gebhart/patrepeval huggingface dataset:
AGU position statement on human impacts on climate (2003)

Human activities are increasingly altering the Earth's climate. These effects add to natural influences that have been present over Earth's history. Scientific evidence strongly indicates that natural influences cannot explain the rapid increase in global near‐surface temperatures observed during the second half of the 20th century. Human impacts on the climate system include increasing concentrations of atmospheric greenhouse gases (e.g., carbon dioxide, chlorofluorocarbons and their substitutes, methane, nitrous oxide, etc.), air pollution, increasing concentrations of airborne particles, and land alteration. A particular concern is that atmospheric levels of carbon dioxide may be rising faster than at any time in Earth's history, except possibly following rare events like impacts from large extraterrestrial objects.
Accurate and comprehensive sequencing of personal genomes (2011)

As whole-genome sequencing becomes commoditized and we begin to sequence and analyze personal genomes for clinical and diagnostic purposes, it is necessary to understand what constitutes a complete sequencing experiment for determining genotypes and detecting single-nucleotide variants. Here, we show that the current recommendation of ∼30× coverage is not adequate to produce genotype calls across a large fraction of the genome with acceptably low error rates. Our results are based on analyses of a clinical sample sequenced on two related Illumina platforms, GAII(x) and HiSeq 2000, to a very high depth (126×). We used these data to establish genotype-calling filters that dramatically increase accuracy. We also empirically determined how the callable portion of the genome varies as a function of the amount of sequence data used. These results help provide a "sequencing guide" for future whole-genome sequencing decisions and metrics by which coverage statistics should be reported.
A new in vivo test method to compare wound dressing fluid handling characteristics and wear time. (2011)

A refined in vivo artificial wound model utilizing artificial wound fluid (AWF) was developed to overcome important limitations such as adhesive-skin interactions, movement, pressure, shear, and varying environmental conditions in in vitro models. Using this model, a study with primary endpoints of wear time and fluid handling capacity was conducted to compare two foam dressings: a high performance (HPF) dressing and an adhesive dressing (AAF). A 10-cm(2) artificial wound bed, created using a nonstick absorbent pad, was applied to the lower back of 24 healthy volunteers and the tip of a 23-gauge catheter was inserted into the pad to administer AWF. The pad and catheter were secured in place with paper tape and covered with the test dressings. This model and 1.0-mL AWF infusions every 12 hours was used to simulate highly exudating wounds. The HPF dressing absorbed 75% more fluid before failure and remained intact for a median of 6.1 days compared to 3.5 days for the AAF dressing (P <0.001, Cox proportional hazard model). Comparisons between dressing outcomes using this model and previously published in vitro results suggest the model may be valid and reliable. Studies to ascertain the ability of this model to predict clinical dressing performance and research to compare other wound outcomes that affect dressing change frequency and cost (eg, healing) are needed.
In vitro Production of Transfusable Red Blood Cells (2008)

Unpredictable adverse results can ensue from blood transfusion therapies because of the donation of cells from a very large number of anonymous volunteers. There is little doubt that transfusable blood cells produced on a large scale in vitro would be candidate materials to replace cells donated from such a large group of anonymous individuals. The recent progress of technology for in vitro production of transfusable red blood cells is reviewed.
Thyroid Function Modulates Thymic Endocrine Activity* (1986)

The thymus produces humoral factors that induce proliferation and differentiation of T-cells, which are responsible for cell-mediated immunity. Recent data in animals suggest that such thymic hormone activity is modulated by the neuroendocrine network and, in particular, by thyroid hormones, but no information is presently available in humans. To study this question, we measured the circulating thymic factor called thymulin (Zn-FTS) in hyperthyroid and hypothyroid patients. Thymulin levels were higher in hyperthyroid patients than in normal subjects, whereas hypothyroid patients had lower thymulin levels than normal subjects. A significant correlation was found between circulating thymulin and serum T4 and T3 levels. Thymulin changes could be reversed by appropriate treatment in both groups of patients. Recent data indicate that zinc is required to confer biological activity on thymic hormone molecules. This raised the question of whether the influence of thyroid status on thymulin activity could be mediated by changes in serum zinc concentrations. No support for such an explanation was obtained by thymulin measurements by a modified bioassay using an optimal zinc concentration in the assay system. In conclusion, thyroid status modulates thymic endocrine function in humans. Whether and to what extent such modulation is relevant to the function of the immune system remain to be established.
Codon usage tabulated from international DNA sequence databases: status for the year 2000 (2000)

The frequencies of each of the 257 468 complete protein coding sequences (CDSs) have been compiled from the taxonomical divisions of the GenBank DNA sequence database. The sum of the codons used by 8792 organisms has also been calculated. The data files can be obtained from the anonymous ftp sites of DDBJ, Kazusa and EBI. A list of the codon usage of genes and the sum of the codons used by each organism can be obtained through the web site http://www.kazusa.or.jp/codon/. The present study also reports recent developments on the WWW site. The new web interface provides data in the CodonFrequency-compatible format as well as in the traditional table format. The use of the database is facilitated by keyword based search analysis and the availability of codon usage tables for selected genes from each species. These new tools will provide users with the ability to further analyze for variations in codon usage among different genomes.
Role of the Phosphatidylserine Receptor TIM-1 in Enveloped-Virus Entry (2013)

The cell surface receptor T cell immunoglobulin mucin domain 1 (TIM-1) dramatically enhances filovirus infection of epithelial cells. Here, we showed that key phosphatidylserine (PtdSer) binding residues of the TIM-1 IgV domain are critical for Ebola virus (EBOV) entry through direct interaction with PtdSer on the viral envelope. PtdSer liposomes but not phosphatidylcholine liposomes competed with TIM-1 for EBOV pseudovirion binding and transduction. Further, annexin V (AnxV) substituted for the TIM-1 IgV domain, supporting a PtdSer-dependent mechanism. Our findings suggest that TIM-1-dependent uptake of EBOV occurs by apoptotic mimicry. Additionally, TIM-1 enhanced infection of a wide range of enveloped viruses, including alphaviruses and a baculovirus. As further evidence of the critical role of enveloped-virion-associated PtdSer in TIM-1-mediated uptake, TIM-1 enhanced internalization of pseudovirions and virus-like proteins (VLPs) lacking a glycoprotein, providing evidence that TIM-1 and PtdSer-binding receptors can mediate virus uptake independent of a glycoprotein. These results provide evidence for a broad role of TIM-1 as a PtdSer-binding receptor that mediates enveloped-virus uptake. Utilization of PtdSer-binding receptors may explain the wide tropism of many of these viruses and provide new avenues for controlling their virulence.
Genetic and Environmental Manipulation of Horticultural Crops (1997)

1: Genetic Approaches to Manipulation of Fruit Development and Quality in Tomato, J J Giovannoni et al., Texas A & M University, USA 2: Improving Tomato Fruit Quality by Cultivation, L C Ho, Horticulture Research International, UK 3: Applications of Molecular Biology and Genetic Manipulation to Understand and Improve Quality of Fruits and Vegetables, D Grierson, University of Nottingham, UK 4: Gene Expression in Ripening Bananas, R Drury, Horticulture Research International, UK, C R Bird, Zeneca Plant Science, UK and G B Seymour, Horticulture Research International, UK 5: Genes for Fruit Quality in Strawberry, K Manning, Horticulture Research International, UK 6: The Tomato Ethylene Receptor Gene Family: It's Not Easy Being a Plant, D Tieman and H Klee, University of Florida, USA 7: Environmental Requirements as Determined by Rooting Potential in Leafy Cuttings, 8: R S Harrison-Murray and B H Howard, Horticulture Research International, UK 9: The Use of Mutants and Molecular Biology to Understand Competence for Root Formation, W P Hackett et al., University of Minnesota, USA 10: Physiological Analysis of the Floral Transition, G Bernier et al., Universite de Liege, Belgium 11: Genetic and Environmental Control of Flowering in Strawberry, N H Battey et al., University of Reading, UK 12: Manipulating the Photoperiodic Control of Plant Reproduction, S D Jackson and B Thomas, Horticulture Research International, UK 13: Regulation of Abscisic Acid and Water Stress Response Genes, P K Busk et al., CID, Barcelona, Spain 14: Manipulation of Growth of Horticultural Crops under Environmental Stress, W J Davies and D S Thompson, Lancaster University, UK and J E Taylor, University of Reading, UK 15: Engineering Phytochrome Genes to Improve Crop Performance, H Smith, University of Leicester, UK 16: Regulation of Stem Extension by Temperature, F Allen Langton, Horticulture Research International, UK 17: Modification of Plant Morphology by Genetic Manipulation of Gibberellin Biosynthesis, P Hedden et al., University of Bristol, UK
Reprogramming of anaerobic metabolism by the FnrS small RNA (2010)

Small RNAs (sRNAs) that act by base pairing with trans-encoded mRNAs modulate metabolism in response to a variety of environmental stimuli. Here, we describe an Hfq-binding sRNA (FnrS) whose expression is induced upon a shift from aerobic to anaerobic conditions and which acts to downregulate the levels of a variety of mRNAs encoding metabolic enzymes. Anaerobic induction in minimal medium depends strongly on FNR but is also affected by the ArcA and CRP transcription regulators. Whole genome expression analysis showed that the levels of at least 32 mRNAs are downregulated upon FnrS overexpression, 15 of which are predicted to base pair with FnrS by TargetRNA. The sRNA is highly conserved across its entire length in numerous Enterobacteria, and mutational analysis revealed that two separate regions of FnrS base pair with different sets of target mRNAs. The majority of the target genes were previously reported to be downregulated in an FNR-dependent manner but lack recognizable FNR binding sites. We thus suggest that FnrS extends the FNR regulon and increases the efficiency of anaerobic metabolism by repressing the synthesis of enzymes that are not needed under these conditions.
RAS isoforms and mutations in cancer at a glance (2016)

RAS proteins (KRAS4A, KRAS4B, NRAS and HRAS) function as GDP-GTP-regulated binary on-off switches, which regulate cytoplasmic signaling networks that control diverse normal cellular processes. Gain-of-function missense mutations in RAS genes are found in ∼25% of human cancers, prompting interest in identifying anti-RAS therapeutic strategies for cancer treatment. However, despite more than three decades of intense effort, no anti-RAS therapies have reached clinical application. Contributing to this failure has been an underestimation of the complexities of RAS. First, there is now appreciation that the four human RAS proteins are not functionally identical. Second, with >130 different missense mutations found in cancer, there is an emerging view that there are mutation-specific consequences on RAS structure, biochemistry and biology, and mutation-selective therapeutic strategies are needed. In this Cell Science at a Glance article and accompanying poster, we provide a snapshot of the differences between RAS isoforms and mutations, as well as the current status of anti-RAS drug-discovery efforts.
Intracranial Haemorrhage in the new-born: A study of diagnosis and differential diagnosis based upon pathological and clinical findings in 126 cases (1938)

Hitherto interest in intracranial haemorrhage in the new-born has been centred mainly upon etiology and pathology.More recently symptomotology has received increasing attention.While the pathology of the subject in its relation to etiological factors has received considerable attention, few attempts have been made to correlate pathological with clinical findings.The present paper is based upon both clinical and pathological observations made by the writer in connexion with 126 new-born infants in whom intracranial haemorrhage was found at autopsy.Of the 126 infants, 110 were born in the Royal Maternity Hospital and ten in the Western General Hospital, Edinburgh.Six infants were born at home, four being subsequently admitted to the Royal Maternity Hospital and two to the Western General Hospital.Infants born in hospital were under observation from the time of birth and were examined daily following the first evidence of failure to progress or of disturbed health.Clinical findings were recorded at the time of examination.A similar routine was adopted in the case of infants born at home and subsequently admitted to hospital.Post- mortem examinations were carried out within thirty-six, forty-eight and seventy-two hours of death in the case of ninety-five, twenty-four and seven infants respectively.A pathological basis has been considered as best suited to the study of the present series.Intracranial haemorrhage found post mortem in the 126 cases included in the investigation differed according as it had taken place into the subdural space, the subarachnoid space, the ventricular system or into the brain substance.Cases have been grouped according to the distribution of the H 89 on July 18,
Near-Infrared Reflectance Analysis by Gauss-Jordan Linear Algebra (1983)

Near-infrared reflectance analysis is an analytical technique that uses the near-infrared diffuse reflectance of a sample at several discrete wavelengths to predict the concentration of one or more of the chemical species in that sample. However, because near-infrared bands from solid samples are both abundant and broad, the reflectance at a given wavelength usually contains contributions from several sample components, requiring extensive calculations on overlapped bands. In the present study, these calculations have been performed using an approach similar to that employed in multi-component spectrophotometry, but with Gauss-Jordan linear algebra serving as the computational vehicle. Using this approach, correlations for percent protein in wheat flour and percent benzene in hydrocarbons have been obtained and are evaluated. The advantages of a linear-algebra approach over the common one employing stepwise regression are explored.
PROSTATE SPECIFIC ANTIGEN: A DECADE OF DISCOVERY-WHAT WE HAVE LEARNED AND WHERE WE ARE GOING (1999)

During the last decade much of the focus has been on improving the ability of this tumor marker to detect prostate cancer. PSA remains the best and most widely used tumor marker in urology today.
Theoretische Chemie 2004 (2005)

Abstract Durch Kombination von klassischen und quantenmechanischen Theorien lassen sich Quantenphänomene mittlerweile auch in komplexen Systemen wie Flüssigkeiten, Nanostrukturen und Biomolekülen beschreiben. Die theoretische Spektroskopie ist das Bindeglied zwischen Molekülphysik und Reaktionsdynamik. Fortschritte in der Methodenentwicklung machen den routinemäßigen Einsatz in Analytik und Strukturchemie absehbar. Die Dichtefunktionaltheorie hat sich zu einem wichtigen Bestandteil der chemischen Forschung entwickelt. Die Suche nach Lösungen für fundamentale Probleme bleibt aber schwierig.
Structures of Neutral O-Linked Polylactosaminoglycans on Human Skim Milk Mucins (1989)

O-Linked oligosaccharides were isolated from human skim milk mucins and from mucin-derived glycopeptides by reductive beta-elimination. The released alditols were fractionated by DEAE-Sephadex chromatography and purified by high performance liquid chromatography on primary amine bonded phase. The structures of the major neutral oligosaccharide alditols could be established by fast atom bombardment and electron impact mass spectrometry, combined with methylation analysis, 500-MHz 1H nuclear magnetic resonance spectroscopy, and endo-beta-galactosidase (from Bacteroides fragilis, EC 3.2.1.103) digestion (where n = 0-3): (formula; see text) Major O-glycosidically linked oligosaccharides on skim milk mucins are of the Gal beta(1-3)[GlcNAc beta(1-6)] GalNAc core type 2 and exhibit linearly extended backbone chains of the poly N-acetyllactosamine type comprizing up to at least four repeating units, which are linked by the hitherto unknown sequence GlcNAc-beta(1-6) Gal rather than GlcNAc beta(1-3)Gal. A considerable portion of neutral alditols is represented by branched isomers of the linear species, which are distinguished by their content of 3,6-disubstituted galactose and their partial resistance to endo-beta-galactosidase digestion.
Plasma from human volunteers subjected to remote ischemic preconditioning protects human endothelial cells from hypoxia–induced cell damage (2015)

Short repeated cycles of peripheral ischemia/reperfusion (I/R) can protect distant organs from subsequent prolonged I/R injury; a phenomenon known as remote ischemic preconditioning (RIPC). A RIPC-mediated release of humoral factors might play a key role in this protection and vascular endothelial cells are potential targets for these secreted factors. In the present study, RIPC-plasma obtained from healthy male volunteers was tested for its ability to protect human umbilical endothelial cells (HUVEC) from hypoxia-induced cell damage. 10 healthy male volunteers were subjected to a RIPC-protocol consisting of 4 × 5 min inflation/deflation of a blood pressure cuff located at the upper arm. Plasma was collected before (T0; control), directly after (T1) and 1 h after (T2) the RIPC procedure. HUVEC were subjected to 24 h hypoxia damage and simultaneously incubated with 5% of the respective RIPC-plasma. Cell damage was evaluated by lactate dehydrogenase (LDH)-measurements. Western blot experiments of hypoxia inducible factor 1 alpha (HIF1alpha), phosphorylated signal transducer and activator of transcription 5 (STAT5), protein kinase B (AKT) and extracellular signal-related kinase 1/2 (ERK-1/2) were performed. Furthermore, the concentrations of hVEGF were evaluated in the RIPC-plasma by sandwich ELISA. Hypoxia-induced cell damage was significantly reduced by plasma T1 (p = 0.02 vs T0). The protective effect of plasma T1 was accompanied by an augmentation of the intracellular HIF1alpha (p = 0.01 vs T0) and increased phosphorylation of ERK-1/2 (p = 0.03 vs T0). Phosphorylation of AKT and STAT5 remained unchanged. Analysis of the protective RIPC-plasma T1 showed significantly reduced levels of hVEGF (p = 0.01 vs T0). RIPC plasma protects endothelial cells from hypoxia-induced cell damage and humoral mediators as well as intracellular HIF1alpha may be involved.
LIM domain-containing protein trip6 can act as a coactivator for the v-Rel transcription factor. (1999)

The retroviral oncoprotein v-Rel is a transcriptional activator in the Rel/NF-kappaB family of eukaryotic transcription factors. v-Rel malignantly transforms a variety of cell types in vitro and in vivo, and its transforming activity is dependent on the ability of v-Rel to bind to DNA and activate transcription. In this report, we used the yeast two-hybrid assay to identify proteins that interact with C-terminal sequences of v-Rel that are needed for transcriptional activation and transformation. One protein, Trip6, that we identified in this screen was previously identified as a thyroid hormone receptor-interacting protein. Trip6 is a member of a subfamily of LIM domain-containing proteins that are thought to transport intracellular signals from the cell surface to the nucleus. By several criteria, we show that sequences from Trip6, which include the LIM domains, behave as a coactivator for transcriptional activation by v-Rel. That is, a GAL4-Trip6 fusion protein can activate transcription in yeast and chicken cells, Trip6 can enable C-terminal sequences of v-Rel to activate transcription in yeast, and Trip6 can enhance activation by v-Rel from a kappaB site reporter plasmid in yeast. Although full-length Trip6 localizes to adhesion plaques, deletion of N-terminal sequences allows human Trip6 to enter the nucleus of chicken cells. Lastly, Northern blotting shows that Trip6 mRNA is expressed in many human tissues. Coexpression of Trip6 does not affect the transforming activity of v-Rel. Taken together, our results indicate that Trip6 may be a protein that is important for the ability of v-Rel to activate transcription and transform cells, and may represent a potential target for blocking Rel-mediated oncogenesis and transcriptional activation.
Completion of Horizontal Drainholes (1988)

ABSTRACT Horizontal drainholes, of which the aim is to collect the fluids over considerable lengths, may cross heterogenous zones of the reservoir. So as to turn to practical effect the advantages which in theory, ensue from horizontal drains, specific techniques must be made available providing solutions to the selective completion problems. Indeed, only a selective production method taking into account the geological heterogeneities of the reservoir will enable high production and recovery rates. This paper presents results concerning three stages of the methodology of selective completion design, i.e., procedures and equipment for cementing or setting external casing packers, methods of reservoir evaluation in order to describe heterogeneities and models to optimize the flow rate distribution according to these heterogeneities.
Effects of stimulation frequency and intensity in sacral neuromodulation on anorectal inputs to the somatosensory cortex in an experimental model (2014)

The effect of SNM in this animal model is governed principally by frequency, with an optimum of 2 Hz. If animal data can be translated to humans, optimization of SNM frequency may offer a clinically relevant improvement in the efficacy of SNM. Surgical relevance Sacral neuromodulation (SNM) for faecal incontinence currently employs stimulation parameters that have been derived empirically and may not be optimal. This study used an animal model of SNM and focused on its acute effect on anal canal cortical evoked potentials (EPs). It was found that SNM potentiated EPs, with a clear optimum at a frequency of 2 Hz. If this finding is applicable to the mechanism of action of human SNM, this suggests that there may be a clinically relevant improvement by reducing stimulus frequency from its typical value of 14 Hz to 2 Hz.