Überblick zur Softwareentwicklung in Wissenschaftlichen Anwendungen

Viele wissenschaftliche Disziplinen müssen heute immer komplexer werdende numerische Probleme lösen. Die Komplexität der benutzten wissenschaftlichen Software steigt dabei kontinuierlich an. Diese Komplexitätssteigerung wird durch eine ganze Reihe sich ändernder Anforderungen verursacht: Die Betrachtung gekoppelter Phänomene gewinnt Aufmerksamkeit und gleichzeitig müssen neue Technologien wie das Grid-Computing oder neue Multiprozessorarchitekturen genutzt werden, um weiterhin in angemessener Zeit zu Berechnungsergebnissen zu kommen. Diese Fülle an neuen Anforderungen kann nicht mehr von kleinen spezialisierten Wissenschaftlergruppen in Isolation bewältigt werden. Die Entwicklung wissenschaftlicher Software muss vielmehr in interdisziplinären Gruppen geschehen, was neue Herausforderungen in der Softwareentwicklung induziert. Ein Paradigmenwechsel zu einer stärkeren Separation von Verantwortlichkeiten innerhalb interdisziplinärer Entwicklergruppen ist bis jetzt in vielen Fällen nur in Ansätzen erkennbar. Die Kopplung partitioniert durchgeführter Simulationen physikalischer Phänomene ist ein wichtiges Beispiel für softwaretechnisch herausfordernde Aufgaben im Gebiet des wissenschaftlichen Rechnens. In diesem Kontext modellieren verschiedene Simulationsprogramme unterschiedliche Teile eines komplexeren gekoppelten Systems. Die vorliegende Arbeit gibt einen Überblick über Paradigmen, die darauf abzielen Softwareentwicklung für Berechnungsprogramme verlässlicher und weniger abhängig voneinander zu machen. Ein spezielles Augenmerk liegt auf der Entwicklung gekoppelter Simulationen.Fields of modern science and engineering are in need of solving more and more complex numerical problems. The complexity of scientific software thereby rises continuously. This growth is caused by a number of changing requirements. Coupled phenomena gain importance and new technologies like the computational Grid, graphical and heterogeneous multi-core processors have to be used to achieve high-performance. The amount of additional complexity can not be handled by small groups of specialised scientists. The interdiciplinary nature of scientific software thereby presents new challanges for software engineering. A paradigm shift towards a stronger separation of concerns becomes necessary in the development of future scientific software. The coupling of independently simulated physical phenomena is an important example for a software-engineering concern in the domain of computational science. In this context, different simulation-programs model only a part of a more complex coupled system. The present work gives overview on paradigms which aim at making software-development in computational sciences more reliable and less interdependent. A special focus is put on the development of coupled simulations

A Robotic System for Solo Surgery in Flexible Ureterorenoscopy

Urolithiasis is a common disease with increasing prevalence across all ages. A common treatment option for smaller kidney stones is flexible ureterorenoscopy (fURS), where a flexible ureteroscope (FU) is used for stone removal and to inspect the renal collecting system. The handling of the flexible ureteroscope and end effectors (EEs), however, is challenging and requires two surgeons. In this article, we introduce a modular robotic system for endoscope manipulation, which enables solo surgery (SSU) and is adaptable to various hand-held FUs. Both the developed hardware components and the proposed workflow and its representation in software are described. We then present and discuss the results of an initial user study. Finally, we describe subsequent developmental steps towards more extensive testing by clinical staff

Clinical and virological characteristics of hospitalised COVID-19 patients in a German tertiary care centre during the first wave of the SARS-CoV-2 pandemic: a prospective observational study

Purpose: Adequate patient allocation is pivotal for optimal resource management in strained healthcare systems, and requires detailed knowledge of clinical and virological disease trajectories. The purpose of this work was to identify risk factors associated with need for invasive mechanical ventilation (IMV), to analyse viral kinetics in patients with and without IMV and to provide a comprehensive description of clinical course. Methods: A cohort of 168 hospitalised adult COVID-19 patients enrolled in a prospective observational study at a large European tertiary care centre was analysed. Results: Forty-four per cent (71/161) of patients required invasive mechanical ventilation (IMV). Shorter duration of symptoms before admission (aOR 1.22 per day less, 95% CI 1.10-1.37, p < 0.01) and history of hypertension (aOR 5.55, 95% CI 2.00-16.82, p < 0.01) were associated with need for IMV. Patients on IMV had higher maximal concentrations, slower decline rates, and longer shedding of SARS-CoV-2 than non-IMV patients (33 days, IQR 26-46.75, vs 18 days, IQR 16-46.75, respectively, p < 0.01). Median duration of hospitalisation was 9 days (IQR 6-15.5) for non-IMV and 49.5 days (IQR 36.8-82.5) for IMV patients. Conclusions: Our results indicate a short duration of symptoms before admission as a risk factor for severe disease that merits further investigation and different viral load kinetics in severely affected patients. Median duration of hospitalisation of IMV patients was longer than described for acute respiratory distress syndrome unrelated to COVID-19

Elements of a Computational Framework for Coupled Simulations

International audienceCoupled problems arise because certain aspects of some systems have previously been modelled separately, assuming (implicitly) an uncoupled behaviour. More often then not, computational approaches and mature software have been developed for each of these aspects in isolation. If one has to consider now the coupled problem, it would be advantageous if this previous work could be put to good use. This, in particular, concerns the developed software. In this presentation we will analyse the requirements for this to be achieved, and outline some of the possible solutions. Several tasks have to be accomplished: Non-matching spatial grids and geometric representations have to be joined, fulfilling certain consistency requirements. Similarly non-matching time-stepping schemes have tobe combined. After outlining a possible mathematical formulation for the coupling, the joining of the software will be considered. We view the original software which is modelling some aspect as a software-engineering component, and we describe a component-based approach to achieve a consistently coupled and (if so desired) distributed computational simulation

Age-Dependent Presentation and Clinical Course of 1465 Patients Aged 0 to Less than 18 Years with Ovarian or Testicular Germ Cell Tumors; Data of the MAKEI 96 Protocol Revisited in the Light of Prenatal Germ Cell Biology

OBJECTIVE To evaluate prognostic factors in pediatric patients with gonadal germ cell tumors (GCT). METHODS Patients <18 years with ovarian and testicular GCT (respectively OGCT and TGCT) were prospectively registered according to the guidelines of MAKEI 96. After resection of the primary tumor, patients staged ≥II received risk-stratified cisplatin-based combination chemotherapy. Patients were analyzed in respect to age (six age groups divided into 3-year intervals), histology, stage, and therapy. The primary end point was overall survival. RESULTS Between January 1996 and March 2016, the following patients were registered: 1047 OGCT, of those, 630 had ovarian teratoma (OTER) and 417 had malignant OGCT (MOGCT); and 418 TGCT, of those, 106 had testicular teratoma (TTER) and 312 had malignant TGCT (MTGCT). Only in MTGCT, older age correlated with a higher proportion of advanced tumors. All 736 teratomas and 240/415 stage I malignant gonadal GCT underwent surgery and close observation alone. In case of watchful waiting, the progression rate of OGCT was higher than that of TGCT. However, death from disease was reported in 8/417 (1.9%) MOGCT and 8/312 (2.6%) MTGCT irrespective of adjuvant chemotherapy and repeated surgery. CONCLUSIONS The different pathogenesis and histogenesis of gonadal GCT reflects sex- and age-specific patterns that define clinically relevant risk groups. Therefore, gender and age should be considered in further research on the biology and clinical practice of pediatric gonadal GCT

A model-based theory on the origin of downbeat nystagmus

The pathomechanism of downbeat nystagmus (DBN), an ocular motor sign typical for vestibulo-cerebellar lesions, remains unclear. Previous hypotheses conjectured various deficits such as an imbalance of central vertical vestibular or smooth pursuit pathways to be causative for the generation of spontaneous upward drift. However, none of the previous theories explains the full range of ocular motor deficits associated with DBN, i.e., impaired vertical smooth pursuit (SP), gaze evoked nystagmus, and gravity dependence of the upward drift. We propose a new hypothesis, which explains the ocular motor signs of DBN by damage of the inhibitory vertical gaze-velocity sensitive Purkinje cells (PCs) in the cerebellar flocculus (FL). These PCs show spontaneous activity and a physiological asymmetry in that most of them exhibit downward on-directions. Accordingly, a loss of vertical floccular PCs will lead to disinhibition of their brainstem target neurons and, consequently, to spontaneous upward drift, i.e., DBN. Since the FL is involved in generation and control of SP and gaze holding, a single lesion, e.g., damage to vertical floccular PCs, may also explain the associated ocular motor deficits. To test our hypothesis, we developed a computational model of vertical eye movements based on known ocular motor anatomy and physiology, which illustrates how cortical, cerebellar, and brainstem regions interact to generate the range of vertical eye movements seen in healthy subjects. Model simulation of the effect of extensive loss of floccular PCs resulted in ocular motor features typically associated with cerebellar DBN: (1) spontaneous upward drift due to decreased spontaneous PC activity, (2) gaze evoked nystagmus corresponding to failure of the cerebellar loop supporting neural integrator function, (3) asymmetric vertical SP deficit due to low gain and asymmetric attenuation of PC firing, and (4) gravity-dependence of DBN caused by an interaction of otolith-ocular pathways with impaired neural integrator function

Biogeography of bacterioplankton in inland waters

Bacteria are among the most abundant groups of organisms. They mediate key ecological processes. Recent molecular advances have provided greater insight into bacterial diversity as well as allowing a more thorough examination of patterns in the spatial and temporal distribution of bacteria. Thus, the study of bacterial biodiversity and biogeographical distribution has stimulated considerable interest and dispute over the last decade. This review summarises the findings obtained from studies on the biogeography of bacterioplankton in inland waters. We examine factors and processes that may determine and maintain bacterial diversity and biogeography, and relate these to the theoretical metacommunity framework. We conclude that the importance of local environmental factors (such as lake character) for local bacterioplankton community compositions (BCC) is much more intensively studied than the importance of regional factors, such as dispersal. Further, few attempts have been made to evaluate simultaneously the relative importance of the two types of factors for BCC. Finally, we summarise gaps in knowledge, delineate challenges and put forward possible future research directions