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Showing papers by "University of Guelph published in 2019"


Journal ArticleDOI
TL;DR: It is confirmed that eukaryotes form at least two domains, the loss of monophyly in the Excavata, robust support for the Haptista and Cryptista, and suggested primer sets for DNA sequences from environmental samples that are effective for each clade are provided.
Abstract: This revision of the classification of eukaryotes follows that of Adl et al., 2012 [J. Euk. Microbiol. 59(5)] and retains an emphasis on protists. Changes since have improved the resolution of many ...

750 citations


Journal ArticleDOI
TL;DR: Current knowledge of how macronutrient metabolism by the gut microbiome influences human health is summarized and knowledge gaps that could contribute to the understanding of overall human wellness will be identified.
Abstract: The human gut microbiome is a critical component of digestion, breaking down complex carbohydrates, proteins, and to a lesser extent fats that reach the lower gastrointestinal tract. This process results in a multitude of microbial metabolites that can act both locally and systemically (after being absorbed into the bloodstream). The impact of these biochemicals on human health is complex, as both potentially beneficial and potentially toxic metabolites can be yielded from such microbial pathways, and in some cases, these effects are dependent upon the metabolite concentration or organ locality. The aim of this review is to summarize our current knowledge of how macronutrient metabolism by the gut microbiome influences human health. Metabolites to be discussed include short-chain fatty acids and alcohols (mainly yielded from monosaccharides); ammonia, branched-chain fatty acids, amines, sulfur compounds, phenols, and indoles (derived from amino acids); glycerol and choline derivatives (obtained from the breakdown of lipids); and tertiary cycling of carbon dioxide and hydrogen. Key microbial taxa and related disease states will be referred to in each case, and knowledge gaps that could contribute to our understanding of overall human wellness will be identified.

594 citations


Journal ArticleDOI
TL;DR: This work presents vConTACT v.2.0, a network-based application utilizing whole genome gene-sharing profiles for virus taxonomy that integrates distance-based hierarchical clustering and confidence scores for all taxonomic predictions, and applies it to analyze 15,280 Global Ocean Virome genome fragments.
Abstract: Microbiomes from every environment contain a myriad of uncultivated archaeal and bacterial viruses, but studying these viruses is hampered by the lack of a universal, scalable taxonomic framework. We present vConTACT v.2.0, a network-based application utilizing whole genome gene-sharing profiles for virus taxonomy that integrates distance-based hierarchical clustering and confidence scores for all taxonomic predictions. We report near-identical (96%) replication of existing genus-level viral taxonomy assignments from the International Committee on Taxonomy of Viruses for National Center for Biotechnology Information virus RefSeq. Application of vConTACT v.2.0 to 1,364 previously unclassified viruses deposited in virus RefSeq as reference genomes produced automatic, high-confidence genus assignments for 820 of the 1,364. We applied vConTACT v.2.0 to analyze 15,280 Global Ocean Virome genome fragments and were able to provide taxonomic assignments for 31% of these data, which shows that our algorithm is scalable to very large metagenomic datasets. Our taxonomy tool can be automated and applied to metagenomes from any environment for virus classification.

434 citations


Journal ArticleDOI
TL;DR: A comprehensive pipeline called Extensive de-novo TE Annotator (EDTA) is created that produces a filtered non-redundant TE library for annotation of structurally intact and fragmented elements and will greatly facilitate TE annotation in eukaryotic genomes.
Abstract: Sequencing technology and assembly algorithms have matured to the point that high-quality de novo assembly is possible for large, repetitive genomes. Current assemblies traverse transposable elements (TEs) and provide an opportunity for comprehensive annotation of TEs. Numerous methods exist for annotation of each class of TEs, but their relative performances have not been systematically compared. Moreover, a comprehensive pipeline is needed to produce a non-redundant library of TEs for species lacking this resource to generate whole-genome TE annotations. We benchmark existing programs based on a carefully curated library of rice TEs. We evaluate the performance of methods annotating long terminal repeat (LTR) retrotransposons, terminal inverted repeat (TIR) transposons, short TIR transposons known as miniature inverted transposable elements (MITEs), and Helitrons. Performance metrics include sensitivity, specificity, accuracy, precision, FDR, and F1. Using the most robust programs, we create a comprehensive pipeline called Extensive de-novo TE Annotator (EDTA) that produces a filtered non-redundant TE library for annotation of structurally intact and fragmented elements. EDTA also deconvolutes nested TE insertions frequently found in highly repetitive genomic regions. Using other model species with curated TE libraries (maize and Drosophila), EDTA is shown to be robust across both plant and animal species. The benchmarking results and pipeline developed here will greatly facilitate TE annotation in eukaryotic genomes. These annotations will promote a much more in-depth understanding of the diversity and evolution of TEs at both intra- and inter-species levels. EDTA is open-source and freely available: https://github.com/oushujun/EDTA.

410 citations


Journal ArticleDOI
Richard Karlsson Linnér1, Richard Karlsson Linnér2, Pietro Biroli3, Edward Kong4, S. Fleur W. Meddens1, S. Fleur W. Meddens2, Robbee Wedow, Mark Alan Fontana5, Mark Alan Fontana6, Maël Lebreton7, Stephen P. Tino8, Abdel Abdellaoui2, Anke R. Hammerschlag2, Michel G. Nivard2, Aysu Okbay2, Cornelius A. Rietveld1, Pascal Timshel9, Pascal Timshel10, Maciej Trzaskowski11, Ronald de Vlaming2, Ronald de Vlaming1, Christian L. Zund3, Yanchun Bao12, Laura Buzdugan3, Laura Buzdugan13, Ann H. Caplin, Chia-Yen Chen4, Chia-Yen Chen14, Peter Eibich15, Peter Eibich16, Peter Eibich17, Pierre Fontanillas, Juan R. González18, Peter K. Joshi19, Ville Karhunen20, Aaron Kleinman, Remy Z. Levin21, Christina M. Lill22, Gerardus A. Meddens, Gerard Muntané23, Gerard Muntané18, Sandra Sanchez-Roige21, Frank J. A. van Rooij1, Erdogan Taskesen2, Yang Wu11, Futao Zhang11, Adam Auton, Jason D. Boardman24, David W. Clark19, Andrew Conlin20, Conor C. Dolan2, Urs Fischbacher25, Patrick J. F. Groenen1, Kathleen Mullan Harris26, Gregor Hasler27, Albert Hofman1, Albert Hofman4, Mohammad Arfan Ikram1, Sonia Jain21, Robert Karlsson28, Ronald C. Kessler4, Maarten Kooyman, James MacKillop29, James MacKillop30, Minna Männikkö20, Carlos Morcillo-Suarez18, Matthew B. McQueen24, Klaus M. Schmidt31, Melissa C. Smart12, Matthias Sutter32, Matthias Sutter33, Matthias Sutter16, Roy Thurik1, André G. Uitterlinden1, Jon White34, Harriet de Wit35, Jian Yang11, Lars Bertram22, Lars Bertram36, Dorret I. Boomsma2, Tõnu Esko37, Ernst Fehr3, David A. Hinds, Magnus Johannesson38, Meena Kumari12, David Laibson4, Patrik K. E. Magnusson28, Michelle N. Meyer39, Arcadi Navarro18, Arcadi Navarro40, Abraham A. Palmer21, Tune H. Pers9, Tune H. Pers10, Danielle Posthuma2, Daniel Schunk41, Murray B. Stein21, Rauli Svento20, Henning Tiemeier1, Paul R. H. J. Timmers19, Patrick Turley4, Patrick Turley14, Patrick Turley42, Robert J. Ursano43, Gert G. Wagner17, Gert G. Wagner16, James F. Wilson44, James F. Wilson19, Jacob Gratten11, Jacob Gratten45, James J. Lee46, David Cesarini47, Daniel J. Benjamin42, Daniel J. Benjamin48, Philipp Koellinger17, Philipp Koellinger2, Jonathan P. Beauchamp8 
TL;DR: This paper found evidence of substantial shared genetic influences across risk tolerance and the risky behaviors: 46 of the 99 general risk tolerance loci contain a lead SNP for at least one of their other GWAS, and general risk-tolerance is genetically correlated with a range of risky behaviors.
Abstract: Humans vary substantially in their willingness to take risks. In a combined sample of over 1 million individuals, we conducted genome-wide association studies (GWAS) of general risk tolerance, adventurousness, and risky behaviors in the driving, drinking, smoking, and sexual domains. Across all GWAS, we identified hundreds of associated loci, including 99 loci associated with general risk tolerance. We report evidence of substantial shared genetic influences across risk tolerance and the risky behaviors: 46 of the 99 general risk tolerance loci contain a lead SNP for at least one of our other GWAS, and general risk tolerance is genetically correlated ([Formula: see text] ~ 0.25 to 0.50) with a range of risky behaviors. Bioinformatics analyses imply that genes near SNPs associated with general risk tolerance are highly expressed in brain tissues and point to a role for glutamatergic and GABAergic neurotransmission. We found no evidence of enrichment for genes previously hypothesized to relate to risk tolerance.

395 citations


Journal ArticleDOI
TL;DR: The MIUViG (Minimum Information about an Uncultivated Virus Genome) as mentioned in this paper standard was developed within the Genomic Standards Consortium framework and includes virus origin, genome quality, genome annotation, taxonomic classification, biogeographic distribution and in silico host prediction.
Abstract: We present an extension of the Minimum Information about any (x) Sequence (MIxS) standard for reporting sequences of uncultivated virus genomes. Minimum Information about an Uncultivated Virus Genome (MIUViG) standards were developed within the Genomic Standards Consortium framework and include virus origin, genome quality, genome annotation, taxonomic classification, biogeographic distribution and in silico host prediction. Community-wide adoption of MIUViG standards, which complement the Minimum Information about a Single Amplified Genome (MISAG) and Metagenome-Assembled Genome (MIMAG) standards for uncultivated bacteria and archaea, will improve the reporting of uncultivated virus genomes in public databases. In turn, this should enable more robust comparative studies and a systematic exploration of the global virosphere.

318 citations


Journal ArticleDOI
TL;DR: Vanadium redox flow batteries (VRFBs) are one of the emerging energy storage techniques being developed with the purpose of effectively storing renewable energy as mentioned in this paper, and there are currently a limited number of papers published addressing the design considerations of the VRFB, the limitations of each component and what has been/is being done to address said limitations.
Abstract: Interest in the advancement of energy storage methods have risen as energy production trends toward renewable energy sources. Vanadium redox flow batteries (VRFB) are one of the emerging energy storage techniques being developed with the purpose of effectively storing renewable energy. There are currently a limited number of papers published addressing the design considerations of the VRFB, the limitations of each component and what has been/is being done to address said limitations. This review briefly discusses the current need and state of renewable energy production, the fundamental principles behind the VRFB, how it works and the technology restraints. The working principles of each component are highlighted and what design aspects/cues are to be considered when building a VRFB. The limiting determinants of some components are investigated along with the past/current research to address these limitations. Finally, critical research areas are highlighted along with future development recommendations.

315 citations


Journal ArticleDOI
TL;DR: This review covers the use of blood flow restriction to enhance muscular strength and hypertrophy via training with resistance and aerobic exercise and preventing muscle atrophy using the technique passively.
Abstract: The current manuscript sets out a position stand for blood flow restriction (BFR) exercise, focusing on the methodology, application and safety of this mode of training. With the emergence of this technique and the wide variety of applications within the literature, the aim of this position stand is to set out a current research informed guide to BFR training to practitioners. This covers the use of BFR to enhance muscular strength and hypertrophy via training with resistance and aerobic exercise and preventing muscle atrophy using the technique passively. The authorship team for this article was selected from the researchers focused in BFR training research with expertise in exercise science, strength and conditioning and sports medicine.

297 citations


Journal ArticleDOI
TL;DR: This Review focuses on the diverse constituents of green tea polyphenols and their molecular mechanisms from the perspective of their potential therapeutic function and recent advances on their bioavailability, bioaccessibility, and microbiota.
Abstract: Tea, leaf, or bud from the plant Camellia sinensis, make up some of the beverages popularly consumed in different parts of the world as green tea, oolong tea, or black tea. More particularly, as a nonfermented tea, green tea has gained more renown because of the significant health benefits assigned to its rich content in polyphenols. As a main constituent, green tea polyphenols were documented for their antioxidant, anti-inflammation, anticancer, anticardiovascular, antimicrobial, antihyperglycemic, and antiobesity properties. Recent reports demonstrate that green tea may exert a positive effect on the reduction of medical chronic conditions such as cardiovascular disease, cancer, Alzheimer's disease, Parkinson's disease, and diabetes. The health benefits of green teas, in particular EGCG, are widely investigated, and these effects are known to be primarily associated with the structure and compositions of its polyphenols. This Review focuses on the diverse constituents of green tea polyphenols and their molecular mechanisms from the perspective of their potential therapeutic function. Recent advances of green tea polyphenols on their bioavailability, bioaccessibility, and microbiota were also summarized in this article. Dietary supplementation with green tea represents an attractive alternative toward promoting human health.

293 citations


Journal ArticleDOI
01 Aug 2019-Nature
TL;DR: Soil radiocarbon dating reveals that combusted ‘legacy carbon’—soil carbon that escaped burning during previous fires—could shift the carbon balance of boreal ecosystems, resulting in a positive climate feedback.
Abstract: Boreal forest fires emit large amounts of carbon into the atmosphere primarily through the combustion of soil organic matter1–3. During each fire, a portion of this soil beneath the burned layer can escape combustion, leading to a net accumulation of carbon in forests over multiple fire events4. Climate warming and drying has led to more severe and frequent forest fires5–7, which threaten to shift the carbon balance of the boreal ecosystem from net accumulation to net loss1, resulting in a positive climate feedback8. This feedback will occur if organic-soil carbon that escaped burning in previous fires, termed ‘legacy carbon’, combusts. Here we use soil radiocarbon dating to quantitatively assess legacy carbon loss in the 2014 wildfires in the Northwest Territories of Canada2. We found no evidence for the combustion of legacy carbon in forests that were older than the historic fire-return interval of northwestern boreal forests9. In forests that were in dry landscapes and less than 60 years old at the time of the fire, legacy carbon that had escaped burning in the previous fire cycle was combusted. We estimate that 0.34 million hectares of young forests (<60 years) that burned in the 2014 fires could have experienced legacy carbon combustion. This implies a shift to a domain of carbon cycling in which these forests become a net source—instead of a sink—of carbon to the atmosphere over consecutive fires. As boreal wildfires continue to increase in size, frequency and intensity7, the area of young forests that experience legacy carbon combustion will probably increase and have a key role in shifting the boreal carbon balance. Soil radiocarbon dating reveals that combusted ‘legacy carbon’—soil carbon that escaped burning during previous fires—could shift the carbon balance of boreal ecosystems, resulting in a positive climate feedback.

260 citations


Journal ArticleDOI
TL;DR: In this article, the authors investigated the ingredients used in the formulation of modern meat analogues, evaluated the nutrient specifications of modernMeat analogue products, and then formed a comparison with traditional meat products.

Journal ArticleDOI
TL;DR: In this article, the development of hydrothermal carbonization with a focus on the practical aspects of the process is reviewed, and many references have been reviewed critically to provide a well-structured source for improving this process.
Abstract: Greenhouse gases emitted from the excessive use of fossil fuels are threatening the environment, and thus alternative resources like biomass are being considered as a replacement. Biomass with high moisture content is better treated by hydrothermal carbonization method than any other process to generate biofuel. Research on this method on a lab scale has progressed recently. However, due to the complex reaction mechanisms and operational barriers, more improvements are required to make it a commercial technology. This paper aims to review the development of hydrothermal carbonization with a focus on the practical aspects of the process. Many references have been reviewed critically to provide a well-structured source for improving this process. After providing information about the biomass structure and general knowledge of hydrothermal carbonization, the challenges faced in attempts to improve the process have been identified as lack of valid kinetic and heat transfer models and insufficient data on continuous and large-scale reactors. Useful and practical suggestions have been presented to tackle all these challenges.

Journal ArticleDOI
TL;DR: The R package amt (animal movement tools) as mentioned in this paper allows users to fit step selection functions (SSFs) to data and simulate space use of animals from fitted models, which can also be used to estimate utilization distributions and mechanistic home ranges.
Abstract: Advances in tracking technology have led to an exponential increase in animal location data, greatly enhancing our ability to address interesting questions in movement ecology, but also presenting new challenges related to data management and analysis. Step-selection functions (SSFs) are commonly used to link environmental covariates to animal location data collected at fine temporal resolution. SSFs are estimated by comparing observed steps connecting successive animal locations to random steps, using a likelihood equivalent of a Cox proportional hazards model. By using common statistical distributions to model step length and turn angle distributions, and including habitat- and movement-related covariates (functions of distances between points, angular deviations), it is possible to make inference regarding habitat selection and movement processes or to control one process while investigating the other. The fitted model can also be used to estimate utilization distributions and mechanistic home ranges. Here, we present the R package amt (animal movement tools) that allows users to fit SSFs to data and to simulate space use of animals from fitted models. The amt package also provides tools for managing telemetry data. Using fisher (Pekania pennanti) data as a case study, we illustrate a four-step approach to the analysis of animal movement data, consisting of data management, exploratory data analysis, fitting of models, and simulating from fitted models.

Journal ArticleDOI
TL;DR: In this paper, the authors describe enabling technologies, provided by the Internet of Things (IoT), which have the potential to increase food production transparency, including blockchain and Big Data analytics.
Abstract: Background Modern food supply chains are complex and contain numerous stakeholders, with each performing specific roles pertaining to food production. As food supply chains become more complex, the importance of food production transparency increases. Several factors contribute to the need for transparency such as an increase in the global population, detection of foodborne illness outbreaks, efficient management of risks and recalls, and satisfying consumer demand. A case in point is the necessity that food production systems become more sustainable through improvements in production efficiency and reducing the wasting of resources and food. Other examples include the need for timely identification of the source of food production, in addition to requiring a more rapid knowledge of the cause of contamination during outbreaks of foodborne illness. Scope and approach This review sets out to describe enabling technologies, provided by the Internet of Things (IoT), which have the potential to increase food production transparency. In addition, other technologies important for managing and using food supply chain data, such as blockchain and Big Data analytics, are reviewed. The IoT is the overarching technology which allows for data collection from multiple phases within supply chains leading to data driven transparent systems of food production. Key findings and conclusions Enabling transparency in food supply chains via implementation of technologies will require considerable effort from all stakeholders involved, resulting in many new challenges and requirements that must be addressed. These challenges and requirements range from technical issues, such as Internet connection, storage requirements, device security, and government requirements and regulations, to those concerning consumer acceptance.

Journal ArticleDOI
01 Feb 2019
TL;DR: This paper proposes an IDS based on feature selection and clustering algorithm using filter and wrapper methods that has a high accuracy and detection rate with a low false positive rate compared to the existing methods in the literature.
Abstract: Due to the widespread diffusion of network connectivity, the demand for network security and protection against cyber-attacks is ever increasing. Intrusion detection systems (IDS) perform an essential role in today's network security. This paper proposes an IDS based on feature selection and clustering algorithm using filter and wrapper methods. Filter and wrapper methods are named feature grouping based on linear correlation coefficient (FGLCC) algorithm and cuttlefish algorithm (CFA), respectively. Decision tree is used as the classifier in the proposed method. For performance verification, the proposed method was applied on KDD Cup 99 large data sets. The results verified a high accuracy (95.03%) and detection rate (95.23%) with a low false positive rate (1.65%) compared to the existing methods in the literature.

Journal ArticleDOI
TL;DR: The present review is focused on the different resistance mechanisms adopted by food pathogens to overcome bacteriocin.

Journal ArticleDOI
TL;DR: The goal is to design a scalable anomaly detection engine suitable for large-scale smart grids, which can differentiate an actual fault from a disturbance and an intelligent cyber-attack.
Abstract: Smart grid technology increases reliability, security, and efficiency of the electrical grids. However, its strong dependencies on digital communication technology bring up new vulnerabilities that need to be considered for efficient and reliable power distribution. In this paper, an unsupervised anomaly detection based on statistical correlation between measurements is proposed. The goal is to design a scalable anomaly detection engine suitable for large-scale smart grids, which can differentiate an actual fault from a disturbance and an intelligent cyber-attack. The proposed method applies feature extraction utilizing symbolic dynamic filtering (SDF) to reduce computational burden while discovering causal interactions between the subsystems. The simulation results on IEEE 39, 118, and 2848 bus systems verify the performance of the proposed method under different operation conditions. The results show an accuracy of 99%, true positive rate of 98%, and false positive rate of less than 2%

Journal ArticleDOI
14 Oct 2019
TL;DR: In this paper, the authors identify five priorities to chart a course towards an environmentally sustainable and socially equitable blue economy, and propose five policies and actions to achieve these goals, including:
Abstract: The global rush to develop the ‘blue economy’ risks harming both the marine environment and human wellbeing. Bold policies and actions are urgently needed. We identify five priorities to chart a course towards an environmentally sustainable and socially equitable blue economy.

Journal ArticleDOI
TL;DR: There is a cluster of four methods that rank significantly better than the other methods, with one clear winner, and the inter-scanner robustness ranking shows that not all the methods generalize to unseen scanners.
Abstract: Quantification of cerebral white matter hyperintensities (WMH) of presumed vascular origin is of key importance in many neurological research studies. Currently, measurements are often still obtained from manual segmentations on brain MR images, which is a laborious procedure. The automatic WMH segmentation methods exist, but a standardized comparison of the performance of such methods is lacking. We organized a scientific challenge, in which developers could evaluate their methods on a standardized multi-center/-scanner image dataset, giving an objective comparison: the WMH Segmentation Challenge. Sixty T1 + FLAIR images from three MR scanners were released with the manual WMH segmentations for training. A test set of 110 images from five MR scanners was used for evaluation. The segmentation methods had to be containerized and submitted to the challenge organizers. Five evaluation metrics were used to rank the methods: 1) Dice similarity coefficient; 2) modified Hausdorff distance (95th percentile); 3) absolute log-transformed volume difference; 4) sensitivity for detecting individual lesions; and 5) F1-score for individual lesions. In addition, the methods were ranked on their inter-scanner robustness; 20 participants submitted their methods for evaluation. This paper provides a detailed analysis of the results. In brief, there is a cluster of four methods that rank significantly better than the other methods, with one clear winner. The inter-scanner robustness ranking shows that not all the methods generalize to unseen scanners. The challenge remains open for future submissions and provides a public platform for method evaluation.

Journal ArticleDOI
TL;DR: In this article, the authors use literature and field data to outline some key trends being observed at the nexus of agricultural production, technology, and labour in North America, with a particular focus on the Canadian context.

Journal ArticleDOI
01 Mar 2019-Geoderma
TL;DR: Wang et al. as discussed by the authors constructed both Cubist and partial least square regression (PLSR) models on electrical conductivity (EC) (150 ground-based measurements as calibration set) using various related covariates (e.g. terrain attributes, remotely sensed spectral indices of vegetation and salinity from landsat8 OLI satellite) that are at the same time period corresponding to soil sampling.

Journal ArticleDOI
08 Jun 2019-Foods
TL;DR: Protein digestibility is currently a hot research topic and is of big interest to the food industry and different scoring methods have been developed to describe protein quality.
Abstract: Protein digestibility is currently a hot research topic and is of big interest to the food industry. Different scoring methods have been developed to describe protein quality. Cereal protein scores are typically low due to a suboptimal amino acid profile and low protein digestibility. Protein digestibility is a result of both external and internal factors. Examples of external factors are physical inaccessibility due to entrapment in e.g., intact cell structures and the presence of antinutritional factors. The main internal factors are the amino acid sequence of the proteins and protein folding and crosslinking. Processing of food is generally designed to increase the overall digestibility through affecting these external and internal factors. However, with proteins, processing may eventually also lead to a decrease in digestibility. In this review, protein digestion and digestibility are discussed with emphasis on the proteins of (pseudo)cereals.

Journal ArticleDOI
TL;DR: An holistic approach across all ruminant livestock industries and long-term commitment is required for control of paratuberculosis.
Abstract: Paratuberculosis, a chronic disease affecting ruminant livestock, is caused by Mycobacterium avium subsp. paratuberculosis (MAP). It has direct and indirect economic costs, impacts animal welfare and arouses public health concerns. In a survey of 48 countries we found paratuberculosis to be very common in livestock. In about half the countries more than 20% of herds and flocks were infected with MAP. Most countries had large ruminant populations (millions), several types of farmed ruminants, multiple husbandry systems and tens of thousands of individual farms, creating challenges for disease control. In addition, numerous species of free-living wildlife were infected. Paratuberculosis was notifiable in most countries, but formal control programs were present in only 22 countries. Generally, these were the more highly developed countries with advanced veterinary services. Of the countries without a formal control program for paratuberculosis, 76% were in South and Central America, Asia and Africa while 20% were in Europe. Control programs were justified most commonly on animal health grounds, but protecting market access and public health were other factors. Prevalence reduction was the major objective in most countries, but Norway and Sweden aimed to eradicate the disease, so surveillance and response were their major objectives. Government funding was involved in about two thirds of countries, but operations tended to be funded by farmers and their organizations and not by government alone. The majority of countries (60%) had voluntary control programs. Generally, programs were supported by incentives for joining, financial compensation and/or penalties for non-participation. Performance indicators, structure, leadership, practices and tools used in control programs are also presented. Securing funding for long-term control activities was a widespread problem. Control programs were reported to be successful in 16 (73%) of the 22 countries. Recommendations are made for future control programs, including a primary goal of establishing an international code for paratuberculosis, leading to universal acknowledgment of the principles and methods of control in relation to endemic and transboundary disease. An holistic approach across all ruminant livestock industries and long-term commitment is required for control of paratuberculosis.

Journal ArticleDOI
TL;DR: Necessary actions include improvements in antimicrobial use, better regulation and policy, as well as improved surveillance, stewardship, infection control, sanitation, animal husbandry, and finding alternatives to antimicrobials.
Abstract: Approaching any issue from a One Health perspective necessitates looking at the interactions of people, domestic animals, wildlife, plants, and our environment. For antimicrobial resistance this includes antimicrobial use (and abuse) in the human, animal and environmental sectors. More importantly, the spread of resistant bacteria and resistance determinants within and between these sectors and globally must be addressed. Better managing this problem includes taking steps to preserve the continued effectiveness of existing antimicrobials such as trying to eliminate their inappropriate use, particularly where they are used in high volumes. Examples are the mass medication of animals with critically important antimicrobials for humans, such as third generation cephalosporins and fluoroquinolones, and the long term, in-feed use of antimicrobials, such colistin, tetracyclines and macrolides, for growth promotion. In people it is essential to better prevent infections, reduce over-prescribing and over-use of antimicrobials and stop resistant bacteria from spreading by improving hygiene and infection control, drinking water and sanitation. Pollution from inadequate treatment of industrial, residential and farm waste is expanding the resistome in the environment. Numerous countries and several international agencies have now included a One Health Approach within their action plans to address antimicrobial resistance. Necessary actions include improvements in antimicrobial use, better regulation and policy, as well as improved surveillance, stewardship, infection control, sanitation, animal husbandry, and finding alternatives to antimicrobials.

DOI
10 Jun 2019
TL;DR: In this article, the authors indicate how much they agree or disagree with EACH of the following statements about the general communication between you and your mother: Strongly Disagree Disagree Agree Strongly Agree 1.
Abstract: Using the scale below, please indicate how much you agree or disagree with EACH of the following statements about the general communication between you and your mother. Response choices: Strongly Disagree Disagree Agree Strongly Agree 1. I can discuss my beliefs with my mother without feeling restrained or embarrassed. 2. Sometimes I have trouble believing everything my mother tells me 3. My mother is always a good listener. 4. I am sometimes afraid to ask my mother for what I want. 5. My mother has a tendency to say things to me which would be better left unsaid. 6. My mother can tell how I'm feeling without asking. 7. I am very satisfied with how my mother and I talk together. 8. If I were in trouble, I could tell my mother. 9. I openly show affection to my mother. 10. When we are having a problem, I often give my mother the silent treatment. 11. I am careful about what I say to my mother. 12. When talking to my mother, I have a tendency to say things that would be better left unsaid. 13. When I asked questions, I get honest answers from my mother. 14. My mother tries to understand my point of view. 15. There are topics I avoid discussing with my mother. 16. I find it easy to discuss problems with my mother. 17. It is very easy for me to express all my true feelings to my mother. 18. My mothers nags/bothers me. 19. My mother sometimes insults me when she is angry with me. 20. I don't think I can tell my mother how I really feel about some things.

Journal ArticleDOI
TL;DR: In this paper, the authors use evidence from ten ecoregions, spanning forests from Canada to Mexico, to review the properties of these forests that reinforced those qualities and highlight geographic similarities and differences in the structure and organization of historical landscapes, their forest types, and in the conditions that have changed resilience and resistance to abrupt or large-scale disruptions.
Abstract: Resilience and resistance concepts have broad application to ecology and society. Resilience is an emergent property that reflects the amount of disruption a system can withstand before its structure or organization uncharacteristically shift. Resistance is a component of resilience. Before the advent of intensive forest management and fire suppression, western North American forests exhibited a naturally occurring resilience to wildfires and other disturbances. Using evidence from ten ecoregions, spanning forests from Canada to Mexico, we review the properties of these forests that reinforced those qualities. We show examples of multi-level landscape resilience, of feedbacks within and among levels, and how conditions have changed under climatic and management influences. We highlight geographic similarities and differences in the structure and organization of historical landscapes, their forest types, and in the conditions that have changed resilience and resistance to abrupt or large-scale disruptions. We discuss the regional climates’ role in episodically or abruptly reorganizing plant and animal biogeography, and forest resilience and resistance to disturbances. We give clear examples of these changes and suggest that managing for resilient forests is a construct that is strongly dependent on scale and social values. It involves human community adaptations that work with the ecosystems they depend on and the processes that shape them. It entails actively managing factors and exploiting mechanisms that drive dynamics at each level as means of adapting landscapes, species, and human communities to climate change, and maintaining core ecosystem functions, processes, and services. Finally, it compels us to prioritize management that incorporates ongoing disturbances and anticipated effects of climatic changes, to support dynamically shifting patchworks of forest and nonforest. Doing so will make these shifting forest conditions and wildfire regimes more gradual and less disruptive to individuals and society.

Journal ArticleDOI
TL;DR: It is argued that generalists’ responses present a powerful and underutilized approach to understanding and predicting the consequences of climate change and may serve as much-needed early warning signals for monitoring the looming impacts of global climate change on entire ecosystems.
Abstract: Climate change is asymmetrically altering environmental conditions in space, from local to global scales, creating novel heterogeneity. Here, we argue that this novel heterogeneity will drive mobile generalist consumer species to rapidly respond through their behaviour in ways that broadly and predictably reorganize — or rewire — food webs. We use existing theory and data from diverse ecosystems to show that the rapid behavioural responses of generalists to climate change rewire food webs in two distinct and critical ways. First, mobile generalist species are redistributing into systems where they were previously absent and foraging on new prey, resulting in topological rewiring — a change in the patterning of food webs due to the addition or loss of connections. Second, mobile generalist species, which navigate between habitats and ecosystems to forage, will shift their relative use of differentially altered habitats and ecosystems, causing interaction strength rewiring — changes that reroute energy and carbon flows through existing food web connections and alter the food web’s interaction strengths. We then show that many species with shared traits can exhibit unified aggregate behavioural responses to climate change, which may allow us to understand the rewiring of whole food webs. We end by arguing that generalists’ responses present a powerful and underutilized approach to understanding and predicting the consequences of climate change and may serve as much-needed early warning signals for monitoring the looming impacts of global climate change on entire ecosystems. Climate change is spatially asymmetrical and so will alter the behaviour of generalist consumer species, affecting food webs in two ways. Movement into novel ecosystems will affect the topology of food webs, while changes within an ecosystem will affect interaction strengths.


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Abstract: Digital technologies are being developed and adopted across the agro‐food system, from farm to fork. Within decision‐making spaces, however, little attention is being paid to political factors arising from such technological developments. This review draws from critical social sciences to examine emerging technologies and big data systems in agriculture and assesses some key issues arising in the field. We begin with an introduction and review of the so‐called ‘digital revolution’ and then briefly outline how political economy is effective for understanding major challenges for governing technologies and data systems in agriculture. These challenges include: (1) data ownership and control, (2) the production of technologies and data development, and (3) data security. We then use literature and examples to consider the extent to which the political and economic landscape can be shifted to support greater equity in agriculture, while reflecting on structural challenges and limits. In doing so, we emphasise that while there are significant systemic tensions between digital ag‐tech development and agroecological approaches, we do not see them as mutually exclusive per se. This article intends to provide decision‐makers, practitioners and scholars from a wide range of disciplines with a timely assessment of agro‐food digitalisation that attends to political economic factors. In doing so, this article contributes to policy and decision‐making discussions, which, from our perspective, continue to be rather technocentric in nature while paying little attention to how digital technologies can support agroecological systems specifically.

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TL;DR: The results studied by differential scanning calorimetry (DSC) and dynamic viscoelasticity revealed that the swelling process of starch granule was restricted by protein, and recrystallization after cold storage was accelerated by protein addition.