Behavioural response of wheat bulb fly (Delia coarctata, Diptera: Anthomyiidae) larvae to the primary plant metabolite carbon dioxide

Wheat bulb fly (WBF) larvae use chemotaxis to orientate towards host-plant root exudates. This study aimed to investigate the role of the primary plant metabolite carbon dioxide (CO2) in host-plant location by WBF. Arena based behavioural experiments were used to identify whether CO2 induced chemotaxis (directional movement in response to a chemical stimulus) or kinesis (non-directional movement in response to a stimulus) from WBF larvae. No chemotactic response was observed when larvae were presented to a point source of CO2. However, elevated levels of CO2 induced kinesis, with both track length and tortuosity (number of twists and turns in the movement path) increasing at elevated CO2 levels of 1000-2000ppm, demonstrating increased searching behaviour. Soil emission of CO2 was quantified to compare soil levels with those identified as eliciting behavioural effects on the larvae. Samples removed from soil gave a mean CO2 concentration of 557 (±46) ppm, which is lower than the lowest concentration of CO2 found to induce a behavioural response and higher than the lowest CO2 concentration tested, which was found not to alter behaviour. It is proposed that increased CO2 concentrations in the soil act as a behavioural trigger, inducing intensive searching of an area by WBF larvae. This increases the likelihood of finding more host-specific identifiers, such as secondary metabolites when near a potential host-plan

Genetic determinants of the molecular portraits of epithelial cancers

The ability to characterize and predict tumor phenotypes is crucial to precision medicine. In this study, we present an integrative computational approach using a genome-wide association analysis and an Elastic Net prediction method to analyze the relationship between DNA copy number alterations and an archive of gene expression signatures. Across breast cancers, we are able to quantitatively predict many gene signatures levels within individual tumors with high accuracy based upon DNA copy number features alone, including proliferation status and Estrogen-signaling pathway activity. We can also predict many other key phenotypes, including intrinsic molecular subtypes, estrogen receptor status, and TP53 mutation. This approach is also applied to TCGA Pan-Cancer, which identify repeatedly predictable signatures across tumor types including immune features in lung squamous and basal-like breast cancers. These Elastic Net DNA predictors could also be called from DNA-based gene panels, thus facilitating their use as biomarkers to guide therapeutic decision making

Amplification of SOX4 promotes PI3K/Akt signaling in human breast cancer

Purpose: The PI3K/Akt signaling axis contributes to the dysregulation of many dominant features in breast cancer including cell proliferation, survival, metabolism, motility, and genomic instability. While multiple studies have demonstrated that basal-like or triple-negative breast tumors have uniformly high PI3K/Akt activity, genomic alterations that mediate dysregulation of this pathway in this subset of highly aggressive breast tumors remain to be determined. Methods: In this study, we present an integrated genomic analysis based on the use of a PI3K gene expression signature as a framework to analyze orthogonal genomic data from human breast tumors, including RNA expression, DNA copy number alterations, and protein expression. In combination with data from a genome-wide RNA-mediated interference screen in human breast cancer cell lines, we identified essential genetic drivers of PI3K/Akt signaling. Results: Our in silico analyses identified SOX4 amplification as a novel modulator of PI3K/Akt signaling in breast cancers and in vitro studies confirmed its role in regulating Akt phosphorylation. Conclusions: Taken together, these data establish a role for SOX4-mediated PI3K/Akt signaling in breast cancer and suggest that SOX4 may represent a novel therapeutic target and/or biomarker for current PI3K family therapies

Qualitative exploration of the potential for adverse events when using an online peer support network for mental health: Cross-sectional survey

Background: Online peer support networks are a growing area of mental health support for offering social connection, identity, and support. However, it has been reported that not all individuals have a positive experience on such networks. The potential for adverse events within a moderated online peer support network is a new area of research exploration. Objective: The objective of the study was to determine if use of an online moderated peer networks leads to adverse events for users. Methods: Four biannual online surveys (October 2014 to March 2016) were conducted by a large national UK mental health charity, with users of their online peer support network exploring personal safety, moderation, experiences on the site, and how the site could be improved. Data were analyzed using thematic analysis by 2 independent researchers using a priori themes: negative experiences of moderation, social exclusion, contagion, negative interactions with other users, online relationships, co-rumination and collusion, and other. Results: In total, 2353 survey responses were logged with 197 (8.37%) documenting an adverse event of negative experience. A dominant theme of negative experiences of moderation emerged (73/197, 37.1%) with evidence of social exclusion (50/197, 25.4%). Reading user posts was shown to be a cause of worry and distress for a few users, and analysis highlighted several instances of depressogenic and emotional contagion as well as some limited evidence of behavioral contagion (46/197, 23.4%). Very limited evidence of co-rumination (1/197, 0.5%) and no evidence of collusion were identified. Conclusions: Evidence of adverse events was identified at low levels in the sample of respondents, although we have no comparison data to indicate if levels are low compared with comparable platforms. Not all users of online peer support networks find them wholly beneficial. Research must explore what works for whom. The next stage of service development should consider which users may be likely to receive no benefit, or even deteriorate, as a result of using the service

Virus expression detection reveals RNA-sequencing contamination in TCGA

Background: Contamination of reagents and cross contamination across samples is a long-recognized issue in molecular biology laboratories. While often innocuous, contamination can lead to inaccurate results. Cantalupo et al., for example, found HeLa-derived human papillomavirus 18 (H-HPV18) in several of The Cancer Genome Atlas (TCGA) RNA-sequencing samples. This work motivated us to assess a greater number of samples and determine the origin of possible contaminations using viral sequences. To detect viruses with high specificity, we developed the publicly available workflow, VirDetect, that detects virus and laboratory vector sequences in RNA-seq samples. We applied VirDetect to 9143 RNA-seq samples sequenced at one TCGA sequencing center (28/33 cancer types) over 5 years. Results: We confirmed that H-HPV18 was present in many samples and determined that viral transcripts from H-HPV18 significantly co-occurred with those from xenotropic mouse leukemia virus-related virus (XMRV). Using laboratory metadata and viral transcription, we determined that the likely contaminant was a pool of cell lines known as the "common reference", which was sequenced alongside TCGA RNA-seq samples as a control to monitor quality across technology transitions (i.e. microarray to GAII to HiSeq), and to link RNA-seq to previous generation microarrays that standardly used the "common reference". One of the cell lines in the pool was a laboratory isolate of MCF-7, which we discovered was infected with XMRV; another constituent of the pool was likely HeLa cells. Conclusions: Altogether, this indicates a multi-step contamination process. First, MCF-7 was infected with an XMRV. Second, this infected cell line was added to a pool of cell lines, which contained HeLa. Finally, RNA from this pool of cell lines contaminated several TCGA tumor samples most-likely during library construction. Thus, these human tumors with H-HPV or XMRV reads were likely not infected with H-HPV 18 or XMRV

Prognostic value of B cells in cutaneous melanoma

Background: Measures of the adaptive immune response have prognostic and predictive associations in melanoma and other cancer types. Specifically, intratumoral T cell density and function have considerable prognostic and predictive value in skin cutaneous melanoma (SKCM). Less is known about the significance of tumor-infiltrating B cells in SKCM. Our goal was to understand the prognostic and predictive value of B cell phenotypic subsets in SKCM using RNA sequencing. Methods: We used our previously published algorithm, V'DJer, to assemble B cell receptor (BCR) repertoires and estimate diversity from short-read RNA sequencing (RNA-seq). We applied machine learning-based cellular phenotype classifiers to measure relative similarity of bulk tumor sample gene expression profiles and different B cell phenotypes. We assessed these aspects of B cell biology in 473 SKCM from the Cancer Genome Atlas Project (TCGA) as well as in RNA-seq data corresponding to tumor samples procured from patients who received CTLA-4 and PD-1 inhibitors for metastatic SKCM. Results: We found that the BCR repertoire was associated with different clinical factors, such as tumor tissue site and sex. However, increased clonality of the BCR repertoire was favorably prognostic in SKCM and was prognostic even after first conditioning on various clinical factors. Mutation burden was not correlated with any BCR measurement, and no specific mutation had an altered BCR repertoire. Lack of an assembled BCR in pre-treatment tumor tissues was associated with a lack of anti-tumor response to a CTLA-4 inhibitor in metastatic SKCM. Conclusions: These findings suggest an important prognostic and predictive role for B cell characteristics in SKCM. This has implications for melanoma immunobiology and potential development of immunogenomics features to predict survival and response to immunotherapy

Regular black holes in quadratic gravity

The first-order correction of the perturbative solution of the coupled equations of the quadratic gravity and nonlinear electrodynamics is constructed, with the zeroth-order solution coinciding with the ones given by Ay\'on-Beato and Garc{\'\i}a and by Bronnikov. It is shown that a simple generalization of the Bronnikov's electromagnetic Lagrangian leads to the solution expressible in terms of the polylogarithm functions. The solution is parametrized by two integration constants and depends on two free parameters. By the boundary conditions the integration constants are related to the charge and total mass of the system as seen by a distant observer, whereas the free parameters are adjusted to make the resultant line element regular at the center. It is argued that various curvature invariants are also regular there that strongly suggests the regularity of the spacetime. Despite the complexity of the problem the obtained solution can be studied analytically. The location of the event horizon of the black hole, its asymptotics and temperature are calculated. Special emphasis is put on the extremal configuration

Lesbian and bisexual women's human rights, sexual rights and sexual citizenship: negotiating sexual health in England.

Lesbian and bisexual women's sexual health is neglected in much Government policy and practice in England and Wales. This paper examines lesbian and bisexual women's negotiation of sexual health, drawing on findings from a small research project. Themes explored include invisibility and lack of information, influences on decision-making and sexual activities and experiences of services and barriers to sexual healthcare. Key issues of importance in this respect are homophobic and heterosexist social contexts. Drawing on understandings of lesbian, gay and bisexual human rights, sexual rights and sexual citizenship, it is argued that these are useful lenses through which to examine and address lesbian and bisexual women's sexual health and related inequalities

A comprehensive categorical and bibliometric analysis of published research articles on pediatric pain from 1975-2010

The field of pediatric pain research began in the mid-1970's and has undergone significant growth and development in recent years as evidenced by the variety of books, conferences, and journals on the topic as well as the number of disciplines engaged in work in this area. Using categorical and bibliometric meta-trend analysis, the current study offers a synthesis of research on pediatric pain published between 1975 and 2010 in peer-reviewed journals. Abstracts from 4256 articles, retrieved from Web of Science, were coded across four categories: article type, article topic, type and age of participants, and pain stimulus. The affiliation of the first author and number of citations were also gathered. The results suggest a significant increase in the number of publications over the time period investigated, with 96% of the included articles published since 1990 and most research being multi-authored publications in pain- focused journals. First authors were most often from the United States, and affiliated with a medical department. The majority of studies were original research articles; the most frequent topics were pain characterization (39.86%), pain intervention (37.49%), and pain assessment (25.00%). Clinical samples were most frequent, with participants most often characterized as children (6-12 years) or adolescents (13-18 years) experiencing chronic or acute pain. The findings provide a comprehensive overview of contributions in the field of pediatric pain research over 35 years and offers recommendations for future research in the area. (C) 2015 International Association for the Study of Pai

Clarifying Some Remaining Questions in the Anomaly Puzzle

We discuss several points that may help to clarify some questions that remain about the anomaly puzzle in supersymmetric theories. In particular, we consider a general N=1 supersymmetric Yang-Mills theory. The anomaly puzzle concerns the question of whether there is a consistent way to put the R-current and the stress tensor in a single supercurrent, even though in the classical theory they are in the same supermultiplet. As is well known, the classically conserved supercurrent bifurcates into two supercurrents having different anomalies in the quantum regime. The most interesting result we obtain is an explicit expression for the lowest component of one of the two supercurrents in 4-dimensional spacetime, namely the supercurrent that has the energy-momentum tensor as one of its components. This expression for the lowest component is an energy-dependent linear combination of two chiral currents, which itself does not correspond to a classically conserved chiral current. The lowest component of the other supercurrent, namely, the R-current, satisfies the Adler-Bardeen theorem. The lowest component of the first supercurrent has an anomaly that we show is consistent with the anomaly of the trace of the energy-momentum tensor. Therefore, we conclude that there is no consistent way to put the R-current and the stress tensor in a single supercurrent in the quantized theory. We also discuss and try to clarify some technical points in the derivations of the two-supercurrents in the literature. These latter points concern the significance of infrared contributions to the NSVZ beta-function and the role of the equations of motion in deriving the two supercurrents.Comment: 22 pages, no figure. v2: minor changes. v3: sections re-organized. new subsections (IVA, IVB) added. references adde