Miracle-dz/UniFAR-FTUs huggingface dataset:
Gene Flow between the Korean Peninsula and Its Neighboring Countries

SNP markers provide the primary data for population structure analysis. In this study, we employed whole-genome autosomal SNPs as a marker set (54,836 SNP markers) and tested their possible effects on genetic ancestry using 320 subjects covering 24 regional groups including Northern ( = 16) and Southern ( = 3) Asians, Amerindians ( = 1), and four HapMap populations (YRI, CEU, JPT, and CHB). Additionally, we evaluated the effectiveness and robustness of 50K autosomal SNPs with various clustering methods, along with their dependencies on recombination hotspots (RH), linkage disequilibrium (LD), missing calls and regional specific markers. The RH- and LD-free multi-dimensional scaling (MDS) method showed a broad picture of human migration from Africa to North-East Asia on our genome map, supporting results from previous haploid DNA studies. Of the Asian groups, the East Asian group showed greater differentiation than the Northern and Southern Asian groups with respect to Fst statistics. By extension, the analysis of monomorphic markers implied that nine out of ten historical regions in South Korea, and Tokyo in Japan, showed signs of genetic drift caused by the later settlement of East Asia (South Korea, Japan and China), while Gyeongju in South East Korea showed signs of the earliest settlement in East Asia. In the genome map, the gene flow to the Korean Peninsula from its neighboring countries indicated that some genetic signals from Northern populations such as the Siberians and Mongolians still remain in the South East and West regions, while few signals remain from the early Southern lineages.
Prediction of adverse events after catheter-based procedures in adolescents and adults with congenital heart disease in the IMPACT registry

Aims We sought to identify factors associated with major adverse events (MAE) after cardiac catheterization in adolescents and adults with congenital heart disease (CHD), and create the first model to individualize risk discussions in this growing population. Methods and results Improving Pediatric and Adult Congenital Treatment (IMPACT), a National Cardiovascular Data Registry, contains congenital catheterization data from over 87 hospitals in the United States. Demographics, pre-procedure, and procedural variables were collected for patients over age 10. Multivariable logistic regression was used to identify significant predictors of MAE, a composite of death, urgent surgery or procedure due to a catheterization complication, transfusion, embolic stroke, tamponade, extracorporeal membrane oxygenation or ventricular assist device placement, and device embolization, malposition or thrombosis requiring surgical intervention. A risk score was built based on the effect sizes of each predictor and validated in a split sample. A MAE occurred in 686 (2.5%) of the 27 293 index procedures meeting inclusion criteria. The independent multivariate predictors of MAE were older age, pre-procedural anticoagulation use, renal disease, lower haemoglobin, lower oxygen saturation, non-elective procedure, higher index procedure risk and having had no prior cardiac procedures. Being underweight or overweight had borderline significance and was added to the model. The C-statistic for the model was robust at 0.787 in the derivation and 0.773 in the validation cohort. Conclusion The factors predicting adverse events after cardiac catheterization in adolescents and adults with CHD are different than in the general population. Validation of this model in other national or multi-institutional datasets is the next step.
Automated Computational Processing of 3‐D MR Images of Mouse Brain for Phenotyping of Living Animals

Magnetic resonance (MR) imaging provides a method to obtain anatomical information from the brain in vivo that is not typically available by optical imaging because of this organ's opacity. MR is nondestructive and obtains deep tissue contrast with 100‐µm3 voxel resolution or better. Manganese‐enhanced MRI (MEMRI) may be used to observe axonal transport and localized neural activity in the living rodent and avian brain. Such enhancement enables researchers to investigate differences in functional circuitry or neuronal activity in images of brains of different animals. Moreover, once MR images of a number of animals are aligned into a single matrix, statistical analysis can be done comparing MR intensities between different multi‐animal cohorts comprising individuals from different mouse strains or different transgenic animals, or at different time points after an experimental manipulation. Although preprocessing steps for such comparisons (including skull stripping and alignment) are automated for human imaging, no such automated processing has previously been readily available for mouse or other widely used experimental animals, and most investigators use in‐house custom processing. This protocol describes a stepwise method to perform such preprocessing for mouse. © 2017 by John Wiley & Sons, Inc.
Accuracy of the urine UCA1 for diagnosis of bladder cancer: a meta-analysis

Urine UCA1 has been reported as a potential novel diagnostic biomarker for bladder cancer in several studies, but their results are inconsistent. As a result of this, a diagnostic meta-analysis to assess the diagnostic performance of urine UCA1 in detecting bladder cancer was conducted. A systematic electronic and manual search was performed for relevant literatures through PubMed, Cochrane library, Chinese Wan Fang and the China National Knowledge Infrastructure (CNKI) databases up to December 30, 2016. The quality of the studies included in this meta-analysis was assessed using the Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) tool. All analyses were conducted using stata12.0 software. Six studies collectively included 578 bladder cancer patients and 562 controls met the eligible criteria. The overall diagnostic accuracy was measured by the following: sensitivity 0.81 (95% CI = 0.75-0.86), specificity 0.86 (95% CI = 0.73-0.93), positive likelihood ratio 5.85 (95% CI = 2.72-12.57), negative likelihood 0.22 (95% CI = 0.15-0.32), diagnostic odds ratio 27.01 (95% CI = 8.69-83.97), and area under the curve 0.88 (95% CI = 0.85-0.91). Meta-regression analysis suggested that ethnicity significantly accounted for the heterogeneity of sensitivity. Deeks’ funnel plot asymmetry test (P = 0.33) suggested no potential publication bias. According to our results, urine UCA1 has greater diagnostic value in diagnosing bladder cancer, however further research studies with more well-designed and large sample sizes are required to confirm our findings.
Local Fringe Frequency Estimation Based on Multifrequency InSAR for Phase-Noise Reduction in Highly Sloped Terrain

The interferometric phases in highly sloped terrain have the characteristics of large fringe density, narrow width, low correlation, and under-sampling. The local fringe frequ- ency (LFF) is a criterion to evaluate the trend and magnitude of the local terrain gradient and can be employed to improve the quality of interferograms. The results of the traditional LFF estimation method can be affected by phase noise, and sometimes the phase unwrapping (PU) operation is also required for some local regions. When it comes to highly sloped terrain, the phenomenon of phase under-sampling may cause incorrectness in the absolute interferometric phase during the operation of PU and may then influence the accuracy of the whole estimation. In order to solve this problem, this letter proposes an extended maximum-likelihood method for LFF estimation based on the multifrequency interferometric synthetic aperture radar (InSAR) data. Through the differences in the LFF between the different frequency InSAR data, the estimation quality map is introduced to modify the large error in certain regions by local 2-D fitting and thus achieves a accurate estimation of LFF in highly sloped terrain. Finally, the estimated results of LFF are used to guide the process of phase filtering. Simulated data and real airborne dual-frequency InSAR data are both employed to validate this proposed method.
Extension of the variational equation to analog/digital circuits: numerical and experimental validation

Conventional shooting methods cannot be used to determine the steady‐state solution of circuits whose model is characterised by a vector field exhibiting zero order discontinuities. In the analysis of circuits working on a stable limit cycle, this limitation prevents the use of methods that exploit Floquet theory to compute the variational model and thus the properties of the fundamental matrix and, for example, phase noise in oscillators. In this paper, we use an improved shooting method that solves this drawback by resorting to saltation matrices and show how this method makes possible the correct computation of the first left eigenfunction (known as ppv) of the fundamental matrix. ppvs are a key aspect in determining phase noise. The results obtained through numerical simulations are compared with measurements on a relaxation oscillator serving as a simple but significant comparison vehicle. Copyright © 2012 John Wiley & Sons, Ltd.
Evaluation of seismic reflector slopes with a Yoyo‐CTD

In spring 2007 a dedicated seismic and oceanographic experiment was conducted in the Gulf of Cadiz. Employing two research vessels seismic and hydrographic observations were made contemporaneously and in close proximity. At a 12 hour long station inside a Meddy a conductivity‐temperature‐depth (CTD) probe was lowered and raised repeatedly while the seismic vessel conducted a repetitive survey on tracks nearby. Over the period 17 CTD profiles were collected covering the depth interval from 500 to 1700 m. The CTD data show the Meddy's elevated temperatures and salinities as well as varying intrusive features. When converted into reflection coefficients and convoluted with the seismic source signal the CTD data agrees well with nearby seismic data. The comparison of the temporal/spatial slopes of CTD‐derived reflectors with those of isopycnals shows a good agreement when the slopes are determined over intervals shorter than 4 hours.
Differences in posttraumatic growth and grief reactions among adolescents by relationship with the deceased

AIM The aim of this study was to examine three hypotheses: (1) adolescents who had experienced the death of a parent would report higher grief reactions than those who had lost a grandparent; (2) adolescents who experienced the death of a parent would report higher posttraumatic growth than those who had lost a grandparent; and (3) posttraumatic growth and grief reactions are positively associated. BACKGROUND To date, no study has investigated adolescents' posttraumatic growth by their relationship with the deceased. DESIGN Cross-sectional web-based survey. METHODS Participants were adolescents who had experienced the death of a parent or grandparent in the last 5 years. Participants completed the Japanese version of the Posttraumatic Growth Inventory and grief reaction items. We conducted a web-based survey during January 2014. We used Pearson product-moment correlations to examine the association between each Posttraumatic Growth Inventory domain and each grief reaction item. Differences in the relationship with the deceased for each Posttraumatic Growth Inventory and grief reaction item were compared with an independent-sample t-test. RESULTS Participants (n = 124) reported grief reactions including 'I began to get frustrated at the little things' (43·5%), 'It was difficult to go to school' (41·1%) and 'I was not able to sleep at night' (33·9%). The independent t-test indicated that parentally bereaved adolescents reported higher grief reactions than those who had lost a grandparent. There were no differences in post-traumatic growth by relationship with the deceased. [corrected]. Pearson's bivariate analysis showed an association between grief reactions and posttraumatic growth. CONCLUSION Parentally bereaved adolescents reported higher grief reactions. [corrected]. Nurses should ensure bereaved adolescents receive appropriate support.
Editor’s Highlight: Transcriptome Profiling Reveals Bisphenol A Alternatives Activate Estrogen Receptor Alpha in Human Breast Cancer Cells

Background Plasticizers with estrogenic activity, such as bisphenol A (BPA), have been reported to have potential adverse health effects in humans. Due to mounting evidence of these health effects and public pressure, BPA is being phased out by the plastics manufacturing industry and replaced by other bisphenol variants in “BPA-free” products. Objectives We have compared estrogenic activity of BPA to 6 bisphenol analogues (bisphenol S, BPS; bisphenol F, BPF; bisphenol AP, BPAP; bisphenol AF, BPAF; bisphenol Z, BPZ; bisphenol B, BPB) in three human breast cancer cell lines. Methods Estrogenicity was assessed by cell growth in an estrogen receptor (ER)-mediated cell proliferation assay, and by the induction of estrogen response element (ERE)-mediated transcription in a luciferase assay. Gene expression profiles were determined in MCF-7 human breast cancer cells by microarray analysis and confirmed by Illumina-based RNA sequencing. Results All bisphenols showed estrogenic activity in promoting cell growth and inducing ERE-mediated transcription. BPAF was the most potent bisphenol, followed by BPB > BPZ ~ BPA > BPF ~ BPAP > BPS. The addition of ICI 182,780 antagonized the activation of ERs by bisphenols. Data mining of ToxCast high-throughput screening assays confirms our results but also shows divergence in the sensitivities of the assays. The comparison of transcriptome profile alterations resulting from BPA alternatives with an ERα gene expression biomarker further indicates that all BPA alternatives act as ERα agonists in MCF-7 cells. These results were confirmed by RNA sequencing. Conclusion In conclusion, BPA alternatives are not necessarily less estrogenic in a human breast cancer cell model. Three bisphenols (BPAF, BPB, and BPZ) were more estrogenic than BPA. The relevance of human exposure to BPA alternatives in hormone-dependent breast cancer risk should be investigated.
Copy Number Variation of UGT 2B Genes in Indian Families Using Whole Genome Scans

Background and Objectives. Uridine diphospho-glucuronosyltransferase 2B (UGT2B) is a family of genes involved in metabolizing steroid hormones and several other xenobiotics. These UGT2B genes are highly polymorphic in nature and have distinct polymorphisms associated with specific regions around the globe. Copy number variations (CNVs) status of UGT2B17 in Indian population is not known and their disease associations have been inconclusive. It was therefore of interest to investigate the CNV profile of UGT2B genes. Methods. We investigated the presence of CNVs in UGT2B genes in 31 members from eight Indian families using Affymetrix Genome-Wide Human SNP Array 6.0 chip. Results. Our data revealed >50% of the study members carried CNVs in UGT2B genes, of which 76% showed deletion polymorphism. CNVs were observed more in UGT2B17 (76.4%) than in UGT2B15 (17.6%). Molecular network and pathway analysis found enrichment related to steroid metabolic process, carboxylesterase activity, and sequence specific DNA binding. Interpretation and Conclusion. We report the presence of UGT2B gene deletion and duplication polymorphisms in Indian families. Network analysis indicates the substitutive role of other possible genes in the UGT activity. The CNVs of UGT2B genes are very common in individuals indicating that the effect is neutral in causing any suspected diseases.
3D dentofacial photogrammetry reference values: a novel approach to orthodontic diagnosis

Background Orthodontic diagnostic standards generally use the cranial base as a reference and rely on samples selected by orthodontists. Objective The purpose of this study was to provide male and female standards for a novel non-radiographic approach for orthodontic diagnosis that utilizes 3D dentofacial photogrammetry using the eyes and natural head orientation as references instead of the cranial base. Methods One hundred and eighty females and 200 males between the ages of 18 and 35 years from 2 modeling agencies were orthodontically screened for near ideal occlusion. Subjects that met the inclusion criteria were rated by a sample of 40 lay people for attractiveness on a visual analogue scale. The final sample that had 3D facial and dental imaging included 49 subjects 25 males and 24 females with near ideal occlusion and considered attractive by the public. Results Inter and Intra-examiner ICC were greater than 0.8 for both landmarking and indexing. Relative to a coronal plane contacting the pupils (MC), the mean sagittal position of the alar curvature (representing the nasomaxillary complex) was 14.36 ± 3.08 mm in males and 12.4 ± 3.58 mm in females. The sagittal position of soft tissue pogonion relative to the pupils was 14.84 ± 3.63 mm in males and 12.78 ± 5.68 mm in females. The angle between the alar curvature and pogonion relative to the pupils was 9° in males and 10° in females. With the exception of the occlusal plane which was steeper in females, no ratios or angular facial measurements showed a significant gender difference. Relative to MC, males had more proclined upper incisors (20° vs 16°) and more retroclined Lower incisors (27° vs 31°; P > 0.05). A Procrustes ANOVA and permutation test showed that the shapes of males and females are different enough to be considered two distinct populations. Conclusions 1. When using the proposed method for orthodontic diagnosis, male and female patients should be compared to their respective dentofacial standards. 2. Validation of the proposed method and standards on an orthodontic population is underway to determine the scope its use.
Location-Specific Responses to Thermal Stress in Larvae of the Reef-Building Coral Montastraea faveolata

Background The potential to adapt to a changing climate depends in part upon the standing genetic variation present in wild populations. In corals, the dispersive larval phase is particularly vulnerable to the effects of environmental stress. Larval survival and response to stress during dispersal and settlement will play a key role in the persistence of coral populations. Methodology/Principal Findings To test the hypothesis that larval transcription profiles reflect location-specific responses to thermal stress, symbiont-free gametes from three to four colonies of the scleractinian coral Montastraea faveolata were collected from Florida and Mexico, fertilized, and raised under mean and elevated (up 1 to 2°C above summer mean) temperatures. These locations have been shown to exchange larvae frequently enough to prevent significant differentiation of neutral loci. Differences among 1,310 unigenes were simultaneously characterized using custom cDNA microarrays, allowing investigation of gene expression patterns among larvae generated from wild populations under stress. Results show both conserved and location-specific variation in key processes including apoptosis, cell structuring, adhesion and development, energy and protein metabolism, and response to stress, in embryos of a reef-building coral. Conclusions/Significance These results provide first insights into location-specific variation in gene expression in the face of gene flow, and support the hypothesis that coral host genomes may house adaptive potential needed to deal with changing environmental conditions.
Effect of bandwidth on seismic imaging of rotating stratified turbulence surrounding an anticyclonic eddy from field data and numerical simulations

The fine resolution of long geoseismic sections should permit the characterization of oceanic turbulence properties over several decades of horizontal scales. The range of horizontal scales actually probed by three different acoustic sources is found to be directly linked to their frequency content. The horizontal inertial range with a spectral slope of kh−5/3 extend up to 3 km wavelength for the most intense acoustic reflectors which surround strong anticyclonic eddies. The in situ data analysis is confirmed by high resolution numerical simulations of oceanic anticyclonic vortices, in a rotating temperature‐stratified fluid (no salt), which show the spontaneous emergence of a concentration of acoustic reflectors above and below the eddy. These show an anisotropy and a spectral slope consistent with the framework of stratified turbulence, which differs from that of Garret and Munk for internal waves. The implications are that a direct energy cascade to smaller spatial scales is occurring at the boundaries of energetic oceanic vortices and may provide a mechanism to drive mixing in the ocean interior.
Use of acetaminophen and risk of endometrial cancer: evidence from observational studies

Previous meta-analyses suggested that aspirin was associated with reduced risk of endometrial cancer. However, there has been no study comprehensively summarize the evidence of acetaminophen use and risk of endometrial cancer from observational studies. We systematically searched electronic databases (PubMed, EMBASE, Web of Science, and Cochrane Library) for relevant cohort or case-control studies up to February 28, 2017. Two independent authors performed the eligibility evaluation and data extraction. All differences were resolved by discussion. A random-effects model was applied to estimate summary relative risks (RRs) with 95% CIs. All statistical tests were two-sided. Seven observational studies including four prospective cohort studies and three case-control studies with 3874 endometrial cancer cases were included for final analysis. Compared with never use acetaminophen, ever use this drug was not associated with risk of endometrial cancer (summarized RR = 1.02; 95% CI: 0.93−1.13, I2 = 0%). Similar null association was also observed when compared the highest category of frequency/duration with never use acetaminophen (summarized RR = 0.88; 95% CI: 0.70−1.11, I2 = 15.2%). Additionally, the finding was robust in the subgroup analyses stratified by study characteristics and adjustment for potential confounders and risk factors. There was no evidence of publication bias by a visual inspection of a funnel plot and formal statistical tests. In summary, the present meta-analysis reveals no association between acetaminophen use and risk of endometrial cancer. More large scale prospective cohort studies are warranted to confirm our findings and carry out the dose-response analysis of aforementioned association.