bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chromosomal‐level assembly of Takifugu obscurus (Abe, 1949) genome using third‐generation DNA sequencing and Hi‐C analysis
Authors: Kang Seunghyun , Kim Jin‐Hyoung , Jo Euna , Lee Seung Jae , Jung Jihye , Kim Bo‐Mi , Lee Jun Hyuck , Oh Tae‐Jin , Yum Seungshic , Rhee Jae‐Sung , Park Hyun 
Published: December 2019

AbstractThe Tetraodontidae family are known to have relatively small and compact genomes compared to other vertebrates. The obscure puffer fish Takifugu obscurus is an anadromous species that migrates to freshwater from the sea for spawning. Thus the euryhaline characteristics of T. obscurus have been investigated to gain understanding of their survival ability, osmoregulation, and other homeostatic mechanisms in both freshwater and seawater. In this study, a high quality chromosome‐level reference genome for T. obscurus was constructed using long‐read Pacific Biosciences (PacBio) Sequel sequencing and a Hi‐C‐based chromatin contact map platform. The final genome assembly of T. obscurus is 381 Mb, with a contig N50 length of 3,296 kb and longest length of 10.7 Mb, from a total of 62 Gb of raw reads generated using single‐molecule real‐time sequencing technology from a PacBio Sequel platform. The PacBio data were further clustered into chromosome‐scale scaffolds using a Hi‐C approach, resulting in a 373 Mb genome assembly with a contig N50 length of 15.2 Mb and and longest length of 28 Mb. When we directly compared the 22 longest scaffolds of T. obscurus to the 22 chromosomes of the tiger puffer Takifugu rubripes, a clear one‐to‐one orthologous relationship was observed between the two species, supporting the chromosome‐level assembly of T. obscurus. This genome assembly can serve as a valuable genetic resource for exploring fugu‐specific compact genome characteristics, and will provide essential genomic information for understanding molecular adaptations to salinity fluctuations and the evolution of osmoregulatory mechanisms.
P2 receptors mRNA expression profiles in macrophages from ankylosing spondylitis patients and healthy individuals
Authors: Akhtari Maryam , Zargar Seyed Jalal , Vojdanian Mahdi , Ashraf‐Ganjouei Amir , Javinani Ali , Hamzeh Elham , Rezaiemanesh Alireza , Jamshidi Ahmadreza , Mahmoudi Mahdi 
Published: December 2019

AbstractBackgroundAnkylosing spondylitis (AS) is a multifactorial rheumatic disease which mainly involves the axial skeleton. Macrophages and extracellular nucleotides have been shown to contribute to the inflammation process in autoimmune diseases. Membrane‐bound purinergic P2 receptors might be involved in the modulation of immune cells in AS. Therefore, we aimed to analyze the messenger RNA (mRNA) expression of P2 receptors in the macrophages of AS patients and healthy controls.MethodsTwenty‐three AS patients and 23 age‐ and sex‐matched healthy individuals were included in our study. Whole blood‐separated monocytes of study participants were stimulated by macrophage colony‐stimulating factor for 7 days and differentiated to macrophages. Monocyte and macrophage markers were analyzed by flow cytometry. SYBR green real‐time polymerase chain reaction was used to measure the relative expression levels of P2RX1, P2RX2, P2RX3, P2RX4, P2RX5, P2RX6, P2RX7, P2RY1, P2RY2, P2RY4, P2RY6, P2RY11, P2RY12, P2RY13, P2RY14, and PANX1 genes.ResultsP2RY13 and P2RY6 genes had the highest expression levels in macrophages among P2RY genes. P2RY1 mRNA expression was significantly down‐regulated (−1.75 fold) and P2RY14 was up‐regulated (2.6 fold) in macrophages of AS patients compared to healthy individuals. P2RX4 gene had the highest expression in monocyte‐derived macrophages, followed by P2RX7 and P2RX1 genes. There was no significant difference in P2X receptor mRNA expression level between macrophages of AS patients and healthy individuals.ConclusionsOur results indicate that AS patients show altered expression levels of P2 receptor genes. Moreover, these changes might be associated with disease activity and patients’ status.
Moving the Conceptual Framework Forward: Accounting for Uncertainty
Authors: Barker Richard , Penman Stephen , Linsmeier Thomas J. , Cooper Stephen 
Published: December 2019

ABSTRACTTo meet the objectives of financial reporting in the IASB's Conceptual Framework, the “balance‐sheet approach” embraced by the Framework is necessary but not sufficient. Critical, but largely overlooked, is the role of uncertainty, which we argue defines the role of accrual accounting as a distinctive source of information for investors when investment outcomes are uncertain. This role is in some sense paradoxical: on the one hand, uncertainty undermines both the balance sheet (because uncertain assets are unrecognized) and the income statement (because mismatching is unavoidable). However, these inevitable accounting effects can be exploited to provide information about uncertainty, though not by a balance‐sheet approach alone. Rather, balance sheet recognition and measurement criteria are established by consideration of the impact of uncertainty on matching and mismatching in the income statement. This combination of balance‐sheet and income‐statement approaches enhances the communication of information to investors under conditions of uncertainty, thereby giving greater clarity and purpose in satisfying the objective of the Framework to provide information about “the amount, timing, and uncertainty of future cash flows.”
THE ANCIENT RECEPTION OF AESCHYLEAN SATYR PLAY
Authors: TOUYZ PAUL 
Published: December 2019

Abstract
In this article, I first discuss the reception of Aeschylus’ satyr plays in classical drama, the evidence for their reperformance, and their place in ancient criticism and scholarship. In the final section, I analyze the factors that contributed to the positive reputation of Aeschylean satyr play. Although the evidence is often very limited, I attempt to establish a framework for understanding this ancient reception. Here I propose that the importance placed on satyr play in Aeschylus’ reception in antiquity can be viewed as an extension of his image as the father of tragedy, through both the association of satyr play with the origins of tragedy and its place in the tetralogy.
Impact of deep breathing on predictability of stroke volume variation in spontaneous breathing patients
Authors: Mukai Akira , Suehiro Koichi , Kimura Aya , Kodama Sae , Tanaka Katsuaki , Mori Takashi , Nishikawa Kiyonobu 
Published: December 2019

BackgroundThis study investigated the ability of stroke volume variation (SVV) during deep breathing to discriminate fluid responders among spontaneously breathing patients.MethodsThirty patients undergoing general anaesthesia were enrolled and assessed before anaesthetic induction. Haemodynamic variables, including stroke volume (SV) and SVV, were measured using the ClearSight system during normal breathing. After these measurements, each patient was required to maintain deep breathing (6 breaths min−1) and haemodynamic variables were recorded. Then, the table was adjusted to the Trendelenburg position (15°) for 2 minutes, and haemodynamic variables were measured. Receiver operating characteristic curves were created for SVV during normal and deep breathing, and the difference in SVV between normal and deep breathing (ΔSVV) to discriminate fluid responders (SV increase >10% after changing position). The correlation between SV increase and ΔSVV was examined using Pearson's correlation coefficient. The grey zone approach was used to assess the inconclusive range of the haemodynamic variables.ResultsReceiver operating characteristic curve analysis indicated that ΔSVV showed good reliability in predicting fluid responsiveness (AUC: 0.850; 95% CI: 0.672‐0.953; threshold: 4%, sensitivity: 75.0%, specificity: 88.9%], while SVV during normal breathing did not (AUC: 0.579; 95% CI: 0.386‐0.756)]. Although SVV during deep breathing exhibited acceptable predictability (AUC: 0.778; 95% CI: 0.589‐0.908), the sensitivity was not good (58.3%). With the grey zone approach, the inconclusive range of ΔSVV was small with the range of 1.4%‐4.2% (23% of patients).ConclusionDeep breathing could improve the reliability of dynamic indices in spontaneously breathing patients.Trial registrationUMIN‐CTR, identifer: UMIN000027970. https://upload.umin.ac.jp/cgi-open-bin/ctr/ctr_view.cgi?recptno=R000032040
ETph: enhancers and their targets in pig and human database
Authors: Sun H. , Liao Y. , Wang Z. , Zhang Z. , Oyelami F. O. , Olasege B. S. , Wang Q. , Pan Y. 
Published: December 2019

SummaryEnhancers, as the genomic non‐coding sequences, play a key role in the activation of gene expression. They have been widely identified in the human genome. Pig is an important biomedical model for human health. Few studies have been performed to explore the enhancers in the pig genome. The human enhancer information may be useful to identify enhancers in the pig genome. In addition, the genetic background of pig traits could be useful to annotate human enhancers and diseases. Thus, in order to further study enhancers and their potential roles in human and pig, we developed a public database, ETph (Enhancers and their Targets in pig and human). ETph integrates the information on human enhancers, pig putative enhancers, target genes, pig QTL terms, human diseases, GO terms and the KEGG pathway. A total of 25 182 enhancers were identified in the pig genome using the human homology sequence information. Among them, 6232 high‐confidence enhancers were used to build the ETph. ETph provides a convenient platform to search, browse and download data. Moreover, a web‐based analytical tool was designed to visualize networks and topology graphs among pig putative enhancers, target genes, pig QTL traits and human diseases. ETph might provide a useful tool for researchers to investigate the genetic background of pig traits and human diseases. ETph is freely accessible at http://klab.sjtu.edu.cn/enhancer/.
Symbiotic collision tumour of the scalp: squamous cell carcinoma and malignant melanoma
Authors: Mangkorntongsakul Varitsara , Tng Er Tsing Vivian , Scurry James , Gourlay Ralph 
Published: December 2019

AbstractCutaneous collision tumours are the co‐existence of two tumours of different histopathological morphologies that coincide at the same or adjacent anatomical sites. A large scalp nodule excised from a 70 year‐old man revealed a collision tumour composed of cells of squamous carcinoma (SCC) and malignant melanoma. Immunohistochemistry using dual staining for melanoma and squamous cell carcinoma demonstrated an unusual pattern; nests of melanoma cells surrounded by a layer of squamous carcinoma cells. The unique architecture observed in the case suggested a relationship between the two tumours.
Increasing incidence of Acanthamoeba keratitis in a large tertiary ophthalmology department from year 1994 to 2018
Authors: Nielsen Stine Elkjær , Ivarsen Anders , Hjortdal Jesper 
Published: December 2019

AbstractPurposeAcanthamoeba (AA) keratitis is a rare and severe infection with poor prognosis. The aim was to investigate the incidence and risk factors of AA keratitis in a large tertiary ophthalmology department in Denmark.MethodsA search was performed in our electronic patient records by the keywords: ‘PHMB/polyhexanid’, ‘Brolene’ or ‘amoeba and chlorhexidine’ from year 1994 to 2018, and afterwards medical records were reviewed. A total of 65 cases of AA keratitis were hereby identified.ResultsPatients were relatively young, median (range) age of 38 (15–70) years. A significant increase of diagnosing AA keratitis occurred from 0.13 cases per million per year in the first 5 years to 2.7 cases per million per year the last 5 years. Eighty‐nine per cent of patients were contact lens users, and 49% had received corticosteroids before the diagnosis was established. Severe pain was present in 34% of patients. Prognosis was poor with final visual acuity of logMAR (mean, 95% CI) 0.30 (0.18–0.41), 18% had transplantation à chaud, and 2% were enucleated.ConclusionThe study indicates that the incidence of AA keratitis is increasing, also in Denmark. Most patients were young contact lens users. The course of the disease is long and often painful, and the prognosis is poor despite relevant treatment.
Increased ferritin levels in non‐transfusion‐dependent β°‐thalassaemia/HbE are associated with reduced CXCR2 expression and neutrophil migration
Authors: Thiengtavor Chayada , Siriworadetkun Sirikwan , Paiboonsukwong Kittiphong , Fucharoen Suthat , Pattanapanyasat Kovit , Vadolas Jim , Svasti Saovaros , Chaichompoo Pornthip 
Published: December 2019

SummarySevere bacterial infection is a major complication causing morbidity and mortality in β‐thalassaemia/HbE patients. Innate immunity constitutes the first line of defence against bacterial infection. This study aimed to comprehensively investigate the innate immune phenotype and function related to factors predisposing to infection in non‐transfusion‐dependent (NTD) β°‐thalassaemia/HbE patients. Twenty‐six patients and 17 healthy subjects were recruited to determine complement activity (C3, C4, mannose‐binding lectin and CH50) and surface receptor expression including markers of phagocytosis (CD11b, CD16 and C3bR), inflammation (C5aR) and migration (CD11b, CXCR1 and CXCR2) on neutrophils and monocytes. In addition, phagocytosis and oxidative burst activity of neutrophils and monocytes against Escherichia coli and neutrophil migration were examined. Decreased C3 and surface expression of CD11b and C3bR on neutrophils were found in patients. However, phagocytosis of neutrophils in patients was still in the normal range. Interestingly, patients displayed a significant reduction of surface expression of CXCR2 [1705 ± 217 mean fluorescent intensity (MFI)] on neutrophils, leading to impaired neutrophil migration (9·2 ± 7·7%) when compared to neutrophils from healthy subjects (2261 ± 627 MFI and 27·8 ± 9% respectively). Moreover, surface expression of CXCR2 on neutrophils was associated with splenectomy status, serum ferritin and haemoglobin levels. Therefore, impaired neutrophil migration could contribute to the increased susceptibility to infection seen in NTD β°‐thalassaemia/HbE patients.
Mucormycosis in children with haematological malignancies is a salvageable disease: a report from the Israeli Study Group of Childhood Leukemia
Authors: Elitzur Sarah , Arad‐Cohen Nira , Barg Assaf , Litichever Naomi , Bielorai Bella , Elhasid Ronit , Fischer Salvador , Fruchtman Yariv , Gilad Gil , Kapelushnik Joseph , Kharit Mira , Konen Osnat , Laor Ruth , Levy Itzhak , Raviv Dror , Shachor‐Meyouhas Yael , Shvartser‐Beryozkin Yulia , Toren Amos , Yaniv Isaac , Nirel Ronit , Izraeli Shai , Barzilai‐Birenboim Shlomit 
Published: December 2019

SummaryMucormycosis has emerged as an increasingly important cause of morbidity and mortality in immunocompromised patients, but contemporary data in children are lacking. We conducted a nationwide multicentre study to investigate the characteristics of mucormycosis in children with haematological malignancies. The cohort included 39 children with mucormycosis: 25 of 1136 children (incidence 2·2%) with acute leukaemias prospectively enrolled in a centralized clinical registry in 2004–2017, and an additional 14 children with haematological malignancies identified by retrospective search of the databases of seven paediatric haematology centres. Ninety‐two percent of mucormycosis cases occurred in patients with acute leukaemias. Mucormycosis was significantly associated with high‐risk acute lymphoblastic leukaemia (OR 3·75; 95% CI 1·51–9·37; P = 0·004) and with increasing age (OR 3·58; 95% CI 1·24–9·77; P = 0·01). Fifteen patients (38%) died of mucormycosis. Rhinocerebral pattern was independently associated with improved 12‐week survival (OR 9·43; 95% CI 1·47–60·66; P = 0·02) and relapsed underlying malignancy was associated with increased 12‐week mortality (OR 6·42; 95% CI, 1·01–40·94; P = 0·05). In patients receiving frontline therapy for their malignancy (n = 24), one‐year cumulative mucormycosis‐related mortality was 21 ± 8% and five‐year overall survival was 70 ± 8%. This largest paediatric population‐based study of mucormycosis demonstrates that children receiving frontline therapy for their haematological malignancy are often salvageable.
Mental and physical health conditions in people with intellectual disabilities: Comparing local and national data
Authors: Perera Bhathika , Audi Salma , Solomou Solomis , Courtenay Ken , Ramsay Hugh 
Published: December 2019

Accessible summaryPeople with intellectual disability have multiple health problems.People with intellectual disability have more physical and mental health conditions than people without intellectual disabilities.People with intellectual disability may need more health checks due to increased prevalence of physical and mental illnesses.More studies are needed to understand what interventions are effective to reduce health problems in people with intellectual disability.AbstractBackgroundStudies have reported increased prevalence of physical and mental health conditions in people with intellectual disabilities (ID) compared to people without intellectual disabilities. However, there are no studies looking into specific health conditions at a national level and comparing with areas that are socio‐economically disadvantaged (e.g. low income and low education attainment). This study examines and compares the prevalence of physical and mental health morbidity in people with and without intellectual disabilities at a local and national level in the UK.MethodThis study was an anecdotal analysis of physical and mental health data and annual health check‐up for England (national), London (regional) and Haringey (inner‐city borough of London) in 2016/17 using data from the NHS Digital database.ResultsPatterns of mental and physical conditions for people with and without intellectual disabilities were similar across Haringey, London and England data. Severe mental illness was more prevalent among people with intellectual disabilities compared to non‐intellectual disability peers. This further increased in the inner‐city London borough for the intellectual disability group. Certain physical health conditions were also more prevalent in people with intellectual disabilities. Certain activities such as monitoring blood pressure, recording body mass index and checking HbA1C were better in people with intellectual disabilities. Uptake of annual health checks for people with intellectual disabilities remained around 50%.DiscussionThis study further highlights the increased prevalence of mental and physical disorders in people with intellectual disabilities compared to people without intellectual disabilities. Further increased risk of mental disorders in an inner London borough compared to national data aligns with existing literature that highlights the negative impact of socio‐economic deprivation on mental and physical health. Further studies are needed to assess the health and social care measures that can reduce the physical and mental health morbidity in people with intellectual disabilities.
Clinical relevance of Aspergillus fumigatus sensitization in cystic fibrosis
Authors: Eickmeier Olaf , Zissler Ulrich M. , Wittschorek Julia , Unger Frederike , Schmitt‐Grohé Sabina , Schubert Ralf , Herrmann Eva , Zielen Stefan 
Published: December 2019

AbstractRationaleThe clinical relevance of sensitization to Aspergillus (A) fumigatus in cystic fibrosis (CF) is unclear. Some researchers propose that specific A fumigatus IgE is an innocent bystander, whereas others describe it as the major cause of TH‐2‐driven asthma‐like disease.ObjectivesLung function parameters in mild CF patients may be different in patients with and without A fumigatus sensitization. We aimed to ascertain whether allergen exposure to A fumigatus by bronchial allergen provocation (BAP) induces TH‐2 inflammation comparable to an asthma‐like disease.MethodsA total of 35 patients, aged 14.8 ± 8.5 years, and 20 healthy controls were investigated prospectively. The patients were divided into two groups: group 1 (n = 18): specific (s)IgE negative, and group 2 (n = 17): sIgE positive (≥0.7 KU/L) for A fumigatus. Lung function, exhaled NO, and induced sputum were analysed. All sensitized patients with an FEV1 > 75% (n = 13) underwent BAP with A fumigatus, and cell counts, and the expression of IL‐5, IL‐13, INF‐γ, and IL‐8 as well as transcription factors T‐bet, GATA‐3, and FoxP3, were measured.ResultsLung function parameters decreased significantly compared to controls, but not within the CF patient group. After BAP, 8 of 13 patients (61%) had a significant asthmatic response and increased eNO 24 hours later. In addition, marked TH‐2‐mediated inflammation involving eosinophils, IL‐5, IL‐13, and FoxP3 became apparent in induced sputum cells.ConclusionOur study demonstrated the clinical relevance of A fumigatus for the majority of sensitized CF patients. A distinct IgE/TH‐2‐dominated inflammation was found in induced sputum after A fumigatus exposure.
New clinical characteristics and novel pathogenic variants of patients with hereditary leukodystrophies
Authors: Xie Juan‐Juan , Ni Wang , Wei Qiao , Ma Huan , Bai Ge , Shen Ying , Wu Zhi‐Ying 
Published: December 2019

AbstractAimLeukodystrophies are a group of inherited white matter disorders with clinical, genetic, and imaging heterogeneity, which usually pose a diagnostic challenge for physicians. We aimed to identify new clinical characteristics and novel pathogenic variants of hereditary leukodystrophies in this study.MethodsWhole exome sequencing (WES) was performed in 28 unrelated patients clinically suspected with leukodystrophies. Leukocytes enzyme activity test, electroencephalogram (EEG), electromyography (EMG), and brain MRI were conducted. Functional analysis was performed, and the pathogenicity of variants was classified according to the American College of Medical Genetics and Genomics (ACMG) standards and guidelines.ResultsWe made definite diagnosis in 8 probands with 12 pathogenic variants and reported new clinical characteristics and imaging features of these patients. Three novel pathogenic variants were identified, including a microdeletion variant c.2654_2654+3del within CSF1R, a nonsense variant c.1321C>T, and a missense variant c.166G>C within GALC.ConclusionOur results have deepened the understanding of clinical, genetic, and imaging heterogeneity of hereditary leukodystrophies, and expanded the spectrum of pathogenic variants and clinical features.