gebhart/patrepeval huggingface dataset:
The immunology of AIDS‐associated lymphomas (1998)

Lymphomas that occur in patients with human immunodeficiency virus (HIV) infection are predominantly of B-cell origin and subsets show evidence for Epstein-Barr virus (EBV) infection or chromosomal translocations in the c-myc locus. The only subset of lymphoma clearly related to the immunodeficiency caused by HIV infection (similar to transplantation-associated lymphomas) is the EBV+ primary central nervous system lymphoma. The systemic AIDS-related lymphomas (ARLs) represent a complex set of disease processes histologically categorized as large cell or small non-cleaved (Burkitt's-like) lymphomas. Molecular analyses of the ARLs have demonstrated polyclonal lymphomas as likely early representatives of monoclonal immunoglobulin (Ig)-expressing B-cell lymphomas. Variable region analysis of lymphoma-associated Ig has shown evidence for extensive somatic mutation with little evidence for appropriate affinity maturation. These observations suggest that abnormal control of B-cell maturation in response to polyclonal antigenic stimulation may play a central role in the pathogenesis of ARL. The recent finding of clonal HIV integrated within macrophages in a subset of early lymphomas also provides evidence for abnormalities outside the B-cell compartment playing roles in this disease. Overall, ARLs generally appear to be outgrowths of antigen-driven B-cells with significant growth control influence provided by abnormal T-cell and antigen-presenting cell processes.
Anti-Diabetic Efficacy and Impact on Amino Acid Metabolism of GRA1, a Novel Small-Molecule Glucagon Receptor Antagonist (2012)

Hyperglucagonemia is implicated in the pathophysiology of hyperglycemia. Antagonism of the glucagon receptor (GCGR) thus represents a potential approach to diabetes treatment. Herein we report the characterization of GRA1, a novel small-molecule GCGR antagonist that blocks glucagon binding to the human GCGR (hGCGR) and antagonizes glucagon-induced intracellular accumulation of cAMP with nanomolar potency. GRA1 inhibited glycogenolysis dose-dependently in primary human hepatocytes and in perfused liver from hGCGR mice, a transgenic line of mouse that expresses the hGCGR instead of the murine GCGR. When administered orally to hGCGR mice and rhesus monkeys, GRA1 blocked hyperglycemic responses to exogenous glucagon. In several murine models of diabetes, acute and chronic dosing with GRA1 significantly reduced blood glucose concentrations and moderately increased plasma glucagon and glucagon-like peptide-1. Combination of GRA1 with a dipeptidyl peptidase-4 inhibitor had an additive antihyperglycemic effect in diabetic mice. Hepatic gene-expression profiling in monkeys treated with GRA1 revealed down-regulation of numerous genes involved in amino acid catabolism, an effect that was paralleled by increased amino acid levels in the circulation. In summary, GRA1 is a potent glucagon receptor antagonist with strong antihyperglycemic efficacy in preclinical models and prominent effects on hepatic gene-expression related to amino acid metabolism.
Supplementary Figure Legends from Promoter Methylation Modulates Indoleamine 2,3-Dioxygenase 1 Induction by Activated T Cells in Human Breast Cancers (2023)

&lt;p&gt;Figure Legends for Supplementary Figures 1-6&lt;/p&gt;
Under a nonadherent state, bone marrow mesenchymal stem cells can be efficiently induced into functional islet-like cell clusters to normalize hyperglycemia in mice: a control study (2014)

Our studies demonstrate that nonadherent induction can greatly promote BMSCs to form pancreatic islet-like cell clusters, thereby improving the differentiation efficiency of BMSCs towards IPCs.
GLUCAGON IS A UNIQUE CARDIOVASCULAR AGENT WITH ANTI-OPIATE ACTIVITY (1985)

Naval Medical Research Institute, Bethesda, Maryland 20814–5055, Walter Reed Army Institute of Research, Washington, D.C., and the Uniformed Services University of the Health Sciences
A Package of Time-Shared Computer Programs for Patient Care (1977)

A collection of time-shared computer programs for patient care has been developed. It contains programs for clinical pharmacology to analyse dosage requirements of digitalis glycosides, kanamycin, gentamicin, streptomycin, cephaloridine, procainamide, lidocaine, and six inhalation anesthetics. Programs for cardiology analyse data from the cardiac catheter laboratory, from echocardiograms, and from systolic time intervals. Those for the pulmonary function laboratory analyse data of blood gases, spirometry, lung volumes, and diffusing capacity. Other programs compute endogneous creatinine clearance for adults and for newborn infants without requiring collection of the usual urine specimen, and others aid in decision analysis, application of Bayes' theorem, and in computing a fever index. The collection can be used over internationally accessible time-sharing facilities.
Seismic reflection surveys to assist nickel and gold exploration in the WA goldfields (2007)

SummaryIn August 2006 pilot high resolution 2D seismic surveys were carried out on Lake Lefroy near Kambalda in WA to provide a “proof-of-concept” for the use of surface reflection surveys for guiding exploration for nickel sulphide and gold in this area.The pilot survey demonstrated the basalt ultramafic boundary is usually a good reflector and mapped a number known and previously unknown faults and shears. A correlation was also noted between zones of reduced reflection and intrusive porphyries.
Endotoxin as a Marker for Water Quality (2022)

We suggest that BacterisK can be used as a convenient risk assessment tool to assess water quality where results are required quickly or access to laboratories is lacking.
Quantum Yield Switching of Fluorescence by Selectively Bridging Single and Double Bonds in Chalcones:  Involvement of Two Different Types of Conical Intersections (1999)

From the fluorescence properties of chalcones as a function of solvent polarity, and by the comparison to derivatives with donors and acceptors and with various selectively bridged bonds, it can be concluded that two emissive and two nonemissive states are needed to describe the fluorescence behavior. Three of these states are connected with bond twisting and lead to species with high or low dipole moment, two of them situated in the proximity of a conical intersection.
Neuronal Network Formation from Reprogrammed Early Postnatal Rat Cortical Glial Cells (2010)

In the subependymal zone and the dentate gyrus of the adult brain of rodents, neural stem cells with glial properties generate new neurons in a life-long process. The identification of glial progenitors outside the neurogenic niches, oligodendrocyte precursors in the healthy brain, and reactive astrocytes after cortical injury led to the idea of using these cells as endogenous cell source for neural repair in the cerebral cortex. Recently, our group showed that proliferating astroglia from the cerebral cortex can be reprogrammed into neurons capable of action potential firing by forced expression of neurogenic fate determinants but failed to develop synapses. Here, we describe a maturation profile of cultured reprogrammed NG2+ and glial fibrillary acidic protein+ glia cells of the postnatal rat cortex that ends with the establishment of a glutamatergic neuronal network. Within 3 weeks after viral expression of the transcription factor neurogenin 2 (Ngn2), glia-derived neurons exhibit network-driven, glutamate receptor-dependent oscillations in Ca(2+) and exhibit functional pre- and postsynaptic specialization. Interestingly, the Ngn2-instructed glutamatergic network also supports the maturation of a γ-aminobutyric acid (GABA)ergic input via GABA(A) receptors in a non-cell autonomous manner. The "proof-of-principle" results imply that a single transcription factor may be sufficient to instruct a neuronal network from a glia-like cell source.
Emission and excitation contributions to enhanced single molecule fluorescence by gold nanometric apertures (2008)

We detail the role of single nanometric apertures milled in a gold film to enhance the fluorescence emission of Alexa Fluor 647 molecules. Combining fluorescence correlation spectroscopy and lifetime measurements, we determine the respective contributions of excitation and emission in the observed enhanced fluorescence. We characterize a broad range of nanoaperture diameters from 80 to 310 nm, and highlight the link between the fluorescence enhancement and the local photonic density of states. These results are of great interest to increase the effectiveness of fluorescence-based single molecule detection and to understand the interaction between a quantum emitter and a nanometric metal structure.
Chronic oral infection with major periodontal bacteria Tannerella forsythia modulates systemic atherosclerosis risk factors and inflammatory markers (2015)

Tannerella forsythia is a Gram-negative anaerobic organism that inhabits the subgingival cavity and initiates connective tissue destruction and alveolar bone resorption in periodontal disease (PD). PD is a chronic immunoinflammatory disease and has been linked to several systemic diseases including atherosclerosis. This study evaluated the effects of a chronic oral infection with T. forsythia ATCC 43037 on the induction of PD, inflammatory markers and atherosclerosis risk factors in hyperlipidemic ApoE(null) mice. Mice were orally infected for 12 and 24 weeks prior to euthanasia. Bacterial colonization of the oral cavity and bacteremia was confirmed via isolation of genomic DNA from oral plaque and tissues. Oral infection elicited significantly elevated levels of serum IgG and IgM antibodies and alveolar bone resorption compared to control mice. Tannerella forsythia-infected mice had increased serum amyloid A, and significantly reduced serum nitric oxide when compared to controls. Tannerella forsythia chronic infection also significantly increased serum lipoproteins suggesting altered cholesterol metabolism and potential for aortic inflammation. Despite enhanced acute phase reactants and altered lipid profiles, T. forsythia infection was associated with decreased aortic plaque. This study investigates the potential of a known periodontal bacterial pathogen found in atherosclerotic plaque in humans to accelerate atherosclerosis in hyperlipdemic mice.
Abstract 1717: Post-Procedural Incomplete Stent Apposition after Implantation of Everolimus-Eluting or Paclitaxel-Eluting Stents: Insights from the Randomized SPIRIT III Trial (2007)

Background : We investigated the morphometric changes of post-procedural incomplete stent apposition (ISA) after implantation of Everolimus-eluting cobalt-chromium alloy XIENCE™ V stents (EES) and Paclitaxel-eluting Taxus ™ stents (PES). Methods : Data were obtained from the SPIRIT III trial (2:1 randomized, multicenter trial comparing EES to PES in de novo native coronary artery lesions). Serial IVUS imaging was performed post-intervention and at 8 months follow-up. ISA was defined as separation of at least 1 stent strut from the vessel wall with evidence of blood speckle behind the strut. The following parameters were obtained from the IVUS analysis: ISA area at the maximum ISA (max ISA) site, ISA angle (angle of the ISA arc at the max ISA site), ISA depth (length between the stent strut and the vessel wall at the max ISA site), and ISA length (longitudinal length of the ISA); vessel, stent, lumen, peri-stent plaque, and neointimal hyperplasia area at the ISA site. Results : At baseline, there were 34 ISA sites in 29 EES (18 at the proximal edge, 9 at the distal edge, and 7 within the stent body), and 16 ISA sites in 11 PES (4 at the proximal edge, 5 at the distal edge, and 7 within the stent body). ISA area, angle, depth, and length decreased between post-procedure and follow-up period in both groups (Table ). Vessel and peri-stent plaque area increased in PES, whereas no changes were observed in EES. There was no difference in the incidence of either persistent or resolved ISA between the 2 groups (p=0.32). Neither stent thrombosis nor in-stent restenosis occurred in the patients with post-procedural ISA over a period of 12 months. Conclusion : This IVUS analysis suggests different vessel responses at the site of post-procedural ISA between EES and PES, but no clinical consequences. Longer term follow-up with larger cohorts is warranted to further validate the clinical implications of ISA with drug-eluting stents.
An exact ray model for oblique incident light on planar films (2020)

During recent years, ray tracing has frequently been used to study the absorption characteristics of structured solar cells. However, wave properties such as absorption enhancement due to resonances in optically thin solar films, cannot be explained by pure classical ray models. Here we present an exact three-dimensional ray model for oblique incidence of a plane electromagnetic wave on a thin film and show that the resonant structure of the absorption cross section calculated from our ray model is identical to exact calculations by electromagnetic wave theory. Both parallel and perpendicular polarized light are described exactly by the ray model presented. We validate the resonant structure of the absorption cross section of our ray model by an experimentally realized layered film, where we obtain perfect agreement between experiment and theory. We demonstrate further that for a beam with a finite beam waist, in accordance with Beer-Lambert's law, absorption occurs along the path of the beam, while, in the case of a plane wave incident on an optically thin film, and contrary to Beer-Lambert's law, absorption occurs along the axis perpendicular to the surface of the film.
Proteome‐wide analysis of nonsynonymous single‐nucleotide variations in active sites of human proteins (2013)

An enzyme's active site is essential to normal protein activity such that any disruptions at this site may lead to dysfunction and disease. Nonsynonymous single-nucleotide variations (nsSNVs), which alter the amino acid sequence, are one type of disruption that can alter the active site. When this occurs, it is assumed that enzyme activity will vary because of the criticality of the site to normal protein function. We integrate nsSNV data and active site annotations from curated resources to identify all active-site-impacting nsSNVs in the human genome and search for all pathways observed to be associated with this data set to assess the likely consequences. We find that there are 934 unique nsSNVs that occur at the active sites of 559 proteins. Analysis of the nsSNV data shows an over-representation of arginine and an under-representation of cysteine, phenylalanine and tyrosine when comparing the list of nsSNV-impacted active site residues with the list of all possible proteomic active site residues, implying a potential bias for or against variation of these residues at the active site. Clustering analysis shows an abundance of hydrolases and transferases. Pathway and functional analysis shows several pathways over- or under-represented in the data set, with the most significantly affected pathways involved in carbohydrate metabolism. We provide a table of 32 variation-substrate/product pairs that can be used in targeted metabolomics experiments to assay the effects of specific variations. In addition, we report the significant prevalence of aspartic acid to histidine variation in eight proteins associated with nine diseases including glycogen storage diseases, lacrimo-auriculo-dento-digital syndrome, Parkinson's disease and several cancers.
Few-mode EDFA Supporting 5 Spatial Modes with Reconfigurable Differential Modal Gain Control (2013)

We experimentally demonstrate a FM-EDFA supporting 5 spatial modes with reconfigurable differential gain control and excellent gain-flatness obtained through mode-selective bi-directional pumping of a custom fiber with a radially-profiled erbium dopant distribution
The molecular basis of fibronectin‐mediated bacterial adherence to host cells (2004)

Many pathogenic Gram-positive bacteria produce cell wall-anchored proteins that bind to components of the extracellular matrix (ECM) of the host. These bacterial MSCRAMMs (microbial surface components recognizing adhesive matrix molecules) are thought to play a critical role in infection. One group of MSCRAMMs, produced by staphylococci and streptococci, targets fibronectin (Fn, a glycoprotein found in the ECM and body fluids of vertebrates) using repeats in the C-terminal region of the bacterial protein. These bacterial Fn-binding proteins (FnBPs) mediate adhesion to host tissue and bacterial uptake into non-phagocytic host cells. Recent studies on interactions between the host and bacterial proteins at the residue-specific level and on the mechanism of host cell invasion are providing a much clearer picture of these processes.
Chemical compositions in convective and nonconvective regions during PEM‐Tropics B (2002)

Four DC‐8 flights during Pacific Exploratory Mission (PEM)‐Tropics B are analyzed in terms of geographical location, meteorological conditions, and chemical compositions. The meteorological conditions are determined using the meteorological analysis of the Florida State University Global Spectral Model, trajectory analysis, and in situ measurements. Typical undisturbed meteorological conditions are found over the northeastern Pacific between 30° and 15°N and southeast of Hawaiian Islands during flights 5 and 6. Disturbed meteorological conditions are found over western and central equatorial Pacific especially over the Intertropical Convergence Zone (ITCZ) and the South Pacific Convergence Zone (SPCZ) during flights 7 and 10. Comparison of the chemical concentrations between disturbed and undisturbed regions revealed remarkable differences. The distribution of the chemical constituents is found to be closely linked to the atmospheric state. Large amounts of pollutants are found to be capped at lower levels due to climatologically persistent trade wind inversion in the undisturbed regions. Transient convective systems are found to be the primary entity that destroys the inversion, causing the vertical transport of the chemicals. The disturbed regions displayed more homogeneous vertical distributions of chemicals resulting from low‐level convergence and associated convection. Trajectory analysis showed that in undisturbed regions centered north of Hawaiian Islands, and in disturbed regions, the interaction between lower‐level easterlies and upper‐level westerlies plays a significant role on atmospheric chemistry over these regions.
Cell composition and expansion strategy can reduce the beneficial effect of AKT-inhibition on functionality of CD8+ T cells (2020)

AKT-inhibition is a promising approach to improve T cell therapies; however, its effect on CD4<sup>+</sup> T cells is insufficiently explored. Previously, we and others showed that AKT-inhibition during ex vivo CD8<sup>+</sup> T cell expansion facilitates the generation of polyfunctional T cells with stem cell memory-like traits. However, most therapeutic T cell products are generated from lymphocytes, containing CD4<sup>+</sup> T cells that can affect CD8<sup>+</sup> T cells dependent on the Th-subset. Here, we investigated the effect of AKT-inhibition on CD4<sup>+</sup> T cells, during separate as well as total T cell expansions. Interestingly, ex vivo AKT-inhibition preserved the early memory phenotype of CD4<sup>+</sup> T cells based on higher CD62L, CXCR4 and CCR7 expression. However, in the presence of AKT-inhibition, Th-differentiation was skewed toward more Th2-associated at the expense of Th1-associated cells. Importantly, the favorable effect of AKT-inhibition on the functionality of CD8<sup>+</sup> T cells drastically diminished in the presence of CD4<sup>+</sup> T cells. Moreover, also the expansion method influenced the effect of AKT-inhibition on CD8<sup>+</sup> T cells. These findings indicate that the effect of AKT-inhibition on CD8<sup>+</sup> T cells is dependent on cell composition and expansion strategy, where presence of CD4<sup>+</sup> T cells as well as polyclonal stimulation impede the favorable effect of AKT-inhibition.
LTE - The UMTS Long Term Evolution: From Theory to Practice (2011)

Where this book is exceptional is that the reader will not just learn how LTE works but why it works Adrian Scrase, ETSI Vice-President, International Partnership Projects LTE - The UMTS Long Term Evolution: From Theory to Practice provides the reader with a comprehensive system-level understanding of LTE, built on explanations of the theories which underlie it. The book is the product of a collaborative effort of key experts representing a wide range of companies actively participating in the development of LTE, as well as academia. This gives the book a broad, balanced and reliable perspective on this important technology. Lucid yet thorough, the book devotes particular effort to explaining the theoretical concepts in an accessible way, while retaining scientific rigour. It highlights practical implications and draws comparisons with the well-known WCDMA/HSPA standards. The authors not only pay special attention to the physical layer, giving insight into the fundamental concepts of OFDMA, SC-FDMA and MIMO, but also cover the higher protocol layers and system architecture to enable the reader to gain an overall understanding of the system. Key Features: Draws on the breadth of experience of a wide range of key experts from both industry and academia, giving the book a balanced and broad perspective on LTE Provides a detailed description and analysis of the complete LTE system, especially the ground-breaking new physical layer Offers a solid treatment of the underlying advances in fundamental communications and information theory on which LTE is based Addresses practical issues and implementation challenges related to the deployment of LTE as a cellular system Includes an accompanying website containing a complete list of acronyms related to LTE, with a brief description of each (http://www.wiley.com/go/sesia_theumts) This book is an invaluable reference for all research and development engineers involved in LTE implementation, as well as graduate and PhD students in wireless communications. Network operators, service providers and R&D managers will also find this book insightful.
Photoaffinity labeling of the Ah receptor. (1986)

A series of halodibenzo-p-dioxins with the photolabile aryl azide functional group were synthesized and screened as potential photoaffinity labels for the Ah receptor, and 2-azido-3-iodo-7,8-dibromodibenzo-p-dioxin was selected for radiosynthesis with 125I (specific activity 2176 Ci/mmol, equilibrium dissociation constant, KD = 0.76 nM). Following incubation of this 125I-labeled photoaffinity ligand with the protamine sulfate-precipitated fraction of C57BL/6J mouse liver cytosol, and irradiation with long wavelength ultraviolet light, the radiolabeled macromolecules were precipitated with acetone and analyzed by denaturing gel electrophoresis and autoradiography. Among the labeled products, two peptides with apparent molecular masses of 95,000 and 70,000 daltons had the following properties: 1) they were selectively labeled at low ligand concentrations; 2) they were labeled in approximately a 1:1 ratio; 3) co-incubation with receptor agonists inhibited the photoaffinity labeling of both peptides to a similar extent, and structure activity relationship for inhibition of labeling by these agonists corresponded to that for their binding affinity to the Ah receptor; 4) upon nondenaturing chromatographic separation of photoaffinity labeled cytosol on high performance liquid chromatography size exclusion and anion exchange columns, the 95- and 70-kDa peptides coelute; 5) the migration of these peptides upon denaturing electrophoresis is the same in the presence or absence of a thiol reducing agent; and 6) proteolysis of the 95- and 70-kDa peptides produces a similar pattern of cleavage peptides. The simplest structure of the Ah receptor in mouse liver cytosol, appears to be a dimer composed of two noncovalently linked subunits of apparent molecular masses of 95 and 70 kDa, which have homologous structure and similar ligand binding sites, but other possibilities are discussed.