Miracle-dz/UniFAR-FTUs huggingface dataset:
Long-term effect of soil and water conservation measures on runoff, sediment and their relationship in an orchard on sloping red soil of southern China

The effect of soil and water conservation measures (SWCMs) is usually dependent on time. Thus the trend in reducing runoff and sediment over time is a very important theoretical problem for evaluating the effectiveness of SWCMs. Moreover, there is still a lack of comprehensive assessment of water erosion dynamics following implementing SWCMs despite their ecological significance. Therefore, the long-term impact of SWCMs on runoff and sediment and their relationships was assessed for an orchard on sloping red soil in southern China. Overland flow and erosion sediment were continuously observed for 15 years on citrus experimental plots under one of four treatments: grass strips, strip intercropping, level terrace and clean-tillage. By means of Mann–Kendall trend tests and double cumulative curves, the time series of runoff and sediment under the different treatments were analyzed. Furthermore, we linked the effect of soil conservation and the relationship between runoff and sediment variation to determine the mechanism of conservation measures on sediment reduction. The results showed that the first 4 years was the key period to prevent soil erosion for this orchard, and then the intensity of soil erosion decreased below 500 t·km–2·a–1. Considering economic costs and ecological effect, grass strips were the best protective measure for this test situation. The fitted curves of the effect of SWCMs on sediment reduction over time showed an ‘L’ form, but on runoff there was an approximately horizontal line. The SWCMs did not change the rainfall–runoff relationship, but did change the runoff–sediment erosion relationship. The erosion reduction mechanism of SWCMs in the early phase was a joint function of reducing runoff and changing the runoff–sediment relationship, and in the post-stable phase it worked mainly by reducing runoff. The results provide the basis for rational allocation of SWCMs considering location and time.
Intronless mRNAs transit through nuclear speckles to gain export competence

Nuclear speckles (NSs) serve as splicing factor storage sites. In this study, we unexpectedly found that many endogenous intronless mRNAs, which do not undergo splicing, associate with NSs. These associations do not require transcription, polyadenylation, or the polyA tail. Rather, exonic splicing enhancers present in intronless mRNAs and their binding partners, SR proteins, promote intronless mRNA localization to NSs. Significantly, speckle targeting of mRNAs promotes the recruitment of the TREX export complex and their TREX-dependent nuclear export. Furthermore, TREX, which accumulates in NSs, is required for releasing intronless mRNAs from NSs, whereas NXF1, which is mainly detected at nuclear pores, is not. Upon NXF1 depletion, the TREX protein UAP56 loses speckle concentration but coaccumulates with intronless mRNAs and polyA RNAs in the nucleoplasm, and these RNAs are trapped in NSs upon UAP56 codepletion. We propose that the export-competent messenger RNP assembly mainly occurs in NSs for intronless mRNAs and that entering NSs serves as a quality control step in mRNA export.
Predictions for the Sky-Averaged Depth of the 21 cm Absorption Signal at High Redshift in Cosmologies with and without Nonbaryonic Cold Dark Matter.

We consider the 21 cm absorption signal expected at high redshift in cosmologies with and without nonbaryonic cold dark matter. The expansion of the early Universe decelerates strongly with dark matter, but approximately coasts without it. This results in a different path length across the epochs when absorption is expected, with the consequence that the absorption is predicted to be a factor of ∼2 greater without dark matter than with it. Observation of such a signal would motivate consideration of extended theories of gravity in lieu of dark matter.
Mining MOOC Lecture Transcripts to Construct Concept Dependency Graphs

This paper addresses the question of identifying a concept dependency graph for a MOOC through unsupervised analysis of lecture transcripts. The problem is important: extracting a concept graph is the ﬁrst step in helping students with varying preparation to understand course material. The problem is challenging: instructors are unaware of the student preparation diversity and may be unable to identify the right resolution of the concepts, necessitating costly updates; inferring concepts from groups suﬀers from polysemy; the temporal order of concepts depends on the concepts in question. We propose innovative unsupervised methods to discover a directed concept dependency within and between lectures. Our main technical innovation lies in exploiting the temporal ordering amongst concepts to discover the graph. We propose two measures—the Bridge Ensemble Measure and the Global Direction Measure—to infer the existence and the direction of the dependency relations between concepts. The bridge ensemble measure identiﬁes concept overlap between lectures, determines concept co-occurrence within short windows, and the lecture where concepts occur ﬁrst. The global direction measure incorporates time directly by analyzing the concept time ordering both globally and within lectures. Experiments over real-world MOOC data show that our method outperforms the baseline in both AUC and precision/recall curves.
Gastric corticotropin-releasing factor influences mast cell infiltration in a rat model of functional dyspepsia

Functional gastrointestinal disorders (FGIDs) are characterized by dysregulated gut-brain interactions. Emerging evidence shows that low-grade mucosal inflammation and immune activation contribute to FGIDs, including functional dyspepsia (FD). Stress plays an important role in the onset of FD symptoms. In human subjects with FD, presence of gastric mast cells has been reported, but factors that influence mast cell infiltration remain uncharacterized. Corticotropin-releasing factor (CRF) initiates the body’s stress response and is known to degranulate mast cells. In this study, we delineated the role of the CRF system in the pathogenesis of FD in a rat model. Gastric irritation in neonate rat pups with iodoacetamide (IA) was used to induce FD-like symptoms. RNA interference (RNAi) was used to silence gastric CRF expression. Mast cell infiltrate in the stomach increased by 54% in IA-treated rats compared to controls and CRF-RNAi tended to decrease gastric mast cell infiltrate. Sucrose intake decreased in IA-treated rats and mast cell numbers showed a negative association with sucrose intake. IA treatment and transient silencing of gastric CRF increased hypothalamic CRF levels. In IA-treated rats, gastric levels of CRF receptor 2 (CRF2) decreased by ~76%, whereas hypothalamic CRF receptor 1 (CRF1) levels increased. Plasma levels of TNF-α showed a positive correlation with plasma CRF levels. Levels of phosphorylated p38 and ERK1/2 in the stomach showed a positive correlation with gastric CRF levels. Thus, CRF may contribute to low grade inflammation via modulating mast cell infiltration, cytokine levels, MAPK signaling, and the gut-brain axis.
The metagenome of the female upper reproductive tract

Abstract Background The human uterus is traditionally believed to be sterile, while the vaginal microbiota plays an important role in fending off pathogens. Emerging evidence demonstrates the presence of bacteria beyond the vagina. However, a microbiome-wide metagenomic analysis characterizing the diverse microbial communities has been lacking. Results We performed shotgun-sequencing of 52 samples from the cervical canal and the peritoneal fluid of Chinese women of reproductive age using the Illumina platform. Direct annotation of sequencing reads identified the taxonomy of bacteria, archaea, fungi and viruses, confirming and extending the results from our previous study. We replicated our previous findings in another 24 samples from the vagina, the cervical canal, the uterus and the peritoneal fluid using the BGISEQ-500 platform revealing that microorganisms in the samples from the same individuals were largely shared in the entire reproductive tract. Human sequences made up more than 99% of the 20GB raw data. After filtering, vaginal microorganisms were well covered in the generated reproductive tract gene catalogue, while the more diverse upper reproductive tract microbiota would require greater depth of sequencing and more samples to meet the full coverage scale. Conclusions We provide novel detailed data on the microbial composition of a largely unchartered body site, the female reproductive tract. Our results indicated the presence of an intra-individual continuum of microorganisms that gradually changed from the vagina to the peritoneal fluid. This study also provides a framework for understanding the implications of the composition and functional potential of the distinct microbial ecosystems of the female reproductive tract in relation to health and disease.
Gene regulation underlies environmental adaptation in house mice

Changes in cis-regulatory regions are thought to play a major role in the genetic basis of adaptation. However, few studies have linked cis-regulatory variation with adaptation in natural populations. Here, using a combination of exome and RNA-seq data, we performed expression quantitative trait locus (eQTL) mapping and allele-specific expression analyses to study the genetic architecture of regulatory variation in wild house mice (Mus musculus domesticus) using individuals from five populations collected along a latitudinal cline in eastern North America. Mice in this transect showed clinal patterns of variation in several traits, including body mass. Mice were larger in more northern latitudes, in accordance with Bergmann's rule. We identified 17 genes where cis-eQTLs were clinal outliers and for which expression level was correlated with latitude. Among these clinal outliers, we identified two genes (Adam17 and Bcat2) with cis-eQTLs that were associated with adaptive body mass variation and for which expression is correlated with body mass both within and between populations. Finally, we performed a weighted gene co-expression network analysis (WGCNA) to identify expression modules associated with measures of body size variation in these mice. These findings demonstrate the power of combining gene expression data with scans for selection to identify genes involved in adaptive phenotypic evolution, and also provide strong evidence for cis-regulatory elements as essential loci of environmental adaptation in natural populations.
A Dietary Assessment App for Hospitalized Patients at Nutritional Risk: Development and Evaluation of the MyFood App

Background Disease-related malnutrition is a common challenge among hospitalized patients. There seems to be a lack of an effective system to follow-up nutritional monitoring and treatment of patients at nutritional risk after risk assessment. We identify a need for a more standardized system to prevent and treat disease-related malnutrition. Objective We aimed to develop a dietary assessment app for tablets for use in a hospital setting and to evaluate the app’s ability to measure individual intake of energy, protein, liquid, and food and beverage items among hospitalized patients for two days. We also aimed to measure patients’ experiences using the app. Methods We have developed the MyFood app, which consists of three modules: 1) collection of information about the patient, 2) dietary assessment function, and 3) evaluation of recorded intake compared to individual needs. We used observations from digital photography of the meals, combined with partial weighing of the meal components, as a reference method to evaluate the app’s dietary assessment system for two days. Differences in the intake estimations of energy, protein, liquid, and food and beverage items between MyFood and the photograph method were analyzed on both group and individual level. Results Thirty-two patients hospitalized at Oslo University Hospital were included in the study. The data collection period ran from March to May 2017. About half of the patients had ≥90% agreement between MyFood and the photograph method for energy, protein, and liquid intake on both recording days. Dinner was the meal with the lowest percent agreement between methods. MyFood overestimated patients’ intake of bread and cereals and underestimated fruit consumption. Agreement between methods increased from day 1 to day 2 for bread and cereals, spreads, egg, yogurt, soup, hot dishes, and desserts. Ninety percent of participants reported that MyFood was easy to use, and 97% found the app easy to navigate. Conclusions We developed the MyFood app as a tool to monitor dietary intake among hospitalized patients at nutritional risk. The recorded intake of energy, protein, and liquid using MyFood showed good agreement with the photograph method for the majority of participants. The app’s ability to estimate intake within food groups was good, except for bread and cereals which were overestimated and fruits which were underestimated. The app was well accepted among study participants and has the potential to be a dietary assessment tool for use among patients in clinical practice.
Student Motivation in High School Physical Education: A Latent Profile Analysis Approach.

Guided by the principles of self-determination theory, the purpose of this study was to identify latent profiles representing high school students' motivational regulations for physical education (PE) and to model putative predictors and outcomes of profile membership. A sample of 532 Australian high school students, age 12-16 years (M = 13.83, SD = 1.13), reported their motivation for PE, perceptions of need satisfaction in PE, and effort expended in PE. Latent profile analysis revealed evidence of 3 distinct profiles that were consistent with continuum expectations outlined in self-determination theory (i.e., the moderately autonomous, moderately controlled, and highly autonomous profiles), alongside 2 profiles characterized by levels of introjected regulation that aligned with autonomous motives (i.e., the mixed motivation and amotivated profiles). Analyses also revealed that, on the whole, greater need satisfaction predicted membership of more autonomous profiles and that membership of such profiles was predictive of greater self-reported effort in PE. Analyses revealed evidence of qualitatively distinct motivation profiles that were differentially predicted by students' psychological need satisfaction and predictive of in-class effort. This study is not only the first to use latent profile analysis to explore the role of psychological need satisfaction in predicting PE motivation profiles. It also provides practical information regarding the prevalence and potential outcomes of students' motivation profiles.
Trough concentration of itraconazole and its relationship with efficacy and safety: a systematic review and meta-analysis

Objectives The optimum trough concentration of itraconazole for clinical response and safty is controversial. The objective of this systematic review and meta-analysis was to determine the optimum trough concentration of itraconazole and evaluate its relationship with efficacy and safety. Methods We searched PubMed, EMBASE, Web of Science, the Cochrane Library, Clinical-Trials.gov, and three Chinese literature databases (CNKI, WanFang, and CBM). We included observational studies that compared clinical outcomes below or above the trough concentration cut-off value which we set as 0.25, 0.5, and 1.0 mg/L. The efficacy outcomes were rate of successful treatment, rate of prophylaxis failure and invasive fungal infection (IFI)-related mortality. The safety outcomes included incidents of hepatotoxicity and other adverse events. Results The study included a total of 29 studies involving 2,346 patients. Our meta-analysis showed that compared with itraconazole trough concentrations (Ctrough) of ≥0.25 mg/L, levels of <0.25 mg/L significantly increased the incidence of IFI for prophylaxis (RR =3.279, 95% confidence interval [CI] 1.73–6.206). Moreover, the success rate of treatment decreased significantly at a cut-off level of 0.5 mg/L (RR =0.396, 95% CI 0.176–0.889). An itraconazole trough level of 1.0 mg/L was associated with hepatotoxicity and other adverse events in a review of many studies. Conclusion An itraconazole trough concentration of 0.25 mg/L should be considered as the lower threshold for prophylaxis, and a target concentration of 0.5 mg/L should be the lower limit for effective treatment. A trough level of 1.0 mg/L is associated with increased hepatotoxicity and other adverse events (using High Performance Liquid Chromatography [HPLC]).
Mathematics Learning through Computational Thinking Activities: A Systematic Literature Review

: Computational Thinking represents a terminology that embraces the complex set of reasoning processes that are held for problem stating and solving through a computational tool. The ability of systematizing problems and solve them by these means is currently being considered a skill to be developed by all students, together with Language, Mathematics and Sciences. Considering that Computer Science has many of its roots on Mathematics, it is reasonable to ponder if and how Mathematics learning can be influenced by offering activities related to Computational Thinking to students. In this sense, this article presents a Systematic Literature Review on reported evidences of Mathematics learning in activities aimed at developing Computational Thinking skills. Forty-two articles which presented didactic activities together with an experimental design to evaluate learning outcomes published from 2006 to 2017 were analyzed. The majority of identified activities used a software tool or hardware device for their development. In these papers, a wide variety of mathematical topics has been being developed, with some emphasis on Planar Geometry and Algebra. Conversion of models and solutions between different semiotic representations is a high level cognitive skill that is most frequently associated to educational outcomes. This review indicated that more recent articles present a higher level of rigor in methodological procedures to assess learning effects. However, joint analysis of evidences from more than one data source is still not frequently used as a validation procedure.
1-, 3-, and 5-year survival among early-stage lung cancer patients treated with lobectomy vs SBRT

Background Lobectomy has traditionally been recommended for fit patients diagnosed with early-stage non-small-cell lung cancer (NSCLC). Recently, however, stereotactic body radiotherapy (SBRT) has been introduced as an alternative treatment option. The purpose of this investigation is to compare survival outcomes for individuals with stage I/II NSCLC treated with lobectomy vs SBRT. Methods This retrospective study included 191 patients (100 surgery, 91 SBRT) identified through the Lung Cancer Evaluation Center, Stony Brook, NY, between 2008 and 2012. Survival and recurrence rates were compared using Kaplan–Meier curves, log-rank tests, and Cox proportional hazard models to adjust for possible confounders. A subset of cases was propensity-matched to address potential differences in health status between groups. Results 1-, 3-, and 5-year survival outcomes were significantly better among patients undergoing lobectomy vs SBRT. Survival rates at 3 years were 92.8% and 59.0% (p<0.001) in the 2 groups, respectively. Propensity-matched analyses indicated similar findings. Recurrence rates were likewise lower among patients undergoing surgery (7.1% vs 21.0%, p<0.01 at 3 years); however, statistical significance was not maintained in the propensity-matched analysis. Conclusion These findings add to a growing evidence base supporting the use of lobectomy vs SBRT in the treatment of lung cancer among healthy, early-stage NSCLC patients.
Evaluation of a smartphone photoscreening app to detect refractive amblyopia risk factors in children aged 1–6 years

Purpose To determine the specificity and sensitivity of a smartphone app (GoCheckKids [GCK] used as a photoscreening tool on the iPhone 7 to detect refractive amblyopia risk factors in children aged 1–6 years. Participants and methods A prospective, multicenter, 10-month evaluation of children aged 1–6 years old who underwent photoscreening with the GCK app to detect amblyopia risk factors. The first acceptable quality photograph of each study subject was evaluated by trained technicians using GCK’s proprietary automated image processing algorithm to analyze for amblyopia risk factors. Trained graders, masked to the cycloplegic clinical data, remotely reviewed photographs taken with the app and compared results to the gold standard pediatric ophthalmology examinations using the 2013 American Association for Pediatric Ophthalmology & Strabismus amblyopia risk factor guidelines. Primary outcome was the ability of the GCK app to identify amblyopia risk factors compared to the cycloplegic refraction. Results There were 287 patient images analyzed. The overall sensitivity and specificity in detecting amblyopia risk factors were 76% and 85%, respectively using manual grading. The overall automated grading results had a sensitivity and sensitivity in detecting amblyopia risk factors of 65% and 83%, respectively. Conclusion The GCK smartphone app is a viable photoscreening device for the detection of amblyopia risk factors in children aged 1–6 years.
Urinary excretion of homocysteine thiolactone and the risk of acute myocardial infarction in coronary artery disease patients: the WENBIT trial

No individual homocysteine (Hcy) metabolite has been studied as a risk marker for coronary artery disease (CAD). Our objective was to examine Hcy‐thiolactone, a chemically reactive metabolite generated by methionyl‐tRNA synthetase and cleared by the kidney, as a risk predictor of incident acute myocardial infarction (AMI) in the Western Norway B‐Vitamin Intervention Trial.
Initial presentation of human papillomavirus‐related head and neck cancer: A retrospective review

Human papillomavirus (HPV) has been identified as a risk factor for oropharyngeal squamous cell carcinoma (OPSCC) and a cause of the recent dramatic rise in the incidence of this disease. HPV‐positive OPSCC typically affects a younger population and has no validated screening test. This study aims to outline the common presenting signs of HPV‐positive OPSCC.