Much effort has been devoted to assess disease risk based on large-scale protein-protein network and genotype-phenotype associations. However, the challenge of risk prediction for complex diseases remains unaddressed. Here, we propose a framework to quantify the risk based on a Voronoi tessellation network analysis, taking into account the disease association scores of both genes and variants. By integrating ClinVar, SNPnexus, and DISEASES databases, we introduce a gene-variant map that is based on the pairwise disease-associated gene-variant scores. This map is clustered using Voronoi tessellation and network analysis with a threshold obtained from fitting the background Voronoi cell density distribution. We define the relative risk of disease that is inferred from the scores of the data points within the related clusters on the gene-variant map. We identify autoimmune-associated clusters that may interact at the system-level. The proposed framework can be used to determine the clusters that are specific to a subtype or contribute to multiple subtypes of complex diseases.
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Punicic acid (PuA; 18: 3Δ 9cis,11trans,13cis ) is an unusual 18-carbon fatty acid bearing three conjugated double bonds. It has been shown to exhibit a myriad of beneficial bioactivities including anti-cancer, anti-diabetes, anti-obesity, antioxidant, and anti-inflammatory properties. Pomegranate (Punica granatum) seed oil contains approximately 80% PuA and is currently the major natural source of this remarkable fatty acid. While both PuA and pomegranate seed oil have been used as functional ingredients in foods and cosmetics for some time, their value in pharmaceutical/medical and industrial applications are presently under further exploration. Unfortunately, the availability of PuA is severely limited by the low yield and unstable supply of pomegranate seeds. In addition, efforts to produce PuA in transgenic crops have been limited by a relatively low content of PuA in the resulting seed oil. The production of PuA in engineered microorganisms with modern fermentation technology is therefore a promising and emerging method with the potential to resolve this predicament. In this paper, we provide a comprehensive review of this unusual fatty acid, covering topics ranging from its natural sources, biosynthesis, extraction and analysis, bioactivity, health benefits, and industrial applications, to recent efforts and future perspectives on the production of PuA in engineered plants and microorganisms.
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The average adult is sedentary between 55 and 71% (9 to 11 hours) of their waking day, many of these in the workplace. Recent research into healthy lifestyles has shifted from measuring time spent in physical activity, to time spent in sedentary behaviours. Independent of regular physical activity, sedentary behaviour contributes to major negative health outcomes, namely obesity, diabetes, cardiovascular disease, cancer, and depression, in addition to reduced workplace productivity and increased absenteeism due to illness. In collaboration with Vivo for Healthier Generations, a community recreation centre in Calgary, Alberta, we performed a pilot project that aimed to reduce sedentary behaviour through feasible and sustainable changes in workplace practice. With the support of their employer, volunteers had their offices retrofitted with sit-stand desks and anti-fatigue mats for a six-month workplace intervention. To complement the workstations, participants were offered motivational support and created individual action plans to personalize their movement goals. Participants in the study were provided workshops, newsletters, and other positive social prompts designed to embed standing and walking into a daily office routine. A mixed-methods approach was used in this six-month pilot study to fully explore the objective measures and the story of the participants. https://viurrspace.ca/bitstream/handle/10613/19604/SheehanEtAl.pdf?sequence=3
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College researcher traces cause of $15m. disease -- Forum opens up issue of who-governs-who -- Unclassifieds -- A salute for Iver Krogstad -- The datebook https://viuspace.viu.ca/bitstream/handle/10613/880/MainlyMalNov22-91.pdf?sequence=3
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Magnetic resonance imaging (MRI) is a non-destructive technique that is capable of localizing pathologies and assessing other anatomical features (e.g., tissue volume, microstructure, and white matter connectivity) in postmortem, ex vivo human brains. However, when brains are removed from the skull and cerebrospinal fluid (i.e., their normal in vivo magnetic environment), air bubbles and air–tissue interfaces typically cause magnetic susceptibility artifacts that severely degrade the quality of ex vivo MRI data. In this report, we describe a relatively simple and cost-effective experimental setup for acquiring artifact-free ex vivo brain images using a clinical MRI system with standard hardware. In particular, we outline the necessary steps, from collecting an ex vivo human brain to the MRI scanner setup, and have also described changing the formalin (as might be necessary in longitudinal postmortem studies). Finally, we share some representative ex vivo MRI images that have been acquired using the proposed setup in order to demonstrate the efficacy of this approach. We hope that this protocol will provide both clinicians and researchers with a straight-forward and cost-effective solution for acquiring ex vivo MRI data from whole postmortem human brains.
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Much effort has been devoted to assess disease risk based on large-scale protein-protein network and genotype-phenotype associations. However, the challenge of risk prediction for complex diseases remains unaddressed. Here, we propose a framework to quantify the risk based on a Voronoi tessellation network analysis, taking into account the disease association scores of both genes and variants. By integrating ClinVar, SNPnexus, and DISEASES databases, we introduce a gene-variant map that is based on the pairwise disease-associated gene-variant scores. This map is clustered using Voronoi tessellation and network analysis with a threshold obtained from fitting the background Voronoi cell density distribution. We define the relative risk of disease that is inferred from the scores of the data points within the related clusters on the gene-variant map. We identify autoimmune-associated clusters that may interact at the system-level. The proposed framework can be used to determine the clusters that are specific to a subtype or contribute to multiple subtypes of complex diseases.
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Punicic acid (PuA; 18: 3Δ 9cis,11trans,13cis ) is an unusual 18-carbon fatty acid bearing three conjugated double bonds. It has been shown to exhibit a myriad of beneficial bioactivities including anti-cancer, anti-diabetes, anti-obesity, antioxidant, and anti-inflammatory properties. Pomegranate (Punica granatum) seed oil contains approximately 80% PuA and is currently the major natural source of this remarkable fatty acid. While both PuA and pomegranate seed oil have been used as functional ingredients in foods and cosmetics for some time, their value in pharmaceutical/medical and industrial applications are presently under further exploration. Unfortunately, the availability of PuA is severely limited by the low yield and unstable supply of pomegranate seeds. In addition, efforts to produce PuA in transgenic crops have been limited by a relatively low content of PuA in the resulting seed oil. The production of PuA in engineered microorganisms with modern fermentation technology is therefore a promising and emerging method with the potential to resolve this predicament. In this paper, we provide a comprehensive review of this unusual fatty acid, covering topics ranging from its natural sources, biosynthesis, extraction and analysis, bioactivity, health benefits, and industrial applications, to recent efforts and future perspectives on the production of PuA in engineered plants and microorganisms.
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The average adult is sedentary between 55 and 71% (9 to 11 hours) of their waking day, many of these in the workplace. Recent research into healthy lifestyles has shifted from measuring time spent in physical activity, to time spent in sedentary behaviours. Independent of regular physical activity, sedentary behaviour contributes to major negative health outcomes, namely obesity, diabetes, cardiovascular disease, cancer, and depression, in addition to reduced workplace productivity and increased absenteeism due to illness. In collaboration with Vivo for Healthier Generations, a community recreation centre in Calgary, Alberta, we performed a pilot project that aimed to reduce sedentary behaviour through feasible and sustainable changes in workplace practice. With the support of their employer, volunteers had their offices retrofitted with sit-stand desks and anti-fatigue mats for a six-month workplace intervention. To complement the workstations, participants were offered motivational support and created individual action plans to personalize their movement goals. Participants in the study were provided workshops, newsletters, and other positive social prompts designed to embed standing and walking into a daily office routine. A mixed-methods approach was used in this six-month pilot study to fully explore the objective measures and the story of the participants. https://viurrspace.ca/bitstream/handle/10613/19604/SheehanEtAl.pdf?sequence=3
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College researcher traces cause of $15m. disease -- Forum opens up issue of who-governs-who -- Unclassifieds -- A salute for Iver Krogstad -- The datebook https://viuspace.viu.ca/bitstream/handle/10613/880/MainlyMalNov22-91.pdf?sequence=3
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Magnetic resonance imaging (MRI) is a non-destructive technique that is capable of localizing pathologies and assessing other anatomical features (e.g., tissue volume, microstructure, and white matter connectivity) in postmortem, ex vivo human brains. However, when brains are removed from the skull and cerebrospinal fluid (i.e., their normal in vivo magnetic environment), air bubbles and air–tissue interfaces typically cause magnetic susceptibility artifacts that severely degrade the quality of ex vivo MRI data. In this report, we describe a relatively simple and cost-effective experimental setup for acquiring artifact-free ex vivo brain images using a clinical MRI system with standard hardware. In particular, we outline the necessary steps, from collecting an ex vivo human brain to the MRI scanner setup, and have also described changing the formalin (as might be necessary in longitudinal postmortem studies). Finally, we share some representative ex vivo MRI images that have been acquired using the proposed setup in order to demonstrate the efficacy of this approach. We hope that this protocol will provide both clinicians and researchers with a straight-forward and cost-effective solution for acquiring ex vivo MRI data from whole postmortem human brains.
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