Nextflow vs. plain bash: different approaches to the parallelization of SNP calling from the whole genome sequence data.

This study compared computational approaches to parallelization of an SNP calling workflow. The data comprised DNA from five Holstein-Friesian cows sequenced with the Illumina platform. The pipeline consisted of quality control, alignment to the reference genome, post-alignment, and SNP calling. Three approaches to parallelization were compared: (i) a plain Bash script in which a pipeline for each cow was executed as separate processes invoked at the same time, (ii) a Bash script wrapped in a single Nextflow process and (iii) a Nextflow script with each component of the pipeline defined as a separate process. The results demonstrated that on average, the multi-process Nextflow script performed 15-27% faster depending on the number of assigned threads, with the biggest execution time advantage over the plain Bash approach observed with 10 threads. In terms of RAM usage, the most substantial variation was observed for the multi-process Nextflow, for which it increased with the number of assigned threads, while RAM consumption of the other setups did not depend much on the number of threads assigned for computations. Due to intermediate and log files generated, disk usage was markedly higher for the multi-process Nextflow than for the plain Bash and for the single-process Nextflow.

Assessing the outcomes of parasacral transcutaneous electrical nerve stimulation (PTENS) in the treatment of enuresis in children: A systematic review and meta-analysis of randomized control trials.

INTRODUCTION: Nocturnal enuresis (NE) is a common pathology in children that can have significant behavioral, emotional, and social impacts on a child's life. Recent studies have assessed PTENS as a potential treatment method for NE, particularly in those who do not respond to initial first-line treatments. Literature has shown varying results with regard to its success. There has been no systematic review and meta-analysis to date assessing outcomes following this treatment. OBJECTIVES: Despite multiple studies showing the potential benefits of PTENS in NE, there has been no consensus regarding its efficacy. The aim of this study was to systematically analyze the effects of PTENS on children with NE. STUDY DESIGN: In September 2021, a search of PubMed, Embase and the Cochrane Library was carried out for studies relating to outcomes following PTENS in children with NE. Studies included were original publication English language randomized controlled trial (RCT's) with at least ten children receiving parasacral transcutaneous electrical nerve stimulation (PTENS). After assessing for relevant studies, data were collated and analyzed from the included studies. Risk of bias was assessed using the Cochrane seven domain assessment. Our primary outcome was response and nonresponse to treatment. These results were combined in a fixed effects meta-analysis model to obtain an overall estimate of the success rate. Information regarding demographics was also collected. There was no external funding for this review. RESULTS: Of 145 studies found initially, four RCT's (208 children) were included. The weighted mean rate of full response to active PTENS was 10.8% (0%-19%). All studies considered, meta-analysis showed no difference between PTENS and controls (RR: 0.70, 95% confidence interval [CI: 0.37-1.32]). Subgroup analysis of monosymptomatic enuresis showed no effect of PTENS compared to controls (RR = 0.58, 95% CI: [0.24-1.42]). When grouped, studies comparing PTENS to sham/behavioral treatment showed no benefit compared to controls (RR = 0.81, 95% CI: [0.05-12.53]) and those comparing PTENS to biofeedback/interferential current (IFC) showed no difference to controls (RR = 0.69, 95% CI: [0.36-1.33]). There was no evidence of a difference between cases and controls between these latter subgroups (RR = 0.70, 95% CI: [0.37-1.32]). DISCUSSION/CONCLUSION: Our results suggest that PTENS has no clear benefit in the management of children with NE compared to controls. Subgroup analysis showed that its use in monosymptomatic NE has no clear advantage. However, this review has highlighted the need for further high quality studies. Limitations to this review included a relatively small sample size and the use of prior or concomitant therapies.

Incidence of Low-Grade Testicular Injury in Orchidectomy Specimens Post-testicular Torsion.

INTRODUCTION: Following detorsion and orchidopexy for testicular torsion, predominantly animal studies have reported a risk of autoimmune and reperfusion injury to the contralateral testis. As a result, when testicular viability is compromised, orchidectomy is readily performed. This practice increases the likelihood of testes with potentially reversible injury being excised. We aim to determine the incidence of such occurrences and review the available evidence for and against early orchidectomy when testicular viability is doubtful. MATERIALS AND METHODS: Data for a 15-year period from two pediatric institutions on testicular torsion in children younger than 16 years were reviewed. Using a previously published grading system, the orchidectomy specimens in this cohort with early low-grade injury were analyzed. Low-grade injury suggests the possibility of restitutio ad integrum implying restoration of exocrine and endocrine function of the affected testes. RESULTS: Between both institutions, 222 scrotal explorations were performed for testicular torsion; 20 neonatal and 202 outside the neonatal period (age range [median]: 1-28 days [3 days] and 3 months-16 years [13 years], respectively). Of these scrotal explorations, 17 neonatal and 66 nonneonatal orchidectomies were required (85 vs. 33%, respectively; p < 0.0001). From these orchidectomy specimens, 5 (6%) were found to have low-grade injury. The ages of these five children ranged from 9 to 16 years (median 15, mean 13.6 years). Their symptom duration ranged from 8 to 37 hours (median 14, mean 18 hours) and two of these children had a preoperative ultrasound documenting no flow to the testis. CONCLUSION: The finding of histopathological features that may represent salvageability of a torted testis occurs relatively rarely. Because of this possibility, appropriate intraoperative steps to check for reperfusion must be undertaken prior to orchidectomy. More evidence for the use of antioxidants and tunica albuginea decompression to improve testes salvage rates is required. The potential for exocrine and endocrine function if partial testicular atrophy occurs and the evidence for contralateral autoimmune testicular damage in pre- and postpubertal males require further investigation.

Effect of abnormal notochord delamination on hindgut development in the Adriamycin mouse model.

BACKGROUND: Adriamycin mouse model (AMM) is a model of VACTERL anomalies. Sonic hedgehog (Shh) pathway, sourced by the notochord, is implicated of anorectal malformations. We hypothesized hindgut anomalies observed in the AMM are the result of abnormal effect of the notochord. METHODS: Time-mated CBA/Ca mice received two intraperitoneal injections of Adriamycin (6 mg/kg) or saline as control on embryonic day (E) 7 and 8. Fetuses were harvested from E9 to E11, stained following whole mount in situ hybridization with labeled RNA probes to detect Shh and Fork head box F1(Foxf1) transcripts. Immunolocalization with endoderm marker Hnf3ß was used to visualize morphology. Embryos were scanned by OPT to obtain 3D representations of expressions. RESULTS: In AMM, the notochord was abnormally displaced ventrally with attachment to the hindgut endoderm in 71 % of the specimens. In 32 % of the treated embryos abnormal hindgut ended blindly in a cystic structure, and both of types were remarked in 29 % of treated embryos. Endodermal Shh and mesenchymal Foxf1 genes expression were preserved around the hindgut cystic malformation. CONCLUSIONS: The delamination of the developing notochord in the AMM is disrupted, which may influence signaling mechanisms from the notochord to the hindgut resulting in abnormal patterning of the hindgut.

The effect of adriamycin exposure on the notochord of mouse embryos.

The notochord has important structural and signaling properties during vertebrate development with key roles in patterning surrounding tissues, including the foregut. The adriamycin mouse model is an established model of foregut anomalies where exposure of embryos in utero to the drug adriamycin leads to malformations including oesophageal atresia and tracheoesophageal fistula. In addition to foregut abnormalities, treatment also causes branching, displacement, and hypertrophy of the notochord. Here, we explore the hypothesis that the notochord may be a primary target of disruption leading to abnormal patterning of the foregut by examining notochord position and structure in early embryos following adriamycin exposure. Treated (n = 46) and control (n = 30) embryos were examined during the crucial period when the notochord normally delaminates away from the foregut endoderm (6-28 somite pairs). Transverse sections were derived from the anterior foregut and analyzed by confocal microscopy following immunodetection of extracellular matrix markers E-cadherin and Laminin. In adriamycin-treated embryos across all stages, the notochord was abnormally displaced ventrally with prolonged attachment to the foregut endoderm. While E-cadherin was normally detected in the foregut endoderm with no expression in the notochord of control embryos, treated embryos up to 24 somites showed ectopic notochordal expression indicating a change in characteristics of the tissue; specifically an increase in intracellular adhesiveness, which may be instrumental in structural changes, affecting mechanical and signaling properties. This is consistent with disruption of the notochord leading to altered signaling to the foregut causing abnormal patterning and congenital foregut malformations.

Abnormal notochord branching is associated with foregut malformations in the adriamycin treated mouse model.

Oesophageal atresia (OA) and tracheooesophageal fistula (TOF) are relatively common human congenital malformations of the foregut where the oesophagus does not connect with the stomach and there is an abnormal connection between the stomach and the respiratory tract. They require immediate corrective surgery and have an impact on the future health of the individual. These abnormalities are mimicked by exposure of rat and mouse embryos in utero to the drug adriamycin. The causes of OA/TOF during human development are not known, however a number of mouse mutants where different signalling pathways are directly affected, show similar abnormalities, implicating multiple and complex signalling mechanisms. The similarities in developmental outcome seen in human infants and in the adriamycin treated mouse model underline the potential of this model to unravel the early embryological events and further our understanding of the processes disturbed, leading to such abnormalities. Here we report a systematic study of the foregut and adjacent tissues in embryos treated with adriamycin at E7 and E8 and analysed between E9 and E12, comparing morphology in 3D in 149 specimens. We describe a spectrum of 8 defects, the most common of which is ventral displacement and branching of the notochord (in 94% of embryos at E10) and a close spatial correspondence between the site of notochord branching and defects of the foregut. In addition gene expression analysis shows altered dorso-ventral foregut patterning in the vicinity of notochord branches. This study shows a number of features of the adriamycin mouse model not previously reported, implicates the notochord as a primary site of disturbance in such abnormalities and underlines the importance of the model to further address the mechanistic basis of foregut congenital abnormalities.

Mesenchymal expression of Tbx4 gene is not altered in Adriamycin mouse model.

PURPOSE: The Adriamycin mouse model (AMM) is a reproducible teratogenic model of esophageal atresia/tracheo-esophageal fistula (EA/TEF). Tbx4 is a member of the T-box family of transcription factor genes, which is reported to play a key role in separation of the respiratory tract and the esophagus. Up-regulation of Tbx4 is reported to cause TEF in the chick. Optical projection tomography (OPT) is a technique that allows three-dimensional (3D) imaging of gene expression in small tissue specimens in an anatomical context. The aim of this study was to investigate the temporo-spatial expression of Tbx4 during the critical period of separation of the trachea and esophagus in normal and Adriamycin treated embryos using OPT. MATERIALS AND METHODS: Time-mated CBA/Ca mice received intraperitoneal injections of Adriamycin (6 mg/kg) or saline on days 7 and 8 of gestation. Embryos were harvested on days 9-12, stained following whole mount in situ hybridization with labeled RNA probes to detect Tbx4 transcripts (n = 5 for each treatment/day of gestation). Immunolocalization with the endoderm marker Hnf3beta was used to visualize morphology. Embryos were scanned by OPT to obtain 3D representations of gene expression domains. Animal licence no. B100/4106. RESULTS: OPT elegantly revealed Tbx4 gene expression in both controls and in the disorganized pulmonary mesenchyme in the treated embryos. Although characteristic morphological abnormalities were observed in Adriamycin treated embryos, there was no significant difference in Tbx4 transcript distribution around lung primordia in comparison with control embryos. CONCLUSION: Although previously reported morphological abnormalities of notochord and esophagus were observed in AMM, Tbx4 gene expression was unaltered, suggesting that esophageal anomalies can occur in the presence of normal Tbx4 gene expression in this model.

Fgf10 gene expression is delayed in the embryonic lung mesenchyme in the adriamycin mouse model.

BACKGROUND: The adriamycin mouse model is a well-established teratogenic model of esophageal atresia/tracheoesophageal fistula. Fibroblast growth factor 10 (Fgf10) plays a key role in branching of the lung buds during lung morphogenesis. Fgf10 knockout mice exhibit the absence of the lungs. Optical projection tomography (OPT) is a technique that allows three-dimensional (3D) imaging of gene expression in small tissue specimens in an anatomical context. The aim of this study was to investigate the temporo-spatial expression of Fgf10 during the critical period of separation of the trachea and esophagus in normal and adriamycin-treated embryos using OPT. METHODS: Time-mated CBA/Ca mice received intraperitoneal injections of adriamycin (6 mg/kg) or saline on days 7 and 8 of gestation. Embryos were harvested on days 10-13, stained after whole mount in situ hybridization with labeled RNA probes to detect Fgf10 transcripts (n = 5 for each treatment/day of gestation). Immunolocalization with endoderm marker Hnf3 beta was used to visualize morphology. Embryos were scanned by OPT to obtain 3D representations of gene expression domains. RESULTS: Computer reconstructed specimens allowed precise staging of developing embryos according to Theiler Staging (TS) criteria. OPT elegantly displayed Fgf10 gene expression in the pulmonary mesenchyme around the tip of the lung buds in both controls and treated embryos in the same spatial territory. Fgf10 gene expression was first detected in the control embryos at TS17. However, Fgf10 gene expression in adriamycin-treated embryos was first only observed at TS18 in 67% of the specimens. CONCLUSION: Delayed Fgf10 gene expression during the critical period of separation of the trachea and esophagus may affect lung bud formation in the adriamycin model leading to tracheoesophageal malformations.

Upregulation of Slit-2 and Slit-3 gene expressions in the nitrofen-induced hypoplastic lung.

PURPOSE: The pathogenesis of pulmonary hypoplasia in the nitrofen-induced congenital diaphragmatic hernia (CDH) is not clearly understood. Slit-2 and Slit-3 are expressed in fetal lung and play a key role in directing the functional organization and differentiation of lung mesenchyme during branching morphogenesis. We hypothesized that the pulmonary gene expression levels of Slit genes are altered in the nitrofen-induced CDH. MATERIALS AND METHODS: Pregnant rats were exposed to either olive oil or nitrofen on day 9 of gestation (D9). Fetal lungs were harvested on D15 and D21 and divided into 2 groups as follows: CDH (n = 9 at each time-point) and control (n = 9 at each time-point). The pulmonary gene expression levels of Slit-2, Slit-3, Robo1, and Robo2 were analyzed by real time reverse transcription polymerase chain reaction. Student's t test or Mann-Whitney U test was used for statistical analysis. RESULTS: Relative messenger RNA expression levels of Slit-2 and Slit-3 were significantly increased in CDH lungs compared to control at both D15 and D21 (P < .05). However, there were no significant differences between CDH and controls in the pulmonary gene expression levels of Robo1 and Robo2 at each time-point. CONCLUSION: Our results provide evidence, for the first time, that Slit genes are upregulated in nitrofen-induced hypoplastic lungs in both early and late stages of lung development. Altered pulmonary Slit gene expression may disrupt branching lung morphogenesis resulting in pulmonary hypoplasia.

Sonic hedgehog gene expression in nitrofen induced hypoplastic lungs in mice.

BACKGROUND: The pathogenesis of congenital diaphragmatic hernia (CDH) is unknown. The sonic hedgehog (Shh) cascade is crucial for the patterning of the early respiratory system in mice. Optical Projection Tomography (OPT) is a new tool for 3D imaging small biological specimens that enables us to visualise both the anatomy of developing organs and gene expression localised in the context of normal or abnormal anatomy. We visualised Shh gene expression patterns in the nitrofen treated and control mouse lung buds at early stages of lung development. MATERIALS AND METHODS: Time-mated CD1 female mice (n = 5) received oral administration of 100 mg of the herbicide 2,4-dichlorophenyl-p-nitrophenylether (nitrofen) (WAKO Chemical, Osaka, Japan) in 1 ml of olive oil or olive oil alone at 7 days of gestation. Embryos were harvested on gestation days 9-12, and stained following whole mount in situ hybridisation with labelled RNA probes to detect Shh transcripts at each stage. Embryos were scanned by OPT to obtain 3D representations of gene expression domains in the context of the changing morphology of the embryo. RESULTS: OPT analysis of Shh transcript distribution clearly revealed gene expression in both groups. In treated embryos, there were no significant changes in Shh transcript distribution in lung buds in comparison with control embryos. CONCLUSION: Although altered Shh expression in the hypoplastic lung has been reported in late gestation, the present study did not reveal any significant alterations in pulmonary Shh spatial transcript distribution or gene expression level during the early gestation in nitrofen CDH model. It would be of great interest in future studies to use OPT approach to investigate pulmonary expression of Shh and other regulatory genes both during early and late stages of lung development in order to provide new insights into the pathogenesis of pulmonary hypoplasia.