gebhart/patrepeval huggingface dataset:
Screening for sexually transmitted diseases and hepatitis in 18–29-year-old men recently released from prison: feasibility and acceptability (2005)

Men entering prisons have high rates of sexually transmitted disease (STD), hepatitis, and HIV. This study sought to determine the acceptability and feasibility of screening for STD and hepatitis in young men released from prison. Participants were interviewed six months after release and offered free screening. Of 42 (56%) eligible men who participated in the qualitative interview, 33 (79%) provided at least a blood or urine specimen. Eight of 33 (24%) men tested had chlamydia, trichomoniasis, hepatitis B or C virus (HBV or HCV). Three of 32 (9%) had chlamydia, three of 32 (9%) had trichomoniasis, two of 28 (7%) had prior syphilis, and two of 28 (7%) had HCV. Of 28 tested for HBV, six (21%) were immune, two (7%) had chronic infection, and 20 (71%) were susceptible. Barriers to screening included lack of forewarning, inconvenience, and insufficient incentive. In conclusion, screening for STD and hepatitis among former inmates can be acceptable and feasible. Forewarning, reducing the time burden, and providing monetary incentives may increase screening rates.
Single-molecule PCR: an artifact-free PCR approach for the analysis of somatic mutations (2005)

A critical review of the clone-by-clone approach to the analysis of complex spectra of somatic mutations is presented. The study of a priori unknown somatic mutations requires painstaking analysis of complex mixtures of multiple mutant and non-mutant DNA molecules. If mutant fractions are sufficiently high, these mixtures can be dissected by the cloning of individual DNA molecules and scanning of the individual clones for mutations (e.g., by sequencing). Currently, the majority of such cloning is performed using PCR fragments. However, post-PCR cloning may result in various PCR artifacts - PCR errors and jumping PCR - and preferential amplification of certain mutations. This review argues that single-molecule PCR is a simple alternative that promises to evade the disadvantages inherent to post-PCR cloning and enhance mutational analysis in the future.
Changes in cell surface antigen expressions during proliferation and differentiation of human erythroid progenitors (1992)

Abstract Cell surface antigen expression during proliferation and differentiation of human erythroid progenitors was examined using a combination of sequential micromanipulations of paired daughter cells derived from erythroid burst-forming units (BFU-E) and immuno-staining with a panel of monoclonal antibodies. Single hematopoietic progenitors were identified in methylcellulose cultures containing human cord blood mononuclear cells and micromanipulated individually to secondary culture. Paired daughter cells, granddaughter cells, and subsequent generations, whose counterparts produced erythroid bursts, were stained with various cytochemical and immuno-alkaline phosphatase stainings. Most paired daughter cells of BFU-E immunostained positively with anti- platelet glycoprotein(GP) IIb, antiplatelet GPIIb/IIIa, anti-HLA-DR, and antitransferrin receptor antibodies. Acid phosphatase staining was also positive. Neither CD34 nor CD33 antigens were identified on the cells. CD36 and blood group A antigens were first identified on cells from aggregates containing 32 to 64 cells after 4 days of secondary culture and preceded the expression of glycophorin A and hemoglobin alpha. These results indicate that various cell surface antigens were sequentially expressed during the proliferation and differentiation of erythroid progenitors, and that our procedure may be useful for clarifying the morphologic and immunologic properties of hematopoietic stem cells.
Oseltamivir- and Amantadine-Resistant Influenza Viruses A (H1N1) (2009)

Surveillance of amantadine and oseltamivir resistance among influenza viruses was begun in Hong Kong in 2006. In 2008, while both A/Brisbane/59/2007-like and A/Hong Kong/2652/2006-like viruses (H1N1) were cocirculating, we detected amantadine and oseltamivir resistance among A/Hong Kong/2652/2006-like viruses (H1N1), caused by genetic reassortment or spontaneous mutation.
Prolonged activity of factor IX as a monomeric Fc fusion protein (2010)

Treatment of hemophilia B requires frequent infusions of factor IX (FIX) to prophylax against bleeding episodes. Hemophilia B management would benefit from a FIX protein with an extended half-life. A recombinant fusion protein (rFIXFc) containing a single FIX molecule attached to the Fc region of immunoglobulin G was administered intravenously and found to have an extended half-life, compared with recombinant FIX (rFIX) in normal mice, rats, monkeys, and FIX-deficient mice and dogs. Recombinant FIXFc protein concentration was determined in all species, and rFIXFc activity was measured in FIX-deficient animals. The half-life of rFIXFc was approximately 3- to 4-fold longer than that of rFIX in all species. In contrast, in mice in which the neonatal Fc receptor (FcRn) was deleted, the half-life of rFIXFc was similar to rFIX, confirming the increased circulatory time was due to protection of the rFIXFc via the Fc/FcRn interaction. Whole blood clotting time in FIX-deficient mice was corrected through 144 hours for rFIXFc, compared with 72 hours for rFIX; similar results were observed in FIX-deficient dogs. Taken together, these studies show the enhanced pharmacodynamic and pharmacokinetic properties of the rFIXFc fusion protein and provide the basis for evaluating rFIXFc in patients with hemophilia B.
Biosynthesis and postsynthetic processing of human C-reactive protein. (1983)

Human C-reactive protein (CRP) is one of several plasma proteins that increase after tissue injury or inflammation. The magnitude of the increase in CRP (100 to 1000-fold over the resting state) makes this an excellent model for studies of eukaryotic gene control. Accordingly, the biosynthesis and postsynthetic processing of human CRP was examined under cellfree conditions and in Xenopus oocytes injected with liver mRNA. The primary translation product is larger than native serum CRP by an 18-amino acid amino terminal extension. The sequence of this signal peptide was derived from nucleotide sequencing of a 1.8-kilobase (Kb) CRP-specific cDNA clone. Northern blot analysis revealed a CRP mRNA of approximately 2.2 Kb, a size more than three times that required (615 bases) to code for the primary translation product. These data form the basis for study of molecular control of the acute phase response.
Pathogenesis of septic shock in Pseudomonas aeruginosa pneumonia (1999)

The pathogenesis of septic shock occurring after Pseudomonas aeruginosa pneumonia was studied in a rabbit model. The airspace instillation of the cytotoxic P. aeruginosa strain PA103 into the rabbit caused a consistent alveolar epithelial injury, progressive bacteremia, and septic shock. The lung instillation of a noncytotoxic, isogenic mutant strain (PA103DeltaUT), which is defective for production of type III secreted toxins, did not cause either systemic inflammatory response or septic shock, despite a potent inflammatory response in the lung. The intravenous injection of PA103 did not cause shock or an increase in TNF-alpha, despite the fact that the animals were bacteremic. The systemic administration of either anti-TNF-alpha serum or recombinant human IL-10 improved both septic shock and bacteremia in the animals that were instilled with PA103. Radiolabeled TNF-alpha instilled in the lung significantly leaked into the circulation only in the presence of alveolar epithelial injury. We conclude that injury to the alveolar epithelium allows the release of proinflammatory mediators into the circulation that are primarily responsible for septic shock. Our results demonstrate the importance of compartmentalization of inflammatory mediators in the lung, and the crucial role of bacterial cytotoxins in causing alveolar epithelial damage in the pathogenesis of acute septic shock in P. aeruginosa pneumonia.
Airborne measurements of peroxy radicals using the PERCA technique (2002)

The Peroxy Radical Chemical Amplifier (PERCA) technique is a proven method for measurement of ambient levels of peroxy radicals at ground level, but there are no published instances of the technique being used on an aerial platform. Here we describe deployment of a PERCA on the former UK Meteorological Office C-130 Hercules research aircraft. The instrument uses the established method of chemical amplification and conversion of peroxy radicals to nitrogen dioxide (NO2) by doping the sample air-flow matrix with CO and NO, subsequently measuring the NO2 yield with an improved 'Luminox' LMA-3 NO2 detector. NO2 from the amplification chemistry is distinguished from other sources of NO2 reaching the detector by periodically injecting CO approximately 1 s downstream of the NO injection point (termination mode). Chain lengths (CL's) for the amplification chemistry were typically approximately 260 (ground level) to approximately 200 (7,000 m). This variation with altitude is less than the variation associated with the 'age' of the PFA inlet material where the amplification chemistry occurs; CL's of approximately 200 with old tubing to approximately 300 with new clean tubing were typical (ground level values). The CL determinations were made in-flight using an onboard calibration unit based on the 254 nm photolysis of 7.5 to 10 parts per billion (by volume, ppbv) of CH3I in air, producing CH3O2 in a quantitative manner. The noise-equivalent detection limit for peroxy radicals (HO2 + RO2) is 2 parts per trillion (by volume, pptv) at 3,650 m when the background ambient ozone levels are stable, based on a 5 min average of five 30 s amplification cycles and five 30 s termination cycles. This detection limit is a function of several factors but is most seriously degraded when there is large variability in the ambient ozone concentration. This paper describes the instrument design, considers its performance and proposes design improvements. It concludes that the performance of an airborne PERCA in the free troposphere can be superior to that of ground-based instruments when similar sampling frequencies are compared.
Synthesis and Optical Properties of Silver Nanoparticles and Arrays (2005)

This Minireview systematically examines optical properties of silver nanoparticles as a function of size. Extinction, scattering, and absorption cross-sections and distance dependence of the local electromagnetic field, as well as the quadrupolar coupling of 2D assemblies of such particles are experimentally measured for a wide range of particle sizes. Such measurements were possible because of the development of a novel synthetic method for the size-controlled synthesis of chemically clean, highly crystalline silver nanoparticles of narrow size distribution. The method and its unique advantages are compared to other methods for synthesis of metal nanoparticles. Synthesis and properties of nanocomposite materials using these and other nanoparticles are also described. Important highlights in the history of the field of metal nanoparticles as well as an examination of the basic principles of plasmon resonances are included.
La genèse du cimetière médiéval urbain : l’exemple de la topographie funéraire de Toulouse (vers 250-1350) (1999)

This article proposes to study the genesis of the medieval cemetery in the concrete case of Toulouse. This is a long-term process. The evolution of the topography of burial places from Antiquity to the Middle Ages allows new questions on the medieval city during the early Middle Ages, notably those that concern the birth of the medieval parish community and the emergence of the ecclesiastical topography.
Oral laquinimod in patients with relapsing-remitting multiple sclerosis: 36-week double-blind active extension of the multi-centre, randomized, double-blind, parallel-group placebo-controlled study (2010)

The good efficacy and the excellent safety and tolerability profiles of laquinimod 0.6 mg/day are confirmed in this extension study.
Touch screens now offer compelling uses (1991)

Research on improving the user interfaces of touch screen applications is described. The advantages of touch screens are discusses, their current capabilities are examined, and possible future developments are considered.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Silicon UTSi/sup (R)/ CMOS RFIC for CDMA wireless communications systems (2003)

Design and performance of UTSi CMOS down converter RFIC for CDMA applications is presented. The down converter consists of a two-stage LNA, RF switch, and mixer integrated with passive matching components. Performance of building blocks have been evaluated. Results show that the stringent requirements for linearity at low power consumption required for CDMA can be achieved using UTSi CMOS technology. By integrating the down converter with PLL fabricated in the same process, it will be possible to realize a single chip transceiver IC. Results show that silicon CMOS UTSi has the on-chip RF performance required for high level of integration of future wireless communications systems.
Crystal Structures of Oxidized and Reduced Stellacyanin from Horseradish Roots (2004)

Umecyanin (UMC) is a type 1 copper-containing protein which originates from horseradish roots and belongs to the stellacyanin subclass of the phytocyanins, a ubiquitous family of plant cupredoxins. The crystal structures of Cu(II) and Cu(I) UMC have been determined at 1.9 and 1.8 A, respectively. The protein has an overall fold similar to those of other phytocyanins. At the active site the cupric ion is coordinated by the N(delta1) atoms of His44 and His90, the S(gamma) of Cys85, and the O(epsilon)(1) of Gln95 in a distorted tetrahedral geometry. Both His ligands are solvent exposed and are surrounded by nonpolar and polar side chains on the protein surface. Thus, UMC does not possess a distinct hydrophobic patch close to the active site in contrast to almost all other cupredoxins. UMC has a large surface acidic patch situated approximately 10-30 A from the active site. The structure of Cu(I) UMC is the first determined for a reduced phytocyanin and demonstrates that the coordination environment of the cuprous ion is more trigonal pyramidal. This subtle change in geometry is primarily due to the Cu-N(delta1)(His44) and Cu-O(epsilon1)(Gln95) bond lengths increasing from 2.0 and 2.3 A in Cu(II) UMC to 2.2 and 2.5 A, respectively, in the reduced form, as a consequence of slight rotations of the His44 and Gln95 side chains. The limited structural changes upon redox interconversion at the active site of this stellacyanin are analogous to those observed in a typical type 1 copper site with an axial Met ligand and along with its surface features suggest a role for UMC in interprotein electron transfer.
Genetic and biochemical characterization of a new extracellular lipase from Streptomyces cinnamomeus (1997)

Streptomyces cinnamomeus Tü89 secretes a 30-kDa esterase and a 50-kDa lipase. The lipase-encoding gene, lipA, was cloned from genomic DNA into Streptomyces lividans TK23 with plasmid vector pIJ702. Two lipase-positive clones were identified; each recombinant plasmid had a 5.2-kb MboI insert that contained the complete lipA gene. The two plasmids differed in the orientation of the insert and the degree of lipolytic activity produced. The lipA gene was sequenced; lipA encodes a proprotein of 275 amino acids (29,213 Da) with a pI of 5.35. The LipA signal peptide is 30 amino acids long, and the mature lipase sequence is 245 amino acids long (26.2 kDa) and contains six cysteine residues. The conserved catalytic serine residue of LipA is in position 125. Sequence similarity of the mature lipases (29% identity, 60% similarity) was observed mainly in the N-terminal 104 amino acids with the group II Pseudomonas lipases; no similarity to the two Streptomyces lipase sequences was found. lipA was also expressed in Escherichia coli under the control of lacZ promoter. In the presence of the inducer isopropyl-beta-D-thiogalactopyranoside (IPTG), growth of the E. coli clone was severely affected, and the cells lysed in liquid medium. Lipase activity in the E. coli clone was found mainly in the pellet fraction. In sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis, three additional protein bands of 50, 29, and 27 kDa were visible. The 27-kDa protein showed lipolytic activity and represents the mature lipase; the 29- and 50-kDa forms showed no activity and very probably represent the unprocessed form and a dimeric misfolded form, respectively. For higher expression of lipA in S. lividans, the gene was cloned next to the strong aphII promoter. In contrast to the lipA-expressing E. coli clone, S. cinnamomeus and the corresponding S. lividans clone secreted only an active protein of 50 kDa. The lipase showed highest activity with C6 and C18 triglycerides; no activity was observed with phospholipids, Tween 20, or p-nitrophenylesters. Upstream of lipA and in the same orientation, an open reading frame, orfA, is found whose deduced protein sequence (519 amino acids) shows similarity to various membrane-localized transporters. Downstream of lipA and in the opposite orientation, an open reading frame, orfB (encoding a 199-amino-acid protein) is found, which shows no conspicuous sequence similarity to known proteins, other than an NAD and flavin adenine dinucleotide binding-site sequence.
Determinants of Gastroesophageal Junction Incompetence: Hiatal Hernia, Lower Esophageal Sphincter, or Both? (1992)

Gastroesophageal junction competence during abrupt increases in intra-abdominal pressure is compromised by both hiatal hernia and low LES pressure. These factors interact with each other to determine susceptibility to reflux.
Probabilistic palm rejection using spatiotemporal touch features and iterative classification (2014)

Tablet computers are often called upon to emulate classical pen-and-paper input. However, touchscreens typically lack the means to distinguish between legitimate stylus and finger touches and touches with the palm or other parts of the hand. This forces users to rest their palms elsewhere or hover above the screen, resulting in ergonomic and usability problems. We present a probabilistic touch filtering approach that uses the temporal evolution of touch contacts to reject palms. Our system improves upon previous approaches, reducing accidental palm inputs to 0.016 per pen stroke, while correctly passing 98% of stylus inputs.
Gold Nanorod Based Selective Identification of Escherichia coli Bacteria Using Two-Photon Rayleigh Scattering Spectroscopy (2009)

The presence of E. coli in foodstuffs and drinking water is a chronic worldwide problem. The worldwide food production industry is worth about U.S. $578 billion, and the demand for biosensors to detect pathogens and pollutants in foodstuffs is growing day by day. Driven by the need, we report for the first time that two-photon Rayleigh scattering (TPRS) properties of gold nanorods can be used for rapid, highly sensitive and selective detection of Escherichia coli bacteria from aqueous solution, without any amplification or enrichment in 50 colony forming units (cfu)/mL level with excellent discrimination against any other bacteria. TPRS intensity increases 40 times when anti- E. coli antibody-conjugated nanorods were mixed with various concentrations of Escherichia coli O157:H7 bacterium. The mechanism of TPRS intensity change has been discussed. This bionanotechnology assay could be adapted in studies using antibodies specific for various bacterial pathogens for the detection of a wide variety of bacterial pathogens used as bioterrorism agents in food, clinical samples, and environmental samples.
The Transcriptional Regulator Np20 Is the Zinc Uptake Regulator in Pseudomonas aeruginosa (2013)

Zinc is essential for all bacteria, but excess amounts of the metal can have toxic effects. To address this, bacteria have developed tightly regulated zinc uptake systems, such as the ZnuABC zinc transporter which is regulated by the Fur-like zinc uptake regulator (Zur). In Pseudomonas aeruginosa, a Zur protein has yet to be identified experimentally, however, sequence alignment revealed that the zinc-responsive transcriptional regulator Np20, encoded by np20 (PA5499), shares high sequence identity with Zur found in other bacteria. In this study, we set out to determine whether Np20 was functioning as Zur in P. aeruginosa. Using RT-PCR, we determined that np20 (hereafter known as zur) formed a polycistronic operon with znuC and znuB. Mutant strains, lacking the putative znuA, znuB, or znuC genes were found to grow poorly in zinc deplete conditions as compared to wild-type strain PAO1. Intracellular zinc concentrations in strain PAO-Zur (Δzur) were found to be higher than those for strain PAO1, further implicating the zur as the zinc uptake regulator. Reporter gene fusions and real time RT-PCR revealed that transcription of znuA was repressed in a zinc-dependent manner in strain PAO1, however zinc-dependent transcriptional repression was alleviated in strain PAO-Zur, suggesting that the P. aeruginosa Zur homolog (ZurPA) directly regulates expression of znuA. Electrophoretic mobility shift assays also revealed that recombinant ZurPA specifically binds to the promoter region of znuA and does not bind in the presence of the zinc chelator N,N',N-tetrakis(2-pyridylmethyl) ethylenediamine (TPEN). Taken together, these data support the notion that Np20 is the P. aeruginosa Zur, which regulates the transcription of the genes encoding the high affinity ZnuABC zinc transport system.
AGL24 acts as a promoter of flowering in Arabidopsis and is positively regulated by vernalization (2003)

MADS-domain-containing transcription factors comprise a large family of regulators that have diverse roles in plant development, including the regulation of flowering time. AGAMOUS-LIKE 20/SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1) and FRUITFUL act to promote flowering, whereas FLOWERING LOCUS C (FLC), FLOWERING LOCUS M/MADS AFFECTING FLOWERING1, and SHORT VEGETATIVE PHASE are inhibitors of flowering. Here we report that AGAMOUS-LIKE 24 (AGL24) also plays a role in the regulation of flowering time. agl24 mutants are late flowering and overexpression of AGL24 causes early flowering in wild-type and late-flowering-mutant backgrounds. The effect of AGL24 overexpression is most pronounced in autonomous-pathway-mutant and FRIGIDA-containing backgrounds. The behavior of AGL24 is most similar to that of SOC1. Like SOC1, AGL24 mRNA levels are upregulated by vernalization. Unlike SOC1, however, AGL24 mRNA levels are not affected by FLC, and therefore AGL24 may represent an FLC-independent target of the vernalization pathway. There is also evidence for cross-talk between AGL24 and SOC1. When overexpressed, SOC1 and AGL24 are able to upregulate each other's expression. Thus, AGL24 represents another component in a network of MADS-domain-containing transcription factors that regulate flowering time.
Isolation of a novel candidate oncogene within a frequently amplified region at 3q26 in ovarian cancer. (2001)

Amplification of 3q25-q26 was one of the most frequent chromosomal alterations in human ovarian carcinoma. A chromosome microdissection-hybrid selection method was applied to isolate transcribed sequences from a primary ovarian cancer containing high-copy-number amplification of 3q26 using 3q26 band-specific DNAs generated by chromosome microdissection. Using this method, we have isolated a novel candidate oncogene eIF-5A2 (eukaryotic initiation factor 5A2). eIF-5A2 shares 82% identity of amino acid sequence with eIF-5A including the minimum domain needed for eIF-5A maturation by hypusine modification at lysine-50 residue. Amplification and overexpression of eIF-5A2 was frequently detected in primary ovarian cancers and ovarian cancer cell lines. The proliferation-related function of eIF-5A supports that eIF-5A2 is a candidate oncogene related to the development of ovarian cancer.