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Abstract Purpose Calibration of radiographs is a critical step in digital templating for hip arthroplasty. Calibration errors of > 1.5% lead to over- or undersizing of the templated implants and may affect logistics and patient safety. Contemporary calibration methods are known to be imprecise with average errors of 6.5% and wide variance. A novel bi-planar radiograph-based calibration method is proposed, and a phantom study was conducted as proof of concept. Methods A spherical external calibration marker (ECM) is placed in front of the pubic symphysis of a pelvic bone model at twelve different positions. For each marker position, standard anteroposterior radiographs and four corresponding lateral radiographs with different degrees of rotation (0°–30°) are taken (overall, 60 radiographs). Calibration factors are calculated for an internal calibration marker (ICM) at the centre of the right hip (reference) and the ECM using a novel algorithm. Rotation and marker positions simulate foreseeable use errors and misplacements and aim to test robustness of the method against these errors. Results ECM calibration factor was 125.9% (range 124.7–127.2), and the mean ICM calibration factor was 126.6% (range 126.2–127.1) ($$p p < 0.001 ). Four images (8.3%) were beyond the 1% error threshold (all with 30° rotation). The mean difference was 0.79% (SD 0.49). Conclusion The bi-planar method precisely predicts the true calibration factor of the hip joint plane under various conditions. In lateral radiographs, rotation of up to 20° did not adversely affect the precision and all images had calibration errors below the threshold for clinical significance.

ZusammenfassungDas Angiosarkom ist eine seltene, maligne Erkrankung, die von den Blutgefäßen ausgeht. Das pulmonale Angiosarkom kann sich diagnostisch initial wie eine chronisch thromboembolische pulmonale Hypertonie (CTEPH) darstellen. Die CTEPH ist eine Erhöhung des pulmonal-arteriellen Drucks und Widerstands als Folge einer persistierenden Obstruktion der Lungenstrombahn nach pulmonalen Thromboembolien trotz adäquater Antikoagulation.In unserer Ambulanz für pulmonale Hypertonie stellte sich ein 76-jähriger Patient mit anamnestisch vor 7 Monaten erlittener subakuter, links zentraler Lungenarterienembolie (LAE) vor, die seitdem mit Apixaban therapiert wurde. Bei persistierender Belastungsdyspnoe wurde der Verdacht auf eine CTEPH gestellt und es erfolgte weitere Diagnostik. Passend zur CTEPH zeigte sich spiroergometrisch eine ineffektive Ventilation und echokardiografisch eine Rechtsherzbelastung. Eine Verlaufs-CT des Thorax ergab einen persistierenden und größenkonstanten Füllungsdefekt der linken Pulmonalarterie mit szintigrafischem Nachweis einer primären Perfusionsstörung des gesamten linken Lungenflügels. Mit dem Verdacht auf ein malignes Geschehen veranlassten wir eine PET-CT, in welcher sich die Läsion der Pulmonalarterie stoffwechselaktiv darstellte. Eine unter endobronchialer Ultraschallkontrolle durchgeführte Punktion der Läsion ergab histologisch den Nachweis eines sarkomatoiden Tumors mit Amplifikation des MDM2-Gens. Wir stellten die Diagnose eines Intimasarkoms der linken Pulmonalarterie und führten den Patienten einer Pneumektomie zu.Die Intimasarkome der Pulmonalarterie sind selten und führen durch Wachstum und Thrombusneigung zur Stenose des Gefäßes. Die damit einhergehende klinische und echokardiografische Präsentation kann eine CTEPH imitieren und stellt somit eine wichtige Differenzialdiagnose zu dieser dar. 2015 wurden weniger als 300 Fallberichte beschrieben.Hinweise auf ein pulmonales Angiosarkom: Kontrastmittel aufnehmende, intraluminale Gewebsformation mit Dilatation der Pulmonalarterie und Infiltration der Gefäßwand, erhöhte Stoffwechselaktivität des Befundes in der FDG-PET CT, Größenprogredienz unter Antikoagulation, anamnestisch keine stattgehabte LAE, B-Symptome.Die Diagnosesicherung erfolgt durch Biopsie. Das mediane Überleben wird mit 1,5–17 Monaten beschrieben, welches mit therapeutischen Interventionen um einige Monate mit Symptomreduktion verlängert werden kann. Als therapeutischer Standard gilt die Resektion des Tumors mit ggf. Metastasenentfernung. Der Nutzen von Radio- und Chemotherapie ist Bestandteil aktueller Forschung. Eine Behandlung ist in erfahrenen Zentren anzustreben und es bedarf weiterer Forschung zur Verbesserung von Diagnostik und Therapie.

Objectives To define and compare growth rates of the distal aorta in Marfan patients with and without aortic root replacement using serial MR angiography (MRA). Methods We retrospectively included 136 Marfan patients with a total of 645 MRAs who underwent a median of five MRAs (range: 2–13) at 1.5 T and 3 T in annual intervals. Of these, 41 patients (34.8 ± 12 years) had undergone aortic root replacement. The remaining 95 patients (29.0 ± 17 years) still had a native aorta and served as the control group. Thoracic aortic diameters were independently measured at eleven predefined levels. Estimated growth rates were calculated using a mixed effects model adjusted for sex, age, BMI, and medication. Results Marfan patients with aortic root replacement revealed the highest mean estimated growth rate in the proximal descending aorta (0.77 mm/year, CI: 0.31–1.21). Mean growth rates at all levels of the distal thoracic aorta were significantly higher in patients with aortic root replacement (0.28–0.77 mm/year) when compared to patients without aortic root replacement (0.03–0.07 mm/year) (all p Conclusion Distal thoracic aortic diameters increase at a significantly higher rate in Marfan patients with aortic root replacement compared to Marfan patients without aortic root replacement. Further studies are warranted to investigate if the increased growth rate of the distal thoracic aorta after aortic root replacement is caused by altered hemodynamics due to the rigid aortic root graft or due to the general genetic disposition of post-operative Marfan patients. Clinical relevance statement High growth rates of the distal aorta after aortic root replacement underline the need for careful life-long aortic imaging of Marfan patients after aortic root replacement. Key Points • Aortic growth rates in Marfan patients with aortic root replacement are highest in the mid-aortic arch, the proximal- and mid-descending aorta. • Growth rates of the distal thoracic aorta are significantly higher in Marfan patients with aortic root replacement compared to Marfan patients without aortic root replacement. • Antihypertensive medication, gender, and BMI have no significant impact on distal aortic growth rates in Marfan patients.

Purpose The medical examination (“medical”) is an important procedure in professional soccer since it has high economic relevance. In addition to clinical tests, magnetic resonance imaging (MRI) is used to assess joint health. In the present study, the reliability of semiquantitative knee MRI during the “medical” in professional soccer was tested, and its relationship with clinical data and days missed due to knee injury was observed. Methods In this cross-sectional study, between 2012 and 2019, 69 newly assigned players (age 18–35 years) from a professional soccer club underwent MRI (3.0 T) of both knee joints during their “medical”. Reported knee injuries and previously missed days due to injury were obtained from player anamnesis and the “transfermarkt.com” database. Based on the established “Whole-Organ Magnetic Resonance Imaging Score” (WORMS), two independent radiologists graded the MRI results. Further evaluation was based on the mean score of both knees. Results The mean WORMS for all subjects was 13.9 (median 10.5, range 0–61). Players with previous injuries had significantly higher scores than players without reported injuries (22.1 ± 17.7 vs. 8.9 ± 4.4, p r: 0.424, p r: 0.489, p r: 0.386, p p = 0.001). The WORMS was a significant predictor of days missed due to injury (p p = 0.006). The intraclass correlation coefficient was excellent (0.89). Conclusion Semiquantitative knee MRI for WORMS determination during the soccer “medical” is a robust and reliable method. Prior injury, even in players without documented trauma, was detected by the WORMS, and previously missed days due to injury were correlated with the semiquantitative MR knee score. Level of evidence Level III.

Im Rahmen der NFDI4Biodiversity All Hands Conference vom 12.-14. Oktober 2022 stellt sich die Projektkoordination (Task Area 5, Measure 1) vor und bieteteinen Überblick über die Projektsteuerung. &nbsp

Persisting patellar maltracking following surgical realignment often remains unseen. The aim of this study was to analyze the effects of realignment procedures on patellofemoral kinematics in patients with patellofemoral instability (PFI) and patellofemoral maltracking (PM) by using dynamic magnetic resonance imaging (MRI). Patients planned for surgical patellar realignment due to PFI and a clinically and radiologically apparent PM between December 2019 and May 2022 were included. Patients without PM, limited range of motion, joint effusion, or concomitant injuries were excluded. Dynamic mediolateral translation (dMPT) and patella tilt (dPT) were measured preoperatively and three months postoperatively. In 24 patients (7 men, 17 women; mean age 23.0 years), 10 tibial tubercle transfers, 5 soft tissue patella tendon transfers, 6 trochleoplasties, 3 lateral lengthenings, 1 varizating distal femoral osteotomy (DFO), and 1 torsional DFO were performed. At final follow-up, dMPT (from 10.95 ± 5.93 mm to 4.89 ± 0.40 mm, p < 0.001) and dPT (from 14.50° ± 10.33° to 8.44° ± 7.46°, p = 0.026) were significantly improved. All static radiological parameters were corrected to physiological values. Surgical patellar realignment contributed to the significant improvement of patellofemoral kinematics, with an approximation to normal values. The postoperative application of dynamic MRI allowed for a quantification of the performed correction, allowing for a postoperative control of success.

Pulmonary angiosarcoma is a rare and malignant disease of the blood vessels. Initially, it can be misdiagnosed as chronic thromboembolic hypertension (CTEPH). In CTEPH, there is increased pressure and resistance of the pulmonary arteries following persistent obstruction of pulmonary circulation from (recurrent) thromboembolism despite adequate anticoagulative treatment.A 76-year-old patient was referred to our centre for pulmonary hypertension after a central, left-sided, subacute pulmonary thromboembolism had been observed 7 months earlier. It was treated with apixaban, but the patient described persistent dyspnoea and cough. We observed severely reduced diffusion capacity, ineffective ventilation during cardiopulmonary exercise testing and right heart strain on echocardiograph, signs that are in agreement with suspected CTEPH. Computer tomography of the chest showed a persistent, size-constant obliteration of the left main pulmonary artery, and ventilation perfusion scan confirmed complete interruption of perfusion. We suspected malignancy; PET-CT scan confirmed metabolically active lesions. Histopathological examination of a sample obtained from the lesion by endobronchial ultrasound-guided needle aspiration showed a sarcomatous tumour with amplification of the MDM2-gene. We diagnosed an intimal angiosarcoma of the left pulmonary artery and referred the patient to pneumectomy.Angiosarcoma of the pulmonary arteries is a rare differential diagnosis of persistent thrombotic lesion and suspected CTEPH. In 2015 there were less than 300 cases described.Pulmonary angiosarcoma should be considered if: lesion occupies the entire lumen of pulmonary arteries with dilatation, contrast enhancement and infiltration of the wall in radiological examination, FDG-PET CT reveals metabolically active lesions, no pulmonary thromboembolism was documented in the anamnesis, increase in size is seen despite anticoagulation, patient presents with B symptoms.Diagnosis confirmed by biopsy, resection of tumour and removal of metastases is the therapeutic standard. Median survival remains poor. Further research is needed for improved diagnosis and treatment.Das Angiosarkom ist eine seltene, maligne Erkrankung, die von den Blutgefäßen ausgeht. Das pulmonale Angiosarkom kann sich diagnostisch initial wie eine chronisch thromboembolische pulmonale Hypertonie (CTEPH) darstellen. Die CTEPH ist eine Erhöhung des pulmonal-arteriellen Drucks und Widerstands als Folge einer persistierenden Obstruktion der Lungenstrombahn nach pulmonalen Thromboembolien trotz adäquater Antikoagulation.In unserer Ambulanz für pulmonale Hypertonie stellte sich ein 76-jähriger Patient mit anamnestisch vor 7 Monaten erlittener subakuter, links zentraler Lungenarterienembolie (LAE) vor, die seitdem mit Apixaban therapiert wurde. Bei persistierender Belastungsdyspnoe wurde der Verdacht auf eine CTEPH gestellt und es erfolgte weitere Diagnostik. Passend zur CTEPH zeigte sich spiroergometrisch eine ineffektive Ventilation und echokardiografisch eine Rechtsherzbelastung. Eine Verlaufs-CT des Thorax ergab einen persistierenden und größenkonstanten Füllungsdefekt der linken Pulmonalarterie mit szintigrafischem Nachweis einer primären Perfusionsstörung des gesamten linken Lungenflügels. Mit dem Verdacht auf ein malignes Geschehen veranlassten wir eine PET-CT, in welcher sich die Läsion der Pulmonalarterie stoffwechselaktiv darstellte. Eine unter endobronchialer Ultraschallkontrolle durchgeführte Punktion der Läsion ergab histologisch den Nachweis eines sarkomatoiden Tumors mit Amplifikation des MDM2-Gens. Wir stellten die Diagnose eines Intimasarkoms der linken Pulmonalarterie und führten den Patienten einer Pneumektomie zu.Die Intimasarkome der Pulmonalarterie sind selten und führen durch Wachstum und Thrombusneigung zur Stenose des Gefäßes. Die damit einhergehende klinische und echokardiografische Präsentation kann eine CTEPH imitieren und stellt somit eine wichtige Differenzialdiagnose zu dieser dar. 2015 wurden weniger als 300 Fallberichte beschrieben.Hinweise auf ein pulmonales Angiosarkom: Kontrastmittel aufnehmende, intraluminale Gewebsformation mit Dilatation der Pulmonalarterie und Infiltration der Gefäßwand, erhöhte Stoffwechselaktivität des Befundes in der FDG-PET CT, Größenprogredienz unter Antikoagulation, anamnestisch keine stattgehabte LAE, B-Symptome.Die Diagnosesicherung erfolgt durch Biopsie. Das mediane Überleben wird mit 1,5–17 Monaten beschrieben, welches mit therapeutischen Interventionen um einige Monate mit Symptomreduktion verlängert werden kann. Als therapeutischer Standard gilt die Resektion des Tumors mit ggf. Metastasenentfernung. Der Nutzen von Radio- und Chemotherapie ist Bestandteil aktueller Forschung. Eine Behandlung ist in erfahrenen Zentren anzustreben und es bedarf weiterer Forschung zur Verbesserung von Diagnostik und Therapie.

Introduction: Incidence of pancreatic neuroendocrine tumours (pNETs) is on the rise. The only curative treatment is surgical resection in localized or oligo-metastatic disease. However, patients may present with locally advanced or unresectable primary tumours. So far, no conversion therapy to achieve resectability has been established, which is partly due to lack of data on primary tumour response to therapies. Here, we specifically evaluate the primary tumour response to streptozocin/5-FU in a large cohort of metastatic pNET patients. Methods: Five ENETS centres in Germany contributed 84 patients to the study cohort for retrospective analysis. Results: Overall response rate (ORR) in primary tumours was 34% and disease control rate (DCR) 88%. ORR was different in metastases at 44% and DCR at 70%. Partial remission in primary tumours was more frequent among those located in pancreatic tail than that in pancreatic head (49% vs. 14%, p = 0.03). Correspondingly, metastases from tumours originating from pancreatic tail responded more frequently than metastases originating from pancreatic head (88.5% vs. 41.7%, p = 0.005). The median PFS of the primary tumours was longer than that in metastases (31 months vs. 16 months; p = 0.04). Considerable downsizing of the primary tumour was rare and occurred primarily in tumours located in the pancreatic tail. Conclusion: STZ/5-FU can achieve disease stabilization in a high proportion of metastatic pNET patients. In the majority of cases however it does not induce substantial downsizing of the primary tumour, thus possibly limiting its potential as conversion chemotherapy. Furthermore, the difference in response rate observed between different primary tumour locations warrants further exploration.

Purpose Adrenal 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 methods Forty-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. Results Correlation 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 (p“ruler” compared to group “no ruler” (all p“expert” (all p>0.05). Conclusions CT/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.

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.

ZusammenfassungDie Spondylodiszitis gilt in der westlichen Welt als ein häufig verzögert diagnostiziertes Krankheitsbild. Jedoch ist eine frühe Diagnosestellung entscheidend, um die Therapie zeitgerecht einzuleiten und so Komplikationen zu vermeiden. Die radiologische Bildgebung spielt dabei – besonders im Frühstadium – eine zentrale Rolle bei der Abgrenzung zu anderen Erkrankungen der Wirbelsäule.

Waterbodies such as lakes and ponds are fragile environments affected by human influences. Suitable conditions can result in massive growth of phototrophs, commonly referred to as phytoplankton blooms. Such events benefit heterotrophic bacteria able to use compounds secreted by phototrophs or their biomass as major nutrient source. One example of such bacteria are Planctomycetes, which are abundant on the surfaces of marine macroscopic phototrophs; however, less data are available on their ecological roles in limnic environments. In this study, we followed a cultivation-independent deep sequencing approach to study the bacterial community composition during a cyanobacterial bloom event in a municipal duck pond. In addition to cyanobacteria, which caused the bloom event, members of the phylum Planctomycetes were significantly enriched in the cyanobacteria-attached fraction compared to the free-living fraction. Separate datasets based on isolated DNA and RNA point towards considerable differences in the abundance and activity of planctomycetal families, indicating different activity peaks of these families during the cyanobacterial bloom. Motivated by the finding that the sampling location harbours untapped bacterial diversity, we included a complementary cultivation-dependent approach and isolated and characterized three novel limnic strains belonging to the phylum Planctomycetes.

OBJECTIVE. The purpose of this study was to introduce a 24-hour teleradiology service for cruise ships as a novel concept in maritime telemedicine. SUBJECTS AND METHODS. One cruise ship equipped with a mobile radiography unit and digital storage imaging plates was involved in this pilot study. Radiographs were transmitted via satellite internet to a tertiary hospital on shore for image interpretation by expert radiologists. Use of a virtual private network (VPN) enabled secure data transfer. Radiographs and patient data were automatically integrated into the PACS and radiology information system of the radiology department at the hospital. Images were analyzed by the staff radiologist at the hospital, and reports were immediately returned via e-mail through the VPN tunnel. RESULTS. Seventy-five radiographs of 47 patients were obtained on board within 2 months. All datasets were successfully transmitted. Most of the examinations (35 [≈ 75%]) were skeletal radiographs; the other 12 (≈ 25%) were chest radiographs. The turnaround time for the radiology reports was within 30 minutes in 43 cases (≈ 92%). In four cases (≈ 8%), delay was due to technical and organizational issues at the tertiary hospital. CONCLUSION. With the objective of supporting ship physicians with expert analyses of radiographs, a secure and stable method of image and radiology report transmission between an onboard hospital and a land-based radiology department was established.

Vortrag vonProf. Dr. Frank Oliver Glöckner,Universität Bremen, AWI Bremerhaven und GFBio e.V., über Aufgaben und Services des NFDI4Biodiversity-Konsortiums, präsentiert im Rahmen der HeFDI Data Talks.

Die in den letzten Jahren beobachteten raschen Veränderungen der Biosphäre werden sowohl durch kleine als auch durch großräumige Faktoren verursacht, wie z. B. Temperaturverschiebungen, Veränderungen in der Landnutzung oder Veränderungen im Energiehaushalt der Systeme. Während sich die letztgenannten Prozesse leicht quantifizieren lassen, ist es schwieriger, den Verlust an biologischer Vielfalt und Gemeinschaftsstrukturen zu dokumentieren. Veränderungen in der Abundanz und Vielfalt von Organismen werden kaum dokumentiert. Zählungen von Arten sind in der Regel lückenhaft und werden durch einfache, räumlich, zeitlich und ökologisch oft unbefriedigende Artenlisten für einzelne Untersuchungsgebiete abgeleitet. So bleiben schädliche globale Prozesse und ihre Triebkräfte oft unentdeckt. Ein Haupthindernis für die Überwachung der Artenvielfalt ist der Mangel an taxonomischem Fachwissen, das für großflächige und feingranulare Bewertungen unbedingt erforderlich ist. Ein weiteres Hindernis ist der hohe Personalaufwand und die damit verbundenen Kosten, die für die Erfassung großer Gebiete erforderlich sind, oder die Unzugänglichkeit entlegener, aber dennoch betroffener Gebiete. Um diese Einschränkungen zu überwinden, schlagen wir ein Netz von automatisierten Multisensor-Stationen zur Überwachung der Artenvielfalt (AMMODs) vor, das den Weg für eine neue Generation von Zentren zur Bewertung der biologischen Vielfalt ebnen soll. Dieses Netzwerk kombiniert Spitzentechnologien mit Biodiversitätsinformatik und Expertensystemen, die das Expertenwissen bewahren. Jede AMMOD-Station kombiniert autonome Probennehmer für Insekten, Pollen und Sporen, Audiorekorder für lautäußernde Tiere, Sensoren für flüchtige organische Verbindungen, die von Pflanzen emittiert werden (pVOC), und Kamerafallen für Säugetiere und kleine Wirbellose. AMMODs sind weitgehend eigenständig und können die Daten vor der Übertragung an die Empfangsstationen zur Speicherung, Integration und Analyse vorverarbeiten (z. B. zur Rauschfilterung). Die Installation an schwer zugänglichen Standorten erfordert ein ausgeklügeltes und anspruchsvolles Systemdesign mit einem optimalen Gleichgewicht zwischen Energiebedarf, Bandbreite für die Datenübertragung, erforderlichem Service und Betrieb unter allen Umweltbedingungen über Jahre hinweg. Eine wichtige Voraussetzung für die automatische Artenbestimmung sind Datenbanken mit DNA-Barcodes, Tierlauten, pVOCs und Bildern, die als Trainingsdaten für die automatische Artenbestimmung dienen. AMMOD-Stationen werden somit zu einer Schlüsselkomponente, um die Überwachung der biologischen Vielfalt für Forschung und Politik voranzutreiben, indem sie Daten zur biologischen Vielfalt mit einer noch nie dagewesenen räumlichen und zeitlichen Auflösung liefern. 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. Bundesministerium für Bildung und Forschung (BMBF)

Zur F��rderung des Dialogs zur NFDI in der Helmholtz-Gemeinschaft veranstaltete das Helmholtz Open Science Office am 8. Dezember 2021 ein zweites virtuelles Helmholtz Open Science Forum unter dem Motto ���Helmholtz in der Nationalen Forschungsdateninfrastruktur (NFDI)���. Alle Mitarbeitenden der Helmholtz-Gemeinschaft waren eingeladen, sich an dem zentren��bergreifenden Austausch zu beteiligen. Aufbauend auf das erste Forum im Mai 2021 lag der Schwerpunkt der Veranstaltung auf der Identifikation und Diskussion von Helmholtzspezifischen Themen und Aktivit��ten bei der Realisierung der NFDI.

Establishing a diagnosis in cases of fever of unknown origin (FUO) in immunocompromised patients can be difficult. In 25-35% infectious diseases are the underlying cause. This article reports the case of a 74-year-old woman with a 5-month history of fever. Through open biopsy of the femoral shaft and microbiological analysis, a diagnosis of neoehrlichiosis could be established. After initiation of treatment with doxycycline, the symptoms quickly resolved resulting in a complete recovery.Fieber unklarer Genese („fever of unknown origin“ [FUO]) kann insbesondere bei immunsupprimierten Patienten eine Vielzahl an Ursachen haben. In ca. 25–35 % der Fälle liegt dabei eine infektiöse Ursache zugrunde. Die Diagnosestellung ist häufig erschwert und wird mit zeitlicher Latenz gestellt. Wir schildern den Fall einer 74-jährigen Patientin mit einem seit 5 Monate bestehenden FUO, bei der mittels offener Femurbiopsie und mikrobiologischer Untersuchung die Diagnose einer Neoehrlichiose gestellt werden konnte. Nach Einleitung einer Therapie mit Doxycyclin kam es zu einer raschen und kompletten Besserung der Beschwerden.

Essential oils of the genus Mentha are extensively used as flavour ingredients in the food, cosmetic and pharmaceutical industry. To avoid the very time and labour-intensive traditional flavour analysis comprising isolation by solvent assisted flavour extraction and comprehensive GC-MS analysis, a new high-throughput approach based on a bead-beater homogenisation followed by SIDA-LC MS/MS has been developed. While terpenes could be directly detected using atmospheric pressure chemical ionisation (APCI), alcohols and carbonyls compounds were quantified following specific derivatisations. For example, the reaction of carbonyl compounds such as menthone and (R,S)-carvone with 3-nitrophenylhydrazine [1] enabled their highly sensitive detection by means of electrospray ionisation. In total, over 50 odour-active analytes responsible for the characteristic flavour of mint could be quantified using fast and robust UHPLC-MS/MS methods in small sample amounts such as a single mint leaf. Application of this procedure to more than 150 different genotypes of the genus Mentha enabled the mapping of flavour alterations depending on e.g. growth stages or environmental conditions.

Freshly brewed coffee is appreciated by consumers all over the world because of its stimulating effect, its characteristic taste centring on sourness and pleasant bitterness and its alluring aroma with characteristic “roasty/sulphurous” odour notes, culminating in the unique flavour sensation of coffee. The molecules responsible for the olfactory sensation of roasted coffee beans and percolated coffee beverages, analysed by means of the molecular sensory science approach are well understood. With previous studies providing qualitative and quantitative data, using aroma extract dilution analysis (AEDA), gas chromatography-olfactometry (GC-O) and headspace GC-MS techniques resulting in comprehensive aroma recombinates consisting of not more than 30 odorants [1-3]. Although the aroma of coffee can be reconstituted rather well, the impact of the melanoidin containing high molecular weight fractions (HMW) on the sensory quality of coffee beverages, is still mostly unclear on a molecular basis. Whereas former studies clearly indicated that especially odour active thiols exhibit high binding affinity to high molecular weight melanoidin fractions of coffee, only covalent interactions have been considered so far. The impact of non-covalent π-π interactions on coffee flavour is still completely unclear [4, 5]. To get detailed insight into the molecular phenomenon of odorant polymer interactions and the sensory impact on coffee flavour perception, a quantitative 1H-NMR based screening approach was developed, which allowed the direct and non-invasive analysis of molecular interactions between key coffee odorants, like 2-furfurylthiol and high molecular weight melanoidin polymers (>10 kDa). A clear distinction between covalent and non-covalent interactions was achieved by monitoring time dependency of odorant polymer interactions, with 2-furfurylthiol exhibiting π-π interactions as well as covalent bindings. In contrast, pyrazines and hydroxyphenols showed only non-covalent π-π stacking, whereas aldehydes incubated with HMW material showed only covalent interactions at prolonged incubation times. Furanones, as well as diketones showed no interactions with the HMW. Human sensory experiments with isolated HMW material >10 kDa and a full aroma recombinate of coffee were well in the line with the findings from the NMR based approach. A drastic reduction of “roasty/sulphurous” aroma notes in combination with a decrease in overall coffee-like odour quality, as well as an increased “sweetish/caramel-like” flavour was perceivable upon incubation of coffee melanoidins with the aroma recombinate. The lack of binding affinity of the sweetish/caramel smelling 4-hydroxy-2,5-dimethyl-3(2H)-furanone in combination with the high binding affinity of coffee thiols provides explanation of the sensory evaluation and might be the reason for the fast disappearance of the “roasty/sulphurous” aroma impressions of a freshly prepared coffee brew.

Objectives: Until today, patellar tracking is characterized based on cadaveric biomechanical studies. Although its objective assessment via dynamic magnetic resonance imaging (MRI) has been proposed, normal values are still lacking. The purpose of this study was to provide normal values for physiological [for full text, please go to the a.m. URL]

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

NFDI4BioDiversity ist ein Konsortium innerhalb der Nationalen Forschungsdateninfrastruktur (NFDI) mit einem Schwerpunkt auf Services für die Biodiversitätsforschung und Ökologie. Unzählige Studien belegen den Rückgang der Biodiversität auf unserem Planeten. Drängende Fragen in diesem Zusammenhang sind unter anderem welche Auswirkungen der Rückgang der Biodiversität auf die betroffenen Ökosysteme hat und welche (anthropogenen) Einflüsse die Biodiversität reduzieren oder fördern. Um die komplexen Zusammenhänge zu verstehen und daraus Handlungsempfehlungen abzuleiten, werden vielfältige, qualitätsgesicherte und FAIRe[1] Daten benötigt. Diese umfassen das Vorkommen von Pflanzen, Tieren und Mikroorganismen, einschließlich ihrer genotypischen, phänotypischen und funktionalen Vielfalt, sowie deren Zusammenspiel in Populationen und Ökosystemen. In NFDI4BioDiversity haben sich 49 Partner aus Wissenschaft, Behörden und Bürgerwissenschaften zusammengeschlossen, um die Mobilisierung und Publikation vorhandener Daten voranzutreiben, effiziente Workflows zu entwickeln und Tools und Services zur Unterstützung von Analysen bereitzustellen. [1] FAIR: Findable, Accessible, Interoperable, Reusable, aus: Wilkinson, Mark D., et al. „The FAIR Guiding Principles for scientific data management and stewardship”, Scientific Data 3:160018 (March 2016), doi: 10.1038/sdata.2016.18

Planctomycetes are bacteria that were long thought to be unculturable, of low abundance, and therefore neglectable in the environment. This view changed in recent years, after it was shown that members of the phylum Planctomycetes can be abundant in many aquatic environments, e.g., in the epiphytic communities on macroalgae surfaces. Here, we analyzed three different macroalgae from the North Sea and show that Planctomycetes is the most abundant bacterial phylum on the alga Fucus sp., while it represents a minor fraction of the surface-associated bacterial community of Ulva sp. and Laminaria sp. Especially dominant within the phylum Planctomycetes were Blastopirellula sp., followed by Rhodopirellula sp., Rubripirellula sp., as well as other Pirellulaceae and Lacipirellulaceae, but also members of the OM190 lineage. Motivated by the observed abundance, we isolated four novel planctomycetal strains to expand the collection of species available as axenic cultures since access to different strains is a prerequisite to investigate the success of planctomycetes in marine environments. The isolated strains constitute four novel species belonging to one novel and three previously described genera in the order Pirellulales, class Planctomycetia, phylum Planctomycetes.

Planctomycetes are bacteria that were long thought to be unculturable, of low abundance, and therefore neglectable in the environment. This view changed in recent years, after it was shown that members of the phylum Planctomycetes can be abundant in many aquatic environments, e.g., in the epiphytic communities on macroalgae surfaces. Here, we analyzed three different macroalgae from the North Sea and show that Planctomycetes is the most abundant bacterial phylum on the alga Fucus sp., while it represents a minor fraction of the surface-associated bacterial community of Ulva sp. and Laminaria sp. Especially dominant within the phylum Planctomycetes were Blastopirellula sp., followed by Rhodopirellula sp., Rubripirellula sp., as well as other Pirellulaceae and Lacipirellulaceae, but also members of the OM190 lineage. Motivated by the observed abundance, we isolated four novel planctomycetal strains to expand the collection of species available as axenic cultures since access to different strains is a prerequisite to investigate the success of planctomycetes in marine environments. The isolated strains constitute four novel species belonging to one novel and three previously described genera in the order Pirellulales, class Planctomycetia, phylum Planctomycetes.

To provide normal values for physiological patellofemoral tracking in a representative group of healthy individuals, as well as sex differences, using real-time 3T-magnetic resonance imaging (MRI) and to test for the reliability of the presented technique.One hundred knees of healthy individuals with no history of patellofemoral symptoms were scanned with dynamic MRI sequences, during repetitive cycles of flexion (40°) and full extension. Within a 30-seconds time-frame, three simultaneous, transverse slices were acquired. Dynamic mediolateral patellar translation (dMPT) and dynamic patellar tilt (dPT) were measured on two occasions by two independent examiners. Common radiological parameters were measured using static MRI, and correlations were calculated.100 knees (53 right, 47 left; age: 26.7 ± 4.4 years; BMI: 22.5 ± 3.1) of 57 individuals (27 females, 30 males) were included. Mean height was 170.1 ± 7.7 cm in women and 181.8 ± 6.4 cm in men. Average patella diameter was 37.9 ± 2.7 (95% CI 37.1-38.7) mm in women and 42.4 ± 3.2 (95% CI 41.5-43.3) mm in men. In females, the patellar diameters and intercondylar distances were significantly smaller than in males (P.001). Radiological parameters for patellar maltracking were within the normal range. During the range of motion, mean dMPT was 1.7 ± 2.4 (95% CI .9-2.5) mm in females and 1.8 ± 2.7 (95% CI 1.1-2.6) mm in males (P = .766). Mean dPT was 1.3 ± 2.9° (95% CI .4-2.1°) in females and -0.2 ± 3.8° (95% CI -1.2-.9°) in males (P = .036). Neither dMPT nor dPT was correlated with height, BMI, or patellar diameter. Intercondylar distance correlated weakly with dPT (r = -.241; P = .041). Intra- and interrater reliability were excellent for dMPT and dPT.Dynamic mediolateral patellar translation is a size- and sex-independent parameter for proximal patellar tracking. In healthy individuals without patellofemoral abnormalities normal dMPT proximal to the trochlea groove was 1.7 ± 2.5 (1.2-2.2) mm, independent of size or sex. Normal dPT showed a dependency on sex and was 1.3 ± 2.9 (.4-2.1)° in women and -0.2 ± 3.8 (-1.2-0.9)° in men.Level II, diagnostic study.

Planctomycetes are bacteria that were long thought to be unculturable, of low abundance, and therefore neglectable in the environment. This view changed in recent years, after it was shown that members of the phylum Planctomycetes can be abundant in many aquatic environments, e.g., in the epiphytic communities on macroalgae surfaces. Here, we analyzed three different macroalgae from the North Sea and show that Planctomycetes is the most abundant bacterial phylum on the alga Fucus sp., while it represents a minor fraction of the surface-associated bacterial community of Ulva sp. and Laminaria sp. Especially dominant within the phylum Planctomycetes were Blastopirellula sp., followed by Rhodopirellula sp., Rubripirellula sp., as well as other Pirellulaceae and Lacipirellulaceae, but also members of the OM190 lineage. Motivated by the observed abundance, we isolated four novel planctomycetal strains to expand the collection of species available as axenic cultures since access to different strains is a prerequisite to investigate the success of planctomycetes in marine environments. The isolated strains constitute four novel species belonging to one novel and three previously described genera in the order Pirellulales, class Planctomycetia, phylum Planctomycetes.

The standard of care treatment for patients with advanced pancreatic neuroendocrine tumors (pNET) is a combination of streptozotocin and 5-FU. Although widely used, little is known about the best long-term strategy with these substances. We here report our experience of 28 patients treated with streptozotocin/5-FU for advanced pNET with special consideration for long-term management using an extended cycle protocol. Standard 6-weekly Moertel protocol resulted in a median progression-free survival of 21 months (range 3–128) and a median overall survival of 69 months (range 3–157+) in the whole cohort. Thirteen of the 28 patients were switched to an extended 3-month cycle protocol for maintenance therapy. Of these 13 patients, 2 achieved complete remission, 1 partial remission, and 8 stable disease as best response while 2 showed progressive disease following switch to the extended protocol, resulting in an additional median progression-free survival of 23 months. Median overall survival after the start of chemotherapy in this patient group was 69 months (21–157+). Patients benefitted from extended periods free of chemotherapy-associated side effects after switching to the extended cycle protocol. Switching to an extended cycle protocol of 3 months for maintenance therapy following initial standard cycles may achieve long-term disease stabilization in selected patients with advanced pNET with good patient acceptance.

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.

Die U Bremen Research Alliance ist Kernbereich der Bremer Wissenschaft. Sie steht für Kooperation auf den Ebenen Forschung, wissenschaftlicher Nachwuchs, Rekrutierung und Infrastruktur. Um kooperative zukunftsorientierte Wissenschaft zu stärken, verfolgt sie gemeinschaftlich die Schaffung eines abgestimmten Raumes für Innovation, Infrastruktur und Forschung. Die Bereiche Forschungsdatenmanagement, Data Science und Digitalisierung bilden einen Schwerpunkt der Arbeit der Mitglieder der U Bremen Research Alliance. Beispiele dieser Entwicklung sind der Bremer Leibniz-WissenschaftsCampus „Digital Public Health“, die Gründung des Data Science Centers (DSC) an der Universität Bremen, der Aufbau der interdisziplinär und interorganisational getragenen Doktorand*innenausbildung „Data Train – Training in Research Data Management and Data Science“ und die aktive Beteiligung der Mitglieder an vier der neun im Juni 2020 ausgewählten Vorhaben zum Aufbau einer Nationalen Forschungsdateninfrastruktur (NFDI). Bremen ist damit im bundesweiten Vergleich einer der erfolgreichsten NFDI-Standorte. Dieses Whitepaper skizziert den aktuellen Status sowie Handlungsfelder für die disziplinübergreifende Etablierung eines kooperativen Forschungsdatenmanagements in der U Bremen Research Alliance.

Purpose: To compare the patient radiation doses during angiographic selective adrenal vein sampling (AVS) before and after a noise reduction imaging technology upgrade.Methods: 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 a noise reduction 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.Results: 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±61frames, 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). ​Conclusion: The angiographic noise reduction 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.

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.

This report outlines the results of a strategy workshop on cross-cutting topics of the National Research Data Infrastructure (NFDI). The workshop took place on 26 August 2020. The participants were the nine consortia from the first of three funding rounds for NFDI and the NFDI Directorate. The report captures 16 cross-cutting topics upon the workshop participants agreed to be most relevant. In particular, the report shows for each cross-cutting topic: consortia’s intended participation as well as willingness to take a coordination role, expected additional financial requirements, and to which degree further specification is needed. The results confirm the importance of the cross-cutting topics for NFDI. They can be seen as a preliminary basis for the further addressing of cross-cutting topics in NFDI’s planned inter-consortial sections and working groups, that will also include the consortia of funding rounds two and three., {"references":["Berlin Declaration on NFDI Cross-Cutting Topics (15/08/2019): https://zenodo.org/record/3457213.","Leipzig-Berlin-Declaration on NFDI Cross-Cutting Topics on Infrastructure Development (15/07/2020): https://zenodo.org/record/3895209.","Agreement of the Federal Government and Länder: https://www.dfg.de/download/pdf/foerderung/programme/nfdi/blv_en.pdf"]}

GFBio (German Federation for Biological Data) hat sich in den letzten sechs Jahren als die zentrale Anlaufstelle für WissenschaftlerInnen und Datenverantwortliche rund um alle Fragen des Forschungsdatenmanagements in der Biodiversitätsforschung etabliert. Zentrales Ziel von GFBio ist die Sensibilisierung der Fachcommunity für die Themen Forschungsdatenmanagement, Langzeitarchivierung und Publikation von Forschungsdaten. Eine bisher nur unzureichend gelöste Herausforderung ist jedoch die Adressierung der Forschenden vor Ort. Die direkte Interaktion mit den Forschenden am jeweiligen Campus wird dabei durch die FDM-Beratenden geleistet. Die Erfahrung hat gezeigt, dass hier bereits hervorragende Arbeit geleistet wird, jedoch für eine in die Tiefe gehende fachspezifische Beratung oft die Ressourcen fehlen. Das von GFBio propagierte “front-office/back-office” Modell mit einer engen Verknüpfung der Aktivitäten von GFBio und der lokalen FDM-Beratenden ist durch seine Arbeitsteiligkeit zu beiderseitigem Vorteil. Im Folgenden wird GFBio mit seinen Kernservices vorgestellt sowie Anknüpfungspunkte für die Zusammenarbeit mit lokalen FDM-Beratenden aufgezeigt.

Microorganisms comprise an immense phylogenetic and metabolic diversity, inhabit every conceivable niche on earth, and play a fundamental role in global biogeochemical processes. Among others, their study is highly relevant to develop biotechnological applications, understand ecosystem processes and monitor environmental systems. Functional traits (FTs) (i.e., measurable properties of an organism that influence its fitness (McGill et al. 2006)) provide complementary information to the taxonomic composition to improve the characterization of microbial communities and study their ecology (Martiny et al. 2012). The application of FT-based approaches can be particularly enhanced when coupled with metagenomics, which as a culture-independent method, allows us to obtain the genetic material of microorganisms from the environment: Metagenomic data can be used to compute functional traits at the genome level from a random sample of individuals in a microbial community, irrespective of their taxonomic affiliation (Fierer et al. 2014). Previous works using FT-based approaches in metagenomics include the study of community assembly processes (Burke et al. 2011) and responses to environmental change (Leff et al. 2015), and ecosystem functioning (Babilonia et al. 2018). In this work, we present the Metagenomic Traits pipeline: Mg-Traits. Mg-Traits is dedicated to the computation of 25 (and counting) functional traits in short-read metagenomic data, ranging from GC content and amino acid composition to functional diversity and average genome size (see Fig. 1). As an example application, we used the Mg-Traits pipeline to process the 139 prokaryotic metagenomes of the TARA Oceans data set (Sunagawa et al. 2015). In this analysis, we observed that the computed metagenomic traits track community changes along the water column, which denote microorganisms’ environmental adaptations. Mg-Traits allows the systematic computation of a comprehensive set of metagenomic functional traits, which can be used to generate a functional and taxonomic fingerprint and reveal the predominant life-history strategies and ecological processes in a microbial community. Mg-Traits contributes to improving the exploitation of metagenomic data and facilitates comparative and quantitative studies. Considering the high genomic plasticity of microorganisms and their capacity to rapidly adapt to changing environmental conditions, Mg-Traits constitutes a valuable tool to monitor environmental systems. The Mg-Traits pipeline is available at https://github.com/pereiramemo/metagenomic_pipelines. It is programmed in AWK, BASH, and R, and it was devised using a modular design to facilitate the integration of new metagenomic traits.

We evaluated the accuracy of preoperative CT in staging colonic diverticulitis (ACD) by using the classification of diverticular disease (CDD) and investigated the diagnostic impact of water enema (WE) and visceral obesity.In this retrospective study, the radiological and hospital information system was searched for patients who underwent CT for clinically suspected ACD prior to surgery between 2009 and 2019. From the initial population (n = 164), we included 155 patients (94.5 %) (85 women; mean age: 58 ± 13 years) matching the following inclusion criteria: i.) clinically suspected ACD, ii.) i.v. contrast-enhanced CT, iii.) surgery for ACD within 1 week after CT, iv.) histopathological report that proved ACD. The remaining 9 patients (5.5 %) were excluded because histopathological reports were lacking (n = 3) or CT was performed without intravenous contrast agent (n = 6). WE (+ butylscopolamine i.v.) was performed in 93 patients (group A, 60 %). 62 patients (group B, 40 %) had no WE. Visceral-to-subcutaneous fat ratio (V/S) was determined for each patient. Two radiologists blinded for final diagnosis independently staged ACD according to CDD and assessed prevalence and confidence ratings of ACD-related CT-findings: pericolonic fat stranding, covered- and free-perforation, local and generalized peritonitis, abscess. Interobserver-agreement of CT-findings were assessed and effects of WE and V/S ratio on the diagnostic accuracy of CT with surgical and histopathological findings as reference were determined by calculating a logistic regression model.CT-staging showed high accuracy (94 %) and excellent interrater-correlation (ICC 0.96) for staging ACD. WE had no positive impact neither on diagnostic accuracy of staging, nor on confidence ratings of ACD-related CT-findings (all p 0.5). Confidence ratings were significantly higher in examinations without WE for perforation, peritonitis as well as abscesses (all p 0.5). Confidence ratings for the assessment of local peritonitis improved significantly with higher V/S (p = 0.049). The increase of V/S significantly correlated with the probability for correct CDD staging of ACD in CT (p = 0.023).Increase of visceral obesity significantly improves accuracy of CT in preoperative staging acute colonic diverticulitis. However, independently of the degree of visceral obesity, water enema has no diagnostic benefit and may therefore be omitted. Overall, CT proves high accuracy in preoperative staging ACD using the classification of diverticular disease.Retrospective study, observational study.

This article describes some use case studies and self-assessments of FAIR status of de.NBI services to illustrate the challenges and requirements for the definition of the needs of adhering to the FAIR (findable, accessible, interoperable and reusable) data principles in a large distributed bioinformatics infrastructure. We address the challenge of heterogeneity of wet lab technologies, data, metadata, software, computational workflows and the levels of implementation and monitoring of FAIR principles within the different bioinformatics sub-disciplines joint in de.NBI. On the one hand, this broad service landscape and the excellent network of experts are a strong basis for the development of useful research data management plans. On the other hand, the large number of tools and techniques maintained by distributed teams renders FAIR compliance challenging.

Modern digital scientific workflows - often implying Big Data challenges - require data infrastructures and innovative data science methods across disciplines and technologies. Diverse activities within and outside HGF deal with these challenges, on all levels. The series of Data Science Symposia fosters knowledge exchange and collaboration in the Earth and Environment research community. We invited contributions to the overarching topics of data management, data science and data infrastructures. The series of Data Science Symposia is a joint initiative by the three Helmholtz Centers HZG, AWI and GEOMAR Organization: Hela Mehrtens and Daniela Henkel (GEOMAR)

Microorganisms produce an immense variety of natural products through the expression of Biosynthetic Gene Clusters (BGCs): physically clustered genes that encode the enzymes of a specialized metabolic pathway. These natural products cover a wide range of chemical classes (e.g., aminoglycosides, lantibiotics, nonribosomal peptides, oligosaccharides, polyketides, terpenes) that are highly valuable for industrial and medical applications1. Metagenomics, as a culture-independent approach, has greatly enhanced our ability to survey the functional potential of microorganisms and is growing in popularity for the mining of BGCs. However, to effectively exploit metagenomic data to this end, it will be crucial to more efficiently identify these genomic elements in highly complex and ever-increasing volumes of data2. Here, we address this challenge by developing the ultrafast Biosynthetic Gene cluster MEtagenomic eXploration toolbox (BiG-MEx). BiG-MEx rapidly identifies a broad range of BGC protein domains, assess their diversity and novelty, and predicts the abundance profile of natural product BGC classes in metagenomic data. We show the advantages of BiG-MEx compared to standard BGC-mining approaches, and use it to explore the BGC domain and class composition of samples in the TARA Oceans3 and Human Microbiome Project datasets4. In these analyses, we demonstrate BiG-MEx’s applicability to study the distribution, diversity, and ecological roles of BGCs in metagenomic data, and guide the exploration of natural products with clinical applications.

NFDI4BioDiversity ist ein Konsortium innerhalb der Nationalen Forschungsdateninfrastruktur (NFDI) mit einem Schwerpunkt auf Services für die Biodiversitätsforschung und Ökologie. Unzählige Studien belegen den Rückgang der Biodiversität auf unserem Planeten. Drängende Fragen in diesem Zusammenhang sind unter anderem welche Auswirkungen der Rückgang der Biodiversität auf die betroffenen Ökosysteme hat und welche (anthropogenen) Einflüsse die Biodiversität reduzieren oder fördern. Um die komplexen Zusammenhänge zu verstehen und daraus Handlungsempfehlungen abzuleiten, werden vielfältige, qualitätsgesicherte und FAIRe[1] Daten benötigt. Diese umfassen das Vorkommen von Pflanzen, Tieren und Mikroorganismen, einschließlich ihrer genotypischen, phänotypischen und funktionalen Vielfalt, sowie deren Zusammenspiel in Populationen und Ökosystemen. In NFDI4BioDiversity haben sich 49 Partner aus Wissenschaft, Behörden und Bürgerwissenschaften zusammengeschlossen, um die Mobilisierung und Publikation vorhandener Daten voranzutreiben, effiziente Workflows zu entwickeln und Tools und Services zur Unterstützung von Analysen bereitzustellen. [1] FAIR: Findable, Accessible, Interoperable, Reusable, aus: Wilkinson, Mark D., et al. „The FAIR Guiding Principles for scientific data management and stewardship”, Scientific Data 3:160018 (March 2016), doi: 10.1038/sdata.2016.18

Microorganisms produce an immense variety of natural products through the expression of Biosynthetic Gene Clusters (BGCs): physically clustered genes that encode the enzymes of a specialized metabolic pathway. These natural products cover a wide range of chemical classes (e.g., aminoglycosides, lantibiotics, nonribosomal peptides, oligosaccharides, polyketides, terpenes) that are highly valuable for industrial and medical applications1. Metagenomics, as a culture-independent approach, has greatly enhanced our ability to survey the functional potential of microorganisms and is growing in popularity for the mining of BGCs. However, to effectively exploit metagenomic data to this end, it will be crucial to more efficiently identify these genomic elements in highly complex and ever-increasing volumes of data2. Here, we address this challenge by developing the ultrafast Biosynthetic Gene cluster MEtagenomic eXploration toolbox (BiG-MEx). BiG-MEx rapidly identifies a broad range of BGC protein domains, assess their diversity and novelty, and predicts the abundance profile of natural product BGC classes in metagenomic data. We show the advantages of BiG-MEx compared to standard BGC-mining approaches, and use it to explore the BGC domain and class composition of samples in the TARA Oceans3 and Human Microbiome Project datasets4. In these analyses, we demonstrate BiG-MEx’s applicability to study the distribution, diversity, and ecological roles of BGCs in metagenomic data, and guide the exploration of natural products with clinical applications.Competing Interest StatementThe authors have declared no competing interest.

Mit der Nationalen Forschungsdateninfrastruktur (NFDI) verfolgen Bund und L��nder das Ziel, Datenbest��nde aus der Forschung f��r das deutsche Wissenschaftssystem nach den FAIR-Prinzipien systematisch zu erschlie��en, damit diese f��r Dritte besser zug��nglich gemacht werden. Die NFDI wird als Netzwerk von Konsortien ��ber einen Zeitraum von drei Jahren ab 2020 in drei aufeinanderfolgenden F��rderphasen aufgebaut. Eine wichtige Rolle spielt dabei auch die Abdeckung disziplin��bergreifender Querschnittsthemen. Zur F��rderung des Dialogs zur NFDI in der Helmholtz-Gemeinschaft veranstaltete das Helmholtz Open Science Office am 4. Mai 2021 ein digitales Helmholtz Open Science Forum unter dem Motto ���Helmholtz in der Nationalen Forschungsdateninfrastruktur (NFDI)���. Als Impuls f��r die weitere Diskussion lud das Helmholtz Open Science Office alle interessierten Mitarbeitenden der Helmholtz-Gemeinschaft zu diesem virtuellen Helmholtz Open Science Forum ein. Neben einer Einf��hrung durch das NFDI-Direktorat stellten Vortr��ge die Bandbreite der NFDI-Beteiligung in Helmholtz dar (z. B. Praxisberichte bereits bewilligter Konsortien sowie Vortr��ge zum Umgang mit der NFDI aus Perspektive eines Zentrums, eines Forschungsbereichs und einer Plattform des Inkubators ���Information & Data Science���); auch wurde das Zusammenspiel von NFDI und European Open Science Cloud (EOSC) vom B��ro Br��ssel der Gemeinschaft beleuchtet. Im Kern stand die Identifikation und Diskussion zu Helmholtz-spezifischen Aspekten bei der Realisierung der NFDI.

Poster about theNFDI4BioDiversity consortium, presented at the HeFDI Plenary 2020.

Natural history collections are leading successful large-scale projects of specimen digitization (images, metadata, DNA barcodes), thereby transforming taxonomy into a big data science. Yet, little effort has been directed towards safeguarding and subsequently mobilizing the considerable amount of original data generated during the process of naming 15,000–20,000 species every year. From the perspective of alpha-taxonomists, we provide a review of the properties and diversity of taxonomic data, assess their volume and use, and establish criteria for optimizing data repositories. We surveyed 4113 alpha-taxonomic studies in representative journals for 2002, 2010, and 2018, and found an increasing yet comparatively limited use of molecular data in species diagnosis and description. In 2018, of the 2661 papers published in specialized taxonomic journals, molecular data were widely used in mycology (94%), regularly in vertebrates (53%), but rarely in botany (15%) and entomology (10%). Images play an important role in taxonomic research on all taxa, with photographs used in >80% and drawings in 58% of the surveyed papers. The use of omics (high-throughput) approaches or 3D documentation is still rare. Improved archiving strategies for metabarcoding consensus reads, genome and transcriptome assemblies, and chemical and metabolomic data could help to mobilize the wealth of high-throughput data for alpha-taxonomy. Because long-term—ideally perpetual—data storage is of particular importance for taxonomy, energy footprint reduction via less storage-demanding formats is a priority if their information content suffices for the purpose of taxonomic studies. Whereas taxonomic assignments are quasifacts for most biological disciplines, they remain hypotheses pertaining to evolutionary relatedness of individuals for alpha-taxonomy. For this reason, an improved reuse of taxonomic data, including machine-learning-based species identification and delimitation pipelines, requires a cyberspecimen approach—linking data via unique specimen identifiers, and thereby making them findable, accessible, interoperable, and reusable for taxonomic research. This poses both qualitative challenges to adapt the existing infrastructure of data centers to a specimen-centered concept and quantitative challenges to host and connect an estimated \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$ \le $\end{document}2 million images produced per year by alpha-taxonomic studies, plus many millions of images from digitization campaigns. Of the 30,000–40,000 taxonomists globally, many are thought to be nonprofessionals, and capturing the data for online storage and reuse therefore requires low-complexity submission workflows and cost-free repository use. Expert taxonomists are the main stakeholders able to identify and formalize the needs of the discipline; their expertise is needed to implement the envisioned virtual collections of cyberspecimens. [Big data; cyberspecimen; new species; omics; repositories; specimen identifier; taxonomy; taxonomic data.]

Patellofemoral maltracking predisposes the patellofemoral joint to instability. The purpose of this study was to provide a reliable dynamic magnetic resonance imaging (MRI) measuring technique for patellofemoral maltracking, and to investigate the influence of anatomical risk factors (AF) on patellar maltracking. Ten patients (2 males,8 females, average 19 years) with clinical maltracking and 20 controls (10 males,10 females,average 28 years) were examined with a dynamic, multi-slice gradient-echo MRI sequence, during repetitive flexion(40°) and full extension, in an open-chain-active-movement. In a 30-s time frame three simultaneous transverse slices were acquired. Dynamic mediolateral translation and dynamic tilt were measured at defined positions, by two independent examiners. Reproducibility was tested in a set of five knees. Common AFs for patellar maltracking (tibial-tuberosity-to-trochlear-groove-(TT-TG)-distances, trochlea-sulcus-angle, trochlea-sulcus-depth, lateral-trochlear-inclination and Caton-Deschamps-Index) were analyzed in consensus, using standard static MRI sequences. In patients, dynamic mediolateral translation was significantly greater in patients (12.4 ± 6.9 mm vs. − 0.1 ± 2.3 mm, p p p p

The German Network for Bioinformatics Infrastructure (de.NBI) is a national and academic infrastructure funded by the German Federal Ministry of Education and Research (BMBF). The de.NBI provides (i) service, (ii) training, and (iii) cloud computing to users in life sciences research and biomedicine in Germany and Europe and (iv) fosters the cooperation of the German bioinformatics community with international network structures. The de.NBI members also run the German node (ELIXIR-DE) within the European ELIXIR infrastructure. The de.NBI / ELIXIR-DE training platform, also known as special interest group 3 (SIG 3) ‘Training & Education’, coordinates the bioinformatics training of de.NBI and the German ELIXIR node. The network provides a high-quality, coherent, timely, and impactful training program across its eight service centers. Life scientists learn how to handle and analyze biological big data more effectively by applying tools, standards and compute services provided by de.NBI. Since 2015, more than 300 training courses were carried out with about 6,000 participants and these courses received recommendation rates of almost 90% (status as of July 2020). In addition to face-to-face training courses, online training was introduced on the de.NBI website in 2016 and guidelines for the preparation of e-learning material were established in 2018. In 2016, ELIXIR-DE joined the ELIXIR training platform. Here, the de.NBI / ELIXIR-DE training platform collaborates with ELIXIR in training activities, advertising training courses via TeSS and discussions on the exchange of data for training events essential for quality assessment on both the technical and administrative levels. The de.NBI training program trained thousands of scientists from Germany and beyond in many different areas of bioinformatics.