Adventures in data citation: sorghum genome data exemplifies the new gold standard

Scientific progress is driven by the availability of information, which makes it essential that data be broadly, easily and rapidly accessible to researchers in every field. In addition to being good scientific practice, provision of supporting data in a convenient way increases experimental transparency and improves research efficiency by reducing unnecessary duplication of experiments. There are, however, serious constraints that limit extensive data dissemination. One such constraint is that, despite providing a major foundation of data to the advantage of entire community, data producers rarely receive the credit they deserve for the substantial amount of time and effort they spend creating these resources. In this regard, a formal system that provides recognition for data producers would serve to incentivize them to share more of their data. The process of data citation, in which the data themselves are cited and referenced in journal articles as persistently identifiable bibliographic entities, is a potential way to properly acknowledge data output. The recent publication of several sorghum genomes in Genome Biology is a notable first example of good data citation practice in the field of genomics and demonstrates the practicalities and formatting required for doing so. It also illustrates how effective use of persistent identifiers can augment the submission of data to the current standard scientific repositories

Metabolic scaling in modular animals

Metabolic scaling is the relationship between organismal metabolic rate and body mass. Understanding the patterns and causes of metabolic scaling provides a powerful foundation for predicting biological processes at the level of individuals, populations, communities, and ecosystems. Despite intense interest in, and debate on, the mechanistic basis of metabolic scaling, relatively little attention has been paid to metabolic scaling in clonal animals with modular construction, such as colonial cnidarians, bryozoans, and colonial ascidians. Unlike unitary animals, modular animals are structural individuals subdivided into repeated morphological units, or modules, each able to acquire, process, and share resources. A modular design allows flexibility in organism size and shape with consequences for metabolic scaling. Furthermore, with careful consideration of the biology of modular animals, the size and shape of individual colonies can be experimentally manipulated to test competing theories pertaining to metabolic scaling. Here, we review metabolic scaling in modular animals and find that a wide range of scaling exponents, rather than a single value, has been reported for a variety of modular animals. We identify factors influencing variation in intraspecific scaling in this group that relate to the general observation that not all modules within a colony are identical. We highlight current gaps in our understanding of metabolic scaling in modular animals, and suggest future research directions, such as manipulating metabolic states and comparisons among species that differ in extent of module integration

Human Acid Sphingomyelinase Structures Provide Insight to Molecular Basis of Niemann-Pick Disease

Acid sphingomyelinase (ASM) hydrolyzes sphingomyelin to ceramide and phosphocholine, essential components of myelin in neurons. Genetic alterations in ASM lead to ASM deficiency (ASMD) and have been linked to Niemann–Pick disease types A and B. Olipudase alfa, a recombinant form of human ASM, is being developed as enzyme replacement therapy to treat the non-neurological manifestations of ASMD. Here we present the human ASM holoenzyme and product bound structures encompassing all of the functional domains. The catalytic domain has a metallophosphatase fold, and two zinc ions and one reaction product phosphocholine are identified in a histidine-rich active site. The structures reveal the underlying catalytic mechanism, in which two zinc ions activate a water molecule for nucleophilic attack of the phosphodiester bond. Docking of sphingomyelin provides a model that allows insight into the selectivity of the enzyme and how the ASM domains collaborate to complete hydrolysis. Mapping of known mutations provides a basic understanding on correlations between enzyme dysfunction and phenotypes observed in ASMD patients

Bermuda 2.0: Reflections from Santa Cruz

In February 1996, the genome community met in Bermuda to formulate principles for circulating genomic data. Although it is now 20 years since the Bermuda Principles were formulated, they continue to play a central role in shaping genomic and data-sharing practices. However, since 1996, “openness” has become an increasingly complex issue. This commentary seeks to articulate three core challenges data-sharing faces today

Is authorship sufficient for today’s collaborative research? A call for contributor roles

Assigning authorship and recognizing contributions to scholarly works is challenging on many levels. Here we discuss ethical, social, and technical challenges to the concept of authorship that may impede the recognition of contributions to a scholarly work. Recent work in the field of authorship shows that shifting to a more inclusive contributorship approach may address these challenges. Recent efforts to enable better recognition of contributions to scholarship include the development of the Contributor Role Ontology (CRO), which extends the CRediT taxonomy and can be used in information systems for structuring contributions. We also introduce the Contributor Attribution Model (CAM), which provides a simple data model that relates the contributor to research objects via the role that they played, as well as the provenance of the information. Finally, requirements for the adoption of a contributorship-based approach are discussed

Report of the 13th Genomic Standards Consortium Meeting, Shenzhen, China, March 4–7, 2012

This report details the outcome of the 13th Meeting of the Genomic Standards Consortium. The three-day conference was held at the Kingkey Palace Hotel, Shenzhen, China, on March 5–7, 2012, and was hosted by the Beijing Genomics Institute. The meeting, titled From Genomes to Interactions to Communities to Models, highlighted the role of data standards associated with genomic, metagenomic, and amplicon sequence data and the contextual information associated with the sample. To this end the meeting focused on genomic projects for animals, plants, fungi, and viruses; metagenomic studies in host-microbe interactions; and the dynamics of microbial communities. In addition, the meeting hosted a Genomic Observatories Network session, a Genomic Standards Consortium biodiversity working group session, and a Microbiology of the Built Environment session sponsored by the Alfred P. Sloan Foundatio

The nature of NV absorbers at high redshift

We present a study of NV absorption systems at 1.5 < z < 2.5 in the optical spectra of 19 QSOs. Our analysis includes both absorbers arising from the intergalactic medium as well as systems in the vicinity of the background quasar. We construct detailed photoionization models to study the physical conditions and abundances in the absorbers and to constrain the spectral hardness of the ionizing radiation. The rate of incidence for intervening NV components is dN/dz = 3.38 +/- 0.43, corresponding to dN/dX = 1.10 +/- 0.14. The column density distribution function is fitted by the slope beta = 1.89 +/- 0.22, consistent with measurements for CIV and OVI. The narrow line widths (b_NV ~ 6 km/s) imply photoionization rather than collisions as dominating ionization process. The column densities of CIV and NV are correlated but show different slopes for intervening and associated absorbers, which indicates different ionizing spectra. Associated systems are found to be more metal-rich, denser, and more compact than intervening absorbers. This conclusion is independent of the adopted ionizing radiation. For the intervening NV systems we find typical values of [C/H] ~ -0.6 and n_H ~ 10^-3.6 cm^-3, and sizes of a few kpc, while for associated NV absorbers we obtain [C/H] ~ +0.7, n_H ~ 10^-2.8 cm^-3, and sizes of several 10 pc. The abundance of nitrogen relative to carbon [N/C] and alpha-elements like oxygen and silicon [N/alpha] is correlated with [N/H], indicating the enrichment by secondary nitrogen. The larger scatter in [N/alpha] in intervening systems suggests an inhomogeneous enrichment of the IGM. There is an anti-correlation between [N/alpha] and [alpha/C], which could be used to constrain the initial mass function of the carbon- and nitrogen-producing stellar population.Comment: accepted by A&A, revised versio

Aortic root surgery in septuagenarians: impact of different surgical techniques

<p>Abstract</p> <p>Background</p> <p>To evaluate the impact and safety of different surgical techniques for aortic root replacement (ARR) on early and late morbidity and mortality in septuagenarians undergoing ARR.</p> <p>Methods</p> <p>Ninety-five patients (73.8 ± 3.2 years) were operated and divided into three groups according to the aortic root procedure; MECH-group (n = 51) patients with a mechanical composite graft, BIO-group (n = 22) patients with a customized biological composite graft, and REIMPL-group (n = 22) patients with a valve sparing aortic root reimplantation (David I). In 42.1% (40/95) of these patients the aortic arch was replaced. Follow-up was completed in 95.2% (79/83) of in-hospital survivors.</p> <p>Results</p> <p>Hospital mortality was 12.6% (12/95) in the entire population (MECH. 15.7% (8/51), BIO 19.7% (4/22), REIMPL 0% (0/22); p = 0.004). Two patients died intraoperatively. The most frequent postoperative complications were prolonged mechanical ventilation ((>48 h) in 16.8% (16/93) (MECH. 7% (7/51), BIO 36.4% (8/22), REIMPL 4.5% (1/22); p = 0.013) and rethoracotomy for postoperative bleeding in 12.6% (12/95) (MECH. 12% (6/51), BIO 22.7% (5/22), REIMPL 4.5% (1/22); p = 0.19). Nineteen late deaths (22.9%) (19/83) (MECH 34.8% (15/43), BIO 16.7% (3/18), REIMPL 4.5% (1/22); p = 0.012) occurred during a mean follow-up of 41 ± 42 months (MECH 48 ± 48 months, BIO 25 ± 37 months, REIMPL 40 ± 28 months, p = 0.028). Postoperative NYHA class decreased significantly (p = 0.017) and performance status (p = 0.027) increased for the entire group compared to preoperative values.</p> <p>Conclusion</p> <p>Our data indicate that valve sparing aortic root reimplantation is safe and effective in septuagenarians, and is associated with low early and late morbidity and mortality.</p