gebhart/patrepeval huggingface dataset:
Extending HyperTransport Protocol for Improved Scalability (2009)

HyperTransport 3.10 is the best open standard communication technology for chip-to-chip interconnects. However, its extraordinary features are of little help when building mid- and large-scale systems because it is unable to natively scale beyond 8 computing nodes. Therefore, it must be complemented by other interconnect technologies. The HyperTransport Consortium has intensively stimulated discussions among its high-level members in order to overcome those shortcomings. The result is the High Node Count HyperTransport Specification, which defines protocol extensions to the HyperTransport I/O Link Specification Rev. 3.10 that enable HyperTransport to natively support high numbers of computing nodes, typical of large scale server clustering and High Performance Computing (HPC) applications. This extension has been carefully designed in such a way that it extends the maximum number of connected devices to a number large enough to support current and future scalability requirements, while preserving the excellent features that made HyperTransport successful and keeping full backward compatibility with it.
Grafting Oligothiophenes on Surfaces by Diazonium Electroreduction: A Step toward Ultrathin Junction with Well-Defined Metal/Oligomer Interface (2009)

The functionalization of electrode materials through diazonium electroreduction using a heteroaromatic compound, without phenyl groups, has been investigated for the first time. The electrochemical reduction of 2-aminoterthiophenyldiazonium cation, generated in situ, coats the electrode (glassy carbon (GC), gold or platinum) with an ultrathin organic layer, shown by X-ray photoelectron spectroscopy (XPS) of that deposited on gold to consist of terthiophene or oligothiophene. The coating is electroactive at potential close to that of terthiophene in solution. The electrochemical response of the modified GC electrode in the presence of various reversible redox couples shows that the attached layer acts as a conductive switch. It behaves as a barrier to electron transfer when the standard redox potential is below 0.5 V/SCE; in this case diode-like behavior is observed. However, for more oxidizing redox probes the layer can be considered as transparent and no barrier effect is observed. The layer deposited on a platinum ultramicroelectrode (UME) behaves similarly to that obtained on the large GC electrode. Scanning electrochemical microscopy (SECM) can be performed using this electroswitchable modified platinum UME which can act as a filter toward competitive redox exchange pathways.
Concentration-Dependent <i>Mycobacterium tuberculosis</i> Killing and Prevention of Resistance by Rifampin (2007)

Rifampin is a cornerstone of modern antituberculosis therapy. However, rifampin's half-life of 3 h is believed to limit its utility for intermittent therapy, so new congeners with long half-lives are being developed. Using an in vitro pharmacokinetic-pharmacodynamic model of tuberculosis, we examined the relationships between rifampin exposure, microbial killing of log-phase-growth Mycobacterium tuberculosis, and suppression of resistance. Rifampin's microbial killing was linked to the area under the concentration-time curve-to-MIC ratio. The suppression of resistance was associated with the free peak concentration (C(max))-to-MIC ratio and not the duration that the rifampin concentration was above MIC. Rifampin prevented resistance to itself at a free C(max)/MIC ratio of > or =175. The postantibiotic effect duration was > or =5.2 days and was most closely related to the C(max)/MIC ratio (r(2) = 0.96). To explain rifampin's concentration-dependent effect, we examined the kinetics of rifampin entry into M. tuberculosis. Rifampin achieved concentration-dependent intracellular steady-state concentrations within 15 min. Our results suggest that doses of rifampin higher than those currently employed would optimize the effect of rifampin, if patients could tolerate them. Another major implication is that in the design of new rifampin congeners for intermittent therapy, the important properties may include (i) the efficient entry of the rifamycin into M. tuberculosis, (ii) the achievement of a free C(max)/MIC of >175 that can be tolerated by patients, and (iii) a long postantibiotic effect duration.
Store-ordered streaming of shared memory (2005)

Coherence misses in shared-memory multiprocessors account for a substantial fraction of execution time in many important scientific and commercial workloads. Memory streaming provides a promising solution to the coherence miss bottleneck because it improves memory level parallelism and lookahead while using on-chip resources efficiently. We observe that the order in which shared data are consumed by one processor is correlated to the order in which they were produced by another. We investigate this phenomenon and demonstrate that it can be exploited to send store-ordered streams (SORDS) of shared data from producers to consumers, thereby eliminating coherent read misses. Using a trace-driven analysis of all user and OS memory references in a cache-coherent distributed shared-memory multiprocessor, we show that SORDS-based memory streaming can eliminate between 36% and 100% of all coherent read misses in scientific workloads and between 23% and 48% in online transaction processing workloads.
Theoretical optical properties of composite metal–NiO films (2003)

This paper reports theoretical optical properties of composite metal (Cu, Ag, Au, Ni, Pd and Pt) nickel oxide thin films, aiming to create a new electrochromic material. Selective absorption was verified only in composites with metals belonging to the IB column of the periodic table. In particular, emphasis was given to the spectral transmission, reflection and absorption, between 0.4 and 2.5 µm, of Au–NiO composite thin films, that showed the narrowest absorption band in the visible spectrum. Au–CoO films presented similar results. The calculations were based on the Maxwell–Garnett effective medium theory, with Au fill factors, f, varying from 0.0 to 0.2. The Au configurations were modelled to be isolated single spheres (ISS), isolated double spheres, single linear chain (SLC), double linear chain and fcc clusters (FCCs). Independent of the aggregate state, the increase in the fill factor enhances the selective absorption and broadens the absorption band of the films. Films with different thicknesses (0.1–0.3 µm), but with the same amount of Au particles per unit area and aggregate state, showed distinct interference patterns in the transmission and reflection spectra. The absorption spectra were almost insensitive to thickness, being very dependent on the gold content and configuration. The tailoring of the optical properties in the visible region of the Au–NiO films was achieved by controlling the Au configuration. A combination of ISS (25%), SLC (25%) and FCC (50%) was also simulated.
Development of a Method for Quantification of Acrolein−Deoxyguanosine Adducts in DNA Using Isotope Dilution-Capillary LC/MS/MS and Its Application to Human Brain Tissue (2005)

Acrolein is a highly reactive alpha,beta-unsaturated aldehyde and is known to react with DNA forming exocyclic acrolein-deoxyguanosine adducts (Acro-dG). These aldehyde-DNA lesions may play a role in mutagenesis, carcinogenesis, and neurodegenerative diseases. In the present work, we described the development and evaluation of a highly sensitive and selective capillary liquid chromatography nanoelectrospray isotope dilution tandem mass spectrometry method for quantitatively analyzing Acro-dG in DNA hydrolysates. This was achieved by applying a stable isotope-labeled analogue Acro-dG-13C10,15N5 as an internal standard to the DNA to be analyzed and then hydrolyzing the DNA enzymatically to nucleosides. The acrolein-modified nucleosides were separated from normal nucleosides by capillary liquid chromatography and quantified by a high-capacity ion trap mass spectrometer in the MS/MS mode. The developed method achieved attomole-level sensitivity (limit of detection was 10 fg, 31 amol on column) for detection of pure Acro-dG adduct standards. The limit of quantification of Acro-dG adducts obtained in 10 mug of DNA hydrolysates was 1.5 fmol, which corresponded to 50 adducts/10(9) normal nucleosides. Application of this method to the analysis of Acro-dG adducts in acrolein (10-fold)-treated calf thymus DNA showed approximately 830 lesion/10(6) DNA nucleosides using as low as 50 ng of DNA. Application of this method to DNA samples (1-2 mug) isolated from brain tissues from Alzheimer's disease subjects and age-matched controls demonstrated 2800-5100 Acro-dG adducts/10(9) DNA nucleosides. Statistically significant differences (P < 0.05) in levels of Acro-dG between AD subjects and controls were observed in DNA isolated from the hippocampus/parahippocampal gyrus.
Development environment for monitoring, data acquisition and simulation of PLC controlled applications (2013)

It is very important to monitor and test the operation of Programmable Logic Controller (PLC) in real time (online). There are many conventional, but expensive monitoring systems for PLC, such as Supervisory Control and Data Acquisition (SCADA) systems, software and hardware simulators (or debuggers), etc. This paper proposes a user friendly and cost-effective development environment for monitoring and data acquisition of applications with PLC. The purpose of this solution is to simulate the process which is controlled by the PLC. The performances of the development environment are presented on the example of washing machine and dishwasher simulators.
Guided wave modulators in Ti ion implanted LiNbO/sub 3/ waveguides (1989)

Electrooptic modulators in Ti-ion-implanted LiNbO/sub 3/ waveguides are discussed. Low loss (<1-dB/cm) planar and channel waveguides were fabricated and compared to indiffused waveguides. Higher Delta n values are obtained, allowing smaller waveguide geometries and tighter mode confinement. Wavelengths of 0.85 and 1.3 mu m are used. The small mode profiles resulting from the Ti doses up to 4*10/sup 17/ Ti/cm/sup 2/ resulted in V-L products of 8.8 V-mm at 0.85 mu m and 20 V-mm at 1.3 mu m. These values are lower than any previously reported for a Mach-Zehnder modulator using a buffer layer. Comparison of diffused and implanted waveguide modulators indicated that modular efficiency can be optimized by electrode gap spacing and enhanced with smaller mode profiles achievable in implanted guides.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Long-acting beta 2-adrenoceptor agonists: a new perspective in the treatment of asthma (1991)

New long-acting beta 2-adrenoceptor agonists, formoterol and salmeterol, may soon appear in several European countries for treatment of asthma. This review examines currently available information and compares the basic pharmacology and describes the clinical effects of these new drugs. The long duration of bronchodilation seen in clinical studies seems to be similar, whereas in isolated tissues there might be a difference in the binding characteristics to the beta 2-adrenoceptor. Long-acting beta 2-agonists could have an inhibitory effect on inflammatory events related to asthma, but the clinical relevance of these effects is not clear at present. Long-term studies up to one year with both new drugs have not shown any unexpected side-effects, and no tachyphylaxis to beta-adrenoceptor stimulation has been reported. Patients appear to strongly prefer the new drugs compared to the short-acting beta 2-agonists. The potential place for these drugs in the treatment of asthma is discussed and some pitfalls pointed out. It is likely that the long-acting beta 2-agonists will be beneficial to many asthmatic patients.
FTIR dosimetry mapping of as-implanted SIMOX wafers (2002)

This report summarizes recent advances in the application of the On-Line's FTIR FilmExpert/sup TM/ metrology tool for the characterization and uniformity control of SIMOX wafers. The SOI buried layer needs to be uniform within +/5%. This translates to +/- 25 A for 500 A SOI films and respectively less for 200 A SOI films over the large diameter wafers. The criterion is related to the requirement for the uniformity of threshold voltage and corresponding doping levels. The advanced FTIR measurements demonstrated the capability to perform fast mapping of oxygen implant dose with high precision (better than 0.5%) and excellent spatial resolution on as-implanted wafers. i.e. before time-consuming annealing which,finalizes SIMOX fabrication. The results illustrate the potential of the FilmExpert/sup TM/ as a process control tool for optimizing low-dose and ultra low-dose SIMOX manufacturing.
Caveolin-1 Triggers T-cell Activation via CD26 in Association with CARMA1 (2007)

CD26 is a widely distributed 110-kDa cell surface glycoprotein with an important role in T-cell costimulation. We demonstrated previously that CD26 binds to caveolin-1 in antigen-presenting cells, and following exogenous CD26 stimulation, Tollip and IRAK-1 disengage from caveolin-1 in antigen-presenting cells. IRAK-1 is then subsequently phosphorylated to up-regulate CD86 expression, resulting in subsequent T-cell proliferation. However, it is unclear whether caveolin-1 is a costimulatory ligand for CD26 in T-cells. Using soluble caveolin-1-Fc fusion protein, we now show that caveolin-1 is the costimulatory ligand for CD26, and that ligation of CD26 by caveolin-1 induces T-cell proliferation and NF-kappaB activation in a T-cell receptor/CD3-dependent manner. We also demonstrated that the cytoplasmic tail of CD26 interacts with CARMA1 in T-cells, resulting in signaling events that lead to NF-kappaB activation. Ligation of CD26 by caveolin-1 recruits a complex consisting of CD26, CARMA1, Bcl10, and IkappaB kinase to lipid rafts. Taken together, our findings provide novel insights into the regulation of T-cell costimulation via the CD26 molecule.
Autopathogenic T Helper Cell Type 1 (Th1) and Protective Th2 Clones Differ in Their Recognition of the Autoantigenic Peptide of Myelin Proteolipid Protein (1997)

We previously generated a panel of T helper cell 1 (Th1) clones specific for an encephalitogenic peptide of myelin proteolipid protein (PLP) peptide 139-151 (HSLGKWLGHPDKF) that induces experimental autoimmune encephalomyelitis (EAE) upon adoptive transfer. In spite of the differences in their T cell receptor (TCR) gene usage, all these Th1 clones required W144 as the primary and most critical TCR contact residue for the activation. In this study, we determined the TCR contact residues of a panel of Th2/Th0 clones specific for the PLP peptide 139-151 generated either by immunization with the PLP 139-151 peptide with anti- B7-1 antibody or by immunization with an altered peptide Q144. Using alanine-substituted peptide analogues of the native PLP peptide, we show that the Th2 clones have shifted their primary contact residue to the NH2-terminal end of the peptide. These Th2 cells do not show any dependence on the W144, but show a critical requirement for L141/G142 as their major TCR contact residue. Thus, in contrast with the Th1 clones that did not proliferate to A144-substituted peptide, the Th2 clones tolerated a substitution at position 144 and proliferated to A144 peptide. This alternative A144 reactive repertoire appears to have a critical role in the regulation of autoimmune response to PLP 139-151 because preimmunization with A144 to expand the L141/G142-reactive repertoire protects mice from developing EAE induced with the native PLP 139-151 peptide. These data suggest that a balance between two different T cell repertoires specific for same autoantigenic epitope can determine disease phenotype, i.e., resistance or susceptibility to an autoimmune disease.
Automatic moving object segmentation using histogram-based graph cut and label maps (2012)

Presented is a novel object segmentation method using a histogram-based graph cut algorithm with automatically generated label maps. The proposed method consists of three steps including: (i) pre-processing, (ii) label map generation and update, and (iii) object segmentation. The pre-processing step over-segments the input image using the median filter-based watershed algorithm. The label map is generated by using optical-flow and morphological skeletonisation, and it is updated using colour histogram and the Bhattacharyya coefficient for the following frame. Moving objects are finally extracted by using the histogram-based graph-cut method. Experimental results show that the proposed method is significantly faster than existing object segmentation methods by removing user interaction.
A dependency‐aware ontology‐based approach for deploying service level agreement monitoring services in Cloud (2011)

SUMMARY Cloud computing offers virtualized computing elements on demand in a pay‐as‐you‐go manner. The major motivations to adopt Cloud services include no upfront investment on infrastructure and transferring responsibility of maintenance, backups, and license management to Cloud Providers. However, one of the key challenges that holds businesses from adopting Cloud computing services is that, by migrating to Cloud, they move some of their information and services out of their direct control. Their main concern is how well the Cloud providers keep their information (security) and deliver their services (performance). To cope with this challenge, several service level agreement management systems have been proposed. However, monitoring service deployment as a major responsibility of those systems have not been deeply investigated yet. Therefore, this paper shows how monitoring services have to be described, deployed (discovered and ranked), and then how they have to be executed to enforce accurate penalties by eliminating service level agreement failure cascading effects on violation detection. Copyright © 2011 John Wiley & Sons, Ltd.
Clonal lines of aneuploid cells in Rothmund‐Thomson syndrome (1990)

We report on a 21-month-old white boy with the Rothmund-Thomson syndrome. The karyotype on fibroblasts from an area of skin with poikiloderma showed the 46,XY,17 + der(17),t(2;17)(q11;p13) pattern. Karyotype on fibroblasts from normal skin showed two different abnormal patterns: 47,XY, + 8 and 47,XY, + i(2q). His lymphocytes had a normal 46,XY pattern. These findings indicate in vitro abnormalities. They are explained by a degree of chromosomal instability.
ADP-ribosylation of <i>Drosophila</i> indirect-flight-muscle actin and arthrin by <i>Clostridium botulinum</i> C2 toxin and <i>Clostridium perfringens</i> iota toxin (1993)

Purified Drosophila indirect-flight-muscle actin and arthrin, an actin-ubiquitin conjugate, were ADP-ribosylated by Clostridium botulinum C2 toxin and Clostridium perfringens iota toxin. Phalloidin treatment inhibited the ADP-ribosylation of Drosophila actin and arthrin. Like actin, the ADP-ribose-arthrin linkage was sensitive towards hydroxylamine treatment, indicating arginine as the amino acid acceptor. Actin translated in vitro from the indirect-flight-muscle-specific gene Act88F was ADP-ribosylated by C. botulinum C2 toxin and C. perfringens iota toxin. Actin from the R177Q mutant of Act88F translated in vivo was not ADP-ribosylated confirming Arg-177 as the ADP-ribose acceptor. Mutant L176M actin was modified by both toxins, indicating that amino acid 176 of actin does not define the substrate specificity of C. botulinum C2 toxin. Whereas the gene products of various C-terminal mutants of Act88F translated in vitro (E334K, V339I, E364K, G368E, R372H) were substrates for ADP-ribosylation by C. botulinum C2 toxin and by C. perfringens iota toxin, neither toxin modified the N-terminal O-12 deletion mutant.
An iterative dual energy CT reconstruction method for a K-edge contrast material (2011)

We present and evaluate an iterative dual energy CT reconstruction algorithm for a K-edge contrast material in microCT imaging. This allows improved discrimination of contrast enhanced structures such as vasculature from surrounding bony structures. The energy dependence of the attenuation is modeled by decomposing the linear attenuation coefficient into three basis functions. Any material without a K-edge in the imaging energy range can be modeled by two basis functions describing the Compton scatter and the photoelectric effect respectively. A K-edge material is described by using its mass attenuation coefficient as third basis function. During reconstruction the basis function coefficients are determined for each voxel of the image by maximizing the likelihood of the data. The relative weights of the Compton and photoelectric components are constrained to those of expected materials to reduce the number of unknowns to two per voxel. The proposed method is validated on simulated and real microCT projections. The presented method was found to perform better than a typical post-reconstruction approach with respect to beam-hardening and noise at the expense of increased computation time.
Nuclease P1-mediated enhancement of sensitivity of <sup>32</sup>P-Postlabeling test for structurally diverse DNA adducts (1986)

Exceedingly sensitive procedures are required to detect the presence of covalent DNA adducts in humans exposed to environmental genotoxicants because of low levels of such derivatives (1 adduct in 10(8)-10(10) DNA nucleotides). A 32P-postlabeling assay for detection and quantitation of carcinogen--DNA adducts with a sensitivity limit of 1 adduct in 10(7)-10(8) nucleotides has been described previously. In the standard procedure, DNA is enzymatically digested to 3'-phosphorylated normal and adducted mononucleotides, which are quantitatively 32P-labeled at their 5'-hydroxyl groups by T4 polynucleotide kinase-catalyzed [32P]phosphate transfer from [gamma-32P]ATP. 32P-labeled derivatives are resolved by t.l.c., detected by autoradiography and quantitated by counting. We now report that a minor modification of this procedure, entailing the postincubation of DNA digests with Penicillium citrinum nuclease P1 before 32P-labeling, enhanced the technique's sensitivity to 1 adduct in approximately 10(10) nucleotides for a 10-micrograms DNA sample. Nuclease P1 cleaves deoxyribonucleoside 3'-monophosphates of normal nucleotides to deoxyribonucleosides which do not serve as substrates for polynucleotide kinase, while most adducted nucleotides were found to be totally or partially resistant to the 3'-dephosphorylating action of nuclease P1. The additional enzymatic step enabled specific labeling of adducts in up to 20 micrograms of DNA with excess carrier-free [gamma-32P]ATP. The enzymatic digestion conditions were standardized to afford optimal adduct recovery. The new procedure was found to be simple, highly reproducible, and applicable to the detection and measurement of aromatic or bulky non-aromatic DNA adducts formed with such structurally diverse carcinogens as benzo[a]pyrene, 7,12-dimethyl-benz[a]anthracene, dibenzo[c,g]carbazole, 4-aminobiphenyl, safrole and mitomycin C; most adducts were recovered quantitatively with a 500- to 1000-fold increase in 32P-count rates as compared with the standard procedure.
Fabrication of Plasmonic Nanodiscs by Photonic Nanojet Lithography (2012)

In this study, we present and demonstrate a new route to the fabrication of plasmonic nanostructures with a controlled size and shape using photonic nanojet lithography. Through the approach of dual-layer lift-off, the achievable size was remarkably reduced to a sub-100 nm scale and the introduction of an engineered diffuser was proved to give a facile and precise way of controlling the anisotropy in shape without a process burden even when the spherical focusing beads are used.