gebhart/patrepeval huggingface dataset:
Assessment of blind predictions of protein–protein interactions: Current status of docking methods (2003)

The current status of docking procedures for predicting protein-protein interactions starting from their three-dimensional structure is assessed from a first major evaluation of blind predictions. This evaluation was performed as part of a communitywide experiment on Critical Assessment of PRedicted Interactions (CAPRI). Seven newly determined structures of protein-protein complexes were available as targets for this experiment. These were the complexes between a kinase and its protein substrate, between a T-cell receptor beta-chain and a superantigen, and five antigen-antibody complexes. For each target, the predictors were given the experimental structures of the free components, or of one free and one bound component in a random orientation. The structure of the complex was revealed only at the time of the evaluation. A total of 465 predictions submitted by 19 groups were evaluated. These groups used a wide range of algorithms and scoring functions, some of which were completely novel. The quality of the predicted interactions was evaluated by comparing residue-residue contacts and interface residues to those in the X-ray structures and by analyzing the fit of the ligand molecules (the smaller of the two proteins in the complex) or of interface residues only, in the predicted versus target complexes. A total of 14 groups produced predictions, ranking from acceptable to highly accurate for five of the seven targets. The use of available biochemical and biological information, and in one instance structural information, played a key role in achieving this result. It was essential for identifying the native binding modes for the five correctly predicted targets, including the kinase-substrate complex where the enzyme changes conformation on association. But it was also the cause for missing the correct solution for the two remaining unpredicted targets, which involve unexpected antigen-antibody binding modes. Overall, this analysis reveals genuine progress in docking procedures but also illustrates the remaining serious limitations and points out the need for better scoring functions and more effective ways for handling conformational flexibility.
A study of graphenes prepared by different methods: characterization, properties and solubilization (2008)

Graphene has been prepared by different methods: pyrolysis of camphor under reducing conditions (CG), exfoliation of graphitic oxide (EG), conversion of nanodiamond (DG) and arc evaporation of SiC (SG). The samples were examined by X-ray diffraction (XRD), transmission electron microscopy, atomic force microscopy, Raman spectroscopy and magnetic measurements. Raman spectroscopy shows EG and DG to exhibit smaller in-plane crystallite sizes, but in combination with XRD results EG comes out to be better. The CG, EG and DG samples prepared by us have BET surface areas of 46, 925 and 520 m2 g−1 respectively and exhibit significant hydrogen uptake up to 3 wt%. EG also exhibits a high CO2 uptake (34.7 wt%). Electrochemical redox properties of the graphene samples have been examined in addition to their use in electrochemical supercapacitors. Functionalization of EG and DG through amidation has been carried out with the purpose of solubilizing them in non-polar solvents. Water-soluble graphene has been produced by extensive acid treatment of EG or treatment with polyethylene glycol.
Electrodeposition of tin alloys from alkaline stannate baths (1935)

R. G. Monk and H. J. T. Ellingham, Trans. Faraday Soc., 1935, 31, 1460 DOI: 10.1039/TF9353101460
Quadratic Programming based data assimilation with passive drifting sensors for shallow water flows (2009)

We present a method for assimilating Lagrangian sensor measurement data into a shallow water equation model. Using our method, the variational data assimilation problem is formulated as a quadratic programming problem with linear constraints. Drifting sensors that gather position and velocity information in the modeled system can then be used to refine the estimate of the initial conditions of the system. A new sensor network hardware platform for gathering flow information is presented. We summarize the results of a field experiment designed to demonstrate the capabilities of our assimilation method with data gathered from the sensors. Validation of the results is performed by comparing them to an estimate derived from an independent set of static sensors.
Amyloid-like Features of Polyglutamine Aggregates and Their Assembly Kinetics (2002)

The repeat length-dependent tendency of the polyglutamine sequences of certain proteins to form aggregates may underlie the cytotoxicity of these sequences in expanded CAG repeat diseases such as Huntington's disease. We report here a number of features of various polyglutamine (polyGln) aggregates and their assembly pathways that bear a resemblance to generally recognized defining features of amyloid fibrils. PolyGln aggregation kinetics displays concentration and length dependence and a lag phase that can be abbreviated by seeding. PolyGln aggregates exhibit classical beta-sheet-rich circular dichroism spectra consistent with an amyloid-like substructure. The fundamental structural unit of all the in vitro aggregates described here is a filament about 3 nm in width, resembling the protofibrillar intermediates in amyloid fibril assembly. We observed these filamentous structures either as isolated threads, as components of ribbonlike sheets, or, rarely, in amyloid-like twisted fibrils. All of the polyGln aggregates described here bind thioflavin T and shift its fluorescence spectrum. Although all polyGln aggregates tested bind the dye Congo red, only aggregates of a relatively long polyGln peptide exhibit Congo red birefringence, and this birefringence is only observed in a small portion of these aggregates. Remarkably, a monoclonal antibody with high selectivity for a generic amyloid fibril conformational epitope is capable of binding polyGln aggregates. Thus, polyGln aggregates exhibit most of the characteristic features of amyloid, but the twisted fibril structure with Congo red birefringence is not the predominant form in the polyGln repeat length range studied here. We also find that polyGln peptides exhibit an unusual freezing-dependent aggregation that appears to be caused by the freeze concentration of peptide and/or buffer components. This is of both fundamental and practical significance. PolyGln aggregation is revealed to be a highly specific process consistent with a significant degree of order in the molecular structure of the product. This ordered structure, or the assembly process leading to it, may be responsible for the cell-specific neuronal degeneration observed in Huntington's and other expanded CAG repeat diseases.
The Association between Laryngopharyngeal Sensory Deficits, Pharyngeal Motor Function, and the Prevalence of Aspiration with Thin Liquids (2003)

Patients with severely diminished laryngopharyngeal sensation and pharyngeal motor function are at an extremely high risk of aspirating thin liquids (100%). Moderate sensory deficits only appear to influence the prevalence of thin liquid aspiration in the presence of pharyngeal motor dysfunction. Severe laryngopharyngeal sensory deficits are associated with the aspiration of thin liquids regardless of the integrity of pharyngeal motor function. We assume that all persons with an insensate laryngopharynx aspirate thin liquids until proved otherwise. These results emphasize the relationship between laryngopharyngeal sensation and pharyngeal motor function in the evaluation of patients for suspected aspiration.
Molecular Genetic Analysis of Populations. A Practical Approach. (1993)

1. Starch Gel Electrophoresis of Allozymes 2. Total DNA Isolation 3. mtDNA Isolation, Separation and Detection of Fragments 4. Genomic Libraries and the Development of Species-specific Probes 5. RFLP Analysis Using Heterologus Probes 6. PCR Protocols and Population Analysis by Direct DNA Sequencing and PCR-based DNA Fingerprinting 7. Microsatellites 8. Detection of Genetic Variation by DNA Conformational and Denaturing Gradient Methods 9. Multi- and Single-locus DNA Fingerprinting 10. Automated DNA Detection with Fluorescence-based Technologies
Immunomodulation by SanPharma Fungal Metabolic Products (2006)

The fungal metabolite products from SanPharma specifically activate human NK cells in vitro.
Hairy Hybrid Nanoparticles of Magnetic Core, Fluorescent Silica Shell, and Functional Polymer Brushes (2009)

ADVERTISEMENT RETURN TO ISSUEPREVNoteNEXTHairy Hybrid Nanoparticles of Magnetic Core, Fluorescent Silica Shell, and Functional Polymer BrushesGuoliang Li, Dawn Liming Zeng, Liang Wang, Baoyu, Zong, K. G. Neoh, and E. T. Kang*View Author Information Department of Chemical & Biomolecular Engineering, National University of Singapore, Kent Ridge, Singapore 119260*To whom correspondence should be addressed. E-mail: [email protected]Cite this: Macromolecules 2009, 42, 21, 8561–8565Publication Date (Web):September 18, 2009Publication History Received21 July 2009Revised4 September 2009Published online18 September 2009Published inissue 10 November 2009https://pubs.acs.org/doi/10.1021/ma901592jhttps://doi.org/10.1021/ma901592jbrief-reportACS PublicationsCopyright © 2009 American Chemical SocietyRequest reuse permissionsArticle Views2726Altmetric-Citations45LEARN 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 SUBJECTS:Fluorescence,Nanocomposites,Nanoparticles,Radical polymerization,Silica Get e-Alerts
MORPHOLOGICAL DEVELOPMENT OF CHIKUNGUNYA VIRUS (1966)

Chikungunya virus was first detected by electron microscopy of primary chick embryo fibroblast cultures 5 hours after inoculation. Two types of particles were observed in the cytoplasm of infected cells, but not in uninoculated cells. The smaller, presumably precursor particles, measured 260 to 280 Å. The larger particles contained dense cores 260 to 280 Å in diameter and outer shells 500 to 560 Å in diameter. In cell lysates stained negatively with phosphotungstic acid 12 and 24 hours after inoculation, virus particles surrounded by fine outer membranes showed diameters of 540 to 580 Å. Infective virus was first detected 5 hours after inoculation and maximum yields of cell-associated and extracellular virus were attained at 8 to 10 hours.
Antagonism of RAGE suppresses peripheral nerve regeneration (2004)

Axotomy of peripheral nerve triggers events that coordinate a limited inflammatory response to axonal degeneration and initiation of neurite outgrowth. Inflammatory and neurite outgrowth-promoting roles for the receptor for advanced glycation end products (RAGE) have been suggested, so we tested its role in peripheral nerve regeneration. Analysis of immunohistochemical localization of RAGE by confocal microscopy revealed that RAGE was expressed in axons and infiltrating mononuclear phagocytes upon unilateral sciatic nerve crush in mice. Administration of soluble RAGE, the extracellular ligand binding domain of RAGE, or blocking F(ab')2 fragments of antibodies raised to either RAGE or its ligands, S100/calgranulins or amphoterin, reduced functional recovery as assessed by motor and sensory nerve conduction velocities and sciatic functional index and reduced regeneration, as assessed by myelinated fiber density after acute crush of the sciatic nerve. In parallel, in mice subjected to RAGE blockade, decreased numbers of mononuclear phagocytes infiltrated the distal nerve segments after crush. These findings provide the first evidence of an innate function of the ligand/RAGE axis and suggest that RAGE plays an important role in regeneration of the peripheral nervous system.
An Affective Interface for Conveying User Feedback (2010)

Capturing and understanding feedback received from customers in an efficient manner plays a critical role in areas such as Customer relationship management (CRM).Measures of customers' attitude towards a product or service are traditionally obtained using questionnaires formatted as x-point Likert scales, with results typically displayed numerically and sometimes presented in graphic forms. Current `affective'CRM solutions have focused on customer emotion detection by recognising non-verbal cues and physiological signals from customers (Input related research). However, these methods, although technologically advanced are only at a conceptual level and lack the viability and flexibility required by current CRM solutions. This paper presents a system prototype for Non-Verbal Affective User Feedback based on output related affective research. The system converts multi-criteria based estimates of a customer's attitude towards a product or service,obtained using traditional CRM surveys, into a non-verbal representation in the form of virtual facial expressions, or emoticons. Real facial expressions provide a feedback in a concise pictorial form whose emotional content is readily recognisable. We focus on enabling the system to choose those emoticons that, with regards to their emotional content, would be unambiguously legible by users. Our approach is intended to improve the efficiency of the representation mode of CRM survey data making it visually comprehensible `at-a-glance'.
“They'll Change What They're Doing If They Know that You're Watching”: Measuring Reactivity in Health Behavior Because of an Observer's Presence— A Case from the Peruvian Amazon (2008)

Social scientists often employ direct observation to study human behavior, but a health researcher who proposes it may face considerable skepticism from colleagues. Concerns about reactivity lead many to question the validity of observational data. Because few studies have measured reactivity, evidence to evaluate this concern is limited. The authors report results from their systematic measurement of reactivity during a Peruvian malaria prevention study. In sixty observations over nine months, observers recorded all behavior they perceived as potentially reactive. The authors then assessed reactivity using iterative coding and analysis. Although they documented 339 reactivity episodes, only two involved behaviors related to study objectives. These findings are consistent with prior research and provide additional evidence that reactivity, though common, need not bias study results. The authors suggest strategies for assessing reactivity that can help reassure skeptics and reinforce the validity of observational data.
Reactions of Benzocyclic β-Keto Esters with Sulfonyl Azides. 2.<sup>1</sup> Further Insight into the Influence of Azide Structure and Solvent on the Reaction Course (1999)

The reactions of 2-ethoxycarbonyl-1-benzosuberone with 4-methoxybenzenesulfonyl, 2,4,6-triisopropylbenzenesulfonyl, methanesulfonyl, and trifluoromethanesulfonyl azide, in the presence of triethylamine, have been investigated in <i>N</i>,<i>N</i>-dimethylformamide, acetonitrile, or tetrahydrofuran with the intent of clarifying the influence of both the azide electrophile and solvent on the reaction course. The present findings, in addition to those previously obtained with tosyl and 4-nitrobenzenesulfonyl azide, indicate that both the electronic features of the sulfonyl azide and the solvent polarity greatly affect the possible occurrence of azidation and/or Favorskii-type ring contraction at the expense of deacylating diazo transfer. Azidation is promoted by the less electrophilic azides, while it is virtually avoided by the more electrophilic ones. Ring contraction occurs to a limited extent with the less electrophilic azides, but it becomes the main process with those more electrophilic. Moreover, azidation is virtually unaffected by the solvent polarity, while ring contraction can markedly be enhanced by a highly polar solvent. Firm evidence has additionally been obtained that, in contrast to a previous claim, trifluoromethanesulfonyl azide can normally perform diazotization of acyclic β-keto esters in preference to azidation.
ABCB1 Is Upregulated in Acquisition of Taxane Resistance: Lessons from Esophageal Squamous Cell Carcinoma Cell Lines (2016)

Esophageal cancer is one of the common malignancies worldwide, particularly in eastern African and Asian countries including Japan. Taxane (paclitaxel or docetaxel) is one of the effective chemotherapeutic reagents for patients with esophageal cancer, but acquisition of chemoresistance frequently occurs; this is one of the most frequent causes for therapeutic failure. In this study, we established three taxane resistant esophageal squamous cell carcinoma cell lines and explored possible mechanisms for the acquisition of chemoresistance. Microarray analyses indicated that the ABCB1 (ATP binding cassette subfamily B member 1) gene was significantly upregulated in taxane resistant esophageal cancer cell lines. Moreover, we found that siRNA mediated ABCB1 knockdown successfully restored drug sensitivity in both paclitaxel and docetaxel resistant esophageal cancer cell lines. In conclusion, we propose that ABCB1 might play a pivotal role in acquisition of taxane resistance and could be a promising target for treatment of patients with esophageal cancer after acquisition of taxane resistance.
Comprehensive Calibration and Registration Procedures for Augmented Reality (2001)

Augmented Reality - best described as adding computer-generated virtual content to the real environment  needs more adjustments to work properly than immersive virtual environments. To be perceived as an augmentation of reality, the virtual environment has to be properly aligned to the real world. This registration process has to be done at least once for every hardware set-up, but may have to be repeated in part or completely for each user, prop or device to be included both in the real and the virtual world. In this paper, we propose a comprehensive process for registration and calibration tasks necessary to implement correct augmentation. This includes procedures for calibrating projective and head-mounted displays, tracking systems, tracked input devices and props. Our method unifies the necessary tasks of world-toaugmentation alignment, display calibration and registration of tracked and static props in one, interactive set-up process, which can easily be conducted by the untrained user.
Exposure of surgeons-in-training to radiation during intramedullary fixation of femoral shaft fractures. (1992)

Owing to the continuous turnover of registrars and radiographers, most of the trauma-related orthopaedic surgery in this academic hospital is done by inexperienced surgeons-in-training and the fluoroscopy by junior radiographers. This could result in excessive radiation doses. Calibrated lithium fluoride thermoluminescent chips were secured to various parts of the primary surgeon's body to quantify the radiation dose received during the insertion of an intramedullary nail. Closed intramedullary fixation of 15 fractures of the femur was done with interlocking as necessary. The total average exposure time was 14 minutes 45 seconds per procedure. Distal locking took up 31% of this time. The mean radiation dose to the surgeon's eyes and thyroid was 0.13 mGy and to the dominant hand 2.10 mGy. This would allow the performance of about 350 such procedures per year before the maximum permissible dose level was reached. Recommendations to decrease irradiation dosage are made.
Presence of HIV-1 Gag-Specific IFN-γ+IL-2+ and CD28+IL-2+ CD4 T Cell Responses Is Associated with Nonprogression in HIV-1 Infection (2002)

HIV immunity is likely CD4 T cell dependent. HIV-specific CD4 T cell proliferative responses are reported to correlate inversely with virus load and directly with specific CD8 responses. However, the phenotype and cytokine profile of specific CD4 T cells that correlate with disease is unknown. We compared the number/function of Gag p24-specific CD4 T cells in 17 HIV-infected long-term nonprogressors (LTNPs) infected for a median of 14.6 years with those of 16 slow progressors (SPs), also HIV infected for a median of 14 years but whose CD4 count had declined to <500 cells/ micro l. Compared with SPs, LTNPs had higher numbers of specific CD4s that were double positive for IFN-gamma and IL-2 as well as CD28 and IL-2. However, CD4 T cells that produced IL-2 alone (IL-2(+)IFN-gamma(-)) or IFN-gamma alone (IFN-gamma(+)IL-2(-)) did not differ between LTNPs and SPs. The decrease in p24-specific CD28(+)IL-2(+) cells with a concomitant increase of p24-specific CD28(-)IL-2(+) cells occurred before those specific for a non-HIV Ag, CMV. p24-specific CD28(-)IL-2(+) cells were evident in LTNPs and SPs, whereas the CMV-specific CD28(-)IL-2(+) response was confined to SPs. The difference between LTNPs and SPs in the Gag p24 IFN-gamma(+)IL-2(+) response was maintained when responses to total Gag (p17 plus p24) were measured. The percentage and absolute number of Gag-specific IFN-gamma(+)IL-2(+) but not of IFN-gamma(+)IL-2(-) CD4s correlated inversely with virus load. The Gag-specific IFN-gamma(+)IL-2(+) CD4 response also correlated positively with the percentage of Gag-specific IFN-gamma(+) CD8 T cells in these subjects. Accumulation of specific CD28(-)IL-2(+) helpers and loss of IFN-gamma(+)IL-2(+) CD4 T cells may compromise specific CD8 responses and, in turn, immunity to HIV.
Possible neuroprotective effect of brimonidine in a mouse model of ischaemic optic neuropathy (2009)

The increase in HO-1 associated with rAION is mitigated with brimonidine treatment, especially when administered intraperitoneally. Topical brimonidine apparently reduces VEGF, Tie-2, HIF-1alpha and GPX-1 expression on day 21. These results agree with published data and may have therapeutic implications for patients diagnosed with AION in the acute phase.
Detoxification on top of enhanced, diamine-extended glutaraldehyde fixation significantly reduces bioprosthetic root calcification in the sheep model. (2003)

It was shown in a circulatory sheep model that a combination of DA-enhanced fixation with an extraction process of excess GA leads to a distinct mitigation of leaflet and aortic wall calcification.