gebhart/patrepeval huggingface dataset:
A novel method for development of species and strain-specific DNA probes and PCR primers for identifying Burkholderia solanacearum (formerly Pseudomonas solanacearum) (1997)

Six Burkholderia solanacearum (formerly Pseudomonas solanacearum) genomic DNA fragments were isolated, using RAPD techniques and cloning, from the three genetically diverse strains: ACH092 (Biovar 4), ACH0158 (Biovar 2) and ACH0171 (Biovar 3) (1). One of these cloned fragments was selected because it was present constantly in all bacterial strains analysed. The remaining five clones were selected because Southern hybridisation revealed that each showed partial or complete specificity towards the strain of origin. A seventh genomic fragment showing a strain-specific distribution in Southern hybridisations was obtained by differential restriction, hybridisation and cloning of genomic DNA. Each of these clones was sequenced and primers to amplify the insert were designed. When DNA from the strain of origin was used as template, PCR amplification for each of these fragments yielded a single band on gel analysis. One pair of primers amplified the species-constant fragment of 281 bp from DNA of all B. solanacearum strains investigated, from DNA of the closely related bacterium which causes ''blood disease'' of banana (BDB) and in P. syzigii. The sensitivity of detection of B. solanacearum using these ubiquitous primers was between 1.3 and 20 bacterial cells. The feasibility and reliability of a PCR approach to detection and identification of B. solanacearum was tested in diverse strains of the bacterium in several countries and laboratories.
Calcium channel blocking drugs in the management of drug dependence, withdrawal and craving. A clinical pilot study with nifedipine and verapamil. (1998)

In this pilot study nifedipine and verapamil appeared to be effective for the in-patient management of withdrawal and craving in a broad spectrum of chronic drug addicts. Verapamil produced fewer disturbing side effects compared with nifedipine and it may prove a safe, non-addicting and rational treatment in the long term management of chronic dependence, withdrawal and craving. As such, it may be especially valuable in offering the motivated chronic addict help and hope for the long term management of this problem in a community setting. The present results warrant the establishment of a verapamil based, double-blind, drug-matched or placebo-controlled clinical trial to test the validity and significance of these preliminary findings.
Sympathetic Modulation of Acute Cutaneous Flare Induced by Intradermal Injection of Capsaicin in Anesthetized Rats (2003)

Much of the acute cutaneous neurogenic inflammation after intradermal injection of capsaicin (CAP) in rats is mediated by dorsal root reflexes (DRRs), which cause the release of inflammatory agents from primary afferent terminals. Sympathetic efferents modulate neurogenic inflammation by interaction with primary afferent terminals. In this study, we examined if DRR-mediated flare after CAP injection is subject to sympathetic modulation. Changes in cutaneous blood flow on the plantar surface of the foot were measured using a laser Doppler flow meter. After CAP injection, cutaneous flare spread more than 20 mm away from the site of CAP injection. However, this CAP-induced flare was significantly reduced after surgical sympathectomy. Decentralization of postganglionic neurons did not affect the flare induced by CAP injection. If the foot of sympathectomized rats was pretreated with an alpha(1)-adrenoceptor agonist (phenylephrine) by intra-arterial injection, the spread of flare induced by CAP injection could be restored. However, if the spinal cord was pretreated with a GABA(A) receptor antagonist, bicuculline, to prevent DRRs, phenylephrine no longer restored the CAP-evoked flare. An alpha(2)-adrenoceptor agonist (UK14,304) did not affect the CAP-evoked flare in sympathectomized rats. In sympathetically intact rats, blockade of peripheral alpha(1)-adrenoceptors with terazosin profoundly reduced the flare induced by CAP injection, whereas blockade of peripheral alpha(2)-adrenoceptors by yohimbine did not obviously affect the flare. Therefore the pathogenesis of acute neurogenic inflammation in the intradermal CAP injection model depends in part on intact sympathetic efferents and alpha(1)-adrenoceptors. Peripheral alpha(1)-adrenoceptors thus modulate the ability of capsaicin sensitive afferents to evoke the release of inflammatory agents from primary afferents by DRRs.
Survivin Reduces Activation-induced T Cell Death in G1 Phase (2003)

A process termed activation-induced cell death (AICD) is responsible for peripheral T cell tolerance after negative selection of self-reactive T cells, and deletion of hyperactivated T cells following the immune response. Cells in G1 phase of the cell cycle are most susceptible to AICD. We have investigated the relationship between the induction of AICD by phorbol 12-myristate 13-acetate plus ionomycin during the cell cycle and the expression of survivin, an inhibitor of the apoptosis protein (LAP) family. AICD was highly induced in cells of the human T cell line Jurkat E6.1 arrested in G1 phase, whereas survivin was hardly expressed in G1 and instead it was highly expressed in G2/M. Moreover, transient over-expression of survivin in G1 partially blocked the induction of AICD. These results suggest that survivin inhibits the induction of AICD, especially in G1 phase.
cAMP and Serum and Glucocorticoid-inducible Kinase (SGK) Regulate the Epithelial Na+ Channel through Convergent Phosphorylation of Nedd4-2 (2004)

The epithelial Na(+) channel (ENaC) functions as a pathway for epithelial Na(+) transport, contributing to Na(+) homeostasis and blood pressure control. Vasopressin increases ENaC expression at the cell surface through a pathway that includes cAMP and cAMP-dependent protein kinase (PKA), but the mechanisms that link PKA to ENaC are unknown. Here we found that cAMP regulates Na(+) transport in part by inhibiting the function of Nedd4-2, an E3 ubiquitin-protein ligase that targets ENaC for degradation. Consistent with this model, we found that cAMP inhibited Nedd4-2 by decreasing its binding to ENaC. Moreover, decreased Nedd4-2 expression (RNA interference) or overexpression of a dominant negative Nedd4-2 construct disrupted ENaC regulation by cAMP. Nedd4-2 was a substrate for phosphorylation by PKA in vitro and in cells; three Nedd4-2 residues were phosphorylated by PKA and were required for cAMP to inhibit Nedd4-2 (relative functional importance Ser-327 > Ser-221 > Thr-246). Previous work found that these residues are also phosphorylated by serum and glucocorticoid-inducible kinase (SGK), a downstream mediator by which aldosterone regulates epithelial Na(+) transport. Consistent with a functional interaction between these pathways, overexpression of SGK blunted ENaC stimulation by cAMP, whereas inhibition of SGK increased stimulation. Conversely, cAMP agonists decreased ENaC stimulation by SGK. The data suggest that cAMP regulates ENaC in part by phosphorylation and inhibition of Nedd4-2. Moreover, Nedd4-2 is a central convergence point for kinase regulation of Na(+) transport.
ANTIBACTERIAL ACTIVITY OF NOVEL HYDROXY SUBSTITUTED BENZOTHIAZOLE DERIVATIVES AGAINST STREPTOCOCCUS PYOGENES (2018)

Synthesis and screening of benzothiazole derivatives have great importance in heterocyclic chemistry because of its potent and significant biological activities against Streptococcus (S) pyogenes especially hydroxy substitution at benzothiazole. Hydroxy-substituted benzothiazole derivatives were synthesized by reaction of 4-amino-2-chlorophenol with potassium thiocyanate under temperature control and presence of bromine in glacial acetic acid and ammonia. Hydroxy-substituted nitrobenzamides then synthesized by condensation of 2-amino-4-chlorobenzothiazol-5-ol with 2(3or4)nitrobenzoylchloride acid in presence of dry pyridine and acetone. Finally, newly synthesized derivatives (A-01 to A-09) were synthesized through replacing of chlorine of nitrobenzamide by reaction with 2-nitroaniline, 3-nitroaniline, and 4-nitroaniline in presence of DMF. Analytical characterization was performed by TLC, melting point, IR and NMR spectra. Antibacterial activity was performed against S. pyogenes by cup plate method (diffusion technique) using procaine penicillin as standard. Compound A-03, A-04 and A-08 showed potent antibacterial activity against S. pyogenes at both concentrations 50g/ml and 100g/ml as compared to standard while the rest of compounds showed moderate to negligible activity when further assessed to determine MIC by broth dilution method.
Patterning GaN Microstructures by Polarity-Selective Chemical Etching (2003)

We have demonstrated GaN microstructures formed by polarity-selective chemical etching in KOH solution. It was found that KOH selectively etches N-polar GaN but not Ga-polar GaN. The polarity-patterned GaN was grown by plasma-assisted molecular beam epitaxy. For intermediate etching times, hexagonal GaN pyramids were formed in the N-polar regions. With prolonged etching, the N-polar GaN can be completely removed. A one-dimensional array of GaN stripes and a two-dimensional array of hexagonal holes formed in a GaN matrix have been fabricated. Extremely smooth vertical sidewalls have been achieved along with an etch depth of up to 4 µm.
Use of Bronchoalveolar Lavage Semiquantitative Cultures in Cystic Fibrosis (1997)

To assess bronchoalveolar lavage (BAL) in adult CF patients with respiratory symptoms, we studied BAL fluid (BALF) culture results from 28 bronchoscopies in 11 patients. Patients were asked to provide sputum for culture. All but two patients were receiving antibiotics at the time of bronchoscopy, with 13 bronchoscopies done on patients who had been receiving antibiotics for more than 10 d. Gram stain of the BALF was positive in 18 cases. In all but one BALF, > 10,000 colony-forming units per milliliter (cfu/ml) BALF of one or more pathogens was identified. The final case grew Burkholderia cepacia, which was not grown in the sputum. In only six cases (21%) were the sputum and BALF culture results the same. Prior to 11 bronchoscopies, the sputum was not adequate. The remaining 11 cases either had different pathogens in the BAL (six cases), or had some but not all of the BALF pathogens in the sputum. BALF cultures changed therapy in 13 (48%) of cases. Semiquantitative culture of BALF was a useful diagnostic tool in CF in patients in whom empiric therapy failed.
Generation of Quiescent Cardiac Fibroblasts From Human Induced Pluripotent Stem Cells for In Vitro Modeling of Cardiac Fibrosis (2019)

This study uncovers unique gene signatures that define tissue-specific identities of fibroblasts. The bona fide quiescent CFs derived from human induced pluripotent stem cells can serve as a faithful in vitro platform to better understand the underlying mechanisms of cardiac fibrosis and to screen anti-fibrotic drugs.
Counteraction of axonal growth inhibitory properties of Semaphorin 3A and myelin‐associated proteins by a synthetic neurotrophic compound (2004)

One of the reasons for the lack of nerve regeneration in the CNS is the formation of a glial scar over-expressing multiple inhibitory factors including myelin-associated proteins and members of the Semaphorin family. Innovative therapeutic strategies must stimulate axon extension across the lesion site despite this inhibitory molecular barrier. We recently developed a synthetic neurotrophic compound combining an omega-alkanol with a retinol-like cycle (3-(15-hydroxy-pentadecyl)-2,4,4,-trimethyl-cyclohexen-2-one (tCFA15)). Here, we demonstrate that tCFA15 is able to promote cortical axon outgrowth in vitro even in the presence of the inhibitory Semaphorin 3A and myelin extracts. This growth-promoting effect is selectively observed in axons and requires multiple growth-associated intracellular pathways. Our results illustrate the potential use of synthetic neurotrophic compounds to promote nerve regeneration by counteracting the axonal growth inhibition triggered by glial scar-associated inhibitory factors.
Wireless smart implants dedicated to multichannel monitoring and microstimulation (2004)

This invited paper covers several techniques and methods employed to build high reliability circuits and systems dedicated to implement advanced implantable and wirelessly controlled smart medical devices such as sensors and microstimulateurs. A global view of typical micro-devices such us neural signals monitoring device, cortical multichannel stimulator, as well as peripheral nerve interfaces to recuperate bladder functions, is given. In addition, case studies related to peripheral and cortical neural systems are reported. In all these devices, special attention is paid to low-power management of involved systems and to the design of corresponding circuits of such typical implantable multi-disciplinary microsystems.
Programming the Microsoft Windows Driver Model, Second Edition (2002)

From the Publisher:
Written for advanced programmers who use C and C++, the second edition of this popular technical guide illustrates and clarifies real-world driver programming issues for current versions of Microsoft Windows. The author offers a solid overview of the Windows Driver Model (WDM) architecture and breaks down the process of writing custom device drivers into manageable pieces-from the basics of loading device drivers to creating and processing I/O request packets. This edition includes updated information about Windows XP, Windows 2000, and Windows Me, plus extensive practical examples, illustrations, and line-by-line analysis of code samples.
Query Optimization for Distributed Data Streams. (2006)

With the recent explosive growth of sensors and instruments, data-driven stream applications are emerging as a new field. Query optimization for such high performance stream applications has not been extensively studied, especially its core component, the cost model. We observe that the cost model for stream query processing should consider two aspects: output rate and computation cost. However, most existing work on evaluating stream queries uses only one or the other. In this paper, we propose a multi-model based optimization framework by leveraging both aspects. Further, we extend it from the centralized environment to the distributed environment by introducing distributed metrics and an algorithm for query plan decomposition. keywords: stream data, query optimization, distributed stream processing
DART-ID increases single-cell proteome coverage (2018)

Abstract Analysis by liquid chromatography and tandem mass spectrometry (LC-MS/MS) can identify and quantify thousands of proteins in microgram-level samples, such as those comprised of thousands of cells. This process, however, remains challenging for smaller samples, such as the proteomes of single mammalian cells, because reduced protein levels reduce the number of confidently sequenced peptides. To alleviate this reduction, we developed Data-driven Alignment of Retention Times for IDentification (DART-ID). DART-ID implements principled Bayesian frameworks for global retention time (RT) alignment and for incorporating RT estimates towards improved confidence estimates of peptide-spectrum-matches. When applied to bulk or to single-cell samples, DART-ID increased the number of data points by 30 – 50% at 1% FDR, and thus decreased missing data. Benchmarks indicate excellent quantification of peptides upgraded by DART-ID and support their utility for quantitative analysis, such as identifying cell types and cell-type specific proteins. The additional datapoints provided by DART-ID boost the statistical power and double the number of proteins identified as differentially abundant in monocytes and T-cells. DART-ID can be applied to diverse experimental designs and is freely available at http://github.com/SlavovLab/DART-ID . Author Summary Identifying and quantifying proteins in single cells gives researchers the ability to tackle complex biological problems that involve single cell heterogeneity, such as the treatment of solid tumors. Mass spectrometry analysis of peptides can identify their sequence from their masses and the masses of their fragment ion, but often times these pieces of evidence are insufficient for a confident peptide identification. This problem is exacerbated when analyzing lowly abundant samples such as single cells. To identify even peptides with weak mass spectra, DART-ID incorporates their retention time – the time when they elute from the liquid chromatography used to physically separate them. We present both a novel method of aligning the retention times of peptides across experiments, as well as a rigorous framework for using the estimated retention times to enhance peptide sequence identification. Incorporating the retention time as additional evidence leads to a substantial increase in the number of samples in which proteins are confidently identified and quantified.
Synthesis and Structure of Cuboctahedral and Anticuboctahedral Cages Containing 12 Quadruply Bonded Dimolybdenum Units (2005)

The syntheses and structures of two clusters containing 12 Mo-Mo quadruple bonds, [Mo(24)(C(12)H(12)O(4))(24)](C(5)H(5)N)(12) and Mo(24)(C(8)H(4)O(4))(24), are reported. The 12 paddlewheel building blocks and 24 ligands self-assemble into cuboctahedral and anticuboctahedral polyhedra, respectively, depending on the manner in which the two halves of the cluster are aligned. These clusters contain twice as many dimolybdenum units as any previously reported cluster. Possible assembly mechanisms are also proposed.
Multiple Sclerosis: Progress, but No Cure. (2015)

Agents are approved to treat exacerbations and symptoms and as disease-modifying therapy. Most therapies in the works would address relapsing forms of the disease.
Theory of loss and gain trimming of resonator-type filters (2000)

The characteristic response of resonator-type filters is determined by the mutual resonator-to-resonator coupling coefficients, which are not readily trimmed once a device is fabricated. We show that loss and/or gain is a mechanism which can mimic the role of the coupling coefficients, and which can therefore be used for post-fabrication tuning or trimming. By using loss-only trimming, the throughput crosstalk performance can be improved by several orders of magnitude while incurring only small signal attenuation.
Structure–Activity Relationship of a Series of Synthetic Lipopeptide Self-Adjuvanting Group A Streptococcal Vaccine Candidates (2007)

The development of 16 self-adjuvanting group A streptococcal vaccine candidates, composed of (i) a universal helper T-cell epitope (P25), (ii) a target GAS B-cell epitope (J14), and (iii) a lipid moiety, is described. Systemic J14-specific IgG antibodies were detected following subcutaneous immunization of BALB/c (H-2 (d)) mice with each construct without the need for an additional adjuvant. The effect of changing the order of P25, J14, and lipid moiety attachment or incorporation of P25 and J14 into a lipid-core peptide system on antibody titers was assessed. The point of lipid moiety attachment had the greatest influence on systemic J14-specific IgG antibody titers. Overall, the best vaccines featured a C-terminal lipid moiety, conjugated through a lysine residue to P25 at the N-terminus, and J14 on the lysine side chain.
Higher Order Frequency Response Functions in Nonlinear System Identification (1991)

This paper describes higher order frequency response functions (FRF's) and their role in the identification of nonlinear systems. Higher order FRF's only exist for nonlinear systems and have the property that they visually demonstrate how energy is transferred from one frequency to another. a unique characteristic of nonlinear structures and systems. The determination of these FRF's can be approached from two principle directions: using sine excitation by directly measuring the higher order transfer functions which approximate to higher order FRF's or using nonlinear time series methods and probing these to extract the FRF's. In this paper, these approaches are described in relation to simple nonlinear problems and their role in future system methodologies discussed. It is shown that if reliable higher order spectra can be obtained they offer a positive and useful means of practically diagnosing a class of nonlinear structural dynamics problems.
RoboTHOR: An Open Simulation-to-Real Embodied AI Platform (2020)

Visual recognition ecosystems (e.g. ImageNet, Pascal, COCO) have undeniably played a prevailing role in the evolution of modern computer vision. We argue that interactive and embodied visual AI has reached a stage of development similar to visual recognition prior to the advent of these ecosystems. Recently, various synthetic environments have been introduced to facilitate research in embodied AI. Notwithstanding this progress, the crucial question of how well models trained in simulation generalize to reality has remained largely unanswered. The creation of a comparable ecosystem for simulation-to-real embodied AI presents many challenges: (1) the inherently interactive nature of the problem, (2) the need for tight alignments between real and simulated worlds, (3) the difficulty of replicating physical conditions for repeatable experiments, (4) and the associated cost. In this paper, we introduce RoboTHOR to democratize research in interactive and embodied visual AI. RoboTHOR offers a framework of simulated environments paired with physical counterparts to systematically explore and overcome the challenges of simulation-to-real transfer, and a platform where researchers across the globe can remotely test their embodied models in the physical world. As a first benchmark, our experiments show there exists a significant gap between the performance of models trained in simulation when they are tested in both simulations and their carefully constructed physical analogs. We hope that RoboTHOR will spur the next stage of evolution in embodied computer vision.
Optimized layout of MOS cells (1988)

A design method using both logical optimization and optimized topological arrangements is described. Starting from a minimized Boolean function, a synthesis of an optimized well-structured network is obtained. The most original aspect of this approach is a transistor merging procedure leading to a nonseries-parallel network while maintaining a systematic layout. An extension to the synthesis of several functions relies on transistor mergings between functions and allows comparisons with a PLA implementation. Gains in both area and performance are obtained.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>