gebhart/patrepeval huggingface dataset:
Measurement of the Free Concentration Using Solid-Phase Microextraction:  Binding to Protein (1996)

A method is described to measure freely dissolved compounds, using solid-phase microextraction (SPME) as sampling technique. Currently applied techniques, like solvent extraction, have the disadvantage of extracting the total amount of a compound that is present in a sample. For many applications, though, the freely dissolved fraction of a compound is of more interest than the overall amount. The procedure described in this work is based on the principle that only the freely dissolved compound is available for partitioning to the SPME fiber. By extracting only a small amount of the freely dissolved fraction, the equilibrium between the fraction of a compound bound to a matrix and the fraction dissolved in the aqueous phase is not perturbed. The procedure was applied to study the binding of four polar compounds, i.e., aniline, nitrobenzene, 4-chloro-3-methylphenol, and 4-n-pentylphenol, to bovine serum albumin to illustrate the possibilities of the method.
Feasibility of 3D tracking of surgical tools using 2D single plane x-ray projections (2008)

Fluoroscopy is widely used for intra-procedure image guidance, however its planar images provide limited information about the location of the surgical tools or targets in three-dimensional space. An iterative method based on the projection-Procrustes technique can determine the three-dimensional positions and orientations of known sparse objects from a single, perspective projection. We assess the feasibility of applying this technique to track surgical tools by measuring its accuracy and precision through <i>in vitro</i> experiments. Two phantoms were fabricated to perform this assessment: a grid plate phantom with numerous point-targets at regular distances from each other; and a sparse object used as a surgical tool phantom. Two-dimensional projections of the phantoms were acquired using an image intensifier-based C-arm x-ray unit. The locations of the markers projected onto the images were identified and measured using an automated algorithm. The three-dimensional location of the phantom tool tip was identified from these images using the projection-Procrustes technique. The accuracy and precision of the tip localization were used to assess our technique. The average three-dimensional root-mean-square target registration error of the phantom tool tip was 1.8 mm. The average three-dimensional root-mean-square precision of localizing the tool tip was 0.5 mm.
The Role of Biomarkers in Clinical Trials for Alzheimer Disease (2006)

Biomarkers are likely to be important in the study of Alzheimer disease (AD) for a variety of reasons. A clinical diagnosis of Alzheimer disease is inaccurate even among experienced investigators in about 10% to 15% of cases, and biomarkers might improve the accuracy of diagnosis. Importantly for the development of putative disease-modifying drugs for Alzheimer disease, biomarkers might also serve as indirect measures of disease severity. When used in this way, sample sizes of clinical trials might be reduced, and a change in biomarker could be considered supporting evidence of disease modification. This review summarizes a meeting of the Alzheimer's Association's Research Roundtable, during which existing and emerging biomarkers for AD were evaluated. Imaging biomarkers including volumetric magnetic resonance imaging and positron emission tomography assessing either glucose utilization or ligands binding to amyloid plaque are discussed. Additionally, biochemical biomarkers in blood or cerebrospinal fluid are assessed. Currently appropriate uses of biomarkers in the study of Alzheimer disease, and areas where additional work is needed, are discussed.
Rapid and scalable scans at 21  m/s in optical low-coherence reflectometry (1997)

An optical low-coherence reflectometer is presented that uses a fiber Michelson interferometer with a rotating cube to generate rapid depth scans at a high repetition rate. A folded optical path geometry allows the reference arm to scale up the scan range, scan speed, and scan repetitiveness. Thickness measurements with a repetitiveness of 384 Hz and a longitudinal scanning speed of 21 m/s in air over a range of ~3 mm are demonstrated.
Cloning and expression of the first anaerobic toxin gene from Clostridium bifermentans subsp. malaysia, encoding a new mosquitocidal protein with homologies to Bacillus thuringiensis delta-endotoxins (1996)

A gene (cbm71) encoding a 71,128-Da mosquitocidal protein (Cbm71) was obtained by screening a size-fractionated XbaI digest of total genomic DNA from Clostridium bifermentans subsp. malaysia CH18 with two gene-specific oligonucleotide probes. The sequence of the Cbm71 protein, as deduced from the sequence of cbm71, corresponds to that of the 66-kDa protein previously described as one of the mosquitocidal components of C. bifermentans subsp. malaysia. Cbm71 shows limited similarities with Bacillus thuringiensis delta-endotoxins, especially in the four first conserved blocks. However, Cbm71 was not immunologically related to any of the Cry toxins and thus belongs to a novel class of mosquitocidal protein. The cbm71 gene was expressed in a nontoxic strain of B. thuringiensis, and Cbm71 was produced during sporulation and secreted to the supernatant of culture. Trichloroacetic-precipitated supernatant preparations were toxic for mosquito larvae of the species Aedes aegypti, Culex pipiens, and Anopheles stephensi.
Gene expression of sterol regulatory element-binding proteins in hamster small intestine (2001)

Gene expression of sterol regulatory element-binding proteins 1a, 1c, and 2 (SREBP-1a, -1c, and -2) and of 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) synthase, HMG-CoA reductase, and the low density lipoprotein (LDL) receptor was examined in hamster small intestine. SREBP-1c transcript predominated over SREBP-1a. mRNA levels for SREBP-1a, -1c, and -2, LDL receptor, and HMG-CoA synthase were highest in jejunum and ileum. Expression of SREBP-1a and SREBP-1c was highest in cells of the upper villus and decreased in cells of the lower villus. Gene expression of SREBP-2 was lowest in cells of the upper villus and increased in cells of the lower villus. Ileal SREBP-2 gene expression was highest in cells of the midvillus. mRNA levels for HMG-CoA synthase and the LDL receptor followed a pattern similar to that of SREBP-2. A positive correlation existed between SREBP-2 gene expression and rates of cholesterol synthesis. Fatty acid synthesis was highest in jejunum and ileum, correlating positively with the expression of SREBP-1c. Sterol influx into intestinal cells decreased mRNA levels of SREBP-2, HMG-CoA reductase, HMG-CoA synthase, and LDL receptor. In ileum, sterol influx decreased gene expression of SREBP-1a and increased expression of SREBP-1c. The results suggest that SREBP-2 regulates cholesterol synthesis in the small intestine. SREBP-1a is a minor transcript and its expression does not correlate with cholesterol-synthesizing activity. SREBP-1c is a major transcript in small intestine and its expression along the length of the gut correlates with fatty acid synthesis. Sterols regulate gene expression of sterol-responsive genes, including SREBP-2, in small intestine. - Field, F. J., E. Born, S. Murthy, and S. N. Mathur. Gene expression of sterol regulatory element-binding proteins in hamster small intestine. J. Lipid Res. 2001. 42: 1;-8.
Autologous bone marrow transplantation for non-transformed low-grade non-Hodgkin's lymphoma. (1995)

The purpose of this study was to evaluate autologous bone marrow transplantation (ABMT) for low-grade non-Hodgkin's lymphoma (NHL). Between 1983 and 1994, 34 patients with non-transformed low-grade NHL received high-dose chemoradiotherapy plus stem cell rescue with marrow or peripheral blood. At transplantation (5-182 months (median 32) after diagnosis), 2 patients were in complete remission (CR), 21 in partial remission (PR) or minimal disease; 11 had bulky/resistant disease. Four patients died from transplant-related causes and 10 from lymphoma progression. After 40 months median follow-up, 20 survive between 3+ and 88+ months after ABMT. One-year survival is 81% (95% confidence interval, 65-96%) and 5-year survival 37% (14-60%). The probability of relapse at 1 and 2 years is 53% (34-72%) and 75% (54-96%), respectively. Twenty-nine patients were in CR following ABMT and 11 survive in continuous CR 3 to 54 months later. Disease-free survival at 1 and 2 years is 35% (19-52%) and 18% (2-31%). Resistant disease was the only factor significantly associated with poor overall (relative risk = 3.0, P = 0.04) and disease-free survival (RR = 5.4, P = 0.003), while resistant disease and high LDH were associated with increased relapse. ABMT yields a high CR rate for patients with progressive low-grade NHL, but relapse is frequent. Even longer follow-up is required to determine its effectiveness in extending survival of patients with pre-transplant responsive disease.
Overexpression of galectin‐1 is associated with poor prognosis in human hepatocellular carcinoma following resection (2012)

Galectin-1 might be a new prognostic factor for HCC after resection and could potentially be a high-priority therapeutic target.
On mitigating TCP Incast in Data Center Networks (2011)

TCP Incast, also known as TCP throughput collapse, is a term used to describe a link capacity under-utilization phenomenon in certain many-to-one communication patterns, typically in many datacenter applications. The main root cause of TCP Incast analyzed by prior works is attributed to packet drops at the congestion switch that result in TCP timeout. Congestion control algorithms have been developed to reduce or eliminate packet drops at the congestion switch. In this paper, the performance of Quantized Congestion Notification (QCN) with respect to the TCP incast problem during data access from clustered servers in datacenters are investigated. QCN can effectively control link rates very rapidly in a datacenter environment. However, it performs poorly when TCP Incast is observed. To explain this low link utilization, we examine the rate fluctuation of different flows within one synchronous reading request, and find that the poor performance of TCP throughput with QCN is due to the rate unfairness of different flows. Therefore, an enhanced QCN congestion control algorithm, called fair Quantized Congestion Notification (FQCN), is proposed to improve fairness of multiple flows sharing one bottleneck link. We evaluate the performance of FQCN as compared to that of QCN in terms of fairness and convergence with four simultaneous and eight staggered source flows. As compared to QCN, fairness is improved greatly and the queue length at the bottleneck link converges to the equilibrium queue length very fast. The effects of FQCN to TCP throughput collapse are also investigated. Simulation results show that FQCN significantly enhances TCP throughput performance in a TCP Incast setup.
Plasminogen is a key proinflammatory regulator that accelerates the healing of acute and diabetic wounds (2012)

Despite decades of research on wound healing, effective biologic agents for the treatment of chronic wounds, especially diabetic wounds, are still lacking. In the present study, we report that the inert plasma protein plasminogen (plg) acts as a key regulatory molecule that potentiates wound healing in mice. Early in the healing process, plg bound to inflammatory cells is transported to the wound area, where the level of plg is increased locally, leading to the induction of cytokines and intracellular signaling events and to a potentiation of the early inflammatory response. Systemic administration of additional plg not only accelerates the healing of acute burn wounds in wild-type mice, but also improves the healing of chronic diabetic wounds in a mouse model of diabetes. Our results suggest that the administration of plg may be a novel therapeutic strategy to treat many different types of wounds, especially chronic wounds such as those caused by diabetes.
Health Status Predicts Long-Term Outcome in Outpatients With Coronary Disease (2002)

SAQ scores are independently associated with 1-year mortality and ACS among outpatients with coronary disease and may serve a valuable role in the risk stratification of such patients.
CD66a Interactions Between Human Melanoma and NK Cells: A Novel Class I MHC-Independent Inhibitory Mechanism of Cytotoxicity (2002)

NK cells are able to kill virus-infected and tumor cells via a panel of lysis receptors. Cells expressing class I MHC proteins are protected from lysis primarily due to the interactions of several families of NK receptors with both classical and nonclassical class I MHC proteins. In this study we show that a class I MHC-deficient melanoma cell line (1106mel) is stained with several Ig-fused lysis receptors, suggesting the expression of the appropriate lysis ligands. Surprisingly, however, this melanoma line was not killed by CD16-negative NK clones. The lack of killing is shown to be the result of homotypic CD66a interactions between the melanoma line and the NK cells. Furthermore, 721.221 cells expressing the CD66a protein were protected from lysis by YTS cells and by NK cells expressing the CD66a protein. Redirected lysis experiments demonstrated that the strength of the inhibitory effect is correlated with the levels of CD66a expression. Finally, the expression of CD66a protein was observed on NK cells derived from patients with malignant melanoma. These findings suggest the existence of a novel class I MHC-independent inhibitory mechanism of human NK cell cytotoxicity. This may be a mechanism that is used by some of the class I MHC-negative melanoma cells to evade attack by CD66a-positive NK cells.
Molecular Characterization of Caveolin Association with the Golgi Complex: Identification of a Cis-Golgi Targeting Domain in the Caveolin Molecule (1999)

Caveolins are integral membrane proteins which are a major component of caveolae. In addition, caveolins have been proposed to cycle between intracellular compartments and the cell surface but the exact trafficking route and targeting information in the caveolin molecule have not been defined. We show that antibodies against the caveolin scaffolding domain or against the COOH terminus of caveolin-1 show a striking specificity for the Golgi pool of caveolin and do not recognize surface caveolin by immunofluorescence. To analyze the Golgi targeting of caveolin in more detail, caveolin mutants were expressed in fibroblasts. Specific mutants lacking the NH2 terminus were targeted to the cis Golgi but were not detectable in surface caveolae. Moreover, a 32-amino acid segment of the putative COOH-terminal cytoplasmic domain of caveolin-3 was targeted specifically and exclusively to the Golgi complex and could target a soluble heterologous protein, green fluorescent protein, to this compartment. Palmitoylation-deficient COOH-terminal mutants showed negligible association with the Golgi complex. This study defines unique Golgi targeting information in the caveolin molecule and identifies the cis Golgi complex as an intermediate compartment on the caveolin cycling pathway.
The HIV Nef protein modulates cellular and exosomal miRNA profiles in human monocytic cells (2014)

This is the first study to report miRnome analysis of HIV Nef expressing monocytes and exosomes. Our results demonstrate that Nef causes large-scale dysregulation of cellular miRNAs, including their secretion through exosomes. We suggest this to be a novel viral strategy to affect pathogenesis and to limit the effects of RNA interference on viral replication and persistence.
Chemical analysis of polycyclic aromatic compounds (1989)

Significance of chemical analysis of polycyclic aromatic compound and related biological systems the fate of polycyclic aromatic compounds in the atmosphere and during sampling gas- and liquid-chromatographic techniques capillary supercritical fluid chromatography methods micelle-mediated methodologies for the preconcentration and separation of polycyclic aromatic compounds ultraviolet absorption and luminescence spectrometry: an overview of recent developments phase-resolved fluorescence spectroscopy mass spectrometry of polycyclic aromatic compounds laser multiphoton ionization of polyatomic molecules multidimensional resonance two-photon ionization mass spectrometric-based analysis photothermal spectroscopy immunological methods for the detection and quantification of exposure to aromatic hydrocarbons recent advances in infrared analysis of polycyclic aromatic compounds Raman spectroscopy surface-enhanced Raman spectroscopy.
Sequence-based heuristics for faster annotation of non-coding RNA families (2005)

The source code is available under GNU Public License at the supplementary web site.
Efficacy of a new prescription-only medical food supplement in alleviating signs and symptoms of dry eye, with or without concomitant cyclosporine A (2011)

Supplementation with the proper balance of omega-3 and omega-6 essential fatty acids improved TBUT and relieved patient symptoms. The addition of topical cyclosporine did not convey any statistically significant improvement in TBUT beyond that achieved by the supplement.
Overcoming scaling barriers through design technology CoOptimization (2016)

Design technology co-optimization (DTCO) is the term used to describe the process of deriving a competitive technology definition out of a number of increasingly complex trade-offs. DTCO is not a specific approach or methodology, but rather a commitment to closer collaboration between designers and process engineers born out of necessity to maintain value in semiconductor scaling. This paper aims to clarify this abstract concept through a series of examples encountered in scaling a logic cell from the N14 to the N3 technology node.
Management of Inherited Disorders of Ureagenesis (2002)

The conversion of ammonia to urea is known to require the function of at least nine proteins. Five of these are urea cycle enzymes (carbamyl phosphate synthetase I, ornithine transcarbamylase, argininosuccinate synthetase, argininosuccinate lyase, and arginase). A sixth enzyme (N-acetylglutamate synthase) catalyzes the formation of N-acetylglutamate, a cofactor for carbamyl phosphate synthetase I. The remaining three proteins are amino acid transporters for ornithine, aspartate/glutamate, and dibasic amino acids, respectively. An inherited deficiency in any of these proteins causes a block in the urea cycle and resultant hyperammonemia. Although the severity of these disorders varies, symptoms, diagnostic testing, and treatments are similar. Common symptoms include episodes of vomiting, lethargy, and coma associated with hyperammonemia. Diagnosis is based on a combination of measurement of plasma ammonia, plasma and urinary amino acids, urinary orotic acid, enzyme analysis, and molecular testing. Therapy involves a nitrogen-restricted diet, supplementation of essential amino acids and l-citrulline/l-arginine (except for hyperargininemia [l-citrulline is not approved by the United States Food and Drug Administration]), alternative pathway therapy with phenylbutyrate (or phenylacetate and benzoate), and, for the most severe cases, liver transplantation.
Overproduction of Geranylgeraniol by Metabolically Engineered Saccharomyces cerevisiae (2009)

(E, E, E)-Geranylgeraniol (GGOH) is a valuable starting material for perfumes and pharmaceutical products. In the yeast Saccharomyces cerevisiae, GGOH is synthesized from the end products of the mevalonate pathway through the sequential reactions of farnesyl diphosphate synthetase (encoded by the ERG20 gene), geranylgeranyl diphosphate synthase (the BTS1 gene), and some endogenous phosphatases. We demonstrated that overexpression of the diacylglycerol diphosphate phosphatase (DPP1) gene could promote GGOH production. We also found that overexpression of a BTS1-DPP1 fusion gene was more efficient for producing GGOH than coexpression of these genes separately. Overexpression of the hydroxymethylglutaryl-coenzyme A reductase (HMG1) gene, which encodes the major rate-limiting enzyme of the mevalonate pathway, resulted in overproduction of squalene (191.9 mg liter(-1)) rather than GGOH (0.2 mg liter(-1)) in test tube cultures. Coexpression of the BTS1-DPP1 fusion gene along with the HMG1 gene partially redirected the metabolic flux from squalene to GGOH. Additional expression of a BTS1-ERG20 fusion gene resulted in an almost complete shift of the flux to GGOH production (228.8 mg liter(-1) GGOH and 6.5 mg liter(-1) squalene). Finally, we constructed a diploid prototrophic strain coexpressing the HMG1, BTS1-DPP1, and BTS1-ERG20 genes from multicopy integration vectors. This strain attained 3.31 g liter(-1) GGOH production in a 10-liter jar fermentor with gradual feeding of a mixed glucose and ethanol solution. The use of bifunctional fusion genes such as the BTS1-DPP1 and ERG20-BTS1 genes that code sequential enzymes in the metabolic pathway was an effective method for metabolic engineering.
The primary structure of rat liver cellular retinol-binding protein. (1985)

The complete amino acid sequence of a cellular retinol-binding protein (CRBP) has been determined for the first time. The primary structure of rat liver CRBP was elucidated by analyses of cyanogen bromide fragments and peptides obtained by tryptic and thermolytic digestions. The single polypeptide chain of rat CRBP consists of 134 amino acid residues. Under reducing conditions, CRBP exists as a monomer, but, in the absence of reducing agents, dimers and multimers of the protein emerge. This is explained by the observation that CRBP contains 3 cysteines, one of which seems to be highly reactive. Whether CRBP contains a disulfide bond is not yet established. The present data extend the previously described homology between CRBP and a family of low molecular weight proteins, all members of which may bind hydrophobic ligands. Since some of these proteins apparently display intracellular transport functions, a similar role for CRBP is envisaged.
Recombinant human complement subcomponent C1s lacking .beta.-hydroxyasparagine, sialic acid, and one of its two carbohydrate chains still reassembles with C1q and C1r to form a functional C1 complex (1992)

In contrast to the human serum protein which is approximately one-half erythro-beta-hydroxyasparagine at asparagine 134 [Theilens et al. (1990) Biochemistry 29, 3570-3578], recombinant C1s expressed by insect cells after infection with recombinant baculovirus entirely lacks posttranslational modification at asparagine 134. It is also incompletely glycosylated, lacking, at least, sialic acid. Site-directed mutagenesis of one of the two sites of carbohydrate attachment (Asn 159 to Gln 159) yields a faster migrating recombinant C1s still abundantly secreted. Furthermore, the mutated protein displays good hemolytic activity when reassembled with C1q and either human serum or recombinant C1r, demonstrating that these posttranslational modifications are not critical for any of the multiple interactions between C1s and C1q, C1r, C2, and C4 required for reassembly of the C1 complex, activation, and initiation of the classical complement pathway. The 4.0S recombinant C1s dimerizes to yield 5.6S C1s2 in the presence of Ca2+ and forms the 9.1S C1s-C1r-C1r-C1s tetramer upon the addition of human serum C1r and the 15.6S C1 complex upon the addition of C1q to the tetramer. The recombinant C1s and human serum C1s have identical N-terminal amino acid sequences, indicating proper recognition by the insect signal peptidase. The recombinant C1s is secreted and isolated as the unactivated zymogen, and it may be activated by human serum C1r which cleaves at Arg422-Ile423 to yield the characteristic heavy and light chains. A very tight complex is formed between C1-inhibitor and the light chain of recombinant C1s.(ABSTRACT TRUNCATED AT 250 WORDS)