gebhart/patrepeval huggingface dataset:
Sporicidal Effects of High‐Intensity 405 nm Visible Light on Endospore‐Forming Bacteria (2012)

Resistance of bacterial endospores to treatments, including biocides, heat and radiation is a persistent problem. This study investigates the susceptibility of Bacillus and Clostridium endospores to 405 nm visible light, wavelengths which have been shown to induce inactivation of vegetative bacterial cells. Suspensions of B. cereus endospores were exposed to high-intensity 405 nm light generated from a light-emitting diode array and results demonstrate the induction of a sporicidal effect. Up to a 4-log(10) CFU mL(-1) reduction in spore population was achieved after exposure to a dose of 1.73 kJ cm(-2). Similar inactivation kinetics were demonstrated with B. subtilis, B. megaterium and C. difficile endospores. The doses required for inactivation of endospores were significantly higher than those required for inactivation of B. cereus and C. difficile vegetative cells, where ca 4-log(10) CFU mL(-1) reductions were achieved after exposure to doses of 108 and 48 J cm(-2), respectively. The significant increase in dose required for inactivation of endospores compared with vegetative cells is unsurprising due to the notorious resilience of these microbial structures. However, the demonstration that visible light of 405 nm can induce a bactericidal effect against endospores is significant, and could have potential for incorporation into decontamination methods for the removal of bacterial contamination including endospores.
Free-space interconnects for high-performance optoelectronic switching (1998)

The authors describe the two architectures they have developed that use and demonstrate free-space optical interconnects for digital logic: a high-performance optoelectronic computing module and a second-generation digital optoelectronic computer. The low-power, high-performance optoelectronic computing (HPOC) module was designed for switching and data processing applications. Its architecture uses global, free-space, smart optical interconnects rather than electronic interconnects. The HPOC modules, which incorporate arrays of microlasers, diffractive optical interconnect elements and detectors, are currently undergoing prototype fabrication. By extending the high fan-in and fan-out capabilities of free-space optical interconnects, HPOC modules-when properly configured-offer a significant reduction in power, while maintaining good algorithmic efficiency and high noise margin.
Cell-bound albumin is the 70-kDa peptidoglycan-, lipopolysaccharide-, and lipoteichoic acid-binding protein on lymphocytes and macrophages. (1994)

The 70-kDa protein that is present on the surface of lymphocytes and macrophages and that binds peptidoglycan, lipopolysaccharide, lipoteichoic acid, heparin, and sulfated heparinoids was identified as cell-bound albumin. It originated from the tissue culture medium or from the serum in vivo and was not produced by the cells. The following results supported this conclusion: (a) mouse and human cell lines grown in serum-free and albumin-free medium did not have this 70-kDa protein and did not bind peptidoglycan and lipopolysaccharide in photoaffinity cross-linking assay; (b) the appearance of the 70-kDa protein in these cells and the ligand binding were restored by 30-min incubation with serum or purified albumin; (c) soluble albumin bound peptidoglycan and lipopolysaccharide, and this binding was inhibited by the same competitive inhibitors that inhibited the binding to the 70-kDa cellular protein; (d) albumin co-migrated with the 70-kDa cellular protein in two-dimensional polyacrylamide gel electrophoresis; (e) peptide maps of albumin and the 70-kDa cellular protein digested with four proteases were identical; (f) the only protein recognized by anti-albumin monoclonal and polyclonal antibodies on Western immunoblots was the 70-kDa protein that exactly matched with the cellular peptidoglycan/lipopolysaccharide-binding protein; (g) anti-albumin monoclonal antibodies immunoprecipitated the 70-kDa cellular protein; and (h) species-specific anti-bovine, anti-human, and anti-mouse albumin antibodies recognized the 70-kDa protein on mouse and human cells according to the species of albumin that was present in the culture medium or in the serum in vivo, but not according to the species of the cells. The cell-bound albumin was not required for cell activation, because macrophage cell lines that were grown in albumin-free medium and did not have the cell-bound albumin (the 70-kDa protein) fully responded to the stimulation by peptidoglycan and lipopolysaccharide with production of tumor necrosis factor-alpha.
The relationship between protein structure and function: a comprehensive survey with application to the yeast genome (1999)

For most proteins in the genome databases, function is predicted via sequence comparison. In spite of the popularity of this approach, the extent to which it can be reliably applied is unknown. We address this issue by systematically investigating the relationship between protein function and structure. We focus initially on enzymes functionally classified by the Enzyme Commission (EC) and relate these to by structurally classified domains the SCOP database. We find that the major SCOP fold classes have different propensities to carry out certain broad categories of functions. For instance, alpha/beta folds are disproportionately associated with enzymes, especially transferases and hydrolases, and all-alpha and small folds with non-enzymes, while alpha+beta folds have an equal tendency either way. These observations for the database overall are largely true for specific genomes. We focus, in particular, on yeast, analyzing it with many classifications in addition to SCOP and EC (i.e. COGs, CATH, MIPS), and find clear tendencies for fold-function association, across a broad spectrum of functions. Analysis with the COGs scheme also suggests that the functions of the most ancient proteins are more evenly distributed among different structural classes than those of more modern ones. For the database overall, we identify the most versatile functions, i.e. those that are associated with the most folds, and the most versatile folds, associated with the most functions. The two most versatile enzymatic functions (hydro-lyases and O-glycosyl glucosidases) are associated with seven folds each. The five most versatile folds (TIM-barrel, Rossmann, ferredoxin, alpha-beta hydrolase, and P-loop NTP hydrolase) are all mixed alpha-beta structures. They stand out as generic scaffolds, accommodating from six to as many as 16 functions (for the exceptional TIM-barrel). At the conclusion of our analysis we are able to construct a graph giving the chance that a functional annotation can be reliably transferred at different degrees of sequence and structural similarity. Supplemental information is available from http://bioinfo.mbb.yale.edu/genome/foldfunc++ +.
Differential Proteolytic Enzyme Activity in Eosinophilic and Neutrophilic Asthma (2005)

Proteolytic enzyme activity in asthma is dependent on the underlying inflammatory phenotype and is differentially regulated with MMP-9 activity a feature of eosinophilic inflammation, and active NE in neutrophilic inflammation.
n-Alkanes Gel n-Alkanes (and Many Other Organic Liquids) (1999)

Thermoreversible gelation of relatively short n-alkanes and a variety of other organic liquids has been accomplished using low concentrations of long n-alkanes (chain lengths from 24 to 36 carbon atoms) as gelators. The stability of the gels is discussed in terms of gelator concentration, gelation temperature, and the duration of time gels persist without bulk phase separation. Generally, stability increases with the chain length of the gelator. n-Alkanes are structurally the simplest organic gelators possible and their gels with n-alkanes as liquids are the simplest organogels that can be made. Their existence demonstrates that London dispersion forces alone can provide colloidal networks whose strength is sufficient to immobilize liquids against the pull of gravity.
Mutatis Mutandis (2007)

This article presents Proteus, a core calculus that models dynamic software updating, a service for fixing bugs and adding features to a running program. Proteus permits a program's type structure to change dynamically but guarantees the updated program remains type-correct by ensuring a property we call con-freeness. We show how con-freeness can be enforced dynamically, and how it can be approximated via a novel static analysis. This analysis can be used to assess the implications of a program's structure on future updates in order to make update success more predictable. We have implemented Proteus for C, and briefly discuss our implementation which we have tested on several well-known programs.
Synthesis of Some 5-Substituted Indoles (1992)

A halogen-metal exchange strategy was employed to prepare several 5-substituted indoles from 5-bromoindole.Additional derivatives were elaborated from the formyl, acetyl.thiomethyl, boronic acid and trimethylstannyl analogues thus prepared.
Reduction of Viscosity in Suspension of Swimming Bacteria (2009)

Measurements of the shear viscosity in suspensions of swimming Bacillus subtilis in free-standing liquid films have revealed that the viscosity can decrease by up to a factor of 7 compared to the viscosity of the same liquid without bacteria or with nonmotile bacteria. The reduction in viscosity is observed in two complementary experiments: one studying the decay of a large vortex induced by a moving probe and another measuring the viscous torque on a rotating magnetic particle immersed in the film. The viscosity depends on the concentration and swimming speed of the bacteria.
VKORC1 haplotypes influence the performance characteristics of PIVKAII for screening of hepatocellular carcinoma (2010)

VKORC1 haplotypes influence the performance characteristics of PIVKAII for screening of HCC. Thus, measurement could be complementary for PIVKAII in HCC screening.
Amniotic Membrane as a Substrate for Cultivating Limbal Corneal Epithelial Cells for Autologous Transplantation in Rabbits (2000)

Autologous transplantation of cultivated corneal epithelium is feasible by using acellular amniotic membrane as a carrier.
Interactions Between Nutrients and Peptide Growth Factors in Intestinal Growth, Repair, and Function (1999)

Several lines of evidence demonstrate that general nutritional status, specific nutrients (eg, zinc, glutamine), and certain trophic growth factors (eg, growth hormone, insulin-like growth factor I, keratinocyte growth factor, and glucagon-like peptide-2) have important interactions relevant for intestinal growth and function. Adequate nutritional status is critical for endogenous growth factor synthesis in the gut and other tissues and is an important mediator of organ responsiveness to exogenous growth factor administration. Both endogenously synthesized and exogenously administered growth factors upregulate nutrient uptake and utilization by gut mucosa, skeletal muscle, and other organs. Emerging data from both animal and human studies indicate that combinations of selected growth factors and specific nutrients may improve the growth, adaptation, and repair of the intestinal mucosa. Additional studies to determine basic mechanisms of nutrient-growth factor interactions and the safety and efficacy of treatment with combinations of specific nutrients and recombinant growth factors are needed. Results of these investigations should define new methods for support of the intestinal tract during short bowel syndrome (SBS), catabolic illness, and malnutrition.
A novel total synthesis of (2R,4'R,8'R)-.alpha.-tocopherol (vitamin E). Construction of chiral chromans from an optically active, nonaromatic precursor (1979)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA novel total synthesis of (2R,4'R,8'R)-.alpha.-tocopherol (vitamin E). Construction of chiral chromans from an optically active, nonaromatic precursorNoal Cohen, Rocco J. Lopresti, and Gabriel SaucyCite this: J. Am. Chem. Soc. 1979, 101, 22, 6710–6716Publication Date (Print):October 1, 1979Publication History Published online1 May 2002Published inissue 1 October 1979https://pubs.acs.org/doi/10.1021/ja00516a037https://doi.org/10.1021/ja00516a037research-articleACS PublicationsRequest reuse permissionsArticle Views876Altmetric-Citations62LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Bacterial Meningitis in Malawian Adults: Pneumococcal Disease is Common, Severe, and Seasonal (2000)

We prospectively collected laboratory details and outcome data on all patients with laboratory-confirmed cases of meningitis that presented to our unit in Blantyre, Malawi, from 1 April 1998 through 31 March 1999. There were 502 patients with cases of meningitis; the most common causative organisms were Cryptococcus neoformans and Streptococcus pneumoniae. This pattern probably reflects the local human immunodeficiency virus (HIV) seroprevalence (31%) and is different from the pattern in 1974, when Neisseria meningitidis was the most common isolate. There has been an 8-fold increase in the number of meningitis cases per year since 1974, and a doubling of the percentage of medical admissions due to meningitis. The inpatient mortality rate among patients with cases of pneumococcal meningitis was 61%, and in the group as a whole was 41%. Despite the HIV-related pattern of infecting pathogens among these cases of meningitis and the increased incidence of the condition, there was evidence that the typical seasonal pattern of pneumococcal meningitis, which peaks in the cold, dry season, was preserved.
T-bet deficiency reduces atherosclerosis and alters plaque antigen-specific immune responses (2005)

The influence of the immune system on atherosclerosis involves both helper T (Th) cell and antibody responses to plaque antigens. These responses may have proatherogenic and protective effects. T-bet is a transcription factor required for Th1 differentiation and regulates the balance between Th1 and Th2 responses in inflammatory diseases. To clarify how helper T cell subset differentiation influences atherosclerosis, we compared lesion development and immune responses to plaque antigens in low-density lipoprotein receptor-deficient (Ldlr-/-) mice with or without functional T-bet genes. Atherosclerosis was significantly reduced in T-bet-deficient Ldlr-/- mice compared with Ldlr-/- controls, and the lesions that did develop in the absence of T-bet had less smooth muscle cell content. Furthermore, T-bet deficiency caused a Th2 switch in the response to the atherosclerosis-associated antigen heat shock protein-60, and a change in T-dependent isotypes of oxidized LDL-specific antibodies. Of particular significance, T-bet deficiency caused a >250% increase in the titer of E06 antibodies, which are known to be atheroprotective and whose production by B-1 B cells is enhanced by IL-5. These findings establish that T cell subset differentiation influences both T cell and antibody responses that modulate atherosclerosis, and validate the therapeutic goal of skewing T responses to atherosclerosis-associated antigens.
Algorithm of defining 1-D indexing for M-D mixed radix FFT implementation (2002)

A novel M-D (multidimensional) to 1-D FFT (fast Fourier transform) signal flow graph mapping is proposed. Thus, the M-D FFT can be efficiently implemented by the unified 1-D indexing, and the address generator design can be simplified. In addition, the matrix transposition is no longer necessary. The addressing sequences can be derived from the factorization of the twiddle factor matrix. The unified indexing concept of the M-D FFT implementation automatically solves the scaling problem of the block floating-point arithmetic. Practical chip design considerations in implementing the algorithm are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Factors influencing immunodominance hierarchies in TCD8+-mediated antiviral responses (2006)

CD8(+) T-lymphocytes (T(CD8+)) perform a critical role in immunity against tumors and virus infections. A central feature of T(CD8+) immune responses is immunodominance: the observation that T(CD8+) responses consist of a limited collection of specificities with a structured hierarchy. These immunodominance hierarchies result from a complex combination of factors. Major roles are played by peptide binding affinity, T-cell repertoire, and antigen processing and presentation. While the bulk of our information comes from mouse model systems, an increasing number of human studies suggest that immunodominance will be even more complicated. This review outlines current knowledge of T(CD8+ )immunodominance to viral antigens and discusses the relevance and importance of a thorough understanding for the rational design of vaccines that elicit effective T(CD8+) responses.
Review of Infectious Bronchitis Virus Around the World (2012)

Infectious bronchitis virus (IBV) is a gamma coronavirus that causes a highly contagious disease in chickens. The virus can affect the upper respiratory tract and the reproductive tract, and some strains can cause a nephritis. Different serotypes and genetic types of the virus have been identified worldwide and for the most part do not cross-protect. In addition, new types of the virus continue to arise due to mutations and recombination events in the viral genome, making this virus difficult to identify and extremely difficult to control. Surveillance and identification of IBV types is extremely important for control of the disease and the advancement of molecular methods have aided in this pursuit. Genetic typing of IBV, which involves reverse transcription-PCR amplification and sequence analysis of the S1 glycoprotein gene, has revolutionized diagnosis and identification of this virus by making it possible to type and compare the relatedness of a large number of virus isolates in a short period of time. The purpose of this review is to give an update on the strains of IBV currently circulating in commercial chickens worldwide and hopefully to present a clear picture of the relationship between many of these viruses. The information on IBV types presented herein is from published manuscripts, submissions to GenBank, our own unpublished data, and personal communications with scientists and diagnosticians working with IBV worldwide.
The Role of Tea in Human Health: An Update (2002)

Tea is an important dietary source of flavanols and flavonols. In vitro and animal studies provide strong evidence that tea polyphenols may possess the bioactivity to affect the pathogenesis of several chronic diseases, especially cardiovascular disease and cancer. However, the results from epidemiological and clinical studies of the relationship between tea and health are mixed. International correlations do not support this relationship although several, better controlled case-referent and cohort studies suggest an association with a moderate reduction in the risk of chronic disease. Conflicting results between human studies may arise, in part, from confounding by socioeconomic and lifestyle factors as well as by inadequate methodology to define tea preparation and intake. Clinical trials employing putative intermediary indicators of disease, particularly biomarkers of oxidative stress status, suggest tea polyphenols could play a role in the pathogenesis of cancer and heart disease.
Distribution of pathogenic microorganisms isolated from dental hospital workers in Korea (2013)

With the significant rise in hospital infection management in dental hospitals as well as in hospitals, and in order to identify the distribution of pathogenic bacteria on hands and nasal cavity of workers in a dental hospital, bacteria from the hands and nasal cavities of six dentists and 44 dental hygienists from four dental hospitals were investigated. The results showed Staphylococcus aureus, Staphylococcus capitis, Staphylococcus epidermidis, Staphylococcus hominis, Staphylococcus warneri, Staphylococcus xylosus, Staphylococcus. Lugdunensis, and Neisseria spp., were isolated from the nasal cavity and Staphylococcus aureus, Staphylococcus capitis, Staphylococcus epidermidis, Staphylococcus hominis, Staphylococcus warneri, Staphylococcus xylosus, Staphylococcus leutus, Micrococcus spp., Staphylococcus cohnii, Serratia marcescens, Pseudomonas aeruginosa, Klebsiella pneumonia and Pseudomonas pneumotropica from the hands. An antimicrobial disk diffusion test was conducted on Staphylococcus aureus isolated from the hands and nasal cavity to detect MRSA by means of oxacillin. Two strains were detected. When the genes of penicillin binding protein 2 (mecA) were detected from the 2 strains, MRSA was found from both strains. The results of this investigation on the distribution of various pathogenic bacteria and MRSA on hands and nasal cavity of workers of a dental hospital, will contribute to the basic data for the future infection management in a dental hospital.
Establishment of a New Interleukin-6 (IL-6) Receptor Inhibitor Applicable to the Gene Therapy for IL-6–Dependent Tumor (2007)

Interleukin-6 (IL-6) is a key molecule involved in the pathogenesis of several inflammatory diseases and malignancies. Treatments that inhibit IL-6 mitigate the clinical conditions of such diseases. Here, we report on the development of a new receptor inhibitor of IL-6 (NRI) by genetically engineering tocilizumab, a humanized anti-IL-6 receptor monoclonal antibody which specifically blocks IL-6 signaling. This NRI consists of VH and VL of tocilizumab in a single-chain fragment format dimerized by fusing to the Fc portion of human immunoglobulin G(1). The binding activity to IL-6 receptor and the biological activity of the purified NRI were found to be similar to those of parental tocilizumab. Because NRI is encoded on a single gene, it is easily applicable to a gene delivery system using virus vehicles. We administered an adenovirus vector encoding NRI to mouse i.p. and monitored the serum NRI level and growth reduction property on S6B45, an IL-6-dependent multiple myeloma cell line, in vivo. Adequate amount of the serum NRI level to exert anti-IL-6 action could be obtained by the NRI gene introduction combined with adenovirus gene delivery, and this treatment inhibited the in vivo S6B45 cell growth significantly. These findings indicate that NRI is a promising agent applicable to the therapeutic gene delivery approach for IL-6-driven diseases.