Proteins in silico-modeling and sampling

Proteins are linear chain molecules made out of amino acids. Only when they fold to their native states, they become functional. This dissertation aims to model the solvent (environment) effect and to develop & implement enhanced sampling methods that enable a reliable study of the protein folding problem in silico. We have developed an enhanced solvation model based on the solution to the Poisson-Boltzmann equation in order to describe the solvent effect. Following the quantum mechanical Polarizable Continuum Model (PCM), we decomposed net solvation free energy into three physical terms– Polarization, Dispersion and Cavitation. All the terms were implemented, analyzed and parametrized individually to obtain a high level of accuracy. In order to describe the thermodynamics of proteins, their conformational space needs to be sampled thoroughly. Simulations of proteins are hampered by slow relaxation due to their rugged free-energy landscape, with the barriers between minima being higher than the thermal energy at physiological temperatures. In order to overcome this problem a number of approaches have been proposed of which replica exchange method (REM) is the most popular. In this dissertation we describe a new variant of canonical replica exchange method in the context of molecular dynamic simulation. The advantage of this new method is the easily tunable high acceptance rate for the replica exchange. We call our method Microcanonical Replica Exchange Molecular Dynamic (MREMD). We have described the theoretical frame work, comment on its actual implementation, and its application to Trp-cage mini-protein in implicit solvent. We have been able to correctly predict the folding thermodynamics of this protein using our approach.

MULTISCALE EXAMINATION AND MODELING OF ELECTRON TRANSPORT IN NANOSCALE MATERIALS AND DEVICES

For half a century the integrated circuits (ICs) that make up the heart of electronic devices have been steadily improving by shrinking at an exponential rate. However, as the current crop of ICs get smaller and the insulating layers involved become thinner, electrons leak through due to quantum mechanical tunneling. This is one of several issues which will bring an end to this incredible streak of exponential improvement of this type of transistor device, after which future improvements will have to come from employing fundamentally different transistor architecture rather than fine tuning and miniaturizing the metal-oxide-semiconductor field effect transistors (MOSFETs) in use today. Several new transistor designs, some designed and built here at Michigan Tech, involve electrons tunneling their way through arrays of nanoparticles. We use a multi-scale approach to model these devices and study their behavior. For investigating the tunneling characteristics of the individual junctions, we use a first-principles approach to model conduction between sub-nanometer gold particles. To estimate the change in energy due to the movement of individual electrons, we use the finite element method to calculate electrostatic capacitances. The kinetic Monte Carlo method allows us to use our knowledge of these details to simulate the dynamics of an entire device— sometimes consisting of hundreds of individual particles—and watch as a device ‘turns on’ and starts conducting an electric current. Scanning tunneling microscopy (STM) and the closely related scanning tunneling spectroscopy (STS) are a family of powerful experimental techniques that allow for the probing and imaging of surfaces and molecules at atomic resolution. However, interpretation of the results often requires comparison with theoretical and computational models. We have developed a new method for calculating STM topographs and STS spectra. This method combines an established method for approximating the geometric variation of the electronic density of states, with a modern method for calculating spin-dependent tunneling currents, offering a unique balance between accuracy and accessibility.

Safety and effectiveness of bariatric surgery: Roux-en-y gastric bypass is superior to gastric banding in the management of morbidly obese patients: a reply to the response by Bhoyrul et al

ABSTRACT: BACKGROUND: We have read the letter by Bhoyrul et al. in response to our recently published article "Safety and effectiveness of bariatric surgery: Roux-en-Y gastric bypass is superior to gastric banding in the management of morbidly obese patients". We strongly disagree with the content of the letter. RESULTS AND DISCUSSION: Bhoyrul et al. base their letter mostly on low level evidence such as single-institutional case series (level IV evidence) and expert opinion (level V evidence). Surprisingly, they do not comment on the randomized controlled trial, which clearly favours gastric bypass over gastric banding. CONCLUSION: The letter by Bhoyrul et al. is based on low level evidence and is itself biased, unsubstantiated, and not supported by the current literature.

Jan Fook: Social Work: Critical Theory and Practice & Karen Healy: Social Work Practices: Contemporary Perspectives on Change

In his recent book on the contemporary politics of social work, Powell (2001) nominates Jan Fook and Karen Healy as two Australian authors who have made significant contributions to the radical or critical social work tradition. I have chosen to review them together, as each, in different ways, attempts to achieve the same purpose. That is, they attempt to provide a convincing account for adopting a critical approach to practice in the contemporary conditions of the 21st century and, in doing so, re-invigorate the radical tradition of social work practice. My first comment, important for the readership of this international journal, is that both books easily 'travel' beyond the Australian context.

Knowledge-Production Processes in Practice Research - Outcomes and Critical Elements

The welfare sector has seen considerable changes in its operational context. Welfare services respond to an increasing number of challenges as citizens are confronted with life’s uncertainties and a variety of complex situations. At the same time the service-delivery system is facing problems of co-operation and the development of staff competence, as well as demands to improve service effectiveness and outcomes. In order to ensure optimal user outcomes in this complex, evolving environment it is necessary to enhance professional knowledge and skills, and to increase efforts to develop the services. Changes are also evident in the new emergent knowledge-production models. There has been a shift from knowledge acquisition and transmission to its construction and production. New actors have stepped in and the roles of researchers are subject to critical discussion. Research outcomes, in other words the usefulness of research with respect to practice development, is a topical agenda item. Research is needed, but if it is to be useful it needs to be not only credible but also useful in action. What do we know about different research processes in practice? What conceptions, approaches, methods and actor roles are embedded? What is the effect on practice? How does ‘here and now’ practice challenge research methods? This article is based on the research processes conducted in the institutes of practice research in social work in Finland. It analyses the different approaches applied by elucidating the theoretical standpoints and the critical elements embedded in them, and reflects on the outcomes in and for practice. It highlights the level of change and progression in practice research, arguing for diverse practice research models with a solid theoretical grounding, rigorous research processes, and a supportive infrastructure.

Effect of MGA on Performance, Sexual Behavior, Carcass Quality and Tenderness in Mixed-Sex Pens of Cattle

The effect of MGA in mixed pens of steers and heifers was evaluated over a three-year period at the ISU Armstrong Research Farm near Lewis, Iowa. Two pens of approximately 40 head were fed diets with or without MGA in each of three replications. Estrus and riding activity was monitored using the Heat Watchâ system. At slaughter, in addition to routine carcass data collection, a rib sample was collected from each carcass for tenderness evaluation. There was no effect on dry matter intake due to MGA treatment. Mixed-sex pens that were fed MGA were 4% more efficient than controls. MGA-fed steers gained similarly to control steers. MGA fed heifers gained 8% faster than control heifers. MGA highly reduced measures of estrus and riding activity throughout the feeding period. MGA feeding improved marbling and tenderness measured in both steers and heifers. These data suggest that MGA has potential to improve performance, quality grade and tenderness in mixed pens of steers and heifers.

Triality, periodicity and stability of SO(8) gauged supergravity

While electromagnetic duality is a symmetry of many supergravity theories, this is not the case for the N = 8 gauged theory. It was recently shown that this rotation leads to a one-parameter family of SO(8) supergravities. It is an open question what the period of this parameter is. This issue is investigated in the SO(4) invariant sectors of the theory. We classify such critical points and find a novel branch of non-supersymmetric and unstable solutions, whose embedding is related via triality to the two known ones. Secondly, we show that the three branches of solutions lead to a π/4 periodicity of the vacuum structure. The general interrelations between triality and periodicity are discussed. Finally, we comment on the connection to other gauge groups as well as the possibility to achieve (non-)perturbative stability around AdS/Mkw/dS transitions.

Curtailing the voices and the need for predictors

Comment on Transcranial magnetic stimulation of Wernicke's and Right homologous sites to curtail "voices": a randomized trial. [Biol Psychiatry. 2013]

Influence of Geographical Origin and Ethnicity on Mortality in Patients on Antiretroviral Therapy in Canada, Europe, and the United States

Our objective was to assess differences in all-cause mortality, as well as AIDS and non-AIDS death rates, among patients started on antiretroviral therapy (ART) according to their geographical origin and ethnicity/race in Europe, Canada, and the United States. METHODS: This was a collaboration of 19 cohort studies of human immunodeficiency virus-positive subjects who have initiated ART (ART Cohort Collaboration) between 1998 and 2009. Adjusted mortality hazard ratios (AHRs) were estimated using Cox regression. A competing risk framework was used to estimate adjusted subdistribution hazard ratios for AIDS and non-AIDS mortality. RESULTS: Of 46 648 European patients, 16.3% were from sub-Saharan Africa (SSA), 5.1% Caribbean and Latin America, 1.6% North Africa and Middle East, and 1.7% Asia/West; of 1371 patients from Canada, 14.9% were First Nations and 22.4% migrants, and of 7742 patients from North America, 55.5% were African American and 6.6% Hispanic. Migrants from SSA (AHR, 0.79; 95% confidence interval [CI], .68-.92) and Asia/West (AHR, 0.62; 95% CI, .41-.92) had lower mortality than Europeans; these differences appeared mainly attributable to lower non-AIDS mortality. Compared with white Canadians, mortality in Canadian First Nations people (AHR, 1.48; 95% CI, .96-2.29) was higher, both for AIDS and non-AIDS mortality rates. Among US patients, when compared with whites, African Americans had higher AIDS and non-AIDS mortality, and hazard ratios for all-cause mortality increased with time on ART. CONCLUSIONS: The lower mortality observed in migrants suggests "healthy migrant" effects, whereas the higher mortality in First Nations people and African Americans in North America suggests social inequality gaps. KEYWORDS: HIV infection, antiretroviral therapy, ethnic minorities, migrants Comment in Addressing disparities in HIV mortality: antiretroviral therapy is necessary but not sufficient. [Clin Infect Dis. 2013]

Federalism and the Concept of Political Territoriality: Towards an Analytical Framework for Comparative Territorial Politics

The core issues comparative territorial politics addresses are how and why territory is used to delimit, maintain, or create political power; and with what kind of consequences for efficiency (output) and legitimacy (input). The aim of this article is to integrate various research strands into the comparative study of territorial politics, with federal studies at its core. As an example of a conceptual payoff, ‘political territoriality’ refers the observer to three dimensions of the strategic use of areal boundaries for political power. By focusing on territory as a key variable of political systems, the actors, processes and institutions are first analytically separated and continuously measured, enhancing internal validity, and then theoretically integrated, which allows more valid external inferences than classic, legal-institutionalist federal studies. After discussing the boundaries and substance of comparative territorial politics as a federal discipline, political territoriality is developed towards an analytical framework applicable to politics at any governmental level. The claims are modest: political territoriality does not serve so much as an explanatory concept as rather an ‘attention-directing device’ for federal studies.

Experimenting and modeling: sharp distinctions, integration or just a mess?

At first sight, experimenting and modeling form two distinct modes of scientific inquiry. This spurs philosophical debates about how the distinction should be drawn (e.g. Morgan 2005, Winsberg 2009, Parker 2009). But much scientific practice casts serious doubts on the idea that the distinction makes much sense. There are two worries. First, the practices of modeling and experimenting are often intertwined in intricate ways because much modeling involves experimenting, and the interpretation of many experiments relies upon models. Second, there are borderline cases that seem to blur the distinction between experiment and model (if there is any). My talk tries to defend the philosophical project of distinguishing models from experiment and to advance the related philosophical debate. I begin with providing a minimalist framework of conceptualizing experimenting and modeling and their mutual relationships. The methods are conceptualized as different types of activities that are characterized by a primary goal, respectively. The minimalist framwork, which should be uncontroversial, suffices to accommodate the first worry. I address the second worry by suggesting several ways how to conceptualize the distinction in a more flexible way. I make a concrete suggestion of how the distinction may be drawn. I use examples from the history of science to argue my case. The talk concentrates and models and experiments, but I will comment on simulations too.

The sleeper effect: Artifact or phenomenon—A brief comment on Bell et al. (2013)

OBJECTIVE: Bell, Marcus, and Goodlad (2013) recently conducted a meta-analysis of randomized controlled additive trials and found that adding an additional component to an existing treatment vis-à-vis the existing treatment produced larger effect sizes on targeted outcomes at 6-months follow-up than at termination, an effect they labeled as a sleeper effect. One of the limitations with Bell et al.'s detection of the sleeper effect was that they did not conduct a statistical test of the size of the effect at follow-up versus termination. METHOD: To statistically test if the differences of effect sizes between the additive conditions and the control conditions at follow-up differed from those at termination, we used a restricted maximum-likelihood random-effect model with known variances to conduct a multilevel longitudinal meta-analysis (k = 30). RESULTS: Although the small effects at termination detected by Bell et al. were replicated (ds = 0.17-0.23), none of the analyses of growth from termination to follow-up produced statistically significant effects (ds < 0.08; p > .20), and when asymmetry was considered using trim-and-fill procedure or the studies after 2000 were analyzed, magnitude of the sleeper effect was negligible (d = 0.00). CONCLUSION: There is no empirical evidence to support the sleeper effect.

Comment: Earnings Returns to Education in Urban China: A Note on Testing Differences among Groups

Comment on Wu and Xie, ASR, June 2003