Identifying Early-Life Behavior to Predict Mothering Ability in Swine Utilizing NUtrack System

Early recognition of indicator traits for swine reproduction and longevity supports economical selection decision making. Gilt activity is a key variable impacting a sow’s herd life and productivity. The purpose of this study was to examine early- life behaviors contributing to farrowing traits including gestation length (GL), number born alive (NBA), number weaned (NW), and herd life (HL). Herd life was a binary trait representing if a gilt was culled after one parity. Beginning at approximately 20 weeks of age, video recordings were taken on 480 gilts for 7 consecutive days and processed using the NUtrack system. Activity traits include angle rotated (degree), average speed (m/s), distance travelled (m), time spent eating (s), lying lateral (s), lying sternal (s), standing (s), and sitting (s). Final daily activity values were averaged across the period under cameras. Parity one data was collected for all gilts considered. Data were analyzed using linear regression models and odds ratios (R version 4.0.2). GL was significantly impacted by angle rotated (p = 0.03), average speed (p = 0.07), distance travelled (p = 0.05), time spent lying lateral (p = 0.003), and lying sternal (0.02). NBA was significantly impacted by time spent lying lateral (p = 0.01), lying sternal (p = 0.07), and time spent sitting (p = 0.08). NW was significantly impacted by time spent eating (p = 0.09), time spent lying lateral (p = 0.04), and time spent sitting (p = 0.007). Estimated odds ratios showed gilts traveling below average speeds and spending below average time lying sternal were positively associated with below average GL. Gilts spending below average time lying lateral are associated with below average NW. Gilts spending below average time sitting were negatively associated with below average NW. Gilts spending below average time lying sternal were negatively associated with below average HL. This analysis suggests early-life gilt behavior is associated with sow productivity traits of importance. Further examination of the link between behavior and reproductive traits is necessitated. Utilization of the NUtrack video monitoring system to isolate behavioral differences offers potential to aide in selection decisions. Advisor: Benny Mot

Leverage Points for Focus Flow and Communitas

Society is running at a high pace, and with it the hamster wheel we sometimes perceive ourselves to be in. In more scientific terms, this is called cognitive overload in combination with artificial deadline pressure. There is a notion of overwhelm in combination with perceived time scarcity in terms of the cognitive load of individuals. However, if we as individuals are not living in a sustainable way, how can we attempt to create a sustainable world?This paper provides an autoethnography of the use of leverage points to reduce cognitive load for a computer worker, with insights from literature and self-experiments, as well as a discussion on what is needed for changes on a bigger scale. An understanding of how cognitive load and resilience can be addressed by choosing and using specific leverage points has the potential to increase individual sustainability and resilience, what can be called focus flow, as well as communitas (group flow)

High-temperature oxygen non-stoichiometry, conductivity and structure in strontium-rich nickelates La2-xSrxNiO4-\delta (x = 1 and 1.4)

Oxygen nonstoichiometry, electrical conductivity and thermal expansion of La2 xSrxNiO4-\delta phases with high levels of strontium substitution (1 =< x =< 1.4) have been investigated in air and oxygen atmosphere in the temperature range 20-1050 degrees C. These phases retain the K2NiF4-type structure of La2NiO4 (tetragonal, space group I4/mmm). The oxygen vacancy fraction was determined independently from thermogravimetric and neutron diffraction experiments, and is found to increase considerably on heating. The electrical resistivity, thermal expansion and cell parameters with temperature show peculiar variations with temperature, and differ notably from La2NiO4$\pm$\delta in this respect. These variations are tentatively correlated with the evolution of nickel oxidation state, which crosses from a Ni3+/Ni4+ to a Ni2+/Ni3+ equilibrium on heating

Identifying Early-Life Behavior to Predict Mothering Ability in Swine Utilizing NU\u3ci\u3etrack\u3c/i\u3e System

Early indicator traits for swine reproduction and longevity support economical selection decision-making. Activity is a key variable impacting a sow’s herd life and productivity. Early-life activities could contribute to farrowing traits including gestation length (GL), number born alive (NBA), and number weaned (NW). Beginning at 20 weeks of age, 480 gilts were video recorded for 7 consecutive days and processed using the NUtrack system. Activity traits included angle rotated (radians), average speed (m/s), distance traveled (m), time spent eating (s), lying lateral (s), lying sternal (s), standing (s), and sitting (s). Final daily activity values were averaged across the period under cameras. Parity one data were collected for all gilts considered. Data were analyzed using linear regression models (R version 4.0.2). GL was significantly impacted by angle rotated (p = 0.03), average speed (p = 0.07), distance traveled (p = 0.05), time spent lying lateral (p = 0.003), and lying sternal (0.02). NBA was significantly impacted by time spent lying lateral (p = 0.01), lying sternal (p = 0.07), and time spent sitting (p = 0.08). NW was significantly impacted by time spent eating (p = 0.09), time spent lying lateral (p = 0.04), and time spent sitting (p = 0.007). This analysis suggests early-life gilt activities are associated with sow productivity traits of importance. Further examination of the link between behaviors compiled utilizing NUtrack and reproductive traits is necessitated to further isolate behavioral differences for potential use in selection decisions

Comparing citation numbers between articles at two stages of a Model Organism Database curation workflow

Model organism databases (MODs) facilitate the connections between published research papers with genes and other biological information. MODs aim to make research data easier to access to the research community, especially for researchers relying on genetic data and other information about a specific species. This paper follows previous research (Beradini, et al. 2016) that attempted to use quantitative data to determine if and how literature curated by a MOD makes a difference to the access and reuse of the curated data. The research addresses whether articles that have been through the detailed curation process of a MOD are more likely to be cited when compared to 'similar' articles that are not curated. For this research, citations for articles curated by FlyBase, a MOD for genetic and molecular data for the Drosophilidae insect family, were compared with articles identified as having similar genetic and molecular data, but not yet given a detailed curation by FlyBase. In addition, citation counts from a larger set of articles retrieved through a title and keyword search for Drosophilidae are also compared.GM is supported by the FlyBase NIH/NHGRI grant U41HG000739 (N. Perrimon, Harvard University, PI; N.H. Brown, University of Cambridge, coPI)

Building a pipeline to solicit expert knowledge from the community to aid gene summary curation.

Brief summaries describing the function of each gene's product(s) are of great value to the research community, especially when interpreting genome-wide studies that reveal changes to hundreds of genes. However, manually writing such summaries, even for a single species, is a daunting task; for example, the Drosophila melanogaster genome contains almost 14 000 protein-coding genes. One solution is to use computational methods to generate summaries, but this often fails to capture the key functions or express them eloquently. Here, we describe how we solicited help from the research community to generate manually written summaries of D. melanogaster gene function. Based on the data within the FlyBase database, we developed a computational pipeline to identify researchers who have worked extensively on each gene. We e-mailed these researchers to ask them to draft a brief summary of the main function(s) of the gene's product, which we edited for consistency to produce a 'gene snapshot'. This approach yielded 1800 gene snapshot submissions within a 3-month period. We discuss the general utility of this strategy for other databases that capture data from the research literature. Database URL: https://flybase.org/

Automatic categorization of diverse experimental information in the bioscience literature

Background: Curation of information from bioscience literature into biological knowledge databases is a crucial way of capturing experimental information in a computable form. During the biocuration process, a critical first step is to identify from all published literature the papers that contain results for a specific data type the curator is interested in annotating. This step normally requires curators to manually examine many papers to ascertain which few contain information of interest and thus, is usually time consuming. We developed an automatic method for identifying papers containing these curation data types among a large pool of published scientific papers based on the machine learning method Support Vector Machine (SVM). This classification system is completely automatic and can be readily applied to diverse experimental data types. It has been in use in production for automatic categorization of 10 different experimental datatypes in the biocuration process at WormBase for the past two years and it is in the process of being adopted in the biocuration process at FlyBase and the Saccharomyces Genome Database (SGD). We anticipate that this method can be readily adopted by various databases in the biocuration community and thereby greatly reducing time spent on an otherwise laborious and demanding task. We also developed a simple, readily automated procedure to utilize training papers of similar data types from different bodies of literature such as C. elegans and D. melanogaster to identify papers with any of these data types for a single database. This approach has great significance because for some data types, especially those of low occurrence, a single corpus often does not have enough training papers to achieve satisfactory performance. Results: We successfully tested the method on ten data types from WormBase, fifteen data types from FlyBase and three data types from Mouse Genomics Informatics (MGI). It is being used in the curation work flow at WormBase for automatic association of newly published papers with ten data types including RNAi, antibody, phenotype, gene regulation, mutant allele sequence, gene expression, gene product interaction, overexpression phenotype, gene interaction, and gene structure correction. Conclusions: Our methods are applicable to a variety of data types with training set containing several hundreds to a few thousand documents. It is completely automatic and, thus can be readily incorporated to different workflow at different literature-based databases. We believe that the work presented here can contribute greatly to the tremendous task of automating the important yet labor-intensive biocuration effort

Exploring confidence: entrepreneurial leadership in news media organisations

Leading a news media business has never been simple, but success in today’s increasingly turbulent and competitive environment requires entrepreneurial leadership distinct from other behavioural forms of leadership. This paper reflects on both entrepreneurship and leadership in order to develop a construct of entrepreneurial leadership in the context of the contemporary news media industry. Then, drawing on original data collected through the 21-question World Newsmedia Innovation Study conducted in 11 languages, it considers the relationship between the the firm’s entrepreneurial orientation and the perceived performance of the organisation’s leadership. Findings provide insights into how entrepreneurial leaders influence perceptions of organisational culture and future success. It also suggests that news media CEOs have work to do to gain the confidence of their staff, including their executive teams

FlyBase: enhancing Drosophila Gene Ontology annotations

FlyBase (http://flybase.org) is a database of Drosophila genetic and genomic information. Gene Ontology (GO) terms are used to describe three attributes of wild-type gene products: their molecular function, the biological processes in which they play a role, and their subcellular location. This article describes recent changes to the FlyBase GO annotation strategy that are improving the quality of the GO annotation data. Many of these changes stem from our participation in the GO Reference Genome Annotation Project—a multi-database collaboration producing comprehensive GO annotation sets for 12 diverse species