gebhart/patrepeval huggingface dataset:
A Family of IFN-γ–Inducible 65-kD GTPases Protects Against Bacterial Infection (2011)

Immune interferon gamma (IFN-γ) is essential for mammalian host defense against intracellular pathogens. IFN-γ induces nearly 2000 host genes, yet few have any assigned function. Here, we examined a complete mouse 65-kilodalton (kD) guanylate-binding protein (Gbp) gene family as part of a 43-member IFN-γ-inducible guanosine triphosphatase (GTPase) superfamily in mouse and human genomes. Family-wide loss-of-function analysis found that at least four Gbps--Gbp1, Gbp6, Gbp7, and Gbp10--conferred cell-autonomous immunity to listerial or mycobacterial infection within macrophages and gene-deficient animals. These Gbps solicited host defense proteins, including the phagocyte oxidase, antimicrobial peptides, and autophagy effectors, to kill intracellular bacteria. Thus, specific 65-kD Gbps coordinate a potent oxidative and vesicular trafficking program to protect the host from infection.
Sources contributing to the average extracellular concentration of dopamine in the nucleus accumbens (2012)

Mesolimbic dopamine neurons fire in both tonic and phasic modes resulting in detectable extracellular levels of dopamine in the nucleus accumbens (NAc). In the past, different techniques have targeted dopamine levels in the NAc to establish a basal concentration. In this study, we used in vivo fast scan cyclic voltammetry (FSCV) in the NAc of awake, freely moving rats. The experiments were primarily designed to capture changes in dopamine caused by phasic firing - that is, the measurement of dopamine 'transients'. These FSCV measurements revealed for the first time that spontaneous dopamine transients constitute a major component of extracellular dopamine levels in the NAc. A series of experiments were designed to probe regulation of extracellular dopamine. Lidocaine was infused into the ventral tegmental area, the site of dopamine cell bodies, to arrest neuronal firing. While there was virtually no instantaneous change in dopamine concentration, longer sampling revealed a decrease in dopamine transients and a time-averaged decrease in the extracellular level. Dopamine transporter inhibition using intravenous GBR12909 injections increased extracellular dopamine levels changing both frequency and size of dopamine transients in the NAc. To further unmask the mechanics governing extracellular dopamine levels we used intravenous injection of the vesicular monoamine transporter (VMAT2) inhibitor, tetrabenazine, to deplete dopamine storage and increase cytoplasmic dopamine in the nerve terminals. Tetrabenazine almost abolished phasic dopamine release but increased extracellular dopamine to ∼500 nM, presumably by inducing reverse transport by dopamine transporter (DAT). Taken together, data presented here show that average extracellular dopamine in the NAc is low (20-30 nM) and largely arises from phasic dopamine transients.
An SOI voltage-controlled bipolar-MOS device (1987)

This paper describes a new operation mode of the SOI MOSFET. Connecting the floating substrate to the gate in a short-channel SOI MOSFET allows lateral bipolar current to be added to the MOS channel current and thereby enhances the current drive capability of the device. Part of the bipolar current emitted by the source terminal merges into the channel before reaching the drain, which renders the base width substantially shorter than the gate length. This novel operating mode of a short-channel SOI transistor is particularly attractive for high-speed operation, since the device is capable of both reduced voltage swing operation and high current drive, n-p-n and p-n-p devices, as well as complementary inverters have been successfully fabricated.
Undecidability of static analysis (1992)

Static analysis of programs is indispensable to any software tool, environment, or system that requires compile-time information about the semantics of programs. With the emergence of languages like C and LISP, static analysis of programs with dynamic storage and recursive data structures has become a field of active research. Such analysis is difficult, and the static-analysis community has recognized the need for simplifying assumptions and approximate solutions. However, even under the common simplifying assumptions, such analyses are harder than previously recognized. Two fundamental static-analysis problems are may alias and must alias . The former is not recursive (is undecidable), and the latter is not recursively enumerable (is uncomputable), even when all paths are executable in the program being analyzed for languages with if statements, loops, dynamic storage, and recursive data structures.
Efficacy of experimentally produced spray-dried plasma on infectivity of porcine circovirus type 21 (2010)

The value of incorporating spray-dried plasma (SDP) into the diet of weanling pigs to improve feed intake and growth performance has been well documented. However, limited work has been done to confirm that the spray-drying process eliminates all viral contaminates including porcine circovirus type 2 (PCV2). To determine the effect of spray-drying on PCV2 infectivity, colostrum-fed, crossbred, specific-pathogen-free (SPF) pigs were inoculated with PCV2-contaminated SDP intraperitoneally (SDP-IP) or by oral gavage (SDP-OG), inoculated intraperitoneally with PCV2-positive plasma (POS), or left uninoculated (NEG). The plasma used for the experimentally produced SDP was collected from a SPF pig experimentally infected with a PCV2b isolate. Pigs in the NEG group remained seronegative, and PCV2 viremia was not detected. All pigs in the POS group became PCV2 viremic by 14 d postinoculation (DPI) and seroconverted by 28 DPI. In the SDP-IP group, all pigs became viremic by 35 DPI and seroconverted by 49 DPI. In the SDP-OG group, all animals became viremic by 35 DPI and 2/3 pigs seroconverted by 35 DPI. There were no significant (P > 0.05) differences between anti-PCV2-IgG antibody sample-to-positive ratios among pigs in the POS, SDP-OG, or SDP-IP groups. This work provides direct evidence that the experimental spray-drying process used in this study was not effective in inactivating PCV2b in the plasma of a PCV2-infected pig based on a swine bioassay using PCV2-naïve pigs. This work suggests that SDP sourced from pigs could represent a biosecurity risk for the industry.
Room temperature bonding of ultra-fine pitch and low-profiled Cu electrodes for bump-less interconnect (2004)

In this research work, direct interconnection of ultra-low profiled Cu electrodes was carried out at room temperature in order to demonstrate the ultra-high density hump-less interconnect. For that purpose, the manufacturing process of bump-less test structure was established and high accuracy flip chip bonder was developed. The bump-less test vehicles were structured by utilizing CMF' process on Cu electrodes and reactive ion beam etching process on insulator layer. Cu electrodes have the diameters of 3 to 30 pm with the pitches of 10 to 100 pm respectively, and the height of 50 MI. 3 p electrodes chain is composed of 100,000 connections. Also, the newly developed bonder enables the alignment accuracy in 21 pm by utilizing Surface Activated Bonding method (SAB). The electrical interconnection was investigated by the chain resistance measurement by 2-wire lime method. It became clear that over 30,000 connections of 3 pm electrodes were consecutively interconnected. The contact resistance of 10 pn electrode was measured by 4-wire line method and it turned out to he 26 pQ with high electrical reliability. From these results, it can he said that the direct bonding technology of CMP-Cu films was successfully applied for ultra-fme pitch interconnection of Cu bump-less test structure.
Identification of four candidate cGMP targets in Dictyostelium (2002)

In Dictyostelium, a transient increase in intracellular cGMP is important for cytoskeletal rearrangements during chemotaxis. There must be cGMP-binding proteins in Dictyostelium that regulate key cytoskeletal components after treatment with chemoattractants, but to date, no such proteins have been identified. Using a bioinformatics approach, we have found four candidate cGMP-binding proteins (GbpA-D). GbpA and -B have two tandem cGMP-binding sites downstream of a metallo beta-lactamase domain, a superfamily that includes cAMP phosphodiesterases. GbpC contains the following nine domains (in order): leucine-rich repeats, Ras, MEK kinase, Ras guanine nucleotide exchange factor N-terminal (RasGEF-N), DEP, RasGEF, cGMP-binding, GRAM, and a second cGMP-binding domain. GbpD is related to GbpC, but is much shorter; it begins with the RasGEF-N domain, and lacks the DEP domain. Disruption of the gbpC gene results in loss of all high-affinity cGMP-binding activity present in the soluble cellular fraction. GbpC mRNA levels increase dramatically 8 h after starvation is initiated. GbpA, -B, and -D mRNA levels show less dramatic changes, with gbpA mRNA levels highest 4 h into starvation, gbpB mRNA levels highest in vegetative cells, and gbpD levels highest at 8 h. The identification of these genes is the first step in a molecular approach to studying downstream effects of cGMP signaling in Dictyostelium.
Quantum Control by Ultrafast Polarization Shaping (2004)

We demonstrate that the use of time-dependent light polarization opens a new level of control over quantum systems. With potassium dimer molecules from a supersonic molecular beam, we show that a polarization-shaped laser pulse increases the ionization yield beyond that obtained with an optimally shaped linearly polarized laser pulse. This is due to the different multiphoton ionization pathways in K2 involving dipole transitions which favor different polarization directions of the exciting laser field. This experiment is a qualitative extension of quantum control mechanisms which opens up new directions giving access to the three-dimensional temporal response of molecular systems.
The Risk of Cancer Associated with Specific Mutations ofBRCA1andBRCA2among Ashkenazi Jews (1997)

Over 2 percent of Ashkenazi Jews carry mutations in BRCA1 or BRCA2 that confer increased risks of breast, ovarian, and prostate cancer. The risks of breast cancer may be overestimated, but they fall well below previous estimates based on subjects from high-risk families.
ReadDepth: A Parallel R Package for Detecting Copy Number Alterations from Short Sequencing Reads (2011)

Copy number alterations are important contributors to many genetic diseases, including cancer. We present the readDepth package for R, which can detect these aberrations by measuring the depth of coverage obtained by massively parallel sequencing of the genome. In addition to achieving higher accuracy than existing packages, our tool runs much faster by utilizing multi-core architectures to parallelize the processing of these large data sets. In contrast to other published methods, readDepth does not require the sequencing of a reference sample, and uses a robust statistical model that accounts for overdispersed data. It includes a method for effectively increasing the resolution obtained from low-coverage experiments by utilizing breakpoint information from paired end sequencing to do positional refinement. We also demonstrate a method for inferring copy number using reads generated by whole-genome bisulfite sequencing, thus enabling integrative study of epigenomic and copy number alterations. Finally, we apply this tool to two genomes, showing that it performs well on genomes sequenced to both low and high coverage. The readDepth package runs on Linux and MacOSX, is released under the Apache 2.0 license, and is available at http://code.google.com/p/readdepth/.
Mechanisms of Genic Male Sterility (1995)

For normal sexual reproductive development, coordination must occur between both male and female organ ontogeny. An abnormality at any point in this process may lead to sterility. Classification of sterility can be divided into heritable and nonheritable sterility. Numerous schemes for mechanisms controlled by nuclear genes (genic male sterility) have been devised to identify the timing and location of the inception of sterility. These schemes are divided into structural (gross organ changes) and functional. The latter may be divided into abnormal changes occurring in the male cells or surrounding anther tissues during microsporogenesis. Even though sterility can be produced by chemicals, ionizing radiation, genetic engineering, etc., the primary examples presented here will be of naturally occurring systems. The objectives of this paper are to review heritable genic male sterility, give examples of naturally occurring genic male sterility systems, and identify their uses and proposed applications in plant breeding.
The epidemiology of invasive pneumococcal disease in children in Far North Queensland (2001)

Although the seven- and 11-valent conjugate pneumococcal vaccines cover only approximately 60 and 70%, respectively, of the isolates that cause invasive disease in indigenous children in Far North Queensland, they nevertheless have the potential to prevent much morbidity in and hospitalization of these children. It will be essential to maintain surveillance following the introduction of conjugate pneumococcal vaccines so as to monitor changes in the incidence of invasive pneumococcal disease, particularly in high-risk children.
Initial Characterization of an 18F-Labeled Myocardial Perfusion Tracer (2008)

The observation of a high and flow-independent first-pass extraction fraction promises linearity between tracer uptake and myocardial blood flow. Sustained myocardial tracer uptake, combined with high image contrast, will allow for imaging protocols with tracer injection at peak exercise followed by delayed imaging. Thus, 18F-BMS-747158-02 is a promising new tracer for the quantitative imaging of myocardial perfusion and can be distributed to imaging laboratories without a cyclotron.
Frequency dividers in radar target stimulator applications (2018)

More and more driver assistance systems are integrated into modern vehicles. This development results in a continuous rise in the complexity of these vehicles, as the functions have to comply to the corresponding safety standards. Testing and validating these functions on an automotive test bench instead of driving tests at closed proving grounds requires comprehensive stimulation of the involved sensors. In this article we are focusing on an approach for stimulating short-range radar sensors of a vehicle located on such a test bench. Coping with the requirements imposed by these types of sensors we investigate the usage of frequency multipliers and dividers in the frequency translation section of the radar stimulator. For this purpose, we provide an overview on different concepts for these multipliers and dividers. After reviewing the advantages and disadvantages of these devices, we provide measurement results of a stimulator setup applying this type of frequency translation.
CNN for very fast ground segmentation in velodyne LiDAR data (2018)

This paper presents a novel method for ground segmentation in Velodyne point clouds. We propose an encoding of sparse 3D data from the Velodyne sensor suitable for training a convolutional neural network (CNN). This general purpose approach is used for segmentation of the sparse point cloud into ground and non-ground points. The LiDAR data are represented as a multi-channel 2D signal where the horizontal axis corresponds to the rotation angle and the vertical axis represents channels - laser beams. Multiple topologies of relatively shallow CNNs (i.e. 3-5 convolutional layers) are trained and evaluated, using a manually annotated dataset we prepared. The results show significant improvement of performance over the state-of-the-art method by Zhang et al. in terms of speed and also minor improvements in terms of accuracy.
Lysophosphatidic acid-induced squamous cell carcinoma cell proliferation and motility involves epidermal growth factor receptor signal transactivation. (2002)

Transactivation of the epidermal growth factor receptor (EGFR) represents the paradigm for cross-talk between G protein-coupled receptors (GPCRs) and receptor tyrosine kinase signaling pathways. In a variety of squamous cell carcinoma cell lines of the head and neck (HNSCCs), we found that treatment with the GPCR agonists lysophosphatidic acid (LPA), bradykinin, thrombin, and carbachol results in rapid tyrosine phosphorylation of the EGFR. In these tumor cells, signal transactivation of the EGFR and the oncoprotein HER2/neu is critically dependent on metalloprotease activity. Using the metalloprotease inhibitor batimastat, the EGFR-specific tyrphostin AG1478, and a dominant-negative EGFR mutant, we show that in HNSCC cell lines, EGFR tyrosine phosphorylation, recruitment of the adaptor proteins SHC and Gab1, and activation of the ERK/mitogen-activated protein kinase pathway in response to LPA depend both on metalloprotease function and EGFR tyrosine kinase activity. Most importantly, critical characteristics of HNSCC cell lines such as DNA synthesis, cell cycle progression and tumor cell migration are stimulated by LPA and can be abrogated by interfering with EGFR signal transmission. Together, our results demonstrate the importance of a mechanism that promotes head and neck cancer cell proliferation and motility by GPCR ligands involving EGFR transactivation. Our findings suggest that highly abundant GPCR ligands such as LPA may function as tumor promoters and determinants of HNSCC progression.
Isolation and characterization of a protease from Pseudomonas fluorescens RO98 (2000)

Pseudomonas fluorescens RO98, a raw milk isolate, was inoculated into McKellar's minimal salts medium and incubated at 25 degrees C for 48 h to allow production of protease. A zinc-metalloacid protease was purified from the cell-free concentrate by anion exchange and gel filtration chromatography. The purified protease was active between 15 and 55 degrees C, and pH 4.5 and 9.0, and was stable to pasteurization. The enzyme had pH and temperature optima for activity of 5.0 and 35 degrees C, respectively. It was heat stable with a D55 of 41 min and a D62.5 of 18 h. Molecular weight of the enzyme was estimated to be 52 kDa by SDS PAGE and size exclusion chromatography. Values for kM of 144.28, 18.73, 110.20 and 35.23 micromol were obtained for whole, alpha-, beta- and kappa-casein, with a Vmax of 8.26, 0.09, 0.42 and 0.70 micromol mg-1 min-1, respectively. The enzyme hydrolysed kappa-casein preferentially when incubated with artificial casein micelles.
Genetic and Physical Map of the pLAFR1 Vector (2004)

This paper presents the complete sequencing and annotation of the pLAFR1 vector. pLAFR is a tetracycline-resistant "cosmid" cloning vector, which is derived from the 20 kb plasmid pRK290, a RK2-derivative. Due to its broad host range, the pLAFR1 vector has been widely used in the genetic analysis of a broad number of gram-negative bacterial species. The availability of the complete pLAFR1 sequence will most definitely help in the construction and analysis of clone librares based on pRK290 or pLAFR vectors.
GEOMETRIC TOTAL KNEE REPLACEMENT: AN EIGHT YEAR EXPERIENCE AT THE NEW ENGLAND BAPTIST HOSPITAL (1980)

Total knee arthoplasty has been accepted as a valuable adjunct in the treatment of knees severely compromised by disease or trauma. One hundred nine geometric total knee replacements were reviewed to determine the efficacy of the device in the relief of pain, the correction of deformity and instability, and the restoration of functional motion in the diseased knee.1.
Peptide Synthesis Based on t-Boc Chemistry and Solution Photogenerated Acids (2000)

Solution reactions using photogenerated reagents (PGRs) (Gao, X.; Yu, P. Y.; Leproust, E.; Sonigo, L.; Pellois, J. P.; Zhang, H. J. Am. Chem. Soc. 1998, 120, 12698) are developed for parallel synthesis of addressable, combinatorial molecular microarrays. To advance the PGR chemistry for general chemical conversions, light-controlled synthesis of peptides, which employs photogenerated acids (PGAs) and/or in combination with photosensitizers for deprotection of N-t-Boc group, is demonstrated. These reactions were performed on resin and glass plates and conveniently monitored by HPLC analysis (reactions on resin) and fluorescence emission after coupling the deprotected NH(2) group with 4(5)-carboxyfluorescein. These results demonstrate the potential of the PGA chemistry for parallel synthesis of addressable peptide libraries on a microarray platform.
From ARIES to MARS (2013)

Transaction-based systems often rely on write-ahead logging (WAL) algorithms designed to maximize performance on disk-based storage. However, emerging fast, byte-addressable, non-volatile memory (NVM) technologies (e.g., phase-change memories, spin-transfer torque MRAMs, and the memristor) present very different performance characteristics, so blithely applying existing algorithms can lead to disappointing performance.
The Molecular Mechanism of B Cell Activation by toll-like Receptor Protein RP-105 (1998)

The B cell-specific transmembrane protein RP-105 belongs to the family of Drosophila toll-like proteins which are likely to trigger innate immune responses in mice and man. Here we demonstrate that the Src-family protein tyrosine kinase Lyn, protein kinase C beta I/II (PKCbetaI/II), and Erk2-specific mitogen-activated protein (MAP) kinase kinase (MEK) are essential and probably functionally connected elements of the RP-105-mediated signaling cascade in B cells. We also find that negative regulation of RP-105-mediated activation of MAP kinases by membrane immunoglobulin may account for the phenomenon of antigen receptor-mediated arrest of RP-105-mediated B cell proliferation.
Role of glutamine in adaptations in nitrogen metabolism during fasting (1986)

The present study examines the effect of glutamine infusion on the interorgan fluxes of glutamine, alanine, urea, and ammonia with progressive fasting. Experiments were carried out in two groups of conscious dogs with catheters previously implanted in an artery and in the hepatic, portal, and renal veins. Group I (n = 12) was fasted for 24 h, and group II (n = 10) was fasted for 96 h. On the day of the study, seven animals of group I and five of group II received a constant infusion of glutamine (3.0 mumol . kg-1 . min-1) for 1 h, and the rest (controls) received saline. Four-day fasting produced ketosis with a compensated metabolic acidosis. The demand for glutamine by the kidneys and gut increased, and the liver switched from net glutamine utilization to that of net production. The kidneys (33%) and gut (230%) increased their production of ammonia, while their release of alanine decreased. The estimated efflux of glutamine by skeletal muscle, however, did not change. All of the infused glutamine was cleared by the splanchnic and renal tissues. In group I, there was increased gut production of alanine, which was matched by increased hepatic alanine uptake and urea production. No such changes were observed in Group II. There was, however, an increase in hepatic uptake of ammonia. Finally, glutamine infusion did not alter glutamine or alanine output by skeletal muscle in group I, while it decreased efflux of alanine but not that of glutamine in group II. The data emphasize the complex interdependence of the liver, gut, kidneys, and skeletal muscle in nitrogen sparing.(ABSTRACT TRUNCATED AT 250 WORDS)