Statistical analysis of SAMBAH survey and associated data

SAMBAH (Static Acoustic Monitoring of the Baltic Sea Harbour Porpoise) was an international project involving all EU countries around the Baltic Sea, funded by those countries and by the EU Life program (Project Number LIFE08 NAT/S/000261). It ran from 1/1/2010 to 30/9/2015. One major goal of the project was to estimate the abundance of Baltic Sea harbour porpoise, by designing and implementing a large-scale multi-year passive acoustic survey. CREEM was contracted to collaborate on the survey design, and provide statistical analysis of resulting data. A number of internal reports were produced and circulated to the project team, detailing aspects of the analysis. In this CREEM technical report, we collate the most recent version of each of these internal reports as a means of making them publicly available.Publisher PD

Loggerhead turtle Caretta caretta density and abundance in Chesapeake Bay and the temperate ocean waters of the southern portion of the Mid-Atlantic Bight

Funding was provided by the NOAA Species Recovery Grants to States program (Award #NA 47200033) issued to the Virginia Department of Game and Inland Fisheries which contracted with the Virginia Aquarium & Marine Science Center Foundation. Additional funding for tags and turtle capture was also provided by US Fleet Forces Command as well as the Virginia Aquarium Batten Collaborative Research Fund and Batten Professional Development Fund.We conducted aerial surveys of sea turtles in 2011 and 2012, incorporating corrections for perception and availability bias in Chesapeake Bay and near-shore continental shelf waters of the Mid-Atlantic Bight off the US states of Virginia and Maryland. Results of these surveys and ancillary research to determine surface times for loggerhead turtles provide us with a new baseline population estimate for turtles in the region. Prior surveys were conducted in Chesapeake Bay in the mid-1980s and early 2000s, and in ocean waters in the late 1970s and early 1980s. Although comparison of density estimates not corrected for availability between prior surveys and this effort suggests that the population of sea turtles, especially loggerhead turtles, is higher than previous estimates, differences between surveys may be the result of survey methodologies and cannot be assumed to be true changes in density. Surface time for availability corrections was calculated using dive summaries from satellite telemetry on 27 loggerhead turtles tracked between 2011 and 2015. We calculated stratified seasonal availability corrections for bay and ocean waters based on assumed differences in turtle behavior and water clarity between the 2 habitats. For each habitat, we provided seasonal corrections for 3 detection depth bins (shallow, moderate, and deep) to account for differences in sub-surface detection ranges. Differences and trends toward differences among availability corrections underscore the need to better understand the many variables that affect surface time for sea turtles in temperate waters, and the effect that availability has on abundance and density estimates.Publisher PDFPeer reviewe

An expert-based system to predict population survival rate from health data

This work was supported by the Office of Naval Research Marine Mammal Biology Program [grant number N00014-17-1-2868].Timely detection and understanding of causes for population decline are essential for effective wildlife management and conservation. Assessing trends in population size has been the standard approach but we propose that monitoring population health could prove more effective. We collated data from seven bottlenose dolphin (Tursiops truncatus) populations in southeastern U.S. to develop the Veterinary Expert System for Outcome Prediction (VESOP), which estimates survival probability using a suite of health measures identified by experts as indices for inflammatory, metabolic, pulmonary, and neuroendocrine systems. VESOP was implemented using logistic regression within a Bayesian analysis framework, and parameters were fit using records from five of the sites that had a robust stranding network and frequent photographic identification (photo-ID) surveys to document definitive survival outcomes. We also conducted capture-mark-recapture (CMR) analyses of photo-ID data to obtain separate estimates of population survival rates for comparison with VESOP survival estimates. VESOP analyses found multiple measures of health, particularly markers of inflammation, were predictive of 1- and 2-year individual survival. The highest mortality risk one year following health assessment related to low alkaline phosphatase, with an odds ratio of 10.2 (95% CI 3.41-26.8), while 2-year mortality was most influenced by elevated globulin (9.60; 95% CI 3.88-22.4); both are markers of inflammation. The VESOP model predicted population-level survival rates that correlated with estimated survival rates from CMR analyses for the same populations (1-year Pearson's r = 0.99; p = 1.52e-05, 2-year r = 0.94; p = 0.001). While our proposed approach will not detect acute mortality threats that are largely independent of animal health, such as harmful algal blooms, it is applicable for detecting chronic health conditions that increase mortality risk. Random sampling of the population is important and advancement in remote sampling methods could facilitate more random selection of subjects, obtainment of larger sample sizes, and extension of the approach to other wildlife species.Publisher PDFPeer reviewe

TESS Discovery of an ultra-short-period planet around the nearby M dwarf LHS 3844

Data from the newly-commissioned \textit{Transiting Exoplanet Survey Satellite} (TESS) has revealed a "hot Earth" around LHS 3844, an M dwarf located 15 pc away. The planet has a radius of $1.32\pm 0.02$ $R_\oplus$ and orbits the star every 11 hours. Although the existence of an atmosphere around such a strongly irradiated planet is questionable, the star is bright enough ($I=11.9$, $K=9.1$) for this possibility to be investigated with transit and occultation spectroscopy. The star's brightness and the planet's short period will also facilitate the measurement of the planet's mass through Doppler spectroscopy.Comment: 10 pages, 4 figures. Submitted to ApJ Letters. This letter makes use of the TESS Alert data, which is currently in a beta test phase, using data from the pipelines at the TESS Science Office and at the TESS Science Processing Operations Cente

People of the British Isles: preliminary analysis of genotypes and surnames in a UK control population

There is a great deal of interest in fine scale population structure in the UK, both as a signature of historical immigration events and because of the effect population structure may have on disease association studies. Although population structure appears to have a minor impact on the current generation of genome-wide association studies, it is likely to play a significant part in the next generation of studies designed to search for rare variants. A powerful way of detecting such structure is to control and document carefully the provenance of the samples involved. Here we describe the collection of a cohort of rural UK samples (The People of the British Isles), aimed at providing a well-characterised UK control population that can be used as a resource by the research community as well as providing fine scale genetic information on the British population. So far, some 4,000 samples have been collected, the majority of which fit the criteria of coming from a rural area and having all four grandparents from approximately the same area. Analysis of the first 3,865 samples that have been geocoded indicates that 75% have a mean distance between grandparental places of birth of 37.3km, and that about 70% of grandparental places of birth can be classed as rural. Preliminary genotyping of 1,057 samples demonstrates the value of these samples for investigating fine scale population structure within the UK, and shows how this can be enhanced by the use of surnames

Hsp90 orchestrates transcriptional regulation by Hsf1 and cell wall remodelling by MAPK signalling during thermal adaptation in a pathogenic yeast

Acknowledgments We thank Rebecca Shapiro for creating CaLC1819, CaLC1855 and CaLC1875, Gillian Milne for help with EM, Aaron Mitchell for generously providing the transposon insertion mutant library, Jesus Pla for generously providing the hog1 hst7 mutant, and Cathy Collins for technical assistance.Peer reviewedPublisher PD

Activating mutation in MET oncogene in familial colorectal cancer

<p>Abstract</p> <p>Background</p> <p>In developed countries, the lifetime risk of developing colorectal cancer (CRC) is 5%, and it is the second leading cause of death from cancer. The presence of family history is a well established risk factor with 25-35% of CRCs attributable to inherited and/or familial factors. The highly penetrant inherited colon cancer syndromes account for approximately 5%, leaving greater than 20% without clear genetic definition. Familial colorectal cancer has been linked to chromosome 7q31 by multiple affected relative pair studies. The <it>MET </it>proto-oncogene which resides in this chromosomal region is considered a candidate for genetic susceptibility.</p> <p>Methods</p> <p><it>MET </it>exons were amplified by PCR from germline DNA of 148 affected sibling pairs with colorectal cancer. Amplicons with altered sequence were detected with high-resolution melt-curve analysis using a LightScanner (Idaho Technologies). Samples demonstrating alternative melt curves were sequenced. A TaqMan assay for the specific c.2975C <b>></b>T change was used to confirm this mutation in a cohort of 299 colorectal cancer cases and to look for allelic amplification in tumors.</p> <p>Results</p> <p>Here we report a germline non-synonymous change in the <it>MET </it>proto-oncogene at amino acid position T992I (also reported as <it>MET </it>p.T1010I) in 5.2% of a cohort of sibling pairs affected with CRC. This genetic variant was then confirmed in a second cohort of individuals diagnosed with CRC and having a first degree relative with CRC at prevalence of 4.1%. This mutation has been reported in cancer cells of multiple origins, including 2.5% of colon cancers, and in <1% in the general population. The threonine at amino acid position 992 lies in the tyrosine kinase domain of MET and a change to isoleucine at this position has been shown to promote metastatic behavior in cell-based models. The average age of CRC diagnosis in patients in this study is 63 years in mutation carriers, which is 8 years earlier than the general population average for CRC.</p> <p>Conclusions</p> <p>Although the <it>MET </it>p.T992I genetic mutation is commonly found in somatic colorectal cancer tissues, this is the first report also implicating this <it>MET </it>genetic mutation as a germline inherited risk factor for familial colorectal cancer. Future studies on the cancer risks associated with this mutation and the prevalence in different at-risk populations will be an important extension of this work to define the clinical significance.</p

Monitoring Winter and Summer Abundance of Cetaceans in the Pelagos Sanctuary (Northwestern Mediterranean Sea) Through Aerial Surveys

Systematic long-term monitoring of abundance is essential to inform conservation measures and evaluate their effectiveness. To instigate such work in the Pelagos Sanctuary in the Mediterranean, two aerial surveys were conducted in winter and summer 2009. A total of 467 (131 in winter, 336 in summer) sightings of 7 species was made. Sample sizes were sufficient to estimate abundance of fin whales in summer (148; 95% CI = 87–254) and striped dolphins in winter (19,462; 95% CI = 12 939–29 273) and in summer (38 488; 95% CI = 27 447–53 968). Numbers of animals within the Sanctuary are significantly higher in summer, when human activities and thus potential population level impacts are highest. Comparisons with data from past shipboard surveys suggest an appreciable decrease in fin whales within the Sanctuary area and an appreciable increase in striped dolphins. Aerial surveys proved to be more efficient than ship surveys, allowing more robust estimates, with smaller CIs and CVs. These results provide essential baseline data for this marine protected area and continued regular surveys will allow the effectiveness of the MPA in terms of cetacean conservation to be evaluated and inform future management measures. The collected data may also be crucial in assessing whether ship strikes, one of the main causes of death for fin whales in the Mediterranean, are affecting the Mediterranean population

Common Familial Colorectal Cancer Linked to Chromosome 7q31: A Genome-Wide Analysis

Present investigations suggest that approximately 30% of colorectal cancer (CRC) cases arise on the basis of inherited factors. We hypothesize that the majority of inherited factors are moderately penetrant genes, common in the population. We use an affected sibling pair approach to identify genetic regions that are coinherited by siblings with CRC. Individuals from families with at least two siblings diagnosed with colorectal adenocarcinoma or high grade dysplasia were enrolled. Known familial CRC syndromes were excluded. A genome-wide scan on 151 DNA samples from 70 kindreds was completed using deCODE's 1100 short tandem repeat marker set at an average 4 cM density. Fine mapping on a total of 184 DNAs from 83 kindreds was done in regions suggesting linkage. Linkage analysis was accomplished with MERLIN analysis package. Linkage analysis revealed three genetic regions with NPL LOD scores ≥ 2.0: Ch. 3q29, LOD 2.61 (p=0.0003); Ch. 4q31.3, LOD 2.13 (p=0.0009); and Ch. 7q31.31, LOD 3.08 (p=0.00008). Affected siblings with increased sharing at the 7q31 locus have an 3.8 year (±3.5) earlier age of CRC onset although this is not statistically significant (p=0.11). No significant linkage was found near genes causing known syndromes or, regions previously reported (8q24, 9q22, and 11q23). The chromosome 3q21-q24 region reported to be linked in CRC relative pairs, is supported by our study, albeit a minor peak (LOD 0.9, p=0.02). No known familial cancer genes reside in the 7q31 locus, thus the identified region may contain a novel susceptibility gene responsible for common familial CRC