gebhart/patrepeval huggingface dataset:
Machine learning based online performance prediction for runtime parallelization and task scheduling (2009)

With the emerging many-core paradigm, parallel programming must extend beyond its traditional realm of scientific applications. Converting existing sequential applications as well as developing next-generation software requires assistance from hardware, compilers and runtime systems to exploit parallelism transparently within applications. These systems must decompose applications into tasks that can be executed in parallel and then schedule those tasks to minimize load imbalance. However, many systems lack a priori knowledge about the execution time of all tasks to perform effective load balancing with low scheduling overhead. In this paper, we approach this fundamental problem using machine learning techniques first to generate performance models for all tasks and then applying those models to perform automatic performance prediction across program executions. We also extend an existing scheduling algorithm to use generated task cost estimates for online task partitioning and scheduling. We implement the above techniques in the pR framework, which transparently parallelizes scripts in the popular R language, and evaluate their performance and overhead with both a real-world application and a large number of synthetic representative test scripts. Our experimental results show that our proposed approach significantly improves task partitioning and scheduling, with maximum improvements of 21.8%, 40.3% and 22.1% and average improvements of 15.9%, 16.9% and 4.2% for LMM (a real R application) and synthetic test cases with independent and dependent tasks, respectively.
MicroRNA function in animal development (2005)

MicroRNAs (miRNAs) are small non-coding RNA molecules that post-transcriptionally regulate gene expression by base-pairing to mRNAs. Hundreds of miRNAs have been identified in various multicellular organisms and many miRNAs are evolutionarily conserved. Although the biological functions of most miRNAs are unknown, miRNAs are predicted to regulate up to 30% of the genes within the human genome. Gradually, we are beginning to understand the functions of individual miRNAs and the general function of miRNA action. Here, we review the recent advances in miRNA biology in animals. Particularly, we focus on the roles of miRNAs in vertebrate development and disease.
A variant human IgG1-Fc mediates improved ADCC (2011)

Ribosome display was applied to the Fc region of human immunoglobulin G (IgG1) to select for improved binding to human FcγRIIIa, the receptor expressed on human natural killer cells that mediates antibody-dependent cellular cytotoxicity (ADCC). A library of human Fcγ1 variants was generated using error-prone polymerase chain reaction, and subjected to multiple rounds of ribosome display selection against progressively decreasing concentrations of soluble human FcγRIIIa, to enrich for improved binders. Radioimmunoassay and alphascreen analyses of the aglycosylated IgG-Fc output revealed variants with improved binding to FcγRIIIa relative to wild-type IgG-Fc. Subsequent expression in human (HEK-EBNA) cells generated glycosylated IgGs with modified activity in ADCC assays. One particular variant, 125_B01 triggered enhanced ADCC (EC(50) up to four-fold reduced with increased maximal lysis) relative to wild-type antibody, having more equal levels of ADCC for each allotype (V158/F158) of FcγRIIIa. Deconvolution of individual replacements within the variant showed that improved function arose from the Phe243Leu replacement within the CH2 domain, rather than the CH3 domain replacements Thr393Ala or His433Pro. Surprisingly, the oligosaccharide profiles of 125_B01 indicated more oligosaccharide chains lacking fucose, or with bisecting N-acetylglucosamine relative to wild-type IgG1, which correlates with improved function and the replacement Phe243Leu that is a carbohydrate contact residue within the C(H)2 domain.
RORγT, a thymus-specific isoform of the orphan nuclear receptor RORγ / TOR, is up-regulated by signaling through the pre-T cell receptor and binds to the TEA promoter (1999)

TEA (T early alpha) is a genetic element located upstream of the TCR-Jalpha cluster. Thymocytes from mice carrying a targeted deletion of TEA do not rearrange their TCRalpha locus on a window spanning the first nine Jalpha segments. This led us to the hypothesis of TEA having a "rearrangement focusing" activity on the 5' side of the TCR-Jalpha region. We analyzed DNAseI and "phylogenetic" footprints within the TEA promoter in an attempt to identify trans-acting factors that could account for its regulatory function on DNA accessibility. One of these footprints corresponded to a putative DNA-binding site for an orphan nuclear receptor of the ROR / RZR family. The RORgammaT cDNA clone was isolated from a thymus library using a probe corresponding to the DNA-binding domain of RORgamma / TOR. RORgammaT is a thymus-specific isoform of RORgamma, expressed almost exclusively in immature double-positive thymocytes. RORgammaT binds, to the TEA promoter in vitro. Lastly, the expression of RORgammaT is stimulated in two situations that mimic activation through the pre-TCR and in which the thymocytes have their TCR-alpha locus in an "open", yet unrearranged DNA configuration. We propose that the expression of RORgammaT may be part of the pre-TCR activation cascade leading to the maturation of alpha / beta T cells and may participate in the regulation of DNA accessibility in the TCR-Jalpha locus.
An automatic sign recognition and translation system (2001)

A sign is something that suggests the presence of a fact, condition, or quality. Signs are everywhere in our lives. They make our lives easier when we are familiar with them. But sometimes they pose problems. For example, a tourist might not be able to understand signs in a foreign country. This paper discusses problems of automatic sign recognition and translation. We present a system capable of capturing images, detecting and recognizing signs, and translating them into a target language. We describe methods for automatic sign extraction and translation. We use a user-centered approach in system development. The approach takes advantage of human intelligence if needed and leverage human capabilities. We are currently working on Chinese sign translation. We have developed a prototype system that can recognize Chinese sign input from a video camera that is a common gadget for a tourist, and translate the signs into English or voice stream. The sign translation, in conjunction with spoken language translation, can help international tourists to overcome language barriers. The technology can also help a visually handicapped person to increase environmental awareness.
Peripheral Blood Progenitor Cell Mobilization Using Stem Cell Factor in Combination With Filgrastim in Breast Cancer Patients (1997)

Abstract The safety and optimal dose and schedule of stem cell factor (SCF ) administered in combination with filgrastim for the mobilization of peripheral blood progenitor cells (PBPCs) was determined in 215 patients with high-risk breast cancer. Patients received either filgrastim alone (10 μg/kg/d for 7 days) or the combination of 10 μg/kg/d filgrastim and 5 to 30 μg/kg/d SCF for either 7, 10, or 13 days. SCF patients were premedicated with antiallergy prophylaxis. Leukapheresis was performed on the final 3 days of cytokine therapy and, after high-dose chemotherapy and infusion of PBPCs, patients received 10 μg/kg/d filgrastim until absolute neutrophil count recovery. The median number of CD34+ cells collected was greater for patients receiving the combination of filgrastim and SCF, at doses greater than 10 μg/kg/d, than for those receiving filgrastim alone (7.7 v 3.2 × 106/kg, P &lt; .05). There were significantly (P &lt; .05) more CD34+ cells harvested for the 20 μg/kg/d SCF (median, 7.9 × 106/kg) and 25 μg/kg/d SCF (median, 13.6 × 106/kg) 7-day combination groups than for the filgrastim alone patients (median, 3.2 × 106/kg). The duration of administration of SCF and filgrastim (7, 10, or 13 days) did not significantly affect CD34+ cell yield. Treatment groups mobilized with filgrastim alone or with the cytokine combination had similar hematopoietic engraftment and overall survival after PBPC infusion. In conclusion, the results of this study indicate that SCF therapy enhances CD34+ cell yield and is associated with manageable levels of toxicity when combined with filgrastim for PBPC mobilization. The combination of 20 μg/kg/d SCF and 10 μg/kg/d filgrastim with daily apheresis beginning on day 5 was selected as the optimal dose and schedule for the mobilization of PBPCs.
The NG2 chondoitin sulfate proteoglycan: role in malignant progression of human brain tumours (1999)

The expression and function of NG2, a transmembrane chondroitin sulfate proteoglycan was studied in human gliomas of various histological types in culture using immunocytochemistry and flow cytometry. NG2 was differentially expressed in the neoplasms, with higher expression in high compared to low-grade gliomas. In acutely isolated cells from human biopsies, NG2 +ve and NG2 -ve populations were morphologically distinct from each other, and NG2 +ve cells were more proliferative than NG2 -ve cells. The mitogens platelet derived growth factor (PDGF-AA) and basic fibroblast growth factor (bFGF) added in combination to serum-free medium (SFM) upregulated NG2 expression on glioblastoma multiforme cells in culture but had little effect on NG2 expression on the anaplastic astrocytoma cells. Furthermore, NG2 was colocalised with the platelet derived growth factor alpha receptor (PDGFalphaR) and antibody blockade of the PDGF-alphaR ablated NG2 expression on the glioblastoma multiforme cells, suggesting that increased NG2 expression in the presence of PDGF-AA is mediated via the PDGF-alphaR. Assays of migration and invasion indicate that NG2 +ve glioma cells migrated more efficiently on collagen IV and that NG2 -ve cells were more invasive than their NG2 +ve counterparts. The results indicate that NG2 may be, respectively, positively and negatively related to the proliferative and invasive capacity of glioma cells. Thus, expression of the NG2 proteoglycan may have major implications for malignant progression in glial neoplasms and may prove a useful target for future therapeutic regimens.
Heme-Dependent Activation of Guanylate Cyclase by Nitric Oxide: A Novel Signal Transduction Mechanism (1991)

The interaction between nitric oxide (NO) synthesized in one cell and cytosolic guanylate-cyclase-bound heme located in adjacent target cells to generate the NO-heme adduct of guanylate cyclase represents a novel and widespread signal transduction mechanism that links extracellular stimuli to the biosynthesis of cyclic GMP in target cells. A variety of chemical factors interact with selective extracellular receptors and trigger the biosynthesis of NO from L-arginine. The unique chemistry of NO endows this molecule with the capacity to diffuse rapidly into nearby cells and stimulate cyclic GMP formation. Cyclic GMP acts as a messenger in each cell type to trigger different but complementary cellular responses within a localized environment. This transcellular signaling is a form of rapid intercellular communication allowing the simultaneous local initiation of increased blood flow, inhibition of platelet-induced thrombosis and other cellular functions.
tert-Butyl Cation Formation in the Hydrolysis of 2-Methyl-2-propanesulfonyl Chloride, the Simplest Tertiary Alkanesulfonyl Chloride (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTtert-Butyl Cation Formation in the Hydrolysis of 2-Methyl-2-propanesulfonyl Chloride, the Simplest Tertiary Alkanesulfonyl ChlorideJames F. King, Joe Y. L. Lam, and Vinod DaveCite this: J. Org. Chem. 1995, 60, 9, 2831–2834Publication Date (Print):May 1, 1995Publication History Published online1 May 2002Published inissue 1 May 1995https://pubs.acs.org/doi/10.1021/jo00114a036https://doi.org/10.1021/jo00114a036research-articleACS PublicationsRequest reuse permissionsArticle Views749Altmetric-Citations21LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Silver Nanowire Networks as Flexible, Transparent, Conducting Films: Extremely High DC to Optical Conductivity Ratios (2009)

We have used aqueous dispersions of silver nanowires to prepare thin, flexible, transparent, conducting films. The nanowires are of length and diameter close to 6.5 μm and 85 nm, respectively. At low thickness, the films consist of networks but appear to become bulk-like for mean film thicknesses above ∼160 nm. These films can be very transparent with optical transmittance reaching as high as 92% for low thickness. The transmittance (550 nm) decreases with increasing thickness, consistent with an optical conductivity of 6472 S/m. The films are also very uniform; the transmittance varies spatially by typically <2%. The sheet resistance decreases with increasing thickness, falling below 1 Ω/◻ for thicknesses above 300 nm. The DC conductivity increases from 2 × 10(5) S/m for very thin films before saturating at 5 × 10(6) S/m for thicker films. Similarly, the ratio of DC to optical conductivity increases with increasing thickness from 25 for the thinnest films, saturating at ∼500 for thicknesses above ∼160 nm. We believe this is the highest conductivity ratio ever observed for nanostructured films and is matched only by doped metal oxide films. These nanowire films are electromechanically very robust, with all but the thinnest films showing no change in sheet resistance when flexed over >1000 cycles. Such results make these films ideal as replacements for indium tin oxide as transparent electrodes. We have prepared films with optical transmittance and sheet resistance of 85% and 13 Ω/◻, respectively. This is very close to that displayed by commercially available indium tin oxide.
LTE-Advanced - Evolving LTE towards IMT-Advanced (2008)

This paper provides a high-level overview of some technology components currently considered for the evolution of LTE including complete fulfillment of the IMT-advanced requirements. These technology components include extended spectrum flexibility, multi-antenna solutions, coordinated multipoint transmission/reception, and the use of advanced repeaters/relaying. A simple performance assessment is also included, indicating potential for significantly increased performance.
The Ets family of proteins: weak modulators of gene expression in quest for transcriptional partners. (1994)

Members of the Ets family of transcriptional regulators play pivotal roles in physiological processes, such as embryonic development or immune response. The Ets family proteins possess unique regulatory features because they bind DNA as monomers and their respective activities rely more on their ability to interact with other transcription factors than on their specific binding to a cognate DNA sequence. This review focuses on such interactions and also explores dysregulated expression of the Ets proteins in human cancers.
Directed evolution of an ultrastable carbonic anhydrase for highly efficient carbon capture from flue gas (2014)

Carbonic anhydrase (CA) is one of nature's fastest enzymes and can dramatically improve the economics of carbon capture under demanding environments such as coal-fired power plants. The use of CA to accelerate carbon capture is limited by the enzyme's sensitivity to the harsh process conditions. Using directed evolution, the properties of a β-class CA from Desulfovibrio vulgaris were dramatically enhanced. Iterative rounds of library design, library generation, and high-throughput screening identified highly stable CA variants that tolerate temperatures of up to 107 °C in the presence of 4.2 M alkaline amine solvent at pH >10.0. This increase in thermostability and alkali tolerance translates to a 4,000,000-fold improvement over the natural enzyme. At pilot scale, the evolved catalyst enhanced the rate of CO2 absorption 25-fold compared with the noncatalyzed reaction.
Chimeric restriction endonuclease. (1994)

Fok I restriction endonuclease recognizes the nonpalindromic pentadeoxyribonucleotide 5'-GGATG-3'.5'-CATCC-3' in duplex DNA and cleaves 9 and 13 nt away from the recognition site. Recently, we reported the presence of two distinct and separable domains within this enzyme: one for the sequence-specific recognition of DNA (the DNA-binding domain) and the other for the endonuclease activity (the cleavage domain). Here, we report the construction of a chimeric restriction endonuclease by linking the Drosophila Ultrabithorax homeodomain to the cleavage domain (FN) of Fok I restriction endonuclease. The hybrid enzyme, Ubx-FN, was purified, and its cleavage properties were characterized. The hybrid enzyme shows the same DNA sequence-binding preference as that of Ubx; as expected, it cleaves the DNA away from the recognition site. On the 5'-TTAATGGTT-3' strand the hybrid enzyme cleaves 3 nt away from the recognition site, whereas it cuts the complementary 5'-AACCATTAA-3' strand 8, 9, or 10 nt away from the binding site. Similarly engineered hybrid enzymes could be valuable tools in physical mapping and sequencing of large eukaryotic genomes.
Early Steps in Proanthocyanidin Biosynthesis in the Model Legume Medicago truncatula (2007)

Oligomeric proanthocyanidins (PAs) composed primarily of epicatechin units accumulate in the seed coats of the model legume Medicago truncatula, reaching maximal levels at around 20 d after pollination. Genes encoding the single Medicago anthocyanidin synthase (ANS; EC 1.14.11.19) and leucoanthocyanidin reductase (LAR; EC 1.17.1.3) were cloned and the corresponding enzymes functionally identified. Recombinant MtANS converted leucocyanidin to cyanidin, and, more efficiently, dihydroquercetin to the flavonol quercetin. Levels of transcripts encoding dihydroflavonol reductase, ANS, and anthocyanidin reductase (ANR), the enzyme responsible for conversion of anthocyanidin to (-)-epicatechin, paralleled the accumulation of PAs in developing seeds, whereas LAR transcripts appeared to be more transiently expressed. LAR, ANS, and ANR proteins were localized to the cytosol in transfected tobacco (Nicotiana tabacum) leaves. Antisense down-regulation of ANS in M. truncatula resulted in reduced anthocyanin and PA levels, but had no impact on flavonol levels. Transgenic tobacco plants constitutively overexpressing MtLAR showed reduced anthocyanin content, but no catechin or increased levels of PAs were detected either in leaves or in flowers. Our results confirm previously ascribed in vivo functions for ANS and ANR. However, the apparent lack of catechin in M. truncatula PAs, the poor correlation between LAR expression and PA accumulation, and the lack of production of catechin monomers or oligomers in transgenic plants overexpressing MtLAR question the role of MtLAR in PA biosynthesis in Medicago.
Application of Alternating-Type Phase Shift Mask to Polysilicon Level for Random Logic Circuits (1994)

Of all phase shift mask techniques, the alternating type is both the best for improving resolution and the most difficult to use. The problems in its use include complicated design modifications, unwanted phase-transition printing and very challenging mask fabrication. This paper is the first report of a solution using an automatic shifter arrangement and a three-step phase-transition technique on etched-quartz alternating-type phase shift mask (PSM). The lithographic results as well as the electrical results presented demonstrate the feasibility of the technique for application to complex circuits and show the capabilities of this kind of mask in printing smaller dimension lines.
Computer aided diagnosis system for lung cancer based on helical CT images (1996)

In this paper we describe a computer assisted automatic diagnosis system for lung cancer that detects tumor candidates at an early stage from helical computerised tomographic (CT) images. This automation of the process reduces the time complexity and increases the diagnosis confidence. Our algorithm consists of an analysis part and a diagnosis part. In the analysis part, we extract the lung and pulmonary blood vessel regions and analyze the features of these regions using image processing techniques. In the diagnosis part, we define diagnosis rules based on these features, and detect tumor candidates using these rules. We have applied our algorithm to 450 patient's data for mass screening. The results show that our algorithm detected lung cancer candidates successfully.
Ex Vivo Activated Human Macrophages Improve Healing, Remodeling, and Function of the Infarcted Heart (2006)

Early after myocardial infarction, injection of AMS accelerates vascularization, tissue repair, and improves cardiac remodeling and function. Our work suggests a novel clinically relevant option to promote the repair of ischemic tissue.
Milestones in molecular dynamics simulations of single-walled carbon nanotube formation: A brief critical review (2009)

We present a brief review of the most important efforts aimed at simulating single-walled carbon nanotube (SWNT) nucleation and growth processes using molecular dynamics (MD) techniques reported in the literature. MD simulations allow the spatio-temporal movement of atoms during nonequilibrium growth to be followed. Thus, it is hoped that a successful MD simulation of the entire SWNT formation process will assist in the design of chirality-specific SWNT synthesis techniques. We give special consideration to the role of the metal catalyst particles assumed in standard theories of SWNT formation, and describe the actual metal behavior observed in the reported MD simulations, including our own recent quantum chemical MD simulations. It is concluded that the use of a quantum potential is essential for a qualitatively correct description of the catalytic behavior of the metal cluster, and that carbide formation does not seem to be a necessary requirement for nucleation and growth of SWNTs according to our most recent quantum chemical MD simulations.