Small coastal marine protected areas offer recurring, seasonal protection to the common stingray (Dasyatis pastinaca)

Marine protected areas (MPAs) are a crucial tool in safeguarding marine biodiversity. However, elasmobranchs are often not the primary protection target of MPAs, and their contribution to protect these species remains to be better understood. In this study we examine the movement patterns of common stingrays in the Professor Luiz Saldanha marine park, a Portuguese temperate coastal MPA. Using acoustic telemetry, we tagged 31 common stingrays and analyzed their spatial and temporal distribution within the MPA and adjacent areas using a long-term data set. Our findings indicate that this species exhibits seasonal site fidelity, with greater presence during the colder months and reduced presence during warmer months. Space use areas did not exceed the size of the fully protected area, and nocturnal and crepuscular activity was significantly higher than during daytime. Additionally, we observed that most individuals seasonally migrated between this MPA and the nearby Sado estuary, likely to reproduce in the latter. These results demonstrate the site fidelity of common stingrays to an area within the marine park, however the protection provided is only seasonal. Seasonal protection of the movement corridor between the marine park and the estuary would improve the management of this species.La Caixa FoundationLCF/BQ/DI20/11780001, Fundacao para a Ciencia e a Tecnologia (FCT) POSEUR-03-2215-FC-000047info:eu-repo/semantics/publishedVersio

Numerical solution of optimal control problems with constant control delays

We investigate a class of optimal control problems that exhibit constant exogenously given delays in the control in the equation of motion of the differential states. Therefore, we formulate an exemplary optimal control problem with one stock and one control variable and review some analytic properties of an optimal solution. However, analytical considerations are quite limited in case of delayed optimal control problems. In order to overcome these limits, we reformulate the problem and apply direct numerical methods to calculate approximate solutions that give a better understanding of this class of optimization problems. In particular, we present two possibilities to reformulate the delayed optimal control problem into an instantaneous optimal control problem and show how these can be solved numerically with a state-of-the-art direct method by applying Bock’s direct multiple shooting algorithm. We further demonstrate the strength of our approach by two economic examples.delayed differential equations, delayed optimal control, numerical optimization, time-to-build

De-novo pathway discovery for multi-omics data

In der vorliegenden Arbeit werden Methoden und Software vorgestellt, die es erlauben, aus Hochdurchsatz Omics-Daten und biomolekularen Interaktionsnetzwerken biologisch relevante Muster zu extrahieren. Es wird ein Algorithmus entwickelt, der es ermöglicht, aus großen gerichteten molekularen Interaktionsnetzwerken sog. deregulierte Teilnetzwerke zu extrahieren. Deregulierung wird hierbei über auf die Knoten des Netzwerkes abgebildete Omics-Daten definiert. Es wird eine statistische Grundlage für den vorgestellten Algorithmus diskutiert und eine Evaluierung hinsichtlich methodisch verwandter Verfahren vorgenommen. Der Algorithmus und seine Implementierung, DeRegNet, beruhen auf fraktionaler ganzzahliger Optimierung und erlauben zahlreiche Anwendungsszenarien. Exemplarisch wird die Anwendung auf öffentlich zugängliche Daten des TCGA-Projekts vorgestellt (TCGA: The Cancer Genome Atlas), hier genauer an Hand der Daten zum hepatozellulären Karzinom (Leberkrebs). Weiterhin werden Anwendungen auf eine Studie des Folate One-Carbon Metabolismus im Leberkrebs, als auch auf die phosphoproteomische Regulierung des Saccharomyces cerevisiae (Backhefe) Zellzyklus beschrieben. Abschließend wird auf die allgemeine Architektur und einige Implementationsdetails einer web-basierten API (Application Programming Interface) zur Bereitstellung von DeRegNet eingegangen.This thesis presents algorithms and software which allow the extraction of biologically meaningful patterns from high-throughput multi-omics data and biomolecular networks. It describes the concept and implementation of an algorithm which allows the extraction of deregulated subnetworks from large directed molecular interaction networks based on node scores derived from omics data. Statistical underpinnings of the algorithms are derived and the algorithm is benchmarked against its closest methodological relative. Relying on fractional integer programming, the algorithm and its implementation, DeRegNet, allow many flexible modes of application. I demonstrate the application of the algorithm in the context of the public TCGA (The Cancer Genome Atlas) liver cancer dataset, a study investigating the role of folate one-carbon metabolism in liver cancer and a study about the phosphoproteomic regulation of the Saccharomyces cerevisiae (baker's yeast) cell cycle. Finally, the general architecture and some implementation details of a web-based API for DeRegNet are presented

Carbon emissions of retail channels: the limits of available policy instruments to achieve absolute reductions

Buying the same product at the neighborhood store or at a shopping mall implies different carbon emissions. This paper quantifies carbon impacts of consumer choices of retail channel and shop location (where to buy), extending footprint assessments of product choices (what to buy). Carbon emissions of shopping situations are shown in the current situation, in a business-as-usual projection in 2020, and in policy scenarios with changed market shares of shopping situations. The analysis covers the product categories: groceries, clothing, and electronics & computers, from the shopping situations: neighborhood store, town center, discount store, shopping mall, and mail order/online selling. Stages of the product life cycle which differ between shopping situations are examined: freight transport, warehousing, store operation, and the last mile of the consumers' trip to the store. Carbon emissions of shopping situations amount to 2.7% of overall Austrian emissions in the base year. Dominant car use on the last mile substantially contributes to the overall footprint. In the business-as-usual scenario, carbon emissions from shopping situations increase by +33% until 2020, corresponding to 4.2% of the overall Austrian emissions target for 2020. Restricting shopping malls or supporting neighborhood stores could limit this increase to +25% and +20%, respectively. Facilitating online selling achieves no notable effects. The study underlines that an absolute reduction in private demand for household goods is necessary, as available policy instruments aiming at shopping situations fail to compensate the steady growth in private consumption

Complete Genome Sequence of the Type Strain Corynebacterium testudinoris DSM 44614, Recovered from Necrotic Lesions in the Mouth of a Tortoise

The complete genome sequence of the type strain Corynebacterium testudinoris DSM 44614 from the mouth of a tortoise comprises 2,721,226 bp with a mean G+C content of 63.14%. The automatic annotation of the genome sequence revealed 4 rRNA operons, 51 tRNA genes, 7 other RNA genes, and 2,561 protein-coding regions.Medical Microbiology and Genomics fund (eKVV 200937)Germany. Federal Ministry of Education and Research (German Network for Bioinformatics Intrastructure Initiative FKZ 031A533A

Virulence Factor Genes Detected in the Complete Genome Sequence of Corynebacterium uterequi DSM 45634, Isolated from the Uterus of a Maiden Mare

The complete genome sequence of the type strain Corynebacterium uterequi DSM 45634 from an equine urogenital tract specimen comprises 2,419,437 bp and 2,163 protein-coding genes. Candidate virulence factors are homologs of DIP0733, DIP1281, and DIP1621 from Corynebacterium diphtheriae and of sialidase precursors from Trueperella pyogenes and Chlamydia trachomatis.Medical Microbiology and Genomics fund (eKVV 200937)Germany. Federal Ministry of Education and Research (German Network for Bioinformatics Intrastructure Initiative FKZ 031A533A

QuestEnvSim: Environment-Aware Simulated Motion Tracking from Sparse Sensors

Replicating a user's pose from only wearable sensors is important for many AR/VR applications. Most existing methods for motion tracking avoid environment interaction apart from foot-floor contact due to their complex dynamics and hard constraints. However, in daily life people regularly interact with their environment, e.g. by sitting on a couch or leaning on a desk. Using Reinforcement Learning, we show that headset and controller pose, if combined with physics simulation and environment observations can generate realistic full-body poses even in highly constrained environments. The physics simulation automatically enforces the various constraints necessary for realistic poses, instead of manually specifying them as in many kinematic approaches. These hard constraints allow us to achieve high-quality interaction motions without typical artifacts such as penetration or contact sliding. We discuss three features, the environment representation, the contact reward and scene randomization, crucial to the performance of the method. We demonstrate the generality of the approach through various examples, such as sitting on chairs, a couch and boxes, stepping over boxes, rocking a chair and turning an office chair. We believe these are some of the highest-quality results achieved for motion tracking from sparse sensor with scene interaction