gebhart/patrepeval huggingface dataset:
Characterization of gelatinase from pig polymorphonuclear leucocytes. A metalloproteinase resembling tumour type IV collagenase (1989)

The metalloproteinase 'gelatinase' stored in the granules of pig polymorphonuclear leucocytes has been purified in the latent form. The enzyme is secreted as an Mr 97,000 proenzyme that can be activated in the presence of 4-aminophenylmercuric acetate (APMA) by self-cleavage to generate lower-Mr species, of which an Mr 88,000 form was the most active. Trypsin-initiated activation generated different Mr gelatinases of much lower specific activity. Activation was slowed but not prevented by the presence of the tissue inhibitor of metalloproteinases, TIMP. The activated gelatinase formed a stable complex (Mr 144,000) with TIMP, in a Zn2+- and Ca2+-dependent manner, and complex formation was inhibited by the presence of the substrate gelatin. Similar to the human granulocyte gelatinase, the organomercurial-activated pig enzyme degraded gelatin and TCA and TCB fragments of type I collagen, as well as elastin and types IV and V collagen. The degradation of type IV collagen was shown, both by polyacrylamide-gel electrophoresis and by electron microscopic analysis, to generate 3/4 and 1/4 fragments as described for mouse tumour type IV collagenase. Furthermore, an antiserum raised to mouse type IV collagenase recognized the pig granulocyte gelatinase. An antiserum to the pig polymorphonuclear leucocyte gelatinase recognized other high-Mr gelatinases, including those from human granulocytes, pig monocytes and rabbit connective tissue cells, but not the Mr 72,000 enzyme from connective tissue cells. These data suggest that there are two distinct major forms of gelatinolytic activity that also cause specific cleavage of type IV collagen. These enzymes are associated with a wide variety of normal connective tissue and haemopoietic cells, as well as many tumour cells.
Increased suicide attempt rate among patients interrupting use of atypical antipsychotics (2003)

Patients who do not refill atypical antipsychotics in time can be identified in the pharmacy and are most likely those with an increased risk to commit suicide.
Stability determinants in the chloroplast psbB/T/H mRNAs of Chlamydomonas reinhardtii (2000)

The chloroplast gene psbB encodes the chlorophyll-a binding protein P5 (CP47), one of the core subunits of photosystem II (PSII). The psbB mRNA and the downstream psbT and psbH transcripts fail to accumulate in the Chlamydomonas reinhardtii nuclear mutant 222E affected in the Mbb1 gene (Monod et al. 1992, Mol. Gen. Genet. 231, 449-459). By introducing chimeric genes consisting of sequences from psbB and the reporter gene aadA into the chloroplast, the target site of Mbb1 was mapped in the psbB 5' untranslated region (UTR). Primer extension analysis indicates that the psbB RNA exists in a less abundant long form and a more abundant short form, with 5' ends at positions -147 and -35 relative to the AUG initiation codon, respectively. The longer transcript is present both in the wild type (WT) and 222E mutant, but the shorter one accumulates only in the WT. Two putative stem-loop structures in the longer 5' UTR can be deleted individually without affecting psbB mRNA accumulation. Insertion of a poly G cassette in the long leader stabilizes a chimeric psbB transcript in the 222E mutant, suggesting the involvement of a 5'-3' exonuclease. We also show that psbH and psbT are transcribed from the upstream psbB gene promoter, and that the psbH mRNA has its own target sequence for Mbb1 function. We discuss the role of this nucleus-encoded factor, required for specific chloroplast gene expression, in the assembly of the multi-protein PSII complex.
Low molecular weight heparin-induced pharmacological modulation of burn wound healing. (2006)

Low molecular weight heparin (LMWH) appears to be a promising solution for reducing inflammatory post-burn episodes and results in improved healing. The clinical examination presented here includes patients with burn wounds ranging from 20 to 35% total body surface area (TBSA) who were categorized into two groups, of which one received subcutaneous LMWH treatment (10,000 units/day) and the other acted as control. The process of healing was assessed through regular examination of clinical features such as regression of erythema and oedema, eschar formation, and rate of re-epithelialization. Various studies have demonstrated an increase in levels of serum IL-6 indicating the severity of the morbid condition. In the present investigation, LMWH-treated patients exhibited a faster decline in levels of serum IL-6 (within 12 days) than control. Infiltration of inflammatory cells at the local wound site was assessed through a histological analysis of tissue samples taken on various days during the healing process. The LMWH-treated groups exhibited an organized healing pattern with better remodelling in a shorter duration (28 days), while control patients took more than 28 days for complete healing. A slight correlation was observed with TBSA to the inflammatory process, which subsided in patients treated with LMWH, favourably modulating the events involved in the inflammatory process of burn wound healing.
The Use of Thermal Infra-Red Imaging to Detect Delayed Onset Muscle Soreness (2012)

Delayed onset muscle soreness (DOMS), also known as exercise induced muscle damage (EIMD), is commonly experienced in individuals who have been physically inactive for prolonged periods of time, and begin with an unexpected bout of exercise, but can also occur in athletes who exercise beyond their normal limits of training. The symptoms associated with this painful phenomenon can range from slight muscle tenderness, to severe debilitating pain. The intensity of these symptoms and the related discomfort increases within the first 24 hours following the termination of the exercise, and peaks between 24 to 72 hours post exercise. For this reason, DOMS is one of the most common recurrent forms of sports injury that can affect an individual's performance, and become intimidating for many. For the last 3 decades, the DOMS phenomenon has gained a considerable amount of interest amongst researchers and specialists in exercise physiology, sports, and rehabilitation fields. There has been a variety of published studies investigating this painful occurrence in regards to its underlying mechanisms, treatment interventions, and preventive strategies. However, it is evident from the literature that DOMS is not an easy pathology to quantify, as there is a wide amount of variability between the measurement tools and methods used to quantify this condition. It is obvious that no agreement has been made on one best evaluation measure for DOMS, which makes it difficult to verify whether a specific intervention really helps in decreasing the symptoms associated with this type of soreness or not. Thus, DOMS can be seen as somewhat ambiguous, because many studies depend on measuring soreness using a visual analog scale (VAS), which is a subjective rather than an objective measure. Even though needle biopsies of the muscle, and blood levels of myofibre proteins might be considered a gold standard to some, large variations in some of these blood proteins have been documented, in addition to the high risks sometimes associated with invasive techniques. Therefore, in the current investigation, we tested a thermal infra-red (IR) imaging technique of the skin above the exercised muscle to detect the associated muscle soreness. Infra-red thermography has been used, and found to be successful in detecting different types of diseases and infections since the 1950's. But surprisingly, near to nothing has been done on DOMS and changes in skin temperature. The main purpose of this investigation was to examine changes in DOMS using this safe and non-invasive technique.
Back‐contacted back‐junction<i>n</i>‐type silicon solar cells featuring an insulating thin film for decoupling charge carrier collection and metallization geometry (2012)

ABSTRACT In this study, back‐contacted back‐junction n ‐type silicon solar cells featuring a large emitter coverage (point‐like base contacts), a small emitter coverage (point‐like base and emitter contacts), and interdigitated metal fingers have been fabricated and analyzed. For both solar cell designs, a significant reduction of electrical shading losses caused by an increased recombination in the non‐collecting base area on the rear side was obtained. Because the solar cell designs are characterized by an overlap of the B‐doped emitter and the P‐doped base with metal fingers of the other polarity, insulating thin films with excellent electrical insulation properties are required to prevent shunting in these overlapping regions. Thus, with insulating thin films, the geometry of the minority charge carrier collecting emitter diffusion and the geometry of the interdigitated metal fingers can be decoupled. In this regard, plasma‐enhanced chemical vapor deposited SiO 2 insulating thin films with various thicknesses and deposited at different temperatures have been investigated in more detail by metal‐insulator‐semiconductor structures. Furthermore, the influence of different metal layers on the insulation properties of the films has been analyzed. It has been found that by applying a SiO 2 insulating thin film with a thickness of more than 1000 nm and deposited at 350 °C to solar cells fabricated on 1 Ω cm and 10 Ω cm n ‐type float‐zone grown silicon substrates, electrical shading losses could be reduced considerably, resulting in excellent short‐circuit current densities of more than 41 mA/cm 2 and conversion efficiencies of up to 23.0%. Copyright © 2012 John Wiley & Sons, Ltd.
Self-assembly technologies with high-precision chip alignment and fine-pitch microbump bonding for advanced die-to-wafer 3D integration (2011)

We have demonstrated surface-tension-driven chip self-assembly for 3D stacking of a large number of known good dies (KGDs) on silicon substrates in batch processing. In this work, we employed small droplets of ultra-pure water as a liquid to precisely align chips having fine-pitch indium/gold microbumps with a size/pitch of 5/10 or 10/20μm. By using the self-assembly technique, these chips were aligned in a face-down configuration and flip-chip bonded onto hydrophilic bonding areas formed on silicon substrates. The hydrophilic areas are surrounded by hydrophobic areas that have above 100° in water contact angle. The wettability contrast between the hydrophilic and hydrophobic areas was found to be a key parameter to obtain high alignment accuracy. All chips having the indium/gold microbump arrays were self-assembled with high alignment accuracy of approximately 1μm or superior accuracy, and then, successfully bonded at 200°C with thermal compression. The resulting resistance measured with the indium/gold daisy chain patterns was sufficiently low (<;20 mΩ/bump) and comparable to one obtained by a conventional mechanical alignment technique.
A Flexible Nanostructured Paper of a Reduced Graphene Oxide–Sulfur Composite for High‐Performance Lithium–Sulfur Batteries with Unconventional Configurations (2016)

Flexible nanostructured reduced graphene oxide-sulfur (rGO-S) composite films are fabricated by synchronously reducing and assembling GO sheets with S nanoparticles on a metal surface. The nanostructured architecture in such composite films not only provides effective pathways for electron transport, but also suppresses the diffusion of polysulfides. Furthermore, they can serve as the cathodes of flexible Li-S batteries.
MPEG-5 EVC (2019)

The MPEG standardization group has produced a large number of standards for video compression over the last three decades. Traditionally, the MPEG standards have either focused on highest available compression efficiency (e.g. MPEG-2, AVC and HEVC) or a desire to produce a royalty-free standard (e.g. IVC and WebVC). In January 2019, MPEG embarked on a new standardization project that can be said to be a hybrid of the two; MPEG-5 Essential Video Coding (EVC). The MPEG-5 EVC standard is being developed with a royalty-free Baseline profile at its base and a royalty bearing Main profile that provides excellent compression performance. The Main profile adds on top of the Baseline profile, 20 different coding tools that each can be individually turned off and, when needed, replaced by a corresponding Baseline profile tool. This structure makes it easy to fall back to a smaller set off tools in the future, if for example licensing complications occur around a specific tool, without breaking compatibility with already deployed decoders.
MITRE system for clinical assertion status classification (2011)

Using semantic attributes of concepts and information about document structure as features for statistical classification of assertions is a good way to leverage rule-based and statistical techniques. In this task, the choice of features may be more important than the choice of classifier algorithm.
Effect of<i>Bacillus subtilis</i>CGMCC 1.1086 on the growth performance and intestinal microbiota of broilers (2015)

The effect of B. subtilis on growth performance of broilers was evaluated and the relationship between growth and caecal microbiota was revealed. The results of this study help to promote application of probiotics in poultry industry.
BioCyc: Online Resource for Genome and Metabolic Pathway Analysis (2016)

BioCyc.org is a genomic resource that contains more than 7600 Pathway/Genome Databases (PGDBs) for organisms whose genomes have been completely sequenced. Although most PGDBs are bacterial, PGDBs exist for key experimental organisms, including humans (HumanCyc), yeast (YeastCyc), and Arabidopsis (AraCyc). Each BioCyc database integrates the genome sequence of one organism with its predicted metabolic network, including metabolic pathways, reactions, and chemical compounds, all presented via a user‐friendly graphical interface. The BioCyc databases contain additional computed information such as predicted operons and candidate enzymes for catalyzing predicted enzymatic steps that have no assigned enzymes in the genome annotation. The BioCyc.org website enables users to perform many types of searches and data analyses online. Analysis tools include comparisons of pathways and genomes among multiple organisms, alignment of orthologous genes in a multi‐genome browser, and searching for minimal‐cost metabolic network routes that connect two substrates. Tools are also provided for visualizing omics data – such as metabolomics and gene expression data – on individual pathway diagrams, on personalized groups of multiple pathway diagrams called pathway collages, and on diagrams depicting the full metabolic network of an organism. A powerful tool in BioCyc is Smart Tables, which are user‐defined groups of metabolites or genes that can be transformed easily into other types of objects, analyzed, saved in a BioCyc account, and shared with other users. All BioCyc databases save one were created computationally using MetaCyc as a reference. MetaCyc (MetaCyc.org) is a comprehensive manually‐curated metabolic database whose contents are derived from experimentally studies. It currently contains more than 2,400 experimentally determined metabolic pathways from more than 2,700 organisms, curated from more than 47,800 scientific publications. It also contains extensive information on metabolic enzymes, reactions, and substrates. The BioCyc databases can be accessed through the BioCyc.org web site and can be downloaded. In addition, the Pathway Tools software can be downloaded and installed locally to create BioCyc‐like databases for more genomes, curate existing databases, or perform additional analyses that are not available online. Support or Funding Information National Institute of General Medical Sciences of the National Institutes of Health (NIH) [GM080746, GM077678, GM75742].
Challenges for blood–brain barrier (BBB) screening (2007)

Whilst blood-brain barrier permeability is an important determinant in achieving efficacious central nervous system drug concentrations, it should not be viewed or measured in isolation. Recent studies have highlighted the need for an integrated approach where optimal central nervous system penetration is achieved through the correct balance of permeability, a low potential for active efflux, and the appropriate physicochemical properties that allow for drug partitioning and distribution into brain tissue. Integrating data from permeability studies performed incorporating an assessment of active efflux by P-glycoprotein in combination with drug-free fraction measurements in blood and brain has furthered the understanding of the impact of the blood-brain barrier on central nervous system uptake and the underlying physicochemical properties that contribute to central nervous system drug disposition. This approach moves away from screening and ranking compounds in assays designed to measure or predict central nervous system penetration in the somewhat arbitrary units of brain-blood (or plasma) ratios.
CREB: A Key Regulator of Normal and Neoplastic Hematopoiesis (2009)

The cAMP response element-binding protein (CREB) is a nuclear transcription factor downstream of cell surface receptors and mitogens that is critical for normal and neoplastic hematopoiesis. Previous work from our laboratory demonstrated that a majority of patients with acute myeloid leukemia (AML) and acute lymphoid leukemia (ALL) overexpress CREB in the bone marrow. To understand the role of CREB in leukemogenesis, we examined the biological effect of CREB overexpression on primary leukemia cells, leukemia cell lines, and CREB overexpressing transgenic mice. Our results demonstrated that CREB overexpression leads to an increase in cellular proliferation and survival. Furthermore, CREB transgenic mice develop a myeloproliferative disorder with aberrant myelopoiesis in both the bone marrow and spleen. Additional research from other groups has shown that the expression of the cAMP early inducible repressor (ICER), a CREB repressor, is also deregulated in leukemias. And, miR-34b, a microRNA that negative regulates CREB expression, is expressed at lower levels in myeloid leukemia cell lines compared to that of healthy bone marrow. Taken together, these data suggest that CREB plays a role in cellular transformation. The data also suggest that CREB-specific signaling pathways could possibly serve as potential targets for therapeutic intervention.
Environmentally Benign, Rapid, and Selective Extraction of Gold from Ores and Waste Electronic Materials (2017)

Abstract The extraction of gold from ores and electronic waste is an important topic worldwide, as this precious metal has immense value in a variety of fields. However, serious environmental pollution and high energy consumption due to the use of toxic oxidation reagents and harsh reaction conditions is a well‐known problem in the gold industry. Herein, we report a new chemical method based on the combined use of N ‐bromosuccinimide (NBS) and pyridine (Py), which has a greatly decreased environmental impact and reagent cost, as well as mild reaction requirements. This method can directly leach Au 0 from gold ore and electronic waste to form Au III in water. The process is achieved in a yield of approximately 90 % at room temperature and a nearly neutral pH. The minimum dose of NBS/Py is as low as 10 m m , which exhibits low toxicity towards mammalian cells and animals as well as aquatic creatures. The high leaching selectivity of Au over other metals during gold leaching is demonstrated, showing that this method has great potential for practical industrial application towards the sustainable refining of gold from ores and electronic waste.
Production of virulence-related proteins by Canadian strains of Streptococcus suis capsular type 2. (1998)

The production of muramidase-released protein (MRP), extracellular protein factor (EF) and hemolysin (suilysin) by 101 Canadian field strains of Streptococcus suis capsular type 2 is described. Most strains (72%) isolated from diseased pigs were MRP-EF- and only 1 strain was MRP+EF+. This strain was also the only 1 to produce the hemolysin. Thirteen strains (15%) were MRP+ EF- and only 3 strains were MRP* EF-. All the strains isolated from clinically healthy pigs as well as a bovine and 2 human isolates had a MRP-EF- phenotype. In addition, 7 strains (8%) had a MRPS phenotype, which had so far been described for S. suis capsular type 1. In conclusion, most Canadian field isolates of S. suis capsular type 2 tested in this study do not produce the virulence-related proteins described so far for this bacterial pathogen.
Modeling Androgen Receptor Flexibility: A Binding Mode Hypothesis of CYP17 Inhibitors/Antiandrogens for Prostate Cancer Therapy (2012)

Prostate Cancer (PCa), a leading cause of cancer death worldwide (www.cancer.gov), is a complex malignancy where a spectrum of targets leads to a diversity of PCa forms. A widely pursued therapeutic target is the Androgen Receptor (AR). As a Steroid Hormone Receptor, AR serves as activator of transcription upon binding to androgens and plays a central role in the development of PCa. AR is a structurally flexible protein, and conformational plasticity of residues in the binding-pocket is a key to its ability to accommodate ligands from various chemical classes. Besides direct modulation of AR activity by antagonists, inhibition of cytochrome CYP17 (17α-hydroxylase/17,20-lyase), essential in androgen biosynthesis, has widely been considered an effective strategy against PCa. Interestingly, Handratta et al. (2005) discovered new, potent inhibitors of CYP17 (C-17 steroid derivatives) with pure AR antagonistic properties. Although the antiandrogenic activity of their lead compound (VN/124-1) has been experimentally proven both in vitro and in vivo, no structural data are currently available to elucidate the molecular determinants responsible for these desirable dual inhibitory properties. We implemented a Structure-based Drug Design (SBDD) approach to generate a valuable hypothesis as to the binding modes of steroidal CYP17 inhibitors/antiandrogens against the AR. To deal with the plasticity of residues buried in the Ligand Binding Domain (LBD), we developed a flexible-receptor Docking protocol based on Induced-Fit (IFD) methodology (www.schrodinger.com/). Our results constitute an ideal starting point for the rational design of next-generation analogues of CYP17 inhibitors/antiandrogens as well as an attractive tool to suggest novel chemical classes of AR antagonists.
High-Throughput Screen for Poly-3-Hydroxybutyrate in <i>Escherichia coli</i> and <i>Synechocystis</i> sp. Strain PCC6803 (2006)

A novel, quantitative method for detecting poly-3-hydroxybutyrate (PHB) amounts in viable cells was developed to allow for high-throughput screening of mutant libraries. The staining technique was demonstrated and optimized for the cyanobacterium Synechocystis sp. strain PCC6803 and the eubacterium Escherichia coli to maximize the fluorescence difference between PHB-accumulating and control cells by flow cytometry. In Synechocystis, the level of nonspecific dye binding was reduced by using nonionic stain buffer that allowed quantitation of fluorescence levels. In E. coli, the use of a mild sucrose shock facilitated uptake of Nile red without significant loss of viability. The optimized staining protocols yielded a linear response for the mean fluorescence against (chemically measured) PHB. The staining protocols are novel methods useful in the high-throughput evaluation of combinatorial libraries of Synechocystis and E. coli using fluorescence-activated cell sorting to identify mutants with increased PHB-accumulating properties.
Influence of number density and transition cross-section on rapid passage effects in pulsed quantum-cascade laser based spectrometers (2004)

We show how rapid passage effects in molecular gases are influenced by the number density, transition cross-section and reorientation lifetime. Data will be presented that compares rapid passage in ammonia and isotopologues of methyl chloride.