gebhart/patrepeval huggingface dataset:
Naturally Occurring IgM Anti-Leukocyte Autoantibodies (IgM-ALA) Inhibit T Cell Activation and Chemotaxis (2008)

The physiological relevance of naturally occurring IgM-ALA remains to be elucidated. These autoantibodies are present from birth and increase in diverse inflammatory states that are both infectious and noninfectious. Clinical observations showing significantly less acute allograft rejections in recipients having high IgM-ALA levels, led us to investigate whether IgM-ALA could have a functional role in attenuating T cell mediated inflammatory responses. In pursuit of this hypothesis, we did studies using IgM purified from the serum of normal individuals, patients with end stage renal disease, and HIV-1 infection. All preparations of IgM immunoprecipitated certain receptors e.g., CD3, CD4, CCR5, and CXCR4 from whole cell lysates but failed to immunoprecipitate IL-2R and HLA Ags. In physiological doses IgM down-regulated CD4, CD2 and CD86 but not CD8 and CD28, inhibited T cell proliferation, decreased production of certain proinflammatory cytokines e.g., TNF-alpha, IL-13 and IL-2, but not IFN- gamma, IL-1beta, GM-CSF, IL-6 and IL-8 and inhibited leukocyte chemotaxis. These inhibitory effects were more pronounced when using IgM from patients with high levels of IgM-ALA and these inhibitory effects were significantly reduced after using IgM preabsorbed with leukocytes. IgM-ALA binding to leukocytes was found to be highly specific, as <10% of IgM secreting B cell clones had IgM-ALA specificity with some clones having specificity for either T cells or monocytes. These findings support the concept that IgM-ALA provides an innate mechanism to regulate T cell mediated inflammatory responses.
Evidence for disease phenotype associated haplotypes (DR.TNF) in sarcoidosis. (2001)

Using theoretical calculations based on actual data, haplotypes, rather than single genes interacting with each other, were found to be a highly likely explanation for the previously published observations. In addition, the results allow the conclusion to be drawn that disease course associated haplotypes in sarcoidosis are highly probable and that further investigation of polymorphisms in the MHC gene region holds the potential of defining prognostic markers.
Solvolytic cyclization of 1-allylindenes (1967)

P. T. Lansbury and E. J. Nienhouse, Chem. Commun. (London), 1967, 1008 DOI: 10.1039/C19670001008
Mathematical model of fetal circulation and oxygen delivery (1985)

To better understand the fetal circulation and its regulation we constructed a dynamic model of fetal circulation as a transport system. The fetal vascular system is divided into 16 compartments which incorporate the peculiarities of the fetal circulation that produce a difference in oxygen concentration in blood supplying the upper and lower body. Recently published data is used to provide a firm experimental base for the model. The model is used to examine how the results on parts of the fetal cardiovascular system and fetal oxygen consumption are compatible and form a coherent description. We also studied the effects of disturbances from the normal steady state produced by changes in patterns of and resistances to blood flow. A maternal placental blood flow of less than 200 ml X min-1 X kg fetal wt-1 produces a steady-state value of oxygen tension in the fetal ascending aorta of less than 17 mmHg, which is incompatible with normal oxygen delivery. A minimal value of umbilical flow providing an adequate oxygen supply to the fetal body is 87 ml X min-1 X kg fetal wt-1. Due to the geometry of the fetal circulation, the highest normal oxygen tension in the fetal ascending aorta is approximately 25 mmHg, only 8 mmHg above the lowest normal tension of 17 mmHg. Dynamic studies using the model demonstrate differences in response of fetal arterial oxygen tension to temporal cord occlusion and temporal decrease in maternal placental flow.
Frequent Detection of Highly Diverse Variants of <i>Cardiovirus</i> , <i>Cosavirus</i> , <i>Bocavirus</i> , and <i>Circovirus</i> in Sewage Samples Collected in the United States (2009)

ABSTRACT Untreated sewage samples from 12 cities in the United States were screened for the presence of recently characterized RNA and DNA viruses found at high prevalence in the stool specimens of South Asian children. Genetic variants of human cosaviruses and cardioviruses in the Picornaviridae family and of DNA circoviruses and human bocaviruses were detected, expanding the known genetic diversity and geographic range of these newly identified viruses. All four virus groups were detected in sewage samples of less than a milliliter from multiple U.S. cities. PCR screening of particle-protected viral nucleic acid in sewage samples could therefore rapidly establish the presence and determine the diversity of four newly described enteric viruses in large urban populations. More frequent and deeper sampling of viral nucleic acids in sewage samples could be used to monitor changes in the prevalence and genetic composition of these and other novel enteric viruses.
Loss of Magel2, a Candidate Gene for Features of Prader-Willi Syndrome, Impairs Reproductive Function in Mice (2009)

Our results suggest that loss of MAGEL2 contributes to the reproductive deficits seen in people with PWS, and further highlights the role of normal circadian rhythm in the maintenance of fertility.
Point of View: An Experimental Study of a Combination Method Using a Pedicle Screw and Laminar Hook for the Osteoporotic Spine (1997)

Associate Professor Director of Spine Research University of California, Davis Sacramento, California
Chemischer Transport von Eisensulfid. III. Der Transport von Bodenkörpern der Zusammensetzung FeS<sub>1,00</sub> (1976)

Abstract Der Transport von FeS 1,0 gelingt mit Transportsystemen, in denen außer S 2 andere schwefelhaltige Spezies in der Gasphase auftreten, wie H 2 S oder Metallsulfide. Die Systeme Fe/S/H/Halogen und Fe/S/Ge (Sn)/Halogen werden experimentell und theoretisch untersucht. Die Rolle des Einflusses der Bodenkörperzusammensetzung auf die Gasphasengleichgewichte und das Transportverhalten wird fur einen Bodenkörper AB x diskutiert.
Implementing a Radiology–Information Technology Project: Mobile Image Viewing Use Case and a General Guideline for Radiologist–Information Technology Team Collaboration (2015)

With an understanding of the types of decisions that benefit from radiologist input, this article outlines an overall project framework to provide a context for how radiologists might engage in the project cycle.
shRNA-seq data analysis with edgeR (2014)

<ns3:p> Pooled short hairpin RNA sequencing (shRNA-seq) screens are becoming increasingly popular in functional genomics research, and there is a need to establish optimal analysis tools to handle such data. Our open-source shRNA processing pipeline in edgeR provides a complete analysis solution for shRNA-seq screen data, that begins with the raw sequence reads and ends with a ranked lists of candidate shRNAs for downstream biological validation. We first summarize the raw data contained in a fastq file into a matrix of counts (samples in the columns, hairpins in the rows) with options for allowing mismatches and small shifts in hairpin position. Diagnostic plots, normalization and differential representation analysis can then be performed using established methods to prioritize results in a statistically rigorous way, with the choice of either the classic exact testing methodology or a generalized linear modelling that can handle complex experimental designs. A detailed users’ guide that demonstrates how to analyze screen data in edgeR along with a point-and-click implementation of this workflow in Galaxy are also provided. The edgeR package is freely available from <ns3:ext-link xmlns:ns4="http://www.w3.org/1999/xlink" ext-link-type="uri" ns4:href="http://www.bioconductor.org/">http://www.bioconductor.org</ns3:ext-link> . </ns3:p>
29th Annual meeting of the Society for Immunotherapy of Cancer (SITC) (2015)

The 29<sup>th</sup> annual meeting of the Society for Immunotherapy of Cancer (SITC) was held November 7-9, 2014 in National Harbor, MD and was organized by Dr. Arthur A. Hurwitz (National Cancer Institute), Dr. Kim A. Margolin (Stanford University), Dr. Daniel E. Speiser (Ludwig Center for Cancer Research, University of Lausanne) and Dr. Walter J. Urba (Earle A. Chiles Research Institute, Providence Cancer Center). This meeting included over 1,600 registered participants from 28 separate countries, making it the largest SITC meeting held to date. It highlighted significant worldwide progress in the development and application of cancer immunology to the practice of clinical oncology, including advances in diagnosis, prognosis and therapy, utilizing several immunological pathways and mechanisms for a variety of oncologic conditions. Presentations and posters demonstrated that many concepts that had been pursued preclinically in the past are now being translated into clinical practice, with clear benefits for patients.
Choline kinase and its functionThis paper is one of a selection of papers published in this special issue entitled “Second International Symposium on Recent Advances in Basic, Clinical, and Social Medicine” and has undergone the Journal's usual peer review process. (2010)

Choline kinase (CK) was discovered in 1953. Progress in understanding the function of CK was slow until its purification in 1984. The subsequent cloning and expression of the cDNA led to the description of the gene structures. Two genes encode choline kinase, Chka and Chkb, and 3 isoforms of the enzyme have been identified - CKalpha-1, CKalpha-2, and CKbeta - and the active form of CK is a hetero- or homo-dimer. More recently, gene-disrupted mice have been described. Mice that lack CKalpha die early in embryogenesis. In contrast, mice that lack CKbeta survive to adulthood, but develop hindlimb muscular dystrophy and forelimb bone deformity. It has been shown that this hindlimb muscular dystrophy is due to decreased biosynthesis of phosphatidylcholine and increased catabolism of phosphatidylcholine in the hindlimbs, but not the forelimbs, of mice. CK and its product phosphocholine have also been implicated in development of numerous cancers. Thus, a possible treatment for some kinds of cancer may involve drug inhibition of CK or targeting the expression of CK with RNA interference. In the mid 1950s it was clear that CK was important for the biosynthesis of phosphatidylcholine, but no one predicted a role for CK in muscular dystrophy, bone deformities, or cancer.
Zeolites: A Primer (2003)

Zeolites are microporous crystalline aluminosilicates, composed of TO4 tetrahedra (T=Si, Al) with O atoms connecting neighboring tetrahedra. For a completely siliceous structure, combination of TO4 (T=Si) units in this fashion leads to silica (SiO2), which is an uncharged solid. Upon incorporation of Al into the silica framework, the +3 charge on the Al makes the framework negatively charged, and requires the presence of extraframework cations (inorganic and organic cations can satisfy this requirement) within the structure to keep the overall framework neutral. The zeolite composition can be best described as having three components:The extraframework cations are ion exchangeable and give rise to the rich ion-exchange chemistry of these materials. The novelty of zeolites stems from their microporosity and is a result of the topology of the framework.
ITS-RFLP pattern of <i>Bursaphelenchus xylophilus</i> (Nematoda: Aphelenchoididae) does not reflect nematode virulence (2012)

Analysis of the restriction fragment length polymorphism of the internal transcribed spacer region of ribosomal DNA (ITS-RFLP) is an efficient tool for classifying Bursaphelenchus nematodes at or below the species level. In B. xylophilus, it has been shown that the ITS-RFLP pattern of Japanese avirulent (nonpathogenic) isolates is different from that of Japanese virulent (pathogenic) isolates. To clarify the relationship between the virulence and the ITS-RFLP pattern of B. xylophilus, an experiment involving inoculation of the nematodes was performed. Two types of nematode subculture that showed the same RFLP pattern as the virulent isolate or the avirulent isolate were produced from a new nematode population obtained in the field and inoculated into healthy pine seedlings. All seedlings inoculated with the nematode subcultures died within six months, irrespective of whether the subculture had the virulent or avirulent RFLP pattern; this indicated that the nematode virulence does not correspond with the ITS-RFLP pattern. This study shows that the ITS-RFLP pattern is not always available to discriminate between avirulent and virulent populations of B. xylophilus.
In-plane electron dynamics and hot electron effects in a quantum cascade laser (1997)

A model of a quantum cascade laser in the near threshold regime is formed. The influence of the thermal population on the threshold current and the gain is estimated by the model. Subband populations and electron dynamics are solved within a rate-equation formalism derived from the non-stationary Boltzmann equation. The model offers a direct account of the dependence of the subband population on the current density and the dependence of the threshold current on the temperature. Very good agreement between the experimental results and our model is obtained.
Two-dimensional hybrid model of inductively coupled plasma sources for etching (1993)

Inductively coupled plasmas (ICPs) are currently being investigated as high density (≳1011–1012 cm−3), low pressure (&lt;1–20 mTorr) sources for semiconductor etching and deposition. We have developed a two-dimensional (r,z) hybrid model for ICP sources and have used the model to investigate Ar/CF4/O2 mixtures for etching applications. The simulation consists of electromagnetic, electron Monte Carlo, and hydrodynamic modules with an ‘‘off-line’’ plasma chemistry Monte Carlo simulation. The model produces the temporally and spatially dependent magnetic and electric fields (both inductively and capacitively coupled), plasma densities, and the energy resolved flux of ions and radicals to the substrate. We discuss results for densities, power deposition, and ion energies to the substrate as a function of position.
Synthesis and reactions of tungsten(IV) bis(imido) complexes: relatives of bent metallocenes (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis and reactions of tungsten(IV) bis(imido) complexes: relatives of bent metallocenesDarryl S. Williams, Mark H. Schofield, Jens T. Anhaus, and Richard R. SchrockCite this: J. Am. Chem. Soc. 1990, 112, 18, 6728–6729Publication Date (Print):August 1, 1990Publication History Published online1 May 2002Published inissue 1 August 1990https://pubs.acs.org/doi/10.1021/ja00174a052https://doi.org/10.1021/ja00174a052research-articleACS PublicationsRequest reuse permissionsArticle Views354Altmetric-Citations79LEARN 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
National mortality rates from chronic liver disease and consumption of alcohol and pig meat (2009)

A correlation between national pig-meat consumption and mortality rates from chronic liver disease (CLD) across developed countries was reported in 1985. One possible mechanism explaining this may be hepatitis E infection spread via pig meat. We aimed to re-examine the original association in more recent international data. Regression models were used to estimate associations between national pig-meat consumption and CLD mortality, adjusting for confounders. Data on CLD mortality, alcohol consumption, hepatitis B virus (HBV) and hepatitis C virus (HCV) seroprevalence for 18 developed countries (1990-2000) were obtained from WHO databases. Data on national pig-meat and beef consumption were obtained from the UN database. Univariate regression showed that alcohol and pig-meat consumption were associated with mortality from CLD, but beef consumption, HBV and HCV seroprevalence were not. A 1 litre per capita increase in alcohol consumption was associated with an increase in mortality from CLD in excess of 1.6 deaths/100,000 population. A 10 kg higher national annual average per capita consumption of pork meat was associated with an increase in mortality from CLD of between 4 and 5 deaths/100,000 population. Multivariate regression showed that alcohol, pig-meat consumption and HBV seroprevalence were independently associated with mortality from CLD, but HCV seroprevalence was not. Pig-meat consumption remained independently associated with mortality from CLD in developed countries in the 1990-2000 period. Further work is needed to establish the mechanism.
A Methodology for the Refinement of Well Locations During Operational Drilling in Presence of Geological Uncertainty (2016)

Abstract In this paper we present a methodology of automated optimal (in terms of NPV maximization) greenfield development strategy construction that takes into account geological uncertainties of the reservoir. The algorithm is based on ensemble of hydrodynamic models and uses the theory of probabilistic graphical models. The proposed methodology allows making dynamic (in the process of field development) decisions about well grid pattern change on the basis of information obtained from the studies on the oil reservoir carried out with the help of the appraisal wells: appraisal boreholes of the development wells and pre-drilling wells (drilling from current pad to the next one for refining geological targets). The decision of the wells pattern option change does not require any additional calculations. The proposed methodology was applied for creating optimal development strategy for one of the new assets (on production stage) of JSC "Gazprom neft". The reservoir development is complicated by the set of uncertain parameters related to the complex heterogeneous structure of the collector. The parameters have very high influence on the optimal decision choice. As result expected NPV is increased by 15%.
Molecular mechanics in the undergraduate curriculum (1991)

The author outlines recent experience with the introduction of molecular mechanics methodology via computer aided analysis of molecular geometry and energy. Students gained appreciation for the interplay of molecular forces that govern equilibrium energy and molecular forces of organic molecules.
Differential Effects of Lipid-lowering Drugs in Modulating Morphology of Cholesterol Particles (2017)

Treatment of dyslipidemia patients with lipid-lowering drugs leads to a significant reduction in low-density lipoproteins (LDL) level and a low to moderate level of increase in high-density lipoprotein (HDL) cholesterol in plasma. However, a possible role of these drugs in altering morphology and distribution of cholesterol particles is poorly understood. Here, we describe the in vitro evaluation of lipid-lowering drug effects in modulating morphological features of cholesterol particles using the plaque array method in combination with imaging flow cytometry. Image analyses of the cholesterol particles indicated that lovastatin, simvastatin, ezetimibe, and atorvastatin induce the formation of both globular and linear strand-shaped particles, whereas niacin, fibrates, fluvastatin, and rosuvastatin induce the formation of only globular-shaped particles. Next, purified very low-density lipoprotein (VLDL) and LDL particles incubated with these drugs showed changes in the morphology and image texture of cholesterol particles subpopulations. Furthermore, screening of 50 serum samples revealed the presence of a higher level of linear shaped HDL cholesterol particles in subjects with dyslipidemia (mean of 18.3%) compared to the age-matched normal (mean of 11.1%) samples. We also observed considerable variations in lipid-lowering drug effects on reducing linear shaped LDL and HDL cholesterol particles formation in serum samples. These findings indicate that lipid-lowering drugs, in addition to their cell-mediated hypolipidemic effects, may directly modulate morphology of cholesterol particles by a non-enzymatic mechanism of action. The outcomes of these results have potential to inform diagnosis of atherosclerosis and predict optimal lipid-lowering therapy.
Übergangsmetall‐Methylen‐Komplexe, XLV. Ein vereinfachtes Syntheseverfahren für μ‐Alkyliden‐Komplexe am Beispiel neuartiger Dimetallaspirane (1984)

Abstract Die Organometall‐Edukte 1a und 1b reagieren an der Metall‐Metall‐Doppelbindung mit den aus den Hydrazonen 2a – i und Mangandioxid erzeugten Diazoalkanen unter Stickstoffabspaltung übersichtlich zu den μ‐Alkyliden‐Komplexen 3a – i bzw. 4a – c , f , i . So sind erstmalig auch Dimetallaspirane zugänglich wie z.B. der μ‐Cyclobutyliden‐rhodium‐Komplex 3a , dessen Struktur durch Röntgenbeugung ermittelt wurde. Der Cyclobutanring ist mit 20° gefaltet und liegt symmetrisch zwischen den Rh‐Atomen.
Telomerase reverse transcriptase induces basal and amino acid starvation-induced autophagy through mTORC1 (2016)

Telomerase is a reverse transcriptase that consists of the telomerase RNA component (TERC) and the reverse transcriptase catalytic subunit (TERT) and specializes in the elongation of telomere ends. New evidence suggests that beyond classical telomere maintenance, TERT also possesses telomere length-independent functions that are executed via interaction with other binding proteins. One such reported TERT-interacting proteins is mTOR, a master nutrient sensor that is upregulated in several cancers; however, the physiological implications of the TERT-mTOR interaction in normal cellular processes as well as in tumorigenesis are poorly understood. Here, we report that TERT inhibits the kinase activity of mTOR complex 1 (mTORC1) in multiple cell lines, resulting in the activation of autophagy under both basal and amino acid-deprived conditions. Furthermore, TERT-deficient cells display the inability to properly execute the autophagy flux. Functionally, TERT-induced autophagy provides a survival advantage to cells in nutrient-deprived conditions. Collectively, these findings support a model in which gain of TERT function modulates mTORC1 activity and induces autophagy, which is required for metabolic rewiring to scavenge the nutrients necessary for fueling cancer cell growth in challenging tumor microenvironments.