gebhart/patrepeval huggingface dataset:
Bromodomains and Their Pharmacological Inhibitors (2014)

Over 60 bromodomains belonging to proteins with very different functions have been identified in humans. Several of them interact with acetylated lysine residues, leading to the recruitment and stabilization of protein complexes. The bromodomain and extra-terminal domain (BET) proteins contain tandem bromodomains which bind to acetylated histones and are thereby implicated in a number of DNA-centered processes, including the regulation of gene expression. The recent identification of inhibitors of BET and non-BET bromodomains is one of the few examples in which effective blockade of a protein-protein interaction can be achieved with a small molecule. This has led to major strides in the understanding of the function of bromodomain-containing proteins and their involvement in diseases such as cancer and inflammation. Indeed, BET bromodomain inhibitors are now being clinically evaluated for the treatment of hematological tumors and have also been tested in clinical trials for the relatively rare BRD-NUT midline carcinoma. This review gives an overview of the newest developments in the field, with a focus on the biology of selected bromodomain proteins on the one hand, and on reported pharmacological inhibitors on the other, including recent examples from the patent literature.
RNA as a Drug Target: The Case of Aminoglycosides (2003)

How to prevent antibiotic therapies from hitting a snag: Most antibiotics target molecular switches on the ribosome. The binding sites are discrete and made of conserved RNA residues rather than ribosomal proteins (see representation of paromycin binding to the ribosome). However, bacteria have evolved and mutated so that the antibiotics cannot bind. At least two types of new molecules could be designed to keep up in this race against evolution: 1) drugs that would bind to the mutated bacterial sites but not (to avoid toxicity) with human cytoplasmic and mitochondrial ribosomes, and 2) drugs that would interfere with other molecular switches involved in translation or regulation pathways.
MIME (Multipurpose Internet Mail Extensions) Part One: Mechanisms for Specifying and Describing the Format of Internet Message Bodies (1993)

STD 11, RFC 822 defines a message representation protocol which specifies considerable detail about message headers, but which leaves the message content, or message body, as flat ASCII text. This document redefines the format of message bodies to allow multi-part textual and non-textual message bodies to be represented and exchanged without loss of information. This is based on earlier work documented in RFC 934 and STD 11, RFC 1049, but extends and revises that work. Because RFC 822 said so little about message bodies, this document is largely orthogonal to (rather than a revision of) RFC 822.
Monocytes provide a novel costimulatory signal to T cells that is not mediated by the CD28/B7 interaction. (1994)

Resting CD4+T cells must receive nonspecific costimulatory signals from APC to produce maximal amounts of IL-2 in response to TCR signaling. The T cell-specific surface molecule CD28 is one protein that transduces a costimulatory signal following interaction with its ligand B7. We report here the identification of another contact-mediated costimulatory signal provided by the human histiocytic line U937 and by purified monocytes. Although this monocyte-derived costimulus is not transduced by the CD28/B7 interaction, it synergizes with the CD28 signal to elicit maximal IL-2 production from freshly isolated T cells. IL-2 production by previously activated CD8+ T cells depends on the monocyte-derived costimulatory signal, although memory CD4+ T cells respond well to either the monocyte-derived costimulus or B7-derived costimulation. In contrast, IL-2 secretion by naive T cells appears to require the synergistic interaction between both costimulatory pathways. These results suggest that the array of costimulatory ligands expressed by various APC affects the magnitude of the T cell response and also which T cell subsets are stimulated.
Erythropoietin in sickle cell disease: relation of erythropoietin levels to crisis and other complications. (1982)

Erythropoietin responsible for the hormonal regulation of red blood cell production. Its formation is largely controlled by the kidneys. A number of assay methods for erythropoietin are available. Asymptomatic patients with sickle cell disease have elevated erythropoietin levels, as expected with chronic hemolysis. When complicated by chronic renal failure, erythropoietin levels do not rise appropriately. Chronic infection has not been studied, but the erythropoietin response in acute infection does not seem to conform to a pattern. Aplastic crises are characterized by very high levels of erythropoietin, suggesting bone marrow suppression, but events that trigger the crises remain obscure. In vaso-occlusive crises, there is also some suggestion of mild and transient lack of bone marrow response. Patients with sickle cell disease, with their chronic high erythropoietin anemia and susceptibility to altered states, are uniquely suited for investigating the physiology of erythropoietin, especially under the constraints of present assay methods.
533. The chemistry of the triterpenes and related compounds. Part XXXIX. Some derivatives of 4,4-dimethylcholestan-3-one (1961)

G. R. Chaudhry, T. G. Halsall and E. R. H. Jones, J. Chem. Soc., 1961, 2725 DOI: 10.1039/JR9610002725
The UCSC Genome Browser database: extensions and updates 2013 (2012)

The University of California Santa Cruz (UCSC) Genome Browser (http://genome.ucsc.edu) offers online public access to a growing database of genomic sequence and annotations for a wide variety of organisms. The Browser is an integrated tool set for visualizing, comparing, analysing and sharing both publicly available and user-generated genomic datasets. As of September 2012, genomic sequence and a basic set of annotation 'tracks' are provided for 63 organisms, including 26 mammals, 13 non-mammal vertebrates, 3 invertebrate deuterostomes, 13 insects, 6 worms, yeast and sea hare. In the past year 19 new genome assemblies have been added, and we anticipate releasing another 28 in early 2013. Further, a large number of annotation tracks have been either added, updated by contributors or remapped to the latest human reference genome. Among these are an updated UCSC Genes track for human and mouse assemblies. We have also introduced several features to improve usability, including new navigation menus. This article provides an update to the UCSC Genome Browser database, which has been previously featured in the Database issue of this journal.
The specificity of proteasomes: impact on MHC class I processing and presentation of antigens (1999)

We have studied polypeptide processing by purified proteasomes, with regard to proteolytic specificity and cytotoxic T-lymphocyte (CTL) epitope generation. Owing to defined preferences with respect to cleavage sites and fragment length, proteasomes degrade polypeptide substrates into cohorts of overlapping oligopeptides. Many of the proteolytic fragments exhibit structural features in common with major histocompatibility complex (MHC) class I ligands including fragment size and frequencies of amino acids at fragment boundaries. Proteasomes frequently generate definitive MHC class I ligands and/or slightly longer peptides, while substantially larger peptides are rare. Individual CTL epitopes are produced in widely varying amounts, often consistent with immunohierarchies among CTL epitopes. We further found that polypeptide processing is remarkably conserved among proteasomes of eukaryotic origin and that invertebrate proteasomes can efficiently produce known high-copy MHC class I ligands, suggesting evolutionary adaptation of the transporter associated with antigen processing and MHC class I to ancient constraints imposed by proteasomal protein degradation.
Over‐expression of ICAM‐1, VCAM‐1 and ELAM‐1 might influence tumor progression in colorectal cancer (1998)

Adhesion molecules might play a role in tumor progression. We investigated expression of the adhesion molecules ICAM-1, VCAM-1 and ELAM-1 in 24 primary colorectal carcinomas using immuno-histochemistry and Northern blot analysis. Normal colonic tissue from the same patients served as controls. ICAM-1 immunostaining was restricted to the intercellular matrix and vascular endothelial cells. The vast majority of normal tissue samples revealed only faint ICAM-1 immunoreactivity. However, moderate to strong immunostaining was found in 86% of cancerous sections. The ICAM-1 immunoreaction was more intense in well-differentiated carcinomas as well as in the adenomatous parts and transition zones of cancers. Similarly, the cancers exhibited markedly enhanced VCAM-1 and ELAM-1 immunostaining in the endothelial cells of small blood vessels. The intense vascular immunostaining by ICAM-1 and VCAM-1 was associated with a strong presence of CD3-positive T lymphocytes, whereas ELAM-1 immunoreactivity did not correlate with round cell infiltration. On Northern blot analysis, ICAM-1, VCAM-1 and ELAM-1 mRNA levels were increased in 67%, 57% and 63% of carcinomas, respectively, in comparison with normal tissue samples. Densitometric analysis of Northern blots revealed an increase in ICAM-1 by 2.1-fold, an increase in VCAM-1 by 3.4-fold and an increase in ELAM-1 by 2.2-fold in cancerous tissues compared to normal controls. Over-expression of ICAM-1 might prevent cell–cell disruption and, hence, tumor dissemination. Furthermore, over-expression of ICAM-1 and VCAM-1, but not ELAM-1, might favor host anti-tumor defense by trafficking of lymphocytes. Int. J. Cancer (Pred. Oncol.) 79:76–81, 1998. © 1998 Wiley-Liss, Inc.
The Pilosebaceous Unit Is Part of the Skin Immune System (1998)

It is well established that the functional state of sebaceous glands in vivo is a tightly regulated process orchestrated through the interaction of male sex hormones and functional androgen receptors expressed on sebocytes. In the last few years, however, it has become increasingly apparent that sebocytes like epidermal keratinocytes express a variety of cytokines which are implicated in inflammatory and immune responses. For example, sebocytes in vivo have been found to highly express tumor necrosis factor alpha (TNF-alpha) as determined by immunohistochemical and electron-microscopic methods. Moreover, certain neuropeptides including vascular intestinal peptide and proopiomelanocortin (POMC) peptides as well as their receptors have been localized within the pilosebaceous unit of murine and human skin. Since POMC peptides such as alpha-melanocyte-stimulating hormone have recently been shown to exert important immunoregulatory effects by antagonizing the function of proinflammatory cytokines (e.g interleukin 1, interleukin 6 and TNF-alpha), induction of immunosuppressive cytokines (like interleukin 10), modulation of costimulatory molecule expression (e.g. B7-2) or suppression of macrophage-derived nitric oxide, complex interactions between these mediators and their target cells within the pilosebaceous gland seem to exist. The successful cultivation of sebocytes will provide a model by which the effect of these mediators can be studied in detail in order to shed light onto the various pathophysiological conditions of sebaceous glands.
Thymosin alpha1: isolation and sequence analysis of an immunologically active thymic polypeptide. (1977)

The amino acid sequence of a biologically active polypeptide isolated from calf thymus, termed thymosin alpha1, has been determined. Thymosin alpha1 is a heat stable, highly acidic molecule composed of 28 amino acid residues. This peptide is one of several present in thymosin fraction 5 that may participate in the regulation, differentiation and function of thymus-dependent lymphocytes (T cells). A nomenclature for the family of polypeptides present in thymosin fraction 5 is suggested.
Plasma wave electronics: novel terahertz devices using two dimensional electron fluid (1996)

We discuss how the propagation of plasma waves in a High Electron Mobility Transistor (HEMT) can be used to implement a new generation of terahertz devices, including sources, resonant detectors, broad band detectors, and frequency multipliers. Our estimates show that these devices should outperform conventional terahertz devices, which use deep submicron Schottky diodes.
Creation of synthetic samples for physical modelling of natural shale (2016)

ABSTRACT Natural shale samples, particularly well‐preserved, drilled core samples, are extremely difficult to obtain for laboratory research. Multiple tests must be carried out on one sample, and some samples are disposed after destructive tests. Therefore, rarity and non‐reusability of samples strongly restrict shale studies. In this study, based on statistical data from the world's major shale block, a new type of synthetic shale was physically constructed via a process of interfusion, stuffing, and compaction using quartz, clay, carbonate, and kerogen as the primary materials, according to statistical data from the world's major shale blocks. Further evaluation of the synthetic shale involved the use of scanning electron microscopy imagery and analysis of its anisotropic characteristics in comparison with natural shale. The synthetic shale had a laminated microstructure similar to natural shale, and its velocity anisotropy corresponded to Thomsen's anisotropy of a transversely isotropic medium. The results of tests for homogeneity and repeatability indicated that the construction process was stable and that several identical synthetic samples, which were satisfactorily similar to natural shale, could be produced for both iterative and destructive tests. The composition of each mineral, as well as the density, porosity, permeability, and anisotropy of the samples, were all variable. Therefore, a series of synthetic samples could be obtained with properties set to meet the requirements of petrophysical experimentation. Moreover, gas or oil saturation was also considered in the construction of the synthetic shale, meaning that the characteristics of gas or oil saturation (or the complete range of data from dry to saturated samples) could be tested using the synthetic shale.
Blobworld: image segmentation using expectation-maximization and its application to image querying (2002)

Retrieving images from large and varied collections using image content as a key is a challenging and important problem. We present a new image representation that provides a transformation from the raw pixel data to a small set of image regions that are coherent in color and texture. This "Blobworld" representation is created by clustering pixels in a joint color-texture-position feature space. The segmentation algorithm is fully automatic and has been run on a collection of 10,000 natural images. We describe a system that uses the Blobworld representation to retrieve images from this collection. An important aspect of the system is that the user is allowed to view the internal representation of the submitted image and the query results. Similar systems do not offer the user this view into the workings of the system; consequently, query results from these systems can be inexplicable, despite the availability of knobs for adjusting the similarity metrics. By finding image regions that roughly correspond to objects, we allow querying at the level of objects rather than global image properties. We present results indicating that querying for images using Blobworld produces higher precision than does querying using color and texture histograms of the entire image in cases where the image contains distinctive objects.
Resistance of Pasteurella multocida A:3,4 to phagocytosis by turkey macrophages and heterophils (1991)

A virulent field isolate and 2 vaccine strains of Pasteurella multocida A:3,4 were compared for resistance to phagocytosis by turkey macrophages and heterophils, using in vitro assays. The least virulent vaccine strain (M-9) was phagocytosed to a greater degree than was the field isolate or the other vaccine strain (Clemson University). All 3 bacteria differed significantly from each other in the amount of capsular material present as measured by polycationic ferritin labeling and electron microscopy. Removal of the capsule with hyaluronidase resulted in a significant increase in phagocytosis of the field isolate.
Inhibitory Cross-talk by cAMP Kinase on the Calmodulin-dependent Protein Kinase Cascade (1997)

The calmodulin-dependent kinase (CaM-K) cascade, a Ca2+-triggered system involving phosphorylation and activation of CaM-KI and CaM-KIV by CaM kinase kinase (CaM-KK), regulates transcription through direct phosphorylation of transcription factors such as cAMP response element-binding protein. We have shown previously that activated CaM-KIV can activate the mitogen-activated protein kinases (Enslen, H., Tokumitsu, H., Stork, P. J. S., Davis, R. J., and Soderling, T. R. (1996) Proc. Natl. Acad. Sci. U. S. A. 93, 10803-10808), and the present paper describes a novel regulatory cross-talk between cAMP kinase (PKA) and CaM-KK. PKA gave rapid phosphorylation in vitro and in cells of recombinant CaM-KK, resulting in 50-75% inhibition of CaM-KK activity, part of which was due to suppression of CaM-binding by phosphorylation of Ser458 in the CaM-binding domain. However, the Ser458 --> Ala mutant, or a truncation mutant in which the CaM-binding and autoinhibitory domains were deleted, was still partially suppressed by PKA-mediated phosphorylation. The second inhibitory site was identified as Thr108 by site-specific mutagenesis. Treatments of COS-7, PC12, hippocampal, or Jurkat cells with the PKA activators forskolin or isoproterenol gave 30-90% inhibition of either endogenous or transfected CaM-KK and/or CaM-KIV activities. These results demonstrate that the CaM kinase cascade is negatively regulated in cells by the cAMP/PKA pathway.
Layer-by-Layer Self-Assembly of Chitosan and Poly(γ-glutamic acid) into Polyelectrolyte Complexes (2011)

Chitosan (Ch) is a nontoxic and biocompatible polysaccharide extensively used in biomedical applications. Ch, as a polycation, can be combined with anionic polymers by layer-by-layer (LbL) self-assembly, giving rise to multilayered complexed architectures. These structures can be used in tissue engineering strategies, as drug delivery systems, or artificial matrices mimicking the extracellular microenvironment. In this work, Ch was combined with poly(γ-glutamic acid) (γ-PGA). γ-PGA is a polyanion, which was microbially produced, and is known for its low immunogenic reaction and low cytotoxicity. Multilayered ultrathin films were assembled by LbL, with a maximum of six layers. The interaction between both polymers was analyzed by: ellipsometry, quartz crystal microbalance with dissipation, Fourier transform infrared spectroscopy, atomic force microscopy, and zeta potential measurements. Ch/γ-PGA polyelectrolyte multilayers (PEMs) revealed no cytotoxicity according to ISO 10993-5. Overall, this study demonstrates that Ch can interact electrostatically with γ-PGA forming multilayered films. Furthermore, this study provides a comprehensive characterization of Ch/γ-PGA PEM structures, elucidating the contribution of each layer for the nanostructured films. These model surfaces can be useful substrates to study cell-biomaterial interactions in tissue regeneration.
Aging-Dependent Exclusion of Antigen-Inexperienced Cells from the Peripheral B Cell Repertoire (2002)

Aging is accompanied by greatly reduced B cell production in the bone marrow, yet peripheral B cell numbers do not decline. We hypothesize that this may reflect filling of the peripheral pool with B cells that are long-lived as a consequence of specificity for, and chronic stimulation by, environmental Ags. To begin to explore this possibility, we analyzed the effects of aging on B cell population dynamics in the anti-H2(k/b) 3-83 mu-delta Ig-transgenic mouse. We predicted that, because they presumably do not bind environmental Ags, B cells bearing the transgenic receptor may be lost in aged animals. As seen in nontransgenic animals, total splenic B cell numbers remained constant with age in the Ig-transgenic animals despite reduced B cell production. Importantly, although the few newly produced B cells in the bone marrow of aged mice are 3-83 positive, the peripheral compartment of these mice is dominated by B cells that express endogenous Ig genes rather than the transgenes. This population includes large numbers of marginal zone-like and CD21(low/-)CD23(low/-)IgM(low) B cells, as well as elevated numbers of CD5+ B cells. Many of these cells express only non-B220 CD45 isoforms, suggesting that they may be memory cells. A significant proportion of aged transgenic animals produce autoantibodies that are reactive with ssDNA, dsDNA, or histones. Results support the hypothesis that, in the face of severely reduced production with age, B cells are selected based on reactivity to environmental Ags, accumulate, and display activated phenotypes. Cells bearing 3-83-transgenic receptors are excluded from this population due to their specificity. Beyond their importance in aging, these findings define a novel form of receptor revision in which B cells are selected rather than deleted based on Ag reactivity.
Developmental and tissue‐specific expression of human CD4 in transgenic rabbits (1995)

A major obstacle to understanding AIDS is the lack of a suitable small animal model for studying HIV-1 infection and the subsequent development of AIDS, and for testing diagnostic, therapeutic, and preventive modalities. Our goal is to produce a rabbit model for the study of AIDS. Here we report on the generation of transgenic rabbits that express the human CD4 (hCD4) gene. The transgene, which contains the coding region for hCD4 and approximately 23 kb of sequence upstream of the translation start site, was used previously to direct hcD4 expression on the surface of CD4+ T cells of transgenic mice (Gillespie et al., 1993: Mol Cell Biol 13:2952-2958). The hCD4 transgene was detected in five males and two females derived from the microinjection in five males and two females derived from the microinjection of 271 rabbit embryos. Both hCD4 RNA and protein were expressed in peripheral blood lymphocytes (PBLs) from all five males but neither of the females. Human CD4 was expressed on PBLs from F1 offspring of all founder males. T-cell subset analysis revealed that hCD4 expression was restricted to rabbit CD4 (rCD4) expressing lymphocytes; mature rCD4- rCD8+ lymphocytes did not express hCD4. In preliminary studies, PBLs from hCD4 transgenic rabbits produced greater amounts of HIV-1 p24 core protein following HIV-1 infection in vitro than HIV-1 p24 antigen in nontransgenic rabbit infected cultures. These results extend to rabbits our previous observation that this transgene contains the sequence elements required for high-level expression in the appropriate cells of transgenic mice. Furthermore, these and previous studies demonstrating that expression of hCD4 protein enhances HIV-1 infection of rabbit T cells in vitro, coupled with reports that normal, nontransgenic rabbits are susceptible to HIV-1 infection, suggests that the hCD4 transgenic rabbits described herein will have an increased susceptibility to HIV-1 infection. In vivo HIV-1 infection studies with these rabbits are under way.
In Vitro Fermentation of Breast Milk Oligosaccharides by Bifidobacterium infantis and Lactobacillus gasseri (2006)

It has been proposed that human milk oligosaccharides (HMO) function as a prebiotic for bifidobacteria, yet this activity has not been adequately investigated. In this study, Bifidobacterium infantis was shown to ferment purified HMO as a sole carbon source, while another gut commensal, Lactobacillus gasseri, did not ferment HMO. Our results support the hypothesis that HMO selectively amplify bacterial populations in the infant intestine.