Repeatability of baited remote underwater video station (BRUVS) results within and between seasons

Baited remote underwater video stations (BRUVS) are increasingly being used to evaluate and monitor reef communities. Many BRUVS studies compare multiple sites sampled at single time points that may differ from the sampling time of another site. As BRUVS use grows in its application to provide data relevant to sustainable management, marine protected area success, and overall reef health, understanding repeatability of sampling results is vital. We examined the repeatability of BRUVS results for the elasmobranch community both within and between seasons and years, and explored environmental factors affecting abundances at two sites in Indonesia. On 956 BRUVS, 1139 elasmobranchs (69% rays, 31% sharks) were observed. We found consistent results in species composition and abundances within a season and across years. However, elasmobranch abundances were significantly higher in the wet season. The elasmobranch community was significantly different between the two sites sampled, one site being more coastal and easily accessed by fishermen. Our results demonstrate that while BRUVS are a reliable and repeatable method for surveying elasmobranchs, care must be taken in the timing of sampling between different regions to ensure that any differences observed are due to inherent differences amongst sampling areas as opposed to seasonal dissimilarities

The relation between athletic sports and prevalence of amenorrhea and oligomenorrhea in Iranian female athletes

<p>Abstract</p> <p>Background</p> <p>In 1992, the concept of female athlete triad was introduced to describe the interrelated problems of amenorrhea, eating disorders and osteoporosis seen in female athletes. To gain a clearer picture of amenorrhea/oligomenorrhea in Iran, one of the main components of the female athlete triad, we therefore established this study on the prevalence of amenorrhea/oligomenorrhea in elite Iranian female athletes, also evaluating the risk factors of these disorders in the same population.</p> <p>Methods</p> <p>This study performed as a cross-sectional study. All elite Iranian female athletes of 34 sports federation, including female athletes in national teams and medalists of Tehran were invited to participate. A total of 788 (95% response rate) returned the questionnaires and were examined. Younger athletes under the age of menarche were excluded. Each athlete completed a self-administered questionnaire, which covered the following questions about participant's demographic information, athletic history, history of injuries and menstrual pattern. In order to diagnose the causes of amenorrhea/Oligomenorrhea including polycystic ovary syndrome(PCOS), participants with amenorrhea/Oligomenorrhea underwent further investigation. They were evaluated by following Para clinic investigation, and an ultrasonographic study of ovary.</p> <p>Results</p> <p>The age ranged from 13–37 (mean = 21.1, SD = 4.5). Seventy one (9.0%) individuals had amenorrhea/oligomenorrhea, among those, 11 (15.5%) had PCOS.</p> <p>There was also a positive association between amenorrhea/oligomenorrhea and the following: age under 20 OR; 2.67, 95%CI(1.47 – 4.85), weight class sports OR; 2.09, 95%CI(1.15 – 3.82), endurance sports OR; 2.89, 95%CI(1.22 – 6.84), late onset of menarche OR; 3.32 95%CI(1.04–10.51), and use of oral contraceptive pills OR; 6.17, 95%CI(3.00 – 12.69). Intensity of training sport or BMI were not risk factors.</p> <p>Conclusion</p> <p>These findings support the previous findings in the literature that the prevalence of amenorrhea/oligomenorrhea is high in athletes. Furthermore, we provided the first report on the prevalence of PCOS in female athletes with amenorrhea/oligomenorrhea. Athletes would be greatly benefited by greater general awareness about the complications of amenorrhea/oligomenorrhea.</p> <p>To increase awareness of exercise-associated menstrual cycle irregularities, it is necessary to design complete and comprehensive education programs for female athletes, their parents, their coaches, and the relevant authorities.</p

Conservation successes and challenges for wide-ranging sharks and rays

Overfishing is the most significant threat facing sharks and rays. Given the growth in consumption of seafood, combined with the compounding effects of habitat loss, climate change, and pollution, there is a need to identify recovery paths, particularly in poorly managed and poorly monitored fisheries. Here, we document conservation through fisheries management success for 11 coastal sharks in US waters by comparing population trends through a Bayesian state-space model before and after the implementation of the 1993 Fisheries Management Plan for Sharks. We took advantage of the spatial and temporal gradients in fishing exposure and fisheries management in the Western Atlantic to analyze the effect on the Red List status of all 26 wide-ranging coastal sharks and rays. We show that extinction risk was greater where fishing pressure was higher, but this was offset by the strength of management engagement (indicated by strength of National and Regional Plan of Action for sharks and rays). The regional Red List Index (which tracks changes in extinction risk through time) declined in all regions until the 1980s but then improved in the North and Central Atlantic such that the average extinction risk is currently half that in the Southwest. Many sharks and rays are wide ranging, and successful fisheries management in one country can be undone by poorly regulated or unregulated fishing elsewhere. Our study underscores that well-enforced, science-based management of carefully monitored fisheries can achieve conservation success, even for slow-growing species

Overfishing Drives Over One-Third of All Sharks and Rays Toward a Global Extinction Crisis

The scale and drivers of marine biodiversity loss are being revealed by the International Union for Conservation of Nature (IUCN) Red List assessment process. We present the first global reassessment of 1,199 species in Class Chondrichthyes-sharks, rays, and chimeras. The first global assessment (in 2014) concluded that one-quarter (24%) of species were threatened. Now, 391 (32.6%) species are threatened with extinction. When this percentage of threat is applied to Data Deficient species, more than one-third (37.5%) of chondrichthyans are estimated to be threatened, with much of this change resulting from new information. Three species are Critically Endangered (Possibly Extinct), representing possibly the first global marine fish extinctions due to overfishing. Consequently, the chondrichthyan extinction rate is potentially 25 extinctions per million species years, comparable to that of terrestrial vertebrates. Overfishing is the universal threat affecting all 391 threatened species and is the sole threat for 67.3% of species and interacts with three other threats for the remaining third: loss and degradation of habitat (31.2% of threatened species), climate change (10.2%), and pollution (6.9%). Species are disproportionately threatened in tropical and subtropical coastal waters. Science-based limits on fishing, effective marine protected areas, and approaches that reduce or eliminate fishing mortality are urgently needed to minimize mortality of threatened species and ensure sustainable catch and trade of others. Immediate action is essential to prevent further extinctions and protect the potential for food security and ecosystem functions provided by this iconic lineage of predators

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment

Plasma microRNAs as biomarkers of pancreatic cancer risk in a prospective cohort study

Accepted manuscript version. Published version available in International Journal of Cancer 2017, 141 (5):905–915 .Noninvasive biomarkers for early pancreatic ductal adenocarcinoma (PDAC) diagnosis and disease risk stratification are greatly needed. We conducted a nested case-control study within the Prospective Investigation into Cancer and Nutrition (EPIC) cohort to evaluate prediagnostic microRNAs (miRs) as biomarkers of subsequent PDAC risk. A panel of eight miRs (miR-10a, -10b, -21-3p, -21-5p, -30c, -106b, -155 and -212) based on previous evidence from our group was evaluated in 225 microscopically confirmed PDAC cases and 225 controls matched on center, sex, fasting status and age/date/time of blood collection. MiR levels in prediagnostic plasma samples were determined by quantitative RT-PCR. Logistic regression was used to model levels and PDAC risk, adjusting for covariates and to estimate area under the receiver operating characteristic curves (AUC). Plasma miR-10b, -21-5p, -30c and -106b levels were significantly higher in cases diagnosed within 2 years of blood collection compared to matched controls (all p-values <0.04). Based on adjusted logistic regression models, levels for six miRs (miR-10a, -10b, -21-5p, -30c, -155 and -212) overall, and for four miRs (-10a, -10b, -21-5p and -30c) at shorter follow-up time between blood collection and diagnosis (≤5 yr, ≤2 yr), were statistically significantly associated with risk. A score based on the panel showed a linear dose-response trend with risk (p-value = 0.0006). For shorter follow-up (≤5 yr), AUC for the score was 0.73, and for individual miRs ranged from 0.73 (miR-212) to 0.79 (miR-21-5p)