Development of a decision support tool to compare diagnostic strategies for establishing the herd status for infectious diseases: An example with Salmonella Dublin infection in dairies.

The diagnosis of infectious diseases at herd level can be challenging as different stakeholders can have conflicting priorities. The current study proposes a "proof of concept" of an approach that considers a reasonable number of criteria to rank plausible diagnostic strategies using multi-criteria decision analysis (MCDA) methods. The example of Salmonella Dublin diagnostic in Québec dairy herds is presented according to two epidemiological contexts: (i) in herds with no history of S. Dublin infection and absence of clinical signs, (ii) in herds with a previous history of infection, but absence of clinical signs at the moment of testing. Multiple multiparty exchanges were conducted to determine: 1) stakeholders' groups; 2) the decision problem; 3) solutions to the problem (options) or diagnostic strategies to be ordered; 4) criteria and indicators; 5) criteria weights; 6) the construction of a performance matrix for each option; 7) the multi-criteria analyses using the visual preference ranking organization method for enrichment of evaluations approach; 8) the sensitivity analyses, and 9) the final decision. A total of nine people from four Québec's organizations (the dairy producers provincial association along with the DHI company, the ministry of agriculture, the association of veterinary practitioners, and experts in epidemiology) composed the MCDA team. The decision problem was "What is the optimal diagnostic strategy for establishing the status of a dairy herd for S. Dublin infection when there are no clinical signs of infection?". Fourteen diagnostic strategies composed of the three following parameters were considered: 1) biological samples (bulk tank milk or blood from 10 heifers aged over three months); 2) sampling frequencies (one to three samples collection visits); 3) case definitions to conclude to a positive status using imperfect milk- or blood-ELISA tests. The top-ranking diagnostic strategy was the same in the two contexts: testing the bulk tank milk and the blood samples, all samples collected during one visit and the herd being assigned a S. Dublin positive status if one sample is ELISA-positive. The final decision favored the top-ranking option for both contexts. This MCDA approach and its application to S. Dublin infection in dairy herds allowed a consensual, rational, and transparent ranking of feasible diagnostic strategies while taking into account the diagnostic tests accuracy, socio-economic, logistic, and perception considerations of the key actors in the dairy industry. This promising tool can be applied to other infectious diseases that lack a well-established diagnostic procedure to define a herd status.

Association between ATP luminometry of feeding equipment and environmental and health parameters of preweaned calves on dairy farms.

The objective of this study was to examine the influence of different environmental factors on ATP luminometry measurements of feeding equipment and to investigate associations with health of preweaned calves and the levels of ATP identified through luminometry. On 50 commercial dairy farms in Quebec, Canada, ATP luminometry measurements (in relative light units (RLU)) were obtained using the direct swabbing technique with Hygiena UltraSnap swabs and a liquid rinsing technique with the same swab for automatic milk feeders (AMF), bottles, buckets, esophageal tube feeders (ET), milk replacer, nipples and water. During this visit, environmental factors (including temperature, air draft, humidity, ammonia, and bacterial count) were collected and a clinical examination (including respiratory score and fecal score) was performed for all preweaned calves present at the farm. This process was repeated 4 times in a year, leading to collection of luminometer results, environmental parameters, and overall health of calves for each season per farm. Overall, a difference in luminometer results was seen between the different periods sampled for all feeding equipment (except the ET), milk replacer and water, showing higher RLU values in spring and summer and lower values in autumn and winter. When comparing RLU measurements with environmental factors, only a low to negligible correlation could be found. When feeding equipment was classified as not contaminated or contaminated based on previously described cut-off values, a good agreement within a farm for the different seasons was noticed only for nipples (Gwet's agreement AC1 = 0.64), with a poor to moderate agreement for other feeding equipment. Regarding the different models of nipples, 'Peach Teat' nipples showed higher RLU values compared with 'Merricks' nipples models. An association was seen between the proportion of preweaned calves suffering from diarrhea on the farm and the contamination of AMF based on ATP luminometry (logistic regression estimate = 0.52, P = 0.04). For other feeding equipment, milk replacer and water, no significant associations were found. This study showed that ATP luminometry measurements of feeding equipment from preweaned calves are susceptible to seasonality and type of nipple. Thus, these factors should be taken into consideration when interpreting results. Additionally, an association could be made between diarrhea in preweaned calves and the contamination of AMF based on ATP luminometry, showing the potential clinical importance of this on-farm hygiene assessment tool.

The post-septic peripheral myeloid compartment reveals unexpected diversity in myeloid-derived suppressor cells.

Introduction: Sepsis engenders distinct host immunologic changes that include the expansion of myeloid-derived suppressor cells (MDSCs). These cells play a physiologic role in tempering acute inflammatory responses but can persist in patients who develop chronic critical illness. Methods: Cellular Indexing of Transcriptomes and Epitopes by Sequencing and transcriptomic analysis are used to describe MDSC subpopulations based on differential gene expression, RNA velocities, and biologic process clustering. Results: We identify a unique lineage and differentiation pathway for MDSCs after sepsis and describe a novel MDSC subpopulation. Additionally, we report that the heterogeneous response of the myeloid compartment of blood to sepsis is dependent on clinical outcome. Discussion: The origins and lineage of these MDSC subpopulations were previously assumed to be discrete and unidirectional; however, these cells exhibit a dynamic phenotype with considerable plasticity.

Single-molecule long-read methylation profiling reveals regional DNA methylation regulated by Elongator Complex Subunit 2 in Arabidopsis roots experiencing spaceflight.

BACKGROUND: The Advanced Plant Experiment-04 - Epigenetic Expression (APEX-04-EpEx) experiment onboard the International Space Station examined the spaceflight-altered cytosine methylation in two genetic lines of Arabidopsis thaliana, wild-type Col-0 and the mutant elp2-5, which is deficient in an epigenetic regulator Elongator Complex Subunit 2 (ELP2). Whole-genome bisulfite sequencing (WGBS) revealed distinct spaceflight associated methylation differences, presenting the need to explore specific space-altered methylation at single-molecule resolution to associate specific changes over large regions of spaceflight related genes. To date, tools of multiplexed targeted DNA methylation sequencing remain limited for plant genomes. RESULTS: To provide methylation data at single-molecule resolution, Flap-enabled next-generation capture (FENGC), a novel targeted multiplexed DNA capture and enrichment technique allowing cleavage at any specified sites, was applied to survey spaceflight-altered DNA methylation in genic regions of interest. The FENGC capture panel contained 108 targets ranging from 509 to 704 nt within the promoter or gene body regions of gene targets derived from spaceflight whole-genome data sets. In addition to genes with significant changes in expression and average methylation levels between spaceflight and ground control, targets with space-altered distributions of the proportion of methylated cytosines per molecule were identified. Moreover, trends of co-methylation of different cytosine contexts were exhibited in the same DNA molecules. We further identified significant DNA methylation changes in three previously biological process-unknown genes, and loss-of-function mutants of two of these genes (named as EMO1 and EMO2 for ELP2-regulated Methylation in Orbit 1 and 2) showed enhanced root growth rate. CONCLUSIONS: FENGC simplifies and reduces the cost of multiplexed, targeted, single-molecule profiling of methylation in plants, providing additional resolution along each DNA molecule that is not seen in population-based short-read data such as WGBS. This case study has revealed spaceflight-altered regional modification of cytosine methylation occurring within single DNA molecules of cell subpopulations, which were not identified by WGBS. The single-molecule survey by FENGC can lead to identification of novel functional genes. The newly identified EMO1 and EMO2 are root growth regulators which may be epigenetically involved in plant adaptation to spaceflight.

ARMC5 controls the degradation of most Pol II subunits, and ARMC5 mutation increases neural tube defect risks in mice and humans.

BACKGROUND: Neural tube defects (NTDs) are caused by genetic and environmental factors. ARMC5 is part of a novel ubiquitin ligase specific for POLR2A, the largest subunit of RNA polymerase II (Pol II). RESULTS: We find that ARMC5 knockout mice have increased incidence of NTDs, such as spina bifida and exencephaly. Surprisingly, the absence of ARMC5 causes the accumulation of not only POLR2A but also most of the other 11 Pol II subunits, indicating that the degradation of the whole Pol II complex is compromised. The enlarged Pol II pool does not lead to generalized Pol II stalling or a generalized decrease in mRNA transcription. In neural progenitor cells, ARMC5 knockout only dysregulates 106 genes, some of which are known to be involved in neural tube development. FOLH1, critical in folate uptake and hence neural tube development, is downregulated in the knockout intestine. We also identify nine deleterious mutations in the ARMC5 gene in 511 patients with myelomeningocele, a severe form of spina bifida. These mutations impair the interaction between ARMC5 and Pol II and reduce Pol II ubiquitination. CONCLUSIONS: Mutations in ARMC5 increase the risk of NTDs in mice and humans. ARMC5 is part of an E3 controlling the degradation of all 12 subunits of Pol II under physiological conditions. The Pol II pool size might have effects on NTD pathogenesis, and some of the effects might be via the downregulation of FOLH1. Additional mechanistic work is needed to establish the causal effect of the findings on NTD pathogenesis.

The Qanuilirpitaa? 2017 Nunavik Health Survey: design, methods, and lessons learned.

OBJECTIVE: To depict the design, methods, sociodemographic characteristics of the population, and lessons learned during the Qanuilirpitaa? 2017 Nunavik Inuit Health Survey, the third major health survey to be conducted among youth and adults residing in Nunavik (Northern Quebec, Canada). METHODS: Qanuilirpitaa? 2017 is a cross-sectional survey that served to update information regarding various aspects of physical health, mental health, and general well-being of Nunavimmiut. The survey was guided by the ethics principles of Ownership, Control, Access, and Possession (OCAP®) ( https://fnigc.ca/ocap ). Questionnaires and clinical tests were administered to residents from the 14 coastal communities onboard the Canadian Coast Guard Ship Amundsen during late summer and early fall 2017. As part of the community component of the survey, qualitative interviews were performed with key respondents, and services and resources supporting health and well-being in the 14 communities were inventoried and characterized. RESULTS: A total of 1326 Nunavimmiut aged 16 and over participated in the survey. Despite difficulties encountered with the recruitment of participants, co-interpretation sessions with Inuit partners revealed that the survey had succeeded in capturing cultural, socio-economic, and lifestyle characteristics of Nunavimmiut. In all, 20 thematic reports have been published covering various aspects of health and well-being of Nunavimmiut. Regional and local reports pertaining to the community component were produced. More in-depth analyses have ensued, and results are presented in articles published in this CJPH supplement issue. CONCLUSION: Information from this survey is being used to update health services and programs in the region and for the development of health policies and public health interventions to tackle key health-related issues faced by Nunavimmiut. Drawing lessons from challenges and successes encountered in Qanuilirpitaa? 2017, this survey paved the way to the upcoming Inuit-led Qanuippitaa? National Inuit Health Survey to be conducted every 5 years throughout Inuit Nunangat.

RéSUMé: OBJECTIF: Décrire la conception, les méthodes, les caractéristiques sociodémographiques de la population et les leçons tirées de l'Enquête sur la santé des Inuits du Nunavik Qanuilirpitaa? 2017, la troisième grande enquête de santé menée auprès de jeunes et d'adultes résidant au Nunavik (Nord du Québec, Canada). MéTHODES: Qanuilirpitaa? 2017 est une enquête transversale qui a permis la mise à jour des informations concernant divers aspects de la santé physique, de la santé mentale et du bien-être général des Nunavimmiut. L'enquête a été guidée par les principes de propriété, de contrôle, d'accès et de possession (OCAP®) ( https://fnigc.ca/ocap ). Des questionnaires et des tests cliniques ont été administrés à des résidents des 14 communautés côtières, à bord du navire Amundsen de la Garde côtière canadienne, à la fin de l'été et au début de l'automne 2017. Des entrevues qualitatives ont également été réalisées avec des répondants clé dans le cadre de la composante communautaire. RéSULTATS: Au total, 1 326 Nunavimmiut âgés de 16 ans et plus ont été recrutés. Malgré les difficultés rencontrées lors du recrutement des participants, les rencontres de co-interprétation ont permis de vérifier que l'enquête avait réussi à capturer les caractéristiques culturelles, socioéconomiques et les habitudes de vie de la population. Au total, 20 rapports thématiques ont été publiés, lesquels couvrent différents aspects de la santé et du bien-être des Nunavimmiut. Un rapport régional et des rapports locaux liés à la composante communautaire ont également été produits. Des analyses plus approfondies ont également été réalisées, dont les résultats sont présentés dans les articles publiés dans ce numéro supplémentaire de la Revue canadienne de santé publique. CONCLUSION: Les informations issues de cette enquête sont utilisées pour la mise à jour des services de santé dans la région et pour le développement de politiques de santé et d'interventions de santé publique, ayant pour cibles les principaux défis auxquels les Nunavimmiut sont confrontés. Grâce aux leçons apprises lors de sa réalisation, cette enquête a pavé la voie aux prochaines enquêtes Qanuippitaa ? qui seront menées tous les 5 ans dans tout l'Inuit Nunangat.

First detection and complete genome sequence of a new potexvirus naturally infecting Adenium obesum.

Here, we report the detection and complete genome sequence of a novel potexvirus, tentatively named "Adenium obesum virus X" (AobVX), isolated from Adenium obesum, that was sent for virus screening at Australian Government post-entry quarantine (PEQ) facilities after being imported into Australia from China. The AobVX genome is 6781 nucleotides in length excluding the poly(A) tail and is predicted to encode conserved potexvirus proteins and sequence motifs across five open reading frames. The RNA-dependent RNA polymerase of this virus shares the highest amino acid sequence similarity with that of nerine potexvirus 1 (58.7% identity) and nerine virus X (58.58% identity). This is the first report of a positive-sense single-stranded RNA virus in A. obesum related to members of the genus Potexvirus in the family Alphaflexiviridae.

Draft genome sequences of four Staphylococcus hyicus strains, SC302, SC304, SC306, and SC310, isolated from swine from Eastern Canada.

The bacterium Staphylococcus hyicus causes porcine exudative epidermitis in piglets, which represents both health and welfare concerns. Few genome sequences of this pathogen are published. We provide four additional ones to help future genomic analysis of S. hyicus. These are genomes of strains isolated from Canadian swine.

Hygiene management practices and adenosine triphosphate luminometry of feeding equipment in preweaning calves on dairy farms in Quebec, Canada.

The objective of this study was to describe the cleaning practices currently used for preweaning calves on dairy farms in Quebec, Canada. In addition, contamination of feeding equipment for preweaning calves was described using ATP (expressed as relative light units, RLU), visual assessment, and bacteriological analysis. A questionnaire was administered on 50 commercial dairy farms in Quebec, Canada, regarding the self-reported cleaning protocol used for feeding equipment of preweaning calves. During the visit, a visual score was given to the feeding equipment available at the farm. Afterward, ATP luminometry measurements were obtained using Hygiene UltraSnap and MicroSnap swabs (Hygiene, Camarillo, CA), and the liquid rinsing technique for buckets, nipples, bottles, esophageal tube feeders (ET), the tube of automatic milk feeders (AMF), water samples, and milk replacer. An additional direct swabbing technique was performed on buckets and nipples. The fluid retrieved from the liquid rinsing technique was also used to determine the total bacterial count (TBC) and total coliform count. Based on the bacteriological analysis, optimal RLU cutoff values to determine contamination were obtained. The median (interquartile range) luminometer measurements using the UltraSnap and direct technique for buckets and nipples were 2,082 (348-7,410) and 3,462 (462-7,518) RLU, respectively; and, using the liquid technique for bottles, ET, AMF, water, and milk replacer were 43 (4-974), 15 (4-121), 301 (137-1,323), 190 (71-358), and 94 (38-218) RLU, respectively. Overall, for all equipment and both techniques used, higher RLU values were seen in UltraSnap samples compared with MicroSnap samples. Additionally, for buckets and nipples, higher RLU values were obtained for the direct swabbing method compared with the liquid sampling method for both swabs used. No differences in the level of contamination were seen between the different feeding equipment used within a farm. Overall, a higher correlation with bacteriological results was noticed for ATP luminometry compared with the visual score, with a high correlation for nipples and bottles using the UltraSnap and liquid technique. Based on the classification of "contaminated" (TBC ≥100,000 cfu/mL) or "not contaminated" (TBC <100,000 cfu/mL), optimal ATP luminometer cutoff values for buckets, nipples, bottles, AMF, water, and milk replacer were 798, 388, 469, 282, 1,432, and 93 RLU, respectively. No clear association was found between ATP measurements and the self-reported cleaning protocol. This study gave new insights into the current cleaning procedures and contamination of feeding equipment for preweaning calves on dairy farms in Quebec. In addition, ATP luminometry cutoff values could help benchmark farms regarding cleaning practices and provide customized advice, improving the overall hygiene management, and thus the health, of preweaning calves on dairy farms.

Clinical utility of overviews on adverse events of pharmacological interventions.

BACKGROUND: Overviews (i.e., systematic reviews of systematic reviews, meta-reviews, umbrella reviews) are a relatively new type of evidence synthesis. Among others, one reason to conduct an overview is to investigate adverse events (AEs) associated with a healthcare intervention. Overviews aim to provide easily accessible information for healthcare decision-makers including clinicians. We aimed to evaluate the clinical utility of overviews investigating AEs. METHODS: We used a sample of 27 overviews exclusively investigating drug-related adverse events published until 2021 identified in a prior project. We defined clinical utility as the extent to which overviews are perceived to be useful in clinical practice. Each included overview was assigned to one of seven pharmacological experts with expertise on the topic of the overview. The clinical utility and value of these overviews were determined using a self-developed assessment tool. This included four open-ended questions and a ranking of three clinical utility statements completed by clinicians. We calculated frequencies for the ranked clinical utility statements and coded the answers to the open-ended questions using an inductive approach. RESULTS: The overall agreement with the provided statements was high. According to the assessments, 67% of the included overviews generated new knowledge. In 93% of the assessments, the overviews were found to add value to the existing literature. The overviews were rated as more useful than the individual included systematic reviews (SRs) in 85% of the assessments. The answers to the open-ended questions revealed two key aspects of clinical utility in the included overviews. Firstly, it was considered useful that they provide a summary of available evidence (e.g., along with additional assessments, or across different populations, or in different settings that have not been evaluated together in the included SRs). Secondly, it was found useful if overviews conducted a new meta-analysis to answer specific research questions that had not been answered previously. CONCLUSIONS: Overviews on drug-related AEs are considered valuable for clinical practice by clinicians. They can make available evidence on AEs more accessible and provide a comprehensive view of available evidence. As the role of overviews evolves, investigations such as this can identify areas of value.

Standardization and validation of ATP luminometry as a diagnostic tool to assess the cleanliness of feeding equipment in preweaning calves.

The objective of this cross-sectional study was to standardize a reliable and repeatable swabbing technique using ATP luminometry (light emission proportional to the amount of ATP with result provided in relative light units [RLU]) to describe the cleanliness of various feeding equipment used for preweaning calves in dairy farms. A total of 7 Québec commercial dairy herds were selected conveniently. Following visual hygiene scoring, the cleanliness of every available piece of feeding equipment was assessed using direct surface swabbing for buckets and nipples with Hygiena UltraSnap swabs. A liquid rinsing technique was used for esophageal feeders, bottles, and automatic milk feeders (AMF) with UltraSnap, AquaSnap, and MicroSnap swabs. To validate direct swabbing technique of buckets, a stage within and between operators was realized, as well as a conventional bacterial culture. A total of 519 swab samples were obtained from 201 pieces of equipment. The median (interquartile range) contamination in RLU for a bottle, esophageal feeder, AMF, bucket and nipple was 2 (1;6), 2 (0;12), 52 (19;269), 886 (128;7,230) and 899 (142;6,928), respectively. The direct swabbing technique, which consists in swabbing directly the surface of an equipment, showed excellent correlation for intrarater reliability (intraclass correlation (ICC) = 0.93; 95% CI: 0.88-0.96). The interoperator (2 sessions with 3 different operators) reliability also showed high correlation (ICC = 0.88; 95% CI: 0.78-0.94 for the first session, and ICC = 0.89; 95% CI: 0.79-0.95 for the second session). Luminometer values were positively associated with the visual score of esophageal feeders, AMF and buckets. A positive correlation between bacterial culture and direct swabbing of buckets was also found for the UltraSnap (rs = 0.653; 95% CI: 0.283-0.873; P = 0.0003) and MicroSnap (rs = 0.569, 95% CI: 0.309-0.765; P = 0.002). This study describes a standardized and practical on-farm swabbing technique for assessing the hygienic status of feeding equipment by luminometry, which can be integrated in the investigation of preweaning dairy calves problems.

Prolactin and the evolution of male pregnancy.

Prolactin (PRL) is a multifunctional hormone of broad physiological importance, and is involved in many aspects of fish reproduction, including the regulation of live birth (viviparity) and both male and female parental care. Previous research suggests that PRL also plays an important reproductive role in syngnathid fishes (seahorses, pipefish and seadragons), a group with a highly derived reproductive strategy, male pregnancy - how the PRL axis has come to be co-opted for male pregnancy remains unclear. We investigated the molecular evolution and expression of the genes for prolactin and its receptor (PRLR) in an evolutionarily diverse sampling of syngnathid fishes to explore how the co-option of PRL for male pregnancy has impacted its evolution, and to clarify whether the PRL axis is also involved in regulating reproductive function in species with more rudimentary forms of male pregnancy. In contrast to the majority of teleost fishes, all syngnathid fishes tested carry single copies of PRL and PRLR that cluster genetically within the PRL1 and PRLRa lineages of teleosts, respectively. PRL1 gene expression in seahorses and pipefish is restricted to the pituitary, while PRLRa is expressed in all tissues, including the brood pouch of species with both rudimentary and complex brooding structures. Pituitary PRL1 expression remains stable throughout pregnancy, but PRLRa expression is specifically upregulated in the male brood pouch during pregnancy, consistent with the higher affinity of pouch tissues for PRL hormone during embryonic incubation. Finally, immunohistochemistry of brood pouch tissues reveals that both PRL1 protein and PRLRa and Na+/K+ ATPase-positive cells line the inner pouch epithelium, suggesting that pituitary-derived PRL1 may be involved in brood pouch osmoregulation during pregnancy. Our data provide a unique molecular perspective on the evolution and expression of prolactin and its receptor during male pregnancy, and provide the foundation for further manipulative experiments exploring the role of PRL in this unique form of reproduction.

Sociodemographic patterning of dietary profiles among Inuit youth and adults in Nunavik, Canada: a cross-sectional study.

OBJECTIVES: Country (traditional) foods are integral to Inuit culture, but market food consumption is increasing. The Qanuilirpitaa? 2017 Nunavik Health Survey (Q2017) reported similar country food consumption frequency compared to that in 2004; however, examining food items individually does not account for diet patterns, food accessibility, and correlations between food items. Our objective was to identify underlying dietary profiles and compare them across sex, age, ecological region, and food insecurity markers, given the links among diet, health, and sociocultural determinants. METHODS: Food frequency and sociodemographic data were derived from the Q2017 survey (N = 1176). Latent profile analysis identified dietary profiles using variables for the relative frequencies of country and market food consumption first, followed by an analysis with those for country food variables only. Multinomial logistic regression examined the associations among dietary profiles, sociodemographic factors, and food insecurity markers (to disassociate between food preferences and food access). RESULTS: Four overall dietary profiles and four country food dietary profiles were identified characterized by the relative frequency of country and market food in the diet. The patterns were stable across several sensitivity analyses and in line with our Inuit partners' local knowledge. For the overall profiles, women and adults aged 30-49 years were more likely to have a market food-dominant profile, whereas men and individuals aged 16-29 and 50+ years more often consumed a country food-dominant profile. In the country food profiles, Inuit aged 16-29 years were more likely to have a moderate country food profile whereas Inuit aged 50+ were more likely to have a high country food-consumption profile. A low country and market food-consumption profile was linked to higher prevalence of food insecurity markers. CONCLUSION: We were able to identify distinct dietary profiles with strong social patterning. The profiles elucidated in this study are aligned with the impact of colonial influence on diet and subsequent country food promotion programs for Inuit youth. These profiles will be used for further study of nutritional status, contaminant exposure, and health to provide context for future public health programs.

RéSUMé: OBJECTIFS: Les aliments traditionnels font partie intégrante de la culture inuite, mais la consommation d'aliments du marché est en augmentation. L'enquête de santé des Inuit Qanuilirpitaa? réalisée en 2017 (Q2017) a mis en évidence que la fréquence de consommation d'aliments traditionnels était similaire à celle rapportée en 2004. Or, les fréquences de consommation des aliments pris individuellement ne tiennent pas compte des habitudes alimentaires, de l'accessibilité des aliments et des corrélations entre les aliments consommés. Notre objectif était d'identifier les profils alimentaires sous-jacents et de les comparer selon le sexe, l'âge, la région écologique et les marqueurs d'insécurité alimentaire, étant donné le lien entre l'alimentation, la santé et les déterminants socioculturels. MéTHODES: Les données sur les fréquences alimentaires et sociodémographiques sont issues de l'enquête Q2017 (N=1176). L'analyse des profils latents a permis d'identifier des profils alimentaires en utilisant les variables pour les fréquences relatives de la consommation d'aliments traditionnels et du marché et uniquement celles pour les aliments traditionnels. Des régressions logistiques multinomiales ont été utilisées pour examiner les associations entre les profils alimentaires, les facteurs sociodémographiques et les marqueurs d'insécurité alimentaire (pour dissocier les préférences alimentaires de l'accès aux aliments). RéSULTATS: Quatre profils alimentaires globaux et quatre profils alimentaires spécifiques à la consommation d'aliments traditionnels ont été identifiés en fonction de la fréquence relative des aliments traditionnels et des aliments du marché dans l'alimentation. Les profils étaient en accord avec les connaissances locales de nos partenaires Inuit. Pour les profils alimentaires globaux, les femmes et les adultes âgés de 30 à 49 ans étaient plus susceptibles d'avoir un profil dominé par les aliments du marché, tandis que les hommes et les personnes âgées de 16 à 29 ans et celles de 50 ans et plus avaient plus fréquemment un profil dominé par les aliments traditionnels. En ce qui concerne les profils de consommation d'aliments traditionnels, les Inuit âgés de 16 à 29 ans étaient plus susceptibles d'avoir un profil modéré de consommation d'aliments traditionnels, tandis que les Inuit âgés de 50 ans et plus étaient plus susceptibles d'avoir un profil élevé de consommation d'aliments traditionnels. Un profil bas de consommation d'aliments traditionnels et de marché était associé à une prévalence plus élevée de marqueurs d'insécurité alimentaire. CONCLUSION: Nous avons identifié différents profils alimentaires et ces derniers étaient associés à des caractéristiques socio-démographiques distinctes. Les profils alimentaires mis en lumière dans cette étude concordent avec l'impact du colonialisme sur l'alimentation au Nunavik et aux programmes subséquents de promotion des aliments traditionnels auprès des jeunes Inuit. Ces profils seront utilisés pour une étude plus approfondie du statut nutritionnel, de l'exposition aux contaminants et des issues de santé afin d'identifier des pistes de solutions pour les futurs programmes de santé publique.

Diagnosing Intramammary Infection: Meta-Analysis and Mapping Review on Frequency and Udder Health Relevance of Microorganism Species Isolated from Bovine Milk Samples.

Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry provides accurate species-level identification of many, microorganisms retrieved from bovine milk samples. However, not all those microorganisms are pathogenic. Our study aimed to: (1) determine the species-specific prevalence of microorganisms identified in bovine milk of apparently healthy lactating quarters vs. quarters with clinical mastitis (CM); and (2) map current information and knowledge gaps on udder health relevance of microorganisms retrieved from bovine milk samples. A mixed study design (meta-analysis and mapping review) was chosen. We gathered several large Canadian, US and Brazilian data sets of MALDI-TOF results for organisms cultured from quarter milk samples. For meta-analysis, two datasets (apparently healthy quarters vs. CM samples) were organized. A series of meta-analyses was conducted to determine microorganisms' prevalence. Then, each species reported was searched through PubMed to investigate whether inflammation (increased somatic cell count (SCC) or signs of CM) was associated with microorganism's recovery from milk. A total of 294 different species of microorganisms recovered from milk samples were identified. Among 50,429 quarter-milk samples from apparently healthy quarters, the 5 most frequent species were Staphylococcus chromogenes (6.7%, 95% CI 4.5-9.2%), Aerococcus viridans (1.6%, 95% CI 0.4-3.5%), Staphylococcus aureus (1.5%, 95% CI 0.5-2.8%), Staphylococcus haemolyticus (0.9%, 95% CI 0.4-1.5%), and Staphylococcus epidermidis (0.7%, 95% CI 0.2-1.6%). Among the 43,924 quarter-milk CM samples, the 5 most frequent species were Escherichia coli (11%, 95% CI 8.1-14.3%), Streptococcus uberis (8.5%, 95% CI 5.3-12.2%), Streptococcus dysgalactiae (7.8%, 95% CI 4.9-11.5%), Staphylococcus aureus (7.8%, 95% CI 4.4-11.9%), and Klebsiella pneumoniae (5.6%, 95% CI 3.4-8.2%). When conducting the PubMed literature search, there were 206 species identified by MALDI-TOF for which we were not able to find any information regarding their association with CM or SCC. Some of them, however, were frequently isolated in our multi-country dataset from the milk of quarters with CM (e.g., Citrobacter koseri, Enterococcus saccharolyticus, Streptococcus gallolyticus). Our study provides guidance to veterinarians for interpretation of milk bacteriology results obtained using MALDI-TOF and identifies knowledge gaps for future research.

Riluzole partially restores RNA polymerase III complex assembly in cells expressing the leukodystrophy-causative variant POLR3B R103H.

The mechanism of assembly of RNA polymerase III (Pol III), the 17-subunit enzyme that synthesizes tRNAs, 5 S rRNA, and other small-nuclear (sn) RNAs in eukaryotes, is not clearly understood. The recent discovery of the HSP90 co-chaperone PAQosome (Particle for Arrangement of Quaternary structure) revealed a function for this machinery in the biogenesis of nuclear RNA polymerases. However, the connection between Pol III subunits and the PAQosome during the assembly process remains unexplored. Here, we report the development of a mass spectrometry-based assay that allows the characterization of Pol III assembly. This assay was used to dissect the stages of Pol III assembly, to start defining the function of the PAQosome in this process, to dissect the assembly defects driven by the leukodystrophy-causative R103H substitution in POLR3B, and to discover that riluzole, an FDA-approved drug for alleviation of ALS symptoms, partly corrects these assembly defects. Together, these results shed new light on the mechanism and regulation of human nuclear Pol III biogenesis.

Implementation of GA-VirReport, a Web-Based Bioinformatics Toolkit for Post-Entry Quarantine Screening of Virus and Viroids in Plants.

High-throughput sequencing (HTS) of host plant small RNA (sRNA) is a popular approach for plant virus and viroid detection. The major bottlenecks for implementing this approach in routine virus screening of plants in quarantine include lack of computational resources and/or expertise in command-line environments and limited availability of curated plant virus and viroid databases. We developed: (1) virus and viroid report web-based bioinformatics workflows on Galaxy Australia called GA-VirReport and GA-VirReport-Stats for detecting viruses and viroids from host plant sRNA extracts and (2) a curated higher plant virus and viroid database (PVirDB). We implemented sRNA sequencing with unique dual indexing on a set of plants with known viruses. Sequencing data were analyzed using GA-VirReport and PVirDB to validate these resources. We detected all known viruses in this pilot study with no cross-sample contamination. We then conducted a large-scale diagnosis of 105 imported plants processed at the post-entry quarantine facility (PEQ), Australia. We detected various pathogens in 14 imported plants and discovered that de novo assembly using 21-22 nt sRNA fraction and the megablast algorithm yielded better sensitivity and specificity. This study reports the successful, large-scale implementation of HTS and a user-friendly bioinformatics workflow for virus and viroid screening of imported plants at the PEQ.

Contributions and perspectives of Indigenous Peoples to the study of mercury in the Arctic.

Arctic Indigenous Peoples are among the most exposed humans when it comes to foodborne mercury (Hg). In response, Hg monitoring and research have been on-going in the circumpolar Arctic since about 1991; this work has been mainly possible through the involvement of Arctic Indigenous Peoples. The present overview was initially conducted in the context of a broader assessment of Hg research organized by the Arctic Monitoring and Assessment Programme. This article provides examples of Indigenous Peoples' contributions to Hg monitoring and research in the Arctic, and discusses approaches that could be used, and improved upon, when carrying out future activities. Over 40 mercury projects conducted with/by Indigenous Peoples are identified for different circumpolar regions including the U.S., Canada, Greenland, Sweden, Finland, and Russia as well as instances where Indigenous Knowledge contributed to the understanding of Hg contamination in the Arctic. Perspectives and visions of future Hg research as well as recommendations are presented. The establishment of collaborative processes and partnership/co-production approaches with scientists and Indigenous Peoples, using good communication practices and transparency in research activities, are key to the success of research and monitoring activities in the Arctic. Sustainable funding for community-driven monitoring and research programs in Arctic countries would be beneficial and assist in developing more research/monitoring capacity and would promote a more holistic approach to understanding Hg in the Arctic. These activities should be well connected to circumpolar/international initiatives to ensure broader availability of the information and uptake in policy development.

Automating Access to Real-World Evidence.

Introduction: Real-world evidence is important in regulatory and funding decisions. Manual data extraction from electronic health records (EHRs) is time-consuming and challenging to maintain. Automated extraction using natural language processing (NLP) and artificial intelligence may facilitate this process. Whereas NLP offers a faster solution than manual methods of extraction, the validity of extracted data remains in question. The current study compared manual and automated data extraction from the EHR of patients with advanced lung cancer. Methods: Previously, we extracted EHRs from 1209 patients diagnosed with advanced lung cancer (stage IIIB or IV) between January 2015 and December 2017 at Princess Margaret Cancer Centre (Toronto, Canada) using the commercially available artificial intelligence engine, DARWEN (Pentavere, Ontario, Canada). For comparison, 100 of 333 patients that received systemic therapy were randomly selected and clinical data manually extracted by two trained abstractors using the same accepted gold standard feature definitions, including patient, disease characteristics, and treatment data. All cases were re-reviewed by an expert adjudicator. Accuracy and concordance between automated and manual methods are reported. Results: Automated extraction required considerably less time (<1 day) than manual extraction (∼225 person-hr). The collection of demographic data (age, sex, diagnosis) was highly accurate and concordant with both methods (96%-100%). Accuracy (for either extraction approach) and concordance were lower for unstructured data elements in EHR, such as performance status, date of diagnosis, and smoking status (NLP accuracy: 88%-94%; Manual accuracy: 78%-94%; concordance: 71%-82%). Concurrent medications (86%-100%) and comorbid conditions (96%-100%), were reported with high accuracy and concordance. Treatment details were also accurately captured with both methods (84%-100%) and highly concordant (83%-99%). Detection of whether biomarker testing was performed was highly accurate and concordant (96%-98%), although detection of biomarker test results was more variable (accuracy 84%-100%, concordance 84%-99%). Features with syntactic or semantic variation requiring clinical interpretation were extracted with slightly lower accuracy by both NLP and manual review. For example, metastatic sites were more accurately identified through NLP extraction (NLP: 88%-99%; manual: 71%-100%; concordance: 70%-99%) with the exception of lung and lymph node metastases (NLP: 66%-71%; manual: 87%-92%; concordance: 58%) owing to analogous terms used in radiology reports not being included in the accepted gold standard definition. Conclusions: Automated data abstraction from EHR is highly accurate and faster than manual abstraction. Key challenges include poorly structured EHR and the use of analogous terms beyond the accepted gold standard definition. The application of NLP can facilitate real-world evidence studies at a greater scale than could be achieved with manual data extraction.

Increased Adipose Tissue Indices of Androgen Catabolism and Aromatization in Women With Metabolic Dysfunction.

CONTEXT: Body fat distribution is a risk factor for obesity-associated comorbidities, and adipose tissue dysfunction plays a role in this association. In humans, there is a sex difference in body fat distribution, and steroid hormones are known to regulate several cellular processes within adipose tissue. OBJECTIVE: Our aim was to investigate if intra-adipose steroid concentration and expression or activity of steroidogenic enzymes were associated with features of adipose tissue dysfunction in individuals with severe obesity. METHODS: Samples from 40 bariatric candidates (31 women, 9 men) were included in the study. Visceral (VAT) and subcutaneous adipose tissue (SAT) were collected during surgery. Adipose tissue morphology was measured by a combination of histological staining and semi-automated quantification. Following extraction, intra-adipose and plasma steroid concentrations were determined by liquid chromatography electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS). Aromatase activity was estimated using product over substrate ratio, while AKR1C2 activity was measured directly by fluorogenic probe. Gene expression was measured by quantitative PCR. RESULTS: VAT aromatase activity was positively associated with VAT adipocyte hypertrophy (P valueadj < 0.01) and negatively with plasma high-density lipoprotein (HDL)-cholesterol (P valueadj < 0.01), while SAT aromatase activity predicted dyslipidemia in women even after adjustment for waist circumference, age, and hormonal contraceptive use. We additionally compared women with high and low visceral adiposity index (VAI) and found that VAT excess is characterized by adipose tissue dysfunction, increased androgen catabolism mirrored by increased AKR1C2 activity, and higher aromatase expression and activity indices. CONCLUSION: In women, increased androgen catabolism or aromatization is associated with visceral adiposity and adipose tissue dysfunction.

Complete genome sequence of a novel potyvirus infecting Miscanthus sinensis (silver grass).

Here, we describe the full-length genome sequence of a novel potyvirus, tentatively named "Miscanthus sinensis mosaic virus" (MsiMV), isolated from Miscanthus sinensis (silver grass) held in a post-entry quarantine facility after being imported into Western Australia, Australia. The MsiMV genome is 9604 nucleotides (nt) in length, encoding a 3071-amino-acid (aa) polyprotein with conserved sequence motifs. The MsiMV genome is most closely related to that of sorghum mosaic virus (SrMV), with 74% nt and 78.5% aa sequence identity to the SrMV polyprotein region. Phylogenetic analysis based on the polyprotein grouped MsiMV with SrMV, sugarcane mosaic virus (SCMV), and maize dwarf mosaic virus (MDMV). This is the first report of a novel monopartite ssRNA virus in Miscanthus sinensis related to members of the genus Potyvirus in the family Potyviridae.