gebhart/patrepeval huggingface dataset:
Full-Length Human Immunodeficiency Virus Type 1 Genomes from Subtype C-Infected Seroconverters in India, with Evidence of Intersubtype Recombination (1999)

The development of an effective human immunodeficiency virus type 1 (HIV-1) vaccine is likely to depend on knowledge of circulating variants of genes other than the commonly sequenced gag and env genes. In addition, full-genome data are particularly limited for HIV-1 subtype C, currently the most commonly transmitted subtype in India and worldwide. Likewise, little is known about sequence variation of HIV-1 in India, the country facing the largest burden of HIV worldwide. Therefore, the objective of this study was to clone and characterize the complete genome of HIV-1 from seroconverters infected with subtype C variants in India. Cocultured HIV-1 isolates were obtained from six seroincident individuals from Pune, India, and virtually full-length HIV-1 genomes were amplified, cloned, and sequenced from each. Sequence analysis revealed that five of the six genomes were of subtype C, while one was a mosaic of subtypes A and C, with multiple breakpoints in env, nef, and the 3' long terminal repeat as determined by both maximal chi2 analysis and phylogenetic bootstrapping. Sequences were compared for preservation of known cytotoxic T lymphocyte (CTL) epitopes. Compared with those of the HIV-1LAI sequence, 38% of well-defined CTL epitopes were identical. The proportion of nonconservative substitutions for Env, at 61%, was higher (P < 0.001) than those for Gag (24%), Pol (18%), and Nef (32%). Therefore, characterized CTL epitopes demonstrated substantial differences from subtype B laboratory strains, which were most pronounced in Env. Because these clones were obtained from Indian seroconverters, they are likely to facilitate vaccine-related efforts in India by providing potential antigens for vaccine candidates as well as for assays of vaccine responsiveness.
Inducing features of random fields (1997)

We present a technique for constructing random fields from a set of training samples. The learning paradigm builds increasingly complex fields by allowing potential functions, or features, that are supported by increasingly large subgraphs. Each feature has a weight that is trained by minimizing the Kullback-Leibler divergence between the model and the empirical distribution of the training data. A greedy algorithm determines how features are incrementally added to the field and an iterative scaling algorithm is used to estimate the optimal values of the weights. The random field models and techniques introduced in this paper differ from those common to much of the computer vision literature in that the underlying random fields are non-Markovian and have a large number of parameters that must be estimated. Relations to other learning approaches, including decision trees, are given. As a demonstration of the method, we describe its application to the problem of automatic word classification in natural language processing.
Lack of linkage between atopy and locus 11q13 (1992)

Atopy as defined in terms of IgE responsiveness was reported to be controlled by a single gene in British families, and this concept was further supported by a significant linkage between atopy and restriction fragment length polymorphism (RFLP) detected by a DNA probe specific to chromosome 11q13. To confirm this observation in a Japanese population, segregation and linkage analyses were done in four large families. Although segregation patterns of atopy were in agreement with the pattern of autosomal dominant inheritance, there was no significant linkage between atopy and locus 11q13. Alterations in the definitions of atopy did not affect the results. These findings suggested the presence of heterogeneity in genetic elements of atopy, even though atopy may be determined mainly by a single dominant gene.
A robust framework for detecting structural variations in a genome (2008)

Our dataset, results and source code are available at http://compbio.cs.toronto.edu/structvar/.
[Antiestrogens (tamoxifen) in the alternative therapy of benign prostatic hyperplasia]. (1993)

In a non-randomized study the authors administered Tamoxifen to 17 patients with benign prostate hyperplasia who met the criteria for administration of the drug. In the group of patients no significant change of symptoms according to Goldenberg's score was recorded nor changes of prostate size and postmiction residues. In uroflowmetry the significant change of values of maximum flow (p < 0.05) was not associated with a change in the mean flow. The authors assume that monotherapy with Tamoxifen is not effective enough and recommended administration of antioestrogen only in combination with other drugs.
Rigid−Flexible Alternating Block Copolymers That Contain Poly(p-phenylene) Units of Defined Length as the Rigid Blocks (2001)

ADVERTISEMENT RETURN TO ISSUEPREVCommunication to the...Communication to the EditorNEXTRigid−Flexible Alternating Block Copolymers That Contain Poly(p-phenylene) Units of Defined Length as the Rigid BlocksZachary R. Wagner, Timothy K. Roenigk, and Felix E. GoodsonView Author Information Department of Chemistry, West Chester University of Pennsylvania, West Chester, Pennsylvania 19383 Cite this: Macromolecules 2001, 34, 17, 5740–5743Publication Date (Web):July 12, 2001Publication History Received6 March 2001Revised5 June 2001Published online12 July 2001Published inissue 1 August 2001https://pubs.acs.org/doi/10.1021/ma010406bhttps://doi.org/10.1021/ma010406brapid-communicationACS PublicationsCopyright © 2001 American Chemical SocietyRequest reuse permissionsArticle Views389Altmetric-Citations20LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Alcohols,Aromatic compounds,Copolymers,Materials,Polymers Get e-Alerts
Epitope‐dependent synergism and antagonism between CD40 antibodies and soluble CD40 ligand for the regulation of CD23 expression and IgE synthesis in human B cells (1999)

This study demonstrates that appropriate targeting of CD40 can modulate IgE synthesis either positively or negatively.
Electrically Conductive Porous Metal–Organic Frameworks (2016)

Owing to their outstanding structural, chemical, and functional diversity, metal-organic frameworks (MOFs) have attracted considerable attention over the last two decades in a variety of energy-related applications. Notably missing among these, until recently, were applications that required good charge transport coexisting with porosity and high surface area. Although most MOFs are electrical insulators, several materials in this class have recently demonstrated excellent electrical conductivity and high charge mobility. Herein we review the synthetic and electronic design strategies that have been employed thus far for producing frameworks with permanent porosity and long-range charge transport properties. In addition, key experiments that have been employed to demonstrate electrical transport, as well as selected applications for this subclass of MOFs, will be discussed.
Gastro-oesophageal reflux and bronchial asthma: current status and future directions (2004)

In recent years there have been several reports suggesting an association between bronchial asthma and gastro-oesophageal reflux; however a cause and effect relationship has not been proven yet. Confirmation of such a relationship is likely to have far reaching implications on the management of asthma. Reliable assessment of this issue is hampered by the presence of various lacunae in most of the published studies. Hence it is essential to carefully examine the strength of data suggesting a link between asthma and reflux. This article critically analyses currently available literature on the subject (including published reviews, meta-analyses, and randomised clinical trials in the English language) and summarises valid conclusions that can be drawn; it also proposes a framework for future studies to resolve the issue.
Molecular Thermodynamic Modeling of Reverse Micelles and Water-in-Oil Microemulsions (2016)

Surfactant aggregation plays an important role in a variety of chemical and biological nanoscale processes. On a larger scale, using small amounts of amphiphiles compared to large volumes of bulk-phase modifiers can improve the efficiency and reduce the environmental impact of many chemical and industrial processes. To model ternary mixtures of polar, nonpolar, and amphiphilic molecules, we develop a molecular thermodynamic theory for polydisperse water-in-oil (W/O) droplet-type microemulsions and reverse micelles based on global minimization of the Gibbs free energy of the system. The incorporation of size polydispersity into the theoretical formulation has a significant effect on the Gibbs free energy landscape and allows us to accurately predict micelle size distributions and micelle size variation with composition. Results are presented for two sample ionic surfactant/water/oil systems and compared with experimental data. By predicting the structural and compositional characteristics of w/o microemulsions, the molecular thermodynamic approach provides an important bridge between the modeling of ternary systems at the molecular and the macroscopic level.
Creating Raster Omnimax Images from Multiple Perspective Views Using the Elliptical Weighted Average Filter (1986)

Creation of Omnimax animation by computer opens up fantastic new visual possibilities. Unfortunately, the fish-eye distortion of Omnimax film images complicates synthesis by computer, since most image-synthesis programs can create only perspective views. As an alternative to modifying existing image-synthesis programs to produce Omnimax projections directly, we present a method for creating them from multiple perspective views. Four perspective views of the environment are created, each a projection onto a face of a cube centered at the camera, and then a mapping program creates an Omnimax projection from them. To minimize aliasing during resampling, the mapping program uses the elliptical weighted average filter, a space-variant filter we developed for this application that computes a weighted average over an arbitrarily oriented elliptical area. This filter can also be used for texture mapping 3D surfaces.
The role of electronic controls for future automotive mechatronic systems (1996)

The merging of electronics and mechanical actuators for automotive applications is driven by environmental and societal influences, customer wants, quality/reliability, and value. Cost-effective mechatronics is made possible by the continuing improvements in the underlying enabling technologies. This paper examines the technology enablers as they influence automotive control systems, and then explores the impact of environmental, customer, and societal drivers as they affect control systems.
Functional capacity of dystrophins carrying deletions in the N-terminal actin-binding domain (2007)

Duchenne muscular dystrophy and Becker muscular dystrophy (BMD) are caused by mutations in the dystrophin gene. Although many in-frame deletions in the dystrophin gene lead to mild cases of BMD, truncations within the N-terminal actin-binding domain (ABD1) typically decrease dystrophin expression and lead to more severe cases of BMD. Because of the large reduction in protein expression, the functional capacity of dystrophin proteins deleted for subportions of ABD1 has been difficult to ascertain. ABD1 contains three actin-binding sequences designated ABS1-3. In the present study, we examined the pathophysiological effects of in-frame actin-binding sequence deletions in the context of a highly functional microdystrophin (DeltaR4-R23/DeltaCT). We delivered microdystrophins into the tibialis anterior muscles of 2-day-old dystrophin-deficient mdx mice using recombinant adeno-associated viral vectors. Muscles expressing microdystrophin with an intact ABD1 displayed normal morphology and specific force generation and were partially protected from contraction-induced injury when evaluated at 4 months of age. In contrast, muscles expressing microdystrophins lacking ABS2 and 3 or ABS3 alone developed significantly lower levels of specific force and were highly susceptible to contraction-induced injury. Microdystrophins with deletions within ABD1 were also less able to protect myofibers from degeneration than was a microdystrophin with the complete ABD1. We conclude that an intact ABD1 is required to support normal contractile properties of skeletal muscle and to protect against myofiber necrosis.
Adenylate Cyclase Toxin Subverts Phagocyte Function by RhoA Inhibition and Unproductive Ruffling (2008)

Adenylate cyclase toxin (CyaA or ACT) is a key virulence factor of pathogenic Bordetellae. It penetrates phagocytes expressing the alpha(M)beta(2) integrin (CD11b/CD18, Mac-1 or CR3) and paralyzes their bactericidal capacities by uncontrolled conversion of ATP into a key signaling molecule, cAMP. Using pull-down activity assays and transfections with mutant Rho family GTPases, we show that cAMP signaling of CyaA causes transient and selective inactivation of RhoA in mouse macrophages in the absence of detectable activation of Rac1, Rac2, or RhoG. This CyaA/cAMP-induced drop of RhoA activity yielded dephosphorylation of the actin filament severing protein cofilin and massive actin cytoskeleton rearrangements, which were paralleled by rapidly manifested macrophage ruffling and a rapid and unexpected loss of macropinocytic fluid phase uptake. As shown in this study for the first time, CyaA/cAMP signaling further caused a rapid and near-complete block of complement-mediated phagocytosis. Induction of unproductive membrane ruffling, hence, represents a novel sophisticated mechanism of down-modulation of bactericidal activities of macrophages and a new paradigm for action of bacterial toxins that hijack host cell signaling by manipulating cellular cAMP levels.
Synthesis and configurational assignments of diastereomeric .beta.-hydroxy sulfones (1970)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis and configurational assignments of diastereomeric .beta.-hydroxy sulfonesWilliam E. Truce and Thomas C. KlinglerCite this: J. Org. Chem. 1970, 35, 6, 1834–1838Publication Date (Print):June 1, 1970Publication History Published online1 May 2002Published inissue 1 June 1970https://pubs.acs.org/doi/10.1021/jo00831a026https://doi.org/10.1021/jo00831a026research-articleACS PublicationsRequest reuse permissionsArticle Views220Altmetric-Citations44LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Identification of a Cell Surface-binding Protein for the Core Protein of the Basement Membrane Proteoglycan (1989)

We have identified a protein(s) on the surface of hepatocytes that binds to the core protein of the heparan sulfate proteoglycan of basement membranes. These cells attached and spread on substrates prepared from the basement membrane heparan sulfate proteoglycan (HSPG) and its core protein (HSPG-core). Three proteins (Mr = 38,000, 36,000, and 26,000) were found to bind to a HSPG-core affinity column using extracts of iodinated hepatocytes, whereas proteins extracted from isolated membranes contained primarily the larger protein (Mr = 38,000). Similar results were obtained using a solid phase binding technique using labeled HSPG-core. Binding of HSPG-core to the protein (Mr = 38,000) was not altered by the presence of an excess of heparin, heparan sulfate, fibronectin, laminin, or collagen IV but was reduced by unlabeled HSPG-core. Similar studies showed that the binding protein (Mr = 3,0000) was present in extracts from the membranes of Engelbreth-Holm-Swarm tumor cells, Madin-Darby canine kidney cells, COS cells, melanoma cells, and rat kidney epithelial cells but not in fibroblasts. The protein was found in increased amounts in 3T3 cells treated with retinoic acid. These observations suggest that a variety of cells that contact basement membrane contain the proteoglycan-binding protein.
Rheumatoid arthritis disease activity measures: American College of Rheumatology recommendations for use in clinical practice (2012)

We recommend the Clinical Disease Activity Index, Disease Activity Score with 28-joint counts (erythrocyte sedimentation rate or C-reactive protein), Patient Activity Scale (PAS), PAS-II, Routine Assessment of Patient Index Data with 3 measures, and Simplified Disease Activity Index because they are accurate reflections of disease activity; are sensitive to change; discriminate well between low, moderate, and high disease activity states; have remission criteria; and are feasible to perform in clinical settings.
Jacalin: an IgA-binding lectin. (1985)

We previously reported that seeds of Artocarpus integrifolia (jackfruit) contain a lectin, which we call jacalin, that is both a potent T cell mitogen and an apparently T cell-independent activator of human B cells for the secretion of immunoglobulins. During the above experiments we noted a massive precipitation in cell cultures stimulated with greater than or equal to 100 micrograms of lectin. In this paper, we show that the precipitate is formed after the interaction of jacalin and the serum protein added to the culture medium. More importantly, we demonstrate that IgA is probably the major serum constituent precipitated by the lectin and that no IgG or IgM can be detected in the precipitates. In secretions such as colostrum, IgA is the only protein precipitated by jacalin. On the basis of this specificity we describe a simple and reliable affinity chromatography procedure for the purification of both human serum and colostrum IgA. Jacalin is a D-Gal binding lectin and should be a useful tool for studying of serum and secretory IgA.
Complex Induction of Bovine Uterine Proteins by Interferon-Tau1 (1998)

Interferon-tau (IFN-tau) is released by the conceptus and induces two uterine proteins during early pregnancy: ubiquitin cross-reactive protein (UCRP) and granulocyte chemotactic protein-2 (GCP-2). The present experiments were designed to determine whether detection (Western blot) of cytosolic UCRP and release of GCP-2 could be used to examine IFN-tau signal transduction in cultured endometrial explants and primary epithelial cells. Recombinant (r) type 1 IFNs (rboIFN-tau and rboIFN-alpha; 5, 25, 100 nM) induced UCRP, but only rboIFN-tau induced GCP-2 in explant culture. Recombinant boIFN-tau and conceptus secretory proteins containing native IFN-tau induced UCRP and GCP-2 in cultured primary epithelial cells. All concentrations of rboIFN-alpha (25, 50, 100 nM) induced UCRP, but only the highest concentration induced GCP-2 in cultured primary epithelial cells. Interestingly, phorbol ester (100, 500, 1000 ng/ml) induced GCP-2, but it had no effect on UCRP. Because type 1 IFNs induce UCRP, IFN-tau probably interacts with the janus kinase (Jak)-associated IFN-alpha receptor to phosphorylate signal transducers and activators of transcription (STAT) and/or interferon regulatory factor-1 (IRF-1). However, IFN-tau-specific induction of GCP-2 may involve a variant type 1 receptor subunit or activators of transcription that are associated with protein kinase C and the Jak/STAT/IRF-1 pathway.
Fine-scale spatial response of CdZnTe radiation detectors (1999)

Several studies have suggested that the uniformity of Cadmium Zinc Telluride (CZT) detectors play an important role in their performance when operated as gamma-ray spectrometers. However, the detailed gamma response of simple planar detectors as a function of position over the device area is largely unknown. To address this issue we have built a system capable of measuring the detector response with a resolution of /spl sim/250 /spl mu/m. The system consists of a highly collimated (/spl sim/200 /spl mu/m) photon source (<150 keV) scanned over the detector using a computer controlled, two-axis translation stage. Fifteen samples configured as planar detectors were examined with the new apparatus. The material grade of the detectors examined varied from "counter" to "select discriminator". Two classes of spatial response variation were observed and are presented here. Infrared (IR) transmission images were also acquired for each sample and correlation between features in the pulse height spectrum and crystalline defects were observed.
High glucose induces DNA damage in cultured human endothelial cells. (1986)

Morphologic and functional abnormalities of vascular endothelium are well recognized in diabetes. In view of our previous finding that high glucose concentrations accelerate death and hamper replication of cultured human endothelial cells, we have investigated in the same model the possibility that exposure to high glucose may result in DNA damage. DNA from human endothelial cells--but not from fibroblasts--exposed to 30 mM glucose for 9-14 d manifested an accelerated rate of unwinding in alkali indicative of an increased number of single strand breaks (P less than 0.001 vs. control). Endothelial cells exposed to high glucose also manifested an increased amount of hydroxy-urea-resistant thymidine incorporation (333 +/- 153 cpm/10(5) cells vs. 88 +/- 42 in control cells, mean +/- SD, P = 0.04), which is indicative of increased DNA repair synthesis. Neither DNA damage nor repair synthesis were increased by medium hypertonicity achieved with 30 mM mannitol. These findings suggest the possibility that, under conditions of high ambient glucose, excess glucose entry in cells that are insulin independent for glucose transport may, directly or indirectly, perturb DNA function. Further, they suggest the possibility that different individual capabilities to repair DNA damage--a process that is under genetic control--may represent a mechanism for different individual susceptibilities to development of diabetic vascular complication.