RawHummus: an R Shiny app for automated raw data quality control in metabolomics.

MOTIVATION: Robust and reproducible data is essential to ensure high-quality analytical results and is particularly important for large-scale metabolomics studies where detector sensitivity drifts, retention time and mass accuracy shifts frequently occur. Therefore, raw data need to be inspected before data processing to detect measurement bias and verify system consistency. RESULTS: Here, we present RawHummus, an R Shiny app for an automated raw data quality control (QC) in metabolomics studies. It produces a comprehensive QC report, which contains interactive plots and tables, summary statistics and detailed explanations. The versatility and limitations of RawHummus are tested with 13 metabolomics/lipidomics datasets and 1 proteomics dataset obtained from 5 different liquid chromatography mass spectrometry platforms. AVAILABILITY AND IMPLEMENTATION: RawHummus is released on CRAN repository (https://cran.r-project.org/web/packages/RawHummus), with source code being available on GitHub (https://github.com/YonghuiDong/RawHummus). The web application can be executed locally from the R console using the command 'runGui()'. Alternatively, it can be freely accessed at https://bcdd.shinyapps.io/RawHummus/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Saliva metabolome alterations after acute stress.

Major stress has systemic effects on the body that can have adverse consequences for physical and mental health. However, the molecular basis of these damaging effects remains incompletely understood. Here we use a longitudinal approach to characterise the acute systemic impact of major psychological stress in a pig model. We perform untargeted metabolomics on non-invasively obtained saliva samples from pigs before and 24 h after transfer to the novel physical and social environment of a slaughterhouse. The main molecular changes occurring include decreases in amino acids, B-vitamins, and amino acid-derived metabolites synthesized in B-vitamin-dependent reactions, as well as yet-unidentified metabolite features. Decreased levels of several of the identified metabolites are implicated in the pathology of human psychological disorders and neurodegenerative disease, suggesting a possible neuroprotective function. Our results provide a fingerprint of the acute effect of psychological stress on the metabolome and suggest candidate biomarkers with potential roles in stress-related disorders.

CCWeights: an R package and web application for automated evaluation and selection of weighting factors for accurate quantification using linear calibration curve.

Summary: The accuracy of any analytical method is highly dependent on the selection of an appropriate calibration model. Here, we present CCWeights, an R package for automated assessment and selection of weighting factors for accurate quantification using linear calibration curve. Additionally, CCWeights includes a web application that allows users to analyze their data using an interactive graphical user interface, without any programming requirements. The workflow and features of CCWeights are illustrated by the analyses of two datasets acquired by liquid chromatography-mass spectrometry (LC-MS). The resulting quantification table can be directly utilized for further model assessment and subsequent data analysis. Availability and implementation: CCWeights is publicly available on CRAN repository (https://cran.r-project.org/web/packages/CCWeights), with source code available on GitHub (https://github.com/YonghuiDong/CCWeights) under a GPL-3 license. The web application can be run locally from R console using a simple command "runGui()". Alternatively, the web application can be freely accessed for direct online use at https://bcdd.shinyapps.io/CCWeights/. Supplementary information: Supplementary data are available at Bioinformatics Advances online.

Short Term Safety, Immunogenicity, and Reproductive Effects of Combined Vaccination With Anti-GnRH (Gonacon) and Rabies Vaccines in Female Feral Cats.

Overpopulation of free-roaming cats is a major problem leading to negative impacts on animal health and welfare, public nuisance, transmission of zoonotic diseases, and well-documented harm to wildlife. Surgical sterilization had failed to provide a practical solution to free-roaming cats' overpopulation under field conditions; therefore, efficient and safe non-surgical immunocontraception methods are aspired. Rabies is a deadly virus that may infect people and animals. However, the safety and efficacy of combined vaccination with anti-GnRH and rabies vaccines in feral cats, which often suffer from disrupted health conditions and experienced high stress level, has never been studied. Therefore, our objective was to examine the short-term safety and efficacy of anti-GnRH vaccine (Gonacon), in combination with rabies vaccine in female feral cats. Mature feral female cats were captured and divided into the following groups: (I) GonaconX1-Rabies: queens vaccinated with both Gonacon and rabies (n = 5); (II) GonaconX2-Rabies: queens vaccinated twice with Gonacon (3 weeks apart) and with Rabies (n = 4); (III) OVx-Rabies: queens ovariohysterectomized and vaccinated with rabies (n = 4); (IV) Intact-Rabies: queens vaccinated against rabies and remained intact (n = 3). Comprehensive veterinary examinations and blood tests were performed every 2 weeks for 14 weeks. Data were analyzed by Repeated-Measures-ANOVA or Fisher-Exact-Test. There were neither systemic nor local adverse reactions at the vaccination sites. Blood count (PCV, TS, RBC, HGB, HCT, WBC) and chemistry (Total protein, Total globulin, Albumin, Urea, Creatinine, Creatine kinase, Bilirubin, GGT, ALT, AST) analyses revealed no differences among groups. There were no differences in serum rabies antibodies titers among groups, and queens kept a protective titer (>0.5 IU/mL) starting at 2-4 weeks after vaccination. Anti-GnRH antibodies were detected in all Gonacon-vaccinated queens, excluding one queen (GonaconX2-Rabies group). Anti-müllerian hormone serum concentrations reduced significantly after ovariohysterectomy, as well as gradually following vaccination with Gonacon, but it remained high in intact queens. Evaluation of vaginal cytology and ovarian histology suggested that reproductive cyclicity was suppressed in Gonacon-vaccinated queens. Our results support the conclusion that in the short term, the combined vaccination with Gonacon and rabies is safe and effective in female feral cats. However, further long-term studies are warranted to test this immunologic regimen in feral cats.

Providing Meaningful Environmental Enrichment and Measuring Saliva Cortisol in Pigs Housed on Slatted Flooring.

As pork is the most consumed meat worldwide, the welfare of animals in the swine industry has increasingly become a major public concern, which imposes a substantial pressure coming from customers, legislators and other stakeholders, to make management changes to improve the well-being of these animals. Several studies have demonstrated that providing environmental enrichment to pigs allows them to express their natural behavior, such as rooting and exploring, as well as nesting prior to farrowing, and is associated with reduced stress and improved production and welfare. However, many considerations should be taken into account when providing environmental enrichment, such as the type of floor, drainage and sewage systems, the pigs' stage in life, the material, as well as its hanging method, height and location within the pen. The objectives of this paper are (1) to give methodologic information on how to provide a relatively simple and practical meaningful environmental enrichment for pigs which are housed on slatted floors during the different stages of their life, and (2) to demonstrate how to collect saliva samples for the measurement of cortisol concentrations, as a biomarker for acute stress. Protocols include information regarding the use of jute, cotton ropes, straw in racks, as well as chewable silicone sticks devices as environmental enrichment in pens of farrowing and lactation, weaners and finishers. In addition, the use of cotton rope for a non-invasive saliva samples collection for cortisol concentrations analysis is detailed. The protocols provided are relevant for professionals aiming to improve and monitor animal welfare, in both research and industrial swine farming.

Physiological and economic benefits of abandoning invasive surgical procedures and enhancing animal welfare in swine production.

Food-animal welfare is a major ethical and social concern. Pork is the most consumed meat worldwide, with over a billion pigs slaughtered annually. Most of these pigs routinely undergo painful surgical procedures (surgical castration, tail docking, teeth clipping), which farmers often reluctant to avoid, claiming it would increase cost and reduce production efficiency. Herein, this study indicates that these procedures compromise pigs' health and condition. Replacing surgical castration with immunocastration, avoiding tail docking and teeth clipping, and providing environmental enrichment, resulted in significant increase in weight gain, lowered risks for injuries and death, and reduced saliva and hair cortisol, both biomarkers for stress. Testosterone and DHEA analyses confirmed that immunocastration was an effective alternative to surgical castration. Economic models for the entire US swine market revealed that following across-the-board acceptance of this management, pork meat price is expected to drop, while the total annual social welfare (combined consumer and producer surplus) is expected to increase by $US 1.48 to 1.92 billion. In conclusion, sustainable swine farming management can be beneficial for both animals and farmers. Applying such welfare-friendly management is expected to reduce stress, enhance piglet/pig welfare and production, and improve the economics of swine operations in the global agro-food system.

Effects of group housing on reproductive performance, lameness, injuries and saliva cortisol in gestating sows.

In many countries sows are kept in individual stalls from insemination up to just few days prior to farrowing. The overall objective of this study was to examine group housing management system for sows during gestation as an alternative for individual confinement stalls, and the possible effects on their welfare, production and reproduction performances. Accordingly, the study included three specific objectives: (1) to compare parameters of production, reproduction, and welfare of sows housed in groups (either 30 or 7 sows/group; Large Group: LG, Small Group: SG, respectively) during gestation as compared to individual confinement stalls (IS); (2) to compare saliva cortisol of pregnant sows throughout gestation, when housed in groups of three different sizes (either 7, 15 or 30 sows per pen group); and (3) to compare sows' production and reproduction performances at the herd level, before, during and after practically transforming from a management of individual confinement stalls to a group housing system, in a large commercial swine farm over a six-year period. Mean cycle length (weaning-to-weaning) was shorter in group housing management as compared to individual stalls (P = 0.0110), but gestation length did not differ among the three groups. Overall farrowing rate (sows farrowed out of those inseminated) was higher (P ≤ 0.0134) for sows housed in groups (either SG or LG). Furthermore, there was a tendency towards a higher number of total born (P = 0.1033), and born alive piglets (P = 0.0862), in group housing system as compared to individual housing management; however, it did not differ between the LG and SG groups. Injuries and lameness index (ILI) of sows improved significantly over the gestation period in group housing management. Group saliva cortisol during gestation did not differ significantly among groups of 7, 15, or 30 sows, except on the first saliva sampling, just after sows were mixed into groups, where cortisol level was significantly higher in sows housed in a pen of 30 sows. Production and reproduction performances at the herd level, over a 6-years period- before, during and after transforming to a group housing system, improved significantly: shortened cycle length, increased farrowing rate, and increased number of total born and born alive piglets. In conclusion, group housing management during gestation was associated with better reproduction, productivity and welfare of sows, as compared to individual stalls. A welfare friendly housing system can be beneficial and effective for both the farmers and the animals.