gebhart/patrepeval huggingface dataset:
Genetic Analysis of Pathogenic Bacteria: A Laboratory Manual (1995)

Overview: approaching genetic analysis of diverse bacteria. Bacterial pathogenesis: general concepts in bacterial pathogenesis paradigms of bacterial pathogenesis - Salmonella typhimurium, Vibrio cholerae. Practical aspects of microbial genetics: genetic nomenclature microbiological procedures culture media antibiotics, antibiotic resistance, and positive resistance, and positive and negative selections bacterial physiology. Genetic mapping: genetic mapping of chromosomal genes generalized transduction genetic mapping by generalized transduction deletion mapping. Mutants and their analysis: mutagenesis broad host range allelic exchange systems suppression genetic complementation polarity. Transposons and fusions: uses of transposons in bacterial genetics bacteriophage mu operon and gene fusions operon and gene fusions with lacZ operon fusions with uidA (gus), gene fusions with phoA, in vivo expression technology. Gene regulation: regulation of virulence genes challenge phage genetic analysis of DNA-protein interactions. Recombinant DNA: plasmids and conjugation transformation and electrotransformation basic molecular biology techniques electrophoresis of DNA polymerase chain reaction. Experiments. Appendices: strains, phage, and plasmids culture media and supplements strain colelctions genetic exchange and mapping enzyme assays recombinant DNA methods plasmid and transposon restriction maps.
Effect of the artificial sweetener, sucralose, on gastric emptying and incretin hormone release in healthy subjects (2009)

The incretin hormones, glucagon-like peptide-1 (GLP-1) and glucose-dependent insulinotropic polypeptide (GIP), play an important role in glucose homeostasis in both health and diabetes. In mice, sucralose, an artificial sweetener, stimulates GLP-1 release via sweet taste receptors on enteroendocrine cells. We studied blood glucose, plasma levels of insulin, GLP-1, and GIP, and gastric emptying (by a breath test) in 7 healthy humans after intragastric infusions of 1) 50 g sucrose in water to a total volume of 500 ml (approximately 290 mosmol/l), 2) 80 mg sucralose in 500 ml normal saline (approximately 300 mosmol/l, 0.4 mM sucralose), 3) 800 mg sucralose in 500 ml normal saline (approximately 300 mosmol/l, 4 mM sucralose), and 4) 500 ml normal saline (approximately 300 mosmol/l), all labeled with 150 mg 13C-acetate. Blood glucose increased only in response to sucrose (P<0.05). GLP-1, GIP, and insulin also increased after sucrose (P=0.0001) but not after either load of sucralose or saline. Gastric emptying of sucrose was slower than that of saline (t50: 87.4+/-4.1 min vs. 74.7+/-3.2 min, P<0.005), whereas there were no differences in t50 between sucralose 0.4 mM (73.7+/-3.1 min) or 4 mM (76.7+/-3.1 min) and saline. We conclude that sucralose, delivered by intragastric infusion, does not stimulate insulin, GLP-1, or GIP release or slow gastric emptying in healthy humans.
Human Fetal Hemoglobin Expression Is Regulated by the Developmental Stage-Specific Repressor BCL11A (2008)

Differences in the amount of fetal hemoglobin (HbF) that persists into adulthood affect the severity of sickle cell disease and the beta-thalassemia syndromes. Genetic association studies have identified sequence variants in the gene BCL11A that influence HbF levels. Here, we examine BCL11A as a potential regulator of HbF expression. The high-HbF BCL11A genotype is associated with reduced BCL11A expression. Moreover, abundant expression of full-length forms of BCL11A is developmentally restricted to adult erythroid cells. Down-regulation of BCL11A expression in primary adult erythroid cells leads to robust HbF expression. Consistent with a direct role of BCL11A in globin gene regulation, we find that BCL11A occupies several discrete sites in the beta-globin gene cluster. BCL11A emerges as a therapeutic target for reactivation of HbF in beta-hemoglobin disorders.
Trie hashing with controlled load (1991)

Trie hashing (TH), a primary key access method for storing and accessing records of dynamic files, is discussed. The key address is computed through a trie. A key search usually requires only one disk access when the trie is in core and two disk accesses for very large files when the trie must be on disk. A refinement to trie hashing, trie hashing with controlled load (THCL), is presented. It is designed to control the load factor of a TH file as tightly as that of a B-tree file, allows high load factor of up to 100% for ordered insertions, and increases the load factor for random insertions from 70% to over 85%. It is shown that these properties make trie hashing preferable to a B-tree.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Isolation and characterization of the factor X Friuli variant (1989)

Factor X Friuli was isolated from plasma by immunoaffinity and ion exchange chromatography and compared with normal factor X purified by the same method. Similar molecular weights were observed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) of the intact or activated factor X molecules including their respective heavy and light chains. These data indicated that there were no gross structural differences between the normal and variant proteins. Immunochemical assays employing either polyclonal or 46 monoclonal antibodies (MoAbs) did not reveal any structural deviations. Two- dimensional peptide maps indicated that while the light chains of normal and Friuli factor X were very similar, the heavy chains of the native and activated molecules contained a limited number of differences. These data suggested that the defect in factor X Friuli may be a point mutation which lies within the activated heavy chain defined by the 195–424 amino acid sequence. Activation of factor X Friuli in purified systems showed that Russell's viper venom cleaved the molecule at 70% of the normal rate, while the rate of proteolysis of the variant protein was reduced 98% and 75% when incubated with the extrinsic and intrinsic activation complexes, respectively. These data support the clinical laboratory findings and the hypothesis that the defect associated with the Friuli variant may reflect an abnormal interaction between factor X Friuli and the nonproteolytic cofactors of the extrinsic and intrinsic factor X activation complexes. Fluorescence polarization studies suggested that a bound dansylated inhibitor of factor Xa was not oriented to the same extent within the active site of the variant enzyme relative to normal factor Xa until the addition of phospholipid and factor Va. Activated factor X Friuli generated thrombin from prothrombin in a purified system, but at one third the normal rate that was attributed to the Kcat suggesting a secondary effect of this defect.
Oral immunization with attenuated vaccine strains of Vibrio cholerae expressing a dodecapeptide repeat of the serine-rich Entamoeba histolytica protein fused to the cholera toxin B subunit induces systemic and mucosal antiamebic and anti-V. cholerae antibody responses in mice (1997)

Entamoeba histolytica is a significant cause of morbidity and mortality worldwide. The serine-rich E. histolytica protein (SREHP) is a surface-expressed trophozoite protein that includes multiple hydrophilic tandem repeats. A purified fusion protein between the dodecapeptide repeat of SREHP and cholera toxin B subunit (CTB) has previously been shown to be immunogenic in mice after oral inoculation when cholera toxin is coadministered as an immunoadjuvant. We engineered a live attenuated El Tor Vibrio cholerae vaccine strain, Peru2, to express the SREHP-12-CTB fusion protein to the supernatant from either a plasmid [Peru2 (pETR5.1)] or from a chromosomal insertion (ETR3). Vector strains were administered orally to germfree mice that were subsequently housed under nongermfree conditions; mice received one (day 0) or two (days 0 and 14) inoculations. No immunoadjuvant or cholera holotoxin was administered. Mice that received two inoculations of Peru2(pETR5.1) had the most pronounced antiamebic systemic and mucosal immunologic responses. Less marked, but significant, anti-SREHP serum immunoglobulin G antibody responses were also induced in mice that received either one or two oral inoculations of strain ETR3. Anti-V. cholerae responses were also induced, as measured by the induction of serum vibriocidal antibodies and by serum and mucosal anti-CTB antibody responses. These results suggest that V. cholerae vector strains can be successful delivery vehicles for the SREHP-12-CTB fusion protein, to induce mucosal and systemic antiamebic and anti-V. cholerae immune responses. The magnitude of these responses is proportional to the amount of SREHP-12-CTB produced by the vector strain.
Induction of Neuronal Differentiation by p73 in a Neuroblastoma Cell Line (2000)

The p53-related p73 and p63 genes encode proteins that share considerable structural and functional homology with p53. Despite similarities, their deletion in mice has different outcomes, implying that the three genes may play distinct roles in vivo. Here we show that endogenous p73 levels increase in neuroblastoma cells induced to differentiate by retinoic acid and that exogenously expressed p73, but not p53, is sufficient to induce both morphological (neurite outgrowth) and biochemical (expression of neurofilaments and neural cell adhesion molecule (N-CAM); down-regulation of N-MYC and up-regulation of pRB) markers of neuronal differentiation. This activity is shared, to different extents, by all p73 isoforms, whereas the transcriptionally inactive mutants of p73 isoforms are ineffective. Conversely, blockage of endogenous p73 isoforms with a dominant negative p73 results in the abrogation of retinoid-induced N-CAM promoter-driven transcription. Our results indicate that the p73 isoforms activate a pathway that is not shared by p53 and that is required for neuroblastoma cell differentiation in vitro.
Human Dectin-1 Deficiency and Mucocutaneous Fungal Infections (2009)

Mucocutaneous fungal infections are typically found in patients who have no known immune defects. We describe a family in which four women who were affected by either recurrent vulvovaginal candidiasis or onychomycosis had the early-stop-codon mutation Tyr238X in the beta-glucan receptor dectin-1. The mutated form of dectin-1 was poorly expressed, did not mediate beta-glucan binding, and led to defective production of cytokines (interleukin-17, tumor necrosis factor, and interleukin-6) after stimulation with beta-glucan or Candida albicans. In contrast, fungal phagocytosis and fungal killing were normal in the patients, explaining why dectin-1 deficiency was not associated with invasive fungal infections and highlighting the specific role of dectin-1 in human mucosal antifungal defense.
Microstrip RF surface coil design for extremely high‐field MRI and spectroscopy (2001)

A new type of high-frequency RF surface coil was developed for in vivo proton or other nuclei NMR applications at 7T. This is a purely distributed-element and transmission line design. The coil consists of a thin strip conductor (copper or silver) and a ground plane separated by a low-loss dielectric material with a thickness (H). Due to its specific semi-open transmission line structure, substantial electromagnetic energy is stored in the dielectric material between the thin conductor and the ground plane, which results in a reduced radiation loss and a reduced perturbation of sample loading to the RF coil compared to conventional surface coils. The coil is characterized by a high Q factor, no RF shielding, small physical coil size, lower cost, and easy fabrication. A brief theoretical description of the microstrip RF coil is given that can be used to guide the coil designs. A set of gradient-recalled echo images were acquired by using the single- and two-turn microstrip RF surface coils from both phantom and human brain at 7T, which show good penetration and sensitivity. The two-turn coil design significantly improves the B1 symmetry as predicted by the microstrip theory. The optimum H for microstrip surface coils is approximately 7 mm. This coil geometry yields a B1 penetration similar to that of conventional surface coils. SNR comparison was made between the microstrip coil and conventional surface coils with and without RF shielding. The results reveal that the novel surface coil design based on the microstrip concept makes very high-field MRI/MRS more convenient and efficient in research and future clinics.
Collectrin, a Collecting Duct-specific Transmembrane Glycoprotein, Is a Novel Homolog of ACE2 and Is Developmentally Regulated in Embryonic Kidneys (2001)

Collectrin, a novel homolog of angiotensin-converting enzyme-related carboxypeptidase (ACE2), was identified during polymerase chain reaction-based cDNA subtraction and up-regulated in 5/6 ablated kidneys at hypertrophic phase. Collectrin, with 222 amino acids, has an apparent signal peptide and a transmembrane domain; the sequence is conserved in mouse, rat, and human and shares 81.9% identity. Human collectrin has 47.8% identity with non-catalytic extracellular, transmembrane, and cytosolic domains of ACE2; however, unlike ACE and ACE2, collectrin lacks active dipeptidyl carboxypeptidase catalytic domains. The collectrin mRNA transcripts are expressed exclusively in the kidney. In situ hybridization reveals its mRNA expression in renal collecting ducts, and immunohistochemistry shows that it is localized to the luminal surface and cytoplasm of collecting ducts. Immunoprecipitation studies, using [35S]methionine-labeled renal cortical and inner medullar collecting duct cells, i.e. M-1 and mIMCD-3, indicate that the protein size is approximately 32 kDa. During the development of mouse kidney, mRNA signal is detectable at day 13 of gestation, and the protein product is observed in the ureteric bud branches. Its expression is progressively increased during later stages of the gestation extending into the neonatal periods and then is decreased in adult life. Up-regulated expression of collectrin in the hypertrophic kidneys after renal ablation and restricted spatio-temporal expression during development indicates a possible role(s)in the process of progressive renal failure and renal organogenesis.
In Support of the Original Medermycin/Lactoquinomycin A Structure (2002)

[structure: see text] Herein we report a significant body of spectroscopic data that supports the originally proposed structure of medermycin/lactoquinomycin A. In addition, we demonstrate that these data are inconsistent with the revised structure reported recently in the literature.
Balancing Trie-Based Policy Representations for Network Firewalls (2006)

Firewalls inspect arriving packets according to a security policy. The complexity of these policies can cause significant delays in the processing of packets, resulting in degraded performance, traffic bottlenecks, and ultimately violating Quality of Service (QoS) constraints. As network capacities continue to increase, the improvement of firewall performance is a main concern. One technique that dramatically reduces required processing is the representation of security policies in software with n-ary tries. This paper describes trie balancing methods that further improve performance by placing more frequently used rules in high precedence positions which require fewer tuple comparisons. A proof of sorted trie integrity is presented along with experimental results showing that on average, sorting reduces the number of comparisons by 27% as compared to the original trie and by 83% as compared to a list representation. Sorting methods are described in detail and their benefits are demonstrated empirically.
Synthesis and biological activity of spiro(isocoumarin-piperidines) and reltaed compounds. I. (1981)

1'-Alkylspiro [isochroman-3, 4'-piperidin]-1-ones (2) and 1'-alkylspiro [isochroman-4, 4'-piperidines] (4 and 5) were prepared and examined for analgesic activity. Several of the 4-spiro compounds (3, 4, and 5) were found to have analgesic activity as potent as that of aminopyrine, while the 3-spiro compounds (2) were inactive. Further pharmacological studies revealed that several of these compounds inhibited the histamine release induced by compound 48/80 from isolated rat peritoneal mast cells.
New York Science Journal (2015)

New York Science Journal is published with English for the scientists and Engineers. The journal aims to present experimental and theoretical findings of science and engineering and to report on advances in technologies of multidisciplinary subjects. The journal was founded in 2008 by Marsland Press. The Editor-in-Chief, Deputy Editor and editors have backgrounds in Philosophy, Science, Technology and Engineering, etc. This interdisciplinary team is ultimately suited for facilitating the publication of the best of your research work. The journal welcomes manuscripts from all fields in science and engineering research. Papers submitted could be reviews, objective descriptions, research reports, opinions/debates, news, letters, and other types of writings that are nature and science related. Manuscripts submitted will be peer reviewed and the valuable papers will be considered for the publication after the peer review.
Evaluation of the Contribution of Platelets to Clot Strength by Thromboelastography in Rabbits: The Role of Tissue Factor and Cytochalasin D (2000)

Rabbits may serve as a model of hemostasis that closely approximates human situations to mechanistically determine the etiology of coagulopathy. The contribution of platelet function to total clot strength is similar to that observed in humans.
Structures of larger proteins, protein‐ligand and protein‐DNA complexes by multidimensional heteronuclear NMR (1994)

The recent development of a whole panoply of multidimensional heteronuclear-edited and -filtered NMR experiments has revolutionized the field of protein structure determination by NMR, making it possible to extend the methodology from the 10-kDa limit of conventional 2-dimensional NMR to systems up to potentially 35-40 kDa. The basic strategy for solving 3-dimensional structures of larger proteins and protein-ligand complexes in solution using 3- and 4-dimensional NMR spectroscopy is summarized, and the power of these methods is illustrated using 3 examples: interleukin-1 beta, the complex of calmodulin with a target peptide, and the specific complex of the transcription factor GATA-1 with its cognate DNA target site.
A climate-based model predicts the spatial distribution of the Lyme disease vector Ixodes scapularis in the United States. (2003)

An understanding of the spatial distribution of the black-legged tick, Ixodes scapularis, is a fundamental component in assessing human risk for Lyme disease in much of the United States. Although a county-level vector distribution map exists for the United States, its accuracy is limited by arbitrary categories of its reported presence. It is unknown whether reported positive areas can support established populations and whether negative areas are suitable for established populations. The steadily increasing range of I. scapularis in the United States suggests that all suitable habitats are not currently occupied. Therefore, we developed a spatially predictive logistic model for I. scapularis in the 48 conterminous states to improve the previous vector distribution map. We used ground-observed environmental data to predict the probability of established I. scapularis populations. The autologistic analysis showed that maximum, minimum, and mean temperatures as well as vapor pressure significantly contribute to population maintenance with an accuracy of 95% (p < 0.0001). A cutoff probability for habitat suitability was assessed by sensitivity analysis and was used to reclassify the previous distribution map. The spatially modeled relationship between I. scapularis presence and large-scale environmental data provides a robust suitability model that reveals essential environmental determinants of habitat suitability, predicts emerging areas of Lyme disease risk, and generates the future pattern of I. scapularis across the United States.
Binding of dioxygen to iron(II). Reversible behavior in solution (1973)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTBinding of dioxygen to iron(II). Reversible behavior in solutionJack E. Baldwin and Joel. HuffCite this: J. Am. Chem. Soc. 1973, 95, 17, 5757–5759Publication Date (Print):August 1, 1973Publication History Published online1 May 2002Published inissue 1 August 1973https://pubs.acs.org/doi/10.1021/ja00798a052https://doi.org/10.1021/ja00798a052research-articleACS PublicationsRequest reuse permissionsArticle Views222Altmetric-Citations71LEARN 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
Genes Involved in the Synthesis and Degradation of Matrix Polysaccharide in Actinobacillus actinomycetemcomitans and Actinobacillus pleuropneumoniae Biofilms (2004)

Biofilms are composed of bacterial cells embedded in an extracellular polysaccharide matrix. A major component of the Escherichia coli biofilm matrix is PGA, a linear polymer of N-acetyl-D-glucosamine residues in beta(1,6) linkage. PGA mediates intercellular adhesion and attachment of cells to abiotic surfaces. In this report, we present genetic and biochemical evidence that PGA is also a major matrix component of biofilms produced by the human periodontopathogen Actinobacillus actinomycetemcomitans and the porcine respiratory pathogen Actinobacillus pleuropneumoniae. We also show that PGA is a substrate for dispersin B, a biofilm-releasing glycosyl hydrolase produced by A. actinomycetemcomitans, and that an orthologous dispersin B enzyme is produced by A. pleuropneumoniae. We further show that A. actinomycetemcomitans PGA cross-reacts with antiserum raised against polysaccharide intercellular adhesin, a staphylococcal biofilm matrix polysaccharide that is genetically and structurally related to PGA. Our findings confirm that PGA functions as a biofilm matrix polysaccharide in phylogenetically diverse bacterial species and suggest that PGA may play a role in intercellular adhesion and cellular detachment and dispersal in A. actinomycetemcomitans and A. pleuropneumoniae biofilms.