gebhart/patrepeval huggingface dataset:
The Pathogenesis of Ventilator-Associated Pneumonia: Its Relevance to Developing Effective Strategies for Prevention (2005)

Ventilator-associated pneumonia (VAP) is the most common nosocomial infection in the intensive care unit and is associated with major morbidity and attributable mortality. Strategies to prevent VAP are likely to be successful only if based upon a sound understanding of pathogenesis and epidemiology. The major route for acquiring endemic VAP is oropharyngeal colonization by the endogenous flora or by pathogens acquired exogenously from the intensive care unit environment, especially the hands or apparel of health-care workers, contaminated respiratory equipment, hospital water, or air. The stomach represents a potential site of secondary colonization and reservoir of nosocomial Gram-negative bacilli. Endotracheal-tube biofilm formation may play a contributory role in sustaining tracheal colonization and also have an important role in late-onset VAP caused by resistant organisms. Aspiration of microbe-laden oropharyngeal, gastric, or tracheal secretions around the cuffed endotracheal tube into the normally sterile lower respiratory tract results in most cases of endemic VAP. In contrast, epidemic VAP is most often caused by contamination of respiratory therapy equipment, bronchoscopes, medical aerosols, water (eg, Legionella) or air (eg, Aspergillus or the severe acute respiratory syndrome virus). Strategies to eradicate oropharyngeal and/or intestinal microbial colonization, such as with chlorhexidine oral care, prophylactic aerosolization of antimicrobials, selective aerodigestive mucosal antimicrobial decontamination, or the use of sucralfate rather than H(2) antagonists for stress ulcer prophylaxis, and measures to prevent aspiration, such as semirecumbent positioning or continuous subglottic suctioning, have all been shown to reduce the risk of VAP. Measures to prevent epidemic VAP include rigorous disinfection of respiratory equipment and bronchoscopes, and infection-control measures to prevent contamination of medical aerosols. Hospital water should be Legionella-free, and high-risk patients, especially those with prolonged granulocytopenia or organ transplants, should be cared for in hospital units with high-efficiency-particulate-arrestor (HEPA) filtered air. Routine surveillance of VAP, to track endemic VAPs and facilitate early detection of outbreaks, is mandatory.
Combining multi-domain statistical machine translation models using automatic classifiers (2010)

This paper presents a set of experiments on Domain Adaptation of Statistical Machine Translation systems. The experiments focus on Chinese-English and two domain-specific&#13;\ncorpora. The paper presents a novel approach for combining multiple domain-trained translation models to achieve improved translation quality for both domain-specific as well as combined sets of sentences. We train a statistical&#13;\nclassifier to classify sentences according to the appropriate domain and utilize the corresponding domain-specific MT models to translate them. Experimental results show that the method achieves a statistically significant&#13;\nabsolute improvement of 1.58 BLEU (2.86% relative improvement) score over a translation model trained on combined data, and considerable improvements over a model using multiple decoding paths of the Moses decoder, for the combined domain test set. Furthermore, even for domain-specific test sets, our approach works almost as well as dedicated domain-specific models and perfect classification.
Soil Fertility and Fertilizers (1966)

Soil fertility and fertilizers , Soil fertility and fertilizers , مرکز فناوری اطلاعات و اطلاع رسانی کشاورزی
Proximal Endovascular Flow Blockage for Cerebral Protection During Carotid Artery Stenting:Results From a Prospective Multicenter Registry (2005)

Cerebral protection with proximal endovascular blood flow blockage during CAS is feasible, with a high procedural success rate.
Somatic Mutation Profiles of MSI and MSS Colorectal Cancer Identified by Whole Exome Next Generation Sequencing and Bioinformatics Analysis (2010)

We conclude that with deep sequencing of tumor exomes one may be able to predict the microsatellite status of CRC and in addition identify potentially clinically relevant mutations.
Formation of dTDP-Rhamnose Is Essential for Growth of Mycobacteria (2002)

It was determined that the dTDP-rhamnose synthesis gene, rmlD, could be inactivated in Mycobacterium smegmatis only in the presence of a rescue plasmid carrying functional rmlD. Hence, dTDP-rhamnose biosynthesis is essential for the growth of mycobacteria and the targeting of dTDP-rhamnose synthesis for new tuberculosis drugs is supported.
Arginine Supplementation Improves Histone and Acute‐Phase Protein Synthesis During Gram‐Negative Sepsis in the Rat (1991)

Mechanisms of nutrient alteration of hepatic protein synthesis during sepsis are unclear. In vitro, arginine downregulates endotoxin-stimulated hepatocyte protein synthesis but in vivo effects are unknown. This study evaluated the effects of supplemental arginine or glycine on fibrinogen (acute-phase protein), histone, albumin, and liver protein synthesis after Gram-negative sepsis in the rat. Adult rats (225 g, n=36) were randomized to receive isonitrogenous isocaloric total parenteral nutrition supplemented with 264 mg of N per kilogram per day as either arginine or glycine. On day 5, each group was further randomized to control or sepsis. Sepsis was induced by injection of 8 x 10(7) Escherichia coli per 100 g body weight, and then a continuous infusion of [1-14C] leucine was started. The rats were sacrificed 4 hours later. The fractional protein synthesis rates (percent per day) of histone, fibrinogen, albumin, and liver were determined. Supplemental arginine led to significantly increased histone (p < 0.05, analysis of variance) and fibrinogen (p < 0.01, analysis of variance) synthesis in the septic rats compared with all other groups. Histone and albumin synthesis were also significantly increased (p < 0.05) in the arginine-supplemented control group compared with the glycine-supplemented control group. Arginine supplementation during sepsis significantly increased (p < 0.05) albumin and liver protein synthesis compared with controls. Histones which are involved in DNA synthesis and are rich in arginine may play a role in the host response to stress and sepsis. These in vivo results appear to contradict hepatocyte-Kupffer cell coculture studies perhaps because of the hormonal and cytokine responses to nutrient substrate and acute septicemia.
A Low Power DC-DC Converter using a Switched-Capacitor Transformer (1983)

A small size DC-DC regulated converter which does not include inductance is descrived. Voltage transformation is achieved by switched capacitors, that is charging capacitors in series and discharging them in parallel or charging them in parallel and discharging them in series. In the case of inverting the polarity of output voltage, the capacitors are connected to the load as the polarity is inverted. The switched capacitors are alternately connected to the source and the load, such that the power is transmitted. Stabilization of the output voltage is achieved by controlling the period of switching `ON' of the switching elements, that is the method of EWM controlling. The DC-DC regulated converter is built in the form of a Hybrid-IC and confirmed good characteristics during the experiment.
MMP-1 activation by serine proteases and MMP-10 induces human capillary tubular network collapse and regression in 3D collagen matrices (2005)

Previous work has shown that endothelial cell (EC)-derived matrix metalloproteinases (MMPs) regulate regression of capillary tubes in vitro in a plasmin- and MMP-1 dependent manner. Here we report that a number of serine proteases can activate MMP-1 and cause capillary tube regression; namely plasma kallikrein, trypsin, neutrophil elastase, cathepsin G, tryptase and chymase. Plasma prekallikrein failed to induce regression without coactivators such as high molecular weight kininogen (HMWK) or coagulation Factor XII. The addition of trypsin, the neutrophil serine proteases (neutrophil elastase and cathepsin G) and the mast cell serine proteases (tryptase and chymase) each caused MMP-1 activation and collagen type I proteolysis, capillary tubular network collapse, regression and EC apoptosis. Capillary tube collapse is accompanied by collagen gel contraction, which is strongly related to the wound contraction that occurs during regression of granulation tissue in vivo. We also report that proMMP-10 protein expression is markedly induced in ECs undergoing capillary tube morphogenesis. Addition of each of the serine proteases described above led to activation of proMMP-10, which also correlated with MMP-1 activation and capillary tube regression. Treatment of ECs with MMP-1 or MMP-10 siRNA markedly delayed capillary tube regression, whereas gelatinase A (MMP-2), gelatinase B (MMP-9) and stromelysin-1 (MMP-3) siRNA-treated cells behaved in a similar manner to controls and regressed normally. Increased expression of MMP-1 or MMP-10 in ECs using recombinant adenoviral delivery markedly accelerated serine protease-induced capillary tube regression. ECs expressing increased levels of MMP-10 activated MMP-1 to a greater degree than control ECs. Thus, MMP-10-induced activation of MMP-1 correlated with tube regression and gel contraction. In summary, our work demonstrates that MMP-1 zymogen activation is mediated by multiple serine proteases and MMP-10, and that these events are central to EC-mediated collagen degradation and capillary tube regression in 3D collagen matrices.
Adjunctive Use of a Surface-Active Agent in Extracorporeal Circulation (1966)

1. A nonionic surfactant, Pluronic F68, was used in prolonged experimental and clinical extracorporeal circulation, and data are presented which support the efficacy of the use of this agent. 2. Hemolysis and fat embolism resulting from prolonged cardiopulmonary bypass with a bubble oxygenator were greatly reduced by use of the surfactant. 3. The surfactant markedly prevented and improved the intravascular "sludging." 4. The surfactant also reduced the fibrin deposition on the filter of the oxygenator. 5. The function of the pump oxygenator was not affected. 6. No adverse physiological effects resulting from the Pluronic were discovered. It may, therefore, have widespread application in extracorporeal circulation.
THE THEORY OF PHOTODYNAMIC THERAPY DOSIMETRY: CONSEQUENCES OF PHOTO‐DESTRUCTION OF SENSITIZER (1987)

Photodynamic dose is defined as the area under the curve of sensitizer level plotted as a function of light dose. This is a photochemical definition of dose. We will show that this definition is useful in predicting photobiological response. The photodestruction of sensitizer during photodynamic therapy is shown to result in an upper limit on the photodynamic dose which can be delivered by an unlimited light dose. This limit results in the opportunity to make total photodynamic dose uniform to considerable depths (one to two centimeters). The existence of thresholds for permanent tissue damage allows protection of normal tissue from the large light doses required to achieve this limiting dose deep in the tissue. Higher sensitizer levels in the tumor permit tumor destruction while the normal tissues are protected. A clinical trial to determine the proper level of injected dose necessary for these results is required. This theory of photodynamic therapy (PDT) dosimetry is tested in the DBA-SMT experimental mouse tumor system. Combinations of drug and light which are not reciprocal but are nearly equal by this theory are shown to give equivalent tumor control at seven days post treatment. Reciprocal combinations of drug and light fail to give equivalent results when they ae selected using the theory to choose a combination where reciprocity should fail.
G 1 /S Transition in Normal Human T-Lymphocytes Requires the Nuclear Protein Encoded by c- myb (1989)

Exposure of peripheral blood mononuclear cells (PBMC) to an 18-base c-myb antisense oligomer before mitogen or antigen stimulation resulted in almost complete inhibition of c-myb messenger RNA and protein synthesis and blockade of T lymphocyte proliferation. Expression of early and late activation markers, interleukin-2 receptor and transferrin receptor, respectively, by PBMC was unaffected by antisense oligomer exposure as was the expression of c-myc messenger RNA. In contrast, histone H3 messenger RNA levels and DNA content were selectively decreased. These results suggest that c-myb protein deprivation does not perturb T lymphocyte activation or early molecular events that may prepare the cell for subsequent proliferation. Rather, it appears to specifically block cells in late G1 or early S phase of the cell cycle.
HCV protein‐induced cytokine predicts treatment outcomes in chronic hepatitis C virus infection (2013)

Abstract Background &amp; Aims Immune‐mediated processes are thought to influence the efficacy of treatment in chronic hepatitis C virus ( HCV ) infection. This study evaluated the association of baseline immune responses with the achievement of a sustained viral response ( SVR ) upon pegylated interferon and ribavirin treatment. Methods Baseline serum and peripheral blood mononuclear cells (PBMC) cytokine activity was assessed. Metabolic and liver injury parameters were evaluated as underlying factors. Results Baseline demographics and disease parameters did not differ between the SVR − ( n = 14) and SVR + ( n = 25) cohorts except for body mass index ( BMI ) values and liver injury scores. Baseline circulating TNF ‐α levels were three‐fold higher with subsequent treatment failure vs. success ( P = 0.124). Baseline peripheral blood mononuclear cells ( PBMC , n = 25) were cultured with HCV core and non‐structural ( NS )3 proteins. Core ( P = 0.0003) and NS 3 ( P = 0.018) induced greater TNF ‐α production within the SVR −, compared with the SVR +, cohorts. Similar findings were noted for interleukin ( IL )‐1β and IL ‐10 synthesis. Furthermore, HCV core‐induced TNF ‐α synthesis correlated with patient BMI values ( r = 0.489, P = 0.015). Core ( r = 0.432, P = 0.065) and NS 3 ( r = 0.530, P = 0.020)‐induced TNF ‐α displayed a positive relationship with serum adiponectin concentrations. In addition, lipopolysaccharide stimulated cytokine synthesis associated with BMI and adiponectin levels. Although unable to predict treatment outcomes, NS 3‐induced IL ‐6 synthesis and serum leptin concentrations corresponded to liver injury scores. Conclusion An enhanced PBMC susceptibility to core and NS 3‐induced TNF ‐α synthesis at baseline was associated with treatment failure. This phenomenon appeared to involve the interaction of virally generated TNF ‐α activity and metabolic disease. In contrast, IL ‐6 activity and leptin levels may indicate liver damage.
Determination of lipase specificity (1983)

Specificity of lipases is controlled by the molecular properties of the enzyme, structure of the substrate and factors affecting binding of the enzyme to the substrate. Types of specificity are as follows. I. Substrate: (a) different rates of lipolysis of TG, DG, and MG by the same enzyme; (b) separate enzymes from the same source for TG, DG and MG. II. Positional: (a) primary esters; (b) secondary esters; and (c) all three esters or nonspecific hydrolysis. III. Fatty acid, preference for similar fatty acids. IV. Stereospecificity: faster hydrolysis of one primary sn ester as compared to the other. V. Combinations of I-IV. Lipases with these specificities are: Ia, pancreatic; Ib, postheparin plasma. IIa, pancreatic; IIb, Geotrichum candidum, for fatty acids with cis-9-unsaturation, and IIc, Candida cylindracea. III, G. candidum for unsaturates. IV. sn-1, postheparin plasma and sn-3 human and rat lingual lipases. V. Rat lingual lipase. Methods for determination involve digestion of natural fats of known structure and synthetic acylglycerols followed by analysis of the lipolysis products. All of the types of specificity have been detected with use of synthetic acylglycerols. Detection of stereospecificity requires enantiomeric acylglycerols which are difficult to synthesize, so other methods have been developed. These involve the generation of 1,2-(2,3)DG and resolution of the enantiomers. Trioleoylglycerol or racemic TG can be used as substrates. If the lipase is stereospecific, then either the sn-1,2- or 2,3-enantiomer will predominate. The relative amounts of the enantiomers can be determined by measurement of specific rotation, and nuclear magnetic resonance spectra. The DG can also be separated by conversion to phospholipids and hydrolysis with phospholipases A-2 or C. Applications of these procedures are discussed and data on the specificity of various lipases presented.
Lithographically-defined gain apertures within selectively oxidized VCSELs (2000)

Summary form only given.Selectively oxidized vertical cavity surface emitting lasers (VCSELs) have demonstrated record performance such as low threshold current/voltage, high efficiency, and high-speed modulation characteristics. Because of the strong index confinement created by buried oxide layers used to define the laser cavity, oxidized VCSELs typically operate in multiple transverse optical modes, whereas single-mode operation is required for many VCSEL applications. One approach to discriminate against higher-order optical modes is to define a small gain region within a larger diameter cavity. We report on high-performance gain-apertured selectively oxidized VCSELs, which exhibit high single-mode operation as high as 3 m with side mode suppression ratios>30 dB.
Therapeutic Strategies to Enhance the Anticancer Efficacy of Histone Deacetylase Inhibitors (2011)

Histone acetylation is a posttranslational modification that plays a role in regulating gene expression. More recently, other nonhistone proteins have been identified to be acetylated which can regulate their function, stability, localization, or interaction with other molecules. Modulating acetylation with histone deacetylase inhibitors (HDACi) has been validated to have anticancer effects in preclinical and clinical cancer models. This has led to development and approval of the first HDACi, vorinostat, for the treatment of cutaneous T cell lymphoma. However, to date, targeting acetylation with HDACi as a monotherapy has shown modest activity against other cancers. To improve their efficacy, HDACi have been paired with other antitumor agents. Here, we discuss several combination therapies, highlighting various epigenetic drugs, ROS-generating agents, proteasome inhibitors, and DNA-damaging compounds that together may provide a therapeutic advantage over single-agent strategies.
Apomyoglobin as a molecular recognition surface: expression, reconstitution and crystallization of recombinant porcine myoglobin in Escherichia coli (1988)

Recombinant porcine myoglobin has been produced in Escherichia coli using the lambda cII fusion expression system of Nagai and Thøgersen [Nature, 309, 810-812 (1984)]. After processing and reconstitution with haem, the protein is gel-electrophoretically and spectrophotometrically indistinguishable from native pig myoglobin. Large crystals of both native and recombinant porcine myoglobin were grown from 50 mM sodium phosphate, pH 7.1, 80% ammonium sulphate. The crystals belong to space group C2 (a = 156.9 A, b = 42.0 A, c = 92.2 A, beta = 127.9 degrees) and diffract to a nominal 2.5 A resolution. We plan to explore apomyoglobin as a binding surface in studies combining site-directed mutagenesis and X-ray analysis. These experiments will be extended by studying the binding of haem analogues to the mutant apoproteins.
Cloning and sequencing of the genes from Salmonella typhimurium encoding a new bacterial ribonucleotide reductase (1994)

A plasmid library of Salmonella typhimurium was used to complement a temperature-sensitive nrdA mutant of Escherichia coli. Complementation was obtained with two different classes of plasmids, one carrying the E. coli nrdAB-like genes and the second containing an operon encoding a new bacterial ribonucleotide reductase. Plasmids harboring these new reductase genes also enable obligately anaerobic nrdB::Mud1 E. coli mutants to grow in the presence of oxygen. This operon consists of two open reading frames, which have been designated nrdE (2,145 bp) and nrdF (969 bp). The deduced amino acid sequences of the nrdE and nrdF products include the catalytically important residues conserved in ribonucleotide reductase enzymes of class I and show 25 and 28% overall identity with the R1 and R2 protein, respectively, of the aerobic ribonucleoside diphosphate reductase of E. coli. The 3' end of the sequenced 4.9-kb fragment corresponds to the upstream region of the previously published proU operon of both S. typhimurium and E. coli, indicating that the nrdEF genes are at 57 min on the chromosomal maps of these two bacterial species. Analysis of the nrdEF and proU sequences demonstrates that transcription of the nrdEF genes is in the clockwise direction on the S. typhimurium and E. coli maps.
A Novel Strategy for Development of Recombinant Antitoxin Therapeutics Tested in a Mouse Botulism Model (2012)

Antitoxins are needed that can be produced economically with improved safety and shelf life compared to conventional antisera-based therapeutics. Here we report a practical strategy for development of simple antitoxin therapeutics with substantial advantages over currently available treatments. The therapeutic strategy employs a single recombinant 'targeting agent' that binds a toxin at two unique sites and a 'clearing Ab' that binds two epitopes present on each targeting agent. Co-administration of the targeting agent and the clearing Ab results in decoration of the toxin with up to four Abs to promote accelerated clearance. The therapeutic strategy was applied to two Botulinum neurotoxin (BoNT) serotypes and protected mice from lethality in two different intoxication models with an efficacy equivalent to conventional antitoxin serum. Targeting agents were a single recombinant protein consisting of a heterodimer of two camelid anti-BoNT heavy-chain-only Ab V(H) (VHH) binding domains and two E-tag epitopes. The clearing mAb was an anti-E-tag mAb. By comparing the in vivo efficacy of treatments that employed neutralizing vs. non-neutralizing agents or the presence vs. absence of clearing Ab permitted unprecedented insight into the roles of toxin neutralization and clearance in antitoxin efficacy. Surprisingly, when a post-intoxication treatment model was used, a toxin-neutralizing heterodimer agent fully protected mice from intoxication even in the absence of clearing Ab. Thus a single, easy-to-produce recombinant protein was as efficacious as polyclonal antiserum in a clinically-relevant mouse model of botulism. This strategy should have widespread application in antitoxin development and other therapies in which neutralization and/or accelerated clearance of a serum biomolecule can offer therapeutic benefit.