Miracle-dz/UniFAR-FTUs huggingface dataset:
The effect of migration on dietary intake, type 2 diabetes and obesity: The Ghanaian health and nutrition analysis in Sydney, Australia (Ghanaisa)

This study aimed to investigate the dietary changes that occur upon migration and their relationship to Type II diabetes and obesity in Ghanaian migrants residing in Sydney, Australia. Eighty subjects (45 male, 35 female) were recruited from a local association. Anthropometric and duplicate fasting blood glucose measurements were obtained from each subject and dietary information collected by food frequency questionnaires. According to the WHO criteria, 20% of men and 11% of women were diabetic, with 22% and 20% sustaining impaired fasting glucose. Self‐reported mean BMI prior to migration to Australia was significantly lower than their current measured BMI. Fruits were consumed 14.2 and 12.6 servings less and fish 3.8 and 5.3 servings less per week in men and women, respectively, compared to when resident in Ghana. Upon migration, tropical root crops were almost exclusively replaced by potato starch. These dietary changes are consistent with an increased risk of Type II diabetes and overweight in this migrant population.
Cardiovascular structural and functional maturation

Cardiovascular defects represent the largest cause of childhood mortality. Of the 25,000 infants diagnosed with cardiovascular abnormalities each year, 5000 (20%) of those infants will die in the first year of life despite the best medical care. Thus, the broad spectrum of research to define cardiovascular structural and functional maturation includes human embryo, fetal, and neonatal studies, as well as experiments using animal, organ, cell, and subcellular protocols in chick embryo, rat, rabbit, dog, pig, and lamb models. New information further details the maturation of myocyte sarcolemmal and sarcoplasmic calcium transport, the composition of the regulatory thin filament, and the distribution of α-actins, β-myosins, and components of the extracellular matrix in the developing and diseased heart. Coronary angiogenesis in the developing and hypertrophied myocardium is more uniform than found in the mature heart. New quantitative data are available on myocardial growth in the embryonic and neonatal myocardium, and following heart transplantation. Investigation of embryonic, fetal, and neonatal cardiovascular function further highlights the dynamic interdependence of the maturing heart and systemic and pulmonary vascular beds. Exciting information continues to accumulate on the role of the endothelium in the regulation of pulmonary vascular tone.
Detailed analysis of p53 pathway defects in fludarabine-refractory chronic lymphocytic leukemia (CLL): dissecting the contribution of 17p deletion, TP53 mutation, p53-p21 dysfunction, and miR34a in a prospective clinical trial.

The prognosis of fludarabine (F)-refractory chronic lymphocytic leukemia (CLL) is very poor, and underlying mechanisms are only partly understood. To assess the contribution of p53 abnormalities to F-refractory CLL, we studied TP53 mutations in the CLL2H trial (subcutaneous alemtuzumab; n = 99). We found TP53 mutations in 37% of patients. Twelve of 67 (18%) patients without the 17p deletion showed a TP53 mutation and 50% showed evidence of uniparental disomy. A total of 75% of cases with TP53 mutation (without 17p-) showed clonal evolution/expansion. TP53 mutations had no impact on overall survival (P = .48). CLL with the 17p deletion or TP53 mutation showed very low miR-34a expression. To investigate the mechanisms underlying refractory CLL beyond p53, we studied cases without 17p-/TP53 mutation in detail. In several paired samples before and after F-refractory disease, no change in p21/p53 induction was observed after DNA damage. Although TP53 mutations and 17p deletions are found in a high proportion of F-refractory CLL, more than half of the cases cannot be explained by p53 defects (deletion or mutation), and alternative mechanisms need to be investigated. Alemtuzumab is effective irrespective of genetic high-risk subgroups with TP53 mutations. These clinical trials are registered at www.clinicaltrials. gov as #NCT00274976.
Hamstring injuries in elite Gaelic football: an 8-year investigation to identify injury rates, time-loss patterns and players at increased risk

Background Hamstring injuries occur frequently in field sports, yet longitudinal information to guide prevention programmes is missing. Aim Investigate longitudinal hamstring injury rates and associated time loss in elite Gaelic football, while identifying subgroups of players at increased risk. Methods 38 data sets from 15 elite male Gaelic football teams were received by the National Gaelic Athletic Association (GAA) Injury Surveillance Database between 2008 and 2015. Injury and exposure data were provided by the team's medical staff via an online platform. Results 391 hamstring injuries were sustained accounting for 21% (95% CI 20.0% to 21.7%) of all injuries. Prevalence was 21% (95% CI 19.2% to 23.4%). Incidences were 2.2 (95% CI 1.9 to 2.4) per 1000 exposure hours, and 7.0 (95% CI 6.5 to 7.1) times greater in match play than in training. Typically each team sustained 9.0 (95% CI 7.0 to 11.0) hamstring injuries per season affecting the: bicep femoris belly (44%; 95% CI 39.4% to 48.7%); proximal musculotendinous junction (13%; 95% CI 9.8% to 16.3%); distal musculotendinous junction (12%; 95% CI 8.6% to 14.9%) and semimembranosis/semitendinosis belly (9%; 95% CI 6.3% to 11.7%). ∼36% (95% CI 31.5% to 41.0%) were recurrent injuries. Mean time loss was 26.0 (95% CI 21.1 to 33.0) days, which varied with age, injury type and seasonal cycle. Hamstring injuries accounted for 31% (95% CI 25.8% to 38.2%) of injury-related time loss. Previously injured players (rate ratio (RR)=3.3), players aged 18–20 years (IRR=2.3) or >30 years (RR=2.3), as well as defensive (IRR=2.0) and midfield players (RR=1.5), were most at risk of sustaining a hamstring injury. Comparisons of 2008–2011 with 2012–2015 seasons revealed a 2-fold increase in hamstring injury incidences. Between 2008 and 2015 training incidence increased 2.3-fold and match-play incidences increased 1.3-fold. Conclusions Hamstring injuries are the most frequent injury in elite Gaelic football, with incidences increasing from 2008–2011 to 2012–2015. Tailoring risk management strategies to injury history, age and playing position may reduce the burden of hamstring injuries.
CHARMM-GUI Ligand Binder for Absolute Binding Free Energy Calculations and Its Application

Advanced free energy perturbation molecular dynamics (FEP/MD) simulation methods are available to accurately calculate absolute binding free energies of protein-ligand complexes. However, these methods rely on several sophisticated command scripts implementing various biasing energy restraints to enhance the convergence of the FEP/MD calculations, which must all be handled properly to yield correct results. Here, we present a user-friendly Web interface, CHARMM-GUI Ligand Binder ( http://www.charmm-gui.org/input/gbinding ), to provide standardized CHARMM input files for calculations of absolute binding free energies using the FEP/MD simulations. A number of features are implemented to conveniently set up the FEP/MD simulations in highly customizable manners, thereby permitting an accelerated throughput of this important class of computations while decreasing the possibility of human errors. The interface and a series of input files generated by the interface are tested with illustrative calculations of absolute binding free energies of three nonpolar aromatic ligands to the L99A mutant of T4 lysozyme and three FK506-related ligands to FKBP12. Statistical errors within individual calculations are found to be small (~1 kcal/mol), and the calculated binding free energies generally agree well with the experimental measurements and the previous computational studies (within ~2 kcal/mol). Therefore, CHARMM-GUI Ligand Binder provides a convenient and reliable way to set up the ligand binding free energy calculations and can be applicable to pharmaceutically important protein-ligand systems.
Enrichment Factor Analyses on G-Protein Coupled Receptors with Known Crystal Structure

G-protein coupled receptors (GPCRs) are highly relevant drug targets. Four GPCRs with known crystal structure were analyzed with docking (AutoDock4) and postdocking (MM-PBSA) in order to evaluate the ability to recognize known antagonists from a larger database of molecular decoys and to predict correct binding modes. Moreover, implications on multitarget drug screening are put forward. The results suggest that these methods may be of interest to the growing field of GPCR structure-based virtual screening.
Non O157:H7 avian pathogenic Shiga toxin‐producing Escherichia coli isolated from lesions on broiler chickens in Brazil

Shiga toxin-producing Escherichia coli strains produce at one or both of the two types of Shiga toxins (Stx1, Stx2). In humans, these pathogens cause diarrhea, hemorrhagic colitis and HUS, the leading cause of acute renal failure in children (1). The natural reservoirs of STEC are ruminants, particularly cattle. Although some authors (2, 3) have reported that E. coli isolated from chickens may harbor Shiga toxin-encoding genes, there is still no consensus on whether these animals can be considered as reservoirs of STEC strains. We genotypically and phenotypically analyzed 110 E. coli isolated in São Paulo, Brazil from chickens with cellulitis (60 isolates) and SHS lesions (50 isolates) to confirm the presence of STEC. These isolates harbored genes considered as minimal predictors of virulence for APEC (4). Thirty-four of these APEC strains [30.90%] harbored the stx genes according to conventional PCR as described by Paton and Paton (5). Eighteen of these [52.94%] were isolated from chickens with cellulitis and 16 [47.06%] from chickens with SHS lesions. The most frequent stx genotype was stx1þ/stx2þ (61.76%) followed by stx1þ/stx2 (38.24%). Cell-free filtrates of the 34 APEC stxþ exhibited cytotoxic activity similar to culture supernatants of E. coli O157:H7 EDL933 in Vero (African green monkey kidney) and human umbilical vein endothelial cells. It is estimated that STEC O157 causes about 36% of infections and non-O157 STEC cause the rest (6). In our study, none of the 34 STEC belonged to the O157:H7 serotype. Moreover, only one of the strains harbored the eae gene encoded in the LEE. Althoughmany authors have reported that the LEE locus is essential for host colonization and virulence of A/E pathogens (7), others state that, because a significant number of cases of severe disease, includingHUS in humans, as well as sporadic outbreaks, are caused by STEC LEE (8) and these sporadic and outbreak cases of severe disease are indistinguishable from those caused by STEC O157:H7 LEEþ (9), the presence of the LEE locus is not essential for pathogenesis. These genotypic and phenotypic data suggest that chickens act as reservoirs of STEC. We here suggest that the nomenclature for AP-STEC (avian pathogenic Shiga toxinproducing E. coli) should be discussed. Our data suggest that, in addition to cattle and goats, broiler chickens are also important reservoirs for STEC, increasing the risk of transmission of these pathogens to human hosts.
New Strategy for Receptor-Based Pharmacophore Query Construction: A Case Study for 5-HT7 Receptor Ligands

In this paper, a new approach for generating receptor-based 3D pharmacophore models for rapid in silico virtual screening is presented. The method combines information from docking poses of known ligands of different structures and further ligand-receptor complexes analyses using structural interaction fingerprints (SIFts). Next, the best linear combination of three-, four-, and five-feature pharmacophores in terms of selected performance parameter (i.e., recall, F-score, and MCC) is constructed. The resultant queries showed significantly better VS performance and new scaffold recognition when compared with the known ligand- and receptor-based pharmacophore models. The approach was developed and validated on 5-HT₇ receptor homology models created on available crystal structure templates. The efficiency of the obtained linear combinations exhibited only a minor dependence on the template selection.
A novel multi‐strain probiotic and synbiotic supplement for prevention of Clostridium difficile infection in a murine model

The protective effect of a multi‐strain probiotic and synbiotic formulation was evaluated in C57BL/6 mice infected with Clostridium difficile (CD) NAP1/027. Antibiotic‐treated mice were divided into the following four groups: Group 1, fed with a synbiotic formulation consisting of Lactobacillus plantarum F44, L. paracasei F8, Bifidobacterium breve 46, B. lactis 8:8, galacto‐oligosaccharides, isomalto‐oligosaccharides, and resistant starch; Group 2, fed with the same four probiotic strains as Group 1; Group 3, fed with the same prebiotic supplements as Group 1 for 7 days before CD infection; and Group 4 (control group) antibiotic treated and infected with NAP1/027 strain. Feces and cecal contents were collected for microbial cell viability, quantitative PCR (qPCR), toxin analyses and histopathology. Synbiotics‐ and probiotics‐fed mice showed a significant increase in total bifidobacteria (P < 0.05). The total lactobacilli count was increased in Group 1. Tests for cecal toxins were negative in Group 2 mice, whereas one sample each from Group 1 and 3 was positive. qPCR of cecal contents showed significant reduction in NAP1/027 DNA copies in Groups 1 and 2 and significantly higher numbers of B. breve 46, L. plantarum F44, and L. paracasei F8 in Groups 1 and 2 (P < 0.05); these changes were much less pronounced in Groups 3 and 4. Our findings indicate that the newly developed synbiotic or multi‐strain probiotic formulation confers protection against NAP1/027 infection in C57BL/6 mice. This holds promise for performing human studies.
High-intensity interval training: how much pain to get a gain?

High intensity interval training (HIIT) can produce similar if not greater improvements in cardiorespiratory fitness, an independent protective factor against premature death, and some health-related parameters compared to conventional, moderate intensity continuous training (MICT). HIIT takes substantially less time to complete and this enhances its potential in public health promotion given that lack of time is one of the barriers to long-term adherence to physical activity and exercise training. HIIT describes exercise bouts of 10 s to 4 min with ‘all-out’ maximal effort or intensities of 85–95% of maximum heart rate (HRmax) interspersed by periods of low activity or rest (30 s to 4 min). MICT describes prolonged continuous exercise at 60–80% HRmax. Despite the accumulated evidence, very little improvement has been made in terms of HIIT implementation in real life settings given that most studies lack the required level of ecological validity (most are of healthy volunteers training under research-based conditions—this is far from …
Retracted: Characterization of carbapenem resistance mechanisms and in vitro synergistic activity of colistin plus meropenem in carbapenem resistant Klebsiella pneumoniae

Retraction statement: ‘Characterization of carbapenem resistance mechanisms and in vitro synergistic activity of colistin plus meropenem in carbapenem resistant Klebsiella pneumoniae’ by Mohammed Ali M. Marie, Lakshmana Gowda Krishnappa, Yazeed A. Al Sheikh and Khaled Homoud M. Dabwan.
Improving discriminality in heart rate variability analysis using simple artifact and trend removal preprocessors

Heart Rate variability (HRV) is important in characterizing heart functions. However, artifacts and trends are regularly observed to contaminate the HRV sequences. This study proposes a simple and effective preprocessor for the removal of artifacts and trend in the HRV sequences. A thresholding filter is applied to remove artifacts to maintain the HRV sequences in a reasonable range. A wavelet filter proceeds to remove the ultra and very low frequency components determined as trends. As a consequence, more reliable low frequency (LF) and high frequency (HF) components can be calculated, which are believed to be close-related to the autonomic nervous system (ANS) regulation of the heart. The result demonstrates that features calculated from the power spectral density of the preprocessed HRV are more separable in feature space when compared with that from the original HRV. A simple KNN classifier is employed to justify the effects of this preprocessor in differentiating congestive heart failure (CHF) from the normal sinus rhythms (NSR). Using five features calculated from LF and HF, the performance of the KNN classifier shows significant improvement after applying the preprocessors. When compared with the other studies published in the literature, the proposed method outperforms them in CHF recognition with a much simpler scheme.
HackaMol: An Object-Oriented Modern Perl Library for Molecular Hacking on Multiple Scales

HackaMol is an open source, object-oriented toolkit written in Modern Perl that organizes atoms within molecules and provides chemically intuitive attributes and methods. The library consists of two components: HackaMol, the core that contains classes for storing and manipulating molecular information, and HackaMol::X, the extensions that use the core. The core is well-tested, well-documented, and easy to install across computational platforms. The goal of the extensions is to provide a more flexible space for researchers to develop and share new methods. In this application note, we provide a description of the core classes and two extensions: HackaMol::X::Calculator, an abstract calculator that uses code references to generalize interfaces with external programs, and HackaMol::X::Vina, a structured class that provides an interface with the AutoDock Vina docking program.
Vibrotactile guidance for trajectory following in computer aided surgery

Most conventional computer-aided navigation systems assist the surgeon visually by tracking the position of an ancillary and by superposing this position into the 3D preoperative imaging exam. This paper aims at adding to such navigation systems a device that will guide the surgeon towards the target, following a complex preplanned ancillary trajectory. We propose to use tactile stimuli for such guidance, with the design of a vibrating belt. An experiment using a virtual surgery simulator in the case of skull base surgery is conducted with 9 naïve subjects, assessing the vibrotactile guidance effectiveness for complex trajectories. Comparisons between a visual guidance and a visual+tactile guidance are encouraging, supporting the relevance of such tactile guidance paradigm.
Training load and structure-specific load: applications for sport injury causality and data analyses

### Definitions #### Training load Training load represents step count, throws, distance run and/or time spent practising sport. This can be used to calculate a change in training load over time (eg, acute:chronic workload ratio or week-to-week changes), which has been used as a time-varying exposure to sports injury recently. #### Structure-specific cumulative load Can be viewed as the sum of step-specific or throw-specific loads that a certain musculoskeletal structure is exposed to during a training session. Estimation of the structure-specific cumulative load per training session involves stepwise or throw-wise quantification of the load distribution and the load magnitude. #### Structure-specific load capacity Can be defined as a certain structure’s ability to withstand structure-specific cumulative load. How should I schedule my training? How much is too much? Coaches and sports medicine clinicians commonly face such questions when considering training and injury risk. These are highly relevant inquiries, as training load is a necessary cause of sports injury.1 2 To provide answers, our analytical approaches should align with causal frameworks. Changes in training load (eg, acute:chronic workload ratio) has been used as an interesting exposure to injury lately3–5 and promoted as proximal in the causal chain to sports injury.2 6 However, the aetiology behind sports injury development is multifactorial.1 Therefore, more variables (eg, body mass, alignment, diet, strength) than training load are necessary to robustly identify ‘how much is too much’. 7 Accordingly, the purpose of this editorial is to describe the differences among the concepts ‘training-load’, ‘structure-specific load’ and ‘load capacity’, including the varied exposures that define them. Sports injury prevention scientists should carefully consider how best to phrase their research questions in aetiological …
Mesoscopic Simulation of Phospholipid Membranes, Peptides, and Proteins with Molecular Fragment Dynamics

Molecular fragment dynamics (MFD) is a variant of dissipative particle dynamics (DPD), a coarse-grained mesoscopic simulation technique for isothermal complex fuids and soft matter systems with particles that are chosen to be adequate fluid elements. MFD choses its particles to be small molecules which may be connected by harmonic springs to represent larger molecular entities in order to maintain a comparatively accurate representation of covalent bonding and molecular characteristics. For this study the MFD approach is extended to accomplish long-term simulations (up to the microsecond scale) of large molecular ensembles (representing millions of atoms) containing phospholipid membranes, peptides, and proteins. For peptides and proteins a generally applicable fragmentation scheme is introduced in combination with specific backbone forces that keep native spatial shapes with adequate levels of flexibility or rigidity. The new approach is demonstrated by MFD simulations of the formation and characteristics of phospholipid membranes and vesicles, vesicle-membrane fusion, the backbone force dependency of the overall structural flexibility of dumbbell-shaped Calmodulin, the stability of subunit-aggregation of tetrameric hemoglobin, and the collaborative interaction of Kalata B1 cyclotides with a phospholipid membrane. All findings are in reasonable agreement with experimental as well as alternative simulation results. Thus, the extended MFD approach may become a new tool for biomolecular system studies to allow for comparatively fast simulative investigations in combination with a comparatively high chemical granularity.
Telehealth technologies for managing chronic disease - experiences from Australia and the UK

In developed countries, chronic disease now accounts for more than 75% of health care expenditure and nearly an equivalent percentage of disease-related deaths [1]. The burden of chronic disease (often, but not exclusively, associated with ageing) includes congestive heart failure (CHF), chronic obstructive pulmonary disease (COPD), hypertension and diabetes. Over the past several decades there has been an epidemiological shift in disease burden from acute to chronic diseases that has rendered acute care models of health service delivery inadequate to address population health needs.