gebhart/patrepeval huggingface dataset:
Comparison of five cultural procedures for isolation of Clostridium difficile from stools (1992)

Several procedures have been described for the culture of Clostridium difficile from stool specimens. The goal of this study was to determine the effectiveness of five of these methods for the isolation of C. difficile from feces of patients suspected of having C. difficile-associated illness. A total of 564 stool specimens were cultured by using heat shock, ethanol treatment (ET), and direct plating on Carr-Scarborough cycloserine-cefoxitin-fructose agar (CCFA) with horse blood (C/S medium), BBL CCFA medium, and Remel C. difficile agar. Cytotoxin assays were performed on all specimens. A total of 113 specimens (20%) were positive for C. difficile by one or more methods. The numbers of positive cultures by using heat shock, ET, and direct plating on C/S medium, BBL CCFA medium, and Remel C. difficile agar were 79 (70%), 89 (79%), 91 (81%), 79 (70%), and 52 (46%), respectively. We concluded that ET and direct plating on C/S medium were the most effective procedures for isolating C. difficile from stool specimens and found significant variation in the performance of modified CCFA from different manufacturers.
Identification of the NADH-binding subunit of NADH-ubiquinone oxidoreductase of Paracoccus denitrificans (1990)

The NADH dehydrogenase complex isolated from Paracoccus denitrificans is composed of approximately 10 unlike polypeptides and contains noncovalently bound FMN, non-heme iron, and acid-labile sulfide [Yagi, T. (1986) Arch. Biochem. Biophys. 250, 302-311]. When the Paracoccus NADH dehydrogenase complex was irradiated by UV light in the presence of [adenylate-32P]NAD, radioactivity was incorporated exclusively into one of three polypeptides of Mr approximately 50,000. Similar results were obtained when [adenylate-32P]NADH was used. The labeling of the Mr 50,000 polypeptide was diminished when UV irradiation of the enzyme with [adenylate-32P]NAD was performed in the presence of NADH, but not in the presence of NADP(H). The labeled polypeptide was isolated by preparative sodium dodecyl sulfate gel electrophoresis and was shown to cross-react with antiserum to the NADH-binding subunit (Mr = 51,000) of bovine NADH-ubiquinone oxidoreductase. Its amino acid composition was also very similar to that of the bovine NADH-binding subunit. These chemical and immunological results indicate that the Mr 50,000 polypeptide is an NADH-binding subunit of the Paracoccus NADH dehydrogenase complex.
One-Step Synthesis of Mesoporous Metal−SiO<sub>2</sub> Particles by an Aerosol-Assisted Self-assembly Process (2005)

Spherical mesoporous silica particles with entrapped metal nanoparticles are synthesized from a one-step aerosol-assisted self-assembly process using sols of an alkoxysilane, ethanol, surfactant, water, HCl, and metal precursors (e.g., salts or complexes). Utilizing nitrogen as a carrier gas, the sol is sent through an atomizer, producing aerosol droplets, which are passed through a tubular furnace heated to 400 °C. Solvent evaporation from the droplets enriches the nonvolatile components and results in the coassembly of silicate and surfactant into 3-dimensional mesostructures with incorporated metal precursors. Lamellar, cubic, and hexagonal mesostructures are achieved by using different surfactants. Subsequent calcination of the surfactant and reduction of the metal result in spherical mesostructured porous silica particles with supported metal nanoparticles. Nitrogen sorption techniques, transmission electron microscopy, scanning electron microscopy, and X-ray diffraction are used to characterize the particles. Mesoporous silica particles with 0.5% Pd are tested as a catalyst in the hydrodechlorination reaction of 1,2-dichloroethane and exhibit ∼100% conversion above 350 °C and ∼100% ethylene selectivity, demonstrating the potential of such nanocomposites as catalysts.
Measurement of Induced Activity to Estimate Personnel Radiation Exposures Received from Accelerator Beams (1972)

A method has been developed at the Lawrence Radiation Laboratory in Berkeley to estimate the dose received by an individual accidentally exposed to an accelerator particle beam. The dose estimate is based on measurement of the gross induced activities, primarily 11C, resulting from nuclear interactions of the particle beam with the body tissues of the exposed individual. The activities are measured with a portable NaI crystal gamma-ray scintillation detector. To achieve maximum sensitivity and counting statistics, the activity measurements are made in the LRL Health Physics Group's Low-Background Counting Enclosure soon after exposure. Doses have been estimated by exposing two tissue-equivalent phantoms, one simulating an arm and the other simulating a torso, to particle beams (protons, and secondary beams of protons, pi+ mesons, and neutrons) of various energies. Results indicate that independent of the part of the body exposed, the beam size (6–81 cm2) or the beam energy from 50 MeV to about 6 GeV, the actual dose can be estimated within a factor of 2. Under favorable conditions the lower limit of sensitivity in estimating the dose is less than 1 rem.
Omni-directional 3D Measurement by Hyperbolic Mirror Cameras and Pattern Projection (2008)

In this paper, we propose an omni-directional depth measurement method using hyperbolic mirror cameras and projectors to develop circumference sensing function for autonomous mobile systems, virtual reality systems, and so on. In this method, we use two omni-directional cameras to take images of patterns projected by projectors, and estimate distances from cameras to objects by the stereo method. Especially, we use the space encoding method, vertical lines and small points as projected patterns, and we discuss appropriate pattern projection for distance measurement with omni-directional cameras. As the results of experiments, small points projection can measure distances more accurately than other projection, and we can show the effectiveness of proposed method by measuring 3D depth surrounding cameras using multiple projectors.
Reconciling scratch space consumption, exposure, and volatility to achieve timely staging of job input data (2010)

Innovative scientific applications and emerging dense data sources are creating a data deluge for high-end computing systems. Processing such large input data typically involves copying (or staging) onto the supercomputer's specialized high-speed storage, scratch space, for sustained high I/O throughput. The current practice of conservatively staging data as early as possible makes the data vulnerable to storage failures, which may entail re-staging and consequently reduced job throughput. To address this, we present a timely staging framework that uses a combination of job startup time predictions, user-specified intermediate nodes, and decentralized data delivery to coincide input data staging with job start-up. By delaying staging to when it is necessary, the exposure to failures and its effects can be reduced. Evaluation using both PlanetLab and simulations based on three years of Jaguar (No. 1 in Top500) job logs show as much as 85.9% reduction in staging times compared to direct transfers, 75.2% reduction in wait time on scratch, and 2.4% reduction in usage/hour.
Prophylaxis in severe forms of von Willebrand's disease: results from the von Willebrand Disease Prophylaxis Network (VWD PN) (2012)

The bleeding patterns of severe von Willebrand's disease (VWD) adversely affect quality of life, and may be life threatening. There is a presumed role for prophylaxis with VWF-containing concentrates, but data are scarce. The von Willebrand Disease Prophylaxis Network (VWD PN) was formed to investigate the role of prophylaxis in clinically severe VWD that is not responsive to other treatment(s).Using a retrospective design, the effect of prophylaxis was studied. Availability of records to document, or reliably assess, the type and frequency of bleeding episodes prior to, and after, the initiation of prophylaxis was required. Annualized bleeding rates were calculated for the period prior to prophylaxis, during prophylaxis and by primary bleeding indication defined as the site accounting for more than half of all bleeding symptoms. The Wilcoxon signed-rank test of differences in the medians was used. Sixty-one subjects from 20 centres in 10 countries were enrolled. Data for 59 were used in the analysis. The median age at onset of prophylaxis was 22.4 years. Type 3 VWD accounted for the largest number (N = 34, 57.6%). Differences in bleeding rates within individuals during compared with before prophylaxis were significant for the total group (P < 0.0001), and for those with primary bleeding indications of epistaxis (P = 0.0005), joint bleeding (P = 0.002) and GI bleeding (P = 0.001). The effect of prophylaxis was similar among those age < 18 years and those ≥ 18. One person developed an inhibitor during treatment. We conclude that prophylactic treatment of VWD is efficacious.
(2,4-<i>cis</i> and <i>trans</i>)-Gigantecinone and 4-Deoxygigantecin, Bioactive Nonadjacent Bis-Tetrahydrofuran Annonaceous Acetogenins, from <i>Goniothalamus giganteus</i> (1997)

Two new acetogenins, (2,4-cis and trans)-gigantecinone (1), isolated as a mixture, and 4-deoxygigantecin (2), a known acetogenin whose absolute stereochemistry has not been determined previously, were isolated using activity-directed fractionation, from the bark of Goniothalamus giganteus. A key step in solving their absolute stereochemistries was the preparation of 1,4-diol formaldehyde acetal derivatives (1b and 2a). Using the advanced Mosher ester method and circular dichroism, the absolute stereochemistries of 1 and 2 were revealed and were found to be the same as that of gigantecin (3), which supports a common biogenetic origin. Both 1 and 1b showed potent and selective cytotoxicities against the PC-3 human prostate adenocarcinoma cell line. Against yellow fever mosquito larvae, 1 and 2 were more potent than rotenone in pesticidal activity. Longimicin C and a mixture of (2,4-cis and trans)-isoannonacin were also isolated for the first time from this species.
A Novel Timing and Frequency Synchronization Scheme for OFDM Systems (2007)

A new training symbol is designed and a novel timing and frequency synchronization scheme for orthogonal frequency division multiplexing systems is proposed. The timing synchronization is accomplished by using the symmetric conjugate of the training symbol in time domain and the frequency synchronization is finished by utilizing the good autocorrelation of the training symbol in frequency domain. The simulation results show that the scheme gives very accurate estimates of symbol timing and carrier frequency offset and provides a very wide acquisition range for the carrier frequency offset.
<i>O</i> -Mannosyltransferase 1 in <i>Aspergillus fumigatus</i> (AfPmt1p) Is Crucial for Cell Wall Integrity and Conidium Morphology, Especially at an Elevated Temperature (2007)

Protein O-mannosyltransferases initiate O mannosylation of secretory proteins, which are of fundamental importance in eukaryotes. In this study, the PMT gene family of the human fungal pathogen Aspergillus fumigatus was identified and characterized. Unlike the case in Saccharomyces cerevisiae, where the PMT family is highly redundant, only one member of each PMT subfamily, namely, Afpmt1, Afpmt2, and Afpmt4, is present in A. fumigatus. Mutants with a deletion of Afpmt1 are viable. In vitro and in vivo activity assays confirmed that the protein encoded by Afpmt1 acts as an O-mannosyltransferase (AfPmt1p). Characterization of the DeltaAfpmt1 mutant showed that a lack of AfPmt1p results in sensitivity to elevated temperature and defects in growth and cell wall integrity, thereby affecting cell morphology, conidium formation, and germination. In a mouse model, Afpmt1 was not required for the virulence of A. fumigatus under the experimental conditions used.
Security of employee entitlements : corporate governance issues (2008)

Following the collapse across the last decade of a number of large organizations such as Enron in the USA and several domestic organizations including Ansett Airlines, HIH Insurance and One.Tel, much discussion has ensued about the need to secure employee entitlements. However, tangible improvements in this area are elusive. Good corporate governance policies would suggest that deferred obligations as well as current debts should not be neglected and that appropriate arrangements be put in place to adequately fund employee entitlements. In this paper we consider recent Australian attempts to introduce better governance of employee entitlements.
Peptide and Amino Acid Transporters Are Differentially Regulated during Seed Development and Germination in Faba Bean (2003)

Two peptide transporter (PTR) homologs have been isolated from developing seeds of faba bean (Vicia faba). VfPTR1 was shown to be a functional peptide transporter through complementation of a yeast mutant. Expression patterns of VfPTR1 and VfPTR2 as well as of the amino acid permease VfAAP1 (Miranda et al., 2001) were compared throughout seed development and germination. In developing seeds, the highest levels of VfPTR1 transcripts were reached during midcotyledon development, whereas VfAAP1 transcripts were most abundant during early cotyledon development, before the appearance of storage protein gene transcripts, and were detectable until late cotyledon development. During early germination, VfPTR1 mRNA appeared first in cotyledons and later, during seedling growth, also in axes and roots. Expression of VfPTR2 and VfAAP1 was delayed compared with VfPTR1, and was restricted to the nascent organs of the seedlings. Localization of VfPTR1 transcripts showed that this PTR is temporally and spatially regulated during cotyledon development. In germinating seeds, VfPTR1 mRNA was localized in root hairs and root epidermal cells, suggesting a role in nutrient uptake from the soil. In seedling roots, VfPTR1 was repressed by a dipeptide and by an amino acid, whereas nitrate was without influence.
Morphological, physiological, and biochemical changes in rhodopsin knockout mice (1999)

Mutations in rod opsin, the visual pigment protein of rod photoreceptors, account for approximately 15% of all inherited human retinal degenerations. However, the physiological and molecular events underlying the disease process are not well understood. One approach to this question has been to study transgenic mice expressing opsin genes containing defined mutations. A caveat of this approach is that even the overexpression of normal opsin leads to photoreceptor cell degeneration. To overcome the problem, we have reduced or eliminated endogenous rod opsin content by targeted gene disruption. Retinas in mice lacking both opsin alleles initially developed normally, except that rod outer segments failed to form. Within months of birth, photoreceptor cells degenerated completely. Retinas from mice with a single copy of the opsin gene developed normally, and rods elaborated outer segments of normal size but with half the normal complement of rhodopsin. Photoreceptor cells in these retinas also degenerated but did so over a much slower time course. Physiological and biochemical experiments showed that rods from mice with a single opsin gene were approximately 50% less sensitive to light, had accelerated flash-response kinetics, and contained approximately 50% more phosducin than wild-type controls.
An approximate deconvolution procedure for large-eddy simulation (1999)

An alternative approach to large-eddy simulation based on approximate deconvolution (ADM) is developed. The main ingredient is an approximation of the nonfiltered field by truncated series expansion of the inverse filter operator. A posteriori tests for decaying compressible isotropic turbulence show excellent agreement with direct numerical simulation. The computational overhead of ADM is similar to that of a scale-similarity model and considerably less than for dynamic models.
Monitoring of Global Cerebral Ischemia Using Wavelet Entropy Rate of Change (2005)

In this paper, the subband wavelet entropy (SWE) and its time difference are proposed as two quantitative measures for analyzing and segmenting the electroencephalographic (EEG) signals. SWE for EEG subbands, namely Delta, Theta, Alpha, Beta, and Gamma, is calculated and segmented using wavelet analysis. In addition, a time difference entropy measure was calculated because it does not require a baseline and equals to zero in all clinical bands as the initial condition. Visual and quantitative results were obtained from 11 rodents that were subjected to 3, 5, and 7 min of global ischemic brain injury by asphyxic cardiac arrest. We found that the time difference of SWE is capable of amplifying the variations between clinical bands during the various stages of the recovery process and may serve as a novel analytical approach to grade and classify brain rhythms during global ischemic brain injury and recovery.
Determinants for Sensitivity of Human Immunodeficiency Virus Coreceptor CXCR4 to the Bicyclam AMD3100 (1998)

The bicyclam AMD3100 is a potent and selective inhibitor of the replication of human immunodeficiency virus type 1 and type 2 (HIV-1 and HIV-2). It was recently demonstrated that the compound inhibited HIV entry through CXCR4 but not through CCR5. Selectivity of AMD3100 for CXCR4 was further indicated by its lack of effect on HIV-1 and HIV-2 infection mediated by the CCR5, CCR3, Bonzo, BOB, and US28, coreceptors. AMD3100 completely blocked HIV-1 infection mediated by a mutant CXCR4 bearing a deletion of most of the amino-terminal extracellular domain. In contrast, relative resistance to AMD3100 was conferred by different single amino acid substitutions in the second extracellular loop (ECL2) or in the adjacent membrane-spanning domain, TM4. Only substitutions of a neutral residue for aspartic acid and of a nonaromatic residue for phenylalanine (Phe) were associated with drug resistance. This suggests a direct interaction of AMD3100 with these amino acids rather than indirect effects of their mutation on the CXCR4 structure. The interaction of aspartic acids of ECL2 and TM4 with AMD3100 is consistent with the positive charge of bicyclams, which might block HIV-1 entry by preventing electrostatic interactions between CXCR4 and the HIV-1 envelope protein gp120. Other features of AMD3100 must account for its high antiviral activity, in particular the presence of an aromatic linker between the cyclam units. This aromatic group might engage in hydrophobic interactions with the Phe-X-Phe motifs of ECL2 or TM4. These results confirm the importance of ECL2 for the HIV coreceptor activity of CXCR4.
Carbon source utilization and inhibitor tolerance of 45 oleaginous yeast species (2014)

Conversion of lignocellulosic hydrolysates to lipids using oleaginous (high lipid) yeasts requires alignment of the hydrolysate composition with the characteristics of the yeast strain, including ability to utilize certain nutrients, ability to grow independently of costly nutrients such as vitamins, and ability to tolerate inhibitors. Some combination of these characteristics may be present in wild strains. In this study, 48 oleaginous yeast strains belonging to 45 species were tested for ability to utilize carbon sources associated with lignocellulosic hydrolysates, tolerate inhibitors, and grow in medium without supplemented vitamins. Some well-studied oleaginous yeast species, as well as some that have not been frequently utilized in research or industrial production, emerged as promising candidates for industrial use due to ability to utilize many carbon sources, including Cryptococcus aureus, Cryptococcus laurentii, Hannaella aff. zeae, Tremella encephala, and Trichosporon coremiiforme. Other species excelled in inhibitor tolerance, including Candida aff. tropicalis, Cyberlindnera jadinii, Metschnikowia pulcherrima, Schwanniomyces occidentalis and Wickerhamomyces ciferrii. No yeast tested could utilize all carbon sources and tolerate all inhibitors tested. These results indicate that yeast strains should be selected based on characteristics compatible with the composition of the targeted hydrolysate. Other factors to consider include the production of valuable co-products such as carotenoids, availability of genetic tools, biosafety level, and flocculation of the yeast strain. The data generated in this study will aid in aligning yeasts with compatible hydrolysates for conversion of carbohydrates to lipids to be used for biofuels and other oleochemicals.
Serum-free transfection and selection in Chinese hamster ovary (CHO) cells. (1993)

In this report a method for transfection and selection of mammalian cells in serum-free medium is described. Chinese hamster ovary (CHO) cells were grown in serum-free medium in plastic dishes coated with one of the following attachment factors: poly-D-lysine, Cell-Tak (polyphenolic proteins extracted from the marine mussel Mytilus edulis), fibronectin or laminin. Cells grown to 80% confluence were transfected with an expression vector encoding the hygromycin resistance gene as a selectable marker and beta-galactosidase as the reporter gene. Transfectants were selected using hygromycin at a concentration of 500 micrograms/ml. Both fibronectin and laminin supported colony formation following selection in serum-free medium. However, poly-D-lysine and Cell-Tak did not. This method can, thus, be used to select for clones producing a recombinant product in cells that are growing in serum-free medium from the onset to provide a better system from which to purify proteins.
Effect of a pyruvate kinase (pykF-gene) knockout mutation on the control of gene expression and metabolic fluxes in Escherichia coli (2004)

The metabolic regulation of Escherichia coli lacking a functional pykF gene was investigated based on gene expressions, enzyme activities, intracellular metabolite concentrations and the metabolic flux distribution obtained based on (13)C-labeling experiments. RT-PCR revealed that the glycolytic genes such as glk, pgi, pfkA and tpiA were down regulated, that ppc, pckA, maeB and mdh genes were strongly up-regulated, and that the oxidative pentose phosphate pathway genes such as zwf and gnd were significantly up-regulated in the pykF mutant. The catabolite repressor/activator gene fruR was up-regulated in the pykF mutant, but the adenylate cyclase gene cyaA was down-regulated indicating a decreased rate of glucose uptake. This was also ascertained by the degradation of ptsG mRNA, the gene for which was down-regulated in the pykF mutant. In general, the changes in enzyme activities more or less correlated with ratios of gene expression, while the changes in metabolic fluxes did not correlate with enzyme activities. For example, high flux ratios were obtained through the oxidative pentose phosphate pathway due to an increased concentration of glucose-6-phosphate rather than to favorable enzyme activity ratios. In contrast, due to decreased availability of pyruvate (and acetyl coenzyme A) in the pykF mutant compared with the wild type, low flux ratios were found through lactate and acetate forming pathways.