gebhart/patrepeval huggingface dataset:
Restrictions in systemic and locomotor skeletal muscle perfusion, oxygen supply andVO2during high‐intensity whole‐body exercise in humans (2008)

Perfusion to exercising skeletal muscle is regulated to match O(2) delivery to the O(2) demand, but this regulation might be compromised during or approaching maximal whole-body exercise as muscle blood flow for a given work rate is blunted. Whether muscle perfusion is restricted when there is an extreme metabolic stimulus to vasodilate during supramaximal exercise remains unknown. To examine the regulatory limits of systemic and muscle perfusion in exercising humans, we measured systemic and leg haemodynamics, O(2) transport, and , and estimated non-locomotor tissue perfusion during constant load supramaximal cycling (498 +/- 16 W; 110% of peak power; mean +/- S.E.M.) in addition to both incremental cycling and knee-extensor exercise to exhaustion in 13 trained males. During supramaximal cycling, cardiac output (Q), leg blood flow (LBF), and systemic and leg O(2) delivery and reached peak values after 60-90 s and thereafter levelled off at values similar to or approximately 6% (P < 0.05) below maximal cycling, while upper body blood flow remained unchanged (approximately 5.5 l min(-1)). In contrast, Q and LBF increased linearly until exhaustion during one-legged knee-extensor exercise accompanying increases in non-locomotor tissue blood flow to approximately 12 l min(-1). At exhaustion during cycling compared to knee-extensor exercise, Q, LBF, leg vascular conductance, leg O(2) delivery and leg for a given power were reduced by 32-47% (P < 0.05). In conclusion, locomotor skeletal muscle perfusion is restricted during maximal and supramaximal whole-body exercise in association with a plateau in Q and limb vascular conductance. These observations suggest that limits of cardiac function and muscle vasoconstriction underlie the inability of the circulatory system to meet the increasing metabolic demand of skeletal muscles and other tissues during whole-body exercise.
Homologs of the Yeast Longevity GeneLAG1inCaenorhabditis elegansand Human (1998)

LAG1 is a longevity gene, the first such gene to be identified and cloned from the yeast Saccharomyces cerevisiae. A close homolog of this gene, which we call LAC1, has been found in the yeast genome. We have cloned the human homolog of LAG1 with the ultimate goal of examining its possible function in human aging. In the process, we have also cloned a homolog from the nematode worm Caenorhabditis elegans. Both of these homologs, LAG1Hs and LAG1Ce-1, functionally complemented the lethality of a lag1delta lac1delta double deletion, despite low overall sequence similarity to the yeast proteins. The proteins shared a short sequence, the Lag1 motif, and a similar transmembrane domain profile. Another, more distant human homolog, TRAM, which lacks this motif, did not complement. LAG1Hs also restored the life span of the double deletion, demonstrating that it functions in establishing the longevity phenotype in yeast. LAG1Hs mapped to 19p12, and it was expressed in only three tissues: brain, skeletal muscle, and testis. This gene possesses a trinucleotide (CTG) repeat within exon 1. This and its expression profile raise the possibility that it may be involved in neurodegenerative disease. This possibility suggests at least one way in which LAG1Hs might be involved in human aging.
Immunohistochemical profiling of node negative breast carcinomas allows prediction of metastatic risk (2010)

The aim of this study was to identify a prognostic immunohistochemical signature indicative of risk of early metastasis in node-negative breast carcinomas that would also be relevant to the development of new tailored therapy. Quantitative measurements of the immunohistochemical expression of 64 markers (selected from literature data) using high-throughput densitometry (as a continuous variable) of digitised microscopic micro-array images were correlated with clinical outcome in 667 node-negative breast carcinomas (mean follow-up 102 months). Multivariable fractional polynomials model of logistic regression allowed the selection of the best combination of markers (in terms of sensitivity and specificity) to predict patient outcome without any categorisation using predefined cut-points for individual marker measurements. A highly predictive ten-marker (out of 64) signature was identified comprising PI3K, pmTOR, pMAPKAPK-2, SHARP-2, P21, HIF-1alpha, Moesin, p4EBP-1, pAKT and P27 that well classified 91.4% of node-negative patients (specificity 90.9%, sensitivity 93.7%, area under ROC curve 0.958) independently of estrogen receptors (ER), and progesterone receptors (PR) and HER-2 status (91.6% well classified patients when ER, PR, HER-2 excluded). It is concluded that quantitative immunoprofiling of node-negative breast carcinomas is helpful in selecting patients who should not receive aggressive adjuvant chemotherapy and provides data for the development of tailored therapy.
Non‐invasive prenatal testing for aneuploidy: current status and future prospects (2013)

Non-invasive prenatal testing (NIPT) for aneuploidy using cell-free DNA in maternal plasma is revolutionizing prenatal screening and diagnosis. We review NIPT in the context of established screening and invasive technologies, the range of cytogenetic abnormalities detectable, cost, counseling and ethical issues. Current NIPT approaches involve whole-genome sequencing, targeted sequencing and assessment of single nucleotide polymorphism (SNP) differences between mother and fetus. Clinical trials have demonstrated the efficacy of NIPT for Down and Edwards syndromes, and possibly Patau syndrome, in high-risk women. Universal NIPT is not cost-effective, but using NIPT contingently in women found at moderate or high risk by conventional screening is cost-effective. Positive NIPT results must be confirmed using invasive techniques. Established screening, fetal ultrasound and invasive procedures with microarray testing allow the detection of a broad range of additional abnormalities not yet detectable by NIPT. NIPT approaches that take advantage of SNP information potentially allow the identification of parent of origin for imbalances, triploidy, uniparental disomy and consanguinity, and separate evaluation of dizygotic twins. Fetal fraction enrichment, improved sequencing and selected analysis of the most informative sequences should result in tests for additional chromosomal abnormalities. Providing adequate prenatal counseling poses a substantial challenge given the broad range of prenatal testing options now available.
Rank Ordering Plate Data Facilitates Data Visualization and Normalization in High-Throughput Screening (2014)

High-throughput screening (HTS) of chemical and microbial strain collections is an indispensable tool for modern chemical and systems biology; however, HTS data sets have inherent systematic and random error, which may lead to false-positive or false-negative results. Several methods of normalization of data exist; nevertheless, due to the limitations of each, no single method has been universally adopted. Here, we present a method of data visualization and normalization that is effective, intuitive, and easy to implement in a spreadsheet program. For each plate, the data are ordered by ascending values and a plot thereof yields a curve that is a signature of the plate data. Curve shape characteristics provide intuitive visualization of the frequency and strength of inhibitors, activators, and noise on the plate, allowing potentially problematic plates to be flagged. To reduce plate-to-plate variation, the data can be normalized by the mean of the middle 50% of ordered values, also called the interquartile mean (IQM) or the 50% trimmed mean of the plate. Positional effects due to bias in columns, rows, or wells can be corrected using the interquartile mean of each well position across all plates (IQMW) as a second level of normalization. We illustrate the utility of this method using data sets from biochemical and phenotypic screens.
A Molecular Defect in the Vasopressin V2-Receptor Gene Causing Nephrogenic Diabetes Insipidus (1993)

Fundamental to the maintenance of water balance in humans is the rate at which the kidneys excrete free water, which is primarily regulated by arginine vasopressin. The antidiuretic action of argin...
Three-dimensional subwavelength confinement of light with dielectric microspheres (2009)

Dielectric microspheres are shown to be capable of confining light in a three-dimensional region of subwavelength dimensions when they are illuminated by tightly focused Gaussian beams. We show that a simple configuration, not involving resonances, permits one to reach an effective volume as small as 0.6 (lambda/n)(3). It is shown that this three-dimensional confinement arises from interferences between the field scattered by the sphere and the incident Gaussian beam containing high angular components.
Methods of cooling: Practical aspects of therapeutic temperature management (2009)

Intensivists should be familiar with techniques to induce, maintain, and withdraw therapeutic temperature management, and select the most appropriate method for a given patient and situation.
Multi-modality web video categorization (2007)

This paper reports a first comprehensive study and large-scale test on web video (so-called user generated video or micro video) categorization. Observing that web videos are characterized by a much higher diversity of quality, subject, style, and genres compared with traditional video programs, we focus on studying the effectiveness of different modalities in dealing with such high variation. Specifically, we propose two novel modalities including a semantic modality and a surrounding text modality, as effective complements to most commonly used low-level features. The semantic modality includes three feature representations, i.e., concept histogram, visual word vector model and visual word Latent Semantic Analysis (LSA), while text modality includes the titles, descriptions and tags of web videos. We conduct a set of comprehensive experiments for evaluating the effectiveness of the proposed feature representations over different classifiers such as Support Vector Machine (SVM), Gaussian Mixture Model (GMM) and Manifold Ranking (MR). Our experiments on a large-scale dataset with 11k web videos (nearly 450 hours in total) demonstrate that (1) the proposed multimodal feature representation is effective for web video categorization, and (2) SVM outperforms GMM and MR on nearly all the modalities.
Expression of p8 protein in medullary thyroid carcinoma. (2005)

These findings suggest that p8 expression plays an important role in the progression of medullary carcinoma, but does not have an anti-apoptotic function.
The NPI-1/NPI-3 (karyopherin alpha) binding site on the influenza a virus nucleoprotein NP is a nonconventional nuclear localization signal (1997)

Two cellular proteins, NPI-1 and NPI-3, were previously identified through their interaction with the influenza virus nucleoprotein (NP) by using the yeast two-hybrid system. These proteins were then shown to act as general transport factors (karyopherin alpha) and nuclear pore-docking proteins to facilitate the transport of the NP and of viral RNA into the nucleus. The yeast two-hybrid assay has now been used to identify the specific domains on the NP that bind to the NPI proteins. Mutational analysis including alanine scanning identified the motifs SxGTKRSYxxM and TKRSxxxM, which are required for binding to NPI-1 and NPI-3, respectively. These sequences were shown to possess nuclear localization signal (NLS) activity following expression of fusion proteins in HeLa cells. These sequences represent a novel nonconventional NLS motif. Another NLS activity not mediated by the NPI binding sites is associated with noncontiguous sequences in the NP.
Asymmetric Localization of Vangl2 and Fz3 Indicate Novel Mechanisms for Planar Cell Polarity in Mammals (2006)

Planar cell polarity (PCP) is a process in which cells develop with uniform orientation within the plane of an epithelium. To begin to elucidate the mechanisms of PCP in vertebrates, the localization of the protein Vangl2 (Van Gogh-like) was determined during the development of the mammalian cochlea. Results indicate that Vangl2 becomes asymmetrically localized to specific cell-cell boundaries along the axis of polarization and that this asymmetry is lost in PCP mutants. In addition, PDZ2 (postsynaptic density/Discs large/zona occludens 1), PDZ3, and PDZ4 of the PCP protein Scrb1 (Scribble) are shown to bind to the C-terminal PDZ binding domain of Vangl2, suggesting that Scrb1 plays a direct role in asymmetric targeting of Vangl2. Finally, Fz3 (Frizzled), a newly demonstrated mediator of PCP, is also asymmetrically localized in a pattern that matches that of Vangl2. The presence and asymmetry of Fz3 at the membrane is shown to be dependent on Vangl2. This result suggests a role for Vangl2 in the targeting or anchoring of Fz3, a hypothesis strengthened by the existence of a physical interaction between the two proteins. Together, our data support the idea that protein asymmetry plays an important role in the development of PCP, but the colocalization and interaction of Fz3 and Vangl2 suggests that novel PCP mechanisms exist in vertebrates.
Exclusion of the First EGF Domain of Factor VII by a Splice Site Mutation Causes Lethal Factor VII Deficiency (1998)

We have studied a family with homozygous lethal, blood coagulation factor VII (FVII) deficiency. To identify the mutation responsible for the deficiency, exons 2 to 8 and the intron-exon junctions of their FVII genes were amplified from peripheral white blood cell DNA by polymerase chain reaction and screened by single-strand conformational polymorphism analysis. The fragment showing aberrant mobility was cloned and sequenced. We detected a single point mutation, a homozygous G to A substitution at nucleotide position 6070, in the invariant GT dinucleotide at the 5' splice site of intron 4. Homozygosity was confirmed by loss of a site for the restriction endonuclease Mlu I. Analysis of the splicing pattern of ectopic transcripts in lymphocytes in the parents revealed that this mutation is associated with skipping of exon 4, which produces an mRNA encoding FVII with an in-frame deletion of the first epidermal growth factor-like domain (EGF 1). Transient transfection of COS-7 cells with an expression vector containing the triangle upEGF 1 FVII cDNA shows that this mutant protein is not expressed. The identification of the molecular basis of the FVII deficiency in this family allowed mutation-specific prenatal diagnosis to be performed in a subsequent pregnancy. In this family complete FVII deficiency is associated with a severe bleeding diathesis but no developmental abnormalities, lending weight to the hypothesis that fetal FVII is not required for the putative angiogenic functions of tissue factor in humans.
P450 superfamily: update on new sequences, gene mapping, accession numbers and nomenclature (1996)

We provide here a list of 481 P450 genes and 22 pseudogenes, plus all accession numbers that have been reported as of October 18, 1995. These genes have been described in 85 eukaryote (including vertebrates, invertebrates, fungi, and plants) and 20 prokaryote species. Of 74 gene families so far described, 14 families exist in all mammals examined to date. These 14 families comprise 26 mammalian subfamilies, of which 20 and 15 have been mapped in the human genome and the mouse genome, respectively. Each subfamily usually represents a cluster of tightly linked genes widely scattered throughout the genome, but there are exceptions. Interestingly, the CYP51 family has been found in mammals, filamentous fungi and yeast, and plants-attesting to the fact that this P450 gene family is very ancient. One functional CYP51 gene and two processed pseudogenes, which are the first examples of intronless pseudogenes within the P450 superfamily, have been mapped to three different human chromosomes. This revision supersedes the four previous updates in which a nomenclature system, based on divergent evolution of the superfamily, has been described. For the gene, we recommend that the italicized root symbol "CYP' for human ("Cyp' for mouse and Drosophila), representing "cytochrome P450', be followed by an Arabic number denoting the family, a letter designating the subfamily (when two or more exist), and an Arabic numeral representing the individual gene within the subfamily. A hyphen is no longer recommended in mouse gene nomenclature. "P' ("ps' in mouse and Drosophila) after the gene number denotes a pseudogene; "X' after the gene number means its use has been discontinued. If a gene is the sole member of a family, the subfamily letter and gene number would be helpful but need not be included. The human nomenclature system should be used for all species other than mouse and Drosophila. The cDNAs, mRNAs and enzymes in all species (including mouse) should include all capital letters, and without italics or hyphens. This nomenclature system is similar to that proposed in our previous updates.
Fabrication of a Cylindrical Display by Patterned Assembly (2002)

We demonstrate the patterned assembly of integrated semiconductor devices onto planar, flexible, and curved substrates on the basis of capillary interactions involving liquid solder. The substrates presented patterned, solder-coated areas that acted both as receptors for the components of the device during its assembly and as electrical connections during its operation. The components were suspended in water and agitated gently. Minimization of the free energy of the solder-water interface provided the driving force for the assembly. One hundred and thirteen GaAlAs light-emitting diodes with a chip size of 280 micrometers were fabricated into a prototype cylindrical display. It was also possible to assemble 1500 silicon cubes, on an area of 5 square centimeters, in less than 3 minutes, with a defect rate of approximately 2%.
Hyperosmolal vaginal lubricants markedly reduce epithelial barrier properties in a three-dimensional vaginal epithelium model (2017)

Most of the widely used vaginal lubricants in the U.S. and Europe are strongly hyperosmolal, formulated with high concentrations of glycerol, propylene glycol, polyquaternary compounds or other ingredients that make these lubricants 4 to 30 times the osmolality of healthy vaginal fluid. Hyperosmolal formulations have been shown to cause marked toxicity to human colorectal epithelia in vivo, and significantly increase vaginal transmission of genital herpes infections in the mouse/HSV model. They also cause toxicity to explants of vaginal epithelia, to cultured vaginal epithelial cells, and increase susceptibility to HIV in target cells in cell cultures. Here, we report that the osmolality of healthy vaginal fluid is 370 ± 40 mOsm/Kg in women with Nugent scores 0-3, and that a well-characterized three-dimensional human vaginal epithelium tissue model demonstrated that vaginal lubricants with osmolality greater than 4 times that of vaginal fluid (>1500 mOsm/Kg) markedly reduce epithelial barrier properties and showed damage in tissue structure. Four out of four such lubricants caused disruption in the parabasal and basal layers of cells as observed by histological analysis and reduced barrier integrity as measured by trans-epithelial electrical resistance (TEER). No epithelial damage to these layers was observed for hypo- and iso-osmolal lubricants with osmolality of <400 mOsm/Kg. The results confirm extensive reports of safety concerns of hyperosmolal lubricants and suggest the usefulness of reconstructed in vitro vaginal tissue models for assessing safety of lubricants in the absence of direct clinical tests in humans.
Transgenic mice carrying the apolipoprotein E3-Leiden gene exhibit hyperlipoproteinemia (1993)

Apolipoprotein (apo) E3-Leiden, described in a large Dutch family, is associated with a dominantly inherited form of familial dysbetalipoproteinemia. To study the effect of the APOE*3-Leiden mutation in vivo, transgenic mice were generated using a genomic 27-kilobase DNA construct isolated from the APOE*3-Leiden proband. This construct carried the APOE gene, the APOC1 gene, and all known regulatory elements including an element that mediates liver expression. Three strains were generated that showed human APOE and APOC1 expression. All strains had significantly elevated levels of total plasma cholesterol and triglycerides on a regular diet. When mice of one strain were fed a semisynthetic cholesterol-rich diet, total plasma cholesterol and triglyceride levels increased dramatically. This increase was observed mainly in the very low density lipoprotein (VLDL)- and low density lipoprotein (LDL)-sized fractions. In cholesterol-fed mice, the apoE3-Leiden protein became equally distributed between the VLDL/LDL and HDL-sized fractions, while in mice kept on a regular diet, apoE3-Leiden protein was mainly associated with HDL-sized fractions. The presence of hyperlipoproteinemia in the APOE*3-Leiden-expressing transgenic mice supports our finding that the apoE3-Leiden variant behaves like a dominant trait in the expression of familial dysbetalipoproteinemia. ApoE3-Leiden transgenic mice may serve as a model to elucidate additional factors involved in the metabolism of apoE containing remnant lipoproteins in general and the etiology of familial dysbetalipoproteinemia in particular.
Inhibition of yeast glyoxalase I by biologically active peptides. (1989)

The antiglyoxylase activity of biologically active peptides f-Met-Leu-Phe-OCH3 and Boc-Phe-Leu-Phe-OCH3 has been evaluated and compared with those of standard inhibitors s-octylglutathione and squaric acid. The inhibitory properties of these peptides are discussed in terms of biological and pharmacological aspects.
Identification of Conserved Residues Required for the Binding of a Tetratricopeptide Repeat Domain to Heat Shock Protein 90 (1999)

The sequential binding of heat shock protein 90 (hsp90) to a series of tetratricopeptide repeat (TPR) proteins is critical to its function as a molecular chaperone. We have used site-directed mutagenesis to clarify the structural basis for the binding of hsp90 to the TPR domain of phosphoprotein phosphatase 5 (PP5). This TPR domain was chosen for study because its three-dimensional structure is known. We examined co-immunoprecipitation of hsp90 with wild type and mutant TPR constructs from transfected cells. Only mutations located on one face of the TPR domain affected hsp90 binding. This allowed the identification of a binding groove. Three basic residues that are highly conserved in hsp90-binding TPR proteins extend prominently into this groove. Lys-97 and Arg-101 were absolutely required for hsp90 binding, while mutation of Arg-74 diminished, but did not abrogate, hsp90 binding. Mutation of Lys-32, another conserved basic residue in the binding groove, also blocked hsp90 binding. The TPR domain of PP5 bound specifically to a 12-kDa C-terminal fragment of hsp90. This binding was reduced by mutation of acidic residues in the hsp90 fragment. These data suggest conservation, among hsp90-binding TPR proteins, of a binding groove containing basic residues that interact with acidic residues near the C terminus of hsp90.