gebhart/patrepeval huggingface dataset:
Markers of Platelet Activation and Granule Secretion (2007)

Platelet activation results in a complex series of changes including a physical redistribution of receptors, changes in the molecular conformation of receptors, secretion of granule contents, development of a procoagulant surface, generation of platelet-derived microparticles, and formation of leukocyte-platelet aggregates. Each of these changes can potentially be used as a marker of platelet activation. Whole blood flow cytometry (1) is the method of choice for the measurement of all these changes, except the secretion of soluble molecules, which are usually measured by enzyme-linked immunosorbent assay (ELISA). Whole blood flow cytometry has many advantages, including: only minuscule volumes (∼5 µL) of blood are required; platelets are directly analyzed in their physiological milieu of whole blood; the minimal manipulation of samples prevents artifactual in vitro activation and potential loss of platelet subpopulations; both the activation state of circulating platelets and the reactivity of circulating platelets can be determined; and a spectrum of different activation-dependent changes can be determined. The specific methodological details of the use of flow cytometry to measure platelet activation are described elsewhere (1–3).
A Family of Six Flagellin Genes Contributes to the Caulobacter crescentus Flagellar Filament (2000)

The Caulobacter crescentus flagellar filament is assembled from multiple flagellin proteins that are encoded by six genes. The amino acid sequences of the FljJ and FljL flagellins are divergent from those of the other four flagellins. Since these flagellins are the first to be assembled in the flagellar filament, one or both might have specialized to facilitate the initiation of filament assembly.
Solvothermal synthesis of ultralong single-crystalline TiO2 nanowires (2005)

Well-defined single crystalline TiO2 nanowires with diameters of 20–50 nm mostly and lengths of up to a few millimeters have been successfully synthesized by a simple, low-cost solvothermal process using the mixed solvent aqueous NaOH–ethanol. The as-synthesized nanowires are structurally uniform, of high purity and show perfect crystallinity. The growth mechanism of the nanowires has been investigated by following the growth steps of the samples at various reaction stages. The solvent significantly influences the morphology and the crystallization behavior of the final products. This novel approach may be applied to the large-scale fabrication of some other oxide nanowires.
Molecular Principles of Animal Development (2002)

1. Introduction: towards a molecular basis of development 2. Programs and regulatory elements in DNA and RNA 3. Decoding the program: transcription 4. Cell surface proteins: receptors, ligands, and their environment 5. Intracellular effectors of cell interactions: signalling pathways and networks 6. Cells and their interactions 7. Basic cellular routines: division, differentiation, and death 8. The generation of lineages: a developmental routine 9. Long- and short-range influences in the generation of cell diversity 10. Cell type specification: a developmental operation 11. Patterns in 'one' and two dimensions 12. Patterns in three dimensions
New method for electro-optical tuning of tunable lasers (1974)

A new scheme for electro-optical tuning of tunable lasers is described. Tuning rates and tuning ranges in cw dye lasers nearly 100 times greater than those previously reported using a comparable-sized electro-optical crystal have been achieved using this method.
Classification of Human Coronary Atherosclerotic Plaques Using Ex Vivo High-Resolution Multicontrast-Weighted MRI Compared With Histopathology (2012)

Ex vivo high-resolution multicontrast-weighted MRI can accurately classify advanced atherosclerotic plaques in human coronary arteries.
Comparison of the Performance of Screening Mammography, Physical Examination, and Breast US and Evaluation of Factors that Influence Them: An Analysis of 27,825 Patient Evaluations (2002)

Mammographic sensitivity for breast cancer declines significantly with increasing breast density and is independently higher in older women with dense breasts. Addition of screening US significantly increases detection of small cancers and depicts significantly more cancers and at smaller size and lower stage than does PE, which detects independently extremely few cancers. Hormonal status has no significant effect on effectiveness of screening independent of breast density.
Very Low Birth Weight Preterm Infants With Early Onset Neonatal Sepsis (2005)

Background: Early onset neonatal sepsis (EOS, occurring in the first 72 hours of life) remains an important cause of illness and death among very low birth weight (VLBW) preterm infants. We previously reported a change in the distribution of pathogens associated with EOS from predominantly Gram-positive to primarily Gram-negative organisms. Objective: To compare rates of EOS and pathogens associated with infection among VLBW infants born at centers of the National Institute of Child Health and Human Development (NICHD) Neonatal Research Network during 3 time periods: 1991–1993; 1998–2000; and 2002–2003. Study Design: Prospectively collected data from the NICHD Neonatal Research Network VLBW registry were retrospectively reviewed. Rates of blood culture confirmed EOS, selected maternal and infant variables and pathogens associated with infection were compared between 2002–2003 and 2 previously published cohorts. Results: During the past 13 years, overall rates of EOS have remained stable (15–19 per 1000 live births of infants 401–1500 g). More than one-half of early infections in the 2002–2003 cohort were caused by Gram-negative organisms (53%), with Escherichia coli the most common organism (41%). Rates of group B streptococcal infections remain low (1.8 per 1000 live births). Between 1991–1993 and 1998–2000, there was a significant increase in rates of E. coli infections; but in 2002–2003, there was no significant change (7.0 per 1000 live births). Infants with EOS continue to be at significantly increased risk for death compared with uninfected infants. Conclusion: EOS remains an uncommon but important cause of morbidity and mortality among VLBW infants. Gram-negative organisms continue to be the predominant pathogens associated with EOS.
Neurotrophin‐7: a novel member of the neurotrophin family from the zebrafish (1998)

A novel member of the neurotrophin family, zebrafish neurotrophin-7 (zNT-7), was isolated from the zebrafish Danio rerio. The amino acid sequence of zNT-7 is more closely related to that of fish nerve growth factor (NGF) and neurotrophin-6 (NT-6) than to that of any other neurotrophin. zNT-7 is, however, equally related to fish NGF and NT-6 (65% and 63% amino acid sequence identity, respectively) indicating that it represents a distinct neurotrophin sequence. zNT-7 contains a 15 amino acid residue insertion in a beta-turn region in the middle of the mature protein. Recombinant zNT-7 was able to bind to the human p75 neurotrophin receptor and to induce tyrosine phosphorylation of the rat TrkA receptor tyrosine kinase, albeit less efficiently than rat NGF. zNT-7 did not interact with rat TrkB or TrkC, indicating a similar receptor specificity as NGF. We propose that a diversification of the NGF subfamily in the neurotrophin evolutionary tree occurred during the evolution of teleost fishes which resulted in the appearance of several additional members, such as zNT-7 and NT-6, structurally and functionally related to NGF.
Integrated interleaving - a novel ECC architecture (2001)

We introduce a coding method which creates a nested sequence of codes whose distances can be adjusted to fit the error statistics of a specified digital communication or storage channel. This construction permits the use of redundancy in a nonuniform manner as required by the actual digital error occurrences in the codewords. In storage applications the codewords are usually distinct interleaves of data sectors. Our construction creates redundancy which is shared by all the interleaves and is used in those interleaves in which the number of errors exceeds the first level code distance, hence the name integrated interleaving. Our construction is, in particular, suited for long block records, where its coding gains are largest. We evaluate the performance and provide a decoding algorithm for this coding scheme.
Comparison of cell‐cycle phase perturbations induced by the DNA‐minor‐groove alkylator tallimustine and by melphalan in the SW626 cell line (1995)

Tallimustine or N-deformyl-N-[4-N-N,N-bis(2-chloroethylamino)benzoyl], a distamycin-A derivative (FCE 24517), is a novel anti-cancer agent which alkylates N3 adenine in the minor groove of DNA. The cell-cycle phase perturbations induced by the drug were investigated and compared with those caused by melphalan (L-PAM) in SW626 human ovarian-cancer cells. By coupling bromodeoxyuridine (BUdR) immunoreaction with biparametric flow-cytometric (FCM) analysis, we investigated the cell-cycle phase perturbation induced by tallimustine or L-PAM, considering separately the cells which, during the 1-hr treatment, were in the S phase or in G1-G2/M phases of the cell cycle. L-PAM delayed the S-phase progression of cells exposed to the drug when they were in S phase, with a consequent accumulation of cells as soon as they reached the G2 phase. In contrast, the S-phase cells treated with tallimustine were not perturbed during the DNA-synthesis phase progression, and were blocked in G2 only after they had passed through the G1/S transition of a new cell cycle. In cells which were in G1 or G2/M phases during drug treatment, tallimustine and L-PAM caused similar accumulation in G2. The differences in the cell-cycle perturbation caused by tallimustine and L-PAM may well be related to the different DNA damage the 2 drugs produced. These findings emphasize the different properties of DNA-minor-groove alkylating agents and conventional ones.
Role of CD4+ T cells and T-independent mechanisms in acquired resistance to Salmonella typhimurium infection. (1990)

Two aspects of acquired resistance to Salmonella typhimurium infection in BALB/c mice, i.e., the ability to clear the primary inoculum from the spleen and resistance to a secondary challenge, were studied with the use of mAb against T cell subsets. The ability to clear a temperature-sensitive mutant of S. typhimurium from the spleen (assessed at day 21) was abrogated by in vivo treatment with anti-CD4 mAb. Accelerated bacterial clearance could be adoptively transferred into naive mice. In vitro depletion experiments also showed the role of CD4+ T cells in this phenomenon. Depletion of CD8+ T cells had only a marginal effect. Resistance to reinfection in the late phase of the primary infection (day 50) was markedly depressed by in vivo treatment with anti-CD4 mAb, whereas this was not the case during the early phase (day 14). Furthermore, during the early phase of infection athymic nude mice showed increased nonspecific resistance to reinfection. Taken together these results suggest that T-independent mechanisms play a major role in acquired resistance during the early phase of infection.
Noninvasive detection of allograft rejection in heart transplant recipients by use of Doppler tissue imaging. (1998)

Moderate allograft rejection results in reduced myocardial relaxation velocities, which can be detected noninvasively with pulsed-wave Doppler tissue imaging. Hence, Doppler tissue imaging is a useful noninvasive tool to exclude allograft rejection.
Novel Uses of Surgical Robotics in Head and Neck Surgery (2005)

Transaxillary, endoscopic, robotically assisted approaches to the head and neck are feasible. The addition of robotics improves surgical dexterity in a difficult-to-reach anatomic region. Patient satisfaction appears high because of the avoidance of a cervical incision.
Polar allele duplication for transcriptional analysis of consecutive essential genes: application to a cluster of Escherichia coli fatty acid biosynthetic genes (1996)

The genes encoding acyl carrier protein and several key fatty acid biosynthetic enzymes are clustered at min 24 of the Escherichia coli chromosome. This cluster of genes is not transcribed as a classical operon, but rather multiple promoters are present and each gene is cotranscribed with at least one other gene. Transcripts specific for single genes ar also present. Transcription of acpP, the gene encoding acyl carrier protein, has been studied in detail. The acpP gene was shown to be transcribed from at least two different promoters by Northern (RNA) blot, primer extension, and deletion analyses, and the major promoter was mapped. We tested whether multiple promoters are necessary to produce acyl carrier protein by use of a new method whereby a transcriptional terminator was integrated into the chromosome upstream of the intact acpP gene. By use of this method (called polar allele duplication), we demonstrate that the promoter located immediately upstream of the coding sequence is sufficient for synthesis of this very abundant protein.
Investigating and Correcting Plasma DNA Sequencing Coverage Bias to Enhance Aneuploidy Discovery (2014)

Pregnant women carry a mixture of cell-free DNA fragments from self and fetus (non-self) in their circulation. In recent years multiple independent studies have demonstrated the ability to detect fetal trisomies such as trisomy 21, the cause of Down syndrome, by Next-Generation Sequencing of maternal plasma. The current clinical tests based on this approach show very high sensitivity and specificity, although as yet they have not become the standard diagnostic test. Here we describe improvements to the analysis of the sequencing data by reducing GC bias and better handling of the genomic repeats. We show substantial improvements in the sensitivity of the standard trisomy 21 statistical tests, which we measure by artificially reducing read coverage. We also explore the bias stemming from the natural cleavage of plasma DNA by examining DNA motifs and position specific base distributions. We propose a model to correct this fragmentation bias and observe that incorporating this bias does not lead to any further improvements in the detection of fetal trisomy. The improved bias corrections that we demonstrate in this work can be readily adopted into existing fetal trisomy detection protocols and should also lead to improvements in sub-chromosomal copy number variation detection.
Washable Multilayer Triboelectric Air Filter for Efficient Particulate Matter PM2.5 Removal (2018)

Abstract Efficient removal of particulate matter (PM) is the major goal for various air cleaning technologies due to its huge impact on human health. Here, a washable high‐efficiency triboelectric air filter (TAF) that can be used multiple times is presented. The TAF consists of five layers of the polytetrafluoroethylene (PTFE) and nylon fabrics. Compared with traditional electrostatic precipitator, which requires a high‐voltage power supply, the TAF can be charged by simply rubbing the PTFE and nylon fabrics against each other. The electrical properties of the TAF are evaluated through the periodic contacting–separating of the PTFE and nylon fabrics using a linear motor, and an open‐circuit voltage of 190 V is achieved. After charging, the TAF has a removal efficiency of 84.7% for PM 0.5 , 96.0% for PM 2.5 , which are 3.22 and 1.39 times as large as the uncharged one. Most importantly, after washing several times, the removal efficiency of the TAF maintains almost the same, while the commercial face mask drops to 70% of its original efficiency. Furthermore, the removal efficiency of the PM 2.5 is very stable under high relative humidity. Therefore, the TAF is promising for fabricating a reusable and high‐efficiency face mask.
Carbimazole and autoantibody synthesis in Hashimoto's thyroiditis. (1980)

Serum thyroxine, thyrotrophin, and thyroid microsomal antibody levels were measured in 20 patients with Hashimoto's thyroiditis and hypothyroidism before, during, and after treatment with carbimazole or placebo. Thyroid microsomal antibody levels fell during treatment in the 10 patients who received carbimazole, while serum thyroxine and thyrotrophin levels did not change. There were no changes in the placebo group. The study proves support for the concept that carbimazole may act directly on autoantibody synthesising lymphocytes localised in the thyroid. Such an effect might be valuable in influencing the autoimmune process in autoimmune thyroid disease.
Comparative mass spectrometric analyses of Photofrin oligomers by fast atom bombardment mass spectrometry, UV and IR matrix-assisted laser desorption/ionization mass spectrometry, electrospray ionization mass spectrometry and laser desorption/jet-cooling photoionization mass spectrometry (1999)

Photofrin® (porfimer sodium) is a porphyrin derivative used in the treatment of a variety of cancers by photodynamic therapy. This oligomer complex and a variety of porphyrin monomers, dimers and trimers were analyzed with five different mass spectral ionization techniques: fast atom bombardment, UV and IR matrix-assisted laser desorption/ionization, electrospray ionization, and laser desorption/jet-cooling photoionization. All five approaches resulted in very similar oligomer distributions with an average oligomer length of 2.7 ± 0.1 porphyrin units. In addition to the Photofrin analysis, this study provides a side-by-side comparison of the spectra for the five different mass spectrometric techniques. Copyright © 1999 John Wiley & Sons, Ltd.
Liver X receptor activation enhances CVB3 viral replication during myocarditis by stimulating lipogenesis (2015)

LXR agonism does not modulate cardiac inflammation, but exacerbates virus-mediated myocardial damage during VM by stimulating lipid biosynthesis and enhancing CVB3 replication.
A public database for gene expression in human cancers. (1999)

A public database, SAGEmap, was created as a component of the Cancer Genome Anatomy Project to provide a central location for depositing, retrieving, and analyzing human gene expression data. This database uses serial analysis of gene expression to quantify transcript levels in both malignant and normal human tissues. By accessing SAGEmap (http://www.ncbi.nlm.nih.gov/SAGE) the user can compare transcript populations between any of the posted libraries. As an initial demonstration of the database's utility, gene expression in human glioblastomas was compared with that of normal brain white matter. Of the 47,174 unique transcripts expressed in these two tissues, 471 (1.0%) were differentially expressed by more than 5-fold (P<0.001). Classification of these genes revealed functions consistent with the biological properties of glioblastomas, in particular: angiogenesis, transcription, and cell cycle related genes.
Scaling up all pairs similarity search (2007)

Given a large collection of sparse vector data in a high dimensional space, we investigate the problem of finding all pairs of vectors whose similarity score (as determined by a function such as cosine distance) is above a given threshold. We propose a simple algorithm based on novel indexing and optimization strategies that solves this problem without relying on approximation methods or extensive parameter tuning. We show the approach efficiently handles a variety of datasets across a wide setting of similarity thresholds, with large speedups over previous state-of-the-art approaches.
Anisyl neighboring-group participation in carbonium ion formation in antimony pentafluoride and sulfur dioxide (1972)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAnisyl neighboring-group participation in carbonium ion formation in antimony pentafluoride and sulfur dioxideBrian G. Ramsey, James A. Cook Jr., and James A. MannerCite this: J. Org. Chem. 1972, 37, 21, 3310–3322Publication Date (Print):October 1, 1972Publication History Published online1 May 2002Published inissue 1 October 1972https://pubs.acs.org/doi/10.1021/jo00986a025https://doi.org/10.1021/jo00986a025research-articleACS PublicationsRequest reuse permissionsArticle Views91Altmetric-Citations2LEARN 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
A New Surface for Immobilizing and Maintaining the Function of Enzymes in a Freeze-Dried State (2009)

We describe a new surface produced by plasma treatment for immobilizing proteins in the dry state. The need for surfaces suitable for immobilizing proteins is increasing because of demand for microarray diagnostic services, biosensors, and chemical processing. Storage of surface attached proteins in the dry state offers benefits of long shelf life, protection from proteases, easier transportation and convenient storage. In this work, we produced plasma-modified polyethylene surfaces and tested them using two important enzymes for which convenient functional assays are available, namely, horseradish peroxidase and catalase. Over 80% of the function of horseradish peroxidase is retained after freeze-drying, and this function is unaltered after 4 months of storage at 4 degrees C on the treated polyethylene surface. The factors important for maintenance of surface attached enzyme stability were (1) plasma immersion ion implantation (PIII) treatment of the surface, (2) freeze-drying with sucrose in the buffer solution, (3) dry storage with desiccant, and (4) maintaining the freeze-dried protein at a reduced temperature. Other than sucrose, no other additives are needed.
Antibodies against the gH/gL/UL128/UL130/UL131 Complex Comprise the Majority of the Anti-Cytomegalovirus (Anti-CMV) Neutralizing Antibody Response in CMV Hyperimmune Globulin (2012)

Anti-cytomegalovirus (anti-CMV) hyperimmune globulin (HIG) has demonstrated efficacy in preventing CMV disease in solid-organ transplant patients as well as congenital disease when administered to pregnant women. To identify the neutralizing component of cytomegalovirus hyperimmune globulin (CMV-HIG), we performed serial depletions of CMV-HIG on cell-surface-expressed CMV antigens as well as purified antigens. Using this approach, we demonstrate that the major neutralizing antibody response is directed at the gH/gL/UL128/UL130/UL131 complex, suggesting little role for anti-gB antibodies in CMV-HIG neutralization.