gebhart/patrepeval huggingface dataset:
Function of Small Hydrophobic Proteins of Paramyxovirus (2006)

Mumps virus (MuV), a rubulavirus of the paramyxovirus family, causes acute infections in humans. MuV has seven genes including a small hydrophobic (SH) gene, which encodes a type I membrane protein of 57 amino acid residues. The function of the SH protein is not clear, although its expression is not necessary for growth of MuV in tissue culture cells. It is speculated that MuV SH plays a role in viral pathogenesis. Simian virus 5 (SV5), a closely related rubulavirus, encodes a 44-amino-acid-residue SH protein. Recombinant SV5 lacking the SH gene (rSV5DeltaSH) is viable and has no growth defect in tissue culture cells. However, rSV5DeltaSH induces apoptosis in tissue culture cells and is attenuated in vivo. Neutralizing antibodies against tumor necrosis factor alpha (TNF-alpha) and TNF-alpha receptor 1 block rSV5DeltaSH-induced apoptosis, suggesting that SV5 SH plays an essential role in blocking the TNF-alpha-mediated apoptosis pathway. Because MuV is closely related to SV5, we hypothesize that the SH protein of MuV has a function similar to that of SV5, even though there is no sequence homology between them. To test this hypothesis and to study the function of MuV SH, we have replaced the open reading frame (ORF) of SV5 SH with the ORF of MuV SH in a SV5 genome background. The recombinant SV5 (rSV5DeltaSH+MuV-SH) was analyzed in comparison with SV5. It was found that rSV5DeltaSH+MuV-SH was viable and behaved like wild-type SV5, suggesting that MuV SH has a function similar to that of SV5 SH. Furthermore, both ectopically expressed SV5 SH and MuV SH blocked activation of NF-kappaB by TNF-alpha in a reporter gene assay, suggesting that both SH proteins can inhibit TNF-alpha signaling.
Blood Coagulation: Hemostasis and Thrombin Regulation (2009)

Perioperative bleeding is a major challenge particularly because of increasing clinical use of potent antithrombotic drugs. Understanding current concepts of coagulation is important in determining the preoperative bleeding risk of patients, and in managing hemostatic therapy perioperatively. The serine protease thrombin plays pivotal roles in the activation of additional serine protease zymogens (inactive enzymatic precursors), cofactors, and cell-surface receptors. Thrombin generation is closely regulated to locally achieve rapid hemostasis after injury without causing uncontrolled systemic thrombosis. During surgery, there are major disturbances in coagulation and inflammatory systems because of hemorrhage/hemodilution, blood transfusion, and surgical stresses. Postoperative bleeding often requires allogeneic blood transfusions, which support thrombin generation and hemostasis. However, procoagulant activity and inflammation are increased postoperatively; thus, antithrombotic therapy may be required to prevent perioperative thrombotic complications. There have been significant advances in the management of perioperative hemostasis and thrombosis because of the introduction of novel hemostatic and antithrombotic drugs. However, a limitation of current treatment is that conventional clotting tests do not reflect the entire physiological processes of coagulation making optimal pharmacologic therapy difficult. Understanding the in vivo regulatory mechanisms and pharmacologic modulation of thrombin generation may help control bleeding without potentially increasing prothrombotic risks. In this review, we focus on the regulatory mechanisms of hemostasis and thrombin generation using multiple, simplified models of coagulation.
Diverse karyotypic abnormalities of the c -myc locus associated with c -myc dysregulation and tumor progression in multiple myeloma (2000)

Translocations involving c-myc and an Ig locus have been reported rarely in human multiple myeloma (MM). Using specific fluorescence in situ hybridization probes, we show complex karyotypic abnormalities of the c-myc or L-myc locus in 19 of 20 MM cell lines and approximately 50% of advanced primary MM tumors. These abnormalities include unusual and complex translocations and insertions that often juxtapose myc with an IgH or IgL locus. For two advanced primary MM tumors, some tumor cells contain a karyotypic abnormality of the c-myc locus, whereas other tumor cells do not, indicating that this karyotypic abnormality of c-myc occurs as a late event. All informative MM cell lines show monoallelic expression of c-myc. For Burkitt's lymphoma and mouse plasmacytoma tumors, balanced translocation that juxtaposes c-myc with one of the Ig loci is an early, invariant event that is mediated by B cell-specific DNA modification mechanisms. By contrast, for MM, dysregulation of c-myc apparently is caused principally by complex genomic rearrangements that occur during late stages of MM progression and do not involve B cell-specific DNA modification mechanisms.
Patterns of pain: Meta-analysis of microarray studies of pain (2011)

Existing microarray gene expression profiling studies of tonic/chronic pain were subjected to meta-analysis to identify genes found to be regulated by these pain states in multiple, independent experiments. Twenty studies published from 2002 to 2008 were identified, describing the statistically significant regulation of 2254 genes. Of those, a total of 79 genes were found to be statistically significant "hits" in 4 or more independent microarray experiments, corresponding to a conservative P<0.01 overall. Gene ontology-based functional annotation clustering analyses revealed strong evidence for regulation of immune-related genes in pain states. A multi-gene quantitative real-time polymerase chain reaction experiment was run on dorsal root ganglion (DRG) and spinal cord tissue from rats and mice given nerve (sciatic chronic constriction; CCI) or inflammatory (complete Freund's adjuvant) injury. We independently confirmed the regulation of 43 of these genes in the rat-CCI-DRG condition; the genetic correlates in all other conditions were largely and, in some cases, strikingly, independent. However, a handful of genes were identified whose regulation bridged etiology, anatomical locus, and/or species. Most notable among these were Reg3b (regenerating islet-derived 3 beta; pancreatitis-associated protein) and Ccl2 (chemokine [C-C motif] ligand 2), which were significantly upregulated in every condition in the rat.
IL-21 Is Produced by Th17 Cells and Drives IL-17 Production in a STAT3-dependent Manner (2007)

CD4(+) helper T cells can differentiate into several possible fates including: Th1, Th2, T regulatory, and Th17 cells. Although, cytokine production by non-T cells is an important factor in helper T cell differentiation, a characteristic feature of both Th1 and Th2 lineages is their ability to secrete cytokines that promote their respective differentiation. However, cytokines produced by T cells that help to sustain Th17 cells have not yet been identified. Here we show that IL-21 is a product of Th17 cells, which is induced in a Stat3-dependent manner. Additionally, Stat3 can directly bind the Il21 promoter. IL-21 also induces IL-17 production and expression of the transcription factor, RORgammat. Furthermore, generation of Th17 cells in the conventional manner is attenuated by blocking IL-21. IL-21 is known to activate Stat3 and its ability to induce Th17 differentiation is abrogated in the absence of Stat3. These data argue that IL-21 serves as an autocrine factor secreted by Th17 cells that promotes or sustains Th17 lineage commitment.
Protection of mouse photoreceptors by survival factors in retinal degenerations. (1998)

The slowing of degeneration in the rd/rd and Q344ter mutant mice demonstrated that intraocularly injected survival factors can protect photoreceptors from degenerating in animal models with the same or similar genetic defects as those in human inherited retinal degenerations.
A Generalized Bradley-Terry Model: From Group Competition to Individual Skill (2004)

The Bradley-Terry model for paired comparison has been popular in many areas. We propose a generalized version in which paired individual comparisons are extended to paired team comparisons. We introduce a simple algorithm with convergence proofs to solve the model and obtain individual skill. A useful application to multi-class probability estimates using error-correcting codes is demonstrated.
Cystic fibrosis mortality and survival in the UK: 1947–2003 (2006)

Data up to 1995 on the survival of 3-yr cohorts of patients with cystic fibrosis (CF) born in the UK in the period 1968-1992 have previously been published. The present study reports survival data up to the end of 2003 together with a 2003 population estimate. All subjects with CF born in the UK in the period 1968-1992 were identified up to 1997 by active enquiry through recognised CF clinics and other hospital consultants. Information from the death certification authorities up to the end of 2003 was added. Death certificates that could not be matched with UK Cystic Fibrosis Survey records were investigated and the data reconciled. The observed survival up to 2003 of CF patients born in 1978 was 55% for males and 49% for females. For 1988 and 1992 the data were 91 and 88%, and 97 and 96%, respectively. The estimated 2003 mid-year CF population was 8,284. The continuing improvement in survival of cystic fibrosis patients in successive cohorts means that the previous prediction of median survival of >50 yrs of age for individuals born in 2000 continues to look realistic, even in the absence of proven effective therapy aimed at correcting the basic cystic fibrosis defect.
Work Ethic Alive and Well, Approach Just Different (1995)

Reduced operational costs, improved customer service, more efficient work processes, and team activities are several of the positive changes that have occurred since TQM. Senior management at Metro Water Services of Nashville, Tennessee committed to changing its focus and adopting the new style of leadership embodied in the TQM philosophy. They unanimously agreed to follow three key principles: commitment to excellence; empowerment of employees; and customer satisfaction. The road hasn't always been easy, considering that we implemented this new way of working and managing while we also expanded three plants and increased our service area. Much remains to be accomplished, but the focus remains the same–excellence through continuous improvement.
Support vector machines applied to face recognition (1998)

Face recognition is a K class problem, where K is the number of known individuals; and support vector machines (SVMs) are a binary classification method. By reformulating the face recognition problem and reinterpreting the output of the SVM classifier, we developed a SVM-based face recognition algorithm. The face recognition problem is formulated as a problem in difference space, which models dissimilarities between two facial images. In difference space we formulate face recognition as a two class problem. The classes are; dissimilarities between faces of the same person, and dissimilarities between faces of different people. By modifying the interpretation of the decision surface generated by SVM, we generated a similarity metric between faces that is learned from examples of differences between faces. The SVM-based algorithm is compared with a principal component analysis (PCA) based algorithm on a difficult set of images from the FERET database. Performance was measured for both verification and identification scenarios. The identification performance for SVM is 77-78% versus 54% for PCA. For verification, the equal error rate is 7% for SVM and 13% for PCA. 1
Anatomy of an extremely fast LVCSR decoder (2005)

We report in detail the decoding strategy that we used for the past two Darpa Rich Transcription evaluations (RT’03 and RT’04) which is based on finite state automata (FSA). We discuss the format of the static decoding graphs, the particulars of our Viterbi implementation, the lattice generation and the likelihood evaluation. This paper is intended to familiarize the reader with some of the design issues encountered when building an FSA decoder. Experimental results are given on the EARS database (English conversational telephone speech) with emphasis on our faster than real-time system.
Metal ion catalyzed decomposition of tetramethyl-1,2-dioxetane in methanol (1974)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMetal ion catalyzed decomposition of tetramethyl-1,2-dioxetane in methanolPaul D. Bartlett, Alfons L. Baumstark, and Michael E. LandisCite this: J. Am. Chem. Soc. 1974, 96, 17, 5557–5558Publication Date (Print):August 1, 1974Publication History Published online1 May 2002Published inissue 1 August 1974https://pubs.acs.org/doi/10.1021/ja00824a037https://doi.org/10.1021/ja00824a037research-articleACS PublicationsRequest reuse permissionsArticle Views126Altmetric-Citations39LEARN 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
The glucan components of the cell wall of baker's yeast (Saccharomyces cerevisiae) considered in relation to its ultrastructure (1969)

1. Commercial pressed baker's yeast, and cell walls prepared from it, were extracted in various ways and the products examined by a number of techniques, including infrared spectroscopy and electron microscopy. 2. The glucan components of the walls cannot be extracted from intact yeast cells by 3% (w/v) sodium hydroxide at 75 degrees , but at least one-third of the glucan of cell wall preparations is dissolved under these conditions, and more will dissolve after ultrasonic treatment. 3. If intact cells are given a preliminary treatment with acid the wall glucans dissolve in dilute aqueous alkali. 4. Acid conditions as mild as sodium acetate buffer, pH5.0, for 3hr. at 75 degrees are sufficient for this preliminary treatment; the glucan then dissolves in 3% sodium hydroxide at 75 degrees leaving a very small residue, which contains chitin and about 1% of the initial glucan of the wall. Dissolution is hindered by exclusion of air, or by a preliminary reduction with sodium borohydride, suggesting that some degradation of the glucan by alkali is taking place. 5. After treatment with 0.5m-acetic acid for 24hr. at 90 degrees the glucan dissolves slowly at room temperature in 3% sodium hydroxide, or in dimethyl sulphoxide. The extraction with acetic acid removes glycogen and a predominantly beta-(1-->6)-linked glucan (not hitherto recognized as a component of baker's yeast), but none of the beta-(1-->3)-glucan, which remains water-insoluble. 6. Without treatment with acid, the glucan is not significantly soluble in dimethyl sulphoxide, but can be induced to dissolve by ultrasonic treatment. 7. These results are interpreted by postulating the presence of an enclosing membrane, composed of chitin and glucan, that when intact acts as a semipermeable membrane preventing the escape of the alkali- and dimethyl sulphoxide-soluble fraction of the glucan. Mild acid treatments damage this membrane, and ultrasonic and ballistic disintegration disrupt it. 8. Some support for this hypothesis is given by the effects of certain enzyme preparations, which have been found to render a substantial part of the glucan extractable by dimethyl sulphoxide.
Current Review of in Vivo GBM Rodent Models: Emphasis on the CNS-1 Tumour Model (2011)

GBM (glioblastoma multiforme) is a highly aggressive brain tumour with very poor prognosis despite multi-modalities of treatment. Furthermore, recent failure of targeted therapy for these tumours highlights the need of appropriate rodent models for preclinical studies. In this review, we highlight the most commonly used rodent models (U251, U86, GL261, C6, 9L and CNS-1) with a focus on the pathological and genetic similarities to the human disease. We end with a comprehensive review of the CNS-1 rodent model.
Comparison of Crystal Structures of Two Homologous Proteins: Structural Origin of Altered Domain Interactions in Immunoglobulin Light-Chain Dimers (1994)

The sequence and structure of a second human kappa 1 immunoglobulin light-chain variable domain, Wat, has been determined. The R-factor is 15.7% for 1.9-A data. One hundred and ninety-five water molecules were identified; 30 water molecules were located in identical positions in each of the monomers. Some of the water molecules are integral parts of the domains. This light chain is encoded by the same variable domain gene that encoded the previously characterized kappa I variable domain, Rei. Due to limited somatic mutation, the two highly homologous proteins differ in only 20 of the 108 residues. Wat crystallized in space group P6(4) while Rei crystallized in space group P6(1); in both crystals, the asymmetric unit was the noncovalent dimer. Although the basic domain structure is the same for both proteins, the relative positions of the domains within the two dimers differ. This difference is most likely accounted for by the replacement of Tyr36 in Rei by Phe in the Wat protein. Residue Tyr36 is part of the hydrogen-bonding network in the interface between the domains in Rei. Losing the hydrogen-bonding capability of residue 36 by replacement of Tyr by Phe alters the network of hydrogen bonds between the domains, resulting in a different domain-domain contact. The details of lattice contacts in the two crystals were compared. One type of contact that extends the beta-sheet of the individual domains was conserved, but because it involved different symmetry elements within the crystal, different crystal packing resulted. In the Wat crystal, one of the contacts shows an example of how a symmetrical binding site can "bind" an asymmetrical object. Further, the examination of the Wat crystal also illustrates how the different crystalline environments of the domains of the dimer results in different distributions of temperature factors for the residues within the domains.
Transgenic Mice Overexpressing the Prolactin Gene Develop Dramatic Enlargement of the Prostate Gland1 (1997)

An altered endocrine status of elderly men has been hypothesized to be important for development of prostate hyperplasia. The present study addresses the question whether increased PRL expression is of importance for development of prostate hyperplasia in mice. Three lines of PRL transgenic mice were generated having serum levels of PRL of approximately 15 ng/ml, 100 ng/ml, and 250 ng/ml, respectively. These mice developed dramatic enlargement of the prostate gland, approximately 20 times the normal prostate weight and they had a 4- to 5-fold increased DNA content. Histologically, the prostate glands in the transgenic mice were distended from secretion, and the amount of interstitial tissue was increased. The levels oftestosterone and IGF-I were increased in the PRL transgenic animals. In mice overexpressing the bovine GH gene, displaying elevated IGF-I levels, the prostate gland was slightly larger compared with normal mice, indicating that the effect of PRL was not primarily mediated through elevated plasma IGF-I levels. The present study suggests that PRL is an important factor in the development of prostate hyperplasia acting directly on the prostate gland or via increased plasma levels of testosterone.
Impact of fluoroquinolones on the diagnosis of pulmonary tuberculosis initially treated as bacterial pneumonia. (2005)

Delay in the initiation of anti-tuberculosis treatment is possible in patients administered fluoroquinolone and initially misdiagnosed as having bacterial pneumonia.
Biomarkers Indicative of Blood‐Brain Barrier Disruption in Multiple Sclerosis (2006)

Blood-brain barrier (BBB) disruption is one of the hallmarks of multiple sclerosis (MS). It is incompletely understood whether BBB disruption is the initial MS event leading to MS lesion formation or whether it is merely a consequence of cellular infiltration in the central nervous system (CNS). The presence of gadolinium enhancing (Gd+) lesions on serial brain MRI scans is frequently used to evaluate BBB disruption. The presence of Gd enhancement has therefore been used as a reference for most works evaluating promising biomarkers of BBB disruption that are reviewed here. These promising biomarkers include cytokines and chemokines, and their receptors, cell surface markers, and matrix metalloproteinases and their natural inhibitors. At this time, none of these markers have been shown as sensitive as the presence of Gd enhancement to reflect BBB disruption. However, MRI scanning is not only unpractical and expensive; it may also under represent the overall extent of BBB disruption. Developing new MS biomarkers that are sensitive and specific for BBB disruption could 1) improve the monitoring of disease activity; 2) improve the monitoring of response to MS therapies which target BBB disruption; and 3) advance our understanding of dynamic MS processes participating in BBB disruption.
Transcriptional control of genes that regulate glycolysis and gluconeogenesis in adult liver (1994)

Research Article| October 01 1994 Transcriptional control of genes that regulate glycolysis and gluconeogenesis in adult liver F P Lemaigre; F P Lemaigre 1Hormone and Metabolic Research Unit, University of Louvain Medical School and International Institute of Cellular and Molecular Pathology, 75 Avenue Hippocrate, B-1200 Brussels, Belgium Search for other works by this author on: This Site PubMed Google Scholar G G Rousseau G G Rousseau 1Hormone and Metabolic Research Unit, University of Louvain Medical School and International Institute of Cellular and Molecular Pathology, 75 Avenue Hippocrate, B-1200 Brussels, Belgium Search for other works by this author on: This Site PubMed Google Scholar Biochem J (1994) 303 (1): 1–14. https://doi.org/10.1042/bj3030001 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter LinkedIn Cite Icon Cite Get Permissions Citation F P Lemaigre, G G Rousseau; Transcriptional control of genes that regulate glycolysis and gluconeogenesis in adult liver. Biochem J 1 October 1994; 303 (1): 1–14. doi: https://doi.org/10.1042/bj3030001 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search nav search search input Search input auto suggest search filter All ContentAll JournalsBiochemical Journal Search Advanced Search This content is only available as a PDF. © 1994 The Biochemical Society, London1994 Article PDF first page preview Close Modal You do not currently have access to this content.