There is a huge demand on bioinformaticians to provide their biologists with user friendly and scalable software infrastructures to capture, exchange, and exploit the unprecedented amounts of new ...*omics data. We here present MOLGENIS, a generic, open source, software toolkit to quickly produce the bespoke MOLecular GENetics Information Systems needed.
The MOLGENIS toolkit provides bioinformaticians with a simple language to model biological data structures and user interfaces. At the push of a button, MOLGENIS' generator suite automatically translates these models into a feature-rich, ready-to-use web application including database, user interfaces, exchange formats, and scriptable interfaces. Each generator is a template of SQL, JAVA, R, or HTML code that would require much effort to write by hand. This 'model-driven' method ensures reuse of best practices and improves quality because the modeling language and generators are shared between all MOLGENIS applications, so that errors are found quickly and improvements are shared easily by a re-generation. A plug-in mechanism ensures that both the generator suite and generated product can be customized just as much as hand-written software.
In recent years we have successfully evaluated the MOLGENIS toolkit for the rapid prototyping of many types of biomedical applications, including next-generation sequencing, GWAS, QTL, proteomics and biobanking. Writing 500 lines of model XML typically replaces 15,000 lines of hand-written programming code, which allows for quick adaptation if the information system is not yet to the biologist's satisfaction. Each application generated with MOLGENIS comes with an optimized database back-end, user interfaces for biologists to manage and exploit their data, programming interfaces for bioinformaticians to script analysis tools in R, Java, SOAP, REST/JSON and RDF, a tab-delimited file format to ease upload and exchange of data, and detailed technical documentation. Existing databases can be quickly enhanced with MOLGENIS generated interfaces using the 'ExtractModel' procedure.
The MOLGENIS toolkit provides bioinformaticians with a simple model to quickly generate flexible web platforms for all possible genomic, molecular and phenotypic experiments with a richness of interfaces not provided by other tools. All the software and manuals are available free as LGPLv3 open source at http://www.molgenis.org.
We report a case of a 49-year-old woman with a rare anomaly, intrathoracic renal ectopia. Her medical history includes a surgically corrected congenital diaphragmatic hernia, which can cause late ...presentations of diaphragmatic hernia in adult life. The Tc-MAG3 renogram demonstrated slower emptying of the dilated pelvis of the ectopic kidney than the normal kidney. The curve confirmed a delayed Tmax, followed by a distinct decline. These features are not indicative of a complete obstruction, but can result from partial obstruction, renal dysfunction with poor response to diuresis, pelvic dilatation (such as in our patient), or a combination.
Management of data to produce scientific knowledge is a key challenge for biological research in the 21st century. Emerging high-throughput technologies allow life science researchers to produce big ...data at speeds and in amounts that were unthinkable just a few years ago. This places high demands on all aspects of the workflow: from data capture (including the experimental constraints of the experiment), analysis and preservation, to peer-reviewed publication of results. Failure to recognise the issues at each level can lead to serious conflicts and mistakes; research may then be compromised as a result of the publication of non-coherent protocols, or the misinterpretation of published data. In this report, we present the results from a workshop that was organised to create an ontological data-modelling framework for Laboratory Protocol Standards for the Molecular Methods Database (MolMeth). The workshop provided a set of short- and long-term goals for the MolMeth database, the most important being the decision to use the established EXACT description of biomedical ontologies as a starting point.
There is a discrepancy between successful recanalization and good clinical outcome after endovascular treatment (EVT) in acute ischemic stroke patients. During removal of a thrombus, a shower of ...microemboli may release and lodge to the distal circulation. The objective of this study was to determine the extent of damage on brain tissue caused by microemboli. In a rat model of microembolization, a mixture of microsphere (MS) sizes (15, 25 and 50 µm diameter) was injected via the left internal carotid artery. A 3D image of the left hemisphere was reconstructed and a point-pattern spatial analysis was applied based on G- and K-functions to unravel the spatial correlation between MS and the induced hypoxia or infarction. We show a spatial correlation between MS and hypoxia or infarction spreading up to a distance of 1000–1500 µm. These results imply that microemboli, which individually may not always be harmful, can interact and result in local areas of hypoxia or even infarction when lodged in large numbers.
Transitioning from the current linear economic development model to a circular economy (CE) is a hot topic in academic literature, public governance, and the corporate domain. Actors have implemented ...CE strategies to reduce their resource use and its associated impacts, while boosting economic competitiveness and generating positive social impact. Companies are identified as key actors in transitioning to a CE, and many academics have proposed tools to assess CE and guide them in this process. This paper critically reviews such academic ‘assessment approaches’ at the micro level in order to reflect on their key properties. Seventy-four approaches are inventoried through a systematic literature review of academic literature. A critical review framework is constructed and applied, containing four perspectives: A general perspective, a descriptive perspective (methodological aspects), a normative perspective (connections to Sustainable Development), and a prescriptive perspective (implementation-focused). Methodologically, the 74 approaches are highly diverse, having various connections to previously established methodologies. Eighteen of the reviewed assessment approaches include all three dimensions of Sustainable Development (SD), in addition to a ‘circular’ dimension. Roughly one quarter of the approaches apply a participatory design approach. Suggested key desired properties of CE assessment approaches include making use of existing assessment methodologies such as Life Cycle Assessment (LCA), and a closer collaboration between science and practitioners to consider end-user needs in the design of CE assessment approaches.
Patients with aneurysmal subarachnoid hemorrhage (SAH) who experience delayed cerebral ischemia (DCI) have an increased risk of poor outcome. Delayed cerebral ischemia is considered to be caused by ...vasospasm. However, not all patients with DCI have vasospasm. Inversely, not all patients with vasospasm develop clinical symptoms and signs of DCI. In the past, treatments aiming at vasospasm were not successful in preventing ischemia. The purpose of this review is to give an overview of clinical data showing that DCI cannot always be attributed to vasospasm, and to present an in-depth analysis of clinical and autopsy studies on the role of microthrombosis in the pathogenesis of DCI. Clinical studies show that DCI is associated with an activation of the coagulation cascade within a few days after SAH, preceding the time window during which vasospasm occurs. Furthermore, impaired fibrinolytic activity, and inflammatory and endothelium-related processes, lead to the formation of microthrombi, which ultimately result in DCI. The presence of microthrombi is confirmed by autopsy studies. Insight in the pathophysiology of DCI is crucial for the development of effective therapies against this complication. Because multiple pathways are involved, future research should focus on drugs with pleiotropic effects.
Firm‐level adoption of circular business models is a crucial part of the transition toward circular economy, but companies that delve into such pursuits often encounter a series of barriers that ...hamper their success. Although multiple studies on barriers to circular economy have been made, there is a lack of understanding of how barriers are formed under firm‐specific characteristics such as sectoral conditions and the type of circular business model adopted. To bridge this gap, we illustrate a barrier framework in a multiple‐case study including nine Swedish firms. We derived about 28 barriers within five categories of circularity approaches (design, waste, service, platform, and nature) across three sectors (furniture, electronics, and garment). This research contributes to the circular economy literature by revealing how adhering to certain sectors and circular business approaches significantly changes the way barriers are perceived by firms. The outcomes may support both practitioners and policymakers as they facilitate circular economy transitions.
Background:
Ankle sprains are a common injury in collegiate sports. Few studies have examined the epidemiology of individual ligament injuries, specifically the lateral ligament complex (LLC) of the ...ankle.
Purpose:
To describe the epidemiology, including the estimated yearly national incidence, of LLC sprains among National Collegiate Athletic Association (NCAA) athletes.
Study Design:
Descriptive epidemiology study.
Methods:
Injury surveillance data for 25 sports from the NCAA Injury Surveillance Program (NCAA-ISP) for the academic years 2009-2010 to 2014-2015 were used for analysis. All injuries included for analysis had a diagnosis of an LLC sprain. LLC sprain rates and rate ratios (RRs) with 95% CIs were calculated. From the sample, national estimates of the annual incidence of LLC sprains across the entire student-athlete body from these 25 sports were also calculated.
Results:
During the 2009-2010 to 2014-2015 academic years, 2429 LLC sprains were reported, for a rate of 4.95 per 10,000 athlete-exposures (AEs). LLC sprains comprised 7.3% of all reported collegiate sports injuries in the NCAA-ISP. Also, an estimated 16,022 LLC sprains occurred annually among the 25 sports. The sports with the highest LLC sprain rates were men’s basketball (11.96/10,000 AEs) and women’s basketball (9.50/10,000 AEs). Most LLC sprains occurred during practices (57.3%); however, the LLC sprain rate was higher in competitions than in practices (RR, 3.29; 95% CI, 3.03-3.56). Also, 11.9% of LLC sprains were identified as recurrent injuries, with the largest proportions of recurrent LLC sprains being found within women’s basketball (21.1%), women’s outdoor track (21.1%), women’s field hockey (20.0%), and men’s basketball (19.1%). In 44.4% of LLC sprains, the athlete returned to play in less than 24 hours; in 3.6%, the athlete required more than 21 days before returning to play (including those who did not return to play at all).
Conclusion:
LLC sprains were the most commonly reported injury diagnosis among United States collegiate student-athletes. Continued examination of interventions that aim to reduce the incidence, severity, and recurrence of LLC sprains, specifically in women, is warranted.
To estimate knee osteoarthritis (OA) risk following anterior cruciate ligament (ACL), meniscus or combined ACL and meniscus injury.
Systematic review and meta-analysis.
MEDLINE, Embase, SPORTDiscus, ...CINAHL and Web of Science until November 2018.
Prospective or retrospective studies with at least 2-year follow-up including adults with ACL injury, meniscal injury or combined injuries. Knee OA was defined by radiographs or clinical diagnosis and compared with the contralateral knee or non-injured controls.
Risk of bias was assessed using the SIGN50 checklist. ORs for developing knee OA were estimated using random effects meta-analysis.
53 studies totalling ∼1 million participants were included: 185 219 participants with ACL injury, mean age 28 years, 35% females, 98% surgically reconstructed; 83 267 participants with meniscal injury, mean age 38 years, 36% females, 22% confirmed meniscectomy and 73% unknown; 725 362 participants with combined injury, mean age 31 years, 26% females, 80% treated surgically. The OR of developing knee OA were 4.2 (95% CI 2.2 to 8.0; I
=92%), 6.3 (95% CI 3.8 to 10.5; I
=95%) and 6.4 (95% CI 4.9 to 8.3; I
=62%) for patients with ACL injury, meniscal injury and combined injuries, respectively.
The odds of developing knee OA following ACL injury are approximately four times higher compared with a non-injured knee. A meniscal injury and a combined injury affecting both the ACL and meniscus are associated with six times higher odds compared with a non-injured knee. Large inconsistency (eg, study design, follow-up period and comparator) and few high-quality studies suggest that future studies may change these estimates.
Patients sustaining a major knee injury have a substantially increased risk of developing knee OA, highlighting the importance of knee injury prevention programmes and secondary prevention strategies to prevent or delay knee OA development.PROSPERO registration number CRD42015016900.
An emerging research area is dedicated to developing approaches for assessing the ‘circularity’ of companies and their products, within the context of sustainability goals. However, empirical ...evidence on the uptake of these assessment approaches remains scarce. Using a purposive sampling, we conducted a survey receiving 155 responses and held 43 semi‐structured interviews with Dutch and Italian companies active in circular economy (CE), pursuing three research aims: to explore the use of CE and sustainability assessment approaches; to study the process of developing assessment approaches; and to uncover benefits of—and barriers to—CE assessment. While we find high variability of assessment approaches, most often, companies develop tailor‐made sustainability indicators and apply life cycle assessments to CE strategies. Importantly, assessment development for CE practices requires and facilitates collaboration with external stakeholders. Finally, we reflect on the paradox of standardisation versus tailoring of assessment approaches within the CE reality and recommend establishing company needs and capabilities before designing assessment approaches.
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