Estimating household contact matrices structure from easily collectable metadata.

Contact matrices are a commonly adopted data representation, used to develop compartmental models for epidemic spreading, accounting for the contact heterogeneities across age groups. Their estimation, however, is generally time and effort consuming and model-driven strategies to quantify the contacts are often needed. In this article we focus on household contact matrices, describing the contacts among the members of a family and develop a parametric model to describe them. This model combines demographic and easily quantifiable survey-based data and is tested on high resolution proximity data collected in two sites in South Africa. Given its simplicity and interpretability, we expect our method to be easily applied to other contexts as well and we identify relevant questions that need to be addressed during the data collection procedure.

Former foodstuffs in feed: a minireview of recent findings.

The sustainability of all productive activities, including livestock farming, becomes a fundamental challenge in the current scenario. Livestock production faces both old and new challenges related to climate change, food safety, and feed-food competition. The latter aspect has recently become a hot topic, and many researchers are turning their attention to this issue. According to circular economy principles, former foodstuffs have characteristics that make them a promising source of raw material for animal feed. The main objective of the present review is to provide a brief overview of the most recent studies (published between 2016 and 2022) addressing the dietary inclusion of former foodstuffs for livestock. The articles analyzed cover key findings from both in vitro and in vivo studies of former foodstuffs included in the diets for pigs, cows, and broilers, and assess the associated safety aspects. The articles provide information on livestock performances and product quality, as well as feed digestibility, fecal microbiota, and blood analysis. Although the evidence supports the inclusion of former foodstuffs in livestock diets as a safe, effective, and sustainable ingredient, this analysis of the most recent literature also highlights gaps in our knowledge that need to be filled. The present overview will help researchers plan future research and standardize and promote the inclusion of former food products in livestock diets.

A Literature Review of Modeling Approaches Applied to Data Collected in Automatic Milking Systems.

Automatic milking systems (AMS) have played a pioneering role in the advancement of Precision Livestock Farming, revolutionizing the dairy farming industry on a global scale. This review specifically targets papers that focus on the use of modeling approaches within the context of AMS. We conducted a thorough review of 60 articles that specifically address the topics of cows' health, production, and behavior/management Machine Learning (ML) emerged as the most widely used method, being present in 63% of the studies, followed by statistical analysis (14%), fuzzy algorithms (9%), deterministic models (7%), and detection algorithms (7%). A significant majority of the reviewed studies (82%) primarily focused on the detection of cows' health, with a specific emphasis on mastitis, while only 11% evaluated milk production. Accurate forecasting of dairy cow milk yield and understanding the deviation between expected and observed milk yields of individual cows can offer significant benefits in dairy cow management. Likewise, the study of cows' behavior and herd management in AMSs is under-explored (7%). Despite the growing utilization of machine learning (ML) techniques in the field of dairy cow management, there remains a lack of a robust methodology for their application. Specifically, we found a substantial disparity in adequately balancing the positive and negative classes within health prediction models.

The "Second Life" of laboratory rats (Rattus norvegicus): Assessment of social behavior of a colony of rats based on social network analysis.

Rattus norvegicus is a social animal and holds a significant economic value, considering its use in scientific research. Here, we use the Social Network Analysis (SNA) approach to study the social interactions of a group of rats held in a post-laboratory animal care facility. We collected interaction data during four study periods, for a total of 60 days. At the group level, rats presented two communities for each study period, consisting mainly of littermates. At individual level, we found that the rats preferred to interact with individuals of the same strain and laboratory of origin and with littermates. At temporal level, we studied how stable social interactions were over time. During the first study period, we found high social stability, whereas the introduction of new individuals in the subsequent period caused social rearrangements; however, the initial social stability was restored. Our findings have shown that studying the social behavior of rats using SNA is a valuable tool for advancing our understanding of the social system of this species, which has the potential to enhance management and welfare practices.

Social behaviour and transmission of lameness in a flock of ewes and lambs.

Introduction: Sheep have heterogenous social connections that influence transmission of some infectious diseases. Footrot is one of the top five globally important diseases of sheep, it is caused by Dichelobacter nodosus and transmits between sheep when infectious feet contaminate surfaces, e.g., pasture. Surfaces remain infectious for a few minutes to a few days, depending on surface moisture levels. Susceptible sheep in close social contact with infectious sheep might be at risk of becoming infected because they are likely to step onto infectious footprints, particularly dams and lambs, as they cluster together. Methods: High resolution proximity sensors were deployed on 40 ewes and their 54 lambs aged 5-27 days, in a flock with endemic footrot in Devon, UK for 13 days. Sheep locomotion was scored daily by using a 0-6 integer scale. Sheep were defined lame when their locomotion score (LS) was ≥2, and a case of lameness was defined as LS ≥2 for ≥2 days. Results: Thirty-two sheep (19 ewes, 9 single, and 4 twin lambs) became lame during the study, while 14 (5 ewes, 5 single, and 4 twin lambs) were lame initially. These 46 sheep were from 29 family groups, 14 families had >1 lame sheep, and transmission from ewes to lambs was bidirectional. At least 15% of new cases of footrot were from within family transmission; the occurrence of lameness was higher in single than twin lambs. At least 4% of transmission was due to close contact across the flock. Most close contact occurred within families. Single and twin lambs spent 1.5 and 0.9 hours/day with their dams, respectively, and twin lambs spent 3.7 hours/day together. Non-family sheep spent only 0.03 hours/day in contact. Lame single lambs and ewes spent less time with non-family sheep, and lame twin lambs spent less time with family sheep. Discussion: We conclude that most transmission of lameness is not attributable to close contact. However, in ewes with young lambs, some transmission occurs within families and is likely due to time spent in close contact, since single lambs spent more time with their dam than twin lambs and were more likely to become lame.

Seasonal fishery facilitates a novel transmission pathway in an emerging animal reservoir of Guinea worm.

Exploitation of natural resources is a driver of human infectious disease emergence. The emergence of animal reservoirs of Guinea worm Dracunculus medinensis, particularly in domestic dogs Canis familiaris, has become the major impediment to global eradication of this human disease. 93% of all Guinea worms detected worldwide in 2020 were in dogs in Chad. Novel, non-classical pathways for transmission of Guinea worm in dogs, involving consumption of fish, have been hypothesized to support the maintenance of this animal reservoir. We quantified and analyzed variation in Guinea worm emergence in dogs in Chad, across three climatic seasons, in multiple villages and districts. We applied forensic stable isotope analyses to quantify dietary variation within and among dogs and GPS tracking to characterize their spatial ecology. At the end of the hot-dry season and beginning of the wet season, when fishing by people is most intensive, Guinea worm emergence rates in dogs were highest, dogs ate most fish, and fish consumption was most closely associated with disease. Consumption of fish by dogs enables a non-classical transmission pathway for Guinea worm in Chad. Seasonal fisheries and the facilitation of dogs eating fish are likely contributing to disease persistence and to this key impediment to human disease eradication. Interrelated natural resource use, climatic variation, companion animal ecology, and human health highlight the indispensability of One Health approaches to the challenges of eradicating Guinea worm and other zoonotic diseases.

Spatial and temporal variation in proximity networks of commercial dairy cattle in Great Britain.

The nature of contacts between hosts can be important in facilitating or impeding the spread of pathogens within a population. Networks constructed from contacts between hosts allow examination of how individual variation might influence the spread of infections. Studying the contact networks of livestock species managed under different conditions can additionally provide insight into their influence on these contact structures. We collected high-resolution proximity and GPS location data from nine groups of domestic cattle (mean group size = 85) in seven dairy herds employing a range of grazing and housing regimes. Networks were constructed from cattle contacts (defined by proximity) aggregated by different temporal windows (2 h, 24 h, and approximately 1 week) and by location within the farm. Networks of contacts aggregated over the whole study were highly saturated but dividing contacts by space and time revealed substantial variation in cattle interactions. Cows showed statistically significant variation in the frequency of their contacts and in the number of cows with which they were in contact. When cows were in buildings, compared to being on pasture, contact durations were longer and cows contacted more other cows. A small number of cows showed evidence of consistent relationships but the majority of cattle did not. In one group where management allowed free access to all farm areas, cows showed asynchronous space use and, while at pasture, contacted fewer other cows and showed substantially greater between-individual variation in contacts than other groups. We highlight the degree to which variations in management (e.g. grazing access, milking routine) substantially alter cattle contact patterns, with potentially major implications for infection transmission and social interactions. In particular, where individual cows have free choice of their environment, the resulting contact networks may have a less-risky structure that could reduce the likelihood of direct transmission of infections.

Combining Wearable Devices and Mobile Surveys to Study Child and Youth Development in Malawi: Implementation Study of a Multimodal Approach.

BACKGROUND: Multimodal approaches have been shown to be a promising way to collect data on child development at high frequency, combining different data inputs (from phone surveys to signals from noninvasive biomarkers) to understand children's health and development outcomes more integrally from multiple perspectives. OBJECTIVE: The aim of this work was to describe an implementation study using a multimodal approach combining noninvasive biomarkers, social contact patterns, mobile surveying, and face-to-face interviews in order to validate technologies that help us better understand child development in poor countries at a high frequency. METHODS: We carried out a mixed study based on a transversal descriptive analysis and a longitudinal prospective analysis in Malawi. In each village, children were sampled to participate in weekly sessions in which data signals were collected through wearable devices (electrocardiography [ECG] hand pads and electroencephalography [EEG] headbands). Additionally, wearable proximity sensors to elicit the social network were deployed among children and their caregivers. Mobile surveys using interactive voice response calls were also used as an additional layer of data collection. An end-line face-to-face survey was conducted at the end of the study. RESULTS: During the implementation, 82 EEG/ECG data entry points were collected across four villages. The sampled children for EEG/ECG were 0 to 5 years old. EEG/ECG data were collected once a week. In every session, children wore the EEG headband for 5 minutes and the ECG hand pad for 3 minutes. In total, 3531 calls were sent over 5 weeks, with 2291 participants picking up the calls and 984 of those answering the consent question. In total, 585 people completed the surveys over the course of 5 weeks. CONCLUSIONS: This study achieved its objective of demonstrating the feasibility of generating data through the unprecedented use of a multimodal approach for tracking child development in Malawi, which is one of the poorest countries in the world. Above and beyond its multiple dimensions, the dynamics of child development are complex. It is the case not only that no data stream in isolation can accurately characterize it, but also that even if combined, infrequent data might miss critical inflection points and interactions between different conditions and behaviors. In turn, combining different modes at a sufficiently high frequency allows researchers to make progress by considering contact patterns, reported symptoms and behaviors, and critical biomarkers all at once. This application showcases that even in developing countries facing multiple constraints, complementary technologies can leverage and accelerate the digitalization of health, bringing benefits to populations that lack new tools for understanding child well-being and development.

High-resolution contact networks of free-ranging domestic dogs Canis familiaris and implications for transmission of infection.

Contact patterns strongly influence the dynamics of disease transmission in both human and non-human animal populations. Domestic dogs Canis familiaris are a social species and are a reservoir for several zoonotic infections, yet few studies have empirically determined contact patterns within dog populations. Using high-resolution proximity logging technology, we characterised the contact networks of free-ranging domestic dogs from two settlements (n = 108 dogs, covering >80% of the population in each settlement) in rural Chad. We used these data to simulate the transmission of an infection comparable to rabies and investigated the effects of including observed contact heterogeneities on epidemic outcomes. We found that dog contact networks displayed considerable heterogeneity, particularly in the duration of contacts and that the network had communities that were highly correlated with household membership. Simulations using observed contact networks had smaller epidemic sizes than those that assumed random mixing, demonstrating the unsuitability of homogenous mixing models in predicting epidemic outcomes. When contact heterogeneities were included in simulations, the network position of the individual initially infected had an important effect on epidemic outcomes. The risk of an epidemic occurring was best predicted by the initially infected individual's ranked degree, while epidemic size was best predicted by the individual's ranked eigenvector centrality. For dogs in one settlement, we found that ranked eigenvector centrality was correlated with range size. Our results demonstrate that observed heterogeneities in contacts are important for the prediction of epidemiological outcomes in free-ranging domestic dogs. We show that individuals presenting a higher risk for disease transmission can be identified by their network position and provide evidence that observable traits hold potential for informing targeted disease management strategies.

Wearable Proximity Sensors for Monitoring a Mass Casualty Incident Exercise: Feasibility Study.

BACKGROUND: Over the past several decades, naturally occurring and man-made mass casualty incidents (MCIs) have increased in frequency and number worldwide. To test the impact of such events on medical resources, simulations can provide a safe, controlled setting while replicating the chaotic environment typical of an actual disaster. A standardized method to collect and analyze data from mass casualty exercises is needed to assess preparedness and performance of the health care staff involved. OBJECTIVE: In this study, we aimed to assess the feasibility of using wearable proximity sensors to measure proximity events during an MCI simulation. In the first instance, our objective was to demonstrate how proximity sensors can collect spatial and temporal information about the interactions between medical staff and patients during an MCI exercise in a quasi-autonomous way. In addition, we assessed how the deployment of this technology could help improve future simulations by analyzing the flow of patients in the hospital. METHODS: Data were obtained and collected through the deployment of wearable proximity sensors during an MCI functional exercise. The scenario included 2 areas: the accident site and the Advanced Medical Post, and the exercise lasted 3 hours. A total of 238 participants were involved in the exercise and classified in categories according to their role: 14 medical doctors, 16 nurses, 134 victims, 47 Emergency Medical Services staff members, and 27 health care assistants and other hospital support staff. Each victim was assigned a score related to the severity of his/her injury. Each participant wore a proximity sensor, and in addition, 30 fixed devices were placed in the field hospital. RESULTS: The contact networks show a heterogeneous distribution of the cumulative time spent in proximity by the participants. We obtained contact matrices based on the cumulative time spent in proximity between the victims and rescuers. Our results showed that the time spent in proximity by the health care teams with the victims is related to the severity of the patient's injury. The analysis of patients' flow showed that the presence of patients in the rooms of the hospital is consistent with the triage code and diagnosis, and no obvious bottlenecks were found. CONCLUSIONS: Our study shows the feasibility of the use of wearable sensors for tracking close contacts among individuals during an MCI simulation. It represents, to our knowledge, the first example of unsupervised data collection-ie, without the need for the involvement of observers, which could compromise the realism of the exercise-of face-to-face contacts during an MCI exercise. Moreover, by permitting detailed data collection about the simulation, such as data related to the flow of patients in the hospital, such deployment provides highly relevant input for the improvement of MCI resource allocation and management.

Close encounters between infants and household members measured through wearable proximity sensors.

Describing and understanding close proximity interactions between infant and family members can provide key information on transmission opportunities of respiratory infections within households. Among respiratory infections, pertussis represents a public health priority. Pertussis infection can be particularly harmful to young, unvaccinated infants and for these patients, family members represent the main sources of transmission. Here, we report on the use of wearable proximity sensors based on RFID technology to measure face-to-face proximity between family members within 16 households with infants younger than 6 months for 2-5 consecutive days of data collection. The sensors were deployed over the course of approximately 1 year, in the context of a national research project aimed at the improvement of infant pertussis prevention strategies. We investigated differences in close-range interactions between family members and we assessed whether demographic variables or feeding practices affect contact patterns between parents and infants. A total of 5,958 contact events were recorded between 55 individuals: 16 infants, 4 siblings, 31 parents and 4 grandparents. The aggregated contact networks, obtained for each household, showed a heterogeneous distribution of the cumulative time spent in proximity with the infant by family members. Contact matrices defined by age and by family role showed that most of the contacts occurred between the infant and other family members (70%), while 30% of contacts was among family members (infants excluded). Many contacts were observed between infants and adults, in particular between infant and mother, followed by father, siblings and grandparents. A larger number of contacts and longer contact durations between infant and other family members were observed in families adopting exclusive breastfeeding, compared to families in which the infant receives artificial or mixed feeding. Our results demonstrate how a high-resolution measurement of contact matrices within infants' households is feasible using wearable proximity sensing devices. Moreover, our findings suggest the mother is responsible for the large majority of the infant's contact pattern, thus being the main potential source of infection for a transmissible disease. As the contribution to the infants' contact pattern by other family members is very variable, vaccination against pertussis during pregnancy is probably the best strategy to protect young, unvaccinated infants.

Pond use by captive African penguins (Spheniscus demersus) in an immersive exhibit adjacent to human bathers.

Nonhuman animals in zoos are exposed to a continuous human presence, which affects their behaviors and welfare. However, little is known about what role the "visitor effect" has on penguins in captivity. The African penguin (Spheniscus demersus) is an endangered species commonly housed in zoos worldwide. The aim of this study was to evaluate whether the abundance of human bathers could reduce the average time spent in the water of a colony of African penguins housed in an exhibit where their pond habitat was adjacent to a swimming pool. Observations were carried out on 7 penguins in the summer of 2009. Data were collected during 3 time periods (Time 1 [T1] = opening of the swimming season, Time 2 [T2] = core of the season, Time 3 [T3] = late season) of 14 days each. The human disturbance caused by bathers strongly reduced the pond use by penguins at T1 and T2, especially when there were large numbers of visitors. However, at T3, we observed that the overall use of the pond by penguins increased, and the average duration of their diving was no longer dependent on the number of visitors.

The vocal repertoire of the African Penguin (Spheniscus demersus): structure and function of calls.

The African Penguin (Spheniscus demersus) is a highly social and vocal seabird. However, currently available descriptions of the vocal repertoire of African Penguin are mostly limited to basic descriptions of calls. Here we provide, for the first time, a detailed description of the vocal behaviour of this species by collecting audio and video recordings from a large captive colony. We combine visual examinations of spectrograms with spectral and temporal acoustic analyses to determine vocal categories. Moreover, we used a principal component analysis, followed by signal classification with a discriminant function analysis, for statistical validation of the vocalisation types. In addition, we identified the behavioural contexts in which calls were uttered. The results show that four basic vocalisations can be found in the vocal repertoire of adult African Penguin, namely a contact call emitted by isolated birds, an agonistic call used in aggressive interactions, an ecstatic display song uttered by single birds, and a mutual display song vocalised by pairs, at their nests. Moreover, we identified two distinct vocalisations interpreted as begging calls by nesting chicks (begging peep) and unweaned juveniles (begging moan). Finally, we discussed the importance of specific acoustic parameters in classifying calls and the possible use of the source-filter theory of vocal production to study penguin vocalisations.