Miracle-dz/UniFAR-FTUs huggingface dataset:
Newcastle disease virus: A promising agent for tumour immunotherapy

Malignant tumours are a major cause of mortality in humans. Currently used therapeutic regimens have not improved survival rates of patients suffering from malignant tumours much because of their limited efficacy and side‐effects. A therapeutic approach that uses Newcastle disease virus (NDV) represents an attractive new tool for tumour immunotherapy. The present review highlights the mechanisms and advances that are likely to have considerable impact on NDV virotherapy. Significant evidence exists regarding the oncolytic effects of NDV, suggesting its potential use in the treatment of various tumours. Furthermore, clinical trials have suggested that several NDV strains have the potential for cancer virotherapy with few side‐effects compared with traditional treatments. Many studies have been performed to investigate the oncolytic mechanisms of NDV. Apoptosis following NDV infection may contribute to the observed oncolytic effects; however, NDV could also stimulate both innate and adaptive antitumour immune responses. For many years, different approaches have been investigated (or are in the process of being developed) regarding the use of NDV for the treatment of malignancies. Recent advances using reverse genetics have provided a means of generating recombinant NDV strains with improved oncolytic and immune regulatory properties.
Effects of Once-Daily Oral and Transdermal Methylphenidate on Sleep Behavior of Children With ADHD

Objective: Methylphenidate is a leading first-line treatment for ADHD (AD/HD). This stimulant has long been suspected to adversely affect sleeping patterns of treated individuals, especially children. There are few studies on the effects of recently developed longer-acting methylphenidate treatments, such as once-daily oral or transdermal formulations, on sleep. Method: The authors examined eight indices of sleep behavior among children treated with either of these two methylphenidate preparations or placebo in a randomized, double-blind, multicenter, parallel-group study. Results: The main predictor of sleep problems was baseline numbers or severity of preexisting sleep problems, whereas the different treatments and placebo varied little in their propensity to elicit such problems. There was no significant relationship between dosage and severity or frequency of sleep problems. Conclusion: The authors found little evidence that methylphenidate treatment (at least in sustained-release forms) was a significant cause of sleep problems in treated children who were carefully titrated to an optimal dose. (J. of Att. Dis. 2009; 12(4) 308-315)
Stem cell profiling by nuclear magnetic resonance spectroscopy

The classification of embryonic and adult stem cells, including their derivatives, is still limited, and often these cells are best defined by their functional properties. Recent gene array studies have yielded contradictory results. Also, very little is known about the metabolic properties of these exciting cells. In this study, proton (1H) NMR spectroscopy was used to identify the major low‐molecular‐weight metabolites in murine embryonic stem cells (ESC) and their neural stem cell (NSC) derivatives. ESC are characterized by an unusually low number of NMR‐detectable metabolites, high phosphocholine (PC) content, and nondetectable glycerophosphocholine (GPC). The metabolic profiles of NSC resemble glial cells and oligodendrocyte progenitors, but with considerably higher PC, GPC, and myo‐inositol content. The results suggest that NMR spectroscopy in vitro can provide markers to study the effects of differentiation on cell metabolism, and potentially to assess stem cell preparations for differentiation status. Magn Reson Med, 2006. © 2006 Wiley‐Liss, Inc.
Co-worker Networks and Agglomeration Externalities

Abstract The present article provides an initial systematic analysis of how social networks influence productivity in regional agglomerations. This is accomplished by means of matched employer–employee data for the entire Swedish economy for the period 1990–2008, allowing us to construct a weighted co-worker network with aggregated tie weights on the plant level. We find evidence that increasing density of the plant-level network has a positive effect on productivity, particularly in large regional industry-clusters with high degrees of specialization. Triadic closure of ties is, however, negatively linked to productivity, suggesting the importance of nonredundant knowledge. Moreover, we find only limited support for the notion that the diversity of linkages within or across regions as such is beneficial for productivity. Instead, we show that the degree of specialization conditions the extent to which both linkages to related industries in the region and nonlocal ties are beneficial. Our results thus suggest that having dense social networks is a crucial feature of high-performing agglomerations, and that interindustry, as well as interregional, linkages are compensatory in cases when sufficient industry specialization is absent.
Government Expenditure and Economic Growth in South Africa: A Vector Error Correction Modelling and Granger Causality Test

Previous studies generally find mixed empirical evidence on the relationship between government spending and economic growth. This study re-examine the relationship between government expenditure and economic growth in South Africa for the period of 1990 to 2015 using the Vector Error Correction Model and Granger Causality techniques. The time series data included in the model were gross domestic Product (GDP), government expenditure, national savings, government debt and consumer price index or inflation. Results obtained from the analysis showed a negative long-run relationship between government expenditure and economic growth in South Africa. Furthermore, the estimate of the speed of adjustment coefficient found in this study has revealed that 49 per cent of the variation in GDP from its equilibrium level is corrected within of a year. Furthermore, the study discovered that the causality relationship run from economic growth to government expenditure. This implied that the Wagner’s law is applicable to South Africa since government expenditure is an effect rather than a cause of economic growth. The results presented in this study are similar to those in the literature and are also sustained by preceding studies.
Alteration of Immune Responses of Rabbits Infected with Bovine Immunodeficiency‐Like Virus

Nine 3‐month‐old rabbits were inoculated with bovine immunodeficiency‐like virus (BIV) to study the pathogenesis of BIV and alteration of the immune responses in experimentally infected rabbits. BIV proviral DNA and anti‐BIV antibodies were detected from all rabbits inoculated with BIV‐infected bovine embryo spleen (BESP) cells. Rabbits inoculated with spleen cells of the BIV‐infected rabbit also converted to proviral DNA‐positive and BIV‐antibody‐positive. The blastogenic responses to concanavalin A of peripheral blood mononuclear cells prepared from BIV‐infected rabbits were not significantly different from those from uninfected controls at 2 and 4 months post‐inoculation (PI). The humoral immune responses against bovine serum albumin (BSA) were depressed in two of four BIV‐infected rabbits at 1 to 3 months PI. The antibody responses against sheep red blood cells (SRBCs) were significantly depressed in all BIV‐infected rabbits at 2 to 4 months PI. BIV was rescued by cocultivation of spleen cells of infected rabbits with BESP cells. Distinct development of lymphoid follicle was observed in lymph nodes and spleens of uninfected rabbits which received BSA and SRBCs. In contrast, moderate lymphoid cell depletion was observed in BIV‐infected rabbits which received the same immunogens.
Protein analysis by dynamic light scattering: Methods and techniques for students

Dynamic light scattering (DLS) analyses are routinely used in biology laboratories to detect aggregates in macromolecular solutions, to determine the size of proteins, nucleic acids, and complexes or to monitor the binding of ligands. This article is written for graduate and undergraduate students with access to DLS and for faculty members who wish to incorporate DLS into a lab activity, a practical course or research. It reviews the basic concepts of light scattering measurements and addresses four critical aspects of the analysis and interpretation of DLS results. To ensure reproducible quantitative data, attention should be paid to controlling the preparation and handling of proteins or assemblies because variations in the state of aggregation, induced by minor changes in experimental condition or technique, might compromise DLS results and affect protein activity. Variables like temperature, solvent viscosity, and inter‐particle interactions may also influence particle size determination. Every point is illustrated by case studies, including a commercially available albumin, a small RNA virus isolated from plants, as well as four soluble proteins and a ribonucleoprotein assembly purified and characterized by students in the frame of their master degree. © 2012 by The International Union of Biochemistry and Molecular Biology
Fast and unintentional evaluation of emotional sounds: evidence from brief segment ratings and the affective Simon task

ABSTRACT In the present study, we raised the question of whether valence information of natural emotional sounds can be extracted rapidly and unintentionally. In a first experiment, we collected explicit valence ratings of brief natural sound segments. Results showed that sound segments of 400 and 600 ms duration—and with some limitation even sound segments as short as 200 ms—are evaluated reliably. In a second experiment, we introduced an auditory version of the affective Simon task to assess automatic (i.e. unintentional and fast) evaluations of sound valence. The pattern of results indicates that affective information of natural emotional sounds can be extracted rapidly (i.e. after a few hundred ms long exposure) and in an unintentional fashion.
Brain structural and microstructural alterations associated with cerebral palsy and motor impairments in adolescents born extremely preterm and/or extremely low birthweight

To elucidate neurobiological changes underlying motor impairments in adolescents born extremely preterm (gestation <28wks) and/or with extremely low birthweight (ELBW, <1000g), our aims were the following: (1) to compare corticospinal tract (CST) microstructure and primary motor cortex (M1) volume, area, and thickness between extremely preterm/ELBW adolescents and a comparison group with normal birthweight (>2499g); (2) to compare CST microstructure and M1 volume, area, and thickness between extremely preterm/ELBW adolescents with cerebral palsy (CP), motor impairment without CP, and no motor impairment; and (3) to investigate associations between CST microstructure and M1 measures.
Identification and functional analysis of CITED2 mutations in patients with congenital heart defects

Recent reports have demonstrated that mice lacking the transcription factor Cited2 die in utero showing various cardiac malformations. We present for the first time functionally relevant mutations of CITED2 in patients with congenital heart defects (CHDs). CITED2 encodes a CREBBP/EP300 interacting transcriptional modulator of HIF1A and TFAP2. To study the potential impact of sequence variations in CITED2 for CHDs in humans, we screened a cohort of 392 well‐characterized patients and 192 control individuals using DHPLC, sequencing, and Amplifluor™ genotyping techniques. We identified 15 CITED2 nucleotide alterations. Seven of these alterations were found only in CHD patients and were not detected in controls, including three mutations leading to alterations of the amino acid sequence (p.Ser170_Gly178del, p.Gly178_Ser179ins9, and p.Ser198_Gly199del). All three of these amino acid changing mutations cluster in the serine‐glycine‐rich junction of the protein, to which no functionality had heretofore been assigned. Here we show that these mutations significantly reduce the capacity of CITED2 to transrepress HIF1A, and that the p.Ser170_Gly178del mutation significantly diminishes TFAP2C coactivation. This reveals a modifying role for the serine‐glycine‐rich region in CITED2 function. In summary, the observation of these mutations in patients with septal defects indicates that CITED2 has a causative impact in the development of CHD in humans. Hum Mutat 26(6), 575–582, 2005. © 2005 Wiley‐Liss, Inc.
Diagnostic Real-Time PCR for Detection of Salmonella in Food

ABSTRACT A robust 5′ nuclease (TaqMan) real-time PCR was developed and validated in-house for the specific detection of Salmonella in food. The assay used specifically designed primers and a probe target within the ttrRSBCA locus, which is located near the Salmonella pathogenicity island 2 at centisome 30.5. It is required for tetrathionate respiration in Salmonella. The assay correctly identified all 110 Salmonella strains and 87 non-Salmonella strains tested. An internal amplification control, which is coamplified with the same primers as the Salmonella DNA, was also included in the assay. The detection probabilities were 70% when a Salmonella cell suspension containing 103 CFU/ml was used as a template in the PCR (5 CFU per reaction) and 100% when a suspension of 104 CFU/ml was used. A pre-PCR sample preparation protocol including a preenrichment step in buffered peptone water followed by DNA extraction-purification was applied when 110 various food samples (chicken rinses, minced meat, fish, and raw milk) were investigated for Salmonella. The diagnostic accuracy was shown to be 100% compared to the traditional culture method. The overall analysis time of the PCR method was approximately 24 h, in contrast to 4 to 5 days of analysis time for the traditional culture method. This methodology can contribute to meeting the increasing demand of quality assurance laboratories for standard diagnostic methods. Studies are planned to assess the interlaboratory performance of this diagnostic PCR method.
Reduction of intra‐ and interlaboratory variation in CD34+ stem cell enumeration using stable test material, standard protocols and targeted training

The European Working Group on Clinical Cell Analysis (EWGCCA) has, in preparation for a multicentre peripheral blood stem cell clinical trial, developed a single‐platform flow cytometric protocol for the enumeration of CD34+ stem cells. Using this protocol, stabilized blood and targeted training, the EWGCCA have attempted to standardize CD34+ stem cell enumeration across 24 clinical sites. Results were directly compared with participants in the UK National External Quality Assessment Scheme (NEQAS) for CD34+ Stem Cell Quantification that analysed the same specimens using non‐standardized methods. Two bead‐counting systems, Flow‐Count and TruCount, were also evaluated by the EWGCCA participants during trials 2 and 3. Using Flow‐Count, the intralaboratory coefficient of variation (CV) was ≤ 5% in 39% of the laboratories (trial 1), increasing to 65% by trial 3. Interlaboratory variation was reduced from 23.3% (trial 1) to 10.8% in trial 3. In trial 2, 70% of laboratories achieved an intralaboratory CV ≤ 5% using TruCount, increasing to 74% for trial 3; the interlaboratory CV was reduced from 23.4% to 9.5%. Comparative analysis of the EWGCCA and the UK NEQAS cohorts revealed that EWGCCA laboratories, using the standardized approach, had lower interlaboratory variation. Thus, the use of a common standardized protocol and targeted training significantly reduced intra‐ and interlaboratory CD34+ cell count variation.
Effect of conjugal bereavement on mortality of the bereaved spouse in participants of the Renfrew/Paisley Study

Objectives: To investigate how loss of a spouse affects mortality risk in the bereaved partner. Design and setting: Prospective cohort study in Renfrew and Paisley in Scotland. Participants: 4395 married couples aged 45–64 years when the study was carried out between 1972 and 1976. Methods: The date of bereavement for the bereaved spouse was the date of death of his or her spouse. Bereavement could occur at any time during the follow-up period, so it was considered as a time-dependent exposure variable and the Cox proportional hazards model for time-dependent variables was used. The relative rate (RR) of mortality was calculated for bereaved versus non-bereaved spouses and adjusted for confounding variables. Main outcome measures: Causes of death to 31 March 2004. Results: Bereaved participants were at higher risk than non-bereaved participants of dying from any cause (RR 1.27; 95% CI 1.2 to 1.35). These risks remained but were attenuated after adjustment for confounding variables. There were raised RRs for bereaved participants dying of cardiovascular disease, coronary heart disease, stroke, all cancer, lung cancer, smoking-related cancer, and accidents or violence. After adjustment for confounding variables, RRs remained higher for bereaved participants for all these causes except for mortality from lung cancer. There was no strong statistical evidence that the increased risks of death associated with bereavement changed with time after bereavement. Conclusions: Conjugal bereavement, in addition to existing risk factors, is related to mortality risk for major causes of death.
Sustained virologic response by direct antiviral agents reduces the incidence of hepatocellular carcinoma in patients with HCV infection

The aim of this study was to assess the rate of development of hepatocellular carcinoma (HCC) in patients who achieved sustained virologic response (SVR) by direct antiviral agents (DAA). We retrospectively evaluated patients who achieved SVR by oral DAA interferon‐free regimens (n = 77) (daclatasvir/asunaprevir [n = 67], ombitasvir/paritaprevir/ritonavir [n = 9], and telaprevir [n = 1]) and by pegylated‐interferon plus ribavirin (Peg‐IFN/RBV, n = 528). In all patients, the background was chronic hepatitis or cirrhosis caused by HCV genotype 1b. During a median follow‐up period of 4.0 years, two (2.6%) of DAA‐treated patients developed HCC. The 3‐ and 5‐year cumulative HCC development rates were 1.30% and 3.03%, respectively, in the DAA group, and 1.02% and 2.19 % in the Peg‐IFN/RBV group (P not significant). In patients with Fib‐4 score of >3.25, the 3‐year HCC development rates were 4.35% and 3.95%, whereas those of the 5 year were 9.66% and 8.37%, in the DAA and Peg‐IFN/RBV group, respectively. In patients with Fib‐4 score of ≤3.25, none of the DAA group developed HCC, whereas 0.48% at 3‐year and 1.05% at 5‐year of patients of the Peg‐IFN/RBV group did. Propensity score analysis using the inverse probability of treatment weights (IPTW) also showed no significant difference in HCC development rate between the two groups. Serum AFP gradually and similarly decreased after initiation of antiviral therapy in both groups. Our data indicate that the HCC risk rate after SVR is similar regardless of whether the latter was achieved by DAA or IFN‐based regimens. J. Med. Virol. 89:476–483, 2017. © 2016 Wiley Periodicals, Inc.
A hierarchical semantic image labeling method via random forests

In this paper, we propose an effective image labeling method with a hierarchical framework consists of two layers of random forests. In the first layer, random forests is performed on superpixel basis. An initial labeling map is efficiently estimated by assigning every superpixel with a unique class label. In the second layer, structured random forests is applied to the image patches locating at superpixel boundaries to make use of the topological distribution of the object classes via local label descriptors. In our work, structured random forests not only generates local label predictions, but also provides us the reliability score of this prediction so that the predictions from two layers can be fused adaptively for a more reliable labeling result. This additional layer makes improvements especially on implausible label configurations and at positions where superpixel segmentation is not accurate enough. In our extensive experiments, the proposed method performs state-of-the-art accuracy.
Calcium gradients and buffers in bovine chromaffin cells.

1. Digital imaging and photometry were used in conjunction with the fluorescent Ca2+ indicator, Fura‐2, to examine intracellular Ca2+ signals produced by depolarization of single adrenal chromaffin cells. 2. Depolarization with a patch pipette produced radial gradients of Ca2+ within the cell, with Ca2+ concentration highest in the vicinity of the plasma membrane. These gradients dissipated within a few hundred milliseconds when the voltage‐gated Ca2+ channels were closed. 3. Dialysis of Fura‐2 into the chromaffin cell caused concentration‐dependent changes in the depolarization‐induced Ca2+ signal, decreasing its magnitude and slowing its recovery time course. These changes were used to estimate the properties of the endogenous cytoplasmic Ca2+ buffer with which Fura‐2 competes for Ca2+. 4. The spatially averaged Fura‐2 signal was well described by a model assuming fast competition between Fura‐2 and an endogenous buffer on a millisecond time scale. Retrieval of calcium by pumps and slow buffers occurs on a seconds‐long time scale. No temporal changes indicative of buffers with intermediate kinetics could be detected. 5. Two independent estimates of the capacity of the fast endogenous Ca2+ buffer suggest that 98‐99% of the Ca2+ entering the cell normally is taken up by this buffer. This buffer appears to be immobile, because it does not wash out of the cell during dialysis. It has a low affinity for Ca2+ ions, because it does not saturate with 1 microM‐Ca2+ inside the cell. 6. The low capacity, affinity and mobility of the endogenous Ca2+ buffer makes it possible for relatively small amounts of exogenous Ca2+ buffers, such as Fura‐2, to exert a significant influence on the characteristics of the Ca2+ concentration signal as measured by fluorescence ratios. On the other hand, even at moderate Fura‐2 concentrations (0.4 mM) Fura‐2 will dominate over the endogenous buffers. Under these conditions radiometric Ca2+ concentration signals are largely attenuated, but absolute fluorescence changes (at 390 nm) accurately reflect calcium fluxes.
Utility Maximization for Layered Transmission Using the Broadcast Approach

We investigate the power allocation problem in layered transmission with successive enhancement using the broadcast approach. This problem is particularly important for multimedia streaming applications and multicasting services over slowly fading channels with partial channel information at the transmitter. We consider the practical scenario of limited and pre-specified source layers, and we propose a generic and efficient solution to optimize the transmission power allocated to each layer in order to maximize the average user satisfaction defined by a utility function of the decoded layers. We assume a block-fading Rayleigh distributed channel model. However, our solution can be extended to a number of other channel distributions. Although the direct formulation of the problem is not convex, we propose change of optimization variable, and we use the dual problem and the perturbation analysis in order to obtain the optimal solution. The solution is based on a one-dimensional bisection search irrespective of the total number of layers. Our optimality analysis indicates that in some cases it may not be optimal to transmit all the layers.