Overview of the PALM model system 6.0

In this paper, we describe the PALM model system 6.0. PALM (formerly an abbreviation for Parallelized Large-eddy Simulation Model and now an independent name) is a Fortran-based code and has been applied for studying a variety of atmospheric and oceanic boundary layers for about 20 years. The model is optimized for use on massively parallel computer architectures. This is a follow-up paper to the PALM 4.0 model description in Maronga et al. (2015). During the last years, PALM has been significantly improved and now offers a variety of new components. In particular, much effort was made to enhance the model with components needed for applications in urban environments, like fully interactive land surface and radiation schemes, chemistry, and an indoor model. This paper serves as an overview paper of the PALM 6.0 model system and we describe its current model core. The individual components for urban applications, case studies, validation runs, and issues with suitable input data are presented and discussed in a series of companion papers in this special issue.Peer reviewe

Temporal and spatial analysis of the 2014-2015 Ebola virus outbreak in West Africa

West Africa is currently witnessing the most extensive Ebola virus (EBOV) outbreak so far recorded. Until now, there have been 27,013 reported cases and 11,134 deaths. The origin of the virus is thought to have been a zoonotic transmission from a bat to a two-year-old boy in December 2013 (ref. 2). From this index case the virus was spread by human-to-human contact throughout Guinea, Sierra Leone and Liberia. However, the origin of the particular virus in each country and time of transmission is not known and currently relies on epidemiological analysis, which may be unreliable owing to the difficulties of obtaining patient information. Here we trace the genetic evolution of EBOV in the current outbreak that has resulted in multiple lineages. Deep sequencing of 179 patient samples processed by the European Mobile Laboratory, the first diagnostics unit to be deployed to the epicentre of the outbreak in Guinea, reveals an epidemiological and evolutionary history of the epidemic from March 2014 to January 2015. Analysis of EBOV genome evolution has also benefited from a similar sequencing effort of patient samples from Sierra Leone. Our results confirm that the EBOV from Guinea moved into Sierra Leone, most likely in April or early May. The viruses of the Guinea/Sierra Leone lineage mixed around June/July 2014. Viral sequences covering August, September and October 2014 indicate that this lineage evolved independently within Guinea. These data can be used in conjunction with epidemiological information to test retrospectively the effectiveness of control measures, and provides an unprecedented window into the evolution of an ongoing viral haemorrhagic fever outbreak.status: publishe

Implementation of sustainable urban drainage systems into local planning processes as a contribution to water sensitive urban design

Transformationsprozesse wie der globale Klimawandel und demographische Verschiebungen führen in urbanen Räumen zu städtebaulichen, stadtklimatischen und gewässerbezogenen Defiziten. Diese Defizite werden maßgeblich durch die Art und Weise der Regenwasserbewirtschaftung beeinflusst. Die dezentrale Bewirtschaftung von Regenwasser mit Maßnahmen der Versickerung, Verdunstung, Rückhaltung und gedrosselten Ableitung ermöglicht einen naturnahen urbanen Wasserkreislauf, in dessen Folge Hitzeinseln, Gewässerbelastungen, aber auch die Belastung von bestehenden Kanalnetzen reduziert werden. Die bei Umsetzung von dezentraler Regenwasserbewirtschaftung (dRWB) geschaffenen Grün- und Wasserflächen haben darüber hinaus ein städtebauliches Aufwertungspotential. Vor dem Hintergrund der mehrdimensionalen Wirkung von dRWB hat sich mit dem Begriff der wassersensiblen Stadtentwicklung ein neues Narrativ und Planungsparadigma entwickelt. Zur Umsetzung von wassersensibler Stadtentwicklung bedarf es einer Implementation von dRWB in alltägliche kommunale Planungsprozesse. Trotz der bekannten Vorteile der dRWB finden vielerorts solche Implementationsprozesse nicht oder nur sehr begrenzt statt. Mit dem Ziel, Treiber und Hindernisse für die Implementation von dRWB in kommunalen Planungsprozessen zu identifizieren, werden daher folgende Forschungsfragen in dieser Arbeit erörtert: - Warum bedarf es wassersensibler Stadtentwicklung bzw. der Implementation von dRWB in kommunale Planungsprozesse? - Wie erfolgt die Implementation von dRWB in kommunale Planungsprozesse? - Wo (räumlich, technisch, prozedural) erfolgt die Implementation von dRWB? - Wann (zeitlich, prozedural) erfolgt die Implementation von dRWB? - Wer (Akteure) implementiert dRWB? Als transdisziplinäre Untersuchung im Spannungsfeld von Siedlungswasserwirtschaft und Raumplanung bedient sich diese Arbeit sowohl etablierter Methoden der Wasserwirtschaft als auch solcher der Politik- und Verwaltungswissenschaft. Bewirtschaftungsszenarien für ein Bestandsquartier werden modelltechnisch abgebildet. Wasserwirtschaftliche Effekte werden quantifiziert und mit planerischen Bedingungen in einen Kontext gesetzt. Über eine Policyanalyse wird dargestellt, welche Elemente der wassersensiblen Stadtentwicklung bereits in existierenden wasserwirtschaftlichen und raumplanerischen Handlungsprogrammen enthalten sind. Anhand einer politikfeldbezogenen Verwaltungsanalyse werden darüber hinaus mit der „Zukunftsvereinbarung Regenwasser“ und der Zukunftsinitiative „Wasser in der Stadt von morgen“ zwei explizit wassersensible Handlungsprogramme analysiert. Es wird eine große Bandbreite an Einflussfaktoren in den Bereichen der Regularien, Anreiz- und Finanzierungssysteme, Verwaltungsstrukturen und Prozessorganisation identifiziert. Hierbei wird fortlaufend die Bedeutung individueller Interessen und Motivationen ersichtlich. Die Analyse mündet in einer Zusammenfassung besonders relevanter Treiber und Hemmnisse aus den Bereichen der Normung, der Leitbilder, der Prozessorganisation und des Akteursverhaltens. Abschließend werden Handlungsempfehlungen ausgesprochen. Die Arbeit skizziert einen transdisziplinären Forschungsansatz der geeignet ist, tiefergehende und kommunenspezifische Implementationstreiber und -hemmnisse zu identifizieren. Eine Anwendung der Methode in Reallaboren wird empfohlen, um die herausgearbeiteten Einflussfaktoren ortsspezifisch zu konkretisieren und zu ergänzen.Transformation processes such as global warming and demographic shifts result in urban climate, urban quality, and water-related deficits. These deficits are influenced by the method and manner of rainwater management. The decentralized management of rainwater with infiltration, evaporation, retention and restricted discharge enables natural circulation. Vegetation and waterbodies created by sustainable urban drainage systems (SUDS) have significant potential to improve urban development. Against the backdrop of SUDS’s multidimensional effect, a new narrative and planning paradigm has developed with the concept of water-sensitive urban design. The implementation of water-sensitive urban design requires the implementation of SUDS in day-to-day planning processes at the municipal level. Despite the known advantages of SUDS, such implementation processes have been used sparingly, if at all. With the aim of identifying drivers and obstacles for the implementation of SUDS in municipal planning processes, the following research questions are discussed in this thesis: - Why is there a need for water-sensitive urban design and the implementation of SUDS in municipal planning processes? - How is SUDS implemented in municipal planning processes? - Where (spatially, technically, procedurally) is SUDS implemented? - When (chronologically, procedurally) is SUDS implemented? - Who (agents) implements SUDS? As a transdisciplinary study between urban water management and spatial planning, this work utilises established methods of water management and those of political and administrative science. Best-practise scenarios for an existing city district are illustrated through models. Water management effects are quantified and put into context with planning conditions. A policy analysis shows which elements of water-sensitive urban design already exist in water management and spatial planning programs. On the basis of an administrative analysis related to the policy field, two explicitly water-sensitive programs of action are also analysed: the “Zukunftsvereinbarung Regenwasser” and “Wasser in der Stadt von morgen” initiatives. A wide range of influencing factors in the areas of regulations, incentive and financing systems, administrative structures and process organization are identified. The importance of individual interests and motivations is con¬tinuously evident. The analysis leads to a summarizing presentation of particularly relevant drivers and obstacles from the areas of standardization, mission statements, process organization and agent behaviour. Finally, recommendations for action are made. The work outlines a transdisciplinary research approach that will assist in the identification deeper and community-specific implementation drivers and barriers. An application of these methods through research by design is recommended in order to concretize and supplement the influencing factors elucidated here on a site-specific basis

Generalization, Mayhems and Limits in Recurrent Proximal Policy Optimization

At first sight it may seem straightforward to use recurrent layers in Deep Reinforcement Learning algorithms to enable agents to make use of memory in the setting of partially observable environments. Starting from widely used Proximal Policy Optimization (PPO), we highlight vital details that one must get right when adding recurrence to achieve a correct and efficient implementation, namely: properly shaping the neural net's forward pass, arranging the training data, correspondingly selecting hidden states for sequence beginnings and masking paddings for loss computation. We further explore the limitations of recurrent PPO by benchmarking the contributed novel environments Mortar Mayhem and Searing Spotlights that challenge the agent's memory beyond solely capacity and distraction tasks. Remarkably, we can demonstrate a transition to strong generalization in Mortar Mayhem when scaling the number of training seeds, while the agent does not succeed on Searing Spotlights, which seems to be a tough challenge for memory-based agents.Comment: 17 pages, 18 figures, preprin

Modeling and Optimizing Data Transfer in GPU-Accelerated Optical Coherence Tomography

Signal processing of optical coherence tomography (OCT) has become a bottleneck for using OCT in medical and industrial applications. Recently, GPUs gained more importance as compute device to achieve video frame rate of 25 frames/s. Therefore, we develop a CUDA implementation of an OCT signal processing chain: We focus on reformulating the signal processing algorithms in terms of high-performance libraries like CUBLAS and CUFFT. Additionally, we use NVIDIAs stream concept to overlap computations and data transfers. Performance results are presented for two Pascal GPUs and validated with a derived performance model. The model gives an estimate for the overall execution time for the OCT signal processing chain, including compute and transfer times

Inhibition of Protein Geranylgeranylation Specifically Interferes with CD40-Dependent B Cell Activation, Resulting in a Reduced Capacity To Induce T Cell Immunity

Ab-independent effector functions of B cells, such as Ag presentation and cytokine production, have been shown to play an important role in a variety of immune-mediated conditions such as autoimmune diseases, transplant rejection, and graft-versus-host disease. Most current immunosuppressive treatments target T cells, are relatively unspecific, and result in profound immunosuppression that places patients at an increased risk of developing severe infections and cancer. Therapeutic strategies, which interfere with B cell activation, could therefore be a useful addition to the current immunosuppressive armamentarium. Using a transcriptomic approach, we identified upregulation of genes that belong to the mevalonate pathway as a key molecular event following CD40-mediated activation of B cells. Inhibition of 3-hydroxy-3-methylglutaryl CoA reductase, the rate-limiting enzyme of the mevalonate pathway, by lipophilic statins such as simvastatin and atorvastatin resulted in a specific inhibition of B cell activation via CD40 and impaired their ability to act as stimulatory APCs for allospecific T cells. Mechanistically, the inhibitory effect resulted from the inhibition of protein geranylgeranylation subsequent to the depletion of mevalonate, the metabolic precursor for geranylgeranyl. Thus, inhibition of geranylgeranylation either directly through geranylgeranyl transferase inhibitors or indirectly through statins represents a promising therapeutic approach for the treatment of diseases in which Ag presentation by B cells plays a role

COVID-19 Infection Induce miR-371a-3p Upregulation Resulting in Influence on Male Fertility

In December 2019, the first case of COVID-19 was reported and since then several groups have already published that the virus can be present in the testis. To study the influence of SARS-CoV-2 which cause a dysregulation of the androgen receptor (AR) level, thereby leading to fertility problems and inducing germ cell testicular changes in patients after the infection. Formalin-Fixed-Paraffin-Embedded (FFPE) testicular samples from patients who died with or as a result of COVID-19 (n = 32) with controls (n = 6), inflammatory changes (n = 9), seminoma with/without metastasis (n = 11) compared with healthy biopsy samples (n = 3) were analyzed and compared via qRT-PCR for the expression of miR-371a-3p. An immunohistochemical analysis (IHC) and ELISA were performed in order to highlight the miR-371a-3p targeting the AR. Serum samples of patients with mild or severe COVID-19 symptoms (n = 34) were analyzed for miR-371a-3p expression. In 70% of the analyzed postmortem testicular tissue samples, a significant upregulation of the miR-371a-3p was detected, and 75% of the samples showed a reduced spermatogenesis. In serum samples, the upregulation of the miR-371a-3p was also detectable. The upregulation of the miR-371a-3p is responsible for the downregulation of the AR in SARS-CoV-2-positive patients, resulting in decreased spermatogenesis. Since the dysregulation of the AR is associated with infertility, further studies have to confirm if the identified dysregulation is regressive after a declining infection

COVID-19 Infection Induce miR-371a-3p Upregulation Resulting in Influence on Male Fertility

In December 2019, the first case of COVID-19 was reported and since then several groups have already published that the virus can be present in the testis. To study the influence of SARSCoV-2 which cause a dysregulation of the androgen receptor (AR) level, thereby leading to fertility problems and inducing germ cell testicular changes in patients after the infection. Formalin-Fixed-Paraffin-Embedded (FFPE) testicular samples from patients who died with or as a result of COVID-19 (n = 32) with controls (n = 6), inflammatory changes (n = 9), seminoma with/without metastasis (n = 11) compared with healthy biopsy samples (n = 3) were analyzed and compared via qRT-PCR for the expression of miR-371a-3p. An immunohistochemical analysis (IHC) and ELISA were performed in order to highlight the miR-371a-3p targeting the AR. Serum samples of patients with mild or severe COVID-19 symptoms (n = 34) were analyzed for miR-371a-3p expression. In 70% of the analyzed postmortem testicular tissue samples, a significant upregulation of the miR-371a-3p was detected, and 75% of the samples showed a reduced spermatogenesis. In serum samples, the upregulation of the miR-371a-3p was also detectable. The upregulation of the miR-371a-3p is responsible for the downregulation of the AR in SARS-CoV-2-positive patients, resulting in decreased spermatogenesis. Since the dysregulation of the AR is associated with infertility, further studies have to confirm if the identified dysregulation is regressive after a declining infection

Quantifying the effects of urban stormwater management - towards a novel approach for integrated planning

ABSTRACT Integrated planning of stormwater management requires a quantitative description of positive and negative effects of possible measures. We suggest quantifying these effects with generic performance indicators within eight categories: building physics and services, landscape quality, urban climate, biodiversity, groundwater, surface water, direct costs and indirect environmental costs. First results indicate that the defined performance indicators allow an objective pre-selection of measures based on their ability to reach local stormwater management goals. The final selection of measures should be based on an evaluation for a specific city quarter (to reduce indicator uncertainty) and reviewed by local stake holders