gebhart/patrepeval huggingface dataset:
Effective methodology for deadlock-free minimal routing in InfiniBand networks (2003)

The InfiniBand Architecture (IBA) defines a switch-based network with point-to-point links whose topology is arbitrarily established by the customer. We propose a simple and effective methodology for designing deadlock-free routing strategies that are able to route packets through minimal paths in InfiniBand networks. This methodology can meet the trade-off between network performance and the number of resources dedicated to deadlock avoidance. Evaluation results show that the resulting routing strategies significantly outperform up*/down* routing. In particular, throughput improvement ranges, on average, from 1.33 for small networks to 4.05 for large networks. Also, it is shown that just two virtual lanes and three service levels are enough to achieve more than 80% of the throughput improvement achieved by the best proposed routing strategy (the one that always provides minimal paths without limiting the number of resources).
ChemInform Abstract: Chemistry of Antisense Oligonucleotides (2000)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
SARS-CoV-2: Structure, Biology, and Structure-Based Therapeutics Development (2020)

The pandemic of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been posing great threats to the world in many aspects. Effective therapeutic and preventive approaches including drugs and vaccines are still unavailable although they are in development. Comprehensive understandings on the life logic of SARS-CoV-2 and the interaction of the virus with hosts are fundamentally important in the fight against SARS-CoV-2. In this review, we briefly summarized the current advances in SARS-CoV-2 research, including the epidemic situation and epidemiological characteristics of the caused disease COVID-19. We further discussed the biology of SARS-CoV-2, including the origin, evolution, and receptor recognition mechanism of SARS-CoV-2. And particularly, we introduced the protein structures of SARS-CoV-2 and structure-based therapeutics development including antibodies, antiviral compounds, and vaccines, and indicated the limitations and perspectives of SARS-CoV-2 research. We wish the information provided by this review may be helpful to the global battle against SARS-CoV-2 infection.
The Discovery of the Factor Xa Inhibitor Otamixaban: From Lead Identification to Clinical Development (2007)

Factor Xa (fXa) is a critical serine protease situated at the confluence of the intrinsic and extrinsic pathways of the blood coagulation cascade. FXa catalyses the conversion of prothrombin to thrombin via the prothrombinase complex. Its singular role in thrombin generation, coupled with its potentiating effects on clot formation render it an attractive target for therapeutic intervention. Otamixaban is a synthetically derived parenteral fXa inhibitor currently in late stage clinical development at Sanofi-Aventis for the management of acute coronary syndrome. Otamixaban is a potent (Ki = 0.5 nM), selective, rapid acting, competitive and reversible fXa inhibitor that effectively inhibits both free and prothrombinase-bound fXa. In vivo experiments have demonstrated that Otamixaban is highly efficacious in rodent, canine and porcine models of thrombosis. In addition, recent clinical findings indicate that Otamixaban is efficacious, safe and well tolerated in humans and therefore has considerable potential for the treatment of acute coronary syndrome. This review article chronicles the discovery and pre-clinical data surrounding the fXa inhibitor Otamixaban as well as the recent clinical findings in humans.
Reduction of Speech Spectra by Analysis-by-Synthesis Techniques (1961)

Procedures are described for reducing the speech wave to a specification in terms of the time-varying vocal-tract resonances and source characteristics. The basic method, which has been called analysis by synthesis, involves the comparison of speech spectra with a series of spectra that are synthesized within the analyzer. Each comparison spectrum is generated according to a set of rules based on an acoustical theory of speech production. The result of the analysis of each input spectrum is a set of parameters that describes the synthesized spectrum providing the best match. In one version of the method convergence, towards the best match is controlled by the experimenter; in another version convergence to a match is accomplished automatically without the intervention of the experimenter. All the operations have been programmed on a general-purpose digital computer and have been applied to the analysis of vowels and some consonants. The advantages of the analysis techniques are discussed.
Murine monoclonal antibodies to Klebsiella pneumoniae protect against lethal endotoxemia and experimental infection with capsulated K. pneumoniae (1990)

To prepare monoclonal antibodies (MAbs) directed against the core-lipid A fractions of smooth lipopoly-saccharide (LPS) from Klebsiella pneumoniae O1:K2, we immunized BALB/c mice with the LPS-associated proteins plus LPS. This preparation exposed the core-lipid A moiety, which is normally hidden in the micellar structure of classical LPS preparations. Among 10 MAbs selected for their reactivity with LPS-associated proteins plus LPS from K. pneumoniae O1:K2, 6 (3A3, 3C2, 3C4, 7D2, 11C3, and 12B6) were directed against the core fraction and 2 (6C5 and 10A5) were directed against the lipid A fraction. Only one (2A4) recognized the O antigen, and one (6D5) had an undefined specificity. When injected before challenge with K. pneumoniae O1:K2 LPS in galactosamine-sensitized mice, five of the MAbs (3C4, 6D5, 7D2, 11C3, and 12B6) provided protection in this model of lethal endotoxemia. MAb 7D2 was also protective in an experimental infection with capsulated K. pneumoniae O1:K2.
Prolonged Skin Graft Survival by Administration of Anti-CD8C Monoclonal Antibody with Cyclosporin A (1999)

Costimulation via the B7/CD28 pathway is an important signal for the activation of T cells. Maximal inhibition of T-cell activation and the induction of alloantigen-specific nonresponsiveness in vitro was achieved using anti-CD80 monoclonal antibody (mAb) in combination with cyclosporin A (CsA). Based on this knowledge, the efficacy of the prophylactic treatment of anti-CD80 mAb and CsA on allogeneic skin graft survival was tested in a preclinical rhesus monkey model. No side effects have been observed. Administration of anti-CD80 mAb resulted in high mAb serum levels that decreased to undetectable values around day 7. At the same time, the anti-mouse antibody response started to develop. The anti-CD80 mAb bound to peripheral blood mononuclear cells and was detectable in lymph node and grafted skin during the treatment period. The skin graft survival time of untreated or suboptimally CsA-treated rhesus monkeys was 10 days. Treatment with CsA (blood levels of 100-160 ng/ml) in combination with anti-CD80 mAb (0.5 mg/kg) resulted in a significantly increased skin graft survival time to 14 days. Eventually, skin grafts in all rhesus monkeys were rejected, which coincided with an increase in helper and cytotoxic T-cell frequency and induction of an antibody response directed against the donor antigens. Therefore, treatment of anti-CD80 mAb in combination with CsA has significant immunosuppressive potency, but was unable to induce donor-specific nonresponsiveness in skin graft recipients.
Photosensitized destruction of human bladder carcinoma cells treated with chlorin e6-conjugated microspheres. (1991)

A photosensitizer conjugate, chlorin e6 (Ce6) covalently bound to 1-micron-diameter polystyrene microspheres, has been investigated in the photodynamic destruction of MGH-U1 human bladder carcinoma cells in vitro. The microspheres were taken up avidly by the carcinoma cells; confocal laser scanning fluorescence microscopy showed them to be localized in the cytoplasm, apparently within lysosomes, visualized by labeling with acridine orange. In contrast, fluorescence of unconjugated Ce6 was present within most cellular membranes. Use of Ce6-microsphere conjugates led to a 20-fold-higher mean intracellular concentration, compared with unconjugated Ce6. Cells incubated in the presence of Ce6-microsphere conjugates (0.43 microM equivalent) and subsequently irradiated at 659 nm with a dye laser pumped by an argon-ion laser showed dose-dependent phototoxicity, leading to total inhibition of colony formation at a radiant exposure of 5J/cm2; in contrast, cells incubated with either unconjugated Ce6 (0.43 microM) or unconjugated microspheres before laser irradiation were unaffected. Cells pretreated with Ce6-microsphere conjugates and irradiated in the presence of 90% 2H2O showed significantly increased phototoxicity, an effect consistent with an important role for excited-state singlet oxygen in the mechanism of injury. In solution, however, photosensitized generation of singlet oxygen with Ce6-microsphere conjugates was 9 times less efficient than with unconjugated Ce6. The markedly greater phototoxicity of Ce6-microsphere conjugates compared to unconjugated Ce6 was therefore a consequence of the high intracellular Ce6 concentration attained by phagocytosis of the conjugates and their particular sites of intracellular localization. Thus, these conjugates are an efficient system for the delivery of photosensitizing drugs to carcinoma cells.
C-Jun NH(2)-terminal kinase mediates proliferation and tumor growth of human prostate carcinoma. (2003)

These results indicate that JNK is required for growth of prostate carcinoma cells in vitro and in vivo, and additionally indicate that JNK2 plays a dominant role. The JNK pathway is a novel target in the treatment of prostate carcinoma.
An access control architecture for programmable routers (2002)

Programmable networks allow the router's functionality to be extended dynamically through the use of active extensions. This flexible architecture facilitates the deployment of new network protocols and services. However, the programmable nature of a network also raises serious safety and security concerns. These concerns must be addressed before programmable networks can be deployed. One particular security question is how we can limit what resources and data active extensions can access on the router. While existing operating systems address this question for end-points and servers, routers have been designed to perform a different task, namely forwarding packets, and the existing OS solutions turn out to be inadequate for routers. We look at how we can restrict active extensions' access to link bandwidth and data traffic. Our solution is based on access control lists that are used to check all active extensions' operations that may affect the use of link bandwidth, or may involve access to user traffic. We implemented these mechanisms in Darwin, an example of a programmable network.
Characterization of Defocused Electron Beams and Welds in Stainless Steel and Refractory Metals using the Enhanced Modified Faraday Cup Diagnostic (2009)

As the first part of a project to compare new generation, continuous wave, laser welding technology to traditional electron beam welding technology, electron beam welds were made on commercially pure vanadium refractory metal and 21-6-9 austenitic stainless steel. The electron beam welds were made while employing EB diagnostics to fully characterize the beams so that direct comparisons could be made between electron beam and laser beams and the welds that each process produces.
Platelet glutathione peroxidase activity is impaired in patients with coronary heart disease (1986)

Platelet glutathione peroxidase (GSH-Px) activity was measured in 25 healthy individuals and in 25 patients affected with well-documented coronary artery stenosis. In parallel, malondialdehyde (MDA) production was assayed on platelets following stimulation with sodium arachidonate. Mean platelet GSH-Px activity was significantly reduced and mean platelet MDA production was significantly increased in the patient group. The difference observed in the GSH-Px activity might be a consequence of different nutritional habits, suggesting an impaired intake of selenium, the inorganic moiety of GSH-Px. As low GSH-Px activities in human platelets may be associated with increased MDA and thromboxane production, we hypothesize that a low enzyme activity may be a risk factor for the development of coronary artery disease.
The microbiology of butyrate formation in the human colon (2002)

Butyrate arising from microbial fermentation is important for the energy metabolism and normal development of colonic epithelial cells and has a mainly protective role in relation to colonic disease. While certain dietary substrates such as resistant starch appear to be butyrogenic in the colon, it is not known to what extent these stimulate butyrate production directly, e.g. by promoting amylolytic species, or indirectly, e.g. through cross-feeding of fermentation products. Cultural and molecular studies indicate that the most numerous butyrate-producing bacteria found in human faeces are highly oxygen-sensitive anaerobes belonging to the Clostridial clusters IV and XIVa. These include many previously undescribed species related to Eubacterium, Roseburia, Faecalibacterium and Coprococcus whose distribution and metabolic characteristics are under investigation. A better understanding of the microbial ecology of colonic butyrate-producing bacteria will help to explain the influence of diet upon butyrate supply, and to suggest new approaches for optimising microbial activity in the large intestine.
Modified belief-propagation algorithm for decoding of irregular low-density parity-check codes (2002)

A modified belief-propagation algorithm is proposed for decoding of irregular low-density parity-check codes. This algorithm effectively reduces the decoding complexity while achieving a BER performance near to or even better than that of the standard belief-propagation algorithm.
Photophysical Properties of Fluorescent DNA-dyes Bound to Single- and Double-stranded DNA in Aqueous Buffered Solution¶ (2001)

The absorption and fluorescence spectra, fluorescence quantum yields, lifetimes and time-resolved fluorescence spectra are reported for nine different fluorescent DNA-dyes. The work was initiated in search of a quantitative method to detect the ratio of single-to-double stranded DNA (ssDNA/dsDNA) in solution based on the photophysics of dye-DNA complexes; the result is a comprehensive study providing a vast amount of information for users of DNA strains. The dyes examined were the bisbenzimide or indole-derived stains (Hoechst 33342, Hoechst 33258 and 4',6-diamidino-2-phenylindole), phenanthridinium stains (ethidium bromide and propidium iodide) and cyanine dyes (PicoGreen, YOYO-1 iodide, SYBR Green I and SYBR Gold). All were evaluated under the same experimental conditions in terms of ionic strength, pH and dye-DNA ratio. Among the photophysical properties evaluated only fluorescence lifetimes for the cyanine stilbene dyes allowed a convenient differentiation between ssDNA and dsDNA. The bisbenzimide dyes showed multiexponential decays when bound to either form of DNA, making lifetime-based analysis cumbersome with inherent errors. These dyes also presented biexponential decay when free in aqueous buffered solutions at different pH. A mechanism for their deactivation is proposed based on two different conformers decaying with different kinetics. The phenanthridinium dyes showed monoexponential decays with ssDNA and dsDNA, but there was no discrimination between them. High dye-DNA ratios (e.g. 1:1) resulted in multiexponential decays for cyanine dyes, resulting from energy transfer or self-quenching deactivation. Shifts in both absorption and fluorescence maxima for both ssDNA and dsDNA DNA-cyanine dye complexes were small. Broadening of dye-ssDNA absorption and fluorescence bands for the cyanine dyes relative to dye-dsDNA bands was detected and attributed to higher degrees of rotational freedom in the former.
A Molecular Basis for Functional Peptide Mimicry of a Carbohydrate Antigen (2000)

Peptides may substitute for carbohydrate antigens in carbohydrate-specific immunological reactions. Using the recognition properties of an anti-Lewis Y (LeY) antibody, BR55-2, as a model system, we establish a molecular perspective for peptide mimicry by comparing the three-dimensional basis of BR55-2 binding to LeY with the binding of the same antibody to peptides. The peptides compete with LeY, as demonstrated by enzyme-linked immunosorbent assay and Biacore analysis. The computer program LUDI was used to epitope map the antibody-combining site, correlating peptide reactivity patterns. This approach identified amino acids interacting with the same BR55-2 functional residue groups that recognize the Fucalpha(1-3) moiety of LeY. Molecular modeling indicates that the peptides adopt an extended turn conformation within the BR55-2 combining site, serving to overlap the peptides with the LeY spatial position. Peptide binding is associated with only minor changes in BR55-2, relative to the BR55-2-LeY complex. Anti-peptide serum distinguishes the Fucalpha(1-3) from the Fucalpha(1-4) linkage, therefore differentiating difucosylated neolactoseries antigens. These results further confirm that peptides and carbohydrates can bind to the same antibody-binding site and that peptides can structurally and functionally mimic salient features of carbohydrate epitopes.
Improved hyper-temporal feature extraction methods for land cover change detection in satellite time series (2012)

The growth in global population inevitably increases the consumption of natural resources. The need to provide basic services to these growing communities leads to an increase in anthropogenic changes to the natural environment. The resulting transformation of vegetation cover (e.g. deforestation, agricultural expansion, urbanisation) has significant impacts on hydrology, biodiversity, ecosystems and climate. Human settlement expansion is the most common driver of land cover change in South Africa, and is currently mapped on an irregular, ad hoc basis using visual interpretation of aerial photographs or satellite images. This thesis proposes several methods of detecting newly formed human settlements using hyper-temporal, multi-spectral, medium spatial resolution MODIS land surface reflectance satellite imagery. The hyper-temporal images are used to extract time series, which are analysed in an automated fashion using machine learning methods. A post-classification change detection framework was developed to analyse the time series using several feature extraction methods and classifiers. Two novel hyper-temporal feature extraction methods are proposed to characterise the seasonal pattern in the time series. The first feature extraction method extracts Seasonal Fourier features that exploits the difference in temporal spectra inherent to land cover classes. The second feature extraction method extracts state-space vectors derived using an extended Kalman filter. The extended Kalman filter is optimised using a novel criterion which exploits the information inherent in the spatio-temporal domain. The post-classification change detection framework was evaluated on different classifiers; both supervised and unsupervised methods were explored. A change detection accuracy of above 85% with false alarm rate below 10% was attained. The best performing methods were then applied at a provincial scale in the Gauteng and Limpopo provinces to produce regional change maps, indicating settlement expansion.
Preparation of Peptides Containing Cysteine (1952)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPreparation of Peptides Containing CysteineL. Carroll King and Fred H. SuydamCite this: J. Am. Chem. Soc. 1952, 74, 21, 5499–5501Publication Date (Print):November 1, 1952Publication History Published online1 May 2002Published inissue 1 November 1952https://pubs.acs.org/doi/10.1021/ja01141a081https://doi.org/10.1021/ja01141a081research-articleACS PublicationsRequest reuse permissionsArticle Views69Altmetric-Citations10LEARN 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
Direct conversion of methane to aromatics in a catalytic co-ionic membrane reactor (2016)

Nonoxidative methane dehydroaromatization (MDA: 6CH4 ↔ C6H6 + 9H2) using shape-selective Mo/zeolite catalysts is a key technology for exploitation of stranded natural gas reserves by direct conversion into transportable liquids. However, this reaction faces two major issues: The one-pass conversion is limited by thermodynamics, and the catalyst deactivates quickly through kinetically favored formation of coke. We show that integration of an electrochemical BaZrO3-based membrane exhibiting both proton and oxide ion conductivity into an MDA reactor gives rise to high aromatic yields and improved catalyst stability. These effects originate from the simultaneous extraction of hydrogen and distributed injection of oxide ions along the reactor length. Further, we demonstrate that the electrochemical co-ionic membrane reactor enables high carbon efficiencies (up to 80%) that improve the technoeconomic process viability.
Sensitivity of Corynespora cassicola, causal agent of Corynespora leaf spot of cucumber, to thiophanate-methyl, diethofencarb and azoxystrobin. (2004)

Sensitivity of Corynespora cassicola, causal agent of Corynespora leaf spot of cucumber, isolated from cucumber plants in Okayama Prefecture to thiophanate-methyl (T) and diethofencarb (D), and azoxystrobin (A) was investigated using the minimum inhibitory concentration (MIC) method and a bioassay. With the MIC method, 29 isolates among 193 isolates were highly resistant to both T and D. In the bioassay test, an isolate resistant to A was isolated from cucumber plants in a field. This report is the first on isolates of the causal fungus that are highly resistant to both T and D and the second report on isolates resistant to A.