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1	The role of dynamics in emergent protein properties Orlando, Gabriele 23 May 2019 (has links) (PDF) Protein structure is not fixed in time, and conformational transitions are the keyto many biological interactions such as enzymatic reactions or signal transduction.Protein dynamics and secondary structure propensities describe these conformationaltransitions, defining how protein structure is likely to evolve in time. Unfortunatelythis kind of information is extremely hard to obtain and the required experimentsare expensive and time consuming.A backbone dynamics and secondary structure propensity predictor that worksfrom sequence only, called DynaMine, has recently been developed. DynaMine addsa new dimension to protein sequences that can, for instance, be exploited to identifyprotein regions involved in specific biological tasks and in protein classification. Thisthesis shows how these predictions can be used to infer emergent properties of pro-teins and how they can highlight hidden evolutionary relationships between remotehomologs.The thesis is divided in 4 parts, corresponding to four different topics in which dy-namics and secondary structure propensities are reported to play a crucial role: thefirst part describes a new pairwise algorithm that uses secondary structure propen-sities and dynamics to align remote homologous proteins. The following three partsdeal with dynamics-related protein emergent behaviours: protein disorder, beta-aggregation and DNA-binding capability in archaea. The results show how backbonedynamics and secondary structure propensities can help improving the prediction ofall the aforementioned subjects. With regard to the identification of DNA-bindingproteins and the prediction of beta-aggregation, experimental validation is also pro-vided and discussed. / Doctorat en Sciences / info:eu-repo/semantics/nonPublished Sciences exactes et naturelles Protein Dynamics Secondary structure propensities
2	Insights into Unfolded Proteins from the Intrinsic ϕ/ψ Propensities of the AAXAA Host-Guest Series Towse, Clare-Louise, Vymetal, J., Vondrasek, J., Daggett, V. 19 January 2016 (has links) No / Various host-guest peptide series are used by experimentalists as reference conformational states. One such use is as a baseline for random-coil NMR chemical shifts. Comparison to this random-coil baseline, through secondary chemical shifts, is used to infer protein secondary structure. The use of these random-coil data sets rests on the perception that the reference chemical shifts arise from states where there is little or no conformational bias. However, there is growing evidence that the conformational composition of natively and nonnatively unfolded proteins fail to approach anything that can be construed as random coil. Here, we use molecular dynamics simulations of an alanine-based host-guest peptide series (AAXAA) as a model of unfolded and denatured states to examine the intrinsic propensities of the amino acids. We produced ensembles that are in good agreement with the experimental NMR chemical shifts and confirm that the sampling of the 20 natural amino acids in this peptide series is be far from random. Preferences toward certain regions of conformational space were both present and dependent upon the environment when compared under conditions typically used to denature proteins, i.e., thermal and chemical denaturation. Moreover, the simulations allowed us to examine the conformational makeup of the underlying ensembles giving rise to the ensemble-averaged chemical shifts. We present these data as an intrinsic backbone propensity library that forms part of our Structural Library of Intrinsic Residue Propensities to inform model building, to aid in interpretation of experiment, and for structure prediction of natively and nonnatively unfolded states. / NIH GM 50789, Ministry of Education, Youth and Sports (MSMT) of the Czech Republic LH11020 Molecular dynamics simulation Conformational propensities Protein and peptide structure
3	Essays on Fiscal and Monetary Policy Ordonez, Brenda Vanessa 25 August 2022 (has links) No description available. Economics
4	Explanation and deduction : a defence of deductive chauvinism Hållsten, Henrik January 2001 (has links) In this essay I defend the notion of deductive explanation mainly against two types of putative counterexamples: those found in genuinely indeterministic systems and those found in complex dynamic systems. Using Railton's notions of explanatory information and ideal explanatory text, deductivism is defended in an indeterministic setting. Furthermore, an argument against non-deductivism that hinges on peculiarities of probabilistic causality is presented. The use of the notion of an ideal explanatory text gives rise to problems in accounting for explanations in complex dynamic systems, regardless of whether they are deterministic or not. These problems are considered in the essay and a solution is suggested. This solution forces the deductivist to abandon the requirement that an explanation consists of a deductive argument, but it is argued that the core of deductivism is saved in so far as we, for full explanations, can still adhere to the fundamental requirement: If A explains B, then A is inconsistent with anything inconsistent with B. Deductive explanation Statistical explanation Chances Propensities Probabilities Sine qua non Probabilistic causality Indeterminism Ideal explanatory text Explanatory information Explanatory sketches Dynamic systems Chaotic systems Approximate solutions Coffa Salmon Railton Humphreys Kitcher Poincaré Suppes Lorenz Hénon.
5	The Use of an Online Readiness Assessment to Determine Necessary Skills, Aptitude, and Propensities for Successful Completion in a Secondary Online Credit Course Vineyard, Tracy Elizabeth 05 1900 (has links) A gap exists in education research in the area of online readiness for secondary courses. In the current study, I examined the use of an online readiness assessment to inform students and educators of the necessary skills, aptitudes, and propensities needed for secondary course completion. In this research study, the perceptions of 17 secondary students in a North Texas public school were examined. Using a three-phase design, qualitative demographic surveys, focus groups, and open-ended end-of-course success questionnaires were collected and analyzed. The findings revealed the Revised McVay Online Readiness Assessment beneficial for providing students with information regarding skills needed for their online course success. Students were interested in how prior online experience influences online readiness and successful completion as well as the influence prior expectations of online learning had on online success. In addition, the study revealed the importance of student readiness relating to more specific self-regulatory skills including time-management, metacognitive self-monitoring, and task-strategies. The study results also revealed students found importance in knowing their comfort with online communication. K-12 school system and curriculum leaders may consider and take action to ensure effective curriculum and programs are implemented to achieve the desired results of student online course completion as well as providing students with necessary skills, such as comfort in online communication, and self-regulation specific to time-management, metacognitive self-monitoring, and task-strategies. The study results suggest an online readiness assessment would prove even more useful with the inclusion of such specific skills. Secondary online readiness K-12 preparation readiness assessment aptitudes skills propensities self-regulation online communication self-management secondary technical skills best-practices Education, Curriculum and Instruction Education, Technology Education, Secondary Web-based instruction. High school students. Academic achievement.
6	CHANGING TACTICS: REHABILITATING CANADIAN JUSTICE FOR TRAUMATIZED VETERANS Samson, J. Jason 22 July 2012 (has links) This thesis examines how military members and veterans with Operational Stress Injuries are treated by Canadian justice systems. It suggests a correlation between mental injuries sustained on operations by military personnel and propensities for military and societal misconduct. By comparing civilian and military processes with American justice counterparts, a plan to improve the existing Canadian legal landscape is proposed. Using an analysis of the underlying philosophy and purpose of military justice, a problem solving diversionary court is recommended, along with legislative and policy amendments. The use of a consent-based “Treatment Standing Court Martial” would place military justice officials parallel to civilian justice alternative measures programs, and in a better position to break the cycle of recidivism among veterans by addressing root causes. Education to reduce stigma along with military-civilian partnerships are also advocated to enhance the detection of mental illness and to foster early treatment for military personnel and veterans. The overall goals of the work include: reducing recidivism, improving operational efficiency and taking care of military members, veterans and their families.

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