Miracle-dz/UniFAR-FTUs huggingface dataset:
Blood biomarkers of methylation in Down syndrome and metabolic simulations using a mathematical model.

SCOPE The study tests the metabolites of the methylation cycle in individuals with Down syndrome (DS) and applies a mathematical model in order to change this cycle by nutritional factors. METHODS AND RESULTS We measured concentrations of the metabolites related to the methylation cycle in the blood of 35 young individuals with DS and 47 controls of comparable age. Moreover, we applied a mathematical model to learn more about the regulation of the methylation cycle in DS. Concentrations of cystathionine, cysteine, betaine, choline, dimethylglycine, S-adenosylhomocysteine (SAH), S-adenosylmethionine (SAM), and holotranscobalamin were significantly higher in DS compared to the controls. The median SAM/SAH ratio was lower in DS and that of methionine and reduced glutathione did not differ significantly between the groups. The mathematical model showed that enhanced methionine turnover and accelerated Hcy-remethylation might explain the shift in the methylation cycle in DS. CONCLUSION In addition to the DS-related excess of cystathionine beta synthase (CBS) activity, increases in the activities of MS and betaine homocysteine methyl transferase, and in methionine input were necessary to account for the changes in metabolite levels observed in DS. A low-methionine diet might offer a perspective for reversing the metabolic imbalance in DS, but this awaits clinical investigations.
Solar Photovoltaic Array Dependent Dual Output Converter Based Water Pumping Using Switched Reluctance Motor Drive

This paper aims at the design and development of an efficient photovoltaic (PV) array powered switched reluctance motor (SRM) driven pump utilizing a dual supply buck–boost converter. The buck–boost converter, having dual supply, is used as an intermediate dc–dc power conditioning stage between PV array and SRM-pump. To optimize the power of the PV array and to provide soft starting to the SRM drive are the two major concerns of this converter. It also provides voltage balancing of split capacitors, owing to which there is considerable reduction in torque ripple and the required size of it. Moreover, the continuous conduction mode operation of dual supply dc–dc converter minimizes current and voltage stresses on converter indices and reduced electromagnetic interference. The electronic commutation of the SRM drive at fundamental frequency offers reduced switching losses in the midpoint converter and, therefore, considerable enhancement in the efficiency of the proposed system. A dwell angle self-starting control algorithm for a four-phase 8/6 SRM is also implemented in the proposed system. A prototype is developed in the laboratory to validate the performance of the proposed system in different environmental conditions.
Causal Inference from Descriptions of Experimental and Non-Experimental Research: Public Understanding of Correlation-Versus-Causation

ABSTRACT The human tendency to conflate correlation with causation has been lamented by various scientists (Kida, 2006; Stanovich, 2009), and vivid examples of it can be found in both the media and peer-reviewed literature. However, there is little systematic data on the extent to which individuals conflate correlation with causation. In three experiments, we presented people with one of four research vignettes generated from the combination of two independent variables: whether the vignette described an experimental or non-experimental design, and whether it revealed a positive or negative association. Upon reading their vignette, participants selected inferences that could be drawn from the findings. Participants drew causal inferences from non-experimental vignettes as often as they did from experimental vignettes, and more frequently for causal statements and directions of association that fit with intuitive notions than for those that did not. We discuss our findings in relation to other biases in human thinking.
The chloroplast ATP synthase features the characteristic redox regulation machinery.

SIGNIFICANCE Regulation of the activity of the chloroplast ATP synthase is largely accomplished by the chloroplast thioredoxin system, the main redox regulation system in chloroplasts, which is directly coupled to the photosynthetic reaction. We review the current understanding of the redox regulation system of the chloroplast ATP synthase. RECENT ADVANCES The thioredoxin-targeted portion of the ATP synthase consists of two cysteines located on the central axis subunit γ. The redox state of these two cysteines is under the influence of chloroplast thioredoxin, which directly controls rotation during catalysis by inducing a conformational change in this subunit. The molecular mechanism of redox regulation of the chloroplast ATP synthase has recently been determined. CRITICAL ISSUES Regulation of the activity of the chloroplast ATP synthase is critical in driving efficiency into the ATP synthesis reaction in chloroplasts. FUTURE DIRECTIONS The molecular architecture of the chloroplast ATP synthase, which confers redox regulatory properties requires further investigation, in light of the molecular structure of the enzyme complex as well as the physiological significance of the regulation system.
Modulation of Apoptotic Signaling by the Hepatitis B Virus X Protein

Worldwide, an estimated 350 million people are chronically infected with the Hepatitis B Virus (HBV); chronic infection with HBV is associated with the development of severe liver diseases including hepatitis and cirrhosis. Individuals who are chronically infected with HBV also have a significantly higher risk of developing hepatocellular carcinoma (HCC) than uninfected individuals. The HBV X protein (HBx) is a key regulatory HBV protein that is important for HBV replication, and likely plays a cofactor role in the development of HCC in chronically HBV-infected individuals. Although some of the functions of HBx that may contribute to the development of HCC have been characterized, many HBx activities, and their putative roles during the development of HBV-associated HCC, remain incompletely understood. HBx is a multifunctional protein that localizes to the cytoplasm, nucleus, and mitochondria of HBV‑infected hepatocytes. HBx regulates numerous cellular signal transduction pathways and transcription factors as well as cell cycle progression and apoptosis. In this review, we will summarize reports in which the impact of HBx expression on cellular apoptotic pathways has been analyzed. Although various effects of HBx on apoptotic pathways have been observed in different model systems, studies of HBx activities in biologically relevant hepatocyte systems have begun to clarify apoptotic effects of HBx and suggest mechanisms that could link HBx modulation of apoptotic pathways to the development of HBV-associated HCC.
Nonlinear feedback linearization controller design for half car suspension system

This paper investigates the nonlinear controller design of a half car suspension system. The half car suspension system is a multiple-input-multiple-output (MIMO) nonlinear system. The proposed controller design is based on a feedback linearization method. Its prime goal is the coordinated control of ride quality and handling performance which are nowadays challenging for suspension systems, for the applications on unpaved roads. The tracking performance of the proposed control technique in the presence of the deterministic road disturbance has been illustrated using simulation results.
Delirium in older emergency department patients is an independent predictor of hospital length of stay.

OBJECTIVES The consequences of delirium in the emergency department (ED) remain unclear. This study sought to determine if delirium in the ED was an independent predictor of prolonged hospital length of stay (LOS). METHODS This prospective cohort study was conducted at a tertiary care, academic ED from May 2007 to August 2008. The study included English-speaking patients aged 65 and older who were in the ED for less than 12 hours at enrollment. Patients were excluded if they refused consent, were previously enrolled, were unable to follow simple commands at baseline, were comatose, or did not have a delirium assessment performed by the research staff. The Confusion Assessment Method for the Intensive Care Unit (CAM-ICU) was used to determine delirium status. Patients who were discharged directly from the ED were considered to have a hospital LOS of 0 days. To determine if delirium in the ED was independently associated with time to discharge, Cox proportional hazard regression was performed adjusted for age, comorbidity burden, severity of illness, dementia, functional impairment, nursing home residence, and surgical procedure. A sensitivity analysis, which included admitted patients only, was also performed. RESULTS A total of 628 patients met enrollment criteria. The median age was 75 years (interquartile range [IQR] = 69-81), 365 (58%) patients were female, 111 (18%) were nonwhite, 351 (56%) were admitted to the hospital, and 108 (17%) were delirious in the ED. Median LOS was 2 days (IQR = 0-5.5) for delirious ED patients and 1 day (IQR = 0-3) for nondelirious ED patients (p < 0.001). The hazard ratio (HR) of delirium for time to discharge was 0.71 (95% confidence interval [CI] = 0.57 to 0.89) after adjusting for confounders, and indicated that ED patients with delirium were more likely to have prolonged hospital LOS compared with those without delirium. For the sensitivity analysis, which included only hospitalized patients, the adjusted HR was 0.76 (95% CI = 0.58 to 0.99). CONCLUSIONS Delirium in older ED patients has negative consequences and is an independent predictor of prolonged hospitalizations.
Focal adhesion kinase

This investigation describes the clinical significance of phosphorylated focal adhesion kinase (FAK) at the major activating tyrosine site (Y397) in epithelial ovarian cancer (EOC) cells and tumor-associated endothelial cells. FAK gene amplification as a mechanism for FAK overexpression and the effects of FAK tyrosine kinase inhibitor VS-6062 on tumor growth, metastasis, and angiogenesis were examined. FAK and phospho-FAKY397 were quantified in tumor (FAK-T; pFAK-T) and tumor-associated endothelial (FAK-endo; pFAK-endo) cell compartments of EOCs using immunostaining and qRT-PCR. Associations between expression levels and clinical variables were evaluated. Data from The Cancer Genome Atlas were used to correlate FAK gene copy number and expression levels in EOC specimens. The in vitro and in vivo effects of VS-6062 were assayed in preclinical models. FAK-T and pFAK-T overexpression was significantly associated with advanced stage disease and increased microvessel density (MVD). High MVD was observed in tumors with elevated endothelial cell FAK (59%) and pFAK (44%). Survival was adversely affected by FAK-T overexpression (3.03 vs 2.06 y, P = 0.004), pFAK-T (2.83 vs 1.78 y, P < 0.001), and pFAK-endo (2.33 vs 2.17 y, P = 0.005). FAK gene copy number was increased in 34% of tumors and correlated with expression levels (P < 0.001). VS-6062 significantly blocked EOC and endothelial cell migration as well as endothelial cell tube formation in vitro. VS-6062 reduced mean tumor weight by 56% (P = 0.005), tumor MVD by 40% (P = 0.0001), and extraovarian metastasis (P < 0.01) in orthotopic EOC mouse models. FAK may be a unique therapeutic target in EOC given the dual anti-angiogenic and anti-metastatic potential of FAK inhibitors.
The Electric Vehicle Routing Problem with Time Windows under Travel Time Uncertainty

Due to environmental friendliness, electric vehicles have become more and more popular nowadays in the transportation system. For many express companies, it is more and more important to meet the predetermined time window of customers. The uncertainty in travel times often causes uncertain energy consumption and uncertain recharging time, thus electric vehicles may miss the time windows of customers. Therefore, this paper addresses the electric vehicle routing problem with time windows under travel time uncertainty, which aims to determine the optimal delivery strategy under travel time uncertainty. To solve this problem, a robust optimization model is built based on the route-dependent uncertainty sets. However, considering the complexity of the problem, the robust model can only solve few instances including the small number of customers. Thus, a hybrid metaheuristic consisting of the adaptive large neighborhood search algorithm and the local search algorithm is proposed. The results show that the algorithm can obtain the optimal solution for the small-sized instances and the large-sized instances.
The Saccharomyces cerevisiae gene PPH3 encodes a protein phosphatase with properties different from ppx, PP1 and PP2A

A clone encoding the catalytic subunit of a protein phosphatase from Saccharomyces cerevisiae was isolated. Except for replacement of IIe‐245 by Met the structure of the phosphatase was identical to that encoded by PPH3 (Ronne, H., Carlberg, M., Hu, G. Z. and Nehlin, J. O. (1991). Mol. Cell. Biochem. 11, 4876–4884) and exhibited 63% sequence identity to PPX cloned from a rabbit liver cDNA library (Brewis, N. D., Street, A. J., Prescott, A. R. and Cohen, P. T. W. (1993). EMBO J. 12, 987–996). Expression of active enzyme was achieved in Escherichia coli mutants which were generated by a genetic selection based on functional complementation of bacterial phosphoserine phosphatase. Though some of the properties of PPH3 resembled those of protein phosphatase 2A and PPX, others were different. PPH3 exhibited lower sensitivity against inhibition by okadaic acid, showed different substrate specificity and required a divalent cation (Mn2+ was preferred before Mg2+ and Ca2+) for activity when assayed with phospho‐histone as a substrate. However, 25% of maximum activity was observed in the absence of divalent cations when the peptide LRRAS(P)LG was used as substrate. The PPH3‐protein was also identified by chromatography of extracts from S. cerevisiae on DEAE–cellulose. Protein immunoreactive with an antiserum raised against the non‐conserved N‐terminal 53 amino acids of PPH3 was coeluted with a single peak of LRRAS(P)LG dephosphorylating activity.
Evaluation of audio-based feedback technologies for bow learning technique in violin beginners

We present a study of the effects of feedback technologies on the learning process of novice violin students. Twenty-one subjects participated in our experiment, divided into two groups: Beginners (participants with no prior violin playing experience, N=14), and experts (participants with more than 6 years of violin playing experience, N=7). The beginners group was further divided into two: a group of beginners learning with Youtube videos (N=7), and a group of beginners with additional feedback related to the quality of their performance (N=7). Participants were asked to perform a violin exercise during 21 trials while their audio was recorded and analyzed. Three different audio descriptors were extracted from each audio in order to evaluate the quality of the performance: Dynamic stability, pitch stability and aperiodicity. Beginners showed a significant improvement during the session(i.e. by comparing the beginning and the end of the session)in the quality of the sound recorded, while experts maintained their results. However, only the beginner group with feedback showed significant improvement between the middle and late part of the session, while the group without feedback remained stable.
Can JSP Code be Generated Using XML Tags?

Over the years, a variety of web services have started using server-side scripting to deliver results back to a client as a paid or free service; one such server-side scripting language is Java Server Pages (JSP). Also Extensible markup language (XML), is being adopted by most web developers as a tool to describe data.Therefore, we present a conversion method which uses predefined XML tags as input and generates the corresponding JSP code. However, the end users are required to have a basic experience with web pages. This conversion method aims to reduce the time and effort spent by the user (web developer) to get acquainted with JSP. The conversion process abstracts the user from the intricacies of JSP and enables him to focus on the business logic.
A Wireless Sensor Network for greenhouse climate monitoring

In the last years, the presence of WSN (Wireless Sensor Network) is spreading worldwide. The reason for this success is that they facilitate the creation of data acquisition networks minimizing the necessary wire infrastructure. However, the WSN distributed modules typically have high dependencies on their batteries consumption. In the other hand, event-based systems are spreading fastly day by day. This kind of system allows to perform asynchronous actions based on a schedule or rules. The WSN distributed modules allow to perform a process before transmitting the data. If a event-based algorithm is used to define when it is necessary to transmit the acquired data, transmissions could be minimized. In this way, modules energy consumption can be reduced, extending the battery life. Therefore, mixing both technologies improves the WSN autonomy. In this work, these ideas are performed and analyzed in the climate monitoring framework.
Imaging Protein‐Protein Interactions by Fluorescence Resonance Energy Transfer (FRET) Microscopy

Detection of specific protein‐protein interactions has long been restricted to bulk biochemical methods such as immunoprecipitation and immunoblotting. Even more sensitive methods using general immunofluorescence are limited, and it is difficult to infer protein‐protein interactions from the results of these tests. Fluoresence Resonance Energy Transfer (FRET) is a photophysical process that can be exploited to obtain highly sensitive information about such interactions. It can sense the presence of acceptor fluorophores in the vicinity of a donor fluorophore within a separation distance that is the size of a single protein molecule. This unit details FRET microscopy based on release of quenched donor fluorescence after acceptor photobleaching, microinjection of reagents into the nucleus or cytosol, and labeling of antibodies for these procedures.
The phenomenology of niche evolution via quantitative traits in a ‘black-hole’ sink

Previous studies of adaptive evolution in sink habitats (in which isolated populations of a species cannot persist deterministically) have highlighted the importance of demographic constraints in slowing such evolution, and of immigration in facilitating adaptation. These studies have relied upon either single–locus models or deterministic quantitative genetic formulations. We use individual–based simulations to examine adaptive evolution in a ‘black–hole’ sink environment where fitness is governed by a polygenic character. The simulations track both the number of individuals and their multi–locus genotypes, and incorporate, in a natural manner, both demographic and genetic stochastic processes. In agreement with previous studies, our findings reveal the central parts played by demographic constraints and immigration in adaptation within a sink (adaptation is more difficult in environments with low absolute fitness, and higher immigration can accelerate adaptation). A novel finding is that there is a ‘punctuational’ pattern in adaptive evolution in sink environments. Populations typically stay maladapted for a long time, and then rapidly shift into a relatively adapted state, in which persistence no longer depends upon recurrent immigration.
Three‐dimensional reconstruction of limited‐view projections for contrast‐enhanced magnetic resonance angiography at high temporal and spatial resolution

The feasibility of reconstructing three‐dimensional (3D) MRI data sets from limited‐view projections is investigated in phantom and in vivo animal studies to improve the temporal resolution of magnetic resonance angiography without sacrificing spatial resolution. Thirty‐two pairs of orthogonal biplane projections are acquired in an interleaved manner during the first pass of a contrast agent. The full data set is reconstructed as a priori 3D information. Each pair of projections is then reconstructed into an individual 3D data set based on a correlation analysis with the a priori data set. In this way, time‐resolved 3D data sets at 1‐ to 2‐s time intervals are reconstructed with submillimeter spatial resolution. Artifacts are limited if the image is simply structured or sparse and if SNR is sufficient in the projection images. With this technique, both high temporal and spatial resolution can be achieved simultaneously. Magn Reson Med, 2005. © 2005 Wiley‐Liss, Inc.
Characterizing Bursts of Aggregate Pairs With Individual Poissonian Activity and Preferential Mobility

The power-law distributions of contact durations and waiting intervals of all pairs of agents together, dubbed as bursts of aggregate pairs, have been found in many realistic opportunistic networks. Many models for such opportunistic networks are under a homogeneous assumption that the distribution from every pair of agents performs the same format as that from all pairs of agents. But our empirical study shows an opposite scenario, e.g., each agent performs Poissonian dynamics while all pairs perform burst dynamics. Therefore, we propose a bottom-up human mobility model to replicate this opportunistic network, and prove that bursts of aggregate pairs can be rooted from individual independent Poissonian self-activity and preferential mobility. Finally we validate our findings with numerical simulations.
Hungary: Crisis Coupled with a Fiscal Squeeze – Effects on Inequality

This book offers a unique combination of research, case studies and policy discussions. An assessment of national trends in 30 European countries precedes case studies of 14 of them, in which noted European specialists report on individual enterprises or sectors. The volume’s survey of national- and local-level policy solutions contributes to identifying those responses that strengthen economic competitiveness, preserve social cohesion and do not deepen inequalities.