gebhart/patrepeval huggingface dataset:
Construction of a new shuttle vector for Lactobacillus (1992)

To clone the malolactic enzyme gene from Lactobacillus sp. 89, construction of a shuttle vector able to express itself in Lactobacillus sp. 89 and Escherichia coli was undertaken. The shuttle plasmid pLE16 resulted from the union of pBR328 and of the pLB10 plasmid extracted from Lactobacillus bulgaricus 10. The bacterial transformation in Lactobacillus sp. 89 was performed by electroporation, and the clones were selected on MRS medium with 30 micrograms.mL-1 chloramphenicol added. Fifty percent of the clones from Lactobacillus sp. 89 lost their resistance to chloramphenicol following 28 generations when the selection pressure was not maintained. The restriction map of pLE16 (7600 bp) was established using several restriction enzymes.
Operational Semantics of the Marte Repetitive Structure Modeling Concepts for Data-Parallel Applications Design (2010)

This paper presents an operational semantics of the repetitive model of computation, which is the basis for the repetitive structure modeling (RSM) package defined in the standard UML Marte profile. It also deals with the semantics of an RSM extension for control-oriented design. The goal of this semantics is to serve as a formal support for i) reasoning about the behavioral properties of models specified in Marte with RSM, and ii) defining correct-by-construction model transformations for the production of executable code in a model-driven engineering framework.
Complementary base-pair-facilitated electron tunneling for electrically pinpointing complementary nucleobases (2005)

Molecular tips in scanning tunneling microscopy can directly detect intermolecular electron tunneling between sample and tip molecules and reveal the tunneling facilitation through chemical interactions that provide overlap of respective electronic wave functions, that is, hydrogen-bond, metal-coordination-bond, and charge-transfer interactions. Nucleobase molecular tips were prepared by chemical modification of underlying metal tips with thiol derivatives of adenine, guanine, cytosine, and uracil and the outmost single nucleobase adsorbate probes intermolecular electron tunneling to or from a sample nucleobase molecule. We found that the electron tunneling between a sample nucleobase and its complementary nucleobase molecular tip was much facilitated compared with its noncomplementary counterpart. The complementary nucleobase tip was thereby capable of electrically pinpointing each nucleobase. Chemically selective imaging using molecular tips may be coined "intermolecular tunneling microscopy" as its principle goes and is of general significance for novel molecular imaging of chemical identities at the membrane and solid surfaces.
Towards Transparent Parallel Processing on Multi-core Computers (2009)

Parallelization of all application types is critical with the trend towards an exponentially increasing number of cores per chip, which needs to be done at multiple levels to address the unique challenges and exploit the new opportunities brought by new architecture advances. In this dissertation, we focus on enhancing the utilization of future-generation, many-core personal computers for high performance and energy effective computing.\n\n\nOn one hand, computation- and/or data-intensive tasks such as scientific data processing and visualization, which are typically performed sequentially on personal workstations, need to be parallelized to take advantage of the increasing hardware parallelism. Explicit parallel programming, however, is labor-intensive and requires sophisticated performance tuning for individual platforms and operating systems. In this PhD study, we made a first step toward transparent parallelization for data processing codes, by developing automatic parallelization tools for scripting languages. More specifically, we present pR, a framework that transparently parallelizes the R language for high-performance statistical computing. We apply parallelizing compiler technology to runtime, whole-program dependence analysis and employ incremental code analysis assisted with evaluation results. Experimental results demonstrate that pR can exploit both task and data parallelism transparently and overall achieve good performance as well as scalability. Further, we attack the performance tuning problem for transparent parallel execution, by proposing and designing a novel online task decomposition and scheduling approach for transparent parallel computing. This approach collects runtime task cost information transparently and performs online static scheduling, utilizing cost estimates generated by ANN-based runtime performance prediction, as well as by loop iteration test runs. We implement the above techniques in the pR framework and our proposed approach is demonstrated to significantly improve task partitioning and scheduling over a variety of benchmarks.\n\n\nOn the other hand, multi-core personal computers will inevitably be under-utilized when their owners perform light-weight tasks such as editing and web browsing, making volunteer computing more appealing than ever. In this study, we made a first step towards a novel computation model, energy-aware volunteer computing on multi-core processors, by evaluating the potential energy/performance trade-off of a more aggressive execution model that selects active nodes over idle nodes for scheduling foreign application tasks, in order to better utilize idle cores and achieve energy savings. Our experiment results suggest that aggressive volunteer computing can bring significant energy saving compared to common existing execution modes and provides an attractive computation model.
Current Diagnostic Uses of Saliva (1987)

Most of the information which has been collected on salivary composition in different disease states (with the notable exception of that in digitalis intoxication) has proved of little practical diagnostic value. Diagnostic use of saliva has become more extensive in recent years, particularly in relation to estimation of systemic levels of lipid-soluble drugs and hormones. Thiocyanate levels have been used to validate self-reported frequency of tobacco-smoking, and nitrate levels have been assayed to estimate dietary nitrate intakes. The estimation of steroid hormone concentrations in saliva is now generally recognized as a means of determining systemic steroid levels which offers many advantages over estimation in serum or urine samples. Immunoassay methods now permit measurement of very small concentrations of biologically active substances in saliva.
Feature Selection for Gene Expression Using Model-Based Entropy (2009)

Gene expression data usually contain a large number of genes but a small number of samples. Feature selection for gene expression data aims at finding a set of genes that best discriminate biological samples of different types. Using machine learning techniques, traditional gene selection based on empirical mutual information suffers the data sparseness issue due to the small number of samples. To overcome the sparseness issue, we propose a model-based approach to estimate the entropy of class variables on the model, instead of on the data themselves. Here, we use multivariate normal distributions to fit the data, because multivariate normal distributions have maximum entropy among all real-valued distributions with a specified mean and standard deviation and are widely used to approximate various distributions. Given that the data follow a multivariate normal distribution, since the conditional distribution of class variables given the selected features is a normal distribution, its entropy can be computed with the log-determinant of its covariance matrix. Because of the large number of genes, the computation of all possible log-determinants is not efficient. We propose several algorithms to largely reduce the computational cost. The experiments on seven gene data sets and the comparison with other five approaches show the accuracy of the multivariate Gaussian generative model for feature selection, and the efficiency of our algorithms.
Deeper understanding of the homography decomposition for vision-based control (2007)

The displacement of a calibrated camera between two images of a planar object&#13;\ncan be estimated by decomposing a homography matrix. The aim of this document is to&#13;\npropose a new method for solving the homography decomposition problem. This new method&#13;\nprovides analytical expressions for the solutions of the problem, instead of the traditional&#13;\nnumerical procedures. As a result, expressions of the translation vector, rotation matrix and&#13;\nobject-plane normal are explicitly expressed as a function of the entries of the homography&#13;\nmatrix. The main advantage of this method is that it will provide a deeper understanding&#13;\non the homography decomposition problem. For instance, it allows to obtain the relations&#13;\namong the possible solutions of the problem. Thus, new vision-based robot control laws can&#13;\nbe designed. For example the control schemes proposed in this report combine the two final&#13;\nsolutions of the problem (only one of them being the true one) assuming that there is no a&#13;\npriori knowledge for discerning among them.
Ultrathin self-assembled anionic polymer membranes for superfast size-selective separation (2013)

Nanoporous membranes with superior separation performance have become more crucial with increasing concerns in functional nanomaterials. Here novel ultrahigh permeable nanoporous membranes have been fabricated on macroporous supports by self-assembly of anionic polymer on copper hydroxide nanostrand templates in organic solution. This facile approach has a great potential for the fabrication of ultrathin anionic polymer membranes as a general method. The as-fabricated self-assembled membranes have a mean pore size of 5-12 nm and an adjustable thickness as low as 85 nm. They allow superfast permeation of water, and exhibit excellent size-selective separation properties and good fouling resistance for negatively-charged solutes during filtration. The 85 nm thick membrane has an ultrahigh water flux (3306 l m(-2) h(-1) bar(-1)) that is an order of magnitude larger than commercial membranes, and can highly efficiently separate 5 and 15 nm gold nanoparticles from their mixtures. The newly developed nanoporous membranes have a wide application in separation and purification of biomacromolecules and nanoparticles.
Structure-based mutagenesis reveals the albumin-binding site of the neonatal Fc receptor (2012)

Albumin is the most abundant protein in blood where it has a pivotal role as a transporter of fatty acids and drugs. Like IgG, albumin has long serum half-life, protected from degradation by pH-dependent recycling mediated by interaction with the neonatal Fc receptor, FcRn. Although the FcRn interaction with IgG is well characterized at the atomic level, its interaction with albumin is not. Here we present structure-based modelling of the FcRn-albumin complex, supported by binding analysis of site-specific mutants, providing mechanistic evidence for the presence of pH-sensitive ionic networks at the interaction interface. These networks involve conserved histidines in both FcRn and albumin domain III. Histidines also contribute to intramolecular interactions that stabilize the otherwise flexible loops at both the interacting surfaces. Molecular details of the FcRn-albumin complex may guide the development of novel albumin variants with altered serum half-life as carriers of drugs.
Complementary metal-oxide-semiconductor thin-film transistor circuits from a high-temperature polycrystalline silicon process on steel foil substrates (2002)

We fabricated CMOS circuits from polycrystalline silicon films on steel foil substrates at process temperatures up to 950/spl deg/C. The substrates were 0.2-mm thick steel foil coated with 0.5-/spl mu/m thick SiO/sub 2/. We employed silicon crystallization times ranging from 6 h (600/spl deg/C) to 20 s (950/spl deg/C). Thin-film transistors (TFTs) were made in either self-aligned or nonself-aligned geometries. The gate dielectric was SiO/sub 2/ made by thermal oxidation or from deposited SiO/sub 2/. The field-effect mobilities reach 64 cm/sup 2//Vs for electrons and 22 cm/sup 2//Vs for holes. Complementary metal-oxide-silicon (CMOS) circuits were fabricated with self-aligned TFT geometries, and exhibit ring oscillator frequencies of 1 MHz. These results lay the groundwork for polycrystalline silicon circuitry on flexible substrates for large-area electronic backplanes.
Leucine Supplementation Differently Modulates Branched-Chain Amino Acid Catabolism, Mitochondrial Function and Metabolic Profiles at the Different Stage of Insulin Resistance in Rats on High-Fat Diet (2017)

The available findings concerning the association between branched-chain amino acids (BCAAs)-particularly leucine-and insulin resistance are conflicting. BCAAs have been proposed to elicit different or even opposite effects, depending on the prevalence of catabolic and anabolic states. We tested the hypothesis that leucine supplementation may exert different effects at different stages of insulin resistance, to provide mechanistic insights into the role of leucine in the progression of insulin resistance. Male Sprague-Dawley rats were fed a normal chow diet, high-fat diet (HFD), HFD supplemented with 1.5% leucine, or HFD with a 20% calorie restriction for 24 or 32 weeks. Leucine supplementation led to abnormal catabolism of BCAA and the incompletely oxidized lipid species that contributed to mitochondrial dysfunction in skeletal muscle in HFD-fed rats in the early stage of insulin resistance (24 weeks). However, leucine supplementation induced no remarkable alternations in BCAA catabolism, but did enhance mitochondrial biogenesis with a concomitant improvement in lipid oxidation and mitochondrial function during the hyperglycaemia stage (32 weeks). These findings suggest that leucine trigger different effects on metabolic signatures at different stages of insulin resistance, and the overall metabolic status of the organisms should be carefully considered to potentiate the benefits of leucine.
Effect of omega-3-acid ethyl esters on the steady-state plasma pharmacokinetics of rosuvastatin in healthy adults (2008)

Administration of P-OM3 with rosuvastatin did not affect the pharmacokinetics of rosuvastatin under steady-state conditions in healthy individuals.
Management ... working day of a health services manager. Plymouth Community Services NHS Trust. (1994)

Rae Wallin is Director of Personnel, Plymouth Community Services NHS Trust, a trust with 2000 staff and a budget of 40m pounds. Ideally, work and home life are strictly compartmentalised but this does not always happen in practice; there is a challenge in balancing the needs of both. Senior managers are under enormous pressure in today's NHS; for women, Opportunity 2000 has not yet really changed things.
Simian immunodeficiency virus (SIVmac251) membrane lipid mixing with human CD4+ and CD4- cell lines in vitro does not necessarily result in internalization of the viral core proteins and productive infection (1993)

The cell binding site of simian immunodeficiency virus (SIV) is believed to be the CD4 molecule. Several CD4+ cell lines are, however, resistant to infection by SIVmac251 in vitro and additional cell membrane molecules have been implicated in SIVmac251 entry. We investigated the binding, envelope fusion and entry of the viral core proteins (p27) of SIVmac251 into two human CD4+ cell lines (H9 and Sup-T1) which are infectible, and one CD4+ (A3.01) and two CD4- cell lines (K562 and Raji) that are resistant to infection. The fusion of the viral and cellular membranes was monitored by a fluorescence assay for lipid mixing. Cell entry of the viral core was evaluated following virus-cell incubation and cell surface trypsinization. We found that SIVmac251 can bind to and fuse (membrane lipid mixing) in a temperature-dependent but pH-independent fashion with CD4+ and CD4- human-derived cell lines. In contrast, lipid mixing with CD4 expressing EL-4 mouse T cells or Mv-1-lu mink lung fibroblasts was absent or limited, suggesting that certain components of human cell membranes in addition to CD4 are involved in SIVmac envelope-cell fusion. Lipid mixing with the human cells was inhibited partially by soluble CD4. Anti-CD4 antibodies inhibited the lipid inter-mixing with H9, but not with Raji cells, whereas neutralizing anti-SIVmac sera inhibited fusion with both CD4+ and CD4- cells. Out of the five human cell lines tested, efficient entry of p27 and productive infection took place only with H9 and Sup-T1 cells. In these two cases, the amounts of p27 internalized during virus-cell fusion correlated with the extent of infection.
Assessing atherosclerotic plaque morphology: comparison of optical coherence tomography and high frequency intravascular ultrasound. (1997)

OCT represents a promising new technology for intracoronary imaging because of its high resolution, broad dynamic range, and ability to be delivered through intravascular catheters.
Structure/function analysis of the transmembrane domain of DAB389-interleukin-2, an interleukin-2 receptor-targeted fusion toxin. The amphipathic helical region of the transmembrane domain is essential for the efficient delivery of the catalytic domain to the cytosol of target cells (1993)

Cassette and deletion mutagenesis were used to analyze the function of the amphipathic alpha-helices in the transmembrane domain of DAB389-interleukin-2 (IL-2), a fusion protein which is targeted to the interleukin-2 receptor. We demonstrate that the in-frame deletion of 60 amino acids, from Asn204 to Glu263 in DAB389-IL-2, results in complete loss of cytotoxic activity, whereas when the amphipathic regions from Asp208 to Ser220 and Ala244 to His258 are replaced with idealized amphipathic helices composed of repeating Glu, Lys, and Leu residues, the mutant fusion toxin has low but detectable activity. DAB389-IL-2 and both variants form channels in artificial phospholipid bilayers with conductances identical to those formed by diphtheria toxin. Both mutant fusion toxins bind to the high affinity IL-2 receptor with affinities similar to that of DAB389-IL-2. The fact that these mutants have markedly reduced or absent cytotoxic activity, but possess "wild type" catalytic activity, binding affinities, and channel conductances, suggests the existence of a step in the intoxication pathway, defective in the mutants, which occurs after DAB389-IL-2 binds to the IL-2 receptor. It is unknown whether this step occurs prior or subsequent to channel formation, but it is essential for the efficient delivery of the ADP-ribosyltransferase from DAB389-IL-2 to the cytosol of target cells.
Exacerbation of Parkinsonism by Tacrine (1992)

A patient with Alzheimer's disease and mild features of parkinsonism was treated with tacrine. Tremor and gait dysfunction worsened but responded to the addition of levodopa without adversely affecting cognitive function. The implications for experimental treatment strategies of patients with combined Alzheimer's and Parkinson's disease are discussed.
Laser Additive Manufacturing Process Planning and Automation 243 (2000)

This paper presents a Laser Additive Manufacturing Process Planning (LAMPP) being developed at the University of Missouri-Rolla. The off-line planning recognizes difficult-to-build features from an STL file, selects optimal part orientation and building directions based on the skeleton information of the object geometry, and optimizes the sub-process sequences for deposition and machining. During the optimization of the subpart building processes, collaboration between the deposition process planner and the machining process planner is needed to check the deposition availability and machinability. As a result, tool paths for both the laser head and the machining head are automatically generated.
Chronic Pruritic Dermatitis in Asthmatic Monkeys: A Subhuman Primate Analogue of Atopic Dermatitis? (1981)

In a group of adult normal rhesus monkeys and monkeys with IgE-mediated asthma observed over a period of 15 years, 2 of the latter group were found to have chronic, generalized pruritus and dermatitis. The skin lesions were recurrent and located on the flexural surfaces of the forearms leading to the thickened, scaling, lichenified dermatitis in that area in the skin of 1 monkey. The pruritus and skin lesions subsided following therapy with depot methylprednisolone but recurred after this therapy was discontinued. Both animals had recurrent severe cutaneous infections in excoriated lesions following scratching without infections in other organs. The cutaneous infections responded to penicillin therapy but recurred with scratching. No deficiencies in immunoglobulin levels, or lymphocyte responses to phytohemagglutinin were found in these 2 monkeys. The 2 animals differed from normal animals by their high titers of immediate skin reactivity to ascaris antigen, persistent and severe asthmatic responses to ascaris antigen, high IgG antibody levels to ascaris antigen but all of the latter findings were also present in asthmatic monkeys without dermatitis. Cutaneous biopsies of lesions were nonspecific but provided no evidence for other explanations for the dermatitis which appears to be an analogue of human atopic dermatitis.
Revisiting an Old Riddle: What Determines Genetic Diversity Levels within Species? (2012)

Understanding why some species have more genetic diversity than others is central to the study of ecology and evolution, and carries potentially important implications for conservation biology. Yet not only does this question remain unresolved, it has largely fallen into disregard. With the rapid decrease in sequencing costs, we argue that it is time to revive it.
Analysis of Probability as an Aid in the Clinical Diagnosis of Coronary-Artery Disease (1979)

The diagnosis of coronary-artery disease has become increasingly complex. Many different results, obtained from tests with substantial imperfections, must be integrated into a diagnostic conclusion about the probability of disease in a given patient. To approach this problem in a practical manner, we reviewed the literature to estimate the pretest likelihood of disease (defined by age, sex and symptoms) and the sensitivity and specificity of four diagnostic tests: stress electrocardiography, cardiokymography, thallium scintigraphy and cardiac fluoroscopy. With this information, test results can be analyzed by use of Bayes' theorem of conditional probability. This approach has several advantages. It pools the diagnostic experience of many physicians ans integrates fundamental pretest clinical descriptors with many varying test results to summarize reproducibly and meaningfully the probability of angiographic coronary-artery disease. This approach also aids, but does not replace, the physician's judgment and may assit in decisions on cost effectiveness of tests.
Meta-Analysis: Obesity and the Risk for Gastroesophageal Reflux Disease and Its Complications (2005)

Obesity is associated with a statistically significant increase in the risk for GERD symptoms, erosive esophagitis, and esophageal adenocarcinoma. The risk for these disorders seems to progressively increase with increasing weight.