bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bounding the average causal effect in Mendelian randomisation studies with multiple proposed instruments: An application to prenatal alcohol exposure and attention deficit hyperactivity disorder
Authors: Diemer Elizabeth W. , Havdahl Alexandra , Andreassen Ole A. , Munafò Marcus R. , Njolstad Pal R. , Tiemeier Henning , Zuccolo Luisa , Swanson Sonja A. 
Published: February 2023

AbstractBackgroundAs large‐scale observational data become more available, caution regarding causal assumptions remains critically important. This may be especially true for Mendelian randomisation (MR), an increasingly popular approach. Point estimation in MR usually requires strong, often implausible homogeneity assumptions beyond the core instrumental conditions. Bounding, which does not require homogeneity assumptions, is infrequently applied in MR.ObjectivesWe aimed to demonstrate computing nonparametric bounds for the causal risk difference derived from multiple proposed instruments in an MR study where effect heterogeneity is expected.MethodsUsing data from the Norwegian Mother, Father and Child Cohort Study (n = 2056) and Avon Longitudinal Study of Parents and Children (n = 6216) to study the average causal effect of maternal pregnancy alcohol use on offspring attention deficit hyperactivity disorder symptoms, we proposed 11 maternal SNPs as instruments. We computed bounds assuming subsets of SNPs were jointly valid instruments, for all combinations of SNPs where the MR model was not falsified.ResultsThe MR assumptions were violated for all sets with more than 4 SNPs in one cohort and for all sets with more than 2 SNPs in the other. Bounds assuming one SNP was an individually valid instrument barely improved on assumption‐free bounds. Bounds tightened as more SNPs were assumed to be jointly valid instruments, and occasionally identified directions of effect, though bounds from different sets varied.ConclusionsOur results suggest that, when proposing multiple instruments, bounds can contextualise plausible magnitudes and directions of effects. Computing bounds over multiple assumption sets, particularly in large, high‐dimensional data, offers a means of triangulating results across different potential sources of bias within a study and may help researchers to better evaluate and emphasise which estimates are compatible with the most plausible assumptions for their specific setting.
High killing rate of nematode and promotion of rice growth by synthetic volatiles from Bacillus strains due to enhanced oxidative stress response
Authors: Ali Qurban , Yu Chenjie , Wang Yujie , Sheng Tao , Zhao Xiaozhen , Wu Xiaohui , Jing Liang , Gu Qin , Wu Huijun , Gao Xuewen 
Published: February 2023

AbstractThe plant parasitic nematode Aphelenchoides besseyi is a major pest that poses serious threats to different vegetables and crop plants. In the present study, volatiles isolated from Bacillus spp. were utilized as green biocontrol agents to overcome nematodes. In in vitro experiment, Bacillus spp. GBSC56, SYST2, and FZB42 showed the strongest nematicidal activity with killing rates of 80.78%, 75.69%, and 60.45%, respectively, as compared with control. The selected synthetic volatile organic compounds (VOCs), namely albuterol, benzaldehyde (BDH), 1,2‐benzisothiazol‐3(2H)‐one (1,2‐HIT), dimethyl disulfide (DMDS), 2‐undecanone (2‐UD), and 1,3‐propanediole (1,3‐PD), exhibited strong nematicidal activity, with A. besseyi killing rate of 85.58%, 82.65%, 81.75%, 80.36%, 84.45%, and 82.36%, respectively, at 400 μg/mL. Microscopic analysis proved that the rapid mortality was due to the production of reactive oxygen species (ROS). Molecular docking attributed this ROS production to the nematicidal effect of synthetic VOCs on NADH DEHYDROGENASE SUBUNIT 2, which is known to play a critical role in the suppression of ROS in nematode models. In a greenhouse experiment, the Bacillus strains GBSC56, SYST2, and FZB42 and their synthetic VOCs significantly improved the physiological parameters in terms of growth promotion traits. In addition, selected genes related to growth promotion and defense genes showed a significant upregulation of their expression in rice seedlings treated with those synthetic VOCs. Overall, these findings revealed that the selected Bacillus strains and their synthetic VOCs possess high potential against A. besseyi. Moreover, this study also sheds new light on the mechanisms by which specific Bacillus nematicidal VOCs influence important genes involved in rice plant growth promotion and could effectively be used to suppress plant parasitic nematodes.
Comprehensive analysis of MAPK gene family in Populus trichocarpa and physiological characterization of PtMAPK3‐1 in response to MeJA induction
Authors: Wu Jing , Liang Xiaoyu , Lin Miao , Lan Yangang , Xiang Yan , Yan Hanwei 
Published: February 2023

AbstractMitogen‐activated protein kinases (MAPKs) play important roles in plant growth and development, as well as hormone and stress responses by signaling to eukaryotic cells, through MAPK cascade, the presence of various cues; thereby, regulating various responses. The MAPK cascade consists mainly of three gene families, MAPK, MAPKK, and MAPKKK, which activate downstream signaling pathways through sequential phosphorylation. Although the MAPK cascade gene family has been reported in several species, there is a lack of comprehensive analysis in poplar. We identified 21 MAPK genes, 11 MAPKK genes, and 104 MAPKKK genes in Populus trichocarpa. The phylogenetic classification was supported by conservative motif, gene structure and motif analysis. Whole genome duplication has an important role in the expansion of MAPK cascade genes. Analysis of promoter cis‐elements and expression profiles indicates that MAPK cascade genes have important roles in plant growth and development, abiotic and biotic stresses, and phytohormone response. Expression profiling revealed a significant upregulation of PtMAPK3‐1 expression in response to drought, salt and disease stresses. Poplar transiently overexpressing PtMAPK3‐1 and treated with methyl jasmonic acid (MeJA) had higher catalase and peroxidase levels than non‐overexpressing poplar. This work represents the first complete inventory of the MAPK cascade in P. trichocarpa, which reveals that PtMAPK3‐1 is induced by the MeJA hormone and participates in the MeJA‐induced enhancement of the antioxidant enzyme system.
Optimizing growth chamber conditions for maintaining Arcticlichen‐dominatedbiocrusts
Authors: Ficko Sarah A. , McClymont Alexandra , Haughland Diane L. , Naeth M. Anne 
Published: February 2023

Optimizing growth chamber conditions for Arctic lichen biocrusts will create new opportunities to assess and prioritize reclamation techniques given the challenges associated with conducting arctic field work. Our study is the first to examine growth chamber conditions for optimizing survival and growth of Arctic lichen biocrusts, as measured by changes in lichen cover. We assessed effects of substrate crossed with substrate depth, substrate sterilization, lichen inoculation and community composition, and watering frequency in four concurrent experiments over 6 weeks on survival of arctic biocrusts collected from Diavik Diamond Mine Inc., Northwest Territories, Canada. Mixed species declined less thanFlavocetraria cucullata, and substrate affectedF. cucullatasurvival over time. Live lichen cover declined least with a 3‐day watering frequency and substrate depth of 1 cm. Sterilization did not affect lichen survival, and no contamination was observed over 6 weeks. Our results highlight the challenges of maintaining and growing lichens under controlled conditions, as only a few treatments showed increases in cover. Our research shows that even short‐term growth chamber experiments have potential to screen reclamation treatments prior to field assessments, permitting reclamation scientists to optimize limited time and resources while in the field.
Preference‐Aligned Fertility Management as a Person‐Centered Alternative to Contraceptive Use‐Focused Measures
Authors: Holt Kelsey , Galavotti Christine , Omoluabi Elizabeth , Challa Sneha , Waiswa Peter , Liu Jenny 
Published: February 2023

AbstractEquating contraceptive use with programmatic success is fundamentally flawed in failing to account for whether individuals desire contraceptive use; this is problematic because nonuse can reflect empowered decision‐making and use may reflect an individual's inability to refuse or discontinue a method. A rights‐based approach demands respect for individuals’ freedom to weigh options and choose how their desire for pregnancy prevention can be accommodated by available methods and within the context of their own personal, social, and material constraints. We offer an alternative construct, preference‐aligned fertility management (PFM), that provides a more holistic indicator of whether one's contraceptive needs are met. PFM is more person‐centered and informative for programming than status quo measures of unmet need, demand satisfied, and contraceptive use which define a positive outcome in relation to pregnancy risk rather than one's stated preferences. The PFM approach goes beyond other recent proposals for modifying the concept of unmet need by refraining from judgment of legitimate reasons for nonuse of contraception and offers a straightforward way to capture whether people act in line with their preferences. We conclude with discussion of how we plan to measure PFM in the Innovations for Choice and Autonomy (ICAN) study in Nigeria and Uganda.
Body Composition Asymmetry in University Rugby Players: Influence of Sex, Position, and Injury
Authors: Cohen Tamara R. , Rosenstein Brent , Rizk Amanda , Frenette Stephane , Fortin Maryse 
Published: February 2023

Context: Measures of side-to-side asymmetry in body composition may help identify players who are predisposed to lower limb injuries (LLI) or lower back pain (LBP). This study aimed to examine (1) side-to-side asymmetry in college rugby players according to sex and position and (2) whether side-to-side asymmetry is associated with LBP or LLI. Design: Cross-sectional study. Methods: Thirty-six rugby players (61% female) underwent a dual-energy X-ray absorptiometry assessment for total and regional (appendicular, truncal) outcomes of fat mass, lean mass, and bone mass. A subsample (n = 23) of players had a second dual-energy X-ray absorptiometry assessment 2 months postbaseline. Two-way analysis of variance was used to assess the effect of position (forward and backs) and sex on body composition asymmetry. Student paired t tests were used to assess side-to-side difference in body composition and compare baseline and follow-up measures. Logistic regression was used to assess possible associations between LLI, LBP, and the degree of side-to-side asymmetry in body composition. Results: Male players had greater asymmetry in arm bone mass compared with female players (P = .026), and trunk fat mass asymmetry was greater in forwards as compared with backs (P = .017). Forwards had significantly greater fat mass (P = .004) and percentage of fat (P = .048) on the right leg compared with the left. Backs had significantly greater bone mass in the right arm compared with the left (P = .015). From baseline to postseason, forwards had a significant increase in side-to-side asymmetry in arm lean mass (P = .006) and a significant decrease in side-to-side asymmetry in leg fat mass (P = .032). In backs, side-to-side asymmetry at baseline compared with postseason was significantly different (P = .011) for trunk fat mass. There were no significant associations between body composition asymmetry, LLI, or LBP by sex or position. Conclusion: Our results revealed the presence of side-to-side asymmetries in body composition in university rugby players between sex and position. The amount of asymmetry, however, was not associated with LBP and LLI.
Prognostic significance ofKMT2A-PTD in patients with acute myeloid leukaemia: a systematic review and meta-analysis
Authors: Ye Wu , Ma Mingzhu , Wu Xia , Deng Jili , Liu Xiaoyan , Zheng Xue , Gong Yuping 
Published: February 2023

ObjectivesWhetherKMT2A-PTD has a prognostic impact on patients with acute myeloid leukaemia (AML) is controversial. Therefore, we conducted a meta-analysis to assess the prognostic value ofKMT2A-PTD in patients with AML.MethodsEligibility criteria: we included studies concerning the prognostic value ofKMT2A-PTD in patients with AML.Information sources: Eligible studies were identified from PubMed, Embase, Medline, Web of Science, Cochrane Library and Chinese Biomedical Database. The systematic search date was 19 December 2020.Risk of bias: Sensitivity analysis was used to evaluate the stability and reliability of the combined results. Begg’s and Egger’s tests were used to assess the publication biases of studies.Synthesis of results: We calculated the pooled HRs and their 95% CIs for overall survival (OS) and event-free survival (EFS) by Stata V.12 software.ResultsIncluded studies: 18 studies covering 6499 patients were included.Synthesis of results:KMT2A-PTD conferred shorter OS in total population (HR=1.30, 95% CI 1.09 to 1.51). In the subgroup analysis,KMT2A-PTD also resulted in shorter OS in karyotypically normal AML patients (HR=2.72, 95% CI 1.83 to 3.61) and old AML patients (HR=1.93, 95% CI 1.44 to 2.42).KMT2A-PTD indicated no prognostic impact on EFS in total population (HR=1.26, 95% CI 0.86 to 1.66). However, in the sensitivity analysis,KMT2A-PTD resulted in poor EFS (HR=1.34, 95% CI 1.04 to 1.64) when deleting the study with a relatively obvious effect on the combined HR. In the subgroup analysis,KMT2A-PTD was associated with poor EFS in old AML patients (HR=1.64, 95% CI 1.25 to 2.03).ConclusionThe findings indicated thatKMT2A-PTD had an adverse impact on the prognosis of patients with AML in the total population, and the conclusion can also be applied to some subgroups including karyotypically normal AML and old AML patients.KMT2A-PTD may be a promising genetic biomarker in patients with AML in the future.Trial registration numberCRD42021227185.
Handling of missing data with multiple imputation in observational studies that address causal questions: protocol for a scoping review
Authors: Mainzer Rheanna , Moreno-Betancur Margarita , Nguyen Cattram , Simpson Julie , Carlin John , Lee Katherine 
Published: February 2023

IntroductionObservational studies in health-related research often aim to answer causal questions. Missing data are common in these studies and often occur in multiple variables, such as the exposure, outcome and/or variables used to control for confounding. The standard classification of missing data as missing completely at random, missing at random (MAR) or missing not at random does not allow for a clear assessment of missingness assumptions when missingness arises in more than one variable. This presents challenges for selecting an analytic approach and determining when a sensitivity analysis under plausible alternative missing data assumptions is required. This is particularly pertinent with multiple imputation (MI), which is often justified by assuming data are MAR. The objective of this scoping review is to examine the use of MI in observational studies that address causal questions, with a focus on if and how (a) missingness assumptions are expressed and assessed, (b) missingness assumptions are used to justify the choice of a complete case analysis and/or MI for handling missing data and (c) sensitivity analyses under alternative plausible assumptions about the missingness mechanism are conducted.Methods and analysisWe will review observational studies that aim to answer causal questions and use MI, published between January 2019 and December 2021 in five top general epidemiology journals. Studies will be identified using a full text search for the term ‘multiple imputation’ and then assessed for eligibility. Information extracted will include details about the study characteristics, missing data, missingness assumptions and MI implementation. Data will be summarised using descriptive statistics.Ethics and disseminationEthics approval is not required for this review because data will be collected only from published studies. The results will be disseminated through a peer reviewed publication and conference presentations.Trial registration numberThis protocol is registered on figshare (https://doi.org/10.6084/m9.figshare.20010497.v1).
Health-related quality of life associated with sensory impairment in Chinese middle-aged and older adults: a cohort study
Authors: Ding Yue , Yan Yuhan , Tian Yong , Du Wei , Fan Lijun 
Published: February 2023

BackgroundThe impact of sensory impairment (SI) on individual multidimensional health has not been adequately explored in developing countries. This study examined the association of hearing or/and visual impairment with health-related quality of life (HRQoL) in the Chinese middle-aged and older population, and further explored potential discrepancies in associations by gender and rural–urban residence.MethodsThis cohort study used four-wave data during 2011–2018 from the China Health and Retirement Longitudinal Study, and enrolled 13 342 community-dwelling adults aged 45 years or older. We employed linear mixed effects models to estimate the longitudinal associations between SI and HRQoL, and conducted interaction tests to assess gender or rural–urban differences in above associations.ResultsHearing impairment (HI) and visual impairment (VI) were separately and jointly associated with deteriorated overall HRQoL and decreased physical/mental component of HRQoL (all β<0, all p<0.05), and in particular, dual sensory impairment (DSI) exhibited greater impacts on HRQoL than either HI or VI alone. The impacts of SI on HRQoL were more evident among women or rural population than their counterparts (all p for interaction<0.05).ConclusionThis study observed decreased HRQoL in association with SI. The greater impact of DSI underlines the need for integrated care for comorbid sensory conditions. Our findings also indicate the necessity to reduce the burden of SI among more vulnerable populations such as females and rural adults.
Risk factors and predictors of intracranial hemorrhage after mechanical thrombectomy in acute ischemic stroke: insights from the Stroke Thrombectomy and Aneurysm Registry (STAR)
Authors: Ironside Natasha , Chen Ching-Jen , Chalhoub Reda M , Wludyka Peter , Kellogg Ryan T , Al Kasab Sami , Ding Dale , Maier Ilko , Rai Ansaar , Jabbour Pascal , Kim Joon-tae , Wolfe Stacey Q , Starke Robert M , Psychogios Marios-Nikos , Shaban Amir , Arthur Adam S , Yoshimura Shinichi , Grossberg Jonathan A , Alawieh Ali , Fragata Isabel , Polifka Adam J , Mascitelli Justin R , Osbun Joshua W , Matouk Charles , Levitt Michael R , Dumont Travis M , Cuellar-Saenz Hugo H , Williamson Richard , Romano Daniele G , Crosa Roberto Javier , Gory Benjamin , Mokin Maxim , Moss Mark , Limaye Kaustubh , Kan Peter , Spiotta Alejandro M , Park Min S 
Published: February 2023

BackgroundReducing intracranial hemorrhage (ICH) can improve patient outcome in acute ischemic stroke (AIS) intervention. We sought to identify ICH risk factors after AIS thrombectomy.MethodsThis is a retrospective review of the Stroke Thrombectomy and Aneurysm Registry (STAR) database. All patients who underwent AIS thrombectomy with available ICH data were included. Multivariable regression models were developed to identify predictors of ICH after thrombectomy. Subgroup analyses were performed stratified by symptom status and European Cooperative Acute Stroke Study (ECASS) grade.ResultsThe study cohort comprised 6860 patients. Any ICH and symptomatic ICH (sICH) occurred in 25% and 7% of patients, respectively. Hemorrhagic infarction 1 (HI1) occurred in 36%, HI2 in 24%, parenchymal hemorrhage 1 (PH1) in 22%, and PH2 in 17% of patients classified by ECASS grade. Intraprocedural complications independently predicted any ICH (OR 3.8083, P<0.0001), PH1 (OR 1.9053, P=0.0195), and PH2 (OR 2.7347, P=0.0004). Race also independently predicted any ICH (black: OR 0.5180, P=0.0017; Hispanic: OR 0.4615, P=0.0148), sICH (non-white: OR 0.4349, P=0.0107), PH1 (non-white: OR 3.1668, P<0.0001), and PH2 (non-white: OR 1.8689, P=0.0176), with white as the reference. Primary mechanical thrombectomy technique also independently predicted ICH. ADAPT (A Direct Aspiration First Pass Technique) was a negative predictor of sICH (OR 0.2501, P<0.0001), with stent retriever as the reference.ConclusionsThis study identified ICH risk factors after AIS thrombectomy using real-world data. There was a propensity towards a reduced sICH risk with direct aspiration. Procedural complications and ethnicity were predictors congruent between categories of any ICH, sICH, PH1, and PH2. Further investigation of technique and ethnicity effects on ICH and outcomes after AIS thrombectomy is warranted.
Characterising airway obstructive, dysanaptic and PRISm phenotypes of prematurity-associated lung disease
Authors: Cousins Michael , Hart Kylie , Kotecha Sarah J , Henderson A John , Watkins W John , Bush Andrew , Kotecha Sailesh 
Published: February 2023

IntroductionAlthough obstructive airway disease has been shown to be associated with prematurity, other spirometry phenotypes are less well described.ObjectivesWe characterised abnormal spirometry phenotypes in preterm-born children, including prematurity-associated obstructive lung disease (POLD, forced expiratory volume in 1 s (FEV1)<lower limit of normal (LLN), FEV1/forced vital capacity (FVC)<LLN), prematurity-associated preserved ratio of impaired spirometry (pPRISm, FEV1<LLN, FEV1/FVC≥LLN) and prematurity-associated dysanapsis (pDysanapsis, FEV1≥LLN, FEV1/FVC<LLN), and associated them with early life factors, bronchodilator responsiveness and fractional exhaled nitric oxide (FENO).Methods768 children, aged 7–12 years, underwent FENOmeasurements and spirometry before and after salbutamol. Groups were compared using parametric tests; multinomial regression was used.Results22.6% of 544 preterm-born (mean gestation: 31 weeks) and 9.2% of 195 term-born children, with satisfactory data available, were classified into one of four abnormal spirometry groups. Each phenotype was generally more prevalent in preterm-born children than in the term-born children. For the preterm group, POLD-reversible (4.4%) was associated with increased FENO, bronchopulmonary dysplasia (BPD) and intrauterine growth restriction. POLD-fixed group (3.3%) did not have increased FENObut was associated with BPD. 41% of the pDysanapsis group (5.9%) had bronchodilator response, 31% had increased FENOand was associated with postnatal weight gain. In the pPRISm group (9%), 13% responded to bronchodilators, FENOwas not increased and was non-significantly associated with body mass index (p=0.064).ConclusionsFurther to airway obstruction, we describe airway dysanapsis and pPRISm spirometry phenotypes in survivors of prematurity, both of which have poor outlook in other disease groups. By identifying specific phenotypes, targeted therapy can be developed to improve long-term outcomes.