Agrammatic but numerate

A central question in cognitive neuroscience concerns the extent to which language enables other higher cognitive functions. In the case of mathematics, the resources of the language faculty, both lexical and syntactic, have been claimed to be important for exact calculation, and some functional brain imaging studies have shown that calculation is associated with activation of a network of left-hemisphere language regions, such as the angular gyrus and the banks of the intraparietal sulcus. We investigate the integrity of mathematical calculations in three men with large left-hemisphere perisylvian lesions. Despite severe grammatical impairment and some difficulty in processing phonological and orthographic number words, all basic computational procedures were intact across patients. All three patients solved mathematical problems involving recursiveness and structure-dependent operations (for example, in generating solutions to bracket equations). To our knowledge, these results demonstrate for the first time the remarkable independence of mathematical calculations from language grammar in the mature cognitive system

The Children and Young People's Health Partnership Evelina London Model of Care: process evaluation protocol

Introduction Children and young people (CYP) in the UK have poor health outcomes, and there is increasing emergency department and hospital outpatient use. To address these problems in Lambeth and Southwark (two boroughs of London, UK), the local Clinical Commissioning Groups, Local Authorities and Healthcare Providers formed The Children and Young People’s Health Partnership (CYPHP), a clinical-academic programme for improving child health. The Partnership has developed the CYPHP Evelina London model, an integrated healthcare model that aims to deliver effective, coordinated care in primary and community settings and promote better self-management to over approximately 90 000 CYP in Lambeth and Southwark. This protocol is for the process evaluation of this model of care. Methods and analysis Alongside an impact evaluation, an in-depth, mixed-methods process evaluation will be used to understand the barriers and facilitators to implementing the model of care. The data collected mapped onto a logic model of how CYPHP is expected to improve child health outcomes. Data collection and analysis include qualitative interviews and focus groups with stakeholders, a policy review and a quantitative analysis of routine clinical and administrative data and questionnaire data. Information relating to the context of the trial that may affect implementation and/or outcomes of the CYPHP model of care will be documented. Ethics and dissemination The study has been reviewed by NHS REC Cornwall & Plymouth (17/SW/0275). The findings of this process evaluation will guide the scaling up and implementation of the CYPHP Evelina London Model of Care across the UK. Findings will be disseminated through publications and conferences, and implementation manuals and guidance for others working to improve child health through strengthening health systems. Trial registration number NCT03461848

Three new species of Nautilus Linnaeus, 1758 (Mollusca, Cephalopoda) from the Coral Sea and South Pacific

Nautiloids are a charismatic group of marine molluscs best known for their rich fossil record, but today they are restricted to a handful of species in the family Nautilidae from around the Coral Triangle. Recent genetic work has shown a disconnect between traditional species, originally defined on shell characters, but now with new findings from genetic structure of various Nautilus populations. Here, three new species of Nautilus from the Coral Sea and South Pacific region are formally named using observations of shell and soft anatomical data augmented by genetic information: N. samoaensis sp. nov. (from American Samoa), N. vitiensis sp. nov. (from Fiji), and N. vanuatuensis sp. nov. (from Vanuatu). The formal naming of these three species is timely considering the new and recently published information on genetic structure, geographic occurrence, and new morphological characters, including color patterns of shell and soft part morphology of hood, and will aid in managing these possibly endangered animals. As recently proposed from genetic analyses, there is a strong geographic component affecting taxonomy, with the new species coming from larger island groups that are separated by at least 200 km of deep water (greater than 800 m) from other Nautilus populations and potential habitats. Nautilid shells implode at depths greater than 800 m and depth therefore acts as a biogeographical barrier separating these species. This isolation, coupled with the unique, endemic species in each locale, are important considerations for the conservation management of the extant Nautilus species and populations

CYGD: the Comprehensive Yeast Genome Database

The Comprehensive Yeast Genome Database (CYGD) compiles a comprehensive data resource for information on the cellular functions of the yeast Saccharomyces cerevisiae and related species, chosen as the best understood model organism for eukaryotes. The database serves as a common resource generated by a European consortium, going beyond the provision of sequence information and functional annotations on individual genes and proteins. In addition, it provides information on the physical and functional interactions among proteins as well as other genetic elements. These cellular networks include metabolic and regulatory pathways, signal transduction and transport processes as well as co-regulated gene clusters. As more yeast genomes are published, their annotation becomes greatly facilitated using S.cerevisiae as a reference. CYGD provides a way of exploring related genomes with the aid of the S.cerevisiae genome as a backbone and SIMAP, the Similarity Matrix of Proteins. The comprehensive resource is available under http://mips.gsf.de/genre/proj/yeast/

Re-evaluating the phylogeny of Sipuncula through transcriptomics

Sipunculans (also known as peanut worms) are an ancient group of exclusively marine worms with a global distribution and a fossil record that dates back to the Early Cambrian. The systematics of sipunculans, now considered a distinct subclade of Annelida, has been studied for decades using morphological and molecular characters, and has reached the limits of Sanger-based approaches. Here, we reevaluate their family-level phylogeny by comparative transcriptomic analysis of eight species representing all known families within Sipuncula. Two data matrices with alternative gene occupancy levels (large matrix with 675 genes and 62% missing data; reduced matrix with 141 genes and 23% missing data) were analysed using concatenation and gene-tree methods, yielding congruent results and resolving each internal node with maximum support. We thus corroborate prior phylogenetic work based on molecular data, resolve outstanding issues with respect to the familial relationships of Aspidosiphonidae, Antillesomatidae and Phascolosomatidae, and highlight the next area of focus for sipunculan systematics

EndoNet: an information resource about regulatory networks of cell-to-cell communication†

EndoNet is an information resource about intercellular regulatory communication. It provides information about hormones, hormone receptors, the sources (i.e. cells, tissues and organs) where the hormones are synthesized and secreted, and where the respective receptors are expressed. The database focuses on the regulatory relations between them. An elementary communication is displayed as a causal link from a cell that secretes a particular hormone to those cells which express the corresponding hormone receptor and respond to the hormone. Whenever expression, synthesis and/or secretion of another hormone are part of this response, it renders the corresponding cell an internal node of the resulting network. This intercellular communication network coordinates the function of different organs. Therefore, the database covers the hierarchy of cellular organization of tissues and organs as it has been modeled in the Cytomer ontology, which has now been directly embedded into EndoNet. The user can query the database; the results can be used to visualize the intercellular information flow. A newly implemented hormone classification enables to browse the database and may be used as alternative entry point. EndoNet is accessible at: http://endonet.bioinf.med.uni-goettingen.de

Nacre tablet thickness records formation temperature in modern and fossil shells

Nacre, the iridescent outer lining of pearls and inner lining of many mollusk shells, is composed of periodic, parallel, organic sheets alternating with aragonite (CaCO_3) tablet layers. Nacre tablet thickness (TT) generates both nacre's iridescence and its remarkable resistance to fracture. Despite extensive studies on how nacre forms, the mechanisms controlling TT remain unknown, even though they determine the most conspicuous of nacre's characteristics, visible even to the naked eye. Thermodynamics predicts that temperature (T) will affect both physical and chemical components of biomineralized skeletons. The chemical composition of biominerals is well-established to record environmental parameters, and has therefore been extensively used in paleoclimate studies. The physical structure, however, has been hypothesized but never directly demonstrated to depend on the environment. Here we observe that the physical TT in nacre from modern and fossil shallow-water shells of the bivalves Pinna and Atrina correlates with T as measured by the carbonate clumped isotope thermometer. Based on the observed TT vs. T correlation, we anticipate that TT will be used as a paleothermometer, useful to estimate paleotemperature in shallow-water paleoenvironments. Here we successfully test the proposed new nacre TT thermometer on two Jurassic Pinna shells. The increase of TT with T is consistent with greater aragonite growth rate at higher T, and with greater metabolic rate at higher T. Thus, it reveals a complex, T-dependent biophysical mechanism for nacre formation

Knowledge-based energy functions for computational studies of proteins

This chapter discusses theoretical framework and methods for developing knowledge-based potential functions essential for protein structure prediction, protein-protein interaction, and protein sequence design. We discuss in some details about the Miyazawa-Jernigan contact statistical potential, distance-dependent statistical potentials, as well as geometric statistical potentials. We also describe a geometric model for developing both linear and non-linear potential functions by optimization. Applications of knowledge-based potential functions in protein-decoy discrimination, in protein-protein interactions, and in protein design are then described. Several issues of knowledge-based potential functions are finally discussed.Comment: 57 pages, 6 figures. To be published in a book by Springe

Human Stressors Are Driving Coastal Benthic Long-Lived Sessile Fan Mussel Pinna nobilis Population Structure More than Environmental Stressors.

Coastal degradation and habitat disruption are severely compromising sessile marine species. The fan shell Pinna nobilis is an endemic, vulnerable species and the largest bivalve in the Mediterranean basin. In spite of species legal protection, fan shell populations are declining. Models analyzed the contributions of environmental (mean depth, wave height, maximum wave height, period of waves with high energy and mean direction of wave source) versus human-derived stressors (anchoring, protection status, sewage effluents, fishing activity and diving) as explanatory variables depicting Pinna nobilis populations at a mesoscale level. Human stressors were explaining most of the variability in density spatial distribution of fan shell, significantly disturbing benthic communities. Habitat protection affected P. nobilis structure and physical aggression by anchoring reveals a high impact on densities. Environmental variables instead played a secondary role, indicating that global change processes are not so relevant in coastal benthic communities as human-derived impacts.Versión del editor4,411