Ten Simple Rules for Digital Data Storage

Data is the central currency of science, but the nature of scientific data has changed dramatically with the rapid pace of technology. This change has led to the development of a wide variety of data formats, dataset sizes, data complexity, data use cases, and data sharing practices. Improvements in high throughput DNA sequencing, sustained institutional support for large sensor networks, and sky surveys with large-format digital cameras have created massive quantities of data. At the same time, the combination of increasingly diverse research teams and data aggregation in portals (e.g. for biodiversity data, GBIF or iDigBio) necessitates increased coordination among data collectors and institutions. As a consequence, “data” can now mean anything from petabytes of information stored in professionally-maintained databases, through spreadsheets on a single computer, to hand-written tables in lab notebooks on shelves. All remain important, but data curation practices must continue to keep pace with the changes brought about by new forms and practices of data collection and storage.</jats:p

STOP-AD portal: Selecting the optimal pharmaceutical for preclinical drug testing in Alzheimer\u27s disease.

We propose an unbiased methodology to rank compounds for advancement into comprehensive preclinical testing for Alzheimer\u27s disease (AD). Translation of compounds to the clinic in AD has been hampered by poor predictive validity of models, compounds with limited pharmaceutical properties, and studies that lack rigor. To overcome this, MODEL-AD\u27s Preclinical Testing Core developed a standardized pipeline for assessing efficacy in AD mouse models. We hypothesize that rank-ordering compounds based upon pharmacokinetic, efficacy, and toxicity properties in preclinical models will enhance successful translation to the clinic. Previously compound selection was based solely on physiochemical properties, with arbitrary cutoff limits, making ranking challenging. Since no gold standard exists for systematic prioritization, validating a selection criteria has remained elusive. The STOP-AD framework evaluates the drug-like properties to rank compounds for in vivo studies, and uses an unbiased approach that overcomes the validation limitation by performing Monte-Carlo simulations. HIGHLIGHTS: Promising preclinical studies for AD drugs have not translated to clinical success. Systematic assessment of AD drug candidates may increase clinical translatability. We describe a well-defined framework for compound selection with clear selection metrics

Ecology under lake ice

Winter conditions are rapidly changing in temperate ecosystems, particularly for those that experience periods of snow and ice cover. Relatively little is known of winter ecology in these systems, due to a historical research focus on summer ‘growing seasons’. We executed the first global quantitative synthesis on under‐ice lake ecology, including 36 abiotic and biotic variables from 42 research groups and 101 lakes, examining seasonal differences and connections as well as how seasonal differences vary with geophysical factors. Plankton were more abundant under ice than expected; mean winter values were 43.2% of summer values for chlorophyll a, 15.8% of summer phytoplankton biovolume and 25.3% of summer zooplankton density. Dissolved nitrogen concentrations were typically higher during winter, and these differences were exaggerated in smaller lakes. Lake size also influenced winter‐summer patterns for dissolved organic carbon (DOC), with higher winter DOC in smaller lakes. At coarse levels of taxonomic aggregation, phytoplankton and zooplankton community composition showed few systematic differences between seasons, although literature suggests that seasonal differences are frequently lake‐specific, species‐specific, or occur at the level of functional group. Within the subset of lakes that had longer time series, winter influenced the subsequent summer for some nutrient variables and zooplankton biomass

A unified dataset of colocated sewage pollution, periphyton, and benthic macroinvertebrate community and food web structure from Lake Baikal (Siberia)

Sewage released from lakeside development can introduce nutrients and micropollutants that can restructure aquatic ecosystems. Lake Baikal, the world’s most ancient, biodiverse, and voluminous freshwater lake, has been experiencing localized sewage pollution from lakeside settlements. Nearby increasing filamentous algal abundance suggests benthic communities are responding to localized pollution. We surveyed 40-km of Lake Baikal’s southwestern shoreline from 19 to 23 August 2015 for sewage indicators, including pharmaceuticals, personal care products, and microplastics, with colocated periphyton, macroinvertebrate, stable isotope, and fatty acid samplings. The data are structured in a tidy format (a tabular arrangement familiar to limnologists) to encourage reuse. Unique identifiers corresponding to sampling locations are retained throughout all data files to facilitate interoperability among the dataset’s 150+ variables. For Lake Baikal studies, these data can support continued monitoring and research efforts. For global studies of lakes, these data can help characterize sewage prevalence and ecological consequences of anthropogenic disturbance across spatial scales

Effects of spatially heterogeneous lakeside development on nearshore biotic communities in a large, deep, oligotrophic lake

Sewage released from lakeside development can reshape ecological communities. Nearshore periphyton can rapidly assimilate sewage-associated nutrients, leading to increases of filamentous algal abundance, thus altering both food abundance and quality for grazers. In Lake Baikal, a large, ultra-oligotrophic, remote lake in Siberia, filamentous algal abundance has increased near lakeside developments, and localized sewage input is the suspected cause. These shifts are of particular interest in Lake Baikal, where endemic littoral biodiversity is high, lakeside settlements are mostly small, tourism is relatively high (~1.2 million visitors annually), and settlements are separated by large tracts of undisturbed shoreline, enabling investigation of heterogeneity and gradients of disturbance. We surveyed sites along 40 km of Baikal’s southwestern shore for sewage indicators—pharmaceuticals and personal care products (PPCPs) and microplastics—as well as periphyton and macroinvertebrate abundance and indicators of food web structure (stable isotopes and fatty acids). Summed PPCP concentrations were spatially related to lakeside development. As predicted, lakeside development was associated with more filamentous algae and lower abundance of sewagesensitive mollusks. Periphyton and macroinvertebrate stable isotopes and essential fatty acids suggested that food web structure otherwise remained similar across sites; yet, the invariance of amphipod fatty acid composition, relative to periphyton, suggested that grazers adjust behavior or metabolism to compensate for different periphyton assemblages. Our results demonstrate that even low levels of human disturbance can result in spatial heterogeneity of nearshore ecological responses, with potential for changing trophic interactions that propagate through the food web

Lake-wide physical and biological trends associated with warming in Lake Baikal

Eutrophication and warming of lakes are occurring globally. Lake Baikal, a large ancient lake composed of three basins, has recently experienced benthic eutrophication at local sites and lake warming in the south basin. Here, we look for signals of warming and pelagic eutrophication across the entire lake using physical and biological data collected at a subset of 79 stations sampled ca. annually (1977–2003) during the period of summer stratification. Lake-wide, surface waters warmed 2.0 °C; and, consistent with this warming, the abundance of two warm-water, cosmopolitan zooplankton taxa increased between two (pelagic cladocerans) and 12-fold (Cyclops kolensis). C. kolensis increased throughout the lake, whereas cladocerans increased significantly only in the north basin. In contrast, abundance of the cold-water endemic copepod, Epischura baikalensis, that dominates the crustacean zooplankton community, did not change. With the exception of one coastal station in the north basin, there is no evidence of pelagic eutrophication. Although chlorophyll concentrations increased 46% lake-wide (0.82 to 1.20 μg/L), the increasing trend was significant only in the south basin. Surprisingly, mean Secchi transparency increased by 1.4 m lake-wide across the 26-year time series with significant deepening of water transparency occurring in the central and north basins. This suggests a decline in productivity in the north and middle basins, but an increase in the south basin. Taken together, these findings suggest that physical and biological changes associatedwithwarming have occurred in Lake Baikal, butwide-spread pelagic eutrophication in the lake\u27s three basins has not

How open science helps researchers succeed

Open access, open data, open source, and other open scholarship practices are growing in popularity and necessity. However, widespread adoption of these practices has not yet been achieved. One reason is that researchers are uncertain about how sharing their work will affect their careers. We review literature demonstrating that open research is associated with increases in citations, media attention, potential collaborators, job opportunities, and funding opportunities. These findings are evidence that open research practices bring significant benefits to researchers relative to more traditional closed practices

A unified dataset of colocated sewage pollution, periphyton, and benthic macroinvertebrate community and food web structure from Lake Baikal (Siberia)

Sewage released from lakeside development can introduce nutrients and micropollutants that can restructure aquatic ecosystems. Lake Baikal, the world’s most ancient, biodiverse, and voluminous freshwater lake, has been experiencing localized sewage pollution from lakeside settlements. Nearby increasing filamentous algal abundance suggests benthic communities are responding to localized pollution. We surveyed 40-km of Lake Baikal’s southwestern shoreline from 19 to 23 August 2015 for sewage indicators, including pharmaceuticals, personal care products, and microplastics, with colocated periphyton, macroinvertebrate, stable isotope, and fatty acid samplings. The data are structured in a tidy format (a tabular arrangement familiar to limnologists) to encourage reuse. Unique identifiers corresponding to sampling locations are retained throughout all data files to facilitate interoperability among the dataset’s 150+ variables. For Lake Baikal studies, these data can support continued monitoring and research efforts. For global studies of lakes, these data can help characterize sewage prevalence and ecological consequences of anthropogenic disturbance across spatial scales