gebhart/patrepeval huggingface dataset:
<i>HLA-B</i> Genotyping to Detect Carbamazepine-Induced Stevens-Johnson Syndrome: Implications for Personalizing Medicine (2005)

Preventing severe adverse drug reactions by identifying people at risk with a simple genetic test is the goal of many pharmacogenomic studies. Stevens-Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN) are related, life-threatening cutaneous adverse reactions, most often caused by medication. The overall incidence and the commonly offending drugs vary among different ethnic populations. Susceptibility to such idiosyncratic reactions is thought to be genetically determined and immune mediated. Finding a strong genetic association between a particular human leukocyte antigen (HLA)-B allele and the reaction to a specific drug provides evidence that the pathogenesis of the severe cutaneous adverse drug reactions involves major histocompatibility complex-restricted presentation of a drug or its metabolites for T-cell activation. In the case of carbamazepine-induced SJS/TEN, the tight association of the HLA-B*1502 allele (sensitivity 100%, specificity 97% and odds ratio 2504) provides a plausible basis for further development of such a test to identify individuals at risk of developing this life-threatening condition.
Maximum energy of protons accelerated by high-power lasers: Thermodynamic approach (2007)

It is shown that the energy of protons accelerated in laser-matter interaction experiments may be significantly increased through the process of splitting the incoming laser pulse into multiple interaction stages of equal intensity. From a thermodynamic point of view, the splitting procedure can be viewed as an effective way of increasing the efficiency of energy transfer from the laser light to protons, which peaks for processes having the least amount of entropy gain. It is predicted that it should be possible to achieve $\apprge 100%$ increase in the energy efficiency in a six-stage laser proton accelerator compared to a single laser-target interaction scheme.
Genetic Control of Reduced Palmitate Content in Soybean (1994)

Reduced palmitate content in soybean [ Glycine max (L.) Merr.] is controlled by two major alleles, fap1 and fap3 . This study was conducted to determine the role that modifying genes may have on the reduced palmitate trait in lines homozygous for the major alleles. Two lines homozygous for fap1 and fap3 , AX5152‐34 and AX5152‐105, were each crossed as donor parents to a high‐yielding cultivar with normal palmitate, ‘Kenwood’ or ‘Marcus’. The F 1 plants were backcrossed to the high‐yielding cultivar. Two experiments were grown in randomized complete‐block designs at three locations in Iowa with two replications per location. The Kenwood experiment consisted of 14 F 4:6 lines from the cross AX5152‐105 × Kenwood, 83 BC 1 F 3:5 lines from five BC 1 families from the backcross Kenwood × (AX5152‐105 × Kenwood), Kenwood and AX5152‐105. The Marcus experiment contained 14 F 4:6 lines from the cross AX5152‐34 × Marcus, 69 BC 1 F 3:5 lines from the backcross Marcus × (AX5152‐34 × Marcus) among six backcross families, Marcus and AX5152‐34. All lines, except Kenwood and Marcus, were homozygous for both fap1 and fap3 . The influence of modifying genes on palmitate content was evident in both experiments. There were significant differences in palmitate content among single‐cross lines, among backcross lines, and among lines within individual backcross families. The palmitate content of each donor parent was significantly different from the means of the corresponding single‐cross and backcross populations. Lines with reduced palmitate were obtained that had higher yield than the recurrent parents, which indicated that reduced palmitate is not detrimental to yield. Lines with reduced palmitate generally had reduced oil content.
[Malaria vaccine]. (2008)

With about 2.2 billion of the world' s population at risk, malaria remains as one of the most infectious disease globally. The failure of existing control strategies necessitates the need for vaccine development. Our efforts have been geared on the development of an effective vaccine using SE36 protein based from the N-terminal domain of Serine Repeat Antigen (SERA5) of Plasmodium falciparum. Immunoepidemiological data underscores the uniqueness of SERA vs. other vaccine candidate, showing a semi-perfect correlation of the naturally induced antibody response to SE36 protein with increased protective immunity in adults and children. GMP-grade SE36 was formulated adsorbed to aluminum hydroxide gel as BK-SE36. Immunological test using squirrel monkeys provided significant protection after P. falciparum challenge infection. No significant safety issues have been identified in healthy, malaria-unexposed adults in a Phase Ia clinical trial in Japan. Cumulative data confirms that the vaccine is safe and highly immunogenic.
Evaluation of a Novel Thermobrachytherapy Seed for Concurrent Administration of Brachytherapy and Magnetically Mediated Hyperthermia in Treatment of Solid Tumors (2011)

Concurrent hyperthermia and radiation therapy in treatment of cancer show a strong evidence of a synergistic enhancement. We designed a new self-regulating Thermo-Brachytherapy seed, which serves as a source of both radiation and heat for concurrent administration of brachytherapy and hyperthermia. The Thermo-Brachytherapy seed has a core of ferromagnetic material which produces heat when subjected to alternating electro-magnetic (EM) field and effectively shuts off after reaching the Curie temperature (TC) of the ferromagnetic material thus realizing the temperature self-regulation. For the thermal characteristics, we considered a model consisting of one seed as well as an array of 16 seeds placed in the central region of a cylindrical water phantom. Isodose distributions of these models were computed using MCNP5 Monte Carlo simulation technique. The modeling for the isothermal distribution computations performed using a finite-element partial differential equation solver package COMSOL Multiphysics. It is shown that by changing frequency and intensity of the alternating applied magnetic field, we can obtain desired isothermal distribution within the target volume. Adjustment of these two parameters allows one to match the desired isosurface dose distribution with an optimized isothermal distribution achieving optimal treatment in both modalities. We also demonstrate that the effect of tissue cooling down due to the blood perfusion could be compensated by adjusting the externally applied magnetic field parameters. In this paper, parameters effecting radiation and thermal distribution on this proposed new seed will be presented.
Reducing energy consumption on mobile devices with WiFi interfaces (2005)

Emergence of mobile handheld devices with WiFi (IEEE 802.11) interfaces such as WiFi phones, WiFi-cellular dual-mode phones and PDAs (personal digital assistants), allow users to take full advantages of heterogeneous radio technologies. WiFi, however, was not originally designed for energy-constrained handheld devices. As a result, the standby times of a handheld device with a WiFi interface is significantly lower than what people typically experience with today's cellular phones. This paper presents and evaluates a system-level power management method devices with WiFi, or other high energy-consuming network interfaces, to significantly increase their standby times without modifications to WiFi and upper layer protocols and implementations.
An image-based method to measure joint deformity in inflammatory arthritis: development and pilot study (2019)

Quantifying joint deformity in people with rheumatoid (RA) and psoriatic arthritis (PsA) remains challenging. Here, we demonstrate a new method to measure bone erosions and abnormal periosteal growths, based on the difference between a predicted healthy and actual diseased joint surface. We optimized the method by creating and measuring artificial bone erosions and growths. Then we measured 46 healthy and diseased patient surfaces. We found average sensitivity errors of ≤0.27 mm when measuring artificial erosions and growths. Patients had significantly more bone erosion than healthy subjects. Surface based outcomes are a novel way to interpret and quantify bone changes in PsA and RA.
The integration of nanowires and nanotubes with microstructures (2009)

A technique for the localised synthesis, self-assembly and direct integration of nanostructures with microstructures employing the localised synthesis of nanostructures onto Microelectromechanical Systems (MEMS) structures is demonstrated. The in-situ guided growth process of the nanostructures is accomplished using a locally applied electric-field realised by using the MEMS structures as electrodes. The self-assembly and self-terminated contact process of nanostructures is achieved when the hot nanostructure makes contact with the cold MEMS structure. This approach is flexible and both Silicon Nanowires (SiNWs) and Carbon Nanotubes (CNTs) have been successfully integrated to form Nanoelectromechanical Systems (NEMS) devices. These systems are potentially available for sensing applications with or without further functionalisation. As such, this approach mitigates integration and manufacturing difficulties which currently plague the fabrication of nanoscale devices.
<title>Design and analysis of optical burst-switched networks</title> (1999)

Optical burst switching (OBS) is a promising solution for building terabit optical routers and realizing IP over D- WDM. In this paper, we describe the basic concept of OBS and a general architecture of optical routers. The key design issues related to the OBS are discussed, notably, burstification, offset-time management and channel scheduling. A simple channel scheduling algorithm called LAUC (Latest Available Unscheduled Channel) algorithm is presented, which is also called Horizon algorithm in the literature. The performance of optical routers under random and self-similar traffic is thoroughly studied via computer simulations. Our study indicates that the distribution of burst length is not exponential any more. For the FDL (fiber delay line) optical buffer, the burst loss ratio is quite sensitive to the traffic characteristic of bursts when using the LAUC algorithm.
Effects of atorvastatin on fasting and postprandial complement component 3 response in familial combined hyperlipidemia (2003)

VLDL overproduction by enhanced hepatic FFA flux is a major characteristic of familial combined hyperlipidemia (FCHL). The postprandial complement component 3 (C3) response has been associated with impaired postprandial FFA metabolism in FCHL. We investigated the effects of 16 weeks of treatment with atorvastatin on postprandial C3 and lipid changes in 12 FCHL patients. Atorvastatin significantly lowered fasting plasma C3 and triglyceride (TG) in FCHL. Fasting TG and insulin sensitivity were the best predictors of fasting and postprandial C3. Postprandial triglyceridemia and C3 response, estimated as area under the curve (AUC), were significantly lowered by atorvastatin by 19% and 12%, respectively, albeit still elevated, compared with 10 matched controls. Postprandial FFA-AUC and postheparin plasma lipolytic activities remained unchanged after atorvastatin, suggesting no major effect on lipolysis. After atorvastatin, postprandial hydroxybutyric acid-AUC, which was elevated in untreated FCHL patients, was decreased, reaching values similar to those in controls. The present data show reduction of postprandial hepatic FFA flux in FCHL by atorvastatin, providing an additional mechanistic explanation for the reduction of VLDL secretion reported previously for atorvastatin. This was accompanied by a decrease in fasting plasma C3 concentrations and a blunted postprandial C3 response to an acute oral fat load.
Toll-like Receptor 2: A Novel Therapeutic Target for Ischemic White Matter Injury and Oligodendrocyte Death (2017)

Despite paramount clinical significance of white matter stroke, there is a paucity of researches on the pathomechanism of ischemic white matter damage and accompanying oligodendrocyte (OL) death. Therefore, a large gap exists between clinical needs and laboratory researches in this disease entity. Recent works have started to elucidate cellular and molecular basis of white matter injury under ischemic stress. In this paper, we briefly introduce white matter stroke from a clinical point of view and review pathophysiology of ischemic white matter injury characterized by OL death and demyelination. We present a series of evidence that Toll-like receptor 2 (TLR2), one of the membranous pattern recognition receptors, plays a cell-autonomous protective role in ischemic OL death and ensuing demyelination. Moreover, we also discuss our recent findings that its endogenous ligand, high-mobility group box 1 (HMGB1), is released from dying OLs and exerts autocrine trophic effects on OLs and myelin sheath under ischemic condition. We propose that modulation of TLR2 and its endogenous ligand HMGB1 can be a novel therapeutic target for ischemic white matter disease.
The immunogenic potential of bacterial flagella for <i>Salmonella</i>‐mediated tumor therapy (2019)

Genetically engineered Salmonella Typhimurium are potent vectors for prophylactic and therapeutic measures against pathogens as well as cancer. This is based on the potent adjuvanticity that supports strong immune responses. The physiology of Salmonella is well understood. It simplifies engineering of both enhanced immune-stimulatory properties as well as safety features, thus, resulting in an appropriate balance between attenuation and efficacy for clinical applications. A major virulence factor of Salmonella is the flagellum. It is also a strong pathogen-associated molecular pattern recognized by extracellular and intracellular receptors of immune cells of the host. At the same time, it represents a serious metabolic burden. Accordingly, the bacteria evolved tight regulatory mechanisms that control flagella synthesis in vivo. Here, we systematically investigated the immunogenicity and adjuvant properties of various flagella mutants of Salmonella in vitro and in a mouse cancer model in vivo. We found that mutants lacking the flagellum-specific ATPase FliHIJ or the inner membrane ring FliF displayed the greatest stimulatory capacity and strongest antitumor effects, while remaining safe in vivo. Scanning electron microscopy revealed the presence of outer membrane vesicles in the ΔfliF and ΔfliHIJ mutants. Finally, the combination of the ΔfliF and ΔfliHIJ mutations with our previously described attenuated and immunogenic background strain SF102 displayed strong efficacy against the highly resistant cancer cell line RenCa. We thus conclude that manipulating flagella biosynthesis has great potential for the construction of highly efficacious and versatile Salmonella vector strains.
Uniform surface acoustic wave transducer configuration having improved frequency selectivity (1981)

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Sulfate reduction is increased in transgenic <i>Arabidopsis thaliana</i> expressing 5′‐adenylylsulfate reductase from <i>Pseudomonas aeruginosa</i> (2002)

The two-electron reduction of sulfate to sulfite in plants is mediated by 5'-adenylylsulfate (APS) reductase, an enzyme theorized to be a control point for cysteine synthesis. The hypothesis was tested by expression in Arabidopsis thaliana under transcriptional control of the CaMV 35S promoter of the APS reductase from Pseudomonas aeruginosa (PaAPR) fused with the rbcS transit peptide for localization of the protein to plastids. PaAPR was chosen for the experiment because it is a highly stable enzyme compared with the endogenous APS reductase of A. thaliana, and because PaAPR is catalytically active in combination with the plant thioredoxins m and f indicating that it would likely be catalytically active in plastids. The results indicate that sulfate reduction and O-acetylserine (OAS) production together limit cysteine synthesis. Transgenic A. thaliana lines expressing PaAPR accumulated sulfite, thiosulfate, cysteine, gamma-glutamylcysteine, and glutathione. Sulfite and thiosulfate increased more than did cysteine, gamma-glutamylcysteine and glutathione. Thiosulfate accumulation was most pronounced in flowers. Feeding of OAS to the PaAPR-expressing plants caused cysteine and glutathione to increase more rapidly than in comparably treated wild type. Both wild-type and transgenic plants accumulated sulfite and thiosulfate in response to OAS feeding. The PaAPR-expressing plants were slightly chlorotic and stunted compared with wild type. An attempt to uncover the source of thiosulfate, which is not thought to be an intermediate of sulfate reduction, revealed that purified beta-mercaptopyruvate sulfurtransferase is able to form thiosulfate from sulfite and beta-mercaptopyruvate, suggesting that this class of enzymes could form thiosulfate in vivo in the presence of excess sulfite.
HIGH RESOLUTION PHONON SPECTROSCOPY AT LOW TEMPERATURES (1978)

A review is given of the techniques of phonon spectroscopy that are capable of high resolution <≈ 1 GHz and of problems for which they could be of value. Particular attention is paid to the frequency crossing technique.
Spatial-Frequency-Domain Imaging for quality assessment of apples (2006)

Spatial-Frequency-Domain Imaging (SFDI) is applied for the first time to the quality assessment of apples. The optical properties obtained are correlated to the physical and chemical properties.
An efficient SQL-based RDF querying scheme (2005)

Devising a scheme for efficient and scalable querying of Resource Description Framework (RDF) data has been an active area of current research. However, most approaches define new languages for querying RDF data, which has the following shortcomings: 1) They are difficult to integrate with SQL queries used in database applications, and 2) They incur inefficiency as data has to be transformed from SQL to the corresponding language data format. This paper proposes a SQL based scheme that avoids these problems. Specifically, it introduces a SQL table function RDF_MATCH to query RDF data. The results of RDF_MATCH table function can be further processed by SQL's rich querying capabilities and seamlessly combined with queries on traditional relational data. Furthermore, the RDF_MATCH table function invocation is rewritten as a SQL query, thereby avoiding run-time table function procedural overheads. It also enables optimization of rewritten query in conjunction with the rest of the query. The resulting query is executed efficiently by making use of B-tree indexes as well as specialized subject-property materialized views. This paper describes the functionality of the RDF_MATCH table function for querying RDF data, which can optionally include user-defined rulebases, and discusses its implementation in Oracle RDBMS. It also presents an experimental study characterizing the overhead eliminated by avoiding procedural code at runtime, characterizing performance under various input conditions, and demonstrating scalability using 80 million RDF triples from UniProt protein and annotation data.
Convolutional Dictionary Learning for Multi-Channel Signals (2018)

There has recently been a rapid growth in interest in the design of efficient algorithms for convolutional sparse coding, and in the application of these methods to signal and image processing inverse problems. Thus far, however, the design of algorithms and methods for multi-channel signals has received very little attention. In this work we extend our initial results in convolutional sparse coding and dictionary learning for this type of data, proposing new algorithms that scale well to signals with large numbers of channels, and demonstrate their performance in an application involving hyperspectral imagery.
DO TESTICUIAR OPIATES REGULATE LEYDIG CELL FUNCTION? (1984)

beta-Endorphin is believed to be synthesized in testicular Leydig cells. To gain more information about the role of this and other endogenous opioid peptides in the testis, opiate antagonists (naloxone and nalmefene, 100 micrograms/testis) were administered intratesticularly to hemicastrated adult rats. Leydig cell function was evaluated by measurement of serum testosterone and testosterone production in vitro. Estimation of androgen binding protein (rABP) was used as an index of Sertoli cell function. Serum testosterone was reduced significantly by intratesticular administration of naloxone and nalmefene in treated animals. Systemic administration of these antagonists had no effect at the doses used. Testes from treated animals incubated in vitro with or without hCG produced significantly less testosterone than vehicle-treated control testes. Hemicastration reduced rABP synthesis and secretion; however, treatment with opiate antagonists did not alter the amount of this protein in the serum or epididymides of these rats. These observations suggest that endogenous testicular opiates modulate testosterone secretion by Leydig cells.
Computerized Identification of Suspicious Regions for Masses in Digitized Mammograms (1996)

Because this method limits the initial number of suspicious mass regions while retaining high sensitivity, it may be applicable to clinically usable computer-aided diagnosis schemes.
Linear Active Disturbance Rejection Control with a Fractional-Order Integral Action (2022)

Linear active disturbance rejection control (LADRC) is a powerful control structure thanks to its performance in uncertainties, internal and external disturbances estimation and cancelation. An extended state observer (ESO) based controller is the key to the LADRC method. In this article, the LADRC scheme combined with a fractional-order integral action (FOI-LADRC) is proposed to improve the robustness of the standard LADRC. Using the robust closed-loop Bode’s ideal transfer function (BITF), an appropriate pole placement method is proposed to design the set-point tracking controller of the FOI-LADRC scheme. Numerical simulations and experimental results on a cart-pendulum system will illustrate the effectiveness of the proposed FOI-LADRC scheme for the disturbance rejection, the set-point tracking and the improved robustness. To illustrate the LADRC control schemes and to verify the performance of the proposed FOI-LADRC, compared to the standard LADRC and IOI-LADRC structures, two tests will be carried out. First, simulation tests on an academic example will be presented to show the effect of the different parameters of the control law on the performance of the closed-loop system. Then, these three control structures are implemented on an experimental test bench, the cart-pendulum system, to show their efficiency and to show the superiority of the proposed method compared to the two other structures.
A DCT-domain filtering algorithm for MPEG-4 encoding (2003)

One of the well-known weaknesses of block-based video compression schemes such as MPEG-4, at low bit-rates, is blocking artifacts. They can be well removed by post-processing solutions offering an efficient deblocking filter, unfortunately at the cost of a significant increase of the decoding process complexity. In this paper, we propose a new method to reduce blocking artifacts (thus increasing the visual quality of sequences or the compression rate) at the encoding stage to get rid of, or to help, the post-processing step. We consider a filtering operation in the DCT domain, applied on blocks before quantization to leave the decoding process unmodified. The solution is adaptive and focuses on regions which would be a priori blocky regarding some texture features and encoding parameters. It is based on the mix of quantization step reduction at the frame level, with DCT coefficients low-pass filtering at the block level, on top of any bit-rate regulation module. Tests showed the efficiency of the method: the sequences encoded with our DCT filter are cleaner, with less ringing and, above all, fewer blocking artifacts than the ones without any processing. Visual quality is therefore better for a constant bit consumption. Depending on cases, post-processing is either useless or improved by our process.