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"Kirk, David J."
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Handbook of mindfulness : theory, research, and practice
This handbook offers both a comprehensive review of the current science of mindfulness and a guide to its ongoing evolution. Scholars explore the topic in the context of contemporary psychological theories of attention, perceptual processing, motivation, and behaviour, as well as within a rich cross-disciplinary dialogue with the contemplative traditions.
Effects of an Immunomodulatory Supplement and Evaporative Cooling on Immune Status, Mammary Gland Microstructure, and Gene Expression of Cows Exposed to Heat Stress During the Dry Period
by
Corra, Fabiana N.
,
Chapman, James D.
,
Laporta, Jimena
in
Analysis
,
Animal lactation
,
Apoptosis
2025
Nutritional and cooling strategies to abate the negative effects of heat stress during the dry period have been used to improve the performance of dairy cattle. The objective of this study was to evaluate the effects of feeding an immunomodulatory supplement (OmniGen-AF®, OMN) before, during, and after exposure to either heat stress or active cooling during the dry period on immune function and mammary development in dairy cows. During late lactation (at least 60 d before dry off), cows were provided with evaporative cooling systems (shade, fans, and soakers) and assigned to two groups: placebo (56 g/d of AB20® top-dressed; CON) or OmniGen-AF® (OMN, 56 g/d top-dressed). Cows were dried off ~46 d before the expected calving date and further split into evaporative cooling (shade, fans, and soakers; CL) or heat stress (only shade; HT) pens. Thus, after dry off, there were four treatment groups: heat stress with placebo (HT, n = 17), HT with OMN supplementation (HT + OMN, n = 19), CL with placebo (CL, n = 16), and CL with OMN supplementation (CL + OMN, n = 11). From a subset of cows (n = 6–8 per group), four blood samples were collected during the dry period (−43, −39, −32, and −21 d relative to calving) to evaluate neutrophil function and blood hematology. In addition, mammary biopsies (4–6 cows/treatment) were collected at −43, −39, −32, and −21 d relative to calving to evaluate mammary gland gene expression and histology, i.e., Tdt dUTP nick-end labeling (TUNEL) and Ki67. Genes related to autophagy, apoptosis, and cell proliferation were analyzed by qRT-PCR. Relative to CL, HT downregulated the expression of beclin-2 (BECN2) but upregulated the expression of beclin-1 (BECN1) on days −43 and −39 relative to calving, respectively. Also, relative to CL, HT upregulated the expression of BAX and FAS on day −39 relative to calving. These differences in gene expression were followed by HT cows having a lower total cell apoptosis rate during involution relative to CL cows. Further to these effects, HT leads to a lower alveoli number relative to CL cows. As in the CL treatment, OMN cows have a higher total cell apoptosis rate and alveoli number relative to CON cows. In addition, OMN cows have higher total cell proliferation relative to CON. Prolactin (PRL) and cortisol concentrations were evaluated during the dry period at days −45, −26, −3, and −1 relative to calving. Relative to CL, HT cows had higher PRL at day −45 but lower PRL on day −1 relative to calving, and a similar trend was observed for cortisol concentrations. In summary, HT impacts mammary gland gene expression, compromises mammary involution, reduces alveoli number, and alters hormone dynamics throughout the dry period. Following the same trends as the CL treatment, OMN increases mammary gland turnover by having a higher cell apoptosis and cell proliferation rate and lower connective tissue relative to CON cows.
Journal Article
Design of a Two-Stroke Cycle Spark Ignition Engine Employing a Scotch-Yoke Crankshaft Mechanism
1985
This paper discusses the design aspects of a two-stroke cycle, spark ignition engine intended for light aircraft propulsion. A modified form of scotch-yoke crank mechanism is employed, and by utilization of two such reciprocating assemblies set at 90 degress to each other, a compact 4-cylinder radial engine configuration results. The unique mechanical design considerations of the scotch-yoke combined with the two-stroke engine cycle are examined in detail. The design offers an inherently balanced, low vibration machine employing a full circulatory lubrication system while retaining basic two-stroke engine simplicity. A prototype has been constructed which meets all initial design criteria and test results are presented.
Journal Article
Assessing the carbon capture potential of a reforestation project
by
Burgess, Paul J
,
Farfan, Jhon
,
Smith, Pete
in
704/106/694/682
,
704/172/4081
,
Anthropogenic factors
2021
The number of reforestation projects worldwide is increasing. In many cases funding is obtained through the claimed carbon capture of the trees, presented as immediate and durable, whereas reforested plots need time and maintenance to realise their carbon capture potential. Further, claims usually overlook the environmental costs of natural or anthropogenic disturbances during the forest’s lifetime, and greenhouse gas (GHG) emissions associated with the reforestation are not allowed for. This study uses life cycle assessment to quantify the carbon footprint of setting up a reforestation plot in the Peruvian Amazon. In parallel, we combine a soil carbon model with an above- and below-ground plant carbon model to predict the increase in carbon stocks after planting. We compare our results with the carbon capture claims made by a reforestation platform. Our results show major errors in carbon accounting in reforestation projects if they (1) ignore the time needed for trees to reach their carbon capture potential; (2) ignore the GHG emissions involved in setting up a plot; (3) report the carbon capture potential per tree planted, thereby ignoring limitations at the forest ecosystem level; or (4) under-estimate tree losses due to inevitable human and climatic disturbances. Further, we show that applications of biochar during reforestation can partially compensate for project emissions.
Journal Article
FilmArray, an Automated Nested Multiplex PCR System for Multi-Pathogen Detection: Development and Application to Respiratory Tract Infection
2011
The ideal clinical diagnostic system should deliver rapid, sensitive, specific and reproducible results while minimizing the requirements for specialized laboratory facilities and skilled technicians. We describe an integrated diagnostic platform, the “FilmArray”, which fully automates the detection and identification of multiple organisms from a single sample in about one hour. An unprocessed biologic/clinical sample is subjected to nucleic acid purification, reverse transcription, a high-order nested multiplex polymerase chain reaction and amplicon melt curve analysis. Biochemical reactions are enclosed in a disposable pouch, minimizing the PCR contamination risk. FilmArray has the potential to detect greater than 100 different nucleic acid targets at one time. These features make the system well-suited for molecular detection of infectious agents. Validation of the FilmArray technology was achieved through development of a panel of assays capable of identifying 21 common viral and bacterial respiratory pathogens. Initial testing of the system using both cultured organisms and clinical nasal aspirates obtained from children demonstrated an analytical and clinical sensitivity and specificity comparable to existing diagnostic platforms. We demonstrate that automated identification of pathogens from their corresponding target amplicon(s) can be accomplished by analysis of the DNA melting curve of the amplicon.
Journal Article
A systematic review of physical activity and quality of life and well-being
by
Vásquez, Priscilla M
,
Sheppard, Bonny Bloodgood
,
Petruzzello, Steven J
in
Dementia
,
Exercise
,
Physical Activity/Bodyweight/Nutrition and Energy Balance
2020
Participation in regular physical activity improves quality of life and well-being in many, including older adults and adults.
Abstract
Maintaining or improving quality of life (QoL) and well-being is a universal goal across the lifespan. Being physically active has been suggested as one way to enhance QoL and well-being. In this systematic review, conducted in part for the 2018 U.S. Health and Human Services Physical Activity Guidelines for Americans Scientific Advisory Committee Report, we examined the relationship between physical activity (PA) and QoL and well-being experienced by the general population across the lifespan and by persons with psychiatric and neurologic conditions. Systematic reviews, meta-analyses, and pooled analyses from 2006 to 2018 were used for the evidence base. Strong evidence (predominantly from randomized controlled trials [RCTs]) demonstrated that, for adults aged 18–65 years and older adults (primarily 65 years and older), PA improves QoL and well-being when compared with minimal or no-treatment controls. Moderate evidence indicated that PA improves QoL and well-being in individuals with schizophrenia and Parkinson’s disease, and limited evidence indicated that PA improves QoL and well-being for youth and for adults with major clinical depression or bipolar disorder. Insufficient evidence existed for individuals with dementia because of a small number of studies with mixed results. Future high-quality research designs should include RCTs involving longer interventions testing different modes and intensities of PA in diverse populations of healthy people and individuals with cognitive (e.g., dementia) and mental health conditions (e.g., schizophrenia) to precisely characterize the effects of different forms of PA on aspects of QoL and well-being.
Journal Article
Functional classification of long non-coding RNAs by k-mer content
2018
The functions of most long non-coding RNAs (lncRNAs) are unknown. In contrast to proteins, lncRNAs with similar functions often lack linear sequence homology; thus, the identification of function in one lncRNA rarely informs the identification of function in others. We developed a sequence comparison method to deconstruct linear sequence relationships in lncRNAs and evaluate similarity based on the abundance of short motifs called k-mers. We found that lncRNAs of related function often had similar k-mer profiles despite lacking linear homology, and that k-mer profiles correlated with protein binding to lncRNAs and with their subcellular localization. Using a novel assay to quantify Xist-like regulatory potential, we directly demonstrated that evolutionarily unrelated lncRNAs can encode similar function through different spatial arrangements of related sequence motifs. K-mer-based classification is a powerful approach to detect recurrent relationships between sequence and function in lncRNAs.
SEEKR is a method that deconstructs linear sequence relationships between lncRNAs and evaluates similarity on the basis of abundance of short motifs called k-mers. LncRNAs of related function often have similar k-mer profiles despite lacking linear homology.
Journal Article
Modelling the potential for soil carbon sequestration using biochar from sugarcane residues in Brazil
2020
Sugarcane (
Saccharum officinarum
L.) cultivation leaves behind around 20 t ha
−1
of biomass residue after harvest and processing. We investigated the potential for sequestering carbon (C) in soil with these residues by partially converting them into biochar (recalcitrant carbon-rich material). First, we modified the RothC model to allow changes in soil C arising from additions of sugarcane-derived biochar. Second, we evaluated the modified model against published field data, and found satisfactory agreement between observed and predicted soil C accumulation. Third, we used the model to explore the potential for soil C sequestration with sugarcane biochar in São Paulo State, Brazil. The results show a potential increase in soil C stocks by 2.35 ± 0.4 t C ha
−1
year
−1
in sugarcane fields across the State at application rates of 4.2 t biochar ha
−1
year
−1
. Scaling to the total sugarcane area of the State, this would be 50 Mt of CO
2
equivalent year
−1
, which is 31% of the CO
2
equivalent emissions attributed to the State in 2016. Future research should (a) further validate the model with field experiments; (b) make a full life cycle assessment of the potential for greenhouse gas mitigation, including additional effects of biochar applications on greenhouse gas balances.
Journal Article
World Health Organization Global Estimates and Regional Comparisons of the Burden of Foodborne Disease in 2010
by
Cawthorne, Amy
,
Kirk, Martyn D.
,
Angulo, Frederick J.
in
2010 AD
,
Campylobacter
,
Collection Review
2015
Illness and death from diseases caused by contaminated food are a constant threat to public health and a significant impediment to socio-economic development worldwide. To measure the global and regional burden of foodborne disease (FBD), the World Health Organization (WHO) established the Foodborne Disease Burden Epidemiology Reference Group (FERG), which here reports their first estimates of the incidence, mortality, and disease burden due to 31 foodborne hazards. We find that the global burden of FBD is comparable to those of the major infectious diseases, HIV/AIDS, malaria and tuberculosis. The most frequent causes of foodborne illness were diarrheal disease agents, particularly norovirus and Campylobacter spp. Diarrheal disease agents, especially non-typhoidal Salmonella enterica, were also responsible for the majority of deaths due to FBD. Other major causes of FBD deaths were Salmonella Typhi, Taenia solium and hepatitis A virus. The global burden of FBD caused by the 31 hazards in 2010 was 33 million Disability Adjusted Life Years (DALYs); children under five years old bore 40% of this burden. The 14 subregions, defined on the basis of child and adult mortality, had considerably different burdens of FBD, with the greatest falling on the subregions in Africa, followed by the subregions in South-East Asia and the Eastern Mediterranean D subregion. Some hazards, such as non-typhoidal S. enterica, were important causes of FBD in all regions of the world, whereas others, such as certain parasitic helminths, were highly localised. Thus, the burden of FBD is borne particularly by children under five years old-although they represent only 9% of the global population-and people living in low-income regions of the world. These estimates are conservative, i.e., underestimates rather than overestimates; further studies are needed to address the data gaps and limitations of the study. Nevertheless, all stakeholders can contribute to improvements in food safety throughout the food chain by incorporating these estimates into policy development at national and international levels.
Journal Article
Twelve or 30 Months of Dual Antiplatelet Therapy after Drug-Eluting Stents
2014
Patients who had received a drug-eluting stent and then dual antiplatelet therapy for 12 months were randomly assigned to 18 more months of therapy or aspirin alone. Continued therapy resulted in lower rates of stent thrombosis and major adverse cardiovascular events but more bleeding.
Millions of patients worldwide undergo coronary stenting each year for the treatment of ischemic heart disease.
1
,
2
Although drug-eluting stents reduce the rate of restenosis as compared with bare-metal stents, there is concern that drug-eluting stents may be associated with a risk of stent thrombosis beyond 1 year after treatment.
3
Stent thrombosis is rare, yet it is frequently associated with myocardial infarction and may be fatal.
3
Furthermore, ischemic events, such as myocardial infarction, stroke, or death from cardiovascular causes, that are unrelated to the treated coronary lesion may also occur beyond 1 year.
4
,
5
The use of dual antiplatelet therapy . . .
Journal Article