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4281. [Article] Genome scale transcriptome analysis and development of reporter systems for studying shoot organogenesis in poplar
Vegetative propagation allows the amplification of selected genotypes for research, breeding, and commercial planting. However, efficient in vitro regeneration and genetic transformation remains a major ...Citation Citation
- Title:
- Genome scale transcriptome analysis and development of reporter systems for studying shoot organogenesis in poplar
- Author:
- Bao, Yanghuan
Vegetative propagation allows the amplification of selected genotypes for research, breeding, and commercial planting. However, efficient in vitro regeneration and genetic transformation remains a major obstacle to research and commercial application in many plant species. Our aims are to improve knowledge of gene regulatory circuits important to meristem organization, and to identify genes that might be useful for improving the efficiency of in vitro regeneration. In this thesis, we have approached these goals in two ways. First, we analyzed gene expression during poplar (Populus) regeneration using an AffymetrixGeneChip® array representing over 56,000 poplar transcripts. We have produced a catalog of regulated genes that can be used to inform studies of gene function and biotechnology. Second, we developed a GUS reporter system for monitoring meristem initiation using promoters of poplar homologs to the meristem-active regulatory genes WUSCHEL (WUS) and SHOOTMERISTEMLESS (STM). This provides plant materials whose developmental state can be assayed with improved speed and sensitivity. For the microarray study, we hybridized cDNAs derived from tissues of a female hybrid poplar clone (INRA 717-1 B4, Populus tremula x P. alba) at five sequential time points during organogenesis. Samples were taken from stems prior to callus induction, at 3 days and 5 days after callus induction, and at 3 and 8 days after the start of shoot induction. Approximately 15% of the monitored genes were significantly up-or down-regulated based on both Extraction and Analysis of Differentially Expressed Gene Expression (EDGE) and Linear Models for Microarray Data (LIMMA, FDR<0.01). Of these, over 3,000 genes had a 5-fold or greater change in expression. We found a very strong and rapid change in gene expression at the first time point after callus induction, prior to detectable morphological changes. Subsequent changes in gene expression at later regeneration stages were more than an order of magnitude smaller. A total of 588 transcription factors that were distributed in 45 gene families were differentially regulated. Genes that showed strong differential expression encoded proteins active in auxin and cytokinin signaling, cell division, and plastid development. When compared with data on in vitro callogenesis from root explants in Arabidopsis, 25% (1,260) of up-regulated and 22% (748) of down- regulated genes were in common with the genes that we found regulated in poplar during callus induction. When ~3kb of the 5' flanking regions of close homologs were used to drive expression of the GUSPlus gene, 50 to 60% of the transgenic events showed expression in apical and axillary meristems. However, expression was also common in other organs, including in leaf veins (40% and 46% of WUS and STM transgenic events, respectively) and hydathodes (56% of WUS transgenic events). Histochemical GUS staining of explants during callogenesis and shoot regeneration using in vitro stems as explants showed that expression was detectable prior to visible shoot development, starting 3 to 15 days after explants were placed onto callus inducing medium. Based on microarray gene expression data, a paralog of poplar WUS was detectably up-regulated during shoot initiation, but the other paralog was not. Surprisingly, both paralogs of poplar STM were down-regulated 3- to 6-fold during early callus initiation, a possible consequence of its stronger expression in the secondary meristem (cambium) than in shoot tissues. We identified 15 to 35 copies of cytokinin response regulator binding motifs (ARR1AT) and one copy of the auxin response element (AuxRE) in both promoters. Several of the WUS and STM transgenic events produced should be useful for monitoring the timing and location of meristem development during natural and in vitro shoot regeneration.
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4282. [Article] Social regulatory processes in adulthood : responding to change and variability in proximal and distal social forces
Adult development and social experiences are intertwined, which has implications for social policy, health, and well-being across the lifespan. This dissertation explores the benefit and risk that close ...Citation Citation
- Title:
- Social regulatory processes in adulthood : responding to change and variability in proximal and distal social forces
- Author:
- Mejía, Shannon T.
Adult development and social experiences are intertwined, which has implications for social policy, health, and well-being across the lifespan. This dissertation explores the benefit and risk that close social partners bring to adults' lives, and the efficacy and consequences of engaging social resources to maintain well-being in the face of variability and change in their proximal and distal social environments. The first study, using a life course perspective and a macro analytic lens, traced experiences of financial loss in middle adulthood during the 2008 recession. Using the 2006 and 2010 waves of the Health and Retirement Study (n = 1,881; age range = 51 - 60 years), this study used conditional change models and path analysis to examine the extent to which increasing household complexity, giving help, receiving help, and relationship quality promoted or hindered the capacity to maintain a sense of control in the face of financial loss. Experiencing financial loss was directly associated with decreased control and giving help, and increased household complexity and receiving help. Experiences of financial loss indirectly decreased control through increased household complexity and decreased giving help. Although the experience of financial loss was distributed across differences in income and education, social resources patterned the engagement of interpersonal resources, which translated to engagement patterns that could compromise the sense of control. However, change in relationship quality, which did not systematically differ across experiences of financial loss, created pathways to support or hinder maintaining a sense of control while engaging interpersonal resources. The second study, informed by lifespan developmental theory and developmental systems theory, applied a micro analytic lens to closely examine the within-person processes that connect daily interactions within the social convoy to emotional well-being in older adulthood. Using data from the Personal Understanding of Life and Social Experiences Project, this study linked older adults' (N = 99; age mean = 63.29, SD = 7.93) satisfaction with their five closest social partners to daily experiences of positive and negative affect across 100 days. Multivariate multilevel models suggest that older adults’ daily affect is more sensitive to the quality of daily interactions with closest compared to other social partners. The relative strength of positive and negative affect sensitivity also varied within levels of closeness. Negative affect was relatively more sensitive to interactions with the closest social partner, and positive affect was relatively more sensitive to interactions with other close social partners. This study also found emotional sensitivity to vary within individuals. Satisfying contact with other social partners dampened emotional sensitivity to the closest social partner on that day. These patterns differed across overall levels of contact satisfaction. Those with lower overall satisfaction had higher emotional sensitivity, and were less able to regulate the sensitivity of positive affect. Together, the findings from these studies suggest that: (a) how individuals engage their interpersonal resources in response to loss can facilitate or hinder the maintenance of control and well-being; (b) the strategies that individuals engage vary by the presence or absence of socioeconomic and socioemotional resources; and (c) social partners contribute to both emotional reaction and recovery, but this sensitivity can be up and down regulated by reaching out to other close social partners. Relationships with others therefore contribute to well-being by supporting (or hindering) the regulation of self, actions, and emotions. Regulation through close interpersonal ties illustrates a process that links developmental and life course trajectories.
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4283. [Article] Disengaged and untrusting? Young adults' feelings of social integration and trust during the Great Recession
Navigating the transition to adulthood is fraught with challenges, especially for those coming of age during an economic crisis. Individuals often rely on support from existing social networks, and establish ...Citation Citation
- Title:
- Disengaged and untrusting? Young adults' feelings of social integration and trust during the Great Recession
- Author:
- Day, Jack K.
Navigating the transition to adulthood is fraught with challenges, especially for those coming of age during an economic crisis. Individuals often rely on support from existing social networks, and establish social capital through deepening and expanding social ties, as they establish footholds in roles marking adulthood. Yet investing in social ties likely depends on levels of social trust, and conversely, social trust emerges from social ties. Additionally, social trust and integration are likely susceptible to change during economic recessions. The aim of this study is to address three research questions related to the relationship between social trust and integration: (1) How does the causal relationship between feelings of social trust and integration fluctuate for young adults amid uncertainty introduced by the Great Recession? (2) How does the relationship between social trust and integration vary in relation to young adults’ economic instability? (3) How does the relationship between feelings of social trust and integration vary in relation to entering roles marking adulthood? Using data from the Panel Study of Income Dynamics (PSID) from 2005 (n = 728), 2007 (n = 638), 2009 (n = 634), and 2011 (n = 606), cross-lagged models are utilized to assess the causal relationship between feelings of social trust and social integration among young adults (aged 17-27) before and during the Great Recession. Although most young adults in the study are not engaged in traditional civic activities, which often promote and emerge from social integration, many report feeling that they belong to a community and have something of value to contribute to society. They also report relatively persistent optimistic feelings of social trust over time, indicating that young adults’ outlooks on society and their own futures did not become more negative during the economic downturn. Most importantly, findings in this study provide evidence of a mutually causal relationship between feelings of social integration and trust, with investments in one domain having a positive effect on the other. The relationship between measures of social trust and integration did not, however, vary in predictable patterns in relation to the economic recession or to levels of individual economic instability. Yet both social trust and integration fluctuate in relation to changes in political climate, suggesting that they may be influenced by macro-level factors. Finally, entry into roles marking adulthood in 2007 is negatively, and in 2011 is positively, associated with feelings of social integration and, to a lesser extent, trust. These findings suggest that younger respondents who enter adult roles may be less trusting and connected to communities, though this trend reverses as the sample ages. The findings from this study have implications for identifying: threats to social trust, and effective means of encouraging and fostering trust through community engagement; ways in which young adults form connections to communities, and barriers to establishing diverse social networks that strengthen social capital; ways in which young adults take an active role in the political process and informing policy; and why they may opt-out of civic participation, especially if they lack social trust. Recommendations are made for developing more sensitive and clearly defined measures of social integration and trust, and for future research.
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4284. [Article] Methods for Efficient Synthesis of Large Reversible Binary and Ternary Quantum Circuits and Applications of Linear Nearest Neighbor Model
This dissertation describes the development of automated synthesis algorithms that construct reversible quantum circuits for reversible functions with large number of variables. Specifically, the research ...Citation Citation
- Title:
- Methods for Efficient Synthesis of Large Reversible Binary and Ternary Quantum Circuits and Applications of Linear Nearest Neighbor Model
- Author:
- Hawash, Maher Mofeid
- Year:
- 2013
This dissertation describes the development of automated synthesis algorithms that construct reversible quantum circuits for reversible functions with large number of variables. Specifically, the research area is focused on reversible, permutative and fully specified binary and ternary specifications and the applicability of the resulting circuit to the physical limitations of existing quantum technologies. Automated synthesis of arbitrary reversible specifications is an NP hard, multiobjective optimization problem, where 1) the amount of time and computational resources required to synthesize the specification, 2) the number of primitive quantum gates in the resulting circuit (quantum cost), and 3) the number of ancillary qubits (variables added to hold intermediate calculations) are all minimized while 4) the number of variables is maximized. Some of the existing algorithms in the literature ignored objective 2 by focusing on the synthesis of a single solution without the addition of any ancillary qubits while others attempted to explore every possible solution in the search space in an effort to discover the optimal solution (i.e., sacrificed objective 1 and 4). Other algorithms resorted to adding a huge number of ancillary qubits (counter to objective 3) in an effort minimize the number of primitive gates (objective 2). In this dissertation, I first introduce the MMDSN algorithm that is capable of synthesizing binary specifications up to 30 variables, does not add any ancillary variables, produces better quantum cost (8-50% improvement) than algorithms which limit their search to a single solution and within a minimal amount of time compared to algorithms which perform exhaustive search (seconds vs. hours). The MMDSN algorithm introduces an innovative method of using the Hasse diagram to construct candidate solutions that are guaranteed to be valid and then selects the solution with the minimal quantum cost out of this subset. I then introduce the Covered Set Partitions (CSP) algorithm that expands the search space of valid candidate solutions and allows for exploring solutions outside the range of MMDSN. I show a method of subdividing the expansive search landscape into smaller partitions and demonstrate the benefit of focusing on partition sizes that are around half of the number of variables (15% to 25% improvements, over MMDSN, for functions less than 12 variables, and more than 1000% improvement for functions with 12 and 13 variables). For a function of n variables, the CSP algorithm, theoretically, requires n times more to synthesize; however, by focusing on the middle k (k by MMDSN which typically yields lower quantum cost. I also show that using a Tabu search for selecting the next set of candidate from the CSP subset results in discovering solutions with even lower quantum costs (up to 10% improvement over CSP with random selection). In Chapters 9 and 10 I question the predominant methods of measuring quantum cost and its applicability to physical implementation of quantum gates and circuits. I counter the prevailing literature by introducing a new standard for measuring the performance of quantum synthesis algorithms by enforcing the Linear Nearest Neighbor Model (LNNM) constraint, which is imposed by the today's leading implementations of quantum technology. In addition to enforcing physical constraints, the new LNNM quantum cost (LNNQC) allows for a level comparison amongst all methods of synthesis; specifically, methods which add a large number of ancillary variables to ones that add no additional variables. I show that, when LNNM is enforced, the quantum cost for methods that add a large number of ancillary qubits increases significantly (up to 1200%). I also extend the Hasse based method to the ternary and I demonstrate synthesis of specifications of up to 9 ternary variables (compared to 3 ternary variables that existed in the literature). I introduce the concept of ternary precedence order and its implication on the construction of the Hasse diagram and the construction of valid candidate solutions. I also provide a case study comparing the performance of ternary logic synthesis of large functions using both a CUDA graphic processor with 1024 cores and an Intel i7 processor with 8 cores. In the process of exploring large ternary functions I introduce, to the literature, eight families of ternary benchmark functions along with a Multiple Valued file specification (the Extended Quantum Specification XQS). I also introduce a new composite quantum gate, the multiple valued Swivel gate, which swaps the information of qubits around a centrally located pivot point. In summary, my research objectives are as follows: * Explore and create automated synthesis algorithms for reversible circuits both in binary and ternary logic for large number of variables. * Study the impact of enforcing Linear Nearest Neighbor Model (LNNM) constraint for every interaction between qubits for reversible binary specifications. * Advocate for a revised metric for measuring the cost of a quantum circuit in concordance with LNNM, where, on one hand, such a metric would provide a way for balanced comparison between the various flavors of algorithms, and on the other hand, represents a realistic cost of a quantum circuit with respect to an ion trap implementation. * Establish an open source repository for sharing the results, software code and publications with the scientific community. With the dwindling expectations for a new lifeline on silicon-based technologies, quantum computations have the potential of becoming the future workhorse of computations. Similar to the automated CAD tools of classical logic, my work lays the foundation for creating automated tools for constructing quantum circuits from reversible specifications.
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4285. [Article] A public elementary school as a cultural context : Japanese children learning to perceive their environment
This thesis examines the cultural context in which Japanese children are constructing their own perspective of the environment because in the development of environmental education in Japan, the perspectives ...Citation Citation
- Title:
- A public elementary school as a cultural context : Japanese children learning to perceive their environment
- Author:
- Sugai, Taichi
This thesis examines the cultural context in which Japanese children are constructing their own perspective of the environment because in the development of environmental education in Japan, the perspectives of children and teachers have not been taken into consideration. Although educators have made efforts to give direction to environmental education, relatively few have focused on the teachers’ and children’s ordinary activities from the point of view of environmental education. This ethnographic study helps education policy makers to understand the actual state of a public elementary school, an institution expected to produce environmentally literate people. The data presented in this study were collected in my fieldwork at a public elementary school in Osaka, Japan between September and December in 2005. Main methods utilized in this research are participant observation in classrooms, school events, and casual conversation, and in- depth interviews with twenty teachers, administrators, parents, and community members. Throughout the research, I have two main objectives in mind. First, I explore whether children are completely removed from nature or not, a question that is dependent on how nature is defined. It is a tendency in Japan to view nature and culture as blending with each other, but in different ways according to the context. Thus, when observing children playing with a small part of nature (e.g., insects and flowers), some argue that children still have a connection with nature while others say that children lack opportunities to feel close to nature. Increasingly, people today accept the latter perspective, and regard nature as something distant from children’s ordinary lives. This view of nature is reinforced by the dramatic images of nature broadcast on TV. Additionally, the social circumstances that prevent parents from allowing their children to play outside freely lead them to think that they need to invest considerable time and money in order to let their children experience nature. As a result, parents tend to believe that nature hardly exists in their This thesis examines the cultural context in which Japanese children are constructing their own perspective of the environment because in the development of environmental education in Japan, the perspectives of children and teachers have not been taken into consideration. Although educators have made efforts to give direction to environmental education, relatively few have focused on the teachers’ and children’s ordinary activities from the point of view of environmental education. This ethnographic study helps education policy makers to understand the actual state of a public elementary school, an institution expected to produce environmentally literate people. The data presented in this study were collected in my fieldwork at a public elementary school in Osaka, Japan between September and December in 2005. Main methods utilized in this research are participant observation in classrooms, school events, and casual conversation, and in- depth interviews with twenty teachers, administrators, parents, and community members. Throughout the research, I have two main objectives in mind. First, I explore whether children are completely removed from nature or not, a question that is dependent on how nature is defined. It is a tendency in Japan to view nature and culture as blending with each other, but in different ways according to the context. Thus, when observing children playing with a small part of nature (e.g., insects and flowers), some argue that children still have a connection with nature while others say that children lack opportunities to feel close to nature. Increasingly, people today accept the latter perspective, and regard nature as something distant from children’s ordinary lives. This view of nature is reinforced by the dramatic images of nature broadcast on TV. Additionally, the social circumstances that prevent parents from allowing their children to play outside freely lead them to think that they need to invest considerable time and money in order to let their children experience nature. As a result, parents tend to believe that nature hardly exists in their neighborhoods. The pervasiveness of this view has led to the strong influence of parents’ sense of values and families’ socioeconomic status on how their children experience nature. Second, I describe what kind of environmental education has actually been implemented at a public elementary school. Children are constructing their perspective of the natural environment not only in the classes officially regarded as environmental education, but also in other aspects of their everyday school lives. Even when teachers do not think that they are teaching about the environment, their words and behavior convey culturally accepted ways to think, act and speak, and make decisions; this in turn influences the way students deal with nature. Thus, teachers are officially and unofficially, consciously and unconsciously, implementing environmental education. Nonetheless, today’s teachers believe that they conduct environmental education only in a weekly “Period of Integrated Learning.” While their preparation time for environmental education is limited, they realize the existence of various obstacles for the implementation of environmental education, such as lack of time and resources and the fact that children do not have enough knowledge and experiences to understand environmental problems. They eventually come to conduct environmental education through the lens of their own values. Yet, because of the lack of efficient criteria to judge whether the activities have a positive influence on the children, teachers do not seem to have confidence in the ongoing environmental education and underestimate the value of environmental education in comparison to other subjects like Japanese and mathematics. Teachers’ perceptions of environmental education have been shaped by the official discourse of environmental education, which has been widely accepted by common people and environmental educators. A significant effect is the pervasive belief that environmental education can be conducted by an add-on approach. This generates the tendency to ignore the fact that the curriculum itself has a deep cultural perspective on the human-nature relationship, which is highly problematic from the point of view of environmental education. In conclusion, I strongly argue that environmental educators and school officials who accept the importance of environmental education should comprehend the status quo of public elementary schools before turning over the responsibility of children’s education to teachers. Japan must build a society that affords the essential needs of education in order for teachers to give all their time and energy for the children they are currently facing. Before teachers can concentrate on environmental education, education officials, policymakers, and the public must understand the limitations of individual schools and teachers in relation to environmental education within the present education system. I recommend that environmental educators pay heed to insiders’ voices and experiences, examine what the voices represent from a broader perspective, and make these findings the basis of future plans for environmental education.
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4286. [Article] Influences of clearcut logging on macroinvertebrates in perennial and intermittent headwaters of the Central Oregon Coast Range
This research was designed to broaden the understanding of how timber-harvest affects aquatic macroinvertebrates in perennial and intermittent headwater streams. This study compared emergent and benthic ...Citation Citation
- Title:
- Influences of clearcut logging on macroinvertebrates in perennial and intermittent headwaters of the Central Oregon Coast Range
- Author:
- Banks, Janel
This research was designed to broaden the understanding of how timber-harvest affects aquatic macroinvertebrates in perennial and intermittent headwater streams. This study compared emergent and benthic macroinvertebrate assemblages from 20 headwater streams in the central Oregon Coast Range that varied by harvest condition and flow duration. Through comparison of the community and functional characteristics of the macroinvertebrates in similar streams under different harvest conditions, logging impacts on adult and immature aquatic macroinvertebrates in perennial and intermittent streams were assessed. Adult insects emerging from the 20 study streams were collected using emergence traps set for four weeks in a 40-meter reach during three sampling periods: August-September 2003, October-November 2003, and April-May 2004. Adult aquatic insects were identified to genus and family taxonomic levels and results were expressed as number of individuals emerging per m2 per day. Benthic samples were taken from each reach in May 2004, insects and non-insects were identified to various taxonomic levels, and results were expressed as number of individuals per m2. Ten streams were located in catchments that were clearcut to the stream bank no more than a year before sampling began; three of these streams were intermittent and seven were perennial. Intermittent streams were summer-dry and retained surface-water for a minimum of eight months during the year, while perennial streams had surface flow year-round. The other ten streams (four intermittent and six perennial) were located in forested catchments that have not been logged for at least 34 years. The physical habitat of each stream reach was assessed in August 2003. Regardless of flow-duration or season, more aquatic insects emerged from streams in logged catchments. The emergence rate of Diptera, predominantly Chironomidae, was especially high from clearcut sites. More Trichoptera also emerged from clearcut sites. Ephemeroptera and Plecoptera did not emerge at rates that varied by logging condition. Plecoptera had higher emergence from intermittent than perennial sites in spring. Taxa richness was higher at clearcut sites, driven primarily by rare taxa encountered in less than 5 of the 10 clearcut sites. Emergent insect functional feeding group composition was affected by harvest condition with collector-filterers emerging at higher rates from clearcut sites. Examination of community patterns through nonmetric multidimensional scaling (NMS) ordination analyses indicated that emergent aquatic macroinvertebrate assemblages differ by season and by harvest condition. The duration of stream flow did not strongly influence adult assemblages. Channel dimensions (active channel and bankfull width) and catchment area were correlated with ordination-axes, but were not different between logged and forested sites. The amount of riparian cover (canopy, understory, and groundcover), stand age, slash, and stream cover were all considerably different between logged and forested sites and were highly influential on emergent assemblages. Substrate size was also influential on adult assemblages. Mean water temperature in summer, fall, and spring was highly correlated with seasonal variation in assemblages. Regardless of harvest-condition, intermittent streams had higher overall benthic macroinvertebrate density. Trichoptera had higher densities at intermittent sites than perennial sites, while Diptera, Plecoptera, and non-insects had similar densities between categories of flow duration and harvest condition. Benthic macroinvertebrate functional composition was also affected by flow-duration, with collector-filterers, collector-gatherers, and predators occurring at higher densities at intermittent sites than perennial sites. The densities of scrapers and shredders did not differ between classes of flow duration or harvest condition. The majority of taxa (72%) were common to both perennial and intermittent sites; however, taxa richness was lower at intermittent sites. NMS-ordination analyses of the benthic macroinvertebrates showed that community patterns differed by harvest condition within the perennial flow-duration class. Benthic communities of intermittent streams did not differ between harvest conditions. Channel dimensions (active channel and bankfull width), mean substrate diameter, percent stream-cover, mean water temperature, elevation, and percent small riparian trees influenced benthic community assemblages. The majority of perennial-clearcut sites had macroinvertebrate community patterns more similar to intermittent-forested and intermittent-clearcut streams than to perennial-forested sites. The two perennial-clearcut sites that did not have benthic assemblages similar to the other five perennial-clearcut sites had larger diameter substrate, higher elevation, larger catchment area, and cooler mean water temperature than other perennial-clearcut sites. This study provides evidence that Oregon’s current timber harvesting practices impact macroinvertebrate assemblages of perennial and intermittent headwaters in the Central Oregon Coast Range within a year following harvest. When the studied streams were clearcut to the streambank, there was increased emergence of adult macroinvertebrates, principally midges, at clearcut sites. Benthic assemblages differed primarily between intermittent and perennial flow-duration. However, within flow-classes, assemblages of benthic aquatic macroinvertebrates in perennial streams were impacted by clearcut logging to a higher degree than intermittent streams. Perennial-clearcut streams had different benthic assemblages from perennial-mature streams and perennial-clearcut streams with coarser substrate and cooler temperatures. Intermittent streams, which generally experience fewer flushing events and accumulate finer substrates than perennial streams, may be affected to a lesser degree by any sedimentation caused by logging activity. Correlations of emergent and benthic macroinvertebrate communities with the measured environmental gradients are suggestive that reduced canopy cover and substrate composition are major influential factors.
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4287. [Article] Cruise ship disturbance to Kittlitz's murrelets (Brachyramphus brevirostris) in Glacier Bay National Park and Preserve, Alaska
The Kittlitz's murrelet (Brachyramphus brevirostris), a small pursuit-diving seabird in the family Alcidae, occurs across much of coastal Alaska and parts of the Russian Far East. Glacier Bay National ...Citation Citation
- Title:
- Cruise ship disturbance to Kittlitz's murrelets (Brachyramphus brevirostris) in Glacier Bay National Park and Preserve, Alaska
- Author:
- Marcella, Timothy K.
The Kittlitz's murrelet (Brachyramphus brevirostris), a small pursuit-diving seabird in the family Alcidae, occurs across much of coastal Alaska and parts of the Russian Far East. Glacier Bay National Park, located in Southeast Alaska, is believed to support approximately 37% of the worldwide breeding population of Kittlitz's murrelets during the summer months. Recent concern over apparent population declines in Alaska, coupled with the Park's dual mandate of resource preservation and visitation, led to this study. Cruise ships, although not the most numerous vessel type operating in Glacier Bay, have previously been identified as the vessel type eliciting the greatest disturbance response from Kittlitz's murrelets. During the murrelet breeding seasons in 2011 and 2012, my field assistants and I collected focal observations of 4,251 Brachyramphus murrelets from the bow of cruise ships traveling through Glacier Bay. Identification of murrelets to species was hampered by both the distance at which murrelets responded to the approaching ship and the type of response to the ship (diving vs. flushing). For roughly 40% of focal observations of murrelets from cruise ships, the species of murrelet (Kittlitz's murrelet or marbled murrelet [B. marmoratus]) could not be identified. Apparent habitat partitioning by the two murrelet species in Glacier Bay resulted in 79% of identified murrelets in the upper section of the Bay (Upper Bay) being Kittlitz's murrelets, while 83% of identified murrelets in the lower section of the Bay (Lower Bay) were marbled murrelets. In the Upper Bay, cruise ships are predicted to disturb 61% of all murrelets within 850 m on either side of the cruise ship's course (i.e., elicited a flushing or diving response), whereas in the Lower Bay, cruise ships are predicted to disturb 72% of murrelets within 850 m of the ship's course. Using Cox multistate models, I demonstrated that murrelets in the Upper Bay (predominantly Kittlitz's murrelets) were more likely to dive than flush in response to approaching cruise ships, whereas murrelets in the Lower Bay (predominantly marbled murrelets) were more likely to flush than dive. Also, murrelets in the Upper Bay responded to cruise ships by flushing or diving at shorter distances from the ship compared to murrelets in the Lower Bay. Murrelets in both areas of Glacier Bay generally reacted to cruise ships at greater distances when the ship approached indirectly, presumably because of the larger profile presented by a passing ship as opposed to a directly advancing ship. Absolute distance of the cruise ship from a focal murrelet was a strong predictor of murrelet disturbance response; no other management-relevant covariates that were measured during this study (e.g., ship velocity, distance to shore, whether a cruise ship had entered the Bay earlier that day) explained a significant proportion of the variation in murrelet response. Inferences based on data collected on-board cruise ships were limited to murrelet disturbance responses that occurred within 1 km of the ship. This was because of limits to the distance from the ship at which behavioral responses could be observed and the a priori assumption that disturbance to murrelets by cruise ships was unlikely at distances greater than 1 km. Results from shipboard observations indicated that some proportion of murrelets encountered at the farthest distance we could make inferences were on occasion disturbed (point estimate at 850 m perpendicular distance from ship's course = 15-30% probability of flushing or diving). This suggests that disturbance of murrelets by cruise ships in Glacier Bay exceeded expected distance thresholds. In order to investigate the effects of cruise ships on murrelet behavior at distances greater than 1 km, my assistants and I collected a total of 643 focal observations of Kittlitz's murrelets during 181 hours of observation from land-based observation sites in the Upper Bay during the 2012 field season. By combining these data with AIS and GPS ship tracks, I was able to append distance to the nearest cruise ship to each focal murrelet observation and search for patterns in murrelet behavior. By collecting data in this manner, I was able to avoid biasing the study based on pre-conceived notions of what constituted a threshold distance for cruise ships to disturb Kittlitz's murrelets. Using a segmented regression model within a logistic regression framework, I found that Kittlitz's murrelets exhibited a disturbance threshold (defined as an increased incidence of flushing from the water) by cruise ships at distances of at least 1.6 km, and perhaps as great as 6.0 km, with a best estimate of threshold disturbance distance at 3.8 km from a cruise ship. When cruise ships were greater than 3.8 km from focal Kittlitz's murrelets, the baseline probability of murrelets flushing during a focal observation period was 12.5%. When cruise ships were less than 3.8 km from focal Kittlitz's murrelets, the probability of flushing increased logistically with decreasing distance to an estimated 48% for the closest approach distances. The unexpectedly long distances at which murrelet behavior was affected by cruise ships in Glacier Bay is most likely attributable to social facilitation by other disturbed murrelets, because similar numbers of murrelets flushed when cruise ships were approaching (n = 30) as when they were receding (n = 27). Once a Kittlitz's murrelet flushed from the water, the subsequent duration of flight did not vary with distance to the nearest cruise ship. Instead, the duration of Kittlitz's murrelet flight was associated with time of day. The strong association between the proximity of cruise ships and the probability of a murrelet flushing, even at distances of several kilometers, demonstrates that Kittlitz's murrelets in Glacier Bay are susceptible to disturbance from cruise ships at distances greater than has previously been published for any seabird.
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4288. [Article] The illicit use of prescription stimulants on college campuses : a theoretical examination
The illicit use of prescription stimulants (IUPS) is a critical Public Health problem in the college population that represents a unique form of substance use. Namely, the primary motives for IUPS by college ...Citation Citation
- Title:
- The illicit use of prescription stimulants on college campuses : a theoretical examination
- Author:
- Bavarian, Niloofar
The illicit use of prescription stimulants (IUPS) is a critical Public Health problem in the college population that represents a unique form of substance use. Namely, the primary motives for IUPS by college students are academic in nature (e.g., Teter, McCabe, LaGrange, Cranford, & Boyd, 2006), which may explain why usage rates as high as 43% have been reported on college campuses (Advokat, Guidry, & Martino, 2008). As the field of IUPS is in its infancy, the IUPS-literature lacks 1) a consistent definition of "illicit use of prescription stimulants", 2) an instrument designed to assess the multiple influences on IUPS behavior, and 3) a theoretical lens (Bavarian, 2010a). Accordingly, the goal of this study was to address these research gaps by examining IUPS at one university located in the Pacific Northwest using the theory of triadic influence (TTI; Flay & Petraitis, 1994; Flay, Snyder, & Petraitis, 2009), an integrated, ecological approach to explaining and predicting health behaviors. The study included five phases of research. The first phase began with a systematic approach to measurement development resulting in a 97-item preliminary instrument, the Behaviors, Expectancies, Attitudes and College Health Questionnaire (BEACH-Q). The measure was reviewed by the dissertation committee, leading to revisions in content and structure. During phase II, the BEACH-Q was evaluated by a convenience sample of five health and measurement professionals, and results suggested good content validity of the instrument (i.e. 35 of the 37 TTI-based covariates received a median rating between "agree" and "strongly agree", and 34 received a mean rating between "agree" and "strongly agree"). In phase III (instrument review by a convenience sample of six undergraduates), all 37 covariates received a median and mean rating between "agree" and "strongly agree", confirming good face validity. In phase IV, one undergraduate classroom was selected to participate in a pilot test of the BEACH-Q, using test-retest methodology. Results from the pilot (N = 39) showed that the instrument had moderate to high internal consistency reliability and modest to high stability reliability. In phase V, the final 96-item version of the BEACH-Q was administered throughout campus using one-stage cluster sampling, with classrooms as the sampling unit and students as the observation unit (N = 520 students in 20 classrooms, eligible student response rate = 96.30%). The prevalence of IUPS during college self-reported by the phase V sample was 25.58%, and the probability of engaging in IUPS did not differ between classrooms (Median Odds Ratio = 1.00). In crude logistic regressions, 24 out of 37 hypothesized theoretical covariates were significantly associated with IUPS in the expected direction, suggesting predictive validity of the BEACH-Q. Nested logistic regression analyses illustrated that, for the full multivariate model including ultimate, distal, and proximal covariates, the following measures in the intrapersonal stream were significantly associated with IUPS during college: race/ethnicity, year in school, academic concern, academic grades, diagnosis with Attention Deficit Disorder, and IUPS avoidance self-efficacy. Significant social situation/context stream covariates in the full model included: residence, varsity sports participation, perceptions of IUPS by friends, family, and faculty, endorsement of IUPS by friends, and perceived prevalence of IUPS among friends. With respect to the sociocultural environment stream, in the full multivariate model, the following covariates were found to be significantly associated with IUPS: financial-related stress, participation in religious activities, positive IUPS expectancies, prescription stimulant knowledge and perceived costs/benefits of IUPS. Lastly, intention to engage in IUPS (an immediate precursor) was positively associated with IUPS. Structural equation modeling was used to test models of IUPS for each of the three streams, as well as one integrated model that included covariates from each stream. The models all demonstrated good model fit, and provided insight into the factors that influence (and suggest the mechanisms of causation) intentions to engage in, and ultimately the behavior of, IUPS. In the intrapersonal stream model, inattention was positively associated with academic concern and inversely associated with avoidance self-efficacy, and avoidance self-efficacy was inversely associated with intentions to engage in IUPS. Moreover, intentions to engage in IUPS and avoidance self-efficacy were both significantly associated with IUPS. In the social situation/context stream model, living on-campus was negatively associated with friends' endorsement of IUPS which was positively associated with perceived prevalence of IUPS among friends, and perceived prevalence was positively associated with intentions to engage in IUPS; all of the direct paths to IUPS, excepting the path from perceived prevalence of IUPS among friends, were significant. In the sociocultural environment model, perception of course demand was significantly associated with both the perception that professors give the most attention to top academic students and attitudes about the impact of prescription stimulants on academics, and these attitudes had a positive association with intentions to engage in IUPS. Moreover, the direct paths from attitudes and intentions to IUPS were significant. The mixed model, including participation in religious activities (sociocultural environment stream), friends' endorsement of IUPS (social situation/context stream), and avoidance self-efficacy (intrapersonal stream), also had significant paths from ultimate to distal to proximal to immediate precursor, and significant direct paths to IUPS. This study successfully achieved its goals. First, the instrument developed was theory-driven, broadly defined IUPS, and was psychometrically strong. The cross-sectional study illustrated that IUPS was prevalent on the campus under investigation, as one in four students had engaged in the behavior during college. Associations of use with theoretical correlates were tested for, and structural equation modeling was used to support one premise of the TTI (i.e. that behavior is multifaceted, and covariates from different streams may interact to influence behavior). The findings also suggest that prevention and intervention plans should be multifaceted in nature. Given that this study's cross-sectional nature limited the ability to make causal inferences, future research involving the BEACH-Q should use longitudinal designs.
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Body size explains much of the interspecific variation in the physiology, behavior, and morphology of birds, such as metabolic rate, diet selection, intake rate, gut size, and bill size. Based on mass-specific ...
Citation Citation
- Title:
- The role of body size in the foraging strategies and management of avian herbivores : a comparison of dusky Canada geese (Branta canadensis occidentalis) and cackling geese (B. hutchinsii minima) wintering in the Willamette Valley of Oregon
- Author:
- Mini, Anne E.
Body size explains much of the interspecific variation in the physiology, behavior, and morphology of birds, such as metabolic rate, diet selection, intake rate, gut size, and bill size. Based on mass-specific metabolic requirements and relative energetic costs of activities, being a certain body size has both advantages and disadvantages. In particular, avian herbivores such as geese possess a relatively simple digestive system, consume foods with low digestibility and poor nutrient content, and have increased energetic demands compared to other bird taxa; therefore, any effects of body size on foraging strategies should be readily apparent in this foraging guild. The influence of body size on the behavior and management of Canada Geese (Branta canadensis) and Cackling Geese (B. hutchinsii) as avian herbivores has not been well studied. My dissertation explores the role of body size in comparative foraging behavior, habitat selection, and winter conservation planning for two congeneric geese, the Dusky Canada Goose (B. c. occidentalis; hereafter Duskys) and the Cackling Goose (B. h. minima; hereafter Cacklers). These two taxa share the same over-winter foraging environment (grass seed fields) in the same restricted geographic area (the Willamette Valley) during winter. Duskys and Cacklers differ by more than a factor of two in body size and have different relative bill sizes and social organization. Because of smaller body size, Cacklers have greater relative energy demands and less fasting endurance compared to Duskys; however, Cacklers have comparatively low energetic costs for flight and transport. Duskys, however, have higher total energy requirements than Cacklers. Additionally, Cacklers form large, high-density flocks and have a total over-wintering population size in the study area of about 200,000. Duskys occur in relatively small family groups and have a total over-wintering population size of about 13,000. My study demonstrated that interspecific differences in body size between Cacklers and Duskys was associated with differences in foraging behavior, movements, and habitat selection. Cacklers foraged a greater percentage of time (30%) in all habitats and across the entire winter compared to Duskys. Cacklers had higher peck rates (up to 100 pecks min⁻¹ greater) than Duskys in all foraging habitats expect pasture. The pecking rate of Cacklers was greatest in fields of young grass (200 pecks min⁻¹), which may indicate that Cacklers had relatively high intake rates in this foraging habitat. Based on differences in foraging behavior among habitats, Cacklers may have the foraging strategy of energy intake maximizers, whereas the foraging strategy of Duskys is more towards time-energy expenditure minimizers, at least for part of the winter. Cacklers moved across the landscape very differently from Duskys, exhibiting less site fidelity and greater commuting distances to foraging areas. Cacklers showed a preference for young grass during all periods of the winter, reaffirming that Cacklers are specialized grazers on short green forage, whereas Duskys preferred young grass and pasture. Fields of young grass were the preferred foraging habitat of Cacklers, had less standing crop biomass, and may have enabled higher foraging efficiencies, which may have led to higher intake rates. The ability of the landscape to support wintering geese changed across the winter because total available plant biomass fluctuated with the rate of grass regrowth. The estimated carrying capacity of the landscape for geese decline by almost one-half during mid-winter (mid-December to mid-February) compared to early winter or late winter periods. Although Cacklers have lower individual energy requirements compared to Duskys, due to a much larger target population size, Cacklers required 89% more foraging habitat than Duskys. Forage requirements encountered a bottleneck during mid-winter, when grass regrowth rates were low and day length was short. Commensurate with this pattern of forage availability, goose body condition declined during the mid-winter period. To support Pacific Flyway target populations for geese, approximately 18,000 ha of total grazing habitat in young and mature grass is needed in the Willamette Valley to support a total over-wintering population composed of 340,000 geese belonging to four subspecies. The role of body size in influencing the foraging behavior and decisions of over-wintering geese has important implications for conservation planning of goose populations. Small-bodied Cacklers are selective in field choice, yet more likely to redistribute across the landscape. Disturbances (e.g., hunting, hazing, or predation) will have a disproportionate effect on the movements of smaller-bodied geese compared to larger geese. These characteristics of Cacklers will make conservation planning to retain geese on public land more difficult. Coordinated management with private landowners and farming practices that maximize preferred goose foraging habitat on public lands may attract geese to utilize protected areas and minimize conflicts with agriculture in the Willamette Valley. Availability of resources during critical periods in winter is an important factor affecting the distribution of geese, but may affect small and large bodied geese differently. Management could be targeted during these critical time periods. By considering the role of body size in the context of life history characteristics, foraging behavior and habitat selection, appropriate management strategies can be developed and implemented to reduce the effects of agricultural depredation by geese, while promoting the future conservation of wintering geese in the Willamette Valley.
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Clostridium perfringens is a Gram-positive, anaerobic, spore-forming bacterium that can produce as many as 17 different toxins and are responsible to cause a wide array of gastrointestinal (GI) and histotoxic ...
Citation Citation
- Title:
- Characterization of Sporulation and Germination Genes in Clostridium perfringens
- Author:
- Talukdar, Prabhat Kumar
Clostridium perfringens is a Gram-positive, anaerobic, spore-forming bacterium that can produce as many as 17 different toxins and are responsible to cause a wide array of gastrointestinal (GI) and histotoxic diseases in humans and animals. As individual strains produce a subset of these toxins, C. perfringens strains can be classified into five toxinotypes (A-E). C. perfringens type A strains that produce C. perfringens enterotoxin (CPE) cause food-poisoning (FP) and non-food borne (NFB) diseases in humans and domestic animals which account for a substantial amount of economic loss every year in the United States. To cause a wide variety of diseases in different hosts, C. perfringens possesses several unique characteristics; i) this bacterium is anaerobic and can survive in many conditions that are not regularly exposed to the air or has limited oxygen concentration, such as soil, sewage, GI tract of humans and animals, ii) it can form spores that are resistant to heat and other environmental stresses, iii) by sensing favorable conditions, spores of C. perfringens can rapidly transform into vegetative cells through a process called germination when conditions are favorable, and iv) it can produce variety of toxins in different conditions. Considering these unique features regarding C. perfringens survival in the environment and pathogenicity towards different hosts, it is important to identify genes and proteins that are involved in C. perfringens sporulation and germination process. Also, identification of potential germinant molecules is important to effectively kill spores with minimal effort. The studies conducted for this dissertation were focused to identify and characterize several putative germination and sporulation specific proteins as well as characterize germinant molecules for C. perfringens isolates from various sources. The initial focus of this dissertation was to investigate the role of two serine proteases of Csp family proteins, CspA and CspC, in C. perfringens spore germination. Previously, it has been shown that another serine protease CspB is involved in the processing of pro-SleC into mature, active SleC. SleC is a cortex lytic enzyme that is involved in the spore cortex hydrolysis in C. perfringens spore germination. Our current study demonstrated that i) cspA and cspC are transcribed as a bicistronic operon during the sporulation and the location of the transcripts are present in mother cell only, ii) both CspA and CspC have role in spore germination, as spores of double cspA-cspC and single cspC mutants exhibited very low extent of germination with different nutrient and non-nutrient germinants than wild-type and complemented strains, iii) cspA and cspC spores were defective in outgrowth and colony formation in nutrient rich media, iv) CspA and CspC are involved in spore cortex hydrolysis by processing of pro-SleC into active SleC, and finally v) CspA and CspC do not activate and regulate the levels of CspB. The second focus of this dissertation was to identify and characterize several putative sporulation proteins in C. perfringens FP strain SM101. Nine genes (ylzA, ymxH, spoIIM, ytxC, ylxY, ytaF, yyaC1, yyaC2 and bkdR) were identified based on the homology with respective genes in Bacillus subtilis. Among the selected genes, promoters of seven genes (ymxH, spoIIM, ytxC, ytaF, yyaC1, yyaC2 and bkdR) were expressed at different time points during sporulation as determined by β-glucuronidase assay. By using group-II intron based TargeTron technique, null mutations were inserted in seven genes (ymxH, spoIIM, ytxC, ytaF, yyaC1, yyaC2 and bkdR) and analyzed for spore formation and germination properties. Results from this study revealed that, ii) SpoIIM plays very crucial role in spore formation as no spores were produced by spoIIM mutant strain, ii) YmxH, YtxC, YtaF, YyaC1 and BkdR have minor role in spore formation as C. perfringens ymxH, ytxC, ytaF, yyaC1 and bkdR strains showed significantly reduced spore formation compared to the wild-type strain, and iv) YyaC2 and YtxC have roles in spore germination as lower germination rate and decreased DPA release compared to wild-type was observed with yyaC2 and ytxC mutant spores. The final focus of this dissertation was to identify the germinants for the spores of C. perfringens strains isolated from diseased animals and investigate the presence and expression of major germination genes in these animal isolates. Spores of C. perfringens animal isolates (horse isolates 106902 and 106903, pig isolates JGS1071 and JGS1807, dog isolates 294442 and 294443, and poultry isolates JGS4122 and JGS4125) were tested with different nutrient and non-nutrient germinants. Spores of C. perfringens animal isolates showed very low germination with different nutrient, non-nutrient germinants, rich media and cell culture media compared to human FP isolate SM101. When spores of four strains (106903, JGS1807, 294442, and JGS4122) of animal isolates were tested with all amino acids at pH 7.0 and pH 6.0, the germination rate varied among strains and was not consistent. However, most of the strains germinated better at pH 6.0 than at pH 7.0 with all amino acids tested. Germination assay with L-cysteine and L-lysine at different pHs (5.0 to 9.0) and different concentrations (1 mM to 200 mM) revealed that except strain JGS4122, all other strains did germinate better with higher concentrations of L-cysteine and L-lysine at pH range of 5.5-7.0. qRT-PCR analyses with RNA extracted from 8 h sporulation culture showed that level of expressions of gerKA, gerKB, gerKC and gerAA were higher in animal isolates compared to SM101. However, the transcript levels of cspA, cspB, cspC and sleC were lower in animal isolates. This finding was further confirmed by the quantitative Western blot analyses as the levels of both CspB and SleC was low in C. perfringens animal isolates than in human isolates. Together this finding suggests that C. perfringens animal isolates may have low activity in cortex hydrolysis that results in the lower spore germination. Collectively, our studies contribute towards understanding the mechanism of sporulation and germination in pathogenic bacterium C. perfringens by 1) dissecting the role of two new Csp proteases in C. perfringens spore germination; 2) identifying and characterizing new sporulation and germination genes in the pathogenic bacterium C. perfringens, and 2) characterizing germination of spores of C. perfringens isolated from diseased animals.