Large-scale structure of time evolving citation networks

In this paper we examine a number of methods for probing and understanding the large-scale structure of networks that evolve over time. We focus in particular on citation networks, networks of references between documents such as papers, patents, or court cases. We describe three different methods of analysis, one based on an expectation-maximization algorithm, one based on modularity optimization, and one based on eigenvector centrality. Using the network of citations between opinions of the United States Supreme Court as an example, we demonstrate how each of these methods can reveal significant structural divisions in the network, and how, ultimately, the combination of all three can help us develop a coherent overall picture of the network's shape.Comment: 10 pages, 6 figures; journal names for 4 references fixe

Metabolite profiling of yam (Dioscorea spp.) accessions for use in crop improvement programmes

Article purchased; Published online: 14 Oct. 2017Introduction Ninety-seven percent of yam (Dioscorea spp.) production takes place in low income food deficit countries (LIFDCs) and the crop provides 200 calories a day to approximately 300 million people. Therefore, yams are vital for food security. Yams have high-yield potential and high market value potential yet current breeding of yam is hindered by a lack of genomic information and genetic resources. New tools are needed to modernise breeding strategies and unlock the potential of yam to improve livelihood in LIFDCs. Objectives Metabolomic screening has been undertaken on a diverse panel of Dioscorea accessions to assess the utility of the approach for advancing breeding strategies in this understudied crop. Methods Polar and lipophilic extracts from tubers of accessions from the global yam breeding program have been comprehensively profiled via gas chromatography-mass spectrometry. Results A visual pathway representation of the measured yam tuber metabolome has been delivered as a resource for biochemical evaluation of yam germplasm. Over 200 compounds were routinely measured in tubers, providing a major advance for the chemo-typing of this crop. Core biochemical redundancy concealed trends that were only elucidated following detailed mining of global metabolomics data. Combined analysis on leaf and tuber material identified a subset of metabolites which allow accurate species classification and highlighted the potential of predicting tuber composition from leaf profiles. Metabolic variation was accessionspecific and often localised to compound classes, which will aid trait-targeting for metabolite markers. Conclusions Metabolomics provides a standalone platform with potential to deliver near-future crop gains for yam. The approach compliments the genetic advancements currently underway and integration with other ‘–omics’ studies will deliver a significant advancement to yam breeding strategies

The Asymptotic D- to S-State Ratio for 3-He

This work was supported by the National Science Foundation Grant NSF PHY 81-14339 and by Indiana Universit

A novel compartment, the 'subqpical stem' of the aerial hyphae, is the location of a sigN-dependent, developmentally distinct transcription in Streptomyces coelicolor.

Streptomyces coelicolor has nine SigB-like RNA polymerase sigma factors, several of them implicated in morphological differentiation and/or responses to different stresses. One of the nine, SigN, is the focus of this article. A constructed sigN null mutant was delayed in development and exhibited a bald phenotype when grown on minimal medium containing glucose as carbon source. One of two distinct sigN promoters, sigNP1, was active only during growth on solid medium, when its activation coincided with aerial hyphae formation. Transcription from sigNP1 was readily detected in several whi mutants (interrupted in morphogenesis of aerial mycelium into spores), but was absent from all bld mutants tested, suggesting that sigNP1 activity was restricted to the aerial hyphae. It also depended on sigN, thus sigN was autoregulated. Mutational and transcription studies revealed no functional significance to the location of sigN next to sigF, encoding another SigB-like sigma factor. We identified another potential SigN target, nepA, encoding a putative small secreted protein. Transcription of nepA originated from a single, aerial hyphae-specific and sigN-dependent promoter. While in vitro run-off transcription using purified SigN on the Bacillus subtilis ctc promoter confirmed that SigN is an RNA polymerase sigma factor, SigN failed to initiate transcription from sigNP1 and from the nepA promoter in vitro. Additional in vivo data indicated that further nepA upstream sequences, which are likely to bind a potential activator, are required for successful transcription. Using a nepA–egfp transcriptional fusion we located nepA transcription to a novel compartment, the ‘subapical stem’ of the aerial hyphae. We suggest that this newly recognized compartment defines an interface between the aerial and vegetative parts of the Streptomyces colony and might also be involved in communication between these two compartments

Uric acid: an old actor for a new role

The role of uric acid as an independent risk factor for cardiovascular events is still debated. In fact, other confounding factors such as glucose intolerance, obesity, dyslipidaemia, hypertension, use of diuretics and insulin resistance may play a role in determining the increased vascular risk associated to elevated uric acid concentrations. These factors (including high uric acid) have been mentioned in one or more definitions of the metabolic syndrome. Recently, much attention has been paid to the metabolic syndrome due to its possible role as a risk factor for the development of type 2 diabetes and cardiovascular disease. The worldwide increase in the prevalence of obesity and diabetes is a reason not only for the increasing prevalence of the metabolic syndrome but also of hyperuricaemia. A better understanding of the role of uric acid in health and in disease states may help physicians to improve their performance in preventing and treating cardiovascular disease

Existing guidance on reporting of consensus methodology: a systematic review to inform ACCORD guideline development

Objective To identify evidence on the reporting quality of consensus methodology and to select potential checklist items for the ACcurate COnsensus Reporting Document (ACCORD) project to develop a consensus reporting guideline.Design Systematic review.Data sources Embase, MEDLINE, Web of Science, PubMed, Cochrane Library, Emcare, Academic Search Premier and PsycINFO from inception until 7 January 2022.Eligibility criteria Studies, reviews and published guidance addressing the reporting quality of consensus methodology for improvement of health outcomes in biomedicine or clinical practice. Reports of studies using or describing consensus methods but not commenting on their reporting quality were excluded. No language restrictions were applied.Data extraction and synthesis Screening and data extraction of eligible studies were carried out independently by two authors. Reporting quality items addressed by the studies were synthesised narratively.Results Eighteen studies were included: five systematic reviews, four narrative reviews, three research papers, three conference abstracts, two research guidance papers and one protocol. The majority of studies indicated that the quality of reporting of consensus methodology could be improved. Commonly addressed items were: consensus panel composition; definition of consensus and the threshold for achieving consensus. Items least addressed were: public patient involvement (PPI); the role of the steering committee, chair, cochair; conflict of interest of panellists and funding. Data extracted from included studies revealed additional items that were not captured in the data extraction form such as justification of deviation from the protocol or incentives to encourage panellist response.Conclusion The results of this systematic review confirmed the need for a reporting checklist for consensus methodology and provided a range of potential checklist items to report. The next step in the ACCORD project builds on this systematic review and focuses on reaching consensus on these items to develop the reporting guideline.Dermatology and Venereolog

A New Faint Milky Way Satellite Discovered in the Pan-STARRS1 3π Survey

We present the discovery of a faint Milky Way satellite, Laevens 2/Triangulum II, found in the Panoramic Survey Telescope And Rapid Response System (Pan-STARRS 1) 3 pi imaging data and confirmed with follow-up wide-field photometry from the Large Binocular Cameras. The stellar system, with an absolute magnitude of M_V=-1.8 +/-0.5, a heliocentric distance of 30 +2/-2 kpc, and a half-mass radius of 34 +9/-8 pc, shows remarkable similarity to faint, nearby, small satellites such as Willman 1, Segue 1, Segue 2, and Bo\"otes II. The discovery of Laevens 2/Triangulum II further populates the region of parameter space for which the boundary between dwarf galaxies and globular clusters becomes tenuous. Follow-up spectroscopy will ultimately determine the nature of this new satellite, whose spatial location hints at a possible connection with the complex Triangulum-Andromeda stellar structures

Nucleon Charge and Magnetization Densities from Sachs Form Factors

Relativistic prescriptions relating Sachs form factors to nucleon charge and magnetization densities are used to fit recent data for both the proton and the neutron. The analysis uses expansions in complete radial bases to minimize model dependence and to estimate the uncertainties in radial densities due to limitation of the range of momentum transfer. We find that the charge distribution for the proton is significantly broad than its magnetization density and that the magnetization density is slightly broader for the neutron than the proton. The neutron charge form factor is consistent with the Galster parametrization over the available range of Q^2, but relativistic inversion produces a softer radial density. Discrete ambiguities in the inversion method are analyzed in detail. The method of Mitra and Kumari ensures compatibility with pQCD and is most useful for extrapolating form factors to large Q^2.Comment: To appear in Phys. Rev. C. Two new figures and accompanying text have been added and several discussions have been clarified with no significant changes to the conclusions. Now contains 47 pages including 21 figures and 2 table

Biological and geophysical feedbacks with fire in the Earth system

Roughly 3% of the Earth's land surface burns annually, representing a critical exchange of energy and matter between the land and atmosphere via combustion. Fires range from slow smouldering peat fires, to low-intensity surface fires, to intense crown fires, depending on vegetation structure, fuel moisture, prevailing climate, and weather conditions. While the links between biogeochemistry, climate and fire are widely studied within Earth system science, these relationships are also mediated by fuels—namely plants and their litter—that are the product of evolutionary and ecological processes. Fire is a powerful selective force and, over their evolutionary history, plants have evolved traits that both tolerate and promote fire numerous times and across diverse clades. Here we outline a conceptual framework of how plant traits determine the flammability of ecosystems and interact with climate and weather to influence fire regimes. We explore how these evolutionary and ecological processes scale to impact biogeochemical and Earth system processes. Finally, we outline several research challenges that, when resolved, will improve our understanding of the role of plant evolution in mediating the fire feedbacks driving Earth system processes. Understanding current patterns of fire and vegetation, as well as patterns of fire over geological time, requires research that incorporates evolutionary biology, ecology, biogeography, and the biogeosciences