gebhart/patrepeval huggingface dataset:
<i>Salmonella</i> and <i>Escherichia coli</i> O157:H7 Contamination on Hides and Carcasses of Cull Cattle Presented for Slaughter in the United States: an Evaluation of Prevalence and Bacterial Loads by Immunomagnetic Separation and Direct Plating Methods (2008)

The hide and carcass hygiene of cull cattle at slaughter in four geographically distant regions of the United States was examined from July 2005 to April 2006 by measuring the aerobic plate counts (APC) and the prevalences and loads of Salmonella and Escherichia coli O157:H7. The geometric mean log(10) APC CFU/100 cm(2) levels on hides and preevisceration and postintervention carcasses ranged from 6.17 to 8.19, 4.24 to 6.47, and 1.46 to 1.96, respectively, and were highest in the summer (P < 0.0001). The average prevalences of Salmonella on hides and preevisceration and postintervention carcasses were 89.6% (95% confidence interval [CI], 85.1 to 94.0), 50.2% (95% CI, 40.9 to 59.5), and 0.8% (95% CI, 0.18 to 1.42), respectively. The prevalences of E. coli O157:H7 were 46.9% (95% CI, 37.3 to 56.6) and 16.7% (95% CI, 9.8 to 23.6) on hides and preevisceration carcasses, respectively. Examination of the concomitant incidence of Salmonella and E. coli O157:H7 showed that, on average, 33.3% (95% CI, 15.9 to 69.8) of cattle hide and 4.1% (95% CI, 0.98 to 17.3) of preevisceration carcass samples were contaminated with both pathogens. The pathogen prevalence on hides and carcasses was not significantly affected by the season; however, significant differences were observed between plants with respect to the incoming pathogen load and the ability to mitigate hide-to-carcass transfer. In spite of these differences, postintervention carcass contamination was significantly reduced (P < 0.001), likely as a result of the use of one or more of the processing interventions employed at each of the four processing plants examined.
Effect of Emulsifier Concentration and Acid Volume Fraction on the Elastic Properties of Emulsified Acids (2011)

Abstract Acid in diesel emulsified acids have been used in the oilfield for many years. Unlike other acid systems, such as gelled and viscoelastic surfactant-based (VES) acids, where the mobility of hydrogen ion controls the overall rate of the reaction, emulsified acid/rock reaction involves the transport of acid droplets in the diesel phase to the rock surface. Upon contact with rock surface, acid droplets breaks and then the actual reaction on the surface occurs. The emulsified acid has several advantages including the minimum number of acid additives and low corrosion rate. The most important properties of emulsified acid are the viscosity, stability and reactivity. These properties are greatly affected by acid droplet size. Based on our knowledge, the effect of the droplet size on the elastic properties of emulsified acid was not studied before. The main objective of this paper is to provide a detailed description of the elastic properties of the emulsified acid. In order to perform that, a HPHT rheometer was used. The oscillatory shear measurements were carried out on a series of emulsified acid samples. Different parameters can affect the behavior of the viscoelastic properties of the emulsified acid; such as emulsifier concentration, acid to diesel volume ratio, and acid additives. The rheological properties depend on the droplet size. At low emulsifier concentration, coarse emulsion, elastic properties were dominant only at high frequency. At high emulsifier concentration, fine emulsions, viscous properties were dominant. Acid additives that affect the droplet size will affect the rheological properties of emulsified acid.
Automatic Detection of Unsafe Dynamic Component Loadings (2011)

Dynamic loading of software components (e.g., libraries or modules) is a widely used mechanism for an improved system modularity and flexibility. Correct component resolution is critical for reliable and secure software execution. However, programming mistakes may lead to unintended or even malicious components being resolved and loaded. In particular, dynamic loading can be hijacked by placing an arbitrary file with the specified name in a directory searched before resolving the target component. Although this issue has been known for quite some time, it was not considered serious because exploiting it requires access to the local file system on the vulnerable host. Recently, such vulnerabilities have started to receive considerable attention as their remote exploitation became realistic. It is now important to detect and fix these vulnerabilities. In this paper, we present the first automated technique to detect vulnerable and unsafe dynamic component loadings. Our analysis has two phases: 1) apply dynamic binary instrumentation to collect runtime information on component loading (online phase), and 2) analyze the collected information to detect vulnerable component loadings (offline phase). For evaluation, we implemented our technique to detect vulnerable and unsafe component loadings in popular software on Microsoft Windows and Linux. Our evaluation results show that unsafe component loading is prevalent in software on both OS platforms, and it is more severe on Microsoft Windows. In particular, our tool detected more than 4,000 unsafe component loadings in our evaluation, and some can lead to remote code execution on Microsoft Windows.
Shadow buttons (2009)

We present Shadow Buttons, an approach to placing WIMP interface elements into gestural and sketch-based interfaces. Utilizing the hover state, supported by pen-based devices such as Tablet PCs, we provide users with important WIMP-based functionality by invoking widgets only when the stylus hovers over "shadow" regions. In this way, every pixel of the display, including the shadows, can be drawn on. By interacting with a shadow region while in the hover state, users can temporarily display and interact with familiar WIMP elements. We explore the Shadow Button design space as it relates to handwritten mathematical expressions and also present an informal evaluation of our technique, examining various Shadow Button parameters including button size, placement, and method of invocation. Preliminary results indicate that users prefer utilizing the hover state over tapping on the Shadow Button and in general, prefer interface elements to be as close to the ink as possible. In addition, the distance between the shadow region and the menu was found to be the most important factor in Shadow Button usability.
Protein Targeting (2014)

Abstract Protein sorting is the process by which cellular proteins, both newly synthesised and recycling, are directed to the appropriate intracellular compartments in which they will perform their function. This process relies upon the targeting signals that are found within each protein. These specific signals can be integrally encoded within the polypeptide sequence or require post‐translational modification of the protein. Targeting signals direct the interaction of proteins with a multitude of accessory factors to ensure the correct delivery of proteins to their appropriate destinations within each cell. Many proteins have multiple targeting signals that are interpreted hierarchically in cellular compartments. Changes in the expression of either the targeting signals or their recognition factors alter the targeting of proteins in different cell types or in response to physiological cues. Key Concepts: Protein targeting signals can be encoded within the polypeptide chain or can be post‐translational modifications or patches. Targeting signals are recognised by cellular factors that direct proteins to their proper site of function. Many proteins have multiple targeting signals. The relative strength of targeting signals can change based on post‐translational modifications such as phosphorylation or accessibility to recognition factors at different locations within cells. Differences in the expression of targeting signals or recognition factors can result in cell‐type dependent, developmental, or acute changes in protein targeting.
Ha-ras proteins exhibit GTPase activity: point mutations that activate Ha-ras gene products result in decreased GTPase activity. (1985)

Several ras genes have been expressed at high levels in Escherichia coli and the resultant ras proteins were shown to be functional with respect to their well-known specific, high-affinity, GDP/GTP binding. We were able to detect a weak GTPase activity associated with the purified proteins. The normal cellular ras protein (p21N) exhibits approximately equal to 10 times higher GTPase activity than the "activated" proteins. Even though the turnover rate of the reaction is very low (0.02 mol of GTP hydrolyzed per mol of p21N protein per minute), the reaction appears to be catalytic; one molecule of p21N hydrolyzes more than one molecule of GTP. The GTPase and the GDP binding activities both have been recovered from a Mr 23,000 protein eluted following NaDodSO4/polyacrylamide gel electrophoresis, suggesting that these two activities are associated with the same protein. Mg2+ ions and dithiothreitol are required for GTPase activity and the optimal pH is between 7 and 8. Guanidine X HCl, which is required for solubilizing bacterially expressed ras protein, is strongly inhibitory to GTPase activity at concentrations higher than 0.5 M.
Small molecule inhibitors of histone acetyltransferases and deacetylases are potential drugs for inflammatory diseases (2013)

Lysine acetylation is a reversible post-translational modification (PTM) of cellular proteins and represents an important regulatory switch in signal transduction. Lysine acetylation, in combination with other PTMs, directs the outcomes as well as the activation levels of important signal transduction pathways such as the nuclear factor (NF)-κB pathway. Small molecule modulators of the 'writers' (HATs) and 'erasers' (HDACs) can regulate the NF-κB pathway in a specific manner. This review focuses on the effects of frequently used HAT and HDAC inhibitors on the NF-κB signal transduction pathway and inflammatory responses, and their potential as novel therapeutics.
Non-alcoholic fatty liver disease short food frequency questionnaire (version 1.0) (2019)

A short food frequency questionnaire (SFFQ) to assess habitual intakes of food items related to non-alcoholic fatty liver disease (NAFLD).
Biochemical and genetic analysis of Streptococcus mutans  -galactosidase (1991)

The aga gene coding for alpha-galactosidase in Streptococcus mutans was detected in a recombinant gene library constructed in phage lambda. The gene was subcloned into plasmid vectors and shown to specify a novel protein of Mr 80,000. Characterization of alpha-galactosidase from S. mutans and from recombinant Escherichia coli expressing aga indicated that the enzyme functions as a tetramer. The amino acid composition of the alpha-galactosidase, deduced from nucleotide sequencing of aga, gave a predicted Mr of 82,022 and revealed regions of homology to alpha-galactosidases encoded by the E. coli Raf plasmids and by Bacillus stearothermophilus. Inactivation of the aga gene in S. mutans resulted in loss of all alpha-galactosidase activity and abolished the ability to ferment melibiose; alpha-glucosidase activity was also lost, due to an indirect effect on the dexB gene.
Antihyperglycemic effects of baicalin on streptozotocin – nicotinamide induced diabetic rats (2010)

The aim of the study was to investigate the effects of baicalin on blood glucose, insulin and cytokine levels. Rat diabetes was induced by intraperitoneal (i.p.) injection of nicotinamide and streptozotocin. Diabetic rats were dosed with i.p. baicalin or oral metformin daily for 8 days. Blood glucose, insulin and hepatic glycogen were determined using conventional methods. The activity of hepatic hexokinase was determined using a coupled assay with glucose-6-phosphate dehydrogenase. Serum levels of interleukin-6 (IL-6), tumor necrosis factor-α (TNF-α) and adiponectin were measured by enzyme-linked immunosorbent assay. Administration of baicalin at 50 or 100 mg/kg significantly decreased plasma glucose levels in a dose dependent manner. The serum insulin level was not increased by baicalin treatment. Administration of baicalin at a high dose (100 mg/kg) resulted in a significant increase of liver glycogen content and a reduction of serum TNF-α. The activity of hepatic hexokinase was significantly increased after dosing baicalin at 25, 50 or 10 mg/kg. Administration of baicalin (50 or 10 mg/kg) or metformin (10 mg/kg) significantly alleviated the morphological injury to the pancreas caused by STZ. The possible mechanisms contributing to the hypoglycemic effect include increasing the hepatic glycogen content and glycolysis, and reducing the serum levels of TNF-α.
Elimination of biofilm and microbial contamination reservoirs in hospital washbasin U-bends by automated cleaning and disinfection with electrochemically activated solutions (2016)

Automated ECA treatment of washbasin U-bends consistently minimizes microbial contamination.
Tetraalkylammonium trihydridocyanoborates. Versatile, selective reagents for reductive aminations in nonpolar media (1981)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTetraalkylammonium trihydridocyanoborates. Versatile, selective reagents for reductive aminations in nonpolar mediaRobert O. Hutchins and Morris MarkowitzCite this: J. Org. Chem. 1981, 46, 17, 3571–3574Publication Date (Print):August 1, 1981Publication History Published online1 May 2002Published inissue 1 August 1981https://pubs.acs.org/doi/10.1021/jo00330a048https://doi.org/10.1021/jo00330a048research-articleACS PublicationsRequest reuse permissionsArticle Views1465Altmetric-Citations40LEARN 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
NG2+ Progenitors Derived From Embryonic Stem Cells Penetrate Glial Scar and Promote Axonal Outgrowth Into White Matter After Spinal Cord Injury (2015)

The glial scar resulting from spinal cord injury is rich in chondroitin sulfate proteoglycan (CSPG), a formidable barrier to axonal regeneration. We explored the possibility of breaching that barrier by first examining the scar in a functional in vitro model. We found that embryonic stem cell-derived neural lineage cells (ESNLCs) with prominent expression of nerve glial antigen 2 (NG2) survived, passed through an increasingly inhibitory gradient of CSPG, and expressed matrix metalloproteinase 9 (MMP-9) at the appropriate stage of their development. Outgrowth of axons from ESNLCs followed because the migrating cells sculpted pathways in which CSPG was degraded. The degradative mechanism involved MMP-9 but not MMP-2. To confirm these results in vivo, we transplanted ESNLCs directly into the cavity of a contused spinal cord 9 days after injury. A week later, ESNLCs survived and were expressing both NG2 and MMP-9. Their axons had grown through long distances (>10 mm), although they preferred to traverse white rather than gray matter. These data are consistent with the concept that expression of inhibitory CSPG within the injury scar is an important impediment to regeneration but that NG2+ progenitors derived from ESNLCs can modify the microenvironment to allow axons to grow through the barrier. This beneficial action may be partly due to developmental expression of MMP-9. We conclude that it might eventually be possible to encourage axonal regeneration in the human spinal cord by transplanting ESNLCs or other cells that express NG2.
Theoretical modeling of thermoelectricity in Bi nanowires (1999)

A theoretical model based on the basic electronic band structure of bulk Bi is developed to predict the dependence of the band structure and thermoelectric properties on nanowire width. By carefully tailoring the Bi wire size and carrier concentration, substantial enhancement in the thermoelectric figure of merit is expected for small nanowire widths.
Daala: A Perceptually-Driven Next Generation Video Codec (2016)

The Daala project is a royalty-free video codec that attempts to compete with the best patent-encumbered codecs. Part of our strategy is to replace core tools of traditional video codecs with alternative approaches, many of them designed to take perceptual aspects into account, rather than optimizing for simple metrics like PSNR. This paper documents some of our experiences with these tools, which ones worked and which did not, and what we've learned from them. The result is a codec which compares favorably with HEVC on still images, and is on a path to do so for video as well.
Excitation energy transfer in DNA: Duplex melting and transfer from normal bases to 2-aminopurine (1993)

Absorption and fluorescence excitation and emission spectra of the B DNA duplex decamer d[CTGA(2AP)TTCAG]2, where emission from the 2AP (2-aminopurine) base dominates, have been measured as a function of temperature. A low-temperature excitation band in the 260-270-nm region disappears near the duplex melting temperature, Tm = 27 degrees C, but then reappears at higher temperatures. Singlet-singlet energy transfer thus occurs between the normal DNA bases and the 2AP base in the B-helical conformation and to a lesser extent in the structurally-mobile melted conformation. The measured efficiency of transfer is 4-5% at 4 degrees C, near 0 at 30 degrees C, and rises again to 1% at 48 degrees C. Nearest-neighbor-only singlet transfer is likely. Such transfer does not offer a likely explanation for UV damage distributions in DNA.
Laser vs. Cold Knife Conization: A Community Hospital Experience (1987)

A retrospective study compared 144 cold knife conizations and 51 laser excisional conizations for postcone infections, healing qualities, surgical techniques, intraoperative and postoperative blood loss, anesthesia and operating time, and the necessity for hospitalization. The relative contributions of these factors to the cost of conization were assessed. There were no postoperative infections in either patient group. The healing qualities of the laser conizations were subjectively considered to be excellent. The majority of laser conizations were performed on outpatients, whereas the majority of patients having cold knife conizations were hospitalized. Intraoperative and postoperative blood loss was less when the laser was used. Although both anesthesia and operating time were shorter with the cold knife techniques, the requirement for hospitalization brought the cost up to that for laser conization.
An Annexin 2 Phosphorylation Switch Mediates p11-dependent Translocation of Annexin 2 to the Cell Surface (2004)

Annexin 2 is a profibrinolytic co-receptor for plasminogen and tissue plasminogen activator that stimulates activation of the major fibrinolysin, plasmin, at cell surfaces. In human subjects, overexpression of annexin 2 in acute promyelocytic leukemia leads to a bleeding diathesis reflective of excessive cell surface annexin 2-dependent generation of plasmin (Menell, J. S., Cesarman, G. M., Jacovina, A. T., McLaughlin, M. A., Lev, E. A., and Hajjar, K. A. (1999) N. Engl. J. Med. 340, 994-1004). In addition, mice completely deficient in annexin 2 display fibrin accumulation within blood vessels and impaired clearance of injury-induced thrombi (Ling Q., Jacovina, A.T., Deora, A.B., Febbraio, M., Simantov, R., Silverstein, R. L., Hempstead, B. L., Mark, W., and Hajjar, K. A. (2004) J. Clin. Investig. 113, 38-48). Here, we show that endothelial cell annexin 2, a protein that lacks a typical signal peptide, translocates from the cytoplasm to the extracytoplasmic plasma membrane in response to brief temperature stress both in vitro and in vivo in the absence of cell death or cell lysis. This regulated response is independent of new protein or mRNA synthesis and does not require the classical endoplasmic reticulum-Golgi pathway. Temperature stress-induced annexin 2 translocation is dependent on both expression of protein p11 (S100A10) and tyrosine phosphorylation of annexin 2 because annexin 2 release is completely eliminated on depletion of p11, inactivation of tyrosine kinase, or mutation of tyrosine 23. Translocation of annexin 2 to the cell surface dramatically increases tissue plasminogen activator-dependent plasminogen activation potential and may represent a novel stress-induced protein secretion pathway.
A Microsatellite Linkage Map of Barramundi, <i>Lates calcarifer</i> (2006)

Barramundi (Lates calcarifer) is an important farmed marine food fish species. Its compact genome (approximately 700 Mb) is among the smallest genomes of food fish species. We established a first-generation genetic linkage map of Barramundi with a mapping panel containing three parents (two males and one female) and 93 progeny. A total of 240 microsatellite markers were mapped into 24 linkage groups. Among these markers, 10 were located in ESTs and known genes. The total lengths of the female and male maps were 873.8 and 414.5 cM with an average marker spacing of 6.20 and 4.70 cM, respectively. Comparing the flanking sequences of the 240 Barramundi microsatellites with the assembled whole-genome sequences of Tetraodon nigrovidiris revealed 55 homologous sequences located in 19 of the 21 chromosomes of T. nigrovidiris. The map will not only enable the mapping of quantitative trait loci, but also provide new resources for understanding the evolution of fish genomes.
PERMEATION OF HYDROGEN THROUGH PALLADIUM/ALUMINA COMPOSITE MEMBRANES (2001)

In this study, the Pd/alumina composite membranes for hydrogen separation were prepared on a disk-type of α-alumina porous support and supported γ-alumina membrane by electroless-plating technique, respectively. The composite membranes with thickness of palladium layer ranging from 7–15 μm are used in the gas permeation experiment under 600–669 K and 50–220 kPa. The experimental results demonstrated that the hydrogen transport through these composite membranes is mainly controlled by solution-diffusion mechanism. It also showed that the selectivity coefficient of H2/N2 in the composite membranes reaches to infinite. The exponential dependency of the hydrogen partial pressure on permeation rate is in the range of 0.627 to 0.688, which is somewhat above that predicted by Sievert's law. Furthermore, the apparent activation energies of hydrogen permeation from the experimental results are within 8.8–9.3 kJ/mol. Additionally, the transport behavior of hydrogen through the bulk Pd layer of Pd/alumina composite membranes were analyzed based on the resistance model. Consequently, the hydrogen flux through a Pd/alumina composite membrane, with a palladium film of 7 μm thick, deviated from Sievert's law. In addition, the hydrogen flux through thick Pd film (15 μm) was observed to be proportional to the difference in the square root of the hydrogen pressure on either side of the film, in accordance with Sievert's law.