bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pregnancy after lung and heart–lung transplantation: a French multicentre retrospective study of 39 pregnancies
Authors: Bry Charlotte , Hubert Dominique , Reynaud-Gaubert Martine , Dromer Claire , Mal Hervé , Roux Antoine , Boussaud Véronique , Claustre Johanna , Le Pavec Jérôme , Murris-Espin Muriel , Danner-Boucher Isabelle 
Published: October 2019

Pregnancy after lung and heart–lung transplantation remains rare. This French study deals with change in lung function after a pregnancy and the maternal and newborn outcomes.We retrospectively included 39 pregnancies in 35 women aged >20 years. Data on patients, course of pregnancies and newborns were collected from nine transplantation centres.Mean age at time of pregnancy was 28 years. Cystic fibrosis affected 71% of patients. Mean±sdtime between transplantation and pregnancy was 63±44 months. 26 births occurred (67%) with a mean term of 36 weeks of amenorrhoea and a mean birthweight of 2409 g. Prematurity was observed in 11 cases (43%). Forced expiratory volume in 1 s was 83.9% of predicted before pregnancy and 77.3% of predicted 1 year after the end of pregnancy (p=0.04). 10 patients developed chronic lung allograft dysfunction after delivery. Nine patients died at a mean±sdtime after transplantation of 8.2±7 years and a mean±sdtime after pregnancy of 4.6±6.5 years.These data show that pregnancy remains feasible in lung and heart–lung transplant recipients, with more frequent maternal and newborn complications than in the general population. Survival in this cohort appears to be similar to the global survival observed in lung transplant recipients. Planned pregnancy and multidisciplinary follow-up are crucial.
The appropriate dosing of erenumab for migraine prevention after multiple preventive treatment failures: a critical appraisal
Authors: Ornello Raffaele , Tiseo Cindy , Frattale Ilaria , Perrotta Giulia , Marini Carmine , Pistoia Francesca , Sacco Simona 
Published: October 2019

AbstractBackgroundErenumab, a fully human monoclonal antibody directed against the calcitonin gene-related peptide receptor, was approved for the prevention of episodic (EM) or chronic migraine (CM) at the monthly dose of 70 mg or 140 mg. We reviewed the available literature to understand if patients with prior preventive treatment failures benefit more from the 140 mg dose than the 70 mg.Main bodyWe searched papers indexed in PubMed and conference abstracts published in the last 2 years which assessed the safety and efficacy of erenumab in patients with prior preventive treatment failures. We reviewed the results of 3 randomized controlled trials and their subgroup analyses and open-label extensions. The 140 mg monthly dose of erenumab had a numerical advantage over the 70 mg monthly dose in patients with prior preventive treatment failures, both in EM and CM (with or without medication overuse) during the double blind phases of the trials and their open-label extensions. The numerical difference between the two doses increased with the increase in the number of prior preventive treatment failures.ConclusionsThe available data suggest that erenumab 140 mg monthly might be preferred over the 70 mg monthly dose in patients with EM or CM and prior preventive treatment failures. Further data are needed to assess the long-term efficacy in clinical practice of the two doses of erenumab, while their safety profile is comparable.
Random forest-based imputation outperforms other methods for imputing LC-MS metabolomics data: a comparative study
Authors: Kokla Marietta , Virtanen Jyrki , Kolehmainen Marjukka , Paananen Jussi , Hanhineva Kati 
Published: October 2019

Abstract

Background
LC-MS technology makes it possible to measure the relative abundance of numerous molecular features of a sample in single analysis. However, especially non-targeted metabolite profiling approaches generate vast arrays of data that are prone to aberrations such as missing values. No matter the reason for the missing values in the data, coherent and complete data matrix is always a pre-requisite for accurate and reliable statistical analysis. Therefore, there is a need for proper imputation strategies that account for the missingness and reduce the bias in the statistical analysis.

Results
Here we present our results after evaluating nine imputation methods in four different percentages of missing values of different origin. The performance of each imputation method was analyzed by Normalized Root Mean Squared Error (NRMSE). We demonstrated that random forest (RF) had the lowest NRMSE in the estimation of missing values for Missing at Random (MAR) and Missing Completely at Random (MCAR). In case of absent values due to Missing Not at Random (MNAR), the left truncated data was best imputed with minimum value imputation. We also tested the different imputation methods for datasets containing missing data of various origin, and RF was the most accurate method in all cases. The results were obtained by repeating the evaluation process 100 times with the use of metabolomics datasets where the missing values were introduced to represent absent data of different origin.

Conclusion
Type and rate of missingness affects the performance and suitability of imputation methods. RF-based imputation method performs best in most of the tested scenarios, including combinations of different types and rates of missingness. Therefore, we recommend using random forest-based imputation for imputing missing metabolomics data, and especially in situations where the types of missingness are not known in advance.
PPR-SSM: personalized PageRank and semantic similarity measures for entity linking
Authors: Lamurias Andre , Ruas Pedro , Couto Francisco M. 
Published: October 2019

Abstract

Background
Biomedical literature concerns a wide range of concepts, requiring controlled vocabularies to maintain a consistent terminology across different research groups. However, as new concepts are introduced, biomedical literature is prone to ambiguity, specifically in fields that are advancing more rapidly, for example, drug design and development. Entity linking is a text mining task that aims at linking entities mentioned in the literature to concepts in a knowledge base. For example, entity linking can help finding all documents that mention the same concept and improve relation extraction methods. Existing approaches focus on the local similarity of each entity and the global coherence of all entities in a document, but do not take into account the semantics of the domain.

Results
We propose a method, PPR-SSM, to link entities found in documents to concepts from domain-specific ontologies. Our method is based on Personalized PageRank (PPR), using the relations of the ontology to generate a graph of candidate concepts for the mentioned entities. We demonstrate how the knowledge encoded in a domain-specific ontology can be used to calculate the coherence of a set of candidate concepts, improving the accuracy of entity linking. Furthermore, we explore weighting the edges between candidate concepts using semantic similarity measures (SSM). We show how PPR-SSM can be used to effectively link named entities to biomedical ontologies, namely chemical compounds, phenotypes, and gene-product localization and processes.

Conclusions
We demonstrated that PPR-SSM outperforms state-of-the-art entity linking methods in four distinct gold standards, by taking advantage of the semantic information contained in ontologies. Moreover, PPR-SSM is a graph-based method that does not require training data. Our method improved the entity linking accuracy of chemical compounds by 0.1385 when compared to a method that does not use SSMs.
Cooperative evolution of two different TEs results in lineage-specific novel transcripts in the BLOC1S2 gene
Authors: Cho Hyeon-Mu , Park Sang-Je , Choe Se-Hee , Lee Ja-Rang , Kim Sun-Uk , Jin Yeung-Bae , Kim Ji-Su , Lee Sang-Rae , Kim Young-Hyun , Huh Jae-Won 
Published: October 2019

AbstractBackgroundTheBLOC1S2gene encodes the multifunctional protein BLOS2, a shared subunit of two lysosomal trafficking complexes: i) biogenesis of lysosome-related organelles complex-1 and i) BLOC-1-related complex. In our previous study, we identified an intriguing unreported transcript of theBLOC1S2gene that has a novel exon derived from two transposable elements (TEs), MIR andAluSp. To investigate the evolutionary footprint and molecular mechanism of action of this transcript, we performed PCR and RT-PCR experiments and sequencing analyses using genomic DNA and RNA samples from humans and various non-human primates.ResultsThe results showed that the MIR element had integrated into the genome of our common ancestor, specifically in theBLOC1S2gene region, before the radiation of all primate lineages and that theAluSp element had integrated into the genome of our common ancestor, fortunately in the middle of the MIR sequences, after the divergence of Old World monkeys and New World monkeys. The combined MIR andAluSp sequences provide a 3′ splice site (AG) and 5′ splice site (GT), respectively, and generate the Old World monkey-specific transcripts. Moreover, branch point sequences for the intron removal process are provided by the MIR andAluSp combination.ConclusionsWe show for the first time that sequential integration into the same location and sequence divergence events of two different TEs generated lineage-specific transcripts through sequence collaboration during primate evolution.
Complete nontuberculous mycobacteria whole genomes using an optimized DNA extraction protocol for long-read sequencing
Authors: Bouso Jennifer M. , Planet Paul J. 
Published: October 2019

Abstract

Background
Nontuberculous mycobacteria (NTM) are a major cause of pulmonary and systemic disease in at-risk populations. Gaps in knowledge about transmission patterns, evolution, and pathogenicity during infection have prompted a recent surge in genomic NTM research. Increased availability and affordability of whole genome sequencing (WGS) techniques provide new opportunities to sequence and construct complete bacterial genomes faster and at a lower cost. However, extracting large quantities of pure genomic DNA is particularly challenging with NTM due to its slow growth and recalcitrant cell wall. Here we report a DNA extraction protocol that is optimized for long-read WGS of NTM, yielding large quantities of highly pure DNA with no additional clean-up steps.

Results
Our DNA extraction method was compared to 6 other methods with variations in timing of mechanical disruption and enzymatic digestion of the cell wall, quantity of matrix material, and reagents used in extraction and precipitation. We tested our optimized method on 38 clinical isolates from the M. avium and M. abscessus complexes, which yielded optimal quality and quantity measurements for Oxford Nanopore Technologies sequencing. We also present the efficient completion of circularized M. avium subspecies hominissuis genomes using our extraction technique and the long-read sequencing MinION platform, including the identification of a novel plasmid.

Conclusions
Our optimized extraction protocol and assembly pipeline was both sufficient and efficient for genome closure. We expect that our finely-tuned extraction method will prove to be a valuable tool in long-read sequencing and completion of mycobacterial genomes going forward. Utilization of comprehensive, long-read based approaches will advance the understanding evolution and pathogenicity of NTM infections.
Analysis of the fecal microbiota of fast- and slow-growing rainbow trout (Oncorhynchus mykiss)
Authors: Chapagain Pratima , Arivett Brock , Cleveland Beth M. , Walker Donald M. , Salem Mohamed 
Published: October 2019

Abstract

Background
Diverse microbial communities colonizing the intestine of fish contribute to their growth, digestion, nutrition, and immune function. We hypothesized that fecal samples representing the gut microbiota of rainbow trout could be associated with differential growth rates observed in fish breeding programs. If true, harnessing the functionality of this microbiota can improve the profitability of aquaculture. The first objective of this study was to test this hypothesis if gut microbiota is associated with fish growth rate (body weight). Four full-sibling families were stocked in the same tank and fed an identical diet. Two fast-growing and two slow-growing fish were selected from each family for 16S rRNA microbiota profiling.
Microbiota diversity varies with different DNA extraction methods. The second objective of this study was to compare the effects of five commonly used DNA extraction methods on the microbiota profiling and to determine the most appropriate extraction method for this study. These methods were Promega-Maxwell, Phenol-chloroform, MO-BIO, Qiagen-Blood/Tissue, and Qiagen-Stool. Methods were compared according to DNA integrity, cost, feasibility and inter-sample variation based on non-metric multidimensional scaling ordination (nMDS) clusters.

Results
Differences in DNA extraction methods resulted in significant variation in the identification of bacteria that compose the gut microbiota. Promega-Maxwell had the lowest inter-sample variation and was therefore used for the subsequent analyses. Beta diversity of the bacterial communities showed significant variation between breeding families but not between the fast- and slow-growing fish. However, an indicator analysis determined that cellulose, amylose degrading and amino acid fermenting bacteria (Clostridium, Leptotrichia, and Peptostreptococcus) are indicator taxa of the fast-growing fish. In contrary, pathogenic bacteria (Corynebacterium and Paeniclostridium) were identified as indicator taxa for the slow-growing fish.

Conclusion
DNA extraction methodology should be carefully considered for accurate profiling of the gut microbiota. Although the microbiota was not significantly different between the fast- and slow-growing fish groups, some bacterial taxa with functional implications were indicative of fish growth rate. Further studies are warranted to explore how bacteria are transmitted and potential usage of the indicator bacteria of fast-growing fish for development of probiotics that may improve fish health and growth.
Microevolution within ST11 group Clostridioides difficile isolates through mobile genetic elements based on complete genome sequencing
Authors: Wu Yuan , Yang Lin , Li Wen-Ge , Zhang Wen Zhu , Liu Zheng Jie , Lu Jin-Xing 
Published: October 2019

AbstractBackgroundClade 5Clostridioides difficilediverges significantly from the other clades and is therefore, attracting increasing attention due its great heterogeneity. In this study, we used third-generation sequencing techniques to sequence the complete whole genomes of three ST11C. difficileisolates, RT078 and another two new ribotypes (RTs), obtained from three independent hospitalized elderly patients undergoing antibiotics treatment. Mobile genetic elements (MGEs), antibiotic-resistance, drug resistance genes, and virulent-related genes were analyzed and compared within these three isolates.ResultsIsolates 10,010 and 12,038 carried a distinct deletion intcdAcompared with isolate 21,062. Furthermore, all three isolates had identical deletions and point-mutations intcdC, which was once thought to be a unique characteristic of RT078. Isolate 21,062 (RT078) had a unique plasmid, different numbers of transposons and genetic organization, and harboring special CRISPR spacers. All three isolates retained high-level sensitivity to 11 drugs and isolate 21,062 (RT078) carried distinct drug-resistance genes and loss of numerous flagellum-related genes.ConclusionsWe concluded that capillary electrophoresis based PCR-ribotyping is important for confirming RT078. Furthermore, RT078 isolates displayed specific MGEs, indicating an independent evolutionary process. In the further study, we could testify these findings with more RT078 isolates of divergent origins.
Inheritance of pre-emergent metribuzin tolerance and putative gene discovery through high-throughput SNP array in wheat (Triticum aestivum L.)
Authors: Bhoite Roopali , Si Ping , Liu Hui , Xu Ling , Siddique Kadambot H. M. , Yan Guijun 
Published: October 2019

Abstract

Background
Herbicide tolerance is an important trait that allows effective weed management in wheat crops in dryland farming. Genetic knowledge of metribuzin tolerance in wheat is needed to develop new cultivars for the industry. Here, we investigated gene effects for metribuzin tolerance in nine crosses of wheat by partitioning the means and variances of six basic generations from each cross into their genetic components to assess the gene action governing the inheritance of this trait. Metribuzin tolerance was measured by a visual senescence score 21 days after treatment. The wheat 90 K iSelect SNP genotyping assay was used to identify the distribution of alleles at SNP sites in tolerant and susceptible groups.

Results
The scaling and joint-scaling tests indicated that the inheritance of metribuzin tolerance in wheat was adequately described by the additive-dominance model, with additive gene action the most significant factor for tolerance. The potence ratio for all the crosses ranged between − 1 and + 1 for senescence under metribuzin-treated conditions indicating a semi-dominant gene action in the inheritance of metribuzin tolerance in wheat. The number of segregating genes governing metribuzin tolerance was estimated between 3 and 15. The consistent high heritability range (0.82 to 0.92) in F5–7 generations of Chuan Mai 25 (tolerant) × Ritchie (susceptible) cross indicated a significant contribution of additive genetic effects to metribuzin tolerance in wheat. Several genes related to photosynthesis (e.g. photosynthesis system II assembly factor YCF48), metabolic detoxification of xenobiotics and cell growth and development (cytochrome P450, glutathione S-transferase, glycosyltransferase, ATP-binding cassette transporters and glutathione peroxidase) were identified on different chromosomes (2A, 2D, 3B, 4A, 4B, 7A, 7B, 7D) governing metribuzin tolerance.

Conclusions
The simple additive–dominance gene effects for metribuzin tolerance will help breeders to select tolerant lines in early generations and the identified genes may guide the development of functional markers for metribuzin tolerance.
Challenges, consequences, and lessons for way–outs to emergencies at hospitals: a systematic review study
Authors: Rasouli Hamid Reza , Aliakbar Esfahani Ali , Abbasi Farajzadeh Mohsen 
Published: October 2019

AbstractBackgroundEmergency Department (ED) overcrowding adversely affects patients’ health, accessibility, and quality of healthcare systems for communities. Several studies have addressed this issue. This study aimed to conduct a systematic review study concerning challenges, lessons and way outs of clinical emergencies at hospitals.MethodsOriginal research articles on crowding of emergencies at hospitals published from 1st January 2007, and 1st August 2018 were utilized. Relevant studies from the PubMed and EMBASE databases were assessed using suitable keywords. Two reviewers independently screened the titles, abstracts and the methodological validity of the records using data extraction format before their inclusion in the final review. Discussions with the senior faculty member were used to resolve any disagreements among the reviewers during the assessment phase.ResultsOut of the total 117 articles in the final record, we excluded 11 of them because of poor quality. Thus, this systematic review synthesized the reports of 106 original articles. Overall 14, 55 and 29 of the reviewed refer to causes, effects, and solutions of ED crowding, respectively. The review also included four articles on both causes and effects and another four on causes and solutions. Multiple individual patients and healthcare system related challenges, experiences and responses to crowding and its consequences are comprehensively synthesized.ConclusionED overcrowding is a multi-facet issue which affects by patient-related factors and emergency service delivery. Crowding of the EDs adversely affected individual patients, healthcare delivery systems and communities. The identified issues concern organizational managers, leadership, and operational level actions to reduce crowding and improve emergency healthcare outcomes efficiently.
Longitudinal inconsistency in responses to survey items that ask women about intimate partner violence
Authors: Loxton Deborah , Powers Jennifer , Townsend Natalie , Harris Melissa L. , Forder Peta 
Published: October 2019

Abstract

Background
Longitudinal research has demonstrated that experiences of abuse and adversity are not consistently reported over time; however, there is a paucity of available evidence regarding the consistency of reporting experiences of intimate partner violence (IPV) over time. This study aimed to investigate the consistency of self-reported IPV involving a partner or spouse. Differences in the health status of women according to consistency of IPV reporting was also investigated.

Methods
Survey data collected from the 1946–51 cohort of the Australian Longitudinal Study on Women’s Health (ALSWH) between 1996 and 2016 were used (n = 13,715). Consistency of self-reported IPV was evaluated by responses to the question “Have you ever been in a violent relationship with a partner/spouse?” Demographic and health characteristics of consistent and inconsistent reporters of IPV were compared. Multinomial logistic regression was used to determine the strength of the association between demographic and health characteristics of the women and their consistency of longitudinal reporting of IPV.

Results
There were 10,966 women who answered IPV questions over six surveys, with 9610 women (87.6%) providing consistent responses. Inconsistent responses were provided by 1356 women (12.4%), of whom 258 (2.4%) reported IPV at all but one survey (Mainly IPV), 587 (5.3%) reported no IPV at all but one survey (Mainly no IPV), and 511 (4.7%) reported Mixed IPV responses over time. Women in the Mainly IPV group, and those in the Mixed IPV group were similar to those in the Consistent IPV group in demographic and health characteristics, whereas women in the Mainly no IPV group were similar to those in the Consistent never IPV group.

Conclusions
IPV data collected at one time point may involve around 12% false negative or false positive responses. To increase reliability, IPV should be measured on more than one occasion, using different techniques and methods that account for intentional and unintentional over- and under-reporting.