gebhart/patrepeval huggingface dataset:
Identification of genes involved in the switch between the smooth and rugose phenotypes of<i>Vibrio cholerae</i> (2003)

Vibrio cholerae can switch to a 'rugose' phenotype characterized by an exopolysaccharide (EPS) matrix, wrinkled colony morphology, increased biofilm formation and increased survival under specific conditions. The vps gene cluster responsible for the biosynthesis of the rugose EPS (rEPS) is positively regulated by VpsR. We recently identified media (APW#3) promoting EPS production and the rugose phenotype and found epidemic strains switch at a higher frequency than non-pathogenic strains, suggesting this switch and the rugose phenotype are important in cholera epidemiology. In this study, transposon mutagenesis on a smooth V. cholerae strain was used to identify mutants that were unable to shift to the rugose phenotype under inducing conditions to better understand the molecular basis of the switch. We identified vpsR, galE and vps previously associated with the rugose phenotype, and also identified genes not previously associated with the phenotype, including rfbD and rfbE having roles in LPS (lipopolysaccharide) synthesis and aroB and aroK with roles in aromatic amino acid synthesis. Additionally, a mutation in amiB encoding N-acetylmuramoyl-L-alanine amidase caused defects in the switch, motility and cell morphology. We also found that a gene encoding a novel regulatory protein we termed RocS (regulation of cell signaling) containing a GGDEF and EAL domains and associated with c-di-GMP levels is important for the rugose phenotype, EPS, biofilm formation and motility. We propose that modulation of cyclic dinucleotide (e.g. c-di-GMP) levels might have application in regulating various phenotypes of prokaryotes. Our study shows the molecular complexity of the switch between the smooth and rugose phenotypes of V. cholerae and may be relevant to similar phenotypes in other species.
Surface immobilization chemistry influences peptide‐based detection of lipopolysaccharide and lipoteichoic acid (2012)

Antimicrobial peptides (AMPs) have recently gained attention as potentially valuable diagnostic and therapeutic agents. The utilization of these peptides for diagnostic purposes relies on the ability to immobilize them on the surface of a detection platform in a predictable and reliable manner that facilitates target binding. The method for attachment of peptides to a solid support is guided by peptide length, amino acid composition, secondary structure, and the nature of the underlying substrate. While immobilization methods that target amine groups of amino acid sequences are widely used, they can result in heterogeneous conjugation at multiple sites on a peptide and have direct implications for peptide presentation and function. Using two types of commercial amine-reactive microtiter plates, we described the effects of analogous immobilization chemistries on the surface attachment of AMPs and their differential binding interaction with Gram-specific bacterial biomarkers, lipopolysaccharide and lipoteichoic acid. As might be expected, differences in overall binding affinities were noted when comparing AMPs immobilized on the two types of plates. However, the two-amine-targeted linking chemistries also affected the specificity of the attached peptides; lipopolysaccharide generally demonstrated a preference for peptides immobilized on one type of plate, while (when observed at all) lipoteichoic acid bound preferentially to AMPs immobilized on the other type of plate. These results demonstrate the potential for tuning not only the binding affinities but also the specificities of immobilized AMPs by simple alterations in linking strategy.
Effect in Man of Anti‐Allergic Drugs on the Immediate and Late Phase Cutaneous Allergic Reactions Induced by Anti‐IgE (1981)

Wheal and flare reactions as well as a late cutaneous allergic reaction (LCAR) were induced by anti-human IgE in healthy subjects. The effect of the beta 2-adrenoceptor stimulant terbutaline, the histamine-1 (H1) receptor blocking agent mepyramine and the synthetic glucocorticoid betamethasone on these reactions was studied. All administrations were given intradermally (i.d.). The immediate reaction to anti-IgE was inhibited by 3 micrograms terbutaline and 30 micrograms mepyramine (P less than 0.01) whereas 50 micrograms betamethasone had no effects. Terbutaline had no effect on the flare response induced by i.d. injected histamine but a slight effect on whealing. Terbutaline and mepyramine weakly reduced the LCAR throughout the observation period of 24 h (P less than 0.01). In contrast, betamethasone almost completely abolished the LCAR. It is concluded that the two phases of the skin reaction to anti-IgE are interrelated since an inhibition of the early phase was followed by an attenuation of the LCAR. The mechanism of action of steroids seems to differ fundamentally from that of other anti-allergic drugs since inhibition of the early step in the reaction is not essential to the action on the late step. It is further suggested that terbutaline inhibits anti-IgE-mediated cutaneous reactions by inhibition of the mast cell release reaction.
The Natural History of Fetomaternal Alloimmunization to the Platelet-Specific Antigen HPA-1a (PlA1, Zwa) as Determined by Antenatal Screening (1998)

Immunization against the human platelet antigen (HPA)-1 alloantigen is the most common cause of severe fetal and neonatal thrombocytopenia. Fetal therapy has substantial risks and its indications need better definition. Of 24,417 consecutive pregnant women, 618 (2.5%) were HPA-1a negative of whom 385 entered an observational study. All were HLA-DRB3*0101 genotyped and screened for anti–HPA-1a. Their partners and neonates were HPA-1 genotyped and the latter were assessed by cord blood platelet counts and cerebral ultrasound scans. Anti–HPA-1a was detected in 46 of 387 pregnancies (12.0%; 95% CI 8.7%-15.2%). All but one were HLA-DRB3*0101 positive (odds ratio 140; 95% CI 19-1035;P< .00001). One baby died in utero, and of 26 HPA-1a–positive babies born to women with persistent antenatal antibodies, 9 were severely thrombocytopenic (8 with a count <10 × 109/L, 1 with a large porencephalic cyst), 10 were mildly thrombocytopenic, whereas 7 had normal platelet counts. Severe thrombocytopenia was significantly associated with a third trimester anti–HPA-1a titer ≥ 1:32 (P = .004), but was not observed in babies of women with either transient or postnatal-only antibodies. HPA-1a alloimmunization complicates 1 in 350 unselected pregnancies, resulting in severe thrombocytopenia in 1:1,200. HPA-1a and HLA-DRB3*0101 typing combined with anti–HPA-1a titration allows selection of the majority of pregnancies at risk of severe thrombocytopenia.
Molecular caps for full quantum mechanical computation of peptide–water interaction energy (2003)

We present a systematic study of numerical accuracy of various forms of molecular caps that are employed in a recently developed molecular fractionation scheme for full quantum mechanical computation of protein-molecule interaction energy. A previously studied pentapeptide (Gly-Ser-Ala-Asp-Val) or P5 interacting with a water molecule is used as a benchmark system for numerical testing. One-dimensional potential energy curves are generated for a number of peptide-water interaction pathways. Our study shows that various forms of caps all give consistently accurate energies compared to the corresponding full system calculation with only small deviations. We also tested the accuracy of cutting peptide backbone at different positions and comparisons of results are presented.
An Automated Tool for Scoring Biomedical Terms Correlation Based on Semantic Analysis (2010)

The considerable improvement in the biotechnogical field and the adoption of screen techniques such as high throughput arrays produced a spread of biological and genetical data and scientific papers, mostly diffused on the Web. Even if the huge amount of available information represents a major step forward for the biomedical research field, the main effort for a scientist is to evaluate the correlation among the concepts both in qualitative and in quantitative terms. In the presented work, exploiting the richness of the UMLS Metathesaurus in combination with the novelty of the literature provided by PubMed, an automatic flow aimed at the scoring the semantic correlation among biomedical terms (e. g. biomolecules and biological processes) is proposed. The experiments show that obtained correlations are fully coherent with the information coming from the biological literature. The accuracy of the results remarks the importance of combining text mining techniques with complete and well structured thesaurus, such as UMLS.
STAT4 Is a Critical Mediator of Early Innate Immune Responses against Pulmonary <i>Klebsiella</i> Infection (2004)

Bacterial pneumonia is a leading cause of morbidity and mortality in the U.S. An effective innate immune response is critical for the clearance of bacteria from the lungs. IL-12, a key T1 cytokine in innate immunity, signals through STAT4. Thus, understanding how STAT4 mediates pulmonary immune responses against bacterial pathogens will have important implications for the development of rational immunotherapy targeted at augmenting innate immunity. We intratracheally administered Klebsiella pneumoniae to wild-type BALB/c and STAT4 knockout (STAT4-/-) mice. Compared with wild-type controls, STAT4-/- mice had decreased survival following intratracheal Klebsiella administration, which was associated with a higher lung and blood bacterial burden. STAT4-/- animals also displayed impaired pulmonary IFN-gamma production and decreased levels of proinflammatory cytokines, including the ELR- CXC chemokines IFN-gamma-inducible protein-10 and monokine induced by IFN-gamma. Although total lung leukocyte populations were similar between STAT4-/- and wild-type animals following infection, alveolar macrophages isolated from infected STAT4-/- mice had decreased production of proinflammatory cytokines, including IFN-gamma, compared with infected wild-type mice. The intrapulmonary overexpression of IFN-gamma concomitant with the systemic administration of IFN-gamma partially reversed the immune deficits observed in STAT4-/- mice, resulting in improved bacterial clearance from the blood. Collectively, these studies demonstrate that STAT4 is required for the generation of an effective innate host defense against bacterial pathogens of the lung.
Comparison of human papillomavirus in situ hybridization and p16 immunohistochemistry in the detection of human papillomavirus‐associated head and neck cancer based on a prospective clinical experience (2010)

A feasible strategy that incorporates p16 IHC and HPV ISH is able to detect HPV in a high percentage of oropharyngeal carcinomas. HPV status is frequently requested by the oncologist to estimate clinical outcome, and used by pathologists to establish tumor classification and determine site of tumor origin.
JTAPI : Java Telephony API : Javaによるテレフォニアプリケーション開発 (1999)

第１部 テレコムプログラミング 第２部 テレフォニＡＰＩ 第３部 ＪＴＡＰＩの実装 第４部 ＪＴＡＰＩによるテレフォニプログラミング 第５部 実世界のテレフォニプログラミング 第６部 Ｊａｖａにおけるテレフォニプログラミングの将来
Effects of Topical Application of Betamethasone on Imiquimod-induced Psoriasis-like Skin Inflammation in Mice. (2016)

Psoriasis is a chronic inflammatory skin disease mediated by dysregulated auto-reactive immune system. In this study, in order to confirm and further extend the pharmacological basis of topical steroids in psoriasis therapy, we investigated the effect of betamethasone ointment on imiquimod (IMQ)-induced skin inflammation in mice. In BALB/c mice, topical IMQ at the dose of 250 µg each on both sides of the ear induced marked psoriasis-like skin inflammation within 5 days. The same dose of IMQ produced only slight to moderate skin inflammation even on Day 7 in CB-17 scid mice. IMQ-induced skin inflammation was associated with increased levels of mRNA transcripts expression of signature cytokines of T helper (Th)1/Th17 cells, i.e., interferon-γ, interleukin (IL)-17 and IL-22 on Day 5. In addition, levels of mRNA expression of the markers of keratinocytes, i.e., IL-1β, S100A8, and S100A9, were dramatically elevated in IMQ-treated mice. The IMQ-induced changes in cytokine expression were significantly suppressed by topical treatment with betamethasone ointment. IMQ failed to produce significant changes in the mRNA levels of tumor necrosis factor-α as a marker of macrophages and NK1.2 as a marker of natural killer cells and natural killer T cells. In contrast, mRNA level of a Th2 cytokine IL-13 was significantly decreased by IMQ treatment and further suppressed by betamethasone. These findings provide the first pharmacological evidence that the topical application of betamethasone prevents IMQ-induced psoriasis-like skin inflammation in mice by inhibiting gene expressions of various cytokines related to Th1 cells, Th17 cells and keratinocytes.
Subcritical (Hot/Liquid) Water Dechlorination of PCBs (Aroclor 1254) with Metal Additives and in Waste Paint (2003)

No disposal option exists for "mixed wastes" such as paint scrapings that are co-contaminated with polychlorinated biphenyls (PCBs) and radioactive metals. Either removal or destruction of the PCBs is required prior to disposal. Comparison of subcritical water dechlorination (350 degrees C, 1 h) of Aroclor 1254 in paint scrapings (180 ppm) and of standard Aroclor 1254 showed significantly enhanced dechlorination in the presence of paint. While no significant degradation was observed for standard Aroclor (no paint), the dechlorination of PCBs in paint was 99, 99, and 80% for the hepta-, hexa-, and pentachlorinated congeners, respectively, indicating that metals in the paint enhanced the dechlorination reactions. Adding metals to the standard Aroclor (no paint) reactions enhanced PCB dechlorination in subcritical water in descending order of activity: Pb approximately = Cu > Al > Zn > Fe. In the presence of both zerovalent and divalent lead and zerovalent copper in subcritical water (350 degrees C, 1 h), 99% of the Aroclor 1254 mixture (tetra- to heptachlorinated biphenyls) was dechlorinated. High dechlorination (ca. 95%) was also achieved with zerovalent aluminum. In contrast to other metals, lead retained its degradation ability at a lower temperature of 250 degrees C after 18 h. The high degradation efficiency achieved using metal additives in water at reasonable temperatures and pressures demonstrates the potential for subcritical water dechlorination of PCBs in paint scrapings and, potentially, in other solid and liquid wastes.
Serum cotinine as a biomarker of tobacco exposure and the association with treatment response in early rheumatoid arthritis (2012)

Among patients enrolled in a large randomized controlled trial of early RA with poor prognostic factors, smoking status did not impact treatment responses for those receiving early combination or initial MTX with step-up therapy at 24 weeks if the disease was still active.
Yarning: A responsive research methodology (2004)

This paper explores 'yarning' as a research method which emerged in a cross-cultural PhD as a means of building a research partnership between feminist and Indigenous leaders in early childhood education. This method created an avenue for the researcher, positioned as both insider and outsider, to hear and understand the voices ofthe Indigenous participants. This responsiveness became a strength of the research which enabled a profound, complex and subtle understanding to emerge across the contact zone (Pratt, 1992: 4) between academic research methods and Indigenous cultures, by bringing them into discursive relations with each other (Griffiths, 1998: 45).
Prolongation of life span of dystrophic hamster by cysteine proteinase inhibitor, loxistatin (EST). (1987)

We studied the effect of loxistation (EST), an orally applicable cysteine proteinase inhibitor, on dystrophic hamsters, UM-X7.1.E-64-c, an active form of EST, was continuously found in plasma when the feed containing EST was given ad libitum. The drug concentration in plasma of dystrophic hamsters receiving EST feed showed distinct dose dependency. A diet containing EST from weaning to death significantly prolonged the survival period of the dystrophic hamsters.
Inhibition of mouse GATA-1 function by the glucocorticoid receptor: possible mechanism of steroid inhibition of erythroleukemia cell differentiation. (1993)

Treatment of mouse erythroleukemia (MEL) cells with hexamethylene bisacetamide induces a program of erythrodifferentiation, as judged by an increase in the synthesis of globins and other erythroid-specific products. This induction can be inhibited by glucocorticoids, e.g. dexamethasone. All globin and other erythroid-specific genes tested contain GATA response elements (GATA-RE) and can be transactivated by GATA-1, a transcription factor. GATA-1 is highly expressed in erythroid cells, including MEL cells. We noted a glucocorticoid receptor (GR) response element motif near a GATA-RE motif in the promoter region of the mouse beta-major and beta-minor globin genes and about 130 bases away from a GATA-RE in the alpha 1-globin gene promoter and, therefore, investigated the possibility that the dexamethasone-induced inhibition of induced MEL cell differentiation may involve effects of the GR on GATA-1 activity. Evidence obtained from transfection assays and DNA electrophoretic mobility shift assays indicates that the GR binds GATA-1 and interferes with its function before any interaction with DNA, but that the presence of a glucocorticoid response element near a GATA-RE augments the GR effect. The N-terminal 106-amino acid domain of the GR was found to be essential for the effect, possibly by binding to GATA-1. Since GATA-1 is autoregulatory, i.e. it has been shown by others to bind to its own promoter and up-regulate its own transcription, the finding that activated GR can interfere with GATA-1 function may provide an explanation for the inhibition by glucocorticoids of the entire program of erythroid differentiation in MEL cells. That is, by interfering with GATA-1 function, the GR inhibits not only the expression of erythroid structural genes, but may also inhibit the expression of a primary erythroid regulatory gene, GATA-1. It was also shown that the GATA-RE in each of the beta-globin promoters responds to mouse GATA-1 in a functional transfection assay.
An a-InGaZnO TFT Pixel Circuit Compensating Threshold Voltage and Mobility Variations in AMOLEDs (2014)

In this paper, we proposed a novel voltage-programmed pixel circuit based on amorphous indium gallium zinc-oxide thin-film transistor (a-InGaZnO TFT) for active-matrix organic light-emitting display (AMOLED) with an enhanced electrical stability and uniformity. Through an extensive simulation work based on a-InGaZnO TFT and OLED experimental data, we confirm that the proposed pixel circuit can compensate for both mobility variation and threshold voltage shift of the driving TFT.
Be13, a human T-leukemia cell line highly sensitive to dexamethasone-induced cytolysis. (1984)

A unique human T-leukemia cell line highly sensitive to dexamethasone-induced lysis is described. The cell line designated Be13 is killed readily within 24 hr by 10(-9) M dexamethasone. No lysis is induced by nonglucocorticoid steroids. The lysis is mediated via specific cytoplasmic receptors and is efficiently blocked by the antagonist cortexolone. The inhibiting effect of actinomycin D and cycloheximide on the lytic process suggests the involvement of gene activation and destruction of the cells by an "autolytic protein." Kinetic studies imply that the lytic process is induced during a distinct phase of the cell cycle. Dexamethasone, however, does not cause an arrest in a distinct phase of the cell cycle. The Be13 cell is a unique human cell line killed directly by glucocorticoids, and it may serve as a suitable in vitro model for studying the lytic effect of glucocorticoids on the proliferating compartment of human leukemias.
Methane fermentation, submerged gas collection, and the fate of carbon in advanced integrated wastewater pond systems (1995)

There are several basic reasons for concern regarding the fate of carbonaceous material in waste stabilization ponds: accumulation of solids; performance and useful life of the pond system; and, the control of methane emissions. In conventional ponds methane fermentation is minimal, and carbon-rich organic matter is integrated by bacteria and microalgae which grow and settle. The integration of carbon decreases pond volume and treatment capacity and causes the ponds to age prematurely, to produce odor, and to require frequent sludge removal; and, any methane produced escapes to the atmosphere. However, if carbon-rich organics are efficiently converted to methane or to harvested microalgae, the pond system will continue to treat wastewater effectively for an extended period of time. Advanced Integrated Wastewater Pond Systems (AIWPSs) developed at the University of California fully utilize methane fermentation and microalgal cultivation to treat wastewater and to reclaim energy and nutrients. First generation AIWPSs have provided reliable municipal sewage treatment at St. Helena and Hollister, California, for 28 and 16 years, respectively, without the need for sludge removal. However, these first generation systems lack the facilities to recover and utilize the carbon-rich treatment byproducts of methane and algal biomass. The recovery of methane using a submerged gas collector was demonstrated using a second generation AIWPS prototype at the University of California, Berkeley, and the optimization of in-pond methane fermentation, the growth of microalgae in High Rate Ponds, and the harvest of microalgae by sedimentation and dissolved air flotation were studied. Preliminary data are presented to quantify the fate of carbon in the second generation AIWPS prototype and to estimate the fate of carbon in a full-scale, 200 MLD second generation AIWPS treating municipal sewage. In the experimental system, 17% of the influent organic carbon was recovered as methane, and an average of 6 g C/m2/d were assimilated into harvestable algal biomass. In a full-scale second generation AIWPS in a climate comparable to Richmond, California, located at 37° N latitude, these values would be significantly higher--as much as 30% of the influent organic carbon would be recovered as methane and as much as 10 g C/m2/d would be assimilated by microalgae. These efficiencies would increase further in warmer climates with more abundant sunlight.
A Visual Programming Language for Novices (1987)

Abstract: "We present Bridge Talk, a new approach to visual languages for novice programmers. The design of Bridge Talk is based on data about how novices learn to program. Bridge Talk allows novices to program with programming plans -- frame-like objects that capture essential program components like 'keep a running total' and 'iterate down a data structure'. Novices are focused on the interactions between plans, not on the implementation details for a particular plan. Beginning with plans as a basis for a novice programming language, we were forced to develop a programming formalism that can deal with multiple levels of detail, merged plan implementations, and interrelationships between plans.The actual visual presentation for the language is based on six 'design, implement, test with students, and redesign' cycles."