gebhart/patrepeval huggingface dataset:
A population-based perspective of the hospital incidence and case-fatality rates of deep vein thrombosis and pulmonary embolism. The Worcester DVT Study. (1991)

A community-wide study was conducted in 16 short-stay hospitals in metropolitan Worcester, Mass, to examine the incidence and case-fatality rates of deep vein thrombosis and pulmonary embolism in patients hospitalized between July 1, 1985, and December 31, 1986. The average annual incidence of deep vein thrombosis alone was 48 per 100,000, while the incidence of pulmonary embolism with or without deep vein thrombosis was 23 per 100,000. The incidence rates of deep vein thrombosis and pulmonary embolism increased exponentially with age. The in-hospital case-fatality rate of venous thromboembolism was 12%. Among patients discharged from the hospital, the long-term case-fatality rates were 19%, 25%, and 30% at 1, 2, and 3 years after hospital discharge. Extrapolation of the data from this population-based study suggests that there are approximately 170,000 new cases of clinically recognized venous thromboembolism in patients treated in short-stay hospitals in the United States each year, and 99,000 hospitalizations for recurrent disease. Because of the silent nature of this disease and the low rate of autopsy in the United States, the total incidence, prevalence, and mortality rates of venous thromboembolism remain elusive.
GeneNetWeaver: in silico benchmark generation and performance profiling of network inference methods (2011)

dario.floreano@epfl.ch.
FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes (2004)

We present a simple but powerful procedure to extract Gene Ontology (GO) terms that are significantly over- or under-represented in sets of genes within the context of a genome-scale experiment (DNA microarray, proteomics, etc.). Said procedure has been implemented as a web application, FatiGO, allowing for easy and interactive querying. FatiGO, which takes the multiple-testing nature of statistical contrast into account, currently includes GO associations for diverse organisms (human, mouse, fly, worm and yeast) and the TrEMBL/Swissprot GOAnnotations@EBI correspondences from the European Bioinformatics Institute.
Asynchronous non-invasive high-speed BCI speller with robust non-control state detection (2019)

Brain-Computer Interfaces (BCIs) enable users to control a computer by using pure brain activity. Recent BCIs based on visual evoked potentials (VEPs) have shown to be suitable for high-speed communication. However, all recent high-speed BCIs are synchronous, which means that the system works with fixed time slots so that the user is not able to select a command at his own convenience, which poses a problem in real-world applications. In this paper, we present the first asynchronous high-speed BCI with robust distinction between intentional control (IC) and non-control (NC), with a nearly perfect NC state detection of only 0.075 erroneous classifications per minute. The resulting asynchronous speller achieved an average information transfer rate (ITR) of 122.7 bit/min using a 32 target matrix-keyboard. Since the method is based on random stimulation patterns it allows to use an arbitrary number of targets for any application purpose, which was shown by using an 55 target German QWERTZ-keyboard layout which allowed the participants to write an average of 16.1 (up to 30.7) correct case-sensitive letters per minute. As the presented system is the first asynchronous high-speed BCI speller with a robust non-control state detection, it is an important step for moving BCI applications out of the lab and into real-life.
Channel Length Scaling in Graphene Field-Effect Transistors Studied with Pulsed Current−Voltage Measurements (2011)

We investigate current saturation at short channel lengths in graphene field-effect transistors (GFETs). Saturation is necessary to achieve low-output conductance required for device power gain. Dual-channel pulsed current-voltage measurements are performed to eliminate the significant effects of trapped charge in the gate dielectric, a problem common to all oxide-based dielectric films on graphene. With pulsed measurements, graphene transistors with channel lengths as small as 130 nm achieve output conductance as low as 0.3 mS/μm in saturation. The transconductance of the devices is independent of channel length, consistent with a velocity saturation model of high-field transport. Saturation velocities have a density dependence consistent with diffusive transport limited by optical phonon emission.
Requirement for Cellular Cyclin-Dependent Kinases in Herpes Simplex Virus Replication and Transcription (1998)

Several observations indicate that late-G1/S-phase-specific cellular functions may be required for herpes simplex virus (HSV) replication: (i) certain mutant HSV strains are replication impaired during infection of cells in the G0/G1 but not in the G1/S phase of the cell cycle, (ii) several late-G1/S-phase-specific cellular proteins and functions are induced during infection, and (iii) the activity of a cellular protein essential for expression of viral immediate-early (IE) genes, HCF, is normally required during the late G1/S phase of the cell cycle. To test the hypothesis that late-G1/S-phase-specific cellular functions are necessary for HSV replication, HEL or Vero cells were infected in the presence of the cell cycle inhibitors roscovitine (Rosco) and olomoucine (Olo). Both drugs inhibit cyclin-dependent kinase 1 (cdk-1) and cdk-2 (required for cell cycle progression into the late G1/S phase) and cdk-5 (inactive in cycling cells) but not cdk-4 or cdk-6 (active at early G1). We found that HSV replication was inhibited by Rosco and Olo but not by lovastatin (a cell cycle inhibitor that does not inhibit cdk activity), staurosporine (a broad-spectrum protein serine-threonine kinase inhibitor), PD98059 (an inhibitor specific for erk-1 and -2) or iso-Olo (a structural isomer of Olo that does not inhibit cdk activity). The concentrations of Rosco and Olo required to inhibit cell cycle progression and viral replication in both HEL and Vero cells were similar. Inhibition of viral replication was found not to be mediated by drug-induced cytotoxicity. Efforts to isolate Rosco- or Olo-resistant HSV mutants were unsuccessful, indicating that these drugs do not act by inhibiting a single viral target. Viral DNA replication and accumulation of IE and early viral RNAs were inhibited in the presence of cell cycle-inhibitory concentrations of Rosco or Olo. We therefore conclude that one or more cdks active from late G1 onward or inactive in nonneuronal cells are required for accumulation of HSV transcripts, viral DNA replication, and production of infectious virus.
HARP syndrome is allelic with pantothenate kinase–associated neurodegeneration (2002)

HARP (hypoprebetalipoproteinemia, acanthocytosis, retinitis pigmentosa, and pallidal degeneration) is a rare syndrome with many clinical similarities to pantothenate kinase-associated neurodegeneration (PKAN, formerly Hallervorden-Spatz syndrome). Despite these common features, lipoprotein abnormalities have not been reported in PKAN. After the recent discovery of the genetic defect in PKAN, we report a homozygous nonsense mutation in exon 5 of the PANK2 gene that creates a stop codon at amino acid 371 (R371X) in the original HARP patient. This finding establishes that HARP is part of the PKAN disease spectrum.
Zyme, a Novel and Potentially Amyloidogenic Enzyme cDNA Isolated from Alzheimer's Disease Brain (1997)

The deposition of the beta amyloid peptide in neuritic plaques and cerebral blood vessels is a hallmark of Alzheimer's disease (AD) pathology. The major component of the amyloid deposit is a 4.2-kDa polypeptide termed amyloid beta-protein of 39-43 residues, which is derived from processing of a larger amyloid precursor protein (APP). It is hypothesized that a chymotrypsin-like enzyme is involved in the processing of APP. We have discovered a new serine protease from the AD brain by polymerase chain reaction amplification of DNA sequences representing active site homologous regions of chymotrypsin-like enzymes. A cDNA clone was identified as one out of one million that encodes Zyme, a serine protease. Messenger RNA encoding Zyme can be detected in some mammalian species but not in mice, rats, or hamster. Zyme is expressed predominantly in brain, kidney, and salivary gland. Zyme mRNA cannot be detected in fetal brain but is seen in adult brain. The Zyme gene maps to chromosome 19q13.3, a region which shows genetic linkage with late onset familial Alzheimer's disease. When Zyme cDNA is co-expressed with the APP cDNA in 293 (human embryonic kidney) cells, amyloidogenic fragments are detected using C-terminal antibody to APP. These co-transfected cells release an abundance of truncated amyloid beta-protein peptide and shows a reduction of residues 17-42 of Abeta (P3) peptide. Zyme is immunolocalized to perivascular cells in monkey cortex and the AD brain. In addition, Zyme is localized to microglial cells in our AD brain sample. The amyloidogenic potential and localization in brain may indicate a role for this protease in amyloid precursor processing and AD.
Dye-Sensitized Solar Cells Based on Oriented TiO2 Nanotube Arrays: Transport, Trapping, and Transfer of Electrons (2008)

Dye-sensitized solar cells fabricated using ordered arrays of titania nanotubes (tube lengths 5, 10, and 20 microm) grown on titanium have been characterized by a range of experimental methods. The collection efficiency for photoinjected electrons in the cells is close to 100% under short circuit conditions, even for a 20 microm thick nanotube array. Transport, trapping, and back transfer of electrons in the nanotube cells have been studied in detail by a range of complementary experimental techniques. Analysis of the experimental results has shown that the electron diffusion length (which depends on the diffusion coefficient and lifetime of the photoinjected electrons) is of the order of 100 microm in the titania nanotube cells. This is consistent with the observation that the collection efficiency for electrons is close to 100%, even for the thickest (20 microm) nanotube films used in the study. The study revealed a substantial discrepancy between the shapes of the electron trap distributions measured experimentally using charge extraction techniques and those inferred indirectly from transient current and voltage measurements. The discrepancy is resolved by introduction of a numerical factor to account for non-ideal thermodynamic behavior of free electrons in the nanostructured titania.
Transcription factor C/EBP‐β mediates downregulation of dipeptidyl‐peptidase III expression by interleukin‐6 in human glioblastoma cells (2014)

Dipeptidyl-peptidase III (DPP III) is a cytosolic metallo-aminopeptidase implicated in various physiological and pathological processes. A previous study from our laboratory indicated an elevated expression of DPP III in glioblastoma (U87MG) cells. In the present study we investigated the role of interleukin-6 (IL-6), a pleiotropic cytokine produced by glial tumors, in the regulation of DPP III expression. Immunohistochemistry, western blotting and quantitative RT-PCR were used for quantitation of DPP III and IL-6 in human glioblastoma cells and tumors. Cell transfections and DPP III promoter reporter assays were performed to study the transcriptional regulation of DPP III by IL-6. Promoter deletion analysis, site directed mutagenesis, chromatin immunoprecipitation assays and small interfering RNA (siRNA) technology was employed to elucidate the molecular mechanism of IL-6 mediated regulation of DPP III expression in glioblastoma cells. Our results for the first time demonstrate a negative correlation (r = 0.632, P = 0.01) between DPP III and IL-6 in both human tumors and cultured glioblastoma cells. Treatment of U87MG cells with IL-6 significantly decreased DPP III expression with a concomitant increase in the levels of transcription factor CCAAT/enhancer binding protein beta (C/EBP-β). Deletion/mutagenesis of C/EBP-β binding motif of DPP III promoter significantly increased its activity and abolished its responsiveness to IL-6. This effect could also be mimicked by C/EBP-β siRNA. In conclusion our study for the first time demonstrates C/EBP-β mediated transcriptional downregulation of DPP III by IL-6. Our results demonstrating a negative correlation between IL-6 and DPP III taken together with the previously reported prognostic significance of this cytokine in glioblastoma suggests that DPP III may prove useful as a prognostic marker.
Metabolic engineering of Saccharomyces cerevisiae for the de novo production of psilocybin and related tryptamine derivatives (2020)

Psilocybin is a tryptamine-derived psychoactive alkaloid found mainly in the fungal genus Psilocybe, among others, and is the active ingredient in so-called "magic mushrooms". Although its notoriety originates from its psychotropic properties and popular use as a recreational drug, clinical trials have recently recognized psilocybin as a promising candidate for the treatment of various psychological and neurological afflictions. In this work, we demonstrate the de novo biosynthetic production of psilocybin and related tryptamine derivatives in Saccharomyces cerevisiae by expression of a heterologous biosynthesis pathway sourced from Psilocybe cubensis. Additionally, we achieve improved product titers by supplementing the pathway with a novel cytochrome P450 reductase from P. cubensis. Further rational engineering resulted in a final production strain producing 627 ± 140 mg/L of psilocybin and 580 ± 276 mg/L of the dephosphorylated degradation product psilocin in triplicate controlled fed-batch fermentations in minimal synthetic media. Pathway intermediates baeocystin, nor norbaeocystin as well the dephosphorylated baeocystin degradation product norpsilocin were also detected in strains engineered for psilocybin production. We also demonstrate the biosynthetic production of natural tryptamine derivative aeruginascin as well as the production of a new-to-nature tryptamine derivative N-acetyl-4-hydroxytryptamine. These results lay the foundation for the biotechnological production of psilocybin in a controlled environment for pharmaceutical applications, and provide a starting point for the biosynthetic production of other tryptamine derivatives of therapeutic relevance.
In Vivo Triple Quantum Filtered Twisted Projection Sodium MRI of Human Articular Cartilage (1999)

In this work, we present the first triple quantum filtered (TQF) sodium MR images of the human knee joint in vivo. A 3D TQF data set of 16 slices was obtained in 20 min using a TQF pulse sequence preencoded to a twisted projection imaging readout. Images clearly demarcate patellar cartilage and also demonstrate fluid signal suppressed by the triple quantum filter. Biexponential transverse relaxation times were calculated by fitting the TQF free induction decay to a theoretical signal expression. The average values from three healthy volunteers were T(2fall)(*) = 9.59 +/- 0.35 ms and T(2rise)(*) = 0.84 +/- 0.06 ms. Application of TQF imaging in biological tissues is discussed.
Dehydration leads to a phase transition in monoclinic factor XIII crystals (1999)

Monoclinic factor XIII crystals have been transferred to a solution containing increasing amounts of the precipitant PEG 6000. At a concentration of about 36%(w/v) PEG 6000, a phase transition was observed. The space group of the crystals was preserved on the transition, but half of the 2(1) screw axes were lost, which meant that the unit-cell volume and the content of the asymmetric unit were doubled. The structure of factor XIII in the new crystal form was solved by molecular replacement. About 80% of the changes accompanying the transition can be explained by a rigid-body rotation of half of the factor XIII dimers in the lattice by about 5 degrees. The remaining changes are mostly small interdomain movements of the four domains which constitute one factor XIII monomer.
Non-Functionalization of Two CYP82E Nicotine N-Demethylase Genes Abolishes Nornicotine Formation in Nicotiana langsdorffii (2012)

Nornicotine is formed from nicotine by nicotine N-demethylase, a CYP82E family monooxygenase, and accumulates to high levels in some tobacco (Nicotiana tabacum) cultivars and many wild Nicotiana species. Nicotiana langsdorffii does not form nornicotine, whereas the closely related species N. alata accumulates this alkaloid abundantly. We show here that the two nicotine N-demethylase genes in N. langsdorffii have been inactivated by different molecular mechanisms. We identified four N. alata CYP82E genes that encode functional nicotine N-demethylases. In N. langsdorffii, however, one CYP82E gene encoding a functional enzyme was not expressed at all, whereas the other was weakly expressed but contained a one-nucleotide deletion in the first exon, yielding a truncated protein. Expression analysis of interspecific F(1) hybrids between N. alata and N. langsdorffii indicated that cis-acting polymorphisms abolish expression of the otherwise functional CYP82E gene in N. langsdorffii. Segregation analysis of tobacco alkaloids and individual CYP82E alleles in F(2) progeny revealed that duplicated CYP82E genes in both species are genetically linked, and provide genetic evidence that CYP82E genes are solely responsible for nornicotine formation in these wild Nicotiana species.
Application of mass spectrometry to the identification and quantification of histone post‐translational modifications (2004)

The core histones are the primary protein component of chromatin, which is responsible for the packaging of eukaryotic DNA. The NH(2)-terminal tail domains of the core histones are the sites of numerous post-translational modifications that have been shown to play an important role in the regulation of chromatin structure. In this study, we discuss the recent application of modern analytical techniques to the study of histone modifications. Through the use of mass spectrometry, a large number of new sites of histone modification have been identified, many of which reside outside of the NH(2)-terminal tail domains. In addition, techniques have been developed that allow mass spectrometry to be effective for the quantitation of histone post-translational modifications. Hence, the use of mass spectrometry promises to dramatically alter our view of histone post-translational modifications.
Clonal growth of normal human epidermal keratinocytes in a defined medium (1982)

Colony formation by normal human epidermal keratinocytes (HK) has been achieved in a medium that contains no deliberately added undefined supplements. The term "defined" is used to describe this medium, although the possibility that trace contaminants in its components could be contributing to the multiplication that it supports cannot yet be ruled out completely. The defined medium consists of a basal medium, MCDB 152, supplemented with 5 ng/ml epidermal growth factor (EGF), 10 micrograms/ml transferrin, 5 micrograms/ml insulin, 1.4 X 10(-6) M hydrocortisone, 1.0 X 10(-5) Methanolamine, 1.0 X 10(-5) M phosphoethanolamine, and 2.0 X 10(-9) M progesterone. MCDB 152 differs from MCDB 151, previously developed for multiplication of HK with small amounts of dialyzed serum (Peehl and Ham, 1980b), only by addition of the trace element mixture from human fibroblast medium MCDB 104 (McKeehan et al., 1977). Most of the requirement for transferrin, which is the least defined component of the defined medium, can be replaced by adding freshly dissolved and sterilized ferrous sulfate to the final medium after it has been filter sterilized. Insulin and EGF are clearly needed for optimal multiplication and hydrocortisone is mildly beneficial. Either ethanolamine or phosphoethanolamine must be present in the defined medium for HK multiplication. There is a greater need for EGF and less for hydrocortisone in the defined medium than in previous partially defined systems that we have worked with. Very large colonies of flattened epithelial cells are obtained in the defined medium, which has a low calcium concentration (0.03 mM) and does not favor keratinocyte differentiation. Less growth and more differentiation are obtained with higher calcium concentrations. The defined medium is highly selective for keratinocyte growth from a mixed inoculum of keratinocytes and fibroblasts.
Inhibition of matrix metalloproteinase 9 expression by a ribozyme blocks metastasis in a rat sarcoma model system. (1996)

Matrix metalloproteinases (MMPs) have been implicated in tumor progression, but the exact roles that each member of this family may play in contributing to the behavior of malignant tumors are only beginning to be understood. MMP-9 (gelatinase B or the 92-kDa gelatinase/type IV collagenase) expression has been associated with metastasis in a variety of model systems including that of rat sarcomas generated by transformation of rat embryo cells with rasH and myc. To determine the effect that expression of MMP-9 has in this system, we inhibited the expression of MMP-9 using a hammerhead ribozyme. Introduction of an expression vector for a ribozyme directed against the rat MMP-9 mRNA sequence into a metastatic rat embryo cell line transformed by rasH and myc (2.10.10) that constitutively secretes MMP-9 resulted in the absence of detectable MMP-9 mRNA and loss of released 92-kDa gelatinase activity. These cells were no longer metastatic in a lung colonization assay but retained tumorigenicity. Introduction of an expression vector for a control hammerhead ribozyme had no effect. These data document the requirement for MMP-9 expression in metastasis in this system.
Biocatalysis and nineteenth century organic chemistry: conversion of D-glucose into quinoid organics (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTBiocatalysis and nineteenth century organic chemistry: conversion of D-glucose into quinoid organicsK. M. Draths, T. L. Ward, and J. W. FrostCite this: J. Am. Chem. Soc. 1992, 114, 24, 9725–9726Publication Date (Print):November 1, 1992Publication History Published online1 May 2002Published inissue 1 November 1992https://pubs.acs.org/doi/10.1021/ja00050a099https://doi.org/10.1021/ja00050a099research-articleACS PublicationsRequest reuse permissionsArticle Views313Altmetric-Citations42LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts