gebhart/patrepeval huggingface dataset:
Digital Quantification of DNA Replication and Chromosome Segregation Enables Determination of Antimicrobial Susceptibility after only 15 Minutes of Antibiotic Exposure (2016)

Abstract Rapid antimicrobial susceptibility testing (AST) would decrease misuse and overuse of antibiotics. The “holy grail” of AST is a phenotype‐based test that can be performed within a doctor visit. Such a test requires the ability to determine a pathogen's susceptibility after only a short antibiotic exposure. Herein, digital PCR (dPCR) was employed to test whether measuring DNA replication of the target pathogen through digital single‐molecule counting would shorten the required time of antibiotic exposure. Partitioning bacterial chromosomal DNA into many small volumes during dPCR enabled AST results after short exposure times by 1) precise quantification and 2) a measurement of how antibiotics affect the states of macromolecular assembly of bacterial chromosomes. This digital AST (dAST) determined susceptibility of clinical isolates from urinary tract infections (UTIs) after 15 min of exposure for all four antibiotic classes relevant to UTIs. This work lays the foundation to develop a rapid, point‐of‐care AST and strengthen global antibiotic stewardship.
Resilience, persistence and unshakeable optimism (2013)

In every quality improvement initiative, leaders will face challenging problems, changing circumstances, and unforeseen difficulties. What sets the successful leader apart is not their superior intellect or natural ability—it's the fact that they do not give up. They stick with an idea or a concept long after the majority have given up and moved onto something easier. As important as what quality improvement leaders do is the fact that they keep doing it. They overcome problems, shrug off setbacks and remain positive. This article explores the much underrated leadership qualities of resilience, persistence and optimism, and explains why these key ingredients are essential to leading a successful quality improvement programme.
High affinity IgG binding by FcgammaRI (CD64) is modulated by two distinct IgSF domains and the transmembrane domain of the receptor (1998)

The high affinity IgG receptor, FcgammaRI, is comprised of three immunoglobulin superfamily (IgSF) domains (EC1, EC2 and EC3), a single transmembrane spanning region, and a short cytoplasmic tail. We have shown a role for three separate domains of FcgammaRI in the high affinity binding of IgG. Affinity measurements of chimeric FcgammaRs in which EC1 and EC2 of FcgammaRI have been replaced with the homologous EC1 and/or EC2 domains of the low affinity IgG receptor, FcgammaRII indicate that both EC2 and EC3 are essential for high affinity binding of monomeric IgG. Identification of EC3 from FcgammaRI as the binding site for the monoclonal antibody 10.1, which blocks IgG binding, provides further evidence for the role of this domain in binding. In addition, we have found that the affinity of FcgammaRI is increased threefold when co-expressed with its accessory molecule, gamma-chain. Affinity measurements of further chimeras indicates that the transmembrane domain of FcgammaRI has a negative influence upon the affinity of the receptor. To account for these observations, we propose that receptor dimerization is required for maximal affinity of FcgammaRI. Dimerization may serve as the mechanism by which IgG binding triggers several FcgammaRI-mediated events.
Long-Term Clinical Outcomes Following Treatment of Actinic Keratosis with Imiquimod 5% Cream (2006)

One and a half years following treatment, imiquimod continued to provide a long-term clinical benefit in a majority of patients who experienced complete clearance of their AK lesions.
Survival of Staphylococcus aureus Inside Neutrophils Contributes to Infection (2000)

Neutrophils have long been regarded as essential for host defense against Staphylococcus aureus infection. However, survival of the pathogen inside various cells, including phagocytes, has been proposed as a mechanism for persistence of this microorganism in certain infections. Therefore, we investigated whether survival of the pathogen inside polymorphonuclear neutrophils (PMN) contributes to the pathogenesis of S. aureus infection. Our data demonstrate that PMN isolated from the site of infection contain viable intracellular organisms and that these infected PMN are sufficient to establish infection in a naive animal. In addition, we show that limiting, but not ablating, PMN migration into the site of infection enhances host defense and that repletion of PMN, as well as promoting PMN influx by CXC chemokine administration, leads to decreased survival of the mice and an increased bacterial burden. Moreover, a global regulator mutant of S. aureus (sar-) that lacks the expression of several virulence factors is less able to survive and/or avoid clearance in the presence of PMN. These data suggest that the ability of S. aureus to exploit the inflammatory response of the host by surviving inside PMN is a virulence mechanism for this pathogen and that modulation of the inflammatory response is sufficient to significantly alter morbidity and mortality induced by S. aureus infection.
Effects of feeding two levels of propionibacteria to dairy cows on plasma hormones and metabolites (2007)

To determine the effect of feeding propionibacteria on metabolic indicators during lactation, multiparous and primiparous Holstein cows were fed one of three dietary treatments in a 2 x 3 factorial design from 2 weeks prepartum to 30 weeks post partum: (1) Control (primiparous n=5, multiparous n=8) fed a total mixed ration (TMR); (2) high-dose group (primiparous n=6, multiparous n=5) fed TMR plus 6 x 10 (11) cfu/head daily (high-dose P169) of propionibacterium strain P169; or (3) low-dose group (primiparous n=8, multiparous n=6) fed TMR plus 6 x 10(10) cfu/head daily (low-dose P169) of P169. Blood samples were collected weekly and analysed for plasma concentrations of glucose, insulin, insulin-like growth factor-I (IGF-I), leptin, nonesterified fatty acids (NEFA) and cholesterol. Between weeks 25 and 30, all groups received bovine somatotropin (bST) every 2 weeks. Low-dose P169 multiparous cows had lower (P<0.05) plasma insulin and glucose concentrations than high-dose P169 multiparous cows, whereas high-dose P169 primiparous cows had lower glucose but greater insulin concentartions than low-dose P169 primiparous cows (P<0.05). Plasma insulinratioglucose molar ratios were 13-18% lower (P<0.05) in low-dose P169 cows than in control or high-dose P169 cows. Plasma IGF-I, NEFA and leptin levels did not differ among diet groups between weeks 1 and 25. Low-dose P169 multiparous cows had 25% greater plasma cholesterol levels than high-dose P169 and control multiparous cows, but cholesterol levels in primiparous cows did not differ. During bST treatment, high-dose P169 multiparous cows and low-dose P169 primiparous cows had lower IGF-I levels than their respective controls and, regardless of parity, high-dose P169 cows had greater NEFA than control cows. Although supplemental feeding of P169 altered plasma hormones and metabolites, the particular effects were dependent on dose of P169 and parity of cows.
Whitney regularity for solutions to the coboundary equation on Cantor sets (2007)

We prove Whitney regularity results for the solutions of the coboundary equation over dynamically defined Cantor sets satisfying a natural geometric regularity condition, in particular hyperbolic basic sets in dimension two. To do this we prove an analogue of Journé’s well-known result in the context of Cantor sets satisfying geometric regularity conditions. 1
Brown adipose tissue thermogenesis in obese animals (1986)

Conference Article| April 01 1986 Brown adipose tissue thermogenesis in obese animals PAUL TRAYHURN; PAUL TRAYHURN 1Dunn Nutrition Laboratory, Medical Research Council and University of Cambridge, Downham's Lane, Milton Road, Cambridge CB4 1XJ, U.K. Search for other works by this author on: This Site PubMed Google Scholar STEWART W. MERCER STEWART W. MERCER 1Dunn Nutrition Laboratory, Medical Research Council and University of Cambridge, Downham's Lane, Milton Road, Cambridge CB4 1XJ, U.K. Search for other works by this author on: This Site PubMed Google Scholar Author and article information Publisher: Portland Press Ltd Online ISSN: 1470-8752 Print ISSN: 0300-5127 © 1986 Biochemical Society1986 Biochem Soc Trans (1986) 14 (2): 236–239. https://doi.org/10.1042/bst0140236 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn Email Cite Icon Cite Get Permissions Citation PAUL TRAYHURN, STEWART W. MERCER; Brown adipose tissue thermogenesis in obese animals. Biochem Soc Trans 1 April 1986; 14 (2): 236–239. doi: https://doi.org/10.1042/bst0140236 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Society Transactions Search Advanced Search Keywords: VMH, ventromedial hypothalamus This content is only available as a PDF. © 1986 Biochemical Society1986 Article PDF first page preview Close Modal You do not currently have access to this content.
Low pH-induced Cell Fusion in Flavivirus-infected Aedes Albopictus Cell Cultures (1990)

Cell-to-cell fusion of Aedes albopictus (mosquito) cells infected with dengue and St Louis encephalitis (SLE) flaviviruses was induced by exposure to low pH. The parameters of this low pH-induced fusion were examined. Syncytium formation was maximal in cultures 36 to 48 h post-infection and occurred when cultures were maintained at the acid pH for 15 min at 35 degrees C. The optimal pH range for fusion was 5.0 to 6.5 for dengue virus-infected cells and 5.0 to 5.5 for SLE virus-infected cells. Syncytia were not observed in vertebrate cells (Vero and BHK) under these conditions despite similar virus yields. Fusion was shown to be ATP-dependent and could be prevented by the addition of either polyclonal antiviral antibodies or monoclonal antibody to the envelope glycoprotein. The lysosomotropic amine ammonium chloride inhibited the replication of SLE virus in both mosquito and vertebrate cells, consistent with the idea that low pH-induced fusion is necessary for virus entry into both types.
Comparison of the efficiency of some novel maize promoters in monocot and dicot plants (2002)

Three novel maize promoters (Gos-2, Enolase and Actin-2) were evaluated for their efficiency in driving the GUS gene expression in plant tissues. Three plasmids were constructed to contain the GUS gene in combination with the three promoters and another three plasmids were constructed to contain the GUS gene in combination with the three promoters and the INTIUBIZM intron. The six plasmids were employed in the transformation of maize immature embryos (as a monocot system) and tomato leaflets (as a dicot system). The transformation was conducted using the biolistic particle delivery system. Our results revealed the efficiency of the newly isolated maize promoters in both monocots and dicots. However, the level of activity of the different promoters was variable in both systems. Among the six plasmids, the Gos-2 was determined as the most efficient promoter in driving the transient GUS gene expression in maize, while maize Actin-2 in the plasmid bearing an intron revealed the highest GUS expression in tomato leaflets.
Assimilation of Cellooligosaccharides by a Cell Surface-Engineered Yeast Expressing β-Glucosidase and Carboxymethylcellulase from Aspergillus aculeatus (1998)

Since Saccharomyces cerevisiae lacks the cellulase complexes that hydrolyze cellulosic materials, which are abundant in the world, two types of hydrolytic enzymes involved in the degradation of cellulosic materials to glucose were genetically co-immobilized on its cell surface for direct utilization of cellulosic materials, one of the final goals of our studies. The genes encoding FI-carboxymethylcellulase (CMCase) and beta-glucosidase from the fungus Aspergillus aculeatus were individually fused with the gene encoding the C-terminal half (320 amino acid residues from the C terminus) of yeast alpha-agglutinin and introduced into S. cerevisiae. The delivery of CMCase and beta-glucosidase to the cell surface was carried out by the secretion signal sequence of the native signal sequence of CMCase and by the secretion signal sequence of glucoamylase from Rhizopus oryzae for beta-glucosidase, respectively. The genes were expressed by the glyceraldehyde-3-phosphate dehydrogenase promoter from S. cerevisiae. The CMCase and beta-glucosidase activities were detected in the cell pellet fraction, not in the culture supernatant. The display of CMCase and beta-glucosidase proteins on the cell surface was confirmed by immunofluorescence microscopy. The cells displaying these cellulases could grow on cellobiose or water-soluble cellooligosaccharides as the sole carbon source. The degradation and assimilation of cellooligosaccharides were confirmed by thin-layer chromatography. This result showed that the cell surface-engineered yeast with these enzymes can be endowed with the ability to assimilate cellooligosaccharides. This is the first step in the assimilation of cellulosic materials by S. cerevisiae expressing heterologous cellulase genes.
New High Voltage Pulse Generators (2009)

The use of High Voltage Pulses has found applications in biotechnology, medicine, industrial applications, and food processing and preservation. Biotechnology application includes electro-chemotherapy, gene transfer, electroinsertion of proteins into cell plasma membrane, electrofusion of cells, transdermal drug delivery, water treatment and food. Industrial applications of High Voltage Pulses include the filtering of flue gas particles using electrostatic precipitators, treatment of metal and polymer materials by plasma immersion ion implantation, exciter lasers fabrication, flash radiography or ionization, polarization source in accelerators, insulation testing and so on. Efficiency of all these applications strongly depends on parameters of electric pulses, which are delivered to the treated object using specially developed electrodes and electronic devices. In this paper, the design and structure of high-voltage pulse generator will be described. We have presented most commonly used techniques of signal generation based on various methods such as: Marx cells and spark gaps, MOSFET series and parallel, IGBT, nonlinear capacitor, static induction thyristor, and modular high voltage. Methods of high voltage pulse generators based on various shape of pulse are also presented. Keywords: Marx generator, MOSFET, IGBT, nonlinear capacitor, pulse shaping network, thyristor
An Ethylene-Inducible Component of Signal Transduction Encoded by Never-ripe (1995)

The ripening-impaired tomato mutant Never-ripe (Nr) is insensitive to the plant hormone ethylene. The gene that cosegregates with the Nr locus encodes a protein with homology to the Arabidopsis ethylene receptor ETR1 but is lacking the response regulator domain found in ETR1 and related prokaryotic two-component signal transducers. A single amino acid change in the sensor domain confers ethylene insensitivity when expressed in transgenic tomato plants. Modulation of NR gene expression during fruit ripening controls response to the hormone ethylene.
Endoscopic screening of relatives of patients with colorectal cancer (1998)

For individuals with two or more first degree relatives, or relatives who have developed colorectal cancer at a young age, colonoscopy appears to be the only satisfactory method of screening, but 60 cm flexible sigmoidoscopy may be useful in those at lower levels of risk.
Prediction of Slug Frequency for Gas/Liquid Flows (2000)

Summary During slug flow, knowledge of the slug frequency is essential for the gas-liquid receiving facility design as well as for predicting various slug flow characteristics such as slug length and pressure drop. Various methods proposed in the literature for predicting the slugging frequency in horizontal and inclined pipes were examined. These included both empirical correlations as well as mechanistic models. Slug flow frequency data taken with an air-water system in a laboratory flow loop together with data from the published literature were compared to the predictions of the various methods. A total of 399 data points were collected covering pipe diameters from 1 to 8 in. and inclinations from 0 to 11° above the horizontal. A total of eight published methods were compared to the data but none was found satisfactory. For this reason, the mechanistic slug frequency model of Taitel and Dukler1 was investigated in detail as an alternative unbiased prediction method. This model required the solution of the unsteady-state equations for mass and momentum by a finite difference technique. This numerical model gave satisfactory results at the expense of considerable computer CPU time. For faster slug frequency calculations a new correlation was developed utilizing all 399 data points. This resulted in 0% average error (bias) and 60% average absolute error. This correlation represents a significant improvement in slug frequency prediction accuracy over the other methods studied.
Accuracy of replication in the polymerase chain reaction. Comparison between Thermotoga maritima DNA polymerase and Thermus aquaticus DNA polymerase (1998)

For certain applications of the polymerase chain reaction (PCR), it may be necessary to consider the accuracy of replication. The breakthrough that made PCR user friendly was the commercialization of Thermus aquaticus (Taq) DNA polymerase, an enzyme that would survive the high temperatures needed for DNA denaturation. The development of enzymes with an inherent 3' to 5' exonuclease proofreading activity, lacking in Taq polymerase, would be an improvement when higher fidelity is needed. We used the forward mutation assay to compare the fidelity of Taq polymerase and Thermotoga maritima (ULTMA) DNA polymerase, an enzyme that does have proofreading activity. We did not find significant differences in the fidelity of either enzyme, even when using optimal buffer conditions, thermal cycling parameters, and number of cycles (0.2% and 0.13% error rates for ULTMA and Taq, respectively, after reading about 3,000 bases each). We conclude that for sequencing purposes there is no difference in using a DNA polymerase that contains an inherent 3' to 5' exonuclease activity for DNA amplification. Perhaps the specificity and fidelity of PCR are complex issues influenced by the nature of the target sequence, as well as by each PCR component.
Purification and Cloning of a Protein Kinase That Phosphorylates and Activates the Polo-Like Kinase Plx1 (1998)

The Xenopus polo-like kinase 1 (Plx1) is essential during mitosis for the activation of Cdc25C, for spindle assembly, and for cyclin B degradation. Polo-like kinases from various organisms are activated by phosphorylation by an unidentified protein kinase. A protein kinase, polo-like kinase kinase 1 or xPlkk1, that phosphorylates and activates Plx1 in vitro was purified to near homogeneity and cloned. Phosphopeptide mapping of Plx1 phosphorylated in vitro by recombinant xPlkk1 or in progesterone-treated oocytes indicates that xPlkk1 may activate Plx1 in vivo. The xPlkk1 protein itself was also activated by phosphorylation on serine and threonine residues, and the kinetics of activation of xPlkk1 in vivo closely paralleled the activation of Plx1. Moreover, microinjection of xPlkk1 into Xenopus oocytes accelerated the timing of activation of Plx1 and the transition from G2 to M phase of the cell cycle. These results define a protein kinase cascade that regulates several events of mitosis.
Intraarterial Administration of Marrow Stromal Cells in a Rat Model of Traumatic Brain Injury (2001)

To test the efficacy of various delivery routes of stem cells to treat cerebral injury, we investigated the parenchymal distribution of marrow stromal cells (MSCs) injected into the internal carotid artery (ICA) of the adult rat after traumatic brain injury (TBI). Bromodeoxyuridine (BrdU)-labeled MSCs were injected via the ipsilateral ICA at 24 h after TBI. Using histology and immunohistochemistry, the distribution of implanted MSCs was analyzed at 7 days after transplantation. Four groups (n = 4/group) were studied: group 1, animals transplanted with MSCs cultured with NGF and BDNF at 24 h after TBI; group 2, animals transplanted with MSCs cultured without NGF and BDNF; group 3, animals injected with a placebo, phosphate buffered saline into the ICA at 24 h after TBI; and group 4, rats subjected to TBI only. In groups 1 and 2, BrdU-positive cells were localized to the boundary zone of the lesion, corpus callosum and cortex of the ipsilateral hemisphere. The number of BrdU-positive cells was significantly higher in the ipsilateral hemisphere than in the contralateral hemisphere. More MSCs infused intraarterially engrafted in group 1 (18.9%) than in group 2 (14.4%, p < 0.05). Using double staining, BrdU-positive cells expressed MAP-2, NeuN, and GFAP in both groups 1 and 2, with this expression being greater in group 1 and the difference between two groups reaching statistical significance in case of MAP-2. Our data suggest that intraarterial transplantation of MSCs is a viable route for the intracerebral administration of MSCs for the treatment of TBI, since MSCs infused intraarterially after TBI survive and migrate into the brain. Some implanted MSCs express proteins specific to neurons and astrocytes. The addition of NGF and BDNF promote migration of MSCs into the brain and subsequent expression of neuronal protein MAP-2.
Sniffing around oxytocin: review and meta-analyses of trials in healthy and clinical groups with implications for pharmacotherapy (2013)

The popularity of oxytocin (OT) has grown exponentially during the past decade, and so has the number of OT trials in healthy and clinical groups. We take stock of the evidence from these studies to explore potentials and limitations of pharmacotherapeutic applications. In healthy participants, intranasally administered OT leads to better emotion recognition and more trust in conspecifics, but the effects appear to be moderated by context (perceived threat of the 'out-group'), personality and childhood experiences. In individuals with untoward childhood experiences, positive behavioral or neurobiological effects seem lowered or absent. In 19 clinical trials, covering autism, social anxiety, postnatal depression, obsessive-compulsive problems, schizophrenia, borderline personality disorder and post-traumatic stress, the effects of OT administration were tested, with doses ranging from 15 IU to more than 7000 IU. The combined effect size was d=0.32 (N=304; 95% confidence interval (CI): 0.18-0.47; P<0.01). However, of all disorders, only studies on autism spectrum disorder showed a significant combined effect size (d=0.57; N=68; 95% CI: 0.15-0.99; P<0.01). We hypothesize that for some of the other disorders, etiological factors rooted in negative childhood experiences may also have a role in the diminished effectiveness of treatment with OT.
A Statistical Model-Based V/UV Decision under Background Noise Environments (2004)

SUMMARY In this letter, we propose an approach to incorporate a statistical model for the voiced/unvoiced (V/UV) speech decision under background noise environments. Our approach consists of splitting the input noisy speech into two separate bands and applying a statistical model for each band. We compute and compare the likelihood ratio (LR) for each band based on the statistical model and estimated noise statistics for the V/UV decision. According to the simulation test, the proposed V/UV decision shows a better performance compared with the selectable mode vocoder (SMV) V/UV decision algorithm, particularly in clean and white