Community-driven development for computational biology at Sprints, Hackathons and Codefests

Background: Computational biology comprises a wide range of technologies and approaches. Multiple technologies can be combined to create more powerful workflows if the individuals contributing the data or providing tools for its interpretation can find mutual understanding and consensus. Much conversation and joint investigation are required in order to identify and implement the best approaches. Traditionally, scientific conferences feature talks presenting novel technologies or insights, followed up by informal discussions during coffee breaks. In multi-institution collaborations, in order to reach agreement on implementation details or to transfer deeper insights in a technology and practical skills, a representative of one group typically visits the other. However, this does not scale well when the number of technologies or research groups is large. Conferences have responded to this issue by introducing Birds-of-a-Feather (BoF) sessions, which offer an opportunity for individuals with common interests to intensify their interaction. However, parallel BoF sessions often make it hard for participants to join multiple BoFs and find common ground between the different technologies, and BoFs are generally too short to allow time for participants to program together. Results: This report summarises our experience with computational biology Codefests, Hackathons and Sprints, which are interactive developer meetings. They are structured to reduce the limitations of traditional scientific meetings described above by strengthening the interaction among peers and letting the participants determine the schedule and topics. These meetings are commonly run as loosely scheduled "unconferences" (self-organized identification of participants and topics for meetings) over at least two days, with early introductory talks to welcome and organize contributors, followed by intensive collaborative coding sessions. We summarise some prominent achievements of those meetings and describe differences in how these are organised, how their audience is addressed, and their outreach to their respective communities. Conclusions: Hackathons, Codefests and Sprints share a stimulating atmosphere that encourages participants to jointly brainstorm and tackle problems of shared interest in a self-driven proactive environment, as well as providing an opportunity for new participants to get involved in collaborative projects

The societal cost of treatment-seeking patients with borderline personality disorder in Germany

According to previous research, borderline personality disorder (BPD) is associated with high cost-of-illness. However, there is still a shortage of cost-of-illness-studies assessing costs from a broad societal perspective, including direct and indirect costs. Further, there are considerable differences in the results among the existing studies. In the present study, 167 German men and women seeking specialized outpatient treatment for BPD were included. We assessed societal cost-of-illness bottom-up through structured face-to-face interviews and encompassed a wide range of cost components. All costs were calculated for the 2015 price level. Cost-of-illness amounted to € 31,130 per patient and year preceding disorder-specific outpatient treatment. € 17,044 (54.8%) were direct costs that were mostly related to hospital treatment. Indirect costs amounted to € 14,086 (45.2%). Within indirect costs, costs related to work disability were the most crucial cost driver. The present study underlines the tremendous economic burden of BPD. According to the present study, both the direct and indirect costs are of significant importance for the societal costs associated with BPD. Besides the need for more disorder-specific treatment facilities for men and women with BPD, we assume that education and employment are topics that should be specifically targeted and individually supported at an early stage of treatment. Trial Registration: German Clinical Trial Registration, DRKS00011534, Date of Registration: 11/01/2017, retrospectively registered

Viral shedding and antibody response in 37 patients with MERS-coronavirus infection

Background. The Middle East respiratory syndrome (MERS) coronavirus causes isolated cases and outbreaks of severe respiratory disease. Essential features of the natural history of disease are poorly understood. Methods. We studied 37 adult patients infected with MERS coronavirus for viral load in the lower and upper respiratory tracts (LRT and URT, respectively), blood, stool, and urine. Antibodies and serum neutralizing activities were determined over the course of disease. Results. One hundred ninety-nine LRT samples collected during the 3 weeks following diagnosis yielded virus RNA in 93% of tests. Average (maximum) viral loads were 5 × 106 (6 × 1010) copies/mL. Viral loads (positive detection frequencies) in 84 URT samples were 1.9 × 104 copies/mL (47.6%). Thirty-three percent of all 108 serum samples tested yielded viral RNA. Only 14.6% of stool and 2.4% of urine samples yielded viral RNA. All seroconversions occurred during the first 2 weeks after diagnosis, which corresponds to the second and third week after symptom onset. Immunoglobulin M detection provided no advantage in sensitivity over immunoglobulin G (IgG) detection. All surviving patients, but only slightly more than half of all fatal cases, produced IgG and neutralizing antibodies. The levels of IgG and neutralizing antibodies were weakly and inversely correlated with LRT viral loads. Presence of antibodies did not lead to the elimination of virus from LRT. Conclusions. The timing and intensity of respiratory viral shedding in patients with MERS closely matches that of those with severe acute respiratory syndrome. Blood viral RNA does not seem to be infectious. Extrapulmonary loci of virus replication seem possible. Neutralizing antibodies do not suffice to clear the infection

Formation of Compressed Flat Electron Beams with High Transverse-Emittance Ratios

Flat beams -- beams with asymmetric transverse emittances -- have important applications in novel light-source concepts, advanced-acceleration schemes and could possibly alleviate the need for damping rings in lepton colliders. Over the last decade, a flat-beam-generation technique based on the conversion of an angular-momentum-dominated beam was proposed and experimentally tested. In this paper we explore the production of compressed flat beams. We especially investigate and optimize the flat-beam transformation for beams with substantial fractional energy spread. We use as a simulation example the photoinjector of the Fermilab's Advanced Superconducting Test Accelerator (ASTA). The optimizations of the flat beam generation and compression at ASTA were done via start-to-end numerical simulations for bunch charges of 3.2 nC, 1.0 nC and 20 pC at ~37 MeV. The optimized emittances of flat beams with different bunch charges were found to be 0.25 {\mu}m (emittance ratio is ~400), 0.13 {\mu}m, 15 nm before compression, and 0.41 {\mu}m, 0.20 {\mu}m, 16 nm after full compression, respectively with peak currents as high as 5.5 kA for a 3.2-nC flat beam. These parameters are consistent with requirements needed to excite wakefields in asymmetric dielectric-lined waveguides or produce significant photon flux using small-gap micro-undulators.Comment: 17

Stronger Neural Modulation by Visual Motion Intensity in Autism Spectrum Disorders

Theories of autism spectrum disorders (ASD) have focused on altered perceptual integration of sensory features as a possible core deficit. Yet, there is little understanding of the neuronal processing of elementary sensory features in ASD. For typically developed individuals, we previously established a direct link between frequency-specific neural activity and the intensity of a specific sensory feature: Gamma-band activity in the visual cortex increased approximately linearly with the strength of visual motion. Using magnetoencephalography (MEG), we investigated whether in individuals with ASD neural activity reflect the coherence, and thus intensity, of visual motion in a similar fashion. Thirteen adult participants with ASD and 14 control participants performed a motion direction discrimination task with increasing levels of motion coherence. A polynomial regression analysis revealed that gamma-band power increased significantly stronger with motion coherence in ASD compared to controls, suggesting excessive visual activation with increasing stimulus intensity originating from motion-responsive visual areas V3, V6 and hMT/V5. Enhanced neural responses with increasing stimulus intensity suggest an enhanced response gain in ASD. Response gain is controlled by excitatory-inhibitory interactions, which also drive high-frequency oscillations in the gamma-band. Thus, our data suggest that a disturbed excitatoryinhibitory balance underlies enhanced neural responses to coherent motion in ASD

Measuring data‑centre workfows complexity through process mining: the Google cluster case

Data centres have become the backbone of large Cloud services and applica-tions, providing virtually unlimited elastic and scalable computational and storage resources. The search for the efficiency and optimisation of resources is one of the current key aspects for large Cloud Service Providers and is becoming more and more challenging, since new computing paradigms such as Internet of Things, Cyber-Physical Systems and Edge Computing are spreading. One of the key aspects to achieve efficiency in data centres consists of the discovery and proper analysis of the data-centre behaviour. In this paper, we present a model to automatically retrieve execution workflows of existing data-centre logs by employing process mining tech-niques. The discovered processes are characterised and analysed according to the understandability and complexity in terms of execution efficiency of data-centre jobs. We finally validate and demonstrate the usability of the proposal by applying the model in a real scenario, that is, the Google Cluster tracesMinisterio de Ciencia y Tecnología RTI2018–094283-B-C33Ministerio de Ciencia y Tecnología RTI2018-098062-A-I00Universidad de Sevilla 2018/0000052

Maritime Logistik im Zeitalter der Nordischen Kreuzzügen

The Limes Saxoniae remained a stable cultural frontier zone until the year 1147, when Danish and German princes managed to subdue the Slavic lands east of the Elbe lastingly in a joint maritime-terrestrial campaign. It was the first papally authorised crusading campaign “contra Sclavos ceterosque paganos habitantes versus Aquilonem” – the last pagans of northern Europe. This expeditio was a precedent, followed by many more campaigns against the Slavs, Prussians, Lithuanians, Livs, Estonians and other pagan nations of the Baltic Rim; a time frame spanning over four centuries, colloquially captured by the umbrella term ‘Northern Crusades’. Most of these campaigns required seaborne transport, which is studied here with an interdisciplinary historical-archaeological approach. The diachronic theme is examined by a number of case studies, which involve different angles: On the one hand, questions of navigation and orientation are addressed, as exemplified by a re-evaluation of a 13th-century Danish itinerary to Estonia. On the other hand, the capabilities and use of ships are assessed, which supplied the Catholic enclaves in the pagan East with crusaders, settlers and goods. Numerous shipwrecks are re-visited to verify the claims of contemporary chroniclers, with discussions on technical aspects of ship-construction, but also with a focus on early trade links. Another major focus lies on timber trade across the Baltic Sea, shedding light on an often overlooked aspect: The Teutonic Order as economic rather than solely militaristic power. This study is concluded by assessing the local maritime transport geography of a Teutonic Order castle and a nearby appertaining shipwreck from a period of political instability and the imminent collapse of the Livonian Confederation.Für Jahrhunderte bildete der Limes Saxoniae eine feste Kulturgrenze, bis ins Jahr 1147, als dänische und deutsche Fürsten die slawischen Länder östlich der Elbe in koordinierten see- und landseitigen Angriffen unter ihre Kontrolle brachten. Es war der erste päpstlich angeordnete Kreuzzug “contra Sclavos ceterosque paganos habitantes versus Aquilonem” – gegen die letzten Heiden Nordeuropas. Dieser Kreuzzug war der Ausgangpunkt für zahlreiche weitere Feldzüge gegen Slawen, Pruzzen, Litauer, Liven, Esten und anderen heidnischen Nationen des Ostseeraumes und charakterisierte eine über vier Jahrhunderte umspannende Epoche, die unter dem Begriff 'Nordische Kreuzzüge' verstanden wird. Für die meisten dieser Feldzüge war die Schifffahrt eine Grundvoraussetzung, die hier durch einen interdisziplinär historisch-archäologischen Ansatz erforscht wird. Die diachronische Thematik wird durch eine Reihe von Fallstudien untergliedert, die unterschiedliche Ansatzpunkte haben: Auf der einen Seite wird der Frage nachgegangen, wie man sich im Mittelalter orientierte und welche Navigationstechniken zum Einsatz kamen, exemplarisch anhand eines dänischen Itinerars nach Estland aus dem 13. Jahrhundert veranschaulicht. Auf der anderen Seite werden die Einsatzmöglichkeiten und Einsatzgebiete von Schiffen untersucht, welche die katholischen Enklaven im heidnischen Osten mit Kreuzfahrern, aber auch Kolonisten und Gütern versorgten. Eine Reihe an mittelalterlichen Schiffwracks werden unter dieser Fragestellung evaluiert, um die Aussagen von zeitgenössischen Chronisten, Diskussionen zu schiffbaulichen Eigenheiten, aber auch frühen Handelsverbindungen zu vergleichen. Ein weiteres Augenmerk liegt auf dem baltischen Holzhandel, der einen oft übersehenen Aspekt aufgreift: Der Deutsche Orden als Handelsmacht. Diese Arbeit schließt mit einer Fallstudie zur maritimen Transportgeografie einer Deutschordensburg und eines zugehörigen Schiffwracks ab, die in eine Zeit der politischen Instabilität und des bevorstehenden Zusammenbruchs der Livländischen Konföderation im Jahre 1561 datieren

Health risk assessment related to hydrogen peroxide presence in the workplace atmosphere - analytical methods evaluation for an innovative monitoring protocol

ObjectivesHydrogen peroxide (HP) accounts for 15% of the total global chemical revenue. According to the National Institute of Occupational Safety and Health, the HP concentration immediately dangerous to human life or health is 75 ppm. Operators exposed to HP should pay attention when choosing the monitoring technique that should be specific and sensitive enough to discriminate the exposure levels from background concentrations. In order to assess the long- and short-term exposure to HP in disinfection processes, the authors compared 6 industrial hygiene monitoring methods to evaluate their efficiency in measuring airborne HP concentrations.Material and MethodsAirborne HP concentrations were evaluated using an on-fiber triphenylphosphine solid-phase microextraction method, and they were compared with those obtained using a 13-mm Swinnex titanium oxysulfate filter holder and 4 portable direct-reading electrochemical sensors. A survey carried out in wood pulp bleaching, food and beverage disinfection processing, and in a hospital department to reduce the risk of spreading nosocomial infections, was performed during routine operations to access the risk of HP occupational exposure.ResultsThrough the generation of HP gaseous dynamic atmospheres (0.1–85 ppm), the authors evaluated the consistency of the results obtained using the 6 methods described. The monitoring campaigns showed that the increase in HP could be relatively high (until 67 ppm) in food and beverage processing.ConclusionsIn the authors’ opinion, the current 8-h time-weighted average limits of 1 ppm for HP do not reflect the actual risk; a short-term exposure limit would, therefore, provide a much better protection