Miracle-dz/UniFAR-FTUs huggingface dataset:
Simulation Modeling and Metamodeling to Inform National and International HIV Policies for Children and Adolescents

Objective and Approach: Computer-based simulation models serve an important purpose in informing HIV care for children and adolescents. We review current model-based approaches to informing pediatric and adolescent HIV estimates and guidelines. Findings: Clinical disease simulation models and epidemiologic models are used to inform global and regional estimates of numbers of children and adolescents living with HIV and in need of antiretroviral therapy, to develop normative guidelines addressing strategies for diagnosis and treatment of HIV in children, and to forecast future need for pediatric and adolescent antiretroviral therapy formulations and commodities. To improve current model-generated estimates and policy recommendations, better country-level and regional-level data are needed about children living with HIV, as are improved data about survival and treatment outcomes for children with perinatal HIV infection as they age into adolescence and adulthood. In addition, novel metamodeling and value of information methods are being developed to improve the transparency of model methods and results, as well as to allow users to more easily tailor model-based analyses to their own settings. Conclusions: Substantial progress has been made in using models to estimate the size of the pediatric and adolescent HIV epidemic, to inform the development of guidelines for children and adolescents affected by HIV, and to support targeted implementation of policy recommendations to maximize impact. Ongoing work will address key limitations and further improve these model-based projections.
The spike onset zone

Objective To determine whether the maximum hemodynamic response to scalp interictal epileptic discharges (IEDs) corresponds to the region where IEDs originate and from where they propagate. Methods We studied 19 patients who underwent first an EEG-fMRI showing responses in the gray matter, and then intracranial EEG (iEEG). We coregistered the hemodynamic responses to the iEEG electrode contacts and analyzed IEDs in the iEEG channel adjacent to a maximum response (labeled the main channel), in relation to IEDs in other channels during a widespread intracranial IED event. IEDs in the main channel were aligned at their peak, and IEDs in each channel were averaged time-locked to these instants. The beginning and peak of IEDs in the averaged trace were identified, blinded to the identity of the main channel. The latency of IEDs was computed between the earliest and all other channels. Results The median latency of IEDs in the main channel was significantly smaller than in other channels for either the peak (15.5 vs 67.5 milliseconds, p = 0.00037) or the beginning (46.5 vs 118.4 milliseconds, p = 0.000048). The latency of IED was significantly correlated to the distance from the maximum hemodynamic response (p < 0.0001 for either the peak or the beginning). Conclusion IED adjacent to a maximum hemodynamic response, which often corresponds to the seizure onset zone, is more likely to precede IEDs in remote locations during a widespread intracranial discharge. Thus, EEG-fMRI is a unique noninvasive method to reveal the origin of IEDs, which we propose to label the spike onset zone.
Saphenous graft atherosclerosis as assessed by optical coherence tomography data for stenotic and non-stenotic lesions from the OCTOPUS registry

Introduction Coronary artery bypass grafting (CABG), although widely used for a long time in diffuse coronary artery disease (CAD), has serious limitations associated with graft aging and its degeneration. Aim The relationship between saphenous vein graft (SVG) plaque morphology assessed by optical coherence tomography (OCT) and clinical findings has not been elucidated yet. Material and methods We compared the morphology of SVG in stenotic vs. non-stenotic lesions using OCT imaging in 29 patients hospitalized in our center within the OCTOPUS registry. Results Stenotic lesions were characterized by higher incidence of thin-cap fibroatheroma (TCFA) (33% vs. 0%, p = 0.0048), thrombus (28% vs. 0%, p = 0.0008), lipid-rich plaque (LRP) (75% vs. 35%, p = 0.0013) and plaque within the SVG valve (19% vs. 0%, p = 0.0114) as compared to non-stenotic lesions. Patients with intimal tearing or rupture (ITR) were older (75.8% vs. 68.9 years, p = 0.047) and had lower left ventricular ejection fraction (LVEF) (32.0% vs. 49.7%, p = 0.001) and glomerular filtration rate (GFR) (36.0 vs. 73.6 ml/min/1.73 m2, p = 0.010). Patients with calcified lesions vs. those without had lower high-density lipoprotein (HDL) cholesterol (33.2 vs. 44.1 mg/dl, p = 0.018), similarly to those with ruptured plaque vs. those without (28.3 vs. 41.7 mg/dl, p = 0.047). Conclusions Presence of ITR was associated with advanced age, decreased LVEF and renal insufficiency. Decreased concentration of HDL was associated with higher occurrence of calcified and ruptured plaque.
The Effect of Problematic Internet Use, Social Appearance Anxiety, and Social Media Use on Nursing Students' Nomophobia Levels

This study examined the effect of problematic Internet use, social appearance anxiety, and social media use on nursing students' nomophobia levels. This study was conducted with 755 undergraduate nursing students. Sociodemographic data were evaluated using percentages and means. The effect of problematic Internet use, social appearance anxiety, and social media use on nomophobia levels was assessed by simple linear regression analysis. The mean age of participants was 21.4 ± 1.3; 82.5% were female, and 59.7% (n = 450) had adequate incomes. According to the regression analysis, nomophobia levels have a strong, positive, and significant relationship with the variables of problematic Internet use (&bgr; = .39, P < .000), social appearance anxiety (&bgr; = .27, P < .001), and social media dependency (&bgr; = .28, P < .001). Examining the correlation between nursing students' problematic Internet use, social appearance anxiety, and social media use levels, nomophobia levels had a positively moderate relationship with problematic Internet use (r = 0.259, P < .001), social appearance anxiety (r = 0.320, P < .001), and social media use levels (r = 0.433, P < .001). There is a direct correlation between nomophobia levels and the variables of problematic Internet use, social appearance anxiety, and social media use.
Impact of Global Mean Normalization on Regional Glucose Metabolism in the Human Brain

Because the human brain consumes a disproportionate fraction of the resting body's energy, positron emission tomography (PET) measurements of absolute glucose metabolism (CMRglc) can serve as disease biomarkers. Global mean normalization (GMN) of PET data reveals disease-based differences from healthy individuals as fractional changes across regions relative to a global mean. To assess the impact of GMN applied to metabolic data, we compared CMRglc with and without GMN in healthy awake volunteers with eyes closed (i.e., control) against specific physiological/clinical states, including healthy/awake with eyes open, healthy/awake but congenitally blind, healthy/sedated with anesthetics, and patients with disorders of consciousness. Without GMN, global CMRglc alterations compared to control were detected in all conditions except in congenitally blind where regional CMRglc variations were detected in the visual cortex. However, GMN introduced regional and bidirectional CMRglc changes at smaller fractions of the quantitative delocalized changes. While global information was lost with GMN, the quantitative approach (i.e., a validated method for quantitative baseline metabolic activity without GMN) not only preserved global CMRglc alterations induced by opening eyes, sedation, and varying consciousness but also detected regional CMRglc variations in the congenitally blind. These results caution the use of GMN upon PET-measured CMRglc data in health and disease.
Future Directions for Indoor Information Systems: A Panel Discussion

Geographic Information Systems (GIS) have enabled a vast range of applications in outdoor spaces, but these systems are bound to accurate localization technologies that are not available inside buildings where people carry 90% of their activities. Additionally, GIS don't address the unique characteristics of complex indoor environments off-the-shelf. At the same time, we witness the uptake of a new class of Indoor Information Systems (IIS), which store indoor spatial models along with sensor signals (e.g., wireless, light and magnetic) used to localize users. Such IIS might be considered as specialized GIS applications that are tailored to the unique challenges pertinent to indoor spaces, namely new indoor data management operators, new indexes, new data privacy schemes, built-in data-driven localization algorithms, models to crowdsource IIS data and these might even use NoSQL architectures. This panel will explore how the academia and industry are tackling the future challenges that rise in the scope of IIS. It will also identify and debate the key challenges and opportunities, in terms of applications, queries, architectures, to which the mobile data management and mobile data mining communities should contribute to.
Eye tracking as a debriefing tool in upset prevention and recovery training (UPRT) for general aviation pilots

Abstract Upset prevention and recovery training (UPRT) is intended to improve the ability of pilots to recognize and avoid situations that can lead to airplane upsets and to improve their ability to recover control of an airplane that has exceeded the normal flight envelope. To this end, a set of different training contents – from theoretical knowledge of aerodynamics and human factors to practice-based flight training – is necessary. In order to support the debriefing with an objective feedback, and because visual scanning is a core competence, two studies on subjective evaluation of aviation pilots – one conducted in a flight simulator and the other one in-flight – focussed on the practical application of eye tracking as a debriefing tool in UPRT. From a practitioner’s perspective, eye tracking appeared to be a useful method in terms of visualising instrument scanning techniques, supporting the instructor with objective debriefing material and fostering self-awareness in human processes. The discussion recommends adjusted UPRT instructor training and further improvements to eye tracking hardware and software. Practitioner Summary: The article focuses on pilot evaluations of eye tracking as a debriefing tool in UPRT and the identification of critical elements in its use. Eye tracking is a promising debriefing tool for UPRT. The discussion points to desirable improvements of eye tracking hardware and software as well as adjustments to instructor training that are pertinent.
Different Anti-Vaping Campaigns Attracting the Same Opponent Community

E-cigarettes (vape) are now the most commonly used tobacco product among youth in the United States. Ads are claiming e-cigarettes help smokers quit, but most of them contain nicotine, which can cause addiction and harm the developing adolescent brain. Therefore, national, state, and local health organizations have proposed anti-vaping campaigns to warn the potential risks of e-cigarettes. However, there is some evidence that these products may reduce harm for adult users who reduce or quit combustible cigarette smoking, and with little evidence that e-cigarettes cause long-term harm, pro-vaping advocates have used this equivocal evidence base to oppose the anti-vaping media campaign messaging, generating a very high volume of oppositional messages on social media. Thus, when we analyze the feedback of anti-vaping campaigns, it is crucial to partition the audience into different clusters according to their attitudes and affiliations. Motivated by this, in this paper, we propose the “community detection on anti-vaping campaign audience” problem and design the “community detection based on social, repost and content relation, (Sorento)” algorithm to solve it. Sorento computes users’ intimacy scores based on their social connections, repost relations, and content similarities. The community detection results achieved by Sorento demonstrate that though anti-vaping campaigns are proposed in different areas at different times, their opponent messages are mainly posted by the same community of pro-vapors.
Non-coeliac gluten sensitivity and the spectrum of gluten-related disorders: an updated overview

Abstract The spectrum of gluten-related disorders includes coeliac disease (CD), wheat allergy (WA) and the suggested entity of non-coeliac gluten sensitivity (NCGS). An increasing number of the world’s population are avoiding gluten due to the assumption of health benefits and self-diagnosed gastrointestinal and/or extra-intestinal symptoms. Unlike CD and WA, NCGS is a relatively new entity with an unknown prevalence and mechanisms, complicated by recent literature suggesting that gluten is not the only food component that may trigger symptoms experienced by this group of patients. The term ‘non-coeliac wheat sensitivity’ has been proposed as a more accurate term, allowing inclusion of other non-gluten wheat components such as fructans and amylase–trypsin inhibitors. There is inconsistent evidence when evaluating the effects of a gluten challenge in patients with suspected NCGS and there is a need for a standardised procedure to confirm the diagnosis, ultimately enabling the optimisation of clinical care. The present review will give an overview of the different gluten-related disorders and discuss the most recent scientific evidence investigating NCGS.
The promiscuous estrogen receptor: Evolution of physiological estrogens and response to phytochemicals and endocrine disruptors

Many actions of estradiol (E2), the principal physiological estrogen in vertebrates, are mediated by estrogen receptor-α (ERα) and ERβ. An important physiological feature of vertebrate ERs is their promiscuous response to several physiological steroids, including estradiol (E2), Δ5-androstenediol, 5α-androstanediol, and 27-hydroxycholesterol. A novel structural characteristic of Δ5-androstenediol, 5α-androstanediol, and 27-hydroxycholesterol is the presence of a C19 methyl group, which precludes the presence of an aromatic A ring with a C3 phenolic group that is a defining property of E2. The structural diversity of these estrogens can explain the response of the ER to synthetic chemicals such as bisphenol A and DDT, which disrupt estrogen physiology in vertebrates, and the estrogenic activity of a variety of plant-derived chemicals such as genistein, coumestrol, and resveratrol. Diversity in the A ring of physiological estrogens also expands potential structures of industrial chemicals that can act as endocrine disruptors. Compared to E2, synthesis of 27-hydroxycholesterol and Δ5-androstenediol is simpler, leading us, based on parsimony, to propose that one or both of these steroids or a related metabolite was a physiological estrogen early in the evolution of the ER, with E2 assuming this role later as the canonical estrogen. In addition to the well-studied role of the ER in reproductive physiology, the ER also is an important transcription factor in non-reproductive tissues such as the cardiovascular system, kidney, bone, and brain. Some of these ER actions in non-reproductive tissues appeared early in vertebrate evolution, long before mammals evolved.
Composition and strain relaxation of InxGa1−xN graded core–shell nanorods

Two InxGa1−xN nanorod samples with graded In compositions of x = 0.5–0 (Ga-rich) and x = 0.5–1 (In-rich) grown by molecular beam epitaxy were studied using transmission electron microscopy. The nanorods had a wurtzite crystal structure with growth along [ 0001 ] and core–shell structures with an In-rich core and Ga-rich shell. Energy-dispersive x-ray analysis confirmed grading over the entire compositional range and showed that the axial growth rate was primarily determined by the In flux, and the radial growth rate by the Ga flux. There was no evidence of misfit dislocations due to grading, but the strain due to the lattice mismatch between the In-rich core and Ga-rich shell was relaxed by edge dislocations at the core–shell interface with Burgers vectors a 〈 11 2 ¯ 0 〉 and c 〈 0001 〉 .
[Analysis of diseases distribution in Medical Information Mart for Intensive Care III database].

OBJECTIVE To study the distribution of diseases in Medical Information Mart for Intensive Care (MIMIC-III) database in order to provide reference for clinicians and engineers who use MIMIC-III database to solve clinical research problems. METHODS The exploratory data analysis technologies were used to explore the distribution characteristics of diseases and emergencies of patients (excluding newborns) in MIMIC-III database were explored; then, neonatal gestational age, weight, length of hospital stay in intensive care unit (ICU) were analyzed with the same method. RESULTS In the MIMIC-III database, 46 428 patients were admitted for the first time, and 49 214 ICU records were recorded. There were 26 076 males and 20 352 females; the median age was 60.5 (38.6, 75.6) years, and most patients were between 60 and 80 years old. The first diagnosis in the disease spectrum analysis was firstly ranked by circulatory diseases (32%), followed by injury and poisoning (14%), digestive system disease (8%), tumor (7%), respiratory disease (6%) and so on. Patients with ischemic heart disease accounted for the largest proportion of circulatory disease (42%), the proportion of these patients gradually increased with age of 60-70 years old, then decreased. However, the proportion of patients with cerebrovascular disease declined first and then increased with age, which was the main cause of death of circulatory system disease (ICU mortality was 22.5%). Injury and poisoning patients showed a significant decrease with age. Digestive system diseases were younger than the general population (most people aged between 50 to 60 years), and non-infectious enteritis and colitis were the main causes of death (ICU mortality was 18.3%). Respiratory infections were predominant in infected patients (34%), but circulatory system infections were the main cause of death (ICU mortality was 25.6%). Secondly, in the neonatal care unit, premature infants accounted for the vast majority (82%). As the gestational age increased, the duration of ICU was decreased, and the mortality was decreased. CONCLUSIONS The diseases distribution of patients can be provided by MIMIC-III database, which helps to grasp the overview of the volume and age distribution of the target patients in advance, and carry out the next step of research. Meanwhile, it points out the important role of exploratory data analysis in electronic health records analysis.
GECO: gene expression correlation analysis after genetic algorithm‐driven deconvolution

Motivation: Large‐scale gene expression analysis is a valuable asset for data‐driven hypothesis generation. However, the convoluted nature of large expression datasets often hinders extraction of meaningful biological information. Results: To this end, we developed GECO, a gene expression correlation analysis software that uses a genetic algorithm‐driven approach to deconvolute complex expression datasets into two subpopulations that display positive and negative correlations between a pair of queried genes. GECO's mutational enrichment and pairwise drug sensitivity analyses functions that follow the deconvolution step may help to identify the mutational factors that drive the gene expression correlation in the generated subpopulations and their differential drug vulnerabilities. Finally, GECO's drug sensitivity screen function can be used to identify drugs that differentially affect the subpopulations. Availability and implementation: http://www.proteinguru. com/geco/ and http://www.proteinguru. com/geco/codes/ Supplementary information: Supplementary data are available at Bioinformatics online.
Different associations between body composition and alcohol when assessed by exposure frequency or by quantitative estimates of consumption

BACKGROUND Alcohol intake is widely assumed to contribute to excess body fatness, especially among young men; however, the evidence is inconsistent. We have addressed this research question by investigating associations between reported alcohol consumption and body composition from large representative national surveys in a high alcohol-consuming country with a high obesity prevalence. METHODS The present study comprised a secondary analysis of combined cross-sectional nationally representative Scottish Health Surveys (1995-2010). Reported alcohol-drinking frequency was divided into five groups: from 'nonfrequent drinking' (reference) to daily/'almost every day' among 35 837 representative adults [mean (SD) age: 42.7 (12.7) years (range 18-64 years)]. Quantitative alcohol consumption was categorised into seven groups: from '1-7 to ≥50 10 g units per week'. Regression models against measured body mass index (BMI) and waist circumference (WC) were adjusted for age, physical activity, income, smoking, deprivation category and economic status. RESULTS Among alcohol-consuming men, heavier drinking (21-28 units per week) was associated with a higher BMI by +1.4 kg m-2 [95% confidence interval (CI) = 1.38-1.43] and higher WC by +3.4 cm (95% CI = 3.2-3.6) than drinking 1-7 units per week. However, those who reported daily drinking frequency were associated with a lower BMI by -2.45 kg m-2 (95% CI = -2.4 to -2.5) and lower WC by -3.7 cm (95% CI = -3.3 to -4.0) than those who reported less-frequent drinking. Similar associations were found for women. Most of these associations were restricted to subjects aged >30 years. Unexplained variances in BMI and WC are large. CONCLUSIONS Quantitative alcohol consumption and frequency of consumption were positively and inversely associated, respectively, with both BMI and WC among alcohol-consuming adults. Surveys are needed that evaluate both the quantity and frequency of consumption. The lowest BMI and WC were associated with a 'Mediterranean' drinking style (i.e. relatively little, but more frequently).
The trehalose protective mechanism during thermal stress in Saccharomyces cerevisiae: the roles of Ath1 and Agt1

ABSTRACT Trehalose on both sides of the bilayer is a requirement for full protection of membranes against stress. It was not known yet how trehalose, synthesized in the cytosol when dividing Saccharomyces cerevisiae cells are shifted from 28°C to 40°C, is transported to the outside and degraded when cells return to 28°C. According to our results, the lack of Agt1, a trehalose transporter, although had not affected trehalose synthesis, reduced cell tolerance to 51°C and increased lipid peroxidation. The damage was reversed when external trehalose was added during 40°C adaptation, confirming that the reason for the agt1&Dgr; sensitivity is the absence of trehalose at the outside of the lipid bilayer. The 40‐28°C condition caused cytosolic trehalase (Nth1) activation, reducing intracellular trehalose and, consequently, the survival rates after 51°C. Although lower than nth1&Dgr; strain, cells deficient in acid trehalase (ath1&Dgr;) maintained increased trehalose levels after 40°C‐28°C shift, which conferred protection against 51°C. Both Ath1 and Agt1 were found into vesicles near to plasma membrane in response to stress. This suggests that Agt1 containing vesicles would fuse with the membrane under 40°C to transport part of the cytosolic trehalose to the outside. By a similar mechanism, Ath1 would reach the cell surface to hydrolyze the external trehalose but only when the stress would be over. Corroborating this conclusion, Ath1 activity in soluble cell‐free extracts increased after 40°C adaptation but decreased when cells returned to 28°C. During 40°C, Ath1 is confined into vesicles, avoiding the cleavage of the outside trehalose.