bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deriving stratified effects from joint models investigating Gene-Environment Interactions
Authors: Laville Vincent , Majarian Timothy , de Vries Paul S. , Bentley Amy R. , Feitosa Mary F. , Sung Yun J. , Rao DC , Manning Alisa , Aschard Hugues ,   on behalf of the CHARGE Gene-Lifestyle Interactions Working Group
Published: July 2019

AbstractBackgroundModels including an interaction term and performing a joint test of SNP and/or interaction effect are often used to discover Gene-Environment (GxE) interactions. When the environmental exposure is a binary variable, analyses from exposure-stratified models which consist of estimating genetic effect in unexposed and exposed individuals separately can be of interest. In large-scale consortia focusing on GxE interactions in which only the joint test has been performed, it may be challenging to get summary statistics from both exposure-stratified and marginal (i.e not accounting for interaction) models.ResultsIn this work, we developed a simple framework to estimate summary statistics in each stratum of a binary exposure and in the marginal model using summary statistics from the “joint” model. We performed simulation studies to assess our estimators’ accuracy and examined potential sources of bias, such as correlation between genotype and exposure and differing phenotypic variances within exposure strata. Results from these simulations highlight the high theoretical accuracy of our estimators and yield insights into the impact of potential sources of bias. We then applied our methods to real data and demonstrate our estimators’ retained accuracy after filtering SNPs by sample size to mitigate potential bias.ConclusionsThese analyses demonstrated the accuracy of our method in estimating both stratified and marginal summary statistics from a joint model of gene-environment interaction. In addition to facilitating the interpretation of GxE screenings, this work could be used to guide further functional analyses. We provide a user-friendly Python script to apply this strategy to real datasets. The Python script and documentation are available at https://gitlab.pasteur.fr/statistical-genetics/J2S.
A common mechanism for efficient N2O reduction in diverse isolates of nodule‐forming bradyrhizobia
Authors: Mania Daniel , Woliy Kedir , Degefu Tulu , Frostegård åsa 
Published: July 2019

SummaryBradyrhizobia are abundant soil bacteria, which can form nitrogen‐fixing symbioses with leguminous plants, including important crops such as soybean, cowpea and peanut. Many bradyrhizobia can denitrify, but studies have hitherto focused on a few model organisms. We screened 39 diverse Bradyrhizobium strains, isolated from legume nodules. Half of them were unable to reduce N2O, making them sources of this greenhouse gas. Most others could denitrify NO3− to N2. Time‐resolved gas kinetics and transcription analyses during transition to anaerobic respiration revealed a common regulation of nirK, norCB and nosZ (encoding NO2−, NO and N2O reductases), and differing regulation of napAB (encoding periplasmic NO3− reductase). A prominent feature in all N2‐producing strains was a virtually complete hampering of NO3− reduction in the presence of N2O. In‐depth analyses suggest that this was due to a competition between electron transport pathways, strongly favouring N2O over NO3− reduction. In a natural context, bacteria with this feature would preferentially reduce available N2O, produced by themselves or other soil bacteria, making them powerful sinks for this greenhouse gas. One way to augment such populations in agricultural soils is to develop inoculants for legume crops with dual capabilities of efficient N2‐fixation and efficient N2O reduction.
Impact of a probiotic product on bowel habits and microbial profile in participants with functional constipation: A randomized controlled trial
Authors: Martoni Christopher J. , Evans Malkanthi , Chow Cheryl‐Emiliane T. , Chan Luisa S. , Leyer Gregory 
Published: July 2019

ObjectiveTo investigate the clinical efficacy of a multi‐strain probiotic product on bowel habits and microbial profile in participants with functional constipation.MethodsThis was a randomized, double‐blind, placebo‐controlled and parallel‐arm study. Altogether 94 otherwise healthy adults aged 18 to 65 years with symptoms of functional constipation were randomized as part of the intention‐to‐treat population. The participants received a placebo or the probiotic product (1.5 × 1010 CFU/day), consisting of Lactobacillus acidophilus DDS‐1, Bifidobacterium animalis subsp. lactis UABla‐12, Bifidobacterium longum UABl‐14 and Bifidobacterium bifidum UABb‐10 over 4 weeks. Outcomes included the patient assessment of constipation‐symptom (PAC‐SYM) questionnaire, stool frequency and consistency, and microbial profile.ResultsThere were no significant between‐group differences in the PAC‐SYM score, despite significant within‐group differences (P < 0.001) over the study period. The probiotic group showed a faster normalization of stool frequency and consistency, with most participants achieving a normalized profile after 1 week. Fecal samples of the probiotic group exhibited higher relative abundance of Ruminococcaceae (P = 0.0047), including the Ruminococcus genus, and lower relative abundance of Erysipelotrichaceae (P = 0.0172) at end‐point compared with baseline. Placebo group samples showed similar abundance profiles over the study, with the exception of Clostridiaceae, which was lower at the study end‐point (P = 0.0033). Among treated participants, all four probiotic strains were significantly more abundant after the intervention.ConclusionsNo significant differences were observed in symptomology, with both groups showing a more than 20% improvement. However, the probiotic helped modulate bowel function earlier than the placebo, with a corresponding shift to a more fibrolytic microbiota.
Direct effects of organic pollutants on the growth and gene expression of the Baltic Sea model bacteriumRheinheimerasp.BAL341
Authors: Karlsson Christofer M. G. , Cerro‐Gálvez Elena , Lundin Daniel , Karlsson Camilla , Vila‐Costa Maria , Pinhassi Jarone 
Published: July 2019

SummaryOrganic pollutants (OPs) are critically toxic, bioaccumulative and globally widespread. Moreover, severalOPs negatively influence aquatic wildlife. Although bacteria are major drivers of the ocean carbon cycle and the turnover of vital elements, there is limited knowledge ofOPeffects on heterotrophic bacterioplankton. We therefore investigated growth and gene expression responses of the Baltic Sea model bacteriumRheinheimerasp.BAL341 to environmentally relevant concentrations of distinct classes ofOPs in 2‐h incubation experiments. During exponential growth, exposure to a mix of polycyclic aromatic hydrocarbons, alkanes and organophosphate esters (denotedMIX) resulted in a significant decrease (between 9% and 18%) in bacterial abundance and production compared with controls. In contrast, combined exposure to perfluorooctanesulfonic acids and perfluorooctanoic acids (denotedPFAS) had no significant effect on growth. Nevertheless,MIXandPFASexposures both induced significant shifts in gene expression profiles compared with controls in exponential growth. This involved several functional metabolism categories (e.g. stress response and fatty acids metabolism), some of which were pollutant‐specific (e.g. phosphate acquisition and alkane‐1 monooxygenase genes). In stationary phase, only two genes in theMIXtreatment were significantly differentially expressed. The substantial direct influence ofOPs on metabolism during bacterial growth suggests that widespreadOPs could severely alter biogeochemical processes governed by bacterioplankton.
Guidelines for the use of acoustic indices in environmental research
Authors: Bradfer‐Lawrence Tom , Gardner Nick , Bunnefeld Lynsey , Bunnefeld Nils , Willis Stephen G. , Dent Daisy H. 
Published: July 2019

Abstract

Ecoacoustics, the study of environmental sound, is a growing field with great potential for biodiversity monitoring. Audio recordings could provide a rapid, cost‐effective monitoring tool offering novel insights into ecosystem dynamics. More than 60 acoustic indices have been developed to date, which reflect distinct attributes of the soundscape, (i.e. the total acoustic energy at a given location, including noise produced by animals, machinery, wind and rain). However, reported patterns in acoustic indices have been contradictory, possibly because there is no accepted best practice for the collection and analysis of audio recordings.

Here, we propose: (a) guidelines for designing studies using audio recordings for the rapid assessment of multiple sites; and (b) a workflow for comparing recordings with seven of the most commonly used indices, permitting discrimination among habitat‐specific soundscapes. We collected and analysed over 26,000 hr of recordings from 117 sites across a range of habitats in a human‐modified tropical landscape in central Panama; an order of magnitude more recordings than used in previously published studies.

We demonstrate that: (a) Standard error variance of indices stabilizes within 120 hr of recordings from a single location. (b) Continuous recording should be used rather than subsample recording on a schedule; sub sampling is a common practice but delays capture of site variability and maximizing total duration of recording should be prioritized. (c) Use of multiple indices to describe soundscape patterns reveals distinct diel and seasonal soundscape patterns among habitats.

We advocate collecting at least 120 hr of continuous recordings per site, and using a range of acoustic indices to categorize the soundscape, including the Acoustic Complexity Index, Acoustic Evenness Index, Acoustic Entropy Index and the Normalized Difference Soundscape Index. Differences among habitat types can be captured if multiple indices are used, and magnitude of variance is often more important than mean values. The workflow we provide will enable successful use of ecoacoustic techniques for environmental monitoring.
Public Deliberation as a Novel Method for an Exception From Informed Consent Community Consultation
Authors: Powers Patricia E. , Shore Karen K. , Perez Susan , Ritley Dominique , Kuppermann Nathan , Holmes James F. , Tzimenatos Leah S. , Shawargga Hiwote , Nishijima Daniel K. 
Published: July 2019

AbstractObjectivesCommunity consultation is required for clinical trials considering federal exception from informed consent (EFIC) procedures. Questions remain about the value of the community consult process and whether it adds intended protections to study subjects. Public deliberation methods that provide baseline participant education and elicit values and opinions about consent options is a novel approach for community consultation. This study evaluated the use of structured public deliberation methods to assess a community's values and opinions about informed consent procedures for a pediatric trauma trial.MethodsThis was a mixed‐methods descriptive study of public deliberation sessions assessing participants’ opinions about informed consent procedures for a pediatric trauma randomized controlled trial (RCT). Participants from communities with high rates of pediatric trauma were recruited via community‐based organizations and social media. Deliberation focused on three consent options for a proposed RCT: 1) enrollment using EFIC procedures with no attempt to obtain informed consent, 2) enrollment using EFIC procedures after attempting to reach a parent, or 3) enrollment only with informed consent. Participant demographic data and their opinions about the proposed study and deliberative session were also collected.ResultsThere were 102 participants across eight sessions (range of nine to 15/session, mean of 13). Most participants were female (n = 78, 76%) and a plurality were black (n = 48, 47%). The majority of participants preferred enrollment using EFIC procedures only after an attempt was made to reach a parent and informed consent was not possible (n = 56, 55%), followed by enrollment using EFIC procedures with no attempt to obtain informed consent (n = 32, 32%), and enrollment only with written informed consent (n = 13, 13%). One participant declined all options. Eighty‐four participants (82%) agreed or strongly agreed that the RCT was important to do, and 79 participants (77%) said that the sessions provided enough information to make an informed decision about the proposed RCT.ConclusionsStructured public deliberation is an effective approach when consulting communities for trials considering EFIC procedures. Future studies are needed to evaluate whether public deliberation methods provide participants with enhanced understanding of clinical trials compared to other community consultation methods.
Genome‐wide association studies of the self‐rating of effects of ethanol (SRE)
Authors: Lai Dongbing , Wetherill Leah , Kapoor Manav , Johnson Emma C. , Schwandt Melanie , Ramchandani Vijay A. , Goldman David , Joslyn Geoff , Rao Xi , Liu Yunlong , Farris Sean , Mayfield R. Dayne , Dick Danielle , Hesselbrock Victor , Kramer John , McCutcheon Vivia V. , Nurnberger John , Tischfield Jay , Goate Alison , Edenberg Howard J. , Porjesz Bernice , Agrawal Arpana , Foroud Tatiana , Schuckit Marc 
Published: July 2019

AbstractThe level of response (LR) to alcohol as measured with the Self‐Report of the Effects of Alcohol Retrospective Questionnaire (SRE) evaluates the number of standard drinks usually required for up to four effects. The need for a higher number of drinks for effects is genetically influenced and predicts higher risks for heavy drinking and alcohol problems. We conducted genome‐wide association study (GWAS) in the African‐American (COGA‐AA, N = 1527 from 309 families) and European‐American (COGA‐EA, N = 4723 from 956 families) subsamples of the Collaborative Studies on the Genetics of Alcoholism (COGA) for two SRE scores: SRE‐T (average of first five times of drinking, the period of heaviest drinking, and the most recent 3 months of consumption) and SRE‐5 (the first five times of drinking). We then meta‐analyzed the two COGA subsamples (COGA‐AA + EA). Both SRE‐T and SRE‐5 were modestly heritable (h2: 21%‐31%) and genetically correlated with alcohol dependence (AD) and DSM‐IV AD criterion count (rg: 0.35‐0.76). Genome‐wide significant associations were observed (SRE‐T: chromosomes 6, rs140154945, COGA‐EA P = 3.30E‐08 and 11, rs10647170, COGA‐AA+EA P = 3.53E‐09; SRE‐5: chromosome13, rs4770359, COGA‐AA P = 2.92E‐08). Chromosome 11 was replicated in an EA dataset from the National Institute on Alcohol Abuse and Alcoholism intramural program. In silico functional analyses and RNA expression analyses suggest that the chromosome 6 locus is an eQTL for KIF25. Polygenic risk scores derived using the COGA SRE‐T and SRE‐5 GWAS predicted 0.47% to 2.48% of variances in AD and DSM‐IV AD criterion count in independent datasets. This study highlights the genetic contribution of alcohol response phenotypes to the etiology of alcohol use disorders.
Increasing primary anastomosis rate over time for the operative management of acute diverticulitis
Authors: Ahmadi Nima , Howden William B. , Ahmadi Nazanin , Byrne Christopher M. , Young Christopher J. 
Published: July 2019

BackgroundOver the past two decades, there has been mounting evidence that primary anastomosis (PA) is a safe alternative to Hartmann's procedure (HP) in acute diverticulitis. In addition, specialized colorectal surgeons are more likely to perform PA. This study aimed to analyse if this evidence has led to an increase in the rate of PA in a major tertiary institution over time.MethodsA retrospective observational study of patients requiring operative management of acute diverticulitis from 1 January 2001 to 31 December 2015 at a tertiary teaching hospital.ResultsOne hundred and eighteen patients underwent surgery for acute diverticulitis. Patients who failed initial conservative management were more likely to have PA (43% versus 21%, P = 0.044). There was no difference in medical or surgical complications, readmission rate or mortality between patients who had a PA compared with HP. Patients were more likely to have a PA if a colorectal surgeon was operating compared with a colorectal surgery fellow or general surgeon (36% versus 19% versus 10%, P = 0.039). In patients with modified Hinchey 0–2, there was an increased PA rate within the study period, 21%, 43%, 63% to 57% from the first to the fourth quartile of patients (P = 0.038).ConclusionsThe mounting evidence for the safety of performing PA has led to an increase in the PA rates for acute diverticulitis. Patients who were operated by a colorectal surgeon were more likely to have a PA. The morbidity and mortality were similar in patients who had PA compared with HP.
Decreased neonatal hepatitis B virus (HBV) viremia by maternal tenofovir treatment predicts reduced chronic HBV infection in children born to highly viremic mothers
Authors: Chang Kai‐Chi , Chang Mei‐Hwei , Lee Chien‐Nan , Chang Chin‐Hao , Wu Jia‐Feng , Ni Yen‐Hsuan , Wen Wan‐Hsin , Shyu Ming‐Kwang , Lai Ming‐Wei , Chen Shih‐Ming , Hu Jen‐Jan , Lin Hans Hsienhong , Hsu Jenn‐Jeih , Mu Shu‐Chi , Lin Yu‐Cheng , Liu Chun‐Jen , Chen Ding‐Shinn , Lin Lung‐Huang , Chen Huey‐Ling ,   The Taiwan Study Group for the Prevention of Mother‐to‐Infant Transmission of HBV (PreMIT study)
Published: July 2019

SummaryBackgroundMaternal anti‐viral treatment prevents mother‐to‐infant transmission of hepatitis B virus (HBV), but the role of neonatal viremia on subsequent HBV infection is not clear.AimsTo investigate the effect of maternal anti‐viral treatment on neonatal serum HBV DNA and hepatitis B surface antigen (HBsAg) in infants born to highly viremic mothers and the roles of neonatal markers in predicting chronic HBV infection in children.MethodsSerum HBV DNA and HBsAg were tested in children. Of the 201 pregnant mothers, 110 received tenofovir during the third trimester. Chronic infection in children was defined by HBsAg seropositivity at 6 or 12 months lasting more than 6 months.ResultsThe maternal HBV viral loads from baseline to delivery were 8.25 ± 0.48 to 4.29 ± 0.98 log10 IU/mL; and 8.29 ± 0.49 to 8.12 ± 0.68 log10 IU/mL in the tenofovir and control group respectively. Of the 208 children, those in the tenofovir group had a lower rate of neonatal HBV DNA seropositivity at birth (5.22% vs 30.11%, P < 0.0001) and HBsAg seropositivity at 6 months (1.74% vs 11.83%, P = 0.003) and 12 months (1.74% vs 10.75%, P = 0.007). In a first multivariate analysis, maternal HBV DNA level at delivery (odds ratio = 1.70, P = 0.0172) and neonatal HBsAg positivity (odds ratio = 19.37, P < 0.0001) were significantly associated with children's chronic HBV infection. In a second model, neonatal HBV DNA positivity was a strong independent influence variable (odds ratio = 61.89, P = 0.0002).ConclusionsMaternal tenofovir therapy decreased maternal viral load and neonatal viremia. Positive neonatal HBV DNA was highly correlated with chronic HBV infection in children. Clinical Trial Identifier: NCT01312012.
Treating hoarding disorder with compassion‐focused therapy: A pilot study examining treatment feasibility, acceptability, and exploring treatment effects
Authors: Chou Chia‐Ying , Tsoh Janice Y. , Shumway Martha , Smith Lauren C. , Chan Joanne , Delucchi Kevin , Tirch Dennis , Gilbert Paul , Mathews Carol A. 
Published: July 2019

ObjectivesHoarding disorder (HD) was recognized as a psychiatric disorder in 2013. Existing literature suggests room for improvement in its treatment. The current pilot study aimed to provide an initial evaluation on the potential of compassion‐focused therapy (CFT) as an intervention for HD, with the primary aim being assessing its feasibility and acceptability, and the secondary being evaluating its effects.DesignBoth CFT and a second round of the current standard of treatment and cognitive behavioural therapy (CBT) were investigated in the current study as follow‐up treatment options for individuals who had completed CBT but were still significantly symptomatic.MethodsForty eligible individuals were enrolled (20 in each treatment). Treatment feasibility and acceptability were assessed by quantitative and qualitative measures. To explore treatment effects, HD symptom severity, HD‐related dysfunctions, and their underlying mechanisms were assessed pre‐treatment and post‐treatment.ResultsRetention rates were 72% for CFT and 37% for CBT. All participants and 79% of the participants rated CFT and CBT, respectively, as good or excellent. After receiving CFT as a follow‐up treatment, HD symptom severity dropped below the cut‐off point for clinically significant HD for 77% of the treatment completers, and 62% achieved clinically significant reduction in symptom severity. In contrast, after completing a second course of CBT, 23% had HD symptom severity dropped below the cut‐off threshold, and 29% achieved clinically significant symptom reduction.ConclusionsThe current study showed satisfactory feasibility and acceptability of CFT. Moreover, it also found promising effects of CFT in addressing hoarding‐related mechanisms that may not have been sufficiently addressed by CBT. The results suggest promising potential of CFT as a treatment for HD. Further investigation on this intervention is needed.Practitioner points

CFT may be a promising treatment option, particularly for those who do not respond well to CBT.

Improving emotion regulation and negative self‐perception by applying CFT interventions may help relieve hoarding symptoms.

Generalization of the findings should be applied with caution given the small convenience sample of the current study.

Statistical comparison on treatment effect measures between CFT and CBT as follow‐up treatments was not available due to small sample size. Therefore, the comparative conclusions based on this pilot study should be made with caution.
Make‐or‐Break: Chasing Risky Goals or Settling for Safe Rewards?
Authors: Analytis Pantelis P. , Wu Charley M. , Gelastopoulos Alexandros 
Published: July 2019

AbstractHumans regularly pursue activities characterized by dramatic success or failure outcomes where, critically, the chances of success depend on the time invested working toward it. How should people allocate time between suchmake‐or‐breakchallenges and safe alternatives, where rewards are more predictable (e.g., linear) functions of performance? We present a formal framework for studying time allocation between these two types of activities, and we explore optimal behavior in both one‐shot and dynamic versions of the problem. In the one‐shot version, we illustrate striking discontinuities in the optimal time allocation policy as we gradually change the parameters of the decision‐making problem. In the dynamic version, we formulate the optimal strategy—defined by agiving‐upthreshold—which adaptively dictates when people should stop pursuing the make‐or‐break goal. We then show that this strategy is computationally inaccessible for humans, and we explore boundedly rational alternatives. We compare the performance of the optimal model against (a) a myopic giving‐up threshold that is easier to compute, and even simpler heuristic strategies that either (b) only decide whether or not to start pursuing the goal and never give up or (c) consider giving up at a fixed number of control points. Comparing strategies across environments, we investigate the cost and behavioral implications of sidestepping the computational burden of full rationality.