gebhart/patrepeval huggingface dataset:
Accelerating Compute-Intensive Applications with GPUs and FPGAs (2008)

Accelerators are special purpose processors designed to speed up compute-intensive sections of applications. Two extreme endpoints in the spectrum of possible accelerators are FPGAs and GPUs, which can often achieve better performance than CPUs on certain workloads. FPGAs are highly customizable, while GPUs provide massive parallel execution resources and high memory bandwidth. Applications typically exhibit vastly different performance characteristics depending on the accelerator. This is an inherent problem attributable to architectural design, middleware support and programming style of the target platform. For the best application-to-accelerator mapping, factors such as programmability, performance, programming cost and sources of overhead in the design flows must be all taken into consideration. In general, FPGAs provide the best expectation of performance, flexibility and low overhead, while GPUs tend to be easier to program and require less hardware resources. We present a performance study of three diverse applications - Gaussian elimination, data encryption standard (DES), and Needleman-Wunsch - on an FPGA, a GPU and a multicore CPU system. We perform a comparative study of application behavior on accelerators considering performance and code complexity. Based on our results, we present an application characteristic to accelerator platform mapping, which can aid developers in selecting an appropriate target architecture for their chosen application.
Silylative Coupling and Cross‐Metathesis of Alkenes and Dienes with Vinyl–Silicon Derivatives — New Catalytic Routes to Synthesis of Organosilicon Compounds (2005)

Recent achievements in two catalytic reactions, i.e., silylative coupling and cross-metathesis of alkenes and dienes with vinyl-silicon compounds, which resulted in new synthetic routes to organosilicon molecular and macromolecular compounds are presented. The silylative coupling, also called dehydrogenative or trans-silylation and silyl group transfer, is catalyzed by metal complexes which either contain or initiate the formation of M-H and M-Si bonds, where M = Ru, Rh, Co and fr. Cross-metathesis, which was developed very recently, proceeds in the presence of metallacarbenes, mainly those of ruthenium (e.g., Grubbs catalyst).
Neuropsychological function in patients with Gerstmann-Sträussler-Scheinker disease from the Indiana Kindred (F198S) (1997)

Three patients with Gerstmann-Sträussler-Scheinker disease (GSS) caused by a serine-for-phenylalanine substitution at codon 198 of the prion protein gene (PRNP) were compared to 9 age- and education-matched non-mutation-carriers from the same large Indiana kindred (GSS-IK) on a comprehensive neuropsychological test battery. Clinically significant impairments in intelligence, secondary memory, attention and cognitive processing speed, executive ability, and manual motor skills were noted in 2 patients. The wide range and the severity of the cognitive deficits indicated generalized cerebral dysfunction consistent with global dementia. One patient, symptomatic for less than 1 year, had more selective deficits involving memory, motor skills, and verbal fluency, suggesting early subcortical involvement.
Detection Of Focal Points In Speech Prosody (2002)

Publication in the conference proceedings of EUSIPCO, Toulouse, France, 2002
PINOT: an intuitive resource for integrating protein-protein interactions (2020)

PINOT is a tool that allows users to survey the curated literature, extracting PPI data in relation to a list of proteins of interest. PINOT extracts a similar numbers of PPIs as other, analogous, tools and incorporates a set of innovative features. PINOT is able to process large queries, it downloads human PPIs live through PSICQUIC and it applies quality control filters on the downloaded PPI data (i.e. removing the need for manual inspection by the user). PINOT provides the user with information on detection methods and publication history for each downloaded interaction data entry and outputs the results in a table format that can be straightforwardly further customised and/or directly uploaded into network visualization software. Video abstract.
Food Security in Cuba: A Comparison of TRDs, Bodegas, and Agricultural Markets (2015)

After the collapse of the Soviet Union, Cuba entered a period of economic hardship known as the Special Period in Times of Peace.  Since then, changes in Cuba’s food policy have reflected a shift away from strictly regulated food rationing to a mixed system including the libreta system or rationing as well as agricultural markets and stores using convertible pesos (TRDs).  This system has lead to overall greater food security but also greater disparities in food accessibility.  This study reviews and analyses food prices in bodegas, agricultural markets, and TRDs in several municipalities in Cuba. Most of the food items found in the TRDs were unavailable in bodegas and agricultural markets.  This confirmed a trend in which more food items are becoming available only in TRDs.  In addition, TRDs only accepted converted pesos (CUCs) as opposed to national pesos (CUPs), creating a disparity between those with access to the tourism industry and those who do not.  While food availability is greater than it was in the early 1990’s, there are still issues surrounding food access for those without access to CUCs, linking food security to the tourism industry in Cuba.  However, policy changes regarding currency unification and changes regarding the libreta system will impact food security issues in the future.
Improvements to radiometric consistency between AVHRR, MODIS, and VIIRS in SST bands using MICROS online near-real time system (2012)

Monitoring of IR Clear-Sky Radiances over Oceans for SST nearreal time web-based system has been established in July 2008. It analyzes Model (Community Radiative Transfer Model, CRTM) minus Observation (M-O) biases in clear-sky ocean brightness temperatures (BT) in AVHRR bands 3.7 (IR37), 11 (IR11), and 12&mu;m (IR12) onboard NOAA-16, -17, -18, -19 and Metop-A. In January 2012, AVHRR-like bands of VIIRS onboard the Suomi National Polar Partnership (S-NPP; launched in October 2012), and two MODIS instruments onboard Terra and Aqua, were included in MICROS. Double-differences are employed to check various sensors for radiometric consistency. The VIIRS and AVHRR have been in-family, and the consistency further improved after the VIIRS IR calibration was fine-tuned on 7 March 2012. However, MODIS M-O biases have been out of family (by -0.6K in IR 11, and -0.3K in IR12). Analyses have shown that these anomalies in MODIS M-O biases are caused by the "M" term, i.e., incorrect MODIS transmittance coefficients in CRTM v2.02. Based on feedback from NESDIS SST and U. Wisconsin Teams, CRTM Team updated transmittance coefficients in CRTM v2.10. As a result, MODIS M-O biases are now in agreement with AVHRR/VIIRS. However, cross-platform Terra/Aqua bias of ~0.3 K in Ch20 (3.9&mu;m) remains, likely due to calibration uncertainties in MODIS L1b product. This paper documents the joint effort by the SST, MODIS Characterization Support and CRTM Teams towards identifying and resolving observed cross-platform inconsistencies.
Shedding Light on How Intelligent Techniques can Support Technical Debt Management and Influence Software Quality Attributes (2022)

Technical Debt (TD) is a consequence of decision-making in the development process that can negatively impact Software Quality Attributes (SQA) in the long term. Technical Debt Management (TDM) is a complex task to minimize TD that relies on a decision process based on multiple and heterogeneous data that are not straightforward to synthesize. Recent studies show that Intelligent Techniques can be a promising opportunity to support TDM activities since they explore data for knowledge discovery, reasoning, learning, or supporting decision-making. Although these techniques can improve TDM activities, there is a need to identify and analyze solutions based on Intelligent Techniques to support TDM activities and their impact on SQA. For doing so, a Systematic Mapping Study was performed, covering publications between 2010 and 2020. From 2276 extracted studies, we selected 111 unique studies. We found a positive trend in applying Intelligent Techniques to support TDM activities being Machine Learning and Reasoning Under Uncertainty the most recurrent ones. Design and Code were the most frequently investigated TD types. TDM activities supported by intelligent techniques impact different characteristics of SQA, mainly Maintainability, Reliability, and Security. Although the research area is up-and-coming, it is still in its infancy, and this study provides a baseline for future research.
Glutathione import in <i>Haemophilus influenzae</i> Rd is primed by the periplasmic heme-binding protein HbpA (2010)

Glutathione (GSH) is a vital intracellular cysteine-containing tripeptide across all kingdoms of life and assumes a plethora of cellular roles. Such pleiotropic behavior relies on a finely tuned spatiotemporal distribution of glutathione and its conjugates, which is not only controlled by synthesis and breakdown, but also by transport. Here, we show that import of glutathione in the obligate human pathogen Haemophilus influenzae, a glutathione auxotrophe, is mediated by the ATP-binding cassette (ABC)-like dipeptide transporter DppBCDF, which is primed for glutathione transport by a dedicated periplasmic-binding protein (PBP). We have identified the periplasmic lipoprotein HbpA, a protein hitherto implicated in heme acquisition, as the cognate PBP that specifically binds reduced (GSH) and oxidized glutathione (GSSG) forms of glutathione with physiologically relevant affinity, while it exhibits marginal binding to hemin. Dissection of the ligand preferences of HbpA showed that HbpA does not recognize bulky glutathione S conjugates or glutathione derivatives with C-terminal modifications, consistent with the need for selective import of useful forms of glutathione and the concomitant exclusion of potentially toxic glutathione adducts. Structural studies of the highly homologous HbpA from Haemophilus parasuis in complex with GSSG have revealed the structural basis of the proposed novel function for HbpA-like proteins, thus allowing a delineation of highly conserved structure-sequence fingerprints for the entire family of HbpA proteins. Taken together, our studies unmask the main physiological role of HbpA and establish a paradigm for glutathione import in bacteria. Accordingly, we propose a name change for HbpA to glutathione-binding protein A.
The capacity of online (causal) q-ary error-erasure channels (2016)

In the q-ary online (causal) channel coding model, a sender wishes to communicate a message to a receiver by transmitting a codeword x = (x <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> , . . . , x <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</sub> ) ∈ {0, 1, . . . , q - 1} <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</sup> symbol-by-symbol via a channel limited to at most p*n errors (symbol changes) and p*n erasures. The channel is "online" (i.e., "causal") in the sense that at the ith step of communication the channel decides whether to corrupt the ith symbol or not only based on its view of the symbols (x <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1,</sub> . . . , x <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">i</sub> ). This is in contrast to the classical adversarial channel in which the corruption is chosen with full knowledge of the sent codeword x. In this work we extend the results obtained in [1]-[4] (in which the capacities of binary online bit-flip-only channels, and separately binary online erasure-only channels were characterized). We here extend those prior results in two important ways. First, we obtain the capacity of q-ary online channels for general q (rather than just q = 2). Second, we analyze combined error-erasure corruption models (rather than studying them separately). Characterization of this much broader class of symmetric online channels gives a fuller understanding of the effects of causality on jamming adversaries. The extensions in this paper require novel approaches for both optimal code designs, and matching information-theoretic converse arguments.
Adhesion of Helicobacter Species to the Human Gastric Mucosa: A Deep Look Into Glycans Role (2021)

Helicobacter species infections may be associated with the development of gastric disorders, such as gastritis, peptic ulcers, intestinal metaplasia, dysplasia and gastric carcinoma. Binding of these bacteria to the gastric mucosa occurs through the recognition of specific glycan receptors expressed by the host epithelial cells. This review addresses the state of the art knowledge on these host glycan structures and the bacterial adhesins involved in Helicobacter spp. adhesion to gastric mucosa colonization. Glycans are expressed on every cell surface and they are crucial for several biological processes, including protein folding, cell signaling and recognition, and host-pathogen interactions. Helicobacter pylori is the most predominant gastric Helicobacter species in humans. The adhesion of this bacterium to glycan epitopes present on the gastric epithelial surface is a crucial step for a successful colonization. Major adhesins essential for colonization and infection are the blood-group antigen-binding adhesin (BabA) which mediates the interaction with fucosylated H-type 1 and Lewis B glycans, and the sialic acid-binding adhesin (SabA) which recognizes the sialyl-Lewis A and X glycan antigens. Since not every H. pylori strain expresses functional BabA or SabA adhesins, other bacterial proteins are most probably also involved in this adhesion process, including LabA (LacdiNAc-binding adhesin), which binds to the LacdiNAc motif on MUC5AC mucin. Besides H. pylori, several other gastric non- Helicobacter pylori Helicobacter s (NHPH), mainly associated with pigs ( H. suis ) and pets ( H. felis , H. bizzozeronii, H. salomonis, and H. heilmannii ) , may also colonize the human stomach and cause gastric disease, including gastritis, peptic ulcers and mucosa-associated lymphoid tissue (MALT) lymphoma. These NHPH lack homologous to the major known adhesins involved in colonization of the human stomach. In humans, NHPH infection rate is much lower than in the natural hosts. Differences in the glycosylation profile between gastric human and animal mucins acting as glycan receptors for NHPH-associated adhesins, may be involved. The identification and characterization of the key molecules involved in the adhesion of gastric Helicobacter species to the gastric mucosa is important to understand the colonization and infection strategies displayed by different members of this genus.
Niaspan increases angiogenesis and improves functional recovery after stroke (2007)

Niacin increases HDL and promotes angiogenesis, which may contribute to improvement of functional outcome after stroke. The Ang1/Tie2, phosphoinositide 3-kinase/Akt, and endothelial NOS pathways appear to mediate Niacin-induced angiogenesis.
Genetic circuit characterization and debugging using <scp>RNA</scp> ‐seq (2017)

Genetic circuits implement computational operations within a cell. Debugging them is difficult because their function is defined by multiple states (e.g., combinations of inputs) that vary in time. Here, we develop RNA-seq methods that enable the simultaneous measurement of: (i) the states of internal gates, (ii) part performance (promoters, insulators, terminators), and (iii) impact on host gene expression. This is applied to a three-input one-output circuit consisting of three sensors, five NOR/NOT gates, and 46 genetic parts. Transcription profiles are obtained for all eight combinations of inputs, from which biophysical models can extract part activities and the response functions of sensors and gates. Various unexpected failure modes are identified, including cryptic antisense promoters, terminator failure, and a sensor malfunction due to media-induced changes in host gene expression. This can guide the selection of new parts to fix these problems, which we demonstrate by using a bidirectional terminator to disrupt observed antisense transcription. This work introduces RNA-seq as a powerful method for circuit characterization and debugging that overcomes the limitations of fluorescent reporters and scales to large systems composed of many parts.
MRI Guided Radiotherapy: A Short SWOT Analysis (2017)

Visit www.philips.com/mr-rt to explore MR only simulation further Today, MRI has even more to offer radiation therapy treatment planning. Innovative MR-only simulation by Philips helps you rely on MRI as a primary imaging modality for planning the treatment of prostate cancer patients. Available as a plug-in extension to the Ingenia MR-RT, MR-only sim provides a fast and automated approach to obtain soft-tissue contrast you trust for target delineation -plus density information for dose calculations you'd expect from CT, all in one MR imaging session.
Ultrashort Nacelles for Low Fan Pressure Ratio Propulsors (2014)

As the propulsor fan pressure ratio (FPR) is decreased for improved fuel burn, reduced emissions and noise, the fan diameter grows and innovative nacelle concepts with short inlets are required to reduce their weight and drag. This paper addresses the uncharted inlet and nacelle design space for low-FPR propulsors where fan and nacelle are more closely coupled than in current turbofan engines. The paper presents an integrated fan–nacelle design framework, combining a spline-based inlet design tool with a fast and reliable body-force-based approach for the fan rotor and stator blade rows to capture the inlet–fan and fan–exhaust interactions and flow distortion at the fan face. The new capability enables parametric studies of characteristic inlet and nacelle design parameters with a short turn-around time. The interaction of the rotor with a region of high streamwise Mach number at the fan face is identified as the key mechanism limiting the design of short inlets. The local increase in Mach number is due to flow acceleration along the inlet internal surface coupled with a reduction in effective flow area. For a candidate short-inlet design with length over diameter ratio L/D = 0.19, the streamwise Mach number at the fan face near the shroud increases by up to 0.16 at cruise and by up to 0.36 at off-design conditions relative to a long-inlet propulsor with L/D = 0.5. As a consequence, the rotor locally operates close to choke resulting in fan efficiency penalties of up to 1.6% at cruise and 3.9% at off-design. For inlets with L/D &lt; 0.25, the benefit from reduced nacelle drag is offset by the reduction in fan efficiency, resulting in propulsive efficiency penalties. Based on a parametric inlet study, the recommended inlet L/D is suggested to be between 0.25 and 0.4. The performance of a candidate short inlet with L/D = 0.25 was assessed using full-annulus unsteady Reynolds-averaged Navier–Stokes (RANS) simulations at critical design and off-design operating conditions. The candidate design maintains the propulsive efficiency of the baseline case and fuel burn benefits are conjectured due to reductions in nacelle weight and drag compared to an aircraft powered by the baseline propulsor.
Application of binning codes to video coding (2005)

There are several problems in video coding that can not be adequately addressed through the use of conventional source coding techniques. For instance, any video coding system that is based on a predictive framework will suffer from performance degradations if there is uncertainty in the predictions. In this paper, we propose a method that incorporates binning codes and channel decoding to address video coding problems that have multiple possible predictions at the decoder. We will propose solutions based on binning codes to three separate problems in video coding and show that the results are superior to pre-existing methods.
Purification and characterization of dimethylamine : 5‐hydroxybenzimidazolyl‐cobamide methyltransferase from <i>Methanosarcina barkeri</i> Fusaro (1998)

Dimethylamine:5-hydroxybenzimidazolylcobamide methyltransferase (DMA-MT) was purified from cells of Methanosarcina barkeri Fusaro grown on trimethylamine. In the presence of methylcobalamine:coenzyme M methyltransferase isoenzyme II [MT2(II)] the enzyme quite specifically catalyzed the stoichiometric conversion of dimethylamine (apparent Km = 0.45 mM) and 2-mercaptoethane-sulfonate (coenzyme M) to monomethylamine and methyl-coenzyme M. Monomethylamine was a competitive inhibitor of the reaction (Ki = 4.5 mM). The apparent molecular mass of DMA-MT was 100 kDa and the enzyme was found to be a dimer, composed of identical 50-kDa subunits. A corrinoid content of 0.9 +/- 0.1 mol B12/mol holoenzyme was calculated from HPLC analysis. The as-isolated methyltransferase was inactive, but it could be reductively reactivated. Activation required the presence of methyltransferase-activating protein, ATP and dimethylamine. Incubation with these compounds resulted in the methylation of the corrinoid prosthetic group.
The Fractal approach to heterogeneous chemistry : surfaces, colloids, polymers (1989)

Part 1 Overview, B.B.Mandelbrot. Part 2 Basic concepts and terminology, P.Pfeifer. Part 3 Methods for determining the fractal dimension: analysis of images, B.H.Kaye scattering - experiments and theory, P.W. Schmidt adsorption - experiments and theory, D.Farin and D.Avnir energy migration - theory, P.Evesque. Part 4 Mechanisms of formation of fractal objects: growth processes - polymerization and aggregation the formation of fractal objects by polymerization and gelation, J.Martin fractal properties of polymers, M.Daoud fractal analysis of proteins aggregation simulations, P.Meakin experimental observations - (redox reactions, polymerizations, etc). Part 5 Disintegration and dissipation processes: dissolutions, evaporations, etchings, G. Daccord flow in colloidal media, H.Van-Damme diffusion fronts, B.Sapoval. Part 6 Processes in fractal environments: reactions and diffusion in fractal environments molecular diffusion and reactions - theory, P.Pfeifer molecular diffusion and reactions - experiments, J.M.Drake energy migration and trapping catalysis, preliminary observations, D.Avnir and D.Farin electrochemistry, A. Le-Mehaute flow and porosimetry porosity and adsorption isotherms, J.J.Fripiat flow in porous media, P.Adler chromatography, M.Sernetz. Part 7 Special topics: fractal aspects of geochemistry, P.A.Burrough fractal analysis of chaotic chemical and biochemical reactions fractions, D.Passoja. Part 8 Concluding remarks: the skeptical eye, D.Avnir.
Synthesis, Structure, and Mössbauer Study of [Fe(H<sub>2</sub>O)<sub>2</sub>(C<sub>9</sub>O<sub>6</sub>H<sub>4</sub>)]·H<sub>2</sub>O:  A Two-Dimensional Iron(II) Trimellitate (MIL-67) (2003)

The two-dimensional (2D) iron trimellitate [Fe(H(2)O)(2)(C(9)O(6)H(4))].H(2)O, labeled MIL-67, has been obtained under hydrothermal conditions (473 K, 48 h). In the 2D structure of MIL-67, the Fe(2+) ions display two different octahedral environments: [FeO(4)(H(2)O)(2)] and [FeO(2)(H(2)O)(4)]. These octahedra share an apical water molecule to form infinite chains. The chains are linked by partly deprotonated C(9)O(6)H(4)(2-) anions to give hybrid organic-inorganic layers; the remaining acidic-CO(2)H group is dangling in the interlayer space. Below 8(1) K, MIL-67 displays a canted antiferromagnetic behavior, according to analyses via magnetic measurements and Mössbauer spectroscopy. Crystal data for MIL-67 are as follows: triclinic; space group P1 (No. 2), with a = 6.9671(2) A, b = 7.3089(3) A, c = 12.5097(3) A, alpha = 78.758(1) degrees, beta = 89.542(2) degrees, and gamma = 65.197(1) degrees; volume V = 565.21(3) A(3); and Z = 2.