Miracle-dz/UniFAR-FTUs huggingface dataset:
Detecting polygenic selection in marine populations by combining population genomics and quantitative genetics approaches

Highly fecund marine species with dispersive life-history stages often display large population sizes and wide geographic distribution ranges. Consequently, they are expected to experience reduced genetic drift, efficient selection fueled by frequent adaptive mutations, and high migration loads. This has important consequences for understanding how local adaptation proceeds in the sea. A key issue in this regard, relates to the genetic architecture underlying fitness traits. Theory predicts that adaptation may involve many genes but with a high variance in effect size. Therefore, the effect of selection on allele frequencies may be substantial for the largest effect size loci, but insignificant for small effect genes. In such a context, the performance of population genomic methods to unravel the genetic basis of adaptation depends on the fraction of adaptive genetic variance explained by the cumulative effect of outlier loci. Here, we address some methodological challenges associated with the detection of local adaptation using molecular approaches. We provide an overview of genome scan methods to detect selection, including those assuming complex demographic models that better describe spatial population structure. We then focus on quantitative genetics approaches that search for genotype–phenotype associations at different genomic scales, including genome-wide methods evaluating the cumulative effect of variants. We argue that the limited power of single locus tests can be alleviated by the use of polygenic scores to estimate the joint contribution of candidate variants to phenotypic variation.
Mitigating the Impact of Member Turnover in Information Systems Development Projects

Team member turnover presents significant risks to the performance of information systems development (ISD) projects. While prior studies have identified various antecedents of turnover with the general objective of reducing its occurrence, turnover cannot be completely prevented in practice. This study examines practices for mitigating the negative impact of turnover when it occurs. Since ISD is knowledge intensive and turnover typically involves knowledge degradation, this study focuses on key practices for reducing such knowledge degradation, i.e., job enlargement, use of electronic knowledge repositories, and succession planning. Our model for explaining the effects of the practices, based on the human capital and organizational forgetting theories, is tested through a survey of 138 project managers of ISD teams experiencing turnover. The results indicate that the use of electronic knowledge repositories and succession planning reduce the negative effect of turnover on the project performance. In contrast, job enlargement does not have a significant mitigating effect. This study contributes to research by looking beyond the antecedents and prevention of turnover to understand how it can be managed effectively. The findings also offer pragmatic suggestions for alleviating the detrimental effects of team member turnover on the ISD project performance.
Age-Related Volumetric Changes in Mandibular Condyles

Abstract A precise knowledge of the condylar changes with advancing age may improve understanding of pathophysiological alterations of the mandibular condyles. However, the majority of studies focusses on morphological changes, although volumetric analysis based upon cone beam computerized tomography may provide important additional data to characterize mandibular condyles. Therefore, we aimed to provide and compare volumetric data of mandibular condyles of a young and old patient group. This is a retrospective chart review of 195 patients with cone beam computerized tomography between 2007 and 2016. Student t test, analysis of variance, and Pearson correlation test were performed to analyze associations between categorical and continuous variables. P values <0.05 were considered as significant. Volume measurement was performed in a semiautomatic segmentation method with the program "ITK-Snap. " Side- and sex-specific significant differences between condylar volumes were found both in the young and old patient cohort. Age and posterior occlusal support did not significantly correlate with the condylar volume. Volumetric measurement of the mandibular condyles may serve as an important additional characteristic, derived from 3-dimensional imaging. Significant differences in volumetric measurement of mandibular condyles exist between sex and side, but not in relation to age and occlusal support.
Low Serum Sex Hormone-Binding Globulin Associated with Insulin Resistance in Men with Nonalcoholic Fatty Liver Disease

Abstract The presence of nonalcoholic fatty liver disease (NAFLD) is a strong risk predictor for type 2 diabetes (T2D). A reduction in sex hormone-binding globulin (SHBG) is associated with NAFLD. Low SHBG is also associated with insulin resistance (IR). However, very limited data are available for the association of SHBG and IR in patients with NAFLD. The study aims to clarify the association between SHBG and IR in patients with NAFLD. In this cross-sectional study, 334 men with NAFLD were recruited. SHBG, total testosterone, free testosterone, total cholesterol, triglyceride, insulin, and glucose concentrations were measured. Homeostatic model assessment (HOMA)-IR and HOMA-β were calculated. Spearman’s correlations and multiple linear regressions were used to analyze the association between SHBG and IR. Men with moderate-severe NAFLD had higher waist circumference, BMI, total cholesterol, triglyceride, insulin, HOMA-IR, HOMA-β, and free testosterone, but lower SHBG than the mild NAFLD. The moderate-severe NAFLD group exhibited higher HOMA-IR (2.38±1.35 vs. 4.16±2.84, p<0.001) and lower SHBG (25.89±11.89 vs. 30.13±12.97 nmol/l, p<0.001) than the other group. SHBG value was negatively correlated with insulin, and HOMA-IR, but was not significantly correlated with glucose and testosterone. The multiple linear regression analysis showed that SHBG was significantly associated with insulin (β=− 0.241, p<0.001), and HOMA-IR (β=− 0.229, p<0.001), even adjusting for potential confounders. In conclusion, low serum SHBG is associated with IR in men with NAFLD.
Effects of occupational exposure to noise and dust on blood pressure in Chinese industrial workers

ABSTRACT Along with the rapid development of economy and urbanization, noise and air pollution are becoming major occupational health hazards in the process of industrial production. In this study, we collected data from 7293 industrial workers in China. The association between occupational exposure of noise and dust and blood pressure was investigated. Controlling for demographic variables, including sex, age, and length of service, a stepwise regression model with backward elimination was constructed. The results showed that both noise and dust decreased the level of systolic blood pressure (p < 0.001). This finding prompted the manufacturing industry to reduce noise and dust hazards and protect the occupational health of workers. Prospective studies in different populations are still required to verify the net contribution of noise and dust to the decrease in blood pressure.
Papanicolaou Society of Cytopathology new guidelines have a greater ability of risk stratification for pancreatic endoscopic ultrasound-guided fine-needle aspiration specimens

The Papanicolaou Society of Cytopathology has recently proposed a standardized terminology and nomenclature guidelines for pancreatic cytology. However the risk of malignancy associated with the new guidelines has been scarcely studied. In this study, a series of pancreatic cytology cases obtained by endoscopic ultrasound-guided fine-needle aspiration from 294 Chinese patients were retrospectively re-categorized into six categories according the new guidelines. The risks of malignancy were 18.1% for “negative,” 20.0% for “neoplastic,” 57.1% for “nondiagnostic,” 69.2% for “atypical,” 87.5% for “suspicious,” and 100.0% for “positive” respectively. The area under the receiver operating characteristic curve was 0.93 (95% Confidence Interval, 0.90-0.96), which was significantly higher than that associated with old classification system (0.82; 95% Confidence Interval, 0.77-0.87) conventionally used in China. Our investigation demonstrated that the new guidelines have a greater ability of risk stratification than the old classification system conventionally used in China. This may be helpful in giving better predictions of malignancy, thus leading to more personalized treatment strategies.
Dissection of the Octoploid Strawberry Genome by Deep Sequencing of the Genomes of Fragaria Species

Cultivated strawberry (Fragaria x ananassa) is octoploid and shows allogamous behaviour. The present study aims at dissecting this octoploid genome through comparison with its wild relatives, F. iinumae, F. nipponica, F. nubicola, and F. orientalis by de novo whole-genome sequencing on an Illumina and Roche 454 platforms. The total length of the assembled Illumina genome sequences obtained was 698 Mb for F. x ananassa, and ∼200 Mb each for the four wild species. Subsequently, a virtual reference genome termed FANhybrid_r1. 2 was constructed by integrating the sequences of the four homoeologous subgenomes of F. x ananassa, from which heterozygous regions in the Roche 454 and Illumina genome sequences were eliminated. The total length of FANhybrid_r1. 2 thus created was 173.2 Mb with the N50 length of 5137 bp. The Illumina-assembled genome sequences of F. x ananassa and the four wild species were then mapped onto the reference genome, along with the previously published F. vesca genome sequence to establish the subgenomic structure of F. x ananassa. The strategy adopted in this study has turned out to be successful in dissecting the genome of octoploid F. x ananassa and appears promising when applied to the analysis of other polyploid plant species.
Asymptomatic Abdominal Aortic Aneurysms Show Histological Signs of Progression: A Quantitative Histochemical Analysis

Objective: Abdominal aortic aneurysm (AAA) is a serious disease due to its covert nature, relatively high prevalence and fatal prognosis in the case of rupture. To obtain new insights into AAA pathogenesis, we examined the relationships between histopathology, multiplex in vitro immunoassay data, diameter and symptomatology. Methods: In a prospective, non-randomised study, we evaluated samples from 6 normal infrarenal aortae and 65 AAA patients (65 walls, 55 thrombi). The AAA patients were either asymptomatic (n = 44), symptomatic (n = 7) or with ruptured AAA (n = 14). The AAA diameter was classified as small (<5 cm, n = 18), medium (5–7 cm, n = 26) and large (>7 cm, n = 21). We quantified the histopathology of the AAA wall and the adjacent thrombus. We assessed the expression of proteins in the same samples. Results: Asymptomatic AAAs had walls with more abundant inflammatory infiltrates, lower amounts of PAI-1, a higher number of tPA-positive elements, a tendency towards decreased collagen content, whereas the adjacent thrombi had a greater concentration of VCAM-1 and MMP-2 when compared with symptomatic AAAs. Compared with the aneurysmatic aorta, the normal aorta contained less collagen and more elastin, actin, desmin and PAI-1-positive elements; in addition, it was more vascular. Medium-sized AAAs were the most actin and vimentin rich, and large AAAs were the most vascular. Conclusion: Our results show that asymptomatic AAA walls often have more potentially deleterious histopathological alterations than symptomatic AAA walls. This result indicates that a progression from an asymptomatic AAA to rupture can be expected and screening patients who are at risk of rupture could be beneficial.
Tumor-Like Presentation of Primary Angiitis of the Central Nervous System

Background and Purpose— We aimed to describe the clinical and imaging features of patients with tumor-like presentation of primary angiitis of the central nervous system. Methods— We retrospectively analyzed 10 patients enrolled in the French primary angiitis of the central nervous system cohort, who initially presented tumor-like brain lesions and compared them with other patients within the cohort. Results— The 10 patients with tumor-like presentation in the cohort were younger and had more seizures at diagnosis than the other 75 patients (median of 37 [30–48] years versus 46 [18–79] years; P=0.008; 9 [90%] with seizures versus 22 [29%], P<0.001; respectively). All 10 patients had a biopsy (stereotactic procedure in 7 and open-wedge surgery in 3). Histological findings suggestive of vasculitis were observed in 9 patients in whom conventional cerebral angiography and magnetic resonance angiography were negative. In the remaining patient, vascular imaging demonstrated diffuse bilateral large- and medium-sized vessel involvement (biopsy did not reveal vasculitis). All patients with tumor-like presentation received glucocorticoids, combined with cyclophosphamide in 9 cases. With a median follow-up of 27 (12–130) months, 5 (50%) patients relapsed, but achieved remission again after treatment intensification. Conclusions— Patients with tumor-like presentation of primary angiitis of the central nervous system represent a subgroup characterized with mainly small-sized vessel disease that requires histological confirmation because vascular imaging is often normal. Although relapses are not uncommon, global outcomes are good under treatment with glucocorticoids and cyclophosphamide.
Outcome Of Traumatic Brain Injury In Children By Using Rotterdam Score On Computed Tomography.

BACKGROUND The Rotterdam Score (RS) on CT head is a new evolving clinical tool as a predictor of mortality in Traumatic Brain Injury (TBI). The objective of this study is to assess the outcome of children with TBI admitted in paediatric intensive care unit (PICU) of a tertiary-care, university hospital by using RS. METHODS This was a prospective observational study conducted on children (age: 1mo -16yr) with TBI admitted in PICU of Aga Khan University Hospital from 2013 to 2016. RS on CT was calculated by a radiologist. All patients were managed according to according to Paediatric Brain Trauma Foundation Guidelines 2012.Demographic data, clinical variables and outcomes were recorded. Logistic regression analysis was applied to assess the association between outcome and R. RESULTS Ninety-two cases were enrolled during four years. The median age was 77 months (3 months to 16 years) and 73 (79%) were male. The main cause of injury was RTA (60.9%) followed by fall (39.1%). Sixty-two patients (67%) had a post-resuscitation GCS of 8 or less. 54% (51) patients were managed conservatively. The RS of 1, 2, 3, 4 and 5 were present in 19, 36,19,15 and 3 patients. The mean RS was 2.4. The higher mortality rate was observed in high RS. The RS was significantly associated with mortality (OR 1.75, 95% CI 1.03-2.95; p<0.04). CONCLUSIONS Rotterdam Score on CT head can be used to predict mortality in paediatric patients with TBI.
Adaptation of Nussbaum's Capabilities Framework to Community Mental Health: A Consumer‐Based Capabilities Measure

The capabilities approach provides a rich evaluative framework to guide transformative change in the community mental health system. This study reports the content and construct validity and psychometric properties of a contextualized measure of the extent to which mental health programs foster achieved capabilities. The Achieved Capabilities Questionnaire for Community Mental Health (ACQ-CMH), adapted from Nussbaum's capabilities framework, was developed previously with consumer collaboration. Content validity was assessed through a collaborative process, involving a panel of eight consumers, staff members, and senior researchers. The resulting shorter version (ACQ-CMH-98) was completed by 332 community mental health consumers sampled throughout Portugal. Factor (PCA) analysis, internal consistency reliability, and test-retest reliability over 2 weeks (N = 33) showed good psychometric properties. The resulting six-factor structure with 48 items explains 48.88% of the total variance (KMO = 0.89; Bartlett p = .00). Internal consistency of the obtained dimensions ranges from . 91 to . 76. Associations of the measure with recovery, quality of life, and psychological distress scales add further evidence of construct validity. The adaptation of Nussbaum's framework stressed specific components that may enhance understanding and change within the community mental health system.
A MECOM variant in an African American child with radioulnar synostosis and thrombocytopenia.

Genomic Medicine Program, Dr John T. Macdonald Foundation Department of Human Genetics, Division of Pediatric Hematology and Oncology, Department of Pediatrics, John P. Hussman Institute for Human Genomics and Department of Otolaryngology, Miller School of Medicine, University of Miami, Miami, Florida, USA Correspondence to Mustafa Tekin, MD, 1501 NW 10th Avenue, BRB-610 (M-860), Miami, FL 33136, USA Tel: + 1 305 243 2381; fax: + 1 305 243 2704; e-mail: mtekin@med.miami. edu
The Influence of Gate Material, SiO2 Fabrication Method and Gate Edge Effect on Interface Trap Density in 3C-SiC MOS Capacitors

This paper reports on results of interface trap analysis of 3C-SiC MOS capacitors fabricated using four different gate materials and two SiO2 oxide preparation methods. The results indicate that post-deposition annealing in wet oxygen of PECVD deposited SiO2 samples increases the near-interface or slow trap densities, compared with wet oxygen thermally oxidized samples. It has also been found that the energy distribution, Dit, of electron states at the oxide/SiC interface of MOS capacitors with different sizes depend on the factor R=P/A, where P stands for the gate perimeter and A for the gate area, which is related to the amount of stress under the edge of the metallic gate.
Investigating the Relationships Between Alcohol Consumption, Cannabis Use, and Circulating Cytokines: A Preliminary Analysis

BACKGROUND In recent years, human and animal studies have converged to support altered inflammatory signaling as a molecular mechanism underlying the pathophysiology of alcohol use disorders (AUDs). Alcohol binds to receptors on immune cells, triggering signaling pathways that produce pro-inflammatory cytokines. Chronic inflammation is associated with tissue damage, which may contribute to negative effects of AUD. Conversely, cannabis is associated with decreased inflammatory signaling, and animal studies suggest that cannabinoids may impact alcohol-induced inflammation. Thus, the impact of cannabis on inflammation in AUDs in humans warrants examination. METHODS We explored the relationship between self-reported alcohol and cannabis use and circulating levels of the pro-inflammatory cytokines interleukin 6 (IL-6), IL-8, and IL-1β in the blood. Among 66 regular drinkers (mean age = 30.08), we examined circulating cytokines and administered questionnaires assessing alcohol consumption and days of cannabis use over the past 90 days. We examined whether alcohol consumption, cannabis use, and gender were associated with changes in circulating cytokines, and whether there was a significant interaction between alcohol and cannabis use predicting blood levels of circulating cytokines. RESULTS A positive association between alcohol and IL-6 emerged. We also observed a negative association between cannabis and IL-1β. Follow-up moderation analyses indicated a cannabis by alcohol interaction predicting circulating IL-6, such that cannabis nonusers showed a stronger relationship between alcohol and IL-6 compared to cannabis users. CONCLUSIONS These preliminary findings suggest that cannabinoid compounds may serve to mitigate inflammation associated with alcohol use. In addition, the present results provide data to inform future investigations, with the goal of ultimately leveraging knowledge of the role of inflammation in AUDs to develop more effective treatments focused on novel immune targets.
Content of Heavy Metal in the Dust of Leisure Squares and Its Health Risk Assessment—A Case Study of Yanta District in Xi’an

Taking Yanta District in Xi’an as the research object, the present study measures the contents of Cadmium (Cd), Lead (Pb), Copper (Cu), Nickel (Ni), and Chromium (Cr) in dust samples and further assesses the health risk of heavy metals intake through dust based on the assessment method of human exposure risk proposed by U.S. EPA, with an aim to investigate the content of heavy metal in the dust of leisure squares and its exposure risk. As the results indicate, the average contents of five heavy metals are obviously higher than the soil background value in Shaanxi Province. Therefore, Cd, Ni, Cu, Pb, and Cr are obviously enriched in urban surface dust in Shaanxi Province, due to the influence of human activities. In addition, it can also be found that the non-carcinogen exposure risk in children is significantly higher than that in adults with the risk values of these five heavy metals all one order of magnitude higher than those of adults. Irrespective of whether addressing the results for children or adults, the non-carcinogen exposure doses of five heavy metals are sorted as Cr > Pb > Cu > Ni > Cd. According to the present situation, for a child, the total non-carcinogenic risk values of five heavy metals have exceeded the safety limit in 11 of the 20 leisure squares in Yanta District of Xi’an. That means the leisure squares are no longer suitable for physical and recreational activities. For the five heavy metals, the average non-carcinogenic risk value of Cr is largest, and causes the largest threat to health in Yanta District, Xi’an. The carcinogenic exposure doses of the heavy metals Cr, Cd, and Ni are very low in respiratory pathways and there is no carcinogenic health risk. In general, the Cr content in dust in domestic cities is higher than that of foreign cities; however, the Pb content is much lower.