Advances in Spatial Data Infrastructure, Acquisition, Analysis, Archiving and Dissemination

The authors review recent contributions to the state-of-thescience and benign proliferation of satellite remote sensing, spatial data infrastructure, near-real-time data acquisition, analysis on high performance computing platforms, sapient archiving, multi-modal dissemination and utilization for a wide array of scientific applications. The authors also address advances in Geoinformatics and its growing ubiquity, as evidenced by its inclusion as a focus area within the American Geophysical Union (AGU), European Geosciences Union (EGU), as well as by the evolution of the IEEE Geoscience and Remote Sensing Society's (GRSS) Data Archiving and Distribution Technical Committee (DAD TC)

Receptors and Other Signaling Proteins Required for Serotonin Control of Locomotion in Caenorhabditis elegans

A better understanding of the molecular mechanisms of signaling by the neurotransmitter serotonin is required to assess the hypothesis that defects in serotonin signaling underlie depression in humans. Caenorhabditis elegans uses serotonin as a neurotransmitter to regulate locomotion, providing a genetic system to analyze serotonin signaling. From large-scale genetic screens we identified 36 mutants of C. elegans in which serotonin fails to have its normal effect of slowing locomotion, and we molecularly identified eight genes affected by 19 of the mutations. Two of the genes encode the serotonin-gated ion channel MOD-1 and the G-protein-coupled serotonin receptor SER-4. mod-1 is expressed in the neurons and muscles that directly control locomotion, while ser-4 is expressed in an almost entirely non-overlapping set of sensory and interneurons. The cells expressing the two receptors are largely not direct postsynaptic targets of serotonergic neurons. We analyzed animals lacking or overexpressing the receptors in various combinations using several assays for serotonin response. We found that the two receptors act in parallel to affect locomotion. Our results show that serotonin functions as an extrasynaptic signal that independently activates multiple receptors at a distance from its release sites and identify at least six additional proteins that appear to act with serotonin receptors to mediate serotonin response.National Institutes of Health (U.S.) (Grant GM24663

Establishing Trustworthy Repositories of Scientific Data: Opportunities and Benefits

Scientific progress often depends on the ability of the scientific community to build on the works of others. Such works include scientific data, published reports of findings, and other research-related information and artifacts that are produced as part of the scientific process. Providing capabilities for accessing and using such scientific works enables the reproducibility of published methods and results to identify opportunities for improvement. Access and use of science products also enables others to build on previous work. In an increasingly digital world, the science community accesses and uses relevant scientific resources that have been obtained from digital repositories, data centers, and archives, as well as from traditional sources such as publishers of journal articles. Digital repositories need to establish capabilities, which provide access to and enable the use of digital resources. These resources are needed by the science community to improve and build o! n the efforts of others. Digital repositories that provide free and unrestricted access to scientific data and research-related information can reduce the barriers to science. By reducing these barriers they will be able to offer opportunities for members of the scientific community to pursue research questions and challenges that were previously unapproachable. These may include opportunities for researchers to gather data from other domains and support interdisciplinary research. Opportunities to use the data products and services offered by digital repositories also can contribute to the development of the scientific community and to the emergence of new areas of study

Onchocerciasis transmission in Ghana: biting and parous rates of host-seeking sibling species of the Simulium damnosum complex

Background: Ghana is renowned for its sibling species diversity of the Simulium damnosum complex, vectors of Onchocerca volvulus. Detailed entomological knowledge becomes a priority as onchocerciasis control policy has shifted from morbidity reduction to elimination of infection. To date, understanding of transmission dynamics of O. volvulus has been mainly based on S. damnosum sensu stricto (s.s.) data. We aim to elucidate bionomic features of vector species of importance for onchocerciasis elimination efforts. Methods: We collected S. damnosum sensu lato from seven villages in four Ghanaian regions between 2009 and 2011, using standard vector collection, and human- and cattle-baited tents. Taxa were identified using morphological and molecular techniques. Monthly biting rates (MBR), parous rates and monthly parous biting rates (MPBR) are reported by locality, season, trapping method and hour of collection for each species. Results: S. damnosum s.s./S. sirbanum were collected at Asubende and Agborlekame, both savannah villages. A range of species was caught in the Volta region (forest-savannah mosaic) and Gyankobaa (forest), with S. squamosum or S. sanctipauli being the predominant species, respectively. In Bosomase (southern forest region) only S. sanctipauli was collected in the 2009 wet season, but in the 2010 dry season S. yahense was also caught. MBRs ranged from 714 bites/person/month at Agborlekame (100% S. damnosum s.s./S. sirbanum) to 8,586 bites/person/month at Pillar 83/Djodji (98.5% S. squamosum). MBRs were higher in the wet season. In contrast, parous rates were higher in the dry season (41.8% vs. 18.4%), resulting in higher MPBRs in the dry season. Daily host-seeking activity of S. damnosum s.s./S. sirbanum was bimodal, whilst S. squamosum and S. sanctipauli had unimodal afternoon peaks. Conclusions: The bionomic differences between sibling species of the S. damnosum complex need to be taken into account when designing entomological monitoring protocols for interventions and parameterising mathematical models for onchocerciasis control and elimination

Vaginal flora morphotypic profiles and assessment of bacterial vaginosis in women at risk for HIV infection.

Specific morphotypic profiles of normal and abnormal vaginal flora, including bacterial vaginosis (BV), were characterized. A prospective study of 350 women yielded concurrent Gram-stain data and clinical assessment (n = 3455 visits). Microbiological profiles were constructed by Gram stain. Eight profile definitions were based on dichotomizing the levels of Lactobacillus, Gardnerella, and curved, Gram-negative bacillus (Mobiluncus) morphotypes. Of these, two were rare, and the other six demonstrated a graded association with the clinical components of BV. The proposed profiles from the Gram stain reflect the morphotypic categories describing vaginal flora that may enable clearer elucidation of gynecologic and obstetric outcomes in various populations

Onchocerciasis transmission in Ghana: Persistence under different control strategies and the role of the simuliid vectors

Background: The World Health Organization (WHO) aims at eliminating onchocerciasis by 2020 in selected African countries. Current control focuses on community-directed treatment with ivermectin (CDTI). In Ghana, persistent transmission has been reported despite long-term control. We present spatial and temporal patterns of onchocerciasis transmission in relation to ivermectin treatment history. Methodology/Principal Findings: Host-seeking and ovipositing blackflies were collected from seven villages in four regions of Ghana with 3–24 years of CDTI at the time of sampling. A total of 16,443 flies was analysed for infection; 5,812 (35.3%) were dissected for parity (26.9% parous). Heads and thoraces of 12,196 flies were dissected for Onchocerca spp. and DNA from 11,122 abdomens was amplified using Onchocerca primers. A total of 463 larvae (0.03 larvae/fly) from 97 (0.6%) infected and 62 (0.4%) infective flies was recorded; 258 abdomens (2.3%) were positive for Onchocerca DNA. Infections (all were O. volvulus) were more likely to be detected in ovipositing flies. Transmission occurred, mostly in the wet season, at Gyankobaa and Bosomase, with transmission potentials of, respectively, 86 and 422 L3/person/month after 3 and 6 years of CDTI. The numbers of L3/1,000 parous flies at these villages were over 100times the WHO threshold of one L3/1,000 for transmission control. Vector species influenced transmission parameters. At Asubende, the number of L3/1,000 ovipositing flies (1.4, 95% CI = 0–4) also just exceeded the threshold despite extensive vector control and 24 years of ivermectin distribution, but there were no infective larvae in host-seeking flies. Conclusions/Significance: Despite repeated ivermectin treatment, evidence of O. volvulus transmission was documented in all seven villages and above the WHO threshold in two. Vector species influences transmission through biting and parous rates and vector competence, and should be included in transmission models. Oviposition traps could augment vector collector methods for monitoring and surveillance

Modelling the impact of larviciding on the population dynamics and biting rates of Simulium damnosum (s.l.): implications for vector control as a complementary strategy for onchocerciasis elimination in Africa

Background: In 2012, the World Health Organization set goals for the elimination of onchocerciasis transmission by 2020 in selected African countries. Epidemiological data and mathematical modelling have indicated that elimination may not be achieved with annual ivermectin distribution in all endemic foci. Complementary and alternative treatment strategies (ATS), including vector control, will be necessary. Implementation of vector control will require that the ecology and population dynamics of Simulium damnosum sensu lato be carefully considered. Methods: We adapted our previous SIMuliid POPulation dynamics (SIMPOP) model to explore the impact of larvicidal insecticides on S. damnosum (s.l.) biting rates in different ecological contexts and to identify how frequently and for how long vector control should be continued to sustain substantive reductions in vector biting. SIMPOP was fitted to data from large-scale aerial larviciding trials in savannah sites (Ghana) and small-scale ground larviciding trials in forest areas (Cameroon). The model was validated against independent data from Burkina Faso/Côte d’Ivoire (savannah) and Bioko (forest). Scenario analysis explored the effects of ecological and programmatic factors such as pre-control daily biting rate (DBR) and larviciding scheme design on reductions and resurgences in biting rates. Results: The estimated efficacy of large-scale aerial larviciding in the savannah was greater than that of ground-based larviciding in the forest. Small changes in larvicidal efficacy can have large impacts on intervention success. At 93% larvicidal efficacy (a realistic value based on field trials), 10 consecutive weekly larvicidal treatments would reduce DBRs by 96% (e.g. from 400 to 16 bites/person/day). At 70% efficacy, and for 10 weekly applications, the DBR would decrease by 67% (e.g. from 400 to 132 bites/person/day). Larviciding is more likely to succeed in areas with lower water temperatures and where blackfly species have longer gonotrophic cycles. Conclusions: Focal vector control can reduce vector biting rates in settings where a high larvicidal efficacy can be achieved and an appropriate duration and frequency of larviciding can be ensured. Future work linking SIMPOP with onchocerciasis transmission models will permit evaluation of the impact of combined anti-vectorial and anti-parasitic interventions on accelerating elimination of the disease

Connecting Researchers to Data Repositories in the Earth, Space, and Environmental Sciences

The Repository Finder tool was developed to help researchers in the domain of Earth, space, and environmental sciences to identify appropriate repositories where they can deposit their research data and to promote practices that implement the FAIR Principles, encouraging progress toward sharing data that are findable, accessible, interoperable, and reusable. Requirements for the design of the tool were gathered through a series of workshops and working groups as a part of the Enabling FAIR Data initiative led by the American Geophysical Union that included the development of a decision tree that researchers may follow in selecting a data repository, interviews with domain repository managers, and usability testing. The tool is hosted on the web by DataCite and enables a researcher to query all data repositories by keyword or to view a list of domain repositories that accept data for deposit, support open access, and provide persistent identifiers. Metadata records from the re3data.org registry of research data repositories and the returned results highlight repositories that have achieved trustworthy digital repository certification through a formal procedure such as the CoreTrust Seal

A Discussion of Value Metrics for Data Repositories in Earth and Environmental Sciences

Despite growing recognition of the importance of public data to the modern economy and to scientific progress, long-term investment in the repositories that manage and disseminate scientific data in easily accessible-ways remains elusive. Repositories are asked to demonstrate that there is a net value of their data and services to justify continued funding or attract new funding sources. Here, representatives from a number of environmental and Earth science repositories evaluate approaches for assessing the costs and benefits of publishing scientific data in their repositories, identifying various metrics that repositories typically use to report on the impact and value of their data products and services, plus additional metrics that would be useful but are not typically measured. We rated each metric by (a) the difficulty of implementation by our specific repositories and (b) its importance for value determination. As managers of environmental data repositories, we find that some of the most easily obtainable data-use metrics (such as data downloads and page views) may be less indicative of value than metrics that relate to discoverability and broader use. Other intangible but equally important metrics (e.g., laws or regulations impacted, lives saved, new proposals generated), will require considerable additional research to describe and develop, plus resources to implement at scale. As value can only be determined from the point of view of a stakeholder, it is likely that multiple sets of metrics will be needed, tailored to specific stakeholder needs. Moreover, economically based analyses or the use of specialists in the field are expensive and can happen only as resources permit