gebhart/patrepeval huggingface dataset:
A Cladistic Analysis of Phenotypic Associations With Haplotypes Inferred From Restriction Endonuclease Mapping. I. Basic Theory and an Analysis of Alcohol Dehydrogenase Activity in Drosophila (1987)

Because some genes have been cloned that have a known biochemical or physiological function, genetic variation can be measured in a population at loci that may directly influence a phenotype of interest. With this measured genotype approach, specific alleles or haplotypes in the probed DNA region can be assigned phenotypic effects. In this paper we address several problems encountered in implementing the measured genotype approach with restriction site data. A number of analytical problems arise in part as a consequence of the linkage disequilibrium that is commonly encountered when dealing with small DNA regions: 1) different restriction site polymorphisms are not statistically independent, 2) the sites being measured are not likely to be the direct cause of the associated phenotypic effects, 3) haplotype classes may be phenotypically heterogeneous, and 4) the sites that are most strongly associated with phenotypic effects are not necessarily the most closely linked to the actual genetic cause of the effects. When recombination and gene conversion are rare, the primary cause of linkage disequilibrium is history (mutational origin, genetic drift, hitchhiking, etc.). We deal with historical association directly by producing a cladogram that partially reconstructs the evolutionary history of the present-day haplotype variability. The cladogram defines a nested analysis of variance that simultaneously detects phenotypic effects, localizes the effects within the cladogram, and identifies haplotypes that are potentially heterogeneous in their phenotypic associations. The power of this approach is illustrated by an analysis of the associations between alcohol dehydrogenase (ADH) activity and restriction site variability in a 13-kb fragment surrounding the ADH locus in Drosophila melanogaster.
A mitochondrial-like aconitase in the bacterium Bacteroides fragilis : Implications for the evolution of the mitochondrial Krebs cycle (2002)

Aconitase and isocitrate dehydrogenase (IDH) enzyme activities were detected in anaerobically prepared cell extracts of the obligate anaerobe Bacteroides fragilis. The aconitase gene was located upstream of the genes encoding the other two components of the oxidative branch of the Krebs cycle, IDH and citrate synthase. Mutational analysis indicates that these genes are cotranscribed. A nonpolar in-frame deletion of the acnA gene that encodes the aconitase prevented growth in glucose minimal medium unless heme or succinate was added to the medium. These results imply that B. fragilis has two pathways for alpha-ketoglutarate biosynthesis-one from isocitrate and the other from succinate. Homology searches indicated that the B. fragilis aconitase is most closely related to aconitases of two other Cytophaga-Flavobacterium-Bacteroides (CFB) group bacteria, Cytophaga hutchinsonii and Fibrobacter succinogenes. Phylogenetic analysis indicates that the CFB group aconitases are most closely related to mitochondrial aconitases. In addition, the IDH of C. hutchinsonii was found to be most closely related to the mitochondrial/cytosolic IDH-2 group of eukaryotic organisms. These data suggest a common origin for these Krebs cycle enzymes in mitochondria and CFB group bacteria.
Neural cell adhesion molecule (N-CAM) domains and intracellular signaling pathways involved in the inhibition of astrocyte proliferation (1998)

The neural cell adhesion molecule (N-CAM) inhibits astrocyte proliferation in vitro and in vivo, and this effect is partially reversed by the glucocorticoid antagonist RU-486. The present studies have tested the hypothesis that N-CAM-mediated inhibition of astrocyte proliferation is caused by homophilic binding and involves the activation of glucocorticoid receptors. It was observed that all N-CAM Ig domains inhibited astrocyte proliferation in parallel with their ability to influence N-CAM binding. The proliferation of other N-CAM-expressing cells also was inhibited by the addition of N-CAM. In contrast, the proliferation of astrocytes from knockout mice lacking N-CAM was not inhibited by added N-CAM. These findings support the hypothesis that it is binding of soluble N-CAM to N-CAM on the astrocyte surface that leads to decreased proliferation. Signaling pathways stimulated by growth factors include activation of mitogen-activated protein (MAP) kinase. Addition of N-CAM inhibited MAP kinase activity induced by basic fibroblast growth factor in astrocytes. In accord with previous findings that RU-486 could partially prevent the proliferative effects of N-CAM, inhibition of MAP kinase activity by N-CAM was reversed by RU-486. The ability of N-CAM to inhibit astrocyte proliferation was unaffected, however, by agents that block the ability of N-CAM to promote neurite outgrowth. Together, these findings indicate that homophilic N-CAM binding leads to inhibition of astrocyte proliferation via a pathway involving the glucocorticoid receptor and that the ability of N-CAM to influence astrocyte proliferation and neurite outgrowth involves different signal pathways.
A Longitudinal Study of Birth Weight and Being Overweight in Late Adolescence (1991)

A total of 33,413 infants born in Jerusalem between 1964 and 1971 were followed up at 17 years of age by matching computerized database files. A logistic regression model was used to estimate the odds ratios for being overweight at 17 years of age for 500-g birth weight categories from less than 2500 g to 4500 g or greater. Information on the ethnic origin, paternal education, birth order, maternal age, and area of residence at birth was available, and these factors were used as possible confounders. The adjusted odds ratios for being overweight (greater than or equal to 90th percentile; body mass index greater than 24.6 kg/m2) and severely overweight (greater than or equal to 97th percentile; body mass index greater than 27.8 kg/m2) at 17 years of age was elevated for the three birth weight categories above the normal reference category of 3000 to 3499 g, with an estimate of 2.16 and 2.30 for male subjects with a birth weight greater than 4500 g and 2.95 and 4.39 for female subjects. The data suggest that higher birth weights correlate strongly with being overweight in late adolescence independently of other factors considered. However, the predictive power of this association is poor.
Modeling the Exchanges of Energy, Water, and Carbon Between Continents and the Atmosphere (1997)

Atmospheric general circulation models used for climate simulation and weather forecasting require the fluxes of radiation, heat, water vapor, and momentum across the land-atmosphere interface to be specified. These fluxes are calculated by submodels called land surface parameterizations. Over the last 20 years, these parameterizations have evolved from simple, unrealistic schemes into credible representations of the global soil-vegetation-atmosphere transfer system as advances in plant physiological and hydrological research, advances in satellite data interpretation, and the results of large-scale field experiments have been exploited. Some modern schemes incorporate biogeochemical and ecological knowledge and, when coupled with advanced climate and ocean models, will be capable of modeling the biological and physical responses of the Earth system to global change, for example, increasing atmospheric carbon dioxide.
Calcification of oral bacteria: an ultra structural study of two strains of Bacterionema matruchotii (1974)

ABSTRACT – The purpose of this study was to test the hypothesis that the pattern of calcification of dental plaque — either intracellularly or extracellularly — is dependent on the type of microorganisms present. Two strains of Bacterionema matruchotii . Strain 13 (Richardson) and Strain 14266 ATCC, were grown in an in vitro system and their calcification studied by transmission electron microscopy. Mineral crystals appeared in the specimens in scattered areas after 2 weeks of incubation, but consistently and in significant amounts after 4 weeks. In Strain 13 the crystals occurred only intracellularly, while in Strain 14266 the crystals were seen both within and around the bacteria. In the Strain 14266 specimens the extracellular crystals were often related to trilaminar vesicles and cell remnants. Differences in potential of calcification between closely related bacterial strains may partly explain the differences observed between calculus formers and non‐formers.
Analysis of condensed tannins using acidified vanillin (1978)

Abstract The acidified vanillin method for determination of plant tannins has been reassessed. Excluding light and controlling the temperature of the reaction mixture increased the colour stability of the vanillin tannin adduct. Selection of optimum concentrations of reactants and solvents enabled the method to be used in the range 5‐500 μg of condensed tannin with a precision and accuracy greater than 1 μg.
The Canadian MSAT Field Trials Program (2003)

The Canadian Department of Communications is providing a multi-year program for implementation of market trials involving the introduction of new MSAT services in Canada. The author describes the Department's Field Trials Program that commenced in late 1990. The Trials Program includes end-users requiring wide-area portable communications or fixed wide-area communications for the monitoring of remote equipment such as weather stations, gas compressor stations and water level monitoring. The Field Trials Program is operated in conjunction with Telsat Mobile Inc., who have introduced Phase I commercial data services using leased satellite capacity from Inmarsat on Marecs B-2 The author describes the existing mobile and fixed satellite terminals and also the results of the Trials Program to date.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Semidominant Suppressors of Srs2 Helicase Mutations of Saccharomyces cerevisiae Map in the RAD51 Gene, Whose Sequence Predicts a Protein with Similarities to Procaryotic RecA Proteins (1992)

Eleven suppressors of the radiation sensitivity of Saccharomyces cerevisiae diploids lacking the Srs2 helicase were analyzed and found to contain codominant mutations in the RAD51 gene known to be involved in recombinational repair and in genetic recombination. These mutant alleles confer an almost complete block in recombinational repair, as does deletion of RAD51, but heterozygous mutant alleles suppress the defects of srs2::LEU2 cells and are semidominant in Srs2+ cells. The results of this study are interpreted to mean that wild-type Rad51 protein binds to single-stranded DNA and that the semidominant mutations do not prevent this binding. The cloning and sequencing of RAD51 indicated that the gene encodes a predicted 400-amino-acid protein with a molecular mass of 43 kDa. Sequence comparisons revealed homologies to domains of Escherichia coli RecA protein predicted to be involved in DNA binding, ATP binding, and ATP hydrolysis. The expression of RAD51, measured with a RAD51-lacZ gene fusion, was found to be UV- and gamma-ray-inducible, with dose-dependent responses.
Simulated 14 C production rates for the troposphere and stratosphere in weak geomagnetic intensity at 26,000 yr BP (2011)

The 14 C ages of single single-yr tree rings ha have ve been measur measuring ing for the Kaminoyama wood sample using AMS, in order to investigate periodic variations of 14 C concentrations relati relating to an 11 ng 11-yr solar cycle at 26,000 yr BP. It is an interesting era because the geomagnetic intensity was approximately 40％ weaker compared with pr present time. sent We have globally simulated the e 14 C production rates as functions of latitude, longitude, and al altitude using E titude EXPACS PACS to investigate the affection of weak geomagnetic intensity to the 14 C production production. The peak altitude of he 14C production rates was approximately 12 km and the production rates at lower alt altitude than tude 20 km were approximately 83 ％ of the total production rate up to 50 km. The troposphere components were 52％ and 48.4％ of total productions at the min mini- imum and maximum of solar modulation, respectively. mum For the geomagnetic inte intensity in the vicinity of 26 sity 26,000 yr BP, the variation rate of solar m modulation increases to 41％ from 37％ at pr odulation present for the air sent air-mass up to 20 km altitude.
Fungal ribotoxins: molecular dissection of a family of natural killers (2007)

RNase T1 is the best known representative of a large family of ribonucleolytic proteins secreted by fungi, mostly Aspergillus and Penicillium species. Ribotoxins stand out among them by their cytotoxic character. They exert their toxic action by first entering the cells and then cleaving a single phosphodiester bond located within a universally conserved sequence of the large rRNA gene, known as the sarcin-ricin loop. This cleavage leads to inhibition of protein biosynthesis, followed by cellular death by apoptosis. Although no protein receptor has been found for ribotoxins, they preferentially kill cells showing altered membrane permeability, such as those that are infected with virus or transformed. Many steps of the cytotoxic process have been elucidated at the molecular level by means of a variety of methodological approaches and the construction and purification of different mutant versions of these ribotoxins. Ribotoxins have been used for the construction of immunotoxins, because of their cytotoxicity. Besides this activity, Aspf1, a ribotoxin produced by Aspergillus fumigatus, has been shown to be one of the major allergens involved in allergic aspergillosis-related pathologies. Protein engineering and peptide synthesis have been used in order to understand the basis of these pathogenic mechanisms as well as to produce hypoallergenic proteins with potential diagnostic and immunotherapeutic applications.
Intracoronary Infusion of CD133 + and CD133 − CD34 + Selected Autologous Bone Marrow Progenitor Cells in Patients with Chronic Ischemic Cardiomyopathy: Cell Isolation, Adherence to the Infarcted Area, and Body Distribution (2006)

Central issues in intracoronary infusion (ICI) of bone marrow (BM)-cells to damaged myocardium for improving cardiac function are the cell number that is feasible and safe to be administrated as well as the retention of cells in the target area. Our study addressed these issues in eight patients with chronic ischemic cardiomyopathy undergoing ICI of selected BM-progenitors. We could immunomagnetically isolate 0.8 +/- 0.32 x 10(7) CD133(+) cells and 0.75 +/- 0.24 x 10(7) CD133(-)CD34(+) cells from 310 +/- 40 ml BM. After labeling these cells with (99m)Tc-hexamethylpropylenamineoxime, they were infused into the infarct-related artery without any complication. Scintigraphic images 1 (eight patients) and 24 hours (four patients) after ICI revealed an uptake of 9.2% +/- 3.6 and 6.8% +/- 2.4 of the total infused radioactivity in the infarcted area of the heart, respectively; the remaining activity was distributed mainly to liver and spleen. We conclude that through ICI of CD133(+) and CD133(-)CD34(+) BM-progenitors a significant number of them are preferentially attracted to and retained in the chronic ischemic myocardium.
2‘-Amino-2‘-deoxyuridine via an Intramolecular Cyclization of a Trichloroacetimidate (1996)

ADVERTISEMENT RETURN TO ISSUEPREVNoteNEXT2'-Amino-2'-deoxyuridine via an Intramolecular Cyclization of a TrichloroacetimidateDanny P. C. McGee, Alecia Vaughn-Settle, Chandra Vargeese, and Yansheng ZhaiView Author Information NeXstar, inc., 2860 Wilderness Place, Boulder, Colorado 80301 Cite this: J. Org. Chem. 1996, 61, 2, 781–785Publication Date (Web):January 26, 1996Publication History Received9 June 1995Published online26 January 1996Published inissue 1 January 1996https://doi.org/10.1021/jo9510548Copyright © 1996 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views1262Altmetric-Citations57LEARN 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 InReddit Read OnlinePDF (207 KB) Get e-AlertsSUBJECTS:Beverages,Chemical reactions,Chemical synthesis,Mixtures,Nucleic acids Get e-Alerts
A review of breast tomosynthesis. Part II. Image reconstruction, processing and analysis, and advanced applications (2013)

Many important post-acquisition aspects of breast tomosynthesis imaging can impact its clinical performance. Chief among them is the reconstruction algorithm that generates the representation of the three-dimensional breast volume from the acquired projections. But even after reconstruction, additional processes, such as artifact reduction algorithms, computer aided detection and diagnosis, among others, can also impact the performance of breast tomosynthesis in the clinical realm. In this two part paper, a review of breast tomosynthesis research is performed, with an emphasis on its medical physics aspects. In the companion paper, the first part of this review, the research performed relevant to the image acquisition process is examined. This second part will review the research on the post-acquisition aspects, including reconstruction, image processing, and analysis, as well as the advanced applications being investigated for breast tomosynthesis.
Enteropathogenic and enterohaemorrhagic Escherichia coli : more subversive elements (1998)

Enteropathogenic (EPEC) and enterohaemorrhagic Escherichia coli (EHEC) constitute a significant risk to human health worldwide. Both pathogens colonize the intestinal mucosa and, by subverting intestinal epithelial cell function, produce a characteristic histopathological feature known as the 'attaching and effacing' (A/E) lesion. Although EPEC was the first E. coli to be associated with human disease in the 1940s and 1950s, it was not until the late 1980s and early 1990s that the mechanisms and bacterial gene products used to induce this complex brush border membrane lesion and diarrhoeal disease started to be unravelled. During the past few months, there has been a burst of new data that have revolutionized some basic concepts of the molecular basis of bacterial pathogenesis in general and EPEC pathogenesis in particular. Major breakthroughs and developments in the genetic basis of A/E lesion formation, signal transduction, protein translocation, host cell receptors and intestinal colonization are highlighted in this review.
Construction of Acetate Auxotrophs of Neisseria meningitidis to Study Host-Meningococcal Endotoxin Interactions (2001)

To facilitate studies of the molecular determinants of host-meningococcal lipooligosaccharide (endotoxin) interactions at patho-physiologically relevant endotoxin concentrations (i.e. < or =10 ng/ml), we have generated acetate auxotrophs NMBACE1 from encapsulated Neisseria meningitidis (serogroup B, strain NMB) and NMBACE2 from an isogenic bacterial mutant lacking the polysialic acid capsule. Growth of the auxotrophs in medium containing [(14)C]acetate yielded (14)C-lipooligosaccharides containing approximately 600 cpm/ng. Gel sieving resolved 14C-lipooligosaccharide-containing aggregates with an estimated molecular mass of > or =20 x 10(6) Da (peak A) and approximately 1 x 10(6) Da (peak B) from both strains. Lipooligosaccharides in peaks A and B had the same fatty acid composition and SDS-polyacrylamide gel electrophoresis profile. 14C-Labeled capsule copurified with (14)C-lipooligosaccharides in peak B from NMBACE1, whereas the other aggregates contained only 14C-lipooligosaccharide. For all aggregates, lipopolysaccharide-binding protein and soluble CD14-induced delivery of lipooligosaccharides to endothelial cells and cell activation correlated with disaggregation of lipooligosaccharides. These processes were inhibited by the presence of capsule but unaffected by the size of the aggregates. In contrast, endotoxin activation of cells containing membrane CD14 was unaffected by capsule but diminished when endotoxin was presented in larger aggregates. These findings demonstrate that the physical presentation of lipooligosaccharide, including possible interactions with capsule, affect the ability of meningococcal endotoxin to interact with and activate specific host targets.
IL-10 inhibits transcription of cytokine genes in human peripheral blood mononuclear cells. (1994)

Upon addition of LPS to human PBMCs, IL-1 beta, IL-6, and TNF-alpha were released in the culture media in a time-dependent manner. Cytokine release began 2 h after LPS addition and maximal release of all three cytokines was observed between 6 and 8 h. Northern analysis revealed that, for each cytokine, mRNA accumulation preceded protein release. When added either 2 h before or at the same time as LPS, IL-10 inhibited both the cytokine release and mRNA accumulation almost completely. Similar inhibition was observed when IL-10 was added 2 h after LPS, a time point that coincided with the onset of the rapid burst of cytokine mRNA accumulation. The inhibitory activity of IL-10 was abrogated by cycloheximide, suggesting an involvement of newly synthesized proteins in IL-10 action. By using nuclear run-on transcription assays, we have found that IL-10 inhibited transcription of all three cytokine genes in LPS-stimulated PBMCs. In contrast, IL-10 moderately enhanced degradation of IL-6 mRNA, but not of mRNAs for IL-1 beta and TNF-alpha. Thus, the present study provides the first evidence that, in human PBMCs, IL-10 inhibits cytokine synthesis by acting mainly at the level of cytokine gene transcription.
WCET-Directed Dynamic Scratchpad Memory Allocation of Data (2007)

Many embedded systems feature processors coupled with a small and fast scratchpad memory. To the difference with caches, allocation of data to scratchpad memory must be handled by software. The major gain is to enhance the predictability of memory accesses latencies. A compile-time dynamic allocation approach enables eviction and placement of data to the scratchpad memory at runtime. Previous dynamic scratchpad memory allocation approaches aimed to reduce average-case program execution time or the energy consumption due to memory accesses. For real-time systems, worst-case execution time is the main metric to optimize. In this paper, we propose a WCET-directed algorithm to dynamically allocate static data and stack data of a program to scratchpad memory. The granularity of placement of memory transfers (e.g. on function, basic block boundaries) is discussed from the perspective of its computation complexity and the quality of allocation.