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• 1371. [Article] Science and efficacy of mild sodium hydroxide treatments in enzyme-based wheat straw-to-glucose processing

  The work described in this dissertation focused on chemistry related to the use of aqueous sodium hydroxide as a treatment in the processing of wheat straw. A major emphasis was the comprehensive evaluation ...

  Citation × Citation Citation Abstract Copy Title: Science and efficacy of mild sodium hydroxide treatments in enzyme-based wheat straw-to-glucose processing Author: Sophonputtanaphoca, Supaporn The work described in this dissertation focused on chemistry related to the use of aqueous sodium hydroxide as a treatment in the processing of wheat straw. A major emphasis was the comprehensive evaluation of straw component partitioning due to sodium hydroxide (NaOH) processing. This was evaluated over a range of NaOH concentrations (0­‐10%, w/v), all at 50°C, 5 h treatment period, and 3% solid loading. Solid and liquid phases resulting from NaOH treatments were evaluated. Total solids recovered in the NaOH­‐treated solid phase ranged from 47.4­‐88.0%. Overall carbohydrate recovery in the combined solid and liquid phases was negatively correlated with the alkali concentration of the treatment liquor. The glucan content of the NaOH‐treated solid phase ranged from 37.2­‐67.4%. Glucan recovery in the solid phase was relatively high in all cases, the minimum value being ~98%. Increasing amounts of xylan partitioned into the liquid phase as sodium hydroxide concentrations increased – it ranged from 31­‐83% of the xylan being recovered in the soluble phase. Carbohydrate analyses of the pretreated liquor revealed that the majority of carbohydrate loss from the solid fraction could be recovered in the liquid phase in form of oligomers and monomers due to alkaline degradation. The interconversion of glucose, fructose, and mannose under the alkaline condition played an important role in the presence of those sugars. Increase in NaOH concentration contributed to increase in amount of cellulose­‐derived and hemicellulose‐derived oligomers in the pretreated liquor. All oligomers except fructooligomers in NaOH pretreated liquor were higher than those found in water extraction at 50°C, 5 h. Total carbohydrate recovery from the solid and liquid fractions was as high as 99% for glucose and glucan in 5% NaOH treatment and 80‐95% for xylose and xylan in 1-­10% NaOH treatment. The presence of NaOH as extraction reagent dramatically induced lignin and ash removal from the pretreated solid with up to 63% acid insoluble lignin (AIL) and 87% ash extraction. Solid fractions resulting from NaOH pretreatments (up to 5% NaOH) were tested for their susceptibility to enzymatic saccharification using cellulase and cellulase/xylanase enzyme preparations. The cellulase/xylanase enzyme preparation was found to be more effective at cellulose saccharification than the cellulase enzyme preparation alone. Maximum glucose yield, which corresponded to the 5% NaOH treatment, was 82% over the standard 48 h saccharification period. Extended saccharifications times to 120 h showed that the conversion yield approached 90%. Sequential treatments of the straw (i.e. initial alkali treatment – first enzyme saccharification – second alkali treatment ‐ second enzyme treatment) revealed the NaOH treatment has the potential to render essentially all (~99%) of the straw glucan susceptible to enzyme saccharification. This suggests that the layered molecular arrangement of cellulose, hemicellulose, and lignin in the cell wall impacts biomass recalcitrance and glucan conversion yield. The other major focus of this dissertation research was the characterization of alkali neutralization, which occurs during the aqueous alkali processing of wheat straw. The approach taken was to evaluate the time course of alkali uptake and to determine the underlying nature of alkali uptake. The knowledge generated from this study is useful for understanding the nature of the alkali‐induced chemistry that is at the heart of alkali processing of agricultural byproducts, foods, and forest products. Alkali uptake/acid generation measurements were monitored for wheat straw suspensions at pH 11 and 30°C. The first phase of alkali uptake corresponded to the 30‐second time period over which the pH of the wheat straw suspension was adjusted from its original pH (~6.6) to pH 11. Alkali neutralization during this period was attributed to the instantaneous ionization of solvent accessible Bronstad acids. Following pH adjustment to 11.0, the time course of subsequent alkali uptake was recorded. The time course appeared biphasic. The early phase, which corresponded to the relatively rapid uptake of alkali, was evident during the first 24 hours. The later phase, which was characterized by the relatively slow uptake of alkali, was maintained for the length of the study (up to 96 hours). Alkali uptake during the early phase of the time course appears to be determined by the rate of hydrolysis of readily accessible esters – primarily acetic acid esters (acetyl groups). Alkali uptake during the later phase of the time course appears to be impacted by the rate of alkali penetration into the straw and the rate of production of alkali‐induced acid degradation products. The uptake of alkali in the pH adjustment phase was ~ 120 μEq per gram wheat straw, the uptake of alkali in the early phase of time course was ~ 1,064 μEq per gram wheat straw, and the rate of uptake in the later phase of the time course 6.10 μEq per gram wheat straw per hour. Amount of acetyl groups, ferulic acid, and p-­coumaric acid generated during 96-­h pretreatment revealed that they are major esters being hydrolyzed under the studied condition. Combined, these ester-­derived acids contributed up to ~ 28% of overall alkali uptake. In addition, alkaline degradation products quantified in this study showed additional ~ 28% contribution to the overall alkali uptake. Title: Science and efficacy of mild sodium hydroxide treatments in enzyme-based wheat straw-to-glucose processing Author: Sophonputtanaphoca, Supaporn The work described in this dissertation focused on chemistry related to the use of aqueous sodium hydroxide as a treatment in the processing of wheat straw. A major emphasis was the comprehensive evaluation of straw component partitioning due to sodium hydroxide (NaOH) processing. This was evaluated over a range of NaOH concentrations (0­‐10%, w/v), all at 50°C, 5 h treatment period, and 3% solid loading. Solid and liquid phases resulting from NaOH treatments were evaluated. Total solids recovered in the NaOH­‐treated solid phase ranged from 47.4­‐88.0%. Overall carbohydrate recovery in the combined solid and liquid phases was negatively correlated with the alkali concentration of the treatment liquor. The glucan content of the NaOH‐treated solid phase ranged from 37.2­‐67.4%. Glucan recovery in the solid phase was relatively high in all cases, the minimum value being ~98%. Increasing amounts of xylan partitioned into the liquid phase as sodium hydroxide concentrations increased – it ranged from 31­‐83% of the xylan being recovered in the soluble phase. Carbohydrate analyses of the pretreated liquor revealed that the majority of carbohydrate loss from the solid fraction could be recovered in the liquid phase in form of oligomers and monomers due to alkaline degradation. The interconversion of glucose, fructose, and mannose under the alkaline condition played an important role in the presence of those sugars. Increase in NaOH concentration contributed to increase in amount of cellulose­‐derived and hemicellulose‐derived oligomers in the pretreated liquor. All oligomers except fructooligomers in NaOH pretreated liquor were higher than those found in water extraction at 50°C, 5 h. Total carbohydrate recovery from the solid and liquid fractions was as high as 99% for glucose and glucan in 5% NaOH treatment and 80‐95% for xylose and xylan in 1-­10% NaOH treatment. The presence of NaOH as extraction reagent dramatically induced lignin and ash removal from the pretreated solid with up to 63% acid insoluble lignin (AIL) and 87% ash extraction. Solid fractions resulting from NaOH pretreatments (up to 5% NaOH) were tested for their susceptibility to enzymatic saccharification using cellulase and cellulase/xylanase enzyme preparations. The cellulase/xylanase enzyme preparation was found to be more effective at cellulose saccharification than the cellulase enzyme preparation alone. Maximum glucose yield, which corresponded to the 5% NaOH treatment, was 82% over the standard 48 h saccharification period. Extended saccharifications times to 120 h showed that the conversion yield approached 90%. Sequential treatments of the straw (i.e. initial alkali treatment – first enzyme saccharification – second alkali treatment ‐ second enzyme treatment) revealed the NaOH treatment has the potential to render essentially all (~99%) of the straw glucan susceptible to enzyme saccharification. This suggests that the layered molecular arrangement of cellulose, hemicellulose, and lignin in the cell wall impacts biomass recalcitrance and glucan conversion yield. The other major focus of this dissertation research was the characterization of alkali neutralization, which occurs during the aqueous alkali processing of wheat straw. The approach taken was to evaluate the time course of alkali uptake and to determine the underlying nature of alkali uptake. The knowledge generated from this study is useful for understanding the nature of the alkali‐induced chemistry that is at the heart of alkali processing of agricultural byproducts, foods, and forest products. Alkali uptake/acid generation measurements were monitored for wheat straw suspensions at pH 11 and 30°C. The first phase of alkali uptake corresponded to the 30‐second time period over which the pH of the wheat straw suspension was adjusted from its original pH (~6.6) to pH 11. Alkali neutralization during this period was attributed to the instantaneous ionization of solvent accessible Bronstad acids. Following pH adjustment to 11.0, the time course of subsequent alkali uptake was recorded. The time course appeared biphasic. The early phase, which corresponded to the relatively rapid uptake of alkali, was evident during the first 24 hours. The later phase, which was characterized by the relatively slow uptake of alkali, was maintained for the length of the study (up to 96 hours). Alkali uptake during the early phase of the time course appears to be determined by the rate of hydrolysis of readily accessible esters – primarily acetic acid esters (acetyl groups). Alkali uptake during the later phase of the time course appears to be impacted by the rate of alkali penetration into the straw and the rate of production of alkali‐induced acid degradation products. The uptake of alkali in the pH adjustment phase was ~ 120 μEq per gram wheat straw, the uptake of alkali in the early phase of time course was ~ 1,064 μEq per gram wheat straw, and the rate of uptake in the later phase of the time course 6.10 μEq per gram wheat straw per hour. Amount of acetyl groups, ferulic acid, and p-­coumaric acid generated during 96-­h pretreatment revealed that they are major esters being hydrolyzed under the studied condition. Combined, these ester-­derived acids contributed up to ~ 28% of overall alkali uptake. In addition, alkaline degradation products quantified in this study showed additional ~ 28% contribution to the overall alkali uptake. Close

• 1372. [Article] Incorporation of diet information derived from Bayesian stable isotope mixing models into mass-balanced marine ecosystem models : a case study from the Marennes-Oléron Estuary, France

  This thesis presents two related studies on the methodology for creating, and subsequently analyzing, an inverse food web model of an intertidal seagrass bed. The first study (Chapter 2) describes, for ...

  Citation × Citation Citation Abstract Copy Title: Incorporation of diet information derived from Bayesian stable isotope mixing models into mass-balanced marine ecosystem models : a case study from the Marennes-Oléron Estuary, France Author: Pacella, Stephen Roger This thesis presents two related studies on the methodology for creating, and subsequently analyzing, an inverse food web model of an intertidal seagrass bed. The first study (Chapter 2) describes, for the first time in the literature, a method for incorporating isotopic information gained from Bayesian mixing models into an inverse food web model. The second study (Chapter 3) analyzes the results of this food web model from an ecological perspective, which includes the first complete description of the carbon budget of an intertidal seagrass food web incorporating isotopic information. Linear inverse modeling (LIM) is a technique that estimates a complete network of flows in an under-determined system (e.g., a food web) using a combination of site-specific data and previously published data. This estimation of complete flow networks of food webs in marine ecosystems is becoming more recognized as a powerful tool for understanding ecosystem functioning. However, diets and consumption rates of organisms are often difficult or impossible to accurately and reliably measure in the field, resulting in a large amount of uncertainty in the magnitude of consumption flows and resource partitioning in food web models. In order to address this issue, Chapter 2 utilized stable isotope data to help aid in estimating these unknown flows. δ¹³C and δ¹⁵N isotope data of consumers and producers in the Marennes-Oleron seagrass system were used in Bayesian mixing models; the output of which were then used to constrain consumption flows in an inverse analysis food web model of the seagrass ecosystem. We hypothesized that incorporating the diet information gained from the stable isotope mixing models would result in a more constrained food web model. In order to test this, two inverse food web models were built to track the flow of carbon through the seagrass food web on an annual basis, with units of mg C m⁻² d⁻¹. The first model (Traditional LIM) included all available data, with the exception of the diet constraints formed from the stable isotope mixing models. The second model (Isotope LIM) was identical to the Traditional LIM, but included the SIAR diet constraints. Both models were identical in structure, and intended to model the same Marennes- Oleron intertidal seagrass bed. Each model consisted of 27 compartments (24 living, 3 detrital) and 175 flows. Comparisons between the outputs of the models showed the addition of the SIAR-derived isotopic diet constraints further constrained the solution range of all food web flows on average by 26%. Flows that were directly affected by an isotopic diet constraint were 45% further constrained on average. These results confirmed our hypothesis that incorporation of the isotope information would result in a more constrained food web model, and demonstrated the benefit of utilizing multi-tracer stable isotope information in ecosystem models. In Chapter 3, Ecological Network Analysis (ENA) was used to investigate the functional ecology of the system. The majority of seagrass food web studies thus far have relied on trophic marker analyses (i.e. stable isotopes, fatty acids) to investigate food sources and trophic positions, and as a result, few studies have examined seagrass beds from a perspective of whole-ecosystem functioning. By quantifying the Marennes- Oleron seagrass food web using linear inverse modeling coupled with results from isotopic mixing models, this study investigated the relative trophic importance of primary producers in the system, the trophic structure of the seagrass bed flora and fauna, the relative importance of allochthonous versus autochthonous carbon, and both the sequestration and export of organic carbon to the surrounding environment. Additionally, results of these analyses were compared with other coastal systems, including a neighboring bare mudflat located in the Marennes-Oleron estuary. Grazing rates indicated that microphytobenthos was directly consumed about 7 times more than Zostera, while a novel metric of total food web dependency derived from network analysis showed the consumer compartments relied upon microphytobenthos 22 time more than on Z. noltii via direct and indirect pathways. Meiofauna was found to provide an important link between primary production and detritus with upper trophic levels (i.e. fish). Autochthonous carbon was utilized over 4 times more than allochthonous carbon by the seagrass food web in total, and the system was shown to be a net carbon sink. Our analysis supported the concept that seagrass meadows have a high metabolic capacity and the ability to accumulate large sedimentary carbon pools (e.g., carbon sequestration), which are important climate-regulating ecosystem services. ENA revealed the Oleron seagrass bed to be a relatively mature, stable system internally, with strong connections via energy transport to and from surrounding environments. To the best of the authors' knowledge, this study was the first to fully characterize the carbon budget of an intertidal seagrass food web utilizing probabilistic methods. Title: Incorporation of diet information derived from Bayesian stable isotope mixing models into mass-balanced marine ecosystem models : a case study from the Marennes-Oléron Estuary, France Author: Pacella, Stephen Roger This thesis presents two related studies on the methodology for creating, and subsequently analyzing, an inverse food web model of an intertidal seagrass bed. The first study (Chapter 2) describes, for the first time in the literature, a method for incorporating isotopic information gained from Bayesian mixing models into an inverse food web model. The second study (Chapter 3) analyzes the results of this food web model from an ecological perspective, which includes the first complete description of the carbon budget of an intertidal seagrass food web incorporating isotopic information. Linear inverse modeling (LIM) is a technique that estimates a complete network of flows in an under-determined system (e.g., a food web) using a combination of site-specific data and previously published data. This estimation of complete flow networks of food webs in marine ecosystems is becoming more recognized as a powerful tool for understanding ecosystem functioning. However, diets and consumption rates of organisms are often difficult or impossible to accurately and reliably measure in the field, resulting in a large amount of uncertainty in the magnitude of consumption flows and resource partitioning in food web models. In order to address this issue, Chapter 2 utilized stable isotope data to help aid in estimating these unknown flows. δ¹³C and δ¹⁵N isotope data of consumers and producers in the Marennes-Oleron seagrass system were used in Bayesian mixing models; the output of which were then used to constrain consumption flows in an inverse analysis food web model of the seagrass ecosystem. We hypothesized that incorporating the diet information gained from the stable isotope mixing models would result in a more constrained food web model. In order to test this, two inverse food web models were built to track the flow of carbon through the seagrass food web on an annual basis, with units of mg C m⁻² d⁻¹. The first model (Traditional LIM) included all available data, with the exception of the diet constraints formed from the stable isotope mixing models. The second model (Isotope LIM) was identical to the Traditional LIM, but included the SIAR diet constraints. Both models were identical in structure, and intended to model the same Marennes- Oleron intertidal seagrass bed. Each model consisted of 27 compartments (24 living, 3 detrital) and 175 flows. Comparisons between the outputs of the models showed the addition of the SIAR-derived isotopic diet constraints further constrained the solution range of all food web flows on average by 26%. Flows that were directly affected by an isotopic diet constraint were 45% further constrained on average. These results confirmed our hypothesis that incorporation of the isotope information would result in a more constrained food web model, and demonstrated the benefit of utilizing multi-tracer stable isotope information in ecosystem models. In Chapter 3, Ecological Network Analysis (ENA) was used to investigate the functional ecology of the system. The majority of seagrass food web studies thus far have relied on trophic marker analyses (i.e. stable isotopes, fatty acids) to investigate food sources and trophic positions, and as a result, few studies have examined seagrass beds from a perspective of whole-ecosystem functioning. By quantifying the Marennes- Oleron seagrass food web using linear inverse modeling coupled with results from isotopic mixing models, this study investigated the relative trophic importance of primary producers in the system, the trophic structure of the seagrass bed flora and fauna, the relative importance of allochthonous versus autochthonous carbon, and both the sequestration and export of organic carbon to the surrounding environment. Additionally, results of these analyses were compared with other coastal systems, including a neighboring bare mudflat located in the Marennes-Oleron estuary. Grazing rates indicated that microphytobenthos was directly consumed about 7 times more than Zostera, while a novel metric of total food web dependency derived from network analysis showed the consumer compartments relied upon microphytobenthos 22 time more than on Z. noltii via direct and indirect pathways. Meiofauna was found to provide an important link between primary production and detritus with upper trophic levels (i.e. fish). Autochthonous carbon was utilized over 4 times more than allochthonous carbon by the seagrass food web in total, and the system was shown to be a net carbon sink. Our analysis supported the concept that seagrass meadows have a high metabolic capacity and the ability to accumulate large sedimentary carbon pools (e.g., carbon sequestration), which are important climate-regulating ecosystem services. ENA revealed the Oleron seagrass bed to be a relatively mature, stable system internally, with strong connections via energy transport to and from surrounding environments. To the best of the authors' knowledge, this study was the first to fully characterize the carbon budget of an intertidal seagrass food web utilizing probabilistic methods. Close

• 1373. [Article] Linkages among land use, riparian zones, and uptake and transformation of nitrate in stream ecosystems

  Land use alters the physical and biological structure of stream ecosystems and potentially alters their capacity to process nitrogen (N), an essential nutrient that has nearly doubled in abundance on the ...

  Citation × Citation Citation Abstract Copy Title: Linkages among land use, riparian zones, and uptake and transformation of nitrate in stream ecosystems Author: Sobota, Daniel J. Land use alters the physical and biological structure of stream ecosystems and potentially alters their capacity to process nitrogen (N), an essential nutrient that has nearly doubled in abundance on the biosphere during the past century from human activities. In this dissertation, I quantified uptake and transformation of nitrate (NO₃⁻) in small (≤ third-order) streams and related these dynamics to aquatic ecosystem processes, including primary production and organic matter decomposition, and attributes of riparian zone structure and vegetation composition. I also analyze patterns of stream NO₃⁻ processing among three classes of adjacent land use practices (forest, agriculture, and urban). In Chapter 2, ambient rates of NO₃⁻ uptake and transformation were measured with 24-hr releases of ¹⁵N-labeled NO₃⁻ in nine stream reaches in the Willamette River Basin of western Oregon during summer low flow (July – August). Three reaches each were surrounded by forested, agricultural or urban land use. After standardizing reaches to a 500-m length, I estimated that ≥ 20% of tracer ¹⁵NO₃⁻ was taken up by detrital and autotrophic biomass in eight of the reaches. In the remaining stream, which had the largest discharge (120 L s⁻¹) in this study, only 8% of the tracer was taken up in 500 m. Tracer labeling of detritus and autotrophic biomass and a positive correlation (rs=0.81) of uptake with gross primary production suggested that assimilation was the dominant uptake pathway in all streams. Denitrification, dissimilatory reduction of NO₃⁻ to N₂ and N₂O gases, composed 3 – 15% of ¹⁵N budgets over 500 m in two agricultural reaches and in one urban reach dominated by large slowly-turning over pools. However, denitrification was below detection limit at five of the remaining six reaches. This study showed that pathways of stream NO₃⁻ uptake and transformation differed among streams adjacent to three diverse land use practices. In Chapter 3, I quantified effects of substrate nutritional quality and inorganic N loading (as NO₃⁻) on wood breakdown in western Oregon streams. Short-term (< 2 month) breakdown rates of wood substrates of high nutritional quality (Alnus rubra; red alder) and low quality (Pseudotsuga menziesii; Douglas-fir) increased with dissolved inorganic N (11 to 111 mg N L⁻¹) across six streams (p = 0.04), but this relationship was confounded with concurrent increases in stream temperature. Across the six streams, breakdown rates of red alder were consistently double that of Douglas-fir. A longer-term study (313 d) in a coniferous forest Oregon Cascades stream suggested effects of increased NO₃⁻ availability on wood breakdown became evident after cellulose and lignin components of woody tissues began to decompose (> 4 months of incubation). Average breakdown rates substrates enriched with NO₃⁻ were higher than those incubated in low NO₃⁻ conditions, but this difference was not statistically significant. However, microbial biofilm respiration rates and activity of two enzymes involved in the breakdown of woody tissues (beta-glucosidase and phenol oxidase) on red alder had significantly greater responses to NO₃⁻ additions than on Douglas-fir after four months of incubation in the stream. Results suggest that increases in N loading to streams bordered by riparian forests with fast-growing deciduous species could increase wood breakdown rates. On the other hand, increases to N loading may have a smaller effect on wood breakdown in streams surrounded by long-lived coniferous species. In Chapter 4, I quantified patterns of stream channel and riparian zone attributes for 72 streams equally distributed among forests or grasslands, agriculture, and urban land use practices on from eight major North American regions. I also related these patterns to stream NO₃⁻ uptake determined from ¹⁵NO₃⁻ tracer releases. Agricultural and urban streams had a simplified channel structure (low width-to-depth ratio, low variation in stream depth, and high stream banks) relative to forest or grassland streams. Agricultural and urban streams also had a significantly smaller median sediment diameter (D₅₀) and fraction of benthic sediments composed by silt than in forest and grassland streams. Overstory canopy cover over the channel and in the riparian zone was lowest for agricultural streams but did not significantly differ between forest or grassland streams and urban streams. A multiple regression model showed that stream NO₃⁻ uptake decreased with increasing canopy cover, but also increased with abundance of silt in benthic sediments. This suggested NO₃⁻ uptake was strongly influenced by in-stream primary production and extent of anoxic environments (conducive for denitrification). A multiple regression model for fractional NO₃⁻ uptake by denitrification further supported the concept that extent of anoxic environments influenced overall NO₃⁻ uptake in streams. Through these studies, I demonstrated that attributes of riparian zone structure and vegetation composition can strongly influence NO₃⁻ uptake and transformation in stream ecosystems by controlling organic matter dynamics. I also have shown that riparian zone attributes vary significantly among three different land use types (forest or grassland, agriculture, and urban). Similarly, pathways of NO₃⁻ uptake and effects of NO₃⁻ on wood breakdown did or were expected to differ among different land use types / riparian zone characteristics. However, other factors besides riparian attributes, particularly level of nutrient loading, alteration of stream channel physical structure, and basin position of the stream, must be considered in concert when evaluating effects of land use on riparian zone and stream ecosystem structure and function. Title: Linkages among land use, riparian zones, and uptake and transformation of nitrate in stream ecosystems Author: Sobota, Daniel J. Land use alters the physical and biological structure of stream ecosystems and potentially alters their capacity to process nitrogen (N), an essential nutrient that has nearly doubled in abundance on the biosphere during the past century from human activities. In this dissertation, I quantified uptake and transformation of nitrate (NO₃⁻) in small (≤ third-order) streams and related these dynamics to aquatic ecosystem processes, including primary production and organic matter decomposition, and attributes of riparian zone structure and vegetation composition. I also analyze patterns of stream NO₃⁻ processing among three classes of adjacent land use practices (forest, agriculture, and urban). In Chapter 2, ambient rates of NO₃⁻ uptake and transformation were measured with 24-hr releases of ¹⁵N-labeled NO₃⁻ in nine stream reaches in the Willamette River Basin of western Oregon during summer low flow (July – August). Three reaches each were surrounded by forested, agricultural or urban land use. After standardizing reaches to a 500-m length, I estimated that ≥ 20% of tracer ¹⁵NO₃⁻ was taken up by detrital and autotrophic biomass in eight of the reaches. In the remaining stream, which had the largest discharge (120 L s⁻¹) in this study, only 8% of the tracer was taken up in 500 m. Tracer labeling of detritus and autotrophic biomass and a positive correlation (rs=0.81) of uptake with gross primary production suggested that assimilation was the dominant uptake pathway in all streams. Denitrification, dissimilatory reduction of NO₃⁻ to N₂ and N₂O gases, composed 3 – 15% of ¹⁵N budgets over 500 m in two agricultural reaches and in one urban reach dominated by large slowly-turning over pools. However, denitrification was below detection limit at five of the remaining six reaches. This study showed that pathways of stream NO₃⁻ uptake and transformation differed among streams adjacent to three diverse land use practices. In Chapter 3, I quantified effects of substrate nutritional quality and inorganic N loading (as NO₃⁻) on wood breakdown in western Oregon streams. Short-term (< 2 month) breakdown rates of wood substrates of high nutritional quality (Alnus rubra; red alder) and low quality (Pseudotsuga menziesii; Douglas-fir) increased with dissolved inorganic N (11 to 111 mg N L⁻¹) across six streams (p = 0.04), but this relationship was confounded with concurrent increases in stream temperature. Across the six streams, breakdown rates of red alder were consistently double that of Douglas-fir. A longer-term study (313 d) in a coniferous forest Oregon Cascades stream suggested effects of increased NO₃⁻ availability on wood breakdown became evident after cellulose and lignin components of woody tissues began to decompose (> 4 months of incubation). Average breakdown rates substrates enriched with NO₃⁻ were higher than those incubated in low NO₃⁻ conditions, but this difference was not statistically significant. However, microbial biofilm respiration rates and activity of two enzymes involved in the breakdown of woody tissues (beta-glucosidase and phenol oxidase) on red alder had significantly greater responses to NO₃⁻ additions than on Douglas-fir after four months of incubation in the stream. Results suggest that increases in N loading to streams bordered by riparian forests with fast-growing deciduous species could increase wood breakdown rates. On the other hand, increases to N loading may have a smaller effect on wood breakdown in streams surrounded by long-lived coniferous species. In Chapter 4, I quantified patterns of stream channel and riparian zone attributes for 72 streams equally distributed among forests or grasslands, agriculture, and urban land use practices on from eight major North American regions. I also related these patterns to stream NO₃⁻ uptake determined from ¹⁵NO₃⁻ tracer releases. Agricultural and urban streams had a simplified channel structure (low width-to-depth ratio, low variation in stream depth, and high stream banks) relative to forest or grassland streams. Agricultural and urban streams also had a significantly smaller median sediment diameter (D₅₀) and fraction of benthic sediments composed by silt than in forest and grassland streams. Overstory canopy cover over the channel and in the riparian zone was lowest for agricultural streams but did not significantly differ between forest or grassland streams and urban streams. A multiple regression model showed that stream NO₃⁻ uptake decreased with increasing canopy cover, but also increased with abundance of silt in benthic sediments. This suggested NO₃⁻ uptake was strongly influenced by in-stream primary production and extent of anoxic environments (conducive for denitrification). A multiple regression model for fractional NO₃⁻ uptake by denitrification further supported the concept that extent of anoxic environments influenced overall NO₃⁻ uptake in streams. Through these studies, I demonstrated that attributes of riparian zone structure and vegetation composition can strongly influence NO₃⁻ uptake and transformation in stream ecosystems by controlling organic matter dynamics. I also have shown that riparian zone attributes vary significantly among three different land use types (forest or grassland, agriculture, and urban). Similarly, pathways of NO₃⁻ uptake and effects of NO₃⁻ on wood breakdown did or were expected to differ among different land use types / riparian zone characteristics. However, other factors besides riparian attributes, particularly level of nutrient loading, alteration of stream channel physical structure, and basin position of the stream, must be considered in concert when evaluating effects of land use on riparian zone and stream ecosystem structure and function. Close

• 1374. [Article] Effects of spatial scale and heterogeneity on avian occupancy dynamics and population trends in forested mountain landscapes

  Population trends and patterns in species distributions are the major currencies used to examine responses by biodiversity to changing environments. Effective conservation recommendations require that ...

  Citation × Citation Citation Abstract Copy Title: Effects of spatial scale and heterogeneity on avian occupancy dynamics and population trends in forested mountain landscapes Author: Frey, Sarah Jean Kiuama Population trends and patterns in species distributions are the major currencies used to examine responses by biodiversity to changing environments. Effective conservation recommendations require that models of both distribution dynamics and population trends accurately reflect reality. However, identification of the appropriate temporal and spatial scales of animal response, and then obtaining data at these scales present two major challenges to developing predictive models. In heterogeneous forested mountain landscapes I examined: A) the relative drivers of climatic variability at fine spatial scales under the forest canopy ('microclimate'), B) the influence of microclimate on local-scale occupancy dynamics of bird communities, and C) the effects of spatial scale and imperfect bird detection on long-term avian population trends. Climate change has been predicted to cause widespread biodiversity declines. However, the capacity of climate envelope models for predicting the future of biodiversity has been questioned due to the mismatch between the scale of available data (i.e., global climate models) and the scales at which organisms experience their environment. Local-scale variation in microclimate is hypothesized to provide potential ‘microrefugia’ for biodiversity, but the relative role of elevation, microtopography, and vegetation structure in driving microclimate is not well known. If the microrefugia hypothesis is true, I expected to see areas on the landscape that remained relatively cooler (i.e., buffered sites). To test this, I collected temperature data at 183 sites across elevation and forest structure gradients in complex terrain of the H. J. Andrews Experimental Forest in the Cascade Mountains of Oregon, USA (Chapter 2). I used boosted regression trees, a novel machine learning approach, to determine the relative influence of vegetation structure, microtopography, and elevation as drivers of microclimate and mapped fine-scale distributions of temperature across the landscape. Models performed extremely well on independent data - cross-validation correlations between testing and training data were 0.69 - 0.98 for ten selected climate variables. Elevation was the dominant driver in fine-scale microclimate patterns, although vegetation and microtopography also showed substantial relative influences. For instance, during the spring-summer transition, maximum monthly temperatures observed in old-growth sites were 2.6°C (95% CI: 1.8 - 3.3°C) cooler than plantation sites and minimum temperatures during winter months were 0.6°C (95% CI: 0.4 - 0.8°C) warmer. This suggests that older forest stands mediate changes in temperature by buffering against warming during summer months and moderating cold temperatures during the winter. Climate is generally considered most influential on species distributions at large spatial scales; however much microclimate variability exists within regional patterns. I tested whether this high degree of microclimate variability has relevance for predicting species distributions and occupancy dynamics of the Andrews Forest bird community. I collected bird occurrence data in 2012 and 2013 at all 183 sites with fine-scale temperature measurements. I used dynamic occupancy models to test the effects of temperature on occupancy and apparent within-season bird movement while statistically accounting for vegetation effects and imperfect bird detection (Chapter 3). Most species (87%) exhibited within-season shifts in response to local-scale temperature metrics. Effects of temperature on within-season occupancy dynamics were as large or larger (1 to 1.7 times) than vegetation. However, individual species were almost as likely to shift toward warmer sites as toward cooler sites, suggesting that microclimate preferences are species-specific. My results emphasize that high-resolution temperature data provide valuable insight into avian distribution dynamics in montane forest environments and that microclimate is an important variable in breeding season habitat selection by forest birds. I hypothesize that microclimate-associated distribution shifts may reflect species' potential for behavioral buffering from climate change in complex terrain. Factors influencing population trends often differ depending on the spatial scale under consideration. Further, accurate estimation of trends requires accounting for biases caused by imperfect detection. To test the degree to which population trends are consistent across scales, I estimated landscape-scale bird population trends from 1999-2012 for 38 species at the Hubbard Brook Experimental Forest (HBEF) in the White Mountains of New Hampshire, USA and compared them to regional and local trends (Chapter 4). I used a new method - open-population binomial mixture models - to test the hypothesis that imperfect detection in bird sampling has the potential to bias trend estimates. I also tested for generalities in species responses by predicting population trends as a function of life history and ecological traits. Landscape-scale trends were correlated with regional and local trends, but generally these correlations were weak (r = 0.12 - 0.4). Further, more species were declining at the regional scale compared to within the relatively undisturbed HBEF. Life history and ecological traits did not explain any of the variability in the HBEF trends. However, at the regional scale, species that occurred at higher elevations were more likely to be declining and species associated with older forests have increased. I hypothesize that these differences could be attributed to both elevated rates of land-use change in the broader region and the fact that the structure of regional data did not permit modeling of imperfect detection. Indeed, accounting for imperfect detection resulted in more accurate population trend estimates at the landscape scale; without accounting for detection we would have both missed trends and falsely identified trends where none existed. These results highlight two important cautions for trend analysis: 1) population trends estimated at fine spatial scales may not be extrapolated to broader scales and 2) accurate trends require accounting for imperfect detection. Title: Effects of spatial scale and heterogeneity on avian occupancy dynamics and population trends in forested mountain landscapes Author: Frey, Sarah Jean Kiuama Population trends and patterns in species distributions are the major currencies used to examine responses by biodiversity to changing environments. Effective conservation recommendations require that models of both distribution dynamics and population trends accurately reflect reality. However, identification of the appropriate temporal and spatial scales of animal response, and then obtaining data at these scales present two major challenges to developing predictive models. In heterogeneous forested mountain landscapes I examined: A) the relative drivers of climatic variability at fine spatial scales under the forest canopy ('microclimate'), B) the influence of microclimate on local-scale occupancy dynamics of bird communities, and C) the effects of spatial scale and imperfect bird detection on long-term avian population trends. Climate change has been predicted to cause widespread biodiversity declines. However, the capacity of climate envelope models for predicting the future of biodiversity has been questioned due to the mismatch between the scale of available data (i.e., global climate models) and the scales at which organisms experience their environment. Local-scale variation in microclimate is hypothesized to provide potential ‘microrefugia’ for biodiversity, but the relative role of elevation, microtopography, and vegetation structure in driving microclimate is not well known. If the microrefugia hypothesis is true, I expected to see areas on the landscape that remained relatively cooler (i.e., buffered sites). To test this, I collected temperature data at 183 sites across elevation and forest structure gradients in complex terrain of the H. J. Andrews Experimental Forest in the Cascade Mountains of Oregon, USA (Chapter 2). I used boosted regression trees, a novel machine learning approach, to determine the relative influence of vegetation structure, microtopography, and elevation as drivers of microclimate and mapped fine-scale distributions of temperature across the landscape. Models performed extremely well on independent data - cross-validation correlations between testing and training data were 0.69 - 0.98 for ten selected climate variables. Elevation was the dominant driver in fine-scale microclimate patterns, although vegetation and microtopography also showed substantial relative influences. For instance, during the spring-summer transition, maximum monthly temperatures observed in old-growth sites were 2.6°C (95% CI: 1.8 - 3.3°C) cooler than plantation sites and minimum temperatures during winter months were 0.6°C (95% CI: 0.4 - 0.8°C) warmer. This suggests that older forest stands mediate changes in temperature by buffering against warming during summer months and moderating cold temperatures during the winter. Climate is generally considered most influential on species distributions at large spatial scales; however much microclimate variability exists within regional patterns. I tested whether this high degree of microclimate variability has relevance for predicting species distributions and occupancy dynamics of the Andrews Forest bird community. I collected bird occurrence data in 2012 and 2013 at all 183 sites with fine-scale temperature measurements. I used dynamic occupancy models to test the effects of temperature on occupancy and apparent within-season bird movement while statistically accounting for vegetation effects and imperfect bird detection (Chapter 3). Most species (87%) exhibited within-season shifts in response to local-scale temperature metrics. Effects of temperature on within-season occupancy dynamics were as large or larger (1 to 1.7 times) than vegetation. However, individual species were almost as likely to shift toward warmer sites as toward cooler sites, suggesting that microclimate preferences are species-specific. My results emphasize that high-resolution temperature data provide valuable insight into avian distribution dynamics in montane forest environments and that microclimate is an important variable in breeding season habitat selection by forest birds. I hypothesize that microclimate-associated distribution shifts may reflect species' potential for behavioral buffering from climate change in complex terrain. Factors influencing population trends often differ depending on the spatial scale under consideration. Further, accurate estimation of trends requires accounting for biases caused by imperfect detection. To test the degree to which population trends are consistent across scales, I estimated landscape-scale bird population trends from 1999-2012 for 38 species at the Hubbard Brook Experimental Forest (HBEF) in the White Mountains of New Hampshire, USA and compared them to regional and local trends (Chapter 4). I used a new method - open-population binomial mixture models - to test the hypothesis that imperfect detection in bird sampling has the potential to bias trend estimates. I also tested for generalities in species responses by predicting population trends as a function of life history and ecological traits. Landscape-scale trends were correlated with regional and local trends, but generally these correlations were weak (r = 0.12 - 0.4). Further, more species were declining at the regional scale compared to within the relatively undisturbed HBEF. Life history and ecological traits did not explain any of the variability in the HBEF trends. However, at the regional scale, species that occurred at higher elevations were more likely to be declining and species associated with older forests have increased. I hypothesize that these differences could be attributed to both elevated rates of land-use change in the broader region and the fact that the structure of regional data did not permit modeling of imperfect detection. Indeed, accounting for imperfect detection resulted in more accurate population trend estimates at the landscape scale; without accounting for detection we would have both missed trends and falsely identified trends where none existed. These results highlight two important cautions for trend analysis: 1) population trends estimated at fine spatial scales may not be extrapolated to broader scales and 2) accurate trends require accounting for imperfect detection. Close

• 1375. [Article] Biochemical conversion of lignocellulosic biomass to ethanol : experimental, enzymatic hydrolysis modeling, techno-economic and life cycle assessment studies

  Ethanol production from lignocellulosic feedstock has been under intense scrutiny as a transportation fuel due to its potential to address concerns of increasing energy consumption, limited fossil energy ...

  Citation × Citation Citation Abstract Copy Title: Biochemical conversion of lignocellulosic biomass to ethanol : experimental, enzymatic hydrolysis modeling, techno-economic and life cycle assessment studies Author: Kumar, Deepak Ethanol production from lignocellulosic feedstock has been under intense scrutiny as a transportation fuel due to its potential to address concerns of increasing energy consumption, limited fossil energy resources, climate changes due to greenhouse gas emissions from fossil fuels, and especially use of non-food biomaterials, which address the biggest limitation of first generation bioethanol. Despite these advantages, the lignocellulosic ethanol production on commercial scale is still on verge because of high processing costs of ethanol production. In the biochemical conversion process, biomass is converted to ethanol by sequential steps of pretreatment (to reduce the recalcitrance of biomass), hydrolysis (conversion of sugar polymers to monomers) and fermentation (sugars to ethanol). Every year, about a million ton of grass straw is available as agricultural residue in Pacific Northwest. There were no previous comprehensive studies to evaluate the technical feasibility, economic viability and environmental sustainability of the bioethanol produced using grass straw in Willamette valley. The focus of this dissertation was to investigate the potential of cellulosic ethanol production from grass straw, assess the techno-economic viability and environmental impacts of the bioethanol production and development of a stochastic molecular model for modeling cellulose hydrolysis. This dissertation was divided into four studies focused on individual aspects of the overall objective. The first study evaluated the ethanol production potential from straws produced from three major grass seed varieties (perennial ryegrass (Lolium perenne L.), tall fescue (Festuca arundinacea Schreb) and bentgrass (Agrostis sp.)) in Pacific Northwest. Feedstocks were pretreated using three chemical pretreatments (dilute acid, dilute alkali, and hot water) and subsequently hydrolyzed enzymatically to investigate the effect of pretreatment and estimate the potential ethanol yields. Carbohydrate content in biomass varied from 40.6 to 52.9%, with tall fescue having the maximum cellulose content of 32.4%. All pretreatment were effective in increasing the hydrolysis yields, and theoretical maximum ethanol yields were in the range of 276 to 360 L per ton of biomass. The second study performed the comprehensive techno-economic analysis of ethanol production from tall fescue using dilute acid, dilute alkali, hot water, and steam explosion pretreatment technologies. Detailed process models incorporating all unit operations in lignocellulosic ethanol plant with 250,000 metric ton biomass/ year processing capacity were developed in SuperPro Designer. The ethanol production cost were estimated from $0.81 to $0.88/ L of ethanol, and were found highly sensitive to biomass price, enzyme cost, and pentose sugar fermentation efficiency. Energy from lignin residue burning was found sufficient to meet the steam requirement in the production process. Third study performed the life cycle assessment for bioethanol production from grass straw considering various pretreatment technology options. The study revealed that ethanol production from grass straw provide environmental benefits compared to use of gasoline, with 57.43–112.67% reduction in fossil energy use to produce 10,000 MJ of fuel. The GHG emissions during life cycle of ethanol production were estimated in the range of -131 to −555.4 kg CO2 eq. per 10,000 MJ of fuel. It was observed that assumptions and allocation procedure used during the analysis had a significant effect on the LCA results. During the techno-economic assessment of bioethanol process, it was found that cost of cellulose enzymes was significant fraction of the total ethanol production cost. A comprehensive enzymatic hydrolysis model can play critical role in optimizing the enzyme composition and dosage, improving understanding of the process mechanism and reducing the cost of enzymes, a major bottleneck in the ethanol production process. A novel approach of stochastic molecular modeling, in which each hydrolysis event is translated into a discrete event, was used to develop a mechanistic model for cellulose hydrolysis in the fourth study. Cellulose structure was modeled as a group of microfibrils consisting of elementary fibrils bundles, where each elementary fibril was represented as a three dimensional matrix of glucose molecules. Major structural properties: crystallinity, degree of polymerization, surface accessibility, and enzyme characteristics: mode of action, binding and surface blockage, inhibition, along with the dynamic morphological changes in structure of cellulose were incorporated in the model. Hydrolysis of cellulose was simulated based on Monte Carlo simulation technique. Hydrolysis results predicted by model simulations had shown a good fit with the experimental data from hydrolysis of pure cellulose using purified enzymes for various hydrolysis conditions. The model was effective in capturing the dynamic behavior of cellulose hydrolysis during action of individual as well as multiple cellulases. Model was able to simulate and validate all the important expected experimental observations: effect of structural properties, enzyme inhibition and enzyme loadings on the hydrolysis and degree of synergism on different substrates. The work from this dissertation proved the significance of choosing technology options, drew a comparison among different pretreatment technologies, identified the critical processes and inputs that have significant effect on the ethanol production cost, net energy, and GHG emissions. Results from the last study confirmed the validity of using the stochastic molecular modeling approach to quantitatively and qualitatively describe the cellulose hydrolysis, which has wide potential application in bioethanol production research to reduce the enzyme cost. Title: Biochemical conversion of lignocellulosic biomass to ethanol : experimental, enzymatic hydrolysis modeling, techno-economic and life cycle assessment studies Author: Kumar, Deepak Ethanol production from lignocellulosic feedstock has been under intense scrutiny as a transportation fuel due to its potential to address concerns of increasing energy consumption, limited fossil energy resources, climate changes due to greenhouse gas emissions from fossil fuels, and especially use of non-food biomaterials, which address the biggest limitation of first generation bioethanol. Despite these advantages, the lignocellulosic ethanol production on commercial scale is still on verge because of high processing costs of ethanol production. In the biochemical conversion process, biomass is converted to ethanol by sequential steps of pretreatment (to reduce the recalcitrance of biomass), hydrolysis (conversion of sugar polymers to monomers) and fermentation (sugars to ethanol). Every year, about a million ton of grass straw is available as agricultural residue in Pacific Northwest. There were no previous comprehensive studies to evaluate the technical feasibility, economic viability and environmental sustainability of the bioethanol produced using grass straw in Willamette valley. The focus of this dissertation was to investigate the potential of cellulosic ethanol production from grass straw, assess the techno-economic viability and environmental impacts of the bioethanol production and development of a stochastic molecular model for modeling cellulose hydrolysis. This dissertation was divided into four studies focused on individual aspects of the overall objective. The first study evaluated the ethanol production potential from straws produced from three major grass seed varieties (perennial ryegrass (Lolium perenne L.), tall fescue (Festuca arundinacea Schreb) and bentgrass (Agrostis sp.)) in Pacific Northwest. Feedstocks were pretreated using three chemical pretreatments (dilute acid, dilute alkali, and hot water) and subsequently hydrolyzed enzymatically to investigate the effect of pretreatment and estimate the potential ethanol yields. Carbohydrate content in biomass varied from 40.6 to 52.9%, with tall fescue having the maximum cellulose content of 32.4%. All pretreatment were effective in increasing the hydrolysis yields, and theoretical maximum ethanol yields were in the range of 276 to 360 L per ton of biomass. The second study performed the comprehensive techno-economic analysis of ethanol production from tall fescue using dilute acid, dilute alkali, hot water, and steam explosion pretreatment technologies. Detailed process models incorporating all unit operations in lignocellulosic ethanol plant with 250,000 metric ton biomass/ year processing capacity were developed in SuperPro Designer. The ethanol production cost were estimated from $0.81 to $0.88/ L of ethanol, and were found highly sensitive to biomass price, enzyme cost, and pentose sugar fermentation efficiency. Energy from lignin residue burning was found sufficient to meet the steam requirement in the production process. Third study performed the life cycle assessment for bioethanol production from grass straw considering various pretreatment technology options. The study revealed that ethanol production from grass straw provide environmental benefits compared to use of gasoline, with 57.43–112.67% reduction in fossil energy use to produce 10,000 MJ of fuel. The GHG emissions during life cycle of ethanol production were estimated in the range of -131 to −555.4 kg CO2 eq. per 10,000 MJ of fuel. It was observed that assumptions and allocation procedure used during the analysis had a significant effect on the LCA results. During the techno-economic assessment of bioethanol process, it was found that cost of cellulose enzymes was significant fraction of the total ethanol production cost. A comprehensive enzymatic hydrolysis model can play critical role in optimizing the enzyme composition and dosage, improving understanding of the process mechanism and reducing the cost of enzymes, a major bottleneck in the ethanol production process. A novel approach of stochastic molecular modeling, in which each hydrolysis event is translated into a discrete event, was used to develop a mechanistic model for cellulose hydrolysis in the fourth study. Cellulose structure was modeled as a group of microfibrils consisting of elementary fibrils bundles, where each elementary fibril was represented as a three dimensional matrix of glucose molecules. Major structural properties: crystallinity, degree of polymerization, surface accessibility, and enzyme characteristics: mode of action, binding and surface blockage, inhibition, along with the dynamic morphological changes in structure of cellulose were incorporated in the model. Hydrolysis of cellulose was simulated based on Monte Carlo simulation technique. Hydrolysis results predicted by model simulations had shown a good fit with the experimental data from hydrolysis of pure cellulose using purified enzymes for various hydrolysis conditions. The model was effective in capturing the dynamic behavior of cellulose hydrolysis during action of individual as well as multiple cellulases. Model was able to simulate and validate all the important expected experimental observations: effect of structural properties, enzyme inhibition and enzyme loadings on the hydrolysis and degree of synergism on different substrates. The work from this dissertation proved the significance of choosing technology options, drew a comparison among different pretreatment technologies, identified the critical processes and inputs that have significant effect on the ethanol production cost, net energy, and GHG emissions. Results from the last study confirmed the validity of using the stochastic molecular modeling approach to quantitatively and qualitatively describe the cellulose hydrolysis, which has wide potential application in bioethanol production research to reduce the enzyme cost. Close

• 1376. [Article] Two-stage flexible flow shop scheduling with blocking constraint and batching machines

  In this dissertation, a two stage flexible flow shop scheduling problem is studied, where in stage 1, there are identical batch processors (burnout ovens) and in stage 2, there are identical discrete processors ...

  Citation × Citation Citation Abstract Copy Title: Two-stage flexible flow shop scheduling with blocking constraint and batching machines Author: Panahi, Hadi In this dissertation, a two stage flexible flow shop scheduling problem is studied, where in stage 1, there are identical batch processors (burnout ovens) and in stage 2, there are identical discrete processors (furnaces). Batch processors perform a pre-heating process on a batch of jobs at a time and discrete processors perform a casting process on only one job at a time. It is assumed there is no intermediate buffer allowed between stages 1 and 2 and there is a blocking constraint between stages one and two. A batch of jobs is loaded into the batch processors based on predefined patterns. Batch processors have capacity limit and only a limited number of jobs can be loaded into the batch processors. This number is determined by the burnout oven size, jobs size and shape, and also by the layout by which they are loaded into the batch processor. It is assumed that the processing times of the batch processors are fixed and independent of the number of jobs loaded. In stage 2, jobs may require a setup time before loading. This setup depends on the job processed last and the job that is going to be processed next. In stage 2 in order to pour the molten metal, pots are used. Larger jobs require larger pots due to higher molten metal volume. Also jobs may have different alloy types and sometimes the pot that is currently being used must be washed before using it for the next job due to the difference between the alloy types of two consecutive jobs. Furthermore, each pot can be used for a predefined number of pot pourings and when it reaches this predefined maximum, it has to be replaced by a new pot. It is assumed that there are different orders of jobs from customers and each customer’s order is associated with a due date. In this problem, several goals have to be attained while producing high quality products that conform to the established production plan. An ideal production plan reduces the blocking times on the batch processors, reduces the number of pot changes and improves the pot efficiency, reduces the maximum weighted completion time of all jobs and at the same time satisfies customers’ due dates. In order to attain all these goals in one production plan, the maximum weighted completion time of all jobs are minimized. The weights are defined based on customers’ due dates. In order to solve this problem and obtain optimal solutions, several mixed-integer programming mathematical models are developed and are solved using CPLEX and GUROBI. In small-size problems, it is possible to find an optimal solution, but as the size of the problem increases, these commercial solvers are not capable of finding an optimal solution by proving optimality of the feasible solution they find. In large-size problems, these solvers are not even capable of finding a feasible solution. This problem is inspired by a real industry problem and in order to solve this problem on an industrial scale, optimal approaches cannot be employed due to their inefficiency in solving large-size problems. In order to solve these problems and obtain at least high quality near-optimal solutions, three different search algorithms, namely TS, LTM_MAX and LTM_MIN, all based on Tabu search are designed and implemented. The quality of the solutions obtained by the search algorithms has to be evaluated against a valid measure. While mathematical modeling is a good tool to obtain such valid measures (optimal solutions), they are not reliable in solving large-size problems and therefore in this research they are used to evaluate the performance of the search algorithms in small-size problems. For large-size problems, a different methodology, based on the identification of valid lower bounds, is used to investigate the performance of the search algorithms. Two lower bounding mechanisms are used for generating lower bounds. These lower bounds are compared against the solutions found by the search algorithms. The first methodology developed in this research is the iterative selective linear relaxation. This methodology starts from solving the problem with some of the variables relaxed, and allows for relaxing another set of selected variables in subsequent iterations. The second methodology developed in this research is based on branch-and-price (B&P) algorithm. B&P can be viewed as an extension of branch-and-bound, wherein a column generation algorithm is developed and implemented to solve each node of the branch-and bound tree, thus enabling the identification of higher quality lower bounds efficiently for the original problem. A comprehensive set of experiments are performed to evaluate the efficiency and efficacy of the search algorithms. In pursuance of such experiments, numerous test problems that are representative of the real problem have been generated. There are several important factors such as structure of the problem, ratio of processing times to setup times, and types of setup times that are considered in generating test problems. Since some of these factors are known to be “hard to change”, a split-plot design is used to perform the design of experiments in this research. The experiments reveal that LTM_MIN outperforms the other two algorithms in terms of the solution quality. On average TS and LTM_MAX deviate from LTM_MIN by 6.51% and 3.44%, respectively, in small and large-size problems. The average gap of LTM_MIN from the optimal solution in small-size problems is 2.81%, which is very promising. Average gap of LTM_MIN from the best lower bound available and B&P are 31.10% and 39.24%, respectively. In large-size problems the average gap of lower bound obtained by B&P from that by B&B is -14.07%, confirming that B&P outperforms B&B in large-size problems. Finally, in large-size problems, the average gap among best of all three algorithms against the best available lower bound is 14.2%. Title: Two-stage flexible flow shop scheduling with blocking constraint and batching machines Author: Panahi, Hadi In this dissertation, a two stage flexible flow shop scheduling problem is studied, where in stage 1, there are identical batch processors (burnout ovens) and in stage 2, there are identical discrete processors (furnaces). Batch processors perform a pre-heating process on a batch of jobs at a time and discrete processors perform a casting process on only one job at a time. It is assumed there is no intermediate buffer allowed between stages 1 and 2 and there is a blocking constraint between stages one and two. A batch of jobs is loaded into the batch processors based on predefined patterns. Batch processors have capacity limit and only a limited number of jobs can be loaded into the batch processors. This number is determined by the burnout oven size, jobs size and shape, and also by the layout by which they are loaded into the batch processor. It is assumed that the processing times of the batch processors are fixed and independent of the number of jobs loaded. In stage 2, jobs may require a setup time before loading. This setup depends on the job processed last and the job that is going to be processed next. In stage 2 in order to pour the molten metal, pots are used. Larger jobs require larger pots due to higher molten metal volume. Also jobs may have different alloy types and sometimes the pot that is currently being used must be washed before using it for the next job due to the difference between the alloy types of two consecutive jobs. Furthermore, each pot can be used for a predefined number of pot pourings and when it reaches this predefined maximum, it has to be replaced by a new pot. It is assumed that there are different orders of jobs from customers and each customer’s order is associated with a due date. In this problem, several goals have to be attained while producing high quality products that conform to the established production plan. An ideal production plan reduces the blocking times on the batch processors, reduces the number of pot changes and improves the pot efficiency, reduces the maximum weighted completion time of all jobs and at the same time satisfies customers’ due dates. In order to attain all these goals in one production plan, the maximum weighted completion time of all jobs are minimized. The weights are defined based on customers’ due dates. In order to solve this problem and obtain optimal solutions, several mixed-integer programming mathematical models are developed and are solved using CPLEX and GUROBI. In small-size problems, it is possible to find an optimal solution, but as the size of the problem increases, these commercial solvers are not capable of finding an optimal solution by proving optimality of the feasible solution they find. In large-size problems, these solvers are not even capable of finding a feasible solution. This problem is inspired by a real industry problem and in order to solve this problem on an industrial scale, optimal approaches cannot be employed due to their inefficiency in solving large-size problems. In order to solve these problems and obtain at least high quality near-optimal solutions, three different search algorithms, namely TS, LTM_MAX and LTM_MIN, all based on Tabu search are designed and implemented. The quality of the solutions obtained by the search algorithms has to be evaluated against a valid measure. While mathematical modeling is a good tool to obtain such valid measures (optimal solutions), they are not reliable in solving large-size problems and therefore in this research they are used to evaluate the performance of the search algorithms in small-size problems. For large-size problems, a different methodology, based on the identification of valid lower bounds, is used to investigate the performance of the search algorithms. Two lower bounding mechanisms are used for generating lower bounds. These lower bounds are compared against the solutions found by the search algorithms. The first methodology developed in this research is the iterative selective linear relaxation. This methodology starts from solving the problem with some of the variables relaxed, and allows for relaxing another set of selected variables in subsequent iterations. The second methodology developed in this research is based on branch-and-price (B&P) algorithm. B&P can be viewed as an extension of branch-and-bound, wherein a column generation algorithm is developed and implemented to solve each node of the branch-and bound tree, thus enabling the identification of higher quality lower bounds efficiently for the original problem. A comprehensive set of experiments are performed to evaluate the efficiency and efficacy of the search algorithms. In pursuance of such experiments, numerous test problems that are representative of the real problem have been generated. There are several important factors such as structure of the problem, ratio of processing times to setup times, and types of setup times that are considered in generating test problems. Since some of these factors are known to be “hard to change”, a split-plot design is used to perform the design of experiments in this research. The experiments reveal that LTM_MIN outperforms the other two algorithms in terms of the solution quality. On average TS and LTM_MAX deviate from LTM_MIN by 6.51% and 3.44%, respectively, in small and large-size problems. The average gap of LTM_MIN from the optimal solution in small-size problems is 2.81%, which is very promising. Average gap of LTM_MIN from the best lower bound available and B&P are 31.10% and 39.24%, respectively. In large-size problems the average gap of lower bound obtained by B&P from that by B&B is -14.07%, confirming that B&P outperforms B&B in large-size problems. Finally, in large-size problems, the average gap among best of all three algorithms against the best available lower bound is 14.2%. Close

• 1377. [Article] Processes of orientation to the informal caregiving role among Mexican-origin women : a qualitative analysis

  This thesis presents the steps that were taken to develop thematic findings using data from a qualitative study. Using a grounded approach, the study focused on qualitatively exploring Mexican origin caregivers' ...

  Citation × Citation Citation Abstract Copy Title: Processes of orientation to the informal caregiving role among Mexican-origin women : a qualitative analysis Author: McDermott, Elizabeth A. This thesis presents the steps that were taken to develop thematic findings using data from a qualitative study. Using a grounded approach, the study focused on qualitatively exploring Mexican origin caregivers' conceptualizations of elder caregiving in terms of role functioning, social norms, cultural beliefs, and familial obligations. Data collected from one-time, semi-structured interviews with 44 caregivers living in East Los Angeles, California were analyzed to develop thematic content. Before the onset of data analysis, all materials related to the study were reviewed to familiarize the researcher with the data. Following the review of the study materials, each transcript was systematically sorted and analyzed in the language of the interview (i.e., Spanish or English), using Atlas.ti, qualitative data management software. The cultural psychological perspective and the research question, "How do Mexican-origin women describe becoming oriented to or familiarized with the caregiving role and its associated responsibilities?" guided the analysis. Four themes related to women’s conceptualization of caregiving and women's personal sense of responsibility for taking care of familial elders emerged from the analysis. These themes include: 1) early and continued caregiving socialization; 2) psyche and personal identification; 3) familial expectations of giving care; and 4) cultural expectations of the family and the responsibility to give care. The first theme, early and continued caregiving socialization, reflects women's reports of becoming familiarized with the practice of giving care early on in their lives, often years before the actual adoption of the familial caregiving role. Women shared that the process of learning to give care involved continued observation of close relatives' caregiving behaviors and skills. Of those who reported learning how to give care through the observation of relatives, most reported having observed mothers modeling caregiving behaviors in support of elderly relatives and some reported having observed the caregiving activities of aunts and grandmothers. Women also became oriented to the caregiving role by actively participating in their families' caregiving responsibilities and activities early on in their lives (e.g., taking care of siblings, preparing family meals). The second theme to emerge from the analysis reflects the personal identification, held by some women in the sample, as primary caregiver within the family. Caregiving was described by these women as an inherent capacity or ability, not merely a set of skills or functions one becomes familiarized with or trained to do. For that reason, many were reluctant to adopt the term caregiver, instead reporting that they were performing familial duties consistent with their conceptualization of what it meant to be in a family, to be a daughter, or to be a granddaughter. The third theme, familial expectations of giving care, reflects the profound influence of familial expectations on women's behaviors and attitudes concerning the care of dependent familial elders. Families varied with respect to the degree to which familial expectations regarding the care of dependent family members were expressed. In some families, familial expectations regarding the care of dependent relatives were expressed clearly and explicitly while, in others, familial caregiving expectations were merely implied. For those belonging to families where caregiving expectations were implied, expectations within the family regarding the care of dependent relatives were generally conveyed through the allocation of caregiving tasks within the family, such as watching over younger siblings and preparing meals for the family. This implicit expression of caregiving expectations within the family made the process of becoming a caregiver a relatively passive process, involving the gradual increase in responsibilities over dependent family members. The fourth theme, cultural expectations of the family and the responsibility to give care, reflects the cultural forces influencing women's conceptualization of caregiving and women’s personal sense of responsibility for taking care of familial elders. Marianisma, the expectation within Latino culture that female members of a family should consider their own wants, desires, and needs as secondary to the needs of the family, particularly male members of the family (Hubbell, 1993; García & de Oliveira, 1997) was alluded to by many of the women in the sample. Similarly, familism, or the Latino cultural value of allegiance, attachment, dedication, reciprocity, and solidarity within the family (Ruiz & Ransford, 2012) was also reflected in women’s reports, with the majority of women in the sample sharing the view that, in times of need, family members should express loyalty to and responsibility for other dependent members of the family, by being available to give care and support. Though the goal of qualitative research is not necessarily to produce generalizable results but to instead describe as many aspects of a topic in detail, as is possible; it should be noted that, because non-random sampling techniques were utilized to recruit the study participants, the generalizability of this analysis' findings is limited. For that reason, while the discovery of common elements, across interviews, related to the processes of becoming oriented to the caregiver role lends some credibility to the findings of this analysis, caution should be taken when interpreting the results of this analysis. Additional research, involving alternative study designs, larger samples, and more diverse samples in terms of socioeconomic status and geographic location, is warranted. Title: Processes of orientation to the informal caregiving role among Mexican-origin women : a qualitative analysis Author: McDermott, Elizabeth A. This thesis presents the steps that were taken to develop thematic findings using data from a qualitative study. Using a grounded approach, the study focused on qualitatively exploring Mexican origin caregivers' conceptualizations of elder caregiving in terms of role functioning, social norms, cultural beliefs, and familial obligations. Data collected from one-time, semi-structured interviews with 44 caregivers living in East Los Angeles, California were analyzed to develop thematic content. Before the onset of data analysis, all materials related to the study were reviewed to familiarize the researcher with the data. Following the review of the study materials, each transcript was systematically sorted and analyzed in the language of the interview (i.e., Spanish or English), using Atlas.ti, qualitative data management software. The cultural psychological perspective and the research question, "How do Mexican-origin women describe becoming oriented to or familiarized with the caregiving role and its associated responsibilities?" guided the analysis. Four themes related to women’s conceptualization of caregiving and women's personal sense of responsibility for taking care of familial elders emerged from the analysis. These themes include: 1) early and continued caregiving socialization; 2) psyche and personal identification; 3) familial expectations of giving care; and 4) cultural expectations of the family and the responsibility to give care. The first theme, early and continued caregiving socialization, reflects women's reports of becoming familiarized with the practice of giving care early on in their lives, often years before the actual adoption of the familial caregiving role. Women shared that the process of learning to give care involved continued observation of close relatives' caregiving behaviors and skills. Of those who reported learning how to give care through the observation of relatives, most reported having observed mothers modeling caregiving behaviors in support of elderly relatives and some reported having observed the caregiving activities of aunts and grandmothers. Women also became oriented to the caregiving role by actively participating in their families' caregiving responsibilities and activities early on in their lives (e.g., taking care of siblings, preparing family meals). The second theme to emerge from the analysis reflects the personal identification, held by some women in the sample, as primary caregiver within the family. Caregiving was described by these women as an inherent capacity or ability, not merely a set of skills or functions one becomes familiarized with or trained to do. For that reason, many were reluctant to adopt the term caregiver, instead reporting that they were performing familial duties consistent with their conceptualization of what it meant to be in a family, to be a daughter, or to be a granddaughter. The third theme, familial expectations of giving care, reflects the profound influence of familial expectations on women's behaviors and attitudes concerning the care of dependent familial elders. Families varied with respect to the degree to which familial expectations regarding the care of dependent family members were expressed. In some families, familial expectations regarding the care of dependent relatives were expressed clearly and explicitly while, in others, familial caregiving expectations were merely implied. For those belonging to families where caregiving expectations were implied, expectations within the family regarding the care of dependent relatives were generally conveyed through the allocation of caregiving tasks within the family, such as watching over younger siblings and preparing meals for the family. This implicit expression of caregiving expectations within the family made the process of becoming a caregiver a relatively passive process, involving the gradual increase in responsibilities over dependent family members. The fourth theme, cultural expectations of the family and the responsibility to give care, reflects the cultural forces influencing women's conceptualization of caregiving and women’s personal sense of responsibility for taking care of familial elders. Marianisma, the expectation within Latino culture that female members of a family should consider their own wants, desires, and needs as secondary to the needs of the family, particularly male members of the family (Hubbell, 1993; García & de Oliveira, 1997) was alluded to by many of the women in the sample. Similarly, familism, or the Latino cultural value of allegiance, attachment, dedication, reciprocity, and solidarity within the family (Ruiz & Ransford, 2012) was also reflected in women’s reports, with the majority of women in the sample sharing the view that, in times of need, family members should express loyalty to and responsibility for other dependent members of the family, by being available to give care and support. Though the goal of qualitative research is not necessarily to produce generalizable results but to instead describe as many aspects of a topic in detail, as is possible; it should be noted that, because non-random sampling techniques were utilized to recruit the study participants, the generalizability of this analysis' findings is limited. For that reason, while the discovery of common elements, across interviews, related to the processes of becoming oriented to the caregiver role lends some credibility to the findings of this analysis, caution should be taken when interpreting the results of this analysis. Additional research, involving alternative study designs, larger samples, and more diverse samples in terms of socioeconomic status and geographic location, is warranted. Close

• 1378. [Article] A comparison of social class differences in adolescents' self-disclosure, parent-cathexis and self-cathexis

  The purpose of this study was to investigate the differences between middle- and lower-class adolescents and the extent of their self-disclosure to their mothers and their fathers; and their feelings both ...

  Citation × Citation Citation Abstract Copy Title: A comparison of social class differences in adolescents' self-disclosure, parent-cathexis and self-cathexis Author: Larsen, George Robert The purpose of this study was to investigate the differences between middle- and lower-class adolescents and the extent of their self-disclosure to their mothers and their fathers; and their feelings both positive and negative toward their parents and themselves. The subjects consisted of 50 middle-class and 50 lower-class adolescents who were randomly selected from 297 sophomores and juniors attending the same high school in a rural town in Oregon. Hollingshead's Index of Social Position (1958), which uses the occupation and education of the father as criteria for social class, was used to classify the adolescents by social class. Sex comparisons were also analyzed for differences between the middle- and lower-class adolescents. In attempting to realize this purpose, two major hypotheses were tested: Hypothesis 1: There are no differences between these middle-class and lower-class adolescents in the extent of self-disclosure to their parents. Hypothesis 2: There are no differences between these middle-class and lower-class adolescent's in the extent of positive and negative feelings toward their parents and themselves. The extent of self-disclosure was measured by Jourard's Self-disclosure Questionnaire (1964). This 60 item instrument which permits the subjects to indicate the extent to which they are willing to talk to another person about themselves on the following six categories: A attitudes and opinions, B tastes and interests, C work or studies, D money, E personality, and F body. Total scores from the questionnaire were used in testing Hypothesis 1. The results indicated that the null hypothesis could not be rejected. Comparison of middle- and lower-class males and middle- and lower-class females also did not indicate any significant differences on total scores from the Self-disclosure Questionnaire. The extent of the adolescents' positive and negative feelings toward their parents and themselves was measured by the use of Jourard's Cathexis Questionnaire. This instrument consists of 40 personality traits such as: sense of humor, philosophy of life, temper, and happiness. Total scores from the questionnaire were used in the test of Hypothesis 2. Once again, the results of the test indicated that the null hypothesis could not be rejected. In addition analysis was made of differences between middle- and lower-class males and middle- and lower-class females on total scores from the Cathexis Questionnaire for mothers, fathers and themselves. No significant differences were found for the social class differences for the middle- and lower-class males and females. The items within each questionnaire were then analyzed for significant differences between the middle- and lower-class adolescents. To test for significant differences between social classes for each item within the questionnaires, Chi Square and the Kolmogrov- Smirnov Test were used. Sixteen of the 60 items on the Self-disclosure Questionnaire were found to be significantly different between the middle- and lower-class adolescents, with the middle-class adolescents talking more extensively to their parents than did the lower-class adolescents. More specifically five items were significantly different for both mothers and fathers which were: attitudes on drinking, feelings about how work is appreciated, feelings about people at work, trouble controlling feelings, being attractive to the opposite sex or not. While these five items were significant for both mothers and fathers the following eight items were of significance for mothers: attitudes on racial integration, tastes in music, style of house, how much money is made, to whom money is owed, amount in savings, aspects of personality that are disliked, and feelings about one's appearance in the past. The following three items were significant for fathers: tastes in food, source of income, and ideals of overall appearance. In addition analysis of differences between middle- and lower-class males and females on the items within the Self-disclosure Questionnaire with the lower-class adolescent indicating no self-disclosure in contrast to the middle-class adolescents extensive self-disclosure. Slightly more items were significantly different on self-disclosure to the parent of the same sex than to the parent of the opposite sex. The items of significance for males to fathers were: religion, food, social gatherings, feelings about people at work, and adequacy in sexual behavior. The items of significance for females to mothers were: style of house, present work, ambitions and goals, choice of a career, people at work, things that makes one furious, and adequacy in sexual behavior. The items of significance for the males to mothers were: appreciation of work, amount of savings, and being attractive to the opposite sex. The items of significance for the females to their fathers were: how much money is made and trouble controlling feelings. For the Cathexis Questionnaire there were three target persons: mother, father, and self. Only four of the 40 items in this questionnaire were significantly different between middle- and lower-class adolescents. The lower-class adolescents indicated negative feelings toward their fathers and themselves in contrast to the positive feelings expressed by the middle-class adolescents. Of the four items three were for fathers' general knowledge, intelligence level, and philosophy of life. The only significant item for the adolescents' feelings about themselves was their ability to control emotions. An additional comparison was made for differences between the middle- and lower-class males and females for feelings about their mothers, fathers and themselves. There were only two significant items for the sex comparisons for the items from the Cathexis Questionnaire. The lower-class males indicated negative feelings toward their fathers' general knowledge in contrast to the positive feelings of the middle-class males. The lower-class females indicated negative feelings for their fathers' intelligence level in contrast to the positive feelings of the middle-class females. An extension of the analysis of the differences between the extreme ends of the social class continuum was done by going back to the original 297 subjects and taking all of those in Classes I and II (N = 20) and all of those in Class V (N = 23). The two hypotheses were again tested by using the Self-disclosure and Cathexis Questionnaires. Total scores from the two questionnaires were used in the test of Hypothesis 1 and 2. The results of the t-test indicated that the null hypotheses could not be rejected, for both Hypothesis 1 and 2. The sex comparisons for the two hypotheses also indicated no significant differences on total scores from the two questionnaires. The analysis of the differences in the extent of self-disclosure between the extreme ends of the social class continuum provided a pattern which was the reverse for the random sample of middle- and lower-class adolescents. For the random sample there were more items of significant difference for mothers than for fathers, while there were more items of significant difference for fathers than for mothers for the extreme ends of the social class continuum. The lower socio-economic adolescents indicated no self-disclosure for the significant items in contrast to the upper socio-economic adolescents' extensive self-disclosure to their parents. The three items which were significantly different on self-disclosure to mothers were: attitudes toward other religious groups, satisfaction from present work, and who owes me money. The nine items which were significantly different on self-disclosure to fathers were: religion, standards of beauty, tastes in food, present work, ambitions and goals, who owes me money, different parts of the body, physical measurements, and adequate sexual behavior. The analysis of the differences in the extent of self-disclosure between the males and females of the upper and lower extremes of the social class continuum showed no significant difference. The analysis of the differences between the extreme ends of the social class continuum on the items within the Cathexis Questionnaire indicated one item for mothers and six items for fathers. For all of the items the lower socio-economic adolescents indicated negative feelings in contrast to the positive feelings of the upper socio-economic adolescents. The one significant item for feelings about mothers was her general knowledge. The six significant items for feelings about fathers were his: general knowledge, intelligence level, capacity to work, ability to meet new people, and business sense. The sex comparisons of the extreme ends of the social class continuum of the items within the Cathexis Questionnaire found two items of significant differences. The lower socio-economic females indicated negative feelings about fathers' general knowledge and intelligence level, while the upper socio-economic females indicated positive feelings on these items. The items within the questionnaires which indicated significant differences agreed with the literature on social class which suggests that there is more communication between middle-class parents and their children than for lower-class parents and their children, and that the lower-class adolescents report more negative feelings toward their parents than do the middle-class adolescents. The findings of this study suggest the necessity of additional studies of social class differences in rural settings and comparisons of rural and urban samples which use the same criteria for measuring social class and which use the same instruments for measuring differences among the social classes. Title: A comparison of social class differences in adolescents' self-disclosure, parent-cathexis and self-cathexis Author: Larsen, George Robert The purpose of this study was to investigate the differences between middle- and lower-class adolescents and the extent of their self-disclosure to their mothers and their fathers; and their feelings both positive and negative toward their parents and themselves. The subjects consisted of 50 middle-class and 50 lower-class adolescents who were randomly selected from 297 sophomores and juniors attending the same high school in a rural town in Oregon. Hollingshead's Index of Social Position (1958), which uses the occupation and education of the father as criteria for social class, was used to classify the adolescents by social class. Sex comparisons were also analyzed for differences between the middle- and lower-class adolescents. In attempting to realize this purpose, two major hypotheses were tested: Hypothesis 1: There are no differences between these middle-class and lower-class adolescents in the extent of self-disclosure to their parents. Hypothesis 2: There are no differences between these middle-class and lower-class adolescent's in the extent of positive and negative feelings toward their parents and themselves. The extent of self-disclosure was measured by Jourard's Self-disclosure Questionnaire (1964). This 60 item instrument which permits the subjects to indicate the extent to which they are willing to talk to another person about themselves on the following six categories: A attitudes and opinions, B tastes and interests, C work or studies, D money, E personality, and F body. Total scores from the questionnaire were used in testing Hypothesis 1. The results indicated that the null hypothesis could not be rejected. Comparison of middle- and lower-class males and middle- and lower-class females also did not indicate any significant differences on total scores from the Self-disclosure Questionnaire. The extent of the adolescents' positive and negative feelings toward their parents and themselves was measured by the use of Jourard's Cathexis Questionnaire. This instrument consists of 40 personality traits such as: sense of humor, philosophy of life, temper, and happiness. Total scores from the questionnaire were used in the test of Hypothesis 2. Once again, the results of the test indicated that the null hypothesis could not be rejected. In addition analysis was made of differences between middle- and lower-class males and middle- and lower-class females on total scores from the Cathexis Questionnaire for mothers, fathers and themselves. No significant differences were found for the social class differences for the middle- and lower-class males and females. The items within each questionnaire were then analyzed for significant differences between the middle- and lower-class adolescents. To test for significant differences between social classes for each item within the questionnaires, Chi Square and the Kolmogrov- Smirnov Test were used. Sixteen of the 60 items on the Self-disclosure Questionnaire were found to be significantly different between the middle- and lower-class adolescents, with the middle-class adolescents talking more extensively to their parents than did the lower-class adolescents. More specifically five items were significantly different for both mothers and fathers which were: attitudes on drinking, feelings about how work is appreciated, feelings about people at work, trouble controlling feelings, being attractive to the opposite sex or not. While these five items were significant for both mothers and fathers the following eight items were of significance for mothers: attitudes on racial integration, tastes in music, style of house, how much money is made, to whom money is owed, amount in savings, aspects of personality that are disliked, and feelings about one's appearance in the past. The following three items were significant for fathers: tastes in food, source of income, and ideals of overall appearance. In addition analysis of differences between middle- and lower-class males and females on the items within the Self-disclosure Questionnaire with the lower-class adolescent indicating no self-disclosure in contrast to the middle-class adolescents extensive self-disclosure. Slightly more items were significantly different on self-disclosure to the parent of the same sex than to the parent of the opposite sex. The items of significance for males to fathers were: religion, food, social gatherings, feelings about people at work, and adequacy in sexual behavior. The items of significance for females to mothers were: style of house, present work, ambitions and goals, choice of a career, people at work, things that makes one furious, and adequacy in sexual behavior. The items of significance for the males to mothers were: appreciation of work, amount of savings, and being attractive to the opposite sex. The items of significance for the females to their fathers were: how much money is made and trouble controlling feelings. For the Cathexis Questionnaire there were three target persons: mother, father, and self. Only four of the 40 items in this questionnaire were significantly different between middle- and lower-class adolescents. The lower-class adolescents indicated negative feelings toward their fathers and themselves in contrast to the positive feelings expressed by the middle-class adolescents. Of the four items three were for fathers' general knowledge, intelligence level, and philosophy of life. The only significant item for the adolescents' feelings about themselves was their ability to control emotions. An additional comparison was made for differences between the middle- and lower-class males and females for feelings about their mothers, fathers and themselves. There were only two significant items for the sex comparisons for the items from the Cathexis Questionnaire. The lower-class males indicated negative feelings toward their fathers' general knowledge in contrast to the positive feelings of the middle-class males. The lower-class females indicated negative feelings for their fathers' intelligence level in contrast to the positive feelings of the middle-class females. An extension of the analysis of the differences between the extreme ends of the social class continuum was done by going back to the original 297 subjects and taking all of those in Classes I and II (N = 20) and all of those in Class V (N = 23). The two hypotheses were again tested by using the Self-disclosure and Cathexis Questionnaires. Total scores from the two questionnaires were used in the test of Hypothesis 1 and 2. The results of the t-test indicated that the null hypotheses could not be rejected, for both Hypothesis 1 and 2. The sex comparisons for the two hypotheses also indicated no significant differences on total scores from the two questionnaires. The analysis of the differences in the extent of self-disclosure between the extreme ends of the social class continuum provided a pattern which was the reverse for the random sample of middle- and lower-class adolescents. For the random sample there were more items of significant difference for mothers than for fathers, while there were more items of significant difference for fathers than for mothers for the extreme ends of the social class continuum. The lower socio-economic adolescents indicated no self-disclosure for the significant items in contrast to the upper socio-economic adolescents' extensive self-disclosure to their parents. The three items which were significantly different on self-disclosure to mothers were: attitudes toward other religious groups, satisfaction from present work, and who owes me money. The nine items which were significantly different on self-disclosure to fathers were: religion, standards of beauty, tastes in food, present work, ambitions and goals, who owes me money, different parts of the body, physical measurements, and adequate sexual behavior. The analysis of the differences in the extent of self-disclosure between the males and females of the upper and lower extremes of the social class continuum showed no significant difference. The analysis of the differences between the extreme ends of the social class continuum on the items within the Cathexis Questionnaire indicated one item for mothers and six items for fathers. For all of the items the lower socio-economic adolescents indicated negative feelings in contrast to the positive feelings of the upper socio-economic adolescents. The one significant item for feelings about mothers was her general knowledge. The six significant items for feelings about fathers were his: general knowledge, intelligence level, capacity to work, ability to meet new people, and business sense. The sex comparisons of the extreme ends of the social class continuum of the items within the Cathexis Questionnaire found two items of significant differences. The lower socio-economic females indicated negative feelings about fathers' general knowledge and intelligence level, while the upper socio-economic females indicated positive feelings on these items. The items within the questionnaires which indicated significant differences agreed with the literature on social class which suggests that there is more communication between middle-class parents and their children than for lower-class parents and their children, and that the lower-class adolescents report more negative feelings toward their parents than do the middle-class adolescents. The findings of this study suggest the necessity of additional studies of social class differences in rural settings and comparisons of rural and urban samples which use the same criteria for measuring social class and which use the same instruments for measuring differences among the social classes. Close

• 1379. [Article] Role of Peroxisome Proliferator-Activated Receptor Gamma on Prevention/Cure of Mastitis

  Mastitis is a major endemic disease in dairy cows resulting in significant economic losses for the dairy industry. The peroxisome proliferator-activated receptor gamma (PPARγ) is a nuclear receptor that ...

  Citation × Citation Citation Abstract Copy Title: Role of Peroxisome Proliferator-Activated Receptor Gamma on Prevention/Cure of Mastitis Author: Trindade da Rosa, Fernanda Mastitis is a major endemic disease in dairy cows resulting in significant economic losses for the dairy industry. The peroxisome proliferator-activated receptor gamma (PPARγ) is a nuclear receptor that is able to bind and be activated by natural (e.g., fatty acids) and synthetic (e.g. thiazolidinedione) compounds. PPARγ plays important roles in adipocyte differentiation, inflammation, and re-epithelialization in monogastric. In ruminants, PPARγ may play a role in milk fat synthesis. The aim of this study was to assess the role of PPARγ in host response to mammary infection and milk fat synthesis in ruminants. Our hypothesis is that activation of PPARγ improves the host response to mastitis and increases milk fat yield. By using a synthetic PPARγ agonist in dairy goats in combination with intramammary infection to induce subclinical mastitis, the objectives of the present experiments were to test if activation of PPARγ improves 1) the response to mastitis and 2) milk fat production. To achieve our objectives we performed two in vivo experiments (Experiments 1 and 2). In Experiment 1, 24 Saanen lactating goats with a low body condition score and getting a low-energy diet without vitamin supplementation received a daily intrajugular injection of either 8 mg of 2,4-thiazolidinedione (TZD) per kg of BW or saline (as a control) and, after a week of TZD injection, an intramammary infusion (IMI) of either Streptococcus uberis to induce subclinical mastitis or saline used as a control (6 goats/group). Milk yield and components, body weight, rectal temperature, leukocyte phagocytosis, blood metabolic and inflammation parameters plus insulin, adipocyte size by histology, and expression by RT-qPCR of PPARγ target genes in adipose tissue obtained through biopsy and in mammary epithelial cells (MEC) isolated from milk were assessed. In MEC, expression of CCL2 and IL8 was also measured. Data were analyzed by GLIMMIX of SAS with Mastitis, TZD, and Time and all interactions as main effects and goat as random effect. Statistical significance and tendencies were declared at P < 0.05 and 0.05 ≤ P ≤ 0.10, respectively. The induction of mastitis was successful achieved as indicated by >5-fold increase of milk somatic cells count (SCC) in goats receiving Strep. uberis and by 30% decrease of % polymorphonuclear leukocytes in blood. The SCC in milk were overall lower in TZD-treated goats. Mastitis induction but not TZD decreased milk yield and production of milk fat. Goats receiving Strep. uberis had increased concentrations of glucose, triglycerides, and non-esterified fatty acids (NEFA) in blood after IMI. NEFA was not affected in TZD goats, which did not receive Strep. uberis. Inflammatory markers increased in blood of all goats but the increase of haptoglobin was overall lower in TZD treated goats. Indicators of liver activity, including albumin, paraoxonase, and cholesterol, overall decreased after IMI but cholesterol did not decrease in TZD-treated goats. The bactericidal myeloperoxidase was higher in TZD-treated goats after mastitis. Insulin sensitivity was not affected by TZD or mastitis. Adipocytes size increased over time and was higher in TZD goats not receiving Strep. uberis. Subclinical mastitis increased expression of CCL2 and prevented a decrease in expression of IL8. MEC from TZD-treated goats tended to have higher expression of PPARG, FASN and SCD1 after 3 weeks of TZD treatment. Neither mastitis nor TZD affected the expression of genes in adipose tissue. Overall the data of Experiment 1 indicated that the subclinical mastitis model was successfully achieved. The treatment with TZD decreased somatic cells in milk, improved the response of liver, decreased the severity of inflammation, and increased the killing capacity of neutrophils after IMI. The data suggested a more lipogenic adipose tissue in TZD-treated goats but also some active, although minor, nutrigenomic effect of TZD on MEC that may have counteracted the competition of lipid substrates between mammary and adipose tissue. Blood metabolic data suggested that goats responded to Strep. uberis intramammary infusion similar to dairy cows in negative energy balance. Data obtained from Experiment 1 indicated that TZD aids with mastitis response. TZD had some effect on milk fat synthesis but, overall, had a smaller-than-expected nutrigenomic effect probably also due to the low body condition and low energy in the diet of the goats. Thus, the effect of PPARγ on milk fat synthesis is still unclear. The rationale to perform Experiment 2 stemmed from the possibility that the limited nutrigenomic response observed in Experiment 1 was due to a potential dietary deficiency. Subsequent in vitro work demonstrated that TZD is a strong activator of PPAR but only in the presence of 9-cis-retinoic acid, a metabolite of vitamin A and the activation of PPARγ obligate heterodimer Retinoic-X-Receptor (RXR). Therefore, we hypothesized that continuous activation of PPARγ by TZD in dairy goats supplemented with adequate amount of vitamin A improves the inflammatory response to subclinical mastitis. In order to test this hypothesis we used 12 Saanen multiparous goats in early lactation. Goats received a diet that met the NRC requirements, including vitamin A, and a daily injection of 8 mg TZD per kg of BW (n=6) or saline (n=6; CTRL). Following 14 days of treatment, all goats received an IMI of Strep. uberis to induce subclinical mastitis in the right half of the udder with the left half used as control. Metabolic, inflammation, and oxidative-status profiling in blood including 20 parameters was performed. Milk yield, SCC, rectal temperature and leukocytes phagocytosis were measured. Expression of several PPARγ target genes and genes involved in inflammation was measured in MEC, macrophages isolated from milk, and liver tissue. Data were analyzed by GLIMMIX of SAS with treatment (TRT) and Time and TRTxTime interaction as main effects and goat as random effect. For milk and SCC, mammary half was also included in the main effect (including interactions). Statistical significance and tendencies were declared at P < 0.05 and 0.05 ≤ P ≤ 0.10, respectively. Milk yield decreased after IMI but the decrease was larger in TZD-treated goats. SCC increased after IMI but was not affected by TZD administration. Milk fat decreased after IMI in all halves except in the untreated half of TZD-treated goats. In blood within 2 days from IMI, ceruloplasmin, haptoglobin, and glucose were increased while Zn was decreased. These data confirmed successful induction of sub-clinical mastitis and a status of slight inflammation after IMI. None of the parameters in blood was affected by TZD with the exception of a lower bilirubin concentration and a tendency for higher haptoglobin in TZD vs. CTRL after IMI, indicating a more robust response of the liver to inflammation. The stronger inflammation was also supported by a tendency for higher reactive oxygen metabolites in TZD vs. CTRL group after IMI. We also detected a tendency for a higher globulin in TZD vs. CTRL indicating a better adaptive immune system. Leukocyte phagocytosis was strongly reduced by TZD treatment. None of the genes measured were affected by TZD in liver. In milk macrophages and MEC, expression of inflammatory genes was higher compared to control in halves receiving Strep. uberis, whereas no effect of TZD was observed with the exception of a lower SCD1 in TZD-treated goats compared to CTRL. We conclude that, contrary to our hypothesis, in goats receiving NRC recommended amount of vitamin A, TZD had a minor effect on the response to mastitis with a likely better liver response, but a lower phagocytosis and minor effect on expression of genes. Considering both in vivo experiments, we can conclude that TZD has an important effect on inflammatory response in dairy goats receiving low energy diet without vitamins supplementation but the effect disappears for the most part in goats receiving adequate feeding, including vitamin A. Furthermore, the lack of effects on expression of PPARγ target genes does not support TZD being a strong PPARγ agonist in dairy goats. Title: Role of Peroxisome Proliferator-Activated Receptor Gamma on Prevention/Cure of Mastitis Author: Trindade da Rosa, Fernanda Mastitis is a major endemic disease in dairy cows resulting in significant economic losses for the dairy industry. The peroxisome proliferator-activated receptor gamma (PPARγ) is a nuclear receptor that is able to bind and be activated by natural (e.g., fatty acids) and synthetic (e.g. thiazolidinedione) compounds. PPARγ plays important roles in adipocyte differentiation, inflammation, and re-epithelialization in monogastric. In ruminants, PPARγ may play a role in milk fat synthesis. The aim of this study was to assess the role of PPARγ in host response to mammary infection and milk fat synthesis in ruminants. Our hypothesis is that activation of PPARγ improves the host response to mastitis and increases milk fat yield. By using a synthetic PPARγ agonist in dairy goats in combination with intramammary infection to induce subclinical mastitis, the objectives of the present experiments were to test if activation of PPARγ improves 1) the response to mastitis and 2) milk fat production. To achieve our objectives we performed two in vivo experiments (Experiments 1 and 2). In Experiment 1, 24 Saanen lactating goats with a low body condition score and getting a low-energy diet without vitamin supplementation received a daily intrajugular injection of either 8 mg of 2,4-thiazolidinedione (TZD) per kg of BW or saline (as a control) and, after a week of TZD injection, an intramammary infusion (IMI) of either Streptococcus uberis to induce subclinical mastitis or saline used as a control (6 goats/group). Milk yield and components, body weight, rectal temperature, leukocyte phagocytosis, blood metabolic and inflammation parameters plus insulin, adipocyte size by histology, and expression by RT-qPCR of PPARγ target genes in adipose tissue obtained through biopsy and in mammary epithelial cells (MEC) isolated from milk were assessed. In MEC, expression of CCL2 and IL8 was also measured. Data were analyzed by GLIMMIX of SAS with Mastitis, TZD, and Time and all interactions as main effects and goat as random effect. Statistical significance and tendencies were declared at P < 0.05 and 0.05 ≤ P ≤ 0.10, respectively. The induction of mastitis was successful achieved as indicated by >5-fold increase of milk somatic cells count (SCC) in goats receiving Strep. uberis and by 30% decrease of % polymorphonuclear leukocytes in blood. The SCC in milk were overall lower in TZD-treated goats. Mastitis induction but not TZD decreased milk yield and production of milk fat. Goats receiving Strep. uberis had increased concentrations of glucose, triglycerides, and non-esterified fatty acids (NEFA) in blood after IMI. NEFA was not affected in TZD goats, which did not receive Strep. uberis. Inflammatory markers increased in blood of all goats but the increase of haptoglobin was overall lower in TZD treated goats. Indicators of liver activity, including albumin, paraoxonase, and cholesterol, overall decreased after IMI but cholesterol did not decrease in TZD-treated goats. The bactericidal myeloperoxidase was higher in TZD-treated goats after mastitis. Insulin sensitivity was not affected by TZD or mastitis. Adipocytes size increased over time and was higher in TZD goats not receiving Strep. uberis. Subclinical mastitis increased expression of CCL2 and prevented a decrease in expression of IL8. MEC from TZD-treated goats tended to have higher expression of PPARG, FASN and SCD1 after 3 weeks of TZD treatment. Neither mastitis nor TZD affected the expression of genes in adipose tissue. Overall the data of Experiment 1 indicated that the subclinical mastitis model was successfully achieved. The treatment with TZD decreased somatic cells in milk, improved the response of liver, decreased the severity of inflammation, and increased the killing capacity of neutrophils after IMI. The data suggested a more lipogenic adipose tissue in TZD-treated goats but also some active, although minor, nutrigenomic effect of TZD on MEC that may have counteracted the competition of lipid substrates between mammary and adipose tissue. Blood metabolic data suggested that goats responded to Strep. uberis intramammary infusion similar to dairy cows in negative energy balance. Data obtained from Experiment 1 indicated that TZD aids with mastitis response. TZD had some effect on milk fat synthesis but, overall, had a smaller-than-expected nutrigenomic effect probably also due to the low body condition and low energy in the diet of the goats. Thus, the effect of PPARγ on milk fat synthesis is still unclear. The rationale to perform Experiment 2 stemmed from the possibility that the limited nutrigenomic response observed in Experiment 1 was due to a potential dietary deficiency. Subsequent in vitro work demonstrated that TZD is a strong activator of PPAR but only in the presence of 9-cis-retinoic acid, a metabolite of vitamin A and the activation of PPARγ obligate heterodimer Retinoic-X-Receptor (RXR). Therefore, we hypothesized that continuous activation of PPARγ by TZD in dairy goats supplemented with adequate amount of vitamin A improves the inflammatory response to subclinical mastitis. In order to test this hypothesis we used 12 Saanen multiparous goats in early lactation. Goats received a diet that met the NRC requirements, including vitamin A, and a daily injection of 8 mg TZD per kg of BW (n=6) or saline (n=6; CTRL). Following 14 days of treatment, all goats received an IMI of Strep. uberis to induce subclinical mastitis in the right half of the udder with the left half used as control. Metabolic, inflammation, and oxidative-status profiling in blood including 20 parameters was performed. Milk yield, SCC, rectal temperature and leukocytes phagocytosis were measured. Expression of several PPARγ target genes and genes involved in inflammation was measured in MEC, macrophages isolated from milk, and liver tissue. Data were analyzed by GLIMMIX of SAS with treatment (TRT) and Time and TRTxTime interaction as main effects and goat as random effect. For milk and SCC, mammary half was also included in the main effect (including interactions). Statistical significance and tendencies were declared at P < 0.05 and 0.05 ≤ P ≤ 0.10, respectively. Milk yield decreased after IMI but the decrease was larger in TZD-treated goats. SCC increased after IMI but was not affected by TZD administration. Milk fat decreased after IMI in all halves except in the untreated half of TZD-treated goats. In blood within 2 days from IMI, ceruloplasmin, haptoglobin, and glucose were increased while Zn was decreased. These data confirmed successful induction of sub-clinical mastitis and a status of slight inflammation after IMI. None of the parameters in blood was affected by TZD with the exception of a lower bilirubin concentration and a tendency for higher haptoglobin in TZD vs. CTRL after IMI, indicating a more robust response of the liver to inflammation. The stronger inflammation was also supported by a tendency for higher reactive oxygen metabolites in TZD vs. CTRL group after IMI. We also detected a tendency for a higher globulin in TZD vs. CTRL indicating a better adaptive immune system. Leukocyte phagocytosis was strongly reduced by TZD treatment. None of the genes measured were affected by TZD in liver. In milk macrophages and MEC, expression of inflammatory genes was higher compared to control in halves receiving Strep. uberis, whereas no effect of TZD was observed with the exception of a lower SCD1 in TZD-treated goats compared to CTRL. We conclude that, contrary to our hypothesis, in goats receiving NRC recommended amount of vitamin A, TZD had a minor effect on the response to mastitis with a likely better liver response, but a lower phagocytosis and minor effect on expression of genes. Considering both in vivo experiments, we can conclude that TZD has an important effect on inflammatory response in dairy goats receiving low energy diet without vitamins supplementation but the effect disappears for the most part in goats receiving adequate feeding, including vitamin A. Furthermore, the lack of effects on expression of PPARγ target genes does not support TZD being a strong PPARγ agonist in dairy goats. Close

• 1380. [Article] Security protocols for linear network coding

  Network coding, as the next generation of data routing protocols, enables each intermediate node in a network to process and encode its received data before forwarding it to the next nodes. Hence, the ...

  Citation × Citation Citation Abstract Copy Title: Security protocols for linear network coding Author: Adeli, Majid Network coding, as the next generation of data routing protocols, enables each intermediate node in a network to process and encode its received data before forwarding it to the next nodes. Hence, the core idea in network coding is to allow a network to encode the data that is being transmitted through it. This revolutionary idea of data routing results in dynamic change in the content of each data packet. That is, in a network coding setting, the original data symbols that are generated at the source nodes evolve hop-by-hop as they travel through the intermediate nodes. This property is clearly in stark contrast with the methods that are used in traditional data routing protocols, where every intermediate node acts as a plain relay. In other words, in the conventional data routing algorithms, every intermediate node solely replicates its incoming data on one or more of its outgoing channels. The criteria and the policies based on which an intermediate node makes decisions about the proper outgoing channels corresponding to each incoming packet depend on the employed routing protocol. Usually, each intermediate node utilizes a set of routing information (such as a routing table) in order to find the most cost effective path or paths to the final destinations. The cost criterion may be defined based on various parameters, but what is fixed is that the general goal is always to find the most optimum route that starts from the node and reaches the final destination at the lowest cost. Upon finding the best output channels, the intermediate node simply copies the pertinent data packet on the optimum channels without inflicting any change in the data payload. This common method of data routing in conventional routing protocols is indeed considered as a very special case in network coding theory. The fact that in network coding every node processes (encodes) its input data to create its outgoing symbols implies that the encoding operation at a given network node can be expressed as a multi-input multi-output function which intakes the node's incoming data symbols as its input arguments and generates the outgoing data symbols departing the node as its outputs. Since each node in the network has its own function, they are called "local encoding function". This way of looking at the network coding operation enables us to simply define linear and nonlinear network coding as the network codes with linear and nonlinear local encoding functions, respectively. Hence, in linear network coding, every node (including the source and the sink nodes) executes a linear function on its incoming data symbols in order to generate its output symbols, while in nonlinear network coding this function is nonlinear. The linearity indicates that every output symbol of a local encoding function can be stated as a unique linear combination of its input symbols. Therefore, in linear network coding, the encoding operations at the intermediate nodes can be stated as matrix multiplications. If linear network coding is applied then each individual network node will have a matrix with known entries and fixed dimensions that represents the network coding operation at that particular node. These matrices will be called "local encoding matrix" in this work, where linear network coding is considered as the employed data routing protocol. The main focus of this thesis is to thoroughly study the security aspects of linear network coding, and propose new ideas and superior solutions for various security challenges that are faced in this class of data routing protocols. In a broad sense, security attacks can be categorized into two major classes: passive attacks and active attacks. In passive attacks (also known as wiretapping or eavesdropping attacks), the attacker threatens the confidentiality aspect of the data; meaning his goal is to obtain illicit access to the content of the data symbols while he is unable or not interested to change (manipulate) the content of the original data symbols. On the other hand, in active attacks (also known as pollution or Byzantine attacks), the attacker threatens the integrity and authenticity of data. That is, while the content of each original data packet is open and visible to everyone (including the attacker), his goal is to change or corrupt the content of data symbols or interrupt the data transmission process by jamming and blocking the flow of data stream in the network. Under assumption of linear network coding being the applied data routing scheme, both of these two attack classes are comprehensively studied in this thesis. Since in linear network coding each and every node in the network mixes up its incoming data to generate its outputs, observing the content of a symbol flowing on a channel usually does not reveal useful information about the original data symbols. This means network coding (and more specifically, linear network coding in our case) offers the network users an inherent and intrinsic level of security which is normally not an option when traditional store-and-forward data routing protocols are employed. In some cases and for some basic applications, this inherent security is enough; however, for many security-aware and sensitive applications that demand tighter security provisions, additional modifications to the base coding scheme are necessary in order to provide higher levels of security. In Chapter 2, six innovative security protocols that are tailored to effectively and efficiently counteract passive attackers in linear network coding are proposed. The solutions proposed in this chapter may be categorized in three main groups. Two protocols (A and B) are designed solely based on the intrinsic security feature of linear network coding. Protocol (A) requires each global encoding vector that is assigned to one of the network channels to have more than one nonzero entry. This stipulation is shown to be satisfied probabilistically with a probability that drastically approaches "1" as the code field, network capacity, or attacker's limitations increase. Protocol (B) is based on re-ordering the original message vector before sending it through the network. The re-ordering process is designed to elaborately scramble the message vector content in such a way that no additional function is required, yet by sending the scrambled message vector, the eavesdropper will not be able to obtain any information about any of the original data symbols. The sink nodes are the only nodes that are able to de-scramble the data and recover the original message vector. Both of these two protocols are extremely light-weight with no throughput reduction. The second group of our security solutions includes two protocols (C and E), each of which utilizes a hash function and a noisy symbol at the source node in order to generate the required random symbols (masking symbols) that are used to conceal the data symbols in the secured message vector. These protocols reduce the data rate by only one unit while they assume very lax conditions on the attacker's ability in accessing the independent network channels. The offered independency between the number of attacked channels and the secure data rate, and also enabling the source node to independently create its own keys and to change them as often as it generates new data packets are two of the remarkable properties of these protocols. The two remaining protocols (D and F) constituting the third group are in fact two variations of the second group protocols. That is, in order to alleviate the computational complexity burden of the algorithms in the second group, the hash functions are substituted by simple light-weight bijective functions in these protocols. Hence, in addition to all the benefits of the algorithms in the second group, these two protocols are also very fast and easy to implement. The fact that in (linear) network coding data symbols are constantly mixed up and intermingled as they travel through the network is indeed a double-edged sword. That is, as mixing and combining the data symbols provides some degree of security against snooping attackers (and this is besides the other advantages of network coding), if a malicious node injects some bogus or invalid data into the main data stream, then the inflicted pollution propagates throughout the network at an enormously great rate and causes the final destination nodes to be unable to recover the original data symbols. This class of attacks in linear network coding (i.e., pollution attacks) is studied in Chapter 3, where we propose a very efficient hierarchical scheme that is able to accurately pinpoint any number of polluting nodes in the network with any locational distribution. Our protocol is also capable of isolating and disconnecting the violating nodes from the rest of the network and therefore fixing the pollution problem in a more fundamental way. Title: Security protocols for linear network coding Author: Adeli, Majid Network coding, as the next generation of data routing protocols, enables each intermediate node in a network to process and encode its received data before forwarding it to the next nodes. Hence, the core idea in network coding is to allow a network to encode the data that is being transmitted through it. This revolutionary idea of data routing results in dynamic change in the content of each data packet. That is, in a network coding setting, the original data symbols that are generated at the source nodes evolve hop-by-hop as they travel through the intermediate nodes. This property is clearly in stark contrast with the methods that are used in traditional data routing protocols, where every intermediate node acts as a plain relay. In other words, in the conventional data routing algorithms, every intermediate node solely replicates its incoming data on one or more of its outgoing channels. The criteria and the policies based on which an intermediate node makes decisions about the proper outgoing channels corresponding to each incoming packet depend on the employed routing protocol. Usually, each intermediate node utilizes a set of routing information (such as a routing table) in order to find the most cost effective path or paths to the final destinations. The cost criterion may be defined based on various parameters, but what is fixed is that the general goal is always to find the most optimum route that starts from the node and reaches the final destination at the lowest cost. Upon finding the best output channels, the intermediate node simply copies the pertinent data packet on the optimum channels without inflicting any change in the data payload. This common method of data routing in conventional routing protocols is indeed considered as a very special case in network coding theory. The fact that in network coding every node processes (encodes) its input data to create its outgoing symbols implies that the encoding operation at a given network node can be expressed as a multi-input multi-output function which intakes the node's incoming data symbols as its input arguments and generates the outgoing data symbols departing the node as its outputs. Since each node in the network has its own function, they are called "local encoding function". This way of looking at the network coding operation enables us to simply define linear and nonlinear network coding as the network codes with linear and nonlinear local encoding functions, respectively. Hence, in linear network coding, every node (including the source and the sink nodes) executes a linear function on its incoming data symbols in order to generate its output symbols, while in nonlinear network coding this function is nonlinear. The linearity indicates that every output symbol of a local encoding function can be stated as a unique linear combination of its input symbols. Therefore, in linear network coding, the encoding operations at the intermediate nodes can be stated as matrix multiplications. If linear network coding is applied then each individual network node will have a matrix with known entries and fixed dimensions that represents the network coding operation at that particular node. These matrices will be called "local encoding matrix" in this work, where linear network coding is considered as the employed data routing protocol. The main focus of this thesis is to thoroughly study the security aspects of linear network coding, and propose new ideas and superior solutions for various security challenges that are faced in this class of data routing protocols. In a broad sense, security attacks can be categorized into two major classes: passive attacks and active attacks. In passive attacks (also known as wiretapping or eavesdropping attacks), the attacker threatens the confidentiality aspect of the data; meaning his goal is to obtain illicit access to the content of the data symbols while he is unable or not interested to change (manipulate) the content of the original data symbols. On the other hand, in active attacks (also known as pollution or Byzantine attacks), the attacker threatens the integrity and authenticity of data. That is, while the content of each original data packet is open and visible to everyone (including the attacker), his goal is to change or corrupt the content of data symbols or interrupt the data transmission process by jamming and blocking the flow of data stream in the network. Under assumption of linear network coding being the applied data routing scheme, both of these two attack classes are comprehensively studied in this thesis. Since in linear network coding each and every node in the network mixes up its incoming data to generate its outputs, observing the content of a symbol flowing on a channel usually does not reveal useful information about the original data symbols. This means network coding (and more specifically, linear network coding in our case) offers the network users an inherent and intrinsic level of security which is normally not an option when traditional store-and-forward data routing protocols are employed. In some cases and for some basic applications, this inherent security is enough; however, for many security-aware and sensitive applications that demand tighter security provisions, additional modifications to the base coding scheme are necessary in order to provide higher levels of security. In Chapter 2, six innovative security protocols that are tailored to effectively and efficiently counteract passive attackers in linear network coding are proposed. The solutions proposed in this chapter may be categorized in three main groups. Two protocols (A and B) are designed solely based on the intrinsic security feature of linear network coding. Protocol (A) requires each global encoding vector that is assigned to one of the network channels to have more than one nonzero entry. This stipulation is shown to be satisfied probabilistically with a probability that drastically approaches "1" as the code field, network capacity, or attacker's limitations increase. Protocol (B) is based on re-ordering the original message vector before sending it through the network. The re-ordering process is designed to elaborately scramble the message vector content in such a way that no additional function is required, yet by sending the scrambled message vector, the eavesdropper will not be able to obtain any information about any of the original data symbols. The sink nodes are the only nodes that are able to de-scramble the data and recover the original message vector. Both of these two protocols are extremely light-weight with no throughput reduction. The second group of our security solutions includes two protocols (C and E), each of which utilizes a hash function and a noisy symbol at the source node in order to generate the required random symbols (masking symbols) that are used to conceal the data symbols in the secured message vector. These protocols reduce the data rate by only one unit while they assume very lax conditions on the attacker's ability in accessing the independent network channels. The offered independency between the number of attacked channels and the secure data rate, and also enabling the source node to independently create its own keys and to change them as often as it generates new data packets are two of the remarkable properties of these protocols. The two remaining protocols (D and F) constituting the third group are in fact two variations of the second group protocols. That is, in order to alleviate the computational complexity burden of the algorithms in the second group, the hash functions are substituted by simple light-weight bijective functions in these protocols. Hence, in addition to all the benefits of the algorithms in the second group, these two protocols are also very fast and easy to implement. The fact that in (linear) network coding data symbols are constantly mixed up and intermingled as they travel through the network is indeed a double-edged sword. That is, as mixing and combining the data symbols provides some degree of security against snooping attackers (and this is besides the other advantages of network coding), if a malicious node injects some bogus or invalid data into the main data stream, then the inflicted pollution propagates throughout the network at an enormously great rate and causes the final destination nodes to be unable to recover the original data symbols. This class of attacks in linear network coding (i.e., pollution attacks) is studied in Chapter 3, where we propose a very efficient hierarchical scheme that is able to accurately pinpoint any number of polluting nodes in the network with any locational distribution. Our protocol is also capable of isolating and disconnecting the violating nodes from the rest of the network and therefore fixing the pollution problem in a more fundamental way. Close