Search

Abstract To determine the diagnostic yield of cone beam computed tomography (CBCT) compared with 3 T magnetic resonance imaging (MRI) for the evaluation of subchondral insufficiency fractures of the knee. Consecutive patients with subchondral insufficiency fractures of the knee examined by 3 T MRI and CBCT of the femoral condyles were reviewed. Two experienced raters graded the lesion severity on 3 T MRI and CBCT images: grade 1: no signs of a subchondral bone lesion; grade 2: subchondral trabecular fracture or cystic changes, but without infraction of the subchondral bone plate; grade 3: collapse of the subchondral bone plate. Ratings were repeated after six weeks to determine reliability. In addition, the bone lesion size was measured as elliptical area (mm2) and compared between CBCT and T1-weighted MRI sequences. Among 30 patients included (43.3% women; mean age: 60.9 ± 12.8 years; body mass index (BMI) 29.0 ± 12.8 kg/m2), the medial femoral condyle was affected in 21/30 patients (70%). The grading of subchondral lesions between MRI and CBCT did not match in 12 cases (40%). Based on MRI images, an underestimation (i.e., undergrading) compared with CBCT was observed in nine cases (30%), whereas overgrading occurred in three cases (10%). Compared to CBCT, routine T1-weighted 3 T sequences significantly overestimated osseus defect zones in sagittal (84.7 ± 68.9 mm2 vs. 35.9 ± 38.2 mm2, p

Abstract Background The combined injury of the medial collateral ligament complex and the anterior cruciate ligament (ACL) is the most common two ligament injury of the knee. Additional injuries to the medial capsuloligamentous structures are associated with rotational instability and a high failure rate of ACL reconstruction. The study aimed to analyze the specific pattern of medial injuries and their associated risk factors, with the goal of enabling early diagnosis and initiating appropriate therapeutic interventions, if necessary. Results Between January 2017 and December 2018, 151 patients with acute ACL ruptures with a mean age of 32 ± 12 years were included in this study. The MRIs performed during the acute phase were analyzed by four independent investigators—two radiologists and two orthopedic surgeons. The trauma impact on the posterolateral tibial plateau and associated injuries to the medial complex (POL, dMCL, and sMCL) were examined and revealed an injury to the medial collateral ligament complex in 34.4% of the patients. The dMCL was the most frequently injured structure (92.2%). A dMCL injury was significantly associated with an increase in trauma severity at the posterolateral tibial plateau (p

Abstract The information system PANGAEA provides targeted support for research data management as well as long-term data archiving and publication. PANGAEA is operated as an open access library for archiving, publishing, and distributing georeferenced data from earth and environmental sciences. It focuses on observational and experimental data. Citability, comprehensive metadata descriptions, interoperability of data and metadata, a high degree of structural and semantic harmonization of the data inventory as well as the commitment of the hosting institutions ensures the long-term usability of archived data. PANGAEA is a pioneer of FAIR and open data infrastructures to enable data intensive science and an integral component of national and international science and technology activities. This paper provides an overview of the recent organisational, structural, and technological advancements in developing and operating the information system.

Abstract To compare the patient radiation doses during angiographic selective adrenal vein sampling (AVS) before and after an imaging technology upgrade. In this retrospective single-center-study, cumulative air kerma (AK), cumulative dose area product (DAP), fluoroscopy time and contrast agent dosage were recorded from 70 patients during AVS. 35 procedures were performed before and 35 after an imaging processing technology upgrade. Mean values were calculated and compared using an unpaired student’s t-test. DSA image quality was assessed independently by two blinded readers using a four-point Likert scale (1 = poor; 4 = excellent) and compared using Wilcoxon signed-rank test. After the technology upgrade we observed a significant reduction of 35% in AK (1.7 ± 0.7 vs. 1.1 ± 0.7 Gy, p = 0.01) and a significant reduction of 28% in DAP (235.1 ± 113 vs. 170.1 ± 94 Gy*cm2, p = 0.01) in comparison to procedures before the upgrade. There were no significant differences between the number of exposure frames (143 ± 86 vs. 132 ± 61 frames, p = 0.53), fluoroscopy time (42 ± 23 vs. 36 ± 18 min, p = 0.22), or the amount of contrast medium used (179.5 ± 84 vs. 198.1 ± 109 ml, p = 0.41). There was also no significant difference regarding image quality (3 (2–4) vs. 3 (2–4), p = 0.67). The angiographic imaging technology upgrade significantly decreases the radiation dose during adrenal vein sampling without increasing time of fluoroscopy or contrast volume and without compromising image quality.

Rapid changes of the biosphere observed in recent years are caused by both small and large scale drivers, like shifts in temperature, transformations in land-use, or changes in the energy budget of systems. While the latter processes are easily quantifiable, documentation of the loss of biodiversity and community structure is more difficult. Changes in organismal abundance and diversity are barely documented. Censuses of species are usually fragmentary and inferred by often spatially, temporally and ecologically unsatisfactory simple species lists for individual study sites. Thus, detrimental global processes and their drivers often remain unrevealed. A major impediment to monitoring species diversity is the lack of human taxonomic expertise that is implicitly required for large-scale and fine-grained assessments. Another is the large amount of personnel and associated costs needed to cover large scales, or the inaccessibility of remote but nonetheless affected areas.To overcome these limitations we propose a network of Automated Multisensor stations for Monitoring of species Diversity (AMMODs) to pave the way for a new generation of biodiversity assessment centers. This network combines cutting-edge technologies with biodiversity informatics and expert systems that conserve expert knowledge. Each AMMOD station combines autonomous samplers for insects, pollen and spores, audio recorders for vocalizing animals, sensors for volatile organic compounds emitted by plants (pVOCs) and camera traps for mammals and small invertebrates. AMMODs are largely self-containing and have the ability to pre-process data (e.g. for noise filtering) prior to transmission to receiver stations for storage, integration and analyses. Installation on sites that are difficult to access require a sophisticated and challenging system design with optimum balance between power requirements, bandwidth for data transmission, required service, and operation under all environmental conditions for years. An important prerequisite for automated species identification are databases of DNA barcodes, animal sounds, for pVOCs, and images used as training data for automated species identification. AMMOD stations thus become a key component to advance the field of biodiversity monitoring for research and policy by delivering biodiversity data at an unprecedented spatial and temporal resolution.

Abstract Urban soil contamination has become an increasing concern within residential developments and with the expansion of urban agriculture, which has grown across the United States. In Salt Lake County, Utah, there are 39 community gardens and urban farms, with more in development. Only limited data exist to determine whether these soils may be considered contaminated. The purpose of this study was to conduct an urban soil survey in Salt Lake County for initial screening of soils in community gardens and urban farms for common contaminants, including the trace elements lead and arsenic (total concentrations), along with organic contaminant benzo (A) pyrene (BAP). Site selection included an emphasis on sites serving at least nine families and those with greater potential for soil contamination based on identified risk factors. Measured soil test concentrations were compared to US EPA regional screening levels (RSLs) and other US background levels. Lead concentrations ranged from 14.8 to 516 mg kg−1, with a mean concentration of 91.8 mg kg−1. Measured arsenic ranged from 2.83 to 39.3 mg kg−1 with a mean of 11.8 mg kg−1. All measured arsenic concentrations exceeded the US EPA RSL of 0.68 mg kg−1. BAP was the primary hydrocarbon of concern, and concentrations above detectable limits ranged from 0.01 to 0.44 mg kg−1, with a mean concentration of 0.09 mg kg−1. By determining the baseline degree of soil contamination in key urban agricultural sites in Utah's most populated county, local screening levels were developed into soil management plans for producers.

Threats to global biodiversity are increasingly recognised by scientists and the public as a critical challenge. Molecular sequencing technologies offer means to catalogue, explore, and monitor the richness and biogeography of life on Earth. However, exploiting their full potential requires tools that connect biodiversity infrastructures and resources. As a research infrastructure developing services and technical solutions that help integrate and coordinate life science resources across Europe, ELIXIR is a key player. To identify opportunities, highlight priorities, and aid strategic thinking, here we survey approaches by which molecular technologies help inform understanding of biodiversity. We detail example use cases to highlight how DNA sequencing is: resolving taxonomic issues; Increasing knowledge of marine biodiversity; helping understand how agriculture and biodiversity are critically linked; and playing an essential role in ecological studies. Together with examples of national biodiversity programmes, the use cases show where progress is being made but also highlight common challenges and opportunities for future enhancement of underlying technologies and services that connect molecular and wider biodiversity domains. Based on emerging themes, we propose key recommendations to guide future funding for biodiversity research: biodiversity and bioinformatic infrastructures need to collaborate closely and strategically; taxonomic efforts need to be aligned and harmonised across domains; metadata needs to be standardised and common data management approaches widely adopted; current approaches need to be scaled up dramatically to address the anticipated explosion of molecular data; bioinformatics support for biodiversity research needs to be enabled and sustained; training for end users of biodiversity research infrastructures needs to be prioritised; and community initiatives need to be proactive and focused on enabling solutions. For sequencing data to deliver their full potential they must be connected to knowledge: together, molecular sequence data collection initiatives and biodiversity research infrastructures can advance global efforts to prevent further decline of Earth’s biodiversity.

Threats to global biodiversity are increasingly recognised by scientists and the public as a critical challenge. Molecular sequencing technologies offer means to catalogue, explore, and monitor the richness and biogeography of life on Earth. However, exploiting their full potential requires tools that connect biodiversity infrastructures and resources. As a research infrastructure developing services and technical solutions that help integrate and coordinate life science resources across Europe, ELIXIR is a key player. To identify opportunities, highlight priorities, and aid strategic thinking, here we survey approaches by which molecular technologies help inform understanding of biodiversity. We detail example use cases to highlight how DNA sequencing is: resolving taxonomic issues; Increasing knowledge of marine biodiversity; helping understand how agriculture and biodiversity are critically linked; and playing an essential role in ecological studies. Together with examples of national biodiversity programmes, the use cases show where progress is being made but also highlight common challenges and opportunities for future enhancement of underlying technologies and services that connect molecular and wider biodiversity domains. Based on emerging themes, we propose key recommendations to guide future funding for biodiversity research: biodiversity and bioinformatic infrastructures need to collaborate closely and strategically; taxonomic efforts need to be aligned and harmonised across domains; metadata needs to be standardised and common data management approaches widely adopted; current approaches need to be scaled up dramatically to address the anticipated explosion of molecular data; bioinformatics support for biodiversity research needs to be enabled and sustained; training for end users of biodiversity research infrastructures needs to be prioritised; and community initiatives need to be proactive and focused on enabling solutions. For sequencing data to deliver their full potential they must be connected to knowledge: together, molecular sequence data collection initiatives and biodiversity research infrastructures can advance global efforts to prevent further decline of Earth’s biodiversity.

Genes of unknown function are among the biggest challenges in molecular biology, especially in microbial systems, where 40–60% of the predicted genes are unknown. Despite previous attempts, systematic approaches to include the unknown fraction into analytical workflows are still lacking. Here, we present a conceptual framework, its translation into the computational workflow AGNOSTOS and a demonstration on how we can bridge the known-unknown gap in genomes and metagenomes. By analyzing 415,971,742 genes predicted from 1749 metagenomes and 28,941 bacterial and archaeal genomes, we quantify the extent of the unknown fraction, its diversity, and its relevance across multiple organisms and environments. The unknown sequence space is exceptionally diverse, phylogenetically more conserved than the known fraction and predominantly taxonomically restricted at the species level. From the 71 M genes identified to be of unknown function, we compiled a collection of 283,874 lineage-specific genes of unknown function for Cand. Patescibacteria (also known as Candidate Phyla Radiation, CPR), which provides a significant resource to expand our understanding of their unusual biology. Finally, by identifying a target gene of unknown function for antibiotic resistance, we demonstrate how we can enable the generation of hypotheses that can be used to augment experimental data.

Threats to global biodiversity are increasingly recognised by scientists and the public as a critical challenge. Molecular sequencing technologies offer means to catalogue, explore, and monitor the richness and biogeography of life on Earth. However, exploiting their full potential requires tools that connect biodiversity infrastructures and resources. As a research infrastructure developing services and technical solutions that help integrate and coordinate life science resources across Europe, ELIXIR is a key player. To identify opportunities, highlight priorities, and aid strategic thinking, here we survey approaches by which molecular technologies help inform understanding of biodiversity. We detail example use cases to highlight how DNA sequencing is: resolving taxonomic issues; Increasing knowledge of marine biodiversity; helping understand how agriculture and biodiversity are critically linked; and playing an essential role in ecological studies. Together with examples of national biodiversity programmes, the use cases show where progress is being made but also highlight common challenges and opportunities for future enhancement of underlying technologies and services that connect molecular and wider biodiversity domains. Based on emerging themes, we propose key recommendations to guide future funding for biodiversity research: biodiversity and bioinformatic infrastructures need to collaborate closely and strategically; taxonomic efforts need to be aligned and harmonised across domains; metadata needs to be standardised and common data management approaches widely adopted; current approaches need to be scaled up dramatically to address the anticipated explosion of molecular data; bioinformatics support for biodiversity research needs to be enabled and sustained; training for end users of biodiversity research infrastructures needs to be prioritised; and community initiatives need to be proactive and focused on enabling solutions. For sequencing data to deliver their full potential they must be connected to knowledge: together, molecular sequence data collection initiatives and biodiversity research infrastructures can advance global efforts to prevent further decline of Earth’s biodiversity.

PurposeAdrenal vein sampling (AVS) is the reference standard for evaluation of lateralized hormone production in primary aldosteronism. We aimed to investigate the impact of pre-interventional right renal vein (RRV) to right adrenal vein (RAV) distance measurement on fluoroscopy time, contrast agent exposure and radiation dose during AVS.Materials and methodsForty-five patients with primary aldosteronism undergoing AVS were enrolled in our retrospective study and divided into three groups. In the group "ruler" (n = 14), RRV-RAV-distances were determined pre-interventionally by cross-sectional imaging (CT/MRI) and AVS was performed by one interventional radiologist with limited experience in AVS. CT/MRI-derived and fluoroscopy-derived RRV-RAV-distances were correlated for aimed cannulation of the RAV. Patients in group "no ruler" (n = 24, three interventional radiologists with limited experience in AVS) and in group "expert", (n = 7, one expert interventional radiologist) underwent AVS without pre-interventional estimation of RRV-RAV-distances. Procedure parameters (fluoroscopy time, contrast agent volume, radiation dose) of group "ruler" were compared to both other groups by Kruskal-Wallis rank-sum test.ResultsCorrelation of CT/MRI-derived and fluoroscopy-derived RRV-RAV-distances was good (r = 0.74;p = 0.003). The median RRV-RAV-distance was 4.5cm at CT/MRI (95%-CI:4.2-5.0cm) and 4.0cm at fluoroscopy (95%-CI:3.8-4.5cm). Fluoroscopy time (p0.05).ConclusionsCT/MRI-derived pre-interventional renal-adrenal vein distance measurements correlate well with angiographic distance measurements. Pre-interventional estimation of the RRV-RAV-distance allows for aimed cannulation of the RAV with potential reduction of fluoroscopy time, contrast agent exposure and radiation-dose during AVS.

BackgroundTo identify magnetic resonance (MR) angiography derived predictors of progressive dilatation and surgery of the aortic root in Marfan syndrome.Material and methodsWe retrospectively included 111 patients (32.7±16.5 years, range: 7-75 years) with a total of 446 MR angiographies. Aortic diameter growth rates of the entire thoracic aorta and Z-scores were estimated from annual diameter measurements. Aortic root shape was subdivided into three different types: (T0) normal; (T1) localized dilatation; (T2) generalized aortic root dilatation. Aortic diameter, Z-score, age, and aortic root shape at baseline were tested as predictors of aortic root dilatation using a multivariate logistic regression model.ResultsThe highest aortic growth rate was observed at the level of the sinuses of Valsalva. Higher aortic root diameters and Z-scores at baseline predicted an increased growth of the aortic root (p = 0.003 and p0.05). However, significantly more patients undergoing surgery had a generalized aortic dilatation (19/28, 76.9%) than a localized aortic root dilatation (9/28, 32.1%) (p = 0.001).ConclusionLarger baseline aortic root diameter and Z-score as well as young age predict solely progressive aortic root dilatation in Marfan patients. MR angiography derived type of aortic root shape does not predict aortic growth, but patients with generalized aortic root dilatation are referred more frequently for aortic surgery.

Die datengetriebene Forschung wird immer bedeutsamer, um die Forschungsfragen unserer Zeit zu beantworten. Dies lässt sich seit längerem beobachten und wird aktuell durch die COVID-19 Pandemie unter Beweis gestellt. In der Wissenschaft und Wirtschaft besteht jedoch ein starkes Defizit an qualifizierten Personen in (Forschungs-)Datenmanagement, Data Science und innovativen Technologien. Diesem Bedarf folgend, hat die U Bremen Research Alliance[1] mit Unterstützung des Landes Bremen für Promovierende der Mitgliedseinrichtungen eine institutions- und disziplinübergreifende Ausbildung „Data Train – Training in Research Data Management and Data Science“[2] aufgebaut. Data Train verfolgt die Mission, Kompetenzen des wissenschaftlichen Nachwuchses in Data Literacy, Datenmanagement und Data Science zu stärken und dabei die Promovierenden interdisziplinär und interinstitutionell zu vernetzen. An der Entwicklung beteiligen sich vier in Bremen vertretene NFDI-Konsortien (NFDI4Health, NFDI4Biodiversity, KonsortSWD und NFDI4Ing). Dieses interinstitutionelle und disziplinübergreifende Ausbildungsmodell, das die gesamte Datenwertschöpfungskette in der Wissenschaft abdeckt und von der auch Wirtschaftsunternehmen profitieren, liefert einen wichtigen Baustein zur Datenkompetenz-Ausbildung. [1] Der U Bremen Research Alliance e.V. ist ein kollaborativer Zusammenschluss der Universität Bremen mit zwölf der von Bund und Ländern getragenen, außeruniversitären Forschungseinrichtungen sowie weiteren von der Freien Hansestadt Bremen finanzierten Instituten und bildet ein Zentrum exzellenter Wissenschaft. (https://www.uni-bremen.de/research-alliance) [2] https://uni-bremen.de/data-train

The co-authors of this paper hereby state their intention to work together to launch the Genomic Observatories Network (GOs Network) for which this document will serve as its Founding Charter. We define a Genomic Observatory as an ecosystem and/or site subject to long-term scientific research, including (but not limited to) the sustained study of genomic biodiversity from single-celled microbes to multicellular organisms.An international group of 64 scientists first published the call for a global network of Genomic Observatories in January 2012. The vision for such a network was expanded in a subsequent paper and developed over a series of meetings in Bremen (Germany), Shenzhen (China), Moorea (French Polynesia), Oxford (UK), Pacific Grove (California, USA), Washington (DC, USA), and London (UK). While this community-building process continues, here we express our mutual intent to establish the GOs Network formally, and to describe our shared vision for its future. The views expressed here are ours alone as individual scientists, and do not necessarily represent those of the institutions with which we are affiliated.