gebhart/patrepeval huggingface dataset:
Deadlock avoidance revisited (1982)

Several new algorithms that utilize wmt-for relations mduced by processes are developed for deadlock avoidance in operating systems. One of the algorithms allows more concurrency than Havender's scheme and Habermann's algorithm; nonetheless, it can still be computed in polynomial time. Further, the deadlock,prediction problem for a set of processes using locks is reduced to a new NP-complete problem, and the deadlock-avoidanceproblemfor processes with branches is shown to be PSPACE-complete, Finally, the relative power of various algorithms is compared.
Nuclease SP: a novel enzyme from spinach that incises damaged duplex DNA preferentially at sites of adenine (1988)

A novel endonuclease has been isolated from extracts of spinach leaves (Spinacia oleracea). The enzyme has been purified by a series of column chromatography steps and has a molecular size of approximately 43,000 daltons. The spinach endonuclease cleaved double stranded DNA damaged by ultraviolet light or cis-diamminedichloroplatinum (II) primarily at sites of adenine when end-labelled DNA fragments of defined sequence were employed as substrates. The nature of the structural distortion contained in damaged, duplex DNA appears to be an important determinant for endonuclease cleavage. DNA helical distortions produced by UV light-induced (6-4) pyrimidine-pyrimidone photoproducts, but not cyclobutane pyrimidine dimers are recognized by the enzyme. The DNA cleavage products generated by the enzyme contain 3'-hydroxyl and 5'-phosphoryl termini. Single stranded DNA and RNA are hydrolyzed by the spinach endonuclease. This enzyme, which we call nuclease SP, is similar in several respects to other single-strand-specific nucleases such as N. crassa and mung bean nucleases and may function in DNA repair and/or recombination events in spinach cells. Nuclease SP should be a useful tool for the analysis of (6-4) photoproducts occurring in duplex DNA.
Interactive multi-pass programmable shading (2000)

Programmable shading is a common technique for production animation, but interactive programmable shading is not yet widely available. We support interactive programmable shading on virtually any 3D graphics hardware using a scene graph library on top of OpenGL. We treat the OpenGL architecture as a general SIMD computer, and translate the high-level shading description into OpenGL rendering passes. While our system uses OpenGL, the techniques described are applicable to any retained mode interface with appropriate extension mechanisms and hardware API with provisions for recirculating data through the graphics pipeline.
Spray-deposited poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) top electrode for organic solar cells (2008)

Spray deposition is emerging as an attractive low-cost and high throughput method for organic solar cell (OSC) fabrication. In this letter, we demonstrate that a highly conductive formulation of poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) can be spray deposited to form the top electrode for an OSC. An inverted solar cell fabricated in this way with a blend of poly(3-hexylthiophene) and [6,6]-phenyl-C61 butyric acid methyl ester as the active layer achieved a power conversion efficiency of 2.0% under AM 1.5 100 mW/cm2 illumination.
Effect of Low-Power Laser Irradiation on Procollagen Synthesis in Human Fibroblasts (1996)

The conflicting views of the effect of low-power laser (LPL) irradiation on procollagen synthesis have existed at the present time, whereas many clinical studies have tested usefulness of LPL irradiation for the wound healing. To evaluate the effect of LPL irradiation on the procollagen synthesis of human fibroblasts in vitro, LPL irradiation on human fibroblast was carried out using two different culture medium, serum-starved medium and fetal calf serum (FCS)-contained medium. In addition, to investigate the mechanism of the LPL on the procollagen synthesis of human fibroblasts, dexamethasone and methylene blue contained medium were used for inhibition of procollagen product at the pretranslational level and cGMP-mediated processes, respectively. Enhanced effect of LPL was consistently observed in the serum-starved medium (50% increase by a 3 min irradiation), not in the FCS-contained medium. The LPL enhanced effect was not blocked by dexamethasone (3% inhibition) but methylene blue (40% inhibition). Our data suggest that some factors in FCS might interfere with the enhanced effect of LPL on procollagen synthesis and the LPL might act as a direct stimulator of the procollagen synthesis. It seems probable that the LPL enhanced effects might be occurred at the translational level or at the pretranslational level, which is not affected by dexamethasone and cGMP, might be involved in the LPL enhanced effect of the procollagen synthesis in fibroblast.
Structure and Differential Expression of two Maize Ferritin Genes in Response to Iron and Abscisic Acid (1995)

International audience
Neuronal Oscillations in Cortical Networks (2004)

Clocks tick, bridges and skyscrapers vibrate, neuronal networks oscillate. Are neuronal oscillations an inevitable by-product, similar to bridge vibrations, or an essential part of the brain's design? Mammalian cortical neurons form behavior-dependent oscillating networks of various sizes, which span five orders of magnitude in frequency. These oscillations are phylogenetically preserved, suggesting that they are functionally relevant. Recent findings indicate that network oscillations bias input selection, temporally link neurons into assemblies, and facilitate synaptic plasticity, mechanisms that cooperatively support temporal representation and long-term consolidation of information.
Peptides Derived from the Complementarity-determining Regions of Anti-Mac-1 Antibodies Block Intercellular Adhesion Molecule-1 Interaction with Mac-1 (1998)

Peptides or small molecules that can block the interaction of the integrin Mac-1 with its receptor, intercellular adhesion molecule-1 (ICAM-1), have not previously been developed. We studied this interaction by measuring the adherence of ICAM-1-expressing Chinese hamster ovary (CHO) cells to immobilized, purified Mac-1. Nucleotide sequence information was obtained for the complementarity determining regions (CDRs) of three antibodies (44aacb, MY904, and 118.1) shown to block Mac-1-mediated cell adherence. Peptides were synthesized based on the predicted amino acid sequences of the CDRs and tested for the ability to block cell adhesion to Mac-1. Peptides derived from CDR1 of 44aacb, CDR2 of 118.1, and CDRs 1 and 3 of MY904 heavy chains were found to possess blocking activity at 10-100 muM. This may indicate that one or two CDRs contribute disproportionately to the antibody binding affinity. The binding of ligands to Mac-1 has been shown to require a region of the alpha-chain known as the I- or A-domain. We have recombinantly produced Mac-1 I-domain, and show that it is also capable of supporting the adherence of ICAM-1-expressing CHO cells. The adherence of ICAM-1-CHO cells to the I-domain is inhibited by 44aacb and 118.1 and by the CDR peptides from 44aacb and 118.1. By using phage display of peptide libraries based on the 118.1 CDR peptide with five residues randomized, we were able to identify a novel peptide inhibitor of Mac-1 with substitutions at all five positions. These peptides provide lead structures for development of Mac-1 antagonists.
A new era: melanoma genetics and therapeutics (2010)

We have recently witnessed an explosion in our understanding of melanoma. Knowledge of the molecular basis of melanoma and the successes of targeted therapies have pushed melanoma care to the precipice of a new era. Identification of significant pathways and oncogenes has translated to the development of targeted therapies, some of which have produced major clinical responses. In this review, we provide an overview of selected key pathways and melanoma oncogenes as well as the targeted agents and therapeutic approaches whose successes suggest the promise of a new era in melanoma and cancer therapy. Despite these advances, the conversion of transient remissions to stable cures remains a vital challenge. Continued progress towards a better understanding about the complexity and redundancy responsible for melanoma progression may provide direction for anti-cancer drug development.
Branched-chain sugar nucleosides. II. 5',5'-Di-C-methyladenosine (1968)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTBranched-chain sugar nucleosides. II. 5',5'-Di-C-methyladenosineRuth F. Nutt and Edward WaltonCite this: J. Med. Chem. 1968, 11, 1, 151–153Publication Date (Print):January 1, 1968Publication History Published online1 May 2002Published inissue 1 January 1968https://pubs.acs.org/doi/10.1021/jm00307a036https://doi.org/10.1021/jm00307a036research-articleACS PublicationsRequest reuse permissionsArticle Views44Altmetric-Citations13LEARN 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
Computing Framework for Dynamic Integration of Reconfigurable Resources in a Cloud (2015)

Integrating FPGAs into clouds or data centers allows easy access to such reconfigurable resources and provides a promising opportunity to improve both performance and energy efficiency of such systems. Although currently the use of FPGAs as hardware accelerators and especially in clouds is mainly a topic of research, the integration of reconfigurable virtualized resources will become a task of growing importance in the future. We developed a cloud management and hypervisor system called RC3E providing FPGA resources as a service. This paper introduces a computing framework which extends our hypervisor and allows multiple (virtual) user designs on a single physical FPGA. The communication between host and FPGA is implemented by a communication API on the host and the integration of high-level synthesis (HLS) to accelerate applications. We demonstrate the usability of our framework by implementing a sample user design on an FPGA and measuring the performance with up to four simultaneous virtual user designs.
A Standardized Method Of Monitoring Water Quality In Sub-Surface Injection Systems (1967)

American Institute of Mining, Metallurgical and Petroleum Engineers, Inc. Abstract A method of programmed data acquisition is presented to help non-specialist engineers monitor water quality. Field tests, sample collection, laboratory procedures and methods of data presentation are standardized. Specifically, a series of profile plots are prepared from which engineers "read-out" pertinent features of plant performance and water quality. The direct "read-out" procedure, after nominal practice, is relatively simple. In many respects, it may be compared with qualitative log interpretation. A manual for using the Standard Data Package is also presented. Included are "rules of thumb" and other empirically derived "yardsticks" covering several important parameters. Introduction The increasing importance of salt water handling, either in disposal or waterflood operations, has demanded development of better methods. A full understanding of basic parameters is fundamental to creating the best plant design and to determining the most effective operating practices. Toward this end various methods have been proposed to define "water quality", diagnose problems, predict potential problems and ultimately, to use these technical method to maximize operating efficiency. It is a major purpose of this paper to present a standardized method of programmed data acquisition that lends itself to direct measurement of water quality by non-specialist engineers. The heart of the program is the collection and preparation of a "Standard Data Package". While involving a comprehensive technical investigation, the interpretation process is simplified so that unusual technical skills are not often required. Specifically, a standardized format is proposed whereby engineers can inspect a series of charts and "read-out" pertinent features of an injection system's performance. While the "read-out" process appears quite simple, the individual is in effect solving partial chemical material balance calculations that logically lead to sound engineering conclusions. The standardized plan is readily adaptable to regular surveillance of water systems. After an initial comprehensive study, data acquisition can be programmed in advance so that attention is focused on an operation at regular intervals. Comparison of standard charts of succeeding studies is done by inspection. Likewise, with all procedures standardized, results between studies of different projects can be directly compared. BASIC CONCEPT The proposed plan of water quality control can be illustrated by noting the physical similarity of water injection systems and chemical manufacturing plants. Both convert raw material to finished products. Either may be simple or highly complex. Systematic collection of basic in-put and out-put data is recognized as a requirement for efficient operation of a manufacturing plant.
Modeling and segmentation of intra-cochlear anatomy in conventional CT (2010)

Cochlear implant surgery is a procedure performed to treat profound hearing loss. Since the cochlea is not visible in surgery, the physician uses anatomical landmarks to estimate the pose of the cochlea. Research has indicated that implanting the electrode in a particular cavity of the cochlea, the scala tympani, results in better hearing restoration. The success of the scala tympani implantation is largely dependent on the point of entry and angle of electrode insertion. Errors can occur due to the imprecise nature of landmark-based, manual navigation as well as inter-patient variations between scala tympani and the anatomical landmarks. In this work, we use point distribution models of the intra-cochlear anatomy to study the inter-patient variations between the cochlea and the typical anatomic landmarks, and we implement an active shape model technique to automatically localize intra-cochlear anatomy in conventional CT images, where intra-cochlear structures are not visible. This fully automatic segmentation could aid the surgeon to choose the point of entry and angle of approach to maximize the likelihood of scala tympani insertion, resulting in more substantial hearing restoration.
A microRNA array reveals extensive regulation of microRNAs during brain development (2003)

Several hundred microRNAs (miRNAs) have recently been cloned from a wide range of organisms across phylogeny. Despite the high degree of conservation of miRNAs, their functions in general, and in mammals particularly, are just beginning to be defined. Here we show that an oligonucleotide DNA array can be successfully used for the simultaneous analysis of miRNA expression profiles from tissues or cells. From a subset of miRNAs expressed in the brain we designed an oligonucleotide array spotted with probes specific for 44 mature miRNAs. These arrays demonstrated precise regulation of miRNA expression at mammalian brain developmental epochs. About 20% of the probed miRNAs changed significantly in their expression during normal brain development, and two of them, miR-9 and miR-131, were dysregulated in presenilin-1 null mice exhibiting severe brain developmental defects. Transcripts with regulated expression patterns on the arrays were validated by Northern blots. Additionally, a bioinformatic analysis of developmentally regulated miRNAs suggested potential mRNA targets. The arrays also revealed miRNAs distributed to translating polyribosomes in primary neurons where they are likely to modulate translation. Therefore, oligonucleotide arrays provide a new tool for studying miRNA expression in a variety of biological and pathobiological settings. Creating clusters of coexpressed miRNAs will contribute to understanding their regulation, functions, and discovery of mRNA targets.
Treatment of systemic fungal infections with liposomal amphotericin B. (1989)

Forty-six patients with systemic fungal infections were treated with liposomal amphotericin B. Twenty-one patients had disseminated candidiasis, 19 had aspergillosis, and the rest had a variety of other fungal infections. Forty patients failed to respond to conventional amphotericin B therapy, and 6 patients were given liposomal amphotericin B because conventional amphotericin B caused severe side effects. Twenty-four patients had a complete response, and 22 patients failed to respond. No short- or long-term toxic reactions were observed. The acute side effects such as fever, chills, and potassium loss were infrequent and milder than those commonly observed with conventional amphotericin B. No chronic renal, hematologic, or central nervous system side effects were observed. Liposomal amphotericin B therapy was effective and less toxic than conventional amphotericin B therapy.
Renal transport of endogenous amino acids. I. Comparison between immature and adult rats. (1992)

In the late neonatal period of male Wistar rats (10 days old) concentrations in plasma were higher for 5 of 24 amino acids compared to adult animals (2 months old): beta-alanine, tyrosine, glycine, histidine, and the dipeptide anserine. The plasma concentrations of tryptophan, valine and leucine were lower in young than in adult rats. The renal clearances of amino acids were lower in young rats, both in relation to 1 g b.w. and related to 1 g kidney weight. In the latter case the differences became more distinct because the relative kidney weight was higher in young than in adult animals (1.17 +/- 0.07 vs. 0.82 +/- 0.03 g/100 g b.w.) and significant age differences in renal water content did not exist. The apparently more effective tubular reabsorption capacity in young rats can be explained as follows: Because of the significantly lower GFR in 10-day-old rats compared with adults (0.46 +/- 0.03 vs. 1.10 +/- 0.09 ml/min/1 g kidney), the glomerularly filtered load of amino acids is generally lower in young rats (exceptions: tyrosine, glycine). Therefore, the amino acid transporting carrier systems are able to reabsorb the absolutely lower amounts of amino acids from the ultrafiltrate in immature animals. This hypothesis is supported if one relates the renal amino acid clearance to the clearance of inulin. In this way it is possible to show that there are absolutely no differences between both age groups indicating mature transport systems for endogenous amino acids as early as in 10-day-old rats.(ABSTRACT TRUNCATED AT 250 WORDS)
Stubby: A Transformation-based Optimizer for MapReduce Workflows (2012)

There is a growing trend of performing analysis on large datasets using workflows composed of MapReduce jobs connected through producer-consumer relationships based on data. This trend has spurred the development of a number of interfaces--ranging from program-based to query-based interfaces--for generating MapReduce workflows. Studies have shown that the gap in performance can be quite large between optimized and unoptimized workflows. However, automatic cost-based optimization of MapReduce workflows remains a challenge due to the multitude of interfaces, large size of the execution plan space, and the frequent unavailability of all types of information needed for optimization. We introduce a comprehensive plan space for MapReduce workflows generated by popular workflow generators. We then propose Stubby, a cost-based optimizer that searches selectively through the subspace of the full plan space that can be enumerated correctly and costed based on the information available in any given setting. Stubby enumerates the plan space based on plan-to-plan transformations and an efficient search algorithm. Stubby is designed to be extensible to new interfaces and new types of optimizations, which is a desirable feature given how rapidly MapReduce systems are evolving. Stubby's efficiency and effectiveness have been evaluated using representative workflows from many domains.
Identification by a random sequencing strategy of the fowlpoxvirus DNA polymerase gene, its nucleotide sequence and comparison with other viral DNA polymerases (1987)

The nucleotide sequence of the DNA polymerase gene of the avipoxvirus fowlpox is presented and the predicted amino acid sequence compared with that of the orthopoxvirus vaccinia. The results have brought to light an error in the vaccinia sequence which has resulted in the ommission of 44 amino acids from the carboxy-terminus of the vaccinia DNA polymerase. There has been extensive conservation of amino acids throughout the enzymes, and regions identified as being present in DNA polymerases from a wide range of viruses are again present here. The method used to identify the fowlpoxvirus gene could have applications towards defining genomic organisations in other viral systems.
Association of PD-1, PD-1 Ligands, and Other Features of the Tumor Immune Microenvironment with Response to Anti–PD-1 Therapy (2014)

Tumor PD-L1 expression reflects an immune-active microenvironment and, while associated other immunosuppressive molecules, including PD-1 and PD-L2, is the single factor most closely correlated with response to anti-PD-1 blockade. Clin Cancer Res; 20(19); 5064-74. ©2014 AACR.
Preparation of Larnthanum β‐Alumina with High Surface Area by Coprecipitation (1987)

Mixtures of La 2 O 3 and Al 2 O 3 with various La contents were prepared by co‐precipitation from La(NO 3 ) 3 and Al(NO 3 ) 3 solutions and calcined at 800° to 1400°C. The addition of small amounts of La 2 O 3 (2 to 10 mol%) to Al 2 O 3 gives rise to the formation of lanthanum β‐alumina (La 2 O 3 ·11–14Al 2 O 3 ) upon heating to above 1000°C and retards the transformation of γ‐Al 2 O 3 to α‐Al 2 O 3 and associated sintering.
Identification of tubulins as substrates of serine protease HtrA1 by mixture‐based oriented peptide library screening (2009)

Serine protease HtrA1 belongs to a family of chymotrypsin-like proteases that were first identified in bacteria and later in mammalian systems. These proteases were identified as components of protein quality control in prokaryotic systems and as regulators of diverse signaling pathways in mammalian systems. In particular, HtrA1 is implicated in trophoblast cell migration and invasion, tumor progression, chemotherapy-induced cytotoxicity, osteoarthritis, age-related macular degeneration, and pathogenesis of Alzheimer's disease. However, systematic analysis of its potential substrates in biological system is still lacking. Therefore, we performed a mixture-based oriented peptide library screening to identify putative substrates of HtrA1. We identified [AEGR]-[LAGR]-[IAMLR]-[TVIAL] as consensus residues for P1 to P4 sites. We identified several putative substrates of HtrA1 involved in the pathogenesis of various diseases. In this study, we report on the identification of tubulins as potential substrates of HtrA1, and validated tubulins as in vitro and intracellular substrates of HtrA1. These results provide initial insights into substrate identification and functional characterization of HtrA1 in pathogenesis of various diseases.