ATACgraph: Profiling genome-wide chromatin accessibility from ATAC-seq

Assay for transposase-accessible chromatin using sequencing data (ATAC-seq) is an efficient and precise method for revealing chromatin accessibility across the genome. Most of the current ATAC-seq tools follow chromatin immunoprecipitation sequencing (ChIP-seq) strategies that do not consider ATAC-seq-specific properties. To incorporate specific ATAC-seq quality control and the underlying biology of chromatin accessibility, we developed a bioinformatics software named ATACgraph for analyzing and visualizing ATAC-seq data. ATACgraph profiles accessible chromatin regions and provides ATAC-seq-specific information including definitions of nucleosome-free regions (NFRs) and nucleosome-occupied regions. ATACgraph also allows identification of differentially accessible regions between two ATAC-seq datasets. ATACgraph incorporates the docker image with the Galaxy platform to provide an intuitive user experience via the graphical interface. Without tedious installation processes on a local machine or cloud, users can analyze data through activated websites using pre-designed workflows or customized pipelines composed of ATACgraph modules. Overall, ATACgraph is an effective tool designed for ATAC-seq for biologists with minimal bioinformatics knowledge to analyze chromatin accessibility. ATACgraph can be run on any ATAC-seq data with no limit to specific genomes. As validation, we demonstrated ATACgraph on human genome to showcase its functions for ATAC-seq interpretation. This software is publicly accessible and can be downloaded at https://github.com/RitataLU/ATACgraph

BETTER POSTURAL CONTROL DURING ACCURATE SHOOTING IN ELITE FEMALE BASKETBALL PLAYERS

The purpose of this study was to evaluate the differences of postural control (PC) during accurate and inaccurate shooting in elite female basketball players. 21 female professional basketball players recruited as subjects. The PC was evaluated by the Accusway as sway radius, velocity, radial and 95% area of the center of pressure (COP) during standard penalty line shooting. The results showed that the COP sway area during accurate shooting was significantly smaller than during inaccurate shooting (74.0 ± 37.9 vs. 110.6 ± 49.1, p < .05). Moreover, no significant differences were found between situations in the COP radius and velocity. This study found that during the accurate shooting, elite female basketball player had better PC which demonstrated that significant smaller COP sway area than inaccurate shooting

In situ reconstruction of septic aortic pseudoaneurysm due to Salmonella or Streptococcus microbial aortitis: long-term follow-up

AbstractObjectiveThis study was undertaken to illustrate the safety of in situ reconstruction of septic aortic pseudoaneurysm (SAP) secondary to microbial aortitis, with or without long-term antibiotic treatment.MethodsData for patients with SAP (11 abdominal, 4 thoracic) operated on between 1993 and 1999 were reviewed. Computed tomography and aortography showed septic pseudoaneurysm in all patients before surgery. After diagnosis of SAP, all patients underwent aneurysm resection and extensive debridement, with in situ prosthetic grafting or patch repair angioplasty. The graft in 10 of the 11 patients with abdominal SAP was also wrapped with an omental pedicle. In vitro active parenteral antibiotic therapy was prescribed for all patients for at least 2 to 8 weeks after surgery.ResultsAll 15 patients had positive preoperative blood cultures or intraoperative tissue cultures for Salmonella spp (n = 12), viridans Streptococcus (n = 1), group G Streptococcus (n = 1), or Streptococcus pneumoniae (n = 1). There were two perioperative deaths (13.3%), one 6 days after surgery and the other 19 days after surgery, and two late deaths, at 8 and 10 months after surgery, neither of which was related to aortic repair. One patient was unavailable for follow-up. The other 10 patients have been regularly followed up with abdominal ultrasound or computed tomography (mean, 84 months; range, 47-118 months). To date, there has been no graft infection, thrombosis, false aneurysm, or subsequent aortic surgery in these 10 patients.ConclusionSAP due to Salmonella and streptococcal microbial arortitis can be successfully treated with resection of the aneurysm and extensive debridement, followed by in situ prosthetic graft interposition or patch repair aortoplasty. This is a safe and effective treatment that may result in complete remission of SAP. Postoperative parenteral antibiotic therapy should be continued for 2 to 8 weeks. Although usually recommended, lifelong suppressive antibiotic therapy appears to be nonessential with this approach

MethylC-analyzer: A comprehensive downstream pipeline for the analysis of genome-wide DNA methylation

DNA methylation is a crucial epigenetic modification involved in multiple biological processes and diseases. Current approaches for measuring genome-wide DNA methylation via bisulfite sequencing (BS-seq) include whole-genome bisulfite sequencing (WGBS), reduced representation bisulfite sequencing (RRBS), and enzymatic methyl-seq (EM-seq). The computational analysis tools available for BS-seq data include customized aligners for mapping bisulfite-converted reads and computational pipelines for downstream data analysis. Current post-alignment methylation tools are specialized for the interpretation of CG methylation, which is known to dominate mammalian genomes, however, non-CG methylation (CHG and CHH, where H refers to A, C, or T) is commonly observed in plants and fungi and is closely associated with gene regulation, transposon silencing, and plant development. Thus, we have developed a MethylC-analyzer to analyze and visualize post-alignment WGBS, RRBS, and EM-seq data focusing on CG. The tool is able to also analyze non-CG sites to enhance deciphering genomes of plants and fungi. By processing aligned data and gene location files, MethylC-analyzer generates a genome-wide view of methylation levels and methylation in user-specified genomic regions. The meta-plot, for example, allows the investigation of DNA methylation within specific genomic elements. Moreover, our tool identifies differentially methylated regions (DMRs) and investigates the enrichment of genomic features associated with variable methylation. MethylC-analyzer functionality is not limited to specific genomes, and we demonstrated its performance on both plant and human BS-seq data. MethylC-analyzer is a Python- and R-based program designed to perform comprehensive downstream analyses of methylation data, providing an intuitive analysis platform for scientists unfamiliar with DNA methylation analysis. It is available as either a standalone version for command-line uses or a graphical user interface (GUI) and is publicly accessible at https://github.com/RitataLU/MethylC-analyzer

The risk of false inclusion of a relative in parentage testing – an in silico population study

Aim To investigate the potential of false inclusion of a close genetic relative in paternity testing by using computer generated families. Methods 10 000 computer-simulated families over three generations were generated based on genotypes using 15 short tandem repeat loci. These data were used in assessing the probability of inclusion or exclusion of paternity when the father is actually a sibling, grandparent, uncle, half sibling, cousin, or a random male. Further, we considered a duo case where the mother’s DNA type was not available and a trio case including the mother’s profile. Results The data showed that the duo scenario had the highest and lowest false inclusion rates when considering a sibling (19.03 ± 0.77%) and a cousin (0.51 ± 0.14%) as the father, respectively; and the rate when considering a random male was much lower (0.04 ± 0.04%). The situation altered slightly with a trio case where the highest rate (0.56 ± 0.15%) occurred when a paternal uncle was considered as the father, and the lowest rate (0.03 ± 0.03%) occurred when a cousin was considered as the father. We also report on the distribution of the numbers for non-conformity (non-matching loci) where the father is a close genetic relative. Conclusions The results highlight the risk of false inclusion in parentage testing. These data provide a valuable reference when incorporating either a mutation in the father’s DNA type or if a close relative is included as being the father; particularly when there are varying numbers of non-matching loci

A novel strategy for sibship determination in trio sibling model

Aim To use a virtually simulated population, generated from published allele frequencies based on 15 short tandem repeats (STR), to evaluate the efficacy of trio sibship testing and sibling assignment for forensic purposes. Methods Virtual populations were generated using 15 STR loci to create a large number of related and unrelated genotypes (10 000 trio combinations). Using these virtual populations, the probability of related and unrelated profiles can be compared to determine the chance of inclusions of being siblings if they are true siblings and the chance of inclusion if they are unrelated. Two specific relationships were tested – two reference siblings were compared to a third true sibling (3S trio, sibling trio) and two reference siblings were compared to an unrelated individual (2S1U trio, non-sibling trio). Results When the likelihood ratio was greater than 1, 99.87% of siblings in the 3S trio population were considered as siblings (sensitivity); 99.88% of non-siblings in the 2S1U trio population were considered as non-siblings (specificity); 99.9% of both populations were identified correctly as siblings and non-siblings; and the accuracy of the test was 99.88%. Conclusions The high sensitivity and specificity figures when using two known siblings compared to a putative sibling are significantly greater than when using only one known relative. The data also support the use of increasing number of loci allowing for greater confidence in genetic identification. The system established in this study could be used as the model for evaluating and simulating the cases with multiple relatives

A novel strategy for sibship determination in trio sibling model

Aim To use a virtually simulated population, generated from published allele frequencies based on 15 short tandem repeats (STR), to evaluate the efficacy of trio sibship testing and sibling assignment for forensic purposes. Methods Virtual populations were generated using 15 STR loci to create a large number of related and unrelated genotypes (10 000 trio combinations). Using these virtual populations, the probability of related and unrelated profiles can be compared to determine the chance of inclusions of being siblings if they are true siblings and the chance of inclusion if they are unrelated. Two specific relationships were tested – two reference siblings were compared to a third true sibling (3S trio, sibling trio) and two reference siblings were compared to an unrelated individual (2S1U trio, non-sibling trio). Results When the likelihood ratio was greater than 1, 99.87% of siblings in the 3S trio population were considered as siblings (sensitivity); 99.88% of non-siblings in the 2S1U trio population were considered as non-siblings (specificity); 99.9% of both populations were identified correctly as siblings and non-siblings; and the accuracy of the test was 99.88%. Conclusions The high sensitivity and specificity figures when using two known siblings compared to a putative sibling are significantly greater than when using only one known relative. The data also support the use of increasing number of loci allowing for greater confidence in genetic identification. The system established in this study could be used as the model for evaluating and simulating the cases with multiple relatives

Effects of Growth Hormone Treatment on Height, Weight, and Obesity in Taiwanese Patients with Prader-Willi Syndrome

BackgroundInformation regarding the efficacy of growth hormone (GH) therapy in Asian Prader-Willi syndrome (PWS) patients is lacking. We report our experience with GH treatment in children with PWS in Taiwan.MethodsForty-six PWS patients (27 males, 19 females; age range, 1 year 4 months to 13 years 7 months) who received and/or who are currently receiving GH treatment (0.1 IU/kg/day subcutaneously) for a period from 1 year to 3 years were retro-spectively analyzed. We evaluated height, weight, body mass index (BMI) and Rohrer index, before and after GH treatment.ResultsAfter patients had received GH for 1, 2 and 3 years, a significant improvement in mean height standard deviation score (SDS) was noted from −1.24 to −0.31 (p <0.01), 0.00 (p <0.001) and −0.26 (p <0.001), respectively. Mean BMI SDS decreased significantly from 1.93 to 1.13 (p <0.05) after 1 year of treatment; however, no significant changes were observed afterward. Mean Rohrer index decreased significantly, from 224.2 to 186.6 (p <0.001), 178.9 (p <0.001) and 169.3 (p <0.001). No significant gender or genotype pattern differences were noted among the 4 parameters examined.ConclusionThis 3-year, retrospective study indicates that PWS patients benefit from GH therapy in height increase and improved body composition

Fly-DPI: database of protein interactomes for D. melanogaster in the approach of systems biology

BACKGROUND: Proteins control and mediate many biological activities of cells by interacting with other protein partners. This work presents a statistical model to predict protein interaction networks of Drosophila melanogaster based on insight into domain interactions. RESULTS: Three high-throughput yeast two-hybrid experiments and the collection in FlyBase were used as our starting datasets. The co-occurrences of domains in these interactive events are converted into a probability score of domain-domain interaction. These scores are used to infer putative interaction among all available open reading frames (ORFs) of fruit fly. Additionally, the likelihood function is used to estimate all potential protein-protein interactions. All parameters are successfully iterated and MLE is obtained for each pair of domains. Additionally, the maximized likelihood reaches its converged criteria and maintains the probability stable. The hybrid model achieves a high specificity with a loss of sensitivity, suggesting that the model may possess major features of protein-protein interactions. Several putative interactions predicted by the proposed hybrid model are supported by literatures, while experimental data with a low probability score indicate an uncertain reliability and require further proof of interaction. Fly-DPI is the online database used to present this work. It is an integrated proteomics tool with comprehensive protein annotation information from major databases as well as an effective means of predicting protein-protein interactions. As a novel search strategy, the ping-pong search is a naïve path map between two chosen proteins based on pre-computed shortest paths. Adopting effective filtering strategies will facilitate researchers in depicting the bird's eye view of the network of interest. Fly-DPI can be accessed at . CONCLUSION: This work provides two reference systems, statistical and biological, to evaluate the reliability of protein interaction. First, the hybrid model statistically estimates both experimental and predicted protein interaction relationships. Second, the biological information for filtering and annotation itself is a strong indicator for the reliability of protein-protein interaction. The space-temporal or stage-specific expression patterns of genes are also critical for identifying proteins involved in a particular situation

Correction of Tetralogy of Fallot with Absent Pulmonary Valve Syndrome in a Young Infant Using a Bicuspid Equine Pericardial Tube

Absent pulmonary valve syndrome (APVS) is an uncommon variant of tetralogy of Fallot (TOF), which manifests morphologically as vestigial pulmonary valve cusps at the right ventricle-pulmonary trunk junction. The aneurysmally dilated pulmonary arteries may compress the tracheobronchial tree and cause severe respiratory distress in the neonatal or infant stage. Early surgical correction in these patients is necessary despite the high operative mortality rate. A 1-day-old male neonate suffered from progressive shortness of breath after birth. Echocardiography confirmed the diagnosis of TOF with APVS. The marked dilatation of pulmonary arteries resulted in airway compression in addition to heart failure. Total surgical correction was performed at 40 days of age, using a homemade bicuspid equine pericardial tube for right ventricular outflow reconstruction. The short-term follow-up echocardiogram demonstrated good motility of the pericardial leaflet. However, patients receiving this type of valved conduit require meticulous long-term follow-up