gebhart/patrepeval huggingface dataset:
Complete Genome Sequence of Francisella tularensis Subspecies holarctica FTNF002-00 (2009)

Francisella tularensis subspecies holarctica FTNF002-00 strain was originally obtained from the first known clinical case of bacteremic F. tularensis pneumonia in Southern Europe isolated from an immunocompetent individual. The FTNF002-00 complete genome contains the RD(23) deletion and represents a type strain for a clonal population from the first epidemic tularemia outbreak in Spain between 1997-1998. Here, we present the complete sequence analysis of the FTNF002-00 genome. The complete genome sequence of FTNF002-00 revealed several large as well as small genomic differences with respect to two other published complete genome sequences of F. tularensis subsp. holarctica strains, LVS and OSU18. The FTNF002-00 genome shares >99.9% sequence similarity with LVS and OSU18, and is also approximately 5 MB smaller by comparison. The overall organization of the FTNF002-00 genome is remarkably identical to those of LVS and OSU18, except for a single 3.9 kb inversion in FTNF002-00. Twelve regions of difference ranging from 0.1-1.5 kb and forty-two small insertions and deletions were identified in a comparative analysis of FTNF002-00, LVS, and OSU18 genomes. Two small deletions appear to inactivate two genes in FTNF002-00 causing them to become pseudogenes; the intact genes encode a protein of unknown function and a drug:H(+) antiporter. In addition, we identified ninety-nine proteins in FTNF002-00 containing amino acid mutations compared to LVS and OSU18. Several non-conserved amino acid replacements were identified, one of which occurs in the virulence-associated intracellular growth locus subunit D protein. Many of these changes in FTNF002-00 are likely the consequence of direct selection that increases the fitness of this subsp. holarctica clone within its endemic population. Our complete genome sequence analyses lay the foundation for experimental testing of these possibilities.
Molecular approaches to environmental microbiology (1996)

Introduction. Modern Molecular Techniques and Environmental Microbiology. Molecular Analysis of Plasmid Ecology and Evolution. Ribosomal RNA and the Molecular Analysis of Genetic Diversity in Microbial Populations. Flow Cytometry and Environmental Microbiology. Reporter Gene Technology in Environmental Microbiology. Detection of Environmentally-Important Micro-organisms through Nucleic Acid Hybridization. Immunological Approaches to the Analysis of Microbial Populations. Identification of Microorganisms using Biomarkers and Biochemical Profiles. Indentification of Cyanobacterial Toxins. Application of Oligonucleotide Probes for the Detection of Individual Microbial Cells in Natural Environments. Detection of Cryptosporidium and Giardia in Water. Occurrence of Legionella in the Environment. Survival of Bacteria in the Aquatic Environment. Molecular Studies on Field Isolated Agrobacterium.
Induction of Vascular Progenitor Cells From Endothelial Cells Stimulates Coronary Collateral Growth (2011)

We conclude that iVPCs, generated by partially reprogramming ECs, are an ideal cell type for cell-based therapy designed to stimulate coronary collateral growth.
Applications of Electronic-Nose Technologies for Noninvasive Early Detection of Plant, Animal and Human Diseases (2018)

The development of electronic-nose (e-nose) technologies for disease diagnostics was initiated in the biomedical field for detection of biotic (microbial) causes of human diseases during the mid-1980s. The use of e-nose devices for disease-diagnostic applications subsequently was extended to plant and animal hosts through the invention of new gas-sensing instrument types and disease-detection methods with sensor arrays developed and adapted for additional host types and chemical classes of volatile organic compounds (VOCs) closely associated with individual diseases. Considerable progress in animal disease detection using e-noses in combination with metabolomics has been accomplished in the field of veterinary medicine with new important discoveries of biomarker metabolites and aroma profiles for major infectious diseases of livestock, wildlife, and fish from both terrestrial and aquaculture pathology research. Progress in the discovery of new e-nose technologies developed for biomedical applications has exploded with new information and methods for diagnostic sampling and disease detection, identification of key chemical disease biomarkers, improvements in sensor designs, algorithms for discriminant analysis, and greater, more widespread testing of efficacy in clinical trials. This review summarizes progressive advancements in utilizing these specialized gas-sensing devices for numerous diagnostic applications involving noninvasive early detections of plant, animal, and human diseases.
Cuprate-Mediated Synthesis and Biological Evaluation of Cyclopropyl- and <i>tert-</i>Butylfarnesyl Diphosphate Analogs (1996)

The novel farnesyl diphosphate (FPP) analog 3-cyclopropyl-3-desmethylfarnesyl diphosphate (3-cpFPP, 1) was designed as a potential mechanism-based inhibitor of the FPP-utilizing enzyme protein-farnesyl transferase (PFTase). The key step in the synthesis of 1 involved the stereoselective coupling of vinyl triflate 8 with a lower order cyclopropyl cyanocuprate to afford the desired cyclopropyl ester 13. The sterically encumbered analog 3-desmethyl-3-tert-butylfarnesyl diphosphate (3-tbFPP, 7) was synthesized via a similar route. The use of the more reactive higher order tert-butyl cyanocuprate led to lower yields of ester 11, the key intermediate in the synthesis of 7. Biological evaluation of 3-cpFPP demonstrates that it is not a time-dependent inhibitor of recombinant yeast PFTase. Instead, 3-cpFPP is an alternative substrate for this enzyme that exhibits a K(m) comparable to FPP and a k(cat) only 5-fold lower than the natural substrate. In contrast, 3-tbFPP is an exceptionally poor substrate for yeast PFTase and acts as an inhibitor of this enzyme.
Maternal and child health. Infertility: from a personal to a public health problem (1999)

The inability to conceive a child is most often viewed as a private matter, but public health perspectives and skills can contribute greatly to our knowledge about infertility, and the development of effective and rational public policy for prevention, access to health care, and regulation of new technologies. We offer a primer of public health aspects of infertility in an effort to encourage the broad spectrum of public health professionals to become more knowledgeable about these topics and join in the national debate about preventive strategies, cost-benefit assessment, resource allocation, and ethics.
Dielectric losses in a polymer-dispersed liquid crystal film (1990)

We have measured the dielectric response of PDLC films containing liquid crystal droplets of E7 in a polymethylmethacrylate (PMMA) matrix as a function of frequency (0-10KHz) and temperature (25°C-11O°C). The liquid crystal composition of the films was varied from 0% to 60%. A principal objective of this study was to understand the dissipation mechanisms in these systems in an effort to control and reduce them. In the light of the experimental results, we discuss the primary dissipation mechanisms, including both DC and AC losses. The major contribution to the losses in these materials comes from the liquid crystal conductivity. Quantitative interpretation of the results can be clouded by a number of factors including incomplete phase separation of the liquid crystal and polymer, percolation effects and a frequency-dependent conductivity due to charge-carrier depletion in the liquid crystal droplets. Using simple two-phase composite formuli to model the dielectric behavior, the contributions of the real and imaginary parts of the dielectric constant to the field inside a droplet are discussed. The model agrees quantitatively with capacitance experiments, indicating that for frequencies below 100 Hz the field inside of a droplet is strongly modified by charge built up at the droplet/polymer interface.
Mass Spectral Reference Libraries: An Ever-Expanding Resource for Chemical Identification (2012)

The basic principles, practices, and pitfalls in the process of compound identification by searching mass spectral reference libraries are presented. Factors affecting the identification process are discussed as members of one of three major contributors to identification confidence: prior probability, risk of false negative results, and risk of false positive results. More general concerns and the problem of "unknown unknowns" are then explored.
Dopamine depolarizes podocytes via a D1-like receptor (1999)

The data indicate that dopamine induces a cAMP-dependent depolarization via a D1-like receptor in podocytes.
Development of a Structural Concept To Resist Impacts From Multiyear Ice Floes, Ridges, and Icebergs (1984)

ABSTRACT Large multi-year ice features and icebergs may have masses ranging up to 20 million tons or more and may move in the open water at speeds up to 1 knot, thus developing tremendous kinetic energy. A stepped structure concept has been developed to resist these impacts and to transfer the resultant forces and moments into the foundation thus developing a relatively high concentrated reaction force against the ice tending to spall and split it, thus causing a multi-modal failure of the ice, as well as using up kinetic energy at a relatively controlled rate. Calculated ice forces and ice failure modes will be presented. The stepped structure concept is primarily applicable to production platforms in water depths of 50 to 200 meters, which are subject to impact of large ice features such as multi-year ridges, floes, and icebergs (fig. 1). The resulting global ice loads are reduced by 50 percent or more as compared to those developed by a vertical or a steep sided structure. Overturning moments are reduced, thus reducing maxima soil bearing values. The structure itself is efficient in its use of structural materials, and is practicable for construction in pre stressed reinforced concrete or steel/concrete hybrid construction. It has acceptable draft during tow and can carry a fully outfitted deck. It is stable during all stages of installation. INTRODUCTION When large moving ice features such as multiyear ice floes, ice island fragments, and icebergs impact fixed-bottom founded structures, the kinetic energy must be absorbed by one or a combination of mechanisms. One such mechanism is the upward displacement of the ice feature itself, which may be produced by its riding up along inclined surface such as a flat-angled cone. In this case, most of the kinetic energy is converted to potential energy, with a small amount being absorbed by friction and by soil deformation. Conical structures have therefore been proposed. However, in deeper water, as will be discussed later, they become extremely large and costly and may be difficult to control during installation. The kinetic energy of impact may also be absorbed by the progressive crushing of ice. During the impact, the contact area is increasing, with consequent changes in the apparent strength of the ice as the confinement (indentation factor) decreases. Smaller amounts of energy absorption may be provided by strain of the foundation soils in shear and bearing, by rotation of the ice feature, and by hydrodynamic effects of water escaping from the contact zone. For the principal mechanisms, the kinetic energy, (1/2MV2) must be equaled by the integration of the forces over the distance over which the impact occurs obviously, if the structure can be configure to increase the distance of impact, the maximum force will be reduced. Even with such design improvements, the maximum ice forces may significantly exceed those developed by storm waves on existing North Sea platforms.
Pertussis Encephalopathy in an Adult: Case Report and Review (1991)

A 39-year-old man developed paroxysmal cough, occasional vomiting after cough, and subconjunctival hemorrhage. His illness was complicated by episodes of seizure, with clonic movements of the arms and legs, brief loss of consciousness, and confusion. The episodes were triggered by mild, unremarkable coughing paroxysms. A diagnosis of pertussis was confirmed serologically by measurement of IgG, IgA, and IgM antibodies to pertussis toxin and filamentous hemagglutinin. Serologic studies confirmed the presence of Bordetella pertussis infection in the patient's 10-year-old daughter and suggested that his wife was infected as well. This case report illustrates the occurrence of typical pertussis with serious complications in an adult. Further research is required to determine the scope of this problem and the need for a program of adult immunization against pertussis.
On the stability of neutral-type uncertain systems with multiple time delays (2005)

The problems of both single and multiple delays for neutral-type uncertain systems are considered. First, for single neutral time delay systems, based on a Razumikhin-type theorem, some delay-dependent stability criteria are derived in terms of the Lyapunov equation for various classes of model transformation and decomposition techniques.
X-ray phase-contrast microscopy and microtomography (2003)

In-line phase contrast enables weakly absorbing specimens to be imaged successfully with x-rays, and greatly enhances the visibility of fine scale structure in more strongly absorbing specimens. This type of phase contrast requires a spatially coherent beam, a condition that can be met by a microfocus x-ray source. We have developed an x-ray microscope, based on such a source, which is capable of high resolution phase-contrast imaging and tomography. Phase retrieval enables quantitative information to be recovered from phase-contrast microscope images of homogeneous samples of known composition and density, and improves the quality of tomographic reconstructions.
Fish Oil and Extruded Soybeans Fed in Combination Increase Conjugated Linoleic Acids in Milk of Dairy Cows More Than When Fed Separately (2002)

Eight multiparous Holstein and four multiparous Brown Swiss (78 +/- 43 DIM) cows were used in a 4 x 4 Latin square with 28-d periods to evaluate if feeding fish oil with a source of linoleic acid (extruded soybeans) would stimulate additional amounts of conjugated linoleic acid in milk. Four treatments consisted of a control diet with a 50:50 ratio of forage to concentrate (DM basis), a control diet with 2% added fat from either menhaden fish oil or extruded soybeans, or a combination of fish oil and extruded soybeans each adding 1% fat. DM intake (24.3, 21.6, 24.5, and 22.5 kg/d, for control, fish oil, extruded soybeans, and combination diets, respectively), milk production (32.1, 29.1,34.6, and 31.1 kg/d), and milk fat content (3.51, 2.79, 3.27, and 3.14%) were lower for cows that consumed either fish oil-containing diet, especially the 2% fish oil diet. The proportion of n-3 fatty acids in milk fat increased similarly among all three fat-supplemented diets. Concentrations of transvaccenic acid (1.00, 4.16, 2.17, and 3.51 g/100 g of fatty acids) and cis-9, trans-11 conjugated linoleic acid (0.60, 2.03, 1.16, and 1.82 g/100 g of fatty acids) in milk fat increased more with fish oil than with extruded soybeans. When fed the combination diet, these fatty acids were approximately 50% higher than expected for Holsteins, whereas concentrations were similar for Brown Swiss compared with feeding each fat source separately. These data indicated that fish oil modifies ruminal or systemic functions, stimulating increased conversion of linoleic acid into transvaccenic and conjugated linoleic acids.
Zirconium Oxide-based Cathode without Platinum Group Metals for PEFC (2009)

Partially oxidized zirconium carbonitrides (Zr-CNO) powders were evaluated as a non-precious cathode for polymer electrolyte fuel cells (PEFCs). Zr-CNO powders were prepared from zirconium carbonitrides (Zr-CN) with heat-treatment under 0.25%O2/2%H2/N2 at 1000 - 1400oC. The slow scan voltammetry was performed to evaluate the catalytic activity for the oxygen reduction reaction (ORR) under nitrogen and oxygen in 0.1 mol dm-3 H2SO4 at 30oC. Although the onset potential of ORR for untreated Zr-CN is 0.55 V vs. reversible hydrogen electrode (RHE), the onset potential of the appropriate oxidized Zr-CNO reached 0.97 V vs. RHE. XRD and XPS data suggested that the surface of the Zr-CNO was oxidized to ZrO2 and Zr-CN remained in the inner part of the each particle. The existence of tetragonal and/or cubic ZrO2 in the XRD patterns of the Zr-CNO suggested that the vacancies on the surface of the Zr-CNO might affect the catalytic activity for the ORR.
Mapping of the carboxyl terminus within the tertiary structure of transducin's alpha subunit using the heterobifunctional cross-linking reagent, 125I-N-(3-iodo-4-azidophenylpropionamido-S-(2-thiopyridyl) cysteine. (1988)

A heterobifunctional cross-linking reagent, 125I-N-(3-iodo-4-azidophenylpropionamido-S-(2-thiopyridyl) cysteine (125-ACTP), has been synthesized. 125I-ACTP has been used to derivative reduced sulfhydryls of the retinal G protein, transducin (Gt), to form a mixed disulfide bond under mild, nondenaturing conditions (pH 7.4, 4 degrees C). The resulting disulfide was easily cleaved using reducing reagents. A 200-fold molar excess of 125I-ACTP relative to Gt resulted in the incorporation of 1-1.3 mol of the 125I-N-(3-iodo-4-azidophenylpropionamido)cysteine moiety of ACTP into Gt alpha. In contrast to 125I-ACTP, dithionitrobenzoate and dithiopyridone derivatized six sulfhydryls in native Gt. Incubation of a 10-fold molar excess of 125I-ACTP relative to Gt resulted in the derivatization of 0.75-0.9 and 0.1 mol of reduced sulfhydryls/mol Gt alpha and beta, respectively. Gt gamma was not derivatized by 125I-ACTP. Thus, Gt alpha was preferentially derivatized by 125I-ACTP. Tryptic digestion and amino acid sequencing of Gt alpha indicated that both Cys-347 near the carboxyl terminus and Cys-210 between the second and third consensus sequences forming the GTP-binding site were derivatized by 125I-ACTP in a ratio of approximately 70 and 30%, respectively. Thus, both Cys-210 and Cys-347 are labeled, even though derivatization by 125I-ACTP does not exceed 1 mol of SH/mol Gt alpha. It appears that derivatization of one sulfhydryl, either Cys-210 or Cys-347, excludes labeling of the second cysteine either by steric hindrance or induced conformational change making the second cysteine inaccessible to 125I-ACTP. Consistent with this finding was the observation that pertussis toxin-catalyzed ADP-ribosylation of Cys-347 inhibited 125I-ACTP derivatization of Cys-210. Derivatization of Gt alpha at either Cys-210 or Cys-347 by 125I-ACTP inhibited rhodopsin-catalyzed guanosine 5'-3-O-(thio)triphosphate binding to Gt, mimicking the effect of ADP-ribosylation of Cys-347 by pertussis toxin. ACTP contains a radioiodinated phenylazide moiety which, upon activation, can cross-link the derivatized cysteine to an adjacent polypeptide domain. Following reduction of the disulfide, the [125I] iodophenyl moiety will be transferred to the azide-inserted polypeptide. When photoactivation of the phenylazide moiety of 125I-ACTP after sulfhydryl derivatization was performed, insertion of the Cys-347 which contains Cys-210, was found.(ABSTRACT TRUNCATED AT 400 WORDS)
Manufacture of Colby and Brick Cheeses from Ultrafiltered Milk (1983)

Skim milk was fractionated to attain a 50% volume reduction by ultrafihration, standardized with cream, and used in the manufacture of brick and Colby cheeses. The traditional curd washing step was eliminated from the manufacturing procedures. Brick cheese made from creamed skim milk retentate exhibited a lower pH and higher whey-fat loss than control cheese. It was more firm and mealy, possessed a greater acid flavor and less intense cheese flavor, and ranked lower in overall preference than control cheese in evaluation by expert graders. Higher whey-fat losses but similar pH were obtained with Colby cheese prepared from creamed skim milk retentate as compared to control cheese. Evaluation by a sensory analysis panel indicated no differences in overall preference between experimental cheese at an age of 3 mo as compared to commercial Cheddar and " Colby cheeses of similar age.
Abrogation of p53 Function Affects gadd Gene Responses to DNA Base-Damaging Agents and Starvation (1996)

The tumor suppressor p53 is required for induction of its downstream effector genes such as GADD45 and CIP1/WAF1 by ionizing radiation (IR). This response is probably mediated through defined p53 binding sites located in the promoter of CIP1/WAF1 and in the third intron of GADD45. In contrast, the gadd gene stress response to base-damaging agents, such as methylmethane sulfonate (MMS) or UV radiation, or medium depletion (starvation) occurs in all mammalian cells examined to date regardless of p53 status for both GADD45 and also GADD153, which is not IR-responsive in many lines with functional p53. These agents strongly induce the p53 protein and raise the possibility that, although p53 is not required for the typical "gadd" response to these agents, p53 may contribute to these non-IR stress responses. This possibility was confirmed by the finding that disruption of p53 function by transfection with dominant-negative vectors expressing HPV E6, mutant p53, or SV40 T Ag reduced the induction of GADD45 and GADD153 as measured by increases in mRNA and protein levels in human lines with wild-type p53. Similarly, induction of these genes by MMS or UV radiation was consistently stronger in the parental mouse embryo fibroblasts compared to cells derived from mice where both p53 alleles had been deleted. Similar qualitative responses were also seen for CIP1/WAF1. In agreement with reduced induction of p53-regulated genes, the G1 checkpoint activated by MMS or UV radiation was markedly abrogated in p53-wt human MCF-7 breast carcinoma cells by E6 expression. Interestingly, induction of reporter constructs driven by the GADD45 or GADD153 promoters was substantially reduced in human cells transfected with mutant p53 or E6 expression vectors or in cells lacking p53 following treatment with MMS, UV radiation, or starvation. Because neither promoter is inducible by IR, and neither contains a strong p53 binding site, these results indicate that p53 has a synergistic or cooperative role in these non-IR stress responses for both GADD45 and GADD153, and that this role is not mediated through identifiable p53-binding sites.
Molecular Physiology of Glucose Transporters (1990)

Molecular cloning of cDNA encoding the human erythrocyte facilitated-diffusion glucose transporter (GT) has elucidated its structure and has permitted a careful study of its tissue distribution and of its involvement in processes such as insulin-stimulated glucose uptake by adipose cells or transformation-induced increase in glucose metabolism. An important outcome of these studies was the discovery that additional isoforms of this transporter were expressed in a tissue-specific manner; these comprise a family of structurally and functionally related molecules. Their tissue distribution, differences in kinetic properties, and differential regulation by ambient glucose and insulin levels suggest that they play specific roles in the control of glucose homeostasis. Herein, we will discuss the structure of three members of the GT family: erythroid/brain GT, liver GT, and adipose cell/muscle GT. In the light of their tissue-specific expression, kinetic parameters, and susceptibility to insulin action, we discuss their possible specific functions.