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

Transmyocardial laser revascularization fails to prevent left ventricular functional deterioration and aneurysm formation after acute myocardial infarction in sheep

AbstractObjective: Transmyocardial laser revascularization is an investigational technique for revascularizing ischemic myocardium in patients with inoperable coronary arterial disease. This study tests the hypothesis that laser revascularization prevents left ventricular functional deterioration and aneurysm formation after acute anteroapical myocardial infarction. Methods: An ultrasonic ascending aortic flow probe and snares around the distal left anterior descending and second diagonal coronary arteries were placed in 26 Dorsett hybrid sheep. Ten to 14 days later, snared arteries were occluded to produce an anteroapical infarction of 23% of left ventricular mass. Before infarction 14 animals had 34 ± 4 transmyocardial perforations in the area of the anticipated infarction made with a carbon dioxide laser. Twelve animals served as controls. Hemodynamic measurements and transdiaphragmatic quantitative echocardiograms were obtained before, immediately after, and 2, 5, and 8 weeks after infarction. Eighteen sheep completed the protocol. Results: All animals had large anteroapical left ventricular aneurysms with massive ventricular enlargement. Immediately after infarction the anterior wall became thinner and dyskinetic in all sheep. At 8 weeks aneurysmal size and shape were indistinguishable between groups. Two days after infarction, laser holes were filled with fibrin. At 5 and 8 weeks the infarct consisted of dense collagen, fibroblasts, scattered calcifications, myocyte fragments, neutrophils, macrophages, and no laser holes. There were no significant differences at any time between groups for cardiac pressures or output, ventricular volumes, ejection fraction, stroke work, and the stroke work–left ventricular end-diastolic pressure index. Conclusion: Transmyocardial laser perforations do not revascularize acute myocardial infarction in sheep. (J Thorac Cardiovasc Surg 1998;116:752-62

The Potential for Reducing the Number of Pneumococcal Conjugate Vaccine Doses While Sustaining Herd Immunity in High-Income Countries.

Stefan Flasche and colleagues consider whether the number of PCV doses in the infant schedule could be reduced without compromising its public health benefit in high-income settings

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

The Canada-UK Deep Submillimetre Survey: The Survey of the 14-hour field

We have used SCUBA to survey an area of 50 square arcmin, detecting 19 sources down to a 3sigma sensitivity limit of 3.5 mJy at 850 microns. We have used Monte-Carlo simulations to assess the effect of source confusion and noise on the SCUBA fluxes and positions, finding that the fluxes of sources in the SCUBA surveys are significantly biased upwards and that the fraction of the 850 micron background that has been resolved by SCUBA has been overestimated. The radio/submillmetre flux ratios imply that the dust in these galaxies is being heated by young stars rather than AGN. We have used simple evolution models based on our parallel SCUBA survey of the local universe to address the major questions about the SCUBA sources: (1) what fraction of the star formation at high redshift is hidden by dust? (2) Does the submillimetre luminosity density reach a maximum at some redshift? (3) If the SCUBA sources are proto-ellipticals, when exactly did ellipticals form? However, we show that the observations are not yet good enough for definitive answers to these questions. There are, for example, acceptable models in which 10 times as much high-redshift star formation is hidden by dust as is seen at optical wavelengths, but also acceptable ones in which the amount of hidden star formation is less than that seen optically. There are acceptable models in which very little star formation occurred before a redshift of three (as might be expected in models of hierarchical galaxy formation), but also ones in which 30% of the stars have formed by this redshift. The key to answering these questions are measurements of the dust temperatures and redshifts of the SCUBA sources.Comment: 41 pages (latex), 17 postscript figures, to appear in the November issue of the Astronomical Journa

Assessing the efficiency of catch-up campaigns for the introduction of pneumococcal conjugate vaccine: a modelling study based on data from PCV10 introduction in Kilifi, Kenya.

BACKGROUND: The World Health Organisation recommends the use of catch-up campaigns as part of the introduction of pneumococcal conjugate vaccines (PCVs) to accelerate herd protection and hence PCV impact. The value of a catch-up campaign is a trade-off between the costs of vaccinating additional age groups and the benefit of additional direct and indirect protection. There is a paucity of observational data, particularly from low- and middle-income countries, to quantify the optimal breadth of such catch-up campaigns. METHODS: In Kilifi, Kenya, PCV10 was introduced in 2011 using the three-dose Expanded Programme on Immunisation infant schedule and a catch-up campaign in children <5 years old. We fitted a transmission dynamic model to detailed local data, including nasopharyngeal carriage and invasive pneumococcal disease (IPD), to infer the marginal impact of the PCV catch-up campaign over hypothetical routine cohort vaccination in that setting and to estimate the likely impact of alternative campaigns and their dose efficiency. RESULTS: We estimated that, within 10 years of introduction, the catch-up campaign among children <5 years old prevents an additional 65 (48-84) IPD cases across age groups, compared to PCV cohort introduction alone. Vaccination without any catch-up campaign prevented 155 (121-193) IPD cases and used 1321 (1058-1698) PCV doses per IPD case prevented. In the years after implementation, the PCV programme gradually accrues herd protection, and hence its dose efficiency increases: 10 years after the start of cohort vaccination alone the programme used 910 (732-1184) doses per IPD case averted. We estimated that a two-dose catch-up among children <1 year old uses an additional 910 (732-1184) doses per additional IPD case averted. Furthermore, by extending a single-dose catch-up campaign to children aged 1 to <2 years and subsequently to those aged 2 to <5 years, the campaign uses an additional 412 (296-606) and 543 (403-763) doses per additional IPD case averted. These results were not sensitive to vaccine coverage, serotype competition, the duration of vaccine protection or the relative protection of infants. CONCLUSIONS: We find that catch-up campaigns are a highly dose-efficient way to accelerate population protection against pneumococcal disease