gebhart/patrepeval huggingface dataset:
H7 antiserum-sorbitol fermentation medium: a single tube screening medium for detecting Escherichia coli O157:H7 associated with hemorrhagic colitis (1985)

Escherichia coli serotype O157:H7 has been isolated from outbreaks and sporadic cases of hemorrhagic colitis. There is convincing evidence that it can cause this diarrheal disease. Because of the interest in hemorrhagic colitis, it has become desirable to detect this particular strain in human feces, which usually contains many other strains of E. coli. Two characteristics of the incriminated E. coli O157:H7 strain have made its isolation and identification easier. It does not ferment D-sorbitol rapidly, in contrast to about 95% of other E. coli strains. In addition, the strain has H antigen 7, but only about 10% of other E. coli strains have this particular antigen. To screen for E. coli O157:H7 we devised H7 antiserum-sorbitol fermentation medium (18 g of enteric fermentation base, 10 g of D-sorbitol, 4 g of agar, 10 ml of Andrade indicator, 989 ml of water; all ingredients were mixed, autoclaved, and cooled; 1 ml of E. coli H7 antiserum was then added). Colonies to be screened were inoculated into this medium. Strains of E. coli O157:H7 gave a characteristic pattern; they did not ferment sorbitol and were immobilized in the semisolid medium because of the reaction of their flagella with the flagella antiserum. Almost all other strains of E. coli gave a different pattern; they fermented sorbitol or were not immobilized by the H7 serum or both. Strains which were presumptive positives (sorbitol negative, H7 positive) were then tested in E. coli O157 serum by slide or tube agglutination. The number of strains which were presumptive positive by H7-sorbitol medium but then were not found to be O157 was less than 1%. A second approach has been helpful in deciding which colonies to screen in H7-sorbitol medium. MacConkey-sorbitol agar (22.2 g MacConkey agar base [which contains no sugar], 10 g of D-sorbitol, 1,000 ml of water) was designed as a plating medium. Stools were plated on MacConkey agar to estimate the number of E. coli colonies and also plated on MacConkey-sorbitol agar to estimate the number of sorbitol-negative colonies of E. coli. These two approaches have proved useful for isolating and identifying E. coli O157:H7 form human feces and from feces of animals infected in the laboratory with this strain. The results suggest that media may be formulated in a similar fashion for detecting other specific strains of E. coli.
Human Immunodeficiency Virus Type 1 Uses Lipid Raft-Colocalized CD4 and Chemokine Receptors for Productive Entry into CD4 + T Cells (2002)

In this report, we describe a crucial role of lipid raft-colocalized receptors in the entry of human immunodeficiency virus type 1 (HIV-1) into CD4(+) T cells. We show that biochemically isolated detergent-resistant fractions have characteristics of lipid rafts. Lipid raft integrity was required for productive HIV-1 entry as determined by (i) semiquantitative PCR analysis and (ii) single-cycle infectivity assay using HIV-1 expressing the luciferase reporter gene and pseudotyped with HIV-1 HXB2 envelope or vesicular stomatitis virus envelope glycoprotein (VSV-G). Depletion of plasma membrane cholesterol with methyl-beta-cyclodextrin (MbetaCD) relocalized raft-resident markers to a nonraft environment but did not significantly change the surface expression of HIV-1 receptors. MbetaCD treatment inhibited productive infection of HIV-1 by 95% as determined by luciferase activity in cells infected with HXB2 envelope-pseudotyped virus. In contrast, infection with VSV-G-pseudotyped virus, which enters the cells through an endocytic pathway, was not suppressed. Biochemical fractionation and confocal imaging of HIV-1 receptor distribution in live cells demonstrated that CD4, CCR5, and CXCR4 colocalized with raft-resident markers, ganglioside GM1, and glycosylphosphatidylinositol-anchored CD48. While confocal microscopy analysis revealed that HIV-1 receptors localized most likely to the same lipid microdomains, sucrose gradient analysis of the receptor localization showed that, in contrast to CD4 and CCR5, CXCR4 was associated preferentially with the nonraft membrane fraction. The binding of HIV-1 envelope gp120 to lipid rafts in the presence, but not in the absence, of cholesterol strongly supports our hypothesis that raft-colocalized receptors are directly involved in virus entry. Dramatic changes in lipid raft and HIV-1 receptor redistribution were observed upon binding of HIV-1 NL4-3 to PM1 T cells. Colocalization of CCR5 with GM1 and gp120 upon engagement of CD4 and CXCR4 by HIV-1 further supports our observation that HIV-1 receptors localize to the same lipid rafts in PM1 T cells.
Structural and functional hepatocyte polarity and liver disease (2015)

Hepatocytes form a crucially important cell layer that separates sinusoidal blood from the canalicular bile. They have a uniquely organized polarity with a basal membrane facing liver sinusoidal endothelial cells, while one or more apical poles can contribute to several bile canaliculi jointly with the directly opposing hepatocytes. Establishment and maintenance of hepatocyte polarity is essential for many functions of hepatocytes and requires carefully orchestrated cooperation between cell adhesion molecules, cell junctions, cytoskeleton, extracellular matrix and intracellular trafficking machinery. The process of hepatocyte polarization requires energy and, if abnormal, may result in severe liver disease. A number of inherited disorders affecting tight junction and intracellular trafficking proteins have been described and demonstrate clinical and pathophysiological features overlapping those of the genetic cholestatic liver diseases caused by defects in canalicular ABC transporters. Thus both structural and functional components contribute to the final hepatocyte polarity phenotype. Many acquired liver diseases target factors that determine hepatocyte polarity, such as junctional proteins. Hepatocyte depolarization frequently occurs but is rarely recognized because hematoxylin-eosin staining does not identify the bile canaliculus. However, the molecular mechanisms underlying these defects are not well understood. Here we aim to provide an update on the key factors determining hepatocyte polarity and how it is affected in inherited and acquired diseases.
Molecular Cloning of Human Plasma Membrane Phospholipid Scramblase (1997)

The rapid movement of phospholipids (PL) between plasma membrane leaflets in response to increased intracellular Ca2+ is thought to play a key role in expression of platelet procoagulant activity and in clearance of injured or apoptotic cells. We recently reported isolation of a approximately 37-kDa protein in erythrocyte membrane that mediates Ca2+-dependent movement of PL between membrane leaflets, similar to that observed upon elevation of Ca2+ in the cytosol (Bassé, F., Stout, J. G., Sims, P. J., and Wiedmer, T. (1996) J. Biol. Chem. 271, 17205-17210). Based on internal peptide sequence obtained from this protein, a 1,445-base pair cDNA was cloned from a K-562 cDNA library. The deduced "PL scramblase" protein is a proline-rich, type II plasma membrane protein with a single transmembrane segment near the C terminus. Antibody against the deduced C-terminal peptide was found to precipitate the approximately 37-kDa red blood cell protein and absorb PL scramblase activity, confirming the identity of the cloned cDNA to erythrocyte PL scramblase. Ca2+-dependent PL scramblase activity was also demonstrated in recombinant protein expressed from plasmid containing the cDNA. Quantitative immunoblotting revealed an approximately 10-fold higher abundance of PL scramblase in platelet ( approximately 10(4) molecules/cell) than in erythrocyte ( approximately 10(3) molecules/cell), consistent with apparent increased PL scramblase activity of the platelet plasma membrane. PL scramblase mRNA was found in a variety of hematologic and nonhematologic cells and tissues, suggesting that this protein functions in all cells.
The Design and Biological Activities of Glucagon Agonists and Antagonists,and their Use in Examining the Mechanisms of Glucose Action (2001)

Glucagon is a crucial hormone in glucose homeostasis and hence has great potential for application to research which seeks to understand its role in normal and diabetic states. Furthermore, antagonists of glucagon, acting at the glucagon receptor, have numerous applications for studying glucagons role in various physiological functions, and as a potential drug for the treatment of diabetes and diabetic syndromes. In this paper we will discuss research done over the last decade or so which has led to development of 1) the first pure glucagon receptor antagonists which have no partial agonist activity even at high concentrations and under conditions where the cAMP signal is greatly enhanced; 2) systematic studies of glucagon structure-function which have greatly extended our knowledge of those amino acids in glucagon which are most responsible for high affinity binding; 3) residues most important for agonist and for antagonist biological activities; 4) the first highly truncated analogues of glucagon which possess high affinity for the glucagon receptor and are antagonists; 5) cyclic analogues of glucagon which provide insight in the role of α-helix and β-turn structures in the binding affinity of glucagon to its receptor; 6) the first glucagon analogues with subnanomolar binding at the glucagon receptor; and 7) insights into those stereostructural properties which are different in agonist and antagonist analogues. We also discuss conformational studies which have been performed on glucagon and its agonist and antagonist analogues using various biophysical methods including NMR, X-ray crystallography and circular dichroism spectroscopy. Finally we briefly discuss the uses of glucagon analogues, especially glucagon antagonists, in examining the mechanisms and roles of glucagon in normal and diabetic states, and some aspects of the molecular biology of the glucagon receptor.
The incidence of thyroid disorders in the community: a twenty‐year follow‐up of the Whickham Survey (1995)

This historical cohort study has provided incidence data for thyroid disease over a twenty-year period for a representative cross-sectional sample of the population, and has allowed the determination of the importance of prognostic risk factors for thyroid disease identified twenty years earlier.
Batch ethanol fermentation: the correlation between the fermentation efficiency and the biomass initial concentration depends on what is considered as produced ethanol (2006)

Although numerous studies have examined many of the factors that affect the efficiency of batch ethanol fermentation, little attention has been paid to the influence of the biomass concentration on this efficiency. This paper shows that the influence of the biomass initial concentration on the fermentation efficiency depends on what is considered "produced ethanol". If only the ethanol present in the medium aqueous phase at fermentation completion is considered, the fermentation efficiency linearly decreases when the biomass initial concentration increases. If, however, the intracellular ethanol is also considered as produced ethanol, the fermentation efficiency is not affected by the biomass concentration.
Safety and Efficacy of the Terminal Complement Inhibitor Eculizumab in Patients with Paroxysmal Nocturnal Hemoglobinuria: Interim Shepherd Phase III Clinical Study. (2006)

Abstract In paroxysmal nocturnal hemoglobinuria (PNH), lack of the GPI-anchored terminal complement inhibitor CD59 from blood cells renders erythrocytes susceptible to chronic hemolysis resulting in anemia, fatigue, thrombosis, poor quality of life (QoL), and a dependency on transfusions. Eculizumab, a terminal complement inhibitor, reduced intravascular hemolysis and transfusion requirements in transfusion dependent patients with normal or near-normal platelet counts in a randomized placebo-controlled trial (TRIUMPH). SHEPHERD, an open-label, non-placebo controlled 52-week phase III clinical study, is underway to evaluate the safety and efficacy of eculizumab in a broader PNH population including patients with significant thrombocytopenia and/or lower transfusion requirements. Eculizumab was dosed as follows: 600 mg IV every 7 days x 4; 900 mg 7 days later; and then 900 mg every 14±2 days. Eculizumab was administered to 97 patients at 33 international sites. In a pre-specified 6-month interim analysis, the most frequent adverse events were headache (50%), nasopharyngitis (23%), and nausea (16%); most were mild to moderate in severity. No infections or serious adverse events were reported as “probably” or “definitely” related to drug. Intravascular hemolysis, the central clinical manifestation in PNH and the primary surrogate efficacy endpoint of the trial, was significantly reduced in eculizumab patients as assessed by change in lactate dehydrogenase (LDH) area under the curve (p&amp;lt;0.001). LDH levels decreased from a median of 2,051 U/L at baseline to 270 U/L at 26 weeks (p&amp;lt;0.001; normal range 103–223 U/L). Control of intravascular hemolysis resulted in an improvement in anemia as transfusion requirements decreased from a median of 4.0 PRBC units/patient pre-treatment to 0.0 during treatment (p&amp;lt;0.001), approximately 50% of the patients were rendered transfusion independent (P&amp;lt;0.001), and hemoglobin levels increased (p&amp;lt;0.001). Fatigue, as measured by both the FACIT-Fatigue and EORTC QLQ-C30 instruments, was significantly improved with eculizumab treatment as compared to baseline (p&amp;lt;0.001 for each). Other EORTC-QLQ-C30 patient reported outcomes demonstrating improvement included global health status (p&amp;lt;0.001), all 5 patient functioning subscales (p&amp;lt;0.001) and 7 of 9 symptom/single item subscales (p≤0.03). These results demonstrate that the beneficial effects of eculizumab in PNH are applicable to a much broader patient population than previously studied and further underscore that eculizumab treatment markedly reduces intravascular hemolysis, thereby providing clinical benefit to treated patients. The trial will complete in September 2006 and the final results from this 52-week study will be presented.
<title>Object-based deformation technique for 3D CT lung nodule detection</title> (1999)

Helical CT scans have shown effectiveness in detecting lung nodules compared with the convention thoracic radiography. However, in a two-dimensional (2-D) image slice, it is difficult to differentiate nodules from the vertically oriented pulmonary blood vessels. This paper reports an object-based deformation method to detect lung nodules from CT images in three-dimension (3-D). Object-based deformation method in this paper consists of preprocessing and nodule detection. CT numbers are used to identify the pulmonary region and the objects of nodules, blood vessels, and airways. Hough transform is used to identify each circle shape within the pulmonary region. The circles in the different slices are then grouped into the same nodule, airway, or blood to be a target object. To differentiate lung nodules from blood vessels and airways, we use a deformable seed object technique. For a given target object within the pulmonary region, the seed object grows within the target object until it is against the wall of the target object. The seed object is then deformed to match the target object. A cost function is used to match the seed object and the target object. Eight patient cases with 18 nodules were included in this study and the average size of the nodules was 2.4 cm approximately.
Programming semantics for multiprogrammed computations (1966)

The semantics are defined for a number of meta-instructions which perform operations essential to the writing of programs in multiprogrammed computer systems. These meta-instructions relate to parallel processing, protecting of separate computations, program debugging, and the sharing among users of memory segments and other computing objects, the names of which are hierarchically structured. The language sophistication contemplated is midway between an assembly language and an advanced algebraic language.
Interleukin-6 as a Therapeutic Target in Human Ovarian Cancer (2011)

IL-6 stimulates inflammatory cytokine production, tumor angiogenesis, and the tumor macrophage infiltrate in ovarian cancer and these actions can be inhibited by a neutralizing anti-IL-6 antibody in preclinical and clinical studies.
Interlaboratory Standardization of the Sandwich Enzyme-Linked Immunosorbent Assay Designed for MATS, a Rapid, Reproducible Method for Estimating the Strain Coverage of Investigational Vaccines (2012)

The meningococcal antigen typing system (MATS) sandwich enzyme-linked immunosorbent assay (ELISA) was designed to measure the immunologic cross-reactivity and quantity of antigens in target strains of a pathogen. It was first used to measure the factor H-binding protein (fHbp), neisserial adhesin A (NadA), and neisserial heparin-binding antigen (NHBA) content of serogroup B meningococcal (MenB) isolates relative to a reference strain, or "relative potency" (RP). With the PorA genotype, the RPs were then used to assess strain coverage by 4CMenB, a multicomponent MenB vaccine. In preliminary studies, MATS accurately predicted killing in the serum bactericidal assay using human complement, an accepted correlate of protection for meningococcal vaccines. A study across seven laboratories assessed the reproducibility of RPs for fHbp, NadA, and NHBA and established qualification parameters for new laboratories. RPs were determined in replicate for 17 MenB reference strains at laboratories A to G. The reproducibility of RPs among laboratories and against consensus values across laboratories was evaluated using a mixed-model analysis of variance. Interlaboratory agreement was very good; the Pearson correlation coefficients, coefficients of accuracy, and concordance correlation coefficients exceeded 99%. The summary measures of reproducibility, expressed as between-laboratory coefficients of variation, were 7.85% (fHbp), 16.51% (NadA), and 12.60% (NHBA). The overall within-laboratory measures of variation adjusted for strain and laboratory were 19.8% (fHbp), 28.8% (NHBA), and 38.3% (NadA). The MATS ELISA was successfully transferred to six laboratories, and a further laboratory was successfully qualified.
Complete heart block and sudden death in mice overexpressing calreticulin (2001)

The expression of calreticulin, a Ca(2+)-binding chaperone of the endoplasmic reticulum, is elevated in the embryonic heart, and because of impaired cardiac development, knockout of the Calreticulin gene is lethal during embryogenesis. The elevated expression is downregulated after birth. Here we have investigated the physiological consequences of continued high expression of calreticulin in the postnatal heart, by producing transgenic mice that overexpress the protein in the heart. These transgenic animals exhibit decreased systolic function and inward I(Ca,L), low levels of connexin43 and connexin40, sinus bradycardia, and prolonged atrioventricular (AV) node conduction followed by complete heart block and sudden death. We conclude that postnatal downregulation of calreticulin is essential in the development of the cardiac conductive system, in particular in the sinus and AV nodes, when an inward Ca(2+) current is required for activation. This work identifies a novel pathway of events, leading to complete heart block and sudden cardiac death, which involves high expression of calreticulin in the heart.
Experiences with an Efficient Rate Management Approach for the 8th Tortonian Reservoir in the Vienna Basin (2013)

Abstract Active well rate management is a simple way to increase recovery in brown fields while minimizing costs and preserving existing field/well fluid handling constraints. In this work, we present the application of an efficient flow-based surveillance technique to drive rate management decisions for the 8th Tortonian reservoir in the Vienna Basin, Austria. The 8th Tortonian is a typical example of a decade-long peripheral water flood on a long, steady decline for which it is difficult to justify expensive drilling/workover programs. Active rate management to improve sweep patterns presents a cheap solution to increase recovery. In case of the 8th Tortonian, Euro 10,000 (US$13,000) were spent to modify well rates resulting in ∼5700 m³ (∼35000 STB) incremental oil recovered over a 30-month period. The current oil rate remains above the oil rate before the start of the project. Our approach takes advantage of streamline-derived well allocation factors (WAF's) that quantify injector-producer connections. It is simple and efficient to estimate WAF's using total historical well fluid rates, well locations, and a geological model. The geological model can vary in complexity from being a single homogenous layer to a sophisticated, 3D geo-model. With the WAF's known, the efficiency of each injector/producer pair can be estimated by using the historical observed phase rates times the well allocation factors. Well pair efficiencies are the starting point for the rate management approach described in this work. A simple, single homogenous layer system was used in conjunction with historical rates and well locations to estimate the WAF's for the 8th Tortonian reservoir. Connections were compared to available tracer data, and an area of interest was subsequently selected based on streamlines and tracer data both indicating recovery by injected water. A key constraint was to maintain the total gross rate of the area selected at current capacity. New target rates we determined and implemented resulting in a 30% increase of oil rate over a 30 month period. Considering the simplicity and efficiency of the approach, this is a notable result. The production response of the selected wells showed an increased recovery in conjunction with a decreasing watercut suggesting contact with previously unswept oil. All operations and modifications were done at minimum cost. There were no perforation changes or acidizing jobs involved and rate changes were obtained simply by changing pump sizes or increasing the number of strokes by changing the V-belt pulley.
A Phosphine‐Mediated Conversion of Azides into Diazo Compounds (2008)

N2 the mild: Diazo compounds are extremely versatile intermediates for synthetic organic chemistry, but their synthesis can be challenging in the presence of delicate functional groups. The Staudinger ligation has inspired a mild method for the conversion of a broad range of azides into their diazo compound derivatives through an acyl triazene intermediate.
A Composite Kernel Approach for Dialog Topic Tracking with Structured Domain Knowledge from Wikipedia (2014)

Dialog topic tracking aims at analyzing and maintaining topic transitions in ongoing dialogs. This paper proposes a composite kernel approach for dialog topic tracking to utilize various types of domain knowledge obtained from Wikipedia. Two kernels are defined based on history sequences and context trees constructed based on the extracted features. The experimental results show that our composite kernel approach can significantly improve the performances of topic tracking in mixed-initiative human-human dialogs.