Miracle-dz/UniFAR-FTUs huggingface dataset:
Unravelling the determinants of human health in French Polynesia: the MATAEA project

Background: French Polynesia is a French overseas collectivity in the Southeast Pacific, comprising 75 inhabited islands across five archipelagoes. The human settlement of the region corresponds to the last massive migration of humans to empty territories, but its timeline is still debated. Despite their recent population history and geographical isolation, inhabitants of French Polynesia experience health issues similar to those of continental countries. Modern lifestyles and increased longevity have led to a rise in non-communicable diseases (NCDs) such as obesity, diabetes, hypertension, and cardiovascular diseases. Likewise, international trade and people mobility have caused the emergence of communicable diseases (CDs) including mosquito-borne and respiratory diseases. Additionally, chronic pathologies including acute rheumatic fever, liver diseases, and ciguatera, are highly prevalent in French Polynesia. However, data on such diseases are scarce and not representative of the geographic fragmentation of the population. Objectives: The MATAEA project aims to estimate the prevalence of several NCDs and CDs in the population of the five archipelagoes, and identify associated risk factors. Moreover, genetic analyses will contribute to determinate the sequence and timings of the peopling history of French Polynesia, and identify causal links between past genetic adaptation to island environments, and present-day susceptibility to certain diseases. Methods: This cross-sectional survey is based on the random selection of 2,100 adults aged 18-69 years and residing on 18 islands from the five archipelagoes. Each participant answered a questionnaire on a wide range of topics (including demographic characteristics, lifestyle habits and medical history), underwent physical measurements (height, weight, waist circumference, arterial pressure, and skin pigmentation), and provided biological samples (blood, saliva, and stool) for biological, genetic and microbiological analyses. Conclusion: For the first time in French Polynesia, the MATAEA project allows to collect a wide range of data to explore the existence of indicators and/or risk factors for multiple pathologies of public health concern. The results will help health authorities to adapt actions and preventive measures aimed at reducing the incidence of NCDs and CDs. Moreover, the new genomic data generated in this study, combined with anthropological data, will increase our understanding of the peopling history of French Polynesia.
Bias reduction studies in nonparametric regression with applications : an empirical approach

The purpose of this study is to determine the effect of three improvement methods on nonparametric kernel regression estimators. The improvement methods are applied to the Nadaraya-Watson estimator with crossvalidation bandwidth selection, the Nadaraya-Watson estimator with plug-in bandwidth selection, the local linear estimator with plug-in bandwidth selection and a bias corrected nonparametric estimator proposed by Yao (2012). The different resulting regression estimates are evaluated by minimising a global discrepancy measure, i.e. the mean integrated squared error (MISE). In the machine learning context various improvement methods, in terms of the precision and accuracy of an estimator, exist. The first two improvement methods introduced in this study are bootstrapped based. Bagging is an acronym for bootstrap aggregating and was introduced by Breiman (1996a) from a machine learning viewpoint and by Swanepoel (1988, 1990) in a functional context. Bagging is primarily a variance reduction tool, i.e. bagging is implemented to reduce the variance of an estimator and in this way improve the precision of the estimation process. Bagging is performed by drawing repetitive bootstrap samples from the original sample and generating multiple versions of an estimator. These replicates of the estimator are then used to obtain an aggregated estimator. Bragging stands for bootstrap robust aggregating. A robust estimator is obtained by using the sample median over the B bootstrap estimates instead of the sample mean as in bagging. The third improvement method aims to reduce the bias component of the estimator and is referred to as boosting. Boosting is a general method for improving the accuracy of any given learning algorithm. The method starts off with a sensible estimator and improves iteratively, based on its performance on a training dataset. Results and conclusions verifying existing literature are provided, as well as new results for the new methods.
Long noncoding RNA HIKER regulates erythropoiesis in Monge’s disease via CSNK2B

Excessive erythrocytosis (EE) is a major hallmark of patients suffering from chronic mountain sickness (CMS, also known as Monge’s disease) and is responsible for major morbidity and even mortality in early adulthood. We took advantage of unique populations, one living at high altitude (Peru) showing EE, with another population, at the same altitude and region, showing no evidence of EE (non-CMS). Through RNA-Seq, we identified and validated the function of a group of long noncoding RNAs (lncRNAs) that regulate erythropoiesis in Monge’s disease, but not in the non-CMS population. Among these lncRNAs is hypoxia induced kinase-mediated erythropoietic regulator (HIKER)/LINC02228, which we showed plays a critical role in erythropoiesis in CMS cells. Under hypoxia, HIKER modulated CSNK2B (the regulatory subunit of casein kinase 2). A downregulation of HIKER downregulated CSNK2B, remarkably reducing erythropoiesis; furthermore, an upregulation of CSNK2B on the background of HIKER downregulation rescued erythropoiesis defects. Pharmacologic inhibition of CSNK2B drastically reduced erythroid colonies, and knockdown of CSNK2B in zebrafish led to a defect in hemoglobinization. We conclude that HIKER regulates erythropoiesis in Monge’s disease and acts through at least one specific target, CSNK2B, a casein kinase.
Infection of primary nasal epithelial cells differentiates among lethal and seasonal human coronaviruses

Significance All respiratory viruses, including human coronaviruses (HCoVs), enter and establish a primary infection in the nasal epithelium. Primary nasal epithelial cells cultured at air–liquid interface (ALI) closely resemble the in vivo nasal epithelium and thus are an optimal system in which to query HCoV–host interactions. We use human nasal ALI cultures to differentiate among lethal (SARS-CoV-2 and MERS-CoV) and seasonal (HCoV-NL63 and HCoV-229E) HCoVs in terms of replication, cellular tropism, and cytotoxicity induction during infection. We further differentiate among these HCoVs using IL-13 treatment to recapitulate an asthmatic or inflamed airway and find that pre-existing disease states can significantly impact HCoV replication. HCoV–host interactions in the nasal epithelium are likely to determine clinical outcomes such as disease severity and transmissibility.
Interaction between slow wave sleep and elevated office blood pressure in non-hypertensive obstructive sleep apnea patients: a cross-sectional study

Abstract Purpose: Reduced slow wave sleep (SWS) has been linked to hypertension in some studies. The aim of the study is to investigate the association between SWS and office blood pressure (BP) in non-hypertensive obstructive sleep apnea (OSA). Methods: This is a retrospective study of 3350 patients who underwent polysomnography (PSG) in our hospital. Based on quartiles of percent SWS, participants were classified into four groups. BP was measured manually on the randomly chosen arm in a seated position with sphygmomanometer after PSG in the morning, and the average of the second and third measurements was used for this analysis. Elevated office BP was defined as a systolic BP≥140 mmHg or diastolic BP≥90 mmHg. Results: There were 1365 patients with OSA and 597 primary snorers included in our study. In OSA group, OSA patients with SWS <13.5% had a significant elevated risk with elevated office BP (OR,1.49[95%CI 1.05-2.10], P=0.025), compared to the highest quartile (percent SWS >39.2%). However, no significant relationship between decreased SWS and elevated office BP was found in primary snorers group. Conclusion: In non-hypertensive OSA patients, decreased SWS is associated with elevated office BP. Plain language summary This is the first study to investigate the association between decreased SWS and incident elevated office BP in non-hypertensive OSA patients. Our results found that in non-hypertensive OSA patients, decreased SWS is associated with elevated office BP. The relationship between decreased SWS and elevated office BP in OSA patients was evident especially in men and in those <60 years old.
A comprehensive revisit of the machine‐learning tools developed for the identification of enhancers in the human genome

Enhancers are non‐coding DNA elements that play a crucial role in enhancing the transcription rate of a specific gene in the genome. Experiments for identifying enhancers can be restricted by their conditions and involve complicated, time‐consuming, laborious, and costly steps. To overcome these challenges, computational platforms have been developed to complement experimental methods that enable high‐throughput identification of enhancers. Over the last few years, the development of various enhancer computational tools has resulted in significant progress in predicting putative enhancers. Thus, researchers are now able to use a variety of strategies to enhance and advance enhancer study. In this review, an overview of machine learning (ML)‐based prediction methods for enhancer identification and related databases has been provided. The existing enhancer‐prediction methods have also been reviewed regarding their algorithms, feature selection processes, validation techniques, and software utility. In addition, the advantages and drawbacks of these ML approaches and guidelines for developing bioinformatic tools have been highlighted for a more efficient enhancer prediction. This review will serve as a useful resource for experimentalists in selecting the appropriate ML tool for their study, and for bioinformaticians in developing more accurate and advanced ML‐based predictors.
Nonlinear Fourier-Transform Spectroscopy of D2 Using High-Order Harmonic Radiation

High-order harmonic radiation is available to investigate ultrafast nonlinear optical phenomena, such as two-photon absorption process, in the vacuum and extreme ultraviolet wavelength region. We have determined the sequential two-photon dissociative ionization pathways of D2 with the simultaneous irradiation of multiple order harmonics of a Ti:sapphire laser in the visible-vacuum ultraviolet region with the aid of both an interferometric autocorrelation measurement and a Fourier-transform spectroscopy. By analyzing the interferometric autocorrelation signals appearing in the measured momentum distribution of D + , we were able to decompose the measured momentum distribution into three momentum distribution images representing the three distinct dissociation pathways, which are sequentially two-photon excitation processes of D2. \({\mathrm{D}}_{2}^{+}\) is prepared in the electronic ground state of \({\mathrm{D}}_{2}^{+}\), and then excited to the first excited state, leading to the dissociation into D + and D.
Active glucose transport varies by small intestinal region and oestrous cycle stage in mice

What is the central question of this study? Body mass and food intake change during the female ovarian cycle: does glucose transport by the small intestine also vary? What is the main finding and its importance? We have optimised Ussing chamber methodology to measure region‐specific active glucose transport in the small intestine of adult C57BL/6 mice. Our study provides the first evidence that jejunal active glucose transport changes during the oestrous cycle in mice, and is higher at pro‐oestrus than oestrus. These results demonstrate adaptation in active glucose uptake, concurrent with previously reported changes in food intake.
Effectiveness of a blended multidisciplinary intervention for patients with moderate medically unexplained physical symptoms (PARASOL): A cluster randomized clinical trial

Introduction In patients with moderate Medically Unexplained Physical Symptoms (MUPS), interventions focusing on both physical and psychological aspects are recommended. A proactive, blended and integrated physical therapy and mental health nurse intervention (PARASOL) might reduce complaints, stimulate self-management and prevent chronicity. Objective To investigate short- and long-term effectiveness of the PARASOL intervention compared to usual care on subjective symptom impact and quality of life in patients with moderate MUPS. Methods We conducted a cluster randomized clinical trial. The 12-week intervention integrated face-to-face sessions with the physical therapist and mental health nurse and access to a web-based program consisting of graded activity, exercises and information modules. Primary outcomes were subjective symptom impact, as registered with the adequate relief question, and quality of life. Secondary outcomes were severity of (psychosocial) symptoms, overall current health, physical behaviour, illness perceptions, and self-management skills. Assessment took place at baseline, after three and twelve months. Results Compared to usual care (n = 80), the number of patients in the PARASOL intervention (n = 80) that reported adequate short-term relief was higher (31.2% in intervention group vs. 13.7% in control group). On quality of life and secondary outcomes no significant between group differences in short- and long-term were found. Conclusions The PARASOL intervention does improve subjective symptom impact of patients with moderate MUPS on short-term. No additional beneficial effects on the other outcomes and the long-term were found.
Unraveling the Pivotal Impacts of Electron-Acceptors on Light Absorption and Carrier Photogeneration in Perylene Dye Sensitized Solar Cells

Understanding the ultrafast dynamics of excited state evolution and carrier generation at the complicated titania/dye/electrolyte interface is crucial for the development of narrow energy-gap organic dyes to enhance the performance of dye-sensitized solar cells (DSCs). We herein modulate the energy-levels of N-annulated perylene dyes in significant measure by use of benzothiadiazole-benzoic acid (BTBA) and pyridothiadiazole-benzoic acid (PTBA) segments as the electron-acceptors. Based on the model of cold vs hot excited states for electron injection in DSCs, we have perceived from femtosecond transient absorption measurements that a driving force diminution does not necessarily cause a deceleration of electron injection from the hot excited state to titania, suggesting a crucial role of electron coupling on interfacial charge transfer kinetics. Moreover, the electron-accetpor variation from BTBA to PTBA brings forth a fast relaxation of the hot excited state as well as a rapid deactivation of the cold exc.
A cost description of the setup costs of community-owned maternity waiting homes in rural Zambia

Maternity waiting homes (MWHs) are one strategy to improve access to skilled obstetric care in low resource settings such as Zambia. The Maternity Homes Access in Zambia project built 10 MWHs at rural health centers in Zambia for women awaiting delivery and postnatal care (PNC) visits. The objective of this paper is to summarize the costs associated with setup of 10 MWHs, including infrastructure, furnishing, stakeholder engagement, and activities to build the capacity of local communities to govern MWHs. We do not present operational costs after setup was complete. We used a retrospective, top-down program costing approach. We reviewed study documentation to compile planned and actual costs by site. All costs were annuitized using a 3% discount rate and organized by cost categories: (1) Capital: infrastructure and furnishing, and (2) Installation: capacity building activities and stakeholder engagement. We assumed lifespans of 30 years for infrastructure; 5 years for furnishings; and 3 years for installation activities. Annuitized costs were used to estimate cost per night stayed and per visit for delivery and PNC-related stays. We also modeled theoretical utilization and cost scenarios. The average setup cost of one MWH was $85,284 (capital: 76%; installation: 24%). Annuitized setup cost per MWH was USD$12,516 per year. At an observed occupancy rate of 39%, setup cost per visit to the MWH was USD$70, while setup cost per night stayed was USD$6. The cost of stakeholder engagement activities was underbudgeted by half at the beginning of this project.This analysis serves as a planning resource for governments and implementers that are considering MWHs as a component of their overall maternal and child health strategy. Planning considerations should include the annuitized cost, value of capacity building and stakeholder engagement, and that cost per bed night and visit are dependent upon utilization.
Is visual gaze in children with autism spectrum disorder related to sequence of emotion intensity presentation? An eye‐tracking study of natural emotion perception processes

Emotion cognitive remediation is a critical component of social skills training for children with autism spectrum disorder (ASD). Visual perception of emotions is highly correlated with the intensity and sequence of presented emotions. However, few studies examined the effect of presentation sequence and intensity on emotion perception. The present study examined the gaze patterns of children with ASD in receiving different sequences of emotion presentation using eye‐tracking technologies. Gaze patterns of ecologically‐valid video clips of silent emotion stimuli by 51 ASD children and 34 typically developing (TD) children were recorded. Results indicated that ASD and TD children showed opposite visual fixation during different intensity presentation modes: children with ASD showed better emotion perception with a weak‐to‐strong emotion sequence when presented. The visual reductions in emotion perception in children with ASD may due to different perceptual threshold to emotional intensity. The extent of the reductions could be related to an individual's Personal‐Social ability. The present study supports the importance of intensity of emotions and the order at which the emotional stimuli were presented in yielding better emotion perceptions in children with ASD, suggesting that the order of emotion presentation may potentially influence emotion processing during ASD rehabilitation. It is anticipated that the present findings could bring more insights to clinicians for intervention planning in the future.
Human mobility increased with vaccine coverage and attenuated the protection of COVID-19 vaccination: A longitudinal study of 107 countries

Background The World Health Organization has raised concerns that vaccinated people may reduce physical and social distancing more than necessary. With imperfect vaccine protection and the lifting of mobility restrictions, understanding how human mobility responded to vaccination and its potential consequence is critical. We estimated vaccination-induced mobility (VM) and examined whether it attenuates the effect of COVID-19 vaccination on controlling case growth. Methods We collected a longitudinal data set of 107 countries between 15 February 2020 and 6 February 2022 from Google COVID-19 Community Mobility Reports, the Oxford COVID-19 Government Response Tracker, Our World in Data, and World Development Indicators. We measured mobility in four categories of location: retail and recreational places, transit stations, grocery stores and pharmacies, and workplaces. We applied panel data models to address unobserved country characteristics and used Gelbach decomposition to evaluate the extent to which VM has offset vaccination effectiveness. Results Across locations, a 10-percentage-point (pp) increase in vaccine coverage was associated with a 1.4-4.3 pp increase in mobility (P < 0.001). VM was greater in lower-income countries (up to 7.9 pps; 95% confidence interval (CI) = 5.3 to 10.5, P < 0.001) and in earlier stages of vaccine rollouts (up to 19.2 pps; 95% CI = 15.1 to 23.2%, P < 0.001). VM decreased the effectiveness of vaccines in controlling case growth by 33.4% in retail and recreation places (P < 0.001), 26.4% in transit stations (P < 0.001), and 15.4% in grocery stores and pharmacies (P = 0.002). Conclusions VM provides support for the Peltzman effect; it attenuates but does not completely counter vaccine effectiveness. Our study findings suggest strategies for mitigating the unintended consequences of VM, including reducing short-term mobility responses after vaccination, prioritizing mobility in grocery-type places and workplaces, and accelerating rollouts at earlier stages of vaccination, especially in lower-income countries.
Soil Microbial Community Involved in Nitrogen Cycling in Rice Fields Treated with Antiozonant under Ambient Ozone

Ethylenediurea (EDU) is hitherto the most efficient phytoprotectant agent against O3 stress. However, the underlying biological mechanisms of its mode of action are not clear, and the effects of EDU on the environment are still unknown, limiting its large-scale application in agriculture. ABSTRACT Ethylenediurea (EDU) can effectively mitigate the crop yield loss caused by ozone (O3), a major, phytotoxic air pollutant. However, the relevant mechanisms are poorly understood, and the effect of EDU on soil ecosystems has not been comprehensively examined. In this study, a hybrid rice variety (Shenyou 63) was cultivated under ambient O3 and sprayed with 450 ppm EDU or water every 10 days. Real time quantitative polymerase chain reaction (RT-qPCR) showed that EDU had no significant effect on the microbial abundance in either rhizospheric or bulk soils. By applying both metagenomic sequencing and the direct assembly of nitrogen (N)-cycling genes, EDU was found to decrease the abundance of functional genes related to nitrification and denitrification processes. Moreover, EDU increased the abundance of genes involved in N-fixing. Although the abundance of some functional genes did not change significantly, nonmetric multidimensional scaling (NMDS) and a principal coordinates analysis (PCoA) suggested that the microbial community structure involved in N cycling was altered by EDU. The relative abundances of nifH-and norB-harboring microbial genera in the rhizosphere responded differently to EDU, suggesting the existence of functional redundancy, which may play a key role in sustaining microbially mediated N-cycling under ambient O3. IMPORTANCE Ethylenediurea (EDU) is hitherto the most efficient phytoprotectant agent against O3 stress. However, the underlying biological mechanisms of its mode of action are not clear, and the effects of EDU on the environment are still unknown, limiting its large-scale application in agriculture. Due to its sensitivity to environmental changes, the microbial community can be used as an indicator to assess the environmental impacts of agricultural practices on soil quality. This study aimed to unravel the effects of EDU spray on the abundance, community structure, and ecological functions of microbial communities in the rhizosphere of rice plants. Our study provides a deep insight into the impact of EDU spray on microbial-mediated N cycling and the structure of N-cycling microbial communities. Our findings help to elucidate the mode of action of EDU in alleviating O3 stress in crops from the perspective of regulating the structure and function of the rhizospheric soil microbial community.