gebhart/patrepeval huggingface dataset:
Technology scaling: The CoolCube<sup>TM</sup> paradigm (2015)

Scaling race towards aggressive nodes is getting more and more difficult as dimensions are getting close to the atoms ones. New solutions have to be investigated to find new ways of scaling while keeping the Moore's law benefits in terms of area, power, performance and cost. These solutions should leverage on existing technologies for reducing their development cost by proposing new usages. Also, as cost of designing complex systems explodes, these new technologies should come with design techniques close to existing ones without increasing their complexity. Finally, current technological issues such as increased complexity of Back-End-Of-Line (BEOL) with the successive delays of Extreme-Ultra-Violet lithography should be solved. This multi-dimensional problem makes candidates difficult to emerge. The sequential 3D CoolCube <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">TM</sup> technology is one of them: bringing very fine pitch 3D interconnects and leveraging on existing technologies, it's opening the door to real 3D-VLSI with the hope of reducing the actual pressure on BEOL while providing real 3D routing possibilities. However, many roadblock in terms of design still exist. In this paper, we show three aspects of design methodology showing its growing maturity and a PPA analysis based on this methodology showing that gains can meet the classical scaling requirements.
Modulation of airway inflammation by CpG oligodeoxynucleotides in a murine model of asthma. (1998)

Asthma has been increasing in industrialized countries. Evidence suggests that asthma is caused by a Th2 immune response to inhaled environmental Ags and that childhood infections protect against this. We have shown that bacterial DNA contains motifs, centered on unmethylated CpG dinucleotides, which induce Th1-type responses. We hypothesized that the Th1 effect of these CpG motifs may oppose the Th2 type allergic response and suggest that this may account for the protective effect of childhood infection against asthma. We examined the effects of CpG-motif oligodeoxynucleotides (CpG ODN) in a murine model of asthma. Airway eosinophilia, Th2 cytokine induction, IgE production, and bronchial hyperreactivity were prevented by coadministration of CpG ODN with the Ag. Significantly, in a previously sensitized mouse, CpG ODN can prevent allergen-induced airway inflammation. These studies suggest that exposure to CpG DNA may protect against asthma.
Regulation of neutrophil apoptosis by Mcl-1 (2004)

Neutrophils rapidly undergo spontaneous apoptosis, but this process can be considerably delayed by exposure to a variety of agents such as pro-inflammatory cytokines. The anti-apoptotic protein of the Bcl-2 family, Mcl-1, plays a key role in the regulation of neutrophil apoptosis. The protein has some unusual properties compared with other family members, including an extremely high turnover rate. Many factors, such as cytokines and local oxygen concentrations, can regulate cellular levels of Mcl-1 via transcription and post-transcriptional modification, control the survival time of neutrophils within tissues and thereby influence the inflammatory response.
Modification of oligosaccharides by reactive oxygen species decreases sialyl lewis x-mediated cell adhesion (2005)

Modification of cell surface oligosaccharides by reactive oxygen species (ROS) and the biological effect of such modifications on cell adhesion were investigated. Treatment of HL60, a human promyelocyte leukemia cell line, with ROS, generated by a combination of hypoxanthine and xanthine oxidase (HX/XO), decreased the sialic acid content on the cell surface, as indicated by a flow cytometric analysis involving sialic acid-specific lectins, and a concomitant increase of free sialic acid was observed in the supernatant. A cell adhesion assay showed that the HX/XO treatment of HL60 cells decreases their capability of binding to human umbilical vein endothelial cells (HUVEC), probably because of an impairment of the interaction involving E-selectin, whereas the decrease in the binding was canceled by the addition of superoxide dismutase (SOD) and catalase. In fact, cell surface sialyl lewis x (sLe x), but not lewis x (Le x), was decreased by HX/XO treatment. Thus, it is more likely that the impaired interaction is based on diminished levels of the selectin ligand. Cleavage of sialic acid by ROS was further verified by the degradation of 4MU-Neu5Ac by HX/XO in the presence of hydrogen peroxide and iron ion. These results indicate that glycosidic linkage of sialic acid is a potential target for superoxide and other related ROS. It is well known that ROS cause cellular damages such as lipid peroxidation and protein oxidation, but, as suggested by the findings reported in the literature, ROS may also regulate cell adhesion via the structural alteration of sialylated oligosaccharides on the cell surface.
Effects of transitional phenomena on the electric field induced strain-electrostrictive response of a segmented polyurethane elastomer (1997)

The electromechanical properties of a segmented polyurethane elastomer were investigated as functions of temperature and frequency. Two transitional phenomena were observed in the temperature range from -50 to 85°C. In these transition regions, the electric field induced strain coefficient exhibits large increases, which indicate that the effect of the transition processes is significant. The experimental analysis suggests that the transitional processes in the polyurethane are related to the chain-segment motions. From the elastic compliance and the dielectric constant data, the contribution of the uniform Maxwell stress was determined. It was found that the contribution of the Maxwell stress effect to the measured strain coefficient increased from about 10% below the glass transition temperature (Tg) (∼ -25°C) to about 50 and 35% for the frequencies of 10 and 100 Hz, respectively, at ∼ 40°C, which is above Tg. The large difference between the measured strain response and the calculated Maxwell stress effect indicates a significant contribution to the field-induced strain from other mechanisms, such as electrostriction. © 1997 John Wiley & Sons, Inc. J Appl Polym Sci 65: 1363–1370, 1997
Potassium Metal Dispersed on Silica: A Versatile Reagent in Organic Chemistry (1981)

The title reagent K/SiO 2 has a greater reactivity and a different selectivity compared to metallic potassium . It is particularly suitable for dimerizations: benzophenone can be converted with K/SiO 2 into benzopinacol in 72% yield; bromo‐ and iodobenzene afford biphenyl in yields of more than 80%.
Doxycycline versus minocycline in the treatment of acne vulgaris: A double-blind study (1989)

The effect of doxycycline and minocycline on moderate to moderately severe acne vulgaris was compared in a double-blind, double-dummy, randomized study. Sixty-four acne patients were treated for 12 weeks with doxycycline or minocycline, 50 mg twice daily for the first 4 weeks and then 50 mg once daily for the remaining 8 weeks. The patients' acne was evaluated before and after 4, 8 and 12 weeks of treatment. Acne lesions were counted on the face, the chest and the back, differentiating between pustules, papules, open comedones and closed comedones. A significant reduction of all types of acne lesions was observed in all areas during the 12 weeks of treatment for both groups. Doxycycline and minocycline were found to be equally effective in the treatment of moderate to moderately severe acne vulgaris.
Parallel deep neural network training for LVCSR tasks using blue gene/Q (2014)

While Deep Neural Networks (DNNs) have achieved tremendous success for LVCSR tasks, training these networks is slow. To date, the most common approach to train DNNs is via stochastic gradient descent (SGD), serially on a single GPU machine. Serial training, coupled with the large number of training parameters and speech data set sizes, makes DNN training very slow for LVCSR tasks. While 2nd order, data-parallel methods have also been explored, these methods are not always faster on CPU clusters due to the large communication cost between processors. In this work, we explore using a specialized hardware/software approach, utilizing a Blue Gene/Q (BG/Q) system, which has thousands of processors and excellent interprocessor communication. We explore using the 2nd order Hessian-free (HF) algorithm for DNN training with BG/Q, for both cross-entropy and sequence training of DNNs. Results on three LVCSR tasks indicate that using HF with BG/Q offers up to an 11x speedup, as well as an improved word error rate (WER), compared to SGD on a GPU.
Effect of sequential transdermal progesterone cream on endometrium, bleeding pattern, and plasma progesterone and salivary progesterone levels in postmenopausal women (2000)

Pro-Feme transdermal progesterone administered in a 16-, 32- or 64-mg daily dose for 14 days in a sequential regimen does not appear to be effective in inducing a secretory change in a proliferative endometrium. Salivary progesterone levels were not of value in managing the therapy of postmenopausal women.
Structure of linkage disequilibrium and phenotypic associations in the maize genome (2001)

Association studies based on linkage disequilibrium (LD) can provide high resolution for identifying genes that may contribute to phenotypic variation. We report patterns of local and genome-wide LD in 102 maize inbred lines representing much of the worldwide genetic diversity used in maize breeding, and address its implications for association studies in maize. In a survey of six genes, we found that intragenic LD generally declined rapidly with distance (r(2) < 0.1 within 1500 bp), but rates of decline were highly variable among genes. This rapid decline probably reflects large effective population sizes in maize during its evolution and high levels of recombination within genes. A set of 47 simple sequence repeat (SSR) loci showed stronger evidence of genome-wide LD than did single-nucleotide polymorphisms (SNPs) in candidate genes. LD was greatly reduced but not eliminated by grouping lines into three empirically determined subpopulations. SSR data also supplied evidence that divergent artificial selection on flowering time may have played a role in generating population structure. Provided the effects of population structure are effectively controlled, this research suggests that association studies show great promise for identifying the genetic basis of important traits in maize with very high resolution.
The development of targeted radiotherapy for central nervous system leukaemia. (1992)

The use of antibodies to specifically deliver cytotoxic agents to tumour cells has been widely investigated as a means of increasing the therapeutic index of cancer therapy. Nowhere is this more likely to be of benefit than in the treatment of central nervous system (CNS) tumours, in which damage to vital structures by conventional therapies often results in significant sequelae. Many factors have, however, been identified which limit the clinical success of such targeted therapies. Some of these obstacles may be avoided by the administration of therapeutic agents into a tumour-bearing body compartment. This thesis examines the potential of antibody-targeted radionuclide therapy in the treatment of meningeal leukaemia. Three monoclonal antibodies (MoAbs) binding to leukaemic cells were fully characterised, and conditions established for antibody labelling with the beta-emitting radionuclide, iodine-131. The specificity of antibody-mediated hUj therapy against a single cell suspension of leukaemic cell lines was demonstrated using an in-vitro cell survival assay. Additional experiments have suggested a relationship between the degree of cell kill and the amount of radioisotope bound to the cell surface. These results were supported by a mathematical model. In recognition of the limitations of in-vitro models, a small animal model of CNS leukaemia was established. Prolonged survival of animals treated with intrathecally administered 151I-MoAbs was observed, as compared to untreated controls. A multicentre phase I/II clinical study was initiated, in which a transient response to a single intrathecal injection of 131I-MoAbs was noted in six of seven children with CNS relapse of acute lymphoblastic leukaemia. Toxicity was&#13;\n2&#13;\nacceptable. The biodistribution of radioconjugates was examined and models developed for the estimation of radiation dose to both cerebrospinal fluid and normal tissues. The results of these investigations, together with those from the in-vitro model, have suggested strategies by which the efficacy of therapy may be improved.
Identification, molecular characterization, clinical prognosis, and therapeutic targeting of human bladder tumor-initiating cells (2009)

Major clinical issues in bladder cancer include the identification of prediction markers and novel therapeutic targets for invasive bladder cancer. In the current study, we describe the isolation and characterization of a tumor-initiating cell (T-IC) subpopulation in primary human bladder cancer, based on the expression of markers similar to that of normal bladder basal cells (Lineage-CD44(+)CK5(+)CK20(-)). The bladder T-IC subpopulation was defined functionally by its enriched ability to induce xenograft tumors in vivo that recapitulated the heterogeneity of the original tumor. Further, molecular analysis of more than 300 bladder cancer specimens revealed heterogeneity among activated oncogenic pathways in T-IC (e.g., 80% Gli1, 45% Stat3, 10% Bmi-1, and 5% beta-catenin). Despite this molecular heterogeneity, we identified a unique bladder T-IC gene signature by gene chip analysis. This T-IC gene signature, which effectively distinguishes muscle-invasive bladder cancer with worse clinical prognosis from non-muscle-invasive (superficial) cancer, has significant clinical value. It also can predict the progression of a subset of recurring non-muscle-invasive cancers. Finally, we found that CD47, a protein that provides an inhibitory signal for macrophage phagocytosis, is highly expressed in bladder T-ICs compared with the rest of the tumor. Blockade of CD47 by a mAb resulted in macrophage engulfment of bladder cancer cells in vitro. In summary, we have identified a T-IC subpopulation with potential prognostic and therapeutic value for invasive bladder cancer.
Lung Cancer Serum Biomarker Discovery Using Glycoprotein Capture and Liquid Chromatography Mass Spectrometry (2010)

Targeted glycoproteomics represents an attractive approach for conducting peripheral blood based cancer biomarker discovery due to the well-known altered pattern of protein glycosylation in cancer and the reduced complexity of the resultant glycoproteome. Here we report its application to a set of pooled nonsmall cell lung cancer (NSCLC) case sera (9 adenocarcinoma and 6 squamous cell carcinoma pools from 54 patients) and matched controls pools, including 8 clinical control pools with computed tomography detected nodules but being nonmalignant as determined by biopsy from 54 patients, and 8 matched healthy control pools from 106 cancer-free subjects. The goal of the study is to discover biomarkers that may enable improved early detection and diagnosis of lung cancer. Immunoaffinity subtraction was used to first deplete the topmost abundant serum proteins; the remaining serum proteins were then subjected to hydrazide chemistry based glycoprotein capture and enrichment. Hydrazide resin in situ trypsin digestion was used to release nonglycosylated peptides. Formerly N-linked glycosylated peptides were released by peptide-N-glycosidase F (PNGase F) treatment and were subsequently analyzed by liquid chromatography (LC)-tandem mass spectrometry (MS/MS). A MATLAB based in-house tool was developed to facilitate retention time alignment across different LC-MS/MS runs, determination of precursor ion m/z values and elution profiles, and the integration of mass chromatograms based on determined parameters for identified peptides. A total of 38 glycopeptides from 22 different proteins were significantly differentially abundant across the case/control pools (P < 0.01, Student's t test) and their abundances led to a near complete separation of case and control pools based on hierarchical clustering. The differential abundances of three of these candidate proteins were verified by commercially available ELISAs applied in the pools. Strong positive correlations between glycopeptide mass chromatograms and ELISA-measured protein abundance was observed for all of the selected glycoproteins.
Analytic performance modeling for a spectrum of multithreaded processor architectures (2002)

The throughput of pipelined processors suffers from delays associated with instruction dependencies and memory latencies. Multithreaded architectures attempt to hide such delays by sharing the processor with multiple instruction streams. In this paper we develop a comprehensive analytic framework to quantitatively evaluate the performance of a wide spectrum of mulithreaded machines, ranging from those that are capable of switching threads every cycle to those that switch threads only on long delays. The models are validated against previously published simulation and modeling results, and then used to assess the performance potential of multithreading given current processor technology.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
6xHis-Ni-NTA Chromatography as a Superior Technique in Recombinant Protein Expressiod/Purification (2003)

The 6xHis/Ni-NTA system is a fast and versatile tool for the affinity purification of recombinant proteins and antigenic peptides. It is based on the high-affinity binding of six consecutive histidine residues (the 6xHis tag) to immobilized nickel ions, giving a highly selective interaction that allows purification of tagged proteins or protein complexes from <1% to >95% homogeneity in just one step (1, 2). The tight association between the tag and the resin allows contaminants to be easily washed away under stringent conditions, yet the bound proteins can be gently eluted by competition with imidazole, or a slight reduction in pH. Moreover, because the interaction is independent of the tertiary structure of the tag, 6xHis labeled proteins can be purified even under the strongly denaturing conditions required to solubilize inclusion bodies.
Expression patterns of synaptic vesicle protein 2A in focal cortical dysplasia and TSC‐cortical tubers (2009)

The pattern of SV2A immunoreactivity with reduced neuropil expression and altered cellular and subcellular distribution suggests a possible contribution of SV2A to the epileptogenicity of these malformations of cortical development. Knowledge of the expression pattern of SV2A in epilepsy-associated pathologies may be valuable for the evaluation of the effectiveness of AEDs targeting this protein.
Synergistic brainstem interactions for morphine analgesia (1993)

Morphine is a potent analgesic when microinjected into the periaqueductal gray (PAG), the rostral ventral medulla (RVM) which contains the nuclei raphe magnus and reticularis gigantocellularis and the dorsolateral pons (DLP) which includes the locus coeruleus. Coadministration of low morphine doses which are inactive alone into combinations of these three regions elicits dramatic analgesic responses, implying the existence of synergy. The most effective combination is the PAG/RVM, whereas the PAG/DLP and RVM/DLP combinations are much less efficacious. In addition to fixed combinations, inclusion of a low morphine dose in one region shifts the analgesic dose-response curves in the others. The marked synergy between the PAG and the RVM is sensitive to naloxonazine, implying a role for mu 1 receptors. Thus, these studies indicate the presence of intrinsic brainstem mu 1 receptor systems with synergistic interactions which can be pharmacologically distinguished from the brainstem mu 2 receptors mediating supraspinal/spinal synergy.
Identification and Characterization of a Novel Human Microsomal Glutathione S-Transferase with Leukotriene C4 Synthase Activity and Significant Sequence Identity to 5-Lipoxygenase-activating Protein and Leukotriene C4 Synthase (1996)

5-Lipoxygenase-activating protein (FLAP) and leukotriene C4 (LTC4) synthase, two proteins involved in leukotriene biosynthesis, have been demonstrated to be 31% identical at the amino acid level. We have recently identified and characterized a novel member of the FLAP/LTC4 synthase gene family termed microsomal glutathione S-transferase II (microsomal GST-II). The open reading frame encodes a 16.6-kDa protein with a calculated pI of 10.4. Microsomal GST-II has 33% amino acid identity to FLAP, 44% amino acid identity to LTC4 synthase, and 11% amino acid identity to the previously characterized human microsomal GST (microsomal GST-I). Microsomal GST-II also has a similar hydrophobicity pattern to FLAP, LTC4 synthase, and microsomal GST-I. Fluorescent in situ hybridization mapped microsomal GST-II to chromosomal localization 4q28-31. Microsomal GST-II has a wide tissue distribution (at the mRNA level) and was specifically expressed in human liver, spleen, skeletal muscle, heart, adrenals, pancreas, prostate, testis, fetal liver, and fetal spleen. In contrast, microsomal GST-II mRNA expression was very low (when present) in lung, brain, placenta, and bone marrow. This differs from FLAP mRNA, which was detected in lung, various organs of the immune system, and peripheral blood leukocytes, and LTC4 synthase mRNA, which could not be detected in any tissues by Northern blot analysis. Microsomal GST-II and LTC4 synthase were expressed in a baculovirus insect cell system, and microsomes from Sf9 cells containing microsomal GST-II or LTC4 synthase were both found to catalyze the production of LTC4 from LTA4 and reduced glutathione. Microsomal GST-II also catalyzed the formation of another product, displaying a conjugated triene UV absorption spectra with a maximum at 283 nm, suggesting less catalytic stereospecificity compared with LTC4 synthase. Also, the apparent Km for LTA4 was higher for microsomal GST-II (41 microM) than LTC4 synthase (7 microM). In addition, unlike LTC4 synthase, microsomal GST-II was able to catalyze the conjugation of 1-chloro-2, 4-dinitrobenzene with reduced glutathione. Therefore, it is proposed that this novel membrane protein is a member of the microsomal glutathione S-transferase family, also including LTC4 synthase, with significant sequence identities to both LTC4 synthase and FLAP.
Prefix Tables: A Simple Mechanism for Locating Files in a Distributed System (1985)

Abstract : Prefix tables provide a mechanism for locating files in a system whose storage is distributed among many servers. The result is a single file system hierarchy visible uniformly and transparently to all clients. Each client of the filesystem maintains a local prefix table that identifies the server for a file based on the initial part of the file name. Prefix tables are built and modified using a simple broadcast protocol that is flexible enough to allow dynamic server reconfiguration and a simple form of replication.
Study of the vibrational modes of subsurface oxygen on Al(111) using diode laser infrared reflection–absorption spectroscopy (1988)

Infrared reflection–absorption spectroscopy, using polarization modulation and tunable diode laser excitation, has been applied to the study of the vibrational modes of subsurface oxygen on Al(111). The dependence of the spectra on O2 exposure and on annealing has been investigated at a resolution of ∼10 to 20 cm−1 (1.2–2.5 meV) and correlated with Auger data. The absorption band (∼780–920 cm−1) consists of overlapping bands at ∼835 and 862 cm−1 associated, respectively, with isolated sites and with clusters of such sites resembling Al2O3. The apparent shift of this band to higher energy with increasing coverage, observed at lower resolution (but higher sensitivity) in electron energy-loss spectroscopy, is found to result from the change in relative intensity of the two modes.