gebhart/patrepeval huggingface dataset:
Crystal structure of human natural cytotoxicity receptor NKp30 and identification of its ligand binding site (2011)

Natural killer (NK) cells are a group of innate immune cells that carry out continuous surveillance for the presence of virally infected or cancerous cells. The natural cytotoxicity receptor (NCR) NKp30 is critical for the elimination of a large group of tumor cell types. Although several ligands have been proposed for NKp30, the lack of a conserved structural feature among these ligands and their uncertain physiological relevance has contributed to confusion in the field and hampered a full understanding of the receptor. To gain insights into NKp30 ligand recognition, we have determined the crystal structure of the extracellular domain of human NKp30. The structure displays an I-type Ig-like fold structurally distinct from the other natural cytotoxicity receptors NKp44 and NKp46. Using cytolytic killing assays against a range of tumor cell lines and subsequent peptide epitope mapping of a NKp30 blocking antibody, we have identified a critical ligand binding region on NKp30 involving its F strand. Using different solution binding studies, we show that the N-terminal domain of B7-H6 is sufficient for NKp30 recognition. Mutations on NKp30 further confirm that residues in the vicinity of the F strand, including part of the C strand and the CD loop, affect binding to B7-H6. The structural comparison of NKp30 with CD28 family receptor and ligand complexes also supports the identified ligand binding site. This study provides insights into NKp30 ligand recognition and a framework for a potential family of unidentified ligands.
Probabilistic Models and Algorithms for Data Synchronization/Broadcast Via Network Coding (2016)

We investigate the problem of data synchronization in which a sender has a set of packets to be distributed to all the receivers via a broadcast channel. Initially, each receiver has some fraction of the packets. At each time slot, the sender might broadcast a packet to all the receivers. The goal is to find a broadcast scheme that minimizes the number of time slots until all the receivers successfully obtain all the packets. We propose two probabilistic models on how the initial fractions of packets at receivers are distributed. These models arise naturally in many large-scale systems, such as peer-to-peer networks, data centers, and distributed storage systems. Based on these models, we establish probabilistic bounds and asymptotic results on the minimum number of time slots to successfully transmit all the packets to all the receivers. Next, we propose and analyze a number of random network coding algorithms for finding the approximately optimal solution. Theoretical analysis and simulations are provided to verify the probabilistic bounds and the proposed algorithms.
Cyclization of Enediyne Radical Cations through Chemical, Photochemical, and Electrochemical Oxidation:  The Role of State Symmetry (1996)

ADVERTISEMENT RETURN TO ISSUEPREVNoteNEXTCyclization of Enediyne Radical Cations through Chemical, Photochemical, and Electrochemical Oxidation: The Role of State SymmetryDhruva Ramkumar, Mahadevan Kalpana, Babu Varghese, Sethuraman Sankararaman, Mavinahalli N. Jagadeesh, and Jayaraman ChandrasekharView Author Information Department of Chemistry and Regional Sophisticated Instrumentation Centre, Indian Institute of Technology, Madras - 600 036, India Department of Organic Chemistry, Indian Institute of Science, Bangalore - 560 012, India Cite this: J. Org. Chem. 1996, 61, 6, 2247–2250Publication Date (Web):March 22, 1996Publication History Received17 August 1995Published online22 March 1996Published inissue 1 January 1996https://doi.org/10.1021/jo951524yCopyright © 1996 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views751Altmetric-Citations53LEARN 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 InReddit Read OnlinePDF (198 KB) Get e-AlertsSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Cations,Charge transfer,Cyclization,Electron paramagnetic resonance spectroscopy,Photodissociation Get e-Alerts
Biochemical and physiological targets for miticides (1994)

Abstract The biorational design of new miticides requires an understanding of the biochemistry and physiology of mites. This review considers the interaction and impact of existing miticides with the cuticle, nervous system, growth and development, metabolism, feeding and behaviour and assesses the potential of these as possible targets for miticide development. Considering the sites of action of some of the major miticides, GABAergic and octopaminergic transmission, and oxidative phosphorylation are attractive targets for further miticide development.
The Herpes Simplex Virus Type 1 Alkaline Nuclease and Single-Stranded DNA Binding Protein Mediate Strand Exchange In Vitro (2003)

The replication of herpes simplex virus type 1 (HSV-1) DNA is associated with a high degree of homologous recombination. While cellular enzymes may take part in mediating this recombination, we present evidence for an HSV-1-encoded recombinase activity. HSV-1 alkaline nuclease, encoded by the UL12 gene, is a 5'-->3' exonuclease that shares homology with Redalpha, commonly known as lambda exonuclease, an exonuclease required for homologous recombination by bacteriophage lambda. The HSV-1 single-stranded DNA binding protein ICP8 is an essential protein for HSV DNA replication and possesses single-stranded DNA annealing activities like the Redbeta synaptase component of the phage lambda recombinase. Here we show that UL12 and ICP8 work together to effect strand exchange much like the Red system of lambda. Purified UL12 protein and ICP8 mediated the complete exchange between a 7.25-kb M13mp18 linear double-stranded DNA molecule and circular single-stranded M13 DNA, forming a gapped circle and a displaced strand as final products. The optimal conditions for strand exchange were 1 mM MgCl(2), 40 mM NaCl, and pH 7.5. Stoichiometric amounts of ICP8 were required, and strand exchange did not depend on the nature of the double-stranded end. Nuclease-defective UL12 could not support this reaction. These data suggest that diverse DNA viruses appear to utilize an evolutionarily conserved recombination mechanism.
Evaluation of cost savings with ferric carboxymaltose in anemia treatment through its impact on erythropoiesis-stimulating agents and blood transfusion: French healthcare payer perspective (2011)

The present economic model suggests that use of intravenous iron, according to recommendations of international guidelines, is cost saving, particularly in chemotherapy-induced anemia in breast cancers.
Ammonia production by intestinal bacteria: the effects of lactose, lactulose and glucose (1980)

Ammonia production by eight groups of intestinal bacteria was measured, and the effect on ammonia production of lowered pH and ambient ammonia concentration was determined. Endogenous ammonia production from bacterial protoplasm was also examined. To examine the mechanisms by which fermentable substrates reduce ammonia formation in a faecal incubation system, the effect of lactose, lactulose or glucose on ammonia release by pure cultures of intestinal bacteria was studied. The largest amounts of ammonia were generated by gram-negative anaerobes, clostridia, enterobacteria, and Bacillus spp. Gram-positive non-sporing anaerobes, streptococci and micrococci formed modest amounts, and lactobacilli and yeasts formed very little ammonia. All groups of bacteria formed less ammonia at pH 5.0 than at pH 7.0 and production of ammonia was not inhibited when 30 mmol ammonia/litre was included in the medium. Small amounts of ammonia were formed due to endogenous metabolism of bacterial cells. Washed cell suspensions of four isolates of Bacteroides, one clostridial isolate and two streptococcal isolates formed less ammonia from alanine, methionine or histidine after growth in the presence of either lactose or lactulose. In contrast, the Bacteroides isolates formed more ammonia from aspartate than from either lactose or lactulose. Also, cultures of gram-negative anaerobes and enterobacteria, and to a lesser extent clostridia and streptococci, formed significantly less ammonia in nutrient broth when lactose, lactulose or glucose was included in the medium. This decrease in ammonia formation was not due to a fall in pH of the medium. Ammonia production by gram-positive non-sporing anaerobes was not affected by carbohydrate fermentation. These results suggest that gram-negative anaerobic bacteria make a major contribution to ammonia generated from peptides and amino acids in vivo, and that ammonia may be formed from bacterial cells in the colon. Fermentation of lactose and lactulose may repress the formation and inhibit the activity of enzymes responsible for ammonia release. In the human colon these substrate effects may decrease the amount of ammonia available to exert a toxic effect on the host, and thus contribute to the beneficial effects of lactulose when it is used in the treatment of portosystemic encephalopathy.
p-Quinonemethide Analog of the CC-1065 and Duocarmycin Alkylation Subunits (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTp-Quinonemethide Analog of the CC-1065 and Duocarmycin Alkylation SubunitsDale L. Boger, Takahide Nishi, and Bradley R. TeegardenCite this: J. Org. Chem. 1994, 59, 17, 4943–4949Publication Date (Print):August 1, 1994Publication History Published online1 May 2002Published inissue 1 August 1994https://pubs.acs.org/doi/10.1021/jo00096a043https://doi.org/10.1021/jo00096a043research-articleACS PublicationsRequest reuse permissionsArticle Views258Altmetric-Citations22LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Bayesian online classifiers for text classification and filtering (2002)

This paper explores the use of Bayesian online classifiers to classify text documents. Empirical results indicate that these classifiers are comparable with the best text classification systems. Furthermore, the online approach offers the advantage of continuous learning in the batch-adaptive text filtering task.
Current mechanism of tunnel m.i.s. solar cells (1980)

Dark current/voltage characteristics have been examined as a function of temperature for two structures of A1-pSi m.i.s. solar cells. The solar cells have been prepared with interfacial oxide thickness ranging from 10 Å to 20 Å. The results show that the diode saturation current Jo for all oxide thicknesses behave as a majority-carrier current, highly dependent on the effective metal-to-semiconductor barrier height øms and the oxide-tunnel exponent X1/2δ. From the illuminated current/voltage characteristics the sum of øms and (KT/q)X1/2δ is found to be in the range of 730–1025 mV, increasing with increasing oxide thicknessand acceptor concentration.
Analysis Of K- And L-Shell Spectra Emitted From Implosions Of Argon Filled And Argon/Krypton Filled Microballoons (1988)

Experimental results from laser driven implosions of argon-and argon/krypton-filled polymer shell targets are presented. Analysis of the results is discussed with regard to the physics involved and the potential use of spectral features as density diagnostics.
No Direct Neuronotoxicity by HIV-1 Virions or Culture Fluids from HIV-1-Infected T Cells or Monocytes (1992)

Macrophages and microglia are the principal target cells for human immunodeficiency virus (HIV) in brain, and as such, are likely participants in the neuropathology of HIV infection. In a model system for this process, we found that fluids from human monocyte cultures enhanced survival and differentiation of the neurons in fetal rat brain explants. In contrast, fluids from HIV-infected monocyte cultures were strongly toxic to neurons and paradoxically enhanced the proliferation of glial cells. Further, neuronotoxic activity in these fluids was mediated through activation of NMDA binding receptors on the neurons and was inhibited by any of several different NMDA antagonists. Neuronotoxic activity was directly related to contamination of the HIV virus stock with Mycoplasma arginini and M. hominis. Pure cultures of mycoplasma, bacterial lipopolysaccharide (LPS), or murine recombinant tumor necrosis factor alpha (rTNF alpha) each induced neuronotoxicity which exactly mirrored that induced by the contaminated HIV stock. It is likely that mycoplasma or components of the mycoplasma plasma membrane stimulate TNF alpha production by the glial cells in the brain explants. Indeed, careful depletion of glial cells in these explants prevented mycoplasma or LPS-mediated neuronotoxicity. No neuronotoxicity was evident with HIV-1 virus stock, HIV-1 gp120, or culture fluids from HIV-infected T cells or monocytes when these preparations were free of contamination by mycoplasma and LPS. These findings suggest caution in interpretation of those experiments in which similar contamination has not been rigorously excluded.
Classical Electrostatics in Biology and Chemistry (1995)

A major revival in the use of classical electrostatics as an approach to the study of charged and polar molecules in aqueous solution has been made possible through the development of fast numerical and computational methods to solve the Poisson-Boltzmann equation for solute molecules that have complex shapes and charge distributions. Graphical visualization of the calculated electrostatic potentials generated by proteins and nucleic acids has revealed insights into the role of electrostatic interactions in a wide range of biological phenomena. Classical electrostatics has also proved to be successful quantitative tool yielding accurate descriptions of electrical potentials, diffusion limited processes, pH-dependent properties of proteins, ionic strength-dependent phenomena, and the solvation free energies of organic molecules.
Leptospiral Outer Membrane Proteins OmpL1 and LipL41 Exhibit Synergistic Immunoprotection (1999)

New vaccine strategies are needed for prevention of leptospirosis, a widespread human and veterinary disease caused by invasive spirochetes belonging to the genus Leptospira. We have examined the immunoprotective capacity of the leptospiral porin OmpL1 and the leptospiral outer membrane lipoprotein LipL41 in the Golden Syrian hamster model of leptospirosis. Specialized expression plasmids were developed to facilitate expression of leptospiral proteins in Escherichia coli as the membrane-associated proteins OmpL1-M and LipL41-M. Although OmpL1-M expression is highly toxic in E. coli, this was accomplished by using plasmid pMMB66-OmpL1, which has undetectable background expression without induction. LipL41-M expression and processing were enhanced by altering its lipoprotein signal peptidase cleavage site to mimic that of the murein lipoprotein. Active immunization of hamsters with E. coli membrane fractions containing a combination of OmpL1-M and LipL41-M was found to provide significant protection against homologous challenge with Leptospira kirschneri serovar grippotyphosa. At 28 days after intraperitoneal inoculation, survival in animals vaccinated with both proteins was 71% (95% confidence interval [CI], 53 to 89%), compared with only 25% (95% CI, 8 to 42%) in the control group (P < 0.001). On the basis of serological, histological, and microbiological assays, no evidence of infection was found in the vaccinated survivors. The protective effects of immunization with OmpL1-M and LipL41-M were synergistic, since significant levels of protection were not observed in animals immunized with either OmpL1-M or LipL41-M alone. In contrast to immunization with the membrane-associated forms of leptospiral proteins, hamsters immunized with His(6)-OmpL1 and His(6)-LipL41 fusion proteins, either alone or in combination, were not protected. These data indicate that the manner in which OmpL1 and LipL41 associates with membranes is an important determinant of immunoprotection.
Review: Functional dyspepsia (2010)

Dyspepsia is a common term used for a heterogeneous group of abdominal symptoms. Functional dyspepsia (FD) is the focus of this review. The 2006 Rome III criteria defined FD and its subgroups, postprandial distress syndrome (PDS) and epigastric pain syndrome (EPS). FD is a very common condition with a high prevalence throughout the world, adversely affecting the quality of life of patients. The pathophysiology of FD has been under investigation during the past two decades. Multiple mechanisms such as abnormal gastric emptying, visceral hypersensitivity, impaired gastric accommodation, and central nervous system factors are likely involved. Several tests are available for the assessment of various physiologic functions possibly involved in the pathogenesis of FD, and some of these could be used in clinical practice, helping to understand the abnormalities underlining patients' complaints. Currently, the possibilities of pharmacological therapy for FD are still limited, however, experience of using prokinetics, tricyclic antidepressants, selective serotonin-reuptake inhibitors (SSRIs), proton-pump inhibitors (PPIs), and several alternative techniques has been accumulated. The different combinations of alterations in physiologic gastrointestinal and central nervous system functions result in the very heterogeneous nature of FD so combined approaches to these patients could be beneficial in challenging cases.
Enhanced dispositioning of reticle defects using the Virtual Stepper with automated defect severity scoring (2001)

As Optical Proximity Correction (OPC0 and Phase Shifting (PSM) become more and more commonly used for producing smaller features on wafer, the photomask (reticle) manufacturing, that is mask writing, inspection and repairing, and quality assurance become more challenging for both mask shops and wafer fabs. Consequently, a powerful defect analysis tool is needed to determine which defect is a nuisance defect, which defect needs to be repaired, and how good is the repair. It should have the capability for defect printability prediction and analysis of defect impact on device performance. In this paper, we will study and characterize the printability prediction of programmed defects on binary OPC masks by the Virtual Stepper System with its newly developed Automated Defect Severity Scoring (ADSS) function. AMD's defect test reticles HellOPC2 were used. The Virtual Stepper simulation and defect impact analysis results (the automatically calculated Defect Severity Score) will be compared to the SEM images and measurements of wafer prints using 193nm lithography. The results demonstrate that the Virtual Stepper System with its ADSS feature can provide its user with an automate, fast and accurate way of analyzing the impact of a defect. The Virtual Stepper System with ADSS function will be a suitable tool for photomask defect critically assessment in mask shops and wafer fabs.
High-quality {20-21} GaN layers on patterned sapphire substrate with wide-terrace (2011)

A {20-21} GaN layer was grown from a c-plane-like sapphire sidewall of a {22-43} patterned sapphire substrate according to the epitaxial relationship between c-GaN and c-sapphire despite {20-21} GaN is not growing on {22-43} sapphire. The as-grown {20-21} GaN layer had an m- and {10-11} facet structure. To improve the {20-21} GaN layer, a wide-terrace was attempted. The defects in the GaN layer were clustered on the m-facets, resulting in a dislocation density of less than 5.6 × 105/cm2 on the {10-11} facets. The {20-21} GaN layer had an excellent photoluminescence spectrum indicating a small number of defects.
In search of an optimized electrolyte for Na-ion batteries (2012)

Electrolytes are essential for the proper functioning of any battery technology and the emerging Na-ion technology is no exception. Hence, a major focus on battery research is to identify the most appropriate formulation so as to minimize interface reactions and enhance both cell performances and safety aspects. In order to identify suitable electrolyte formulations for Na-ion chemistry we benchmarked various electrolytes containing diverse solvent mixtures (cyclic, acyclic carbonates, glymes) and Na-based salts having either F-based or perchlorate anions and measured viscosity, ionic conductivity, and thermal and electrochemical stability. The binary EC:PC solvent mixture has emerged as the best solvent formulation and has been used to test the performance of Na/hard carbon cells with both NaClO4 and NaPF6 as dissolved salts. Hard carbon electrodes having reversible capacities of 200 mA h g−1 with decent rate capability and excellent capacity retention (>180 cycles) were demonstrated. Moreover, DSC heating curves demonstrated that fully sodiated hard carbon cycled in NaPF6–EC:PC exhibits the highest exothermic onset temperature and nearly the lowest enthalpy of reaction, thus making this electrolyte most attractive for the development of Na-ion batteries.