Miracle-dz/UniFAR-FTUs huggingface dataset:
Standardization of Hepatitis C Virus RNA Quantification

It was recently recommended that hepatitis C virus (HCV) RNA quantification be used to tailor the duration of combined interferon alfa (IFN‐α)/ribavirin therapy in patients infected by HCV genotypes 1, 4, and 5. This recommendation has been difficult to implement in the absence of standardized quantitative units for HCV RNA. The aim of this work was to define clinically relevant HCV RNA loads in standardized international units (IU), for use in routine clinical and research applications based on standardized quantitative assays. Two hepatitis C virus RNA quantitative assays were used: (1) the Superquant assay (National Genetics Institute, Los Angeles, CA), for which possibly relevant thresholds were established; and (2) the semi‐automated Cobas Amplicor HCV Monitor assay version 2.0 (Cobas v2.0, Roche Molecular Systems, Pleasanton, CA) that measures HCV RNA loads in IU/mL. Quantification in the Cobas v2.0 assay was linear over the entire range of values tested, including viral loads higher than 850,000 IU/mL after 100‐fold dilution. The accuracy and precision of the measures in IU/mL were satisfactory with Cobas v2.0. The results obtained with Superquant and Cobas v2.0 correlated (r = .932; P < .0001). A value of 2,000,000 copies/mL (6.3 log10 copies/mL) with Superquant was converted to nearly 800,000 IU/mL (5.9 log10 IU/mL). In conclusion, all HCV RNA quantitative assays should give HCV RNA loads in international units and be validated with appropriate calibrated panels; 800,000 IU/mL in any of these assays should be used as the decision threshold to tailor the IFN‐α/ribavirin treatment duration in patients infected by HCV genotypes 1, 4, and 5.
Demand Response Management for multiple utility companies and multi-type users in smart grid

Demand Response Management (DRM) improves the reliability and efficiency of the grid by shaping user's electricity load profiles and reducing generation cost, which has been a significant component of smart grid. In this paper, we study the case of DRM with multiple utility companies and multi-type users, where the relationship of utility companies is modeled as a non-cooperative game, and users consisting of residential users, commercial users and industrial users, pay different prices even from the same utility company. We propose a management algorithm to enable the utility companies and users to converge to a stable state in which the balance of power supply and demand is reached.
Acceleration of Sensitivity Analysis by Distributed Computation Table of contents

1 Corresponding author.2 2 Abstract. 2 3 Introduction.2 4 Methods.3 5 Results.4 6 Discussion. 4 7 Acknowledgment. 5 8 References.5
Buckling response of electrothermally actuated micro-beams to parallel and transverse flow

We explore both theoretically and experimentally the role of the flow direction on the performance of a novel flow sensor based on post buckling deflection monitoring of electro-thermally actuated double-clamped micro beams. Single crystal Si beams were buckled by a compressive stress arising due to Joule's heating. In the case of a flow directed along the beam, increase of the stream velocity resulted in decrease of the deflection due to the cooling of the beam by conductive heat transfer and convection. In the case of a transverse flow the drag force acting on the structure had a competing effect and deflection decrease was less pronounced. In the case of parallel flow, the deflection sensitivity of 1.5 μm/(m/s) and the critical current sensitivity of 0.4 mA/(m/s) were registered in the experiments. The results were qualitatively consistent with the predictions of the coupled nonlinear reduced order structural, fluidic and heat transfer models.
The Microanalysis of Memory Span and Its Development in Childhood

It is not clear from the literature why, as children develop, there are important increases in memory span, the number of just-presented items that the participant can repeat in the correct serial order. To understand this, some recent results on capacity limits and processing rates were re-analyzed. We first describe results using a conventional measure of performance in immediate memory tasks that is affected by the list length (proportion correct). Next we describe results using a less conventional measure (number correct) that is unaffected by list length under circumstances in which attention to the list during its presentation is curtailed. This measure can estimate an individual's limited-capacity storage ability. Last, we examine measures of spoken response timing that do and do not change with list length. We show that unconventional measures that do not change with list length, but do change with development, are especially useful in assessing basic changes in information processing parameters, .
Comments on health-related quality of life measures for children and adolescents with epilepsy.

The progress of pediatric health-related quality of life (HRQOL) assessments was well described in this issue [1]. However, the section about epilepsy specific instruments needs clarifications. First, the Child Epilepsy Questionnaire—Parental form is not an HRQOL measure. It contains one part, Child Seizure Profile, assessing seizure description and medication side effects, and the other one specifically assessing the HRQOL of children with epilepsy, named the Quality of Life in Childhood Epilepsy Questionnaire (QOLCE) [2]. The QOLCE passed substantial validations for reliability, validity, and responsiveness, and it was approved as an epilepsy HRQOL measure. Second, the Quality of Life in Epilepsy (QOLIE-89) inventory is an epilepsy specific measure for the HRQOL assessment of adults with epilepsy, who are 17 years old and over [3]. This questionnaire was not used in the study of Wildrick et al., but the one developed specifically for that study [4]. I could not find any reference that this measure was psychometrically evaluated or ever again used. Finally, the review omitted to mention the HRQOL in Pediatric Epilepsy Scale [5] and HRQOL Instrument for Children with Epilepsy (HRQL-C-Ep) [6]. The first one is a self-report/parent measure for the HRQOL assessment of everyday living. Its psychometric properties were not tested. The other one is a self-/proxyreport measure for children (8–15 years) assessing HRQOL in interpersonal/social, worries/concerns, emotional, secrecy, and behavior domains. For this measure were demonstrated good reliability and validity. If the inclusion/exclusion criteria from the review are further applied, above all theoretical background, development, and validation, the QOLCE, HRQL-CEp, and QOLIE-AD48 [7] are the current gold standards for HRQOL assessment in children and adolescents with epilepsy. —Dejan Stevanovic, Health Care Center Odzaci—Family Medicine, Odzaci, Serbia. –– Dejan Stevanovic, MD, Health Care Center Odzaci, Family Medicine, Mostong Street 25 Odzaci 25250, Serbia And Montenegro.
Using design rationales for agile documentation

Agile software processes have been discussed as flexible and light-weight alternatives to establish software engineering approaches, in order to overcome the obstacles created by the cost of producing and maintaining documents on higher abstraction levels. Depending on requirements and needs on the documents itself, agile documentation becomes a key issue and brings up questions on how to create, maintain and distribute documents among the team members without creating unnecessary or unjustifiable cost. This paper describes a technique allowing to produce documentation automatically, by conducting analysis on the series of development step taken during project planning and enactment.
HER2-Overexpressing Breast Cancers Amplify FGFR Signaling upon Acquisition of Resistance to Dual Therapeutic Blockade of HER2

Purpose: Dual blockade of HER2 with trastuzumab and lapatinib or pertuzumab has been shown to be superior to single-agent trastuzumab. However, a significant fraction of HER2-overexpressing (HER2+) breast cancers escape from these drug combinations. In this study, we sought to discover the mechanisms of acquired resistance to the combination of lapatinib + trastuzumab. Experimental Design: HER2+ BT474 xenografts were treated with lapatinib + trastuzumab long-term until resistance developed. Potential mechanisms of acquired resistance were evaluated in lapatinib + trastuzumab-resistant (LTR) tumors by targeted capture next-generation sequencing. In vitro experiments were performed to corroborate these findings, and a novel drug combination was tested against LTR xenografts. Gene expression and copy-number analyses were performed to corroborate our findings in clinical samples. Results: LTR tumors exhibited an increase in FGF3/4/19 copy number, together with an increase in FGFR phosphorylation, marked stromal changes in the tumor microenvironment, and reduced tumor uptake of lapatinib. Stimulation of BT474 cells with FGF4 promoted resistance to lapatinib + trastuzumab in vitro. Treatment with FGFR tyrosine kinase inhibitors reversed these changes and overcame resistance to lapatinib + trastuzumab. High expression of FGFR1 correlated with a statistically shorter progression-free survival in patients with HER2+ early breast cancer treated with adjuvant trastuzumab. Finally, FGFR1 and/or FGF3 gene amplification correlated with a lower pathologic complete response in patients with HER2+ early breast cancer treated with neoadjuvant anti-HER2 therapy. Conclusions: Amplification of FGFR signaling promotes resistance to HER2 inhibition, which can be diminished by the combination of HER2 and FGFR inhibitors. Clin Cancer Res; 23(15); 4323–34. ©2017 AACR.
The Role of Oxygen‐free Radicals in Ischemic Tissue Injury in Island Skin Flaps

The contribution of free radical-mediated reperfusion injury to the ischemic damage caused by total venous occlusion of island skin flaps was investigated in a standardized rat model. Control flaps subjected to 8 hours of total venous occlusion showed complete, full thickness necrosis when followed for 7 days following release of the vascular occlusion. Treatment with superoxide dismutase, a scavenger of superoxide radicals, prior to and immediately following the onset of reperfusion, significantly enhanced island flap survival from 0/11 (0%) to 8/15 (53%), p < 0.005, and from 0/9 (0%) to 6/12 (50%), p < 0.02, respectively. These findings are consistent with the hypothesis that oxygen free radicals generated at the time of reperfusion following a period of ischemia contribute significantly to the ultimate damage caused by ischemic injury. Such findings are consistent with similar reported observations on other tissues and suggest a means by which ischemic tissue injury might be therapeutically modified, even after the period of ischemia.
Electrochemical modification of single carbon nanotubes.

However, up to now all of thesechemicalmodificationmethodswereperformedonlyonbulkSWCNTmaterial,notonindividualtubes.Herein we describe a versatile approach to the electro-chemicalmodificationofindividualcarbonnanotubes(smallSWCNT bundles), as demonstrated bythe attachment ofsubstituted phenyl groups. The electrochemical approach isparticularlysuitable for the chemical alteration of single-molecular objects, as their electrochemical potential, whichdeterminestheextentofreaction,canbedirectlyadjustedbyanappliedpotential.Ourresultsshowthatfunctionalgroupscan be controllablyattached to appropriatelycontactednanotubes,whichresultsinhomogeneousmolecularcoatingsofuptoseveralnanometersinthickness.Wepresenttwotypesof coupling reactions, working under oxidative (anodic) orreductive (cathodic) conditions. The corresponding electro-chemical reactions are illustrated schematicallyin Figure1.Inbothcasesaradicalspeciesisproducedonthesurfaceofthe nanotube, which attacks the carbon lattice to form acovalent bond. When the potential is applied for a suitablelength of time, polymerization of the radicals leads tomultilayer coating. This situation is similar to the multi-layer growth of aryl films observed in the electrochemicalmodification of highly oriented pyrolytic graphite(HOPG).
Identification of Proteins from Prunus persica That Interact with Peach Latent Mosaic Viroid

ABSTRACT Peach latent mosaic viroid (PLMVd) is a small, single-stranded, circular RNA pathogen that infects Prunus persica trees. As with all other known viroids, the PLMVd genome does not encode any proteins. Consequently, it must interact with host cellular factors in order to ensure its life cycle. With the objective of identifying cellular proteins that interact with PLMVd, Northwestern hybridizations were performed using partially purified peach leaf extracts. Mass spectrometric analysis of the detected RNA-protein complexes led to the identification of six putative RNA-binding proteins. One of these was found to be elongation factor 1-alpha (eEF1A), and because of its known involvement in the replication and translation of various RNA viruses, further characterizations were performed. Initially, the existence of this interaction received support from an experiment that immunoprecipitated the eEF1A from a crude extract of infected peach leaves, coupled with reverse transcription-PCR detection of the PLMVd. Subsequently, eEF1A interaction with PLMVd strands of both polarities was confirmed in vitro by electrophoresis mobility shift assays, fluorescence spectroscopy, and the prediction of an altered PLMVd RNase mapping profile in the presence of the protein. The potential contribution of eEF1A to the molecular biology of PLMVd, including for viroid replication, is discussed.
Evaluating Qualitative Research: Education of the Guard

Despite a well-established tradition within the information systems discipline and wider management investigations, researchers are frequently required to remind if not educate reviewers as to how qualitative research should be evaluated. This paper reviews and discusses criteria that have been proposed for grounded theory, ethnographic, confessional, postmodern, and interpretive and positivist case studies.
Búsqueda y recomendación de contenido educativo en entornos virtuales de aprendizaje

Resumen. Los entornos de aprendizaje virtual utilizados tanto en el desarrollo de cursos a distancia, como en el soporte al dictado de asignaturas presenciales, poseen una gran cantidad de informacion util para el desarrollo de las diferentes actividades desempenadas por los estudiantes en las distintas etapas del proceso de aprendizaje. Sin embargo, carecen de medios de busqueda adecuados dentro del entorno, por lo que se dificulta encontrar la informacion para todos aquellos estudiantes que poseen una duda puntual. Si a estos entornos se les incorpora un mecanismo de busqueda y recomendacion que combine tecnicas de inteligencia artificial, se pueden convertir en una herramienta muy potente que ayude a los estudiantes a evacuar sus dudas. Es por esto, que el presente trabajo propone un Enfoque para la Busqueda y Recomendacion que combina tecnicas de Mineria de Contenido Web y Recuperacion de Informacion, para asistir a los estudiantes en la busqueda de informacion adecuada, a partir del ingreso de una consulta.
Tryptophan fluorescence monitors multiple conformational changes required for glutamine phosphoribosylpyrophosphate amidotransferase interdomain signaling and catalysis.

Single tryptophan residues were incorporated into each of three peptide segments that play key roles in the structural transition of ligand-free, inactive glutamine phosphoribosylpyrophosphate (PRPP) amidotransferase to the active enzyme-substrate complex. Intrinsic tryptophan fluorescence and fluorescence quenching were used to monitor changes in a phosphoribosyltransferase (PRTase) "flexible loop", a "glutamine loop", and a C-terminal helix. Steady state fluorescence changes resulting from substrate binding were used to calculate binding constants and to detect the structural rearrangements that coordinate reactions at active sites for glutamine hydrolysis and PRTase catalysis. Pre-steady state kinetics of enzyme.PRPP and enzyme.PRPP. glutamine complex formation were determined from stopped-flow fluorescence measurements. The kinetics of the formation of the enzyme.PRPP complex were consistent with a model with two or more steps in which rapid equilibrium binding of PRPP is followed by a slow enzyme isomerization. This isomerization is ascribed to the closing of the PRTase flexible loop and is likely the rate-limiting step in the reaction of PRPP with NH(3). The pre-steady state kinetics for binding glutamine to the binary enzyme. PRPP complex could also be fit to a model involving rapid equilibrium binding of glutamine followed by an enzyme isomerization step. The changes monitored by fluorescence account for the interconversions between "end state" structures determined previously by X-ray crystallography and define an intermediate enzyme.PRPP conformer.
Glucose Stability Study: NaF/Citrate Plasma Versus Serum.

BACKGROUND Clinical laboratories often face practical concerns regarding the shipment condition of clinical specimens when considering the accuracy of glucose concentration test results. Therefore, the aims of this study were to explore whether the choice of the sample collection method has any effect on subsequent glucose measurements and to compare glucose stability in different shipment conditions at room temperature for up to 10 hours. METHODS Paired fasting venous blood samples from 58 volunteers were collected in NaF/citrate tubes and in serum tubes without any additive. At 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, and 10 hours, glucose levels were measured on a Hitachi 7600-020 analyzer using the Glucose GOD-PAP method. RESULTS The mean measured glucose concentration was significantly higher in plasma than in serum (5.07 ? 0.33 mmol/L vs. 4.79 ? 0.38 mmol/L, respectively, p < 0.001) at 0 hours. Passing-Bablok regression revealed a significant difference between the plasma and serum samples. The regression equation was y = 0.765 + 0.893 x (intercept A 95% CI: 0.405 -1.158; slope B 95% CI: 0.812-0.968). A negative bias of 0.28 mmol/L (95% CI: 0.00-0.56) was observed for samples collected in serum tubes. Similar results were found at the other ten time points (1, 2, 3, 4, 5, 6, 7, 8, 9, and 10 hours). Glycolysis was higher in serum tubes (13.4%) than in NaF/citrate tubes (2%) after 10 hours at room temperature. CONCLUSIONS Compared to the serum tube, NaF/citrate plasma tube is suitable for shipping venous whole blood samples within 10 hours at room temperature without undergoing significant glycolysis.
Dietary Niche Shifts of Multiple Marine Predators under Varying Prey Availability on the Northeast Newfoundland Coast

Understanding species interactions among top marine predators and interactions with their prey can provide important insight into community-level responses to changing prey availability and the role of apex predators as indicators of ecosystem change. On the northeast Newfoundland coast, marine predators rely on capelin (Mallotus villosus), a dominant forage fish, as a food source. Capelin migrate into coastal regions to spawn during July, essentially transforming food supply from low during early summer (i.e. pre-spawning) to high later in the summer (i.e. spawning). During July-August, 2016, we used stable isotopic ratios of nitrogen (δ15N) and carbon (δ13C) to investigate shifts in dietary niche metrics at the predator group-level (trophic position, dietary niche breadth) and community-level (niche overlap, trophic diversity) for multiple marine predators under varying capelin availability. Predator groups included non-breeding shearwaters (great shearwater Ardenna gravis, sooty shearwater A. grisea), humpback whales (Megaptera novaeangliae), and gull chicks (herring gull Larus argentatus, great black-backed gull L. marinus). We also tested the sensitivity of community-level dietary metrics to a variety of published trophic discrimination factors. Tissue samples from shearwaters (blood cellular component), gull chicks (whole blood), and whales (skin), representing average diets over 2-3 weeks, were collected during three periods (early, mid, late) corresponding to increasing capelin availability. Isotopic niche breadth (Standard Ellipse Area, SEAb) narrowed and trophic position shifted toward higher δ15N for all predator groups as capelin availability increased, suggesting a higher reliance on capelin. Trophic diversity (distance to centroid) decreased with increased capelin availability, while pairwise niche overlap between predator groups was highly variable and sensitive to varying trophic discrimination factors. Findings suggest that although capelin is the dominant forage fish during the summer, predators rely on capelin as prey to varying degrees. Combining species- and community-level metrics of dietary niche and trophic diversity may provide a more complete picture of predator responses to prey availability and, thus, may be important monitoring tools to indicate changes in the food supply of marine predators.
Analysis of electromagnetic performance of flux-switching permanent-magnet Machines by nonlinear adaptive lumped parameter magnetic circuit model

A nonlinear adaptive lumped parameter magnetic circuit model is developed to predict the electromagnetic performance of a flux-switching permanent-magnet machine. It enables the air-gap field distribution, the back-electromotive force (back-EMF) waveform, the winding inductances, and the electromagnetic torque to be calculated. Results from the model are compared with finite-element predictions and validated experimentally. The influence of end effects is also investigated, and optimal design parameters, such as the rotor pole width, the stator tooth width, and the ratio of the inner to outer diameter of the stator, are discussed.
A Self-Organizing Particle Swarm Optimization Algorithm and Application

A self-organizing particle swarm optimization algorithm is developed for solving premature convergence of particle swarm optimization. According to adaptively adjusting acceleration coefficients and inertia weight, the particles are organized to track the domain of attraction of local optimum and the domain of attraction global optimum respectively during the search. Meanwhile the corresponding strategies with mutation are adopted in different stages of this algorithm to further enhance diversity of population. Experimental results for complex function optimization and nonlinear system identification show that this algorithm improves the global convergence ability and efficiently prevents the algorithm from the local optimization and early maturation.
Treatment of children with acute lymphoblastic leukemia with risk group based intensification and omission of cranial irradiation: A Korean study of 295 patients

Recent studies indicate 70–80% event‐free survival (EFS) for pediatric acute lymphoblastic leukemia (ALL). In this study, we report the outcome of 295 children and adolescents treated at our institution, with stratification into four risk groups, and omission of cranial irradiation in all patients.