Chemical information matters: an e-Research perspective on information and data sharing in the chemical sciences

Recently, a number of organisations have called for open access to scientific information and especially to the data obtained from publicly funded research, among which the Royal Society report and the European Commission press release are particularly notable. It has long been accepted that building research on the foundations laid by other scientists is both effective and efficient. Regrettably, some disciplines, chemistry being one, have been slow to recognise the value of sharing and have thus been reluctant to curate their data and information in preparation for exchanging it. The very significant increases in both the volume and the complexity of the datasets produced has encouraged the expansion of e-Research, and stimulated the development of methodologies for managing, organising, and analysing "big data". We review the evolution of cheminformatics, the amalgam of chemistry, computer science, and information technology, and assess the wider e-Science and e-Research perspective. Chemical information does matter, as do matters of communicating data and collaborating with data. For chemistry, unique identifiers, structure representations, and property descriptors are essential to the activities of sharing and exchange. Open science entails the sharing of more than mere facts: for example, the publication of negative outcomes can facilitate better understanding of which synthetic routes to choose, an aspiration of the Dial-a-Molecule Grand Challenge. The protagonists of open notebook science go even further and exchange their thoughts and plans. We consider the concepts of preservation, curation, provenance, discovery, and access in the context of the research lifecycle, and then focus on the role of metadata, particularly the ontologies on which the emerging chemical Semantic Web will depend. Among our conclusions, we present our choice of the "grand challenges" for the preservation and sharing of chemical information

Scientific and technical data sharing: a trading perspective

It is arguably a precept that the open sharing of data maximises the scientific utility of the research that generated that data. Indeed, progress depends on individual scientists being able to build on the results produced by others. The means to facilitate sharing undoubtedly exist, but various studies have identified reluctance among researchers to share information with their peers, at least until the professional priorities of the original researchers have been accommodated. With a view to encouraging less inhibited collaboration, we appraise the processes of data exchange from the perspective of a trading environment and consider how data exchanges might promote (or perhaps hinder) collaboration in data-rich scientific research disciplines and how such an exchange might be set up. We suggest an exchange with trusted brokers (akin to the commodity markets) as a way to overcome the challenges of the current environment. We conclude by encouraging the scientific and technical community to debate the merits of a trading perspective on data sharing and exchange

Water-Food-Energy Nexus

The proposed SDGs on water, food and energy security all include targets on increasing efficiencies. Yet the water–food–energy nexus has multiple dimensions that, if managed in isolation, will compromise a nation’s ability to achieve the full portfolio of SDGs. Climate change introduces additional uncertainties, further increasing tensions between sectors for access to water. Conventional energy and food production are emitters of greenhouse gases, but measures to reduce emissions—including renewable energy interventions, such as subsidies for biofuel production—can have adverse consequences on food prices. To achieve desirable and sustainable outcomes for water, food, and energy requires investigating these elements as an integrated whole, across sectors and scales. The nexus approach is part of broader systems thinking; it features a pragmatic focus on the relatively limited number of policy choices that are constrained by political realities. This approach recognizes and minimizes trade-offs, builds synergies, and increases resource use efficiencies

Highly efficient 5\u27 capping of mitochondrial RNA with NAD+ and NADH by yeast and human mitochondrial RNA polymerase

Bacterial and eukaryotic nuclear RNA polymerases (RNAPs) cap RNA with the oxidized and reduced forms of the metabolic effector nicotinamide adenine dinucleotide, NAD+ and NADH, using NAD+ and NADH as non-canonical initiating nucleotides for transcription initiation. Here, we show that mitochondrial RNAPs (mtRNAPs) cap RNA with NAD+ and NADH, and do so more efficiently than nuclear RNAPs. Direct quantitation of NAD+- and NADH-capped RNA demonstrates remarkably high levels of capping in vivo: up to ~60% NAD+ and NADH capping of yeast mitochondrial transcripts, and up to ~15% NAD+ capping of human mitochondrial transcripts. The capping efficiency is determined by promoter sequence at, and upstream of, the transcription start site and, in yeast and human cells, by intracellular NAD+ and NADH levels. Our findings indicate mtRNAPs serve as both sensors and actuators in coupling cellular metabolism to mitochondrial transcriptional outputs, sensing NAD+ and NADH levels and adjusting transcriptional outputs accordingly. © 2018, Bird et al

Late-Holocene floodplain development, land-use, and hydroclimate–flood relationships on the lower Ohio River, US

Floodplain development, land-use, and flooding on the lower Ohio River are investigated with a 3100-year-long sediment archive from Avery Lake, a swale lake on the Black Bottom floodplain in southern Illinois, US. In all, 12 radiocarbon dates show that Avery Lake formed at 1130 BCE (3100 cal. yr BP), almost 3000 years later than previously thought, indicating that the Black Bottom floodplain is younger and more dynamic than previously estimated. Three subsequent periods of extensive land clearance were identified by changes in pollen composition, corresponding to Native American occupations before 1500 CE and the current Euro-American occupation beginning in the 18th century. Sedimentation rates prior to 1820 CE changed independently of land clearance events, suggesting natural as opposed to land-use controls. Comparison with high-resolution paleoclimate data from Martin Lake, IN, indicates that lower Ohio River flooding was frequent when cold-season precipitation originating from the Pacific/Arctic predominated when atmospheric circulation resembled positive Pacific North American (PNA) conditions and the Pacific Decadal Oscillation (PDO) was in a positive mean state (1130 BCE to 350 CE and 1150–1820 CE). Conversely, Ohio River flooding was less frequent when warm-season precipitation from the Gulf of Mexico prevailed during negative PDO- and PNA-like mean states (350 and 1150 CE). This flood dynamic appears to have been fundamentally altered after 1820 CE. We suggest that extensive land clearance in the Ohio River watershed increased runoff and landscape erosion by reducing interception, infiltration, and evapotranspiration, thereby increasing flooding despite a shift to negative PDO- and PNA-like mean states. Predicted increases in average precipitation and extreme rainfall events across the mid-continental US are likely to perpetuate current trends toward more frequent flood events, because anthropogenic modifications have made the landscape less resilient to changing hydroclimatic conditions

Pre-Columbian lead pollution from Native American galena processing and land use in the midcontinental United States

The presence and sources of pre-Columbian (before 1492 CE) lead (Pb) pollution in the midcontinental United States were investigated using geochemical and Pb isotope analyses on sediment cores recovered from Avery Lake, a floodplain lake located directly adjacent to the Kincaid Mounds archaeological site on the lower Ohio River, Illinois. Geochemical results indicate the presence of Pb pollution during the Baumer (300 BCE to 300 CE) and Mississippian (1150–1450 CE) occupations, and since the 1800s. Pb isotope results link Mississippian Pb pollution to the processing and use of galena primarily from southeastern and/or central Missouri, and to a lesser extent the upper Mississippi River valley, with ∼1.5 t (metric tons) of galena-derived Pb deposited in Avery Lake during this time. Pb pollution during the Baumer phase, equating to ∼0.4 t of Pb, was not accompanied by a Pb isotope excursion and most likely originated from local biomass burning. These results provide new information about the environmental impacts associated with pre-Columbian Native Americans’ interaction with and utilization of their landscape and its resources

SPRAYTRAN 1.0 User’s Guide: A GIS-Based Atmospheric Spray Droplet Dispersion Modeling System

SPRAY TRANsport (SPRAYTRAN) is a comprehensive dispersion modeling system that is used to simulate the offsite drift of pesticides from spray applications. SPRAYTRAN functions as a console application within Environmental System Research Institute’s ArcMap Geographic Information System (Version 9.x) and integrates the widely-used, U.S. Environmental Protection Agency (EPA)-approved CALifornia PUFF (CALPUFF) dispersion model and model components to simulate longer-range transport and diffusion in variable terrain and spatially/temporally varying meteorological (e.g., wind) fields. Area sources, which are used to define spray blocks in SPRAYTRAN, are initialized using output files generated from a separate aerial-spray-application model called AGDISP (AGricultural DISPersal). The AGDISP model is used for estimating the amount of pesticide deposited to the spray block based on spraying characteristics (e.g., pesticide type, spray nozzles, and aircraft type) and then simulating the near-field (less than 300-m) drift from a single pesticide application. The fraction of pesticide remaining airborne from the AGDISP near-field simulation is then used by SPRAYTRAN for simulating longer-range (greater than 300 m) drift and deposition of the pesticide

The Fourteenth Data Release of the Sloan Digital Sky Survey: First Spectroscopic Data from the extended Baryon Oscillation Spectroscopic Survey and from the second phase of the Apache Point Observatory Galactic Evolution Experiment

The fourth generation of the Sloan Digital Sky Survey (SDSS-IV) has been in operation since July 2014. This paper describes the second data release from this phase, and the fourteenth from SDSS overall (making this, Data Release Fourteen or DR14). This release makes public data taken by SDSS-IV in its first two years of operation (July 2014-2016). Like all previous SDSS releases, DR14 is cumulative, including the most recent reductions and calibrations of all data taken by SDSS since the first phase began operations in 2000. New in DR14 is the first public release of data from the extended Baryon Oscillation Spectroscopic Survey (eBOSS); the first data from the second phase of the Apache Point Observatory (APO) Galactic Evolution Experiment (APOGEE-2), including stellar parameter estimates from an innovative data driven machine learning algorithm known as "The Cannon"; and almost twice as many data cubes from the Mapping Nearby Galaxies at APO (MaNGA) survey as were in the previous release (N = 2812 in total). This paper describes the location and format of the publicly available data from SDSS-IV surveys. We provide references to the important technical papers describing how these data have been taken (both targeting and observation details) and processed for scientific use. The SDSS website (www.sdss.org) has been updated for this release, and provides links to data downloads, as well as tutorials and examples of data use. SDSS-IV is planning to continue to collect astronomical data until 2020, and will be followed by SDSS-V.Comment: SDSS-IV collaboration alphabetical author data release paper. DR14 happened on 31st July 2017. 19 pages, 5 figures. Accepted by ApJS on 28th Nov 2017 (this is the "post-print" and "post-proofs" version; minor corrections only from v1, and most of errors found in proofs corrected