gebhart/patrepeval huggingface dataset:
Accelerator (2006)

GPUs are difficult to program for general-purpose uses. Programmers can either learn graphics APIs and convert their applications to use graphics pipeline operations or they can use stream programming abstractions of GPUs. We describe Accelerator, a system that uses data parallelism to program GPUs for general-purpose uses instead. Programmers use a conventional imperative programming language and a library that provides only high-level data-parallel operations. No aspects of GPUs are exposed to programmers. The library implementation compiles the data-parallel operations on the fly to optimized GPU pixel shader code and API calls.We describe the compilation techniques used to do this. We evaluate the effectiveness of using data parallelism to program GPUs by providing results for a set of compute-intensive benchmarks. We compare the performance of Accelerator versions of the benchmarks against hand-written pixel shaders. The speeds of the Accelerator versions are typically within 50% of the speeds of hand-written pixel shader code. Some benchmarks significantly outperform C versions on a CPU: they are up to 18 times faster than C code running on a CPU.
Expandable external support device to improve Saphenous Vein Graft Patency after CABG (2013)

The expandable SVG external support system was found to be efficacious in reducing SVG's non-uniform dilatation and neointimal formation in an animal model early after CABG. This novel technology may have the potential to improve SVG patency rates after surgical myocardial revascularization.
Modulation of Murine Allergic Rhinosinusitis by CpG Oligodeoxynucleotides (2002)

CpG ODN prevents the development of TH-2-mediated eosinophilic inflammation and symptoms in a murine model of allergic rhinosinusitis.
A language and character set determination method based on N-gram statistics (2002)

An N-gram-based language, script, and encoding scheme-detection method is introduced in this article. The method detects language, script, and encoding schemes using a target text document encoded by computer by checking how many byte sequences of the target match the byte sequences that can appear in the texts belonging to a language, script, and encoding scheme. This detection mechanism is different from conventional N-gram-based methods in that its threshold for any category is uniquely predetermined. The method was originally created for a survey of web pages conducted to find how many web pages are written in a particular language, script, and encoding scheme. The requirement is that the method must be able to respond to either "correct answer" or "unable to detect" where "unable to detect" includes "other than registered." There are some minor problems with this method, but its effectiveness as a language, script, and encoding scheme-detection method has been confirmed by experiments.
T-cell Inhibitors: A Bench-to-Bedside Review (2012)

Allergic contact dermatitis is the quintessential example of a delayed-in-time and T-cell-mediated immune response. In the last decade, many of the molecular events required to initiate (or block) such a response have been uncovered. Textbook and journal reviews have emphasized the costimulatory requirements, with less focus on the coinhibitory signals that are of equal importance in understanding this central event of adaptive immunity. To fill this gap, we offer a compendium of discoveries characterizing the ligand-receptor pairs inhibiting T-cell activation and of selected illnesses and therapeutic applications that illuminate their role in health and disease.
An Application of Random Projection to Parameter Estimation in Partial Differential Equations (2012)

In this article, we use a dimension reduction technique called random projection to reduce the computational cost of estimating unknown parameters in models based on partial differential equations (PDEs). In this setting, the repeated numerical solution of the discrete PDE model dominates the cost of parameter estimation. In turn, the size of the discretized PDE corresponds directly to the number of physical experiments. As the number of experiments grows, parameter estimation becomes prohibitively expensive. In order to reduce this cost, we develop an algorithmic technique based on random projection that solves the parameter estimation problem using a much smaller number of so-called encoded experiments. Encoded experiments amount to nothing more than random sums of physical experiments. Using this construction, we provide a lower bound for the required number of encoded experiments. This bound holds in a probabilistic sense and is independent of the number of physical experiments. Finally, we demonstrate our approach on a parameter estimation problem governed by Poisson's equation.
Fatty acids and eicosanoids regulate gene expression through direct interactions with peroxisome proliferator-activated receptors α and γ (1997)

Peroxisome proliferator-activated receptors (PPARs) alpha and gamma are key regulators of lipid homeostasis and are activated by a structurally diverse group of compounds including fatty acids, eicosanoids, and hypolipidemic drugs such as fibrates and thiazolidinediones. While thiazolidinediones and 15-deoxy-Delta12, 14-prostaglandin J2 have been shown to bind to PPARgamma, it has remained unclear whether other activators mediate their effects through direct interactions with the PPARs or via indirect mechanisms. Here, we describe a novel fibrate, designated GW2331, that is a high-affinity ligand for both PPARalpha and PPARgamma. Using GW2331 as a radioligand in competition binding assays, we show that certain mono- and polyunsaturated fatty acids bind directly to PPARalpha and PPARgamma at physiological concentrations, and that the eicosanoids 8(S)-hydroxyeicosatetraenoic acid and 15-deoxy-Delta12,14-prostaglandin J2 can function as subtype-selective ligands for PPARalpha and PPARgamma, respectively. These data provide evidence that PPARs serve as physiological sensors of lipid levels and suggest a molecular mechanism whereby dietary fatty acids can modulate lipid homeostasis.
Probing the Function of Asp128 in the Low Molecular Weight Protein-Tyrosine Phosphatase-Catalyzed Reaction. A Pre-Steady-State and Steady-State Kinetic Investigation (1996)

The role of Asp128 in the catalytic mechanism of the low Mr protein-tyrosine phosphatase (PTPase) from the fission yeast Schizosaccharomyces pombe has been investigated by a combination of site-directed mutagenesis and pre-steady-state and steady-state kinetic analysis. The corresponding aspartic acid in the bovine enzyme is located on a loop adjacent to the phosphate-binding loop and forms a hydrogen bond with the oxygen atom of the bound sulfate or phosphate that is structurally homologous to the ester oxygen in substrates [Su et al. (1994) Nature 370, 575-578; Zhang, M., et al. (1994) Biochemistry 33, 11097-11105]. Asp128 has been replaced by a Glu, an Asn, and an Ala. The kcat for the hydrolysis of p-nitrophenyl phosphate (pNPP) decreases by factors of 6.7, 400, and 650 for the mutants D128E, D128N, and D128A, respectively. Compared to the wild type, the binding affinity for phosphate is decreased 2 and 4.3-fold, respectively, for the D128A and D128N mutants, whereas no change in affinity is observed for the D128E mutant. An evaluation of the burst kinetics demonstrates that Asp128 plays a role in both the phosphoenzyme intermediate formation (k2) and breakdown (k3). Thus, substitution at Asp128 by a Glu, an Asn, or an Ala reduces k2 by 17, 7480, and 11900 and reduces k3 by 6.2, 380, and 40. The greater effect on k2 and k3 is consistent with a dissociative transition-state for the low M(r)PTPase-catalyzed reaction. Results from the rapid kinetics, partition experiments, and leaving group dependence experiments suggest that for the wild type and D128E mutant, the rate-limiting step is k3, whereas k2 has become rate-limiting for the D128N mutant. With the exception of pNPP, k2 may also be rate-limiting for D128A. Taken together, these results are consistent with Asp128 or Glu128 acting as a general acid to donate a proton to the phenolate leaving group in the phosphorylation step, and the carboxylate side chain plays a role as a general base to activate a nucleophilic water molecule in the dephosphorylation step. The presence of the general acid ensures productive partitioning toward phosphoenzyme formation. In the absence of the general acid, the nature of the transition-state for the phosphorylation step is sensitive to the pKa of the attacking active site thiol group and changes with the structure of the leaving group.
Ischaemia–reperfusion is an event triggered by immune complexes and complement (2003)

Evidence now points to complement and immune complexes as critical players in mediating reperfusion injury. Ischaemia is postulated to induce a phenotypical cellular change through the surface expression of a neoantigen. Preformed circulating natural IgM antibodies are then trapped and complement is activated. Final events leading to reperfusion injury include formation of the membrane attack complex and mast cell degranulation.
Designing Implicit Interfaces for Physiological Computing (2015)

A growing body of recent work has shown the feasibility of brain and body sensors as input to interactive systems. However, the interaction techniques and design decisions for their effective use are not well defined. We present a conceptual framework for considering implicit input from the brain, along with design principles and patterns we have developed from our work. We also describe a series of controlled, offline studies that lay the foundation for our work with functional near-infrared spectroscopy (fNIRS) neuroimaging, as well as our real-time platform that serves as a testbed for exploring brain-based adaptive interaction techniques. Finally, we present case studies illustrating the principles and patterns for effective use of brain data in human--computer interaction. We focus on signals coming from the brain, but these principles apply broadly to other sensor data and in domains such as aviation, education, medicine, driving, and anything involving multitasking or varying cognitive workload.
Synthesis of parazoanthoxanthins and pseudozoanthoxanthins (1978)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of parazoanthoxanthins and pseudozoanthoxanthinsManfred Braun, George Buechi, and Dean F. BusheyCite this: J. Am. Chem. Soc. 1978, 100, 13, 4208–4213Publication Date (Print):June 1, 1978Publication History Published online1 May 2002Published inissue 1 June 1978https://pubs.acs.org/doi/10.1021/ja00481a033https://doi.org/10.1021/ja00481a033research-articleACS PublicationsRequest reuse permissionsArticle Views392Altmetric-Citations39LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
FeRh/FePt exchange spring films for thermally assisted magnetic recording media (2003)

The temperature-dependent magnetic response of exchange-coupled FePt/FeRh thin films is described. The FePt forms a high magnetocrystalline anisotropy, high-coercivity ferromagnetic layer. The FeRh layer is antiferromagnetic at room temperature but, upon heating above a transition temperature, becomes ferromagnetic with a large magnetic moment and low magnetocrystalline anisotropy, forming an exchange–spring system and significantly lowering the coercive field of the composite system. This feature opens intriguing possibilities for media applications for thermally assisted magnetic recording where the ferromagnetic phase of FeRh is exploited to help write the media while the antiferromagnetic phase supports the long-time stability.
Motor signs during the course of Alzheimer disease (2004)

Most motor signs occur frequently and progress rapidly in Alzheimer disease. Tremor is an exception in that it occurs less frequently and advances at slower rates.
Study Of The Effect Of Ethanol Addition And Solution Heating On The Determination Of Ammonia In Water By Indophenol Blue Method = Studi Pengaruh Penambahan Etanol dan Pemanasan Pada Penentuan Amonia dalam Air dengan... (2002)

ABSTRACT\nThe effect of ethanol addition and solution heating on the analytical performance of the determination of ammonia in water by indophenol blue method was studied. The addition of ethanol and solution heating was intended to overcome the problem of reproducibility and sensitivity ussually found in the determination of ammonia by indophenol blue method which is carried out in 100 % aqueous media. The determination of ammonia was done indirectly by reacting ammonia in the sample with hypochloride and phenol using nitroprussida as catalyst to yield blue color-intense chromophore of indophenol: The chromophore was then detected by UV-Visible spectrophotometer. The proposed method was applied for the determination of ammonia in various samples of river water located in Yogyakarta and Makassar.\nResults of the study showed that ethanol addition into analytical solution and solution heating enhanced the formation of indophenol blue. The optimal heating was achieved after 90 minutes of mixing. In ethanol/water medium (50/50, v/v), indophenol blue exhibited maximum absorbance at 648 nm. The analytical performance of ammonia determination by indophenol blue method in this medium is as followed: detection limit = 0.03 ppm, relative standard deviation (RSD) = 2.50 % and the calibration curve was linear in the concentration range of 0.0 â 0.4 ppm with correlation coefficient (r) = 0.9968. Results of ammonia determination in various samples of river water showed that the highest concentration of ammonia (2.421 ppm) was found in Tallo river, Makassar, while the lowest (0.359 ppm) was shown by the river near SGM factory, Yogyakarta.\n\nKeywords: Ammonia, Ethanol, Spectrophotometry, Indophenol blue
Mobile address management and billing for personal communications (2003)

Use of a 'location authority' and a separate 'billing authority' for personal identification numbers (PIDs) is proposed to exploit the existing telephone infrastructure. A mobile PID has no inherent location or routing information. A 'location authority' is responsible for tracking the PID's current location and detecting duplicate PID usage. A 'billing authority' operates like a credit card company, offering on-line credit and service profile verification. A PID could have several 'billing authorities' responsible for maintaining the users service profile and guaranteeing payment to service providers. The author examines transactions, database requirements, and billing for log-in and call set-up under the proposed concept.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Modelling the immunogenicity of therapeutic proteins using T cell epitope mapping. (2003)

A new approach to designing therapeutic proteins is emerging, due to an improved understanding of T cell modulation of the immune response and new methods for modelling T cell epitopes using bioinformatics. In silico T cell epitope-mapping using the bioinformatics, when combined with other ex silico means of evaluating MHC-peptide and T cell interaction such as tetramers and HLA transgenic mice, enables the evaluation of dysfunctional immune responses to therapeutic proteins. This approach may even permit researchers to develop means of modulating anticipated adverse effects. The pocket profile method for developing T cell epitope prediction tools is reviewed here, and a comparison between the pocket profile method and the extended anchor method for epitopes restricted by the class II allele HLA DR B*0101 is described.
Cancer‐testis antigen expression and its epigenetic modulation in acute myeloid leukemia (2011)

Cancer-testis antigens (CTA) represent attractive targets for tumor immunotherapy. However, a broad picture of CTA expression in acute myeloid leukemia (AML) is missing. CTA expression was analyzed in normal bone marrow (BM) as well as in AML cell lines before and after treatment with demethylating agents and/or histone acetylase inhibitors. Presence of selected CTA with a strictly tumor-restricted expression was then determined in samples of patients with AML before and after demethylating therapy. Screening AML cell lines for the expression of 20 CTA, we identified six genes (MAGE-A3, PRAME, ROPN1, SCP-1, SLLP1, and SPO11) with an AML-restricted expression. Analyzing the expression of these CTA in blast-containing samples from AML patients (N = 64), we found all samples to be negative for MAGE-A3 and SPO11 while a minority of patients expressed ROPN1 (1.6%), SCP-1 (3.1%), or SLLP1 (9.4%). The only CTA expressed in substantial proportion of patients (53.1%) was PRAME. Following demethylating treatment with 5'-aza-2'-deoxycytidine, we observed an increased or de novo expression of CTA, in particular of SSX-2, in AML cell lines. In AML patients, we detected increased expression of PRAME and induction of SSX-2 after demethylating therapy with 5-azacytidine. With the exception of PRAME, CTA are mostly absent from AML blasts. However, demethylating treatment induces strong expression of CTA, particularly of SSX-2, in vitro and in vivo. Therefore, we propose that CTA-specific immunotherapy for AML should preferentially target PRAME and/or should be combined with the application of demethylating agents opening the perspective for alternative targets like CTA SSX-2.
Intracellular Glycosylphosphatidylinositols Accumulate on Endosomes: Toxicity of Alpha-Toxin toLeishmania major (2005)

Glycosylphosphatidylinositols (GPIs) are ubiquitous glycolipids in eukaryotes. In the protozoan Leishmania major, GPIs occur "free" or covalently linked to proteins (e.g., gp63) and polysaccharides. While some free GPIs are detected on the plasma membrane, specific sites where GPIs accumulate intracellularly are unknown in most cells, although the glycolipids are synthesized within the secretory system. Herein, we describe a protocol for identifying intracellular sites of GPI accumulation by using alpha-toxin (from Clostridium septicum). Alpha-toxin bound to gp63 and GPIs from L. major. Intracellular binding sites for alpha-toxin were determined in immunofluorescence assays after removal of GPI-anchored macromolecules (e.g., gp63) from the plasma membrane of fixed cells by using detergent. Endosomes were a major site for GPI accretion in L. major. GPI-less gp63 was detected at the endoplasmic reticulum. In studies with live parasites, alpha-toxin killed L. major with a 50% lethal concentration of 0.77 nM.
A microscopic and biochemical study of fragmentation phenotypes in stage-appropriate human embryos (2001)

The occurrence of a pleiomorphic population of cytoplasmic fragments is a common characteristic of early human embryos fertilized in vitro. Here, temporal, spatial, fine structural, and biochemical aspects of fragmentation were examined in fragmented monospermic and dispermic pronuclear to early cleavage stages human embryos classified as stage-appropriate during the first 3.5 days of culture. The morphodynamics of certain common patterns of fragmentation and the movement and composition of fragments were analysed by time-lapse video, mitochondrial fluorescent probes, and transmission electron microscopy. Plasma membrane and nuclear DNA integrity were assessed by annexin V staining, and terminal deoxynucleotidyl transferase-mediated dUTP nick end-labelling (TUNEL) and single-cell alkaline gel electrophoresis ('comet') assays respectively. Developmental competence for affected embryos was related to outcome after embryo transfer. The results demonstrate that certain common forms of spontaneous fragmentation affecting early human embryos are not lethal, and that clusters of apparent fragments are often transient structures, which disappear by resorption or lysis. The findings suggest that the occurrence and fate of fragments characteristic of these phenotypes may be related to oncosis-like processes associated with transient and focal ATP deficiencies in blastomeres and mitochondrial deficiencies or absence in extracellular fragments.
Proteomic Analysis of Cervical−Vaginal Fluid:  Identification of Novel Biomarkers for Detection of Intra-amniotic Infection (2006)

Intra-amniotic infection (IAI) is associated with preterm birth and perinatal mortality. To identify potential biomarkers, we performed a comprehensive survey of the cervical-vaginal fluid (CVF) proteome from a primate IAI model utilizing multidimensional protein identification technology (LC/LC-MS/MS) and MALDI-TOF-MS analyses. Analyses of CVF proteome identified 205 unique proteins and differential expression of 27 proteins in controls and IAI samples. Protein expression signatures and immunodetection of specific biomarkers identified can be employed for noninvasive detection of IAI.
Inhibition of Trehalase Activity Enhances Trehalose Accumulation in Transgenic Plants (1997)

As a first step toward the exploitation of the disaccharide trehalose as a stress-protective and preservative agent in plants, we engineered trehalose biosynthesis in tobacco (Nicotiana tabacum) and potato (Solanum tuberosum) by introducing the otsA and otsB genes from Escherichia coli, which encode trehalose-6-phosphate synthase and trehalose-6-phosphate phosphatase, respectively. In leaves of transgenic tobacco plants, very low levels of trehalose accumulation were obtained (0.11 mg g-1 fresh weight), whereas in transgenic potato tubers, no trehalose accumulated at all. Plant trehalase activity was shown to affect the accumulation of trehalose in these plants. An increase in trehalose accumulation, up to 0.41 and 4.04 mg g-1 fresh weight in tobacco leaves and potato micro-tubers, respectively, was noted when the potent trehalase inhibitor validamycin A was added to in vitro plants and to hydroponically grown greenhouse plants. Stunted growth and the formation of lancet-shaped leaves by trehalose-accumulating tobacco plants suggest a negative effect of trehalose biosynthesis on N. tabacum development. It is surprising that experiments with wild-type plants cultured in the presence of validamycin A indicate that, despite current belief, the capacity to synthesize trehalose may not be restricted to primitive phyla of vascular plants and certain "resurrection plants," but may exist throughout the angiosperms.
A 3 patch near field antenna for conveyor bottom read in RFID sortation application (2006)

The antenna presented in this paper is a 3 patch near field design for the conveyor bottom read. It is an RFID reader path antenna array for RFID sortation application. It is a slim design (28 /spl times/ 20 /spl times/ 0.8") and is inserted under the belt. The intentions of this design are: 1) to reduce the far field gain to meet FCC requirement and, 2) to control the field strength distribution to let a RFID reader read only the box above the antenna while not read the adjacent box.