Expanding aquatic observations through recreation

This is the final version. Available on open access from Frontiers Media via the DOI in this recordAccurate observations of the Earth system are required to understand how our planet is changing and to help manage its resources. The aquatic environment-including lakes, rivers, wetlands, estuaries, coastal and open oceans-is a fundamental component of the Earth system controlling key physical, biological, and chemical processes that allow life to flourish. Yet, this environment is critically undersampled in both time and space. New and cost-effective sampling solutions are urgently needed. Here, we highlight the potential to improve aquatic sampling by tapping into recreation. We draw attention to the vast number of participants that engage in aquatic recreational activities and argue, based on current technological developments and recent research, that the time is right to employ recreational citizens to improve large-scale aquatic sampling efforts. We discuss the challenges that need to be addressed for this strategy to be successful (e.g., sensor integration, data quality, and citizen motivation), the steps needed to realize its potential, and additional societal benefits that arise when engaging citizens in scientific sampling.UK National Centre for Earth ObservationSmartfin/Lostbird FoundationDefr

Peatlands of Southern South America: a review

This is the final version. Available from International Peatland Society (IPS) / International Mire Conservation Group via the DOI in this recordSouthern South American peatlands (SSAP) play a key role in the ecological dynamics of Patagonia. They mostly comprise of undisturbed environments which provide important ecosystem services, including carbon sequestration, water reservoir and habitat for both widespread and endemic organisms. When compared with boreal peatlands, our knowledge of the functioning of SSAP is poor, and it is necessary to raise awareness about their scientific and ecological value and to ensure their conservation. This article examines a broad base of historical and contemporary published research literature on the peatlands of Chile and Argentina, from 1843 onwards, to identify gaps in knowledge, implications for the assessment of peatland functioning, and targets for peatland conservation and management. To achieve this goal, we reviewed a total of 196 research papers/reports from across the peer-reviewed and grey literature. We conclude that gaps in our knowledge and understanding of SSAP have deeply undermined the development of effective conservation strategies for these understudied ecosystems. To reverse this situation, we recommend that future research and management efforts should aim: (1) to build an inventory of the peatlands that exist in SSAP, including their location and area; (2) to ensure land use planning prioritises the maintenance of SSAP ecosystem services; (3) to improve existing legislation and protocols of good and sustainable practice for extractive activities; and (4) to carry out an extensive awareness campaign aimed at the local population and key decision makers

Frequency and genotypic distribution of GB virus C (GBV-C) among Colombian population with Hepatitis B (HBV) or Hepatitis C (HCV) infection

<p>Abstract</p> <p>Background</p> <p>GB virus C (GBV-C) is an enveloped positive-sense ssRNA virus belonging to the <it>Flaviviridae </it>family. Studies on the genetic variability of the GBV-C reveals the existence of six genotypes: genotype 1 predominates in West Africa, genotype 2 in Europe and America, genotype 3 in Asia, genotype 4 in Southwest Asia, genotype 5 in South Africa and genotype 6 in Indonesia. The aim of this study was to determine the frequency and genotypic distribution of GBV-C in the Colombian population.</p> <p>Methods</p> <p>Two groups were analyzed: i) 408 Colombian blood donors infected with HCV (n = 250) and HBV (n = 158) from Bogotá and ii) 99 indigenous people with HBV infection from Leticia, Amazonas. A fragment of 344 bp from the 5' untranslated region (5' UTR) was amplified by nested RT PCR. Viral sequences were genotyped by phylogenetic analysis using reference sequences from each genotype obtained from GenBank (n = 160). Bayesian phylogenetic analyses were conducted using Markov chain Monte Carlo (MCMC) approach to obtain the MCC tree using BEAST v.1.5.3.</p> <p>Results</p> <p>Among blood donors, from 158 HBsAg positive samples, eight 5.06% (n = 8) were positive for GBV-C and from 250 anti-HCV positive samples, 3.2%(n = 8) were positive for GBV-C. Also, 7.7% (n = 7) GBV-C positive samples were found among indigenous people from Leticia. A phylogenetic analysis revealed the presence of the following GBV-C genotypes among blood donors: 2a (41.6%), 1 (33.3%), 3 (16.6%) and 2b (8.3%). All genotype 1 sequences were found in co-infection with HBV and 4/5 sequences genotype 2a were found in co-infection with HCV. All sequences from indigenous people from Leticia were classified as genotype 3. The presence of GBV-C infection was not correlated with the sex (p = 0.43), age (p = 0.38) or origin (p = 0.17).</p> <p>Conclusions</p> <p>It was found a high frequency of GBV-C genotype 1 and 2 in blood donors. The presence of genotype 3 in indigenous population was previously reported from Santa Marta region in Colombia and in native people from Venezuela and Bolivia. This fact may be correlated to the ancient movements of Asian people to South America a long time ago.</p

Using random forest and decision tree models for a new vehicle prediction approach in computational toxicology

yesDrug vehicles are chemical carriers that provide beneficial aid to the drugs they bear. Taking advantage of their favourable properties can potentially allow the safer use of drugs that are considered highly toxic. A means for vehicle selection without experimental trial would therefore be of benefit in saving time and money for the industry. Although machine learning is increasingly used in predictive toxicology, to our knowledge there is no reported work in using machine learning techniques to model drug-vehicle relationships for vehicle selection to minimise toxicity. In this paper we demonstrate the use of data mining and machine learning techniques to process, extract and build models based on classifiers (decision trees and random forests) that allow us to predict which vehicle would be most suited to reduce a drug’s toxicity. Using data acquired from the National Institute of Health’s (NIH) Developmental Therapeutics Program (DTP) we propose a methodology using an area under a curve (AUC) approach that allows us to distinguish which vehicle provides the best toxicity profile for a drug and build classification models based on this knowledge. Our results show that we can achieve prediction accuracies of 80 % using random forest models whilst the decision tree models produce accuracies in the 70 % region. We consider our methodology widely applicable within the scientific domain and beyond for comprehensively building classification models for the comparison of functional relationships between two variables

Genome-wide association study identifies multiple susceptibility loci for glioma

Previous genome-wide association studies (GWASs) have shown that common genetic variation contributes to the heritable risk of glioma. To identify new glioma susceptibility loci, we conducted a meta-analysis of four GWAS (totalling 4,147 cases and 7,435 controls), with imputation using 1000 Genomes and UK10K Project data as reference. After genotyping an additional 1,490 cases and 1,723 controls we identify new risk loci for glioblastoma (GBM) at 12q23.33 (rs3851634, near POLR3B, P=3.02 × 10−9) and non-GBM at 10q25.2 (rs11196067, near VTI1A, P=4.32 × 10−8), 11q23.2 (rs648044, near ZBTB16, P=6.26 × 10−11), 12q21.2 (rs12230172, P=7.53 × 10−11) and 15q24.2 (rs1801591, near ETFA, P=5.71 × 10−9). Our findings provide further insights into the genetic basis of the different glioma subtypes

Noninvasive Assessment of Coronary Artery Disease in Women: What’s Next?

Significant progress in research has been made in the areas of sex-specific aspects of cardiovascular disease. Despite these advances, coronary artery disease (CAD) is the leading cause of death of women in the Western world. Over the past decade, the focused research on women at risk for ischemic heart disease has helped to clarify our understanding of some of the sex-specific factors, which are important in detecting CAD. In women, the detection and evaluation of physiologically significant CAD is challenging, especially given that traditional tests designed to detect focal areas of coronary artery stenosis are less sensitive and specific in female patients who have a lower prevalence of obstructive coronary disease, greater burden of symptoms, and a high atherosclerotic burden. In this article, we review the available evidence on the role of contemporary cardiovascular imaging techniques in evaluating ischemic heart disease in women

A genome-wide association study identifies risk loci for childhood acute lymphoblastic leukemia at 10q26.13 and 12q23.1.

Genome-wide association studies (GWASs) have shown that common genetic variation contributes to the heritable risk of childhood acute lymphoblastic leukemia (ALL). To identify new susceptibility loci for the largest subtype of ALL, B-cell precursor ALL (BCP-ALL), we conducted a meta-analysis of two GWASs with imputation using 1000 Genomes and UK10K Project data as reference (totaling 1658 cases and 7224 controls). After genotyping an additional 2525 cases and 3575 controls, we identify new susceptibility loci for BCP-ALL mapping to 10q26.13 (rs35837782, LHPP, P=1.38 × 10(-11)) and 12q23.1 (rs4762284, ELK3, P=8.41 × 10(-9)). We also provide confirmatory evidence for the existence of independent risk loci at 9p21.3, but show that the association marked by rs77728904 can be accounted for by linkage disequilibrium with the rare high-impact CDKN2A p.Ala148Thr variant rs3731249. Our data provide further insights into genetic susceptibility to ALL and its biology

Multi-laboratory efforts for the standardization of performance assessment of diffuse optics instruments - The BitMap Exercise

A multi-laboratory exercise, involving 29 diffuse optical instruments, aimed at performance assessment of diffuse optics instruments on standardized protocols is presented. The overarching methodology and future actions will also be discussed

A multi-laboratory comparison of photon migration instruments and their performances – the BitMap Exercise

Performance assessment and standardization are indispensable for instruments of clinical relevance in general and clinical instrumentation based on photon migration/diffuse optics in particular. In this direction, a multi-laboratory exercise was initiated with the aim of assessing and comparing their performances. 29 diffuse optical instruments belonging to 11 partner institutions of a European level Marie Curie Consortium BitMap1 were considered for this exercise. The enrolled instruments covered different approaches (continuous wave, CW; frequency domain, FD; time domain, TD and spatial frequency domain imaging, SFDI) and applications (e.g. mammography, oximetry, functional imaging, tissue spectroscopy). 10 different tests from 3 well-accepted protocols, namely, the MEDPHOT2, the BIP3, and the nEUROPt4 protocols were chosen for the exercise and the necessary phantoms kits were circulated across labs and institutions enrolled in the study. A brief outline of the methodology of the exercise is presented here. Mainly, the design of some of the synthetic descriptors, (single numeric values used to summarize the result of a test and facilitate comparison between instruments) for some of the tests will be discussed.. Future actions of the exercise aim at deploying these measurements onto an open data repository and investigating common analysis tools for the whole dataset

Infected Dendritic Cells Facilitate Systemic Dissemination and Transplacental Passage of the Obligate Intracellular Parasite Neospora caninum in Mice

The obligate intracellular parasite Neospora caninum disseminates across the placenta and the blood-brain barrier, to reach sites where it causes severe pathology or establishes chronic persistent infections. The mechanisms used by N. caninum to breach restrictive biological barriers remain elusive. To examine the cellular basis of these processes, migration of different N. caninum isolates (Nc-1, Nc-Liverpool, Nc-SweB1 and the Spanish isolates: Nc-Spain 3H, Nc-Spain 4H, Nc-Spain 6, Nc-Spain 7 and Nc-Spain 9) was studied in an in vitro model based on a placental trophoblast-derived BeWo cell line. Here, we describe that infection of dendritic cells (DC) by N. caninum tachyzoites potentiated translocation of parasites across polarized cellular monolayers. In addition, powered by the parasite's own gliding motility, extracellular N. caninum tachyzoites were able to transmigrate across cellular monolayers. Altogether, the presented data provides evidence of two putative complementary pathways utilized by N. caninum, in an isolate-specific fashion, for passage of restrictive cellular barriers. Interestingly, adoptive transfer of tachyzoite-infected DC in mice resulted in increased parasitic loads in various organs, e.g. the central nervous system, compared to infections with free parasites. Inoculation of pregnant mice with infected DC resulted in an accentuated vertical transmission to the offspring with increased parasitic loads and neonatal mortality. These findings reveal that N. caninum exploits the natural cell trafficking pathways in the host to cross cellular barriers and disseminate to deep tissues. The findings are indicative of conserved dissemination strategies among coccidian apicomplexan parasites