Open Data, Collaborative Working Platforms, and Interdisciplinary Collaboration: Building an Early Career Scientist Community of Practice to Leverage Ocean Observatories Initiative Data to Address Critical Questions in Marine Science

Ocean observing systems are well-recognized as platforms for long-term monitoring of near-shore and remote locations in the global ocean. High-quality observatory data is freely available and accessible to all members of the global oceanographic community—a democratization of data that is particularly useful for early career scientists (ECS), enabling ECS to conduct research independent of traditional funding models or access to laboratory and field equipment. The concurrent collection of distinct data types with relevance for oceanographic disciplines including physics, chemistry, biology, and geology yields a unique incubator for cutting-edge, timely, interdisciplinary research. These data are both an opportunity and an incentive for ECS to develop the computational skills and collaborative relationships necessary to interpret large data sets. Here, we use observatory data to demonstrate the potential for these interdisciplinary approaches by presenting a case study on the water-column response to anomalous atmospheric events (i.e., major storms) on the shelf of the Mid-Atlantic Bight southwest of Cape Cod, United States. Using data from the Ocean Observatories Initiative (OOI) Pioneer Array, we applied a simple data mining method to identify anomalous atmospheric events over a four-year period. Two closely occurring storm events in late 2018 were then selected to explore the dynamics of water-column response using mooring data from across the array. The comprehensive ECS knowledge base and computational skill sets allowed identification of data issues in the OOI data streams and technologically sound characterization of data from multiple sensor packages to broadly characterize ocean-atmosphere interactions. An ECS-driven approach that emphasizes collaborative and interdisciplinary working practices adds significant value to existing datasets and programs such as OOI and has the potential to produce meaningful scientific advances. Future success in utilizing ocean observatory data requires continued investment in ECS education, collaboration, and research; in turn, the ECS community provides feedback, develops knowledge, and builds new tools to enhance the value of ocean observing systems. These findings present an argument for building a community of practice to augment ECS ocean scientist skills and foster collaborations to extend the context, reach, and societal utility of ocean science

LSST: from Science Drivers to Reference Design and Anticipated Data Products

(Abridged) We describe here the most ambitious survey currently planned in the optical, the Large Synoptic Survey Telescope (LSST). A vast array of science will be enabled by a single wide-deep-fast sky survey, and LSST will have unique survey capability in the faint time domain. The LSST design is driven by four main science themes: probing dark energy and dark matter, taking an inventory of the Solar System, exploring the transient optical sky, and mapping the Milky Way. LSST will be a wide-field ground-based system sited at Cerro Pach\'{o}n in northern Chile. The telescope will have an 8.4 m (6.5 m effective) primary mirror, a 9.6 deg$^2$ field of view, and a 3.2 Gigapixel camera. The standard observing sequence will consist of pairs of 15-second exposures in a given field, with two such visits in each pointing in a given night. With these repeats, the LSST system is capable of imaging about 10,000 square degrees of sky in a single filter in three nights. The typical 5$\sigma$ point-source depth in a single visit in $r$ will be $\sim 24.5$ (AB). The project is in the construction phase and will begin regular survey operations by 2022. The survey area will be contained within 30,000 deg$^2$ with $\delta<+34.5^\circ$, and will be imaged multiple times in six bands, $ugrizy$, covering the wavelength range 320--1050 nm. About 90\% of the observing time will be devoted to a deep-wide-fast survey mode which will uniformly observe a 18,000 deg$^2$ region about 800 times (summed over all six bands) during the anticipated 10 years of operations, and yield a coadded map to $r\sim27.5$. The remaining 10\% of the observing time will be allocated to projects such as a Very Deep and Fast time domain survey. The goal is to make LSST data products, including a relational database of about 32 trillion observations of 40 billion objects, available to the public and scientists around the world.Comment: 57 pages, 32 color figures, version with high-resolution figures available from https://www.lsst.org/overvie

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Large-scale sequencing identifies multiple genes and rare variants associated with Crohn’s disease susceptibility

peer reviewe

Prioritising and mapping barriers to achieve equitable surgical care in South Africa:a multi-disciplinary stakeholder workshop

BACKGROUND: Surgical healthcare in South Africa is inequitable with a considerable lack of resources in the public health sector. Identifying barriers to care and creating research priorities to mitigate these barriers can contribute to strategic interventions to improve equitable access to quality surgical care. OBJECTIVE: To use the Four Delays Framework to map barriers to surgical care and identify priorities to achieve equitable and timely access to quality surgical care in South Africa. METHODS: A multi-disciplinary stakeholder workshop was held in Cape Town, South Africa in January 2020. A Four Delays Framework (delays in seeking care, reaching care, receiving care, and remaining in care) was used to identify barriers that occur at each delay and the top 10 priorities for intervention. Barriers were categorised into overarching themes and schematically mapped. RESULTS: Thirty-four stakeholders including health service users, health service providers, and community members participated in this exercise. In total, 34 barriers were identified with 73 connections to various delays. Specifically, 14 barriers were related to delays in seeking care, 11 were related to delays in reaching care, 20 were related to delays in receiving care, and 28 were related to delays in remaining in care. The highest priority barriers across the delays were Lack of service provider’s knowledge, training and experience, and Limited surgical outreach. The barrier Lack of decentralised services was related to all four delays. Barriers were interconnected and potentially reinforcing. CONCLUSIONS: This workshop is the first of its kind to generate evidence on the delays to surgical care in South Africa. Mapping crucial interconnected, potentially reinforcing barriers, and priority interventions demonstrated how a multifaceted approach may be required to address delays to access. Further research focused on the identified priorities will contribute to efforts to promote equitable access to quality surgical care in South Africa

Use of public health service increased risk kidneys in pediatric renal transplant recipients

With the opioid epidemic and expansion of "IR" classification, 25% of deceased donors are categorized PHS-IR. Studies have assessed utilization of PHS-IR organs among adults, but little is known about pediatric recipients. This retrospective cohort study from 2004-2016 (IR period) aimed to: (a) assess IR kidney utilization patterns between adults and children; (b) identify recipient factors associated with transplant from IR donors among pediatric kidney recipients; and (c) determine geography's role in IR kidney utilization for children. The proportion of pediatric recipients receiving IR kidneys was significantly lower than adults (P < 0.001), even when stratified by donor mechanism of death (non-overdose/overdose) and era. In mixed effects models accounting for clustering within centers and regions, older recipient age, later era (post-PHS-IR expansion), and blood type were associated with significantly higher odds of receiving an IR kidney (17 years era 5: OR 5.16 [CI 2.05-13.1] P < 0.001; 18-21 years era 5: OR 2.72 [CI 1.05-7.06] P = 0.04; blood type O: OR 1.32 [CI 1.06-1.64] P = 0.013). The median odds ratio for center within region was 1.77 indicating that when comparing two patients in a region, the odds of receiving an IR kidney were 77% higher for a patient from a center with higher likelihood of receiving an IR kidney. Utilization of PHS-IR kidneys is significantly lower among pediatric recipients versus adult counterparts. More work is needed to understand the reasons for these differences in children in order to continue their access to this life-prolonging therapy

Direct observations of microbial community succession on sinking marine particles.

Microbial community dynamics on sinking particles control the amount of carbon that reaches the deep ocean and the length of time that carbon is stored, with potentially profound impacts on Earths climate. A mechanistic understanding of the controls on sinking particle distributions has been hindered by limited depth- and time-resolved sampling and methods that cannot distinguish individual particles. Here, we analyze microbial communities on nearly 400 individual sinking particles in conjunction with more conventional composite particle samples to determine how particle colonization and community assembly might control carbon sequestration in the deep ocean. We observed community succession with corresponding changes in microbial metabolic potential on the larger sinking particles transporting a significant fraction of carbon to the deep sea. Microbial community richness decreased as particles aged and sank; however, richness increased with particle size and the attenuation of carbon export. This suggests that the theory of island biogeography applies to sinking marine particles. Changes in POC flux attenuation with time and microbial community composition with depth were reproduced in a mechanistic ecosystem model that reflected a range of POC labilities and microbial growth rates. Our results highlight microbial community dynamics and processes on individual sinking particles, the isolation of which is necessary to improve mechanistic models of ocean carbon uptake