Categorization of species as native or nonnative using DNA sequence signatures without a complete reference library.

New genetic diagnostic approaches have greatly aided efforts to document global biodiversity and improve biosecurity. This is especially true for organismal groups in which species diversity has been underestimated historically due to difficulties associated with sampling, the lack of clear morphological characteristics, and/or limited availability of taxonomic expertise. Among these methods, DNA sequence barcoding (also known as "DNA barcoding") and by extension, meta-barcoding for biological communities, has emerged as one of the most frequently utilized methods for DNA-based species identifications. Unfortunately, the use of DNA barcoding is limited by the availability of complete reference libraries (i.e., a collection of DNA sequences from morphologically identified species), and by the fact that the vast majority of species do not have sequences present in reference databases. Such conditions are critical especially in tropical locations that are simultaneously biodiversity rich and suffer from a lack of exploration and DNA characterization by trained taxonomic specialists. To facilitate efforts to document biodiversity in regions lacking complete reference libraries, we developed a novel statistical approach that categorizes unidentified species as being either likely native or likely nonnative based solely on measures of nucleotide diversity. We demonstrate the utility of this approach by categorizing a large sample of specimens of terrestrial insects and spiders (collected as part of the Moorea BioCode project) using a generalized linear mixed model (GLMM). Using a training data set of known endemic (n = 45) and known introduced species (n = 102), we then estimated the likely native/nonnative status for 4,663 specimens representing an estimated 1,288 species (412 identified species), including both those specimens that were either unidentified or whose endemic/introduced status was uncertain. Using this approach, we were able to increase the number of categorized specimens by a factor of 4.4 (from 794 to 3,497), and the number of categorized species by a factor of 4.8 from (147 to 707) at a rate much greater than chance (77.6% accuracy). The study identifies phylogenetic signatures of both native and nonnative species and suggests several practical applications for this approach including monitoring biodiversity and facilitating biosecurity

Particle acceleration during merging-compression plasma start-up in the Mega Amp Spherical Tokamak

Magnetic reconnection occurred during merging-compression plasma start-up in the Mega Amp Spherical Tokamak (MAST), resulting in the prompt acceleration of substantial numbers of ions and electrons to highly suprathermal energies. Accelerated field-aligned ions (deuterons and protons) were detected using a neutral particle analyser at energies up to about 20 keV during merging in early MAST pulses, while nonthermal electrons have been detected indirectly in more recent pulses through microwave bursts. However no increase in soft X-ray emission was observed until later in the merging phase, by which time strong electron heating had been detected through Thomson scattering measurements. A test-particle code CUEBIT is used to model ion acceleration in the presence of an inductive toroidal electric field with a prescribed spatial profile and temporal evolution based on Hall-MHD simulations of the merging process. The simulations yield particle distributions with properties similar to those observed experimentally, including strong field alignment of the fast ions and the acceleration of protons to higher energies than deuterons. Particle-in-cell modelling of a plasma containing a dilute field-aligned suprathermal electron component suggests that at least some of the microwave bursts can be attributed to the anomalous Doppler instability driven by anisotropic fast electrons, which do not produce measurable enhancements in soft X-ray emission either because they are insufficiently energetic or because the nonthermal bremsstrahlung emissivity during this phase of the pulse is below the detection threshold. There is no evidence of runaway electron acceleration during merging, possibly due to the presence of three-dimensional field perturbations

A multi-centre qualitative study exploring the experiences of UK South Asian and White Diabetic Patients referred for renal care

Background An exploration of renal complications of diabetes from the patient perspective is important for developing quality care through the diabetic renal disease care pathway. Methods Newly referred South Asian and White diabetic renal patients over 16 years were recruited from nephrology outpatient clinics in three UK centres - Luton, West London and Leicester – and their experiences of the diabetes and renal care recorded. A semi-structured qualitative interview was conducted with 48 patients. Interview transcripts were analysed thematically and comparisons made between the White and South Asian groups. Results 23 South Asian patients and 25 White patients were interviewed. Patient experience of diabetes ranged from a few months to 35 years with a mean time since diagnosis of 12.1 years and 17.1 years for the South Asian and White patients respectively. Confusion emerged as a response to referral shared by both groups. This sense of confusion was associated with reported lack of information at the time of referral, but also before referral. Language barriers exacerbated confusion for South Asian patients. Conclusions The diabetic renal patients who have been referred for specialist renal care and found the referral process confusing have poor of awareness of kidney complications of diabetes. Healthcare providers should be more aware of the ongoing information needs of long term diabetics as well as the context of any information exchange including language barriers

Needle(s) in the Haystack – Synchronous Multifocal Tumor Induced Osteomalacia

This is the author accepted manuscript. The final version is available from Endocrine Society via http://dx.doi.org/10.1210/jc.2015-3854MG is supported by the NIHR Cambridge Biomedical Research Centre

The Reproducibility of Lists of Differentially Expressed Genes in Microarray Studies

Reproducibility is a fundamental requirement in scientific experiments and clinical contexts. Recent publications raise concerns about the reliability of microarray technology because of the apparent lack of agreement between lists of differentially expressed genes (DEGs). In this study we demonstrate that (1) such discordance may stem from ranking and selecting DEGs solely by statistical significance (P) derived from widely used simple t-tests; (2) when fold change (FC) is used as the ranking criterion, the lists become much more reproducible, especially when fewer genes are selected; and (3) the instability of short DEG lists based on P cutoffs is an expected mathematical consequence of the high variability of the t-values. We recommend the use of FC ranking plus a non-stringent P cutoff as a baseline practice in order to generate more reproducible DEG lists. The FC criterion enhances reproducibility while the P criterion balances sensitivity and specificity

Landscape science: a Russian geographical tradition

The Russian geographical tradition of landscape science (landshaftovedenie) is analyzed with particular reference to its initiator, Lev Semenovich Berg (1876-1950). The differences between prevailing Russian and Western concepts of landscape in geography are discussed, and their common origins in German geographical thought in the late nineteenth and early twentieth centuries are delineated. It is argued that the principal differences are accounted for by a number of factors, of which Russia's own distinctive tradition in environmental science deriving from the work of V. V. Dokuchaev (1846-1903), the activities of certain key individuals (such as Berg and C. O. Sauer), and the very different social and political circumstances in different parts of the world appear to be the most significant. At the same time it is noted that neither in Russia nor in the West have geographers succeeded in specifying an agreed and unproblematic understanding of landscape, or more broadly in promoting a common geographical conception of human-environment relationships. In light of such uncertainties, the latter part of the article argues for closer international links between the variant landscape traditions in geography as an important contribution to the quest for sustainability

Trials and tribulations of recruiting 2,000 older women onto a clinical trial investigating falls and fractures : vital D study

Background Randomised, placebo-controlled trials are needed to provide evidence demonstrating safe, effective interventions that reduce falls and fractures in the elderly. The quality of a clinical trial is dependent on successful recruitment of the target participant group. This paper documents the successes and failures of recruiting over 2,000 women aged at least 70 years and at higher risk of falls or fractures onto a placebo-controlled trial of six years duration. The characteristics of study participants at baseline are also described for this study.Methods The Vital D Study recruited older women identified at high risk of fracture through the use of an eligibility algorithm, adapted from identified risk factors for hip fracture. Participants were randomised to orally receive either 500,000 IU vitamin D3 (cholecalciferol) or placebo every autumn for five consecutive years. A variety of recruitment strategies were employed to attract potential participants.Results Of the 2,317 participants randomised onto the study, 74% (n = 1716/2317) were consented onto the study in the last five months of recruiting. This was largely due to the success of a targeted mail-out. Prior to this only 541 women were consented in the 18 months of recruiting. A total of 70% of all participants were recruited as a result of targeted mail-out. The response rate from the letters increased from 2 to 7% following revision of the material by a public relations company. Participant demographic or risk factor profile did not differ between those recruited by targeted mail-outs compared with other methods.Conclusion The most successful recruitment strategy was the targeted mail-out and the response rate was no higher in the local region where the study had extensive exposure through other recruiting strategies. The strategies that were labour-intensive and did not result in successful recruitment include the activities directed towards the GP medical centres. Comprehensive recruitment programs employ overlapping strategies simultaneously with ongoing assessment of recruitment rates. In our experience, and others direct mail-outs work best although rights to privacy must be respected. <br /

Single-lipid tracking reveals heterogeneities in the nanoscale dynamics of colloid-supported lipid bilayers

In this work, we utilize single-particle tracking photoactivated localization microscopy (sptPALM) to explore lipid dynamics in colloid-supported lipid bilayers (CSLBs) with liquid-like (DOPC), gel-like (DPPC), and phase-separated (DOPC:DPPC:cholesterol) membranes. Using total internal reflection fluorescence illumination, we tracked photoactivatable fluorescent dyes conjugated to lipids within these membranes. Analysis of tracked lipids revealed that bilayers across all compositions have heterogeneous dynamics, with lipid mobility varying over three orders of magnitude. We leveraged the temperature-dependent phase behavior of DPPC to transform gel-like membranes at room temperature into liquid-like membranes above 41 °C, which resulted in increased diffusivity and a surprising decrease in heterogeneity. Finally, we perform single lipid tracking in fluid-rich phases within gel-phase regions to demonstrate their dynamics with reduced lipid mobility because of soft confinement within phase-separated microdomains. Our findings have implications for colloidal assembly strategies that exploit ligand mobility to create controlled and reproducible colloidal superstructures.</p

Recent emergence and worldwide spread of the red tomato spider mite, [i]Tetranychus evansi[/i]: genetic variation and multiple cryptic invasions

Publication Inra prise en compte dans l'analyse bibliométrique des publications scientifiques mondiales sur les Fruits, les Légumes et la Pomme de terre. Période 2000-2012. http://prodinra.inra.fr/record/256699Plant biosecurity is increasingly challenged by emerging crop pests. The spider mite Tetranychus evansi has recently emerged as a new threat to solanaceous crops in Africa and the Mediterranean basin, with invasions characterized by a high reproductive output and an ability to withstand a wide range of temperatures. Mitochondrial (868 bp of COI) and nuclear (1,137 bp of ITS) loci were analyzed in T. evansi samples spanning the current geographical distribution to study the earliest stages of the invasive process. The two sets of markers separate the samples into two main clades that are only present together in South America and Southern Europe. The highest COI diversity was found in South America, consistent with the hypothesis of a South American origin of T. evansi. Among the invaded areas, the Mediterranean region displayed a high level of genetic diversity similar to that present in South America, that is likely the result of multiple colonization events. The invasions of Africa and Asia by T. evansi are characterized by a low genetic variation associated with distinct introductions. Genetic data demonstrate two different patterns of invasions: (1) populations in the Mediterranean basin that are a result of multiple cryptic introductions and (2) emerging invasions of Africa and Asia, each likely the result of propagules from one or limited sources. The recent invasions of T. evansi illustrate not only the importance of human activities in the spread of agricultural pests, but also the limits of international quarantine procedures, particularly for cryptic invasion

School dropout, problem behaviour and poor academic achievement : a longitudinal view of portuguese male offenders

This study examines school drop outs from the perspective of male adults themselves through interviews with offenders currently serving sentences. Participants were 10 Portuguese male inmates, between the ages of 19 and 46 years of age, incarcerated in two prison facilities of the Azores. Qualitative and interpretative methods were carried out using a semi-structured in-depth individual interview that was audiorecorded and conducted on the basis of a list of topics. Interview transcripts and thematic analysis were used in data treatment and analysis. The findings primarily indicate that poor academic achievement and emotional and behavioural difficulties of participants played a particular role in early school drop out. The trajectories these individuals followed within the education system presented problem behaviour, learning disabilities, and/or foster care interventions. While school drop out circumstances were apparently various, analysis showed that they were underpinned by three distinct sets of conditions generally not addressed by the education system. The analysis of the triggering factors and the maintenance dynamics of school drop outs indicated three distinct types: retention/absenteeism, life turning points and positive resolution. Implications for secondary prevention and screening practices are discussed.FCT (SFRH/ BD/ 44245/ 2008)CIEC - unidade de investigação 317 da FC