gebhart/patrepeval huggingface dataset:
An Integrative Approach for Identifying Network Biomarkers of Breast Cancer Subtypes Using Genomic, Interactomic, and Transcriptomic Data (2017)

Breast cancer is a complex disease that can be classified into at least 10 different molecular subtypes. Appropriate diagnosis of specific subtypes is critical for ensuring the best possible patient treatment and response to therapy. Current computational methods for determining the subtypes are based on identifying differentially expressed genes (i.e., biomarkers) that can best discriminate the subtypes. Such approaches, however, are known to be unreliable since they yield different biomarker sets when applied to data sets from different studies. Gathering knowledge about the functional relationship among genes will identify "network biomarkers" that will enrich the criteria for biomarker selection. Cancer network biomarkers are subnetworks of functionally related genes that "work in concert" to perform functions associated with a tumorigenic. We propose a machine learning framework that can be used to identify network biomarkers and driver genes for each specific breast cancer subtype. Our results show that the resulting network biomarkers can separate one subtype from the others with very high accuracy.
Polymeric Gas Separation Membrances (1994)

Synthetic gas separation membranes have developed tremendously since the first commercial system was introduced just 15 years ago. Factors affecting the permeabilities and selectivities of new “tailor‐made” membrane materials are discussed. For example, because the p ‐isomer is more rod‐like than the m ‐isomer chain shown in the figure, the resulting membranes have a higher permeability. magnified image
Muddy water animation with different details (2015)

Abstract Muddy water is an example of suspension, which is a mixture containing particles that separate into distinct layers if left undisturbed. When stirred, however, the mud substance flows like a liquid and again begins settling out. Mud is composed of various sized particles, and they produce different effects when it is blended with water. This paper classifies the mud particles into three types and proposes different simulation methods for the types. The experimental results demonstrate that the proposed methods effectively produce visually plausible muddy water effects. Copyright © 2015 John Wiley &amp; Sons, Ltd.
Prolonged Exposure to NMDAR Antagonist Suppresses Inhibitory Synaptic Transmission in Prefrontal Cortex (2008)

Postmortem studies have shown that schizophrenia produces a reduction in the 67-kilodalton isoform of glutamic acid decarboxylase (GAD67), a key enzyme for gamma-aminobutyric acid (GABA) synthesis. N-methyl-d-aspartate receptor (NMDAR) antagonists have been extensively used to study schizophrenia because they can induce many aspects of the disease, including the decrease in GAD67. It is generally thought that this reduction in GAD implies a reduction in functional inhibition, but direct evidence had been lacking. We have therefore performed physiological studies in slices of prefrontal cortex taken from rats treated with the NMDAR antagonist ketamine. Both frequency and amplitude of miniature inhibitory postsynaptic currents were reduced. Consistent with a reduction of inhibition, we observed an increase in postsynaptic excitability. The increased excitability is likely to result from disinhibition because miniature excitatory postsynaptic current properties and intrinsic excitability were not changed. Ketamine did not affect inhibition or GAD levels in young rats, indicating a developmental regulation that may be related to the developmental increase in ketamine sensitivity that occurs in humans. Our results show that NMDAR antagonist produces biochemical changes in the GABA system that lead to a functional disinhibition. Such disinhibition would be expected to decrease gamma oscillations, which are reduced in schizophrenia.
Imazethapyr at Different Rates and Timings in Drill- and Water-Seeded Imidazolinone-Tolerant Rice (2004)

Imazethapyr applied to the soil at 0, 35, 53, 70, 87, 105, and 140 g ai/ha followed by (fb) early-postemergence (EPOST) or late-postemergence (LPOST) applications at 140, 105, 87, 70, 53, 35, and 0 g ai/ha, respectively, was evaluated for weed control, crop tolerance, and grain yield in imidazolinone-tolerant rice. In drill- and water-seeded rice, imazethapyr effectively controlled barnyardgrass 91 to 97% with a soil fb EPOST or LPOST application except when applied at 105 fb 35 g/ha EPOST at 49 d after late-postemergence treatment. Rice yields were 5,920 and 3,920 kg/ ha in the drill-seeded study with a single application of imazethapyr at 140 g/ha EPOST in 2000 and 2001, respectively. These yields were greater than or equal to those from treatments with two imazethapyr applications.
Fear (2000)

The author recounts the details of the burglary that struck the apartment in which he lived twice which completely shattered his sense of security. He observes that crime and violence were not uncommon in this area, but they always seemed to happen elsewhere and could be avoided. He realizes that break-ins were not a common occurrence for most families in America and that having bars on the windows was not normal. He studied karate and took lessons from a black Muslim sensei named Rahim, formerly Robert, with the express purpose of becoming tough enough to feel secure. He had moved up a rank in the karate hierarchy, his association with Rahim did not achieve the intended goal of feeling safe and secure in the neighborhood, and for a simple reason: within a year Rahim was shot and killed.
Migratory selectivity in the ring expansion of .alpha.,.beta.-unsaturated cyclic ketones via .beta.-hydroxy selenides (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMigratory selectivity in the ring expansion of .alpha.,.beta.-unsaturated cyclic ketones via .beta.-hydroxy selenidesLeo A. Paquette, John R. Peterson, and Robert J. RossCite this: J. Org. Chem. 1985, 50, 25, 5200–5204Publication Date (Print):December 1, 1985Publication History Published online1 May 2002Published inissue 1 December 1985https://pubs.acs.org/doi/10.1021/jo00225a043https://doi.org/10.1021/jo00225a043research-articleACS PublicationsRequest reuse permissionsArticle Views264Altmetric-Citations18LEARN 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
Genetic mutations in the K1 and K10 genes of patients with epidermolytic hyperkeratosis. Correlation between location and disease severity. (1994)

Epidermolytic hyperkeratosis (EH) is a skin disease caused by mutations in the genes encoding K1 and K10, the differentiation-specific keratins of epidermis. To explore the heterogeneity of mutations and to assess whether a correlation exists between disease severity and the extent to which a mutation interferes with keratin network formation, we determined the genetic bases of four severe incidences of EH and one unusually mild case. Two severe cases have the same mutation, K10-R156:C, at a conserved arginine that we previously showed was mutated to a histidine in two unrelated EH families. An additional severe case has a mutation six residues away, still within the amino end of the alpha-helical rod domain of K10. The other severe case has a mutation in the conserved carboxy end of the K1 rod. In contrast, affected members of the atypically mild family have a mutation just proximal to the conserved carboxy end of the K10 rod. By genetic engineering and gene transfection, we demonstrate that each mutation is functionally responsible for the keratin filament aberrations that are typical of keratinocytes cultured from these patients. Moreover, we show that the mild EH mutation less severely affects filament network formation. Taken together, our studies strengthen the link between filament perturbations, cell fragility, and degeneration.
GATA1 and PU.1 Bind to Ribosomal Protein Genes in Erythroid Cells: Implications for Ribosomopathies (2015)

The clear connection between ribosome biogenesis dysfunction and specific hematopoiesis-related disorders prompted us to examine the role of critical lineage-specific transcription factors in the transcriptional regulation of ribosomal protein (RP) genes during terminal erythroid differentiation. By applying EMSA and ChIP methodologies in mouse erythroleukemia cells we show that GATA1 and PU.1 bind in vitro and in vivo the proximal promoter region of the RPS19 gene which is frequently mutated in Diamond-Blackfan Anemia. Moreover, ChIPseq data analysis also demonstrates that several RP genes are enriched as potential GATA1 and PU.1 gene targets in mouse and human erythroid cells, with GATA1 binding showing an association with higher ribosomal protein gene expression levels during terminal erythroid differentiation in human and mouse. Our results suggest that RP gene expression and hence balanced ribosome biosynthesis may be specifically and selectively regulated by lineage specific transcription factors during hematopoiesis, a finding which may be clinically relevant to ribosomopathies.
Distribution Pattern of Plasmodium falciparum Chloroquine Transporter (pfcrt) Gene Haplotypes in Sri Lanka 1996–2006 (2011)

Widespread antimalarial resistance has been a barrier to malaria elimination efforts in Sri Lanka. Analysis of genetic markers in historic parasites may uncover trends in the spread of resistance. We examined the frequency of Plasmodium falciparum chloroquine transporter (pfcrt; codons 72-76) haplotypes in Sri Lanka in 1996-1998 and 2004-2006 using a high-resolution melting assay. Among 59 samples from 1996 to 1998, we detected the SVMNT (86%), CVMNK (10%), and CVIET (2%) haplotypes, with a positive trend in SVMNT and a negative trend in CVMNK frequency (P = 0.004) over time. Among 24 samples from 2004 to 2006, we observed only the SVMNT haplotype. This finding indicates selection for the SVMNT haplotype over time and its possible fixation in the population.
A tunable approximately piecewise linear model derived from the modified probabilistic neural network (2002)

A simple model, which can be adjusted by a single smoothing parameter continuously from the best piecewise linear model in each linear subregion to the best approximately piecewise linear model overall, is developed for multivariate general nonlinear regression. The model provides an accurate, smooth, approximately piecewise linear model to cover the entire data space. It provides a logical basis for extrapolation to regions not represented by training data, based on the closest piecewise linear model. This model has been developed by making relatively minor changes to the form of a modified probabilistic neural network (MPNN), which is a network that id used for general nonlinear regression. The MPNN structure allows it to model data by weighting piecewise linear models associated with each of the network's radial basis functions in the data space.
IGBT Power Stack Integrity Assessment Method for High-Power Magnet Supplies (2019)

This paper proposes a method for assessing the integrity of a series of insulated-gate bipolar transistor (IGBT) power stacks during factory-acceptance tests and service stops. The key challenge that is addressed in this paper is detecting common assembly issues that affect the power stack thermal path as well as distinguishing the acute aging effects of bond-wire lift-off and solder delamination. The method combines offline V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">ce</sub> measurements with current in the extended Zero Temperature Coefficient (ZTC) operating region as well as with sensing current without modifications to the power stack. It also employs on-the-stack V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">ce</sub> calibration for both the measurements. Additionally, only a fixed duty cycle pattern is needed to control the switches. The paper also presents a sensitivity analysis of the method to various parameters such as the current level in the extended ZTC operating region, the precision of the V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">ce</sub> measurement, as well as the ambient, the cooling-water, and the junction temperatures. The experimental results are obtained from a high-current IGBT power stack used in a magnet power supply for particle accelerators and are compared favorably to results from finite element method and lumped parameter network simulations confirming the applicability of the method.
Faculty Opinions recommendation of Structural decomposition and heterogeneity of commercial lipoteichoic Acid preparations. (2003)

Fractionation of commercial preparations of lipoteichoic acids (LTA) by hydrophobic interaction chromatography (HIC) and nuclear magnetic resonance spectroscopy revealed very inhomogeneous compositions and decomposition of the LTA structure: LTA content of the preparations averaged 61% for Streptococcus pyogenes, 16% for Bacillus subtilis, and 75% for Staphylococcus aureus. The decomposition was characterized by a loss of glycerophosphate units as well as alanine and N-acetylglucosamine substituents. All preparations contained-to varying degrees-non-LTA, non-lipopolysaccharide (LPS) immunostimulatory components as indicated by their elution profile in HIC, lack of phosphate, and negative Limulus amoebocyte lysate (LAL) test results. After purification, the commercial LTA from Bacillus subtilis and S. pyogenes but not LTA from S. aureus induced the release of tumor necrosis factor alpha, interleukin 1 beta (IL-1beta), IL-6, and IL-10 in human blood. While pure LTA are negative in the LAL assay, endotoxin equivalents of more than 10 ng of LPS/mg of LTA were found in the commercial preparations. Taken together, these data indicate that these crude preparations with relatively high endotoxin contamination are not suitable for characterizing the activation of immune cells by LTA. PMID: 11796629
163A: FAT ECM AS A NOVEL SCAFFOLD FOR SOFT TISSUE RECONSTRUCTION (2010)

Plastic and Reconstructive Surgery 125(6):p 109, June 2010. | DOI: 10.1097/01.prs.0000371897.79745.e8
T helper cell cytokine responses during intestinal nematode infection: induction, regulation and effector function. (2001)

Four disease models, Trichuris muris, Heligomosoides polygyrus, Nippostrongylus brasiliensis and Trichinella spiralis, have prompted key developments in the understanding of immunity to nematode infections. This article reviews current findings on the induction and regulation of immunity to these infections based on studies employing these animal models, and highlights areas of the immune response that require further research. T cell and cytokine regulation of host protective immunity; regulation of helper T cell responses during nematode infection; and immune effector mechanisms involving antibodies, mast cells, eosinophils, and cytokines and enterocytes are discussed.
A New Surgical Technique for Anterior Segment Ectasia: Tectonic Lamellar Sclerokeratoplasty (2006)

A 41-year-old patient with severe anterior segment ectasia and a previous history of failed corneal graft was treated by placing a 14-mm tectonic corneoscleral allograft in the eye to support both the corneal and the scleral thinning. Nylon 10-0 interrupted sutures were used at the sclero-scleral junction. The host conjunctiva, including the limbal area, was carefully sutured to the donor limbal area. Three months postoperatively, the graft was stable with no progression of the ectasia. The suturing of a corneoscleral graft over a severely ectatic cornea may be an acceptable technique for providing tectonic tissue support and stabilizing eyes with severe anterior segment ectasia.
Making sense of zebrafish neural development in the Minervois (2007)

The meeting 'From sensory perception to motor output: genetic bases of behavior in the zebrafish embryo' was held at Minerve (South of France) on March 16-18, 2007. The meeting site was beautifully situated in the heart of the Minervois wine country, and its remoteness promoted conversations and interaction over the course of the program. The meeting covered neurogenesis and eye development on day 1, ear and lateral line development on day 2, and brain connectivity and behavior on day 3. Underlying all sessions, however, ran the growing importance of live imaging, an approach that takes full advantage of the transparency of fish embryos and early larvae, as illustrated by several movies and links in this report.
Nanostructured TiO2/CH3NH3PbI3 heterojunction solar cells employing spiro-OMeTAD/Co-complex as hole-transporting material (2013)

For using 2,2′,7,7′-tetrakis(N,N′-di-p-methoxyphenylamine)-9,9′-spirobifluorene (spiro-OMeTAD) as a hole conductor in solar cells, it is necessary to improve its charge-transport properties through electrochemical doping. With the aim of fabricating efficient mesoscopic TiO2/CH3NH3PbI3 heterojunction solar cells, we used tris[2-(1H-pyrazol-1-yl)-4-tert-butylpyridine)cobalt(III) tris(bis(trifluoromethylsulfonyl) imide)] (FK209) as a p-dopant for spiro-OMeTAD. The mixture of spiro-OMeTAD, FK209, lithium bis(trifluoromethylsulfonyl)imide (Li-TFSI), and 4-tert-butylpyridine (TBP) exhibited significantly higher performance than mixtures of pristine spiro-OMeTAD, spiro-OMeTAD, and FK209, and spiro-OMeTAD, Li-TFSI, and TBP. Such a synergistic effect between the Co-complex and Li-TFSI in conjunction with spiro-OMeTAD effectively improved the power conversion efficiency (PCE) of the fabricated solar cells. As a result, we achieved PCE of 10.4%, measured under standard solar conditions (AM 1.5G, 100 mW cm−2).
Novel Kumada Coupling Reaction to Access Cyclic (2‐Azaallyl)stannanes. Cycloadditions of Cyclic Nonstabilized 2‐Azaallyllithium Species Derived from Cyclic (2‐Azaallyl)stannanes. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Generation of pokeweed antiviral protein mutations in Saccharomyces cerevisiae: evidence that ribosome depurination is not sufficient for cytotoxicity (2004)

Pokeweed antiviral protein (PAP) is a ribosome-inactivating protein that depurinates the highly conserved alpha-sarcin/ricin loop in the large rRNA. Here, using site-directed mutagenesis and systematic deletion analysis from the 5' and the 3' ends of the PAP cDNA, we identified the amino acids important for ribosome depurination and cytotoxicity of PAP. Truncating the first 16 amino acids of PAP eliminated its cytotoxicity and the ability to depurinate ribosomes. Ribosome depurination gradually decreased upon the sequential deletion of C-terminal amino acids and was abolished when a stop codon was introduced at Glu-244. Cytotoxicity of the C-terminal deletion mutants was lost before their ability to depurinate ribosomes. Mutations in Tyr-123 at the active site affected cytotoxicity without altering the ribosome depurination ability. Total translation was not inhibited in yeast expressing the non-toxic Tyr-123 mutants, although ribosomes were depurinated. These mutants depurinated ribosomes only during their translation and could not depurinate ribosomes in trans in a translation-independent manner. A mutation in Leu-71 in the central domain affected cytotoxicity without altering the ability to depurinate ribosomes in trans and inhibit translation. These results demonstrate that the ability to depurinate ribosomes in trans in a catalytic manner is required for the inhibition of translation, but is not sufficient for cytotoxicity.
Sensibility following Innervated Free TRAM Flap for Breast Reconstruction (2006)

Innervation of the free TRAM flap provides improved sensation to the reconstructed breast and is a simple adjunct to breast reconstruction.
A computationally efficient platform for inertial sensor calibration (2015)

This paper presents the new open-source statistical software package for inertial sensor calibration. This platform is based on the Generalized Method of Wavelet Moments that was recently proposed to estimate simple and composite stochastic models that are typically used in sensor calibration. As opposed to existing techniques, this new package allows to easily and efficiently visualize, estimate and test a wide range of stochastic models that are used to describe and predict the error signals coming from accelerometers and gyroscopes that characterize inertial sensors. The availability of this new tool is of considerable importance since, given the growing use of low-cost IMUs, correctly identifying and precisely estimating the models for the error signals of these sensors allows to greatly improve their navigation accuracy.
The Emergence of Bacterial “Hopeful Monsters” (2014)

The global spread of antibiotic-resistant bacteria has largely been driven by the dissemination of successful lineages. A particularly important example is sequence type (ST) 258 of Klebsiella pneumoniae, a common cause of health care-associated infections. Representatives of this lineage carry a variable array of plasmid-borne resistance genes, typically including a carbapenemase effective against the full range of clinically important β-lactams. In their recent mBio article, Chen et al. [mBio 5(3):e01355-14] described how ST258 emerged through "hybridization" between two other strains, with a second recombination resulting in the diversification of a key antigen. This commentary describes the findings in the context of other examples where saltational evolution has resulted in the sudden emergence of important pathogenic bacteria.