gebhart/patrepeval huggingface dataset:
Blue Gene system software---Design and implementation of a one-sided communication interface for the IBM eServer Blue Gene® supercomputer (2006)

This paper discusses the design and implementation of a one-sided communication interface for the IBM Blue Gene/L supercomputer. This interface facilitates ARMCI and the Global Arrays toolkit and can be used by other one-sided communication libraries. New protocols, interrupt driven communication, and compute node kernel enhancements were required to enable these libraries. Three possible methods for enabling ARMCI on the Blue Gene/L software stack are discussed. A detailed look into the development process shows how the implementation of the one-sided communication interface was completed. This was accomplished on a compressed time scale with the collaboration of various organizations within IBM and open source communities. In addition to enabling the one-sided libraries, bandwidth enhancements were made for communication along a diagonal on the Blue Gene/L torus network. The maximum bandwidth improved by a factor of three. This work will enable a variety of one-sided applications to run on Blue Gene/L.
Release of xenotropic type C RNA virus in response to lipopolysaccharide: acitivity of lipid-A portion upon B lymphocytes. (1976)

The present studies demonstrate that lipopolysaccharide (LPS) causes the release of endogenous xenotropic type-C RNA virus from BALB/c spleen cells. The evidence suggests that virus release is stimulated by the lipid-A portion of LPS and primarily involves an action of LPS on B lymphocytes. LPS had little or no effect on virus release by T lymphocytes, macrophages, or fibroblasts. These results indicate that the differentiated state of the cell plays an important role in the regulation of endogenous virus release.
Radiation-induced Luminescence Properties of SrBr2 Transparent Ceramics Doped with Different Eu Concentrations (2020)

We successfully developed Eu-doped SrBr 2 transparent ceramics with different Eu concentrations by spark plasma sintering and evaluated their optical and scintillation properties. As optical properties, the diffuse transmittance of the 0.01% Eu-doped sample was ~60% in the visible range. All the samples showed two absorption bands at around 250 and 350 nm, the origin of which was the 4f-5d (e g , t 2g ) transitions of Eu 2+ . Regarding scintillation spectra, the spectral shapes of all the Eu-doped SrBr 2 transparent ceramics were similar to that of single crystals. In pulse height spectra, the photoabsorption peak of the 0.01 and 0.1% Eu-doped samples was confirmed, and the estimated light yields were 6600 and 13300 photons/MeV, respectively. Regarding afterglow properties, the afterglow levels of the 0.01 and 0.1% Eudoped samples were comparable to that of a conventional Tl-doped CsI scintillator.
Multisite Organic–Inorganic Hybrid Catalysts for the Direct Sustainable Synthesis of GABAergic Drugs (2014)

Multisite organic-inorganic hybrid catalysts have been prepared and applied in a new general, practical, and sustainable synthetic procedure toward industrially relevant GABA derivatives. The domino sequence is composed of seven chemical transformations which are performed in two one-pot reactions. The method produces both enantiomeric forms of the product in high enantiopurity as well as the racemate in good yields after a single column purification step. This protocol highlights major process intensification, catalyst recyclability, and low waste generation.
A phase-Ib study of TRK-950 combined with anticancer treatment regimens in patients with gastric and gastro-esophageal junction (GEJ) cancer. (2023)

361 Background: TRK-950 is a first-in-class humanized antibody raised against CAPRIN-1 which we have identified as a novel and universal target for cancer therapies. TRK-950 strongly and specifically binds to various cancer cells and shows anti-tumor effects via engagement of immune cells. A series of pre-clinical studies demonstrates its potency and safety. In the phase I study of TRK-950 monotherapy (NCT02990481), it appears safe and well tolerated. No DLT was observed and MTD was not reached at doses of 3-30mg/kg IV weekly. Here, we report on select cohort of the ongoing, multicenter phase Ib study of TRK-950 combined with standard of care (SOC) regimens in patients (pts) with gastric cancer including GEJ cancer (NCT03872947). Methods: Patients with gastric or gastro-esophageal junction (GEJ) cancer and measurable disease were enrolled in phase Ib study, and received paclitaxel on D1, 8, 15 and ramucirumab on D1, 15 of 28-day cycles. In addition TRK-950 was given 10 mg/kg IV weekly. DLT was evaluated during the first cycle. Response was assessed every 2 cycles up to Cycle 6 and every 3 cycles thereafter. Primary endpoint was safety and tolerability. Secondary endpoints included overall response rate (ORR), disease control rate (DCR) per REClST v1.1. Tumor CAPRIN-1 expression was retrospectively assessed by IHC. Results: Nine patients were enrolled, median age 58 yrs; Karnofsky performance status 80 (11%), 90 (67%), 100 (22%); 89% male, 11% female; median number of prior treatments 2 [1, 4]. TRK-950 in combination with ramucirumab and paclitaxel was well tolerated with no DLTs. Most common all-grade treatment-related AEs (TRAEs) were fatigue (67%), vomiting (33%), anemia (22%), nausea (22%), diarrhea (22%), neutrophil count decreased (22%) and decreased appetite (22%). Most common grade ≥ 3 TRAE in ≥ 20% of pts were anemia (22%) and neutrophil count decreased (22%). In 9 response-evaluable pts, ORR was 55.6% and DCR was 100%. Four patients had a screening CAPRIN-1 score of 3+, and all achieved partial response. Conclusions: TRK-950 binds to a newly described target, CAPRIN-1, and has an acceptable safety and tolerability profile when combined with ramucirumab and paclitaxel in gastric cancer including GEJ cancer. Preliminary clinical activity is demonstrated in pre-treated patients with encouraging response rates, particularly enriched by the expression of CAPRIN-1. Further antitumor activity is being confirmed by limiting patients to only 1 prior treatment regimen with an eye towards a randomized trial. Clinical trial information: NCT03872947 .
DNA sequence-level analyses reveal potential phenotypic modifiers in a large family with psychiatric disorders (2018)

Psychiatric disorders are a group of genetically related diseases with highly polygenic architectures. Genome-wide association analyses have made substantial progress towards understanding the genetic architecture of these disorders. More recently, exome- and whole-genome sequencing of cases and families have identified rare, high penetrant variants that provide direct functional insight. There remains, however, a gap in the heritability explained by these complementary approaches. To understand how multiple genetic variants combine to modify both severity and penetrance of a highly penetrant variant, we sequenced 48 whole genomes from a family with a high loading of psychiatric disorder linked to a balanced chromosomal translocation. The (1;11)(q42;q14.3) translocation directly disrupts three genes: DISC1, DISC2, DISC1FP and has been linked to multiple brain imaging and neurocognitive outcomes in the family. Using DNA sequence-level linkage analysis, functional annotation and population-based association, we identified common and rare variants in GRM5 (minor allele frequency (MAF) > 0.05), PDE4D (MAF > 0.2) and CNTN5 (MAF < 0.01) that may help explain the individual differences in phenotypic expression in the family. We suggest that whole-genome sequencing in large families will improve the understanding of the combined effects of the rare and common sequence variation underlying psychiatric phenotypes.
Fantastic-5G: Flexible Air Interface For Scalable Service Delivery Within Wireless Communication Networks Of The 5Th Generation (2016)

5th generation mobile networks will have to cope with a high degree of heterogeneity in terms of: services, mobility, number of devices, etc. Thus diverse and often contradicting key performance indicators need to be supported, but having multiple radio access technologies for multi-service support below 6GHz will be too costly. FANTASTIC-5G will develop a new multi-service Air Interface (AI) through a modular design. To allow the system to adapt to the anticipated heterogeneity, some properties need to be pursued, like: simplicity, flexibility, scalability, versatility, efficiency and future-proofness. Based on these properties a selected set of use cases and link and network design will be presented. The paper will also comprise validation and system level simulations through some indicative results; and will conclude with the overall impact to 5G standardization.
Unusual Analyte-Matrix Adduct Ions and Mechanism of Their Formation in MALDI TOF MS of Benzene-1,3,5-Tricarboxamide and Urea Compounds (2013)

Analyte-matrix adducts are normally absent under typical matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI TOF MS) conditions. Interestingly, though, in the analysis of several types of organic compounds synthesized in our laboratory, analyte-matrix adduct ion peaks were always recorded when common MALDI matrices such as 4-hydroxy-α-cyanocinnamic acid (CHCA) were used. These compounds are mainly those with a benzene-1,3,5-tricarboxamide (BTA) or urea moiety, which are important building blocks to make new functional supramolecular materials. The possible mechanism of the adduct formation was investigated. A shared feature of the compounds studied is that they can form intermolecular hydrogen bonding with matrices like CHCA. The intermolecular hydrogen bonding will make the association between analyte ions and matrix molecules stronger. As a result, the analyte ions and matrix molecules in MALDI clusters will become more difficult to be separated from each other. Furthermore, it was found that analyte ions were mainly adducted with matrix salts, which is probably due to the much lower volatility of the salts compared with that of their corresponding matrix acids. It seems that the analyte-matrix adduct formation for our compounds are caused by the incomplete evaporation of matrix molecules from the MALDI clusters because of the combined effects of enhanced intermolecular interaction between analyte-matrix and of the low volatility of matrix salts. Based on these findings, strategies to suppress the analyte-matrix adduction are briefly discussed. In return, the positive results of using these strategies support the proposed mechanism of the analyte-matrix adduct formation.
Robust partial Fourier reconstruction for diffusion‐weighted imaging using a recurrent convolutional neural network (2021)

This work demonstrates that robust PF reconstruction of DW data is feasible even at strong PF factors in anatomies prone to phase variations. Since the proposed method does not rely on smoothness priors of the phase but uses learned recurrent convolutions instead, artifacts of conventional PF methods can be avoided.
Consolidation, Microstructure and Crystallography of Dense NaNbO<sub>3</sub> Ceramics with Ultra-Fine Grain Size (2006)

The present study reports on the preparation and structural characterization of dense NaNbO3 ceramics with ultrafine grain size. Nanocrystalline raw powders obtained via microemulsion mediated synthesis were consolidated to green compacts, sinterforged to ceramic pellets with high density and ultra-fine microstructure and finally annealed under different thermal regimes in order to systematically increase the average grain size in the range from several hundreds of nm up to a few μm. Structural characterization of these materials included electron-microscopic observation and X-ray diffraction in combination with temperature tuning Raman-spectroscopy in order to detect both the global and local crystallographic symmetry in dependence of the grain size. The results show that ceramics with an average grain size from approximately 360 nm to 1-2 μm consist of a phase mixture of the anti-ferroelectric phase with the space group Pbcm, which is also observed for the conventional case of coarse NaNbO3, and secondly of a new polar polymorph described by the space group Pmc21. The volume fraction of the second polar modification appears to increase with decreasing grain size suggesting an enhancement of the piezoelectric response of ultra-fine grained NaNbO3 ceramics in comparison to coarse grained material of the same composition.
One‐Step Dimerization of Linear Furanocoumarins. (2002)

Abstract For Abstract see ChemInform Abstract in Full Text.
VIP attenuation of the severity of experimental pancreatitis is due to VPAC1 receptor-mediated inhibition of cytokine production. (2005)

VIP attenuated the experimental acute pancreatitis enzymatically and morphologically by inhibiting proinflammatory cytokine production from monocytes mainly through the VPAC1-R.
Cross-validated stepwise regression for identification of novel non-nucleoside reverse transcriptase inhibitor resistance associated mutations (2011)

We successfully identified and validated novel NNRTI resistance associated mutations by developing parsimonious resistance prediction models in which repeated cross-validation within the stepwise regression was applied. Our model selection technique is computationally feasible for large data sets and provides an approach to the continued identification of resistance-causing mutations.
Postcritical-Angle AVO for Carbonate Reservoirs (1998)

Abstract Most carbonate reefs under shale have small critical angle and small amplitude variation with offset (AVO) in the precritical offset range.
Microwave optimized liquid crystals for space and terrestrial communication (2023)

Driven by the need for new low-cost data communication technologies, liquid crystals are used not only by the display industry but also by companies in the satellite and telecommunications area. Recent developments in liquid crystal mixtures for tunable microwave components have led to material classes with substantially increased performance. High performance materials provide a high tunability with low associated dielectric losses meeting requirements of commercial applications. This presentation gives an overview about the state-of-the-art in liquid crystal materials for microwave applications, future development targets as well as emerging fields of applications.
Analysis of Genetic Interactions on a Genome-Wide Scale in Budding Yeast: Diploid-Based Synthetic Lethality Analysis by Microarray (2008)

Comprehensive collections of open reading frame (ORF) deletion mutant strains exist for the budding yeast Saccharomyces cerevisiae. With great prescience, these strains were designed with short molecular bar codes or TAGs that uniquely mark each deletion allele, flanked by shared priming sequences. These features have enabled researchers to handle yeast mutant collections as complex pools of approximately 6000 strains. The presence of any individual mutant within a pool can be assessed indirectly by measuring the relative abundance of its corresponding TAG(s) in genomic DNA prepared from the pool. This is readily accomplished by wholesale polymerase chain reaction (PCR) amplification of the TAGs using fluorescent oligonucleotide primers that recognize the common flanking sequences, followed by hybridization of the labeled PCR products to a TAG oligonucleotide microarray. Here we describe a method-diploid-based synthetic lethality analysis by microarray (dSLAM)-whereby such pools can be manipulated to rapidly construct and assess the fitness of 6000 double-mutant strains in a single experiment. Analysis of double-mutant strains is of growing importance in defining the spectrum of essential cellular functionalities and in understanding how these functionalities interrelate.
ChemInform Abstract: Surface Diffusion of Hydrogen on Ru(00l) Studied Using Laser‐Induced Thermal Desorption. (1986)

Abstract The surface diffusion coefficients for hydrogen on Ru(00l) at low coverage display Arrhenius behaviour in the temp. range 260‐330 K. The activation energy of diffusion is found to be 4 kcal mol ‐1 and the preexponential factor is 6.3·10 ‐4 cm 2 s ‐1 .
Modeling of Cavitating Flow through Waterjet Propulsors (2012)

A computational-fluid-dynamics-based modeling effort to capture flow through an axial flow waterjet propulsor is presented. The effort covered the waterjet flow over a wide range of flow coefficients and into cavitation-driven breakdown. The computations are presented in cavitation at two values of flow coefficient through a series of decreasing operating inlet total pressure. The computational results are compared to experimental measurements. Suction-surface and tip-gap cavitation patterns are presented and compared to experimental photographs. Presented computational solutions are blade-passage steady and periodic. The computational results apply a powering iteration methodology to facilitate coupling of rotor, stator, and inflow and outflow ducting.
Electrical characterization of dry and wet processed interface layer in Ge/High-K devices (2016)

In this work, the dry and wet processed interface layers for three different p type Ge/atomic layer deposition (ALD) 1 nm-Al2O3/ALD 3.5 nm-ZrO2/ALD TiN gate stacks on 300 mm wafers were studied at low temperatures by capacitance–voltage (CV), conductance–voltage measurement, and deep level transient spectroscopy. The interface treatments were (1) simple chemical oxidation (Chemox); (2) chemical oxide removal (COR) followed by 1 nm oxide by slot-plane-antenna (SPA) plasma (COR and SPAOx); and (3) COR followed by vapor O3 treatment (COR and O3). Since low temperature measurements are more reliable, several parameters like equivalent oxide thickness, flatband voltage, bulk doping, and surface potential as a function of gate voltage are reported. Different temperature CV measurement suggests that all the samples are pinned at flat band voltage (Cit give a pseudoaccumulation region) due to large Dit (larger than 1013 cm−2/eV). Room temperature measurement indicates that superior results were observed for slot-plane-plasma-oxidation processed samples.
Entrapment of Chlorella vulgaris cells within graphene oxide layers (2013)

Confinement of microalgae cells within layers of graphene oxide (GO) effectively reduces the rate of cell division, with the microalgal wrapping being more efficient in a vortex fluidic device than using mild sonication, as determined by the cell growth and the level of nitrate removal from the liquid effluent.
GTO based DC feeders for remote loads (2002)

A multiterminal DC transmission scheme using gate turn-off device based inverters is proposed. The scheme utilizes single wire DC transmission and is intended for supplying power to generationless loads in remote locations. A suitable inverter topology is identified and its performance is investigated. Control and protection methods for the scheme are developed for system start-up, AC and DC faults, load voltage regulation and loss of load. The system performance is evaluated using a digital electromagnetic transient analysis program and is found to be satisfactory.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Ground deformation analyzed in heterogeneous finite element models: an application to Darwin volcano (2006)

Magma intrusions into volcanoes may cause relevant surface deformations detectable by geodetic InSAR, GPS or tilt data. Studying the amount and the pattern of surface deformation allow locating magma intrusions, to understand the entity of the magma body, as well as to forecast a possible eruption. Inverse numerical models use geodetic data as the base of their calculations, but most of the previous modeling attempts are made in isotropic elastic half-space (e.g. using Mogi point source). However, can we neglect material heterogeneities such as piles of lava, pyroclastic deposits and sediments? How does material heterogeneities affect the surface deformations and our assessment of volcanic unrest? 
In this work we use finite element models (FEM) to study the importance of mechanical heterogeneities on displacement redistribution. We use InSAR data of Darwin volcano (Galapagos Islands) and we compare inversion models based on homogeneous half-space model to heterogeneous multi layered models. We show that mechanical heterogeneities have important effects on the estimation of the magma chamber depth and on the volume of the magma inflation. 
Our results suggest that the interpretation of geodetic data depends on the crust mechanical characteristics, which is influencing the correct evaluation of volcanic hazard potential.
Streptococcal M1 protein triggers chemokine formation, neutrophil infiltration, and lung injury in an NFAT-dependent manner (2015)

Streptococcus pyogenes of the M1 serotype can cause STSS, which is associated with significant morbidity and mortality. The purpose of the present study was to examine the role of NFAT signaling in M1 protein-induced lung injury. NFAT-luc mice were treated with the NFAT inhibitor A-285222 before administration of the M1 protein. Neutrophil infiltration, edema, and CXC chemokines were quantified in the lung, 4 h after challenge with the M1 protein. Flow cytometry was used to determine Mac-1 expression. Challenge with the M1 protein increased NFAT-dependent transcriptional activity in the lung, spleen, and liver in NFAT-luc mice. Administration of the NFAT inhibitor A-285222 abolished M1 protein-evoked NFAT activation in the lung, spleen, and liver. M1 protein challenge induced neutrophil recruitment, edema, and CXC chemokine production in the lung, as well as up-regulation of Mac-1 on circulating neutrophils. Inhibition of NFAT activity attenuated M1 protein-induced neutrophil infiltration by 77% and edema formation by 50% in the lung. Moreover, administration of A-285222 reduced M1 protein-evoked pulmonary formation of CXC chemokine >80%. In addition, NFAT inhibition decreased M1 protein-triggered Mac-1 up-regulation on neutrophils. These findings indicate that NFAT signaling controls pulmonary infiltration of neutrophils in response to streptococcal M1 protein via formation of CXC chemokines and neutrophil expression of Mac-1. Thus, the targeting of NFAT activity might be a useful way to ameliorate lung injury in streptococcal infections.
Acidification of the interior of Ehrlich ascites tumor cells by nigericin inhibits DNA synthesis (1987)

In Ehrlich ascites carcinoma cells, acidification of the cytoplasm down to pH 6.2-6.3 arrests DNA synthesis. Such acidification can be obtained by decreasing the pH outside the cell or, alternatively, by addition of a micromolar concentration of the K+/H+ antiporter nigericin. Thus, nigericin may be regarded as a new type of cytostatic, the effect of which is mediated by alteration of the intracellular pH.
Physical Properties of Two Isomers of Conjugated Linoleic Acid (2007)

Abstract Thermal properties, powder X‐ray diffraction patterns and FT‐IR absorption spectra of crystals of two isomers of conjugated linoleic acid (CLA), 9‐ cis , 11‐ trans ‐CLA (c9t11), 10‐ trans , 12‐ cis ‐CLA (t10c12) were examined. To search for polymorphic modifications, we carefully performed crystallization from melt and solution phases, and isolated one type of crystalline form in c9t11 and t10c12. The melting temperature ( T m ) was 14.9 °C, enthalpy of fusion (Δ H ) was 38.7 kJ/mol, and entropy of fusion (Δ S ) was 134 J/mol K for c9t11, and T m = 19.8 °C, Δ H = 35.6 kJ/mol and Δ S = 122 J/mol K for t10c12. The X‐ray diffraction and FT‐IR measurements indicated O ⊥ subcell packing in the crystals of c9t11 and t10c12, and long spacing values of 4.22 nm for c9t11 and 3.88 nm for t10c12. The unique molecular structures of the two isomers of CLA are discussed in comparison to the polymorphism of oleic acid, petroselinic acid, elaidic acid and linoleic acid, all of which are unsaturated fatty acids having the same carbon number of 18 as that of the two CLA isomers.