Miracle-dz/UniFAR-FTUs huggingface dataset:
Multi-factor evaluation for the water yield properties of coal floor aquifers, based on GIS

Groundwater inrush in mines directly threatens safe coal production. Aquifer yield plays a crucial role during water inrush. Significant accidents occur in areas where aquifer yields are strong. The yield of an aquifer is influenced by many things and, in this study, five for which data are easily acquired were selected as evaluation indices for coal-seam floor aquifer yield. They comprise specific yield, permeability, drilling fluid consumption, aquifer thickness, and fault and fold distribution. Based on these indices, a comprehensive model for evaluating water yield was constructed. Using the Ordovician limestone aquifer below the coal floor of Danhou coal mine, Hebei province, China, as an example, index data relating to aquifer yield were collected and the index weight determined. A geographic information system was used to prepare a thematic map for each driving factor and, subsequently, to superimpose them. Comprehensive water yield evaluation indexes were obtained and, finally, a zonal map of different water yield properties was developed for the research area.
A zero-agnostic model for copy number evolution in cancer

Motivation New low-coverage single-cell DNA sequencing technologies enable the measurement of copy number profiles from thousands of individual cells within tumors. From this data, one can infer the evolutionary history of the tumor by modeling transformations of the genome via copy number aberrations. Copy number aberrations alter multiple adjacent genomic loci, violating the standard phylogenetic assumption that loci evolve independently. Thus, specialized models to infer copy number phylogenies have been introduced. A widely used model is the copy number transformation (CNT) model in which a genome is represented by an integer vector and a copy number aberration is an event that either increases or decreases the number of copies of a contiguous segment of the genome. The CNT distance between a pair of copy number profiles is the minimum number of events required to transform one profile to another. While this distance can be computed efficiently, no efficient algorithm has been developed to find the most parsimonious phylogeny under the CNT model. Results We introduce the zero-agnostic copy number transformation (ZCNT) model, a simplification of the CNT model that allows the amplification or deletion of regions with zero copies. We derive a closed form expression for the ZCNT distance between two copy number profiles and show that, unlike the CNT distance, the ZCNT distance forms a metric. We leverage the closed-form expression for the ZCNT distance and an alternative characterization of copy number profiles to derive polynomial time algorithms for two natural relaxations of the small parsimony problem on copy number profiles. While the alteration of zero copy number regions allowed under the ZCNT model is not biologically realistic, we show on both simulated and real datasets that the ZCNT distance is a close approximation to the CNT distance. Extending our polynomial time algorithm for the ZCNT small parsimony problem, we develop an algorithm, Lazac, for solving the large parsimony problem on copy number profiles. We demonstrate that Lazac outperforms existing methods for inferring copy number phylogenies on both simulated and real data.
Advanced approaches to overcome biological barriers in respiratory and systemic routes of administration for enhanced nucleic acid delivery to the lung

ABSTRACT Introduction Numerous delivery strategies, primarily novel nucleic acid delivery carriers, have been developed and explored to enable therapeutically relevant lung gene therapy. However, its clinical translation is yet to be achieved despite over 30 years of efforts, which is attributed to the inability to overcome a series of biological barriers that hamper efficient nucleic acid transfer to target cells in the lung. Areas covered This review is initiated with the fundamentals of nucleic acid therapy and a brief overview of previous and ongoing efforts on clinical translation of lung gene therapy. We then walk through the nature of biological barriers encountered by nucleic acid carriers administered via respiratory and/or systemic routes. Finally, we introduce advanced strategies developed to overcome those barriers to achieve therapeutically relevant nucleic acid delivery efficiency in the lung. Expert opinion We are now stepping close to the clinical translation of lung gene therapy, thanks to the discovery of novel delivery strategies that overcome biological barriers via comprehensive preclinical studies. However, preclinical findings should be cautiously interpreted and validated to ultimately realize meaningful therapeutic outcomes with newly developed delivery strategies in humans. In particular, individual strategies should be selected, tailored, and implemented in a manner directly relevant to specific therapeutic applications and goals.
Applications of Repetitive Transcranial Magnetic Stimulation to Improve Upper Limb Motor Performance After Stroke: A Systematic Review

Background Noninvasive brain stimulation (NIBS) is a promising technique for improving upper limb motor performance post-stroke. Its application has been guided by the interhemispheric competition model and typically involves suppression of contralesional motor cortex. However, the bimodal balance recovery model prompts a more tailored application of NIBS based on ipsilesional corticomotor function. Objective To review and assess the application of repetitive transcranial magnetic stimulation (rTMS) protocols that aimed to improve upper limb motor performance after stroke. Methods A PubMed search was conducted for studies published between 1st January 2005 and 1st November 2022 using rTMS to improve upper limb motor performance of human adults after stroke. Studies were grouped according to whether facilitatory or suppressive rTMS was applied to the contralesional hemisphere. Results Of the 492 studies identified, 70 were included in this review. Only 2 studies did not conform to the interhemispheric competition model, and facilitated the contralesional hemisphere. Only 21 out of 70 (30%) studies reported motor evoked potential (MEP) status as a biomarker of ipsilesional corticomotor function. Around half of the studies (37/70, 53%) checked whether rTMS had the expected effect by measuring corticomotor excitability (CME) after application. Conclusion The interhemispheric competition model dominates the application of rTMS post-stroke. The majority of recent and current studies do not consider bimodal balance recovery model for the application of rTMS. Evaluating CME after the application rTMS could confirm that the intervention had the intended neurophysiological effect. Future studies could select patients and apply rTMS protocols based on ipsilesional MEP status.
The appendicularian Oikopleura dioica can enhance carbon export in a high CO2 ocean.

Gelatinous zooplankton are increasingly recognized to play a key role in the ocean's biological carbon pump. Appendicularians, a class of pelagic tunicates, are among the most abundant gelatinous plankton in the ocean, but it is an open question how their contribution to carbon export might change in the future. Here, we conducted an experiment with large volume in situ mesocosms (~55-60 m3 and 21 m depth) to investigate how ocean acidification (OA) extreme events affect food web structure and carbon export in a natural plankton community, particularly focusing on the keystone species Oikopleura dioica, a globally abundant appendicularian. We found a profound influence of O. dioica on vertical carbon fluxes, particularly during a short but intense bloom period in the high CO2 treatment, during which carbon export was 42%-64% higher than under ambient conditions. This elevated flux was mostly driven by an almost twofold increase in O. dioica biomass under high CO2 . This rapid population increase was linked to enhanced fecundity (+20%) that likely resulted from physiological benefits of low pH conditions. The resulting competitive advantage of O. dioica resulted in enhanced grazing on phytoplankton and transfer of this consumed biomass into sinking particles. Using a simple carbon flux model for O. dioica, we estimate that high CO2 doubled the carbon flux of discarded mucous houses and fecal pellets, accounting for up to 39% of total carbon export from the ecosystem during the bloom. Considering the wide geographic distribution of O. dioica, our findings suggest that appendicularians may become an increasingly important vector of carbon export with ongoing OA.
Valproate use associated with frontal and cerebellar gray matter volume reductions: A voxel‐based morphometry study

Recent morphometric magnetic resonance imaging (MRI) studies suggested the possibility that valproate (VPA) use is associated with parieto‐occipital cortical thinning in patients with heterogeneous epilepsy syndromes. In this study, we examined the effect of VPA on the brain volume using a large number of homogenous patients with idiopathic generalized epilepsy. Voxel‐based morphometry was used to compare regional gray matter (GM) volume between 112 patients currently taking VPA (VPA+ group), 81 patients not currently taking VPA (VPA– group), and 120 healthy subjects (control group). The VPA+ group showed a significant GM volume reduction in the bilateral cerebellum, hippocampus, insula, caudate nucleus, medial frontal cortex/anterior cingulate cortex, primary motor/premotor cortex, medial occipital cortex, and anteromedial thalamus, as compared to the control group. The VPA– group showed a significant GM volume reduction in the anteromedial thalamus and right hippocampus/temporal cortex, as compared to the control group. Compared to the VPA– group, the VPA+ group had a significant GM volume reduction in the bilateral cerebellum, primary motor/premotor cortex, and medial frontal cortex/anterior cingulate cortex. We have provided evidence that VPA use could result in GM volume reductions in the frontal cortex and cerebellum. Our findings should be acknowledged as a potential confounding factor in morphometric MRI studies that include subjects taking VPA.
Mapping Weather-Type Influence on Senegal Precipitation Based on a Spatial–Temporal Statistical Model*

AbstractSenegal is particularly vulnerable to precipitation variability. To investigate the influence of large-scale circulation on local-scale precipitation, a full spatial–statistical description of precipitation occurrence and amount for Senegal is developed. These regression-type models have been built on the basis of daily records at 137 locations and were developed in two stages: (i) a baseline model describing the expected daily occurrence probability and precipitation amount as spatial fields from monsoon onset to offset, and (ii) the inclusion of weather types defined from the NCEP–NCAR reanalysis 850-hPa winds and 925-hPa relative humidity establishing the link to the synoptic-scale atmospheric circulation. During peak phase, the resulting types appear in two main cycles that can be linked to passing African easterly waves. The models allow the investigation of the spatial response of precipitation occurrence and amount to a discrete set of preferred states of the atmospheric circulation. As suc.
Risk factors for anastomotic leak and postoperative morbidity after right hemicolectomy for colon cancer: results from a prospective, multi-centre, snapshot study in China

Abstract Background Right hemicolectomy is the standard treatment for right-sided colon cancer. There is variation in the technical aspects of performing right hemicolectomy as well as in short-term outcomes. It is therefore necessary to explore best clinical practice following right hemicolectomy in expert centres. Methods This snapshot study of right hemicolectomy for colon cancer in China was a prospective, multicentre cohort study in which 52 tertiary hospitals participated. Eligible patients with stage I–III right-sided colon cancer who underwent elective right hemicolectomy were consecutively enrolled in all centres over 10 months. The primary endpoint was the incidence of postoperative 30-day anastomotic leak. Results Of the 1854 patients, 89.9 per cent underwent laparoscopic surgery and 52.3 per cent underwent D3 lymph node dissection. The overall 30-day morbidity and mortality were 11.7 and 0.2 per cent, respectively. The 30-day anastomotic leak rate was 1.4 per cent. In multivariate analysis, ASA grade > II (P < 0.001), intraoperative blood loss > 50 ml (P = 0.044) and D3 lymph node dissection (P = 0.008) were identified as independent risk factors for postoperative morbidity. Extracorporeal side-to-side anastomosis (P = 0.031), intraoperative blood loss > 50 ml (P = 0.004) and neoadjuvant chemotherapy (P = 0.004) were identified as independent risk factors for anastomotic leak. Conclusion In high-volume expert centres in China, laparoscopic resection with D3 lymph node dissection was performed in most patients with right-sided colon cancer, and overall postoperative morbidity and mortality was low. Further studies are needed to explore the optimal technique for right hemicolectomy in order to improve outcomes further.
COVID-19 infodemic and health-related quality of life in patients with chronic respiratory diseases: A multicentre, observational study

Background The explosion of information, misinformation and disinformation (the “infodemic”) related to the coronavirus disease 2019 (COVID-19) pandemic on digital and social media is reported to affect mental health and quality of life. However, reports assessing the COVID-19 infodemic on health-related quality of life (HRQL) in patients with chronic diseases are scarce. In this study, we investigated the associations between the infodemic and HRQL in uninfected individuals with pre-existing chronic respiratory diseases (CRDs) such as asthma, chronic obstructive pulmonary disease (COPD) and other CRDs. Methods We conducted a multi-national, cross-sectional, observational study in Canada, India, New Zealand and the United Kingdom where we distributed a set of digitised questionnaires among 1018 participants with chronic respiratory diseases who were not infected with the SARS-CoV-2 virus at least three months prior to the study. We collected information about the infodemic such as news watching or social media use more than usual during the pandemic. HRQL was assessed using the short form of the chronic respiratory questionnaire (SF-CRQ). Demographic information, comorbidities, compliance, mental health, behavioural function, and social support were also recorded. We analysed the direct and indirect relationships between infodemic and HRQL using structural equation models (SEM). Results Of all participants, 54% were females and had a mean (standard deviation (SD)) age of 53 (17) years. We found that higher infodemic was associated with worse emotional function (regression coefficient β = -0.08; 95% confidence interval (CI) = -0.14 to -0.01), which means a one SD change of the higher infodemic latent variable was associated with a 0.08 SD change of emotional function level. The association between higher infodemic and worse emotional function was mediated by worse mental health and behavioural functions but is marginally ameliorated by improved social support. In stratification analysis, we found significant disease and country-wise variations in the associations between infodemic and SF-CRQ domain scores. Conclusions These results provide new evidence that the COVID-19 infodemic significantly influences the HRQL in patients with CRDs through a complex interplay between mental health, behavioural function, and social support. This new dimension of research also opens avenues for further research on infodemic-related health effects in other chronic diseases.
Sample size and predictive performance of machine learning methods with survival data: A simulation study

Prediction models are increasingly developed and used in diagnostic and prognostic studies, where the use of machine learning (ML) methods is becoming more and more popular over traditional regression techniques. For survival outcomes the Cox proportional hazards model is generally used and it has been proven to achieve good prediction performances with few strong covariates. The possibility to improve the model performance by including nonlinearities, covariate interactions and time‐varying effects while controlling for overfitting must be carefully considered during the model building phase. On the other hand, ML techniques are able to learn complexities from data at the cost of hyper‐parameter tuning and interpretability. One aspect of special interest is the sample size needed for developing a survival prediction model. While there is guidance when using traditional statistical models, the same does not apply when using ML techniques. This work develops a time‐to‐event simulation framework to evaluate performances of Cox regression compared, among others, to tuned random survival forest, gradient boosting, and neural networks at varying sample sizes. Simulations were based on replications of subjects from publicly available databases, where event times were simulated according to a Cox model with nonlinearities on continuous variables and time‐varying effects and on the SEER registry data.
Intrahepatic cholestasis of pregnancy and theory of inheritance of the disease. Literature review

Abstract Intrahepatic cholestasis during pregnancy is associated with a higher risk of prenatal and maternal complications. There are several new publications and guidelines on the detection and thresholds of intrahepatic cholestasis during pregnancy. However, the genetic background of this disease has rarely been investigated. This is a comprehensive review of the roles of genes in intrahepatic cholestasis during pregnancy.
Prevalence and adverse effects of sport-related nutritional supplements (sport drinks, bars, and gels) in the military before and during the COVID-19 pandemic: the US Military Dietary Supplement Use Study

ABSTRACT Background Sport-related nutritional supplements (SRNS) include sport drinks, sport bars, and sport gels. This investigation examined temporal patterns in SRNS use and adverse effects (AEs) reported by a single cohort of United States active-duty service members (SMs) surveyed before and during the coronavirus disease 2019 (COVID-19) pandemic. Methods A stratified random sample (n = 22,858) of SMs (Air Force, Army, Navy, and Marine Corps) who completed a questionnaire on their SRNS use and AE experiences and were still on active duty were asked to complete the identical questionnaire on a second occasion. Twenty-five percent of successfully contacted SMs completed both questionnaires (n = 5,778) and were included in this investigation. The average ± standard deviation time between questionnaires was 1.3 ± 0.2 years. Results Prevalence of reported SRNS use ≥1 time/week in the baseline (BL) and follow-up (FU) phases were as follows: any SRNS: BL = 46%, FU = 41%; sport drinks: BL = 31%, FU = 28%; sport bars: BL = 30%, FU = 24%; sport gels: BL = 4%, FU = 4%. Reported weekly aerobic and resistance training durations were reduced in the FU period (8% and 26%, respectively). The proportion of SMs reporting SRNS use in both study phases was as follows: any SRNS = 62%, sport drinks = 54%, sport bars = 50%, sport gels = 35%. Prevalence of reported AEs in the BL and FU phases were as follows: any SRNS: BL = 1.9%, FU = 1.9%; sport drinks: BL = 1.0%, FU = 1.3%; sport bars: BL = 1.7%, FU = 1.4%; sport gels: BL = 3.3%, FU = 2.5%. The proportion of SMs reporting AEs in both phases was as follows: any SRNS = 14%, sport drinks = 11%, sport bars = 17%, sport gels = 0%. Conclusions Overall SRNS use prevalence decreased slightly in the FU period, possibly because of reduced physical training related to military restrictions imposed during the emergence of COVID-19 between surveys. A large proportion of SMs reported changing their use patterns in the FU with some discontinuing use and others initiating use. The AE incidence was similarly low in the BL and FU phases, and few SMs reported AEs in both phases suggesting AEs were transitory. AE reporting for SRNSs was much lower than previously found for dietary supplements, possibly because of greater government regulatory control over SRNSs.
Effect of anterior quadratus lumborum block with ropivacaine on the immune response after laparoscopic surgery in colon cancer: a substudy of a randomized clinical trial

Background Surgery induces a temporal change in the immune system, which might be modified by regional anesthesia. Applying a bilateral preoperative anterior quadratus lumborum block has proven to be a safe and effective technique in pain management after abdominal and retroperitoneal surgery, but the effect on the immune response is not thoroughly investigated. Methods This study is a substudy of a randomized, controlled, double-blinded trial of patients undergoing laparoscopic hemicolectomy due to colon cancer. Twenty-two patients were randomized to undergo either a bilateral anterior quadratus lumborum nerve block with a total of 60 mL ropivacaine 0.375% or placebo with corresponding isotonic saline injections. The main objective of this exploratory substudy was to investigate the systemic immune response in the first postoperative day by examining changes in blood transcript levels (n=750) and stimulated secretion of cytokines (n=17) on ex vivo activation with microbial ligands and anti-CD3/CD28. Results Using unsupervised data analysis tools, we observed no effect of the bilateral anterior quadratus lumborum nerve block on gene expression in immune cells (permutational multivariate analysis of variance using distance matrices: F=0.52, p=0.96), abundances of major immune cell populations (Wilcoxon rank-sum test: p>0.05), and stimulated cytokine secretion (Wilcoxon rank-sum test: p>0.05). Conclusions Our study provides evidence that administration of bilateral anterior quadratus lumborum nerve block as a part of a multimodal analgesic regimen in an enhanced recovery after surgery for laparoscopic hemicolectomy in this cohort does not alter the systemic immune response. Trial registration number NCT03570541.
Movement patterns of common cranes at European stopover sites

The common crane Grus grus is a migratory bird with a wide distribution across Europe and Asia. During the migration the cranes rest at stopover sites were they roost in wetlands and forage on surrounding fields in the farmland. Due to an increase of the European population over the last decades, damage to crops has increased and so the conflicts between cranes and farmers. Therefore, knowledge about the movement of cranes is not only important for an increased understanding of the ecology and behaviour of the species, but also important from a crop damage preventative management perspective. This study has investigated the size of activity areas and flight distances from the roost of juvenile cranes on different stopover sites during the autumn migration, by using GPS transmitters. The results showed that average size of activity area was 31.5 km2 and the average flight distance from the roost was 4.5 km. I found significant variation in both size of activity area and flight distance from roost between the countries along the flyway. Activity areas also varied between stopover sites and no clear latitudinal trend was found, which indicates that the variation rather depend on differences in local conditions. My study provides insight into the movement pattern of cranes, which could be applied when planning crop preventative measures in agricultural areas.