Decifering mega-ripple variability in an anthropogenically steered environment: implications for mine burial studies

In 2007 the Ministery of Defence, in collaboration with Ghent University, developed a project on the understanding of mega-ripple variability in view of improving mine burial prediction models in sandbank areas. Results will assist in the monitoring of sea-mines, heritage of two World Wars, nowadays partially or totally buried by sandy bedforms

Burial Recording Mines: a valid technique to study bedform migration and storm impact above the sea-floor

Initially, Burial Recording Mines (BRMs) were used to understand the sea mine burial. It was a technique predominantly related to military purpose. The first experiment was made 1974. Now a day, it is used as a valid tool for marine science. This methodology gives the rare opportunity to observe and analyze the processes acting on the seafloor directly, making the estimation closer to the reality. During MARIDIV, we present the results of 3 months experiment using burial recording mines. The experiment was performed between September 2008 and January 2009. The Wandelaar region on the Belgian Continental Shelf was chosen as suitable test area. 10,000 measurements of the sediment height around the cylindrical object were recorded, each one of those every 15 minutes. The dataset collected, together with sediment characterization and hydrological and meteorological information, allowed the understanding of the bedform migration. During the experiment, 2 storms passed the test area, in October and November 2008. Using Burial Recording Mines gave the rare opportunity to observe and analyze the storm impact directly on the sea-floor. Processes during and after the second storm will be revealed

Recognizing the seafloor’s characteristics using habitat signatures

Seafloor images become increasingly available, both derived from video or photographs and from acoustic remote sensing. Very-high resolution acoustic imagery has indeed the potential of depicting a recognisable sign on an image that relates to a physical and biological nature, i.e. its habitat signature. Still, most of this information is stored at institutes or universities and no up-to-date comprehensive compilation is yet available. Moreover, the acoustic imagery often remains hard to interpret; this is mainly because of the multitude of factors influencing the image and the lack of reference material. When an interpreter studies a remote sensing image, he indeed needs to refer to particular textures and patterns that are recognisable on the image and relate that to reality. Ground truthing remains crucial; still comparison with a large number of similar cases is a necessity. In the framework of marine environmental issues this becomes increasingly important and the need for sound interpretations is real. To anticipate on this need, a web-based catalogue of seabed habitat signatures is being built in the framework of the MESH project (Mapping European Seabed Habitats), for both scientists and non-scientists. The catalogue contains a collection of images produced by different remote sensing techniques (acoustic and optically derived images, photographs and video). As such, the results of the different techniques can be compared and can strengthen interpretations in view of seabed assessments. The catalogue has a comprehensive list of metadata per habitat signature, both in terms of its physical and biological environment and the conditions under which the signatures were generated. The web catalogue is easy manageable. Habitats can be searched using their own name or by typing a key word or choosing a EUNIS code or making a query on physical factors. For every habitat one or more significant locations in the Mesh area are chosen and every location displays all the signatures available. Every location is identified by its coordinates (lat., long.) to be easily positioned on the MESH webGIS (http://www.searchmesh.net/webGIS). The signatures are presented as little thumbnails to let the web user have an easy overview. These link to a page where a description of the image, an enlarged image and all technical data referred to it can be found. The catalogue will largely increase the visibility of how the seafloor looks like, but above all it is hoped that it will assist in the interpretation of newly acquired data in view of - 48 - environmental assessments. Any potential contributor to this catalogue is invited to share their images to a wider European community. The web-catalogue is developed at Ifremer (http://www.ifremer.fr/meshmalo/ essai_signatures). RCMG is responsible for the input of imagery related to the Belgian part of the North Sea

A public early intervention approach to first-episode psychosis: Treated incidence over 7 years in the Emilia-Romagna region

AimTo estimate the treated incidence of individuals with first-episode psychosis (FEP) who contacted the Emilia-Romagna public mental healthcare system (Italy); to examine the variability of incidence and user characteristics across centres and years. MethodsWe computed the raw treated incidence in 2013-2019, based on FEP users aged 18-35, seen within or outside the regional program for FEP. We modelled FEP incidence across 10 catchment areas and 7 years using Bayesian Poisson and Negative Binomial Generalized Linear Models of varying complexity. We explored associations between user characteristics, study centre and year comparing variables and socioclinical clusters of subjects. ResultsThousand three hundred and eighteen individuals were treated for FEP (raw incidence: 25.3 / 100.000 inhabitant year, IQR: 15.3). A Negative Binomial location-scale model with area, population density and year as predictors found that incidence and its variability changed across centres (Bologna: 36.55; 95% CrI: 30.39-43.86; Imola: 3.07; 95% CrI: 1.61-4.99) but did not follow linear temporal trends or density. Centers were associated with different user age, gender, migrant status, occupation, living conditions and cluster distribution. Year was associated negatively with HoNOS score (R = -0.09, p < .001), duration of untreated psychosis (R = -0.12, p < .001) and referral type. ConclusionsThe Emilia-Romagna region presents a relatively high but variable incidence of FEP across areas, but not in time. More granular information on social, ethnic and cultural factors may increase the level of explanation and prediction of FEP incidence and characteristics, shedding light on social and healthcare factors influencing FEP

Habitat signature catalogue: Belgian part of the North Sea

The Habitat Signature catalogue has been set-up in accordance with a European need for a better visibility of existing seafloor imagery. With 'signature', any record is meant that demonstrates a particular characteristic of a habitat feature, ideally with a biological connotation. Through the MESH project ('Mapping European Seabed Habitats'), a compilation was made on the scale of the NW European seas and its results can be consulted on-line. The present publication comprises the Belgian contribution; however with additional examples and more sitespecific information. Focus is on subtidal acoustic imagery, acquired using very-high resolution side-scan sonar and multibeam technology. With the catalogue, it is aimed at providing existing knowledge of the seabed to a wider community: from the professional surveyor up to the public at large. Each signature comprises its geographic location, the type of technique and, where possible, its interpretation in terms of the physical and biological nature of the seabed. The catalogue does not comprise imagery of wrecks

SINCERITIES: inferring gene regulatory networks from time-stamped single cell transcriptional expression profiles

Abstract Motivation Single cell transcriptional profiling opens up a new avenue in studying the functional role of cell-to-cell variability in physiological processes. The analysis of single cell expression profiles creates new challenges due to the distributive nature of the data and the stochastic dynamics of gene transcription process. The reconstruction of gene regulatory networks (GRNs) using single cell transcriptional profiles is particularly challenging, especially when directed gene-gene relationships are desired. Results We developed SINCERITIES (SINgle CEll Regularized Inference using TIme-stamped Expression profileS) for the inference of GRNs from single cell transcriptional profiles. We focused on time-stamped cross-sectional expression data, commonly generated from transcriptional profiling of single cells collected at multiple time points after cell stimulation. SINCERITIES recovers directed regulatory relationships among genes by employing regularized linear regression (ridge regression), using temporal changes in the distributions of gene expressions. Meanwhile, the modes of the gene regulations (activation and repression) come from partial correlation analyses between pairs of genes. We demonstrated the efficacy of SINCERITIES in inferring GRNs using in silico time-stamped single cell expression data and single cell transcriptional profiles of THP-1 monocytic human leukemia cells. The case studies showed that SINCERITIES could provide accurate GRN predictions, significantly better than other GRN inference algorithms such as TSNI, GENIE3 and JUMP3. Moreover, SINCERITIES has a low computational complexity and is amenable to problems of extremely large dimensionality. Finally, an application of SINCERITIES to single cell expression data of T2EC chicken erythrocytes pointed to BATF as a candidate novel regulator of erythroid development. Availability and implementation MATLAB and R version of SINCERITIES are freely available from the following websites: http://www.cabsel.ethz.ch/tools/sincerities.html and https://github.com/CABSEL/SINCERITIES. The single cell THP-1 and T2EC transcriptional profiles are available from the original publications (Kouno et al., 2013; Richard et al., 2016). The in silico single cell data are available on SINCERITIES websites. Supplementary information Supplementary data are available at Bioinformatics online