gebhart/patrepeval huggingface dataset:
Locality-Aware Reduce Task Scheduling for MapReduce (2011)

MapReduce offers a promising programming model for big data processing. Inspired by functional languages, MapReduce allows programmers to write functional-style code which gets automatically divided into multiple map and/or reduce tasks and scheduled over distributed data across multiple machines. Hadoop, an open source implementation of MapReduce, schedules map tasks in the vicinity of their inputs in order to diminish network traffic and improve performance. However, Hadoop schedules reduce tasks at requesting nodes without considering data locality leading to performance degradation. This paper describes Locality-Aware Reduce Task Scheduler (LARTS), a practical strategy for improving MapReduce performance. LARTS attempts to collocate reduce tasks with the maximum required data computed after recognizing input data network locations and sizes. LARTS adopts a cooperative paradigm seeking a good data locality while circumventing scheduling delay, scheduling skew, poor system utilization, and low degree of parallelism. We implemented LARTS in Hadoop-0.20.2. Evaluation results show that LARTS outperforms the native Hadoop reduce task scheduler by an average of 7%, and up to 11.6%.
Packet classification on multiple fields (1999)

Routers classify packets to determine which flow they belong to, and to decide what service they should receive. Classification may, in general, be based on an arbitrary number of fields in the packet header. Performing classification quickly on an arbitrary number of fields is known to be difficult, and has poor worst-case performance. In this paper, we consider a number of classifiers taken from real networks. We find that the classifiers contain considerable structure and redundancy that can be exploited by the classification algorithm. In particular, we find that a simple multi-stage classification algorithm, called RFC (recursive flow classification), can classify 30 million packets per second in pipelined hardware, or one million packets per second in software.
Characterization of the Prolyl Dipeptidyl Peptidase Gene ( dppIV ) from the Koji Mold Aspergillus oryzae (1998)

The koji mold Aspergillus oryzae secretes a prolyl dipeptidyl peptidase (DPPIV) when the fungus is cultivated in a medium containing wheat gluten as the sole nitrogen and carbon source (MMWG). We cloned and sequenced the DPPIV gene from an A. oryzae library by using the A. fumigatus dppIV gene as a probe. Reverse transcriptase PCR experiments showed that the A. oryzae dppIV gene consists of two exons, the first of which is only 6 bp long. The gene encodes an 87.2-kDa polypeptide chain which is secreted into the medium as a 95-kDa glycoprotein. Introduction of this gene into A. oryzae leads to overexpression of prolyl dipeptidyl peptidase activity, while disruption of the gene abolishes all prolyl dipeptidyl peptidase activity in MMWG. The dppIV null mutants did not exhibit any change in phenotype other than the absence of prolyl dipeptidyl peptidase activity, suggesting that this activity is not essential. This loss of activity diminished the number of dipeptides and increased the number of larger peptides present in the MMWG culture broth. These effects were reversed by the addition of purified, recombinant DPPIV from the methylotrophic yeast expression vector Pichia pastoris. Our results suggest that the DPPIV enzyme may be of importance in industrial hydrolysis of what gluten-based substrates, which are rich in Pro residues.
Determination of tryptophan in feeds and feed ingredients by high-performance liquid chromatography (1981)

A high-performance liquid chromatographic procedure for the determination of tryptophan has been developed using the native fluorescence of the molecule as a means of detection. Proteins were hydrolysed with 6 M sodium hydroxide solution in the presence of maltodextrin, which has been demonstrated to prevent tryptophan degradation. Comparison of results from the proposed method with those from an existing procedure developed by Slump and Schreuder showed the two methods to be statistically equivalent. A wide range of feeds and feed ingredients were analysed, and the measured tryptophan levels were within the range expected from published data. The proposed method is rapid, sensitive and specific, and is recommended for routine laboratory use.
An Octadentate Luminescent Eu(III) 1,2-HOPO Chelate with Potent Aqueous Stability (2007)

The synthesis, characterization, and photophysical properties of two novel ligands, 5LINMe-1,2-HOPO (1) and H(2,2)-1,2-HOPO (2), which utilize the 1,2-HOPO chelate as a sensitizer for Eu(III) are reported. In addition, the former ligand was structurally characterized as the Eu(III) complex by X-ray crystallography. The [Eu(1)2]- complex of the tetradentate ligand (1) is stable in aqueous solution, to a limiting concentration of ca. 7x10(-9) M, and retains the superior photophysical performance noted for the 1,2-HOPO sensitizer. By contrast, the octadentate ligand (2) has vastly improved stability as the [Eu(2)]- complex upon further dilution, to a limiting concentration of ca. 5x10(-17) M, which is beyond the minimum detectable concentration of most fluorimeters. The presence of a single coordinated water molecule for the latter complex reduces the overall metal-centered luminescence.
Etching behavior of CdTe in aqueous H2O2-HI-C6H8O7 solutions (2010)

This paper examines the dissolution behavior of the (111)A, (111)B, (110), and (100) surfaces of CdTe single crystals in aqueous H2O2-HI-C6H8O7 (citric acid) solutions. We have determined the dissolution rate of the crystals as a function of temperature and solution concentration, located the composition regions of polishing and selective etchants, and studied the microstructure and roughness of surfaces polished with optimized etchants. The etching behavior of CdTe is shown to depend on its crystallographic orientation.
Cytokine inhibition of the hepatitis B virus core promoter (1996)

Hepatitis B virus (HBV) DNA contains consensus elements for transactivating proteins whose binding activity in other systems is regulated by inflammatory cytokines. Because HBV replicates within an environment of provoked inflammation, we speculated that the HBV core/pregenomic promoter may be regulated by cytokines produced in response to infection. To evaluate this hypothesis, the HBV core/pregenomic (C/P) promoter and associated cis-acting elements were placed upstream of a luciferase-encoding plasmid. This reporter construct was transfected into cytokine-sensitive hepatoma cells permissive for HBV replication, which were exposed to stimulated mononuclear cell-conditioned medium or human recombinant cytokines. Conditioned medium reduced luciferase expression by 80%. Tumor necrosis factor alpha (TNF-alpha), interferon gamma (IFN-gamma), and interferon alfa (IFN-alpha) each reduced luciferase activity by 40%. Combinations of TNF-alpha and interferons mimicked the extent of conditioned medium inhibition. Non-specific effects from diminished cellular viability or growth were not responsible for decreased luciferase activity. Retention of HBV DNA 330 basepairs upstream of the C/P transcription start site was required to maintain the TNF-alpha effect. A 60% reduction in HBV replicative forms within intracellular core particles was demonstrated with TNF-alpha treatment of Hep G2 cells stably transfected with HBV DNA. The inhibitory action of these cytokines implicates a noncytolytic mechanism by which antigen-nonspecific immune responses in part regulate HBV replication in infected hepatocytes. This function may be beneficial in accelerating viral clearance, but in alternative circumstances could contribute to viral persistence by attenuating immunogen recognition.
EXPLORATORY SIMULATOR STUDY ON THE USE OF ACTIVE CONTROL DEVICES IN CAR DRIVING (1992)

The present study deals with the question whether at the handling Level of car driving active control devices (i.e. active steering wheel, active gas-pedal) may serve as a part of an integrated, intelligent codriver system, that may help the driver to behave safety and efficiently in tomorrow's traffic. The experiment, which was carried out in the TNO driving simulator was divided into three blocks: a lateral control task (Lane-change manoeuvre) supported by the active steering wheel, a longitudinaL control task (speed control) supported by the active gas-pedal, a combined control task (Lane-change manoeuvre and speed control) supported by both active controls. Different force feedback characteristics for the active control devices served as the main independent variable. The results indicate that steering support may be fruitfully applied as a warning system preventing drivers to Leave their Lane. Furthermore, intelligent force feedback from the accelerator pedal appeared to be useful in speed-error reduction. Continuous force changes which are directly related to speed error seem most promising. Interference effects may occur in case of simultaneous presentation of vibrating signals on both steering wheel and accelerator. The present simulator findings need further verification in field studies. Perceptual Motor Skills, Proprioception, Simulators, Vehicle Driving.
Strategies to Improve the Clinical Utility of Saporin-Based Targeted Toxins (2018)

Plant Ribosome-inactivating proteins (RIPs) including the type I RIP Saporin have been used for the construction of Immunotoxins (ITxs) obtained via chemical conjugation of the toxic domain to whole antibodies or by generating genetic fusions to antibody fragments/targeting domains able to direct the chimeric toxin against a desired sub-population of cancer cells. The high enzymatic activity, stability and resistance to conjugation procedures and especially the possibility to express recombinant fusions in yeast, make Saporin a well-suited tool for anti-cancer therapy approaches. Previous clinical work on RIPs-based Immunotoxins (including Saporin) has shown that several critical issues must be taken into deeper consideration to fully exploit their therapeutic potential. This review focuses on possible combinatorial strategies (chemical and genetic) to augment Saporin-targeted toxin efficacy. Combinatorial approaches may facilitate RIP escape into the cytosolic compartment (where target ribosomes are), while genetic manipulations may minimize potential adverse effects such as vascular-leak syndrome or may identify T/B cell epitopes in order to decrease the immunogenicity following similar strategies as those used in the case of bacterial toxins such as Pseudomonas Exotoxin A or as for Type I RIP Bouganin. This review will further focus on strategies to improve recombinant production of Saporin-based chimeric toxins.
Steroidal Sapogenins. XVII. Stereochemistry of the Spiroketal Side Chain2 (1955)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSteroidal Sapogenins. XVII. Stereochemistry of the Spiroketal Side Chain2Monroe E. Wall, Samuel Serota, and C. Roland EddyCite this: J. Am. Chem. Soc. 1955, 77, 5, 1230–1237Publication Date (Print):March 1, 1955Publication History Published online1 May 2002Published inissue 1 March 1955https://pubs.acs.org/doi/10.1021/ja01610a040https://doi.org/10.1021/ja01610a040research-articleACS PublicationsRequest reuse permissionsArticle Views80Altmetric-Citations12LEARN 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
Heparanase enhances the generation of activated factor X in the presence of tissue factor and activated factor VII (2010)

Overall, our results support the notion that heparanase is a potential modulator of blood hemostasis, and suggest a novel mechanism by which heparanase increases the generation of activated factor X in the presence of tissue factor and activated factor VII.
Endothelin receptors as novel targets in tumor therapy (2004)

The endotelin (ET) axis, that includes ET-1, ET-2, ET-3, and the ET receptors, ETA and ETB, plays an important physiological role, as modulator of vasomotor tone, tissue differentiation and development, cell proliferation, and hormone production. Recently, investigations into the role of the ET axis in mitogenesis, apoptosis inhibition, invasiveness, angiogenesis and bone remodeling have provided evidence of the importance of the ET-1 axis in cancer. Data suggest that ET-1 participates in the growth and progression of a variety of tumors such as prostatic, ovarian, renal, pulmonary, colorectal, cervical, breast carcinoma, Kaposi's sarcoma, brain tumors, melanoma, and bone metastases. ET-1 receptor antagonists beside providing ideal tools for dissecting the ET axis at molecular level have demonstrated their potential in developing novel therapeutic opportunity. The major relevance of ETA receptor in tumor development has led to an extensive search of highly selective antagonists. Atrasentan, one of such antagonists, is orally bioavailable, has suitable pharmacokinetic and toxicity profiles for clinical use. Preliminary data from clinical trials investigating atrasentan in patients with prostate cancer are encouraging. This large body of evidence demonstrates the antitumor activity of endothelin receptor antagonists and provides a rationale for the clinical evaluation of these molecules alone and in combination with cytotoxic drugs or molecular inhibitors leading to a new generation of anticancer therapies targeting endothelin receptors.
Reading Wikipedia to Answer Open-Domain Questions (2017)

This paper proposes to tackle open- domain question answering using Wikipedia as the unique knowledge source: the answer to any factoid question is a text span in a Wikipedia article. This task of machine reading at scale combines the challenges of document retrieval (finding the relevant articles) with that of machine comprehension of text (identifying the answer spans from those articles). Our approach combines a search component based on bigram hashing and TF-IDF matching with a multi-layer recurrent neural network model trained to detect answers in Wikipedia paragraphs. Our experiments on multiple existing QA datasets indicate that (1) both modules are highly competitive with respect to existing counterparts and (2) multitask learning using distant supervision on their combination is an effective complete system on this challenging task.
Tolane oligomers: Model thermotropic liquid crystals (1996)

Abstract The liquid crystalline phases of several rigid-rod, non-polar tolane oligomers are characterized by differential scanning calorimetry and transmitted polarized light microscopy. We determine that a stable nematic phase can be formed at ambient pressure if the molecular axial ratio (length-to-width ratio) is greater than 4.5. A smectic phase forms in addition to the nematic phase if the axial ratio exceeds 6.1. Symmetrical fluorination of the terminal phenyl groups reveals that the liquid crystalline phase behaviour of these rigid rods is highly sensitive to perturbations of the charge distribution along the molecules. Nematic tolane oligomers can exhibit high stregth disclinations (s = ±3/2 and ±2) in their schlieren textures, and we discuss conditions that promote the stability of these defects.
Effect of the porous structure of graphite on atomic hydrogen diffusion and inventory (2007)

A multi-scale model for particle diffusion in porous structures is used to study the effect of the internal structure of graphite on atomic hydrogen transport and inventory in graphite. The diffusion of trace amounts of atomic hydrogen are modelled as a trapping–detrapping mechanism within the porous network typical in graphites. Activation energies for the different traps are taken from experiments and from molecular dynamics simulations. Different diffusion mechanisms dominate at different graphite temperatures. It is seen that the trace diffusion coefficient of hydrogen scales as the square of the jump lengths of the dominant mechanism. Depending on the detrapping mechanism and on the internal structure of graphite, the jump lengths after each detrapping event can vary over a few orders of magnitude. This gives rise to the possibility of anomalous diffusion in graphite. The effect of closing the pores of graphite on atomic hydrogen diffusion is also presented.
Design of neo‐glycoconjugates that target the mannose receptor and enhance TLR‐independent cross‐presentation and Th1 polarization (2011)

Cross-presentation is an important mechanism by which DCs present exogenous antigens on MHC-I molecules, and activate CD8(+) T cells, cells that are crucial for the elimination of tumors. We investigated the feasibility of exploiting the capacity of the mannose receptor (MR) to improve both cross-presentation of tumor antigens and Th polarization, processes that are pivotal for the anti-tumor potency of cytotoxic T cells. To this end, we selected two glycan ligands of the MR, 3-sulfo-Lewis(A) and tri-GlcNAc (N-acetylglucosamine), to conjugate to the model antigen OVA and assessed in vitro the effect on antigen presentation and Th differentiation. Our results demonstrate that conjugation of either 3-sulfo-Lewis(A) or tri-GlcNAc specifically directs antigen to the MR. Both neo-glycoconjugates showed, even at low doses, improved uptake as compared with native OVA, resulting in enhanced cross-presentation. Using MR(-/-) and MyD88-TRIFF(-/-) bone marrow-derived DCs (BMDCs), we show that the cross-presentation of the neo-glycoconjugates is dependent on MR and independent of TLR-mediated signaling. Whereas proliferation of antigen-specific CD4(+) T cells was unchanged, stimulation with neo-glycoconjugate-loaded DCs enhanced the generation of IFN-γ-producing T cells. We conclude that modification of antigen with either 3-sulfo-Lewis(A) or tri-GlcNAc enhances cross-presentation and permits Th1 skewing, through specific targeting of the MR, which may be beneficial for DC-based vaccination strategies to treat cancer.
Conjugation of an antibody Fv fragment to a virus coat protein: cell-specific targeting of recombinant polyoma-virus-like particles (2001)

The development of cell-type-specific delivery systems is highly desirable for gene-therapeutic applications. Current virus-based vector systems show broad cell specificity, which results in the need to restrict the natural tropism of these viral systems. Here we demonstrate that tumour-cell-specific virus-like particles can be functionally assembled in vitro from recombinant viral coat protein expressed in Escherichia coli. The insertion of a negatively charged peptide in the HI loop of polyoma VP1 interferes with the binding of VP1 to the natural recognition site on mammalian cells and also serves as an adapter for the coupling of antibody fragments that contain complementary charged fusion peptides. A recombinant antibody fragment of the tumour-specific anti-(Lewis Y) antibody B3 could be coupled to the mutant VP1 by engineered polyionic peptides and an additional disulphide bond. With this system an entirely recombinant cell-specific delivery system assembled in vitro could be generated that transfers genes preferentially to cells presenting the tumour-specific antigen on the cell surface.
Structure and biosynthesis of cytoplasmic and secreted variants of gelsolin. (1984)

Gelsolin is an actin-fragmenting cytoplasmic protein. A functionally similar protein has also been identified in plasma. We have compared the structure of the cytoplasmic and plasma forms of gelsolin and examined their biosynthetic relationships. Plasma gelsolin is larger than cytoplasmic gelsolin (Mr 93,000 versus 90,000, respectively) and is more positively charged. Partial amino acid sequencing analyses show that the two gelsolins share a common 29 amino acid sequence which lies at the NH2-terminal end of cytoplasmic gelsolin and spans residues 26-55 of plasma gelsolin. Compared with cytoplasmic gelsolin, plasma gelsolin contains an additional peptide of 25 amino acids at its NH2 terminus. The human hepatoma-derived cell line, HepG2, synthesizes both the 90-kDa and the 93-kDa gelsolins but secretes only the 93-kDa form. Pulse-chase experiments demonstrate that the rate of disappearance of the 93-kDa gelsolin from the cells corresponds with the rate of appearance of the 93-kDa gelsolin in the medium, whereas the rate of disappearance of the 90-kDa gelsolin is independent of and slower than that of the secreted plasma protein. We conclude that cytoplasmic and plasma gelsolins are structurally similar but not identical, that after synthesis these proteins are processed independently, and that the fate of each is distinct.
Cloning and expression of the gene for the Avi-3 antigen of Mycobacterium avium and mapping of its epitopes (1992)

The Avi-3 antigen, which is found only in Mycobacterium avium culture sonic extracts, is species specific and results in strong skin test activity in guinea pigs sensitized with heat-killed M. avium. Its gene was cloned by using a previously developed single-probe method and was sequenced. The gene encoded a 194-amino-acid polypeptide with a molecular weight of 21,500. A recombinant Avi-3 antigen expressed in Escherichia coli reacted with monoclonal and polyclonal antibodies raised against the native Avi-3 antigen. To identify epitopes on this protein for immunodiagnostic purposes, various parts of the Avi-3 antigen were expressed as beta-galactosidase fusion proteins, using pUR and pURS expression vectors. The clones screened by both antibody reactivity and T-cell proliferative activity defined fragments with coexisting B- and T-cell epitopes. A B-cell epitope (Asn-176 to Ala-186) and two T-cell epitopes (Glu-75 to Ile-86 and Arg-155 to Leu-164) were thus defined. The synthetic polymerized peptides of the T-cell epitopes were proven to elicit a delayed cutaneous hypersensitivity reaction in guinea pigs. This mapping method would be useful in the development of a subunit vaccine consisting of an immunodominant B-cell epitope linked to a T-cell epitope in the vicinity.
Dopant-Free Planar n–i–p Perovskite Solar Cells with Steady-State Efficiencies Exceeding 18% (2017)

In this Letter, we demonstrate a planar n–i–p perovskite solar cell design with a steady-state efficiency of up to 18.8% in the absence of any electronic dopants. In the device stack, solution-processed SnO2 is used as an electron-accepting n-type layer. The absorber layer is a perovskite with both mixed organic A-site cations and mixed halides (FA0.83MA0.17Pb(I0.83Br0.17)3). The hole-transporting p-type layer is a double-layer structure of polymer-wrapped single-walled carbon nanotubes and undoped spiro-OMeTAD. We show that this approach can deliver steady-state efficiencies as high as and even higher than those of traditionally doped spiro-OMeTAD, providing a pathway for dopant-free perovskite solar cells crucial for long-term stability.