Miracle-dz/UniFAR-FTUs huggingface dataset:
Safety and tolerability of regadenoson CMR

Aims Knowledge of adverse events associated with regadenoson perfusion cardiac magnetic resonance (CMR) and patient tolerability has implications for patient safety and staff training. We sought to assess the safety and tolerability of regadenoson stress CMR. Materials and methods A group of 728 consecutive patients (median age 58, 44% female) and 25 normal volunteers (median age 21, 24% female) were recruited from August 2009 to March 2012 using a prospective, cross-sectional study design. Subjects were stressed using fixed-dose regadenoson and imaged using a 1.5T MRI scanner. Symptoms and adverse events including death, myocardial infarction (MI), ventricular tachycardia (VT)/ventricular fibrillation (VF), hospitalization, arrhythmias, and haemodynamic stability were assessed. Results There were no occurrences of death, MI, VT/VF, high-grade atrioventricular block, or stress-induced atrial fibrillation. Notable adverse events included one case of bronchospasm and one case of heart failure exacerbation resulting in hospitalization. The most common symptoms in patients were dyspnoea (30%, n = 217), chest discomfort (27%, n = 200), and headache (15%, n = 111). There was minimal change between baseline and peak systolic and diastolic blood pressure in both patients and volunteers (P > 0.05). A blunted heart rate response to regadenoson was noted in patients with body mass index (BMI) ≥30 kg/m2 (P < 0.001), and diabetes (P = 0.001). Conclusions Regadenoson CMR is well tolerated and can be performed safely with few adverse events.
Informational Complexity and Functional Activity of RNA Structures

Very little is known about the distribution of functional DNA, RNA, and protein molecules in sequence space. The question of how the number and complexity of distinct solutions to a particular biochemical problem varies with activity is an important aspect of this general problem. Here we present a comparison of the structures and activities of eleven distinct GTP-binding RNAs (aptamers). By experimentally measuring the amount of information required to specify each optimal binding structure, we show that defining a structure capable of 10-fold tighter binding requires approximately 10 additional bits of information. This increase in information content is equivalent to specifying the identity of five additional nucleotide positions and corresponds to an ∼1000-fold decrease in abundance in a sample of random sequences. We observe a similar relationship between structural complexity and activity in a comparison of two catalytic RNAs (ribozyme ligases), raising the possibility of a general relationship between the complexity of RNA structures and their functional activity. Describing how information varies with activity in other heteropolymers, both biological and synthetic, may lead to an objective means of comparing their functional properties. This approach could be useful in predicting the functional utility of novel heteropolymers.
PROTEUS2: a web server for comprehensive protein structure prediction and structure-based annotation

PROTEUS2 is a web server designed to support comprehensive protein structure prediction and structure-based annotation. PROTEUS2 accepts either single sequences (for directed studies) or multiple sequences (for whole proteome annotation) and predicts the secondary and, if possible, tertiary structure of the query protein(s). Unlike most other tools or servers, PROTEUS2 bundles signal peptide identification, transmembrane helix prediction, transmembrane β-strand prediction, secondary structure prediction (for soluble proteins) and homology modeling (i.e. 3D structure generation) into a single prediction pipeline. Using a combination of progressive multi-sequence alignment, structure-based mapping, hidden Markov models, multi-component neural nets and up-to-date databases of known secondary structure assignments, PROTEUS is able to achieve among the highest reported levels of predictive accuracy for signal peptides (Q2 = 94%), membrane spanning helices (Q2 = 87%) and secondary structure (Q3 score of 81.3%). PROTEUS2's homology modeling services also provide high quality 3D models that compare favorably with those generated by SWISS-MODEL and 3D JigSaw (within 0.2 Å RMSD). The average PROTEUS2 prediction takes ∼3 min per query sequence. The PROTEUS2 server along with source code for many of its modules is accessible a http://wishart.biology. ualberta.ca/proteus2.
The Physiological Effect of Human Grooming on the Heart Rate and the Heart Rate Variability of Laboratory Non-Human Primates: A Pilot Study in Male Rhesus Monkeys

Grooming is a widespread, essential, and complex behavior with social and affiliative valence in the non-human primate world. Its impact at the autonomous nervous system level has been studied during allogrooming among monkeys living in a semi-naturalistic environment. For the first time, we investigated the effect of human grooming to monkey in a typical experimental situation inside laboratory. We analyzed the autonomic response of male monkeys groomed by a familiar human (experimenter), in terms of the heart rate (HR) and heart rate variability (HRV) at different body parts. We considered the HRV in both the time (SDNN, RMSSD, and RMSSD/SDNN) and the frequency domain (HF, LF, and LF/HF). For this purpose, we recorded the electrocardiogram of two male rhesus monkeys seated in a primate chair while the experimenter groomed their mouth, chest, or arm. We demonstrated that (1) the grooming carried out by a familiar human determined a decrement of the HR and an increment of the HRV; (2) there was a difference in relation to the groomed body part. In particular, during grooming the mouth the HRV was higher than during grooming the arm and the chest. Taken together, the results represent the first evidence that grooming carried out by a familiar human on experimental monkeys has the comparable positive physiological effect of allogrooming between conspecifics. Moreover, since the results underlined the positive modulation of both HR and HRV, the present study could be a starting point to improve the well-being of non-human primates in experimental condition by means of grooming by a familiar person.
GeneXpert MTB/Rif to Diagnose Tuberculous Meningitis: Perhaps the First Test but not the Last.

Tuberculous meningitis (TBM) is the most severe form of tuberculous with substantial mortality. In May 2015, 54 researchers from 10 countries met in Da Lat, Vietnam, to discuss advances in TBM. Among the attendees were researchers involved in pivotal studies on the use of Xpert MTB/Rif for TBM diagnosis. Attendees discussed the 2014 World Health Organization strong recommendation favoring the use of Xpert "in preference to conventional microscopy and culture as the initial diagnostic test for cerebrospinal fluid (CSF) if the sample volume is low or if additional specimens cannot be obtained to make a quick diagnosis. " Attendees were concerned that the limitations of Xpert testing for TBM are not emphasized. Clear guidance is needed for the investigational pathway for TBM, including recommendations on the diagnostic package of investigations, which does not stop with Xpert testing. Second, emphasis on the large CSF volumes (ideally 8-10 mL) needed for Xpert testing is required. Guidelines should also emphasize that TBM is a medical emergency and early treatment reduces mortality.
Comparison of Surrogate Markers as Measures of Uncomplicated Insulin Resistance in Korean Adults

Background Metabolic syndrome (MS) is known to increase the risk of various cardiometabolic diseases and in-sulin resistance (IR) has known to have central role in the development of MS. Many surrogate indices of IR have been proposed and the detection of MS might be a suitable model for assessing the accuracy of surrogate indices. The aims of our study are to invest the most appropriate index by assessment of the diagnostic capacity of IR among each surrogate index and identifying cut-off values for discriminating uncomplicated MS in Korean adults. Methods A cross-sectional study was performed, assessing 294 Korean adults, 85 of whom were diagnosed with uncomplicated MS. The sensitivities and specificities of five surrogate IR indices were compared to discriminate MS from healthy subjects; these included fasting serum insulin, homeostasis model assessment–insulin resistance index, quantitative insulin sensitivity check index, McAuley index, and Disse index. Correlations between each index value were assessed using Pearson's and Spearman's correlation methods. Results The McAuley index showed the highest area under the curve (0.85), specificity (86.12%), accuracy (82.31%), positive predictive value (68.13%), and negative predictive value (88.67%) to distinguish MS, with a cut-off point of 5.3 defined. Correlation coefficients of the five indices showed that the McAuley index had the strongest correlation with IR. Conclusion The McAuley index showed the best accuracy in the detection of MS as a surrogate marker of IR. To establish more effective and accurate standards of measuring IR, comprehensive and multi-scaled studies are required.
Racial Disparities in Age at Time of Homicide Victimization

This study sought the factors associated with race/ethnicity disparities in the age at which homicide deaths tend to occur. We used the multiple disadvantage model to take race into account as we evaluated associations between age at time of homicide victimization and several social structural, mental health−related, and lifestyle factors. Data were derived from the 1993 National Mortality Followback Survey, a cross-sectional interview study of spouses, next of kin, other relatives, and close friends of individuals 15 years and older who died in the United States in 1993. Our results showed age at time of homicide mortality to be related to the three types of factors; race moderated some of these relationships. In general, being employed, married, and a homeowner appeared associated with reduced victimization while young. The relationship of victimization age and employment was not uniform across racial groups, nor was the relationship of victimization age and marital status uniform across groups. Among Blacks, using mental health services was associated with longer life. Homicide by firearm proved important for our Black and Hispanic subsamples, while among Whites, alcohol’s involvement in homicide exerted significant effects. Our results suggest that programs and policies serving the various racial/ethnic groups can alleviate multiple disadvantages relevant in homicide victimization at an early age.
Protein–protein docking with multiple residue conformations and residue substitutions

The protein docking problem has two major aspects: sampling conformations and orientations, and scoring them for fit. To investigate the extent to which the protein docking problem may be attributed to the sampling of ligand side‐chain conformations, multiple conformations of multiple residues were calculated for the uncomplexed (unbound) structures of protein ligands. These ligand conformations were docked into both the complexed (bound) and unbound conformations of the cognate receptors, and their energies were evaluated using an atomistic potential function. The following questions were considered: (1) does the ensemble of precalculated ligand conformations contain a structure similar to the bound form of the ligand? (2) Can the large number of conformations that are calculated be efficiently docked into the receptors? (3) Can near‐native complexes be distinguished from non‐native complexes? Results from seven test systems suggest that the precalculated ensembles do include side‐chain conformations similar to those adopted in the experimental complexes. By assuming additivity among the side chains, the ensemble can be docked in less than 12 h on a desktop computer. These multiconformer dockings produce near‐native complexes and also non‐native complexes. When docked against the bound conformations of the receptors, the near‐native complexes of the unbound ligand were always distinguishable from the non‐native complexes. When docked against the unbound conformations of the receptors, the near‐native dockings could usually, but not always, be distinguished from the non‐native complexes. In every case, docking the unbound ligands with flexible side chains led to better energies and a better distinction between near‐native and non‐native fits. An extension of this algorithm allowed for docking multiple residue substitutions (mutants) in addition to multiple conformations. The rankings of the docked mutant proteins correlated with experimental binding affinities. These results suggest that sampling multiple residue conformations and residue substitutions of the unbound ligand contributes to, but does not fully provide, a solution to the protein docking problem. Conformational sampling allows a classical atomistic scoring function to be used; such a function may contribute to better selectivity between near‐native and non‐native complexes. Allowing for receptor flexibility may further extend these results.
Information diffusion, Facebook clusters, and the simplicial model of social aggregation: a computational simulation of simplicial diffusers for community health interventions

Abstract By integrating the simplicial model of social aggregation with existing research on opinion leadership and diffusion networks, this article introduces the constructs of simplicial diffusers (mathematically defined as nodes embedded in simplexes; a simplex is a socially bonded cluster) and simplicial diffusing sets (mathematically defined as minimal covers of a simplicial complex; a simplicial complex is a social aggregation in which socially bonded clusters are embedded) to propose a strategic approach for information diffusion of cancer screenings as a health intervention on Facebook for community cancer prevention and control. This approach is novel in its incorporation of interpersonally bonded clusters, culturally distinct subgroups, and different united social entities that coexist within a larger community into a computational simulation to select sets of simplicial diffusers with the highest degree of information diffusion for health intervention dissemination. The unique contributions of the article also include seven propositions and five algorithmic steps for computationally modeling the simplicial model with Facebook data.
Part 15: neonatal resuscitation: 2010 American Heart Association Guidelines for Cardiopulmonary Resuscitation and Emergency Cardiovascular Care.

The following guidelines are an interpretation of the evidence presented in the 2010 International Consensus on Cardiopulmonary Resuscitation and Emergency Cardiovascular Care Science With Treatment Recommendations1). They apply primarily to newly born infants undergoing transition from intrauterine to extrauterine life, but the recommendations are also applicable to neonates who have completed perinatal transition and require resuscitation during the first few weeks to months following birth. Practitioners who resuscitate infants at birth or at any time during the initial hospital admission should consider following these guidelines. For the purposes of these guidelines, the terms newborn and neonate are intended to apply to any infant during the initial hospitalization. The term newly born is intended to apply specifically to an infant at the time of birth. Approximately 10% of newborns require some assistance to begin breathing at birth. Less than 1% require extensive resuscitative measures.2,3 Although the vast majority of newly born infants do not require intervention to make the transition from intrauterine to extrauterine life, because of the large total number of births, a sizable number will require some degree of resuscitation. Those newly born infants who do not require resuscitation can generally be identified by a rapid assessment of the following 3 characteristics:
Oral Magnesium Therapy Improves Endothelial Function in Patients With Coronary Artery Disease

BackgroundMagnesium blocks many of the physiological actions of calcium. Nevertheless, the impact of magnesium supplementation on endothelial function and exercise tolerance in stable coronary artery disease (CAD) patients has not been assessed. Methods and ResultsIn a randomized, double-blind, placebo-controlled trial, 50 stable CAD patients (41 men and 9 women, mean±SD age 67±11 years, age range 42 to 82 years) were randomized to receive either magnesium (n=25) (30 mmol/d Magnosolv-Granulat; Asta Medica Company, Inc) or placebo (n=25) for 6 months. Before and after 6 months, endothelium-dependent brachial artery flow-mediated vasodilation (FMD) and endothelium-independent NTG-mediated vasodilation were assessed with high-resolution (10-MHz) ultrasound. Exercise stress testing was performed with use of the Bruce protocol. Intracellular magnesium concentrations ([Mg2+]i) were assessed from sublingual cells through x-ray dispersion (EXA) (normal mean±SD values 37.9±4.0 mEq/L). The magnesium therapy significantly increased postintervention ([Mg2+]i versus placebo (36.2±5.0 versus 32.7±2.7 mEq/L, P <0.02). There was a significant correlation in the total population between baseline [Mg2+]i and baseline FMD (r =0.48, P <0.01). The magnesium intervention resulted in a significant improvement in postintervention FMD (15.5±12.0%, P =0.02 compared with baseline), which was not evident with placebo (4.4±2.5%, P =0.78 compared with baseline). There was better exercise tolerance (9.3±2.0 versus 7.3±3.1 minutes, P =0.05) and less ischemic ST-segment changes (4 versus 10 patients, P =0.05) in the magnesium versus placebo groups, respectively. ConclusionsOral magnesium therapy in CAD patients is associated with significant improvement in brachial artery endothelial function and exercise tolerance, suggesting a potential mechanism by which magnesium could beneficially alter outcomes in CAD patients.
The epidemiology of chronic syndromes that are frequently unexplained: do they have common associated factors?

BACKGROUND Syndromes for which no physical or pathological changes can be found tend to be researched and managed in isolation although hypotheses suggest that they may be one entity. The objectives of our study were to investigate the co-occurrence, in the general population, of syndromes that are frequently unexplained and to evaluate whether they have common associated factors. METHODS We conducted a population-based cross-sectional survey that included 2,299 subjects who were registered with a General Medical Practice in North-west England and who completed full postal questionnaires (response rate 72%). The study investigated four chronic syndromes that are frequently unexplained: chronic widespread pain, chronic oro-facial pain, irritable bowel syndrome, and chronic fatigue. Validated instruments were used to measure the occurrence of syndromes and to collect information on a variety of associated factors: demographic (age, gender), psychosocial (anxiety, depression, illness behaviour), life stressors, and reporting of somatic symptoms. RESULTS We found that 587 subjects (27%) reported one or more syndromes: 404 (18%) reported one, 134 (6%) reported two, 34 (2%) reported three, and 15 (1%) reported all four syndromes. The occurrence of multiple syndromes was greater than would be expected by chance (P < 0.001). There were factors that were common across syndromes: female gender [odds ratio (OR) = 1.8; 95% confidence interval (95% CI) 1.5-2.2], high levels of aspects of health anxiety like health worry preoccupation (OR = 3.5; 95% CI 2.8-4.4) and reassurance seeking behaviour (OR = 1.4; 95% CI 1.1-1.7), reporting of other somatic symptoms (OR = 3.6; 95% CI 2.9-4.4), and reporting of recent adverse life events (OR = 2.3; 95% CI 1.9-2.8). CONCLUSION This study has shown that chronic syndromes that are frequently unexplained co-occur in the general population and share common associated factors. Primary care practitioners need to be aware of these characteristics so that management is appropriate at the outset.
Determinants of technical efficiency in beef cattle production in Kenya

The stochastic metafrontier method is applied to estimate technical efficiency levels in beef cattle production in Kenya. Subsequently, a Tobit model is used to assess factors that might influence efficiency. Results show that the average efficiency level is 0.69, suggesting that there is considerable scope to improve beef production in Kenya. Considering the importance of the livestock enterprise to rural livelihoods and its potential role in poverty reduction, there is need for appropriate development strategies for enhanced efficiency. In particular, livestock development policies should focus on provision of technology-related services. For instance, promoting use of controlled cattle crossbreeding methods would enhance productivity gains. Effective institutional support is also necessary in order to improve efficiency, including improved access to market contracts, better farm management skills and off-farm income opportunities. Key words: Beef production; technical efficiency determinants; Kenya. JEL classifications: D24; O32; Q18.
Just-in-Time Concrete Delivery: Mapping Alternatives for Vertical Supply Chain Integration

This paper explains concepts underlying a just-in-time production system. Just-in-time production systems as implemented by Toyota are pull systems in which ‘kanban’ convey the need to replenish the right inventory at the right time and in the right amount. In this paper, symbols from manufacturing are introduced to map resource flows in order to help distinguish traditionalfrom lean production processes. These symbols are then applied to construction. Ready-mix concrete provides a prototypical example of a just-in-time construction process. Ready-mix concrete is a perishable commodity, batched to specifications upon customer demand. This makes just-in-time delivery necessary. Based on data from industry case studies, alternative forms of vertical supply chain integration were investigated. The most common one is where the batch plant also delivers the mix to the contractor’s project site. An alternative is for the contractor to haul the mix from the batch plant to the project site with their own revolving-drum trucks. One alternative is favored over the other depending on the amount of control the contractor wants in terms of on-time site delivery of concrete and the variability in the contractor’s demand for concrete project after project. Insights can be gained from these two examples on how the construction industry has adopted a just-in-time production system for at least one part of the concrete supply chain. The examples provided will help the reader think through issues pertaining to the need for having information, materials, and time buffers at strategic locations in construction processes.
Object-Oriented Analysis, Modeling, and Simulation of a Notional Air Defense System

This paper describes the analysis, modeling, and simulation of a notional air defense system using SMOOCHES (State Machines for Object-Oriented, Concurrent, Hierarchical Engineering Specifications). SMOOCHES is an object- oriented environment based on hierarchical state machines and extensions to Statecharts, specifically developed as an environment to specify, model, simulate and analyze / evaluate distributed, reactive systems. Using a high level system specification language, an object- oriented, hierarchical state specification of a radar tracking system with realistic constraints is derived. A graphical statechart representation of the tracking system behavior is also derived and implemented within the SMOOCHES environment.