Increased diversity of libraries from libraries: chemoinformatic analysis of bis-diazacyclic libraries

Combinatorial libraries continue to play a key role in drug discovery. To increase structural diversity, several experimental methods have been developed. However, limited efforts have been performed so far to quantify the diversity of the broadly used diversity-oriented synthetic (DOS) libraries. Herein we report a comprehensive characterization of 15 bis-diazacyclic combinatorial libraries obtained through libraries from libraries, which is a DOS approach. Using MACCS keys, radial and different pharmacophoric fingerprints as well as six molecular properties, it was demonstrated the increased structural and property diversity of the libraries from libraries over the individual libraries. Comparison of the libraries to existing drugs, NCI Diversity and the Molecular Libraries Small Molecule Repository revealed the structural uniqueness of the combinatorial libraries (mean similarity < 0.5 for any fingerprint representation). In particular, bis-cyclic thiourea libraries were the most structurally dissimilar to drugs retaining drug-like character in property space. This study represents the first comprehensive quantification of the diversity of libraries from libraries providing a solid quantitative approach to compare and contrast the diversity of DOS libraries with existing drugs or any other compound collection.

A smart sensing platform for the discrimination of human movement

This thesis documents the design, implementation and testing of a smart sensing platform that is able to discriminate between differences or small changes in a persons walking. The distributive tactile sensing method is used to monitor the deflection of the platform surface using just a small number of sensors and, through the use of neural networks, infer the characteristics of the object in contact with the surface. The thesis first describes the development of a mathematical model which uses a novel method to track the position of a moving load as it passes over the smart sensing surface. Experimental methods are then described for using the platform to track the position of swinging pendulum in three dimensions. It is demonstrated that the method can be extended to that of real-time measurement of balance and sway of a person during quiet standing. Current classification methods are then investigated for use in the classification of different gait patterns, in particular to identify individuals by their unique gait pattern. Based on these observations, a novel algorithm is developed that is able to discriminate between abnormal and affected gait. This algorithm, using the distributive tactile sensing method, was found to have greater accuracy than other methods investigated and was designed to be able to cope with any type of gait variation. The system developed in this thesis has applications in the area of medical diagnostics, either as an initial screening tool for detecting walking disorders or to be able to automatically detect changes in gait over time. The system could also be used as a discrete biometric identification method, for example identifying office workers as they pass over the surface.

The pharmacology of centrally acting drugs in animals of altered thyroid status

The pharmacological effects of a number of centrally acting drugs have been compared in euthyroid mice and mice made hyperthyroid by pretreatment with sodium-1-thyroxine. The potencies of two barbiturates, pentobarbitone and thiopentone - as indicated by the duration of their hypnotic actions and their acute toxicities - are increased in hyperthyroid mice. An acutely active uncoupler of phosphorylative oxidation is 2, 4-dinitrophenol, an agent which proved to be a potent hypnotic when administered intracerebrally. An attempt has been made to relate the mechanism of action of the barbiturates to the uncoupling effects of thyroxine and 2, 4-dinitrophenol. The pharmacological effects of chlorpromazine, reserpine and amphetamine-like drugs have also been studied in hyperthyroid mice. After pretreatment with thyroxine, mice show a reduced tendency to become hypothermic after chlorpromazine or reserpine; in fact, under suitable laboratory conditions these agents produce a hyperthermic effect. Yet their known depressant effects upon locomotor activity were not substantially altered. Thus it appeared that depression of locomotor activity and hypothermia are not necessarily correlated, an observation at variance with previously held opinion. These results have been discussed in the light of our knowledge of the role of the thyroid gland in thermoregulation. The actions of tremorine and its metabolite, oxotremorine, have also been examined. Hyperthyroid animals are less susceptible to both the hypothermia and tremor produced by these agents. An attempt is made to explain these observations, in view of the known mechanism of action of oxotremorine and the tremorgenic actions that thyroxine may have. A number of experimental methods have been used to study the anti-nociceptive (analgesic) effects of drugs in euthyroid and hyperthyroid mice. The sites and mechanisms of action of these drugs and the known actions of thyroxine have been discussed.

Study on fatigue and energy-dissipation properties of nanolayered Cu/Nb thin films

Energy dissipation and fatigue properties of nano-layered thin films are less well studied than bulk properties. Existing experimental methods for studying energy dissipation properties, typically using magnetic interaction as a driving force at different frequencies and a laser-based deformation measurement system, are difficult to apply to two-dimensional materials. We propose a novel experimental method to perform dynamic testing on thin-film materials by driving a cantilever specimen at its fixed end with a bimorph piezoelectric actuator and monitoring the displacements of the specimen and the actuator with a fibre-optic system. Upon vibration, the specimen is greatly affected by its inertia, and behaves as a cantilever beam under base excitation in translation. At resonance, this method resembles the vibrating reed method conventionally used in the viscoelasticity community. The loss tangent is obtained from both the width of a resonance peak and a free-decay process. As for fatigue measurement, we implement a control algorithm into LabView to maintain maximum displacement of the specimen during the course of the experiment. The fatigue S-N curves are obtained.

Breaking out of the silo mentality

The return to methods focusing on language and experience following the dominance of experimental methods has in the last few decades led to debate, dialogue, and disagreement regarding the status of qualitative and quantitative methods. However, a recent focus on impact has brought an air of pragmatism to the research arena. In what ways, then, is psychology moving from entrenched mono methods approaches that have epitomised its development until recently, to describing and discussing ways in which mixed and pluralistic research can advance and contribute to further, deeper psychological understanding?.

In situ diagnostics and prognostics of wire bonding faults in IGBT modules for electric vehicle drives

This paper presents a diagnostic and prognostic condition monitoring method for insulated-gate bipolar transistor (IGBT) power modules for use primarily in electric vehicle applications. The wire-bond-related failure, one of the most commonly observed packaging failures, is investigated by analytical and experimental methods using the on-state voltage drop as a failure indicator. A sophisticated test bench is developed to generate and apply the required current/power pulses to the device under test. The proposed method is capable of detecting small changes in the failure indicators of the IGBTs and freewheeling diodes and its effectiveness is validated experimentally. The novelty of the work lies in the accurate online testing capacity for diagnostics and prognostics of the power module with a focus on the wire bonding faults, by injecting external currents into the power unit during the idle time. Test results show that the IGBT may sustain a loss of half the bond wires before the impending fault becomes catastrophic. The measurement circuitry can be embedded in the IGBT drive circuits and the measurements can be performed in situ when the electric vehicle stops in stop-and-go, red light traffic conditions, or during routine servicing.

La kabala dentro del discurso contemporaneo y urbano: El ejemplo de Marcos Ricardo Barnatan

This dissertation analyzes the relationship between several mystic Sephardic texts called the Kabalah which include the three basic mystic books of Judaism: Sefer Yetsira, Sefer Bahir, and Sefer Zohar, and Argentine writer of Jewish descent, Marcos Ricardo Barnatan’s experimental work. The premise is that several mystic Sephardic texts have certain literary characteristics that make them fertile sources for the inspiration of writers like Barnatan. This thesis proves that Barnatan’s poetry and his first novel El Laberinto De Sion both use the most general concepts of the Kabalah in developing his literary and artistic creations. ^ This study is focuses on the concept that there exists a possibility of reading kabalistic texts not only in an exegetical way, but also in a poetic way. Barnatan’s literature is prone to this kind of reading of the texts. He creates a surprisingly expressive structure without ties to established models. This expressive structure is built on a vast amount of symbols, which results from this freedom. Barnatan adopts multiple symbols from cosmogenic theories and makes use of them, thus incorporating both the spirit and style of kabalistic texts into his own work. ^ Instead of addressing some of the main concerns of Kabbalistic study and its commentary, Barnatan avoids the concern for Law, the study of the Torah and its commentaries, while avoiding the use of the Hebrew language. For this reason Barnatan is too deviant to be considered an extension from the mainstream Kabbalistic commentary. Barnatan’s work is destined for a reader who cannot only understand his experimental methods, but who can also assemble a disjointed text while accepting a fundamental instability of space and time.^

Multimode Analysis of Nanoscale Biomolecular Interactions

Biomolecular interactions, including protein-protein, protein-DNA, and protein-ligand interactions, are of special importance in all biological systems. These interactions may occer during the loading of biomolecules to interfaces, the translocation of biomolecules through transmembrane protein pores, and the movement of biomolecules in a crowded intracellular environment. The molecular interaction of a protein with its binding partners is crucial in fundamental biological processes such as electron transfer, intracellular signal transmission and regulation, neuroprotective mechanisms, and regulation of DNA topology. In this dissertation, a customized surface plasmon resonance (SPR) has been optimized and new theoretical and label free experimental methods with related analytical calculations have been developed for the analysis of biomolecular interactions. Human neuroglobin (hNgb) and cytochrome c from equine heart (Cyt c) proteins have been used to optimize the customized SPR instrument. The obtained Kd value (~13 µM), from SPR results, for Cyt c-hNgb molecular interactions is in general agreement with a previously published result. The SPR results also confirmed no significant impact of the internal disulfide bridge between Cys 46 and Cys 55 on hNgb binding to Cyt c. Using SPR, E. coli topoisomerase I enzyme turnover during plasmid DNA relaxation was found to be enhanced in the presence of Mg2+. In addition, a new theoretical approach of analyzing biphasic SPR data has been introduced based on analytical solutions of the biphasic rate equations. In order to develop a new label free method to quantitatively study protein-protein interactions, quartz nanopipettes were chemically modified. The derived Kd (~20 µM) value for the Cyt c-hNgb complex formations matched very well with SPR measurements (Kd ~16 µM). The finite element numerical simulation results were similar to the nanopipette experimental results. These results demonstrate that nanopipettes can potentially be used as a new class of a label-free analytical method to quantitatively characterize protein-protein interactions in attoliter sensing volumes, based on a charge sensing mechanism. Moreover, the molecule-based selective nature of hydrophobic and nanometer sized carbon nanotube (CNT) pores was observed. This result might be helpful to understand the selective nature of cellular transport through transmembrane protein pores.

Factors Affecting Current and Future Treeline Locations and Dynamics in the Peruvian Andes

The elevational distributions of tropical treelines are thought to be determined by temperature, and are predicted to shift upslope in response to global warming. In contrast to this hypothesis, global-scale studies have shown that only half of all studied treelines are shifting upslope. Understanding how treelines will respond to climate change has important implications for global biodiversity, especially in the tropics, because tropical treelines generally represent the upper-elevation distribution limit of the hyper-diverse cloudforest ecosystem. In Chapter 1, I introduce the idea that grasslands found above tropical treelines may represent a potential grass ceiling which forest species cannot cross or invade. I use an extensive literature review to outline potential mechanisms which may be acting to stabilize treeline and prevent forest expansion into high-elevation grasslands. In Chapters 2-4, I begin to explore these potential mechanisms through the use of observational and experimental methods. In Chapter 2, I show that there are significant numbers of seedlings occurring just outside of the treeline in the open grasslands and that seed rain is unlikely to limit seedling recruitment above treeline. I also show that microclimates outside of the closed-canopy cloudforest are highly variable and that mean temperatures are likely a poor explanation of tropical treeline elevations. In Chapter 3, I show that juvenile trees maintain freezing resistances similar to adults, but nighttime radiative cooling near the ground in the open grassland results in lower cold temperatures relative to the free atmosphere, exposing seedlings of some species growing above treeline to lethal frost events. In Chapter 4, I use a large-scale seedling transplant experiment to test the effects of mean temperature, absolute low temperature and shade on transplanted seedling survival. I find that increasing mean temperature negatively affects seedling survival of two treeline species while benefiting another. In addition, low temperature extremes and the presence of shade also appear to be important factors affecting seedling survival above tropical treelines. This work demonstrates that mean temperature is a poor predictor of tropical treelines and that temperature extremes, especially low temperatures, and non-climatic variables should be included in predictions of current and future tropical treeline dynamics.

Fixed vs. variable noise in 2AFC contrast discrimination: lessons from psychometric functions.

Recent discussion regarding whether the noise that limits 2AFC discrimination performance is fixed or variable has focused either on describing experimental methods that presumably dissociate the effects of response mean and variance or on reanalyzing a published data set with the aim of determining how to solve the question through goodness-of-fit statistics. This paper illustrates that the question cannot be solved by fitting models to data and assessing goodness-of-fit because data on detection and discrimination performance can be indistinguishably fitted by models that assume either type of noise when each is coupled with a convenient form for the transducer function. Thus, success or failure at fitting a transducer model merely illustrates the capability (or lack thereof) of some particular combination of transducer function and variance function to account for the data, but it cannot disclose the nature of the noise. We also comment on some of the issues that have been raised in recent exchange on the topic, namely, the existence of additional constraints for the models, the presence of asymmetric asymptotes, the likelihood of history-dependent noise, and the potential of certain experimental methods to dissociate the effects of response mean and variance.

The Political Economy of Ethnic Empowerment in India

This dissertation consists of three papers, which together examine whether policies meant to address inequality, succeed in mitigating the impact of traditional institutions such as caste and enable ethnic minorities to claim their rights. Using experimental and quasi-experimental methods with data from a variety of primary and secondary sources, this dissertation analyzes whether policies meant to empower vulnerable groups in India have succeeded in doing so. The findings suggest that while legislations in the form of mandated political representation or freedom of information laws are necessary in terms of increasing the accountability of government towards citizens, they may not be sufficient in ensuring adequate and uniform delivery of public services, especially to citizens belonging to marginalized groups. Further, empowering citizens – especially those belonging to groups that have faced historic discrimination – to actively participate in civic and political life may require more active and intensive policy and programmatic interventions.

Theory and Practice in Sustainability Science: Influence of Urban Form on the Urban Heat Island and Implications for Urban Systems

As the world population continues to grow past seven billion people and global challenges continue to persist including resource availability, biodiversity loss, climate change and human well-being, a new science is required that can address the integrated nature of these challenges and the multiple scales on which they are manifest. Sustainability science has emerged to fill this role. In the fifteen years since it was first called for in the pages of Science, it has rapidly matured, however its place in the history of science and the way it is practiced today must be continually evaluated. In Part I, two chapters address this theoretical and practical grounding. Part II transitions to the applied practice of sustainability science in addressing the urban heat island (UHI) challenge wherein the climate of urban areas are warmer than their surrounding rural environs. The UHI has become increasingly important within the study of earth sciences given the increased focus on climate change and as the balance of humans now live in urban areas.

In Chapter 2 a novel contribution to the historical context of sustainability is argued. Sustainability as a concept characterizing the relationship between humans and nature emerged in the mid to late 20th century as a response to findings used to also characterize the Anthropocene. Emerging from the human-nature relationships that came before it, evidence is provided that suggests Sustainability was enabled by technology and a reorientation of world-view and is unique in its global boundary, systematic approach and ambition for both well being and the continued availability of resources and Earth system function. Sustainability is further an ambition that has wide appeal, making it one of the first normative concepts of the Anthropocene.

Despite its widespread emergence and adoption, sustainability science continues to suffer from definitional ambiguity within the academe. In Chapter 3, a review of efforts to provide direction and structure to the science reveals a continuum of approaches anchored at either end by differing visions of how the science interfaces with practice (solutions). At one end, basic science of societally defined problems informs decisions about possible solutions and their application. At the other end, applied research directly affects the options available to decision makers. While clear from the literature, survey data further suggests that the dichotomy does not appear to be as apparent in the minds of practitioners.

In Chapter 4, the UHI is first addressed at the synoptic, mesoscale. Urban climate is the most immediate manifestation of the warming global climate for the majority of people on earth. Nearly half of those people live in small to medium sized cities, an understudied scale in urban climate research. Widespread characterization would be useful to decision makers in planning and design. Using a multi-method approach, the mesoscale UHI in the study region is characterized and the secular trend over the last sixty years evaluated. Under isolated ideal conditions the findings indicate a UHI of 5.3 ± 0.97 °C to be present in the study area, the magnitude of which is growing over time.

Although urban heat islands (UHI) are well studied, there remain no panaceas for local scale mitigation and adaptation methods, therefore continued attention to characterization of the phenomenon in urban centers of different scales around the globe is required. In Chapter 5, a local scale analysis of the canopy layer and surface UHI in a medium sized city in North Carolina, USA is conducted using multiple methods including stationary urban sensors, mobile transects and remote sensing. Focusing on the ideal conditions for UHI development during an anticyclonic summer heat event, the study observes a range of UHI intensity depending on the method of observation: 8.7 °C from the stationary urban sensors; 6.9 °C from mobile transects; and, 2.2 °C from remote sensing. Additional attention is paid to the diurnal dynamics of the UHI and its correlation with vegetation indices, dewpoint and albedo. Evapotranspiration is shown to drive dynamics in the study region.

Finally, recognizing that a bridge must be established between the physical science community studying the Urban Heat Island (UHI) effect, and the planning community and decision makers implementing urban form and development policies, Chapter 6 evaluates multiple urban form characterization methods. Methods evaluated include local climate zones (LCZ), national land cover database (NCLD) classes and urban cluster analysis (UCA) to determine their utility in describing the distribution of the UHI based on three standard observation types 1) fixed urban temperature sensors, 2) mobile transects and, 3) remote sensing. Bivariate, regression and ANOVA tests are used to conduct the analyses. Findings indicate that the NLCD classes are best correlated to the UHI intensity and distribution in the study area. Further, while the UCA method is not useful directly, the variables included in the method are predictive based on regression analysis so the potential for better model design exists. Land cover variables including albedo, impervious surface fraction and pervious surface fraction are found to dominate the distribution of the UHI in the study area regardless of observation method.

Chapter 7 provides a summary of findings, and offers a brief analysis of their implications for both the scientific discourse generally, and the study area specifically. In general, the work undertaken does not achieve the full ambition of sustainability science, additional work is required to translate findings to practice and more fully evaluate adoption. The implications for planning and development in the local region are addressed in the context of a major light-rail infrastructure project including several systems level considerations like human health and development. Finally, several avenues for future work are outlined. Within the theoretical development of sustainability science, these pathways include more robust evaluations of the theoretical and actual practice. Within the UHI context, these include development of an integrated urban form characterization model, application of study methodology in other geographic areas and at different scales, and use of novel experimental methods including distributed sensor networks and citizen science.

Causalité et explication causale chez James Woodward

Certains philosophes affirment que les relations causales sont fondées sur les lois de la nature. Cette conception cadre mal avec la réalité des sciences biomédicales et des sciences humaines. Pour se rapprocher de la pratique réelle des diverses sciences, James Woodward propose une conception de la causalité et de l’explication causale fondée sur une relation beaucoup moins exigeante que celle de loi de la nature, qu’il appelle l’invariance. Le but de ce mémoire est de présenter le concept d’invariance et les autres concepts causaux qui s’y rattachent et, d’identifier certaines difficultés, dans le but de cerner l’usage approprié de cette famille de concepts. La conception causale de Woodward suppose que le but de la recherche des causes est pratique plutôt que simplement épistémique : il s’agit pour les agents de s’appuyer sur les causes pour modifier les phénomènes. Cette conception est également non-réductive; elle utilise des contrefactuels et reflète les méthodes expérimentales des diverses sciences. La cohérence de cette conception avec les généralisations causales réelles des sciences fait en sorte qu’elle abandonne l’objectif d’universalité rattaché à la notion de loi de la nature, en faveur d’un objectif de fiabilité temporaire. De plus, comme le critère d’invariance est peu exigeant, d’autres critères doivent lui être ajoutés pour identifier, parmi les relations causales (c’est-à-dire invariantes), les relations les plus susceptibles d’être employées pour modifier les phénomènes de façon fiable.

Mesure de sections efficaces absolues vibrationnelles pour la collision d’électrons de basse énergie (1-19 eV) avec le tétrahydrofurane (THF) condensé

Résumé: Ce mémoire de maîtrise est une étude des probabilités d’interactions (sections efficaces) des électrons de basse énergie avec une molécule d’intérêt biologique. Cette molécule est le tétrahydrofurane (THF) qui est un bon modèle de la molécule constituant la colonne vertébrale de l’ADN; le désoxyribose. Étant donné la grande quantité d’électrons secondaires libérés lors du passage des radiations à travers la matière biologique et sachant que ceux-ci déposent la majorité de l’énergie, l’étude de leurs interactions avec les molécules constituant l’ADN devient rapidement d’une grande importance. Les mesures de sections efficaces sont faites à l’aide d’un spectromètre à haute résolution de pertes d’énergie de l’électron. Les spectres de pertes d’énergie de l’électron obtenus de cet appareil permettent de calculer les valeurs de sections efficaces pour chaque vibration en fonction de l’énergie incidente de l’électron. L’article présenté dans ce mémoire traite de ces mesures et des résultats. En effet, il présente et explique en détail les conditions expérimentales, il décrit la méthode de déconvolution qui est utilisée pour obtenir les valeurs de sections efficaces et il présente et discute des 4 résonances observées dans la dépendance en énergie des sections efficaces. En effet, cette étude a permis de localiser en énergie 4 résonances et celles-ci ont toutes été confirmées par des recherches expérimentales et théoriques antérieures sur le sujet des collisions électrons lents-THF. En outre, jamais ces résonances n’avaient été observées simultanément dans une même étude et jamais la résonance trouvée à basse énergie n’avait été observée avec autant d’intensité que cette présente étude. Cette étude a donc permis de raffiner notre compréhension fondamentale des processus résonants impliqués lors de collisions d’électrons secondaires avec le THF. Les valeurs de sections efficaces sont, quant à elles, très prisées par les théoriciens et sont nécessaires pour les simulations Monte Carlo pour prédire, par exemple, le nombre d’ions formées après le passage des radiations. Ces valeurs pourront justement être utilisées dans les modèles de distribution et dépôt d’énergie au niveau nanoscopique dans les milieux biologiques et ceux-ci pourront éventuellement améliorer l’efficacité des modalités radiothérapeutiques.

Telefone celular como recurso didático no ensino de física

Currently, there are several factors that suggest the need for the school to review their teaching practices: 1) the speed with which information and communication technologies - ICT are spread throughout society and in particular the increasing use of mobile phone by groups in school age;2) the scope and power of integrating ICT convergence of these technological resources, that can be used as teaching resources; 3) the fact that nowadays students grow up in a technological world and make their thought patterns operating in accordance with this reality, etc... In contrast, there are educators unrelated to the appropriation of ICT, presenting, in many cases, resistance to them. There is a incongruity between how individuals use mobile phones, for example, inside and outside the school. There are also educators, schools, public educational departments claiming to be against mobile phones usage; bills and laws regulating their use in educational space, etc... For these controversial aspects we have investigated whether cell phone use as a teaching resource practices mediator in Physics teaching. For this purpose, we developed an applied research with qualitative and exploratory approach about the objectives, adopting participant and the technical procedures. A documental and bibliographical research was taken. First of all, data were collected by e-mail, through a multiple choice questionnaire applied to private school teachers in southern Brazil, to identify the researched reality and develop teaching practices likely to be applied in the studied corpus. Then, such practices were applied in workshops located in Curitiba and Ponta Grossa cities, in Paraná state. During the application, data was collected by the researcher's field notes. Then, we recorded chats about the workshops from an instant message software (msn messenger), and we took photographic records. Data analysis was performed by triangulation. The results showed the need to enhance continuing education courses for teachers and the production of national academic literature, such as articles, dissertations, theses and books that explore the theme of the cell phone and its functionality in educational spaces as an educational resource mediator in the practices of teaching Physics. They are available in the dissertation defended in 2012, and now are also systematized in this book, organized as a final product of research conducted by the Graduate Program in Science Education and Technology UTFPR, Campus Ponta Grossa-PR.