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[This corrects the article DOI: 10.1371/journal.pone.0309964.].

Global food production needs to increase in order to meet the demands of an ever growing global population. As resources are finite, the most feasible way to meet this demand is to minimize losses and improve efficiency. Regular monitoring of factors like animal health, soil and water quality for example, can ensure that the resources are being used to their maximum efficiency. Existing monitoring techniques however have limitations, such as portability, turnaround time and requirement for additional reagents. In this work, we explore the use of micro- and nano-scale electrode devices, for the development of an electrochemical sensing platform to digitalize a wide range of applications within the agri-food sector. With this platform, we demonstrate the direct electrochemical detection of pesticides, specifically clothianidin and imidacloprid, with detection limits of 0.22 ng/mL and 2.14 ng/mL respectively, and nitrates with a detection limit of 0.2 µM. In addition, interdigitated electrode structures also enable an in-situ pH control technique to mitigate pH as an interference and modify analyte response. This technique is applied to the analysis of monochloramine, a common water disinfectant. Concerning biosensing, the sensors are modified with bio-molecular probes for the detection of both bovine viral diarrhea virus species and antibodies, over a range of 1 ng/mL to 10 µg/mL. Finally, a portable analogue front end electronic reader is developed to allow portable sensing, with control and readout undertaken using a smart phone application. Finally, the sensor chip platform is integrated with these electronics to provide a fully functional end-to-end smart sensor system compatible with emerging Agri-Food digital decision support tools.

Cattle vary in their susceptibility to infection and immunopathology, but our ability to measure and longitudinally profile immune response variation is limited by the lack of standardized immune phenotyping assays for high-throughput analysis. Here we report longitudinal innate immune response profiles in cattle using a low-blood volume, whole blood stimulation system—the ImmunoChek (IChek) assay. By minimizing cell manipulation, our standardized system minimizes the potential for artefactual results and enables repeatable temporal comparative analysis in cattle. IChek successfully captured biological variation in innate cytokine (IL-1β and IL-6) and chemokine (IL-8) responses to 24-hr stimulation with either Gram-negative (LPS), Gram-positive (PamCSK4) bacterial or viral (R848) pathogen-associated molecular patterns (PAMPs) across a 4-month time window. Significant and repeatable patterns of inter-individual variation in cytokine and chemokine responses, as well as consistent high innate immune responder individuals were identified at both baseline and induced levels. Correlation coefficients between immune response read-outs (IL-1β, IL-6 and IL-8) varied according to PAMP. Strong significant positive correlations were observed between circulating monocytes and IL-6 levels for null and induced responses (0.49–0.61) and between neutrophils and cytokine responses to R848 (0.38–0.47). The standardized assay facilitates high-throughput bovine innate immune response profiling to identify phenotypes associated with disease susceptibility and responses to vaccination.

Neonatal calf diarrhea (NCD) is a major problem to calf health worldwide, in terms of both morbidity and mortality. A five-point ordinal scale clinical assessment scoring (CAS) chart was utilized to assess calves suffering from NCD-related clinical abnormalities (acidosis and dehydration) on commercial farms. The objective of this research was to determine the predictive capability of this CAS chart against gold standard blood gas parameters, designed to assist farmers in the accurate assessment of the clinical consequences of NCD. A total of 443 diarrheic and non-diarrheic calves were enrolled in the study. The CAS chart rated a calf's health from no clinical signs to varying degrees of clinical severity on a 0 (clinically normal) to 4 (grave) scale, based on clinical indicators including calf demeanour, ear position, mobility, suckle reflex, desire-to-feed, and enophthalmos. Blood gas analysis was conducted for individual calves, consisting of pH, base excess, Na+, K+, Ca2+, Cl-, glucose, total hemoglobin, bicarbonate, anion gap, and strong ion difference. Statistical evaluation was performed by comparison of the CAS score with blood gas profiles using ordinal logistic regression and a non-parametric estimation of the Receiver Operating Characteristics (ROC). The ROC analysis indicated that the CAS chart had acceptable specificity (>95%) with low sensitivity (<60%) in differentiating clinically normal from acidotic/dehydrated cases. Assessment of individual severity classes indicated that the chart can predict and differentiate both clinically normal and advanced cases from the other severity classes (peak estimations >80%) but had reduced accuracy in differentiating mild and moderate cases (peak estimations >50%). The chart, as presented, provides a simple tool to differentiate clinically normal from calves suffering the consequences of diarrhea, but fails to accurately differentiate severity for NCD related acidosis and dehydration. Further efforts are required to enhance the sensitivity and differential diagnostic value of this type of chart.

Background The threat of antimicrobial resistance is triggering the need for behavioural change towards antimicrobial use on Irish farms. Newly introduced veterinary medicine regulations are mandating the restricted and more prudent use of antimicrobials in the animal health sector. The need to reduce antimicrobials has placed a greater emphasis on the importance of animal health testing, however, issues with current testing practices are affecting diagnosis and subsequent drug usage. There is potential for digital technologies to address these issues and reduce antimicrobial use on farms, however, for these tools to be successful, they would need to be developed in collaboration with future end users. Results Using qualitative approaches (focus groups), this study engages with dairy farmers and farm veterinary practitioners to detail current challenges with animal health diagnosis and to explore the initial development of a rapid, on-farm animal health testing tool to address these challenges. Issues with timing and testing, the role of knowledge and experience, and veterinarian availability all affect the ability of farmers and veterinarians to diagnose animal health issues on farm. These issues are having negative implications including the increased and unnecessary use of antimicrobials. An on-farm testing tool would help mitigate these effects by allowing veterinarians to achieve rapid diagnosis, facilitating the timely and targeted treatment of animal illnesses, helping to reduce overall antimicrobial use on farms. However, engagement with end users has highlighted that if a tool like this is not developed correctly, it could have unintended negative consequences such as misdiagnosis, increased antimicrobial use, challenges to farmer-veterinarian relationships, and data misuse. This study outlines initial end user needs and requirements for a testing tool but suggests that in order to successfully design and develop this tool, co-design approaches such as Design Thinking should be applied; to mitigate future negative impacts, and to ensure a testing tool like this is designed specifically to address Irish dairy farmers and farm veterinarians’ values and needs, ensuring responsible and successful uptake and use. Conclusions Digital tools can be effective in reducing antimicrobial use on farms, however, to be successful, these tools should be designed in a user centred way.

Bovine respiratory disease (BRD) is a leading cause of mortality and compromised welfare in bovines. It is a polymicrobial syndrome resulting from a complex interplay of viral and bacterial pathogens with environmental factors. Despite the availability of vaccines, incidence and severity in young calves remains unabated. A more precise analysis of host innate immune responses during infection will identify improved diagnostic and prognostic biomarkers for early intervention and targeted treatments to prevent severe disease and loss of production efficiency. Here, we investigate hematological and innate immune responses using standardized ex-vivo whole blood assays in calves diagnosed with BRD. A total of 65 calves were recruited for this study, all between 2–8 weeks of age with 28 diagnosed with BRD by a thoracic ultrasonography score (TUS) and 19 by Wisconsin health score (WHS) and all data compared to 22 healthy controls from the same 9 study farms. Haematology revealed circulating immune cell populations were similar in both TUS positive and WHS positive calves compared to healthy controls. Gene expression analysis of 48 innate immune signalling genes in whole blood stimulated with TLR ligands was completed in a subset of calves. TLR1/2 stimulation with Pam3CSK4 showed a decreased pattern of expression in IL-1 and inflammasome related genes in addition to chemokine genes in calves with BRD. In response to TLR ligands LPS, Pam3CSK4 and R848, protein analysis of supernatant collected from all calves with BRD revealed significantly increased IL-6, but not IL-1β or IL-8, compared to healthy controls. This hyper-induction of IL-6 was observed most significantly in response to TLR1/2 stimulation in TUS positive calves. ROC analysis identified this induced IL-6 response to TLR1/2 stimulation as a potential diagnostic for BRD with a 74% true positive and 5% false positive detection rate for an IL-6 concentration >1780pg/mL. Overall, these results show altered immune responses specifically upon TLR1/2 activation is associated with BRD pathology which may contribute to disease progression. We have also identified induced IL-6 as a potentially informative biomarker for improved early intervention strategies for BRD.

Sensor technologies that measure grazing and ruminating behaviour as well as physical activities of individual cows are intended to be included in precision pasture management. One of the advantages of sensor data is they can be analysed to support farmers in many decision-making processes. This article thus considers the performance of a set of RumiWatchSystem recorded variables in the prediction of insufficient herbage allowance for spring calving dairy cows. Several commonly used models in machine learning (ML) were applied to the binary classification problem, i.e., sufficient or insufficient herbage allowance, and the predictive performance was compared based on the classification evaluation metrics. Most of the ML models and generalised linear model (GLM) performed similarly in leave-out-one-animal (LOOA) approach to validation studies. However, cross validation (CV) studies, where a portion of features in the test and training data resulted from the same cows, revealed that support vector machine (SVM), random forest (RF) and extreme gradient boosting (XGBoost) performed relatively better than other candidate models. In general, these ML models attained 88% AUC (area under receiver operating characteristic curve) and around 80% sensitivity, specificity, accuracy, precision and F-score. This study further identified that number of rumination chews per day and grazing bites per minute were the most important predictors and examined the marginal effects of the variables on model prediction towards a decision support system.

Vitamin D deficiency at birth, followed by prolonged insufficiency in early life may predispose bovine calves to infection and disease. However, the effects of vitamin D levels on innate immunity are unclear due to the lack of long-term supplementation trials in vivo and reliable approaches for reproducibly assessing immune function. Here, a standardized whole blood immunophenotyping assay was used to compare innate immune responses to infection relevant ligands (LPS, Pam3CSK4 and R848) between Holstein–Friesian calves supplemented with vitamin D (n = 12) from birth until 7 months of age and control calves (n = 10) raised on an industry standard diet. Transcriptomic analysis in unstimulated whole blood cells revealed increased expression of type I interferons and chemokines in vitamin D supplemented calves, while IL-1 and inflammasome gene expression was decreased. In response to stimulation with the bacterial ligand LPS, supplemented calves had significantly increased expression of CASP1 , CX3CR1 , CAT , whereas STAT1 was decreased . Stimulation with the bacterial ligand Pam3CSK4 revealed increased expression of IL1A , IL1B and CAT genes; and decreased C5AR1 expression. In response to the viral ligand R848, STAT1 and S100A8 expression was significantly decreased. An increased IL-1 and inflammasome gene expression signature in vitamin D supplemented calves in response to LPS and Pam3CSK4 was also found, with ELISA confirming increased IL-1β protein production. In contrast, a decreased chemokine gene expression signature was found in response to R848 in supplemented animals, with decreased IL-8 protein expression exhibited in response to all PAMPs also found. These results demonstrated expression of several cytokine, chemokine and inflammasome genes were impacted by vitamin D supplementation in the first 7 months of life, with IL-8 expression particularly responsive to vitamin D. Overall, vitamin D supplementation induced differential innate immune responses of blood immune cells that could have important implications for disease susceptibility in cattle.

It is unknown whether calf rearing facilities in the Republic of Ireland are fit for purpose, or if facilities sufficiently consider calf and farmer welfare. The aim of this study was to review current calf housing facilities and management practices on Irish farms to determine if calves are reared in structurally appropriate facilities with management decisions that safeguard calf and farmer welfare. Fifty-one farms located in the Munster region in the Republic of Ireland were visited twice: (1) Pre-calving (December–January) and (2) During peak calving (January–March). During visit one, herd owners completed a questionnaire regarding calf housing and management practices on-farm and each facility used to rear calves was measured (measurement of cubic air capacity, ventilation, pen area, drainage etc.) without calves being present. Visit two consisted of a short interview with the principal calf manager to validate previously asked questions and environmental based measurements of each calf house that had been recorded, with any deviation from the first visit noted (measurements of temperature, wind speed, light intensity, facility provisions in-house and in-pen; calves present). Average herd size was 254, operating a spring calving system with a median calving season length of 11.6 weeks. While most farms expanded (88%; N = 51), this did not appear to have negatively affected calf space allowances (9.9% houses overcrowded at a space allowance of 1.5 m2/calf; N = 121). Calves were most commonly housed in group sizes of <12 (71.6% of all groupings; N = 394), with farmers moving away from individual housing for a period immediately post-birth, to grouping them immediately instead (58.8%; N = 51). The number of farmers testing colostrum was 31.4% (N = 51). Although the calving season was compact, most farmers were unconcerned about the upcoming spring workload (58.8%; N = 51). Farms appeared sufficiently prepared for spring, with most using the same number or less sheds during visit two than declared in visit one (76.5%; N = 51). To conclude, farmers made sufficient provision for calf housing and space allowances for calves that facilitated group housing post-birth. While structural and management components of rearing systems appear in line with sectoral recommendations, certain areas require attention on many farms (e.g., colostrum testing) to safeguard calf welfare and reduce the workload associated with calf rearing for farmers.

Despite the fact that pneumonia remains a leading cause of mortality and morbidity in pre-weaned calves, relatively little is known regarding the effects of the concurrent administration of intranasal pneumonia virus vaccines, particularly in calves with high levels of maternally derived antibodies. The objective of this study was to use a cohort of 40 dairy and dairy-beef female and male calves (27 females and 13 males) to determine serological responses to concurrent administration at 3 weeks of age (22 ± 4.85 days) of two commercially available intranasal (IN) vaccines for the viruses: bovine respiratory syncytial virus (BRSV), bovine herpes virus 1 (BoHV-1), and parainfluenza-3-virus (PI3-V). The study groups were as follows: (i) Bovilis IBR Marker Live only® (IO), (ii) Bovilis INtranasal RSP Live® only (RPO), (iii) Concurrent vaccination with Bovilis IBR Marker Live® & Bovilis Intranasal RSP Live® (CV), and (iv) a control group of non-vaccinated calves (CONT). The calves’ serological response post-IN vaccination, clinical health scores, rectal temperatures, and weights were measured. Data were analyzed in SAS using mixed models and logistic regression. The CV calves had an average daily weight gain (ADG) of 0.74 (±0.02) kg, which was similar to CONT (0.77 ± 0.02 kg). Despite no significant differences in the antibody levels between study groups 3 weeks post-IN vaccination, following the administration of subsequent parenteral injections in the form of Bovilis Bovipast RSP®(antigens; inactivated BRSV, inactivated PI3-V, inactivated Mannheimia haemolytica ) and Bovilis IBR Marker Live®, the antibody levels of the BRSV and PI3-V increased in both the CV and RPO study groups. Concurrent vaccination resulted in no increase in fever and no difference in health scores when compared to CONT.