gebhart/patrepeval huggingface dataset:
User manual for finite element and finite difference programs: (2003)

This document contains the descriptions, algorithms, user information and listings of the parallel Fortran90/MPI versions of the suite of programs found in NIST-IR 6269 [1], Finite Element and Finite Difference Programs for Computing the Linear Electric and Elastic Properties of Digital Images of Random Materials. These programs use 3-D digital image data on random materials as input and then calculate the effective properties of the random material when subjected to applied fields (for example, mechanical/thermal stresses and AC/DC electric fields).
GroEL (Hsp60) of Clostridium difficile is involved in cell adherence (2001)

Previous results have demonstrated that adherence of Clostridium difficile to tissue culture cells is augmented by various stresses; this study focussed on whether the GroEL heat shock protein is implicated in this process. The 1940 bp groESL operon of C. difficile was isolated by PCR. The 1623 bp groEL gene is highly conserved between various C. difficile isolates as determined by RFLP-PCR and DNA sequencing, and the operon is present in one copy on the bacterial chromosome. The 58 kDa GroEL protein was expressed in Escherichia coli in fusion with glutathione S:-transferase and the fusion protein was purified from IPTG-induced bacterial lysates by affinity chromatography on glutathione-Sepharose. A polyclonal, monospecific antiserum was obtained for GroEL which established by immunoelectron microscopy, indirect immunofluorescence and immunoblot analysis that GroEL is released extracellularly after heat shock and can be surface associated. Cell fractionation experiments suggest that GroEL is predominantly cytoplasmic and membrane bound. GroEL-specific antibodies as well as the purified protein partially inhibited C. difficile cell attachment and expression of the protein was induced by cell contact, suggesting a role for GroEL in cell adherence.
Accuracy of clinical diagnosis of idiopathic Parkinson's disease: a clinico-pathological study of 100 cases. (1992)

Few detailed clinico-pathological correlations of Parkinson's disease have been published. The pathological findings in 100 patients diagnosed prospectively by a group of consultant neurologists as having idiopathic Parkinson's disease are reported. Seventy six had nigral Lewy bodies, and in all of these Lewy bodies were also found in the cerebral cortex. In 24 cases without Lewy bodies, diagnoses included progressive supranuclear palsy, multiple system atrophy, Alzheimer's disease, Alzheimer-type pathology, and basal ganglia vascular disease. The retrospective application of recommended diagnostic criteria improved the diagnostic accuracy to 82%. These observations call into question current concepts of Parkinson's disease as a single distinct morbid entity.
1-Phenylcarbamoyl-2-pyrazolines: a new class of insecticides. 1. Synthesis and insecticidal properties of 3-phenyl-1-phenylcarbamoyl-2-pyrazolines (1977)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXT1-Phenylcarbamoyl-2-pyrazolines: a new class of insecticides. 1. Synthesis and insecticidal properties of 3-phenyl-1-phenylcarbamoyl-2-pyrazolinesKobus Wellinga, Arnold C. Grosscurt, and Roelof Van HesCite this: J. Agric. Food Chem. 1977, 25, 5, 987–992Publication Date (Print):May 1, 1977Publication History Published online1 May 2002Published inissue 1 May 1977https://pubs.acs.org/doi/10.1021/jf60213a018https://doi.org/10.1021/jf60213a018research-articleACS PublicationsRequest reuse permissionsArticle Views196Altmetric-Citations38LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Factor VIIa Inhibitors: Gaining Selectivity within the Trypsin Family. (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Convergence of TCR and cytokine signaling leads to FOXO3a phosphorylation and drives the survival of CD4+ central memory T cells (2006)

The molecular events involved in the establishment and maintenance of CD4+ central memory and effector memory T cells (TCM and TEM, respectively) are poorly understood. In this study, we demonstrate that ex vivo isolated TCM are more resistant to both spontaneous and Fas-induced apoptosis than TEM and have an increased capacity to proliferate and persist in vitro. Using global gene expression profiling, single cell proteomics, and functional assays, we show that the survival of CD4+ TCM depends, at least in part, on the activation and phosphorylation of signal transducer and activator of transcription 5a (STAT5a) and forkhead box O3a (FOXO3a). TCM showed a significant increase in the levels of phosphorylation of STAT5a compared with TEM in response to both IL-2 (P<0.04) and IL-7 (P<0.002); the latter is well known for its capacity to enhance T cell survival. Moreover, ex vivo TCM express higher levels of the transcriptionally inactive phosphorylated forms of FOXO3a and concomitantly lower levels of the proapoptotic FOXO3a target, Bim. Experiments aimed at blocking FOXO3a phosphorylation confirmed the role of this phosphoprotein in protecting TCM from apoptosis. Our results provide, for the first time in humans, an insight into molecular mechanisms that could be responsible for the longevity and persistence of CD4+ TCM.
High-Throughput Models for Exposure-Based Chemical Prioritization in the ExpoCast Project (2013)

The United States Environmental Protection Agency (U.S. EPA) must characterize potential risks to human health and the environment associated with manufacture and use of thousands of chemicals. High-throughput screening (HTS) for biological activity allows the ToxCast research program to prioritize chemical inventories for potential hazard. Similar capabilities for estimating exposure potential would support rapid risk-based prioritization for chemicals with limited information; here, we propose a framework for high-throughput exposure assessment. To demonstrate application, an analysis was conducted that predicts human exposure potential for chemicals and estimates uncertainty in these predictions by comparison to biomonitoring data. We evaluated 1936 chemicals using far-field mass balance human exposure models (USEtox and RAIDAR) and an indicator for indoor and/or consumer use. These predictions were compared to exposures inferred by Bayesian analysis from urine concentrations for 82 chemicals reported in the National Health and Nutrition Examination Survey (NHANES). Joint regression on all factors provided a calibrated consensus prediction, the variance of which serves as an empirical determination of uncertainty for prioritization on absolute exposure potential. Information on use was found to be most predictive; generally, chemicals above the limit of detection in NHANES had consumer/indoor use. Coupled with hazard HTS, exposure HTS can place risk earlier in decision processes. High-priority chemicals become targets for further data collection.
Why Nonoxynol-9 May Have Failed to Prevent Acquisition of Neisseria gonorrhoeae in Clinical Trials (2005)

N gonorrhoeae and H2O2-producing strains of vaginal lactobacilli were not killed by nonoxynol-9 at concentrations greater than those achievable in vivo. Earlier studies that formed the basis for subsequent trials most likely did not detect resistance because too few isolates were evaluated. Large numbers of clinical isolates should be examined before the initiation of clinical trial using microbicidal products.
Drusen complement components C3a and C5a promote choroidal neovascularization (2006)

Age-related macular degeneration (AMD) is the leading cause of irreversible blindness in industrialized nations, affecting 30-50 million people worldwide. The earliest clinical hallmark of AMD is the presence of drusen, extracellular deposits that accumulate beneath the retinal pigmented epithelium. Although drusen nearly always precede and increase the risk of choroidal neovascularization (CNV), the late vision-threatening stage of AMD, it is unknown whether drusen contribute to the development of CNV. Both in patients with AMD and in a recently described mouse model of AMD, early subretinal pigmented epithelium deposition of complement components C3 and C5 occurs, suggesting a contributing role for these inflammatory proteins in the development of AMD. Here we provide evidence that bioactive fragments of these complement components (C3a and C5a) are present in drusen of patients with AMD, and that C3a and C5a induce VEGF expression in vitro and in vivo. Further, we demonstrate that C3a and C5a are generated early in the course of laser-induced CNV, an accelerated model of neovascular AMD driven by VEGF and recruitment of leukocytes into the choroid. We also show that genetic ablation of receptors for C3a or C5a reduces VEGF expression, leukocyte recruitment, and CNV formation after laser injury, and that antibody-mediated neutralization of C3a or C5a or pharmacological blockade of their receptors also reduces CNV. Collectively, these findings establish a mechanistic basis for the clinical observation that drusen predispose to CNV, revealing a role for immunological phenomena in angiogenesis and providing therapeutic targets for AMD.
PPARα Activator Effects on Ang II–Induced Vascular Oxidative Stress and Inflammation (2002)

Docosahexaenoic acid (DHA), a peroxisome proliferator-activated receptor-alpha (PPARalpha) activator, reduces blood pressure (BP) in some hypertensive models by unclear mechanisms. We tested the hypothesis that DHA would prevent BP elevation and improve vascular dysfunction in angiotensin (Ang) II-infused rats by modulating of NADPH oxidase activity and inflammation in vascular wall. Sprague-Dawley rats received Ang II (120 ng/kg per minute SC) with or without DHA (2.5 mL of oil containing 40% DHA/d PO) for 7 days. Systolic BP (mm Hg), elevated in Ang II-infused rats (172+/-3) versus controls (108+/-2, P<0.01), was reduced by DHA (112+/-4). In mesenteric small arteries studied in a pressurized myograph, media/lumen ratio was increased (P<0.05) and acetylcholine-induced relaxation impaired in Ang II-infused rats (P<0.05); both were normalized by DHA. In blood vessels of Ang II-infused rats, NADPH oxidase activity measured by chemiluminescence and expression of adhesion molecules intercellular adhesion molecule and vascular cell adhesion molecule-1 were significantly increased. These changes were abrogated by DHA. PPARalpha activator DHA attenuated the development of hypertension, corrected structural abnormalities, and improved endothelial dysfunction induced by Ang II. These effects are associated with decreased oxidative stress and inflammation in the vascular wall.
Antigenicity and immunogenicity of modified synthetic peptides containing D-amino acid residues. Antibodies to a D-enantiomer do recognize the parent L-hexapeptide and reciprocally. (1993)

The effect of introducing D-amino acid residues in an hexapeptide was examined both at the antigenic and immunogenic levels. A series of D-analogues of the model peptide of sequence IRGERA corresponding to the COOH-terminal residues 130-135 of histone H3 were produced. Four analogues contained a single change of an L-residue by the corresponding enantiomer, one peptide contained two D-residues and another one contained only D-residues (D-enantiomer). A peptide analogue was also synthesized in which the 2 Arg residues were replaced by Lys residues. The parent peptide and peptide analogues were injected into mice after covalent coupling to small unilamellar liposomes containing monophosphoryl lipid A as adjuvant. The substitution of L-Arg131 to Lys or D-Arg was found to change neither the antigenic nor immunogenic properties of the resulting peptides. In contrast, the substitution of Glu133, Arg134, and Ala135 by the respective enantiomers drastically altered the antigenicity of the modified peptides. Each of the six D-analogues induced an immune response with an unusually high level of IgG3 antibodies. The D-enantiomer produced IgG3 antibodies which reacted with the homologous peptide as well as with the all L-peptide and the parent protein H3 in solution but not with analogues containing one or two D-residues only. IgG3 antibodies produced against the all L-peptide reacted with the free all D-peptide but not with the other analogues containing D-residues in position 133, 134, and 135.
Transcription termination and anti‐termination in E. coli (2002)

Transcription termination in Escherichia coli is controlled by many factors. The sequence of the DNA template, the structure of the transcript, and the actions of auxiliary proteins all play a role in determining the efficiency of the process. Termination is regulated and can be enhanced or suppressed by host and phage proteins. This complex reaction is rapidly yielding to biochemical and structural analysis of the interacting factors. Below we review and attempt to unify into basic principles the remarkable recent progress in understanding transcription termination and anti-termination.
Histologic findings in patients with head and neck squamous cell carcinoma receiving perilymphatic natural cytokine mixture (IRX-2) prior to surgery. (1998)

The pathologic changes viewed in the context of the clinical findings indicate that this immunotherapy protocol induces immune regression of the tumor, mediated predominantly by T and B lymphocytes, and thus elicits a tumor-specific immune reaction.
The development of an in-pipe microrobot applying the motion of an earthworm (2002)

This paper describes an in-pipe microrobot to which the motion of an earthworm is applied. A new locomotive unit for the robot is proposed, and the unit was made of two plates connected with an Flexible Micro Actuator (FMA) and four linkages as the legs. The static and dynamic characteristics of FMA were experimentally investigated, and the nonlinear stiffness and the viscous damping were identified. From the driving experiments with a prototype of the robot, which was composed of the three locomotive units, the maximum speed of 2.2mm/s and the maximum traction load of 0.22N were obtained in a pipe 21mm in diameter. The speed of the robot was also theoretically analyzed by taking account of the delay of shrinking of FMA, which was estimated with the identified characteristics, the theoretical speed agreed well with the measured speed.
Synthetic Mimics of Antimicrobial Peptides from Triaryl Scaffolds (2011)

In this report, we describe the synthesis of a new series of small amphiphilic aromatic compounds that mimic the essential properties of cationic antimicrobial peptides using Suzuki-Miyaura coupling. The new design allowed the easy tuning of the conformational restriction, controlled by introduction of intramolecular hydrogen bonds, and the overall hydrophobicity by modifications to the central ring and the side chains. This approach allowed us to better understand the influence of these features on the antimicrobial activity and selectivity. We found that the overall hydrophobicity had a more significant impact on antimicrobial and hemolytic activity than the conformational stiffness. A novel compound was discovered which has MICs of 0.78 μg/mL against S. Aureus and 6.25 μg/mL against E. Coli, similar to the well-known antimicrobial peptide, MSI-78.
Capecitabine and lapatinib uptake in surgically resected brain metastases from metastatic breast cancer patients: a prospective study (2014)

This is the first study to demonstrate that capecitabine and lapatinib penetrate to a significant though variable degree in human BCBM. Drug delivery to BCBM is variable and in many cases appears partially limiting. Elucidating mechanisms that limit drug concentration and innovative approaches to overcome limited drug uptake will be important to improve clinical efficacy of these agents in the central nervous system. Trial registration ID: NCT00795678.
Yersinia Enterocolitica (1989)

YERSINIA ENTEROCOLITICA is rapidly emerging worldwide as an enteric pathogen associated with a wide spectrum of clinical and immunologic manifestations. The clinical illness caused by this pathogen ranges from self-limited enterocolitis to potentially fatal systemic infection; post-infection manifestations include erythema nodosum and reactive arthritis. The organism was first described by Schleifstein and Coleman in 1939 as "an unidentified microorganism resembling Bacterium lignieri and Pasteurella pseudotuberculosis, and pathogenic for man."1 Isolates were variously named Bacterium enterocoliticum, P. X, P. pseudotuberculosis type b, Germe X, and P. pseudotuberculosis X, until 1964, when Frederiksen proposed the name Yersinia enterocolitica.2 In . . .
Purification and properties of the luciferase and of a protein cofactor in the bioluminescence system of Latia neritoides (1968)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPurification and properties of the luciferase and of a protein cofactor in the bioluminescence system of Latia neritoidesOsamu. Shimomura and Frank H. JohnsonCite this: Biochemistry 1968, 7, 7, 2574–2580Publication Date (Print):July 1, 1968Publication History Published online1 May 2002Published inissue 1 July 1968https://pubs.acs.org/doi/10.1021/bi00847a019https://doi.org/10.1021/bi00847a019research-articleACS PublicationsRequest reuse permissionsArticle Views212Altmetric-Citations33LEARN 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
Schooling Behavior of Light‐Powered Autonomous Micromotors in Water (2009)

A new school of thought: Micrometer-sized silver chloride (AgCl) particles (red) in deionized water move under UV illumination by self-diffusiophoresis (see picture). Each AgCl particle secretes ions to which the other particles respond, and they are observed to "school" into regions with higher concentrations of particles. Photo-inactive silica particles (blue) also respond to the chemical secretion by swimming towards and surrounding individual AgCl particles.
Gene Expression Patterns in Deceased Donor Kidneys Developing Delayed Graft Function After Kidney Transplantation (2008)

Cold ischemia time was a predictor of DGF independently of the preservation method. We identified a set of 36 genes candidates of DGF in DDK, with genes involved in the inflammatory response being the more important.
Revision of the Infant Temperament Questionnaire (1978)

The Infant Temperament Questionnaire, originally published in 1970, has been revised to improve its psychometric characteristics. The number of items was increased from 70 to 95, rating options were increased from three to six, more items have high-low reversals, and they are randomized as to content area. The new form was standardized on 203 4- to 8-month-old infants. Good test-retest reliability was maintained and internal consistency of the nine categories was raised to a higher level, thereby assuring a greater reliability of the instrument. These improvements should enhance the questionnaire's use in clinical and research applications.
Preparation and Characterization of Microcellular Polystyrene Foams Processed in Supercritical Carbon Dioxide (1998)

The foaming of polystyrene using supercritical (SC) CO2 has been studied to better understand the microcellular foaming process, as we plan future studies that involve the creation of composite microcellular foams. Rapid decompression of SC CO2-saturated polystyrene at sufficiently high temperatures (above the depressed Tg) yields expanded microcellular foams. The resulting foam structures can be controlled by manipulating processing conditions. Experiments varying the foaming temperature while holding other variables constant show that higher temperatures produce larger cells and reduced densities. Structures range from isotropic cells in samples retaining their initial geometry to highly expanded foams recovered in the shape of the foaming vessel and having oriented, anisotropic cells and limited density reduction. Higher saturation pressures lead to higher nucleation densities and hence smaller cells. Decreasing the rate of depressurization permits a longer period of cell growth and therefore larger cell sizes. Foams having a bimodal distribution of cell sizes can be created by reducing the pressure in two stages.
Species-specific Alternative Splice Mimicry at the Growth Hormone Receptor Locus Revealed by the Lineage of Retroelements during Primate Evolution (2000)

In humans, growth hormone receptor (GHR) transcripts exist in two isoforms differing by the retention (GHRfl) or exclusion (GHRd3) of exon 3, whereas in mice GHRfl is solely expressed. This species-specific expression pattern is believed to result from an alternative splice event that, on the basis of conflicting data obtained in humans, has been considered to be tissue-, developmentally, and/or individual-specific. To decipher the molecular basis of this unusual trait, we isolated a 6.8-kilobase fragment spanning exon 3 from individuals expressing GHRfl. Sequence analysis revealed the existence of two 99% identical retroelements flanking this exon. Unexpectedly, individuals expressing GHRd3 displayed a 2.7-kilobase deletion involving exon 3, which most likely results from an ancestral homologous recombination between the two retroelements. The lineage of these retroelements during primate evolution revealed the species specificity of the GHRd3 allele. These findings led us to propose a model underlying the existence of the sole GHRfl allele in most species. Such a retrovirus-mediated alternative splice mimicry, which clears up several as yet unexplained phenomena (i.e. the above-mentioned expression data, the Mendelian inheritance of GHR expression patterns, and the deletion of nonconsecutive exons in growth hormone resistant patients), represents a novel physiological mechanism accounting for protein diversity between and within species.