Seismic surveys and marine turtles: An underestimated global threat?

Seismic surveys are widely used in marine geophysical oil and gas exploration, employing airguns to produce sound-waves capable of penetrating the sea floor. In recent years, concerns have been raised over the biological impacts of this activity, particularly for marine mammals. While exploration occurs in the waters of at least fifty countries where marine turtles are present, the degree of threat posed by seismic surveys is almost entirely unknown. To investigate this issue, a mixed-methods approach involving a systematic review, policy comparison and stakeholder analysis was employed and recommendations for future research were identified. This study found that turtles have been largely neglected both in terms of research and their inclusion in mitigation policies. Few studies have investigated the potential for seismic surveys to cause behavioural changes or physical damage, indicating a crucial knowledge gap. Possible ramifications for turtles include exclusion from critical habitats, damage to hearing and entanglement in seismic survey equipment. Despite this, the policy comparison revealed that only three countries worldwide currently include turtles in their seismic mitigation guidelines and very few of the measures they specify are based on scientific evidence or proven effectiveness. Opinions obtained from stakeholder groups further highlight the urgent need for directed, in-depth empirical research to better inform and develop appropriate mitigation strategies. As seismic surveying is becoming increasingly widespread and frequent, it is important and timely that we evaluate the extent to which marine turtles, a taxon of global conservation concern, may be affected.This work was supported by NERC (QBEX code NE/J012319/1) and the Darwin Initiative (DI 20-009)

Generation and quality control of lipidomics data for the alzheimers disease neuroimaging initiative cohort.

Alzheimers disease (AD) is a major public health priority with a large socioeconomic burden and complex etiology. The Alzheimer Disease Metabolomics Consortium (ADMC) and the Alzheimer Disease Neuroimaging Initiative (ADNI) aim to gain new biological insights in the disease etiology. We report here an untargeted lipidomics of serum specimens of 806 subjects within the ADNI1 cohort (188 AD, 392 mild cognitive impairment and 226 cognitively normal subjects) along with 83 quality control samples. Lipids were detected and measured using an ultra-high-performance liquid chromatography quadruple/time-of-flight mass spectrometry (UHPLC-QTOF MS) instrument operated in both negative and positive electrospray ionization modes. The dataset includes a total 513 unique lipid species out of which 341 are known lipids. For over 95% of the detected lipids, a relative standard deviation of better than 20% was achieved in the quality control samples, indicating high technical reproducibility. Association modeling of this dataset and available clinical, metabolomics and drug-use data will provide novel insights into the AD etiology. These datasets are available at the ADNI repository at http://adni.loni.usc.edu/

Targeting condom distribution at high risk places increases condom utilization-evidence from an intervention study in Livingstone, Zambia

Background: The PLACE-method presumes that targeting HIV preventive activities at high risk places is effective in settings with major epidemics. Livingstone, Zambia, has a major HIV epidemic despite many preventive efforts in the city. A baseline survey conducted in 2005 in places where people meet new sexual partners found high partner turnover and unprotected sex to be common among guests. In addition, there were major gaps in on-site condom availability. This study aimed to assess the impact of a condom distribution and peer education intervention targeting places where people meet new sexual partners on condom use and sexual risk taking among people socializing there. Methods: The 2005 baseline survey assessed the presence of HIV preventive activities and sexual risk taking in places where people meet new sexual partners in Livingstone. One township was selected for a non-randomised intervention study on condom distribution and peer education in high risk venues in 2009. The presence of HIV preventive activities in the venues during the intervention was monitored by an external person. The intervention was evaluated after one year with a follow-up survey in the intervention township and a comparison township. In addition, qualitative interviews and focus group discussions were conducted. Results: Young people between 17-32 years of age were recruited as peer educators, and 40% were females. Out of 72 persons trained before the intervention, 38 quit, and another 11 had to be recruited. The percentage of venues where condoms were reported to always be available at least doubled in both townships, but was significantly higher in the intervention vs. the control venues in both surveys (84% vs. 33% in the follow-up). There was a reduction in reported sexual risk taking among guests socializing in the venues in both areas, but reporting of recent condom use increased more among people interviewed in the intervention (57% to 84%) than in the control community (55% to 68%). Conclusions: It is likely that the substantial increase in reported condom use in the intervention venues was partially due to the condom distribution and peer education intervention targeting these places. However, substantial changes were observed also in the comparison community over the five year period, and this indicates that major changes had occurred in overall risk taking among people socializing in venues where people meet new sexual partners in Livingstone

Distribution of variation over populations

Understanding the significance of the distribution of genetic or phenotypic variation over populations is one of the central concerns of population genetic and ecological research. The import of the research decisively depends on the measures that are applied to assess the amount of variation residing within and between populations. Common approaches can be classified under two perspectives: differentiation and apportionment. While the former focuses on differences (distances) in trait distribution between populations, the latter considers the division of the overall trait variation among populations. Particularly when multiple populations are studied, the apportionment perspective is usually given preference (via FST/GST indices), even though the other perspective is also relevant. The differences between the two perspectives as well as their joint conceptual basis can be exposed by referring them to the association between trait states and population affiliations. It is demonstrated that the two directions, association of population affiliation with trait state and of trait state with population affiliation, reflect the differentiation and the apportionment perspective, respectively. When combining both perspectives and applying the suggested measure of association, new and efficient methods of analysis result, as is outlined for population genetic processes. In conclusion, the association approach to an analysis of the distribution of trait variation over populations resolves problems that are frequently encountered with the apportionment perspective and its commonly applied measures in both population genetics and ecology, suggesting new and more comprehensive methods of analysis that include patterns of differentiation and apportionment

Comparative analysis of microsatellite variability in five macaw species (Psittaciformes, Psittacidae): Application for conservation

Cross-amplification was tested and variability in microsatellite primers (designed for Neotropical parrots) compared, in five macaw species, viz., three endangered blue macaws (Cyanopsitta spixii [extinct in the wild], Anodorhynchus leari [endangered] and Anodorhynchus hyacinthinus [vulnerable]), and two unthreatened red macaws (Ara chloropterus and Ara macao). Among the primers tested, 84.6% successfully amplified products in C. spixii, 83.3% in A. leari, 76.4% in A. hyacinthinus, 78.6% in A. chloropterus and 71.4% in A. macao. The mean expected heterozygosity estimated for each species, and based on loci analyzed in all the five, ranged from 0.33 (A. hyacinthinus) to 0.85 (A. macao). As expected, the results revealed lower levels of genetic variability in threatened macaw species than in unthreatened. The low combined probability of genetic identity and the moderate to high potential for paternity exclusion, indicate the utility of the microsatellite loci set selected for each macaw species in kinship and population studies, thus constituting an aid in planning in-situ and ex-situ conservation

Scenario of the spread of the invasive species Zaprionus indianus Gupta, 1970 (Diptera, Drosophilidae) in Brazil

Zaprionus indianus was first recorded in Brazil in 1999 and rapidly spread throughout the country. We have obtained data on esterase loci polymorphisms (Est2 and Est3), and analyzed them, using Landscape Shape Interpolation and the Monmonier Maximum Difference Algorithm to discover how regional invasion occurred. Hence, it was apparent that Z. indianus, after first arriving in São Paulo state, spread throughout the country, probably together with the transportation of commercial fruits by way of the two main Brazilian freeways, BR 153, to the south and the surrounding countryside, and the BR 116 along the coast and throughout the north-east

Developing a manually annotated clinical document corpus to identify phenotypic information for inflammatory bowel disease

<p>Abstract</p> <p>Background</p> <p>Natural Language Processing (NLP) systems can be used for specific Information Extraction (IE) tasks such as extracting phenotypic data from the electronic medical record (EMR). These data are useful for translational research and are often found only in free text clinical notes. A key required step for IE is the manual annotation of clinical corpora and the creation of a reference standard for (1) training and validation tasks and (2) to focus and clarify NLP system requirements. These tasks are time consuming, expensive, and require considerable effort on the part of human reviewers.</p> <p>Methods</p> <p>Using a set of clinical documents from the VA EMR for a particular use case of interest we identify specific challenges and present several opportunities for annotation tasks. We demonstrate specific methods using an open source annotation tool, a customized annotation schema, and a corpus of clinical documents for patients known to have a diagnosis of Inflammatory Bowel Disease (IBD). We report clinician annotator agreement at the document, concept, and concept attribute level. We estimate concept yield in terms of annotated concepts within specific note sections and document types.</p> <p>Results</p> <p>Annotator agreement at the document level for documents that contained concepts of interest for IBD using estimated Kappa statistic (95% CI) was very high at 0.87 (0.82, 0.93). At the concept level, F-measure ranged from 0.61 to 0.83. However, agreement varied greatly at the specific concept attribute level. For this particular use case (IBD), clinical documents producing the highest concept yield per document included GI clinic notes and primary care notes. Within the various types of notes, the highest concept yield was in sections representing patient assessment and history of presenting illness. Ancillary service documents and family history and plan note sections produced the lowest concept yield.</p> <p>Conclusion</p> <p>Challenges include defining and building appropriate annotation schemas, adequately training clinician annotators, and determining the appropriate level of information to be annotated. Opportunities include narrowing the focus of information extraction to use case specific note types and sections, especially in cases where NLP systems will be used to extract information from large repositories of electronic clinical note documents.</p

Instant availability of patient records, but diminished availability of patient information: A multi-method study of GP's use of electronic patient records

<p>Abstract</p> <p>Background</p> <p>In spite of succesful adoption of electronic patient records (EPR) by Norwegian GPs, what constitutes the actual benefits and effects of the use of EPRs in the perspective of the GPs and patients has not been fully characterized. We wanted to study primary care physicians' use of electronic patient record (EPR) systems in terms of use of different EPR functions and the time spent on using the records, as well as the potential effects of EPR systems on the clinician-patient relationship.</p> <p>Methods</p> <p>A combined qualitative and quantitative study that uses data collected from focus groups, observations of primary care encounters and a questionnaire survey of a random sample of general practitioners to describe their use of EPR in primary care.</p> <p>Results</p> <p>The overall availability of individual patient records had improved, but the availability of the information within each EPR was not satisfactory. GPs' use of EPRs were efficient and comprehensive, but have resulted in transfer of administrative work from secretaries to physicians. We found no indications of disturbance of the clinician-patient relationship by use of computers in this study.</p> <p>Conclusion</p> <p>Although GPs are generally satisfied with their EPRs systems, there are still unmet needs and functionality to be covered. It is urgent to find methods that can make a better representation of information in large patient records as well as prevent EPRs from contributing to increased administrative workload of physicians.</p