gebhart/patrepeval huggingface dataset:
Characterization of an inducible vancomycin resistance system in Streptomyces coelicolor reveals a novel gene (vanK) required for drug resistance (2004)

Vancomycin is the front-line therapy for treating problematic infections caused by methicillin-resistant Staphylococcus aureus (MRSA), and the spread of vancomycin resistance is an acute problem. Vancomycin blocks cross-linking between peptidoglycan intermediates by binding to the D-Ala-D-Ala termini of bacterial cell wall precursors, which are the substrate of transglycosylase/transpeptidase. We have characterized a cluster of seven genes (vanSRJKHAX) in Streptomyces coelicolor that confers inducible, high-level vancomycin resistance. vanHAX are orthologous to genes found in vancomycin-resistant enterococci that encode enzymes predicted to reprogramme peptidoglycan biosynthesis such that cell wall precursors terminate in D-Ala-D-Lac rather than D-Ala-D-Ala. vanR and vanS encode a two-component signal transduction system that mediates transcriptional induction of the seven van genes. vanJ and vanK are novel genes that have no counterpart in previously characterized vancomycin resistance clusters from pathogens. VanK is a member of the Fem family of enzymes that add the cross-bridge amino acids to the stem pentapeptide of cell wall precursors, and vanK is essential for vancomycin resistance. The van genes are organized into four transcription units, vanRS, vanJ, vanK and vanHAX, and these transcripts are induced by vancomycin in a vanR-dependent manner. To develop a sensitive bioassay for inducers of the vancomycin resistance system, the promoter of vanJ was fused to a reporter gene conferring resistance to kanamycin. All the inducers identified were glycopeptide antibiotics, but teicoplanin, a membrane-anchored glycopeptide, failed to act as an inducer. Analysis of mutants defective in the vanRS and cseBC cell envelope signal transduction systems revealed significant cross-talk between the two pathways.
A new input switching scheme for a capacitive micro-g accelerometer (2004)

The design and implementation of a new input switching capacitive microaccelerometer interface circuit with /spl mu/g resolution is presented. The accelerometers were fabricated on 50 /spl mu/m thick silicon-on-insulator (SOI) substrates using a two-mask, dry-release and low temperature process. Fabricated devices were interfaced with a high resolution, low noise and low power switched-capacitor integrated circuit (IC) implemented in a 2.5V 0.25 /spl mu/m N-well CMOS process with the chip size of 0.5/spl times/1.3mm/sup 2/. The measured sensitivity is 0.45V/g and the output noise floor is 4.4/spl mu/g//spl radic/Hz at 150Hz. The total power consumption is 5mW.
Transplanting the N-terminus from Kv1.4 to Kv1.1 generates an inwardly rectifying K+ channel (1999)

A chimeric channel, 4N/1, was generated from two outwardly rectifying K+ channels by linking the N-terminal cytoplasmic domain of hKv1.4 (N terminus ball and chain of hKv1.4) with the transmembrane body of hKv1.1 (delta78N1 construct of hKv1.1). The recombinant channel has properties similar to the six transmembrane inward rectifiers and opens on hyperpolarization with a threshold of activation at -90 mV. Outward currents are seen on depolarization provided the channel is first exposed to a hyperpolarizing pulse of -100 mV or more. Hyperpolarization at and beyond -130 mV provides evidence of channel deactivation. Delta78N1 does not show inward currents on hyperpolarization but does open on depolarizing from -80 mV with characteristics similar to native hKv1.1. The outward currents seen in both delta78N1 and 4N/1 inactivate slowly at rates consistent with C-type inactivation. The inward rectification of the 4N/1 chimera is consistent with the inactivation gating mechanism. This implies that the addition of the N-terminus from hKv1.4 to hKv1.1 shifts channel activation to hyperpolarizing potentials. These results suggest a mechanism involving the N-terminal cytoplasmic domain for conversion of outward rectifiers to inward rectifiers.
Complex genetics cause and constrain fungal persistence in different parts of the mammalian body (2022)

Abstract Determining how genetic polymorphisms enable certain fungi to persist in mammalian hosts can improve understanding of opportunistic fungal pathogenesis, a source of substantial human morbidity and mortality. We examined the genetic basis of fungal persistence in mice using a cross between a clinical isolate and the lab reference strain of the budding yeast Saccharomyces cerevisiae . Employing chromosomally-encoded barcodes, we tracked the relative abundances of 822 genotyped, haploid segregants in multiple organs over time and performed linkage mapping of their persistence in hosts. Detected loci showed a mix of general and antagonistically pleiotropic effects across organs. General loci showed similar effects across all organs, while antagonistically pleiotropic loci showed contrasting effects in the brain and the kidneys, liver, and spleen. Persistence in an organ required both generally beneficial alleles and organ-appropriate pleiotropic alleles. This genetic architecture resulted in many segregants persisting in the brain or in non-brain organs, but few segregants persisting in all organs. These results show complex combinations of genetic polymorphisms collectively cause and constrain fungal persistence in different parts of the mammalian body.
A superscalar RISC processor with 160 FPRs for large scale scientific processing (2003)

We have developed a superscalar RISC processor for the super technical server HITACHI SR8000. The processor includes architectural features specialized in scientific applications, in which massive amounts of data in the main memory must be processed. These features are a slide-windowed-registers scheme and a simultaneous execution of up to 16 prefetch instructions. The slide-windowed-registers scheme enables instructions of the processor to access any of 160 floating point registers (FPRs). The execution mechanism for prefetch instructions produces high efficiency of the out-of-order superscalar processor despite the long latency of the main memory. A logic simulation showed that the performance of the processor reaches over 3 floating-point operations per cycle and the memory throughput of over 12 bytes per cycle.
Numerical Solution of the Parametric Diffusion Equation by Deep Neural Networks (2021)

Abstract We perform a comprehensive numerical study of the effect of approximation-theoretical results for neural networks on practical learning problems in the context of numerical analysis. As the underlying model, we study the machine-learning-based solution of parametric partial differential equations. Here, approximation theory for fully-connected neural networks predicts that the performance of the model should depend only very mildly on the dimension of the parameter space and is determined by the intrinsic dimension of the solution manifold of the parametric partial differential equation. We use various methods to establish comparability between test-cases by minimizing the effect of the choice of test-cases on the optimization and sampling aspects of the learning problem. We find strong support for the hypothesis that approximation-theoretical effects heavily influence the practical behavior of learning problems in numerical analysis. Turning to practically more successful and modern architectures, at the end of this study we derive improved error bounds by focusing on convolutional neural networks.
Schottky Barrier on n-Type Al0.14Ga0.86N Grown by Organometalic Vapor Phase Epitaxy (1995)

Schottky barrier diodes of Au-n-Al 0.14 Ga 0.86 N grown by Organometallic Vapor Phase Epitaxy were obtained and characterized between 77 K and 373 K. Under forward bias the value of the ideality parameter n=1.41 and the threshold voltage is 0.75 V. The reverse bias leak current is below 10 -10 A on a reverse bias of 10 V. The barrier height (Φ B ) was determined to be (1.17±0.03) eV and (1.3±0.05) eV by the current-voltage and the capacitance-voltage measurement repectively.
Computational Models And Tools For Developing Sophisticated Stimulation Strategies For Retinal Neuroprostheses (2018)

Improvements to the efficacy of retinal neuroprostheses can be achieved by developing more sophisticated neural stimulation strategies to enable selective or preferential activation of specific retinal ganglion cells (RGCs). Computational models are particularly well suited for these investigations. The electric field can be accurately described by mathematical formalisms, and the population-based neural responses to the electrical stimulation can be investigated at resolutions well beyond those achievable by current state-of-the-art biological techniques. In this study, we used a biophysically-and morphologically-detailed RGC model to explore the ability of high frequency electrical stimulation (HFS) to preferentially activate ON and OFF RGC subtypes, the two major information pathways of the retina. The performance of a wide range of electrical stimulation amplitudes (0 - $100~\mu \mathbf {A}$) and frequencies (1 - 10 kHz) on functionally-distinct RGC responses were evaluated. We found that ON RGCs could be preferentially activated at relatively higher stimulation amplitudes $( > 50 {\mu } \mathrm {A})$ and frequencies $( >2$ kHz) while OFF RGCs were activated by lower stimulation amplitudes (10 to $50 {\mu } \mathrm {A})$ across all tested frequencies. These stimuli also show great promise in eliciting RGC responses that parallel RGC encoding: one RGC type exhibited an increase in spiking activity during electrical stimulation whilst another exhibited decreased spiking activity, given the same stimulation parameters.
Supplementary Data from Biological characterization of AT7519, a small-molecule inhibitor of cyclin-dependent kinases, in human tumor cell lines (2023)

Supplementary Data from Biological characterization of AT7519, a small-molecule inhibitor of cyclin-dependent kinases, in human tumor cell lines
An extended priority data partition scheme for MPEG video connections over ATM (2002)

Transmission of compressed video over ATM networks requires efficient data priority partition techniques. In association with intelligent cell discard schemes, these techniques aim to minimize the loss probability of critical information in the situation of congestion. We propose a new video-oriented priority data partition mechanism named the extended priority assignation scheme (ExPAS). This mechanism better uses the cell header and allows the definition of up to three service classes per connection. To evaluate its performance, we have also designed an adaptive cell dropping scheme which takes benefits of the new features. In comparison with previous priority partition techniques based on the cell loss probability (CLP) mechanism, ExPAS with the adaptive selective cell discard (A-SDC) scheme shows better results in minimizing cell losses of intra-coded frames.
Improving parallel job scheduling by combining gang scheduling and backfilling techniques (2002)

Two different approaches have been commonly used to address problems associated with space sharing scheduling strategies: (a) augmenting space sharing with backfilling, which performs out of order job scheduling; and (b) augmenting space sharing with time sharing, using a technique called coscheduling or gang scheduling. With three important experimental results-impact of priority queue order on backfilling, impact of overestimation of job execution times, and comparison of scheduling techniques-this paper presents an integrated strategy that combines backfilling with gang scheduling. Using extensive simulations based on detailed models of realistic workloads, the benefits of combining backfilling and gang scheduling are clearly demonstrated over a spectrum of performance criteria.
Characterization of biosynthesis and modes of action of prostaglandin E2and prostacyclin in guinea pig mesenteric lymphatic vessels (2009)

Our findings characterized the inhibition of lymphatic pumping induced by PGE(2) or prostacyclin in guinea pig mesenteric lymphatics. This action is likely to impair oedema resolution and to contribute to the pro-inflammatory actions of these prostaglandins.
Normalization of Dialysis Dose for Daily Dialysis (2001)

The equilibrated Kt/V (eKtV) is widely used in hemodialysis (HD) as a measure of the intensity (magnitude) of an individual dialysis treatment. Adequate eKt/V for thrice-weekly hemodialysis (twHD) has been extensively studied, and a value in the range 1.0 – 1.1 per treatment (3.0 – 3.3 weekly) is generally considered to represent adequate therapy for this specific frequency of dialysis. However, for other schedules, summing eKt/V's and time-averaging the clearance is not appropriate. This was first demonstrated several years ago by the observation that a weekly eKt/V of 2.0 in continuous ambulatory peritoneal dialysis (CAPD) is therapeutically equal to a weekly eKt/V of 3.0 in twHD. That paradox has been resolved by the standard Kt/V (stdKt/V), which accounts for the first order nature of solute removal by dialysis, and which correctly predicts a normalized weekly stdKt/V of 2.0 for both CAPD and twHD. The equivalent renal clearance (EKR) has also been advanced as a method to normalize dose for varying treatment schedules. However, mathematical consideration shows that EKR is an exact time-averaged clearance. Analysis of data reported for daily dialysis by Piccoli et al. in the present issue of Hemodialysis International shows that the EKRct/V calculated for daily dialysis is identical to the sum of eKt/V's for the individual dialyses. We therefore conclude that EKR is not a suitable parameter for normalizing the dialysis dose, because it fails to reflect the effect of dialysis frequency in HD therapy.
Interferometric redatuming with simultaneous and missing sources using sparsity promotion in the curvelet domain (2012)

Interferometric redatuming is a velocity-independent method to turn downhole receivers into virtual sources. Accurate redatuming involves solving an inverse problem, which can be highly ill-posed, especially in the presence of noise, incomplete data and limited aperture. We address these issues by combining interferometric redatuming with transform-domain sparsity promotion, leading to a formulation that deals with data imperfections. We show that sparsity promotion improves the retrieval of virtual shot records under a salt flank. To reduce acquisition costs, it can be beneficial to reduce the number of sources or shoot them simultaneously. It is shown that sparse inversion can still provide a stable solution in such cases.
Growth characteristics of pulmonary artery smooth muscle cells from fawn-hooded rats (1995)

We compared the proliferative rates of vascular smooth muscle cells (VSMC) from pulmonary arteries of pulmonary hypertensive fawn-hooded rats (FHR) with VSMC from normotensive Sprague-Dawley rats (SDR). VSMC from FHR grew at increased rates and reached higher densities at all serum concentrations studied (5-20%) than the VSMC from SDR. The VSMC from FHR also responded to epidermal growth factor (EGF) at low serum concentrations, as evidenced by significantly greater DNA synthetic rates, than the control VSMC. The increased growth in these cells could be due to increased number and/or affinity of EGF receptors because of the higher specific binding of 125I-EGF to the VSMC from FHR. The VSMC from FHR and SDR were equally sensitive to the antiproliferative effects of heparin, suggesting that the heparin-sensitive pathways are not altered in the VSMC from FHR. These results suggest that the development of pulmonary hypertension in FHR may be related to the higher proliferative capacity of the pulmonary VSMC, which may be coupled to increased activity of the EGF receptors on these cells.
The role of mass spectrometry in the study of non‐enzymatic protein glycation in diabetes (2000)

Mass spectrometry has been applied successfully to the study of non-enzymatic protein glycation, which is a topic of wide interest in the diabetes field. Low- and high-resolution mass spectra, GC/MS, and collisional activation spectroscopy allow the structural identification and quantitative evaluation of advanced glycation end-products, which represent important molecules for monitoring diabetes. More recently available techniques, such as ESI and MALDI/MS, have had a significant impact on analytical problems in diabetes. In particular, MALDI has been applied to the study of protein glycation in in vitro and in vivo conditions, because the number of glucose molecules that condense onto the protein can be easily determined by this approach. In the former case, glycation kinetics have been studied in various sugars and sugar concentrations, proteins, and buffer concentrations; in the latter, comparisons of MALDI spectra of circulating proteins from healthy and diabetic subjects determine the exposure of patients to high glucose levels. The method has been applied to an evaluation of the glycation level of immunoglobulins, and indicates that glycation takes place preferentially on the Fab fragment of the protein; data are relevant in relating immunological impairment with glycation-induced changes in the functionality of immunoglobulins. © 2000 John Wiley & Sons, Inc., Mass Spec Rev 19: 279–304, 2000
INTERLEUKIN-18 (IL-18) ACTIVATES NATURAL KILLER (NK) CELLA AND INDUCES TUMOR APOPTOSIS (2003)

我々はヒト末梢血単核球をIL-18とIL-2とで刺激培養することにより, ヒトでの抗腫瘍効果について検討した。末梢血単核球をIL-18 (500ng/ml) とIL-2 (30U/ml) とで培養し, 細胞表面マーカーの変化を検討したところ, NK細胞 (CD56-CD161-CD3-細胞) の著明な増加と培養上清中に多量のIFN-γ産生が認められた。次に, このIL-2とIL-18とで活性化された単核球と腫瘍細胞とを共培養したところ, 標的細胞に効率良く細胞死を誘導することが明らかになり, さらに腫瘍細胞に効率良くカスパーゼ活性の増強が誘導され, 舌扁平上皮癌細胞株に対して, 効率良くアポトーシスを誘導できることが明らかになった。以上の結果は舌癌を含む頭頸部腫瘍に対する, IL-18の免疫療法の可能性を強く示唆するものであり, 今後のさらなる研究が期待される。
Treatment-resistant eosinophilic oesophagitis successfully managed with tofacitinib (2019)

We present a case of a 34-year-old man with long-term diagnosis of eosinophilic oesophagitis (EoE) who did not achieve control of disease after multiple therapies including topical and systemic steroids, immune modulators and biologics. Initial endoscopic findings showed signs of active eosinophilic oesophagitis and biopsies were significant for up to 100 eosinophils per high power field during his various treatments. There was a significant improvement in the appearance of the oesophagus as well as the least number of eosinophils found in oesophagus biopsies after 3 months of treatment with tofacitinib. There are no cases of EoE treated with tofacitinib. Tofacitinib should be considered for the treatment of eosinophilic oesophagitis given its evolving role as an immunosuppressive agent.
Lipid is heterogeneously distributed in muscle and associates with low radiodensity in cancer patients (2020)

Repeated measures revealed wide variation in radiodensity of RA muscle, both vertically and horizontally. Low muscle radiodensity reflects high level of TG in patients with cancer. Non-uniform distribution of intramyocellular and extramyocellular lipids was evident using light microscopy. These results warrant investigation of mechanisms resulting in lipid deposition in muscles of cancer patients.
Assessment of weed root extracts for allelopathic activity against Orobanche and Phelipanche species (2021)

Broomrapes (Orobanche and Phelipanche species) are holoparasitic weeds that infect roots of crop hosts from Asteraceae, Brassicaceae, Apiaceae, Fabaceae, and Solanaceae. The parasitic weeds are difficult to control selectively without crop damage once attached to their roots. Identification of natural compounds with herbicidal activity against pre-attached broomrape stages can provide control alternatives. With the aim to identify plant species with efficacy for broomrape control, organic and residual aqueous phase extracts from roots of seventeen weed species common in south Spanish broomrape-infested fields were assessed as potential inducers of suicidal broomrape germination and as inhibitors of broomrape radicle growth. Assessments were carried out in vitro using seeds and seedlings of four noxious broomrape species, Orobanche crenata Forsk., Orobanche cumana Wallr., Orobanche minor Sm. and Phelipanche ramosa (L.) Pomel. While root extracts from all the weed species did not induce suicidal germination on O. crenata seeds, most of the extracts induced germination of P. ramosa except for those obtained from Amaranthus albus L., Amaranthus retroflexus L. and Convolvulus arvensis L. Moderate levels of germination activity were induced in O. cumana and O. minor seeds by some of the root extracts tested, with strongest induction obtained from Heliotropium europaeum L. on O. cumana seeds, and from Silybum marianum (L.) Gaertn. on O. minor seeds. For root extract inhibition of broomrape radicles, the extract from C. arvensis roots strongly inhibited radicles of all the broomrape species. While extracts from the other weed species induced low or negligible inhibition of O. cumana and O. crenata radicle growth, many inhibited P. ramosa and O. minor radicles. Exceptions were root extracts from Datura stramonium L., Heliotropium europaeum L., Malva sylvestris L., Solanum nigrum L. and Urtica dioica L., which did not inhibit P. ramosa radicles, and those from A. retroflexus, Datura stramonium L., Malva sylvestris L., Portulaca oleracea L. and S. nigrum, which did not inhibit O. minor radicles. Among the active organic extracts assessed, those showing promising chemical profiles were selected for future studies to characterize natural compounds with potential herbicidal activity on early stages of broomrape growth.
Reinforcement learning in BitTorrent systems (2011)

In this paper, we propose a BitTorrent-like protocol that replaces the peer selection mechanisms in the regular BitTorrent protocol with a novel reinforcement learning based mechanism. The inherent operation of P2P systems, which involves repeated interactions among peers over a long time period, allows peers to efficiently identify free-riders as well as desirable collaborators by learning the behavior of their associated peers. Thus, it can help peers improve their download rates and discourage free-riding (FR), while improving fairness. We model the peers' interactions in the BitTorrent-like network as a repeated interaction game, where we explicitly consider the strategic behavior of the peers. A peer that applies the reinforcement learning based mechanism uses a partial history of the observations on associated peers' statistical reciprocal behaviors to determine its best responses and estimate the corresponding impact on its expected utility. The policy determines the peer's resource reciprocations with other peers, which would maximize the peer's long-term performance.