gebhart/patrepeval huggingface dataset:
Cutting Edge: The Metalloproteinase ADAM17/TNF-α-Converting Enzyme Regulates Proteolytic Shedding of the MHC Class I-Related Chain B Protein (2009)

MHC class I-related chain (MIC) A/B are transmembrane proteins expressed in pathological conditions that are ligands for the activating receptor NKG2D found on cytotoxic lymphocytes. Soluble NKG2D ligands are detected in sera of patients suffering from multiple types of cancer where they are associated with reduced levels of receptor expression and compromised function of NK and CTLs. In this study, we report the identification of a metalloproteinase involved in the cleavage process of MIC; inhibition and knockdown of ADAM17/TACE blocks the shedding of these proteins. Strikingly, the recruitment of both enzyme and substrate to detergent-resistant membrane microdomains is crucial for efficient proteolysis. These findings provide a novel insight into the molecular mechanisms of MIC shedding.
A complete basis set model chemistry. VI. Use of density functional geometries and frequencies (1999)

The recently introduced complete basis set, CBS-Q, model chemistry is modified to use B3LYP hybrid density functional geometries and frequencies, which give both improved reliability (maximum error for the G2 test set reduced from 3.9 to 2.8 kcal/mol) and increased accuracy (mean absolute error reduced from 0.98 to 0.87 kcal/mol), with little penalty in computational speed. The use of a common method for geometries and frequencies makes the modified model applicable to transition states for chemical reactions.
Macrophages as Susceptible Targets for HIV Infection, Persistent Viral Reservoirs in Tissue, and Key Immunoregulatory Cells that Control Levels of Virus Replication and Extent of Disease (1990)

Although macrophages are major targets for human immunodeficiency virus (HIV) infection in vivo, study of HIV-macrophage interactions in vitro was hindered because many laboratory strains of HIV would not replicate in macrophages, and because survival of macrophages in culture was poor. Addition of purified macrophage colony-stimulating factor (M-CSF) to cultured macrophages markedly improves their survival, but does not induce proliferation. HIV isolates that replicate in macrophages will also replicate in lymphocytes; however, isolates adapted to lymphoid cells (such as HIV-HTLVIIIB) will not replicate in macrophages. The envelope gene appears to be a major determinant of the cell tropism of viral isolates. T-cell grown virus stocks synthesize abundant gp120, while virus grown in macrophages contains relatively much less gp120. Electron microscopy of virions from macrophages shows them to be depleted of gp120 surface "spikes." Recombination studies show that the portion of the genome coding for the envelope glycoprotein appears to determine cell tropism. Lastly, rsCD4 neutralized macrophage-tropic isolates less efficiently than T-cell tropic isolates. HIV replication in macrophages is partially under the control of cellular factors, although these have been less well characterized than they have in lymphocytes.
Resistance to anti‐IgM‐induced apoptosis in a WEHI‐231 subline is due to insufficient production of ceramide (1995)

We describe the properties of a physiological cell death (PCD)-resistant subline of WEHI-231 generated from the PCD-susceptible WEHI-231.7 JM cell line maintained in our laboratory. The PCD-resistant WEHI-231.7 JMRE subline was uniquely resistant to anti-immunoglobulin (Ig)M-induced PCD but not to irradiation and etoposide. In these sublines, we compared the expression of genes implicated in regulating PCD. Northern analysis of c-myc, c-fos, egr-1, Fas, p53 and retinoblastoma revealed similar basal levels of expression in all sublines tested and comparable responses to anti-IgM treatment. Similarly, the expression of bcl-2, bcl-x, bax and IL-1 beta converting enzyme did not correlate with susceptibility to anti-IgM-induced PCD. Next, we systematically studied signal transduction events including: tyrosine phosphorylation, Ca++ flux, and ceramide production in the Jm and JMRE sublines. The tyrosine phosphorylation patterns and the Ca++ influx generated following sIgM engagement were very similar in the JM and JMRE sublines. In contrast, the generation of ceramide differed in the PCD-resistant and PCD-susceptible sublines. Ceramide is produced following cross-linking sIgM on WEHI-231.7 JM cells and causes PCD. Ceramide levels in anti-IgM-treated WEHI-231.7 JMRE cells are low and appear to be insufficient to induce PCD.
Novel RNA aptamers targeting gastrointestinal cancer biomarkers CEA, CA50 and CA72-4 with superior affinity and specificity (2018)

Gastric cancer is the third most common cause of death from cancer in the world and it remains difficult to cure in Western countries, primarily because most patients present with advanced disease. Currently, CEA, CA50 and CA72-4 are commonly used as tumor markers for gastric cancer by immunoassays. However, the drawback and conundrum of immunoassay are the unceasing problem in standardization of quality of antibodies and time/effort for the intensive production. Therefore, there is an urgent need for the development of a standardized assay to detect gastric cancer at the early stage. Aptamers are DNA or RNA oligonucleotides with structural domain which recognize ligands such as proteins with superior affinity and specificity when compared to antibodies. In this study, SELEX (Systematic Evolution of Ligands by Exponential enrichment) technique was adopted to screen a random 30mer RNA library for aptamers targeting CEA, CA50 and CA72-4 respectively. Combined with high-throughput sequencing, we identified 6 aptamers which specifically target for these three biomarkers of gastrointestinal cancer. Intriguingly, the predicted secondary structures of RNA aptamers from each antigen showed significant structural similarity, suggesting the structural recognition between the aptamers and the antigens. Moreover, we determined the dissociation constants of all the aptamers to their corresponding antigens by fluorescence spectroscopy, which further demonstrated high affinities between the aptamers and the antigens. In addition, immunostaining of gastric adenocarcinoma cell line AGS using CEA Aptamer probe showed positive fluorescent signal which proves the potential of the aptamer as a detection tool for gastric cancer. Furthermore, substantially decreased cell viability and growth were observed when human colorectal cell line LS-174T was transfected with each individual aptamers. Taking together, these novel RNA aptamers targeting gastrointestinal cancer biomarker CEA, CA50 and CA72-4 will aid further development and standardization of clinical diagnostic method with better sensitivity and specificity, and potentially future therapeutics development of gastric cancer.
Chronic Treatment with Flavonoids Prevents Endothelial Dysfunction in Spontaneously Hypertensive Rat Aorta (2005)

Flavonoids are known to possess cardioprotective properties. Vascular endothelial function is a surrogate marker for cardiovascular diseases, including hypertension. We have studied the effects of chronic flavonoid treatment on vascular endothelial functions in spontaneously hypertensive rats (SHR). Starting from 6-7 weeks old, SHR were given flavonoids (baicalein, flavone, or quercetin) orally (10 mg/kg, once daily) to the SHRs for 4 weeks. Aortas from all the flavonoid-treated animals showed remarkably higher endothelium-dependent relaxations to acetylcholine, to a similar extent as those pretreated with the angiotensin-converting enzyme inhibitor, captopril. However, in contrast to other experimental groups, flavone pretreatment also enhanced the endothelium-independent relaxations to sodium nitroprusside. In addition, treatment with either flavone or quercetin induced a significant attenuation in systolic blood pressure of the hypertensive animals. The present results suggest that chronic treatment with the flavonoids (baicalein, flavone, and quercetin) preserves vascular endothelial functions in hypertensive animals through several possible actions, including increasing endothelial nitric oxide production and bioavailability and reduction in blood pressure.
A format for quality (1996)

Catherine Gleeson and Liz Wright describe the pros and cons of a multidisciplinary group to improve care of people with asthma
Evaluation of stereo confidence indoors and outdoors (2010)

We present an extensive evaluation of 13 confidence metrics for stereo matching that compares the most widely used metrics as well as four novel techniques proposed here. We begin by categorizing the methods according to which aspects of stereo computation they take into account and, then, assess their strengths and weaknesses. The evaluation is conducted on indoor and outdoor datasets with ground truth and measures the capability of each confidence metric to rank depth estimates according to their likelihood for being correct, to detect occluded pixels and to generate low-error depth maps by selecting among multiple hypotheses for each pixel. We believe that such an evaluation is missing from the rapidly maturing stereo literature and that our findings will be helpful to researchers in binocular and multi-view stereo.
Controlled Multicenter Study of the Antihypertensive Effects of Lisinopril, Hydrochlorothiazide, and Lisinopril plus Hydrochlorothiazide in the Treatment of 394 Patients with Mild to Moderate Essential Hypertension (1987)

Lisinopril (LIS) is a lysine analog of enalaprilat, the active metabolite of enalapril, an angiotensin-converting enzyme inhibitor (ACEI). Unlike enalapril, the precursor of enalaprilat, LIS is not a prodrug but has equal ACEI efficacy and potency and a slightly longer duration of action after oral administration. Short-term (12 weeks) and long-term (24 weeks) blood pressure control has been studied with LIS, hydrochlorothiazide (HCTZ), and LIS + HCTZ when given once a day. Drug treatment had three phases: (i) 2-4 weeks of single-blind placebo washout; (ii) 12 weeks of double-blind comparison therapy with LIS 20, 40, and 80 mg vs. HCTZ 12.5, 25, and 50 mg, vs. LIS + HCTZ 20 + 12.5, 40 + 25, and 80 + 50 mg; (iii) 13-24 weeks single-blind LIS vs. LIS + HCTZ. Starting double-blind therapy at the lowest dose, all three groups doubled the dose at weeks 4 and 8 if BP was not controlled with sitting diastolic BP (SDBP) less than 90 mm Hg. At the end of 12 weeks of double-blind therapy, uncontrolled HCTZ-only and LIS-only treatment groups were advanced to combination LIS + HCTZ therapy but uncontrolled LIS + HCTZ patients were dropped. Mean BP reductions (systolic/diastolic, mm Hg) for all three groups after 12 weeks of double-blind comparison therapy were: (i) LIS (n = 162), -16.6/-12.5; (ii) HCTZ (n = 155), -10.4/-6.8; (iii) LIS + HCTZ (n = 74), -23.9/-18.2 with p less than 0.01 for all groups compared to baseline.(ABSTRACT TRUNCATED AT 250 WORDS)
Evaluation of amino-phosphine compounds as antioxidants and antifatigue agents in NR and SBR vulcanizates (2002)

Abstract Amino-phosphine derivatives such as tri (di-phenyl amino) phosphine and tri (di-cymyl-di-phenyl amino) phosphine were prepared. These compounds were incorporated into natural rubber (NR) and styrene–butadiene rubber (SBR) mixes. The rheometric characteristics of the green rubber mixes were determined using the oscillating disc rheometer. The prepared compounds were evaluated as antifatigue and antioxidant agents in NR and SBR vulcanizates. It was found from the obtained results that the investigated compounds are good antioxidant and antifatigue agents and their efficiencies are better than that obtained from phenyl-β-naphthyl amine, which is used widely in the rubber industry. Keywords: AminophosphinesAntifatigueAntioxidantsNatural rubberStyrene–butadiene rubber Acknowledgments
A novel chitosan‐poly(lactide) copolymer and its submicron particles as imidacloprid carriers (2011)

Conjugation of PLA to chitosan was shown to be an available method for the preparation of submicron particles for lipophilic pesticide delivery. The imidacloprid-loaded submicron particles showed a sustained release process. As the mass ratio of copolymer to imidacloprid increased, the submicron particles size and LC decreased. The chitosan-PLA submicron particles could be useful as pesticide carriers for imidacloprid delivery systems.
Unusual Regulation of a Leaderless Operon Involved in the Catabolism of Dimethylsulfoniopropionate in Rhodobacter sphaeroides (2011)

Rhodobacter sphaeroides strain 2.4.1 is a widely studied bacterium that has recently been shown to cleave the abundant marine anti-stress molecule dimethylsulfoniopropionate (DMSP) into acrylate plus gaseous dimethyl sulfide. It does so by using a lyase encoded by dddL, the promoter-distal gene of a three-gene operon, acuR-acuI-dddL. Transcription of the operon was enhanced when cells were pre-grown with the substrate DMSP, but this induction is indirect, and requires the conversion of DMSP to the product acrylate, the bona fide co-inducer. This regulation is mediated by the product of the promoter-proximal gene acuR, a transcriptional regulator in the TetR family. AcuR represses the operon in the absence of acrylate, but this is relieved by the presence of the co-inducer. Another unusual regulatory feature is that the acuR-acuI-dddL mRNA transcript is leaderless, such that acuR lacks a Shine-Dalgarno ribosomal binding site and 5'-UTR, and is translated at a lower level compared to the downstream genes. This regulatory unit may be quite widespread in bacteria, since several other taxonomically diverse lineages have adjacent acuR-like and acuI-like genes; these operons also have no 5' leader sequences or ribosomal binding sites and their predicted cis-acting regulatory sequences resemble those of R. sphaeroides acuR-acuI-dddL.
New driving parameters for diamond deposition reactors: pulsed mode versus continuous mode (2003)

Experimental investigation and modeling of pulsed H2/CH4 plasmas used for diamond deposition are presented. Two plasma configurations are studied : a 2.45 GHz microwave cavity configuration and a 915 MHz surface-wave configuration. Time-resolved measurements of the gas temperature determined from the Doppler broadening of the Balmer Ha line, of the H-atom relative density and of the discharge volume (Vpl) are reported. The experimental time-variations of the gas temperature are characterized by a sharp increase at the beginning of the pulse (t < 250 µs) and a decrease down to a stable value at steady state (t > 1 ms). The simulations enable us to estimate time-variations of the electron energy distribution function, gas temperature and chemical species densities. The in-pulse steady state temperature obtained from the model is in agreement with the measured one, although a discrepancy is obtained on the shape of the early time-variation. Calculations were carried out in order to study the effects of the in-pulse power, the duty cycle and the off-plasma time on the H-atom and CH3-radical densities. It is seen that, at a constant power density averaged over a period, low duty cycles favor high H-atom and CH3 - radical densities, while too long off-plasma times reduce the H-atom density during the pulse. In addition, the production of H atoms was seen to be governed by thermal dissociation in the 2.45 GHz microwave cavity system, and by electronic impact dissociation in the 915 MHz surface wave system, the latter operating under high gas velocities.
Open source tools for standardized privacy protection of medical images (2011)

In addition to the primary care context, medical images are often useful for research projects and community healthcare networks, so-called "secondary use". Patient privacy becomes an issue in such scenarios since the disclosure of personal health information (PHI) has to be prevented in a sharing environment. In general, most PHIs should be completely removed from the images according to the respective privacy regulations, but some basic and alleviated data is usually required for accurate image interpretation. Our objective is to utilize and enhance these specifications in order to provide reliable software implementations for de- and re-identification of medical images suitable for online and offline delivery. DICOM (Digital Imaging and Communications in Medicine) images are de-identified by replacing PHI-specific information with values still being reasonable for imaging diagnosis and patient indexing. In this paper, this approach is evaluated based on a prototype implementation built on top of the open source framework DCMTK (DICOM Toolkit) utilizing standardized de- and re-identification mechanisms. A set of tools has been developed for DICOM de-identification that meets privacy requirements of an offline and online sharing environment and fully relies on standard-based methods.
Hemagglutinin of swine influenza virus: a single amino acid change pleiotropically affects viral antigenicity and replication. (1983)

The complete nucleotide sequence has been obtained of the H1 hemagglutinin (HA) gene of a high-yielding (H) mutant of the A/NJ/11/76(H1N1) strain of swine influenza virus in studies of a viral reassortant (X-53a) bearing this gene. This determination has permitted comparison with human influenza H1N1 prototype viruses A/WSN/33 and A/PR/8/34, with which 80% and 94% amino acid homology was found between HA1 and HA2, respectively. Partial sequences have been determined for other viral reassortants containing either H or L (low-yielding phenotype) genes derived from A/NJ/11/76. Sequence of the HA1 region of an L mutant prototype was virtually completed and differed from that of the H mutant by only four amino acid changes. Sequence analysis of four other viruses was restricted to regions of the HA with which monoclonal antibodies capable of distinguishing L and H mutants are presumed to react. Therefore, changes in these sequences are relevant to changes in viral phenotype. Change at residue 155 from Gly to Glu is associated with change from L to H HA phenotype. This site, structurally equivalent to amino acid 158 on the Wiley et al. HA model [Wiley, D. C., Wilson, I. A. & Skehel, J. J. (1981) Nature (London) 289, 373-378] is near the tip of the HA monomer adjacent to the proposed receptor binding site and therefore credibly could influence both viral antigenicity and replication. Because both L and H variants exist in nature and because revertants may be selected in the laboratory as replication variants in the absence of immunoselection, these studies provide evidence for fortuitous antigenic change in association with change in biological function, which is determined by a single base change.
[Studies on the chemical constituents of Annona muricata]. (1997)

Annonaceous acetogenin (or polyketide) is a kind of potential antineoplastic agents from Annonaceae plants. Two new acetogenins, Muricatalicin (I) and muricatalin (VI), a mesitoate of a new acetogenin, annonacin-B mesitoate (Vb), and three known acetogenins, annonacin (II), annonacin-A (III) and annonacin-10-one (IV) have been isolated from Annona muricata L. The structures and relative stereochemistry of I, VI and Vb were elucidated on the basis of spectral analysis and examination of their acetates and/or mesitoate.
Domain adaptation from multiple sources via auxiliary classifiers (2009)

We propose a multiple source domain adaptation method, referred to as Domain Adaptation Machine (DAM), to learn a robust decision function (referred to as target classifier) for label prediction of patterns from the target domain by leveraging a set of pre-computed classifiers (referred to as auxiliary/source classifiers) independently learned with the labeled patterns from multiple source domains. We introduce a new data-dependent regularizer based on smoothness assumption into Least-Squares SVM (LS-SVM), which enforces that the target classifier shares similar decision values with the auxiliary classifiers from relevant source domains on the unlabeled patterns of the target domain. In addition, we employ a sparsity regularizer to learn a sparse target classifier. Comprehensive experiments on the challenging TRECVID 2005 corpus demonstrate that DAM outperforms the existing multiple source domain adaptation methods for video concept detection in terms of effectiveness and efficiency.
A review of symbolic analysis of experimental data (2003)

This review covers the group of data-analysis techniques collectively referred to as symbolization or symbolic time-series analysis. Symbolization involves transformation of raw time-series measurements (i.e., experimental signals) into a series of discretized symbols that are processed to extract information about the generating process. In many cases, the degree of discretization can be quite severe, even to the point of converting the original data to single-bit values. Current approaches for constructing symbols and detecting the information they contain are summarized. Novel approaches for characterizing and recognizing temporal patterns can be important for many types of experimental systems, but this is especially true for processes that are nonlinear and possibly chaotic. Recent experience indicates that symbolization can increase the efficiency of finding and quantifying information from such systems, reduce sensitivity to measurement noise, and discriminate both specific and general classes of proposed models. Examples of the successful application of symbolization to experimental data are included. Key theoretical issues and limitations of the method are also discussed.
CrystalBall: predicting and preventing inconsistencies in deployed distributed systems (2009)

We propose a new approach for developing and deploying distributed systems, in which nodes predict distributed consequences of their actions, and use this information to detect and avoid errors. Each node continuously runs a state exploration algorithm on a recent consistent snapshot of its neighborhood and predicts possible future violations of specified safety properties. We describe a new state exploration algorithm, consequence prediction, which explores causally related chains of events that lead to property violation. This article describes the design and implementation of this approach, termed CrystalBall. We evaluate CrystalBall on RandTree, BulletPrime, Paxos, and Chord distributed system implementations. We identified new bugs in mature Mace implementations of three systems. Furthermore, we show that if the bug is not corrected during system development, CrystalBall is effective in steering the execution away from inconsistent states at runtime.
Lead Acid-NiMH Hybrid Battery System Using Gel Electrolyte (2012)

A hybrid battery system with gel electrolytes is proposed here to alleviate some limitations on conventional batteries, such as maintenance cost and acid stratification for the lead-acid battery, high self-discharge and short life cycles for high current discharge for nickel-metal hydride battery. This hybrid battery consists of a lead-acid positive electrode and a nickel-metal hydride negative electrode, operating in H2SO4-silica gel and KOH-potassium salt poly(acrylic acid) gel electrolytes via monopolar ion exchange membranes, respectively. The hybrid battery using gel electrolyte maintained stable discharge plateau at 2.27 V and longer discharge capacity than wet electrolyte system. This improved performance may be due to the gel electrolyte which can prevent acid stratification, reduce the corrosion rate of electrodes, and resolve the problem of salting-out in the central chamber for aqueous electrolyte system.