gebhart/patrepeval huggingface dataset:
Combinations of Cyclophilin Inhibitor NIM811 with Hepatitis C Virus NS3-4A Protease or NS5B Polymerase Inhibitors Enhance Antiviral Activity and Suppress the Emergence of Resistance (2008)

Chronic hepatitis C virus (HCV) infection remains a major global health burden while current interferon-based therapy is suboptimal. Efforts to develop more effective antiviral agents mainly focus on two viral targets: NS3-4A protease and NS5B polymerase. However, resistant mutants against these viral specific inhibitors emerge quickly both in vitro and in patients, particularly in the case of monotherapy. An alternative and complementary strategy is to target host factors such as cyclophilins that are also essential for viral replication. Future HCV therapies will most likely be combinations of multiple drugs of different mechanisms to maximize antiviral activity and to suppress the emergence of resistance. Here, the effects of combining a host cyclophilin inhibitor NIM811 with other viral specific inhibitors were investigated in vitro using HCV replicon. All of the combinations led to more pronounced antiviral effects than any single agent, with no significant increase of cytotoxicity. Moreover, the combination of NIM811 with a nucleoside (NM107) or a non-nucleoside (thiophene-2-carboxylic acid) polymerase inhibitor was synergistic, while the combination with a protease inhibitor (BILN2061) was additive. Resistant clones were selected in vitro with these inhibitors. Interestingly, it was much more difficult to develop resistance against NIM811 than viral specific inhibitors. No cross-resistance was observed among these inhibitors. Most notably, NIM811 was highly effective in blocking the emergence of resistance when used in combination with viral protease or polymerase inhibitors. Taken together, these results illustrate the significant advantages of combining inhibitors targeting both viral and host factors as key components of future HCV therapies.
Porcine reproductive and respiratory syndrome virus entry into the porcine macrophage (2010)

Porcine reproductive and respiratory syndrome virus (PRRSV) emerged in the late 1980s and rapidly became one of the most significant viral pathogens in the swine industry. In vivo, the virus shows a very narrow cell tropism and targets specific subsets of porcine macrophages. The entry of PRRSV into its host cell is the first crucial step in infection and has been the focus of many fundamental studies. This review provides a comprehensive overview of the current knowledge on PRRSV entry into the porcine macrophage, covering virus binding, internalization and genome release, and integrates these findings into a general model of the entry process.
Type 1 Fimbriation and Phase Switching in a Natural Escherichia coli fimB Null Strain, Nissle 1917 (1999)

Escherichia coli Nissle 1917 has been used as a probiotic against intestinal disorders for many decades. It is a good colonizer of the human gut and has been reported to be able to express type 1 fimbriae. Type 1 fimbriae are surface organelles which mediate alpha-D-mannose-sensitive binding to various host cell surfaces. The expression is phase variable, and two tyrosine recombinases, FimB and FimE, mediate the inversion of the fimbrial phase switch. Current evidence suggests that FimB can carry out recombination in both directions, whereas FimE-catalyzed switching is on to off only. We show here that under liquid shaking growth conditions, Nissle 1917 did not express type 1 fimbriae, due to a truncation of the fimB gene by an 1,885-bp insertion element. Despite its fimB null status, Nissle 1917 was still capable of off-to-on switching of the phase switch and expressing type 1 fimbriae when grown under static conditions. This phase switching was not catalyzed by FimE, by truncated FimB, or by information residing within the insertion element. No further copies of fimB seemed to be present on the chromosome of Nissle 1917, suggesting that another tyrosine recombinase in Nissle 1917 is responsible for the low-frequency off-to-on inversion of the phase switch that is strongly favored under static growth conditions. This is the first report documenting the non-FimB- or non-FimE-catalyzed inversion of the fim switch.
The Protein Data Bank (2002)

The Protein Data Bank [PDB; Berman, Westbrook et al. (2000), Nucleic Acids Res. 28, 235-242; http://www.pdb.org/] is the single worldwide archive of primary structural data of biological macromolecules. Many secondary sources of information are derived from PDB data. It is the starting point for studies in structural bioinformatics. This article describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource. The reader should come away with an understanding of the scope of the PDB and what is provided by the resource.
Cardiomyocyte Cell Cycle Regulation (2002)

Although rapid progress is being made in many areas of molecular cardiology, issues pertaining to the origins of heart-forming cells, the mechanisms responsible for cardiogenic induction, and the pathways that regulate cardiomyocyte proliferation during embryonic and adult life remain unanswered. In the present study, we review approaches and studies that have shed some light on cardiomyocyte cell cycle regulation. For reference, an initial description of cardiomyogenic induction and morphogenesis is provided, which is followed by a summary of published cell cycle analyses during these stages of cardiac ontology. A review of studies examining cardiomyocyte cell cycle analysis and de novo cardiomyogenic induction in the adult heart is then presented. Finally, studies in which cardiomyocyte cell cycle activity was experimentally manipulated in vitro and in vivo are reviewed. It is hoped that this compilation will serve to stimulate thought and experimentation in this intriguing area of cardiomyocyte cell biology.
Highly efficient iron(0) nanoparticle-catalyzed hydrogenation in water in flow (2013)

Highly efficient catalytic hydrogenations are achieved by using amphiphilic polymer-stabilized Fe(0) nanoparticle (Fe NP) catalysts in ethanol or water in a flow reactor. Alkenes, alkynes, aromatic imines and aldehydes were hydrogenated nearly quantitatively in most cases. Aliphatic amines and aldehydes, ketone, ester, arene, nitro, and aryl halide functionalities are not affected, which provides an interesting chemoselectivity. The Fe NPs used in this system are stabilized and protected by an amphiphilic polymer resin, providing a unique system that combines long-term stability and high activity. The NPs were characterized by TEM of microtomed resin, which established that iron remains in the zero-valent form despite exposure to water and oxygen. The amphiphilic resin-supported Fe(0) nanoparticles in water and in flow provide a novel, robust, cheap and environmentally benign catalyst system for chemoselective hydrogenations.
Characterization of freshly isolated and cultured cells derived from the fatty and fluid portions of liposuction aspirates (2006)

Liposuction aspirates (primarily saline solution, blood, and adipose tissue fragments) separate into fatty and fluid portions. Cells isolated from the fatty portion are termed processed lipoaspirate (PLA) cells and contain adipose-derived adherent stromal cells (ASCs). Here we define cells isolated from the fluid portion of liposuction aspirates as liposuction aspirate fluid (LAF) cells. Stromal vascular fractions (SVF) were isolated separately from both portions and characterized under cultured and non-cultured conditions. A comparable number of LAF and PLA cells were freshly isolated, but fewer LAF cells were adherent. CD34+ CD45- cells from fresh LAF isolates were expanded by adherent culture, suggesting that LAF cells contain ASCs. Although freshly isolated PLA and LAF cells have distinct cell surface marker profiles, adherent PLA and LAF cells have quite similar characteristics with regard to growth kinetics, morphology, capacity for differentiation, and surface marker profiles. After plating, both PLA and LAF cells showed significant increased expression of CD29, CD44, CD49d, CD73, CD90, CD105, and CD151 and decreased expression of CD31 and CD45. Multicolor FACS analysis revealed that SVF are composed of heterogeneous cell populations including blood-derived cells (CD45+), ASCs (CD31- CD34+ CD45- CD90+ CD105- CD146-), endothelial (progenitor) cells (CD31+ CD34+ CD45- CD90+ CD105low CD146+), pericytes (CD31- CD34- CD45- CD90+ CD105- CD146+), and other cells. After plating, ASCs showed a dramatic increase in CD105 expression. Although some adherent ASCs lost CD34 expression with increasing culture time, our culture method maintained CD34 expression in ASCs for at least 10-20 weeks. These results suggest that liposuction-derived cells may be useful and valuable for cell-based therapies.
Birth of a male lamb derived from an in vitro matured oocyte fertilised by intracytoplasmic injection of a single presumptive male sperm (1996)

The developmental competence of in vitro matured ovine oocytes, cytoplasmically injected with single male or female chromosome-bearing sperm, was investigated. Eighty-five unsorted, 92 'female-sorted' and 74 'male-sorted' ram sperm were injected into in vitro matured sheep oocytes and, two to four hours later, placed into the oviducts of 28 oestrous sheep. The sperm were separated according to sex by analysis of their DNA content with a flow cytometer. One pregnancy was diagnosed by ultrasound after 55 days and a 3 kg male lamb was born after 150 days gestation. This lamb was derived from an oocyte injected with 'male-sorted' sperm.
Mifepristone Reduces Weight Gain and Improves Metabolic Abnormalities Associated With Risperidone Treatment in Normal Men (2010)

Antipsychotic medications are associated with significant weight gain, type 2 diabetes mellitus, dyslipidemia, and increased cardiovascular risk. The objective of this study was to determine whether mifepristone, a glucocorticoid receptor antagonist, could prevent risperidone-induced weight gain. Using a 2:2:1 randomization scheme, 76 lean, healthy men (BMI 18-23 kg/m(2)) age 18-40 years were randomized to risperidone (n = 30), risperidone plus mifepristone (n = 30) or mifepristone (n = 16) daily for 28 days in an institutional setting. Subjects were provided food ad libitum. Body weight was measured daily. Metabolic measures were taken at study onset, midpoint, and end. Analyses of covariance indicated that the group receiving risperidone plus placebo gained significantly more weight (P < 0.001) and exhibited a significantly greater increase in waist circumference (P < 0.05) than the group receiving risperidone plus mifepristone. Significant differences were also observed for metabolic measures including fasting insulin (P < 0.001) and triglyceride levels (P < 0.05). Mifepristone attenuated increases in weight and reduced the metabolic changes induced by risperidone use, replicating results from a prior study of olanzapine-induced weight gain. These findings suggest mechanistic involvement of the hypothalamic-pituitary-adrenal axis in the weight and cardiometabolic side effects of antipsychotic medications. Future research should continue to test the potential of glucocorticoid antagonists to alleviate the deleterious side effects associated with use of antipsychotic medications.
The FLP protein of the 2-micron plasmid of yeast. Inter- and intramolecular reactions. (1985)

We have studied the mechanism of reaction of the FLP protein of the yeast 2-micron plasmid on linear substrates. The products of the reaction are dependent upon the concentration of FLP protein. At low concentrations of FLP, products resulting from intramolecular recombination between two FLP target sites accumulate. At higher concentrations of FLP, intermolecular recombination results in the accumulation of products which are larger than the starting substrate. At higher concentrations still, FLP-promoted recombination is inhibited. Potassium chloride (0.15 M) inhibits the intermolecular reaction and also prevents the inhibition of FLP-mediated recombination caused by high concentrations of FLP protein. We present a model that explains these findings.
Inline hologram reconstruction with sparsity constraints (2009)

Inline digital holograms are classically reconstructed using linear operators to model diffraction. It has long been recognized that such reconstruction operators do not invert the hologram formation operator. Classical linear reconstructions yield images with artifacts such as distortions near the field-of-view boundaries or twin images. When objects located at different depths are reconstructed from a hologram, in-focus and out-of-focus images of all objects superimpose upon each other. Additional processing, such as maximum-of-focus detection, is thus unavoidable for any successful use of the reconstructed volume. In this Letter, we consider inverting the hologram formation model in a Bayesian framework. We suggest the use of a sparsity-promoting prior, verified in many inline holography applications, and present a simple iterative algorithm for 3D object reconstruction under sparsity and positivity constraints. Preliminary results with both simulated and experimental holograms are highly promising.
COM+: the evolution of component services (1999)

COM+ encompasses two areas: a fundamental programming architecture for building software components (first defined by the original COM specification) and an integrated suite of component services replete with an associated runtime environment. For many developers, however, the fundamental COM model is insufficient. In the typical corporation, developers build business components that operate as part of a larger application. Developers expend a great deal of effort to build even the simplest of components. They must also create a robust and secure framework for it and ensure that only clients with the proper authorization can perform certain privileged operations using the component. The problem with the bare-bones component model is that developers are left to implement an enormous amount of functionality that has little to do with the goals of the application itself. To reduce the amount of work required to build a complex distributed application, Microsoft developed the Microsoft Transaction Server (MTS), the first Windows-based implementation of a runtime environment to provide component services. These component services operate within a general set of tools and technologies that, together with COM+, form what Microsoft calls the Distributed Internet Applications (DNA) architecture.
A Method of Moments Estimator for Random Effect Multivariate Meta‐Analysis (2012)

Meta-analysis is a powerful approach to combine evidence from multiple studies to make inference about one or more parameters of interest, such as regression coefficients. The validity of the fixed effect model meta-analysis depends on the underlying assumption that all studies in the meta-analysis share the same effect size. In the presence of heterogeneity, the fixed effect model incorrectly ignores the between-study variance and may yield false positive results. The random effect model takes into account both within-study and between-study variances. It is more conservative than the fixed effect model and should be favored in the presence of heterogeneity. In this paper, we develop a noniterative method of moments estimator for the between-study covariance matrix in the random effect model multivariate meta-analysis. To our knowledge, it is the first such method of moments estimator in the matrix form. We show that our estimator is a multivariate extension of DerSimonian and Laird's univariate method of moments estimator, and it is invariant to linear transformations. In the simulation study, our method performs well when compared to existing random effect model multivariate meta-analysis approaches. We also apply our method in the analysis of a real data example.
Inhaled NO as a therapeutic agent (2007)

In 1991, Frostell and colleagues reported that breathing low concentrations of nitric oxide (NO) decreased pulmonary artery pressure (PAP) in awake lambs with experimental pulmonary hypertension (PH) [Frostell C, Fratacci MD, Wain JC, Jones R, Zapol WM. Inhaled nitric oxide. A selective pulmonary vasodilator reversing hypoxic pulmonary vasoconstriction. Circulation 1991;83:2038-47]. Subsequently, efforts of multiple research groups studying animals and patients led to approval of inhaled NO by the US Food and Drug Administration in 1999 and the European Medicine Evaluation Agency and European Commission in 2001. Inhaled NO is currently indicated for the treatment of term and near-term neonates with hypoxemia and PH. Since regulatory approval, several studies have suggested that NO inhalation can prevent chronic lung disease in premature infants. In addition, unanticipated systemic effects of inhaled NO may lead to treatments for a variety of disorders including ischemia-reperfusion injury. This review summarizes the pharmacology and physiological effects of breathing NO. The application of inhaled NO to hypoxemic neonates with PH is discussed including recent studies exploring the use of inhaled NO to prevent bronchopulmonary dysplasia in premature infants. This review also highlights the application of inhaled NO to treat adults with cardiopulmonary disease, strategies to augment the efficacy of inhaled NO, and potential applications of the systemic effects of the gas.
Leukocyte Telomere Length and Mortality in the Cardiovascular Health Study (2011)

These data weakly corroborate prior findings of associations between LTL and mortality in the elderly.
RNA interference in practice (2004)

RNA interference in practice , RNA interference in practice , مرکز فناوری اطلاعات و اطلاع رسانی کشاورزی
The Neurospora crassa carotenoid biosynthetic gene (albino 3) reveals highly conserved regions among prenyltransferases. (1991)

In the filamentous fungus Neurospora crassa the biosynthesis of carotenoids is regulated by blue light. Here we report the characterization of the albino-3 (al-3) gene of N. crassa, which encodes the carotenoid biosynthetic enzyme geranylgeranyl-pyrophosphate synthetase. This is the first geranylgeranyl-pyrophosphate synthetase gene isolated. Nucleotide sequence comparison of al-3 genomic and cDNA clones revealed that the al-3 gene is not interrupted by introns. Transcription of the al-3 gene has been examined in dark-grown and light-induced mycelia. The analysis revealed that the al-3 gene is not expressed in the dark and that its transcription is induced by blue light (Nelson, M. A., Morelli, G., Carattoli, A., Romano, N., and Macino, G. (1989) Mol. Cell. Biol. 9, 1271-1276). The al-3 gene encodes a polypeptide of 428 amino acids. Comparison of the deduced amino acid sequence of al-3 with the sequences of prenyltransferases of other species, from bacteria to humans, showed three highly conserved homologous regions. These homologous regions may be involved in the formation of the catalytic site of the prenyltransferases.
Spin torque switching of perpendicular Ta∣CoFeB∣MgO-based magnetic tunnel junctions (2011)

Spin torque switching is investigated in perpendicular magnetic tunnel junctions using Ta∣CoFeB∣MgO free layers and a synthetic antiferromagnet reference layer. We show that the Ta∣CoFeB interface makes a key contribution to the perpendicular anisotropy. The quasistatic phase diagram for switching under applied field and voltage is reported. Low switching voltages, Vc 50 ns=290 mV are obtained, in the range required for spin torque magnetic random access memory. Switching down to 1 ns is reported, with a rise in switching speed from increased overdrive that is eight times greater than for comparable in-plane devices, consistent with expectations from a single-domain model.
Branch classification (1994)

There is wide agreement that one of the most important impediments to the performance of current and future pipelined superscalar processors is the presence of conditional branches in the instruction stream. Speculative execution seems to be one solution of choice to the branch problem, but speculative work is discarded if a branch is mispredicted. Therefore, we need a very accurate branch predictor; 95% accuracy is not good enough. This paper proposes branch classification to help improve the accuracy of branch predictors. Branch classification allows an individual branch instruction to be associated with the branch predictor best suited to predict its direction. Using this approach, a hybrid branch predictor can be constructed such that each component branch predictor predicts those branches for which it is best suited. This paper suggests one classification scheme, analyzes several branch predictors, and proposes a hybrid branch predictor that achieves higher prediction accuracy than any branch predictor previously reported in the literature.
Satellite Constellation Design Tradeoffs Using Multiple-Objective Evolutionary Computation (2006)

Covers advancements in spacecraft and tactical and strategic missile systems, including subsystem design and application, mission design and analysis, materials and structures, developments in space sciences, space processing and manufacturing, space operations, and applications of space technologies to other fields.
XOMA 052, an anti‐IL‐1β monoclonal antibody, prevents IL‐1β‐mediated insulin resistance in 3T3‐L1 adipocytes (2013)

IL-1β inhibited insulin-induced activation of Akt phosphorylation, glucose transport, and fatty acid uptake. IL-1β also blocked insulin-mediated downregulation of suppressor of cytokine signaling-3 expression. Co-preincubation of IL-1β with XOMA 052 neutralized nearly all of these inhibitory effects in 3T3-L1 adipocytes. These studies provide evidence, therefore, that IL-1β is a key proinflammatory cytokine that is involved in inducing insulin resistance. These studies also suggest that the monoclonal antibody XOMA 052 may be a possible therapeutic to effectively neutralize cytokine-mediated insulin resistance in adipose tissue.
Importance of complement source in bactericidal activity of human antibody and murine monoclonal antibody to meningococcal group B polysaccharide (1983)

The bactericidal activity of human antibody and murine monoclonal antibody to meningococcal group B polysaccharide was investigated as a function of the complement source. The immunoglobulin M murine monoclonal antibody 2-2-B was shown by several different methods to be highly specific for meningococcal group B and Escherichia coli K1 capsular polysaccharides. It had strong bactericidal activity in conjunction with either rabbit or human complement, but gave a higher titer with rabbit complement. A strong prozone was observed in each case. Human postvaccination antibody to meningococcal group B polysaccharide was strongly bactericidal with rabbit complement, but had little or no bactericidal activity in conjunction with human complement. Antibodies in adult normal human sera that were bactericidal with rabbit complement were also found to be predominantly directed against the meningococcal group B capsular polysaccharide. Human antibodies that were bactericidal with human complement appeared to be primarily directed against noncapsular antigens.