Dramatic decline and limited recovery of a green crab (Carcinus maenas) population in the Minas Basin, Canada after the summer of 2013

This paper reports the results of a ten-year monitoring program of an Atlantic Canadian population of green crabs, Carcinus maenas, in the Minas Basin of the Bay of Fundy. Intertidal densities, sex and reproductive ratios, juvenile recruitment, subtidal catch-per-unit-effort (CPUE), and sizes of crabs in this population were recorded from 2008 to 2017. In 2013 intertidal densities, mean crab sizes, subtidal CPUE, and proportions of crabs mature and reproducing all dramatically decreased to all-time lows, and large crabs virtually disappeared from the population. From 2014 to 2017 the population partially recovered but remained in an altered state. Potential causes of interannual changes to this population were investigated by correlating intertidal densities to 257 monthly environmental variables and performing stepwise multiple regression analyses. Crab densities in a given year were best explained by potential settlement during the summer and the maximum sea-surface temperature during March of the same year. However, potential roles of other factors (e.g., autumn winds, summer temperatures, North Atlantic Oscillation index) could not be ruled out. Changes in abundances of other species in the area, particularly predators and prey of green crabs, have also been observed and present possible alternative causative agents that should be investigated. Populations of other marine species in the Gulf of Maine-Bay of Fundy region within which the Minas Basin is situated have also been reported to have undergone dramatic changes in and after 2013, suggesting the occurrence of some oceanographic event or regime shift in the region. Declines to the monitored crab population in this study may have resulted from this same 2013 event. These observations have implications for recruitment to marine populations in this region

General-relativistic coupling between orbital motion and internal degrees of freedom for inspiraling binary neutron stars

We analyze the coupling between the internal degrees of freedom of neutron stars in a close binary, and the stars' orbital motion. Our analysis is based on the method of matched asymptotic expansions and is valid to all orders in the strength of internal gravity in each star, but is perturbative in the ``tidal expansion parameter'' (stellar radius)/(orbital separation). At first order in the tidal expansion parameter, we show that the internal structure of each star is unaffected by its companion, in agreement with post-1-Newtonian results of Wiseman (gr-qc/9704018). We also show that relativistic interactions that scale as higher powers of the tidal expansion parameter produce qualitatively similar effects to their Newtonian counterparts: there are corrections to the Newtonian tidal distortion of each star, both of which occur at third order in the tidal expansion parameter, and there are corrections to the Newtonian decrease in central density of each star (Newtonian ``tidal stabilization''), both of which are sixth order in the tidal expansion parameter. There are additional interactions with no Newtonian analogs, but these do not change the central density of each star up to sixth order in the tidal expansion parameter. These results, in combination with previous analyses of Newtonian tidal interactions, indicate that (i) there are no large general-relativistic crushing forces that could cause the stars to collapse to black holes prior to the dynamical orbital instability, and (ii) the conventional wisdom with respect to coalescing binary neutron stars as sources of gravitational-wave bursts is correct: namely, the finite-stellar-size corrections to the gravitational waveform will be unimportant for the purpose of detecting the coalescences.Comment: 22 pages, 2 figures. Replaced 13 July: proof corrected, result unchange

Science Applications Forum Enhancing fisheries education through the Canadian Fisheries Research Network: a student perspective on interdisciplinarity, collaboration and 4 inclusivity 5 6

Abstract 31 Fisheries sciences and management involve complex problems not easily addressed by a single 32 set of stakeholders or methodologies from one discipline; accordingly, the Canadian Fisheries 33 Research Network (CFRN) was initiated to increase fisheries research capacity in Canada 34 through interdisciplinary and inclusive research collaborations. We compared the value of the 35 CFRN students' learning experience to that offered in traditional fisheries programs at Canadian 36 universities in training post-graduate students to tackle complex fisheries problems. This paper 37 presents 1) a review of the current state of fisheries education across Canada and 2) reflections 38 on our training within the CFRN, and challenges to implementing its innovative approach to 39 fisheries education. We found few dedicated fisheries programs in Canada and concluded that 40 fisheries research typically relies on securing a supervisor with an interest in fisheries. In 41 contrast, the CFRN enhanced our university training through interdisciplinary and inclusive 42 research collaborations, and by exposure to the realities of industry, government and academics 43 collaborating for sustainable fisheries. We propose a new approach to post-graduate level 44 fisheries education, one that combines interdisciplinarity, collaboration, and inclusivity to 45 produce more capable fisheries scientists and managers. Furthermore, we made 46 recommendations on how universities, researchers, and funding agencies can successfully 47 incorporate these themes into fisheries education. 4

Physics, Astrophysics and Cosmology with Gravitational Waves

Gravitational wave detectors are already operating at interesting sensitivity levels, and they have an upgrade path that should result in secure detections by 2014. We review the physics of gravitational waves, how they interact with detectors (bars and interferometers), and how these detectors operate. We study the most likely sources of gravitational waves and review the data analysis methods that are used to extract their signals from detector noise. Then we consider the consequences of gravitational wave detections and observations for physics, astrophysics, and cosmology.Comment: 137 pages, 16 figures, Published version <http://www.livingreviews.org/lrr-2009-2

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

Ireland: Submerged Prehistoric Sites and Landscapes

Evidence of Ireland's drowned landscapes and settlements presently comprises 50 sites spread across the entire island. These comprise mainly intertidal find spots or small collections of flint artefacts. A handful of fully subtidal sites are known, generally from nearshore regions and consisting, with one exception, of isolated single finds. Evidence of organic remains is also sparse, with the exception of Mesolithic and Neolithic wooden fish traps buried in estuarine sediments under Dublin. The relatively small number of sites is probably due to lack of research as much as taphonomic issues, and thus the current evidence hints at the potential archaeological record which may be found underwater. Such evidence could contribute to knowledge of the coastal adaptations and seafaring abilities of Ireland's earliest inhabitants. Nonetheless, taphonomic considerations, specifically relating to Ireland's history of glaciation, sea-level change and also modern oceanographic conditions likely limit the preservation of submerged landscapes and their associated archaeology. Realistically, the Irish shelf is likely characterised by pockets of preservation, which makes detection and study of submerged landscapes difficult but not impossible. A range of potential routes of investigation are identifiable, including site-scale archaeological survey, landscape-scale seabed mapping, archival research and community engagement