gebhart/patrepeval huggingface dataset:
Effects of acid type on physical and biological properties of collagen scaffolds (2008)

Different acid types, hydrochloric acid and acetic acid, were used to prepare collagen solutions. The effects of acid types on physical and biological properties of collagen scaffolds were investigated. The collagen solution prepared with hydrochloric acid (C-HCl) was much more viscous than that prepared with acetic acid (C-Acetic). The conformation of collagen chains was expected to be different due to differences in ionic strength of collagen solutions. Morphology of the scaffolds analyzed by scanning electron microscopy (SEM) revealed that C-HCl scaffolds had larger pore sizes (around 100 microm) than C-Acetic scaffolds (around 50 microm). The more viscous C-HCl solution resulted in harder scaffolds shown by higher compressive modulus. However, the swelling ability of the C-Acetic scaffolds was higher in phosphate-buffered saline solution. The results from in vitro L929 cell culture showed that C-HCl scaffolds could promote cell initial attachment while the C-Acetic scaffolds enhanced cell proliferation. Therefore, the type of acid used as a solvent to form collagen solution affects the morphology, physical and biological properties of the resulting collagen scaffolds.
p65: A C3b-binding protein on murine cells that shares antigenic determinants with the human C3b receptor (CR1) and is distinct from murine C3b receptor. (1985)

Abstract Affinity-purified rabbit antibody to the human C3b receptor (CR1) cross-reacted with an antigen that was expressed on murine splenocytes, lymph node cells, thymocytes, peritoneal macrophages, erythrocytes, and L929 cells, as assessed by flow cytofluorographic analysis of indirectly stained cells. The cell surface antigen recognized by antihuman CR1 had a Mr of 60,000 to 65,000 on each cell type, and the cross-reactive epitope(s) was sensitive to reduction with dithiothreitol but not to oxidation with NaIO4. Analysis by affinity chromatography of murine splenic B lymphocytes identified two cell surface proteins capable of binding to guinea pig C3b (C3bgp). The larger polypeptide had a Mr of 210,000, was not present in L929 cells, and may represent the murine CR1. The smaller polypeptide of 65,000 Mr was also present on L929 cells and was shown to constitute the cross-reactive antigen. Adsorption of detergent lysates of L929 cells with C3bgp-Sepharose depleted by 44% the antigen recognized by anti-human CR1; the C3bgp-binding protein and the cross-reactive antigen exhibited similar patterns on two-dimensional gel electrophoresis; and the isolated C3b-binding protein could be immunoprecipitated with anti-human CR1. Thus, the murine cell surface protein, termed p65, that is antigenically cross-reactive with human CR1 shares a capacity for binding to C3b in its detergent-solubilized form but is distinct from murine CR1 in its lower Mr, wider cellular distribution, and inability to mediate the adherence of C3b-coated particles in its native, membrane-associated form.
Identification of effector cell protease receptor-1. A leukocyte-distributed receptor for the serine protease factor Xa. (1990)

Mitogenesis, cell differentiation and immune-inflammatory responses are regulated by the coordinated assembly of proteases with specific cellular receptors. We have investigated the possibility that immune effector cells may express a high-affinity protease receptor. To address this hypothesis, we have generated mAb to factor V and its activated form Va, a circulating plasma protein that binds the serine protease of the coagulation cascade, factor Xa. Further, by flow microfluorimetry screening, we have isolated a panel of these mAb that recognize a surface molecule expressed on transformed monocytic cells. We now show that these mAb bind to blood monocytes, to CD3- CD16+ CD56+ NK cells, and with considerable heterogeneity, to neutrophils. A small subset of CD3+ cells (5 to 10%) was also identified by these probes and further phenotypically characterized by two-color flow microfluorimetry as predominantly coexpressing CD2, CD4 or CD8, CD57, CD11b, and alpha/beta TCR. This subset of CD3+ cells was expanded in vitro by both lectin- or Ag-specific stimulation. In addition, long term alloreactive stimulation resulted in approximately 8- to 10-fold increased expression of the molecule recognized by these mAb. Functional analyses were performed on a selected T cell clonal derivative of the transformed cell line HuT 78. These cells bound 125I-factor Xa in a specific reaction saturated at 194,000 +/- 26,000 molecules/cell with a Kd approximately 10 to 20 nM and inhibited by the mAb panel described above. These data suggest that immune effector cells express a dynamically regulated protease receptor that is immunologically related to the plasma coagulation protein factor V and its activated form Va. We propose the term effector cell protease receptor-1 to tentatively identify this molecule, and we speculate on its possible involvement in specialized protease-mediated effector functions.
Distinct roles for RDE-1 and RDE-4 during RNA interference in Caenorhabditis elegans. (2001)

RNA interference (RNAi) is a cellular defense mechanism that uses double-stranded RNA (dsRNA) as a sequence-specific trigger to guide the degradation of homologous single-stranded RNAs. RNAi is a multistep process involving several proteins and at least one type of RNA intermediate, a population of small 21-25 nt RNAs (called siRNAs) that are initially derived from cleavage of the dsRNA trigger. Genetic screens in Caenorhabditis elegans have identified numerous mutations that cause partial or complete loss of RNAi. In this work, we analyzed cleavage of injected dsRNA to produce the initial siRNA population in animals mutant for rde-1 and rde-4, two genes that are essential for RNAi but that are not required for organismal viability or fertility. Our results suggest distinct roles for RDE-1 and RDE-4 in the interference process. Although null mutants lacking rde-1 show no phenotypic response to dsRNA, the amount of siRNAs generated from an injected dsRNA trigger was comparable to that of wild-type. By contrast, mutations in rde-4 substantially reduced the population of siRNAs derived from an injected dsRNA trigger. Injection of chemically synthesized 24- or 25-nt siRNAs could circumvent RNAi resistance in rde-4 mutants, whereas no bypass was observed in rde-1 mutants. These results support a model in which RDE-4 is involved before or during production of siRNAs, whereas RDE-1 acts after the siRNAs have been formed.
Pyrogen from Mouse Macrophages Causes Fever in Mice (1976)

Mouse peritoneal macrophages, after phagocytosis, release an endogenous (leucocyte) pyrogen. Intravenous injection of stimulated cell culture supernatant produces a prompt, monophasic fever in mice maintained in a 35 degree environment. The pyrogen is distinct from endotoxin, and resembles cell pyrogens of other species in heat-lability and pronase sensitivity. Human leucocyte pyrogen produces identical responses in mice. Measurement of fever in mice appears to provide a sensitive biological assay for endogenous pyrogens.
Grayscale laser image formation using a programmable binary mask (2012)

We present grayscale laser image formation from a programmable binary mask using a digital micromirror device (DMD) followed by a telescope with an adjustable pinhole low-pass filter. System performance was measured by comparing the intensity conformity with respect to the target image and by the energy conversion efficiency. A theoretical analysis of image precision proved high-precision image formation and inspired the iterative pattern refinement process based on the point spread function of a single DMD pixel to seek optimized image quality. We derived the diffraction efficiency formula of the DMD and discussed the overall system energy efficiency with operation wavelengths. Actual image precision performance was evaluated by measuring the root-mean-square (RMS) error of a series of sinusoidal-flattop profiles with different system bandwidths. We produced grayscale laser images with different spatial spectral content using intensity profiles of Laguerre-Gaussian, Hermite-Gaussian, and Lena-flattop beams. Measured RMS errors of all examples of various bandwidths were consistent with the image precision of the sinusoidal reference patterns. The ripple effect caused by the sharp-edged pinhole was the major contributor to the residual error in the output images. Error histograms had a zero-mean Gaussian distribution with standard deviation equal to the value of the RMS error.
Digital licensing [software reuse] (2005)

Questions of ownership can block widespread software reuse. Forced to choose between negotiating rights to an existing component and reimplementing it, developers often take the latter option. At least in part, this is because they have less control when negotiating with an unknown party, and such negotiations can be expensive - in time, legal fees, knowledge, and the bookkeeping required to monitor usage. How can we dramatically reduce these costs? A digital license protects an author or owner's intellectual property rights to regulate how content is sold or used, monitors compliance to terms and conditions, and regulates compensation. The goal of digital license automation is to provide an infrastructure that makes it easy for programs to negotiate with each other when they need services, taking the human at least partly out of the loop. A pervasive, low-overhead digital licensing infrastructure could enlarge the component software marketplace and lead to greater availability of reusable software components.
Robust question answering over the web of linked data (2013)

Knowledge bases and the Web of Linked Data have become important assets for search, recommendation, and analytics. Natural-language questions are a user-friendly mode of tapping this wealth of knowledge and data. However, question answering technology does not work robustly in this setting as questions have to be translated into structured queries and users have to be careful in phrasing their questions. This paper advocates a new approach that allows questions to be partially translated into relaxed queries, covering the essential but not necessarily all aspects of the user's input. To compensate for the omissions, we exploit textual sources associated with entities and relational facts. Our system translates user questions into an extended form of structured SPARQL queries, with text predicates attached to triple patterns. Our solution is based on a novel optimization model, cast into an integer linear program, for joint decomposition and disambiguation of the user question. We demonstrate the quality of our methods through experiments with the QALD benchmark.
Glycosylated Haemoglobins: Biochemical Evaluation and Clinical Utility (1984)

A review is given of the biochemical background of the glycosylated haemoglobins, their methods of determination, and their clinical significance. Special attention is paid to the sample preparation. For all methods except the colorimetric TBA-method, the removal of the labile pre-HbA1c fraction is essential. Under proper conditions, high-performance liquid chromatography, agar-gel electrophoresis and affinity chromatography are suitable methods for use in the clinical laboratory for the estimation of HbA1c and HbA1. However, the colorimetric TBA-method must be considered to be the method of choice. The clinical utility of the test is stressed with special respect to the management of diabetic pregnancies, the control of home-monitoring of blood glucose, and the objective measurement of the effect of changing diabetic therapy.
Fast networking with socket-outsourcing in hosted virtual machine environments (2009)

This paper proposes a novel method of achieving fast networking in hosted virtual machine (VM) environments. This method, called socket-outsourcing, replaces the socket layer in a guest operating system (OS) with the socket layer of the host OS. Socket-outsourcing increases network performance by eliminating duplicate message copying in both the host OS and the guest OS. Furthermore, socket-outsourcing significantly enhances inter-VM communication within the same host OS since it enables network packets to bypass the protocol stack in guest OSes. Socket-outsourcing was implemented in two representative operating systems (Linux and NetBSD) and on two virtual machine monitors (Linux KVM and PansyVM). These virtual machine monitors provided support for socket-outsourcing through shard memory, event queues, and VM-specific Remote Procedure Call between a guest OS and a host OS. The experimental results revealed that a guest OS outsourcing the socket layer achieved the same network throughput as a native OS using up to four Gigabit Ethernet links. Moreover, the benchmark results obtained from an N-tier Web application that generated a significant amount of inter-VM communication indicated that socket-outsourcing improved performance by up to 45 percent compared with conventional hosted VM environments.
Recognition of Partially Occluded and Rotated Images With a Network of Spiking Neurons (2010)

In this paper, we introduce a novel system for recognition of partially occluded and rotated images. The system is based on a hierarchical network of integrate-and-fire spiking neurons with random synaptic connections and a novel organization process. The network generates integrated output sequences that are used for image classification. The proposed network is shown to provide satisfactory predictive performance given that the number of the recognition neurons and synaptic connections are adjusted to the size of the input image. Comparison of synaptic plasticity activity rule (SAPR) and spike timing dependant plasticity rules, which are used to learn connections between the spiking neurons, indicates that the former gives better results and thus the SAPR rule is used. Test results show that the proposed network performs better than a recognition system based on support vector machines.
Effects of simvastatin on the metabolism of polyunsaturated fatty acids and on glycerolipid, cholesterol, and de novo lipid synthesis in THP-1 cells (1997)

In the monocytic THP-1 cells, the 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) reductase inhibitor simvastatin (5 microM) enhances the conversion of exogenous linoleic (18:2 n-6) and eicosapentaenoic (20:5 n-3) acids to their long-chain polyunsaturated fatty acid (LC-PUFA) derivatives, and this effect is associated with changes in the desaturation steps. In addition, formation of monounsaturated fatty acids from endogenously synthesized precursors is increased. These metabolic changes lead to elevated LC-PUFA and fatty acid (FA) unsaturation in cells. The effects of simvastatin on FA metabolism are associated with increased synthesis of triglycerides from glycerol. The dose-effect relationships for the activity of simvastatin on total linoleic acid (LA) conversion and cholesterol synthesis reveal that enhancement of PUFA metabolism is already maximal at 0.5 microM simvastatin, whereas cholesterol synthesis is further inhibited by concentrations of simvastatin up to 5 microM. The effects of 5 microM simvastatin on PUFA metabolism are partially prevented by mevalonate (1 mM) and geranylgeraniol (5 microM) but not by farnesol (10 microM). These data indicate that HMG-CoA inhibitors have profound effects on PUFA metabolism, and that the pathways for cholesterol and PUFA synthesis are mutually modulated.
Immunogenicity of an Inactivated Oil-Emulsion Canine Distemper Vaccine in African Wild Dogs (2004)

The immunogenicity of an inactivated oil-emulsion vaccine against canine distemper virus was evaluated in nine captive African wild dogs (Lycaon pictus). Antibody levels were determined by neutralization test in Vero cells. No significant local or systemic adverse reactions were observed in the animals. Virus neutralizing antibody levels >1:20 were detected, especially in animals that were vaccinated twice. The use of oil adjuvants is suggested as a good way to enhance the immune response to inactivated canine distemper vaccine.
Co-registration of PET and MRI in different courses of MS using Cobalt-55 as a Calcium-tracer. (1997)

Multiple Sclerosis (MS) is an auto-immune central nervous system (CNS) inflammation. At this moment, MRI is the most accurate paraclinical test in MS to monitor disease activity, although poorly correlated with clinical impairment. PET using Co-55 as a Ca-tracer may visualize Co-transport across the neuronal membrane, Ca-mediated inflammatory processes and passive leakage through a breach in the blood-brain barrier. Co-registration of MRI and Co-PET may actually allow identification of clinically active lesions. MRI and Co-PET were performed as described elsewhere. Based on a statistic parametric mapping (SPM-96)-software package, MRI and Co-PET were superimposed. A semi-automated technique was used to count the MS-lesions. We included four groups of eight MS-patients with relapsing-remitting (RR), primary progressive (PP), progressive relapsing (PR) and secondary progressive (SP) courses and eight healthy volunteers. MS was assessed in terms of impairment using Kurtzke's Expanded Disability Status Scale (EDSS) and Scripps Neurological Rating Scale (NRS). Co-PET displayed focal uptake throughout the MS brain, both in the grey and white matter. All four patients groups (as compared to controls) demonstrated a more inhomogeneous distribution of Co-spots with a tendency to show clustering, most evident in RR-MS. SPM-analysis revealed an essentially different distribution pattern of MS spots on MRI and Co-PET. (Merging of) Co-PET and MRI may eventually form complementary tools for identifying clinically relevant lesions, thus providing a more reliable secondary outcome measure in MS.
Protein L, a bacterial immunoglobulin-binding protein and possible virulence determinant (1990)

Protein L, an immunoglobulin kappa light chain-binding protein, is expressed on the surfaces of certain strains of Peptostreptococcus magnus. Thirty strains of P. magnus were isolated from clinical specimens, and four of them were found to express protein L. Among the 30 strains, 7 were isolated from the vaginas of patients with bacterial vaginosis, and the 4 immunoglobulin-binding strains all belonged to this group, results demonstrating that expression of protein L is correlated to peptostreptococcal virulence (P less than 0.001 in the chi-square test) and indicating that the molecule could be a virulence determinant. Similar amounts of protein L were expressed by the four strains, and when protein L was isolated from three of them and analyzed in Western blots, the same immunoglobulin-binding patterns were obtained. The N-terminal amino acid sequences of tryptic fragments of protein L were determined, and on the basis of these sequence data, oligonucleotides were synthesized and used to screen a genomic library of peptostreptococcal DNA in the lambda ZAP vector. The nucleotide sequence was determined for one of the clones detected in this way. In dot blots and Southern blots of peptostreptococcal DNA, another synthetic oligonucleotide probe based on this sequence showed no hybridization with DNA samples from the nonexpressing strains, whereas similar Southern blot patterns were seen when DNA samples from protein L-expressing strains were analyzed. These results suggest that the protein L gene is missing rather than being down regulated in protein L-negative strains of P. magnus. Finally, the probe did not hybridize with DNA purified from immunoglobulin-binding streptococcal and staphylococcal strains or with Escherichia coli DNA, suggesting that the protein L gene is unique to protein L-expressing strains of P. magnus.
Structural Systems Biology Evaluation of Metabolic Thermotolerance in Escherichia coli (2013)

Genome-scale network reconstruction has enabled predictive modeling of metabolism for many systems. Traditionally, protein structural information has not been represented in such reconstructions. Expansion of a genome-scale model of Escherichia coli metabolism by including experimental and predicted protein structures enabled the analysis of protein thermostability in a network context. This analysis allowed the prediction of protein activities that limit network function at superoptimal temperatures and mechanistic interpretations of mutations found in strains adapted to heat. Predicted growth-limiting factors for thermotolerance were validated through nutrient supplementation experiments and defined metabolic sensitivities to heat stress, providing evidence that metabolic enzyme thermostability is rate-limiting at superoptimal temperatures. Inclusion of structural information expanded the content and predictive capability of genome-scale metabolic networks that enable structural systems biology of metabolism.
Analysis of magnetic stimulation of a concentric axon in a nerve bundle (1995)

The authors present an analysis of magnetic stimulation of an axon located at the center of a nerve bundle. A three-dimensional axisymmetric volume conductor model is used to determine the transmembrane potential response along an axon due to induced electric fields produced by a toroidal coil. The authors evaluate four such models of an axon located in: (1) an isotropic nerve bundle with no perineurium, (2) an anisotropic nerve bundle without a perineurium, (3) an isotropic nerve bundle surrounded by a perineurium, and (4) an anisotropic nerve bundle surrounded by a perineurium. The transmembrane polarization computed along an axon for the above four models is compared to that for an axon located in an infinite homogenous medium. These calculations indicate that a nerve bundle with no sheath has little effect on the transmembrane potential. However, the presence of a perineurium around the nerve bundle and anisotropy in the bundle significantly affects the shape of the transmembrane response. Therefore, during magnetic stimulation, nerve bundle anisotropy and the presence of perineurium must be taken into account for calculation of stimulus intensities for threshold excitation.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Optical coherent-transient true-time-delay regenerator (1996)

We propose a novel all-optical true-time-delay regeneration technique that is well suited for control of phasedarray antennas with time-delay beam steering. Using coherent transients, this versatile technique has the ability to regenerate a variable delay onto an optical waveform of arbitrary shape and high bandwidth. We performed simulations indicating that future research could extend the delay resolution to the subpicosecond regime. We also present proof-of-concept experimental results for a true-time-delay regenerator combined with signal processing.