Experiences with workflows for automating data-intensive bioinformatics

High-throughput technologies, such as next-generation sequencing, have turned molecular biology into a data-intensive discipline, requiring bioinformaticians to use high-performance computing resources and carry out data management and analysis tasks on large scale. Workflow systems can be useful to simplify construction of analysis pipelines that automate tasks, support reproducibility and provide measures for fault-tolerance. However, workflow systems can incur significant development and administration overhead so bioinformatics pipelines are often still built without them. We present the experiences with workflows and workflow systems within the bioinformatics community participating in a series of hackathons and workshops of the EU COST action SeqAhead. The organizations are working on similar problems, but we have addressed them with different strategies and solutions. This fragmentation of efforts is inefficient and leads to redundant and incompatible solutions. Based on our experiences we define a set of recommendations for future systems to enable efficient yet simple bioinformatics workflow construction and execution.Pubblicat

Modeling the response of the induced magnetosphere of Venus to changing IMF direction using MESSENGER and Venus Express observations

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/95427/1/grl25556.pd

Transforming scholarship in the archives through handwritten text recognition:Transkribus as a case study

Purpose: An overview of the current use of handwritten text recognition (HTR) on archival manuscript material, as provided by the EU H2020 funded Transkribus platform. It explains HTR, demonstrates Transkribus, gives examples of use cases, highlights the affect HTR may have on scholarship, and evidences this turning point of the advanced use of digitised heritage content. The paper aims to discuss these issues. - Design/methodology/approach: This paper adopts a case study approach, using the development and delivery of the one openly available HTR platform for manuscript material. - Findings: Transkribus has demonstrated that HTR is now a useable technology that can be employed in conjunction with mass digitisation to generate accurate transcripts of archival material. Use cases are demonstrated, and a cooperative model is suggested as a way to ensure sustainability and scaling of the platform. However, funding and resourcing issues are identified. - Research limitations/implications: The paper presents results from projects: further user studies could be undertaken involving interviews, surveys, etc. - Practical implications: Only HTR provided via Transkribus is covered: however, this is the only publicly available platform for HTR on individual collections of historical documents at time of writing and it represents the current state-of-the-art in this field. - Social implications: The increased access to information contained within historical texts has the potential to be transformational for both institutions and individuals. - Originality/value: This is the first published overview of how HTR is used by a wide archival studies community, reporting and showcasing current application of handwriting technology in the cultural heritage sector

Bilateral Synovitis in symptomatic unilateral transient synovitis of the hip: an ultrasonographic study in 56 children

56 children with a clinical diagnosis of unilateral transient synovitis of the hip underwent bilateral sonographic assessment. On the anterior scan, the distance between the femoral neck and the fibrous joint capsule was measured. This distance, which we call the synovial capsular complex distance, was compared with age-dependent normal values. An in-creased distance was found in all 56 symptomatic hips (mean 10 mm, SD 1.8). This distance was also increased in 14 hips on the contralateral side (mean 8 mm, SD 1.6). An effusion was demonstrated in 53 symptomatic hips and in 8 hips on the contralateral side. These findings indicate that in one quarter of children with symptoms of unilateral transient synovitis the contralateral hip may have an increased synovial capsular complex distance due to synovial swelling or joint effusion, suggesting an asymptomatic synovitis. We therefore recommend a comparison of the synovial capsular complex distance on the symptomatic side with age-related normal values, in addition to a comparison with the asymptomatic hip.Stefan Ehrendorfer, Garry Lequesne, Mario Penta, Paul Smith and Peter Cund

Intrahost Monkeypox Virus Genome Variation in Patient with Early Infection, Finland, 2022

Monkeypox virus was imported into Finland during late May–early June 2022. Intrahost viral genome variation in a sample from 1 patient comprised a major variant with 3 lineage B.1.3–specific mutations and a minor variant with ancestral B.1 nucleotides. Results suggest either ongoing APOBEC3 enzyme–mediated evolution or co-infection.Peer reviewe

Severe signs of hyponatremia secondary to desmopressin treatment for enuresis: a systematic review

OBJECTIVE: Dilutional hyponatremia is a serious adverse effect of desmopressin, a vasopressin analog that is widely prescribed to manage monosymptomatic enuresis. The presentation of hyponatremia, largely related to cerebral dysfunction, can include severe signs like altered mental status and seizures. METHODS: We reviewed the literature dealing with altered mental status or seizures in enuretic subjects on desmopressin. The retained publications included patients who were described individually, revealing data on mode of administration, further identifiable factors predisposing to hyponatremia, presentation and clinical course. RESULTS: We found 54 cases of hyponatremia secondary to desmopressin treatment presenting with altered mental status or seizures. In most cases the complication developed 14 days or less after starting desmopressin. An intranasal formulation had been used in 47 patients. Excess fluid intake was documented as a contributing factor in at least 22 cases. In 6 cases severe signs of hyponatremia developed in the context of intercurrent illnesses. CONCLUSION: Altered mental status or seizures are very rare but recognized complications of desmopressin in enuresis. This complication mostly develops in subjects managed with the intranasal formulation 14 days or less after starting the medication, following excess fluid intake and during intercurrent illnesses

Infant Formula Feeding Increases Hepatic Cholesterol 7α Hydroxylase (CYP7A1) Expression and Fecal Bile Acid Loss in Neonatal Piglets

International audienceBackground: During the postnatal feeding period, formula-fed infants have higher cholesterol synthesis rates and lower circulating cholesterol concentrations than their breastfed counterparts. Although this disparity has been attributed to the uniformly low dietary cholesterol content of typical infant formulas, little is known of the underlying mechanisms associated with this altered cholesterol metabolism phenotype.Objective: We aimed to determine the molecular etiology of diet-associated changes in early-life cholesterol metabolism with the use of a postnatal piglet feeding model.Methods: Two-day-old male and female White-Dutch Landrace piglets were fed either sow milk (Sow group) or dairy-based (Milk group; Similac Advance powder) or soy-based (Soy group; Emfamil Prosobee Lipil powder) infant formulas until day 21. In addition to measuring serum cholesterol concentrations, hepatic and intestinal genes involved in enterohepatic circulation of cholesterol and bile acids were analyzed by real-time reverse-transcriptase polymerase chain reaction and Western blot. Bile acid concentrations were measured by liquid chromatography-mass spectrometry in serum, liver, and feces.Results: Compared with the Sow group, hepatic cholesterol 7a hydroxylase (CYP7A1) protein expression was 3-fold higher in the Milk group (P < 0.05) and expression was 10-fold higher in the Soy group compared with the Milk group (P < 0.05). Likewise, fecal bile acid concentrations were 3-fold higher in the Soy group compared with the Milk group (P < 0.05). Intestinal mRNA expression of fibroblast factor 19 (Fgf19) was reduced in the Milk and Soy groups, corresponding to 54% and 67% decreases compared with the Sow group. In the Soy group, small heterodimer protein (SHP) protein expression was 30% lower compared with the Sow group (P < 0.05).Conclusions: These results indicate that formula feeding leads to increased CYP7A1 protein expression and fecal bile acid loss in neonatal piglets, and this outcome is linked to reduced efficacy in inhibiting CYP7A1 expression through FGF19 and SHP transcriptional repression mechanisms