Geolocator wetness data accurately detect periods of migratory flight in two species of shorebird

While the principal use of light-recording geolocators is to determine geographical locations of migratory birds, supplementary wetness data have been used to refine estimates of minimum flight duration, on the assumption that a wet logger indicates the bird is on the ground. We provide a test of this assumption, by comparing wetness values against directly observed migratory departures of logger-equipped Bar-tailed Godwits Limosa lapponica and Red Knots Calidris canutus from the Manawatu River Estuary, New Zealand. Loggers recorded wetness every 10 min (Biotrack MK4093 and MK5093) or every one or four hours (Migrate Technology C65K). We retrieved loggers from 41 godwits from 2008– 2014 and from seven Red Knots in 2013–2014 for which we had corresponding departure information; in total there were 51 departures of godwits and seven of knots that we could match to actual departure times (this included multiple years for some godwits). Overall, 10-min wetness data were very accurate for both godwits and knots (median estimated departure times were 14 min and one min later than true departure, respectively), as were the 60-min and 240-min loggers on godwits if corrected by the wet counts that are recorded within measurement intervals (medians of 16 min earlier and 8 min earlier, respectively). These longer-interval loggers were still reasonably accurate without this adjustment (medians of 37 min and 74 min later, respectively). There was substantial variation between individuals and logger types, with 10-min loggers going dry up to 148 min (godwit) or 55 min (knot) earlier than true departure, while the 60-min and 240-min loggers recorded wetness up to 142 min or 124 min later than true departure (or 195 min or 232 min later, if unadjusted). Some of this variation simply reflects the interval over which wetness is recorded, but bird behaviour and/or logger performance must play a role in some cases (e.g. the logger going dry before departure or remaining wet after departure). Given observed bird behaviour upon arrival after migration (feeding on wet tidal flats), the wetness recording of geolocators is likely to give an accurate estimate of migratory flight duration, at least for species that frequent wet, particularly marine, habitats

WikiPathways: building research communities on biological pathways.

Here, we describe the development of WikiPathways (http://www.wikipathways.org), a public wiki for pathway curation, since it was first published in 2008. New features are discussed, as well as developments in the community of contributors. New features include a zoomable pathway viewer, support for pathway ontology annotations, the ability to mark pathways as private for a limited time and the availability of stable hyperlinks to pathways and the elements therein. WikiPathways content is freely available in a variety of formats such as the BioPAX standard, and the content is increasingly adopted by external databases and tools, including Wikipedia. A recent development is the use of WikiPathways as a staging ground for centrally curated databases such as Reactome. WikiPathways is seeing steady growth in the number of users, page views and edits for each pathway. To assess whether the community curation experiment can be considered successful, here we analyze the relation between use and contribution, which gives results in line with other wiki projects. The novel use of pathway pages as supplementary material to publications, as well as the addition of tailored content for research domains, is expected to stimulate growth further

BridgeDb: standardized access to gene, protein and metabolite identifier mapping services

Many interesting problems in bioinformatics require integration of data from various sources. For example when combining microarray data with a pathway database, or merging co-citation networks with protein-protein interaction networks. Invariably this leads to an identifier mapping problem, where different datasets are annotated with identifiers that are related, but originate from different databases.

Solutions for the identifier mapping problem exist, such as Biomart, Synergizer, Cronos, PICR, HMS and many more. This creates an opportunity for bioinformatics tool developers. Tools can be made to flexibly support multiple mapping services or mapping services could be combined to get broader coverage. This approach requires an interface layer between tools and mapping services. BridgeDb provides such an interface layer, in the form of both a Java and REST API.

Because of the standardized interface layer, BridgeDb is not tied to a specific source of mapping information. You can switch easily between flat files, relational databases and several different web services. Mapping services can be combined to support multi-omics experiments or to integrate custom microarray annotations. BridgeDb isn't just yet another mapping service: it tries to build further on existing work, and integrate multiple partial solutions. The framework is intended for customization and adaptation to any identifier mapping service. 

BridgeDb makes it easy to add an important capability to existing tools. BridgeDb has already been integrated into several popular bioinformatics applications, such as Cytoscape, WikiPathways, PathVisio, Vanted and Taverna. To encourage tool developers to start using BridgeDb, we've created code examples, online documentation, and a mailinglist to ask questions. 

We believe that, to meet the challenges that are encountered in bioinformatics today, the software development process should follow a few essential principles: user friendliness, code reuse, modularity and open source. BridgeDb adheres to these principles, and can serve as a useful model for others to follow. BridgeDb can function to increase user-friendliness of graphical applications. It re-uses work from other projects such as BioMart and MIRIAM. BridgeDb consists of several small modules, integrated through a common interface (API). Components of BridgeDb can be left out or replaced, for maximum flexibility. BridgeDb was open source from the very beginning of the project. The philosophy of open source is closely aligned to academic values, of building on top of the work of giants. 

Many interesting problems in bioinformatics require integration of data from various sources. For example when combining microarray data with a pathway database, or merging co-citation networks with protein-protein interaction networks. Invariably this leads to an identifier mapping problem, where different datasets are annotated with identifiers that are related, but originate from different databases.

Solutions for the identifier mapping problem exist, such as Biomart, Synergizer, Cronos, PICR, HMS and many more. This creates an opportunity for bioinformatics tool developers. Tools can be made to flexibly support multiple mapping services or mapping services could be combined to get broader coverage. This approach requires an interface layer between tools and mapping services. BridgeDb provides such an interface layer, in the form of both a Java and REST API.

Because of the standardized interface layer, BridgeDb is not tied to a specific source of mapping information. You can switch easily between flat files, relational databases and several different web services. Mapping services can be combined to support multi-omics experiments or to integrate custom microarray annotations. BridgeDb isn't just yet another mapping service: it tries to build further on existing work, and integrate multiple partial solutions. The framework is intended for customization and adaptation to any identifier mapping service. 

BridgeDb makes it easy to add an important capability to existing tools. BridgeDb has already been integrated into several popular bioinformatics applications, such as Cytoscape, WikiPathways, PathVisio, Vanted and Taverna. To encourage tool developers to start using BridgeDb, we've created code examples, online documentation, and a mailinglist to ask questions. 

We believe that, to meet the challenges that are encountered in bioinformatics today, the software development process should follow a few essential principles: user friendliness, code reuse, modularity and open source. BridgeDb adheres to these principles, and can serve as a useful model for others to follow. BridgeDb can function to increase user-friendliness of graphical applications. It re-uses work from other projects such as BioMart and MIRIAM. BridgeDb consists of several small modules, integrated through a common interface (API). Components of BridgeDb can be left out or replaced, for maximum flexibility. BridgeDb was open source from the very beginning of the project. The philosophy of open source is closely aligned to academic values, of building on top of the work of giants. 

The BridgeDb library is available at "http://www.bridgedb.org":http://www.bridgedb.org.
A paper about BridgeDb was published in BMC _Bioinformatics_, 2010 Jan 4;11(1):5.

BridgeDb blog: "http://www.helixsoft.nl/blog/?tag=bridgedb":http://www.helixsoft.nl/blog/?tag=bridged

Spatially distributed water-balance and meteorological data from the Wolverton catchment, Sequoia National Park, California

Accurate water-balance measurements in the seasonal, snow-dominated Sierra Nevada are important for forest and downstream water management. However, few sites in the southern Sierra offer detailed records of the spatial and temporal patterns of snowpack and soil-water storage and the fluxes affecting them, i.e., precipitation as rain and snow, snowmelt, evapotranspiration, and runoff. To explore these stores and fluxes we instrumented the Wolverton basin (2180-2750 m) in Sequoia National Park with distributed, continuous sensors. This 2006-2016 record of snow depth, soil moisture and soil temperature, and meteorological data quantifies the hydrologic inputs and storage in a mostly undeveloped catchment. Clustered sensors record lateral differences with regards to aspect and canopy cover at approximately 2250 and 2625 m in elevation, where two meteorological stations are installed. Meteorological stations record air temperature, relative humidity, radiation, precipitation, wind speed and direction, and snow depth. Data are available at hourly intervals by water year (1 October-30 September) in non-proprietary formats from online data repositories (https://doi.org/10.6071/M3S94T)

Development of a single-session, transdiagnostic preventive intervention for young adults at risk for emotional disorders

Cognitive-behavioral prevention programs have demonstrated efficacy in reducing subclinical symptoms of anxiety and depression, and there is some evidence to suggest that they can lower the risk of future disorder onset. However, existing interventions tend to be relatively lengthy and target specific disorders or problem areas, both of which limit their potential for widespread dissemination. To address these limitations, we aimed to develop a single-session, transdiagnostic preventive intervention based on the Unified Protocol for Transdiagnostic Treatment of Emotional Disorders for young adults at risk for developing anxiety and/or depressive disorders within a college setting. Results from this proof-of-concept study indicated that the intervention was viewed as highly satisfactory and acceptable. The intervention also was successful at delivering adaptive emotion management skills in its 2-hr workshop format. Future studies evaluating the efficacy of this novel transdiagnostic, emotion-focused prevention program are warranted.Accepted manuscrip

Scaffolding School Pupils’ Scientific Argumentation with Evidence-Based Dialogue Maps

This chapter reports pilot work investigating the potential of Evidence-based Dialogue Mapping to scaffold young teenagers’ scientific argumentation. Our research objective is to better understand pupils’ usage of dialogue maps created in Compendium to write scientific ex-planations. The participants were 20 pupils, 12-13 years old, in a summer science course for “gifted and talented” children in the UK. Through qualitative analysis of three case studies, we investigate the value of dialogue mapping as a mediating tool in the scientific reasoning process during a set of learning activities. These activities were published in an online learning envi-ronment to foster collaborative learning. Pupils mapped their discussions in pairs, shared maps via the online forum and in plenary discussions, and wrote essays based on their dialogue maps. This study draws on these multiple data sources: pupils’ maps in Compendium, writings in science and reflective comments about the uses of mapping for writing. Our analysis highlights the diversity of ways, both successful and unsuccessful, in which dialogue mapping was used by these young teenagers

A Longitudinal Study of the Evolution of Organizational Values of Ohio State University Extension Educators

A 2001 replication of a 1991 study investigated the evolution of OSU Extension organizational values. For almost a decade, the 1991 values were used by administrators for decision making and policy development. The authors used a census and Values Questionnaire to collect data. The authors identified 10 of the 12 original organizational values as current OSU Extension organizational values. The strength and stability of its organizational values may be both a source of continuity for OSU Extension during times of rapid social and fiscal change, as well as a source of frustration for leaders seeking to reshape the organization\u27s culture

Climate Change and Land Management Impact Rangeland Condition and Sage-Grouse Habitat in Southeastern Oregon

Contemporary pressures on sagebrush steppe from climate change, exotic species, wildfire, and land use change threaten rangeland species such as the greater sage-grouse (Centrocercus urophasianus). To effectively manage sagebrush steppe landscapes for long-term goals, managers need information about the potential impacts of climate change, disturbances, and management activities. We integrated information from a dynamic global vegetation model, a sage-grouse habitat climate envelope model, and a state-and-transition simulation model to project broad-scale vegetation dynamics and potential sage-grouse habitat across 23.5 million acres in southeastern Oregon. We evaluated four climate scenarios, including continuing current climate and three scenarios of global climate change, and three management scenarios, including no management, current management and a sage-grouse habitat restoration scenario. All climate change scenarios projected expansion of moist shrub steppe and contraction of dry shrub steppe, but climate scenarios varied widely in the projected extent of xeric shrub steppe, where hot, dry summer conditions are unfavorable for sage-grouse. Wildfire increased by 26% over the century under current climate due to exotic grass encroachment, and by two- to four-fold across all climate change scenarios as extreme fire years became more frequent. Exotic grasses rapidly expanded in all scenarios as large areas of the landscape initially in semi-degraded condition converted to exotic-dominated systems. Due to the combination of exotic grass invasion, juniper encroachment, and climatic unsuitability for sage-grouse, projected sage-grouse habitat declined in the first several decades, but increased in area under the three climate change scenarios later in the century, as moist shrub steppe increased and rangeland condition improved. Management activities in the model were generally unsuccessful in controlling exotic grass invasion but were effective in slowing woodland expansion. Current levels of restoration treatments were insufficient to prevent some juniper expansion, but increased treatment rates under the restoration scenario maintained juniper near initial levels in priority treatment areas. Our simulations indicate that climate change may have both positive and negative implications for maintaining sage-grouse habitat