gebhart/patrepeval huggingface dataset:
Phase III Trial in Metastatic Gastroesophageal Adenocarcinoma with Fluorouracil, Leucovorin Plus Either Oxaliplatin or Cisplatin: A Study of the Arbeitsgemeinschaft Internistische Onkologie (2008)

FLO reduced toxicity as compared with FLP. In older adult patients, FLO also seemed to be associated with improved efficacy.
TravTek Evaluation Modeling Study (1996)

This report describes a modeling study that was performed to extrapolate, from the TravTek operational test data, a set of system wide benefits and performance values for a wider-scale deployment of a TravTek-like system. A model was produced whose driver and in-vehicle system parameters were representative of the behavior that was quantified by various TravTek field tests in Orlando. In the second part of the study, a coded traffic network was created with properties that were representative of the traffic conditions observed in Orlando during the course of the TravTek operational field test.
Cloning of a Delta Opioid Receptor by Functional Expression (1992)

Opiate drugs have potent analgesic and addictive properties. These drugs interact with receptors that also mediate the response to endogenous opioid peptide ligands. However, the receptors for opioids have eluded definitive molecular characterization. By transient expression in COS cells and screening with an iodinated analog of the opioid peptide enkephalin, a complementary DNA clone encoding a functional delta opioid receptor has been identified. The sequence shows homology to G protein-coupled receptors, in particular the receptors for somatostatin, angiotensin, and interleukin-8.
Excitation of size selected nanocrystallites in porous silicon (1998)

We prepared silicon that exhibits green-to-red rainbow luminescence along the sample, reflecting gradients in the crystallite size. The excitation has a size-dependent feature, riding a smooth bulklike continuum. For the size-dependent contribution, we measured absorption band edges of 3.75 and 3.0–3.25 eV at the meniscus and opposite end. Excitation in the meniscus, monitored at the edge of the blue emission, isolates ultrasmall sizes, with “excitation coefficients” quadratic with energy, and emission encompassing much of the visible spectrum. Results are discussed in terms of quantum-confinement-induced restructuring of the diamondlike bonds to form radiative Si–Si surface states.
Divergent transcription of pdxB and homology between the pdxB and serA gene products in Escherichia coli K-12 (1989)

We report the DNA sequence and in vivo transcription start of pdxB, which encodes a protein required for de novo biosynthesis of pyridoxine (vitamin B6). The DNA sequence confirms results from previous minicell experiments showing that pdxB encodes a 41-kilodalton polypeptide. RNase T2 mapping of in vivo transcripts and corroborating experiments with promoter expression vector pKK232-8 demonstrated that the pdxB promoter shares its -10 region with an overlapping, divergent promoter. Thus, pdxB must be the first gene in the complex pdxB-hisT operon. The steady-state transcription level from these divergent promoters, which probably occlude each other, is approximately equal in bacteria growing in rich medium at 37 degrees C. The divergent transcript could encode a polypeptide whose amino-terminal domain is rich in proline and glutamine residues. Similarity searches of protein data bases revealed a significant number of amino acid matches between the pdxB gene product and D-3-phosphoglycerate dehydrogenase, which is encoded by serA and catalyzes the first step in the phosphorylated pathway of serine biosynthesis. FASTA and alignment score analyses indicated that PdxB and SerA are indeed homologs and share a common ancestor. The amino acid alignment between PdxB and SerA implies that PdxB is a 2-hydroxyacid dehydrogenase and suggests possible NAD+, substrate binding, and active sites of both enzymes. Furthermore, the fact that 4-hydroxythreonine, a probable intermediate in pyridoxine biosynthesis, is structurally related to serine strongly suggests that the pdxB gene product is erythronate-4-phosphate dehydrogenase. The homology between PdxB and SerA provides considerable support for Jensen's model of enzyme recruitment as the basis for the evolution of different biosynthetic pathways.
Molten salt synthesis of nano-sized Li4Ti5O12 doped with Fe2O3 for use as anode material in the lithium-ion battery (2014)

Fe<sub>2</sub>O<sub>3</sub> modified Li<sub>4</sub>Ti<sub>5</sub>O<sub>12</sub> anode material with differing content of Fe<sub>2</sub>O<sub>3</sub> was synthesized for the first time by the molten salt method. The Li<sub>4</sub>Ti<sub>4.8</sub>Fe<sub>0.2</sub>O<sub>12</sub> electrode showed the best rate performance and superior cycling stability.
Minimal Effort Back Propagation for Convolutional Neural Networks (2017)

As traditional neural network consumes a significant amount of computing resources during back propagation, \citet{Sun2017mePropSB} propose a simple yet effective technique to alleviate this problem. In this technique, only a small subset of the full gradients are computed to update the model parameters. In this paper we extend this technique into the Convolutional Neural Network(CNN) to reduce calculation in back propagation, and the surprising results verify its validity in CNN: only 5\% of the gradients are passed back but the model still achieves the same effect as the traditional CNN, or even better. We also show that the top-$k$ selection of gradients leads to a sparse calculation in back propagation, which may bring significant computational benefits for high computational complexity of convolution operation in CNN.
Optical study of polypyrrole perchlorate (1983)

The optical transmittance spectra of polypyrrole perchlorate have been measured at various stages in the reduction to neutral polypyrrole at 300 and 120 K and at high pressure. Analysis of the results suggests that the polypyrrole chain is composed of conjugated segments of various lengths. The optical conductivity spectrum of polypyrrole perchlorate was obtained by the Kramers–Kronig transformation of the transmittance data from 0.025 to 6.25 eV. The spectrum is not consistent with Drude-like free carriers. The conduction mechanism probably involves hopping between the conjugated segments.
Comprehensive School Health Education Programs: Innovative Practices and Issues in Standard Setting (1994)

“In the great work of education…our physical condition, if not the first step in point of importance, is the first in order of time. On the broad and firm foundation of health alone, can the loftiest and most enduring structures of the intellect be reared.”
Robust estimation of road friction coefficient (2011)

Vehicle active safety systems stabilize the vehicle by controlling tire forces. They work well only when the commanded tire forces are within the friction limit. Therefore, knowledge of the tire/road friction is important to improve the performance of vehicle active safety systems. This paper presents two methods to estimate the friction coefficient: one based on lateral dynamics, and one based on longitudinal dynamics. The two methods are then integrated to improve working range of the estimator and robustness. The first method is a nonlinear observer based on vehicle lateral/yaw dynamics and Brush Tire model, the second method is a recursive least squares method based on the relationship between tire longitudinal slip and traction force. The performance of the estimation algorithm is verified using test data under a wide range of friction and speed conditions.
Pectate lyase from Bacillus subtilis: molecular characterization of the gene, and properties of the cloned enzyme (1993)

Pectate lyases (PL) initiate soft-rot diseases in plants by cleaving pectin which is the major component of the plant cell wall. The present paper reports the first cloning and characterization of a pectate lyase (pel) gene from the Bacillus genus. This gene was isolated from a Bacillus subtilis genomic library constructed in pUC18 as vector and Escherichia coli as host. By Southern hybridization this gene was shown to be present in a single copy in the B. subtilis genome. The nucleotide sequence of a 1.6 kb-pair HindIII restriction fragment, which confers pectate lyase activity to E. coli, indicated a 1,260 bp open reading frame encoding a 420 amino acid polypeptide which includes a 21 amino acid signal sequence. The 45,605 Da deduced protein displays homologies to PLs from Erwinia chrysanthemi. The B. subtilis PL cloned in E. coli was located in the periplasm. It was purified to homogeneity in a one-step procedure from the E. coli periplasmic fluid after overproduction using the pT7 system. Biochemical properties of the purified enzyme were similar to those found for the PL isolated from B. subtilis extracellular media.
BADGE, BeadsArray for the Detection of Gene Expression, a High-Throughput Diagnostic Bioassay (2001)

Several methods are presently available for gene expression analysis. However, few of them are suitable for detection of moderate numbers of genes in thousands of samples with high speed and low cost. There is great demand for such a method for use in diagnostics and screening. To address this need, we have developed an assay for gene expression analysis using microspheres and a fluidic instrument made by Luminex. The assay is named Beads Array for the Detection of Gene Expression (BADGE). BADGE can monitor up to 100 genes in a single reaction, and it takes only 1 h to hybridize and <20 sec to read the results of all 100 genes in a sample for the detection process. For the genes detected in five independent replicate experiments, the standard deviation was <35% of the mean. We have monitored multiple pathogenesis-related genes simultaneously in chemical-treated and control Arabidopsis samples employing the BADGE assay. The data were compared with those obtained from an established technology, Affymetrix GeneChip. The changes in expression profiles were very similar. Our study showed that the BADGE assay was capable of profiling expression of multiple genes at affordable cost and rapid speed.
Retrieving documents by plausible inference: a priliminary study (1988)

Choosing an appropriate document representation and search strategy for document retrieval has been largely guided by achieving good average performance instead of optimizing the results for each individual query. A model of retrieval based on plausible inference gives us a different perspective and suggests that techniques should be found for combining multiple sources of evidence (or search strategies) into an overall assessment of a document's relevance, rather than attempting to pick a single strategy. In this paper, we explain our approach to plausible inference for retrieval and describe some preliminary experiments designed to test this approach. The experiments use a spreading activation search to implement the plausible inference process. The results show that significant effectiveness improvements are possible using this approach.
A Recombinant Glycoprotein Vaccine for Herpes Simplex Type 2: Safety and Efficacy (1995)

This subunit vaccine induces both humoral and cellular responses to HSV-2 that are equal to or greater than those of persons with naturally acquired HSV-2 infection. Studies to evaluate this vaccine for the prevention of genital herpes appear warranted.
Structural analysis of monomeric retroviral reverse transcriptase in complex with an RNA/DNA hybrid (2013)

A key step in proliferation of retroviruses is the conversion of their RNA genome to double-stranded DNA, a process catalysed by multifunctional reverse transcriptases (RTs). Dimeric and monomeric RTs have been described, the latter exemplified by the enzyme of Moloney murine leukaemia virus. However, structural information is lacking that describes the substrate binding mechanism for a monomeric RT. We report here the first crystal structure of a complex between an RNA/DNA hybrid substrate and polymerase-connection fragment of the single-subunit RT from xenotropic murine leukaemia virus-related virus, a close relative of Moloney murine leukaemia virus. A comparison with p66/p51 human immunodeficiency virus-1 RT shows that substrate binding around the polymerase active site is conserved but differs in the thumb and connection subdomains. Small-angle X-ray scattering was used to model full-length xenotropic murine leukaemia virus-related virus RT, demonstrating that its mobile RNase H domain becomes ordered in the presence of a substrate-a key difference between monomeric and dimeric RTs.
Combined X-ray, NMR, and Kinetic Analyses Reveal Uncommon Binding Characteristics of the Hepatitis C Virus NS3-NS4A Protease Inhibitor BI 201335 (2011)

Hepatitis C virus infection, a major cause of liver disease worldwide, is curable, but currently approved therapies have suboptimal efficacy. Supplementing these therapies with direct-acting antiviral agents has the potential to considerably improve treatment prospects for hepatitis C virus-infected patients. The critical role played by the viral NS3 protease makes it an attractive target, and despite its shallow, solvent-exposed active site, several potent NS3 protease inhibitors are currently in the clinic. BI 201335, which is progressing through Phase IIb trials, contains a unique C-terminal carboxylic acid that binds noncovalently to the active site and a bromo-quinoline substitution on its proline residue that provides significant potency. In this work we have used stopped flow kinetics, x-ray crystallography, and NMR to characterize these distinctive features. Key findings include: slow association and dissociation rates within a single-step binding mechanism; the critical involvement of water molecules in acid binding; and protein side chain rearrangements, a bromine-oxygen halogen bond, and profound pK(a) changes within the catalytic triad associated with binding of the bromo-quinoline moiety.
Evaluation of a Transposase Protocol for Rapid Generation of Shotgun High-Throughput Sequencing Libraries from Nanogram Quantities of DNA (2011)

Construction of DNA fragment libraries for next-generation sequencing can prove challenging, especially for samples with low DNA yield. Protocols devised to circumvent the problems associated with low starting quantities of DNA can result in amplification biases that skew the distribution of genomes in metagenomic data. Moreover, sample throughput can be slow, as current library construction techniques are time-consuming. This study evaluated Nextera, a new transposon-based method that is designed for quick production of DNA fragment libraries from a small quantity of DNA. The sequence read distribution across nine phage genomes in a mock viral assemblage met predictions for six of the least-abundant phages; however, the rank order of the most abundant phages differed slightly from predictions. De novo genome assemblies from Nextera libraries provided long contigs spanning over half of the phage genome; in four cases where full-length genome sequences were available for comparison, consensus sequences were found to match over 99% of the genome with near-perfect identity. Analysis of areas of low and high sequence coverage within phage genomes indicated that GC content may influence coverage of sequences from Nextera libraries. Comparisons of phage genomes prepared using both Nextera and a standard 454 FLX Titanium library preparation protocol suggested that the coverage biases according to GC content observed within the Nextera libraries were largely attributable to bias in the Nextera protocol rather than to the 454 sequencing technology. Nevertheless, given suitable sequence coverage, the Nextera protocol produced high-quality data for genomic studies. For metagenomics analyses, effects of GC amplification bias would need to be considered; however, the library preparation standardization that Nextera provides should benefit comparative metagenomic analyses.
Progress in the development of metamorphic multi‐junction III–V space solar cells (2002)

Abstract Theoretical calculations have shown that highest‐efficiency III–V multi‐junction solar cells require alloy structures that cannot be grown on a lattice‐matched substrate. Ever since the first demonstration of high‐efficiency metamorphic single‐ junction 1.1 and 1.2 eV InGaAs solar cells, interest has grown in the development of multi‐junction cells of this type, using graded buffer layer technology. Essential Research Incorporated (ERI) is currently developing a dual‐junction 1.6 eV InGaP/1.1 eV InGaAs tandem cell (projected practical air‐mass zero (AM0), one‐sun efficiency of 27%, and 100‐sun efficiency of 31.1%) under a Ballistic Missile Defense Command (BMDO) SBIR Phase II program. A second ongoing research effort involves the development of a 2.1 eV AlGaInP/1.6 eV InGaAsP/1.2 eV InGaAs triple‐junction concentrator tandem cell (projected practical AM0 efficiency 36.5% under 100 suns) under a SBIR Phase II program funded by the Air Force. We are in the process of optimizing the dual‐junction cell performance. For the triple‐junction cell, we have developed the bottom and the middle cell, and are in the process of developing the layer structures needed for the top cell. A progress report is presented in this paper. Copyright © 2002 John Wiley &amp; Sons, Ltd.
Cross-linking in Progressive Keratoconus Using an Epithelial Debridement or Intrastromal Pocket Technique After Previous Corneal Ring Segment Implantation (2011)

Cross-linking surgery with creation of an intrastromal pocket seems to provide similar clinical outcomes compared to the classic CXL technique.
Stages of the Pathologic Process in Alzheimer Disease: Age Categories From 1 to 100 Years (2011)

Two thousand three hundred and thirty two nonselected brains from 1- to 100-year-old individuals were examined using immunocytochemistry (AT8) and Gallyas silver staining for abnormal tau; immunocytochemistry (4G8) and Campbell-Switzer staining were used for the detection ofβ-amyloid. A total of 342 cases was negative in the Gallyas stain but when restaged for AT8 only 10 were immunonegative. Fifty-eight cases had subcortical tau predominantly in the locus coeruleus, but there was no abnormal cortical tau (subcortical Stages a-c). Cortical involvement (abnormal tau in neurites) was identified first in the transentorhinal region (Stage 1a, 38 cases). Transentorhinal pyramidal cells displayed pretangle material (Stage 1b, 236 cases). Pretangles gradually became argyrophilic neurofibrillary tangles (NFTs) that progressed in parallel with NFT Stages I to VI. Pretangles restricted to subcortical sites were seen chiefly at younger ages. Of the total cases, 1,031 (44.2%) had β-amyloid plaques. The first plaques occurred in the neocortex after the onset of tauopathy in the brainstem. Plaques generally developed in the 40s in 4% of all cases, culminating in their tenth decade (75%). β-amyloid plaques and NFTs were significantly correlated (p < 0.0001). These data suggest that tauopathy associated with sporadic Alzheimer disease may begin earlier than previously thought and possibly in the lower brainstem rather than in the transentorhinal region.
Antipyrine congeners as antidepressant agents. (1993)

1-(N-Antipyrinylglycyl)-3-arylideneamino)-2-thiobarbituric acids (III) were synthesized from 1-arylidene-4-(N-antipyrinyl glycyl)-3-thiosemicarbazones (II). Compounds II in turn were prepared from 4-amino antipyrine. Compounds III were finally converted into 1-(N-antipyrinylglycyl)-3-[(3'-chloro-4-aryl)azitidinyl]-2-t hiobarbituric acids (IV). 4-Aminoantipyrine was also treated with different N-protected amino acids in the presence of N,N'-dicyclohexylcarbodiimide to yield N-(antipyrinylcarbamoyl) substituted alkyl benzamides (V); their debenzoylation yielded 2-(amino-N-antipyrinyl) substituted acetamides (VI). The compounds were screened for their antidepressant activity. Compounds IIId, Va and Vb exhibited activity better than imipramine with less toxicity (ALD50 > 1000 mg/kg).
Electrochemical detection of kinase-catalyzed thiophosphorylation using gold nanoparticles (2007)

An electrochemical biosensor for kinase-catalyzed reactions is coupled with the thiophosphorylation of the substrate peptide using adenosine 5'-[gamma-thio] triphosphate (ATP-S) as the co-substrate.
Two monomers of yeast transcription factor ADR1 bind a palindromic sequence symmetrically to activate ADH2 expression. (1991)

ADR1 is a transcription factor from Saccharomyces cerevisiae that regulates ADH2 expression through a 22-bp palindromic sequence (UAS1). Size fractionation studies revealed that full-length ADR1 and a truncated ADR1 protein containing the first 229 amino acids, which has the complete DNA-binding domain, ADR1:17-229, exist as monomers in solution. However, two complexes were formed with target DNA-binding sites. UV-cross-linking studies suggested that these two complexes represent one and two molecules of ADR1 bound to DNA. Studies of ADR1 complexes formed with wild-type UAS1, asymmetrically altered UAS1, and one half of UAS1 showed that ADR1 can bind to one half of UAS1 and gives rise to a complex containing one molecule of ADR1. Dimethyl sulfate interference studies were consistent with this interpretation and in addition indicated that purine contact sites in each half of UAS1 were identical. Increasing the distance between the two halves of UAS1 had at most a minor effect of the thermodynamics of formation of the two complexes. These data are more consistent with ADR1 binding as two independent monomers, one to each half of UAS1. However, binding of two ADR1 monomers at UAS1 is apparently essential for transactivation in vivo. Further, we have identified a stretch of 18 amino acid residues amino terminal to the zinc two-finger domains of ADR1 which is essential for DNA-binding activity. Single amino acid substitutions of residues in this region resulted in severely reduced DNA-binding activity.
IL-10 Is Induced in the Reperfused Myocardium and May Modulate the Reaction to Injury (2000)

Reperfusion of the ischemic myocardium is associated with a dramatic inflammatory response leading to TNF-alpha release, IL-6 induction, and subsequent neutrophil-mediated cytotoxic injury. Because inflammation is also an important factor in cardiac repair, we hypothesized the presence of components of the inflammatory reaction with a possible role in suppressing acute injury. Thus, we investigated the role of IL-10, an anti-inflammatory cytokine capable of modulating extracellular matrix biosynthesis, following an experimental canine myocardial infarction. Using our canine model of myocardial ischemia and reperfusion, we demonstrated significant up-regulation of IL-10 mRNA and protein in the ischemic and reperfused myocardium. IL-10 expression was first detected at 5 h and peaked following 96-120 h of reperfusion. In contrast, IL-4 and IL-13, also associated with suppression of acute inflammation and macrophage deactivation, were not expressed. In the ischemic canine heart, CD5-positive lymphocytes were the predominant source of IL-10 in the myocardial infarct. In the absence of reperfusion, no significant induction of IL-10 mRNA was noted. In addition, IL-12, a Th1-related cytokine associated with macrophage activation, was not detected in the ischemic myocardium. In vitro experiments demonstrated late postischemic cardiac-lymph-induced tissue inhibitor of metalloproteinases (TIMP)-1 mRNA expression in isolated canine mononuclear cells. This effect was inhibited when the incubation contained a neutralizing Ab to IL-10. Our findings suggest that lymphocytes infiltrating the ischemic and reperfused myocardium express IL-10 and may have a significant role in healing by modulating mononuclear cell phenotype and inducing TIMP-1 expression.
Multi-level transcriptome sequencing identifies COL1A1 as a candidate marker in human heart failure progression (2020)

Our results suggested that COL1A1 might be a plasma biomarker of HF and associated with HF progression, especially to predict the 1-year survival from HF onset to transplantation.