Miracle-dz/UniFAR-FTUs huggingface dataset:
Community factors associated with stunting, overweight and food insecurity: a community-based mixed-method study in four Andean indigenous communities in Ecuador

Objectives We aimed to implement participatory research to answer a question posed by four Kichwa indigenous communities in Andean Ecuador about what actionable factors are associated with childhood stunting, overweight and food insecurity among their people. Design We used mixed methods including household questionnaires, discussion groups with respondents of the questionnaires and anthropometric measurement of children (6 months to 12 years) from surveyed households. Setting The study involved four Andean indigenous communities transitioning from traditional to Western lifestyles. They subsist mainly on small-scale agriculture and have a rich cultural heritage including their traditional language. Participants Anthropometric data were collected from 298 children from 139 households in four communities; all households completed the questionnaire. We held five discussion groups (6–10 participants each): three composed of mothers and two of farmers. Primary and secondary outcome measures Primary outcomes were stunting, overweight, food insecurity and their relationship with demographics, dietary habits and agricultural habits. Results Of 298 children, 48.6% were stunted and 43.3% overweight for age. Stunted children were more likely to live in households that sold livestock (ORa 1.77, 95% CIa 1.06 to 2.95) and with illiterate primary caretakers (ORa 1.81, 95% CIa 1.07 to 3.06), but were less likely to live in households with irrigation (ORa 0.47, 95% CIa 0.27 to 0.81). Overweight children were more likely to be male (ORa 1.87, 95% CIa 1.02 to 3.43) and live in a household that sold livestock (ORa 2.14, 95% CIa 1.14 to 4.02). Some 67.8% of children lived in a household with food insecurity, more frequently in those earning below minimum wage (ORa 2.90, 95% CIa 1.56 to 5.41) and less frequently in those that ate quinoa in the past 24 hours (ORa 0.17, 95% CIa 0.06 to 0.48). Discussion groups identified irrigation and loss of agricultural and dietary traditions as important causes of poor childhood nutrition. Conclusion Many indigenous communities face tumultuous cultural, nutritional and epidemiological transitions. Community-based interventions on factors identified here could mitigate negative health outcomes.
Transcriptome profile analysis identifies candidate genes for the melanin pigmentation of breast muscle in Muchuan black-boned chicken

Melanin-based coloration in the meat of black-boned chicken is a major economic issue in China. Variation in the pigmentation (hypopigmentation) of chicken muscle causes direct economic losses every year. To determine the molecular mechanisms involved in the melanogenesis of muscle tissue, this study used high-throughput sequencing to compare differences in the transcriptome between black (BM) and white (WM) chicken breast muscles. We constructed 6 cDNA libraries from BM and WM groups in Muchuan black-boned chickens. A comparison between the BM and WM groups revealed 264 differentially expressed genes, of which 152 were upregulated, whereas 112 were downregulated in black muscle. Gene ontology and a Kyoto Encyclopedia of Genes and Genomes pathway analysis identified several differentially enriched biological functions and processes of the 2 muscles. Seven promising candidate genes [PMEL, Ras-related protein RAB29, and 5 solute carrier superfamily genes: SLC6A9, SLC38A4, SLC22A5, SLC35F3, and SLC16A3] may play an important role in the melanogenesis of chicken muscle. Our data provide a valuable resource for identifying genes whose functions are critical for muscle melanogenesis, and will assist studies of the molecular mechanisms of melanogenesis regulation in chicken muscle.
Recent Advancements in Our Understanding of the Ergogenic Effect of Respiratory Muscle Training in Healthy Humans: A Systematic Review

Abstract Shei, R-J. Recent advancements in our understanding of the ergogenic effect of respiratory muscle training in healthy humans: a systematic review. J Strength Cond Res 32(9): 2674–2685, 2018—Respiratory muscle training (RMT) has been shown to be an effective ergogenic aid for sport performance. Respiratory muscle training has been documented to improve performance in a wide range of exercise modalities including running, cycling, swimming, and rowing. The physiological effects of RMT that may explain the improvements in performance have been proposed to include diaphragm hypertrophy, muscle fiber–type switching, improved neural control of the respiratory muscles, increased respiratory muscle economy, attenuation of the respiratory muscle metaboreflex, and decreases in perceived breathlessness and exertion. This review summarizes recent studies on the ergogenicity and mechanisms of RMT since 2013 when the topic was last systematically reviewed. Recent evidence confirms the ergogenic effects of RMT and explores different loading protocols, such as concurrent exercise and RMT (i.e., “functional” RMT). These studies suggest that adapting new training protocols may have an additive improvement effect, but evidence of the efficacy of such an approach is conflicting thus far. Other recent investigations have furthered our understanding of the mechanisms underpinning RMT-associated improvements in performance. Importantly, changes in ventilatory efficiency, oxygen delivery, cytokine release, motor recruitment patterns, and respiratory muscle fatigue resistance are highlighted as potential mechanistic factors linking RMT with performance improvements. It is suggested that future investigations focus on development of sport-specific RMT loading protocols, and that further work be undertaken to better understand the mechanistic basis of RMT-induced performance improvements.
Mutation of FOP/FGFR1OP in mice recapitulates human short rib-polydactyly ciliopathy

Skeletal dysplasias are a clinically and genetically heterogeneous group of bone and cartilage disorders. A total of 436 skeletal dysplasias are listed in the 2015 revised version of the nosology and classification of genetic skeletal disorders, of which nearly 20% are still genetically and molecularly uncharacterized. We report the clinical and molecular characterization of a lethal skeletal dysplasia of the short-rib group caused by mutation of the mouse Fop gene. Fop encodes a centrosomal and centriolar satellite (CS) protein. We show that Fop mutation perturbs ciliogenesis in vivo and that this leads to the alteration of the Hedgehog signaling pathway. Fop mutation reduces CSs movements and affects pericentriolar material composition, which probably participates to the ciliogenesis defect. This study highlights the role of a centrosome and CSs protein producing phenotypes in mice that recapitulate a short rib-polydactyly syndrome when mutated.
Urine volume and nitrogen excretion are altered by feeding birdsfoot trefoil compared to alfalfa in lactating dairy cows.

Legumes that contain condensed tannins may have lower ruminal protein degradation than alfalfa. The present study investigated the effects of feeding birdsfoot trefoil (Lotus corniculatus L.) hay on lactational performance and N utilization and excretion. Eight multiparous Holstein cows in mid-lactation (150 ± 22.3 d-in-milk) were randomly assigned to two treatments [alfalfa hay-based total mixed ration (AHT) or birdsfoot trefoil hay-based total mixed ration (BHT)] in a crossover design with two experimental periods. Each experimental period lasted 17 d (14 d of adaptation and 3 d of sampling and total collection). Hays comprised approximately 50% of DM in experimental diets. There were no treatment effects on dry matter intake (DMI; 21.4 vs. 20.7 kg/d), milk yield (29.4 vs. 28.1 kg/d), milk fat concentration (3.20 vs. 3.21%), and milk protein concentration (3.20 vs. 3.16%) for AHT and BHT, respectively. In addition, dietary treatments did not affect milk yield/DMI or energy-corrected milk yield/DMI. In contrast, apparent crude protein digestion decreased in cows fed BHT compared to those fed AHT (60.7 vs. 69.1%). Concentration of milk urea-N decreased by feeding BHT compared with AHT (11.9 vs. 13.3 mg/100 mL), whereas total N excretion did not differ between AHT and BHT diets. However, cows fed BHT excreted more N in feces (194 vs. 168 g/d), while urinary N excretion was lower compared with cows fed AHT. Shift of N to feces resulted in a decrease in urinary-N:fecal-N ratio in cows fed BHT relative to those fed AHT. Overall results in the current study suggest that feeding birdsfoot trefoil in dairy diets shifts routes of N from urine to feces compared with feeding alfalfa hay, with little effect on lactational performance. Reduction in urinary N and any impact on environment may be attributed to functional effect of condensed tannins in birdsfoot trefoil hay.
Increased jejunal permeability in human obesity is revealed by a lipid challenge and is linked to inflammation and type 2 diabetes

Obesity and its metabolic complications are characterized by subclinical systemic and tissue inflammation. In rodent models of obesity, inflammation and metabolic impairments are linked with intestinal barrier damage. However, whether intestinal permeability is altered in human obesity remains to be investigated. In a cohort of 122 severely obese and non‐obese patients, we analyzed intestinal barrier function combining in vivo and ex vivo investigations. We found tight junction impairments in the jejunal epithelium of obese patients, evidenced by a reduction of occludin and tricellulin. Serum levels of zonulin and LPS binding protein, two markers usually associated with intestinal barrier alterations, were also increased in obese patients. Intestinal permeability per se was assessed in vivo by quantification of urinary lactitol/mannitol (L/M) and measured directly ex vivo on jejunal samples in Ussing chambers. In the fasting condition, L/M ratio and jejunal permeability were not significantly different between obese and non‐obese patients, but high jejunal permeability to small molecules (0.4 kDa) was associated with systemic inflammation within the obese cohort. Altogether, these results suggest that intestinal barrier function is subtly compromised in obese patients. We thus tested whether this barrier impairment could be exacerbated by dietary lipids. To this end, we challenged jejunal samples with lipid micelles and showed that a single exposure increased permeability to macromolecules (4 kDa). Jejunal permeability after the lipid load was two‐fold higher in obese patients compared to non‐obese controls and correlated with systemic and intestinal inflammation. Moreover, lipid‐induced permeability was an explicative variable of type 2 diabetes. In conclusion, intestinal barrier defects are present in human severe obesity and exacerbated by a lipid challenge. This paves the way to the development of novel therapeutic approaches to modulate intestinal barrier function or personalize nutrition therapy to decrease lipid‐induced jejunal leakage in metabolic diseases. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Activation functions and their characteristics in deep neural networks

Deep neural networks have gained remarkable achievements in many research areas, especially in computer vision, and natural language processing. The great successes of deep neural networks depend on several aspects in which the development of activation function is one of the most important elements. Being aware of this, a number of researches have concentrated on the performance improvements after the revision of a certain activation function in some specified neural networks. We have noticed that there are few papers to review thoroughly the activation functions employed by the neural networks. Therefore, considering the impact of improving the performance of neural networks with deep architectures, the status and the developments of commonly used activation functions will be investigated in this paper. More specifically, the definitions, the impacts on the neural networks, and the advantages and disadvantages of quite a few activation functions will be discussed in this paper. Furthermore, experimental results on the dataset MNIST are employed to compare the performance of different activation functions.
Outcomes of Pregnancies With Maternal/Paternal Exposure in the Tofacitinib Safety Databases for Ulcerative Colitis

Abstract Background Active inflammatory bowel disease increases the risk of adverse pregnancy outcomes. Tofacitinib is an oral, small molecule Janus kinase inhibitor for the treatment of ulcerative colitis (UC). As a small molecule, tofacitinib is likely to cross the placental barrier; however, information on the effects of tofacitinib on pregnancy outcomes is limited. We report pregnancy and newborn outcomes among patients in UC clinical studies with prenatal (maternal/paternal) exposure to tofacitinib. Methods Pregnancies with maternal/paternal exposure to tofacitinib were identified and outcomes reported in 5 tofacitinib UC interventional studies (up to March 2017). Outcomes from tofacitinib rheumatoid arthritis (RA), psoriasis, and psoriatic arthritis interventional studies, and RA noninterventional postapproval safety studies, spontaneous adverse event reporting, and registry data are also reported. Results Of 1157 patients enrolled in the UC interventional studies, 301 were women of childbearing age. Eleven cases of maternal exposure and 14 cases of paternal exposure to tofacitinib (doses of 5 mg or 10 mg twice daily) before/at the time of conception or during pregnancy were identified. Outcomes included 15 healthy newborns, no fetal deaths, no neonatal deaths, no congenital malformations, 2 spontaneous abortions, and 2 medical terminations. Outcomes across other tofacitinib studies and postmarketing cases were consistent, with a healthy newborn being the most common outcome and no fetal deaths. Conclusions Based on the limited data available, pregnancy and newborn outcomes among patients with prenatal (maternal/paternal) exposure to tofacitinib in UC studies appear similar to those reported for other tofacitinib clinical study populations and the general population.
Is parental oral health literacy a predictor of children's oral health outcomes? Systematic review of the literature

BACKGROUND The scientific evidence regarding the association between parental oral health literacy (OHL) and children's oral health is unclear. AIM To evaluate the scientific evidence concerning the association between parental OHL and children's oral health outcomes. DESIGN Eight databases were searched. Studies that evaluated oral health outcomes among children and measured parental OHL through a validated tool were included. Two independent reviewers selected studies, extracted data and analysed the risk of bias. RESULTS Eleven studies were included. Most (n = 6) had a high risk of bias. Most studies evaluating dental caries found association between lower parental OHL and higher prevalence/experience of dental caries. Poor oral health-related quality of life was associated with decreased parental OHL (P < 0.05). Studies diverged on the association between OHL and the number of filled, extracted teeth, and dental visits. There was no association between children's tooth brushing frequency, use of toothpaste, oral health claim, oral health expenditures and parental OHL. The literature was inconclusive regarding the association between night bottle feeding, negative parental perception of the child's oral health and OHL. CONCLUSION Low parental OHL was associated with dental caries among their children. It is too soon to assume an association between OHL and the remaining outcomes.
Iron Homeostasis Pathways as Therapeutic Targets in Acute Kidney Injury

Background: Iron is critical for fundamental biologic functions such as cell division and mitochondrial electron transport. However, by the virtue of its ability to donate electrons, iron is probably the most effective oxidant in biologic systems. Summary: To avoid damage from iron-mediated oxidative injury or ferroptosis, multiple defense mechanisms exist including iron binding proteins and robust glutathione-dependent intracellular pathways. Hepcidin, through its ability to sequester iron within macrophages and induce H-ferritin, serves as an endogenous protective molecule against ferroptosis. Key Messages: Recent studies have demonstrated the protective role of hepcidin in both ischemic reperfusion injury and heme-mediated models of acute kidney injury (AKI). Ferroptosis-inhibiting drugs and hepcidin offer exciting novel prospects to treat AKI.
Does Early Active Bilingualism Enhance Inhibitory Control and Monitoring? A Propensity-Matching Analysis

Prior research suggesting that longer bilingual experience benefits inhibitory control and monitoring has been criticized for a lack of control over confounding variables. We addressed this issue by using a propensity-score matching procedure that enabled us to match early and late bilinguals on 18 confounding variables—for example, demographic characteristics, immigration status, fitness, extracurricular training, motivation, and emotionality—that have been shown to influence cognitive control. Before early and late bilinguals were matched (N = 196), we found early active bilingual advantages in flanker effects (in accuracy), global accuracy, and sensitivity (d′) on the Attention Network Test for Interaction and Vigilance and global accuracy on the saccade task. After matching (n = 113), many of the early active bilingual advantages that had been identified before matching were either attenuated or disappeared. However, we observed that early active bilingual advantages in flanker effects (in response time) were strengthened after matching. These results stress robust early active bilingual advantages in inhibitory control and highlight the importance of matching language groups on nonlinguistic covariates.
Effects of copper and zinc on ischemic heart disease and myocardial infarction: a Mendelian randomization study.

Background Despite great progress in prevention and control, ischemic heart disease (IHD) remains a leading cause of global morbidity and mortality. Diet plays a key role in IHD, but a comprehensive delineation of the role of dietary factors in IHD is not yet quite complete. Objective The aim of this study was to test the long-standing hypothesis that copper is protective and zinc harmful in IHD. Design We used separate-sample instrumental variable analysis with genetic instruments (Mendelian randomization). We obtained single nucleotide polymorphisms (SNPs) from a genome wide association study, strongly (P value < 5 × 10-8) and independently associated with erythrocyte copper and zinc. We applied these genetic predictors of copper and zinc to the largest, most extensively genotyped IHD case (n ≤ 76014)-control (n ≤ 264785) study, based largely on CARDIoGRAMplusC4D 1000 Genomes and the UK Biobank SOFT CAD, to obtain SNP-specific Wald estimates for the effects of copper and zinc on IHD, which were combined through the use of inverse variance weighting. Sensitivity analysis included use of the MR-Egger method, and reanalysis including SNPs independently associated with erythrocyte copper and zinc at P value < 5 × 10-6. Results Genetically instrumented copper was negatively associated with IHD (OR: 0.94; 95% CI: 0.90, 0.98). Genetically instrumented zinc was positively associated with IHD (OR: 1.06; 95% CI: 1.02, 1.11). Sensitivity analysis via MR-Egger gave no indication of unknown pleiotropy; less strongly associated SNPs gave similar results for copper. Conclusion Genetic validation of a long-standing hypothesis suggests that further investigation of the effects, particularly of copper, on IHD may provide a practical means of reducing the leading cause of mortality and morbidity.
Thromboelastometric prediction of mortality using the kinetics of clot growth in critically ill septic patients

&NA; Sepsis induces alterations in blood coagulation which are associated with mortality. Using rotational thromboelastometry (ROTEM), these states are often characterized by changes in parameters representing terminal clot lysis. However, the ROTEM changes are often subtle, making them difficult to recognize and interpret. The objective of this study is to evaluate a new ROTEM clot velocity parameter representing clot formation kinetics in septic ICU patients. We hypothesized that this time-based parameter was significantly different in critically ill septic survivors vs. nonsurvivors. This retrospective observational study included severe sepsis and septic shock patients having a minimum of two organ dysfunctions by Sequential Organ Failure Assessment criteria (study group), and a control group of healthy adults without infection . ROTEM with EXTEM activation was performed in all groups. The time from maximal clot formation velocity to zero velocity, representing the latter portion of time during active clot formation prior to achieving maximal clot firmness (t-AUCi) was calculated along with other ROTEM parameters and compared between septic survivors, nonsurvivors and healthy controls. A total of 76 septic patients, of which 26.3%, survived, were included in the study group, and 26 healthy control individuals were included in the control group. t-AUCi correlated with terminal clot lysis (P < 0.001), and was significantly prolonged in septic nonsurvivors compared with survivors and healthy controls (P < 0.001). t-AUCi also differentiated nonsurvivors vs. survivors among those patients having similar ROTEM lysis indices. t-AUCi was useful to differentiate critically ill septic patients, and could be useful to identify septic patients with high-risk of ICU mortality.
Soil Type Mediates the Effectiveness of Biological Control Against Limonius californicus (Coleoptera: Elateridae)

Abstract Wireworms, the larval stage of click beetles (Coleoptera: Elateridae), are a considerable threat to cereal and vegetable production in the Pacific Northwest and Intermountain regions of the United States. As insecticides are generally ineffective, alternative controls are needed to improve wireworm management. Wireworms are continuously exposed to a wide range of subterranean pathogenic organisms in the soil; identifying these organisms and determining their impact would contribute to the development of biological control for wireworms. Here, we evaluated the efficacy of an entomopathogenic nematode, Steinernema carpocapsae (Weiser) (Rhabditida: Steinernematidae), and a fungus, Metarhizium brunneum Petch (strain F52) (Hypocreales: Clavicipitaceae), for control of the Pacific Northwest predominant wireworm species Limonius californicus, in two different soil media. We also examined whether diatomaceous earth (DE) increases the efficacy of entomopathogens through facilitating their penetration into the host integument. Treatments containing M. brunneum (F52) resulted in the highest rates of wireworm mortality, indicating that the fungus may be more effective than the nematode at reducing population size. However, results were impacted by soil media. In peatmoss-dominated medium, M. brunneum-containing treatments were more effective in reducing feeding damage than treatments containing S. carpocapsae. However, in sand-dominated medium, treatments with S. carpocapsae provided relatively better seedling protection. No consistent effect of DE was detected. Our results suggest that the effectiveness of wireworm biological control agents depends on soil media, such that the application of biological control against wireworms must be made with knowledge of field soil type.