Horse Feeding and Management

Horses perform variety of roles in our society, serving people in several ways. Proper nutrition and feeding management are some of the main objectives to ensure the well-being and performance of horses. Thus, the link between equine health and good dietary treatment must be recognized to increase our understanding of the needs of the horse. It is important to ensure science-based knowledge is available to all stakeholders and people working in the horse industry. This book presents research papers published in the Special Issue of Animals entitled ‘Horse Nutrition and Management’

An overview of the BioCreative 2012 Workshop Track III: interactive text mining task

In many databases, biocuration primarily involves literature curation, which usually involves retrieving relevant articles, extracting information that will translate into annotations and identifying new incoming literature. As the volume of biological literature increases, the use of text mining to assist in biocuration becomes increasingly relevant. A number of groups have developed tools for text mining from a computer science/linguistics perspective, and there are many initiatives to curate some aspect of biology from the literature. Some biocuration efforts already make use of a text mining tool, but there have not been many broad-based systematic efforts to study which aspects of a text mining tool contribute to its usefulness for a curation task. Here, we report on an effort to bring together text mining tool developers and database biocurators to test the utility and usability of tools. Six text mining systems presenting diverse biocuration tasks participated in a formal evaluation, and appropriate biocurators were recruited for testing. The performance results from this evaluation indicate that some of the systems were able to improve efficiency of curation by speeding up the curation task significantly (∼1.7- to 2.5-fold) over manual curation. In addition, some of the systems were able to improve annotation accuracy when compared with the performance on the manually curated set. In terms of inter-annotator agreement, the factors that contributed to significant differences for some of the systems included the expertise of the biocurator on the given curation task, the inherent difficulty of the curation and attention to annotation guidelines. After the task, annotators were asked to complete a survey to help identify strengths and weaknesses of the various systems. The analysis of this survey highlights how important task completion is to the biocurators’ overall experience of a system, regardless of the system’s high score on design, learnability and usability. In addition, strategies to refine the annotation guidelines and systems documentation, to adapt the tools to the needs and query types the end user might have and to evaluate performance in terms of efficiency, user interface, result export and traditional evaluation metrics have been analyzed during this task. This analysis will help to plan for a more intense study in BioCreative IV

WormBase 2012: more genomes, more data, new website

Since its release in 2000, WormBase (http://www.wormbase.org) has grown from a small resource focusing on a single species and serving a dedicated research community, to one now spanning 15 species essential to the broader biomedical and agricultural research fields. To enhance the rate of curation, we have automated the identification of key data in the scientific literature and use similar methodology for data extraction. To ease access to the data, we are collaborating with journals to link entities in research publications to their report pages at WormBase. To facilitate discovery, we have added new views of the data, integrated large-scale datasets and expanded descriptions of models for human disease. Finally, we have introduced a dramatic overhaul of the WormBase website for public beta testing. Designed to balance complexity and usability, the new site is species-agnostic, highly customizable, and interactive. Casual users and developers alike will be able to leverage the public RESTful application programming interface (API) to generate custom data mining solutions and extensions to the site. We report on the growth of our database and on our work in keeping pace with the growing demand for data, efforts to anticipate the requirements of users and new collaborations with the larger science community

Detection of Crosslinks within and between Proteins by LC-MALDI-TOFTOF and the Software FINDX to Reduce the MSMS-Data to Acquire for Validation

Lysine-specific chemical crosslinking in combination with mass spectrometry is emerging as a tool for the structural characterization of protein complexes and protein-protein interactions. After tryptic digestion of crosslinked proteins there are thousands of peptides amenable to MSMS, of which only very few are crosslinked peptides of interest. Here we describe how the advantage offered by off-line LC-MALDI-TOF/TOF mass spectrometry is exploited in a two-step workflow to focus the MSMS-acquisition on crosslinks mainly. In a first step, MS-data are acquired and all the peak list files from the LC-separated fractions are merged by the FINDX software and screened for presence of crosslinks which are recognized as isotope-labeled doublet peaks. Information on the isotope doublet peak mass and intensity can be used as search constraints to reduce the number of false positives that match randomly to the observed peak masses. Based on the MS-data a precursor ion inclusion list is generated and used in a second step, where a restricted number of MSMS-spectra are acquired for crosslink validation. The decoupling of MS and MSMS and the peptide sorting with FINDX based on MS-data has the advantage that MSMS can be restricted to and focused on crosslinks of Type 2, which are of highest biological interest but often lowest in abundance. The LC-MALDI TOF/TOF workflow here described is applicable to protein multisubunit complexes and using 14N/15N mixed isotope strategy for the detection of inter-protein crosslinks within protein oligomers

SUNRISE: The rich molecular inventory of high-redshift dusty galaxies revealed by broadband spectral line surveys

Understanding the nature of high-$z$ dusty galaxies requires a comprehensive view of their ISM and molecular complexity. However, the molecular ISM at high redshifts is commonly studied using only a few species beyond CO, limiting our understanding of the ISM in these objects. In this paper, we present the results of deep 3 mm spectral line surveys using the NOEMA targeting two lensed dusty galaxies: APM 08279+5255 (APM), a quasar at redshift $z=3.911$, and NCv1.143 (NC), a $z=3.565$ starburst galaxy. The spectral line surveys cover rest-frame frequencies from about 330-550 GHz. We report the detection of 38 and 25 emission lines in APM and NC, respectively. The spectra reveal the chemical richness and the complexity of the physical properties of the ISM. By comparing the spectra of the two sources and combining the gas excitation analysis, we find that the physical properties and the chemical imprints of the ISM are different between them: the molecular gas is more excited in APM, exhibiting higher molecular-gas temperatures and densities compared to NC; the chemical abundances in APM are akin to the values of local AGN, showing boosted relative abundances of the dense gas tracers that might be related to high-temperature chemistry and/or XDRs, while NC more closely resembles local starburst galaxies. The most significant differences are found in H2O, where the 448 GHz H2O line is significantly brighter in APM, likely linked to the intense far-infrared radiation from the dust powered by AGN. Our astrochemical model suggests that, at such high column densities, UV radiation is less important in regulating the ISM, while CRs (and/or X-rays and shocks) are the key players in shaping the abundance of the molecules. Such deep spectral line surveys open a new window to study the physical and chemical properties of the ISM and the radiation field of galaxies in the early Universe. (abridged)Comment: Submitted to A&A; under review. Abstract abridged. Comments are welcome

Family-focused contextual factors associated with lifestyle patterns in young children from two mother-offspring cohorts : GUSTO and EDEN

Background Integrated patterns of energy balance-related behaviours of preschool children in Asia are sparse, with few comparative analyses. Purpose Using cohorts in Singapore (GUSTO) and France (EDEN), we characterized lifestyle patterns of children and investigated their associations with family-focused contextual factors. Methods Ten behavioural variables related to child's diet, walking, outdoor play and screen time were ascertained by parental questionnaires at age 5-6 years. Using principal component analysis, sex-specific lifestyle patterns were derived independently for 630 GUSTO and 989 EDEN children. Contextual variables were organised into distal (family socio-economics, demographics), intermediate (parental health, lifestyle habits) and proximal (parent-child interaction factors) levels of influence and analysed with hierarchical linear regression. Results Three broadly similar lifestyle patterns were identified in both cohorts: "discretionary consumption and high screen time", "fruit, vegetables, and low screen time" and "high outdoor playtime and walking". The latter two patterns showed small differences between cohorts and sexes. The "discretionary consumption and high screen time" pattern was consistently similar in both cohorts; distal associated factors were lower maternal education (EDEN boys), no younger siblings (GUSTO boys) and Malay/Indian ethnicity (GUSTO), while intermediate and proximal associated factors in both cohorts and sexes were poor maternal diets during pregnancy, parents allowing high child control over food intake, snacking between meals and having television on while eating. Conclusions Three similar lifestyle patterns were observed among preschool children in Singapore and France. There were more common associated proximal factors than distal ones. Cohort specific family-focused contextual factors likely reflect differences in social and cultural settings. Findings will aid development of strategies to improve child health.Peer reviewe