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Showing papers by "University College Cork published in 2019"


Journal ArticleDOI
TL;DR: Future studies will focus on understanding the mechanisms underlying the microbiota-gut-brain axis and attempt to elucidate microbial-based intervention and therapeutic strategies for neuropsychiatric disorders.
Abstract: The importance of the gut-brain axis in maintaining homeostasis has long been appreciated. However, the past 15 yr have seen the emergence of the microbiota (the trillions of microorganisms within ...

1,775 citations


Journal ArticleDOI
TL;DR: Shortcuts to adiabaticity (STA) as mentioned in this paper is a systematic approach to accomplish the same final state transfer in a faster manner, which is used for atomic and molecular physics.
Abstract: Adiabatic evolution along the instantaneous eigenstate of a time-dependent Hamiltonian is used for robust and high fidelity state transfer in atomic and molecular physics. Shortcuts to adiabaticity (STA) are systematic approaches to accomplish the same final state transfer in a faster manner. This article presents an introduction to STA and reviews different theoretical approaches and applications of STA to a range of scientific and engineering tasks in quantum physics and beyond.

662 citations


Journal ArticleDOI
TL;DR: It is suggested that ecological barriers and particularly human disturbance likely constrain the capacity of herbivorous waterfowl to track the green wave in some regions, highlighting key challenges in conserving migratory birds.
Abstract: Tracking seasonally changing resources is regarded as a widespread proximate mechanism underpinning animal migration. Migrating herbivores, for example, are hypothesized to track seasonal foliage dynamics over large spatial scales. Previous investigations of this green wave hypothesis involved few species and limited geographical extent, and used conventional correlation that cannot disentangle alternative correlated effects. Here, we introduce stochastic simulations to test this hypothesis using 222 individual spring migration episodes of 14 populations of ten species of geese, swans and dabbling ducks throughout Europe, East Asia, and North America. We find that the green wave cannot be considered a ubiquitous driver of herbivorous waterfowl spring migration, as it explains observed migration patterns of only a few grazing populations in specific regions. We suggest that ecological barriers and particularly human disturbance likely constrain the capacity of herbivorous waterfowl to track the green wave in some regions, highlighting key challenges in conserving migratory birds.

654 citations


Journal ArticleDOI
Hunna J. Watson1, Hunna J. Watson2, Hunna J. Watson3, Zeynep Yilmaz3  +255 moreInstitutions (99)
TL;DR: The genetic architecture of anorexia nervosa mirrors its clinical presentation, showing significant genetic correlations with psychiatric disorders, physical activity, and metabolic (including glycemic), lipid and anthropometric traits, independent of the effects of common variants associated with body-mass index.
Abstract: Characterized primarily by a low body-mass index, anorexia nervosa is a complex and serious illness1, affecting 0.9-4% of women and 0.3% of men2-4, with twin-based heritability estimates of 50-60%5. Mortality rates are higher than those in other psychiatric disorders6, and outcomes are unacceptably poor7. Here we combine data from the Anorexia Nervosa Genetics Initiative (ANGI)8,9 and the Eating Disorders Working Group of the Psychiatric Genomics Consortium (PGC-ED) and conduct a genome-wide association study of 16,992 cases of anorexia nervosa and 55,525 controls, identifying eight significant loci. The genetic architecture of anorexia nervosa mirrors its clinical presentation, showing significant genetic correlations with psychiatric disorders, physical activity, and metabolic (including glycemic), lipid and anthropometric traits, independent of the effects of common variants associated with body-mass index. These results further encourage a reconceptualization of anorexia nervosa as a metabo-psychiatric disorder. Elucidating the metabolic component is a critical direction for future research, and paying attention to both psychiatric and metabolic components may be key to improving outcomes.

517 citations


Journal ArticleDOI
TL;DR: The European Calcified Tissue Society (ECTS) as mentioned in this paper recommends that the measurement of serum 25-hydroxyvitamin D (25(OH)D) be standardized, for example, by the Vitamin D Standardization Program.
Abstract: Vitamin D deficiency (serum 25-hydroxyvitamin D (25(OH)D) 10% of Europeans. The European Calcified Tissue Society (ECTS) advises that the measurement of serum 25(OH)D be standardized, for example, by the Vitamin D Standardization Program. Risk groups include young children, adolescents, pregnant women, older people (especially the institutionalized) and non-Western immigrants. Consequences of vitamin D deficiency include mineralization defects and lower bone mineral density causing fractures. Extra-skeletal consequences may be muscle weakness, falls and acute respiratory infection, and are the subject of large ongoing clinical trials. The ECTS advises to improve vitamin D status by food fortification and the use of vitamin D supplements in risk groups. Fortification of foods by adding vitamin D to dairy products, bread and cereals can improve the vitamin D status of the whole population, but quality assurance monitoring is needed to prevent intoxication. Specific risk groups such as infants and children up to 3 years, pregnant women, older persons and non-Western immigrants should routinely receive vitamin D supplements. Future research should include genetic studies to better define individual vulnerability for vitamin D deficiency, and Mendelian randomization studies to address the effect of vitamin D deficiency on long-term non-skeletal outcomes such as cancer.

391 citations


Journal ArticleDOI
TL;DR: This Review summarizes the available methods and main findings regarding taxonomic composition, community structure, and population dynamics in the human gut phageome, and discusses the main challenges in the field and identify promising avenues for future research.

367 citations


Journal ArticleDOI
TL;DR: This study performed longitudinal metagenomic analysis of fecal viruses in healthy adults that reveal high temporal stability, individual specificity, and correlation with the bacterial microbiome.

364 citations


Journal ArticleDOI
TL;DR: The need to enhance methods for designing and tailoring implementation strategies, and conduct more effectiveness research on discrete, multi-faceted, and tailored implementation strategies is suggested, to advance implementation science.
Abstract: The field of implementation science was developed to better understand the factors that facilitate or impede implementation and generate evidence for implementation strategies. In this article, we briefly review progress in implementation science, and suggest five priorities for enhancing the impact of implementation strategies. Specifically, we suggest the need to: (1) enhance methods for designing and tailoring implementation strategies; (2) specify and test mechanisms of change; (3) conduct more effectiveness research on discrete, multi-faceted, and tailored implementation strategies; (4) increase economic evaluations of implementation strategies; and (5) improve the tracking and reporting of implementation strategies. We believe that pursuing these priorities will advance implementation science by helping us to understand when, where, why, and how implementation strategies improve implementation effectiveness and subsequent health outcomes.

298 citations


Journal ArticleDOI
20 Mar 2019-Neuron
TL;DR: The vagus nerve is discussed, which connects the visceral organs and the brain, as an important communication pathway for the gut microbiota to influence brain and behavior.

280 citations


Journal ArticleDOI
TL;DR: Comparisons using multi-model regarding the role of DACCS in 1.5 and 2 degree scenarios are made and it is found that DACCS allows to postpone mitigation and reduce the climate policy costs.
Abstract: The feasibility of large-scale biological CO2 removal to achieve stringent climate targets remains unclear. Direct Air Carbon Capture and Storage (DACCS) offers an alternative negative emissions technology (NET) option. Here we conduct the first inter-model comparison on the role of DACCS in 1.5 and 2 °C scenarios, under a variety of techno-economic assumptions. Deploying DACCS significantly reduces mitigation costs, and it complements rather than substitutes other NETs. The key factor limiting DACCS deployment is the rate at which it can be scaled up. Our scenarios’ average DACCS scale-up rates of 1.5 GtCO2/yr would require considerable sorbent production and up to 300 EJ/yr of energy input by 2100. The risk of assuming that DACCS can be deployed at scale, and finding it to be subsequently unavailable, leads to a global temperature overshoot of up to 0.8 °C. DACCS should therefore be developed and deployed alongside, rather than instead of, other mitigation options. Direct Air Carbon Capture and Storage (DACCS) is not considered in Integrated Assessment Models. Here the authors make comparisons using multi-model regarding the role of DACCS in 1.5 and 2 degree scenarios and find that DACCS allows to postpone mitigation and reduce the climate policy costs.

273 citations


Journal ArticleDOI
Susana Santos1, Ellis Voerman1, Pilar Amiano, Henrique Barros2, Lawrence J. Beilin3, Anna Bergström4, Marie-Aline Charles5, Leda Chatzi6, Cécile Chevrier7, George P. Chrousos8, Eva Corpeleijn9, Olga Costa10, Nathalie Costet7, Sarah Crozier11, Graham Devereux12, Myriam Doyon13, Merete Eggesbø14, Maria Pia Fantini15, Sara Farchi, Francesco Forastiere, Vagelis Georgiu16, Keith M. Godfrey17, Davide Gori15, Veit Grote18, Wojciech Hanke19, Irva Hertz-Picciotto20, Barbara Heude5, Marie-France Hivert21, Daniel O. Hryhorczuk22, Rae-Chi Huang3, Hazel Inskip17, Anne M. Karvonen23, Louise C. Kenny, Berthold Koletzko18, Leanne K. Küpers24, Hanna Lagström25, Irina Lehmann26, Per Magnus14, Renata Majewska27, Johanna Mäkelä28, Yannis Manios29, Fionnuala M. McAuliffe30, Sheila McDonald31, John Mehegan30, Erik Melén32, Monique Mommers6, Camilla Schmidt Morgen33, George Moschonis, Deirdre M. Murray34, Carol Ní Chaoimh34, Ellen A. Nohr, Anne-Marie Nybo Andersen, Emily Oken21, Adriëtte J J M Oostvogels35, Agnieszka Pac27, Eleni Papadopoulou14, Juha Pekkanen36, Costanza Pizzi37, Kinga Polańska19, Daniela Porta, Lorenzo Richiardi37, Sheryl L. Rifas-Shiman21, Nel Roeleveld38, Luca Ronfani39, Ana Cristina Santos2, Marie Standl, Hein Stigum14, Camilla Stoltenberg40, Elisabeth Thiering18, Carel Thijs6, Maties Torrent, Suzanne Tough31, Tomas Trnovec41, Steve Turner32, Marleen M.H.J. van Gelder38, Lenie van Rossem42, Andrea von Berg, Martine Vrijheid43, Tanja G. M. Vrijkotte35, Jane West44, Alet H. Wijga, John Wright44, Oleksandr Zvinchuk, Thorkild I. A. Sørensen33, Debbie A Lawlor45, Romy Gaillard1, Vincent W. V. Jaddoe1, Vincent W. V. Jaddoe38 
TL;DR: In this paper, the separate and combined associations of maternal pre-pregnancy body mass index (BMI) and gestational weight gain with the risks of pregnancy complications and their population impact were assessed.

Journal ArticleDOI
TL;DR: A meta-analysis focussing on birds suggests that global warming has not systematically affected morphological traits, but has advanced phenological traits and indicates that the evolutionary load imposed by incomplete adaptive responses to ongoing climate change may already be threatening the persistence of species.
Abstract: Biological responses to climate change have been widely documented across taxa and regions, but it remains unclear whether species are maintaining a good match between phenotype and environment, i.e. whether observed trait changes are adaptive. Here we reviewed 10,090 abstracts and extracted data from 71 studies reported in 58 relevant publications, to assess quantitatively whether phenotypic trait changes associated with climate change are adaptive in animals. A meta-analysis focussing on birds, the taxon best represented in our dataset, suggests that global warming has not systematically affected morphological traits, but has advanced phenological traits. We demonstrate that these advances are adaptive for some species, but imperfect as evidenced by the observed consistent selection for earlier timing. Application of a theoretical model indicates that the evolutionary load imposed by incomplete adaptive responses to ongoing climate change may already be threatening the persistence of species.

Journal ArticleDOI
Ellis Voerman1, Susana Santos1, Bernadeta Patro Golab2, Bernadeta Patro Golab1, Pilar Amiano, Ferran Ballester3, Henrique Barros4, Anna Bergström5, Marie-Aline Charles6, Marie-Aline Charles7, Leda Chatzi8, Leda Chatzi9, Leda Chatzi10, Cécile Chevrier11, George P. Chrousos12, Eva Corpeleijn13, Nathalie Costet11, Sarah Crozier14, Graham Devereux15, Merete Eggesbø16, Sandra Ekström17, Maria Pia Fantini18, Sara Farchi, Francesco Forastiere, Vagelis Georgiu10, Keith M. Godfrey14, Keith M. Godfrey19, Davide Gori18, Veit Grote20, Wojciech Hanke21, Irva Hertz-Picciotto22, Barbara Heude7, Barbara Heude6, Daniel O. Hryhorczuk23, Rae-Chi Huang24, Hazel Inskip14, Hazel Inskip19, Nina Iszatt16, Anne M. Karvonen25, Louise C. Kenny26, Berthold Koletzko20, Leanne K. Küpers27, Hanna Lagström28, Irina Lehmann29, Per Magnus16, Renata Majewska30, Johanna Mäkelä31, Yannis Manios32, Fionnuala M. McAuliffe33, Sheila McDonald34, John Mehegan33, Monique Mommers35, Camilla Schmidt Morgen36, Camilla Schmidt Morgen37, Trevor A. Mori24, George Moschonis38, Deirdre M. Murray26, Carol Ní Chaoimh26, Ellen A. Nohr37, Anne-Marie Nybo Andersen36, Emily Oken39, Adriette J. J. M. Oostvogels35, Agnieszka Pac30, Eleni Papadopoulou16, Juha Pekkanen40, Costanza Pizzi41, Kinga Polańska21, Daniela Porta, Lorenzo Richiardi41, Sheryl L. Rifas-Shiman39, Luca Ronfani42, Ana Cristina Santos4, Marie Standl, Camilla Stoltenberg43, Elisabeth Thiering20, Carel Thijs35, Maties Torrent, Suzanne Tough34, Tomas Trnovec44, Steve Turner45, Lenie van Rossem46, Andrea von Berg, Martine Vrijheid47, Tanja G. M. Vrijkotte35, Jane West48, Alet H. Wijga, John Wright48, Oleksandr Zvinchuk, Thorkild I. A. Sørensen36, Debbie A Lawlor27, Romy Gaillard1, Vincent W. V. Jaddoe1 
TL;DR: In this article, the authors conducted an individual participant data meta-analysis of data from 162,129 mothers and children from 37 pregnancy and birth cohort studies from Europe, North-America and Australia, using multilevel binary logistic regression models with a random intercept at cohort level adjusted for maternal socio-demographic and life style related characteristics.
Abstract: Background: Maternal obesity and excessive gestational weight gain may have persistent effects on offspring fat development. However, it remains unclear whether these risks differ by severity of obesity, and whether these effects are restricted to the extremes of maternal body mass index (BMI) and gestational weight gain. We aimed to assess the separate and combined associations of maternal BMI and gestational weight gain with the risk of overweight/obesity throughout childhood, and their population impact. Methods and Findings: We conducted an individual participant data meta-analysis of data from 162,129 mothers and children from 37 pregnancy and birth cohort studies from Europe, North-America and Australia. We assessed the individual and combined associations of maternal pre-pregnancy BMI and gestational weight gain, both in clinical categories and across their full ranges with the risks of overweight/obesity in early- (2.0-5.0 years), mid- (5.0-10.0 years) and late childhood (10.0-18.0 years), using multilevel binary logistic regression models with a random intercept at cohort level adjusted for maternal socio-demographic and life style related characteristics. We observed that a higher maternal pre-pregnancy BMI and gestational weight gain both in clinical categories and across their full ranges were associated with higher risks of childhood overweight/obesity, with the strongest effects in late childhood (Odds Ratios (OR) for overweight/obesity in early-, mid- and late childhood, respectively: 1.66 (95% Confidence Interval (CI): 1.56, 1.78), OR 1.91 (95% CI: 1.85, 1.98), and OR 2.28 (95% CI: 2.08, 2.50) for maternal overweight, OR 2.43 (95% CI: 2.24, 2.64), OR 3.12 (95% CI: 2.98, 3.27), and OR 4.47 (95% CI: 3.99, 5.23) for maternal obesity, and OR 1.39 (95% CI: 1.30, 1.49), OR 1.55 (95% CI: 1.49, 1.60), and 1.72 (95% CI: 1.56, 1.91) for excessive gestational weight gain. The proportions of childhood overweight/obesity prevalence attributable to maternal overweight, maternal obesity and excessive gestational weight gain ranged from 10.2 to 21.6%. Relative to the effect of maternal BMI, excessive gestational weight gain only slightly increased the risk of childhood overweight/obesity within each clinical BMI category (P-values for interactions of maternal BMI with gestational weight gain: p=0.038, p<0.001 and p=0.637, in early-, mid- and late childhood, respectively). Limitations of this study include the self-report of maternal BMI and gestational weight gain for some of the cohorts, and the potential of residual confounding. Also, as this study only included participants from Europe, North-America and Australia, results need to be interpreted with caution with respect to other populations. Conclusions: In this study, higher maternal pre-pregnancy BMI and gestational weight gain were associated with an increased risk of childhood overweight/obesity, with the strongest effects at later ages. The additional effect of gestational weight gain in women who are overweight or obese before pregnancy is small. Given the large population impact, future intervention trials aiming to reduce the prevalence of childhood overweight and obesity should focus on maternal weight status before pregnancy, in addition to weight gain during pregnancy.

Journal ArticleDOI
01 Nov 2019-Science
TL;DR: It is proposed that a trans-species analysis may aid in the understanding of human sociability and the hypothesis that targeting the microbiota through dietary or live biotherapeutic interventions can improve the associated behavioral symptoms in such neurodevelopmental disorders.
Abstract: Sociability can facilitate mutually beneficial outcomes such as division of labor, cooperative care, and increased immunity, but sociability can also promote negative outcomes, including aggression and coercion. Accumulating evidence suggests that symbiotic microorganisms, specifically the microbiota that reside within the gastrointestinal system, may influence neurodevelopment and programming of social behaviors across diverse animal species. This relationship between host and microbes hints that host-microbiota interactions may have influenced the evolution of social behaviors. Indeed, the gastrointestinal microbiota is used by certain species as a means to facilitate communication among conspecifics. Further understanding of how microbiota influence the brain in nature may be helpful for elucidating the causal mechanisms underlying sociability and for generating new therapeutic strategies for social disorders in humans, such as autism spectrum disorders (ASDs).

Journal ArticleDOI
TL;DR: In this article, the authors performed whole-virome analysis on a published keystone inflammatory bowel disease (IBD) cohort and an in-house ulcerative colitis dataset to shed light on the composition of the human gut virome in IBD beyond this identifiable minority.

Proceedings ArticleDOI
02 May 2019
TL;DR: Findings from a series of semi-structured interviews show people make a clear dichotomy between social and functional roles of conversation, emphasising the long-term dynamics of bond and trust along with the importance of context and relationship stage in the types of conversations they have.
Abstract: Conversational agents promise conversational interaction but fail to deliver. Efforts often emulate functional rules from human speech, without considering key characteristics that conversation must encapsulate. Given its potential in supporting long-term human-agent relationships, it is paramount that HCI focuses efforts on delivering this promise. We aim to understand what people value in conversation and how this should manifest in agents. Findings from a series of semi-structured interviews show people make a clear dichotomy between social and functional roles of conversation, emphasising the long-term dynamics of bond and trust along with the importance of context and relationship stage in the types of conversations they have. People fundamentally questioned the need for bond and common ground in agent communication, shifting to more utilitarian definitions of conversational qualities. Drawing on these findings we discuss key challenges for conversational agent design, most notably the need to redefine the design parameters for conversational agent interaction.

Journal ArticleDOI
Nuno Queiroz1, Nuno Queiroz2, Nicolas E. Humphries2, Ana Rita Couto1  +163 moreInstitutions (61)
22 Aug 2019-Nature
TL;DR: It is concluded that pelagic sharks have limited spatial refuge from current levels of fishing effort in marine areas beyond national jurisdictions (the high seas), demonstrating an urgent need for conservation and management measures at high-seas hotspots of shark space use.
Abstract: Effective ocean management and the conservation of highly migratory species depend on resolving the overlap between animal movements and distributions, and fishing effort. However, this information is lacking at a global scale. Here we show, using a big-data approach that combines satellite-tracked movements of pelagic sharks and global fishing fleets, that 24% of the mean monthly space used by sharks falls under the footprint of pelagic longline fisheries. Space-use hotspots of commercially valuable sharks and of internationally protected species had the highest overlap with longlines (up to 76% and 64%, respectively), and were also associated with significant increases in fishing effort. We conclude that pelagic sharks have limited spatial refuge from current levels of fishing effort in marine areas beyond national jurisdictions (the high seas). Our results demonstrate an urgent need for conservation and management measures at high-seas hotspots of shark space use, and highlight the potential of simultaneous satellite surveillance of megafauna and fishers as a tool for near-real-time, dynamic management.

Journal ArticleDOI
TL;DR: The role of diet in shaping the microbiome and the influence of specific dietary components, namely protein, fat and carbohydrates, on gut microbiota composition are looked at.
Abstract: The gut microbiota is a highly complex community which evolves and adapts to its host over a lifetime. It has been described as a virtual organ owing to the myriad of functions it performs, including the production of bioactive metabolites, regulation of immunity, energy homeostasis and protection against pathogens. These activities are dependent on the quantity and quality of the microbiota alongside its metabolic potential, which are dictated by a number of factors, including diet and host genetics. In this regard, the gut microbiome is malleable and varies significantly from host to host. These two features render the gut microbiome a candidate ‘organ’ for the possibility of precision microbiomics—the use of the gut microbiome as a biomarker to predict responsiveness to specific dietary constituents to generate precision diets and interventions for optimal health. With this in mind, this two-part review investigates the current state of the science in terms of the influence of diet and specific dietary components on the gut microbiota and subsequent consequences for health status, along with opportunities to modulate the microbiota for improved health and the potential of the microbiome as a biomarker to predict responsiveness to dietary components. In particular, in Part I, we examine the development of the microbiota from birth and its role in health. We investigate the consequences of poor-quality diet in relation to infection and inflammation and discuss diet-derived microbial metabolites which negatively impact health. We look at the role of diet in shaping the microbiome and the influence of specific dietary components, namely protein, fat and carbohydrates, on gut microbiota composition.

Journal ArticleDOI
TL;DR: This review aims to integrate the contribution of the gut microbiome in health and disease to xenobiotic metabolism focusing on therapeutic interventions, pharmacological drug action, and chemical biotransformations that collectively will have implications for the future practice of precision medicine.
Abstract: The microbiome plays a key role in health and disease, and there has been considerable interest in therapeutic targeting of the microbiome as well as mining this rich resource in drug discovery efforts. However, a growing body of evidence suggests that the gut microbiota can itself influence the actions of a range of xenobiotics, in both beneficial and potentially harmful ways. Traditionally, clinical studies evaluating the pharmacokinetics of new drugs have mostly ignored the important direct and indirect effects of the gut microbiome on drug metabolism and efficacy. Despite some important observations from xenobiotic metabolism in general, there is only an incomplete understanding of the scope of influence of the microbiome specifically on drug metabolism and absorption, and how this might influence systemic concentrations of parent compounds and toxic metabolites. The significance of both microbial metabolism of xenobiotics and the impact of the gut microbiome on host hepatic enzyme systems is nonetheless gaining traction and presents a further challenge in drug discovery efforts, with implications for improving treatment outcomes or counteracting adverse drug reactions. Microbial factors must now be considered when determining drug pharmacokinetics and the impact that an evolving and dynamic microbiome could have in this regard. In this review, we aim to integrate the contribution of the gut microbiome in health and disease to xenobiotic metabolism focusing on therapeutic interventions, pharmacological drug action, and chemical biotransformations that collectively will have implications for the future practice of precision medicine.

Journal ArticleDOI
12 Mar 2019-JAMA
TL;DR: Among peanut-allergic children aged 4 to 11 years, the percentage difference in responders at 12 months with the 250-&mgr;g peanut-patch therapy vs placebo was 21.7% and was statistically significant, but did not meet the prespecified lower bound of the confidence interval criterion for a positive trial result.
Abstract: Importance There are currently no approved treatments for peanut allergy. Objective To assess the efficacy and adverse events of epicutaneous immunotherapy with a peanut patch among peanut-allergic children. Design, Setting, and Participants Phase 3, randomized, double-blind, placebo-controlled trial conducted at 31 sites in 5 countries between January 8, 2016, and August 18, 2017. Participants included peanut-allergic children (aged 4-11 years [n = 356] without a history of a severe anaphylactic reaction) developing objective symptoms during a double-blind, placebo-controlled food challenge at an eliciting dose of 300 mg or less of peanut protein. Interventions Daily treatment with peanut patch containing either 250 μg of peanut protein (n = 238) or placebo (n = 118) for 12 months. Main Outcomes and Measures The primary outcome was the percentage difference in responders between the peanut patch and placebo patch based on eliciting dose (highest dose at which objective signs/symptoms of an immediate hypersensitivity reaction developed) determined by food challenges at baseline and month 12. Participants with baseline eliciting dose of 10 mg or less were responders if the posttreatment eliciting dose was 300 mg or more; participants with baseline eliciting dose greater than 10 to 300 mg were responders if the posttreatment eliciting dose was 1000 mg or more. A threshold of 15% or more on the lower bound of a 95% CI around responder rate difference was prespecified to determine a positive trial result. Adverse event evaluation included collection of treatment-emergent adverse events (TEAEs). Results Among 356 participants randomized (median age, 7 years; 61.2% male), 89.9% completed the trial; the mean treatment adherence was 98.5%. The responder rate was 35.3% with peanut-patch treatment vs 13.6% with placebo (difference, 21.7% [95% CI, 12.4%-29.8%;P Conclusions and Relevance Among peanut-allergic children aged 4 to 11 years, the percentage difference in responders at 12 months with the 250-μg peanut-patch therapy vs placebo was 21.7% and was statistically significant, but did not meet the prespecified lower bound of the confidence interval criterion for a positive trial result. The clinical relevance of not meeting this lower bound of the confidence interval with respect to the treatment of peanut-allergic children with epicutaneous immunotherapy remains to be determined. Trial Registration ClinicalTrials.gov Identifier:NCT02636699

Journal ArticleDOI
TL;DR: Both the pro- and anti-tumorigenic effects identified for almost all members of the IL-1 family of cytokines are highlighted, and potential underlying mechanisms accounting for these divergent effects are explored.
Abstract: The IL-1 family of cytokines currently comprises of seven ligands with pro-inflammatory activity (IL-1α and IL-1β, IL-18, IL-33, IL-36α, IL-36β, IL-36γ) as well as two ligands with anti-inflammatory activity (IL-37, IL-38). These cytokines are known to play a key role in modulating both the innate and adaptive immunes response, with dysregulation linked to a variety of autoimmune and inflammatory diseases. Given the increasing appreciation of the link between inflammation and cancer, the role of several members of this family in the pathogenesis of cancer has been extensively investigated. In this review, we highlight both the pro- and anti-tumorigenic effects identified for almost all members of this family, and explore potential underlying mechanisms accounting for these divergent effects. Such dual functions need to be carefully assessed when developing therapeutic intervention strategies targeting these cytokines in cancer.

Journal ArticleDOI
TL;DR: The findings from recent studies are synthesized, potential underlying mechanisms are discussed, and look to the future regarding novel applications of the adult and children’s DII (C-DII) scores and new avenues of investigation in this field of nutritional research.
Abstract: There are over 1,000,000 publications on diet and health and over 480,000 references on inflammation in the National Library of Medicine database. In addition, there have now been over 30,000 peer-reviewed articles published on the relationship between diet, inflammation, and health outcomes. Based on this voluminous literature, it is now recognized that low-grade, chronic systemic inflammation is associated with most non-communicable diseases (NCDs), including diabetes, obesity, cardiovascular disease, cancers, respiratory and musculoskeletal disorders, as well as impaired neurodevelopment and adverse mental health outcomes. Dietary components modulate inflammatory status. In recent years, the Dietary Inflammatory Index (DII®), a literature-derived dietary index, was developed to characterize the inflammatory potential of habitual diet. Subsequently, a large and rapidly growing body of research investigating associations between dietary inflammatory potential, determined by the DII, and risk of a wide range of NCDs has emerged. In this narrative review, we examine the current state of the science regarding relationships between the DII and cancer, cardiometabolic, respiratory and musculoskeletal diseases, neurodevelopment, and adverse mental health outcomes. We synthesize the findings from recent studies, discuss potential underlying mechanisms, and look to the future regarding novel applications of the adult and children's DII (C-DII) scores and new avenues of investigation in this field of nutritional research.

Journal ArticleDOI
TL;DR: The antibiotic susceptibility patterns of 182 Lactobacillus type strains were determined and these phenotypes were compared to their genotypes based on genome-wide annotations of AR genes, providing evidence for rationally revising the regulatory guidelines for safety assessment of lactobacilli entering the food chain as starter cultures, food preservatives, or probiotics.
Abstract: Lactobacillus species are widely used as probiotics and starter cultures for a variety of foods, supported by a long history of safe usage. Although more than 35 species meet the European Food Safety Authority (EFSA) criteria for qualified presumption of safety status, the safety of Lactobacillus species and their carriage of antibiotic resistance (AR) genes is under continuing ad hoc review. To comprehensively update the identification of AR in the genus Lactobacillus, we determined the antibiotic susceptibility patterns of 182 Lactobacillus type strains and compared these phenotypes to their genotypes based on genome-wide annotations of AR genes. Resistances to trimethoprim, vancomycin, and kanamycin were the most common phenotypes. A combination of homology-based screening and manual annotation identified genes encoding resistance to aminoglycosides (20 sequences), tetracycline (18), erythromycin (6), clindamycin (60), and chloramphenicol (42). In particular, the genes aac(3) and lsa, involved in resistance to aminoglycosides and clindamycin, respectively, were found in Lactobacillus spp. Acquired determinants predicted to code for tetracycline and erythromycin resistance were detected in Lactobacillus ingluviei, Lactobacillus amylophilus, and Lactobacillus amylotrophicus, flanked in the genome by mobile genetic elements with potential for horizontal transfer. IMPORTANCELactobacillus species are generally considered to be nonpathogenic and are used in a wide variety of foods and products for humans and animals. However, many of the species examined in this study have antibiotic resistance levels which exceed those recommended by the EFSA, suggesting that these cutoff values should be reexamined in light of the genetic basis for resistance discussed here. Our data provide evidence for rationally revising the regulatory guidelines for safety assessment of lactobacilli entering the food chain as starter cultures, food preservatives, or probiotics and will facilitate comprehensive genotype-based assessment of strains for safety screening.

Journal ArticleDOI
Robert Edwards1, Alejandro A. Vega1, Holly M. Norman1, Maria Ohaeri1, Kyle Levi1, Elizabeth A. Dinsdale1, Ondrej Cinek2, Ramy K. Aziz3, Katelyn McNair1, Jeremy J. Barr4, Kyle Bibby5, Stan J. J. Brouns6, Adrian Cazares7, Patrick A. de Jonge8, Patrick A. de Jonge9, Christelle Desnues10, Samuel L. Díaz Muñoz11, Samuel L. Díaz Muñoz12, Peter C. Fineran13, Alexander Kurilshikov14, Rob Lavigne15, Karla Mazankova2, David Thomas McCarthy4, Franklin L. Nobrega6, Alejandro Reyes Muñoz16, German Tapia17, Nicole Trefault18, Alexander V. Tyakht19, Pablo Vinuesa20, Jeroen Wagemans15, Alexandra Zhernakova14, Frank Møller Aarestrup21, Gunduz Ahmadov, Abeer Alassaf22, Josefa Antón23, Abigail E. Asangba24, Emma Billings1, Vito Adrian Cantu1, Jane M. Carlton11, Daniel Cazares20, Gyu Sung Cho, Tess Condeff1, Pilar Cortés25, Mike Cranfield12, Daniel A. Cuevas1, Rodrigo De la Iglesia26, Przemyslaw Decewicz27, Michael P. Doane1, Nathaniel J. Dominy28, Lukasz Dziewit27, Bashir Mukhtar Elwasila29, A. Murat Eren30, Charles M. A. P. Franz, Jingyuan Fu14, Cristina García-Aljaro31, Elodie Ghedin11, Kristen M. Gulino11, John M. Haggerty1, Steven R. Head32, Rene S. Hendriksen21, Colin Hill33, Heikki Hyöty34, Elena N. Ilina, Mitchell T. Irwin35, Thomas C. Jeffries36, Juan Jofre31, Randall E. Junge37, Scott T. Kelley1, Mohammadali Khan Mirzaei38, Martin M. Kowalewski, Deepak Kumaresan39, Steven R. Leigh40, David A. Lipson1, Eugenia S. Lisitsyna, Montserrat Llagostera25, Julia M. Maritz11, Linsey C. Marr41, Angela McCann33, Shahar Molshanski-Mor42, Silvia Monteiro43, Benjamin Moreira-Grez39, Megan M. Morris1, Lawrence Mugisha44, Maite Muniesa31, Horst Neve, Nam Nguyen45, Olivia D. Nigro46, Anders S. Nilsson47, Taylor O'Connell1, Rasha Odeh22, Andrew Oliver48, Mariana Piuri49, Aaron J. Prussin41, Udi Qimron42, Zhe Xue Quan50, Petra Rainetova, Adán Ramírez-Rojas, Raúl R. Raya, Kim Reasor1, Gillian A.O. Rice28, Alessandro Rossi8, Alessandro Rossi51, Ricardo Santos43, John Shimashita41, Elyse Stachler52, Lars C. Stene17, Ronan Strain33, Rebecca M. Stumpf24, Pedro J. Torres1, Alan Twaddle11, Mary Ann Ugochi Ibekwe53, Nicolás A. Villagra54, Stephen Wandro48, Bryan A. White24, Andrew S. Whiteley39, Katrine Whiteson48, Cisca Wijmenga14, María Mercedes Zambrano, Henrike Zschach55, Bas E. Dutilh8, Bas E. Dutilh56 
San Diego State University1, Charles University in Prague2, Cairo University3, Monash University4, University of Notre Dame5, Delft University of Technology6, University of Liverpool7, Utrecht University8, Kavli Institute of Nanoscience9, Aix-Marseille University10, New York University11, University of California, Davis12, University of Otago13, University of Groningen14, Katholieke Universiteit Leuven15, University of Los Andes16, Norwegian Institute of Public Health17, Universidad Mayor18, Saint Petersburg State University of Information Technologies, Mechanics and Optics19, National Autonomous University of Mexico20, Technical University of Denmark21, University of Jordan22, University of Alicante23, University of Illinois at Urbana–Champaign24, Autonomous University of Barcelona25, Pontifical Catholic University of Chile26, University of Warsaw27, Dartmouth College28, University of Khartoum29, University of Chicago30, University of Barcelona31, Scripps Research Institute32, University College Cork33, University of Tampere34, Northern Illinois University35, University of Sydney36, Columbus Zoo and Aquarium37, McGill University38, University of Western Australia39, University of Colorado Boulder40, Virginia Tech41, Tel Aviv University42, Instituto Superior Técnico43, Makerere University44, University of California, San Diego45, Hawaii Pacific University46, Stockholm University47, University of California, Irvine48, University of Buenos Aires49, Fudan University50, University of Padua51, University of Pittsburgh52, Ebonyi State University53, Andrés Bello National University54, University of Copenhagen55, Radboud University Nijmegen56
TL;DR: It is concluded that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome.
Abstract: Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world's countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome.

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TL;DR: High fat and high SFA diets can exert unfavorable effects on the gut microbiota and are associated with an unhealthy metabolic state, while high MUFA diets may negatively affect gut microbiota whereas PUFA do not seem to negatively affect the Gut microbiota or metabolic health outcomes.

Journal ArticleDOI
01 Sep 2019-Gut
TL;DR: In this paper, an international panel of experts delivered their opinions on key questions concerning the contribution of the human microbiome to carcinogenesis, including the relevance of dysbiosis/analtered gut, potential mechanisms of microbiota-induced carcinogenesis and future directions for research in the field.
Abstract: Objective In this consensus statement, an international panel of experts deliver their opinions on key questions regarding the contribution of the human microbiome to carcinogenesis. Design International experts in oncology and/or microbiome research were approached by personal communication to form a panel. A structured, iterative, methodology based around a 1-day roundtable discussion was employed to derive expert consensus on key questions in microbiome-oncology research. Results Some 18 experts convened for the roundtable discussion and five key questions were identified regarding: (1) the relevance of dysbiosis/analtered gut microbiome to carcinogenesis; (2) potential mechanisms of microbiota-induced carcinogenesis; (3) conceptual frameworks describing how the human microbiome may drive carcinogenesis; (4) causation versus association; and (5) future directions for research in the field. The panel considered that, despite mechanistic and supporting evidence from animal and human studies, there is currently no direct evidence that the human commensal microbiome is a key determinant in the aetiopathogenesis of cancer. The panel cited the lack of large longitudinal, cohort studies as a principal deciding factor and agreed that this should be a future research priority. However, while acknowledging gaps in the evidence, expert opinion was that the microbiome, alongside environmental factors and an epigenetically/genetically vulnerable host, represents one apex of a tripartite, multidirectional interactome that drives carcinogenesis. Conclusion Data from longitudinal cohort studies are needed to confirm the role of the human microbiome as a key driver in the aetiopathogenesis of cancer.

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TL;DR: It is concluded that an experimental medicine approach and a mechanistic understanding is required to provide solid evidence on which future policies on diet and nutrition for mental health can be based.

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TL;DR: It is agreed that ethical use of AI in radiology should promote well-being, minimize harm, and ensure that the benefits and harms are distributed among stakeholders in a just manner and the radiology community should start now to develop codes of ethics and practice for AI.
Abstract: This statement highlights our consensus that ethical use of AI in radiology should promote well-being, minimize harm, and ensure that the benefits and harms are distributed among stakeholders in a ...

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TL;DR: Hypertensive disorders of pregnancy, including preeclampsia, have a similar pattern of increased risk across all 12 cardiovascular disorders and chronic hypertension, and the impact was evident soon after pregnancy.
Abstract: Background: The associations between pregnancy hypertensive disorders and common cardiovascular disorders have not been investigated at scale in a contemporaneous population. We aimed to investigat...

Journal ArticleDOI
19 Nov 2019-JAMA
TL;DR: This post hoc analysis of a prematurely terminated randomized clinical trial of umbilical cord milking vs delayed umbilicals cord clamping among preterm infants born at less than 32 weeks' gestation found there was no statistically significant difference in the rate of a composite outcome of death or severe intraventricular hemorrhage.
Abstract: Importance Umbilical cord milking as an alternative to delayed umbilical cord clamping may provide equivalent benefits to preterm infants, but without delaying resuscitation. Objective To determine whether the rates of death or severe intraventricular hemorrhage differ among preterm infants receiving placental transfusion with umbilical cord milking vs delayed umbilical cord clamping. Design, Setting, and Participants Noninferiority randomized clinical trial of preterm infants (born at 23-31 weeks’ gestation) from 9 university and private medical centers in 4 countries were recruited and enrolled between June 2017 and September 2018. Planned enrollment was 750 per group. However, a safety signal comprising an imbalance in the number of severe intraventricular hemorrhage events by study group was observed at the first interim analysis; enrollment was stopped based on recommendations from the data and safety monitoring board. The planned noninferiority analysis could not be conducted and a post hoc comparison was performed instead. Final date of follow-up was December 2018. Interventions Participants were randomized to umbilical cord milking (n = 236) or delayed umbilical cord clamping (n = 238). Main Outcomes and Measures The primary outcome was a composite of death or severe intraventricular hemorrhage to determine noninferiority of umbilical cord milking with a 1% noninferiority margin. Results Among 540 infants randomized, 474 (88%) were enrolled and completed the trial (mean gestational age of 28 weeks; 46% female). Twelve percent (29/236) of the umbilical cord milking group died or developed severe intraventricular hemorrhage compared with 8% (20/238) of the delayed umbilical cord clamping group (risk difference, 4% [95% CI, −2% to 9%];P = .16). Although there was no statistically significant difference in death, severe intraventricular hemorrhage was statistically significantly higher in the umbilical cord milking group than in the delayed umbilical cord clamping group (8% [20/236] vs 3% [8/238], respectively; risk difference, 5% [95% CI, 1% to 9%];P = .02). The test for interaction between gestational age strata and treatment group was significant for severe intraventricular hemorrhage only (P = .003); among infants born at 23 to 27 weeks’ gestation, severe intraventricular hemorrhage was statistically significantly higher with umbilical cord milking than with delayed umbilical cord clamping (22% [20/93] vs 6% [5/89], respectively; risk difference, 16% [95% CI, 6% to 26%];P = .002). Conclusions and Relevance In this post hoc analysis of a prematurely terminated randomized clinical trial of umbilical cord milking vs delayed umbilical cord clamping among preterm infants born at less than 32 weeks’ gestation, there was no statistically significant difference in the rate of a composite outcome of death or severe intraventricular hemorrhage, but there was a statistically significantly higher rate of severe intraventricular hemorrhage in the umbilical cord milking group. The early study termination and resulting post hoc nature of the analyses preclude definitive conclusions. Trial Registration ClinicalTrials.gov Identifier:NCT03019367