Interaction between Cape hake spawning and the circulation in the northern Benguela upwelling ecosystem

Cape hake in Namibian waters are demersal and mesopelagic spawners, spawning peaking offshore between 100 and 400 m deep, depending on local environmental conditions. The cross-shelf circulation, low-oxygen layers and mesoscale gyres are three important environmental factors influencing hake spawning behaviour and subsequent transport of the spawning products. Normally, hake spawn offshore near the bottom at depths of 150–400 m. However, during one cruise, spawning was concentrated below several subsurface mesoscale gyres, resulting in reduced dispersion of the eggs and larvae. When the low-oxygen layer above the bottom is pronounced, hake spawning has been observed close to the top of the layer at oxygen concentrations as low as 0.2–0.3 ml l-1. The relatively small size of the eggs and their high specific gravity make them ascend quite slowly from the spawning depths, 10–40 m per day. Consequently, hake eggs spawned deeper than 200 m hatch before they reach the upper mixed layer. The newly hatched larvae are relatively undeveloped, without functional eyes or mouth, and display little swimming activity during their first hours, but laboratory observations have revealed subsequent periods of downward swimming activity. Based on current field observations, on buoyancy measurements of eggs and larvae and on observed larval behaviour, it is concluded that hake eggs and larvae are transported onshore by features of the upwelling subsurface circulation that compensate for offshore movement of surface water. This may be the basic mechanism concentrating early juvenile hake nearshore. Spawning activity near the low-oxygen layer might be a behavioural adaptation to minimize egg predation, because few other species are expected to survive such low concentrations of oxygen.Keywords: buoyancy, eggs, larvae, recruitment processes, retention, vertical distributionAfrican Journal of Marine Science 2001, 23: 317–33

Contextuality-by-Default: A Brief Overview of Ideas, Concepts, and Terminology

This paper is a brief overview of the concepts involved in measuring the degree of contextuality and detecting contextuality in systems of binary measurements of a finite number of objects. We discuss and clarify the main concepts and terminology of the theory called "contextuality-by-default," and then discuss a possible generalization of the theory from binary to arbitrary measurements.Comment: Lecture Notes in Computer Science 9535 (with the corrected list of authors) (2016

Billiards in a general domain with random reflections

We study stochastic billiards on general tables: a particle moves according to its constant velocity inside some domain ${\mathcal D} \subset {\mathbb R}^d$ until it hits the boundary and bounces randomly inside according to some reflection law. We assume that the boundary of the domain is locally Lipschitz and almost everywhere continuously differentiable. The angle of the outgoing velocity with the inner normal vector has a specified, absolutely continuous density. We construct the discrete time and the continuous time processes recording the sequence of hitting points on the boundary and the pair location/velocity. We mainly focus on the case of bounded domains. Then, we prove exponential ergodicity of these two Markov processes, we study their invariant distribution and their normal (Gaussian) fluctuations. Of particular interest is the case of the cosine reflection law: the stationary distributions for the two processes are uniform in this case, the discrete time chain is reversible though the continuous time process is quasi-reversible. Also in this case, we give a natural construction of a chord "picked at random" in ${\mathcal D}$, and we study the angle of intersection of the process with a $(d-1)$-dimensional manifold contained in ${\mathcal D}$.Comment: 50 pages, 10 figures; To appear in: Archive for Rational Mechanics and Analysis; corrected Theorem 2.8 (induced chords in nonconvex subdomains

Metric properties of discrete time exclusion type processes in continuum

A new class of exclusion type processes acting in continuum with synchronous updating is introduced and studied. Ergodic averages of particle velocities are obtained and their connections to other statistical quantities, in particular to the particle density (the so called Fundamental Diagram) is analyzed rigorously. The main technical tool is a "dynamical" coupling applied in a nonstandard fashion: we do not prove the existence of the successful coupling (which even might not hold) but instead use its presence/absence as an important diagnostic tool. Despite that this approach cannot be applied to lattice systems directly, it allows to obtain new results for the lattice systems embedding them to the systems in continuum. Applications to the traffic flows modelling are discussed as well.Comment: 27 pages, 4 figures; minor errors corrected; details added to proofs of Theorems 4.1 and 5.

SNPLogic: an interactive single nucleotide polymorphism selection, annotation, and prioritization system

SNPLogic (http://www.snplogic.org) brings together single nucleotide polymorphism (SNP) information from numerous sources to provide a comprehensive SNP selection, annotation and prioritization system for design and analysis of genotyping projects. SNPLogic integrates information about the genetic context of SNPs (gene, chromosomal region, functional location, haplotypes tags and overlap with transcription factor binding sites, splicing sites, miRNAs and evolutionarily conserved regions), genotypic data (allele frequencies per population and validation method), coverage of commercial arrays (ParAllele, Affymetrix and Illumina), functional predictions (modeled on structure and sequence) and connections or established associations (biological pathways, gene ontology terms and OMIM disease terms). The SNPLogic web interface facilitates construction and annotation of user-defined SNP lists that can be saved, shared and exported. Thus, SNPLogic can be used to identify and prioritize candidate SNPs, assess custom and commercial arrays panels and annotate new SNP data with publicly available information. We have found integration of SNP annotation in the context of pathway information and functional prediction scores to be a powerful approach to the analysis and interpretation of SNP-disease association data

European Society of Coloproctology: guidelines for the management of diverticular disease of the colon

The guideline was developed during several working phases including three voting rounds and one consensus meeting. The two project leads (JKS and EA) appointed by the ESCP guideline committee together with one member of the guideline committee (WB) agreed on the methodology, decided on six themes for working groups (WGs) and drafted a list of research questions. Senior WG members, mostly colorectal surgeons within the ESCP, were invited based on publication records and geographical aspects. Other specialties were included in the WGs where relevant. In addition, one trainee or PhD fellow was invited in each WG. All six WGs revised the research questions if necessary, did a literature search, created evidence tables where feasible, and drafted supporting text to each research question and statement. The text and statement proposals from each WG were arranged as one document by the first and last authors before online voting by all authors in two rounds. For the second voting ESCP national representatives were also invited. More than 90% agreement was considered a consensus. The final phrasing of the statements with < 90% agreement was discussed in a consensus meeting at the ESCP annual meeting in Vienna in September 2019. Thereafter, the first and the last author drafted the final text of the guideline and circulated it for final approval and for a third and final online voting of rephrased statements

Very rapid long-distance sea crossing by a migratory bird

Landbirds undertaking within-continent migrations have the possibility to stop en route, but most long-distance migrants must also undertake large non-stop sea crossings, the length of which can vary greatly. For shorebirds migrating from Iceland to West Africa, the shortest route would involve one of the longest continuous sea crossings while alternative, mostly overland, routes are available. Using geolocators to track the migration of Icelandic whimbrels (Numenius phaeopus), we show that they can complete a round-trip of 11,000 km making two non-stop sea crossings and flying at speeds of up to 24 m s-1; the fastest recorded for shorebirds flying over the ocean. Although wind support could reduce flight energetic costs, whimbrels faced headwinds up to twice their ground speed, indicating that unfavourable and potentially fatal weather conditions are not uncommon. Such apparently high risk migrations might be more common than previously thought, with potential fitness gains outweighing the costs

Genetic influences on attention deficit hyperactivity disorder symptoms from age 2 to 3: A quantitative and molecular genetic investigation

<p>Abstract</p> <p>Background</p> <p>A twin study design was used to assess the degree to which additive genetic variance influences ADHD symptom scores across two ages during infancy. A further objective in the study was to observe whether genetic association with a number of candidate markers reflects results from the quantitative genetic analysis.</p> <p>Method</p> <p>We have studied 312 twin pairs at two time-points, age 2 and age 3. A composite measure of ADHD symptoms from two parent-rating scales: The Child Behavior Checklist/1.5 - 5 years (CBCL) hyperactivity scale and the Revised Rutter Parent Scale for Preschool Children (RRPSPC) was used for both quantitative and molecular genetic analyses.</p> <p>Results</p> <p>At ages 2 and 3 ADHD symptoms are highly heritable (<it>h</it>^{<it>2 </it>}<it>= </it>0.79 and 0.78, respectively) with a high level of genetic stability across these ages. However, we also observe a significant level of genetic change from age 2 to age 3. There are modest influences of non-shared environment at each age independently (<it>e</it>^{<it>2 </it>}= 0.22 and 0.21, respectively), with these influences being largely age-specific. In addition, we find modest association signals in <it>DAT1 </it>and <it>NET1 </it>at both ages, along with suggestive specific effects of <it>5-HTT </it>and <it>DRD4 </it>at age 3.</p> <p>Conclusions</p> <p>ADHD symptoms are heritable at ages 2 and 3. Additive genetic variance is largely shared across these ages, although there are significant new effects emerging at age 3. Results from our genetic association analysis reflect these levels of stability and change and, more generally, suggest a requirement for consideration of age-specific genotypic effects in future molecular studies.</p

PADB : Published Association Database

<p>Abstract</p> <p>Background</p> <p>Although molecular pathway information and the International HapMap Project data can help biomedical researchers to investigate the aetiology of complex diseases more effectively, such information is missing or insufficient in current genetic association databases. In addition, only a few of the environmental risk factors are included as gene-environment interactions, and the risk measures of associations are not indexed in any association databases.</p> <p>Description</p> <p>We have developed a published association database (PADB; <url>http://www.medclue.com/padb</url>) that includes both the genetic associations and the environmental risk factors available in PubMed database. Each genetic risk factor is linked to a molecular pathway database and the HapMap database through human gene symbols identified in the abstracts. And the risk measures such as odds ratios or hazard ratios are extracted automatically from the abstracts when available. Thus, users can review the association data sorted by the risk measures, and genetic associations can be grouped by human genes or molecular pathways. The search results can also be saved to tab-delimited text files for further sorting or analysis. Currently, PADB indexes more than 1,500,000 PubMed abstracts that include 3442 human genes, 461 molecular pathways and about 190,000 risk measures ranging from 0.00001 to 4878.9.</p> <p>Conclusion</p> <p>PADB is a unique online database of published associations that will serve as a novel and powerful resource for reviewing and interpreting huge association data of complex human diseases.</p