Enhancing the FAIRness of Arctic Research Data Through Semantic Annotation

The National Science Foundation’s Arctic Data Center is the primary data repository for NSF-funded research conducted in the Arctic. There are major challenges in discovering and interpreting resources in a repository containing data as heterogeneous and interdisciplinary as those in the Arctic Data Center. This paper reports on advances in cyberinfrastructure at the Arctic Data Center that help address these issues by leveraging semantic technologies that enhance the repository’s adherence to the FAIR data principles and improve the Findability, Accessibility, Interoperability, and Reusability of digital resources in the repository. We describe the Arctic Data Center’s improvements. We use semantic annotation to bind metadata about Arctic data sets with concepts in web-accessible ontologies. The Arctic Data Center’s implementation of a semantic annotation mechanism is accompanied by the development of an extended search interface that increases the findability of data by allowing users to search for specific, broader, and narrower meanings of measurement descriptions, as well as through their potential synonyms. Based on research carried out by the DataONE project, we evaluated the potential impact of this approach, regarding the accessibility, interoperability, and reusability of measurement data. Arctic research often benefits from having additional data, typically from multiple, heterogeneous sources, that complement and extend the bases – spatially, temporally, or thematically – for understanding Arctic phenomena. These relevant data resources must be ‘found’, and ‘harmonized’ prior to integration and analysis. The findings of a case study indicated that the semantic annotation of measurement data enhances the capabilities of researchers to accomplish these tasks

The commonness of rarity: Global and future distribution of rarity across land plants

A key feature of life’s diversity is that some species are common but many more are rare. Nonetheless, at global scales, we do not know what fraction of biodiversity consists of rare species. Here, we present the largest compilation of global plant diversity to quantify the fraction of Earth’s plant biodiversity that are rare. A large fraction, ~36.5% of Earth’s ~435,000 plant species, are exceedingly rare. Sampling biases and prominent models, such as neutral theory and the k-niche model, cannot account for the observed prevalence of rarity. Our results indicate that (i) climatically more stable regions have harbored rare species and hence a large fraction of Earth’s plant species via reduced extinction risk but that (ii) climate change and human land use are now disproportionately impacting rare species. Estimates of global species abundance distributions have important implications for risk assessments and conservation planning in this era of rapid global change

Modified triangular posterior osteosynthesis of unstable sacrum fracture.

We report preliminary results for unstable sacral fractures treated with a modified posterior triangular osteosynthesis. Seven patients were admitted to our trauma center with an unstable sacral fracture. The average age was 31 years (22-41). There were four vertical shear lesions of the pelvis and three transverse fracture of the upper sacrum. The vertical shear injuries were initially treated with an anterior external fixator inserted at the time of admission. Definitive surgery was performed at a mean time of 9 days after trauma. The operation consisted in a posterior fixation combining a vertebropelvic distraction osteosynthesis with pedicle screws and a rod system, whereby the transverse fixation was obtained using a 6 mm rod as a cross-link between the two main rods. Late displacement of the posterior pelvis or fracture was measured on X-ray films according to the criteria of Henderson. The patients were followed-up for a minimum time of 12 months. Four patients who presented with a pre-operative perineal neurological impairment made a complete recovery. No iatrogenic nerve injury was reported. One case of deep infection was managed successfully with surgical debridement and local antibiotics. All patients complained of symptoms related to the prominence of the iliac screws. The metalwork was removed in all cases after healing of the fracture, at a mean time of 4.3 months after surgery. No loss of reduction of fracture was seen at final radiological follow-up. The preliminary results are promising. The fixation is sufficiently stable to allow an immediate progressive weight-bearing, and safe nursing care in polytrauma cases. The only problem seems to be related to prominent heads of the distal screws

2D-fluoroscopic navigated percutaneous screw fixation of pelvic ring injuries - a case series

<p>Abstract</p> <p>Background</p> <p>Screw fixation of pelvic ring fractures is a common, but demanding procedure and navigation techniques were introduced to increase the precision of screw placement. The purpose of this case series was the evaluation of screw misplacement rate and functional outcome of percutaneous screw fixation of pelvic ring disruptions using a 2D navigation system.</p> <p>Methods</p> <p>Between August 2004 and December 2007, 44 of 442 patients with pelvic injuries were included for closed reduction and percutaneous screw fixation of disrupted pelvic ring lesions using an optoelectronic 2D-fluoroscopic based navigation system. Operating and fluoroscopy time were measured, as well as peri- and postoperative complications documented. Screw position was assessed by postoperative CT scans. Quality of live was evaluated by SF 36-questionnaire in 40 of 44 patients at mean follow up 15.5 ± 1.2 month.</p> <p>Results</p> <p>56 iliosacral- and 29 ramus pubic-screws were inserted (mean operation time per screw 62 ± 4 minutes, mean fluoroscopy time per screw 123 ± 12 seconds). In post-operative CT-scans the screw position was assessed and graded as follows: I. secure positioning, completely in the cancellous bone (80%); II. secure positioning, but contacting cortical bone structures (14%); III. malplaced positioning, penetrating the cortical bone (6%). The malplacements predominantly occurred in bilateral overlapping screw fixation. No wound infection or iatrogenic neurovascular damage were observed. Four re-operations were performed, two of them due to implant-misplacement and two of them due to implant-failure.</p> <p>Conclusion</p> <p>2D-fluoroscopic navigation is a safe tool providing high accuracy of percutaneous screw placement for pelvic ring fractures, but in cases of a bilateral iliosacral screw fixation an increased risk for screw misplacement was observed. If additional ramus pubic screw fixations are performed, the retrograde inserted screws have to pass the iliopubic eminence to prevent an axial screw loosening.</p

The Tao of open science for ecology

The field of ecology is poised to take advantage of emerging technologies that facilitate the gathering, analyzing, and sharing of data, methods, and results. The concept of transparency at all stages of the research process, coupled with free and open access to data, code, and papers, constitutes “open science.” Despite the many benefits of an open approach to science, a number of barriers to entry exist that may prevent researchers from embracing openness in their own work. Here we describe several key shifts in mindset that underpin the transition to more open science. These shifts in mindset include thinking about data stewardship rather than data ownership, embracing transparency throughout the data life‐cycle and project duration, and accepting critique in public. Though foreign and perhaps frightening at first, these changes in thinking stand to benefit the field of ecology by fostering collegiality and broadening access to data and findings. We present an overview of tools and best practices that can enable these shifts in mindset at each stage of the research process, including tools to support data management planning and reproducible analyses, strategies for soliciting constructive feedback throughout the research process, and methods of broadening access to final research products

Habitat area and climate stability determine geographical variation in plant species range sizes

Despite being a fundamental aspect of biodiversity, little is known about what controls species range sizes. This is especially the case for hyperdiverse organisms such as plants. We use the largest botanical data set assembled to date to quantify geographical variation in range size for ∼ 85 000 plant species across the New World. We assess prominent hypothesised range-size controls, finding that plant range sizes are codetermined by habitat area and long- and short-term climate stability. Strong short- and long-term climate instability in large parts of North America, including past glaciations, are associated with broad-ranged species. In contrast, small habitat areas and a stable climate characterise areas with high concentrations of small-ranged species in the Andes, Central America and the Brazilian Atlantic Rainforest region. The joint roles of area and climate stability strengthen concerns over the potential effects of future climate change and habitat loss on biodiversity

Early Weight Bearing of Calcaneal Fractures Treated by Intraoperative 3D-Fluoroscopy and Locked-Screw Plate Fixation

Operative therapy of intraarticular fractures of the calcaneus is an established surgical standard. The aim is an accurate reduction of the fracture with reconstruction of Boehler’s angle, length, axis and subtalar joint surface. Intraoperative 3D-fluoroscopy with the Siremobil Iso-C 3D® mobile C-arm system is a valuable assistant for accurate reconstruction of these anatomical structures. Remaining incongruities can be recognized and corrected intraoperatively. The achieved reduction can be fixed by the advantages of an internal fixator (locked-screw plate interface). In the period of October 2002 until April 2007 we operated 136 patients with intraarticular fractures of the calcaneus by means of anatomical reduction, and internal plate fixator under intraoperative control of 3D-fluoroscopy. All patients were supplied with an orthesis after the operation which allowed weight bearing of 10 kg for 12 weeks for the patients operated between October 2002 and October 2004 (Group A). Transient local osteoporosis was observed in all X-Rays at follow-up after an average of 8,6 months. Therefore we changed our postoperative treatment plan for the patients operated between November 2004 and April 2007 (Group B). Weight bearing started with 20 KG after 6 weeks, was increased to 40 KG after 8 weeks and full weight bearing was allowed after 10 weeks for these patients. In no case a secondary dislocation of the fracture was seen. No bone graft was used. At follow up the average American Foot and Ankle Society Score (AOFAS) were 81 for Group_A, compared to 84 for Group B, treated with earlier weight bearing. Autologous bone graft was not necessary even if weight bearing was started after a period of six weeks postoperatively. The combination of 3D-fluoroscopy with locked internal fixation showed promising results. If the rate of patients developing subtalar arthrosis will decrease by this management will have to be shown in long term follow up

Semantics in Support of Biodiversity Knowledge Discovery: An Introduction to the Biological Collections Ontology and Related Ontologies

The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers