A standardisation framework for bio‐logging data to advance ecological research and conservation

Bio‐logging data obtained by tagging animals are key to addressing global conservation challenges. However, the many thousands of existing bio‐logging datasets are not easily discoverable, universally comparable, nor readily accessible through existing repositories and across platforms, slowing down ecological research and effective management. A set of universal standards is needed to ensure discoverability, interoperability and effective translation of bio‐logging data into research and management recommendations. We propose a standardisation framework adhering to existing data principles (FAIR: Findable, Accessible, Interoperable and Reusable; and TRUST: Transparency, Responsibility, User focus, Sustainability and Technology) and involving the use of simple templates to create a data flow from manufacturers and researchers to compliant repositories, where automated procedures should be in place to prepare data availability into four standardised levels: (a) decoded raw data, (b) curated data, (c) interpolated data and (d) gridded data. Our framework allows for integration of simple tabular arrays (e.g. csv files) and creation of sharable and interoperable network Common Data Form (netCDF) files containing all the needed information for accuracy‐of‐use, rightful attribution (ensuring data providers keep ownership through the entire process) and data preservation security. We show the standardisation benefits for all stakeholders involved, and illustrate the application of our framework by focusing on marine animals and by providing examples of the workflow across all data levels, including filled templates and code to process data between levels, as well as templates to prepare netCDF files ready for sharing. Adoption of our framework will facilitate collection of Essential Ocean Variables (EOVs) in support of the Global Ocean Observing System (GOOS) and inter‐governmental assessments (e.g. the World Ocean Assessment), and will provide a starting point for broader efforts to establish interoperable bio‐logging data formats across all fields in animal ecology

Chlamydia trachomatis as a cause of neonatal conjunctivitis in Dutch infants.

Contains fulltext : 69691.pdf (publisher's version ) (Open Access)BACKGROUND: Chlamydia trachomatis is the most common sexually transmitted pathogen in adults, which at delivery may be transmitted from mother to child and cause conjunctivitis and pneumonia. In The Netherlands, prenatal chlamydial screening and treatment of pregnant women is not routine practice. The contribution of C. trachomatis to neonatal ophthalmic disease has not been studied in The Netherlands and remains unclear. METHODS: At the Sophia Children's Hospital and Rotterdam Eye Hospital, 2 cohorts of infants <3 months of age presenting with conjunctivitis were studied, 1 retrospectively (July 1996 to July 2001) and 1 prospectively (September 2001 to September 2002). Laboratory diagnosis was based on bacterial culture and polymerase chain reaction for C. trachomatis. RESULTS: C. trachomatis was detected in 27 (64%) of 42 retrospectively studied infants and 14 (61%) of 23 prospectively studied infants. Mucopurulent discharge was present in 35 (95%) of 37, swelling of the eyes in 27 (73%) of 37, conjunctival erythema in 24 (65%) of 37, respiratory symptoms in 14 (38%) of 37, and feeding problems in 5 (14%) of 37 infants respectively. Before microbiological diagnosis, general practitioners prescribed antichlamydial antibiotics locally to 5 (12%) of 41 and systemically to 4 (10%) of 41 infants who tested positive for chlamydia, and ophthalmologists prescribed to 21 (51%) of 41 and 7 (17%) of 41, respectively. CONCLUSIONS: C. trachomatis was the major cause of bacterial conjunctivitis in this population. Clinically, differentiation from other pathogens was not possible. Many infants who tested positive for chlamydia did not receive appropriate antibiotic treatment

Chlamydia trachomatis respiratory infection in Dutch infants.

Contains fulltext : 79971.pdf (publisher's version ) (Open Access)Chlamydia trachomatis is the most common bacterial pathogen causing sexually transmitted infections in Dutch adults. As prenatal screening for C trachomatis and treatment of pregnant women is not routine practice in The Netherlands, perinatal transmission of C trachomatis may therefore occur. The presence of C trachomatis in infants less than 6 months of age who presented with respiratory complaints to the Erasmus MC-Sophia hospital was evaluated. Respiratory specimens, primarily nasopharyngeal swabs, were tested for C trachomatis, respiratory viruses and Mycoplasma pneumoniae using PCR, viral isolation in cell cultures and direct immunofluorescence. C trachomatis respiratory tract infection was confirmed to be relatively common with detection in 10 of 148 (7%) infants tested. C trachomatis had not been tested for by the attending physicians, but was the second most frequently detected respiratory pathogen after human Respiratory Syncitial Virus, which was found in 41 (28%) infants

Social Network Analysis Reveals the Subtle Impacts of Tourist Provisioning on the Social Behavior of a Generalist Marine Apex Predator

Shark dive ecotourism is a lucrative industry in many regions around the globe. In some cases, sharks are provisioned using bait, prompting increased research on how baited dives influence shark behavior and yielding mixed results. Effects on patterns of habitat use and movement seemly vary across species and locations. It is unknown, however, whether wide-ranging, marine apex predators respond to provisioning by changing their patterns of grouping or social behavior. We applied a tiered analytical approach (aggregation-gregariousness-social preferences) examining the impact of provisioning on the putative social behavior of tiger sharks (Galeocerdo cuvier) at a dive tourism location in The Bahamas. Using network inference on three years of acoustic tracking data from 48 sharks, we tested for non-random social structure between non-provisioned and provisioned monitoring sites resulting in 12 distinct networks. Generally considered a solitary nomadic predator, we found evidence of sociality in tiger sharks, which varied spatiotemporally. We documented periods of both random (n = 7 networks) and non-random aggregation (n = 5 networks). Three of five non-random aggregations were at locations unimpacted by provisioning regardless of season, one occurred at an active provisioning site during the dry season and one at the same receivers during the wet season when provision activity is less prevalent. Aggregations lasted longer and occurred more frequently at provisioning sites, where gregariousness was also more variable. While differences in gregariousness among individuals was generally predictive of non-random network structure, individual site preferences, size and sex were not. Within five social preference networks, constructed using generalized affiliation indices, network density was lower at provisioning sites, indicating lower connectivity at these locations. We found no evidence of size assortment on preferences. Our data suggest that sociality may occur naturally within the Tiger Beach area, perhaps due to the unusually high density of individuals there. This study demonstrates the existence of periodic social behavior, but also considerable variation in association between tiger sharks, which we argue may help to mitigate any long-term impacts of provisioning on this population. Finally, we illustrate the utility of combining telemetry and social network approaches for assessing the impact of human disturbance on wildlife behavior

Large sharks exhibit varying behavioral responses to major hurricanes

Under global climate change, storm events are predicted to increase in strength and frequency. Although aquatic animals can be affected by acute natural disturbances, information on the immediate consequences of these weather systems on the behavioral ecology of highly mobile aquatic predators remains limited. Here we examine the spatial distributions, activity spaces, and ecological change-points of four large shark species (mean: 193 cm fork length ± 70 SD) via passive acoustic telemetry in two different locations in the subtropical Atlantic (Little Bahama Bank, Bahamas, and Biscayne Bay, Florida, USA) in relation to two separate major hurricane events (category 4 and 5). We tested whether sharks would evacuate shallow coastal habitats (and thus exit the acoustic arrays) during the hurricanes and exhibit comparable size of activity spaces pre- and post-storms, as has been previously found for smaller (50–150 cm fork length) sharks elsewhere. Located on the northwest edge of the Little Bahama Bank, Bahamas, an acoustic array consisting of 32 acoustic telemetry receivers tracking tiger sharks Galeocerdo cuvier sustained a direct hit from Hurricane Matthew in 2016. Daily detections of tagged tiger sharks within the array were consistent before and during the hurricane. Immediately following the storm, daily tiger shark detections approximately doubled. Size and extent of tiger shark activity space within the array were consistent pre- and post-storm. Located off Miami, within Biscayne Bay, an array of 32 acoustic receivers tracking bull Carcharhinus leucas, nurse Ginglymostoma cirratum, and great hammerhead sharks Sphyrna mokarran was exposed to tropical-storm-force winds from Hurricane Irma in 2017. As the eye of the storm passed 140 km to the west, most sharks previously present in the array were no longer detected, while two nurse sharks remained at receivers near Miami. Numbers of tagged bull sharks declined following Hurricane Irma, whereas other species did not. Ecological change point analyses indicated that seasonal changes - rather than storm conditions - cannot be ruled out as the primary driver of post-storm shark behavior. Unlike smaller shark species which have previously been found to evacuate shallow water habitats during storms, we found variable responses of large sharks to storm events. •The behavioral effects of tropical storms have not been evaluated for large shark species.•Acoustic telemetry was used to study the behavior of large sharks at two sites hit by hurricanes.•Species-specific responses were observed.•Several species did not evacuate shallow water as reported in small species.•Interspecific behavior, including why some sharks failed to evacuate stormimpacted areas, is discussed

Functional gene-set analysis does not support a major role for synaptic function in attention deficit/Hyperactivity disorder (ADHD)

Attention Deficit/Hyperactivity Disorder (ADHD) is one of the most common childhood-onset neuropsychiatric disorders. Despite high heritability estimates, genome-wide association studies (GWAS) have failed to find significant genetic associations, likely due to the polygenic character of ADHD. Nevertheless, genetic studies suggested the involvement of several processes important for synaptic function. Therefore, we applied a functional gene-set analysis to formally test whether synaptic functions are associated with ADHD. Gene-set analysis tests the joint effect of multiple genetic variants in groups of functionally related genes. This method provides increased statistical power compared to conventional GWAS. We used data from the Psychiatric Genomics Consortium including 896 ADHD cases and 2455 controls, and 2064 parent-affected offspring trios, providing sufficient statistical power to detect gene sets representing a genotype relative risk of at least 1.17. Although all synaptic genes together showed a significant association with ADHD, this association was not stronger than that of randomly generated gene sets matched for same number of genes. Further analyses showed no association of specific synaptic function categories with ADHD after correction for multiple testing. Given current sample size and gene sets based on current knowledge of genes related to synaptic function, our results do not support a major role for common genetic variants in synaptic genes in the etiology of ADHD