Miracle-dz/UniFAR-FTUs huggingface dataset:
Killeen's probability of replication and predictive probabilities: how to compute, use, and interpret them.

P. R. Killeen's (2005a) probability of replication (prep) of an experimental result is the fiducial Bayesian predictive probability of finding a same-sign effect in a replication of an experiment. prep is now routinely reported in Psychological Science and has also begun to appear in other journals. However, there is little concrete, practical guidance for use of prep, and the procedure has not received the scrutiny that it deserves. Furthermore, only a solution that assumes a known variance has been implemented. A practical problem with prep is identified: In many articles, prep appears to be incorrectly computed, due to the confusion between 1-tailed and 2-tailed p values. Experimental findings reveal the risk of misinterpreting prep as the predictive probability of finding a same-sign and significant effect in a replication (p srep). Conceptual and practical guidelines are given to avoid these pitfalls. They include an extension to the case of unknown variance. Moreover, other uses of fiducial Bayesian predictive probabilities for analyzing, designing ("how many subjects? "), and monitoring ("when to stop? ") experiments are presented. Concluding remarks emphasize the role of predictive procedures in statistical methodology.
Anti-HIV Antibody Responses and the HIV Reservoir Size during Antiretroviral Therapy

Background A major challenge to HIV eradication strategies is the lack of an accurate measurement of the total burden of replication-competent HIV (the “reservoir”). We assessed the association of anti-HIV antibody responses and the estimated size of the reservoir during antiretroviral therapy (ART). Methods We evaluated anti-HIV antibody profiles using luciferase immunoprecipitation systems (LIPS) assay in relation to several blood-based HIV reservoir measures: total and 2-LTR DNA (rtPCR or droplet digital PCR); integrated DNA (Alu PCR); unspliced RNA (rtPCR), multiply-spliced RNA (TILDA), residual plasma HIV RNA (single copy PCR), and replication-competent virus (outgrowth assay). We also assessed total HIV DNA and RNA in gut-associated lymphoid tissue (rtPCR). Spearman correlations and linear regressions were performed using log-transformed blood- or tissue-based reservoir measurements as predictors and log-transformed antibody levels as outcome variables. Results Among 51 chronically HIV-infected ART-suppressed participants (median age = 57, nadir CD4+ count = 196 cells/mm3, ART duration = 9 years), the most statistically significant associations were between antibody responses to integrase and HIV RNA in gut-associated lymphoid tissue (1.17 fold-increase per two-fold RNA increase, P = 0.004) and between antibody responses to matrix and integrated HIV DNA in resting CD4+ T cells (0.35 fold-decrease per two-fold DNA increase, P = 0.003). However, these associations were not statistically significant after a stringent Bonferroni-adjustment of P<0.00045. Multivariate models including age and duration of ART did not markedly alter results. Conclusions Our findings suggest that anti-HIV antibody responses may reflect the size of the HIV reservoir during chronic treated HIV disease, possibly via antigen recognition in reservoir sites. Larger, prospective studies are needed to validate the utility of antibody levels as a measure of the total body burden of HIV during treatment.
ChIP-Seq : The new way to ‘ seq ’ genome wide for transcription factor binding patterns

Understanding the transcription regulatory network at the genome level has been a focus of many researchers over the past decade and it remains rightly so. By unlocking how genomic information is translated into gene regulation will allow us to better understand evolution, development and biological processes that have gone astray leading to diseases such as cancer. So far, our understanding of gene regulation has been derived from studies that have focused on detailed characterizations of a specific gene or gene family, but genome-scale analyses are now hinting the re-evaluation of such principles. For example, it is previously thought that a typical RNA polymerase II promoter contains a TATA box that is located 30bp upstream of the transcription start site. However, this may not be entirely true as recent genomic studies have shown that ~50% of human genes have alternative promoters (Kimura et al., 2006). To make matters even more complex, it has been estimated that there are 200-300 transcription factors in humans that bind to core promoters to drive gene transcription (Farnham, 2009). Thus, to fully comprehend the regulatory network of these transcription factors, it is of utmost importance to study the machinery of these proteins at the genomic level. Fortunately, the technological advancement of chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) has allowed investigators to create a global map of specific protein DNA-interactions in a given cell type. ChIP-seq has been widely used to study transcription factor binding, histone modifications and DNA methylation
Measuring Temporal Lags in Delay-Tolerant Networks

Delay-tolerant networks (DTNs) are characterized by a possible absence of end-to-end communication routes at any instant. Yet, connectivity can be achieved over time and space, leading to evaluate a given route both in terms of topological length or temporal length. The problem of measuring temporal distances in a social network was recently addressed through postprocessing contact traces like email data sets, in which all contacts are punctual in time (i.e., they have no duration). We focus on the distributed version of this problem and address the more general case that contacts can have arbitrary durations (i.e., be nonpunctual). Precisely, we ask whether each node in a network can track in real time how "out-of-dateâ it is with respect to every other. Although relatively straightforward with punctual contacts, this problem is substantially more complex with arbitrarily long contacts: consecutive hops of an optimal route may either be disconnected (intermittent connectedness of DTNs) or connected (i.e., the presence of links overlaps in time, implying a continuum of path opportunities). The problem is further complicated (and yet, more realistic) by the fact that we address continuous-time systems and nonnegligible message latencies (time to propagate a single message over a single link); however, this latency is assumed fixed and known. We demonstrate the problem is solvable in this general context by generalizing a time-measurement vector clock construct to the case of "nonpunctualâ causality, which results in a tool we call T-Clocks, of independent interest. The remainder of the paper shows how T-Clocks can be leveraged to solve concrete problems such as learning foremost broadcast trees (BTs), network backbones, or fastest broadcast trees in periodic DTNs.
A Trk/HKT-Type K+ Transporter from Trypanosoma brucei

ABSTRACT The molecular mechanisms of K+ homeostasis are only poorly understood for protozoan parasites. Trypanosoma brucei subsp. parasites, the causative agents of human sleeping sickness and nagana, are strictly extracellular and need to actively concentrate K+ from their hosts’ body fluids. The T. brucei genome contains two putative K+ channel genes, yet the trypanosomes are insensitive to K+ antagonists and K+ channel-blocking agents, and they do not spontaneously depolarize in response to high extracellular K+ concentrations. However, the trypanosomes are extremely sensitive to K+ ionophores such as valinomycin. Surprisingly, T. brucei possesses a member of the Trk/HKT superfamily of monovalent cation permeases which so far had only been known from bacteria, archaea, fungi, and plants. The protein was named TbHKT1 and functions as a Na+-independent K+ transporter when expressed in Escherichia coli, Saccharomyces cerevisiae, or Xenopus laevis oocytes. In trypanosomes, TbHKT1 is expressed in both the mammalian bloodstream stage and the Tsetse fly midgut stage; however, RNA interference (RNAi)-mediated silencing of TbHKT1 expression did not produce a growth phenotype in either stage. The presence of HKT genes in trypanosomatids adds a further piece to the enigmatic phylogeny of the Trk/HKT superfamily of K+ transporters. Parsimonial analysis suggests that the transporters were present in the first eukaryotes but subsequently lost in several of the major eukaryotic lineages, in at least four independent events.
The dimensional structure of the lexicon

Past research indicates that the lexical access of emotion words is influenced by the dimensions of evaluation and activity. Increased reaction time to a lexical decision task using emotion words and nonwords was predicted by low loadings on evaluation and activity as determined by ratings on semantic differential scales [L. H. Wurm and D. A. Vakoch, J. Acoust. Soc. Am. 95, 2974 (1994)]. The current study examines the extent to which evaluation, activity, and potency influence lexical access of words more representative of the entire lexicon [C. E. Osgood, J. Pers. Soc. Psychol. 12, 194–199 (1969)]. Implications for a dimensional model of the structure of the lexicon are discussed.
Discussion of the Kähler-Einstein problem

2 Sequences of Kähler-Einstein metrics 2 2.1 Differential Geometric input . 3 2.2 The main argument . 5 2.2.1 The Chow weight and stability . 5 2.2.2 Bound on the Chow weight . 7 2.3 Limit in the Hilbert scheme . 8 2.3. 1 General theory for group actions . 11 2.3. 2 Partial proof in the reduced irreducible case . 13
The Feasibility of Tissue Doppler Acceleration as a New Predictor of Thrombogenesis in the Left Atrial Appendage Associated with Nonvalvular Atrial Fibrillation

Background: Tissue acceleration utilizing the tissue Doppler imaging (TDI) technique is a new marker of ventricular contraction. We evaluated whether the left atrial appendage (LAA) wall acceleration was associated with thrombosis in patients with nonvalvular atrial fibrillation (NVAF). Methods: Seven NVAF patients with thromboembolism (TE), eight without TE, and eight with normal sinus rhythm (NSR) were studied using transesophageal echocardiography. TDI was used to evaluate the LAA wall acceleration. Results: There was a decrease in the peak flow velocity in the TE group compared with the other two groups. There was greater LAA expansion in NVAF with TE groups (with TE [8.9 ± 2.1 cm2] compared with the group without TE [7.3 ± 2.8 cm2]), but the difference was not statistically significant; the difference was statistically significant compared with the NSR group (5.3 ± 1.2 cm2; P = 0.0035). The average of the continuous 40‐frames area where tissue Doppler acceleration (TDA) was >0.024 cm/sec2 was significantly lower in the TE group (0.12 ± 0.05 cm2) compared to the group without TE (0.33 ± 0.17 cm2; P = 0.0017) and NSR group (0.30 ± 0.13 cm2; P = 0.0042), although wall velocity was not significantly different comparing the two NVAF groups. Furthermore, peak flow velocity of LAA was well correlated with LAA wall acceleration (r = 0.864, P < 0.0001). Conclusions: LAA wall acceleration obtained utilizing the TDI technique may be a new predictor of thrombogenesis in patients with NVAF.
Impact of Rapid Viral Testing for Influenza A and B Viruses on Management of Febrile Infants Without Signs of Focal Infection

Background: The objective of this study was to assess the effect of rapid testing for influenza virus on management of febrile young infants. Methods: During 2 influenza seasons (November to December 2003 and December 2004 to February 2005), we studied prospectively infants who were 0 to 36 months of age who presented to the emergency department (ED) with fever in the absence of signs of focal infection. The Directigen Flu A+B test was used to determine infection with influenza virus types A or B. Confirmatory viral cultures were not done. Results: Rapid influenza testing was performed in 206 infants and 84 (40.7%) of them were influenza-positive. Infants with a positive and a negative influenza test showed a similar mean (standard deviation) age (6.86 [6.3] versus 6.55 [6.8] months) and mean temperature (39.38°C [0.6] versus 39.32°C [0.8]), but there were significant differences (P < 0.01) in the percentage of patients undergoing blood tests (33.3% versus 100%), urinalysis (80.9% versus 100%), chest roentgenogram (14.2% versus 32%), cerebrospinal fluid analysis (1.33% versus 21.3%), mean length of stay in the ED (116.2 [75.5] versus 192.9 [76.3] minutes), admission to the ED observation ward (8.3% versus 21.3%), inpatient care (2.3% versus 16.4%) and antibiotic treatment (0% versus 38.5%). All positive bacterial cultures occurred among influenza-negative patients. Conclusions: The inclusion of rapid influenza testing for the evaluation of febrile young infants without signs of focal infection during influenza season decreases the need for additional studies and reduces the length of stay in the ED, the use of antibiotic treatment and unnecessary hospitalizations.
Sister chromatid exchange.

EARLY RESULTS . 1 83 Sister Chromatid Exchange in Meiosis 1 83 Sister Chromatid Exchange in Somatic Cells 1 84 Isolabeling 1 86 Sister Chromatid Exchanges-Spontaneous or Induced? 1 86 RESULTS FROM NEW METHODS FOR DETECTING SISTER CHROMA TID EXCHANGES . 1 86 Reasons for Differential Staining . 1 87 Harlequin Chromosomes and Chromosome Structure . 1 89 Multiple sister chromatid exchanges 1 90 Autoradiographic image spread . 1 90 Labeling for more than one replication cycle . 1 90 The Question 0/ Spontaneous Levels 0/ Sister Chromatid Exchanges . 1 9 1 Location 0/ Sister Chromosome Exchanges in the Chromosome . 1 93 Sister Chromatid Exchanges and Human Genetic Diseases . 1 93 Sister Chromatid Exchanges as Indicators 0/ Mutagenic Carcinogens . 1 94 Lesions Responsible for Sister Chromatid Exchange Formation . 1 96 CONCLUSION . 1 97
Nuclear Power in France

3 Main players 2 3.1 Public players . 2 3.1. 1 “Atomic Energy and Alternative Energies Commission” (CEA) . 2 3.1. 2 “Nuclear Safety Authority” (ASN) . 4 3.1. 3 “Institute for Radioprotection and Nuclear Safety” (IRSN) . 4 3.1. 4 "National radioactive Waste Management Agency" (ANDRA) . 4 3.2 Industry . 5
Management of Acute Malnutrition in Infants (MAMI) Project

Executive Summary . 11 Chapter 1: Introduction . 41 1.1 Background to the MAMI Project . 15 1.2 Aim, objectives & long term vision . 15 1.3 The process . 16 1.4 MAMI Project framework . 16
Cardiorespiratory Fitness, Blood Pressure and Ethnicity Are Related to Salivary Cortisol Responses after an Exercise Test in Children: The ExAMIN Youth SA Study

Background: Childhood elevated circulatory stress mediators such as cortisol seem to play an important role in the development of hypertension and metabolic disorders later in life. Little is known about the association of body composition, cardiorespiratory fitness (CRF), blood pressure (BP) and ethnicity with cortisol reactivity in young children. Methods: In this cross-sectional study, 324 black and 227 white school children (aged 7.4 ± 1.0 years) were screened for salivary cortisol reactivity, body mass index, BP and CRF (shuttle run) by standardised assessments for children. Results: Children in the lower cortisol reactivity percentile (<25th) had a higher heart rate (87.0 ± 12.9 bpm) and a lower CRF (3.1 ± 1.3 stages) compared to children in the upper (>25th) percentile (86.2 ± 11.5 bpm and 3.5 ± 1.7 stages, respectively). At baseline, children of black ethnicity had a higher cortisol level (p < 0.001). Immediately before the exercise test, no associations of obesity, BP, CRF and ethnicity with cortisol levels were found. In analysis of covariance (ANCOVA) we found that low CRF, high BP and black ethnicity were independently associated with lower cortisol reactivity by performing the shuttle run test (p < 0.01). Conclusion: Low CRF and high BP were associated with lower cortisol reactivity after a cardiorespiratory exercise test. Black children showed a lower cortisol reactivity which may contribute to the earlier onset of hypertension reported in black compared to white populations. Primary prevention programs need to focus on improving physical fitness to reduce the growing prevalence of cardiometabolic disorders during childhood.
CISDA Development Process for decision aids to support self-care decision making

The self-care management of chronic disease patients is complicated by various everyday decisions that range from routine ill-structured problems, e.g., “What to eat? ” to uncertain symptoms-related decisions, e.g., “Why do I feel tired? ” Such decisions can have significant consequences on a patient’s health, treatment, care, and associated medical costs. Due to the complexity involved in understanding and analysing everyday decision making, there is a lack of empirical research to guide the development of self-care decision aids. This thesis aims to address this problem by formulating and illustrating the Critical Illness Self-care Decision Aid (CISDA) process through a coherent, structured, integrated design and development process using a case study. Following a literature review, the problems in current approaches and the criteria needed for the development were derived from evidence-based frameworks such as chronic disease management, decision aids standards and complex interventions development process for future designs. Mixed methods were used including: focus groups, interviews, questionnaire, Cognitive Work Analysis and case scenarios for not only constructing an account of self-care needs and decisions but also to evaluate the development process and the decision support provided involving patients, doctors, caregivers, non-medical experts like psychologists and IT/Systems engineers. The CISDA process consists of: (i) needs assessment, (ii) theory formation, (iii) modelling, (iv) integration, (v) interface design and development, and (vi) evaluation for addressing the relevant intersection of human factors, systems engineering, and software engineering. This thesis should prove useful to not only systems engineers but also to a range of practitioners concerned about decision making, maintaining a user's cognitive perspective during specification and analysis of a complex system.
Power Consumption in WSN Based on Data Compression

— ireless sensor networks are extensively used almost everywhere. WSN’s advantages in certain applications and fields are so crucial that no other system can take its place. They are well known for its portable and scalable nature. Word wireless gives us the notion about self capable device working autonomously. Remotely situated sensors are programmed in such a way that they should work independently as a separate unit collaborating with the other nodes spread in the area. Nodes situated remotely are small in size and limit in the resources. Tiny sensor nodes are unable to carry large memory, high processing speed and bigger power source. Power consumption of WSN is important area, because power plays main role in properly working of a sensor node. Sensor nodes situated in remote areas are out of reach so maintenance is always not possible. Thus we need a strategy to make sensor node work as long as possible without interruption. Due to low battery, sensor nodes ability to sense and ability to communicate weaken and it leads to wrong result or no result. So reducing the power consumption at each sensor node can eventually end up decreasing overall power consumption of a network as well as increasing availability of network. This goal can be reached by reducing the power consumption of data transmission. Data compression is the key to decrease power consumption in network. This paper gives an algorithm which works on redundancy removal of data in network eventually compressing the data.
Application of Intravoxel Incoherent Motion in the Evaluation of Hepatocellular Carcinoma after Transarterial Chemoembolization

(1) Background: To assess the efficacy of the quantitative parameters of intravoxel incoherent motion (IVIM) diffusion-weighted imaging for hepatocellular carcinoma (HCC) diagnosis after transarterial chemoembolization (TACE). (2) Methods: Fifty HCC patients after TACE were included and underwent MRI. All of the patients were scanned with the IVIM-DWI sequence and underwent TACE retreatment within 1 week. Referring to digital subtraction angiography (DSA) and MR enhanced images, two readers measured the f, D, and D* values of the tumor active area (TAA), tumor necrotic area (TNA), and adjacent normal hepatic parenchyma (ANHP). Then, the distinctions of the TAA, TNA, and ANHP were compared and we analyzed the differential diagnosis of the parameters in three tissues. (3) Results: For values of f and D, there were significant differences between any of the TAA, TNA, and ANHP (p < 0.05). The values of f and D were the best indicators for identifying the TAA and TNA, with AUC values of 0.959 and 0.955, respectively. The values of f and D performed well for distinguishing TAA from ANHP, with AUC values of 0.835 and 0.753, respectively. (4) Conclusions: Quantitative IVIM-DWI was effective for evaluating tumor viability in HCC patients treated with TACE and may be helpful for non-invasive monitoring of the tumor viability.
Avaliação da infiltração bacteriana em técnicas de obturação do canal radicular

Introducao: Levando em consideracao a necessidade de que o selamento do sistema de canais e um fator decisivo para o sucesso da terapia endodontica, o presente estudo tem como objetivo avaliar a infiltracao em dentes obturados com tres tecnicas de obturacao: condensacao lateral e vertical a frio, onda continua decondensacao aquecida (E & Q Plus) e cone unico (sistema Protaper Universalri). Metodos: Quarenta e oito dentes tiveram seu comprimento e instrumentacao padronizados. Os dentes foram divididos aleatoriamente de acordo com a tecnica de obturacao: G1 - Condensacao lateral e vertical a frio, G2 u Termoplastica (E & Q Plus)e G3 u Cone unico, grupos-controle negativo e positivo, e obturados com o mesmo cimento (AH-Plus);. Osdentes foram montados em um modelo de dupla câmara, onde a infiltracao de Enterococus faecalis foi avaliada por um periodo de 30 dias pelo teste de turbidez de EVA. Resultados: Os resultados foram estatisticamente tabulados e analisados pelos teste Exato de Fisher e Kruskal-Wallis, usando-se o programa BioEstat 3.0 onde se revelou nao haver diferenca estatistica significante entre os grupos experimentais G1, G2 e G3, quando as tecnicas foram avaliadas separadamente ou entre os grupos. Nao houve diferenca entre as tecnicas avaliadas quando utilizado o cimento AH-Plus. (AU) Intrduction: Taking into consideration that the sealing of the canal system is a decisive factor for the success of endodontic therapy, this study ains to evaluate the microleakage in filled teeth with three obturation techniques:lateral and vertical condensation of cold, the continuoes wave condensation heat (E & Q Plus) and single cone system (ProTaper Universalri). Methods: Forty-eight teeth had their length and standard instrumentation. The teeth were randomly divided according to the technique of closure: G1 - Cold lateral and vertical condensation, G2 - Thermoplasticized (E & Q Plus) and G3 - Single cone, with the same sealer (AH-Plus); and control groups negative and positive. The teeth were mounted on a model of dual chamber where the infiltration of Enterococus faecalis was evaluated for a period of 30 days by testing the turbidity of EVA. Results:The results were statistical tabulated and analysised by Fisher Exact test and Kruskal-Wallis using the program BioEstat where 3.0 showed no statistically significant difference between the experimental groups G1, G2 and G3, when the techniques were evaluated separately or between groups. There was no difference between the techniques evaluated when the AH-Plus cement was used. (AU)