gebhart/patrepeval huggingface dataset:
Crystallization of immunoglobulin Fab fragments specific for DNA. (1988)

The purification and crystallization of Fab fragments of two mouse monoclonal immunoglobulins specific for different DNA structures are described. In each case, papain digestion of the immunoglobulins produced a mixture of Fab species differing in their isoelectric points. Purification of one of these species was required to obtain suitable crystals. One of these antibodies, Jel 72, is specific for right-handed duplex poly(dG).poly(dC). An Fab fragment of Jel 72 with a pI of 8.8 was purified by anion-exchange chromatography and used to obtain crystals from 56% saturated ammonium sulfate and 50 mM sodium acetate, pH 4.2, that diffract to 2.6-A resolution. They belong to the orthorhombic space group P2(1)2(1)2(1), with cell dimensions of a = 94.6, b = 102.6, c = 92.4 A. The other antibody, Jel 318, binds triple-stranded DNA poly[d(Tm5C)].poly[d(GA)].poly[d(m5C + T)]. Jel 318 Fab fragments with isoelectric points of 7.6 and 7.8 were also purified by anion-exchange chromatography, and crystals were obtained from 12% polyethylene glycol 8000, 50 mM NaCl, and 10 mM Tris.HCl, pH 7.8. These crystals diffract to about 2.4-A resolution and also belong to the orthorhombic space group P2(1)2(1)2(1), with cell dimensions of a = 82.4, b = 139.5, and c = 42.0 A. For both Fab fragments, crystal size and quality improved dramatically upon purification of an individual isoelectric species.
Half-Sandwich Ruthenium Phenolate–Oxazoline Complexes: Experimental and Theoretical Studies in Catalytic Transfer Hydrogenation of Nitroarene (2017)

In this work, five ruthenium complexes [Ru(p-cymene)LCl] containing phenolate-oxazoline ligands [L = 2-(4,5-dihydrooxazol-2-yl)phenol (1); L = 2-(4-methyl-4,5-dihydrooxazol-2-yl)phenol (2); L = 2-(4-ethyl-4,5-dihydrooxazol-2-yl)phenol (3); L = 2-(4-phenyl-4,5-dihydrooxazol-2-yl)phenol (4); and 2-(4,4-dimethyl-4,5-dihydrooxazol-2-yl)phenol (5)] were synthesized and characterized. The solid-state structures of all ruthenium complexes were determined by single-crystal X-ray diffraction. The catalytic activities of these complexes in the transfer hydrogenation reaction of nitroarene to aniline were investigated. Aniline and their derivatives were obtained in good to excellent yields with isopropanol as the hydride source. The present protocol provides an environmentally benign synthetic method for the reduction of nitroarenes to anilines without employing harsh reaction conditions. Theoretical studies employing density functional theory were carried with the aim to propose a feasible reaction mechanism and to draw insights into the reactivity of the half-sandwich ruthenium catalyst.
VE-Cadherin Regulates Endothelial Actin Activating Rac and Increasing Membrane Association of Tiam (2002)

Previously published reports support the concept that, besides promoting homotypic intercellular adhesion, cadherins may transfer intracellular signals. However, the signaling pathways triggered by cadherin clustering and their biological significance are still poorly understood. We report herein that transfection of VE-cadherin (VEC) cDNA in VEC null endothelial cells induces actin rearrangement and increases the number of vinculin positive adhesion plaques. VEC expression augments the level of active Rac but decreases active Rho. Microinjection of a dominant negative Rac mutant altered stress fiber organization, whereas inhibition of Rho was ineffective. VEC expression increased protein and mRNA levels of the Rac-specific guanosine exchange factor Tiam-1 and induced its localization at intercellular junctions. In addition, in the presence of VEC, the amounts of Tiam, Rac, and the Rac effector PAK as well as the level of PAK phosphorylation were found increased in the membrane/cytoskeletal fraction. These observations are consistent with a role of VEC in localizing Rac and its signaling partners in the same membrane compartment, facilitating their reciprocal interaction. Through this mechanism VEC may influence the constitutive organization of the actin cytoskeleton.
Increased Interferon Alpha Expression in Circulating Plasmacytoid Dendritic Cells of HIV-1-Infected Patients (2008)

Circulating pDC decline sharply in the course of HIV-1 disease, but express high levels of IFN alpha, which may represent a hallmark of systemic immune dysfunction.
Nonvisual Alternative Display Techniques for Output from Graphics-Based Computers (1989)

In the past, computer displays consisted mostly of unformatted text or simple row-column displays of information. This made providing access for persons who were blind a relatively straightforward task. As computers become more visually complex, however, new strategies are needed to augment the standard approaches to provide access. This article reviews the different types of information that are currently presented visually on computer systems and then discusses possible alternative display mechanisms for each that would be usable by blind persons. Some of the techniques described are commercially available; some exist as research prototypes; others, however, are still conceptual in nature. This article provides an overview and a summary of techniques identified as a result of the planning conference. The information present was compiled as a part of a state-of-the-art session, held in Madison, Wisconsin, on access to visual graphic computer interfaces by blind persons; the session was cosponsored by the Trace R&amp;D Center, the Veterans Administration, the National Federation of the Blind, the American Foundation for the Blind, and Smith-Kettlewell Institute.
The Ynet: an interconnect structure for a highly concurrent data base computer system (2003)

The author describes the design considerations for the Ynet, an interconnect structure for a highly concurrent database system which also requires high availability and real-time operation. The Ynet is the basis of a multiple-instruction, multiple-data (MIMD) concurrent processing architecture which can connect up to 1024 high-performance microprocessors to form a very-high performance system. Most of the functionality of the Ynet results from the logic implemented in the processor interface. The processor interface is divided into three sections, each of which is implemented by a finite-state machine. Example message flows are presented to show how various features of the Ynet operate for sending messages through the system. It is demonstrated how the Ynet design responds to the challenges of a highly concurrent environment, but also to the challenges of real-time, high-availability, multiuser applications. In this regard, the Ynet addresses problems usually not considered in the design of existing concurrent processing architectures.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Membrane Surface Modification by Plasma-Induced Polymerization of Acrylamide for Improved Surface Properties and Reduced Protein Fouling (2002)

Hydrophilic modification of porous polyethersulfone (PES) membranes was achieved by Ar-plasma treatment followed by graft copolymerization with acrylamide (AAm) in the vapor phase. Both surfaces of the modified membranes were found to be highly hydrophilic, the permanency of which depends on the grafting yield. The graft reaction was confirmed by X-ray photoelectron spectroscopy (XPS) and Fourier transform infrared (FTIR) spectroscopy. The grafting rate was dependent on plasma exposure time. The surface and pore structures of PES membranes were viewed using scanning electron microscopy (SEM), revealing no surface damage and only a slight alteration in pore structure. As a result of the incorporation of polar functionalities, the glass transition temperature (Tg) of both the Ar-plasma treated and AAm grafted membranes increased. A moderate change in the tensile strength of the modified membranes was also observed. Most importantly, the AAm grafting made the membrane surface less susceptible to adsorption of BSA proteins. The grafted membranes also give greater flux recoveries after cleaning, indicating that the protein fouling layer was reversible because of the hydrophilic nature of the modified membranes.
Nonradiative exciton energy transfer in hybrid organic-inorganic heterostructures (2008)

Nonradiative energy transfer from a GaAs quantum well to a thin overlayer of an infrared organic semiconductor dye is unambiguously demonstrated. The dynamics of exciton transfer are studied in the time domain by using pump-probe spectroscopy at the donor site and fluorescence spectroscopy at the acceptor site. The effect is observed as simultaneous increase in the population decay rate at the donor and of the rise time of optical emission at the acceptor sites. The hybrid configuration under investigation provides an alternative nonradiative, noncontact pumping route to electrical carrier injection that overcomes the losses imposed by the associated low carrier mobility of organic emitters.
New explanation of the infrared and Raman .nu.(XH) band shape of hydrogen-bonded complexes (1973)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNew explanation of the infrared and Raman .nu.(XH) band shape of hydrogen-bonded complexesJ. Lascombe, J. C. Lassegues, and P. V. HuongCite this: J. Phys. Chem. 1973, 77, 23, 2779–2782Publication Date (Print):November 1, 1973Publication History Published online1 May 2002Published inissue 1 November 1973https://doi.org/10.1021/j100641a012RIGHTS & PERMISSIONSArticle Views23Altmetric-Citations16LEARN 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 PDF (485 KB) Get e-Alerts
A Multithreaded Implementation of Assist Functions to Control a Virtual Reality Model of a 6-DoF Robot Arm for Rehabilitation Applications (2023)

This paper describes a multithreaded platform to implement a haptic interface to control a Virtual Reality (VR) model of a 6-DoF arm with applications towards rehabilitation robotics. The approach allows the defined threads to execute concurrently, resulting in increased utilization of the processor resources and higher instruction execution rates consistent with a realistic rendering of the touch sensation and smooth graphics transitions for the VR simulation. The haptic interface allows for physical rendering of the human–machine interactions through force feedback and velocity scaling enhancing the manipulation capabilities of persons with disabilities. Assist functions are modeled through the use of physical simulation of springs, spring with damping, and velocity scaling. The level of assistance is calculated by concurrent threads running the virtual model of the arm and the haptic loop at two different update rates.
Emerging role of obeticholic acid in the management of nonalcoholic fatty liver disease (2016)

Nonalcoholic fatty liver disease (NAFLD) is the commonest chronic liver disease and its prevalence is increasing driven by the pandemic of obesity and type 2 diabetes mellitus. NAFLD can progress to cirrhosis and is associated with increased risk for cardiovascular disease and hepatocellular cancer. Diet and exercise are limited by suboptimal long-term adherence in patients with NAFLD. On the other hand, current pharmacological treatment of NAFLD has limited efficacy and unfavorable safety profile. In this context, obeticholic acid (OCA), a selective agonist of the farnesoid X receptors, might represent a useful option in these patients. Preclinical studies suggest that OCA improves hepatic steatosis, inflammation and fibrosis. A proof-of-concept study and the randomized, placebo-controlled Farnesoid X Receptor Ligand Obeticholic Acid in non-alcoholic steatohepatitis Treatment (FLINT) trial also showed improvements in liver histology in patients with NAFLD who received OCA. Weight loss and reduction in blood pressure were also observed. However, the effects of OCA on insulin resistance are conflicting and the lipid profile is adversely affected by this agent. In addition, pruritus is frequently observed during treatment with OCA and might lead to treatment discontinuation. However, given the limitations of existing treatments for NAFLD, OCA might represent a useful therapeutic option in selected patients with NAFLD.
Backtransforming Rank Order Kriging Estimates (2010)

A krigagem de dados apresentando distribuições com assimetria positiva deve ser evitada devido à forte influência dos poucos valores altos nas estimativas resultantes. A solução é a transformada de dados que muda a forma da distribuição original para uma distribuição simétrica. A krigagem dos dados transformados é realizada e então transformada de volta para a escala original de medida. Nesse artigo, nós examinamos a transformada uniforme que resulta em uma distribuição uniforme. A krigagem ordinária de dados uniformes resulta numa distribuição em forma de sino, haja vista as caudas da distribuição terem sido perdidas no processo de estimativa devido ao efeito de suavização. A transformada reversa dos valores apresentando essa distribuição em sino resultará em estimativas enviesadas. Portanto, a solução proposta nesse artigo passa pela correção do efeito de suavização das estimativas ranqueadas antes de transformá-las para a escala dos dados originais. Os resultados obtidos mostraram que esse algoritmo é confiável e as estimativas transformadas para a escala original não são enviesadas em relação aos dados amostrais.
Expression of an Entire Bacterial Operon in Plants (2012)

Multigene expression is required for metabolic engineering, i.e. coregulated expression of all genes in a metabolic pathway for the production of a desired secondary metabolite. To that end, several transgenic approaches have been attempted with limited success. Better success has been achieved by transforming plastids with operons. IL-60 is a platform of constructs driven from the geminivirus Tomato yellow leaf curl virus. We demonstrate that IL-60 enables nontransgenic expression of an entire bacterial operon in tomato (Solanum lycopersicum) plants without the need for plastid (or any other) transformation. Delivery to the plant is simple, and the rate of expressing plants is close to 100%, eliminating the need for selectable markers. Using this platform, we show the expression of an entire metabolic pathway in plants and delivery of the end product secondary metabolite (pyrrolnitrin). Expression of this unique secondary metabolite resulted in the appearance of a unique plant phenotype disease resistance. Pyrrolnitrin production was already evident 2 d after application of the operon to plants and persisted throughout the plant's life span. Expression of entire metabolic pathways in plants is potentially beneficial for plant improvement, disease resistance, and biotechnological advances, such as commercial production of desired metabolites.
Site-directed mutagenesis of a calcium binding site modifies specifically the different biochemical properties of annexin I (1994)

All the functions of annexins in vitro as well as in vivo are mediated and probably regulated by calcium. We have used recombinant annexin I, synthesized by Escherichia coli, and we have performed site-directed mutagenesis. We have mutated the endonexin fold of domain 2 that binds calcium. Mutations were performed in this domain of the molecule because it perfectly matches the calcium binding consensus sequence. The two glycines of this fold were mutated into glutamic acid. The helix content and the stability of the mutants are identical to those of the wild-type, suggesting that the mutations did not drastically affect the structure of the protein. The two mutants showed modified calcium binding affinities. However, the calcium binding affinity of the G131E mutant was far more altered than that of the G129E mutant. Furthermore, other biochemical properties of these mutants were modified to different extents. The binding to phospholipid was not seriously affected, whereas the self-association was lost by the G131E mutant. In the same way, liposome aggregation is conserved, but modified, while the calcium affinity measured by equilibrium dialysis is dramatically altered.
Vanadium oxide nanorods as an electrode material for solid state supercapacitor (2022)

The electrochemical properties of metal oxides are very attractive and fascinating in general, making them a potential candidate for supercapacitor application. Vanadium oxide is of particular interest because it possesses a variety of valence states and is also cost effective with low toxicity and a wide voltage window. In the present study, vanadium oxide nanorods were synthesized using a modified sol-gel technique at low temperature. Surface morphology and crystallinity studies were carried out by using scanning electron microscopy, transmission electron microscopy, X-ray diffraction and X-ray photoelectron spectroscopy analysis. To the best of our knowledge, the as-prepared nanorods were tested with magnesium ion based polymer gel electrolyte for the first time. The prepared supercapacitor cell exhibits high capacitance values of the order of ~ 141.8 F g<sup>-1</sup> with power density of ~ 2.3 kW kg<sup>-1</sup> and energy density of ~ 19.1 Wh kg<sup>-1</sup>. The cells show excellent rate capability and good cycling stability.
Generative Adverserial Analysis of Phishing Attacks on Static and Dynamic Content of Webpages (2021)

In this paper, we studied the phishing problem from data analytics and AI-powered adversarial attacks perspectives. We evaluated several static and dynamic features that can be used as good models' predictors. Unlike the URL, which can be easily crafted to evade detection, the page static and dynamic content cannot be easily changed without changing what is presented to the potential victim. We evaluated several conventional and ensemble-based models and reported the best models and settings of models that showed high prediction accuracy. We then analyzed the feasibility of evading phishing classifiers by perturbing static and dynamic features using AI generative models then test both conventional and ensemble classifiers. Our results shows that the analysis of static and dynamic features of web pages has good potential in the area adversarial learning to generate phishing attacks. The results yield that it is more challenging to evade phishing classifiers relying on dynamic content features, which offers a good level of robustness against evasion tactics.
Synthesis of Micelle Templated Silico−Aluminas with Different Alumina Contents (2006)

The computer aided analysis of the EPR spectra of radical surfactant probes inserted in cetyltrimethylammonium bromide micelles provided information on the kinetics of formation of micelle templated silico-aluminas (MTSA) at 343 K, obtained by means of silica and alumina alkaline solutions at different Si/Al ratios (from infinity to 4). Mainly two spectral components were analyzed and relatively quantified in the EPR spectra: (1) the micellar component, due to probes inserted in the surfactant aggregates, whose mobility decreases over the synthesis time, thus reporting on the progressive modification of the micelle structure and the solid condensation; (2) the interacting component, mainly arising from the electrostatic interactions between the surfactant heads and the charged surface sites. This last component increases its relative intensity over the synthesis time, informing about condensation and structuration of the silico-alumina at the micelle surface. X-ray diffraction (XRD), nitrogen sorption isotherms at 77 K, thermogravimetric analysis, TEM and chemical analysis were performed to characterize both as-synthesized and calcined MTSA materials. Nitrogen sorption isotherms allowed us to evaluate the pore diameter, the specific surface area and the pore volume. At Si/Al<15 a decrease in pore volume and specific surface area was interpreted as due to the contemporaneous presence of a hexagonal MTSA and an amorphous material, which was ascertained by means of XRD as the only present at Si/Al=4. The amorphous structure at Si/Al<15 used Na+ as contraions, whereas the surfactants are no more needed to neutralize the negatively charged groups at the solid surface. The hypothesis of a "break" at Si/Al=15 was supported by EPR: the interactions between the surfactant probe heads and the negatively charged surface groups are drastically reduced at Si/Al<15. On the contrary, at Si/Al>15, increasing amounts of alumina slow the kinetics of the synthesis but enhance electrostatic interactions between the surfactant heads and the negatively charged surface groups. Dilution of the synthesis mixture decreased the extent of the interactions, due to partial protonation of the silanol groups, and slowed the synthesis process.
Analyzing Group and Individual Contributions within Group Programming (2022)

In this work, we focus on developing resources for group programming and software engineering education which are important topics within Computer Science curriculums. Our goal is to help educators to be able to understand and assess their students' software projects. To achieve this goal, my advisor and I have developed a web-based application that processes student code repositories and visualizes the resulting data. In our analysis, we use coding metrics such as the number of commits made and number of lines coded (this includes insertions and deletions) along with commit frequency. From this analysis, we are able to curate specific information to help the educator answer questions about fairness, timeliness, consistency, and overall contribution from each student. In the future, we hope to make our application available for all educators.