MIRA: Dual wavelength band instrument

MIRA is a dual wavelength band instrument operated by Technische Universität München TUM, which provides neutrons over a wide range of wavelengths 3.5 Å < λ < 20 Å combining the two beam ports of MIRA-1 and MIRA-2. The instrument´s setup is modular and allows for various different cold neutron experiments such as diffraction, spectroscopy or reflectometry

9 year old girl with progressive weakness: Com july 2009 case 1

A 9-year-old female patient experienced progressive weakness and myalgias of shoulders and back of several months duration. Her medical history was notable for spina bifida in association with a Chiari type II malformation and hydrocephalus. Developmental motor milestones were delayed whereby walking began at age 2. She had mild bowel and bladder dysfunction. At presentation, her neurological exam was notable for weak shoulder adduction, hip and knee flexion and she demonstrated a partial Gower\u27s maneuver. A muscle biopsy showed dystrophic changes and immunohistochemical findings of a Duchenne\u27s mosaic which was confirmed by DNA analysis. The proposed pathogenesis in this case is unfavourable lyonization, which was corroborated by X-inactivation studies. © 2010 International Society of Neuropathology

The openCARP CDE: Concept for and implementation of a sustainable collaborativedevelopment environment for research software

This work describes the setup of an advanced technical infrastructure for collabora-tive software development in large, distributed projects based on GitLab. We presentits customization and extension, additional features and processes like code review,continuous automated testing, DevOps practices, and sustainable life-cycle manage-ment including long-term preservation and citable publishing of software releasesalong with relevant metadata. The collaborative development environment (CDE) iscurrently used for developing the open cardiac simulation software openCARP and anevaluation showcases its capability and utility for collaboration and coordination ofsizeable heterogeneous teams. As such, it could be a suitable and sustainable infras-tructure solution for a wide range of research software projects

Informationsgewinn aus Herbizidversuchen - Auswertung von Feldversuchen der Bezirksstelle Hannover aus den Jahren 2003 – 2009

Pflanzenschutzdienste erheben im Rahmen des Zulassungsverfahrens und für die Beratung von Landwirten Daten von Pflanzenschutzmitteln in einer spezifischen Region. Die Bezirksstelle Hannover legt dazu Feldversuche an: In Abhängigkeit der Initiatoren als Gemeinschaftsprogramme, orientierende und amtliche Mittelprüfungen sowie bezirksstellenindividuelle Versuche. Ziel dieser Arbeit war es, herauszustellen, in wie weit eine übergreifende Sekundärauswertung zusätzlichen Erkenntnisgewinn liefern kann. Die Ergebnisse, die von 2003 bis 2009 in 89 Versuchen an 40 Standorten in einem Umkreis von 50 km um Hannover erhoben worden waren, wurden in 1076 Datensätzen zusammengestellt. Die Versuchsregion lag in zwei Boden-Klima-Räumen.Regionsspezifische Unterschiede im Anbau- und Herbizidmanagement konnten festgestellt werden. Etwa die Hälfte aller Standorte wurde zur Herbizidprüfung nur einmalig aufgesucht und ca. 70 % aller Prüfvarianten wurden nur einjährig geprüft, so dass mögliche Jahreseinflüsse der Herbizidwirkungen unentdeckt blieben. Besonders viele Daten waren zu den Ungräsern Alopecurus myosuroides (ALOMY) und Apera spica-venti (APESV) vorhanden. In den Versuchen wies ALOMY in 74 % aller Fälle einen Starkbefall von mehr als 200 Ähren je m² auf. APESV produzierte nur in 5 % der Versuche mehr als 200 Rispen je m². Bei gleicher Anzahl generativer Sprosse führte APESV zu stärkeren Ertragsdepressionen als ALOMY. Zudem wurde festgestellt, dass Standorte, auf denen ALOMY auftrat, ein höherer Ertrag erreichbar war, als auf APESV-Habitaten. Analysen der Vorhersagegenauigkeit unterschiedlicher Zeitpunkte der Befallsbonitur zeigten, dass der Ertrag am besten mit Deckungsgradbonituren im frühen Frühjahr korrelierte (R² = 0,54), während bei der Herbstbonitur das Bestimmtheitsmaß nur bei 0,25 lag.Die Schlussfolgerung ist, dass die Sekundärauswertung von Herbizid-Feldversuchen im Bereich von Befall-Ertrags-Relationen aktuelle Werte liefern kann. Einer zusammenfassenden Auswertung der Wirkungen einzelner Herbizide steht jedoch die geringe Wiederholung einzelner Prüfglieder über die Zeit im Weg. Stichwörter: Alopecurus myosuroides, Apera spica-venti, Feldversuche, Herbizide, Niedersachsen, Ungräser, UnkrautbekämpfungGaining extra information from herbicide trials - analysing field trials of the region Hannover from 2003 to 2009Crop protection services gather data on pesticides in the context of product registration and for region-specific extension. For this purpose, the region Hannover conducts field trials, which depending on the initiators can be based on different designs. The purpose of this study was to see if it is possible to extract additional data from these data sets by joint analysis.The 1076 data sets are based on 89 trials conducted in 40 locations in a radius of 50 km around the city of Hannover from 2003 to 2009. The region is situated in two ecoregional zones.There were area-specific differences in crop- and herbicide management. About half of the locations were chosen as trial location for herbicides only once and about 70 % of all treatments were tested only in one year. Consequently, possible year-effects remained hidden. Data with regard to the grass weeds, Alopecurus myosuroides (ALOMY) and Apera spica-venti (APESV), were particularly abundant. In 74 % of the trials, the density of ALOMY was &gt; 200 ears per square meter. In contrast, in only 5 % of the trials was the density of APESV &gt; 200 panicles per square meter. However, APESV will lead to higher yield losses than ALOMY at similar ear density. Furthermore, ALOMY predominantly occurred in locations that had the potential to produce higher crop yields than locations with APESV. Analyses of the timing of the surveys showed that crop yield could be best predicted based on weed surveys in early spring (R² = 0.54), whereas correlations with surveys conducted in autumn were weak (R² = 0.25).The results of this study show that the joint analysis of herbicide trials can yield valuable new insights. Joint analysis of herbicide efficiency over all trials could not be conducted due to lack of replication of trials with identical variants over time. Keywords: Alopecurus myosuroides, Apera spica-venti, field trials, grass weeds, herbicides, Lower Saxony, weed contro

SuLMaSS - Sustainable Lifecycle Management for Scientific Software

The SuLMaSS project [1] will advance, develop, build, evaluate, and test infrastructure for sustainable lifecycle management of scientific software. The infrastructure is tested and evaluated by an existing cardiac electrophysiology simulation software project, which is currently in the prototype state and will be advanced towards optimal usability and a large and active user community. Thus, SuLMaSS is focused on designing and implementing application-oriented e-research technologies and the impact is three-fold: - Provision of a high quality, user-friendly cardiac electrophysiology simulation software package that accommodates attestable needs of the scientific community. - Delivery of infrastructure components for testing, safe-keeping, referencing, and versioning of all phases of the lifecycle of scientific software. - Serve as a best practice example for sustainable scientific software management. Scientific software development in Germany and beyond shall benefit through both the aforementioned best practice role model and the advanced infrastructure that will, in part, be available for external projects as well. With adding value for the wider scientific cardiac electrophysiology community, the software will be available under an open source license and be provided for a large share of people and research groups that can potentially leverage computational cardiac modeling methods. Institutional infrastructure will be extended to explore, evaluate and establish the basis for research software development regarding testing, usage, maintenance and support. The cardiac electrophysiology simulator will drive and showcase the infrastructure formation, thus serving as a lighthouse project. The developed infrastructure can be used by other scientific software projects in future and aims to support the full research lifecycle from exploration through conclusive analysis and publication, to archival, and sharing of data and source code, thus increasing the quality of research results. Moreover it will foster a community-based collaborative development and improve sustainability of research software. References: [1]­‌‌‌‌‌‌‌‌‌ http://www.dfg.de/dfg_magazin/aus_der_wissenschaft/impulse_fuer_das_digitale_lis_jb17/02_aus_der_foerderung/index.htm

Genomic analysis of Klebsiella pneumoniae isolates from Malawi reveals acquisition of multiple ESBL determinants across diverse lineages

Objectives ESBL-producing Klebsiella pneumoniae (KPN) pose a major threat to human health globally. We carried out a WGS study to understand the genetic background of ESBL-producing KPN in Malawi and place them in the context of other global isolates. Methods We sequenced genomes of 72 invasive and carriage KPN isolates collected from patients admitted to Queen Elizabeth Central Hospital, Blantyre, Malawi. We performed phylogenetic and population structure analyses on these and previously published genomes from Kenya (n = 66) and from outside sub-Saharan Africa (n = 67). We screened for presence of antimicrobial resistance (AMR) genetic determinants and carried out association analyses by genomic sequence cluster, AMR phenotype and time. Results Malawian isolates fit within the global population structure of KPN, clustering into the major lineages of KpI, KpII and KpIII. KpI isolates from Malawi were more related to those from Kenya, with both collections exhibiting more clonality than isolates from the rest of the world. We identified multiple ESBL genes, including blaCTX-M-15, several blaSHV, blaTEM-63 and blaOXA-10, and other AMR genes, across diverse lineages of the KPN isolates from Malawi. No carbapenem resistance genes were detected; however, we detected IncFII and IncFIB plasmids that were similar to the carbapenem resistance-associated plasmid pNDM-mar. Conclusions There are multiple ESBL genes across diverse KPN lineages in Malawi and plasmids in circulation that are capable of carrying carbapenem resistance. Unless appropriate interventions are rapidly put in place, these may lead to a high burden of locally untreatable infection in vulnerable populations

Hrs and SNX3 Functions in Sorting and Membrane Invagination within Multivesicular Bodies

After internalization, ubiquitinated signaling receptors are delivered to early endosomes. There, they are sorted and incorporated into the intralumenal invaginations of nascent multivesicular bodies, which function as transport intermediates to late endosomes. Receptor sorting is achieved by Hrs—an adaptor-like protein that binds membrane PtdIns3P via a FYVE motif—and then by ESCRT complexes, which presumably also mediate the invagination process. Eventually, intralumenal vesicles are delivered to lysosomes, leading to the notion that EGF receptor sorting into multivesicular bodies mediates lysosomal targeting. Here, we report that Hrs is essential for lysosomal targeting but dispensable for multivesicular body biogenesis and transport to late endosomes. By contrast, we find that the PtdIns3P-binding protein SNX3 is required for multivesicular body formation, but not for EGF receptor degradation. PtdIns3P thus controls the complementary functions of Hrs and SNX3 in sorting and multivesicular body biogenesis

Whole genome analysis reveals the diversity and evolutionary relationships between necrotic enteritis-causing strains of Clostridium perfringens

BACKGROUND: Clostridium perfringens causes a range of diseases in animals and humans including necrotic enteritis in chickens and food poisoning and gas gangrene in humans. Necrotic enteritis is of concern in commercial chicken production due to the cost of the implementation of infection control measures and to productivity losses. This study has focused on the genomic analysis of a range of chicken-derived C. perfringens isolates, from around the world and from different years. The genomes were sequenced and compared with 20 genomes available from public databases, which were from a diverse collection of isolates from chickens, other animals, and humans. We used a distance based phylogeny that was constructed based on gene content rather than sequence identity. Similarity between strains was defined as the number of genes that they have in common divided by their total number of genes. In this type of phylogenetic analysis, evolutionary distance can be interpreted in terms of evolutionary events such as acquisition and loss of genes, whereas the underlying properties (the gene content) can be interpreted in terms of function. We also compared these methods to the sequence-based phylogeny of the core genome. RESULTS: Distinct pathogenic clades of necrotic enteritis-causing C. perfringens were identified. They were characterised by variable regions encoded on the chromosome, with predicted roles in capsule production, adhesion, inhibition of related strains, phage integration, and metabolism. Some strains have almost identical genomes, even though they were isolated from different geographic regions at various times, while other highly distant genomes appear to result in similar outcomes with regard to virulence and pathogenesis. CONCLUSIONS: The high level of diversity in chicken isolates suggests there is no reliable factor that defines a chicken strain of C. perfringens, however, disease-causing strains can be defined by the presence of netB-encoding plasmids. This study reveals that horizontal gene transfer appears to play a significant role in genetic variation of the C. perfringens chromosome as well as the plasmid content within strains

Whole genome analysis reveals the diversity and evolutionary relationships between necrotic enteritis-causing strains of Clostridium perfringens

BACKGROUND: Clostridium perfringens causes a range of diseases in animals and humans including necrotic enteritis in chickens and food poisoning and gas gangrene in humans. Necrotic enteritis is of concern in commercial chicken production due to the cost of the implementation of infection control measures and to productivity losses. This study has focused on the genomic analysis of a range of chicken-derived C. perfringens isolates, from around the world and from different years. The genomes were sequenced and compared with 20 genomes available from public databases, which were from a diverse collection of isolates from chickens, other animals, and humans. We used a distance based phylogeny that was constructed based on gene content rather than sequence identity. Similarity between strains was defined as the number of genes that they have in common divided by their total number of genes. In this type of phylogenetic analysis, evolutionary distance can be interpreted in terms of evolutionary events such as acquisition and loss of genes, whereas the underlying properties (the gene content) can be interpreted in terms of function. We also compared these methods to the sequence-based phylogeny of the core genome. RESULTS: Distinct pathogenic clades of necrotic enteritis-causing C. perfringens were identified. They were characterised by variable regions encoded on the chromosome, with predicted roles in capsule production, adhesion, inhibition of related strains, phage integration, and metabolism. Some strains have almost identical genomes, even though they were isolated from different geographic regions at various times, while other highly distant genomes appear to result in similar outcomes with regard to virulence and pathogenesis. CONCLUSIONS: The high level of diversity in chicken isolates suggests there is no reliable factor that defines a chicken strain of C. perfringens, however, disease-causing strains can be defined by the presence of netB-encoding plasmids. This study reveals that horizontal gene transfer appears to play a significant role in genetic variation of the C. perfringens chromosome as well as the plasmid content within strains