gebhart/patrepeval huggingface dataset:
HOSPITAL-ACQUIRED PNEUMONIA (1989)

A total of 1,001 consecutive episodes of nosocomial pneumonia in 901 patients was identified by routine surveillance at the University of Virginia Medical Center between 1979 and 1983 (8.6 episodes/1,000 admissions). When only initial episodes were examined, 890 patients comprised the study sample. The overall case fatality rate was 30%. Stepwise logistic regression indicated that time from admission to pneumonia (p = 0.0006), age (p less than 0.0001), prior use of mechanical ventilation (p = 0.0032), and neoplastic disease (p = 0.0062) were associated with mortality. Multiple regression analysis indicated that the factors associated with increased length of hospitalization included posttracheostomy status (p = 0.0001), prior mechanical ventilation (p = 0.0001), immunosuppressive or leukopenic status (p = 0.0009), nasogastric intubation (p = 0.0003), and prior bacteremia (p = 0.0127). A sampled, individually matched cohort study (n = 74 pairs) was conducted to determine the proportion of mortality in cases that was attributable to infections (33%) and to determine excess hospital stay (seven days) among the patients with nosocomial pneumonia. Excess stay was statistically significant (p less than 0.0001), but proportional mortality was only marginally significant (p = 0.0892). Our findings suggest that nosocomial pneumonia accounts for approximately 33% of the crude mortality and contributes significantly to the economic burden associated with prolonged hospitalization.
Identification of receptor-binding residues in the inflammatory complement protein C5a by site-directed mutagenesis. (1989)

C5a is an inflammatory mediator potentially involved in a number of diseases. To help define which of its 74 residues are important for receptor binding and response triggering, changes in the amino acid sequence of C5a were introduced by site-directed mutagenesis. Synthetic C5a-encoding genes incorporating point mutations were expressed in Escherichia coli, and the mutant proteins were purified to homogeneity. Modifications of the C5a molecule causing parallel reductions in binding to polymorphonuclear leukocyte membranes and in stimulation of polymorphonuclear leukocyte locomotion (chemokinesis) suggest that carboxyl-terminal residues Lys-68, Leu-72, and Arg-74 interact with the receptor. Substitutions in the disulfide-linked core of C5a revealed involvement of Arg-40 or nearby residues, because potency losses were associated with only localized conformational changes as detected by NMR. Surprisingly, a substitution at core residue Ala-26, which did not alter C5a core structure, appeared from NMR results to reduce potency by causing a long-distance conformational change centered on residue His-15. Thus, at least three discontinuous regions of the C5a molecule appear to act in concert to achieve full potency.
Quantitative Determination of Proteins by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTQuantitative Determination of Proteins by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass SpectrometryRandall W. Nelson, Matthew A. McLean, and T. William. HutchensCite this: Anal. Chem. 1994, 66, 9, 1408–1415Publication Date (Print):April 1, 1994Publication History Published online1 May 2002Published inissue 1 April 1994https://pubs.acs.org/doi/10.1021/ac00081a008https://doi.org/10.1021/ac00081a008research-articleACS PublicationsRequest reuse permissionsArticle Views356Altmetric-Citations114LEARN 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
Influence of the Zn(II) Cofactor on the Refolding of Bovine Carbonic Anhydrase after Denaturation with Sodium Dodecyl Sulfate (2004)

This paper uses capillary electrophoresis to follow a globular metalloprotein--bovine carbonic anhydrase II (BCA, EC 4.2.1.1)--on unfolding upon treatment with sodium dodecyl sulfate (SDS) and refolding upon removal of SDS, both in the presence and the absence of its Zn(II) cofactor. This research demonstrates that the Zn(II) cofactor is not required for refolding into a nativelike conformation, does not remain associated with the unfolded protein, and does not significantly change the rate of refolding. The presence of the Zn(II) cofactor, however, does increase the total amount of recovered protein by a factor of 2. Capillary electrophoresis could distinguish between native and denatured protein, based on the difference in electrophoretic mobility between the native protein and the aggregate of denatured protein and SDS. In addition, the active site was probed by observing binding of BCA to a charged arylsulfonamide using affinity capillary electrophoresis. These studies provide a foundation for future physical-organic studies using BCA as a model to examine interactions between proteins and SDS.
The inhibition of gamma-secretase as a therapeutic approach to Alzheimer's disease (2004)

Alzheimer's disease is a dementing neurodegenerative disorder for which there is no effective treatment at present. Genetic and biological studies provide evidence that the production and deposition of amyloid-beta peptides (Abeta contribute to the etiology of Alzheimer's disease. gamma-Secretase is the pivotal enzyme in generating the C terminus of Abeta which determines its aggregability and speed of deposition. Drugs that regulate the production of Abeta by inhibiting gamma-secretase activity could provide an effective therapy for Alzheimer's disease, although recent studies suggest that gamma-secretase plays important roles in cellular signaling. This review focuses on studies of the gamma-secretase biology and provides the direction for developing effective and selective gamma-secretase inhibitors as drugs for the treatment of Alzheimer's disease.
Structure of the variant glycoproteins and surface coat of Trypanosoma brucei (1984)

The pathogenic African trypanosomes have a unique mechanism for antigenic variation. Each cell is covered by a surface coat consisting of about seven million essentially identical glycoprotein molecules drawn from a large repertoire of variants, each encoded by an individual gene. Amino acid sequence variation extends throughout the molecule but reduces from the amino terminus to the carboxy terminus, where certain features, especially the grouping of cysteine residues, are quite conserved. The range of diversity within the thousand or so variant glycoprotein genes that exist in each cell is large. New variants may arise instantaneously by segmental gene conversion. Variant surface glycoproteins are synthesized with amino terminal signal sequences and hydrophobic carboxy terminal tails. The tails are extraordinarily conserved. After synthesis, they are replaced by a complex glycolipid structure in which myristic (dodecanoic) acid serves to anchor the polypeptide to the surface membrane. Enzymic cleavage of myristic acid releases variant glycoproteins from the surface coat.
Improved High-Efficiency Organic Solar Cells via Incorporation of a Conjugated Polyelectrolyte Interlayer (2011)

The power conversion efficiencies of bulk heterojunction (BHJ) solar cells can be increased from 5 to 6.5% by incorporating an ultrathin conjugated polyelectrolyte (CPE) layer between the active layer and the metal cathode. Poly[N-9''-heptadecanyl-2,7-carbazole-alt-5,5-(4',7'-di-2-thienyl-2',1',3'-benzothiadiazole)] (PCDTBT) and [6,6]-phenyl C(71) butyric acid methyl ester (PC(71)BM) were chosen for the photoactive layer. CPEs with cationic polythiophenes, in both homopolymer and block copolymer configurations, were used to improve the electronic characteristics. The significant improvement in device performance and the simplicity of fabrication by solution processing suggest a promising and practical pathway for improving polymer solar cells with high efficiencies.
Interaction of Estrogenic Chemicals and Phytoestrogens with Estrogen Receptor β (1998)

The rat, mouse and human estrogen receptor (ER) exists as two subtypes, ER alpha and ER beta, which differ in the C-terminal ligand-binding domain and in the N-terminal transactivation domain. In this study, we investigated the estrogenic activity of environmental chemicals and phytoestrogens in competition binding assays with ER alpha or ER beta protein, and in a transient gene expression assay using cells in which an acute estrogenic response is created by cotransfecting cultures with recombinant human ER alpha or ER beta complementary DNA (cDNA) in the presence of an estrogen-dependent reporter plasmid. Saturation ligand-binding analysis of human ER alpha and ER beta protein revealed a single binding component for [3H]-17beta-estradiol (E2) with high affinity [dissociation constant (Kd) = 0.05 - 0.1 nM]. All environmental estrogenic chemicals [polychlorinated hydroxybiphenyls, dichlorodiphenyltrichloroethane (DDT) and derivatives, alkylphenols, bisphenol A, methoxychlor and chlordecone] compete with E2 for binding to both ER subtypes with a similar preference and degree. In most instances the relative binding affinities (RBA) are at least 1000-fold lower than that of E2. Some phytoestrogens such as coumestrol, genistein, apigenin, naringenin, and kaempferol compete stronger with E2 for binding to ER beta than to ER alpha. Estrogenic chemicals, as for instance nonylphenol, bisphenol A, o, p'-DDT and 2',4',6'-trichloro-4-biphenylol stimulate the transcriptional activity of ER alpha and ER beta at concentrations of 100-1000 nM. Phytoestrogens, including genistein, coumestrol and zearalenone stimulate the transcriptional activity of both ER subtypes at concentrations of 1-10 nM. The ranking of the estrogenic potency of phytoestrogens for both ER subtypes in the transactivation assay is different; that is, E2 >> zearalenone = coumestrol > genistein > daidzein > apigenin = phloretin > biochanin A = kaempferol = naringenin > formononetin = ipriflavone = quercetin = chrysin for ER alpha and E2 >> genistein = coumestrol > zearalenone > daidzein > biochanin A = apigenin = kaempferol = naringenin > phloretin = quercetin = ipriflavone = formononetin = chrysin for ER beta. Antiestrogenic activity of the phytoestrogens could not be detected, except for zearalenone which is a full agonist for ER alpha and a mixed agonist-antagonist for ER beta. In summary, while the estrogenic potency of industrial-derived estrogenic chemicals is very limited, the estrogenic potency of phytoestrogens is significant, especially for ER beta, and they may trigger many of the biological responses that are evoked by the physiological estrogens.
New Aminoimidazoles as β-Secretase (BACE-1) Inhibitors Showing Amyloid-β (Aβ) Lowering in Brain (2012)

Amino-2H-imidazoles are described as a new class of BACE-1 inhibitors for the treatment of Alzheimer's disease. Synthetic methods, crystal structures, and structure-activity relationships for target activity, permeability, and hERG activity are reported and discussed. Compound (S)-1m was one of the most promising compounds in this report, with high potency in the cellular assay and a good overall profile. When guinea pigs were treated with compound (S)-1m, a concentration and time dependent decrease in Aβ40 and Aβ42 levels in plasma, brain, and CSF was observed. The maximum reduction of brain Aβ was 40-50%, 1.5 h after oral dosing (100 μmol/kg). The results presented highlight the potential of this new class of BACE-1 inhibitors with good target potency and with low effect on hERG, in combination with a fair CNS exposure in vivo.
Cytokine response by human monocytes to Clostridium difficile toxin A and toxin B (1991)

Clostridium difficile toxins A and B isolated from strain VPI 10463 were tested for induction of cytokine release by human monocytes. Toxin B at 10(-12) M activated human monocytes as measured by release of interleukin-1 (IL-1), tumor necrosis factor (TNF), or IL-6. These effects of toxin B were heat labile (51 degrees C, 30 min). Toxin B was as effective as bacterial lipopolysaccharides in inducing IL-1 beta but less effective in inducing TNF or IL-6. Toxin B and lipopolysaccharides were synergistic in induction of IL-1 beta, TNF, and IL-6. The toxin A preparation used was 1,000-fold less active than toxin B. Apart from the difference in activity, the two toxins showed identical patterns of reaction and there was no synergism between them. A short pulse with toxin B was sufficient to trigger IL-1 release. Toxin B was also extremely toxic for monocytes. The toxicity and the induced proinflammatory monokines (IL-1 and TNF) may contribute to the pathogenic mechanisms of C. difficile infection and pseudomembranous colitis.
Prospective Analysis of Adoptive TIL Therapy in Patients with Metastatic Melanoma: Response, Impact of Anti-CTLA4, and Biomarkers to Predict Clinical Outcome (2018)

<b>Purpose:</b> Adoptive cell therapy (ACT) using tumor-infiltrating lymphocytes (TIL) has consistently demonstrated clinical efficacy in metastatic melanoma. Recent widespread use of checkpoint blockade has shifted the treatment landscape, raising questions regarding impact of these therapies on response to TIL and appropriate immunotherapy sequence.<b>Patients and Methods:</b> Seventy-four metastatic melanoma patients were treated with autologous TIL and evaluated for clinical response according to irRC, overall survival, and progression-free survival. Immunologic factors associated with response were also evaluated.<b>Results:</b> Best overall response for the entire cohort was 42%; 47% in 43 checkpoint-naïve patients, 38% when patients were exposed to anti-CTLA4 alone (21 patients) and 33% if also exposed to anti-PD1 (9 patients) prior to TIL ACT. Median overall survival was 17.3 months; 24.6 months in CTLA4-naïve patients and 8.6 months in patients with prior CTLA4 blockade. The latter patients were infused with fewer TIL and experienced a shorter duration of response. Infusion of higher numbers of TIL with CD8 predominance and expression of BTLA correlated with improved response in anti-CTLA4 naïve patients, but not in anti-CTLA4 refractory patients. Baseline serum levels of IL9 predicted response to TIL ACT, while TIL persistence, tumor recognition, and mutation burden did not correlate with outcome.<b>Conclusions:</b> This study demonstrates the deleterious effects of prior exposure to anti-CTLA4 on TIL ACT response and shows that baseline IL9 levels can potentially serve as a predictive tool to select the appropriate sequence of immunotherapies. <i>Clin Cancer Res; 24(18); 4416-28. ©2018 AACR</i>.
Directly coupled multiple resonator wide-band microstrip antennas (1985)

Three new configurations for increasing the impedance bandwidth of the microstrip patch antennas are described. In these configurations, additional resonators are directly coupled through short sections of microstrip line to the radiating edges, nonradiating edges, and all the four edges of the rectangular patch antennas, respectively. Green's function approach and segmentation method are used for the analysis. The experimental results are in reasonable agreement with the analysis and impedance bandwidths of 548 MHz, 605 MHz, and 810 MHz are obtained for these three configurations, respectively in <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">S</tex> -band (substrate thickness = 0.318 cm and <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">\epsilon_{r} = 2.55</tex> ). The variation in the radiation pattern over this impedance bandwidth is discussed.
Exploiting web search to generate synonyms for entities (2009)

Tasks recognizing named entities such as products, people names, or locations from documents have recently received significant attention in the literature. Many solutions to these tasks assume the existence of reference entity tables. An important challenge that needs to be addressed in the entity extraction task is that of ascertaining whether or not a candidate string approximately matches with a named entity in a given reference table.
Randomized, Controlled Crossover Trial of Dronabinol, 2.5 mg, for Agitation in 2 Patients With Dementia (2011)

Walther, Sebastian MD; Schüpbach, Brigitte MD; Seifritz, Erich MD; Homan, Philipp MD; Strik, Werner MD Author Information
Intervening sequences increase efficiency of RNA 3' processing and accumulation of cytoplasmic RNA (1990)

Two expression vectors were constructed that differ only in the presence (+) or absence (-) of an intervening sequence (IVS) in their 5'-untranslated leaders. Transient transfection into four mammalian cell lines resulted in higher levels of the indicator protein (CAT) from the IVS(+) vector (6 to 50-fold). Cytoplasmic RNA concentrations in 293s and HeLa cell lines corresponded directly to resultant protein levels; measurements in 293s cells of transcription initiation and elongation, steady-state total nuclear RNA, and cytoplasmic RNA stability, were equivalent for the two vectors. Surprisingly, the amount of poly(A)+ nuclear RNA was greater from the IVS(+) vector. Since this difference matches the ratio seen with polyadenylated cytoplasmic RNA, our results imply that splicing is coupled to a polyadenylation/transport pathway.
Automatic Detection of Seizure ONSET in Pediatric EEG (2012)

This paper proposes a method for automatic detection of seizure onset. Two statistical features: skewness and kurtosis with a wavelet based feature: normalized coefficient of variation (NCOV) were extracted from the data. The classification between normal and seizure EEGs was performed using simple linear classifier. The performance of the algorithm was tested on the 10 patient's data of CHB-MIT scalp EEG database. The data consisted of 55 seizures of 10646 seconds duration. The results show a mean latency of 3.2 seconds, a mean false detection rate of 1.1 false detections per hour and 100% sensitivity.
Fighting gender-based violence in South Sudan (2007)

Decades of under-development and conflict have left SouthSudanese women – in the words of the late John Garang– “the poorest of the poor and the marginalised of themarginalised.” It is in this context that violence againstwomen and girls breeds.
Identification of new volatile thiols in the aroma ofVitis vinifera L. var. Sauvignon blanc wines (1998)

Three new flavour-active mercapto-alcohols have been identified in Sauvignon blanc wines: 4-mercapto-4-methylpentan-2-ol, 3-mercaptohexan-1-ol and 3-mercapto-3-methylbutan-1-ol. The first two have a perception threshold of the order of 60 ng/l in an aqueous alcohol solution and their respective odours are reminiscent of citrus zest and grapefruit. The perception threshold of 3-mercapto-3-methylbutan-1-ol, with its odour of cooked leeks, is higher (1500 ng/l in the same solution). These three compounds may contribute towards the typical aroma of Sauvignon blanc wines. © 1998 John Wiley & Sons, Ltd.
Evaluation of Near-surface Converted-mode Seismic Reflection Imaging Potential (2004)

The potential for improving near-surface characterization through converted-mode (P-S and S-P) seismic reflection imaging was tested experimentally and assessed numerically. High-resolution nine-component reflection data were acquired over a geologic sequence type (flat-lying unsaturated and saturated overburden materials above consolidated units) commonly encountered during geotechnical investigations. Interface energy partitioning analyses, event predictions, and elastic-wave modeling were conducted using parameters derived from field data. Common-mode (P-P and S-S) reflections from known lithologic boundaries were observed in field data; however, predicted converted-mode events were not. Modeling demonstrated that in theory, potential benefits of converted-mode reflection imaging exist for the tested subsurface conditions, but that such benefits were unable to be practically realized using field measurements, due to the low amplitudes of converted-mode reflections and the detrimental affects of random and coherent noise modes. This study shows and explains why it is not practical to use converted-mode reflection imaging for improving characterization under such subsurface conditions. The developed analysis methods can be applied to investigate converted-wave imaging potential under different conditions, and to identify near-surface media situations that may yield converted-mode reflections with amplitudes comparable (at
Role of Integrin αvβ3 in Vascular Biology (1998)

Introduction A defining characteristic of vascular cells is their adhesive status. The predominant cells of the blood vessel, endothelial cells (EC) and smooth muscle cells (SMC), are normally adherent but can be induced to migrate in response to vascular injury and angiogenic stimuli. The circulating blood cells are ordinarily nonadhesive but can rapidly acquire an adhesive phenotype in response to physiologic and pathophysiologic stimuli. As prime examples, platelets become adherent to the subendothelial matrix and to one another during thrombus formation, and leukocytes first adhere to EC and then transmigrate during the inflammatory response. At a molecular level, the adhesive properties of the vascular cells are determined by the adhesion receptors on their cell-surface and the functional state of these receptors. To match the variety of requisite cellular adhesive reactions, the repertoire of adhesion receptors expressed by vascular cells is broad. Multiple representatives of the immunoglobulin-like, the selectin, the cadherin and the integrin families of adhesion receptors are present on and have been implicated in the functions of the vascular cells. The importance of these adhesion receptors in vascular cell function is underscored by the severe pathogenetic consequences of their congenital deficiencies, such as in Glanzmann’s thrombasthenia, LAD (Leucocyte Adhesion deficiency) I and LAD II (1-3). The integrins are the largest and most broadly distributed of the families of cellular adhesion receptors. Of the integrins, αvβ3, originally identified as the vitronectin receptor, is particularly widely distributed. It is expressed at variable density on many types of vascular cells. Obviously, the adhesive properties of a cell are determined by its full repertoire of adhesion receptors. As an example, the adhesion of EC to fibrinogen/fibrin is mediated by no fewer than five receptors. Nevertheless, it is possible to dissect out the contributions of individual adhesion receptors, and αvβ3 has been implicated in many functional responses of vascular cells. This review focusses upon the role of αvβ3 in vascular cell biology. Other contributions of this multifunctional receptor, such as its role in neoplastic growth and invasion and in osteoclast-mediated bone resorption, are beyond the scope of this article and have been reviewed elsewhere (4, 5).