gebhart/patrepeval huggingface dataset:
Rapid, Single-Cell Analysis and Discovery of Vectored mRNA Transfection In Vivo with a loxP-Flanked tdTomato Reporter Mouse (2017)

mRNA therapeutics hold promise for the treatment of diseases requiring intracellular protein expression and for use in genome editing systems, but mRNA must transfect the desired tissue and cell type to be efficacious. Nanoparticle vectors that deliver the mRNA are often evaluated using mRNA encoding for reporter genes such as firefly luciferase (FLuc); however, single-cell resolution of mRNA expression cannot generally be achieved with FLuc, and, thus, the transfected cell populations cannot be determined without additional steps or experiments. To more rapidly identify which types of cells an mRNA formulation transfects in vivo, we describe a Cre recombinase (Cre)-based system that permanently expresses fluorescent tdTomato protein in transfected cells of genetically modified mice. Following in vivo application of vectored Cre mRNA, it is possible to visualize successfully transfected cells via Cre-mediated tdTomato expression in bulk tissues and with single-cell resolution. Using this system, we identify previously unknown transfected cell types of an existing mRNA delivery vehicle in vivo and also develop a new mRNA formulation capable of transfecting lung endothelial cells. Importantly, the same formulations with mRNA encoding for fluorescent protein delivered to wild-type mice did not produce sufficient signal for any visualization in vivo, demonstrating the significantly improved sensitivity of our Cre-based system. We believe that the system described here may facilitate the identification and characterization of mRNA delivery vectors to new tissues and cell types.
Optimizing CNN model inference on CPUs (2019)

The popularity of Convolutional Neural Network (CNN) models and the ubiquity of CPUs imply that better performance of CNN model inference on CPUs can deliver significant gain to a large number of users. To improve the performance of CNN inference on CPUs, current approaches like MXNet and Intel OpenVINO usually treat the model as a graph and use the high-performance libraries such as Intel MKL-DNN to implement the operations of the graph. While achieving reasonable performance on individual operations from the off-the-shelf libraries, this solution makes it inflexible to conduct optimizations at the graph level, as the local operation-level optimizations are predefined. Therefore, it is restrictive and misses the opportunity to optimize the end-to-end inference pipeline as a whole. This paper presents \emph{NeoCPU}, a comprehensive approach of CNN model inference on CPUs that employs a full-stack and systematic scheme of optimizations. \emph{NeoCPU} optimizes the operations as templates without relying on third-parties libraries, which enables further improvement of the performance via operation- and graph-level joint optimization. Experiments show that \emph{NeoCPU} achieves up to 3.45$\times$ lower latency for CNN model inference than the current state-of-the-art implementations on various kinds of popular CPUs.
Fe2O3-CNT composite nanofibers as anodes for lithium ion batteries (2019)

Fe<sub>2</sub>O<sub>3</sub>-CNT composite nanofibers are prepared by electrospinning as anodes for lithium-ion batteries. CNTs with high electrical conductivity were distributed homogeneously in Fe<sub>2</sub>O<sub>3</sub>-CNT composite nanofibers. Therefore, electrons could be transferred efficiently by CNTs network during repeated cycles. Moreover, the pores between CNTs facilitate penetration of electrolyte into the structure. The initial discharge capacity of Fe<sub>2</sub>O<sub>3</sub>-CNT composite nanofibers at a current density of 100 mA g<sup>-1</sup> was 770 mA h g<sup>-1</sup>. Additionally, the Coulombic efficiency of the cell maintained above 99 % during 300 cycles. The synergistic effects of Fe<sub>2</sub>O<sub>3</sub>-CNT composite nanofibers containing CNTs and pores efficiently could improve the lithium ion storage property of the cell.
OXA-24 Carbapenemase Gene Flanked by XerC/XerD-Like Recombination Sites in Different Plasmids from Different <i>Acinetobacter</i> Species Isolated during a Nosocomial Outbreak (2010)

A clinical strain of Acinetobacter calcoaceticus resistant to carbapenems was isolated from a blood culture sample from an inpatient in a hospital in Madrid (Spain) during a large outbreak of infection (affecting more than 300 inpatients), caused by a multidrug-resistant Acinetobacter baumannii clone. The carbapenem resistance in both the A. calcoaceticus and A. baumannii clones was due to a bla(OXA-24) gene harbored in different plasmids. The plasmids were fully sequenced, revealing the presence of site-specific recombination binding sites putatively involved in mobilization of the bla(OXA-24) gene. Comparison of plasmids contained in the two strains revealed possible horizontal transmission of resistance genes between the Acinetobacter species.
PGC-1α regulation by exercise training and its influences on muscle function and insulin sensitivity (2010)

The peroxisome proliferator-activated receptor-gamma (PPARgamma) coactivator-1alpha (PGC-1alpha) is a major regulator of exercise-induced phenotypic adaptation and substrate utilization. We provide an overview of 1) the role of PGC-1alpha in exercise-mediated muscle adaptation and 2) the possible insulin-sensitizing role of PGC-1alpha. To these ends, the following questions are addressed. 1) How is PGC-1alpha regulated, 2) what adaptations are indeed dependent on PGC-1alpha action, 3) is PGC-1alpha altered in insulin resistance, and 4) are PGC-1alpha-knockout and -transgenic mice suitable models for examining therapeutic potential of this coactivator? In skeletal muscle, an orchestrated signaling network, including Ca(2+)-dependent pathways, reactive oxygen species (ROS), nitric oxide (NO), AMP-dependent protein kinase (AMPK), and p38 MAPK, is involved in the control of contractile protein expression, angiogenesis, mitochondrial biogenesis, and other adaptations. However, the p38gamma MAPK/PGC-1alpha regulatory axis has been confirmed to be required for exercise-induced angiogenesis and mitochondrial biogenesis but not for fiber type transformation. With respect to a potential insulin-sensitizing role of PGC-1alpha, human studies on type 2 diabetes suggest that PGC-1alpha and its target genes are only modestly downregulated (< or =34%). However, studies in PGC-1alpha-knockout or PGC-1alpha-transgenic mice have provided unexpected anomalies, which appear to suggest that PGC-1alpha does not have an insulin-sensitizing role. In contrast, a modest ( approximately 25%) upregulation of PGC-1alpha, within physiological limits, does improve mitochondrial biogenesis, fatty acid oxidation, and insulin sensitivity in healthy and insulin-resistant skeletal muscle. Taken altogether, there is substantial evidence that the p38gamma MAPK-PGC-1alpha regulatory axis is critical for exercise-induced metabolic adaptations in skeletal muscle, and strategies that upregulate PGC-1alpha, within physiological limits, have revealed its insulin-sensitizing effects.
Packaging Technologies for High Temperature Electronics and Sensors (2013)

This paper reviews ceramic substrates and thick-film metallization based packaging technologies in development for 500degC silicon carbide (SiC) electronics and sensors. Prototype high temperature ceramic chip-level packages and printed circuit boards (PCBs) based on ceramic substrates of aluminum oxide (Al2O3) and aluminum nitride (AlN) have been designed and fabricated. These ceramic substrate-based chiplevel packages with gold (Au) thick-film metallization have been electrically characterized at temperatures up to 550degC. A 96% alumina based edge connector for a PCB level subsystem interconnection has also been demonstrated recently. The 96% alumina packaging system composed of chip-level packages and PCBs has been tested with high temperature SiC devices at 500degC for over 10,000 hours. In addition to tests in a laboratory environment, a SiC JFET with a packaging system composed of a 96% alumina chip-level package and an alumina printed circuit board mounted on a data acquisition circuit board was launched as a part of the MISSE-7 suite to the International Space Station via a Shuttle mission. This packaged SiC transistor was successfully tested in orbit for eighteen months. A spark-plug type sensor package designed for high temperature SiC capacitive pressure sensors was developed. This sensor package combines the high temperature interconnection system with a commercial high temperature high pressure stainless steel seal gland (electrical feed-through). Test results of a packaged high temperature capacitive pressure sensor at 500degC are also discussed. In addition to the pressure sensor package, efforts for packaging high temperature SiC diode-based gas chemical sensors are in process.
Glycine maintains mitochondrial activity and bile composition following warm liver ischemia‐reperfusion injury (2010)

Intravenous glycine administration reduces liver warm I/R injury by reducing the systemic inflammatory response, and maintaining cellular energy production.
Purification and properties of 3 alpha-hydroxysteroid dehydrogenase from rat brain cytosol. Inhibition by nonsteroidal anti-inflammatory drugs and progestins. (1985)

The 3 alpha-hydroxysteroid dehydrogenase (EC 1.1.1.50) of rat brain cytosol has been purified to apparent homogeneity. The purification procedure involves six successive steps, includes one affinity chromatography, and yields enzyme which displays a 1,550-fold enhancement in specific activity. The homogeneous enzyme has a Km of 8.0 microM for 5 alpha-dihydrotestosterone, a Vmax of 1.3 mumol of 3 alpha-androstanediol formed per h/mg of protein, and displays a preference for NADPH. It appears to be the major activity responsible for the reduction of 5 alpha-dihydrotestosterone in this tissue and may play a pivotal role in brain androgen metabolism. The homogeneous enzyme has several properties in common with the 3 alpha-hydroxysteroid dehydrogenase purified from rat liver cytosol (Penning, T. M., Mukharji, I., Barrows, S., and Talalay, P. (1984) Biochem. J. 222, 601-611). It is a monomer with a molecular weight of 31,000, it has a pI of 5.5, and it is potently inhibited by the nonsteroidal anti-inflammatory drugs (IC50 value for indomethacin = 2.0 microM). The potency of inhibition observed for the brain enzyme parallels that observed for cyclooxygenase: indomethacin greater than fenamates greater than l-methylpyrrole acetic acids greater than arylpropionic acids greater than salicylates greater than acetaminophen. Examination of a variety of steroidal contraceptives as modulators of the dehydrogenase indicates that ethinylestradiol is a very poor inhibitor (IC50 = 100 microM), while 6-medroxyprogesterone acetate (Provera) is an extremely potent inhibitor (IC50 = 0.2 microM). The possibility exists that brain androgen metabolism may be altered by the nonsteroidal anti-inflammatory drugs and synthetic progestins.
Vinyl azides in heterocyclic synthesis. Part 8. Synthesis of the naturally occurring phosphodiesterase inhibitors PDE-I and PDE-II (1987)

The synthesis of the naturally occurring pyrrolo[3,2-e]indole phosphodiesterase inhibitors PDE-I (1) and PDE-II (2) from isovanillin is described. The route involves the construction of both pyrrole rings by vinylnitrene cyclisations, the key cyclisation substrates being the azidoacrylates (5) and (11), prepared from the aldehydes (4) and (10) respectively. The tricyclic intermediate (12) is converted into both PDE-I and PDE-II by selective reduction, followed by carbamoylation or acetylation respectively, and deprotection.
Amino acid sequence of a mouse immunoglobulin mu chain. (1979)

The complete amino acid sequence of the mouse mu chain from the BALB/c myeloma tumor MOPC 104E is reported. The C mu region contains four consecutive homology regions of approximately 110 residues and a COOH-terminal region of 19 residues. A comparison of this mu chain from mouse with a complete mu sequence from human (Ou) and a partial mu chain sequence from dog (Moo) reveals a striking gradient of increasing homology from the NH2-terminal to the COOH-terminal portion of these mu chains, with the former being the least and the latter the most highly conserved. Four of the five sites of carbohydrate attachment appear to be at identical residue positions when the constant regions of the mouse and human mu chains are compared. The mu chain of MOPC 104E has a carbohydrate moiety attached in the second hypervariable region. This is particularly interesting in view of the fact that MOPC 104E binds alpha-(1 leads to 3)-dextran, a simple carbohydrate. The structural and functional constraints imposed by these comparative sequence analyses are discussed.
Therapeutic Hypothermia after Cardiac Arrest: Experience at an Academically Affiliated Community-Based Veterans Affairs Medical Center (2011)

At laboratory and clinical levels, therapeutic hypothermia has been shown to improve neurologic outcomes and mortality following cardiac arrest. We reviewed each cardiac arrest in our community-based Veterans Affairs Medical Center over a three-year period. The majority of cases were in-hospital arrests associated with initial pulseless electrical activity or asystole. Of a total of 100 patients suffering 118 cardiac arrests, 29 arrests involved comatose survivors, with eight patients completing therapeutic cooling. Cerebral performance category scores at discharge and six months were significantly better in the cooled cohort versus the noncooled cohort, and, in every case except for one, cooling was offered for appropriate reasons. Mean time to initiation of cooling protocol was 3.7 hours and mean time to goal temperature of 33°C was 8.8 hours, and few complications clearly related to cooling were noted in our case series. While in-patient hospital mortality of cardiac arrest was high at 65% mortality during hospital admission, therapeutic hypothermia was safe and feasible at our center. Our cooling times and incidence of favorable outcomes are comparable to previously published reports. This study demonstrates the feasibility of implementing, a cooling protocol a community setting, and the role of neurologists in ensuring effective hospital-wide implementation.
Factors Influencing Customers' Use of Electronic Commerce in Stock Trading: An Empirical Study in Korea (2001)

In recognizing the power of electronic commerce in continuously provided service context, this paper examines personal and situational factors as well as transactional characteristics influencing customers' use of electronic commerce in stock trading.Empirical data were collected from an intercept field survey of individual customers of two major Korean stock trading brokers.Our results show that customer knowledge, price sensitivity, access capacity, and frequency of order are crucial conditions for customers' use of electronic commerce in stock trading.Moreover, customer knowledge and price sensitivity appear to predict use of electronic commerce in stock trading most significantly, controlling some demographic variables.Despite several limitations, including cross-sectional design conducted only in Korea, this study advances the understanding of factors encouraging increased use of electronic commerce in continuously provided service context.
Some observations on the calcium aluminate carbonate hydrates (1960)

Two calcium aluminate carbonate hydrates, previously reported in the literature, were prepared and various properties determined. The compound 3CaO·Al<sub>2</sub>O<sub>3</sub>·CaCO<sub>3</sub>·11H<sub>2</sub>O, was prepared by precipitation from mixtures of solutions of calcium aluminate, calcium hydroxide and sodium carbonate; and, in less pure form, by several other means. It forms thin hexagonal plates having refractive indices 1.532 and 1.554. From X-ray diffraction, cell parameters, calculated on the assumption of hexagonal symmetry, are <i>a</i>=8.716, <i>c</i>=7.565. On continued exposure to atmospheric carbon dioxide it is decomposed to calcium carbonate and hydrated alumina. The compound 3CaO·Al<sub>2</sub>O<sub>3</sub>·3CaCO<sub>3</sub>·32H<sub>2</sub>O, was prepared by precipitation from mixtures of ammonium bicarbonate, calcium aluminate, and calcium hydroxide in aqueous sucrose solution. It crystallized as spherulites of minute needles. Other methods produced individual crystals, some tubular, but only in minute quantities or mixed with other phases. X-ray diffraction indicates isomorphism with 3CaO·Al<sub>2</sub>O<sub>3</sub>·3CaSO<sub>4</sub>·32H<sub>2</sub>O. 3CaO·Al<sub>2</sub>O<sub>3</sub>·3CaCO<sub>3</sub>·32H<sub>2</sub>O is, in general, less stable than the monocarbonate complex. The needle-form "silicoaluminate" reported by Flint and Wells was re-examined. It was concluded that the phase probably contains CO<sub>2</sub> as well as SiO<sub>2</sub>, but the exact composition is in doubt.
Globally distributed object identification for biological knowledgebases (2004)

The World-Wide Web provides a globally distributed communication framework that is essential for almost all scientific collaboration, including bioinformatics. However, several limits and inadequacies have become apparent, one of which is the inability to programmatically identify locally named objects that may be widely distributed over the network. This shortcoming limits our ability to integrate multiple knowledgebases, each of which gives partial information of a shared domain, as is commonly seen in bioinformatics. The Life Science Identifier (LSID) and LSID Resolution System (LSRS) provide simple and elegant solutions to this problem, based on the extension of existing internet technologies. LSID and LSRS are consistent with next-generation semantic web and semantic grid approaches. This article describes the syntax, operations, infrastructure compatibility considerations, use cases and potential future applications of LSID and LSRS. We see the adoption of these methods as important steps toward simpler, more elegant and more reliable integration of the world's biological knowledgebases, and as facilitating stronger global collaboration in biology.
Trout Ovulatory Proteins Are Partially Responsible for the Anti-Proteolytic Activity Found in Trout Coelomic Fluid1 (1998)

After ovulation in salmonids, the eggs are held in the peritoneal cavity and bathed in coelomic fluid. Using a chromogenic peptide substrate, the anti-protease activity of brook trout coelomic fluid was measured. Trypsin, chymotrypsin, and pancreatic elastase activities were significantly inhibited by coelomic fluid containing 5.0, 10.0, and 25.0 microgram of total protein, respectively. Using subtractive cDNA cloning, we have previously characterized a set of ovarian proteins called TOPs (trout ovulatory proteins) that are secreted into the coelomic fluid after ovulation. TOPs are most homologous to mammalian antileukoprotease, a heat- and acid-stable serine protease inhibitor. On the basis of this homology, we hypothesized that the anti-trypsin activity observed in the coelomic fluid was related to the presence of TOPs. In the present study, this hypothesis was supported by the acid- and heat-stability of the anti-trypsin activity present in coelomic fluid. Coelomic fluid could be heated to 50 degrees C or treated at a pH less than 5.2 without a significant decrease in the inhibitory activity. Further, coelomic fluid from which TOPs were immunoprecipitated had significantly less anti-trypsin activity than nonimmunoprecipitated controls. We propose that TOP proteins are uniquely produced by the ovary and secreted into the coelomic fluid to act as protease inhibitors following ovulation.
HIGH-ENERGY ACCELERATORS (1960)

<div class="section abstract"><div class="htmlview paragraph">HIGH-ENERGY particle accelerators are among the most important, most complex, and most expensive research tools now used in scientific research. This paper presents a summary of the subject to date.</div><div class="htmlview paragraph">To accelerate atomic particles to energies of billions of volts, it is necessary to provide some means whereby the particles can be given successive kicks in energy — the total of the energy received in all of these kicks adding up to the desired final energy. Such high-energy accelerators can be classified into two categories: linear and circular. The author discusses the advantages and disadvantages of both.<span class="xref">*</span></div></div>
<i>Clostridium difficile</i> infection diagnostics – evaluation of the <i>C. DIFF</i> Quik Chek Complete assay, a rapid enzyme immunoassay for detection of toxigenic <i>C. difficile</i> in clinical stool samples (2016)

Diagnostic testing for Clostridium difficile infection (CDI) has, in recent years, seen the introduction of rapid dual-EIA (enzyme immunoassay) tests combining species-specific glutamate dehydrogenase (GDH) with toxin A/B. In a prospective study, we compared the C. DIFF Quik Chek Complete test to a combination of selective culture (SC) and loop-mediated isothermal amplification (LAMP) of the toxin A gene. Of 419 specimens, 68 were positive in SC including 62 positive in LAMP (14.7%). The combined EIA yielded 82 GDH positives of which 47 were confirmed toxin A/B positive (11%) corresponding to a sensitivity and specificity of 94% for GDH EIA compared to SC and for toxin A/B EIA a sensitivity of 71% and a specificity of 99% compared to LAMP. Twenty different PCR ribotypes were evenly distributed except for UK 081 where only 25% were toxin A/B positive compared to LAMP. We propose a primary use of a combined GDH toxin A/B EIA permitting a sensitive 1-h result of 379 of 419 (90%, all negatives plus GDH and toxin EIA positives) referred specimens. The remaining 10% being GDH positive should be tested for toxin A/B gene on the same day and positive results left to a final decision by the physician.
Bioelectrical impedance techniques in medicine. Part III: Impedance imaging. Second section: reconstruction algorithms. (1996)

This section is devoted to the reconstruction algorithms published in the literature and developed for reconstructing the electrical conductivity and permittivity inside a body from measurements made on the body surface. These algorithms fall into two main categories. The first, based on linear approximations, are noniterative methods assuming that conductivity does not differ very much from a constant. Examples of noniterative methods are the Barber-Brown back-projection method and related methods, the Calderon's approach, the moment method, and one-step Newton methods. The second class of methods consists of iterative methods, which typically include output least squares for various functions. A related class includes the adaptive methods, in which the applied patterns of current are adjusted to get the best signal. A review of all these different alternatives is presented.
Fast Bit Compression and Expansion with Parallel Extract and Parallel Deposit Instructions (2006)

Current microprocessor instruction set architectures are word oriented, with some subword support. Many important applications, however, can realize substantial performance benefits from bitoriented instructions. We propose the parallel extract (pex) and parallel deposit (pdep) instructions to accelerate compressing and expanding selections of bits. We show that these instructions can be implemented by the fast inverse butterfly and butterfly network circuits. We evaluate latency and area costs of alternative functional units for implementing subsets of advanced bit manipulation instructions. We show applications exhibiting significant speedup, 3.41x on average over a basic RISC architecture, and 2.48x on average over an instruction set architecture (ISA) that supports extract and deposit instructions.