gebhart/patrepeval huggingface dataset:
Modeling by homology of RNA binding domain in A1 hnRNP protein (1990)

Eukaryotic nuclear RNA binding proteins share a common sequence motif thought to be implicated in RNA binding. One of the two domains present in A1 hnRNP protein, has been modelled by homology in order to make a prediction of the main features of the RNA binding site. Acylphosphatase (EC 3.6.1.7) was selected as template for the modeling experiment. The predicted RNA binding site is a beta-sheet containing the two RNP consensus sequences as well as lysines and arginines conserved among the family.
Endoscopic treatment of postoperative enterocutaneous fistulas after bariatric surgery with the use of a fistula plug: report of five cases (2009)

Anastomotic leaks frequently occur after bariatric surgery and their management includes different options. The present study describes the management of enterocutaneous fistulas in patients in whom surgical or endoscopic treatments have failed, by insertion of a biomaterial (Surgisis fistula plug) to facilitate healing of the gastrocutaneous fistula. Five patients with leaks after bariatric surgery were treated. All patients had undergone previous failed surgical or endoscopic attempt(s) at closure. Our technique entailed insertion of the Surgisis fistula plug into the fistula tract by a "rendezvous" procedure, via both percutaneous and endoscopic routes. The data were collected retrospectively. Initially, two patients were treated by fistula plug alone and three received fistula plug plus a self-expanding stent. In two patients, cutaneous fistula outflow ceased within a few days. The other three patients required one additional endoscopic procedure. At the end we observed healed leaks in four of the five patients (80 %). The median follow-up duration was 18 months. In conclusion, the combined therapy consisting of fistula plug implantation with optional stenting helps closure in these difficult refractory cases of gastrocutaneous fistula.
Role of TNF-α in vascular dysfunction (2009)

Healthy vascular function is primarily regulated by several factors including EDRF (endothelium-dependent relaxing factor), EDCF (endothelium-dependent contracting factor) and EDHF (endothelium-dependent hyperpolarizing factor). Vascular dysfunction or injury induced by aging, smoking, inflammation, trauma, hyperlipidaemia and hyperglycaemia are among a myriad of risk factors that may contribute to the pathogenesis of many cardiovascular diseases, such as hypertension, diabetes and atherosclerosis. However, the exact mechanisms underlying the impaired vascular activity remain unresolved and there is no current scientific consensus. Accumulating evidence suggests that the inflammatory cytokine TNF (tumour necrosis factor)-alpha plays a pivotal role in the disruption of macrovascular and microvascular circulation both in vivo and in vitro. AGEs (advanced glycation end-products)/RAGE (receptor for AGEs), LOX-1 [lectin-like oxidized low-density lipoprotein receptor-1) and NF-kappaB (nuclear factor kappaB) signalling play key roles in TNF-alpha expression through an increase in circulating and/or local vascular TNF-alpha production. The increase in TNF-alpha expression induces the production of ROS (reactive oxygen species), resulting in endothelial dysfunction in many pathophysiological conditions. Lipid metabolism, dietary supplements and physical activity affect TNF-alpha expression. The interaction between TNF-alpha and stem cells is also important in terms of vascular repair or regeneration. Careful scrutiny of these factors may help elucidate the mechanisms that induce vascular dysfunction. The focus of the present review is to summarize recent evidence showing the role of TNF-alpha in vascular dysfunction in cardiovascular disease. We believe these findings may prompt new directions for targeting inflammation in future therapies.
An information retrieval model using the fuzzy proximity degree of term occurences (2005)

Based on the idea that the closer the query terms in a document are, the more relevant this document is, we propose a mathematical model of information retrieval based on a fuzzy proximity degree of term occurences. Our model is able to deal with Boolean queries, but contrary to the traditional extensions of the basic Boolean information retrieval model, it does not explicitly use a proximity operator. A single parameter allows to control the proximity degree required. With conjunctive queries, setting this parameter to low values requires a proximity at the phrase level and with high values, the required proximity can continuously be relaxed to the sentence or paragraph levels. We conducted some experiments and present the results.
Laplace Transform of Product of Generalized Marcum Q, Bessel I, and Power Functions with Applications (2014)

The evaluation of integral transforms of special functions is required in different research and practical areas. Analyzing the $κ$-$μ$ fading distribution also khown as the generalized Rician distribution, we find out that the assessment of a few different performance metrics, such as the probability of energy detection of unknown signals and outage probability under co-channel interference, involves the evaluation of an infinite-range integral, which has the form of Laplace transform of product of Marcum Q, Bessel I, and power functions. We evaluate this integral in a closed-form and present numerical estimates.
Effects of overexpression of the alkyl hydroperoxide reductase AhpC on the virulence and isoniazid resistance of Mycobacterium tuberculosis (1997)

Mutations to the regulatory region of the ahpC gene, resulting in overproduction of alkyl hydroperoxide reductase, were encountered frequently in a large collection of isoniazid (INH)-resistant clinical isolates of Mycobacterium tuberculosis but not in INH-susceptible strains. Overexpression of ahpC did not seem to be important for INH resistance, however, as most of these strains were already defective for catalase-peroxidase, KatG, the enzyme required for activation of INH. Transformation of the INH-susceptible reference strain, M. tuberculosis H37Rv, with plasmids bearing the ahpC genes of M. tuberculosis or M. leprae did not result in a significant increase in the MIC. Two highly INH-resistant mutants of H37Rv, BH3 and BH8, were isolated in vitro and shown to produce no or little KatG activity and, in the case of BH3, to overproduce alkyl hydroperoxide reductase as the result of an ahpC regulatory mutation that was also found in some clinical isolates. The virulence of H37Rv, BH3, and BH8 was studied intensively in three mouse models: fully immunocompetent BALB/c and Black 6 mice, BALB/c major histocompatibility complex class II-knockout mice with abnormally low levels of CD4 T cells and athymic mice producing no cellular immune response. The results indicated that M. tuberculosis strains producing catalase-peroxidase were considerably more virulent in immunocompetent mice than the isogenic KatG-deficient mutants but that loss of catalase-peroxidase was less important when immunodeficient mice, unable to produce activated macrophages, were infected. Restoration of virulence was not seen in an INH-resistant M. tuberculosis strain that overexpressed ahpC, and this finding was confirmed by experiments performed with appropriate M. bovis strains in guinea pigs. Thus, in contrast to catalase-peroxidase, alkyl hydroperoxide reductase does not appear to act as a virulence factor in rodent infections or to play a direct role in INH resistance, although it may be important in maintaining peroxide homeostasis of the organism when KatG activity is low or absent.
How the Rise of Federal Bureaucratic Powers Challenges the Role of Courts in Adjudicating Claims of Injury Inflicted by Prescription Drugs (2004)

This Comment uses the recent Paxil litigation as an example of how the rise of federal bureaucratic powers, specifically those exercised by the FDA to administer the Food Drug and Cosmetic Act (hereinafter "FDCA"), increasingly challenge the role of courts in adjudicating tort claims of injury inflicted by prescription drugs. Part I explains the current labeling requirements for prescription drugs. Part II describes product liability law regarding claims involving prescription drugs. Part III analyzes the drug manufacturers' and FDA's defenses to state tort claims, specifically preemption and primary jurisdiction. Part IV discusses the current law as it applies to the recent Paxil litigation. Part V analyzes alternative interpretations that would achieve fairer results. Finally, Part VI of this Comment concludes that FDA prescription drug labeling requirements should be viewed as minimal guidelines subject to enhancement by state court jury verdicts.
A genome-wide association study identifies a novel locus at 6q22.1 associated with ulcerative colitis (2014)

The genetic analysis of ulcerative colitis (UC) has provided new insights into the etiology of this prevalent inflammatory bowel disease. However, most of the heritability of UC (>70%) has still not been characterized. To identify new risk loci for UC we have performed the first genome-wide association study (GWAS) in a Southern European population and undertaken a meta-analysis study combining the newly genotyped 825 UC patients and 1525 healthy controls from Spain with the six previously published GWAS comprising 6687 cases and 19 718 controls from Northern-European ancestry. We identified a novel locus with genome-wide significance at 6q22.1 [rs2858829, P = 8.97 × 10(-9), odds ratio (OR) (95% confidence interval, CI] = 1.12 (1.08-1.16)] that was validated with genotype data from a replication cohort of the same Southern European ancestry consisting in 1073 cases and 1279 controls [combined P = 7.59 × 10(-10), OR (95% CI) = 1.12 (1.08-1.16)]. Furthermore, we confirmed the association of 33 reported associations with UC and we nominally validated the GWAS results of nine new risk loci (P < 0.05, same direction of effect). SNP rs2858829 lies in an intergenic region and is a strong cis-eQTL for FAM26F gene, a gene that is shown to be selectively upregulated in UC colonic mucosa with active inflammation. Our results provide new insight into the genetic risk background of UC, confirming that there is a genetic risk component that differentiates from Crohn's Disease, the other major form of inflammatory bowel disease.
Human Micro-Range/Micro-Doppler Signature Extraction, Association, and Statistical Characterization for High-Resolution Radar (2011)

Extraction, Association, and Statistical Characterization for High-Resolution Radar
Chemical Proteomics-Based Analysis of Off-Target Binding Profiles for Rosiglitazone and Pioglitazone: Clues for Assessing Potential for Cardiotoxicity (2012)

Drugs exert desired and undesired effects based on their binding interactions with protein target(s) and off-target(s), providing evidence for drug efficacy and toxicity. Pioglitazone and rosiglitazone possess a common functional core, glitazone, which is considered a privileged scaffold upon which to build a drug selective for a given target—in this case, PPARγ. Herein, we report a retrospective analysis of two variants of the glitazone scaffold, pioglitazone and rosiglitazone, in an effort to identify off-target binding events in the rat heart to explain recently reported cardiovascular risk associated with these drugs. Our results suggest that glitazone has affinity for dehydrogenases, consistent with known binding preferences for related rhodanine cores. Both drugs bound ion channels and modulators, with implications in congestive heart failure, arrhythmia, and peripheral edema. Additional proteins involved in glucose homeostasis, synaptic transduction, and mitochondrial energy production were detected and potentially contribute to drug efficacy and cardiotoxicity.
Studies on the Status of Periodontal Disease from the Lymphocytes Functions Concerned with Immunoglobulin Synthesis. (1991)

歯周病患者の抗体産生に関連する免疫ネットワーク諸因子間の関わりを知ることを目的に, 歯周病原性細菌に対して低い血清抗体価を示す歯周病患者18名と高い血清抗体価を示す患者14名, および健常者18名について, 末梢血レベルにおける抗体産生能, 単核球サブセットの割合, およびT細胞と単球の機能を調べた。健常者群と比較して, 患者群はサプレッサーT細胞数の低下と抗体産生能の亢進を示す特徴を有していた。また, 調べた諸機能の亢進あるいは低下を示す被験者の割合は血清抗体価の高低に関わらず患者群に多かった。しかし, 調べた諸機能値はいずれも個体差によるばらつきが大きかった。体液性免疫応答に関連する個体のリンパ球因子間の関わりは, 個体毎に明らかにされなければならないと考えられる。
A novel design of a microstrip microwave broadband power amplifier for DCS, PCS and UMTS bands (2017)

A RF-microwave broadband power amplifier using the Si-Bipolar transistor is presented in this work. The power amplifier operates in several frequency ranges 1.70–2.20GHz. Which covers the following bands: DCS (Digital Cellular System) (1710MHz–1880MHz) in Europe, PCS (Personal communication Services/System) (1850MHz–1990MHZ) in the United States, UMTS (Universal Mobile Telecommunication System) (1920MHz–2170MHz). The broadband matching networks of this amplifier consist of microstrip transmission lines. This BPA based on the analysis of scattering parameters, also with using analytical and computer-aided optimization techniques. A typical broadband amplifier has been designed with a nominal power gain of 11.5dB with a maximum deviation of 1dB, covering the 1.70–2.20GHz band. The high gain, good performances for input and output matching networks impedance and stability are achieved.
Effects of underwater turbulence on laser beam propagation and coupling into single-mode optical fiber (2010)

We characterize and compare the effects of turbulence on underwater laser propagation with theory. Measurements of the coupling efficiency of the focused beam into a single-mode fiber are reported. A simple tip-tilt control system, based on the position of the image centroid in the focal plane, was shown to maintain good coupling efficiency for a beam radius equal to the transverse coherence length, r(0). These results are relevant to high bandwidth communication technology that requires good spatial mode quality.
Repeatability of 3D OCT Pachymetry in Eyes with and without Contact Lens Induced Corneal Swelling (2013)

Introduction: Corneal thickness measurement is an indirect assessment of the physiological corneal function in human eye. This value, especially in the central area, is an important data for clinical diagnosis, treatment and monitoring of anterior segment pathologies. There are several technologies for non-invasively measuring corneal thickness like optical coherence tomography (OCT). However, there is little information available describing the effect of contact lens induced corneal swelling in OCT measures. The purpose of this study was to evaluate the repeatability of OCT corneal pachymetry in eyes with and without contact lens induced corneal swelling. Material and Methods: This study included five visits over one week in six healthy subjects: baseline and after sleeping with four different CL of +0.50 D, +2.00 D, +5.00 D and +8.00 D (Acuvue 2, Johnson & Johnson Vision Care) on four different days. Corneal pachymetry OCT 3D (Topcon) were measured three consecutive times during each visit. Besides, this measurement was repeated in 12 meridians (Scans #1 to #12), between 0°and 165°with 15° intervals. Results: Corneal pachymetry was significant different between before and after contact lens wear (p < 0.001 ANOVA). High repeatability was found without corneal swelling [Coefficient of variation (CV) = 0.68% p = 0.93] and with corneal swelling [CL -0.50 D (CV = 0.78% p = 0.95; 590 ± 46 μm CI 95% 548 to 596), with CL + 2.00 D (CV = 0.72% p = 0.97; 601 ± 46 μm CI 95% 595 to 607), with CL + 5.00 D (CV = 0.78% p = 0.66; 608 ± 50 μm CI 95% 601 to 615) and with CL + 8.00 D (CV = 0.77% p = 0.97; 607 ± 44 μm CI 95% 601 to 613)]. There were no differences (p = 1.00) in central corneal thickness along the 12 scans corneal [Scan #0 (593 ± 50 μm CI 95% 582 to 603), #1 (592 ± 50 μm CI 95% 581 to 603), #2 (591 ± 50 μm IC 95% 580 to 602), #3 (590 ± 49 μm CI 95% 579 to 600), #4 (590 ± 50 μm CI 95% 579 to 600), #5 (591 ± 50 μm CI 95% 581 to 602), #6 (590 ± 51 μm CI 95% 580 to 601), #7 (589 ± 50 μm CI 95% 578 to 600), #8 (590 ± 50 μm CI 95% 579 to 600), #9 (589 ± 50 μm CI 95% 579 to 600), #10 (592 ± 50 μm CI 95% 581 to 602) and #11 (591 ± 50 μm CI 95% 580 to 601). Conclusions: 3D OCT showed a high repeatability (CV < 1%) to measure central thickness in corneas with and without contact lens induced corneal swelling. This technology presents advantages over other clinical devices used to measure corneal thickness and could be the “gold standard” for future clinical studies and clinical practice for eye care practitioners.
Red-blue pebbling revisited: near optimal parallel matrix-matrix multiplication (2019)

We propose COSMA: a parallel matrix-matrix multiplication algorithm that is near communication-optimal for all combinations of matrix dimensions, processor counts, and memory sizes. The key idea behind COSMA is to derive an optimal (up to a factor of 0.03\% for 10MB of fast memory) sequential schedule and then parallelize it, preserving I/O optimality. To achieve this, we use the red-blue pebble game to precisely model MMM dependencies and derive a constructive and tight sequential and parallel I/O lower bound proofs. Compared to 2D or 3D algorithms, which fix processor decomposition upfront and then map it to the matrix dimensions, it reduces communication volume by up to $\sqrt{3}$ times. COSMA outperforms the established ScaLAPACK, CARMA, and CTF algorithms in all scenarios up to 12.8x (2.2x on average), achieving up to 88\% of Piz Daint's peak performance. Our work does not require any hand tuning and is maintained as an open source implementation.
Finding and Certifying (Near-)Optimal Strategies in Black-Box Extensive-Form Games (2020)

Often -- for example in war games, strategy video games, and financial simulations -- the game is given to us only as a black-box simulator in which we can play it. In these settings, since the game may have unknown nature action distributions (from which we can only obtain samples) and/or be too large to expand fully, it can be difficult to compute strategies with guarantees on exploitability. Recent work \cite{Zhang20:Small} resulted in a notion of certificate for extensive-form games that allows exploitability guarantees while not expanding the full game tree. However, that work assumed that the black box could sample or expand arbitrary nodes of the game tree at any time, and that a series of exact game solves (via, for example, linear programming) can be conducted to compute the certificate. Each of those two assumptions severely restricts the practical applicability of that method. In this work, we relax both of the assumptions. We show that high-probability certificates can be obtained with a black box that can do nothing more than play through games, using only a regret minimizer as a subroutine. As a bonus, we obtain an equilibrium-finding algorithm with $\tilde O(1/\sqrt{T})$ convergence rate in the extensive-form game setting that does not rely on a sampling strategy with lower-bounded reach probabilities (which MCCFR assumes). We demonstrate experimentally that, in the black-box setting, our methods are able to provide nontrivial exploitability guarantees while expanding only a small fraction of the game tree.
Analysis of associative reinforcement learning in neural networks using iterated function systems (1992)

A mathematical theory of associative reinforcement learning in neural networks is developed in terms of random iterated function systems (IFSs), which are finite sets of random maps on metric spaces. In particular, the stochastic search for an associative mapping that maximizes the expected pay-off arising from reinforcement is formulated as a random IFS on weight-space. The dynamical evolution of the weights is described by a Markov process. If this process is ergodic then the limiting behavior of the system is described by an invariant probability measure on weight space that can have a fractal-like structure. A class of associative reinforcement learning algorithms is constructed that is an extension of the nonassociative schemes used in stochastic automata theory. The issue of generalization is discussed within the IFS framework and related to the stochastic and possibly fractal nature of the learning process.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Supervisory hybrid systems (1999)

Supervisory hybrid systems are systems generating a mixture of continuous-valued and discrete-valued signals. This systems paradigm is particularly useful in modeling applications where high-level decision making is used to supervise process behavior. Hybrid system methodologies are also applicable to switched systems where the system switches between various setpoints or operational modes to extend its effective operating range. Hybrid systems, therefore, embrace a diverse set of applications. There has been considerable activity in the area of hybrid systems theory, and this article provides an introduction to some of the basic concepts and trends in this emergent field. The term hybrid refers to a mixing of two fundamentally different types of objects or methods. The paper deals with supervisory hybrid systems. Supervisory hybrid systems are systems that combine discrete event and continuous-valued dynamics. The article is organized as follows. We first provide an example of a hybrid system, to be used throughout as a pedagogical tool illustrating various concepts in hybrid systems theory. We then discuss modeling frameworks for hybrid systems, paying specific attention to the hybrid automaton. Not only may the system have a hybrid character, but the specifications on desired system behaviors may also be hybrid. The article also discusses specification logics that express system requirements on both the discrete and continuous states of the system. The article continues with a survey of current methods and concepts used to verify or validate desired system behaviors, and concludes with a survey of current methods for hybrid control system synthesis.
Delft-Java dynamic translation (1999)

This paper describes the DELFT-JAVA processor and the mechanisms required to dynamically translate JVM instructions into DELFT-JAVA instructions. Using a form of hardware register allocation, we transform stack bottlenecks into pipeline dependencies which are later removed using register renaming and interlock collapsing arithmetic units. When combined with superscalar techniques and multiple instruction issue, we remove up to 60% of translated dependencies. When compared with a realizable stack-based implementation, our approach accelerates a Vector Multiply execution by 3.2/spl times/ for out-of-order execution with register renaming and 2.7/spl times/ when hardware constraints were considered. In addition, for translated instruction streams, we realized a 50% performance improvement for out-of-order execution when compared with in-order execution.