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• 2021. [Article] Lents: Alternatives for the Future

  This document is the complement to the Issues Analysis. The Issues Analysis looked at the problems and issues which confront the Lents neighborhood. This document proposes actions that can be taken to ...

  Citation × Citation Citation Abstract Copy Title: Lents: Alternatives for the Future Author: Healy, Kent, Gumusoglu, Shea, Dane, Mark, Kelley, Steve, Holycross, Jim, Zhou, Ning-Sheng, Ray, Michael, Loughran, Sean, Bairnsfather, Kyle, Scolnick, Peggy, Zybas, Matt Year: 1993 This document is the complement to the Issues Analysis. The Issues Analysis looked at the problems and issues which confront the Lents neighborhood. This document proposes actions that can be taken to address the issues identified in the previous analysis. Each section, e.g. Environment, Transportation, etc., has its own goals and subsequent objectives and actions. A goal is a broad statement of what is the desired outcome for the neighborhood. More specific objectives identify what needs to be done to improve things and to remedy the identified problems. The actions are means to achieve an objective. Specific potential implementers are then proposed for each action suggested. Interconnections between different sections exist for many problems and solutions. For example, the light rail alignment is a transportation issue but has ramifications in all aspects of life. Because of the inter-relatedness of the urban system, it was concluded that a unifying vision would be the best vehicle to present the means of addressing the neighborhood's issues. Three distinct visions of potential futures for the neighborhood of Lents are presented below. The time scale for these visions is long, approximately 50 years. This allows for three distinctly different visions for Lents. The three visions are; Status Quo, Urban Villages and Regional Attractor. The visions act to encompass all the linkages and provide direction towards a unified future state of existence for the neighborhood. An urban system, like any system, needs to have connection and continuity between its various parts for it to function efficiently. The visions are a means of achieving this. In the Status Quo vision the neighborhood will continue to move through time without major adjustments to its existing state. The actions for change are congruent with the existing state of the neighborhood. Goals and objectives for this vision relate directly to current neighborhood concerns. The suggested actions work towards alleviating current problems and making the neighborhood a better place to live, work and do business. The land use structure and neighborhood function would be not be altered in any significant way. The Urban Village's fundamental idea is to strive for neighborhood selfsufficiency. The neighborhood is separated into "nodes" or "activity centers." A node or activity center is a relatively small area of diverse and intense activity. The nodes help to define residents' sense of neighborhood. A node might have a public open space, such as a developed park, which would be surrounded by mixed-use development, commercial on the first floor and residential above. The nodes would be linked by pedestrian friendly greenways (streets improved with trees and flora) encouraging walking as the preferred mode of transportation. Density would be increased around the nodes to further encourage pedestrian travel and make businesses economically viable to customers using this mode of travel. Educational facilities would be linked closely to neighborhood needs, and cottage industries would be encouraged. In the Regional Attractor vision, the neighborhood would serve a specialized function to the whole metropolitan region. The focus would switch from mainly residential concerns to primaily employment generating concerns. Industry and business would be the critical elements in this neighborhood vision. Automobile or transit use would be the major modes of travel to ensure the neighborhood has regional accessibility. The neighborhood would serve as a single component within a regional system. This document will explore each of these visions in greater depth and present the means to making the vision a reality. While no single vision of Lents will seem preferable to everyone, the hope in presenting these three distinctly different potential futures for the neighborhood, is to reinforce an understanding of the tradeoffs that must be considered when developing a Lents plan. The intent is not to actually see the implementation of one of these visions, but rather to make the choices that must be made between one action and another more explicit. Our sincere hope is that any dialoque this document provokes will be one in which the interests of all Lents residents, present and future, are considered. Title: Lents: Alternatives for the Future Author: Healy, Kent, Gumusoglu, Shea, Dane, Mark, Kelley, Steve, Holycross, Jim, Zhou, Ning-Sheng, Ray, Michael, Loughran, Sean, Bairnsfather, Kyle, Scolnick, Peggy, Zybas, Matt Year: 1993 This document is the complement to the Issues Analysis. The Issues Analysis looked at the problems and issues which confront the Lents neighborhood. This document proposes actions that can be taken to address the issues identified in the previous analysis. Each section, e.g. Environment, Transportation, etc., has its own goals and subsequent objectives and actions. A goal is a broad statement of what is the desired outcome for the neighborhood. More specific objectives identify what needs to be done to improve things and to remedy the identified problems. The actions are means to achieve an objective. Specific potential implementers are then proposed for each action suggested. Interconnections between different sections exist for many problems and solutions. For example, the light rail alignment is a transportation issue but has ramifications in all aspects of life. Because of the inter-relatedness of the urban system, it was concluded that a unifying vision would be the best vehicle to present the means of addressing the neighborhood's issues. Three distinct visions of potential futures for the neighborhood of Lents are presented below. The time scale for these visions is long, approximately 50 years. This allows for three distinctly different visions for Lents. The three visions are; Status Quo, Urban Villages and Regional Attractor. The visions act to encompass all the linkages and provide direction towards a unified future state of existence for the neighborhood. An urban system, like any system, needs to have connection and continuity between its various parts for it to function efficiently. The visions are a means of achieving this. In the Status Quo vision the neighborhood will continue to move through time without major adjustments to its existing state. The actions for change are congruent with the existing state of the neighborhood. Goals and objectives for this vision relate directly to current neighborhood concerns. The suggested actions work towards alleviating current problems and making the neighborhood a better place to live, work and do business. The land use structure and neighborhood function would be not be altered in any significant way. The Urban Village's fundamental idea is to strive for neighborhood selfsufficiency. The neighborhood is separated into "nodes" or "activity centers." A node or activity center is a relatively small area of diverse and intense activity. The nodes help to define residents' sense of neighborhood. A node might have a public open space, such as a developed park, which would be surrounded by mixed-use development, commercial on the first floor and residential above. The nodes would be linked by pedestrian friendly greenways (streets improved with trees and flora) encouraging walking as the preferred mode of transportation. Density would be increased around the nodes to further encourage pedestrian travel and make businesses economically viable to customers using this mode of travel. Educational facilities would be linked closely to neighborhood needs, and cottage industries would be encouraged. In the Regional Attractor vision, the neighborhood would serve a specialized function to the whole metropolitan region. The focus would switch from mainly residential concerns to primaily employment generating concerns. Industry and business would be the critical elements in this neighborhood vision. Automobile or transit use would be the major modes of travel to ensure the neighborhood has regional accessibility. The neighborhood would serve as a single component within a regional system. This document will explore each of these visions in greater depth and present the means to making the vision a reality. While no single vision of Lents will seem preferable to everyone, the hope in presenting these three distinctly different potential futures for the neighborhood, is to reinforce an understanding of the tradeoffs that must be considered when developing a Lents plan. The intent is not to actually see the implementation of one of these visions, but rather to make the choices that must be made between one action and another more explicit. Our sincere hope is that any dialoque this document provokes will be one in which the interests of all Lents residents, present and future, are considered. Close

• 2022. [Article] Ecomorphology and Mating Behavior of Two Species of Night-stalking Tiger Beetles, Omus audouini and O. dejeanii

  Night-stalking tiger beetles (Cicindelinae: Omus) are among the least studied members of the highly diverse Carabid sub-family Cicindelinae, the tiger beetles. Despite populations of Omus being common ...

  Citation × Citation Citation Abstract Copy Title: Ecomorphology and Mating Behavior of Two Species of Night-stalking Tiger Beetles, Omus audouini and O. dejeanii Author: Richardson, Robert Kent Year: 2013 Night-stalking tiger beetles (Cicindelinae: Omus) are among the least studied members of the highly diverse Carabid sub-family Cicindelinae, the tiger beetles. Despite populations of Omus being common in the forest floor habitats of the west coast of North America and their conspicuous predatory role within terrestrial arthropod communities, little is known about the biology and ecology of Omus. Field studies showed that two species of Omus existed in the forested areas of Powell Butte Nature Park, Portland, Oregon, USA: Omus audouiniand O. dejeanii. The co-occurrence of sympatric, and likely syntopic, species allowed for a comparative approach in examining and analyzing previously unknown or unaddressed aspects of the biology of Omus. Both morphometric and behavioral analysis was used to address specific questions regarding niche partitioning and mating behaviors in the genus. On the basis of the competitive exclusion principle, I predicted that these closely related species with similar ecological requirements would experience selective pressure to minimize niche overlap and competitive pressures through morphological character displacement. In particular, the mandibles of male tiger beetles serve a dual role: one as tools for feeding-- including prey capture and prey processing--and another role as secondary sexual organs whereby the males use their mandibles to grasp the female and maintain amplexus. A geometric morphometric approach was used to evaluate and compare shape differences between the two species as well as identify trends of sexual dimorphism and species differences in context of prey base. Tiger beetles obligatorily engage in male-superior mounted mating behavior. Body size was used to first address trends of female-biased sexual size dimorphism within the Carabid subfamily Cicindelinae. Female tiger beetles may be expected to experience proportionally greater stress during mating among larger bodied than smaller bodied species and selection would favor increasingly pronounced female-biased sexual size dimorphism among larger-bodied species. The mating duration of Omuswas anecdotally reported as an order of magnitude greater than any other tiger beetle but has never been experimentally confirmed. I performed a series of pairings under laboratory setting to (1) establish a baseline of mating duration for the two species and test the effects of (2) time of day mating was initiated, (3) food deprivation and (4) operational sex ratio on mating duration. Morphometric analysis suggested niche partitioning existed between the two species due to an average body size scaling factor of x1.3 and an average mandible length scaling factor of x1.5, i.e. "Hutchinsonian Ratios"-- an observed minimum scaling threshold of niche differentiation seen in several natural predator populations. Similar minimum values were not seen between the sexes of either species suggesting an absence of sexual niche dimorphism. Geometric morphometric analysis of the mandibles revealed two distinct regions subject to selective adaptation: the distal region of the mandible (including the apical incisor) was consistently sexually dimorphic between the examined species while the proximal region involving the terebral teeth showed interspecific differences independent of sex and likely associated with prey processing, further supporting the hypothesis of niche partitioning between the two species but not necessarily between the sexes. The magnitude of sexual size dimorphism was found to be constant within Cicindelinae regardless of species body size. Behavioral analysis of mating established thatO. audouiniandO. dejeaniihave average (± SD) mating durations of 10.6 (± 1.8) and 29.4 (± 5.6) hours, respectively. Time of initiation of mating (whether morning or evening), food deprivation and operational sex ratio did not have any statistically significant effect on mating duration for either species. The absence of effect operational sex ratios on mating duration by suggests that mate guarding may not be a universal factor for all tiger beetles and, instead, syn- copulatory courtship, as opposed to pre- or post-copulatory courtship, as a female-choice reproductive mechanism may serve as a better explanation for the mating behaviors seen in Omus. Title: Ecomorphology and Mating Behavior of Two Species of Night-stalking Tiger Beetles, Omus audouini and O. dejeanii Author: Richardson, Robert Kent Year: 2013 Night-stalking tiger beetles (Cicindelinae: Omus) are among the least studied members of the highly diverse Carabid sub-family Cicindelinae, the tiger beetles. Despite populations of Omus being common in the forest floor habitats of the west coast of North America and their conspicuous predatory role within terrestrial arthropod communities, little is known about the biology and ecology of Omus. Field studies showed that two species of Omus existed in the forested areas of Powell Butte Nature Park, Portland, Oregon, USA: Omus audouiniand O. dejeanii. The co-occurrence of sympatric, and likely syntopic, species allowed for a comparative approach in examining and analyzing previously unknown or unaddressed aspects of the biology of Omus. Both morphometric and behavioral analysis was used to address specific questions regarding niche partitioning and mating behaviors in the genus. On the basis of the competitive exclusion principle, I predicted that these closely related species with similar ecological requirements would experience selective pressure to minimize niche overlap and competitive pressures through morphological character displacement. In particular, the mandibles of male tiger beetles serve a dual role: one as tools for feeding-- including prey capture and prey processing--and another role as secondary sexual organs whereby the males use their mandibles to grasp the female and maintain amplexus. A geometric morphometric approach was used to evaluate and compare shape differences between the two species as well as identify trends of sexual dimorphism and species differences in context of prey base. Tiger beetles obligatorily engage in male-superior mounted mating behavior. Body size was used to first address trends of female-biased sexual size dimorphism within the Carabid subfamily Cicindelinae. Female tiger beetles may be expected to experience proportionally greater stress during mating among larger bodied than smaller bodied species and selection would favor increasingly pronounced female-biased sexual size dimorphism among larger-bodied species. The mating duration of Omuswas anecdotally reported as an order of magnitude greater than any other tiger beetle but has never been experimentally confirmed. I performed a series of pairings under laboratory setting to (1) establish a baseline of mating duration for the two species and test the effects of (2) time of day mating was initiated, (3) food deprivation and (4) operational sex ratio on mating duration. Morphometric analysis suggested niche partitioning existed between the two species due to an average body size scaling factor of x1.3 and an average mandible length scaling factor of x1.5, i.e. "Hutchinsonian Ratios"-- an observed minimum scaling threshold of niche differentiation seen in several natural predator populations. Similar minimum values were not seen between the sexes of either species suggesting an absence of sexual niche dimorphism. Geometric morphometric analysis of the mandibles revealed two distinct regions subject to selective adaptation: the distal region of the mandible (including the apical incisor) was consistently sexually dimorphic between the examined species while the proximal region involving the terebral teeth showed interspecific differences independent of sex and likely associated with prey processing, further supporting the hypothesis of niche partitioning between the two species but not necessarily between the sexes. The magnitude of sexual size dimorphism was found to be constant within Cicindelinae regardless of species body size. Behavioral analysis of mating established thatO. audouiniandO. dejeaniihave average (± SD) mating durations of 10.6 (± 1.8) and 29.4 (± 5.6) hours, respectively. Time of initiation of mating (whether morning or evening), food deprivation and operational sex ratio did not have any statistically significant effect on mating duration for either species. The absence of effect operational sex ratios on mating duration by suggests that mate guarding may not be a universal factor for all tiger beetles and, instead, syn- copulatory courtship, as opposed to pre- or post-copulatory courtship, as a female-choice reproductive mechanism may serve as a better explanation for the mating behaviors seen in Omus. Close

• 2023. [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 Citation Abstract Copy 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. 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. Close

• 2024. [Article] Employment of Crystallographic Image Processing Techniques to Scanning Probe Microscopy Images of Two-Dimensional Periodic Objects

  Thin film arrays of molecules or supramolecules are active subjects of investigation because of their potential value in electronics, chemical sensing, catalysis, and other areas. Scanning probe microscopes ...

  Citation × Citation Citation Abstract Copy Title: Employment of Crystallographic Image Processing Techniques to Scanning Probe Microscopy Images of Two-Dimensional Periodic Objects Author: Moon, Bill Year: 2011 Thin film arrays of molecules or supramolecules are active subjects of investigation because of their potential value in electronics, chemical sensing, catalysis, and other areas. Scanning probe microscopes (SPMs), including scanning tunneling microscopes (STMs) and atomic force microscopes (AFMs) are commonly used for the characterization and metrology of thin film arrays. As opposed to transmission electron microscopy (TEM), SPMs have the advantage that they can often make observations of thin films in air or liquid, while TEM requires highly specialized techniques if the sample is to be in anything but vacuum. SPM is a surface imaging technique, while TEM typically images a 2D projection of a thin 3D sample. Additionally, variants of SPM can make observations of more than just topography; for instance, magnetic force microscopy measures nanoscale magnetic properties. Thin film arrays are typically two-dimensionally periodic. A perfect, infinite two-dimensionally periodic array is mathematically constrained to belong to one of only 17 possible 2D plane symmetry groups. Any real image is both finite and imperfect. Crystallographic Image Processing (CIP) is an algorithm that Fourier transforms a real image into a 2D array of complex numbers, the Fourier coefficients of the image intensity, and then uses the relationship between those coefficients to first ascertain the 2D plane symmetry group that the imperfect, finite image is most likely to possess, and then adjust those coefficients that are symmetry-related so as to perfect the symmetry. A Fourier synthesis of the symmetrized coefficients leads to a perfectly symmetric image in direct space (when accumulated rounding and calculation errors are ignored). The technique is, thus, an averaging technique over the direct space experimental data that were selected from the thin film array. The image must have periodicity in two dimensions in order for this technique to be applicable. CIP has been developed over the past 40 years by the electron crystallography community, which works with 2D projections from 3D samples. Any periodic sample, whether it is 2D or 3D has an "ideal structure" which is the structure absent any crystal defects. The ideal structure can be considered one average unit cell, propagated by translation into the whole sample. The "real structure" is an actual sample containing vacancies, dislocations, and other defects. Typically the goal of electron and other types of microscopy is examination of the real structure, as the ideal structure of a crystal is already known from X-ray crystallography. High resolution transmission electron microscope image based electron crystallography, on the other hand, reveals the ideal crystal structure by crystallographic averaging. The ideal structure of a 2D thin film cannot be easily in a spatially selective fashion examined by grazing incidence X-ray or low energy electron diffraction based crystallography. SPMs straightforwardly observe thin films in direct space, but SPM accuracy is hampered by blunt or multiple tips and other unavoidable instrument errors. Especially since the film is often of a supramolecular system whose molecules are weakly bonded (via pi bonds, hydrogen bonds, etc.) both to the substrate and to each other, it is relatively easy for a molecule from the film to adhere to the scanning tip during the scan and become part of the tip during subsequent observation. If the thin film array has two-dimensional periodicity, CIP is a unique and effective tool both for image enhancement (determination of ideal structure) and for the quantification of overall instrument error. In addition, if a sample of known 2D periodicity is scanned, CIP can return information about the contribution of the instrument itself to the image. In this thesis we show how the technique is applied to images of two dimensionally periodic samples taken by SPMs. To the best of our knowledge, this has never been done before. Since 2D periodic thin film arrays have an ideal structure that is mathematically constrained to belong to one of the 17 plane symmetry groups, we can use CIP to determine that group and use it for a particularly effective averaging algorithm. We demonstrate that the use of this averaging algorithm removes noise and random error from images more effectively than translational averaging, also known as "lattice averaging" or "Fourier filtering". We also demonstrate the ability to correct systematic errors caused by hysteresis in the scanning process. These results have the effect of obtaining the ideal structure of the sample, averaging out the defects crystallographically, by providing an average unit cell which, when translated, represents the ideal structure. In addition, if one has recorded a scanning probe image of a 2D periodic sample of known symmetry, we demonstrate that it is possible to use the Fourier coefficients of the image transform to solve the inverse problem and calculate the point spread function (PSF) of the instrument. Any real scanning probe instrument departs from the ideal PSF of a Dirac delta function, and CIP allows us to quantify this departure as far as point symmetries are concerned. The result is a deconvolution of the "effective tip", which includes any blunt or multiple tip effects, as well as the effects caused by adhesion of a sample molecule to the scanning tip, or scanning irregularities unrelated to the physical tip. We also demonstrate that the PSF, once known, can be used on a second image taken by the same instrument under approximately the same experimental conditions to remove errors introduced during that second imaging process. The preponderance of two-dimensionally periodic samples as subjects of SPM observation makes the application of CIP to SPM images a valuable technique to extract a maximum amount of information from these images. The improved resolution of current SPMs creates images with more higher-order Fourier coefficients than earlier, "softer" images; these higher-order coefficients are especially amenable to CIP, which can then effectively magnify the resolution improvement created by better hardware. The improved resolution combined with the current interest in supramolecular structures (which although 3D usually start building on a 2D periodic surface) appears to provide an opportunity for CIP to significantly contribute to SPM image processing. Title: Employment of Crystallographic Image Processing Techniques to Scanning Probe Microscopy Images of Two-Dimensional Periodic Objects Author: Moon, Bill Year: 2011 Thin film arrays of molecules or supramolecules are active subjects of investigation because of their potential value in electronics, chemical sensing, catalysis, and other areas. Scanning probe microscopes (SPMs), including scanning tunneling microscopes (STMs) and atomic force microscopes (AFMs) are commonly used for the characterization and metrology of thin film arrays. As opposed to transmission electron microscopy (TEM), SPMs have the advantage that they can often make observations of thin films in air or liquid, while TEM requires highly specialized techniques if the sample is to be in anything but vacuum. SPM is a surface imaging technique, while TEM typically images a 2D projection of a thin 3D sample. Additionally, variants of SPM can make observations of more than just topography; for instance, magnetic force microscopy measures nanoscale magnetic properties. Thin film arrays are typically two-dimensionally periodic. A perfect, infinite two-dimensionally periodic array is mathematically constrained to belong to one of only 17 possible 2D plane symmetry groups. Any real image is both finite and imperfect. Crystallographic Image Processing (CIP) is an algorithm that Fourier transforms a real image into a 2D array of complex numbers, the Fourier coefficients of the image intensity, and then uses the relationship between those coefficients to first ascertain the 2D plane symmetry group that the imperfect, finite image is most likely to possess, and then adjust those coefficients that are symmetry-related so as to perfect the symmetry. A Fourier synthesis of the symmetrized coefficients leads to a perfectly symmetric image in direct space (when accumulated rounding and calculation errors are ignored). The technique is, thus, an averaging technique over the direct space experimental data that were selected from the thin film array. The image must have periodicity in two dimensions in order for this technique to be applicable. CIP has been developed over the past 40 years by the electron crystallography community, which works with 2D projections from 3D samples. Any periodic sample, whether it is 2D or 3D has an "ideal structure" which is the structure absent any crystal defects. The ideal structure can be considered one average unit cell, propagated by translation into the whole sample. The "real structure" is an actual sample containing vacancies, dislocations, and other defects. Typically the goal of electron and other types of microscopy is examination of the real structure, as the ideal structure of a crystal is already known from X-ray crystallography. High resolution transmission electron microscope image based electron crystallography, on the other hand, reveals the ideal crystal structure by crystallographic averaging. The ideal structure of a 2D thin film cannot be easily in a spatially selective fashion examined by grazing incidence X-ray or low energy electron diffraction based crystallography. SPMs straightforwardly observe thin films in direct space, but SPM accuracy is hampered by blunt or multiple tips and other unavoidable instrument errors. Especially since the film is often of a supramolecular system whose molecules are weakly bonded (via pi bonds, hydrogen bonds, etc.) both to the substrate and to each other, it is relatively easy for a molecule from the film to adhere to the scanning tip during the scan and become part of the tip during subsequent observation. If the thin film array has two-dimensional periodicity, CIP is a unique and effective tool both for image enhancement (determination of ideal structure) and for the quantification of overall instrument error. In addition, if a sample of known 2D periodicity is scanned, CIP can return information about the contribution of the instrument itself to the image. In this thesis we show how the technique is applied to images of two dimensionally periodic samples taken by SPMs. To the best of our knowledge, this has never been done before. Since 2D periodic thin film arrays have an ideal structure that is mathematically constrained to belong to one of the 17 plane symmetry groups, we can use CIP to determine that group and use it for a particularly effective averaging algorithm. We demonstrate that the use of this averaging algorithm removes noise and random error from images more effectively than translational averaging, also known as "lattice averaging" or "Fourier filtering". We also demonstrate the ability to correct systematic errors caused by hysteresis in the scanning process. These results have the effect of obtaining the ideal structure of the sample, averaging out the defects crystallographically, by providing an average unit cell which, when translated, represents the ideal structure. In addition, if one has recorded a scanning probe image of a 2D periodic sample of known symmetry, we demonstrate that it is possible to use the Fourier coefficients of the image transform to solve the inverse problem and calculate the point spread function (PSF) of the instrument. Any real scanning probe instrument departs from the ideal PSF of a Dirac delta function, and CIP allows us to quantify this departure as far as point symmetries are concerned. The result is a deconvolution of the "effective tip", which includes any blunt or multiple tip effects, as well as the effects caused by adhesion of a sample molecule to the scanning tip, or scanning irregularities unrelated to the physical tip. We also demonstrate that the PSF, once known, can be used on a second image taken by the same instrument under approximately the same experimental conditions to remove errors introduced during that second imaging process. The preponderance of two-dimensionally periodic samples as subjects of SPM observation makes the application of CIP to SPM images a valuable technique to extract a maximum amount of information from these images. The improved resolution of current SPMs creates images with more higher-order Fourier coefficients than earlier, "softer" images; these higher-order coefficients are especially amenable to CIP, which can then effectively magnify the resolution improvement created by better hardware. The improved resolution combined with the current interest in supramolecular structures (which although 3D usually start building on a 2D periodic surface) appears to provide an opportunity for CIP to significantly contribute to SPM image processing. Close

• 2025. [Article] Responses of Aquatic Non-Native Species to Novel Predator Cues and Increased Mortality

  Lethal biotic interactions strongly influence the potential for aquatic non-native species to establish and endure in habitats to which they are introduced. Predators in the recipient area, including native ...

  Citation × Citation Citation Abstract Copy Title: Responses of Aquatic Non-Native Species to Novel Predator Cues and Increased Mortality Author: Turner, Brian Christopher Year: 2017 Lethal biotic interactions strongly influence the potential for aquatic non-native species to establish and endure in habitats to which they are introduced. Predators in the recipient area, including native and previously established non-native predators, can prevent establishment, limit habitat use, and reduce abundance of non-native species. Management efforts by humans using methods designed to cause mass mortality (e.g., trapping, biocide applications) can reduce or eradicate non-native populations. However, the impacts of predator and human induced mortality may be mitigated by the behavior or population-level responses of a given non-native species. My dissertation examined the responses of non-native aquatic species to the risk of predation by novel (i.e., no previous exposure) predators in the recipient community and indicators of potential compensatory responses by non-native populations to increased mortality resulting from removal efforts. My dissertation addresses four primary questions. 1) Can first generation, naïve invaders recognize and defend against predators found within the region of invasion through the expression of inducible defenses? 2) Can the overcompensatory potential of a population be predicted though examinations of intraspecific interactions of individuals from the population? 3) What is the relationship between removal effort outcome (i.e., successful or unsuccessful reduction of the target population) and compensatory population responses? 4) Is there a relationship between characteristics of removal efforts that are typically available to managers (e.g., target area size, target area connectivity, removal methodology) and compensatory population responses that could indicate the relative likelihood of compensation resulting from removal efforts? An invading species should be more likely to establish if it can successfully identify and defend against predators in the recipient range, such as through the expression of inducible defenses. Inducible defenses are behavioral or physiological changes that reduce an organism's susceptibility to predation. Through a series of laboratory experiments, I tested whether inducible defenses, in the form of increased burrowing depth, may have benefited the early stage of invasion of Nuttallia obscurata (purple varnish clam), an established Northeast Pacific invader. Specimens of N. obscurata were collected from introduced populations in the Northeast Pacific and from a native population in Japan. The clams were exposed to chemical and physical cues from Northeast Pacific crab predators, including the native Metacarcinus magister (Dungeness crab), an abundant and frequent predator of N. obscurata. While introduced N. obscurata increased their burrowing depth in the physical presence of M. magister, clams collected from their native range showed no such response. This lack of increased burrowing depth by naïve clams in response to a predator native to the newly invaded range, but a significant increase in depth for clams from populations established in the range suggests that while inducible defenses likely did not contribute to the initial establishment of N. obscurata in the Northeast Pacific, they may contribute to their continued persistence and expansion in their introduced range. Some efforts to reduce invasive populations have paradoxically led to population increases. This phenomenon, referred to as overcompensation, occurs when strong negative density-dependent interactions are reduced through increased mortality within a population, resulting in an increase in the population's recruitment rate sufficient to increase the population's overall abundance. Increases in a population's recruitment rate can result from reduced cannibalism of juveniles resulting in lower mortality of new recruits, from increased adult reproductive output, which increases the number of potential recruits, or from reductions in size and/or age at maturity of the unharvested population, which increases the number of reproductive individuals. I predicted the overcompensatory potential of a population of Carcinus maenas (European green crab) in Bodega Harbor, California, using a series of laboratory and field experiments examining intraspecific pressures of adults on juveniles in the population. This measure of intraspecific pressure was used to predict the overcompensatory potential of the population in response to increased mortality from ongoing removal efforts. This prediction was then assessed using pre- and post-removal surveys of juvenile recruitment in Bodega Harbor compared to nearby populations, testing for evidence of overcompensation. While adult C. maenas in Bodega Harbor had limited negative impacts on juveniles, I concluded it was unlikely to result in overcompensation. Relative juvenile abundance did not statistically increase in removal compared to reference populations, consistent with my conclusion from the experiments. Increases in recruitment rates can occur as a result of efforts to remove non-native species. This increase in recruitment can result in overcompensation, but more commonly results in compensation, where recruitment rates increase relative to pre-removal recruitment but does not result in in the population's abundance exceeding pre-removal levels. However, a detailed and accurate prediction of the response of a population to harvest is time consuming and data intensive. This is not feasible for most efforts to eradicate non-native species, which have the greatest chance of success when enacted rapidly after detection. For my final chapter, I performed a literature review and accompanying statistical analysis to determine if typically available information related to the removal effort (site size, site connectivity, and removal technique) could be used to determine increased risk of compensation for a given effort to remove aquatic invasive species. Compensation was closely linked to unsuccessful removal efforts and was observed only among efforts utilizing physical removal methods. However, the frequency with which compensation occurred varied with the exact technique employed, occurring most frequently in removal utilizing electrofishing. Additionally, evidence of compensation was more frequent among larger removal areas with variable connectivity. While other predictors (temperature, effort, etc) might add to the predicative power, the findings of the review provide criteria for managers to determine the relative risk of compensation prior to the start of removal. Further understanding of how invasive species respond to lethal biotic interactions, including anthropogenically mediated control measures, can aid in assessing the risk of invasion for a given species and inform managers of the risk of complications resulting from removal efforts. While inducible defenses may contribute to the long-term success of an introduced species in their recipient range, my findings did not support the idea that inducible defenses triggered by predator cues contributed to their initial introduction in this case. However, research on other non-native species and offspring of previously naïve prey would allow for a clearer picture of the role of inducible defenses in the invasion process. Compensation resulting from removal efforts does not guarantee failure, and certain characteristics of removal efforts seem to indicate increased risk of compensation. Together these components help identify how biotic interactions surrounding mortality risk of an invading species help shape the trajectory of invasion. Title: Responses of Aquatic Non-Native Species to Novel Predator Cues and Increased Mortality Author: Turner, Brian Christopher Year: 2017 Lethal biotic interactions strongly influence the potential for aquatic non-native species to establish and endure in habitats to which they are introduced. Predators in the recipient area, including native and previously established non-native predators, can prevent establishment, limit habitat use, and reduce abundance of non-native species. Management efforts by humans using methods designed to cause mass mortality (e.g., trapping, biocide applications) can reduce or eradicate non-native populations. However, the impacts of predator and human induced mortality may be mitigated by the behavior or population-level responses of a given non-native species. My dissertation examined the responses of non-native aquatic species to the risk of predation by novel (i.e., no previous exposure) predators in the recipient community and indicators of potential compensatory responses by non-native populations to increased mortality resulting from removal efforts. My dissertation addresses four primary questions. 1) Can first generation, naïve invaders recognize and defend against predators found within the region of invasion through the expression of inducible defenses? 2) Can the overcompensatory potential of a population be predicted though examinations of intraspecific interactions of individuals from the population? 3) What is the relationship between removal effort outcome (i.e., successful or unsuccessful reduction of the target population) and compensatory population responses? 4) Is there a relationship between characteristics of removal efforts that are typically available to managers (e.g., target area size, target area connectivity, removal methodology) and compensatory population responses that could indicate the relative likelihood of compensation resulting from removal efforts? An invading species should be more likely to establish if it can successfully identify and defend against predators in the recipient range, such as through the expression of inducible defenses. Inducible defenses are behavioral or physiological changes that reduce an organism's susceptibility to predation. Through a series of laboratory experiments, I tested whether inducible defenses, in the form of increased burrowing depth, may have benefited the early stage of invasion of Nuttallia obscurata (purple varnish clam), an established Northeast Pacific invader. Specimens of N. obscurata were collected from introduced populations in the Northeast Pacific and from a native population in Japan. The clams were exposed to chemical and physical cues from Northeast Pacific crab predators, including the native Metacarcinus magister (Dungeness crab), an abundant and frequent predator of N. obscurata. While introduced N. obscurata increased their burrowing depth in the physical presence of M. magister, clams collected from their native range showed no such response. This lack of increased burrowing depth by naïve clams in response to a predator native to the newly invaded range, but a significant increase in depth for clams from populations established in the range suggests that while inducible defenses likely did not contribute to the initial establishment of N. obscurata in the Northeast Pacific, they may contribute to their continued persistence and expansion in their introduced range. Some efforts to reduce invasive populations have paradoxically led to population increases. This phenomenon, referred to as overcompensation, occurs when strong negative density-dependent interactions are reduced through increased mortality within a population, resulting in an increase in the population's recruitment rate sufficient to increase the population's overall abundance. Increases in a population's recruitment rate can result from reduced cannibalism of juveniles resulting in lower mortality of new recruits, from increased adult reproductive output, which increases the number of potential recruits, or from reductions in size and/or age at maturity of the unharvested population, which increases the number of reproductive individuals. I predicted the overcompensatory potential of a population of Carcinus maenas (European green crab) in Bodega Harbor, California, using a series of laboratory and field experiments examining intraspecific pressures of adults on juveniles in the population. This measure of intraspecific pressure was used to predict the overcompensatory potential of the population in response to increased mortality from ongoing removal efforts. This prediction was then assessed using pre- and post-removal surveys of juvenile recruitment in Bodega Harbor compared to nearby populations, testing for evidence of overcompensation. While adult C. maenas in Bodega Harbor had limited negative impacts on juveniles, I concluded it was unlikely to result in overcompensation. Relative juvenile abundance did not statistically increase in removal compared to reference populations, consistent with my conclusion from the experiments. Increases in recruitment rates can occur as a result of efforts to remove non-native species. This increase in recruitment can result in overcompensation, but more commonly results in compensation, where recruitment rates increase relative to pre-removal recruitment but does not result in in the population's abundance exceeding pre-removal levels. However, a detailed and accurate prediction of the response of a population to harvest is time consuming and data intensive. This is not feasible for most efforts to eradicate non-native species, which have the greatest chance of success when enacted rapidly after detection. For my final chapter, I performed a literature review and accompanying statistical analysis to determine if typically available information related to the removal effort (site size, site connectivity, and removal technique) could be used to determine increased risk of compensation for a given effort to remove aquatic invasive species. Compensation was closely linked to unsuccessful removal efforts and was observed only among efforts utilizing physical removal methods. However, the frequency with which compensation occurred varied with the exact technique employed, occurring most frequently in removal utilizing electrofishing. Additionally, evidence of compensation was more frequent among larger removal areas with variable connectivity. While other predictors (temperature, effort, etc) might add to the predicative power, the findings of the review provide criteria for managers to determine the relative risk of compensation prior to the start of removal. Further understanding of how invasive species respond to lethal biotic interactions, including anthropogenically mediated control measures, can aid in assessing the risk of invasion for a given species and inform managers of the risk of complications resulting from removal efforts. While inducible defenses may contribute to the long-term success of an introduced species in their recipient range, my findings did not support the idea that inducible defenses triggered by predator cues contributed to their initial introduction in this case. However, research on other non-native species and offspring of previously naïve prey would allow for a clearer picture of the role of inducible defenses in the invasion process. Compensation resulting from removal efforts does not guarantee failure, and certain characteristics of removal efforts seem to indicate increased risk of compensation. Together these components help identify how biotic interactions surrounding mortality risk of an invading species help shape the trajectory of invasion. Close