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Search Results: 1 - 10 of 3487 matches for " Stephan "
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T cell receptor variable β20-1 harbors a nucleotide binding pocket in the CDR2β loop  [PDF]
Stephan Watkins, Werner J. Pichler
Open Journal of Immunology (OJI) , 2013, DOI: 10.4236/oji.2013.33021
Abstract:

Novel aspects of T cells containing TCRVβ20-1 are numerous, ranging from pathogen specific reactivity to specific tissue homing, or possible T cell subsets. Recently, it was demonstrated that TCR itself could become reactive by binding to small molecules free of the pHLA interface. Our work here was to identify a natural ligand binding to an identified pocket on the CDR2β loop of these TCR. Using docking of suspected ligands, we were able to show Guanine and Adenine diand tri-nucleotides readily bind to the identified site. Comparing these with small molecule sites found on other TCR types, we show this interaction is novel. With further molecular dynamic simulations, these sites are shown to be plausible by conducting simple computational based solubility tests as cross validation. Combined with simple proliferative responses, the identified nucleotides are also shown to have functional consequences by inducing T cell proliferation for CD4/Vβ20-1 + T cells, while failing to induce proliferation in other T cell isolates. Merging computational and simple cell assays, this work establishes a role of nucleotides in T cells found to contain this TCR subtype.

Monitoring Endangered Species Populations: Gene Dispersal Can Have Pronounced Effects on the Relationship between Census Size and Genetic Diversity  [PDF]
Steven H. Rogstad, Stephan Pelikan
American Journal of Plant Sciences (AJPS) , 2013, DOI: 10.4236/ajps.2013.410238
Abstract:

Anthropogenic activities are increasing habitat fragmentation, as well as the number of threatened and endangered species. Thus, isolated fragments with natural remnant stands, or in situ or ex situ endangered species rescue populations, are on the rise. The most common method for assessing the “conservation health” of such populations is to determine or estimate the census size. However, while it is known that the census size of a population does not always correlate with its genetic diversity, methods for modeling how different factors can drive variation in the relationship of census size to genetic diversity in plant populations are needed. Here we use the computer program NEWGARDEN to investigate how the relationship of stand size versus genetic diversity (measured as both the percent of the founding alleles retained and FIT) can be extremely variable depending on founder number, founder density, and gene dispersal distances. Populations of endangered species that appear to have the same conservation health in terms of similar population numbers may differ greatly in their conservation health as indicated by the genetic diversity they retain. NEWGARDEN can be used to explore how different founding and intra- or interspecific life history characteristics can affect genetic diversity relative to census size. If proper historical data exist, NEWGARDEN can also be used to estimate the percent of founding genetic diversity remaining in a given stand.

Activating interactions of sulfanilamides with T cell receptors  [PDF]
Stephan Watkins, Werner J. Pichler
Open Journal of Immunology (OJI) , 2013, DOI: 10.4236/oji.2013.33019
Abstract:

Activation and expansion of drug reactive T cells are key features in drug hypersensitivity reactions. Drugs may interact directly with immune receptors such as the human leukocyte antigens (HLA) or the T-cell receptors (TCR) itself, the pharmacological interaction [p-i] concept. To analyze whether the drug sulfamethoxazole (SMX) interacts directly with the TCR and thereby contributing to signaling and T cell activation, we analyze two SMX specific T cell clones (TCC “1.3”and “H13”). Proliferation to SMX and 11 related sulfanilamides, Ca++ influx in drug stimulated T-cells and the inhibitory effect of non-reactive sulfanilamides on SMX stimulation were analyzed. In silico docking of SMX and related sulfanilamide to the TCR were used to identify possible drug binding sites, and correlated to in vitro data to find the correct docking. In Ca++ influx assays, reactions occurred as early as 14 sec after adding SMX to TCC and APC. The broadly reactive clone (“H13”) was stimulated by 5 additional sulfanilamide, while one TCC (“1.3”) was reactive exclusively with SMX but not other sulfanilamides. Competition experiments with sulfanilamide inhibited SMX induced Ca++ influx and proliferation of the TCC1.3 ina dose dependent way. Docking experiments with SMX and related sulfanilamides confirmed and explained the in vitro data as docking localized binding sites for SMX and the 5 stimulating sulfanilamides on the CDR2β domain of the clone H13, while the 6 non-stimulatory SA failed to bind. In TCC 1.3, SMX could be docked on the CDR3α of the TCR. The other, non-stimulatory but inhibitory SA could also be docked to the same site. The combined analysis of in vitro and in silico

Segmenting Salient Objects in 3D Point Clouds of Indoor Scenes Using Geodesic Distances  [PDF]
Shashank Bhatia, Stephan K. Chalup
Journal of Signal and Information Processing (JSIP) , 2013, DOI: 10.4236/jsip.2013.43B018
Abstract:

Visual attention mechanisms allow humans to extract relevant and important information from raw input percepts. Many applications in robotics and computer vision have modeled human visual attention mechanisms using a bottom-up data centric approach. In contrast, recent studies in cognitive science highlight advantages of a top-down approach to the attention mechanisms, especially in applications involving goal-directed search. In this paper, we propose a top-down approach for extracting salient objects/regions of space. The top-down methodology first isolates different objects in an unorganized point cloud, and compares each object for uniqueness. A measure of saliency using the properties of geodesic distance on the object’s surface is defined. Our method works on 3D point cloud data, and identifies salient objects of high curvature and unique silhouette. These being the most unique features of a scene, are robust to clutter, occlusions and view point changes. We provide the details of the proposed method and initial experimental results.

 

Spectral Crop Coefficient Approach for Estimating Daily Crop Water Use  [PDF]
Nithya Rajan, Stephan J. Maas
Advances in Remote Sensing (ARS) , 2014, DOI: 10.4236/ars.2014.33013
Abstract: While the amount of water used by a crop can be measured using lysimeters or eddy covariance systems, it is more common to estimate this quantity based on weather data and crop-related factors. Among these approaches, the standard crop coefficient method has gained widespread use. A limitation of the standard crop coefficient approach is that it applies to “standard conditions” that are invariant from field to field. In this article, we describe a method for estimating daily crop water use (CWU) that is specific to individual fields. This method, the “spectral crop coefficient” approach, utilizes a crop coefficient numerically equivalent to the crop ground cover observed in a field using remote sensing. This “spectral crop coefficient” Ksp is multiplied by potential evapotranspiration determined from standard weather observations to estimate CWU. We present results from a study involving three farmers' fields in the Texas High Plains in which CWU estimated using the Ksp approach is compared to observed values obtained from eddy covariance measurements. Statistical analysis of the results suggests that the Ksp approach can produce reasonably accurate estimates of daily CWU under a variety of irrigation strategies from fully irrigated to dryland. These results suggest that the Ksp approach could be effectively used in applications such as operational irrigation scheduling, where its field-specific nature could minimize over-irrigation and support water conservation.
Abstract not submitted for online publication
Stephan Schuster
Genome Biology , 2010, DOI: 10.1186/gb-2010-11-s1-i16
Abstract:
The POETICs of industrial carbon dioxide emissions in Japan: an urban and institutional extension of the IPAT identity
Stephan Scholz
Carbon Balance and Management , 2006, DOI: 10.1186/1750-0680-1-11
Abstract: Results suggest the weak existence of an environmental Kuznets curve, in which the wealthiest cities are reducing their emissions through increased efficiency. Significant institutional impacts are also found to hold in the predicted directions. Specifically, panel and cross-sectional regressions indicate that membership in the International Council for Local Environmental Initiatives and non-profit organizational presence have negative effects on industrial carbon dioxide emissions.The presence of institutional drivers at the city level provides empirical support for the POETICs rubric, which recasts the ecological framing of the IPAT identity in a more sociological mold. The results also indicate that Japanese civil society has a role to play in carbon mitigation. More refined studies need to take into consideration an expanded set of methods, drivers, and carbon budgets, as applied to a broader range of cases outside of Japan, to more accurately assess how civil society can bridge the issue of scale that separates local level policy concerns from global level climate dynamics.The flow of carbon through the Earth's eco-systems is one of the most complex and important of the global cycles. It challenges researchers to be interdisciplinary and synthesize information from both the natural and social sciences in order to understand how it works and what causes it to change. One of the greatest challenges in this task is measuring and accounting for the increasingly skewed contribution of human activities. It is now widely accepted that anthropogenic causes have pushed the atmospheric concentration of carbon dioxide (CO2), the main greenhouse gas responsible for global warming and associated climate changes, to its highest level in 420,000 years at 380 parts per million [1].Rapid population growth coupled with industrialization has clearly been taking its toll. While the developed world has passed through the demographic transition to a low fertility regime defined by
Microproteins (miPs) – the next big thing
Stephan Feller
Cell Communication and Signaling , 2012, DOI: 10.1186/1478-811x-10-42
Abstract: In case you do not know what they are, no need to worry: nobody does.However, with proto-genes recently entering the stage [1] it seems just a small step for mankind to assume that those dye fronts of protein gels you have been cutting off and binning for decades now harbour a plethora of precious little gems and thus an amazing potential for discovering exciting regulatory molecules that will bind to proteins etc. to regulate their conformations and activities, their binding partners, their subcellular localisation and so on.They can be expected to steer embryonic development and stem cell differentiation, to play a role in cancers and neurodegenerative diseases and should also make great leads for future drugs. Clearly, miPs are yet another Nobel Prize lurking, and begging for attention.To study them is easy: just mass spec your protein gel dye fronts to death, synthesise all found miP candidates, biotinylate them and go fishing for binding partners. Then introduce your miPs into cells using cell-penetrating shuttle peptides or transfections and watch their interaction partners misbehave in cells. Finally, do miP knock-outs and -ins in animals of your fancy and observe what happens to them. Alternatively, if you do not have access to mass spec-omics, look for short transcribed ORFs of unknown function in the genome, synthesise those ORFs as biotinylated peptides on a vast scale and then go fishing.That is all there is to it really,…so…would someone look, PLEASE.Of course, if you actually find something, we told you so, and we would want to share the glory and the financial rewards; and do not dare to simply call these newly found, super-exciting, sparkling entities merely regulatory peptides or christen them with another boring name like that, or you shall never be grand.Merry Christmas and a healthy, happy and very productive 2013 to all of you.
Science and policy in substance abuse
Stephan Arndt
Substance Abuse Treatment, Prevention, and Policy , 2006, DOI: 10.1186/1747-597x-1-1
Abstract: Separate and often disparate public systems deal with substance abuse as well as provide substance abuse treatment and prevention. These include: legislation pertaining to substance abuse; correctional supervision of substance abusers; medical treatment and screening; mental health services; research and evaluation of substance abuse programs; interdiction efforts, and so on. These varied systems share a common goal – to reduce the burden of substance abuse on the abuser, their family, and society. Unfortunately, these systems often operate in isolation of one another. This journal will provide an environment for the exchange of ideas, new research, consensus papers, and critical reviews that bridge fields that share a common goal of reducing the problems caused by substance abuse.We are interested in articles on research and evaluation of issues pertaining to treatment, recovery, and prevention, but with an emphasis on items such as: evidence-based practices; stigma reduction; how public policy and law making have implications for treatment and recovery; removing barriers to treatment and recovery; how decision makers can implement new treatment practices; and the epidemiological trends in substance abuse in special populations (e.g., corrections offenders, women, elders). We will consider original data driven articles, consensus topics, literature reviews – all with a policy flavor. These papers may come from, but are not limited to, psychology, psychiatry, sociology, medicine, social work, law, forensics, corrections, education, health policy, and public health.There are many potential papers that go unpublished in the scholarly literature that can find a home here. For example, the Robert Woods Johnson Foundation "Substance Abuse Policy Research Program" funds a very large number of projects that would yield perfectly relevant and potentially publishable findings http://www.rwjf.org/files/publications/annual/2004/portfolio_addiction_01.jsp webcite.Governmental a
Stereotyping and the treatment of missing data for drug and alcohol clinical trials
Stephan Arndt
Substance Abuse Treatment, Prevention, and Policy , 2009, DOI: 10.1186/1747-597x-4-2
Abstract: Stigma and stereotyping of marginalized groups is alive and well in the 21st century. Oftentimes, it is insidious. As researchers, we sometimes like to think that negative attitudes and bias are the afflictions of the less enlightened. Like addiction though, these afflictions sometimes show up in the least likely places.A fair number of clients drop out of treatment and clinical trial studies. We typically do not know why subjects drop out; whether or not they are using again and if they are, at what level; and can make no direct assessments about outcomes. Their data are missing. How clinical trials in addiction research treat missing data depends on presumptions about why the data are missing. Too often, we pass over the assumptions because they are imbedded in the analysis. Even when the presumptions are explicit, it is sometimes too easy to skim over the Methods Sections of papers and not question the underlying assumptions of the statistical analyses.A close examination of the assumptions in a surprisingly large number of published studies finds what can only be described as stigma and stereotyping of individuals because they are no longer participating in studies. There are several options for how the dropouts and their data are handled. The decision depends on the intent of the study and presumptions about why the data are missing.To find out how research reports in substance abuse/dependence clinical trials generally dealt with their missing data, I did an informal review of recent clinical trials. I selected 4 prominent journals (i.e. Alcoholism: Clinical and Experimental Research, Alcohol and Alcoholism, Journal of Studies on Alcohol and Drugs, Journal of Substance Abuse Treatment) dealing with substance misuse. For each journal, I went back from the most recent issues until I found 10 reports of clinical trials or went back 6 issues, whichever occurred first. This resulted in 34 articles on clinical trials. I reviewed the reports' method of handling the m
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