gebhart/patrepeval huggingface dataset:
HADDOCK versus HADDOCK: New features and performance of HADDOCK2.0 on the CAPRI targets (2007)

Here we present version 2.0 of HADDOCK, which incorporates considerable improvements and new features. HADDOCK is now able to model not only protein-protein complexes but also other kinds of biomolecular complexes and multi-component (N > 2) systems. In the absence of any experimental and/or predicted information to drive the docking, HADDOCK now offers two additional ab initio docking modes based on either random patch definition or center-of-mass restraints. The docking protocol has been considerably improved, supporting among other solvated docking, automatic definition of semi-flexible regions, and inclusion of a desolvation energy term in the scoring scheme. The performance of HADDOCK2.0 is evaluated on the targets of rounds 4-11, run in a semi-automated mode using the original information we used in our CAPRI submissions. This enables a direct assessment of the progress made since the previous versions. Although HADDOCK performed very well in CAPRI (65% and 71% success rates, overall and for unbound targets only, respectively), a substantial improvement was achieved with HADDOCK2.0.
Homocysteine and coronary artery disease (1994)

Whether measuring plasma homocysteine levels in patients with coronary artery disease should be routine and whether treating hyperhomocysteinemia in these patients may reduce the risk of coronary events remains to be determined.
Resolution of Bronchial Hyperresponsiveness and Pulmonary Inflammation Is Associated with IL-3 and Tissue Leukocyte Apoptosis (2001)

We have used two models of murine pulmonary inflammation to investigate the signals responsible for the resolution of bronchial hyperresponsiveness (BHR). Both protocols involved two sensitizations with OVA followed by serial aerosolized challenge with OVA. We determined that administration of the second sensitization by aerosol (model A) was associated with a transient response, whereas administration by the i.p. route (model B) induced a sustained response, in the form of BHR and eosinophilia. This difference in kinetics was due solely to the route of the second Ag administration and was not associated with Ag dose or adjuvant. Differences in kinetics of lung eosinophilia/BHR were shown to be independent of IgE levels and IL-4 or IL-5. However, IL-3 levels in model A closely correlated with the rate of leukocyte clearance by apoptosis and were observed concomitant with a decline in BHR. Blockage of IL-3 in model B increased leukocyte apoptosis but reduced tissue eosinophilia and BHR. The use of mouse models in which a single different administration of allergen is associated with a failure/success to resolve inflammation and BHR by 72 h postchallenge indicates a link between IL-3 production, leukocyte apoptosis, and BHR responses.
Conserved arginine-516 of Penicillium amagasakiense glucose oxidase is essential for the efficient binding of β-d-glucose (2000)

The effects of mutation of key conserved active-site residues (Tyr-73, Phe-418, Trp-430, Arg-516, Asn-518, His-520 and His-563) of glucose oxidase from Penicillium amagasakiense on substrate binding were investigated. Kinetic studies on the oxidation of β-D-glucose combined with molecular modelling showed the side chain of Arg-516, which forms two hydrogen bonds with the 3-OH group of β-D-glucose, to be absolutely essential for the efficient binding of β-D-glucose. The R516K variant, whose side chain forms only one hydrogen bond with the 3-OH group of β-D-glucose, exhibits an 80-fold higher apparent Km (513 mM) but a Vmax only 70% lower (280 units/mg) than the wild type. The complete elimination of a hydrogen-bond interaction between residue 516 and the 3-OH group of β-D-glucose through the substitution R516Q effected a 120-fold increase in the apparent Km for glucose (to 733 mM) and a decrease in the Vmax to 1/30 (33 units/mg). None of the other substitutions, with the exception of variant F418A, affected the apparent Km more than 6-fold. In contrast, the removal of aromatic or bulky residues at positions 73, 418 or 430 resulted in decreases in the maximum rates of glucose oxidation to less than 1/90. Variants of the potentially catalytically active His-520 and His-563 were completely, or almost completely, inactive. Thus, of the residues forming the active site of glucose oxidase, Arg-516 is the most critical amino acid for the efficient binding of β-D-glucose by the enzyme, whereas aromatic residues at positions 73, 418 and 430 are important for the correct orientation and maximal velocity of glucose oxidation.
A system for various visual classification tasks based on neural networks (2002)

A three stage recognition architecture that can be trained to different recognition or segmentation tasks is presented. It consists of an adaptive feature extraction based on vector quantization and local PCA. The features are classified by neural expert networks. It is shown that the system can be applied to object classification, segmentation of partially occluded objects and classification of object parts without modifications in the architecture.
Tonkinecin, a Novel Bioactive Annonaceous Acetogenin from Uvaria tonkinesis (1996)

A novel bioactive monotetrahydrofuran acetogenin named tonkinecin (1) and two known compounds, uvariamicins I and II, have been isolated from the roots of Uvaria tonkinesis. The structure of 1 was elucidated using spectral methods and its absolute stereochemistry established by 1H-NMR experiments utilizing Mosher ester methodology.
SASI-Seq: sample assurance Spike-Ins, and highly differentiating 384 barcoding for Illumina sequencing (2014)

SASI-Seq is a simple, inexpensive and flexible tool that enables sample assurance, allows deconvolution of sample mix-ups and reports levels of cross-contamination between samples throughout NGS workflows.
Identification of specific Rp-phosphate oxygens in the tRNA anticodon loop required for ribosomal P-site binding (1997)

tRNA binding to the ribosomal P site is dependent not only on correct codon-anticodon interaction but also involves identification of structural elements of tRNA by the ribosome. By using a phosphorothioate substitution-interference approach, we identified specific nonbridging Rp-phosphate oxygens in the anticodon loop of tRNA(Phe) from Escherichia coli which are required for P-site binding. Stereospecific involvement of phosphate oxygens at these positions was confirmed by using synthetic anticodon arm analogues at which single Rp- or Sp-phosphorothioates were incorporated. Identical interference results with yeast tRNA(Phe) and E. coli tRNA(fMet) indicate a common backbone conformation or common recognition elements in the anticodon loop of tRNAs. N-ethyl-N-nitrosourea modification-interference experiments with natural tRNAs point to the importance of the same phosphates in the loop. Guided by the crystal structure of tRNA(Phe), we propose that specific Rp-phosphate oxygens are required for anticodon loop ("U-turn") stabilization or are involved in interactions with the ribosome on correct tRNA-mRNA complex formation.
Role of alveolar macrophages in chronic obstructive pulmonary disease (2014)

Alveolar macrophages (AMs) represent a unique leukocyte population that responds to airborne irritants and microbes. This distinct microenvironment coordinates the maturation of long-lived AMs, which originate from fetal blood monocytes and self-renew through mechanisms dependent on GM-CSF and CSF-1 signaling. Peripheral blood monocytes can also replenish lung macrophages; however, this appears to occur in a stimuli specific manner. In addition to mounting an appropriate immune response during infection and injury, AMs actively coordinate the resolution of inflammation through efferocytosis of apoptotic cells. Any perturbation of this process can lead to deleterious responses. In chronic obstructive pulmonary disease (COPD), there is an accumulation of airway macrophages that do not conform to the classic M1/M2 dichotomy. There is also a skewed transcriptome profile that favors expression of wound-healing M2 markers, which is reflective of a deficiency to resolve inflammation. Endogenous mediators that can promote an imbalance in inhibitory M1 vs. healing M2 macrophages are discussed, as they are the plausible mechanisms underlying why AMs fail to effectively resolve inflammation and restore normal lung homeostasis in COPD.
Generation of a Hybrid Sequence-Specific Single-Stranded Deoxyribonuclease (1987)

The relatively nonspecific single-stranded deoxyribonuclease, staphylococcal nuclease, was selectively fused to an oligonucleotide binding site of defined sequence to generate a hybrid enzyme. A cysteine was substituted for Lys116 in the enzyme by oligonucleotide-directed mutagenesis and coupled to an oligonucleotide that contained a 3'-thiol. The resulting hybrid enzyme cleaved single-stranded DNA at sites adjacent to the oligonucleotide binding site.
Chikungunya fever: A re-emerging viral infection (2008)

Chikungunya (CHIK) fever is a re-emerging viral disease characterized by abrupt onset of fever with severe arthralgia followed by constitutional symptoms and rash lasting for 1-7 days. The disease is almost self-limiting and rarely fatal. Chikungunya virus (CHIKV) is a RNA virus belonging to family Togaviridae, genus Alphavirus. Molecular characterization has demonstrated two distinct lineages of strains which cause epidemics in Africa and Asia. These geographical genotypes exhibit differences in the transmission cycles. In contrast to Africa where sylvatic cycle is maintained between monkeys and wild mosquitoes, in Asia the cycle continues between humans and the Aedes aegypti mosquito. CHIKV is known to cause epidemics after a period of quiescence. The first recorded epidemic occurred in Tanzania in 1952-1953. In Asia, CHIK activity was documented since its isolation in Bangkok, Thailand in 1958. Virus transmission continued till 1964. After hiatus, the virus activity re-appeared in the mid-1970s and declined by 1976. In India, well-documented outbreaks occurred in 1963 and 1964 in Kolkata and southern India, respectively. Thereafter, a small outbreak of CHIK was reported from Sholapur district, Maharashtra in 1973. CHIKV emerged in the islands of South West Indian Ocean viz. French island of La Reunion, Mayotee, Mauritius and Seychelles which are reporting the outbreak since February, 2005. After quiescence of about three decades, CHIKV re-emerged in India in the states of Andhra Pradesh, Karnataka, Maharashtra, Madhya Pradesh and Tamil Nadu since December, 2005. Cases have also been reported from Rajasthan, Gujarat and Kerala. The outbreak is still continuing. National Institute of Communicable Diseases has conducted epidemiological, entomological and laboratory investigations for confirmation of the outbreak. These have been discussed in detail along with the major challenges that the country faced during the current outbreak.
Darstellung binärer Variablen durch elektrische Größen (1997)

Logiksysteme zeichnen sich durch eine große Vielzahl und durch große Unterschiedlichkeit in der technischen Realisierung aus. Eine Übersicht gibt Bild 2.1. Bei elektronischen Systemen werden die binären Variablen allgemein durch zwei unterschiedliche elektrische Spannungsniveaus festgelegt, bei deren Wahl man im Prinzip völlig frei ist. Nebenbedingungen sind:
Fructose 2,6-bisphosphate 2 years after its discovery (1982)

Research Article| July 15 1982 Fructose 2,6-bisphosphate 2 years after its discovery H G Hers; H G Hers Search for other works by this author on: This Site PubMed Google Scholar E Van Schaftingen E Van Schaftingen Search for other works by this author on: This Site PubMed Google Scholar Author and article information Publisher: Portland Press Ltd Online ISSN: 1470-8728 Print ISSN: 0264-6021 © 1982 London: The Biochemical Society1982 Biochem J (1982) 206 (1): 1–12. https://doi.org/10.1042/bj2060001 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn Email Cite Icon Cite Get Permissions Citation H G Hers, E Van Schaftingen; Fructose 2,6-bisphosphate 2 years after its discovery. Biochem J 15 July 1982; 206 (1): 1–12. doi: https://doi.org/10.1042/bj2060001 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Journal Search Advanced Search This content is only available as a PDF. © 1982 London: The Biochemical Society1982 Article PDF first page preview Close Modal You do not currently have access to this content.
The Reactions of Carbobenzoxyamino Acid Amides with Carbonyl Compounds (1961)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Reactions of Carbobenzoxyamino Acid Amides with Carbonyl CompoundsURI ZEHAVI and DOV BEN-ISHAICite this: J. Org. Chem. 1961, 26, 4, 1097–1101Publication Date (Print):April 1, 1961Publication History Published online1 May 2002Published inissue 1 April 1961https://pubs.acs.org/doi/10.1021/jo01063a029https://doi.org/10.1021/jo01063a029research-articleACS PublicationsRequest reuse permissionsArticle Views389Altmetric-Citations35LEARN 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
Immunization Against Infectious Disease (1978)

Mortality and morbidity from infectious diseases in the United States have declined more than 90 percent since 1900. Factors believed to be responsible for this decline include changes in the natural history of disease, sanitation, quarantine measures, control of nonhuman vectors, antibacterial drugs, and immunization. The contributions of each of these factors differ among the various infectious diseases; except for smallpox and diphtheria control, immunization had little effect until after World War II. The success of present and future immunization programs is endangered by public and physician complacency and by complex legal and ethical problems related to informed consent and responsibility for rare, vaccine-related injury.
Discount Anonymous On Demand Routing for Mobile Ad hoc Networks (2006)

Recent years have seen a large number of proposals for anonymity mechanisms operating on the application layer. Given that anonymity is no stronger than its weakest link, such proposals are only meaningful if one can offer anonymity guarantees on the communication layer as well. ANODR - or anonymous on demand routing - is one of the leading proposals to deal with this issue. In this paper, we propose a novel technique to address the same problem, but at a lower cost. Our proposal, which we dub discount-ANODR, is built around the same set of techniques as ANODR is. Our proposal has the benefit of achieving substantially lower computation and communication complexities at the cost of a slight reduction of privacy guarantees. In particular, discount-ANODR achieves source anonymity and routing privacy. A route is "blindly generated" by the intermediaries on the path between an anonymous source and an identified destination. Route requests in discount-ANODR bear strong similarities to route requests in existing source routing protocols, with the limitation that intermediaries only know the destination of the request and the identity of the previous intermediary - but not whether the latter was the originator of the request. The response to a route request protects the compiled route by means of iterated symmetric encryption, drawing on how messages are prepared before being submitted to a typical synchronous mix network (or onion router). The communication of data subsequently uses such "route onions" to channel the packet to the intended destination. We do not use any key exchange, nor do we utilize public key operations at any time; consequently, we do not need to rely on any PKI, CRL or related constructions
Introduction (2010)

In the forty years since these words were first published, The Dialectic of Sex has had a strange history. Written by the then twenty-five-year-old Shulamith Firestone, it first appeared in the autumn of 1970, the same year as Kate Millett's Sexual Politics and Germaine Greer's The Sexual Eunuch. Like those other founding texts of Women's Liberation, The Dialectic of Sex became a bestseller, but unlike them it became the object of attack and misrepresentation from both conservatives and feminists. Moreover, despite its pioneering critique of binary gender, The Dialectic of Sex is also missing from the bibliographies of Queer Theory. This volume is the first sustained discussion of its contents and their implications for the politics of another age.
Biological lithography: Improvements in DNA synthesis methods (2004)

We have recently succeeded in synthesizing long oligonucleotides (90-mers) with high yield. This synthesis requires 360 virtual masks, and thus puts challenges on image placement and local contrast. We have updated our DNA synthesis modeling to Monte Carlo simulation from numerical approach. We also devised a method, called “Inverted Capping,” to remove sequence errors from edge scattering of light, which provides a large error reduction and the possibility of fabrication of higher resolutions. Finally, we have also implemented an image locking method to eliminate image drifts.
Possible Antimigraine Mechanisms of Action of the 5HT1F Receptor Agonist LY334370 (1999)

This study investigated whether the selective 5HT1F receptor agonist LY334370 has other possible antimigraine mechanisms in addition to the proposed inhibition of dural plasma extravasation. LY334370 (up to 10(-5) M) had no vasoconstrictor effects on human cerebral arteries in vitro. It had no effect (up to 10 mg kg-1, i.v.) on neurogenic vasodilation of dural blood vessels produced by electrical stimulation of the dura mater in anesthetized rats. Nor had it any effect (at 3 mg kg-1, i.v.) on the hyperalgesia produced by injection of carrageenan into the paw of conscious rats or on nociceptive reflex responses in the spinalized, decerebrate rabbit (up to 3 mg kg-1, i.v.), indicating that it has no general analgesic properties. However, it significantly inhibited activation of second-order neurons in the trigeminal nucleus caudalis produced by electrical stimulation of the dura mater in anesthetised rats at 3 mg kg-1, i.v. These results provide evidence to suggest that LY334370 has a central mechanism of action in blocking the transmission of nociceptive impulses within the trigeminal nucleus caudalis and that this may represent a mechanism through which it has its antimigraine effect.
Activation of the Factor VIIIa-Factor IXa Enzyme Complex of Blood Coagulation by Membranes Containing Phosphatidyl-L-serine (1996)

Factor IXa, a serine protease of blood coagulation, functions at least 100,000 times more efficiently when bound to factor VIIIa on a phospholipid membrane than when free in solution. We have utilized the catalytic activity of the factor VIIIa-factor IXa complex to report the effect of phospholipid membranes on binding of factor IXa to factor VIIIa and on enzymatic cleavage of the product. The apparent affinity of factor IXa for factor VIIIa was 10-fold lower in the absence of phospholipid membranes with a KD of 46 nM versus 4.3 nM with phospholipid membranes. The Km for activation of factor X by the factor VIIIa-factor IXa complex was 1700 nM in solution, 70-fold higher than the value of 28 nM when bound to membranes containing phosphatidyl-L-serine, phosphatidylethanolamine, and phosphatidylcholine at a ratio of 4:20:76. The largest effect of phosphatidyl-L-serine-containing membranes on the factor VIIIa-factor IXa complex was the accelerated rate of peptide bond cleavage, with the k(cat) increased by 1,500-fold from 0.022 to 33 min-1. Membranes in which phosphatidyl-L-serine was replaced by phosphatidyl-D-serine, phosphatidic acid, or phosphatidylglycerol were at least 10-fold less effective for enhancing the k(cat). Thus, while membranes containing phosphatidyl-L-serine enhance condensation of the enzyme with its cofactor and substrate, their largest effect is activation of the assembled factor VIIIa-factor IXa enzyme complex.
Multimedia summaries of broadcast news (2002)

Increasing amounts of text, audio, and video content has fueled efforts to provide direct, content based access to these materials. Summaries are often necessary to enable timely relevancy assessments, information extraction, or information analysis from source material. Whereas text summarization research is receiving increasing attention, comparatively few investigators have examined video summarization. We report on the extension of a broadcast news access system to provide multimedia summaries. We briefly overview our system for video analysis, focusing on our novel integration of image, speech and language processing techniques to support automated video summarization. We outline algorithms for proper name and keyphrase extraction, story segmentation, and key frame extraction which together underpin our current ability to automatically summarize video. We describe the systems ability to generate multimedia video summaries tailored to a user query. We discuss evaluation metrics for measuring the (quality) value of these summary artifacts.
Hermetic Wafer-Level Packaging for RF MEMs: Effects on Resonator Performance. (2016)

Abstract not provided.
Differential Inhibition of Aminopeptidase A and Aminopeptidase N by New .beta.-Amino Thiols (1994)

Aminopeptidase A (APA) is a highly selective peptidase, which cleaves the N-terminal Glu or Asp residues of biologically active peptides, and has therefore been proposed to be involved in angiotensin II and CCK8 metabolism. Highly potent and selective APA inhibitors are consequently required to study the physiological regulation of these two peptides. Using, as a model, Glu-thiol (4-amino-5-mercaptopentanoic acid), which was the first efficient APA inhibitor described but is however equipotent on APA (0.14 microM) and aminopeptidase N (APN) (0.12 microM), several beta-amino thiol inhibitors have been synthesized. In these molecules, the length of the side chain was varied and the carboxylate group of Glu-thiol was replaced by other negatively charged groups, such as phosphonate, sulfonate, hydroxamate, and thiol. The inhibitory potency of one of these compounds, 22h (S)-3-amino-4-mercaptobutanesulfonate, was found to be nearly 100-fold better for APA than for APN, with an affinity (0.29 microM) almost equivalent to that of Glu-thiol. Hence, this compound is the first selective APA inhibitor reported, and as such, it should be an interesting probe to explore the physiological involvement of APA in the metabolism of neuropeptides like angiotensin II and CCK8.
Hyperhomocysteinemia Increases Risk of Death, Especially in Type 2 Diabetes (2000)

Hyperhomocysteinemia is related to 5-year mortality independent of other major risk factors and appears to be a stronger (1.9-fold) risk factor for mortality in type 2 diabetic patients than in nondiabetic subjects.