gebhart/patrepeval huggingface dataset:
Polydom/SVEP1 Is a Ligand for Integrin α9β1 (2012)

A variety of proteins, including tenascin-C and osteopontin, have been identified as ligands for integrin α9β1. However, their affinities for integrin α9β1 are apparently much lower than those of other integrins (e.g. α3β1, α5β1, and α8β1) for their specific ligands, leaving the possibility that physiological ligands for integrin α9β1 still remain unidentified. In this study, we found that polydom (also named SVEP1) mediates cell adhesion in an integrin α9β1-dependent manner and binds directly to recombinant integrin α9β1 with an affinity that far exceeds those of the known ligands. Using a series of recombinant polydom proteins with N-terminal deletions, we mapped the integrin-binding site to the 21st complement control protein domain. Alanine-scanning mutagenesis revealed that the EDDMMEVPY sequence (amino acids 2636-2644) in the 21st complement control protein domain was involved in the binding to integrin α9β1 and that Glu(2641) was the critical acidic residue for the integrin binding. The importance of this sequence was further confirmed by integrin binding inhibition assays using synthetic peptides. Immunohistochemical analyses of mouse embryonic tissues showed that polydom colocalized with integrin α9 in the stomach, intestine, and other organs. Furthermore, in situ integrin α9β1 binding assays using frozen mouse tissues showed that polydom accounts for most, but not all, of the integrin α9β1 ligands in tissues. Taken together, the present findings indicate that polydom is a hitherto unknown ligand for integrin α9β1 that functions as a physiological ligand in vivo.
Modeling of a Competitive Microfluidic Heterogeneous Immunoassay: Sensitivity of the Assay Response to Varying System Parameters (2009)

We present a fractional sensitivity analysis of a competitive microfluidic heterogeneous immunoassay for a small molecule analyte. A simple two-dimensional finite element model is used to determine the fractional sensitivity of the assay signal with respect to analyte concentration, flow rate, initial surface density of binding sites, and antibody concentration. The fractional sensitivity analysis can be used to identify (1) the system parameters for which it is most crucial to control or quantify the variability between assays and (2) operating ranges for these parameters that improve assay sensitivity (within the constraints of the experimental system). Experimental assay results for the drug phenytoin, obtained using surface plasmon resonance imaging, are shown to be consistent with the predictions of the model.
Method for yielding a database of location fingerprints in WLAN (2005)

Location fingerprinting in wireless LAN positioning has received much attention recently. One of the key issues of this technique is generating the database of fingerprints. The conventional method does not utilise the spatial correlation of measurements sampled at adjacent reference points, and the training process is not an easy task. A new method based on kriging is presented which can not only achieve more accurate estimation, but can also greatly reduce the workload and save training time. This can make the fingerprinting technique more flexible and easier to implement.
An Evaluation of Narrowing Following Intradiskal Injection of Chymopapain (1977)

Lateral X-rays of lumbosacral spines of 76 patients who received chymopapain injection for lumbar disk lesions after a positive myelogram and diskogram were examined and measured to determine the degree of narrowing which occurred after injection of the enzyme. There were 2 groups of patients, those with clinically good results after injection, and those with poor results. Measurements were made of the injected and adjacent noninjected disk spaces. The validity of the method used with established by a correlation of 0.95 over a period of time for the uninjected disks. The narrowing after injection was significant at the p less than 0.01 level for both clinical successes and failures, but the degree of narrowing was significantly greater for the clinically good results.
Neural network simulation on a massively parallel cellular array processor: AAP-2 (1989)

An implementation of error backpropagation on a massively parallel cellular array processor, AAP-2, is described. Parallel operations of a neural network simulation on the AAP-2 are described, including: allocation of the processors, computing the activation value with a stable-lookup method, and communication between processors. Currently, this simulator on the AAP-2 can run at approximately 18 MCPS (million connections per second), which is 45 times faster at a learning phase than that of the IBM-3090. The results indicate that fine-grained, cellular array computers consisting of a large number of simple processors can be efficient neural network simulators.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Large Aggregated Ions Found in Some Protic Ionic Liquids (2009)

Large aggregated parent ions, for example, C(8)A(7)(+) (C = cation and A = anion), have been observed within some protic ionic liquids (PILs) using electrospray ionization mass spectrometry (ESI-MS). We have shown that the formation and size of aggregates is dependent on the nature of the anion and cation. Solvent structuring in select PILs through aggregation can contribute to their classification as "poor ionic liquids" and can also strongly influence the entropic component to the free energy of amphiphile self-assembly in select PILs.
Ion transporting proteins of human bronchial epithelium (2011)

The electrolyte transport system across human airway epithelium followed by water movement is essential for the normal mucociliary clearance that allows the maintenance of the aseptic condition of the respiratory tract. The function of epithelial cells is to control and regulate ionic composition and volume of fluids in the airways. Various types of proteins taking part in assuring effective ions and water transport in apical and basolateral membranes of the airway epithelium have been found (e.g., CFTR, ENaC, CaCC, ORCC, potassium channels, NaKATPase, aquaporins). The paper reviews the current state of the art in the field of ion channels, transporters, and other signaling proteins identified in the human bronchial epithelium.
X-ray analysis (1. 4-Å resolution) of avian pancreatic polypeptide: Small globular protein hormone (1981)

The crystal structure of avian pancreatic polypeptide (aPP), a 36-residue polypeptide with some hormonal properties, has been determined by using single isomorphous replacement and anomalous scattering to 2.1-A resolution. The phases were extended to 1.4-A resolution by using a modified tangent formula. The molecule contains two regions of secondary structure-an extended polyproline-like helix (residues 1-8) and an alpha-helix (residues 14-31)-that run roughly antiparallel. The packing together of nonpolar groups from these regions gives the molecule a hydrophobic core in spite of its small size. The aPP molecules form a symmetrical dimer in the crystal stabilized principally by interlocking of nonpolar groups from the alpha-helices. The aPP dimers are crosslinked by coordination of Zn(2+); three aPP molecules contribute ligands to each zinc. The coordination geometry is a distorted trigonal bipyramid. The properties of the aPP molecule in solution are consistent with expectations based on the crystal structure. The aPP molecule has several general features in common with the pancreatic hormones insulin and glucagon. All three hormones have complex mechanisms for self-association. Like insulin, aPP seems to have a stable monomeric structure but its biological activity seems to depend on the more flexible COOH-terminal region analogous to the flexible NH(2)-terminal region of glucagon.
Meal‐induced peptide tyrosine tyrosine inhibition of pancreatic secretion in the rat (1989)

In the present studies we examined the distribution, release, and biological actions of peptide tyrosine tyrosine (PYY) in the rat. The concentration and distribution of PYY was highest in the ileum and colon as determined by both radioimmunoassay of rat tissue extracts and immunocytochemistry. An ultrastructural comparison of rat and dog colonic PYY cells revealed a bipolar distribution of peptide-containing secretory granules in both species. Serum PYY and pancreatic exocrine secretory responses were monitored after presentation of a meal to meal-trained rats (n = 12). A significant increase in PYY concentrations was not observed until 120 min after meal presentation, a delayed response similar to that previously observed in the dog. PYY responses were also observed in rats after perfusion of the intestine at the level of the duodenum and ileum with an 80 mOsm micellar solution of sodium oleate. Duodenal instillations of the fatty acids resulted in a maximum PYY response after 120 min, whereas rats subject to ileal perfusion of fat exhibited maximum PYY release within the first hour. In other experiments, infusion of exogenous PYY at 100 pmol.kg-1.h-1, which reproduced plasma PYY levels observed after a meal and perfusion of the gut with fat, significantly inhibited CCK-stimulated bile pancreatic volume (P less than 0.02), protein (P less than 0.01), and amylase (P less than 0.01) output. These studies demonstrate a bipolar distribution of PYY-containing secretory granules in cells of the jejunal, ileal, and colonic mucosa, and show that PYY is released in response to a meal in amounts sufficient to inhibit cholecystokinin-stimulated pancreatic secretion. Evidence is presented that PYY may mediate the delayed inhibition of pancreatic secretion that is observed in the rat after ingestion of a meal.
Reduction of fibrous adhesion formation by a copolymer possessing an affinity for anionic surfaces (1998)

Postsurgical adhesions represent a common complication following a variety of surgical procedures. We sought to develop and evaluate a water-soluble polymer that could self-assemble onto tissue surfaces, forming a barrier on the surface. A copolymer was synthesized so as to contain two components: one component adsorbed to the tissue surface, and the other created a steric barrier, thereby preventing cell interactions with the tissue surface, and perhaps altering the wound-healing response that leads to the formation of fibrous adhesions. The component selected for tissue binding was a water-soluble polycation, poly-L-lysine, which can bind to negative sites on glycoproteins, proteoglycans, and cells; and the component selected for steric stabilization was polyethylene glycol, a nonionic polymer that interacts poorly with proteins. Efficacy of lavage with an aqueous solution of the copolymer for the prevention of postsurgical abdominopelvic adhesions was assessed following a standard electrocautery injury of the uterine horns of rats. The copolymer resulted in an 88% reduction in the extent of adhesions that formed. In vitro studies designed to investigate the mechanism of this efficacy indicated that the copolymer may both hinder cell-tissue adhesive interactions and alter the process of fibrin formation.
A geometry calibration and visual seamlessness method based on multi-projector tiled display wall (2009)

Multi-projector virtual environment based on PC cluster has characteristics of low cost, high resolution and widely visual angle, which has become a research hotspot in Virtual Reality application. Geometric distortion calibration and seamless splicing is key problems in multi-projector display. The paper does research on geometry calibration method and edge blending. It proposes an automatic calibration preprocessing algorithm based on a camera, which projects images to the regions expected in terms of the relation between a plane surface and a curved surface and texture mapping method. In addition, overlap regions, which bring about intensity imbalance regions, may be adjusted by an edge blending function. Implementation indicates that the approach can accomplish geometry calibration and edge blending on an annular screen.
Lipoprotein Size and Atherosclerosis Susceptibility in Apoe −/− and Ldlr −/− Mice (2001)

Two hypercholesterolemic mouse models, the apo-E-deficient mouse (Apoe(-/-)) and the LDL receptor-deficient mouse (Ldlr(-/-)), have been used extensively as animal models of atherogenesis. Total plasma cholesterol levels in chow-fed Apoe(-/-) mice are much higher than in Ldlr(-/-) mice. In a recent study, we managed to even-up the cholesterol levels in Apoe(-/-) mice and Ldlr(-/-) mice by making both models homozygous for the Apob(100) (apo B-100-only) allele. On a chow diet, apo-E-deficient apo B-100-only mice (Apoe(-/-)Apob(100/100)) and LDL receptor-deficient apo B-100-only mice (Ldlr(-/-)Apob(100/100)) had similar total plasma cholesterol levels ( approximately 300 mg/dL). The plasma of Ldlr(-/-)Apob(100/100) mice contained large numbers of small lipoproteins, whereas the plasma of Apoe(-/-)Apob(100/100) mice contained much lower levels of much larger lipoproteins. Interestingly, the Ldlr(-/-)Apob(100/100) mice developed far more extensive atherosclerotic lesions than the Apoe(-/-)Apob(100/100) mice. The finding of substantially more atherosclerosis in Ldlr(-/-)Apob(100/100) mice than in Apoe(-/-)Apob(100/100) mice, despite nearly identical cholesterol levels, suggests that large numbers of small apo B-100-containing lipoproteins are far more atherogenic than lower numbers of large apo B-100-containing lipoproteins.
The Impact of Dynamically Heterogeneous Multicore Processors on Thread Scheduling (2008)

Although most current multicore processors are homogeneous, microarchitects are now proposing heterogeneous core implementations, including systems in which heterogeneity is introduced at runtime. This article shows that operating system schedulers must consider dynamic heterogeneity or suffer significant power-efficiency and performance losses.
Minocycline in Rheumatoid Arthritis: A 48-Week, Double-Blind, Placebo-Controlled Trial (1995)

Minocycline was safe and effective for patients with mild to moderate rheumatoid arthritis. Its mechanisms of action remain to be determined.
New Algorithms and Integrated Workflow for Tight Gas and Shale Completions (2011)

Abstract Multi-stage stimulation has become the norm for unconventional reservoir development. How many fracture treatment stages and perforation clusters are optimal? What is the ideal spacing between perforation clusters? Where is the best location for each fracture treatment stage? These are critical and difficult questions to answer when designing completions for tight gas and shale reservoirs and the approach to answering these questions can differ considerably for vertical and horizontal wells in different lithologies. In the past, optimizing the number and location of fracture treatment stages has been primarily a manual, time intensive process, resulting in a "cookie cutter" approach that may not properly account for vertical and lateral heterogeneity. This paper details new algorithms and an integrated workflow that could improve fracture treatment staging in both vertical and horizontal wells. The primary obstacles to optimizing completions in tight gas and shale reservoirs have been the absence of hydraulic fracture models that properly simulate complex fracture propagation which is common in many reservoirs, efficient methods to create discrete reservoir simulation grids to rigorously model the hydrocarbon production from complex hydraulic fractures, automated fracture treatment staging algorithms, and the ability to efficiently integrate microseismic mapping measurements with geological and geophysical data. One of these obstacles has been overcome with the recent development of complex hydraulic fracture models (Meyer and Bazan, 2011, Weng et al., 2011, Xu et al., 2010). However, the remaining obstacles are just now being addressed. Algorithms for efficient and rigorous design of multi-stage completions are detailed in the paper. Separate staging algorithms have been developed for vertical and horizontal wells that utilize detailed stress, rock mechanical, and image measurements (i.e. - natural fracture identification) to select stage intervals and perforation locations. The staging algorithms incorporate "fit-for-purpose" hydraulic fracture models ranging from standard planar pseudo 3D models to newly developed complex fracture models, depending on the environment. The algorithms are seamlessly integrated with microseismic measurements, a common Earth Model, and automated routines to discretely grid the complex fracture geometry for reservoir simulation. A common software platform enables the efficient utilization of multiple data sources from multiple disciplines. The application of the newly developed algorithms and integrated workflow is illustrated using examples from tight gas and shale reservoirs.
Spatial variations in oxygen precipitation in silicon after high temperature rapid thermal annealing (1997)

Spatial variations of oxygen precipitation have been studied in silicon wafers submitted to rapid thermal annealing (RTA) in nitrogen ambients at a temperature above 1150 °C prior to a two-step precipitation treatment. The samples submitted to high temperature preannealing show a consistent enhancement of oxygen precipitation, which is dependent on the RTA time and temperature. Oxygen precipitate density measurements show that oxygen precipitation is not homogeneous inside the wafer, but peaks near the surfaces, with a minimum in the bulk. The high treatment in N2 results in the formation of defects which act as precursors for the subsequent nucleation and growth of oxygen precipitates. There is strong evidence that these precursors are generated by the thermal nitridation of the silicon surface and subsequent vacancy injection into the bulk of the wafer.
Analysis of heterologous and homologous promoters and enhancers in vitro and in vivo by gene transfer into Japanese medaka (Oryzias latipes) Xiphophorus. (1993)

Efficient expression systems are required for analysis of gene regulation and function in teleost fish. To develop such systems, a number of inducible or constitutive promoter and enhancer sequences of fish or higher vertebrate origin were tested for activity in a variety of fish cell lines and in embryos of the Japanese medaka fish (Oryzias latipes) and Xiphophorus. The activity of the different promoter-enhancer combinations were quantitated. Considerable differences were found for some constructs if tested in vitro or in vivo. Fro the data obtained, a set of expression vectors for basic research as well as for aquaculture purposes were established.
Isolated Subtalar Arthrodesis* (2000)

To the best of our knowledge, the present study includes the largest reported series of isolated subtalar arthrodeses in adults. Our results suggest that the outcome following isolated subtalar arthrodesis is not as favorable as has been reported in previous studies. The rate of union was significantly diminished by smoking, the presence of more than two millimeters of avascular bone at the arthrodesis site, and the failure of a previous subtalar arthrodesis (p < 0.05 for all). Other factors that probably affect the union rate include the use of structural allograft and performance of the arthrodesis adjac
Extracellular Level of GABA and Glu: In Vivo Microdialysis-HPLC Measurements (2006)

In spite of several studies showing specific physiological functions of changes in the extracellular level of the major excitatory and inhibitory transmitters, Glu and GABA within the brain ([Glu](EXT), [GABA](EXT)) the exact origin (neuronal vs. astroglial, synaptic vs. extrasynaptic) of Glu and GABA present in dialysate samples is still a matter of debate. For better understanding the significance of in vivo microdialysis data, here we discuss methodological details and problems in addition to regulation of [Glu](EXT) and [GABA](EXT). Changes in [Glu](EXT) and [GABA](EXT) under pathological conditions such as ischemia and epilepsy are also reviewed. Based on recent in vivo microdialysis data we argue that ambient [Glu](EXT) and [GABA](EXT)may have a functional role. It is suggested that specific changes in concentrations of Glu and GABA in dialysate samples together with their alterations independent of neuronal activity indicate the involvement of Glu and GABA in the information processing of the brain as essential signaling molecules of nonsynaptic transmission as well. Since various drugs are able to interfere with extrasynaptic signals in vivo, studying the extracellular cell-to-cell communication of brain cells represents a new aspect to improve drugs modulating Gluergic as well as GABAergic neurotransmission.
Lexicase parsing (1986)

This paper presents a lexicon-based approach to syntactic analysis, Lexicase, and applies it to a lexicon-driven computational parsing system. The basic descriptive mechanism in a Lexicase grammar is lexical features. The properties of lexical items are represented by contextual and non-contextual features, and generalizations are expressed as relationships among sets of these features and among sets of lexical entries. Syntactic tree structures are representaed as notworks of pairwise dependency relationships among the words in a sentence. Possible dependencies are marked as contextual features on individual lexical items, and Lexicase parsing is a process of picking out words in a string and attaching dependents to them in accordance with their contextual features. Lexicase is an appropriate vehicle for parsing because Lexicase analyses are monostratal, flat, and relatively non-abstract, and it is well suited to machine translation because grammatical representations for corresponding sentences in two languages will be very similar to each other in structure and inter-constituent relations, and thus far easier to interconvert.
Dissecting the Genetic Basis of Rheumatoid Arthritis in Mouse Models (2006)

Rheumatoid Arthritis, RA, is a common polygenic multi-factorial chronic inflammatory disorder that involves complex interactions between genetic and environmental factors. Despite major advances, the aetiology of the disease is still not completely understood. In this post-genome era, the sequencing of the human and some murine genomes as well as advances in global screening technologies offer an opportunity to accelerate the search for new pathological pathways and to identify new therapeutic targets. Animal models of RA offer an opportunity to dissect the genetic basis of disease in a simplified genome and controlled environment with the aim of identifying new pathological pathways and thus new therapeutic targets. Linkage analysis in the mouse model has identified more than 60 Loci, controlling disease phenotypes, immune response and cytokines. This indicates that gene variations among inbred mice strains affect the disease and that those polymorphic genes could be potential therapeutic targets. However, progress in identification of susceptibility genes in mouse models is slow. The progress is hampered by the complexity of disease as well as the traditional genetic dissection strategies. In this post-genome era, the sequencing of the human and some murine genomes as well as advances in global screening technologies offer an opportunity to accelerate the progress.
DNA fingerprinting by hybridisation to oligonucleotide arrays (1995)

Most methods for analysing variation in DNA sequences rely on gel electrophoresis, a method which is difficult to automate and to quantify. Hybridisation to oligonucleotides bound to a solid surface offers alternatives, with the advantage that they can be more readily automated and lend themselves to powerful statistical analytical procedures. In this paper, we discuss a number of different ways in which oligonucleotide arrays could be used for DNA typing for applications in forensic science.