gebhart/patrepeval huggingface dataset:
Constellation: A secure self-optimizing framework for genomic processing (2016)

The Constellation framework is designed for process automation, secure workload distribution, and performance optimization for genomic processing. The goal of Constellation is to provide a flexible platform for the processing of custom ”write once run anywhere” genomic pipelines, across a range of computational resources and environments, through the agent-based management of genomic processing containers. An implementation of the Constellation framework is currently in use at the University of Kentucky Medical Center for clinical diagnostic and research genomic processing.
Fast Complex Valued Matrix Inversion for Multi-User STBC-MIMO Decoding (2007)

This paper studies the efficient complex matrix inversion for multi-user STBC-MIMO decoding. A novel method called Alamouti blockwise analytical matrix inversion (ABAMI) and its programmable VLSI implementation are proposed for the inversion of (in this context) large complex matrices with Alamouti sub-blocks. Our solution significantly reduces the number of operations which makes it more than 4 times faster than several other solutions in the literature. Furthermore, compared to these fixed function VLSI implementations, our solution is more flexible and consumes less silicon area because the hardware can be reused for many other operations. In addition to the routine analysis of the general computational complexity based on the number of basic operations, the computational latency is also measured in clock cycles based on the conceptual hardware for real-time matrix inversion
Polymyalgia Rheumatica and Giant Cell Arteritis (2016)

Diagnosis of PMR/GCA is made by clinical features and elevated inflammatory markers. In PMR, ultrasound imaging may improve diagnostic accuracy. In GCA, temporal artery biopsy may not be required in patients with typical disease features accompanied by characteristic ultrasound or MRI findings. Consensus-based recommendations suggest glucocorticoids as the most effective therapy for PMR/GCA. Methotrexate may be added to glucocorticoids in patients at risk for relapse and in those with glucocorticoid-related adverse effects or need for prolonged glucocorticoid therapy.
The L- and R-type isozymes of rat pyruvate kinase are produced from a single gene by use of different promoters. (1987)

cDNA clones for rat R-type pyruvate kinase and a genomic clone encoding both L- and R-type isozyme mRNAs were isolated. Their sequences were compared with that of the L-type isozyme cDNA to determine the sequences of mRNA and protein of the R-type isozyme and the organizations of the L- and R-type genes. Results showed that the R-type isozyme mRNA had an identical nucleotide sequence to that of the L-type except in the 5'-terminal region including the coding sequence and the length of the 3'-untranslated region. The sequence upstream of the 5th coding residue of the L-type was replaced by a 98-nucleotide coding sequence plus a 5'-untranslated region in the R-type isozyme. Therefore, the R-type subunit consists of 574 amino acids, which is 31 residues longer than the L-type at the amino terminus. The pyruvate kinase L gene is present as a single copy per haploid genome and is composed of 12 exons and 11 introns with a length of about 9.3 kilobase pairs. The first (exon R) and second (exon L) exons encode the 5'-terminal sequences specific for the R- and L-types, respectively. The remaining downstream exons encode a sequence common to both isozymes. The last exon contains the entire 3'-untranslated region, including several putative polyadenylation signals. Alternative use of these signals is reported to be responsible for generation of multiple mRNA species for the L-type, whereas the R-type uses only the first signal. The cap site is mapped 16 nucleotides upstream from the translation initiation site for the L-type, whereas multiple cap sites were suggested for the R-type. The canonical promoter of the TATA box was identified in the upstream sequence of exon L, but not in that of exon R. Instead, the 5'-flanking region of exon R contained another promoter sequence of the CAT box. Thus, we conclude that the L- and R-type isozymes of pyruvate kinase are produced from a single gene by use of different promoters.
Effects of Dietary Weight Loss on Sympathetic Activity and Cardiac Risk Factors Associated with the Metabolic Syndrome (2005)

Weight loss by a hypocaloric diet with moderate sodium restriction diminishes SNS activity in MetS subjects. This may be due to the consequences of decreased leptin concentration, enhanced insulin sensitivity, or improvements in cardiac baroreflex function.
Arterial smooth muscle cells express nitric oxide synthase in response to endothelial injury. (1994)

Endothelial cells regulate vascular tone by secreting paracrine mediators that control the contractility of arterial smooth muscle cells. Nitric oxide (NO) is an important vasodilating agent that is generated from L-arginine by the enzyme nitric oxide synthase (NOS), which is expressed constitutively by the endothelium. NO also inhibits platelet aggregation, contributing to the antithrombotic properties of the endothelial surface. It would therefore be expected that loss of the endothelium during arterial injury would lead to vasospasm and thrombosis but instead, the neointima formed after injury has a nonthrombogenic surface and a maintained vascular patency. We report here that arterial smooth muscle cells in the neointima formed after a deendothelializing balloon injury to the rat carotid artery express the cytokine-inducible isoform of NOS. Expression was detectable by reverse transcription-polymerase chain reaction from day 1-14 after injury and in situ hybridization showed expression of NOS mRNA by neointimal smooth muscle cells, particularly at the surface of the lesion. This was associated with systemically detectable NO production as revealed by electron paramagnetic resonance spectroscopic analysis of nitrosylated red cell hemoglobin. Local NO production by intimal smooth muscle cells after endothelial injury could represent an important mechanism for the maintenance of arterial patency and nonthrombogenicity in the injured artery.
Validation of a Vertical Progression Porcine Burn Model (2011)

A major potential goal of burn therapy is to limit progression of partial- to full-thickness burns. To better test therapies, the authors developed and validated a vertical progression porcine burn model in which partial-thickness burns treated with an occlusive dressing convert to full-thickness burns that heal with scarring and wound contraction. Forty contact burns were created on the backs and flanks of two young swine using a 150 g aluminum bar preheated to 70°C, 80°C, or 90°C for 20 or 30 seconds. The necrotic epidermis was removed and the burns were covered with a polyurethane occlusive dressing. Burns were photographed at 1, 24, and 48 hours as well as at 7, 14, 21, and 28 days postinjury. Full-thickness biopsies were obtained at 1, 4, 24, and 48 hours as well as at 7 and 28 days. The primary outcomes were presence of deep contracted scars and wound area 28 days after injury. Secondary outcomes were depth of injury, reepithelialization, and depth of scars. Data were compared across burn conditions using analysis of variance and χ(2) tests. Eight replicate burns were created with the aluminum bar using the following temperature/contact-time combinations: 70/20, 70/30, 80/20, 80/30, and 90/20. The percentage of burns healing with contracted scars were 70/20, 0%; 70/30, 25%; 80/20, 50%; 80/30, 75%; and 90/20, 100% (P = .05). Wound areas at 28 days by injury conditions were 70/20, 8.1 cm(2); 70/30, 7.8 cm(2); 80/20, 6.6 cm(2); 80/30, 4.9 cm(2); and 90/20, 4.8 cm(2) (P = .007). Depth of injury judged by depth of endothelial damage for the 80/20 and 80/30 burns at 1 hour was 36% and 60% of the dermal thickness, respectively. The depth of injury to the endothelial cells 1 hour after injury was inversely correlated with the degree of scar area (Pearson's correlation r = -.71, P < .001). Exposure of porcine skin to an aluminum bar preheated to 80°C for 20 or 30 seconds results initially in a partial-thickness burn that when treated with an occlusive dressing progresses to a full-thickness injury and heals with significant scarring and wound contracture.
Novel Inhibitors of Dengue Virus Methyltransferase: Discovery by in Vitro-Driven Virtual Screening on a Desktop Computer Grid (2010)

Dengue fever is a viral disease that affects 50-100 million people annually and is one of the most important emerging infectious diseases in many areas of the world. Currently, neither specific drugs nor vaccines are available. Here, we report on the discovery of new inhibitors of the viral NS5 RNA methyltransferase, a promising flavivirus drug target. We have used a multistage molecular docking approach to screen a library of more than 5 million commercially available compounds against the two binding sites of this enzyme. In 263 compounds chosen for experimental verification, we found 10 inhibitors with IC(50) values of <100 microM, of which four exhibited IC(50) values of <10 microM in in vitro assays. The initial hit list also contained 25 nonspecific aggregators. We discuss why this likely occurred for this particular target. We also describe our attempts to use aggregation prediction to further guide the study, following this finding.
Introduction (1989)

Although they almost certainly met at Bristol in the summer of 1795, the close friendship between Wordsworth and Coleridge began in the summer of 1797 when Coleridge leaped over a gate and bounded across a pathless field' to Racedown (LY, IV, 719 [III, 1263]),1 the house in Dorset where Wordsworth was living with his sister Dorothy. By this time Wordsworth's youthful adventures in France were well behind him. His involvement with the French Revolution had been complicated by his liaison with Annette Vallon, who became an ardent royalist. When his uncles stopped sending him money he was forced to leave France, leave Annette and his baby daughter, Caroline, and return to England. His disillusionment, first when England failed to support the revolution and then when he realised the full horrors of the atrocities committed by it, pushed him to the verge of mental breakdown. A legacy of £900 from his friend Raisley Calvert allowed him to rejoin Dorothy and regain some peace of mind in the tranquillity of the West Country. Coleridge, too, had virtually finished with his dreams of setting up a democratic republic on the shores of the Susquehanna with a group of friends, including his future brother-in-law, Robert Southey.
Microbial Transformations of Metals (1978)

Human coronavirus (HCoV) infection causes respiratory diseases with mild to severe outcomes. In the last 15 years, we have witnessed the emergence of two zoonotic, highly pathogenic HCoVs: severe acute respiratory syndrome coronavirus (SARS-CoV) and ...Read More
Nitric Oxide Mediates Excitotoxic and Anoxic Damage in Rat Retinal Ganglion Cells Cocultured With Astroglia (1999)

Neuroprotective agents may play a role in patients with glaucoma who have progressive visual field loss, despite satisfactory control of intraocular pressure. Inhibition of nitric oxide synthase at the level of the optic nerve head may contribute to a clinically significant level of neuroprotection.
Phenotyping of Clinical Notes with Improved Document Classification Models Using Contextualized Neural Language Models (2019)

Clinical notes contain an extensive record of a patient's health status, such as smoking status or the presence of heart conditions. However, this detail is not replicated within the structured data of electronic health systems. Phenotyping, the extraction of patient conditions from free clinical text, is a critical task which supports avariety of downstream applications such as decision support and secondary use of medical records. Previous work has resulted in systems which are high performing but require hand engineering, often of rules. Recent work in pretrained contextualized language models have enabled advances in representing text for a variety of tasks. We therefore explore several architectures for modeling pheno-typing that rely solely on BERT representations of the clinical note, removing the need for manual engineering. We find these architectures are competitive with or outperform existing state of the art methods on two phenotyping tasks.
Immobilization of Leuconostoc Oenos ml 34 in Calcium Alginate Gels and its Application to Wine Technology (1982)

Leuconostoc oenos ML 34 cells were immobilized in 1.67% calcium alginate gels to test their ability to convert L-malic acid into L-lactic acid in wine. Activity of the immobilized cells, assayed in standard buffers, was highest at pH 4.0 and 15% ethanol (v/v), and it stayed constant for 540 min. The sequential replacement of the spent incubation medium with fresh medium gave rise to an increase in activity during the first two days and to a decrease in activity thereafter. After 36 days, the activity was 60% of the maximum. About 45% to 60% of the L-malic acid was transformed into L-lactic acid by the immobilized cells in wine, and the decrease in titratable acidity was equivalent to 50% of the L-malic acid originally present, in accordance with the mechanism of malolactic fermentation in winemaking. After stirring the gels in wine several times, the activity of the immobilized cells gradually decreased until no activity was detectable. The living cells inside the gel were 2 x 10 8 /mL, and only 0.1% leakage occurred during use.
Spectral interferometry-based surface plasmon resonance sensing of liquid analyte refractive index change (2013)

Theoretical study of a polarimetric setup intended to measure the refractive index change of a liquid analyte is presented. The detection scheme is based on the excitation of surface plasmon resonance in Kretschmann configuration combined with spectral interferometry. The principle of the method is to observe the spectral interference fringes as a result of mixing of two orthogonal linearly polarized waves with an analyzer. The waves are reflected from the base of a coupling prism covered by a thin metal layer used for generation of surface plasmon waves. The polarimetric setup consists of a linear polarizer, a birefringent crystal, a SF10 coupling prism covered by a gold layer and a linear analyzer. The attenuated total reflection at the prism base serves for the excitation of surface plasmon waves. The output optical field is then analyzed by a spectrometer. The phase change of resulting interference spectrum contains the information about the refractive index change of investigated analyte. The shift of phase curve is related to the analyte refractive index change. The model computation is performed in the frame of thin-film optics and the dispersion properties of all included materials are taken into account.
Assessment of waveguide thermal response by interrogation of UV written planar gratings (2005)

The technique of direct grating writing, based on direct ultraviolet writing, is demonstrated as a tool for highly accurate measurement of waveguide and material properties. Silica-on-silicon planar samples are processed using hydrogen loading and thermal locking before Bragg channel waveguides are defined in the photosensitive core layer. The refractive index is accurately probed to compare different thermal locking procedures and characterize waveguide thermal stability.
Piroxicam Therapy in 34 Dogs With Transitional Cell Carcinoma of the Urinary Bladder (1994)

Thirty-four dogs with histopathologically confirmed, measurable, nonresectable transitional cell carcinoma of the urinary bladder were treated with piroxicam (0.3 mg/kg PO sid) and were evaluated for tumor response and drug toxicity. Dogs were evaluated at the Purdue University Veterinary Teaching Hospital by means of physical examination, thoracic and abdominal radiography, cystography, complete blood count, serum biochemistry profile, and urinalysis. In selected cases, prostaglandin E2 (PGE2) concentrations in plasma and in supernatants of stimulated monocytes, and natural killer cell activity were quantified. Dogs were evaluated before therapy and at 28 and 56 days after initiation of therapy. Dogs with stable disease or remission at 56 days remained on the study and were evaluated at 1 to 2 months intervals. Tumor responses were 2 complete remissions, 4 partial remissions, 18 stable diseases, and 10 progressive diseases. The median survival of all dogs was 181 days (range, 28 to 720+ days), with 2 dogs still alive. Piroxicam toxicity consisted of gastrointestinal irritation in 6 dogs and renal papillary necrosis (detected at necropsy) in 2 dogs. Monocyte production of PGE2 appeared to decrease with therapy in dogs whose tumors were decreasing in size, and increased in dogs with tumor progression. A consistent pattern in natural killer cell activity was not observed. In vitro cytotoxicity assays against 4 canine tumor cell lines revealed no direct antitumor effects of piroxicam. In summary, antitumor activity, which was not likely the result of a direct cytotoxic effect, was observed in dogs with transitional cell carcinoma of the bladder treated with piroxicam.
Neuromyelitis optica MOG-IgG causes reversible lesions in mouse brain (2014)

These differences mirror the better outcomes for MOG-IgG compared with AQP4-IgG patients and raise the possibility that MOG-IgG contributes to pathology in some neuromyelitis optica patients.
Surviving Intensive Care (2013)

Wide variation in methodological approaches limited study comparability and external validity of findings. We found substantial variation in the cost of resource use, especially among countries. Careful description of patient cohorts and healthcare systems is required to maximize generalizability. We give recommendations for a more standardized approach to improve design and reporting of future studies.
Infectious Disease Genomics (2010)

The history and development of infectious disease genomics are discussed in this chapter. HGP must not be restricted to the human genome and should include model organisms including mouse, bacteria, yeast, fruit fly, and worm. The completed or ongoing genome projects will provide enormous opportunities for the discovery of novel vaccines and drug targets against human pathogens as well as the improvement of diagnosis and discovery of infectious agents and the development of new strategies for invertebrate vector control. The polysaccharide capsule is important for meningococci to escape from complement-mediated killing. With the completion of the genome sequence of a virulent MenB strain, a “reverse vaccinology” approach was applied for the development of a universal MenB vaccine by Novartis. The indispensable fatty acid synthase (FAS) pathway in bacteria has been regarded as a promising target for the development of antimicrobial agents. Through a systematic screening of 250,000 natural product extracts, a Merck team identified a potent and broad-spectrum antibiotic, platensimycin, which is derived from Streptomyces platensis. Vector Biology Network was formed to achieve three goals (1) to develop basic tools for the stable transformation of anopheline mosquitoes by the year 2000; (2) to engineer a mosquito incapable of carrying the malaria parasite by 2005; and (3) to run controlled experiments to test how to drive the engineered genotype into wild mosquito populations by 2010. The most immediate impact of a completely sequenced pathogen genome is for infectious disease diagnosis.
Novel Synthetic Dermal Fillers Based on Sodium Carboxymethylcellulose (2007)

BACKGROUND The persistence of dermal fillers containing crosslinked hyaluronic acid (XLHA) correlates linearly to the concentration of polymer in solution. For dermal fillers composed of XLHA, a polymer concentration above approximately 25 mg/mL is not practical because it cannot be easily injected through a small-bore needle. OBJECTIVE Formulating dermal fillers from mixtures of carboxymethylcellulose (CMC) and polyethylene oxide (PEO) has several advantages over XLHA. We hypothesize that increasing the concentration of CMC/PEO will increase the persistence in the dermis. These polymers of CMC and PEO can be formulated at higher concentrations than XLHA to produce smooth, particulate-free gels resulting in easier, more controllable injection. Second, these gels are not required to be covalently crosslinked; CMC/PEO forms a stable gel-like structure in solution without crosslinking. Materials and Methods Here we have prepared dermal fillers from CMC/PEO polymer blends at concentrations of 20 mg/mL (dermal filler 1), 29 mg/mL (dermal filler 2), 37 mg/mL (dermal filler 3), and 45 mg/mL (dermal filler 4) and measured their rheologic properties compared to commercial XLHA dermal fillers. RESULTS AND CONCLUSIONS The data here demonstrate that it is possible to duplicate the rheologic properties of commercial XLHA fillers using CMC/PEO at different polymer concentrations to formulate improved dermal fillers. All of the dermal filler formulations prepared can be easily injected through 30-gauge needles.
<i>piggyBac</i> is a flexible and highly active transposon as compared to <i>Sleeping Beauty</i> , <i>Tol2</i> , and <i>Mos1</i> in mammalian cells (2006)

A nonviral vector for highly efficient site-specific integration would be desirable for many applications in transgenesis, including gene therapy. In this study we directly compared the genomic integration efficiencies of piggyBac, hyperactive Sleeping Beauty (SB11), Tol2, and Mos1 in four mammalian cell lines. piggyBac demonstrated significantly higher transposition activity in all cell lines whereas Mos1 had no activity. Furthermore, piggyBac transposase coupled to the GAL4 DNA-binding domain retains transposition activity whereas similarly manipulated gene products of Tol2 and SB11 were inactive. The high transposition activity of piggyBac and the flexibility for molecular modification of its transposase suggest the possibility of using it routinely for mammalian transgenesis.
Strategy for Selecting Optimised Technologies for Gas Turbine Air Inlet Filtration Systems (2011)

With continuous advances in gas turbine technology, wider breadth of fuel quality burnt and ever growing expectations of; longer life, higher efficiency and reduced maintenance requirements, the filtration of the air entering the gas turbine (GT) has never been more important to meeting its operational requirements. Gas turbines are used throughout the world in an ever increasing diversity of application and environment. This presents a number of challenges to the air filtration system, that require unique solutions for each subset of environment specific challenge, gas turbine platform technology and fuel quality being burnt. This paper discusses the importance of air filtration to a modern GT and how this has changed over time and it’s shifting operational requirements. It explores the challenges facing the air filtration system presented by the different; environments, GT technologies and fuel quality. The paper details what approaches and filtration technologies are currently used to address these challenges, with strengths and weaknesses explained as appropriate, to finally present a strategy for specifying an optimized filtration system to meet the challenges of the modern GT.
UAV Task Assignment (2008)

Unmanned aerial vehicles (UAVs) are becoming vital warfare and homeland security platforms because they have the potential to significantly reduce cost and risk to human life while amplifying warfighter and first-responder capabilities. This article builds on the very active area of planning and control for autonomous multiagent systems. This work represents a step toward enabling robust decision making for distributed autonomous UAVs by improving the team's operational reliability and capabilities through better system self-awareness and adaptive mission planning. The health-aware task assignment algorithm developed in this article was demonstrated to be effective both in simulation and flight experiments.