gebhart/patrepeval huggingface dataset:
Emerging patterns and implications of HIV-1 integrase inhibitor resistance (2012)

Integrase inhibitors provide a potent option for the treatment of HIV infection. Drug resistance remains a challenge, which may be partially overcome by the introduction of second-generation compounds. Prompt management of RAL and EVG failure is required to prevent the accumulation of multiple resistance mutations that reduce DTG susceptibility.
Efficacy of a Fibrin Hemostatic Bandage in Controlling Hemorrhage From Experimental Arterial Injuries (1995)

Bandages containing fibrinogen and thrombin significantly reduced the amount of blood loss and allowed mean arterial pressures to be maintained in animals with uncontrolled hemorrhage from femoral artery lacerations. A hemostatic bandage may be an important adjuvant for controlling severe extremity hemorrhage in the prehospital setting.
Synthesis of 3-Indolyl and 5-Bromo-3-indolyl Phosphate for Histochemical Demonstration of Alkaline Phosphatase (1967)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of 3-Indolyl and 5-Bromo-3-indolyl Phosphate for Histochemical Demonstration of Alkaline PhosphataseK. C. Tsou, Helen C. F. Su, Dorothy J. Rabiger, Hans. Heymann, and Arnold M. SeligmanCite this: J. Med. Chem. 1967, 10, 4, 662–664Publication Date (Print):July 1, 1967Publication History Published online1 May 2002Published inissue 1 July 1967https://pubs.acs.org/doi/10.1021/jm00316a031https://doi.org/10.1021/jm00316a031research-articleACS PublicationsRequest reuse permissionsArticle Views108Altmetric-Citations9LEARN 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
Abundance of Gal 1,3GalNAc in O-Linked Oligosaccharide on Hinge Region of Polymerized IgA1 and Heat-Aggregated IgA1 from Normal Human Serum (1996)

Gas-phase hydrazinolysis was used to analyze the glycoform of the O-linked oligosaccharide of human serum IgA1. In our previous report, only one glycoform was obtained from the IgA1 of healthy individuals. However, it was found to be composed of heterogeneous IgA1 components having mutually different glycoforms. First, the IgA1 was separated into two subfractions having different affinities toward jacalin. Among them, the high-affinity subfraction was mainly composed of polymerized IgA1. Comparative study of the carbohydrate chain showed a relative abundance of Gal beta 1,3GalNAc in the polymerized form. A simultaneous analysis of the N-glycan of these subfractions was also carried out. Three major components, two biantennary and one triantennary oligosaccharides, were obtained from both subfractions and the relative contents of these components were almost the same. On the other hand, IgA1 was artificially polymerized by heating at 63 degrees C for 2 h. The heat-stable IgA1 was separated from the heat-aggregated material on a Sephacryl S-300 column. The obtained heat-stable IgA1 (approximately 20%) was not further aggregated by more heating under the same conditions. The heat-stable IgA1 contained a much higher amount of the sialylated Gal beta 1,3GalNAc. Thus, it was shown that the degree of completeness of the hinge O-linked oligosaccharide might be correlated with the stability and polymerization process of the IgA1 molecule.
Peptide sequences selected by BA4, a tropoelastin-specific monoclonal antibody, are ligands for the 67-kilodalton bovine elastin receptor (1993)

A 67-kDa cell-surface elastin/laminin receptor is expressed by fetal bovine ligamentum nuchae fibroblasts and neutrophils. Two hexapeptides, VGVAPG and PGAIPG, contained within hydrophobic domains of tropoelastin are binding sites for this receptor. Studies of recombinant tropoelastin proteins and synthetic peptides demonstrated that a monoclonal antibody, BA4, recognized peptide sequences similar to those recognized by the 67-kDa receptor. Taking advantage of this similarity, an "epitope library" containing random hexapeptides was screened with BA4. Four BA4-selected peptides (VGAMPG, VGMAPG, VGSLPG, and VGLSPG) were synthesized; studies of fibroblast and neutrophil migration support the hypothesis that these peptides are ligands of the 67-kDa receptor present on ligamentum nuchae fibroblasts and neutrophils. Two additional, physically similar tropoelastin peptides,AGAIPG and PGAVGP, were also identified as peptide ligands, and hence potential binding sites within tropoelastin, of the elastin receptor. These data suggest that the 67-kDa elastin/laminin receptor may interact with a wide range of structurally similar peptides containing amino acid substitutions involving small nonpolar and uncharged amino acids.
Inhibition of PI3Kδ Restores Glucocorticoid Function in Smoking-induced Airway Inflammation in Mice (2009)

These data show that therapeutic inhibition of PI3Kdelta may restore glucocorticoid function in oxidative stress-induced glucocorticoid insensitivity.
Identification of Adipophilin as a Potential Plasma Biomarker for Colorectal Cancer Using Label-Free Quantitative Mass Spectrometry and Protein Microarray (2011)

The combination of HFM and 2DICAL enables the comprehensive analysis of plasma proteins and is ideal for use in all biomarker discovery studies.
Thymus-autonomous T cell development in the absence of progenitor import (2012)

Thymus function is thought to depend on a steady supply of T cell progenitors from the bone marrow. The notion that the thymus lacks progenitors with self-renewal capacity is based on thymus transplantation experiments in which host-derived thymocytes replaced thymus-resident cells within 4 wk. Thymus grafting into T cell-deficient mice resulted in a wave of T cell export from the thymus, followed by colonization of the thymus by host-derived progenitors, and cessation of T cell development. Compound Rag2(-/-)γ(c)(-/-)Kit(W/Wv) mutants lack competitive hematopoietic stem cells (HSCs) and are devoid of T cell progenitors. In this study, using this strain as recipients for wild-type thymus grafts, we noticed thymus-autonomous T cell development lasting several months. However, we found no evidence for export of donor HSCs from thymus to bone marrow. A diverse T cell antigen receptor repertoire in progenitor-deprived thymus grafts implied that many thymocytes were capable of self-renewal. Although the process was most efficient in Rag2(-/-)γ(c)(-/-)Kit(W/Wv) hosts, γ(c)-mediated signals alone played a key role in the competition between thymus-resident and bone marrow-derived progenitors. Hence, the turnover of each generation of thymocytes is not only based on short life span but is also driven via expulsion of resident thymocytes by fresh progenitors entering the thymus.
Structural Basis for Inhibition of Protein-tyrosine Phosphatase 1B by Isothiazolidinone Heterocyclic Phosphonate Mimetics (2006)

Crystal structures of protein-tyrosine phosphatase 1B in complex with compounds bearing a novel isothiazolidinone (IZD) heterocyclic phosphonate mimetic reveal that the heterocycle is highly complementary to the catalytic pocket of the protein. The heterocycle participates in an extensive network of hydrogen bonds with the backbone of the phosphate-binding loop, Phe(182) of the flap, and the side chain of Arg(221). When substituted with a phenol, the small inhibitor induces the closed conformation of the protein and displaces all waters in the catalytic pocket. Saturated IZD-containing peptides are more potent inhibitors than unsaturated analogs because the IZD heterocycle and phenyl ring directly attached to it bind in a nearly orthogonal orientation with respect to each other, a conformation that is close to the energy minimum of the saturated IZD-phenyl moiety. These results explain why the heterocycle is a potent phosphonate mimetic and an ideal starting point for designing small nonpeptidic inhibitors.
Conjugation of soluble CD4 without loss of biological activity via a novel carbohydrate-directed cross-linking reagent. (1992)

Chemical conjugates of recombinant soluble CD4 (sCD4) with toxins, or with antibodies that activate cytotoxic T cells, can be used to direct selective killing of human immunodeficiency virus (HIV)-infected cells. This approach takes advantage of the ability of sCD4 to bind with high affinity to gp120, the envelope protein of HIV-1, which is expressed on actively infected cells. However, conjugation of sCD4 via reagents that target amino groups may reduce its affinity for gp120, since at least one such group is important for gp120 binding. Here, we describe a novel cross-linking reagent which enables the conjugation of sCD4 via its carbohydrate moieties rather than its free amino groups. This heterobifunctional reagent, 4-(4-N-maleimidophenyl)butyric acid hydrazide (MPBH), combines a nucleophilic hydrazide with an electrophilic maleimide, thereby allowing coupling of carbohydrate-derived aldehydes to free thiols. We describe conditions by which MPBH is coupled selectively to the sialic acid residues of sCD4, and exemplify the use of MPBH by conjugating sCD4 to hemoglobin and to beta-galactosidase. We show that, whereas conjugation of sCD4 via amino groups markedly reduces its gp120 binding affinity, conjugation via the carbohydrate chains using MPBH does not affect binding. Moreover, we demonstrate the ability of a sCD4-MPBH-fluorescein conjugate to label HIV-infected human CEM cells selectively. These results indicate that, by targeting its carbohydrate moieties, sCD4 can be cross-linked to other molecules without compromising its function. The approach described here can be useful for glycoproteins in which amino groups, but not carbohydrates, are important for function. More generally, this approach can be considered for use in cross-linking glycoconjugates to compounds which either contain thiols, or to which thiols can be added.
Sorting of Phaseolin to the Vacuole Is Saturable and Requires a Short C-Terminal Peptide (1998)

Lorenzo Frigerio, Maddalena de Virgilio, Alessandra Prada, Franco Faoro, Alessandro Vitale, Sorting of Phaseolin to the Vacuole Is Saturable and Requires a Short C-Terminal Peptide, The Plant Cell, Vol. 10, No. 6 (Jun., 1998), pp. 1031-1042
Developmental Regulation of Neural Response to FGF-1 and FGF-2 by Heparan Sulfate Proteoglycan (1993)

Murine neural precursor cells and cell lines derived from them are stimulated by members of the heparin-binding fibroblast growth factor (FGF) family. The activity of FGF is regulated by heparan sulfate proteoglycans (HSPGs), and this interaction is an essential prerequisite for the binding of growth factor to the signal transducing receptors. Messenger RNA for FGF-2 was detectable in the neuroepithelium at embryonic day 9, and the HSPGs produced by these cells at this time preferentially bound FGF-2. However, at embryonic day 11, when messenger RNA for FGF-1 was first detectable, there was a switch in the binding specificity of the HSPG to FGF-1. Thus, a single species of HSPG undergoes a rapid, tightly controlled change in growth factor-binding specificity concomitant with the temporal expression of the FGFs.
Biomechanical Comparison of Posterior Lumbar Interbody Fusion Cages (1997)

This study revealed the two cages to have similar biomechanical characteristics immediately after posterior insertion and warrant further clinical studies.
Intent detection using semantically enriched word embeddings (2016)

State-of-the-art targeted language understanding systems rely on deep learning methods using 1-hot word vectors or off-the-shelf word embeddings. While word embeddings can be enriched with information from semantic lexicons (such as WordNet and PPDB) to improve their semantic representation, most previous research on word-embedding enriching has focused on improving intrinsic word-level tasks such as word analogy and antonym detection. In this work, we enrich word embeddings to force semantically similar or dissimilar words to be closer or farther away in the embedding space to improve the performance of an extrinsic task, namely, intent detection for spoken language understanding. We utilize several semantic lexicons, such as WordNet, PPDB, and Macmillan Dictionary to enrich the word embeddings and later use them as initial representation of words for intent detection. Thus, we enrich embeddings outside the neural network as opposed to learning the embeddings within the network, and, on top of the embeddings, build bidirectional LSTM for intent detection. Our experiments on ATIS and a real log dataset from Microsoft Cortana show that word embeddings enriched with semantic lexicons can improve intent detection.
A novel class of secreted hydrophobic proteins is involved in aerial hyphae formation in Streptomyces coelicolor by forming amyloid-like fibrils (2003)

Streptomycetes exhibit a complex morphological differentiation. After a submerged mycelium has been formed, filaments grow into the air to septate into spores. A class of eight hydrophobic secreted proteins, ChpA-H, was shown to be instrumental in the development of Streptomyces coelicolor. Mature forms of ChpD-H are up to 63 amino acids in length, and those of ChpA-C are larger (+/-225 amino acids). ChpA-C contain two domains similar to ChpD-H, as well as a cell-wall sorting signal. The chp genes were expressed in submerged mycelium (chpE and chpH) as well as in aerial hyphae (chpA-H). Formation of aerial hyphae was strongly affected in a strain in which six chp genes were deleted (DeltachpABCDEH). A mixture of ChpD-H purified from cell walls of aerial hyphae complemented the DeltachpABCDEH strain extracellularly, and it accelerated development in the wild-type strain. The protein mixture was highly surface active, and it self-assembled into amyloid-like fibrils at the water-air interface. The fibrils resembled those of a surface layer of aerial hyphae. We thus conclude that the amyloid-like fibrils of ChpD-H lower the water surface tension to allow aerial growth and cover aerial structures, rendering them hydrophobic. ChpA-C possibly bind ChpD-H to the cell wall.
Myocardial T2 quantitation in patients with iron overload at 3 Tesla (2009)

Myocardial T2 quantitation is feasible at 3T. Given the substantially decreased T2 and increased B0 inhomogeneity, the rapid myocardial T2 measurement protocol demonstrated here may present a robust alternative to study cardiac iron overload at 3T.
Thermotolerant Hydrogenases: Biological Diversity, Properties, and Biotechnological Applications (2008)

Hydrogenases are metalloproteins that catalyze the oxidation and reduction of molecular hydrogen and play a crucial role in many microbial metabolic processes. A subset of hydrogenases capable of functioning at temperatures from 50 to 125 degrees C is found in thermophilic microorganisms. Most known thermotolerant hydrogenases contain a [NiFe] active site and are either bidirectional or uptake type. Although no exhaustive survey has been done of the ecological diversity of thermophilic hydrogen-reducing or oxidizing bacteria, they appear to exist in virtually every thermophilic environment examined to date. Thermotolerant hydrogenases share many similarities with their mesophilic counterparts, but they have several features in addition to thermotolerance that make them especially well suited for biotechnological applications. Ongoing research is focused on potential applications of thermotolerant H2 ases in biosynthesis, H2 production, bioremediation, and biosensors.
Tumor necrosis factor alpha is involved in mouse growth and lymphoid tissue development. (1992)

Tumor necrosis factor alpha (TNF-alpha), a major mediator of inflammation, also possesses a wide pleiotropism of actions, suggesting its involvement in physiological conditions. TNF-alpha mRNA is present in mouse embryonic tissues and also in fetal thymus and spleen. Repeated injections of a monospecific polyclonal rabbit anti-mouse TNF-alpha antibody in mice, starting either during pregnancy or at birth, led to a severe but transient growth retardation, already present at birth, reaching a 35% decrease in body weight at 3 wk, with complete recovery at 8 wk. The insulin growth factor I (IGF-I) blood levels were decreased to about 50%; growth hormone release and other endocrine functions were unaltered. A marked atrophy of the thymus, spleen, and lymph nodes was also observed, with lymphopenia and impaired development of T and B cell peripheral lymphoid structures. The pathways involving TNF-alpha in IGF-I release and early body growth are probably distinct from those by which TNF-alpha participates in early development of lymphoid tissues, where its low physiological release may contribute to enhance lymphoid cell expansion.
Lysyl Oxidase: Mechanism, Regulation and Relationship to Liver Fibrosis (1994)

Lysyl oxidase oxidizes peptidyl lysine in collagen and elastin substrates to residues of alpha-aminoadipic-delta-semialdehyde. The peptidyl aldehydes can then undergo spontaneous condensations with unreacted epsilon-amino groups and with neighboring aldehyde functions, thus forming the covalent crosslinkages which convert elastin and collagen into insoluble fibers. The unique role of lysyl oxidase in the post-translational modification of these proteins qualifies this enzymatic reaction as a potentially pivotal site of biological and/or chemotherapeutic control of collagen fiber deposition. Recent advances in the study of the catalytic mechanism, in the development of active site inhibitors, and in the biosynthesis and regulation of this unusual catalyst are reviewed as are studies on the response of lysyl oxidase in fibrotic liver.
Multi-resolution motion estimation (2002)

Spatial multi-resolution video sequences provide video at multiple frame sizes, allowing extraction of only the resolution or bit rate required by the user. This paper proposes fine-to-coarse motion estimation (ME) for multi-resolution video coding. While coarse-to-fine ME, used in previously proposed coding themes, can provide a better estimate at the coarsest resolution, it is outperformed by fine-to-coarse ME at finer resolutions due to the inability of coarse-to-fine ME to accurately track motion at finer resolutions. At the finest resolution, fine-to-coarse ME provides a PSNR improvement of up to 1 dB, for the sequences tested, and better visual quality at all resolutions. In addition, fine-to-coarse ME provides more accurate and thus more compressible motion estimates.
Steroid-Associated Side Effects in Patients With Multiple Myeloma: Consensus Statement of the IMF Nurse Leadership Board (2008)

Steroids have been the foundation of multiple myeloma therapy for more than 30 years and continue to be prescribed as single agents and in combination with other antimyeloma drugs, including novel therapies. Steroids cause a wide range of side effects that affect almost every system of the body. Identification and prompt management of the toxicities contribute to the success of steroid-containing antimyeloma regimens. By following patients carefully and educating them and their caregivers, nurses can promote adherence to therapy and improve quality of life. The International Myeloma Foundation's Nurse Leadership Board developed this consensus statement for the management of steroid-associated side effects to be used by healthcare providers in any medical setting.
New Insights on the Mechanical Characterization of Kerogen-Rich Shale, KRS (2015)

Abstract In the past decade, chemical, physical and mechanical characterization of source rock reservoirs has moved towards micro- and nano-scale analyses, primarily driven by the fact that the representative elementary volume (REV) for characterizing shales is at the nanometer scale. Nanoindentation is now widely used in many industrial and university laboratories to measure both stiffness and strength and other mechanical properties of shales, such as anisotropic Young's Moduli and plastic yielding parameters. However, to date, tensile failures of shales have not been studied at the micro- or nanoscale. In this work, a nanoindenter is used to bring organic-rich shale (preserved Woodford shale from a well site in Ada, Oklahoma) to failure in tension. Micro-cantilever beam geometries (~25 microns in length and ~5 microns in width) were milled and loaded to failure while monitoring in-situ via scanning electron microscopy (SEM). The force-displacement curves were analyzed in light of the high resolution images collected during fracture initiation, propagation, and ultimate failure. Complementary studies of the mineralogical composition, particularly at the failure faces, as well as the organic content were also performed. Failure planes and tensile fracture initiation in the micro-beam were associated with the various phases of the mineral and organic cluster components. The micro-beam tests of this composite natural material demonstrate linear elastic behavior followed by plastic yielding before complete failure. This behavior was clearly observed to correlate with the amount of organic matter at the fractured surface. Energy dispersive X-ray spectroscopy (EDS) analyses were conducted at the post-failure stage on the resulting fracture faces and the relationship between mechanical behavior and composition was established. It was observed that when high mineral content was found at the faces, a brittle failure took place, while when the fixed support had high kerogen content the micro-beam failed in a ductile mode. These results reinforce our growing understanding of the heterogeneous nature of shale and the importance of nano- and micro-scale analyses to understand our reservoir source rocks.
Abnormalities of plasma lipoproteins in a new genetically obese rat with non-insulin-dependent diabetes mellitus (Wistar fatty rat). (1991)

We investigated plasma lipoprotein profiles and the activities of tissue cholesterol regulating enzymes in Wistar fatty rats, an animal model for non-insulin-dependent diabetes mellitus (NIDDM). Wistar fatty rats were made by transfer of the fa gene to the Wistar Kyoto rats by backcross-breeding. Wistar fatty and control non-diabetic littermates were given a laboratory chow or an atherogenic diet containing 1 percent (weight percent) cholesterol, 0.5 percent cholic acid, and 5 percent lard. Under the chow diet, plasma fasting glucose and immunoreactive insulin concentrations in Wistar fatty rats were 1.5- and 6-fold higher than controls, respectively. Plasma cholesterol was significantly increased in Wistar fatty rats compared with controls. Elevated plasma cholesterol levels in Wistar fatties was accounted for by the increases of cholesterol content in the d less than 1.006 g/ml lipoprotein and high-density lipoproteins. Under the atherogenic diet, plasma cholesterol levels in Wistar fatties were further increased by 129 percent compared with controls. The diet-induced increase of cholesterol contents was shown in all lipoprotein classes for Wistar fatty rats. The activities of regulatory enzymes for cholesterol biosynthesis or absorption were measured in Wistar fatty rats. Both hepatic and intestinal 3-hydroxy-3-methylglutaryl (HMG)-CoA reductase activities were significantly higher in Wistar fatty rats than those in controls (P less than 0.05 and P less than 0.01, respectively). ACAT activities in Wistar fatties were significantly increased in the intestine (P less than 0.05) and decreased in the liver in comparison with controls (P less than 0.01).(ABSTRACT TRUNCATED AT 250 WORDS)