bluuebunny/crossref_metadata_2025_split huggingface dataset:
Suboptimal care for chronic pancreatitis patients revealed by moderate to low adherence to the United European Gastroenterology evidence‐based guidelines (HaPanEU): A Netherlands nationwide analysis
Authors: de Rijk Florence EM , Kempeneers Marinus A , Bruno Marco J , Besselink Marc GH , van Goor Harry , Boermeester Marja A , van Geenen Erwin JM , van Hooft Jeanin E , van Santvoort Hjalmar C , Verdonk Robert C ,   Dutch Pancreatitis Study Group
Published: June 2020

Background and objectiveThe 2016, United European Gastroenterology evidence‐based guidelines for the diagnosis and therapy of chronic pancreatitis (HaPanEU) provided evidence‐based recommendations for the management of chronic pancreatitis and allowed for the objective evaluation of the quality of care in several domains of disease management through assessment of guideline adherence. Therefore, the aim of this study is to evaluate the current level and the variety of care for chronic pancreatitis patients in the Netherlands using the HaPanEU guidelines as a reference standard. The majority of these patients were diagnosed before the publication of these guidelines. Therefore, in most patients, the results of the present study with respect to those recommendations regarding the diagnostic process of chronic pancreatitis represent guideline correspondence and not adherence.MethodsA subgroup of patients from the Dutch nationwide chronic pancreatitis registry (CARE) was included in a retrospective cross‐sectional observational cohort study. A total of 39 recommendations concerning the non‐invasive management of chronic pancreatitis were appointed as quality indicators (QIs). Per patient, the number of relevant QIs was determined and guideline adherence was assessed. Data were analyzed to identify factors associated with guideline adherence.ResultsOverall, 97 patients with chronic pancreatitis from 11 hospitals were included. Per patient, a mean number of 26 relevant QIs was applicable, with an average adherence rate of 53%. In 45% of the patients, guideline adherence was less than 50%. The majority of suboptimal managed QIs concerned the management of chronic pancreatitis complications. Guideline adherence was not associated with hospital type, sex, age or etiology of pancreatitis.ConclusionIn the Netherlands, adherence to the HaPanEU recommendations for the management of chronic pancreatitis is moderate to low for all non‐invasive domains, which may indicate suboptimal care for these patients. Closer guideline adherence could improve the level of care and the clinical outcomes of these patients. A nationwide approach to increase awareness of the key guideline recommendations among clinicians and patients is needed.
Can Tissue Expansion Reconstruction in the Trunk of Children Increase the Risk of Scoliosis?
Authors: Yen Paul , Bucevska Marija , Reilly Christopher , Verchere Cynthia 
Published: June 2020

Introduction: We hypothesize that treatment of significant truncal lesions with truncal tissue expanders and subsequent flap surgery in pediatric patients may increase the risk of scoliosis. This study aims to investigate any relationship between tissue expansion (TE) and scoliosis and to compare the prevalence of scoliosis in our tissue expander population to the general population. Methods: Health records of patients who underwent truncal TE at BC Children’s Hospital between 1997 and 2017 were retrospectively reviewed and analyzed. The cross-sectional component of the study consisted of radiological imaging to establish the presence or absence of scoliosis. Results: We identified 28 patients who underwent truncal TE over the study period. Ten had a scoliosis X-ray on their chart or as a part of the study. Three (10.7%) patients were identified as having developed scoliosis after TE. Conclusions: We recommend that pediatric TE patients be made aware of the potential complication of scoliosis and be followed closely in the years during and after their treatment, in order to allow for preventative measures, early diagnosis and early management (if required).
A rapid response-type doctor car system shortened time to intravenous thrombolytic therapy for patients with ischemic stroke: an observational study at a single emergency center in Japan
Authors: Yoshioka Yuki , Gamo Mina , Yoneda Ryuhei , Matsunaga Naoki , Takada Tadaaki , Fukuta Yasushi , Sato Koichi 
Published: June 2020

Abstract
Background
For patients with ischemic stroke, rapid reperfusion therapy is extremely important. In April 2015, our medical center introduced a rapid response-type doctor car (RRC) system. Here, an emergency medical team, including a physician, is dispatched to the patient’s prehospital location. The team then assesses the patient and, if necessary, initiates infusion therapy, excluding thrombolytic therapy. Before arriving at the hospital, a prehospital physician orders the preparation of diagnostic tools and conducts an early consultation to a neurologist in order to begin thrombolytic therapy more swiftly. This study aimed to determine whether the RRC system shortened the time to commence intravenous reperfusion therapy in patients with ischemic stroke. This was a retrospective observational study conducted at a tertiary emergency center in Japan. Cases of patients with ischemic stroke who underwent intravenous thrombolytic therapy from January 2015 to December 2018 were enrolled. They were divided into two groups: RRC group (intervened by RRC system) and non-RRC group (not intervened by RRC system). The groups’ door-to-needle (DTN) time was compared.

Results
During the study period, 140 patients received intravenous thrombolytic therapy. Among those, 28 were in the RRC group and 28 received the usual prehospital care. Of 56 patients, the median age was 82 years old, and 42.9% of patients were male. The median NIHSS was 14 (IQR 10–21). As for demographics, there were no significant differences between the two groups. Median DTN time was 67 min (IQR 55–79) in RRC group vs. 81 min (IQR 69–107) in usual care group, respectively (P < 0.05).

Conclusion
In this study, patients with ischemic stroke in RRC group received intravenous thrombolytic therapy in a shorter time compared to the group that received usual care.
Alteration of gut microbiota affects expression of adiponectin and resistin through modifying DNA methylation in high-fat diet-induced obese mice
Authors: Yao Hongyang , Fan Chaonan , Lu Yuanyuan , Fan Xiuqin , Xia Lulu , Li Ping , Wang Rui , Tang Tiantian , Wang Yuanyuan , Qi Kemin 
Published: June 2020

Abstract
Background
Adiponectin and resistin are typically secreted by the adipose tissue and are abnormally expressed in obesity. However, the underlying influential factors and mechanisms are to be elucidated. It is well known that the expression of genes is regulated by epigenetics while gut microbiota participates in epigenetic processes through its metabolites such as folate, biotin, and short-chain fatty acids (SCFAs). Therefore, we supposed that alteration of gut microbiota might affect the transcriptional expression of adiponectin and resistin through epigenetic regulation in obesity.

Methods
C57BL/6J mice were fed either a high-fat diet (34.9% fat by wt., 60% kcal) or a normal-fat diet (4.3% fat by wt., 10% kcal) for 16 weeks, with ampicillin and neomycin delivered via drinking water to interfere with gut microbiota development. Fecal microbiota was analyzed by 16S rRNA high-throughput sequencing. The mRNA expression levels of genes were measured by real-time quantitative RT-PCR. SCFA contents in feces were examined using gas chromatography.

Results
Alteration of the gut microbiota induced by antibiotic use, characterized by a dramatic reduction of the phylum Firmicutes and Actinobacteria and an increase of Proteobacteria with reductions of genera including Lactobacillus, norank_f_Bacteroidales_S24-7_group, Alistipes, Desulfovibrio, Helicobacter, etc., and increases in Bacteroides, Enterobacter, Klebsiella, inhibited the body weight gain in mice fed the high-fat diet instead of the normal-fat diet. The mRNA expression of adiponectin and resistin was upregulated by antibiotic use in mice fed the high-fat diet, accompanied by increased expression of fat oxidation and thermogenesis-related genes (PPAR-α, Pgc-1α, and Atgl) in the fat and/or liver, whereas no change in the expression of adiponectin and resistin was found in mice fed the normal-fat diet. Furthermore, antibiotic use reduced DNA methylation fractions of the adiponectin and resistin promoters and downregulated the expression of DNA methyltransferase 1 and 3a (DNMT1 and DNMT3a) with the high-fat diet feeding.

Conclusion
Alteration of gut microbiota induced by antibiotic use may affect the expression of adiponectin and resistin in mice fed the high-fat diet by modifying promoter DNA methylation, thus leading to increased fatty acid oxidation and less body weight gain.
Genetic parameters of resistance to pasteurellosis using novel response traits in rabbits
Authors: Shrestha Merina , Garreau Hervé , Balmisse Elodie , Bed’hom Bertrand , David Ingrid , Guitton Edouard , Helloin Emmanuelle , Lenoir Guillaume , Maupin Mickaël , Robert Raphaël , Lantier Frédéric , Gunia Mélanie 
Published: June 2020

Abstract
Background
Pasteurellosis (Pasteurella infection) is one of the most common bacterial infections in rabbits on commercial farms and in laboratory facilities. Curative treatments using antibiotics are only partly efficient, with frequent relapses. Breeding rabbits for improved genetic resistance to pasteurellosis is a sustainable alternative approach. In this study, we infected 964 crossbred rabbits from six sire lines experimentally with Pasteurella multocida. After post-mortem examination and bacteriological analyses, abscess, bacteria, and resistance scores were derived for each rabbit based on the extent of lesions and bacterial dissemination in the body. This is the first study to use such an experimental design and response traits to measure resistance to pasteurellosis in a rabbit population. We investigated the genetic variation of these traits in order to identify potential selection criteria. We also estimated genetic correlations of resistance to pasteurellosis in the experimental population with traits that are under selection in the breeding populations (number of kits born alive and weaning weight).

Results
Heritability estimates for the novel response traits, abscess, bacteria, and resistance scores, ranged from 0.08 (± 0.05) to 0.16 (± 0.06). The resistance score showed very strong negative genetic correlation estimates with abscess (− 0.99 ± 0.05) and bacteria scores (− 0.98 ± 0.07). A very high positive genetic correlation of 0.99 ± 0.16 was estimated between abscess and bacteria scores. Estimates of genetic correlations of the resistance score with average daily gain traits for the first and second week after inoculation were 0.98 (± 0.06) and 0.70 (± 0.14), respectively. Estimates of genetic correlations of the disease-related traits with average daily gain pre-inoculation were favorable but with high standard errors. Estimates of genetic and phenotypic correlations of the disease-related traits with commercial selection traits were not significantly different from zero.

Conclusions
Disease response traits are heritable and are highly correlated with each other, but do not show any significant genetic correlations with commercial selection traits. Thus, the prevalence of pasteurellosis could be decreased by selecting more resistant rabbits on any one of the disease response traits with a limited impact on the selection traits, which would allow implementation of a breeding program to improve resistance to pasteurellosis in rabbits.
Whole-genome sequencing of European autochthonous and commercial pig breeds allows the detection of signatures of selection for adaptation of genetic resources to different breeding and production systems
Authors: Bovo Samuele , Ribani Anisa , Muñoz Maria , Alves Estefania , Araujo Jose P. , Bozzi Riccardo , Čandek-Potokar Marjeta , Charneca Rui , Di Palma Federica , Etherington Graham , Fernandez Ana I. , García Fabián , García-Casco Juan , Karolyi Danijel , Gallo Maurizio , Margeta Vladimir , Martins José Manuel , Mercat Marie J. , Moscatelli Giulia , Núñez Yolanda , Quintanilla Raquel , Radović Čedomir , Razmaite Violeta , Riquet Juliette , Savić Radomir , Schiavo Giuseppina , Usai Graziano , Utzeri Valerio J. , Zimmer Christoph , Ovilo Cristina , Fontanesi Luca 
Published: June 2020

Abstract
Background
Natural and artificial directional selection in cosmopolitan and autochthonous pig breeds and wild boars have shaped their genomes and resulted in a reservoir of animal genetic diversity. Signatures of selection are the result of these selection events that have contributed to the adaptation of breeds to different environments and production systems. In this study, we analysed the genome variability of 19 European autochthonous pig breeds (Alentejana, Bísara, Majorcan Black, Basque, Gascon, Apulo-Calabrese, Casertana, Cinta Senese, Mora Romagnola, Nero Siciliano, Sarda, Krškopolje pig, Black Slavonian, Turopolje, Moravka, Swallow-Bellied Mangalitsa, Schwäbisch-Hällisches Schwein, Lithuanian indigenous wattle and Lithuanian White old type) from nine countries, three European commercial breeds (Italian Large White, Italian Landrace and Italian Duroc), and European wild boars, by mining whole-genome sequencing data obtained by using a DNA-pool sequencing approach. Signatures of selection were identified by using a single-breed approach with two statistics [within-breed pooled heterozygosity (HP) and fixation index (FST)] and group-based FST approaches, which compare groups of breeds defined according to external traits and use/specialization/type.

Results
We detected more than 22 million single nucleotide polymorphisms (SNPs) across the 23 compared populations and identified 359 chromosome regions showing signatures of selection. These regions harbour genes that are already known or new genes that are under selection and relevant for the domestication process in this species, and that affect several morphological and physiological traits (e.g. coat colours and patterns, body size, number of vertebrae and teats, ear size and conformation, reproductive traits, growth and fat deposition traits). Wild boar related signatures of selection were detected across all the genome of several autochthonous breeds, which suggests that crossbreeding (accidental or deliberate) occurred with wild boars.

Conclusions
Our findings provide a catalogue of genetic variants of many European pig populations and identify genome regions that can explain, at least in part, the phenotypic diversity of these genetic resources.
Museomics of tree squirrels: a dense taxon sampling of mitogenomes reveals hidden diversity, phenotypic convergence, and the need of a taxonomic overhaul
Authors: de Abreu-Jr Edson Fiedler , Pavan Silvia E. , Tsuchiya Mirian T. N. , Wilson Don E. , Percequillo Alexandre R. , Maldonado Jesús E. 
Published: June 2020

AbstractBackgroundTree squirrels (Sciuridae, Sciurini), in particular the highly diverse Neotropical lineages, are amongst the most rapidly diversifying branches of the mammal tree of life but also some of the least known. Negligence of this group by systematists is likely a product of the difficulties in assessing morphological informative traits and of the scarcity or unavailability of fresh tissue samples for DNA sequencing. The highly discrepant taxonomic arrangements are a consequence of the lack of phylogenies and the exclusive phenotypic-based classifications, which can be misleading in a group with conservative morphology. Here we used high-throughput sequencing and an unprecedented sampling of museum specimens to provide the first comprehensive phylogeny of tree squirrels, with a special emphasis on Neotropical taxa.ResultsWe obtained complete or partial mitochondrial genomes from 232 historical and modern samples, representing 40 of the 43 currently recognized species of Sciurini. Our phylogenetic analyses—performed with datasets differing on levels of missing data and taxa under distinct analytical methods—strongly support the monophyly of Sciurini and consistently recovered 12 major clades within the tribe. We found evidence that the diversity of Neotropical tree squirrels is underestimated, with at least six lineages that represent taxa to be named or revalidated. Ancestral state reconstructions of number of upper premolars and number of mammae indicated that alternative conditions of both characters must have evolved multiple times throughout the evolutionary history of tree squirrels.ConclusionsComplete mitogenomes were obtained from museum specimens as old as 120 years, reinforcing the potential of historical samples for phylogenetic inferences of elusive lineages of the tree of life. None of the taxonomic arrangements ever proposed for tree squirrels fully corresponded to our phylogenetic reconstruction, with only a few of the currently recognized genera recovered as monophyletic. By investigating the evolution of two morphological traits widely employed in the taxonomy of the group, we revealed that their homoplastic nature can help explain the incongruence between phylogenetic results and the classification schemes presented so far. Based on our phylogenetic results we suggest a tentative supraspecific taxonomic arrangement for Sciurini, employing 13 generic names used in previous taxonomic classifications.
Alternative splicing is highly variable among Daphnia pulex lineages in response to acute copper exposure
Authors: Suresh Sneha , Crease Teresa J. , Cristescu Melania E. , Chain Frédéric J. J. 
Published: June 2020

Abstract
Background
Despite being one of the primary mechanisms of gene expression regulation in eukaryotes, alternative splicing is often overlooked in ecotoxicogenomic studies. The process of alternative splicing facilitates the production of multiple mRNA isoforms from a single gene thereby greatly increasing the diversity of the transcriptome and proteome. This process can be important in enabling the organism to cope with stressful conditions. Accurate identification of splice sites using RNA sequencing requires alignment to independent exonic positions within the genome, presenting bioinformatic challenges, particularly when using short read data. Although technological advances allow for the detection of splicing patterns on a genome-wide scale, very little is known about the extent of intraspecies variation in splicing patterns, particularly in response to environmental stressors. In this study, we used RNA-sequencing to study the molecular responses to acute copper exposure in three lineages of Daphnia pulex by focusing on the contribution of alternative splicing in addition to gene expression responses.

Results
By comparing the overall gene expression and splicing patterns among all 15 copper-exposed samples and 6 controls, we identified 588 differentially expressed (DE) genes and 16 differentially spliced (DS) genes. Most of the DS genes (13) were not found to be DE, suggesting unique transcriptional regulation in response to copper that went unnoticed with conventional DE analysis. To understand the influence of genetic background on gene expression and alternative splicing responses to Cu, each of the three lineages was analyzed separately. In contrast to the overall analysis, each lineage had a higher proportion of unique DS genes than DE genes suggesting that genetic background has a larger influence on DS than on DE. Gene Ontology analysis revealed that some pathways involved in stress response were jointly regulated by DS and DE genes while others were regulated by only transcription or only splicing.

Conclusions
Our findings suggest an important role for alternative splicing in shaping transcriptome diversity in response to metal exposure in Daphnia, highlighting the importance of integrating splicing analyses with gene expression surveys to characterize molecular pathways in evolutionary and environmental studies.
Molecular genetic analysis of spring wheat core collection using genetic diversity, population structure, and linkage disequilibrium
Authors: Mourad Amira M. I. , Belamkar Vikas , Baenziger P. Stephen 
Published: June 2020

AbstractBackgroundWheat (Triticum aestiviumL.) is an important crop globally which has a complex genome. To identify the parents with useful agronomic characteristics that could be used in the various breeding programs, it is very important to understand the genetic diversity among global wheat genotypes. Also, understanding the genetic diversity is useful in breeding studies such as marker-assisted selection (MAS), genome-wide association studies (GWAS), and genomic selection.ResultsTo understand the genetic diversity in wheat, a set of 103 spring wheat genotypes which represented five different continents were used. These genotypes were genotyped using 36,720 genotyping-by-sequencing derived SNPs (GBS-SNPs) which were well distributed across wheat chromosomes. The tested 103-wheat genotypes contained three different subpopulations based on population structure, principle coordinate, and kinship analyses. A significant variation was found within and among the subpopulations based on the AMOVA. Subpopulation 1 was found to be the more diverse subpopulation based on the different allelic patterns (Na,Ne,I,h, anduh). No high linkage disequilibrium was found between the 36,720 SNPs. However, based on the genomic level, D genome was found to have the highest LD compared with the two other genomes A and B. The ratio between the number of significant LD/number of non-significant LD suggested that chromosomes 2D, 5A, and 7B are the highest LD chromosomes in their genomes with a value of 0.08, 0.07, and 0.05, respectively. Based on the LD decay, the D genome was found to be the lowest genome with the highest number of haplotype blocks on chromosome 2D.ConclusionThe recent study concluded that the 103-spring wheat genotypes and their GBS-SNP markers are very appropriate for GWAS studies and QTL-mapping. The core collection comprises three different subpopulations. Genotypes in subpopulation 1 are the most diverse genotypes and could be used in future breeding programs if they have desired traits. The distribution of LD hotspots across the genome was investigated which provides useful information on the genomic regions that includes interesting genes.
Transcriptomic analysis reveals hub genes and subnetworks related to ROS metabolism in Hylocereus undatus through novel superoxide scavenger trypsin treatment during storage
Authors: Li Xin , Liu Xueru , Pang Xinyue , Yin Yong , Yu Huichun , Yuan Yunxia , Li Bairu 
Published: June 2020

Abstract
Background
It was demonstrated in our previous research that trypsin scavenges superoxide anions. In this study, the mechanisms of storage quality improvement by trypsin were evaluated in H. undatus.

Results
Trypsin significantly delayed the weight loss and decreased the levels of ROS and membrane lipid peroxidation. Transcriptome profiles of H. undatus treated with trypsin revealed the pathways and regulatory mechanisms of ROS genes that were up- or downregulated following trypsin treatment by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) enrichment analyses. The current results showed that through the regulation of the expression of hub redox enzymes, especially thioredoxin-related proteins, trypsin can maintain low levels of endogenous active oxygen species, reduce malondialdehyde content and delay fruit aging. In addition, the results of protein-protein interaction networks suggested that the downregulated NAD(P) H and lignin pathways might be the key regulatory mechanisms governed by trypsin.

Conclusions
Trypsin significantly prolonged the storage life of H. undatus through regulatory on the endogenous ROS metabolism. As a new biopreservative, trypsin is highly efficient, safe and economical. Therefore, trypsin possesses technical feasibility for the quality control of fruit storage.

Graphical abstract