Screening and quantification of micro(nano)plastics and plastic additives in the seawater of Mar Menor lagoon

In this work a suspect-screening approach was employed to assess the polymers and plastic additives of micro(nano)plastics (NPL/MPLs) of size ranges from the nm range to 20 μm present in seawater from the top 5 cm of the Mar Menor lagoon during two sampling campaigns (summer and winter), as well of other potentially adsorbed compounds onto the plastic particles surfaces and suspended material. The identification of NPL/MPLs has been based on characteristic Kendrick Mass Defect analysis for each polymer type in mass spectra. The applied methodology allowed to identify NPLs/MPLs of polystyrene (PS), polyethylene (PE), polyisoprene (PI), polybutadiene (PBD), polypropylene (PP), polyamides (PA), polyvinylchloride (PVC), n-isopropylacrylamide (PNIPAm), and polydimethylsiloxanes. In addition, PS, PE, PI, PBD, PP, PA, and PVC were confirmed with standards, and the equivalent concentrations were quantified. The results of this study showed that most frequently found compounds were PP, PE, PA and PNIPAm, while the compound found at higher concentrations was by far PP reaching the 9,303 ± 366 ng/mL in one of the samples. A total number of 135 chemical compounds were tentatively identified, 74 of them plastic additives and compounds used in the polymers manufacture or coming from the polymer’s decomposition. In relation to plastic additives, the more frequently tentatively identified compounds were plasticizers such as phthalates group; stabilizers such as antioxidants (e.g., distearyl 3,3′-thiodipropionate, 2,5-di-tert-butylhydroquinone), and UV filters as benzotriazoles. Several flame retardants of the group of phosphates were as well detected. The other compounds tentatively identified in the samples were pharmaceuticals, pesticides, food additives, flavors and natural products that were attached onto the plastic particles and particulate matter from surrounding waters. In regards to the seasonal variation, during the summer a major number of compounds were tentatively detected, while de concentrations of polymers were slightly higher in winter. The spatial distribution showed higher contamination in the southern part of the coastal lagoon.Postprin

GeoTriples: a Tool for Publishing Geospatial Data as RDF Graphs Using R2RML Mappings

In this paper we present the tool GeoTriples that allows the transformation of Earth Observation data and geospatial data into RDF graphs, by using and extending the R2RML mapping language to be able to deal with the specificities of geospatial data. GeoTriples is a semi-automated tool that transforms geospatial information into RDF following the state of the art vocabularies like GeoSPARQL and stSPARQL, but at the same time it is not tightly coupled to a specific vocabulary

The Biomarker Toolkit - an evidence-based guideline to predict cancer biomarker success and guide development

BACKGROUND: An increased number of resources are allocated on cancer biomarker discovery, but very few of these biomarkers are clinically adopted. To bridge the gap between Biomarker discovery and clinical use, we aim to generate the Biomarker Toolkit, a tool designed to identify clinically promising biomarkers and promote successful biomarker translation. METHODS: All features associated with a clinically useful biomarker were identified using mixed-methodology, including systematic literature search, semi-structured interviews, and an online two-stage Delphi-Survey. Validation of the checklist was achieved by independent systematic literature searches using keywords/subheadings related to clinically and non-clinically utilised breast and colorectal cancer biomarkers. Composite aggregated scores were generated for each selected publication based on the presence/absence of an attribute listed in the Biomarker Toolkit checklist. RESULTS: Systematic literature search identified 129 attributes associated with a clinically useful biomarker. These were grouped in four main categories including: rationale, clinical utility, analytical validity, and clinical validity. This checklist was subsequently developed using semi-structured interviews with biomarker experts (n=34); and 88.23% agreement was achieved regarding the identified attributes, via the Delphi survey (consensus level:75%, n=51). Quantitative validation was completed using clinically and non-clinically implemented breast and colorectal cancer biomarkers. Cox-regression analysis suggested that total score is a significant driver of biomarker success in both cancer types (BC: p>0.0001, 95.0% CI: 0.869-0.935, CRC: p>0.0001, 95.0% CI: 0.918-0.954). CONCLUSIONS: This novel study generated a validated checklist with literature-reported attributes linked with successful biomarker implementation. Ultimately, the application of this toolkit can be used to detect biomarkers with the highest clinical potential and shape how biomarker studies are designed/performed

GeoTriples: Transforming geospatial data into RDF graphs using R2RML and RML mappings

A lot of geospatial data has become available at no charge in many countries recently. Geospatial data that is currently made available by government agencies usually do not follow the linked data paradigm. In the few cases where government agencies do follow the linked data paradigm (e.g., Ordnance Survey in the United Kingdom), specialized scripts have been used for transforming geospatial data into RDF. In this paper we present the open source tool GeoTriples which generates and processes extended R2RML and RML mappings that transform geospatial data from many input formats into RDF. GeoTriples allows the transformation of geospatial data stored in raw files (shapefiles, CSV, KML, XML, GML and GeoJSON) and spatially-enabled RDBMS (PostGIS and MonetDB) into RDF graphs using well-known vocabularies like GeoSPARQL and stSPARQL, but without being tightly coupled to a specific vocabulary. GeoTriples has been developed in European projects LEO and Melodies and has been used to transform many geospatial data sources into linked data. We study the performance of GeoTriples experimentally using large publicly available geospatial datasets, and show that GeoTriples is very efficient and scalable especially when its mapping processor is implemented using Apache Hadoop

Generalized dynamical density functional theory for classical fluids and the significance of inertia and hydrodynamic interactions

We study the dynamics of a colloidal fluid including inertia and hydrodynamic interactions, two effects which strongly influence the non-equilibrium properties of the system. We derive a general dynamical density functional theory (DDFT) which shows very good agreement with full Langevin dynamics. In suitable limits, we recover existing DDFTs and a Navier-Stokes-like equation with additional non-local terms.Comment: 5 pages, 4 figures, 4 supplementary movie files, I supplementary pd

COL4A5 and LAMA5 variants co-inherited in familial hematuria: Digenic inheritance or genetic modifier effect?

Background: About 40-50% of patients with familial microscopic hematuria (FMH) caused by thin basement membrane nephropathy (TBMN) inherit heterozygous mutations in collagen IV genes (COL4A3, COL4A4). On long follow-up, the full phenotypic spectrum of these patients varies a lot, ranging from isolated MH or MH plus low-grade proteinuria to chronic renal failure of variable degree, including end-stage renal disease (ESRD). Methods: Here, we performed Whole Exome Sequencing (WES) in patients of six families, presenting with autosomal dominant FMH, with or without progression to proteinuria and loss of renal function, all previously found negative for severe collagen IV mutations. Hierarchical filtering of the WES data was performed, followed by mutation prediction analysis, Sanger sequencing and genetic segregation analysis. Results: In one family with four patients, we found evidence for the contribution of two co-inherited variants in two crucial genes expressed in the glomerular basement membrane (GBM); LAMA5-p.Pro1243Leu and COL4A5-p.Asp654Tyr. Mutations in COL4A5 cause classical X-linked Alport Syndrome, while rare mutations in the LAMA5 have been reported in patients with focal segmental glomerulosclerosis. The phenotypic spectrum of the patients includes hematuria, proteinuria, focal segmental glomerulosclerosis, loss of kidney function and renal cortical cysts. Conclusions: A modifier role of LAMA5 on the background of a hypomorphic Alport syndrome causing mutation is a possible explanation of our findings. Digenic inheritance is another scenario, following the concept that mutations at both loci more accurately explain the spectrum of symptoms, but further investigation is needed under this concept. This is the third report linking a LAMA5 variant with human renal disease and expanding the spectrum of genes involved in glomerular pathologies accompanied by familial hematurias. The cystic phenotype overlaps with that of a mouse model, which carried a Lama5 hypomorphic mutation that caused severely reduced Lama5 protein levels and produced kidney cysts. 2018 The Author(s).The work was supported from the Cyprus Research Promotion Foundation through the grant NEW INFRASTRUCTURE/STRATEGIC/0308/24 to CD (co-funded by the European Regional Development Fund and the Republic of Cyprus). The funding body did not contribute to the design of study, collection, analysis and interpretation of data, or in manuscript writing.Scopu

Unification of dynamic density functional theory for colloidal fluids to include inertia and hydrodynamic interactions: derivation and numerical experiments.

Starting from the Kramers equation for the phase-space dynamics of the N-body probability distribution, we derive a dynamical density functional theory (DDFT) for colloidal fluids including the effects of inertia and hydrodynamic interactions (HI). We compare the resulting theory to extensive Langevin dynamics simulations for both hard rod systems and three-dimensional hard sphere systems with radially symmetric external potentials. As well as demonstrating the accuracy of the new DDFT, by comparing with previous DDFTs which neglect inertia, HI, or both, we also scrutinize the significance of including these effects. Close to local equilibrium we derive a continuum equation from the microscopic dynamics which is a generalized Navier–Stokes-like equation with additional non-local terms governing the effects of HI. For the overdamped limit we recover analogues of existing configuration-space DDFTs but with a novel diffusion tensor