Development of a Species Distribution Model for the East Pacific Green Sea Turtle using Ecological Geoprocessing Tools

East Pacific green sea turtles, Chelonia mydas, play ecologically important roles in marine habitats which range from grazing (and thus regularly "mowing") algae and seagrass beds to cycling nutrients between the ocean and land. However, these important grazers have been hunted to ecological extinction in some places for their eggs, meat, and skin. The conservation initiative for the survival of sea turtles requires the protection of their primary habitats in conjunction with a decrease in their interaction with humans. One way these objectives can be met is through the creation of species distribution maps (SDMs). For this thesis, a SDM was created from a generalized additive model used to identify major feeding areas for East Pacific green turtles residing in the Galapagos Islands. The input for the model was green turtle sighting locations during a June 2010 marine life observation survey and remotely sensed values of four oceanographic parameters obtained from satellite sensors (Bathymetry, Sea Surface Temperature, Chlorophyll a, and Current Speed). Line transects of intertidal and subtidal shoreline regions of the islands of Isabela, San Cristobal, and Floreana were also completed, to describe similarities and differences in macroalgal abundance between the locations. A generalized additive model (GAM) explained 56% of the data's null deviance and had a true positive rate of 0.83. The corresponding species distribution map indicated that East Pacific green sea turtles prefer to forage in warm, low chlorophyll a, slow moving waters at depths mostly less than 250m throughout the archipelago. ANOVA analyses showed that macroalgal abundance was statistically different (p-value < 0.01) between the islands of San Cristobal and Isabela. The line transects analysis also documented that red algae was the most prominent phyla at the sites and that the macroalgal abundance did not vary much between months June 2010 and April/May 2011. With these results, potential foraging areas for East Pacific green turtles can be identified and protected. Future studies will be focused on the collection of macroalgae from coastal areas outlined in the SDM and the interactions between green turtles and their competitors and/or predators. This information can be used to validate the areas delineated by the model and to further the understanding of the spatial-temporal effects on macroalgal abundance

Report of Working Group on Widely Distributed Stocks (WGWIDE).

As a consequence of the impact of the COVID pandemic on international travel which prevented the traditional meeting from taking place, the Working Group on Widely Distributed Stocks (WGWIDE) met online via WebEx hosted by ICES. Prior to the 2020 meeting, the generic ToRs for species and regional working groups were re-prioritised by ACOM to allow the WG to focus primarily on those ToRs most applicable to the provision of advice. WGWIDE reports on the status and considerations for management of Northeast Atlantic mackerel, blue whiting, Western and North Sea horse mackerel, Northeast Atlantic boarfish, Norwegian springspawning herring, striped red mullet (Subareas 6, 8 and Divisions 7.a-c, e-k and 9.a), and red gurnard (Subareas 3, 4, 5, 6, 7, and 8) stocks. Northeast Atlantic (NEA) Mackerel. This stock is highly migratory and widely distributed throughout the Northeast Atlantic with significant fisheries is most ICES subareas. A diverse range of fleets from smaller artisanal, handline vessels to large (100m+) factory freezer vessels and modern RSW trawlers and purse seiners take part in what is one of the most valuable European fisheries. The assessment conducted in 2020 is an update assessment, based on the configuration agreed during the most recent inter-benchmark exercise in 2019 and incorporates the most recent data available from sampling of the commercial catch in 2019, the final 2019 egg survey SSB estimate, an updated recruitment index and tagging time series along with 2020 survey data from the IESSNS swept area survey. Advice is given based on stock reference points which were updated during a management strategy evaluation carried out in 2020. Following a strong increase from 2007 to 2014, SSB has been declining although it remains well above MSY Btrigger. Fishing mortality has been below FMSY since 2016. There have been a number of large year classes since 2001 with above average recruitment over much of the most recent decade. Blue Whiting. This pelagic gadoid is widely distributed in the eastern part of the North Atlantic. The 2020 update assessment followed the protocol from the most recent inter-benchmark in 2016 and used preliminary catch data from 2020. Due to the cancellation of the 2020 acoustic survey, this data was not available. The effect on the assessment was minimal and limited to increases in uncertainty of the terminal year estimates. The SSB continues to decrease from the most recent maximum in 2017 mainly due to below average recruitment since 2017, although it remains above MSY Btrigger. Fishing mortality has been above FMSY since 2014. Norwegian Spring Spawning Herring. This is one of the largest herring stocks in the world. It is highly migratory, spawning along the Norwegian coast and feeding throughout much of the Norwegian Sea. The 2020 assessment is based on an implementation of the XSAM assessment model introduced at the benchmark in 2016. This years’ assessment indicates that the stock is continuing to decline from the peak in 2008 of 7Mt to just above MSY Btrigger due to successive years of average or below average recruitment. Catch advice for 2021 is given on the basis of the agreed management plan and represents a substantial increase over the 2020 advice due to an upward revision in the estimate of the 2016 year-class which is considered to be the most significant year-class since 2004

Improving Medicines use in People with Polypharmacy in Primary Care (IMPPP): Protocol for a multicentre cluster randomised trial comparing a complex intervention for medication optimization against usual care.

IntroductionPolypharmacy is increasingly common, and associated with undesirable consequences. Polypharmacy management necessitates balancing therapeutic benefits and risks, and varying clinical and patient priorities. Current guidance for managing polypharmacy is not supported by high quality evidence. The aim of the Improving Medicines use in People with Polypharmacy in Primary Care (IMPPP) trial is to evaluate the effectiveness of an intervention to optimise medication use for patients with polypharmacy in a general practice setting.MethodsThis trial will use a multicentre, open-label, cluster-randomised controlled approach, with two parallel groups. Practices will be randomised to a complex intervention comprising structured medication review (including interprofessional GP/pharmacist treatment planning and patient-facing review) supported by performance feedback, financial incentivisation, clinician training and clinical informatics (intervention), or usual care (control). Patients with polypharmacy and triggering potentially inappropriate prescribing (PIP) indicators will be recruited in each practice using a computerised search of health records. 37 practices will recruit 50 patients, and review them over a 26-week intervention delivery period. The primary outcome is the mean number of PIP indicators triggered per patient at 26 weeks follow-up, determined objectively from coded GP electronic health records. Secondary outcomes will include patient reported outcome measures, and health and care service use. The main intention-to-treat analysis will use linear mixed effects regression to compare number of PIP indicators triggered at 26 weeks post-review between groups, adjusted for baseline (pre-randomisation) values. A nested process evaluation will explore implementation of the intervention in primary care.Ethics and disseminationThe protocol and associated study materials have been approved by the Wales REC 6, NHS Research Ethics Committee (REC reference 19/WA/0090), host institution and Health Research Authority. Research outputs will be published in peer-reviewed journals and relevant conferences, and additionally disseminated to patients and the public, clinicians, commissioners and policy makers.Isrctn registration90146150 (28/03/2019)

Horizontal gene transfer in Histophilus somni and its role in the evolution of pathogenic strain 2336, as determined by comparative genomic analyses

<p>Abstract</p> <p>Background</p> <p>Pneumonia and myocarditis are the most commonly reported diseases due to <it>Histophilus somni</it>, an opportunistic pathogen of the reproductive and respiratory tracts of cattle. Thus far only a few genes involved in metabolic and virulence functions have been identified and characterized in <it>H. somni </it>using traditional methods. Analyses of the genome sequences of several <it>Pasteurellaceae </it>species have provided insights into their biology and evolution. In view of the economic and ecological importance of <it>H. somni</it>, the genome sequence of pneumonia strain 2336 has been determined and compared to that of commensal strain 129Pt and other members of the <it>Pasteurellaceae</it>.</p> <p>Results</p> <p>The chromosome of strain 2336 (2,263,857 bp) contained 1,980 protein coding genes, whereas the chromosome of strain 129Pt (2,007,700 bp) contained only 1,792 protein coding genes. Although the chromosomes of the two strains differ in size, their average GC content, gene density (total number of genes predicted on the chromosome), and percentage of sequence (number of genes) that encodes proteins were similar. The chromosomes of these strains also contained a number of discrete prophage regions and genomic islands. One of the genomic islands in strain 2336 contained genes putatively involved in copper, zinc, and tetracycline resistance. Using the genome sequence data and comparative analyses with other members of the <it>Pasteurellaceae</it>, several <it>H. somni </it>genes that may encode proteins involved in virulence (<it>e.g</it>., filamentous haemaggutinins, adhesins, and polysaccharide biosynthesis/modification enzymes) were identified. The two strains contained a total of 17 ORFs that encode putative glycosyltransferases and some of these ORFs had characteristic simple sequence repeats within them. Most of the genes/loci common to both the strains were located in different regions of the two chromosomes and occurred in opposite orientations, indicating genome rearrangement since their divergence from a common ancestor.</p> <p>Conclusions</p> <p>Since the genome of strain 129Pt was ~256,000 bp smaller than that of strain 2336, these genomes provide yet another paradigm for studying evolutionary gene loss and/or gain in regard to virulence repertoire and pathogenic ability. Analyses of the complete genome sequences revealed that bacteriophage- and transposon-mediated horizontal gene transfer had occurred at several loci in the chromosomes of strains 2336 and 129Pt. It appears that these mobile genetic elements have played a major role in creating genomic diversity and phenotypic variability among the two <it>H. somni </it>strains.</p

Basic science232. Certolizumab pegol prevents pro-inflammatory alterations in endothelial cell function

Background: Cardiovascular disease is a major comorbidity of rheumatoid arthritis (RA) and a leading cause of death. Chronic systemic inflammation involving tumour necrosis factor alpha (TNF) could contribute to endothelial activation and atherogenesis. A number of anti-TNF therapies are in current use for the treatment of RA, including certolizumab pegol (CZP), (Cimzia ®; UCB, Belgium). Anti-TNF therapy has been associated with reduced clinical cardiovascular disease risk and ameliorated vascular function in RA patients. However, the specific effects of TNF inhibitors on endothelial cell function are largely unknown. Our aim was to investigate the mechanisms underpinning CZP effects on TNF-activated human endothelial cells. Methods: Human aortic endothelial cells (HAoECs) were cultured in vitro and exposed to a) TNF alone, b) TNF plus CZP, or c) neither agent. Microarray analysis was used to examine the transcriptional profile of cells treated for 6 hrs and quantitative polymerase chain reaction (qPCR) analysed gene expression at 1, 3, 6 and 24 hrs. NF-κB localization and IκB degradation were investigated using immunocytochemistry, high content analysis and western blotting. Flow cytometry was conducted to detect microparticle release from HAoECs. Results: Transcriptional profiling revealed that while TNF alone had strong effects on endothelial gene expression, TNF and CZP in combination produced a global gene expression pattern similar to untreated control. The two most highly up-regulated genes in response to TNF treatment were adhesion molecules E-selectin and VCAM-1 (q 0.2 compared to control; p > 0.05 compared to TNF alone). The NF-κB pathway was confirmed as a downstream target of TNF-induced HAoEC activation, via nuclear translocation of NF-κB and degradation of IκB, effects which were abolished by treatment with CZP. In addition, flow cytometry detected an increased production of endothelial microparticles in TNF-activated HAoECs, which was prevented by treatment with CZP. Conclusions: We have found at a cellular level that a clinically available TNF inhibitor, CZP reduces the expression of adhesion molecule expression, and prevents TNF-induced activation of the NF-κB pathway. Furthermore, CZP prevents the production of microparticles by activated endothelial cells. This could be central to the prevention of inflammatory environments underlying these conditions and measurement of microparticles has potential as a novel prognostic marker for future cardiovascular events in this patient group. Disclosure statement: Y.A. received a research grant from UCB. I.B. received a research grant from UCB. S.H. received a research grant from UCB. All other authors have declared no conflicts of interes

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Workshop on Raising Data using the RDBES and TAF (WKRDBESRaiseTAF; outputs from 2022 meeting)

41 páginasThe Workshop on Raising Data using the RDBES and TAF (WKRDBES-Raise&TAF) met online (26–30 of September 2022) to evaluate the use of the Regional Database and Estimation System (RDBES) format to reproduce the 2022 InterCatch input and output, identifying a Transparent Assessment Framework (TAF) structure to organize the intermediate steps and to propose standardized output formats. The main outcomes of WKRDBES-Raise&TAF were: · RDBES provides sufficient support for current national estimation protocols. However, some minor issues were reported that hampered an exact reproduction of the estimates. Therefore, adaptations of the data model should not be excluded completely. · All the input to stock assessment that InterCatch currently provides, could be reproduced. The participants started from the current stock extracts that can be downloaded from InterCatch. · A workflow was proposed with a national TAF repository for each country, a stock estimation repository and a stock assessment repository. The intermediate output of those repositories will be stored in an ‘intermediate output database’ and depending on the user role, you will get access to the relevant stages in this workflow. · The following requirements for the standard output formats were defined: they cannot be more restrictive than the InterCatch input and output format; they should present measures of uncertainty and sample sizes (for national estimates) and should have a configurable domain definition (for national estimates). Despite those successful outcomes, the current plan for transition to an operational system was concluded to be too optimistic. WKRDBES-Raise&TAF therefore recommends to the Working Group on Governance of the Regional Database and Estimation System (WGRDBESGOV) to revise the roadmap and allow RDBES to be in a test phase also for 2023. WKRDBES-Raise&TAF felt the need to test the proposed workflow on a small scale and therefore recommends to the WGRDBESGOV to arrange a workshop where two stocks (pok.27.3a46 (Saithe (Pollachius virens) in Subareas 4, 6 and Division 3.a (North Sea, Rockall and West of Scotland, Skagerrak and Kattegat) and wit.27.3a47d (Witch (Glyptocephalus cynoglossus) in Subarea 4 and Divisions 3.a and 7.d (North Sea, Skagerrak and Kattegat, eastern English Channel)) will be set up to go through the whole flow.Peer reviewe

Marine mammal distribution in Ecuador: surveys aboard a ship of opportunity as a means of monitoring relative abundance

Five marine mammal surveys between 2008 and 2011 were conducted aboard the Buque de Investigación Orion (the research vessel for the Oceanographic Institute of the Ecuadorian Navy) within oceanic waters adjacent to mainland Ecuador and the Galápagos Islands. The surveys dedicated extensive time in deep, offshore waters where cetaceans were not densely present. Sightings of 12 species were compared with an earlier survey aboard the B/I Orion in 2001 as well as with a subset of published data from three NOAA STAR (Stenella Abundance Research) surveys between 1999 and 2003. Additionally, a small boat, near-shore survey, was conducted during June 2010 among andnear the Galápagos Islands. Encounter rates ranged annually from 0.012 cetacean/km to 0.027 cetacean/km. The highest encounter rate aboard the B/I Orion took place during the April 2009 survey. In order to compare sightingrates between the B/I Orion and NOAA platforms, the average effective half-strip widths were used to determine encounter rates per area effectively searched. A zonation within the study region was observed between odontocete andbalaenopterid cetaceans as well as between striped (Stenella coeruleoalba) and short-beaked common dolphins (Delphinus delphis). Several methodological aspects of surveys and geographical features that may influence encounter rates and subsequent abundance estimates are discussed. This study demonstrates that vessels of opportunity provide a valuable means of studying open-ocean and coastal distributions of marine mammals. Possible methodological improvements, such as the use of high-power binoculars, that could increase the absolute number of sightings, the efficiency of these opportunistic surveys, and improve the sighting rates of more evasive species are discussed