bluuebunny/crossref_metadata_2025_split huggingface dataset:
Systematic Review of Stress Radiographic Modalities Stability Assessment in Supination External Rotation Ankle Fractures
Authors: Yousaf Sohail , Saleh Alan , Ahluwalia Aashish , Haleem Shahnawaz , Hayat Zara , Ramesh Palanisamy 
Published: December 2019

Background: Isolated distal fibular fractures resulting from supination external rotation (SER) injuries without evidence of obvious talar shift on standard radiographs present a diagnostic dilemma for clinicians. The status of the deep deltoid ligament, the main stabilizer of the ankle joint, is assessed by an increase in medial clear space (MCS) on radiographs. Therefore, these injuries can be either stable or unstable. In recent years, considerable clinical and research efforts have been made to determine ankle stability following SER fracture. The purpose of this systematic review was to evaluate and compare the role of different stress radiograph modalities in assessing stability of the ankle with SER fractures with no obvious talar subluxation on standard radiographs. Methods: The electronic databases MEDLINE, EMBASE, Ovid, Cochrane Central, CINAHL, and Google Scholar were searched from January 2000 to January 2018 to identify literature relating to radiologic assessment of stability of SER ankle fractures. Results: Our literature search revealed 10 peer-reviewed articles that fulfilled inclusion criteria. This yielded a total of 698 patients. The systematic review found 3 broad categories of radiographic investigations in the assessment of ankle joint stability: external rotation (ER) stress radiographs, gravity stress views (GSV), and weightbearing (WB) radiographs. Proponents of WB radiographs have demonstrated how axial load can normalize ankle joint alignment in cases of proven instability. There was a consistently high grade of evidence for using a medial clear space (MCS) value of more than 4 to 5 mm to indicate an unstable ankle following SER fracture. Conclusion: In conclusion, the results of this systematic review support an MCS value of less than 4 to 5 mm as a good indicator of stability, regardless of choice of stress imaging modality. These patients can be allowed early weightbearing with expected good functional outcomes. Recent published literature favors WB stress radiographs as a reliable and safe technique for assessing stability in SER ankle fractures. However, it should be kept in mind that this is based on studies with relatively low grades of evidence. Level of Evidence: Level II, systematic review of variable quality studies.
Normative data for multiple breath washout outcomes in school-aged Caucasian children
Authors: Anagnostopoulou Pinelopi , Latzin Philipp , Jensen Renee , Stahl Mirjam , Harper Alana , Yammine Sophie , Usemann Jakob , Foong Rachel E. , Spycher Ben , Hall Graham L. , Singer Florian , Stanojevic Sanja , Mall Marcus A. , Ratjen Felix , Ramsey Kathryn A. 
Published: December 2019

BackgroundThe multiple breath nitrogen washout (N2MBW) technique is increasingly used to assess the degree of ventilation inhomogeneity in school-aged children with lung disease. However, reference values for healthy children are currently not available. The aim of this study was to generate reference values for N2MBW outcomes in a cohort of healthy Caucasian school-aged children.MethodsN2MBW data from healthy Caucasian school-age children between 6 and 18 years old were collected from four experienced centres. Measurements were performed using an ultrasonic flowmeter (Exhalyzer D, Eco Medics AG, Duernten, Switzerland) and were analysed with commercial software (Spiroware version 3.2.1, Eco Medics AG). Normative values and upper limits of normal (ULN) were generated for lung clearance index (LCI) at 2.5% (LCI2.5%) and at 5% (LCI5%) of the initial nitrogen concentration and for moment ratios (M1/M0and M2/M0). A prediction equation was generated for functional residual capacity (FRC).ResultsAnalysis used 485 trials from 180 healthy Caucasian children aged from 6 to 18 years old. While LCI increased with age, this increase was negligible (0.04 units·year–1for LCI2.5%) and therefore fixed ULN were defined for this age group. These limits were 7.91 for LCI2.5%, 5.73 for LCI5%, 1.75 for M1/M0and 6.15 for M2/M0, respectively. Height and weight were found to be independent predictors of FRC.ConclusionWe report reference values for N2MBW outcomes measured on a commercially available ultrasonic flowmeter device (Exhalyzer D, Eco Medics AG) in healthy school-aged children to allow accurate interpretation of ventilation distribution outcomes and FRC in children with lung disease.
Increased risk of active tuberculosis during pregnancy and postpartum: a register-based cohort study in Sweden
Authors: Jonsson Jerker , Kühlmann-Berenzon Sharon , Berggren Ingela , Bruchfeld Judith 
Published: December 2019

RationaleStudies investigating the risk of active tuberculosis (TB) in association with pregnancy have not been conclusive. We aimed to investigate this risk in a large retrospective register-based cohort study in Sweden.MethodsData from women of 15–49 years of age who had given birth in Sweden between 2005 and 2013 were extracted from the national childbirth register and linked to the national TB register. Cohort time was divided into three exposure periods: during pregnancy, six months (180 days) postpartum and time neither pregnant nor postpartum. We calculated incidence rates (IRs) per 100 000 person-years for each period and incidence rate ratios (IRRs) with IRs neither pregnant nor postpartum as the reference.ResultsThe cohort included 649 342 women, of whom 553 were registered as cases of active TB, 389 when neither pregnant nor postpartum, 85 during pregnancy and 79 when postpartum. Overall IRs were 9, 12 and 17 cases per 100 000 person-years, respectively, giving IRR 1.4, 95% CI 1.1–1.7 (during pregnancy) and IRR 1.9, 95% CI 1.5–2.5 (when postpartum). Stratification by TB incidence in country of origin showed that the increased risk was concentrated amongst women from countries with a TB incidence of 100 or higher, where IRs per 100 000 person-years were 137 (when neither pregnant nor postpartum), 182 (during pregnancy) and 233 (when postpartum).ConclusionWe show a significant increase in risk of active TB during both pregnancy and postpartum in women from high incidence countries and recommend TB screening in pregnant women belonging to this risk group.
M3S: a comprehensive model selection for multi-modal single-cell RNA sequencing data
Authors: Zhang Yu , Wan Changlin , Wang Pengcheng , Chang Wennan , Huo Yan , Chen Jian , Ma Qin , Cao Sha , Zhang Chi 
Published: December 2019

AbstractBackgroundVarious statistical models have been developed to model the single cell RNA-seq expression profiles, capture its multimodality, and conduct differential gene expression test. However, for expression data generated by different experimental design and platforms, there is currently lack of capability to determine the most proper statistical model.ResultsWe developed an R package, namely Multi-Modal Model Selection (M3S), for gene-wise selection of the most proper multi-modality statistical model and downstream analysis, useful in a single-cell or large scale bulk tissue transcriptomic data. M3S is featured with (1) gene-wise selection of the most parsimonious model among 11 most commonly utilized ones, that can best fit the expression distribution of the gene, (2) parameter estimation of a selected model, and (3) differential gene expression test based on the selected model.ConclusionA comprehensive evaluation suggested that M3S can accurately capture the multimodality on simulated and real single cell data. An open source package and is available through GitHub athttps://github.com/zy26/M3S.
BayesMetab: treatment of missing values in metabolomic studies using a Bayesian modeling approach
Authors: Shah Jasmit , Brock Guy N. , Gaskins Jeremy 
Published: December 2019

Abstract
Background
With the rise of metabolomics, the development of methods to address analytical challenges in the analysis of metabolomics data is of great importance. Missing values (MVs) are pervasive, yet the treatment of MVs can have a substantial impact on downstream statistical analyses. The MVs problem in metabolomics is quite challenging and can arise because the metabolite is not biologically present in the sample, or is present in the sample but at a concentration below the lower limit of detection (LOD), or is present in the sample but undetected due to technical issues related to sample pre-processing steps. The former is considered missing not at random (MNAR) while the latter is an example of missing at random (MAR). Typically, such MVs are substituted by a minimum value, which may lead to severely biased results in downstream analyses.

Results
We develop a Bayesian model, called BayesMetab, that systematically accounts for missing values based on a Markov chain Monte Carlo (MCMC) algorithm that incorporates data augmentation by allowing MVs to be due to either truncation below the LOD or other technical reasons unrelated to its abundance. Based on a variety of performance metrics (power for detecting differential abundance, area under the curve, bias and MSE for parameter estimates), our simulation results indicate that BayesMetab outperformed other imputation algorithms when there is a mixture of missingness due to MAR and MNAR. Further, our approach was competitive with other methods tailored specifically to MNAR in situations where missing data were completely MNAR. Applying our approach to an analysis of metabolomics data from a mouse myocardial infarction revealed several statistically significant metabolites not previously identified that were of direct biological relevance to the study.

Conclusions
Our findings demonstrate that BayesMetab has improved performance in imputing the missing values and performing statistical inference compared to other current methods when missing values are due to a mixture of MNAR and MAR. Analysis of real metabolomics data strongly suggests this mixture is likely to occur in practice, and thus, it is important to consider an imputation model that accounts for a mixture of missing data types.
Integrate multi-omics data with biological interaction networks using Multi-view Factorization AutoEncoder (MAE)
Authors: Ma Tianle , Zhang Aidong 
Published: December 2019

Abstract
Background
Comprehensive molecular profiling of various cancers and other diseases has generated vast amounts of multi-omics data. Each type of -omics data corresponds to one feature space, such as gene expression, miRNA expression, DNA methylation, etc. Integrating multi-omics data can link different layers of molecular feature spaces and is crucial to elucidate molecular pathways underlying various diseases. Machine learning approaches to mining multi-omics data hold great promises in uncovering intricate relationships among molecular features. However, due to the “big p, small n” problem (i.e., small sample sizes with high-dimensional features), training a large-scale generalizable deep learning model with multi-omics data alone is very challenging.

Results
We developed a method called Multi-view Factorization AutoEncoder (MAE) with network constraints that can seamlessly integrate multi-omics data and domain knowledge such as molecular interaction networks. Our method learns feature and patient embeddings simultaneously with deep representation learning. Both feature representations and patient representations are subject to certain constraints specified as regularization terms in the training objective. By incorporating domain knowledge into the training objective, we implicitly introduced a good inductive bias into the machine learning model, which helps improve model generalizability. We performed extensive experiments on the TCGA datasets and demonstrated the power of integrating multi-omics data and biological interaction networks using our proposed method for predicting target clinical variables.

Conclusions
To alleviate the overfitting problem in deep learning on multi-omics data with the “big p, small n” problem, it is helpful to incorporate biological domain knowledge into the model as inductive biases. It is very promising to design machine learning models that facilitate the seamless integration of large-scale multi-omics data and biomedical domain knowledge for uncovering intricate relationships among molecular features and clinical features.
Listening to women’s voices: the experience of giving birth with paramedic care in Queensland, Australia
Authors: Flanagan Belinda , Lord Bill , Reed Rachel , Crimmins Gail 
Published: December 2019

Abstract
Background
Unplanned out-of-hospital birth is generally assumed to occur for women who are multiparous, have a history of a short pushing phase of labour or are experiencing a precipitate birth. However, there is little research that examines the woman’s perspective regarding factors that influenced their decision on when to access care. This research aimed to explore women’s experience of unplanned out-of-hospital birth in paramedic care. Due to the size of the data in the larger study of ‘Women’s experience of unplanned out-of-hospital birth in paramedic care’ [1], this paper will deal directly with the women’s narrative concerning her decision to access care and how previous birth experience and interactions with other healthcare professionals influenced her experience.

Method
Narrative inquiry, underpinned from a feminist perspective, was used to guide the research. Twenty-two women who had experienced an unplanned out-of-hospital birth within the last 5 years in Queensland, Australia engaged in this research.

Results
The decision of a woman in labour to attend hospital to birth her baby is influenced by information received from healthcare providers, fear of unnecessary medical intervention in birth, and previous birth experience. All themes and subthemes that emerged in the women’s narratives relate to the notion of birth knowledge. These specifically include perceptions of what constitutes authoritative knowledge, who possesses the authoritative knowledge on which actions are based, and when and how women use their own embodied knowledge to assess the validity of healthcare workers’ advice and the necessity for clinical intervention.

Conclusions
The women interviewed communicated a tension between women’s knowledge, beliefs and experience of the birth process, and the professional models of care traditionally associated with the hospital environment. It is essential that information provided to women antenatally is comprehensive and comprehensible. The decisions women make concerning their birth plan represent the women’s expectations for their birth and this should be used as a means to openly communicate issues that may impact the birth experience.
Association of cleft lip and palate on mother-to-infant bonding: a cross-sectional study in the Japan Environment and Children’s Study (JECS)
Authors:   Japan Environment & Children’s Study Group, Tsuchiya Shinobu , Tsuchiya Masahiro , Momma Haruki , Koseki Takeyoshi , Igarashi Kaoru , Nagatomi Ryoichi , Arima Takahiro , Yaegashi Nobuo 
Published: December 2019

Abstract
Background
Cleft lip and/or palate is among the most prevalent congenital birth defects, and negatively affects maternal psychological status and may consequently result in higher prevalence of child maltreatment. However, the association of childbirths of infants with cleft lip and/or palate with maternal emotional involvement still remains unclear. We examined the association between childbirths of infants with cleft lip and/or palate and mother-to-infant bonding, using data from the Japan Environment and Children’s Study, a nationwide birth cohort study.

Methods
A cross-sectional study using the jecs-an-20,180,131 dataset was performed. A total 104,065 fetuses in 15 regional centres in Japan were enrolled after obtaining informed written consent. The Mother-to-Infant Bonding Scale, a self-report scale consisting of 10 items, was used to evaluate maternal bonding at one year after childbirth. Finally, the participants consisted of 79,140 mother-infant pairs, of which 211 mothers of infants with cleft lip and/or palate were included in our analyses. Multivariable logistic regression analysis using multiple imputation for missing data was performed to calculate the odds ratio and 95% confidence interval in the estimation of the association between bonding disorders and childbirths with cleft lip and/or palate.

Results
No increased risk of bonding disorders was observed among all the mothers of infants with cleft lip and/or palate (odds ratio [95% confidence interval]; 0.97 [0.63–1.48], p = 0.880), however, advanced maternal age or multiple parity may adversely affect the associations between bonding disorders and cleft lip and/or palate, respectively. After stratification with a combination of maternal age and parity, a significant association of cleft lip and/or palate with bonding disorders was found only among advanced-age multiparae (odds ratio [95% confidence interval] = 2.51 [1.17–5.37], p = 0.018), but it was weakened after additional adjustment for maternal depression.

Conclusions
Childbirths of infants with cleft lip and/or palate may increase the risk of bonding disorders among advanced-age multiparae, possibly through maternal depression. This finding provides valuable information for the provision of multidisciplinary cleft care.
Exercise prescription for weight management in obese adults at risk for osteoarthritis: synthesis from a systematic review
Authors: Barrow Dylan R. , Abbate Lauren M. , Paquette Max R. , Driban Jeffrey B. , Vincent Heather K. , Newman Connie , Messier Stephen P. , Ambrose Kirsten R. , Shultz Sarah P. 
Published: December 2019

AbstractBackgroundThe aim of this systematic review was to identify principles of exercise interventions associated with improved physical function, weight management or musculoskeletal pain relief among young and middle-aged adults with obesity and propose an evidence-based exercise prescription that could assist in secondary prevention of osteoarthritis.MethodsA structured electronic review was conducted using MEDLINE, PubMed, and SPORTDiscus. The search string included 1) “obes*” AND “exercise” AND “interven*” AND “musculoskeletal pain OR knee pain OR hip pain”. Studies 1) were randomized controlled trials of humans, with a non-exercise control, 2) included participants aged 18–50 years, and 3) had outcomes that included physical function, musculoskeletal pain, and/or body composition. Studies were excluded if participants had peri-menopausal status, cancer, or obesity-related co-morbidities. A recommended exercise prescription was developed based on common principles used in the included exercise interventions with greatest change in function or pain.ResultsSeven studies were included. Similarities in exercise intensity (40–80% VO2max), frequency (three times per week), duration (30–60 min), and exercise mode (treadmill, cross-trainer, stationary bike, aquatic exercise) were observed in exercise interventions that resulted in improved physical function and/or pain, compared to non-exercise control groups.ConclusionCommon principles in exercise prescription for improvements in weight management, physical function and pain relief among otherwise healthy people with obesity. Exercise prescription including moderate intensity exercise for 30–60 min, three times per week can be considered an effective treatment for weight management and obesity-related musculoskeletal symptoms. Exercise should be recommended to at-risk individuals as part of secondary prevention of osteoarthritis.
The effectiveness of Reslizumab in severe asthma treatment: a real-world experience
Authors: Ibrahim H. , O’Sullivan R. , Casey D. , Murphy J. , MacSharry J. , Plant B. J. , Murphy D. M. 
Published: December 2019

Abstract
Background
Increased numbers of blood and sputum eosinophils are associated with higher exacerbation frequency and increased asthma severity. In clinical trials, targeting Interleukin-5 has been shown to be a useful therapeutic strategy for patients with severe eosinophilic asthma.

Methods
Twenty-six patients have been commenced on Reslizumab in our institution since early 2017. Safety and clinical efficacy parameters were recorded at regular intervals.

Results
Mean ACQ-6 score at the start of treatment was 3.5. The average number of exacerbations in the year preceding treatment was 8.3 per person. 30% of patients had been admitted to hospital at least once over the 12 months preceding therapy. 54% of our patients were on long term oral steroid.
Our data showed sustained improvement of Asthma control (Mean improvement in ACQ-6 was 1.7 at 1 year, and 2.0 at 2 years, P = 0.0001). Of the patients who were on long term systemic steroids, 35.7% discontinued steroids completely, with a mean reduction of prednisolone dose of 5.2 mg at 1 year. There was a 79% reduction in the annual exacerbation frequency at 1 year, and 88% at 2 years (P = < 0.0001). Modest, albeit statistically significant increases in creatine kinase which seemed to plateau by 1 year were noted.

Conclusions
Overall, Reslizumab was well tolerated with discontinuation of treatment due to side effects recorded in only one patient. Our data confirm the utility of anti-IL5 therapy in a carefully selected phenotype of severe asthma with evidence of eosinophilic airway inflammation.
Synergistic effects of APOE and sex on the gut microbiome of young EFAD transgenic mice
Authors: Maldonado Weng Juan , Parikh Ishita , Naqib Ankur , York Jason , Green Stefan J. , Estus Steven , LaDu Mary Jo 
Published: December 2019

AbstractBackgroundAlzheimer’s disease (AD) is a fatal neurodegenerative disease.APOE4is the greatest genetic risk factor for AD, increasing risk up to 15-fold compared to the commonAPOE3.Importantly, female (♀)APOE4carriers have a greater risk for developing AD and an increased rate of cognitive decline compared to male (♂)APOE4carriers. While recent evidence demonstrates that AD,APOEgenotype, and sex affect the gut microbiome (GM), howAPOEgenotype and sex interact to affect the GM in AD remains unknown.MethodsThis study analyzes the GM of 4-month (4 M) ♂ and ♀ E3FAD and E4FAD mice, transgenic mice that overproduce amyloid-β 42 (Aβ42) and express humanAPOE3+/+orAPOE4+/+. Fecal microbiotas were analyzed using high-throughput sequencing of 16S ribosomal RNA gene amplicons and clustered into operational taxonomic units (OTU). Microbial diversity of the EFAD GM was compared acrossAPOE,sex and stratified byAPOE + sex, resulting in 4-cohorts (♂E3FAD, ♀E3FAD, ♂E4FAD and ♀E4FAD). Permutational multivariate analysis of variance (PERMANOVA) evaluated differences in bacterial communities between cohorts and the effects ofAPOE + sex. Mann-Whitney tests and machine-learning algorithms identified differentially abundant taxa associated withAPOE + sex.ResultsSignificant differences in the EFAD GM were associated withAPOEgenotype and sex. Stratification byAPOE + sex revealed thatAPOE-associated differences were exhibited in ♂EFAD and ♀EFAD mice, and sex-associated differences were exhibited in E3FAD and E4FAD mice. Specifically, the relative abundance of bacteria from the generaPrevotellaandRuminococcuswas significantly higher in ♀E4FAD compared to ♀E3FAD, while the relative abundance ofSutterellawas significantly higher in ♂E4FAD compared to ♂E3FAD. Based on 29 OTUs identified by the machine-learning algorithms, heatmap analysis revealed significant clustering of ♀E4FAD separate from other cohorts.ConclusionsThe results demonstrate that the 4 M EFAD GM is modulated byAPOE + sex. Importantly, the effect ofAPOE4on the EFAD GM is modulated by sex, a pattern similar to the greater AD pathology associated with ♀E4FAD. While this study demonstrates the importance of interactive effects ofAPOE + sex on the GM in young AD transgenic mice, changes associated with the development of pathology remain to be defined.