bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bile acid synthesis disorders in Japan: long-term outcome and chenodeoxycholic acid treatment
Authors: Kimura Akihiko , Mizuochi Tatsuki , Takei Hajime , Ohtake Akira , Mori Jun , Shinoda Kunihiro , Hashimoto Takuji , Kasahara Mureo , Togawa Takao , Murai Tsuyoshi , Iida Takashi , Nittono Hiroshi 
Published: January 2020

Abstract
Background: We encountered 7 Japanese patients with bile acid synthesis disorders (BASD) over 21 years between 1996 and 2017. Diagnoses were made by bile acid and genetic analyses. We gave low-dose, long-term chenodeoxycholic acid (CDCA) treatment to 5 of the patients, who had 3β-hydroxy-Δ 5 -C 27 -steroid dehydrogenase/isomerase (3β-HSD) deficiency (n=3) or Δ 4 -3-oxosteroid 5β-reductase (5β-reductase) deficiency (n=2). Another patient with the latter diagnosis whose bile acid analyses had mitigating features was maintained on ursodeoxycholic acid according to parental preferences and now remains healthy after discontinuation of treatment. A patient with oxysterol 7α-hydroxylase deficiency developed liver failure and fully recovered after successful liver transplantation. We used clinical records to clarify long-term outcome and value of CDCA in the other patients. Efficacy of CDCA treatment was evaluated in the 5 patients given a low dose (5 to 10 mg/kg/day) for a long term. Results: Medians with ranges of current patient ages and duration of CDCA treatment are10 years (8 to 43) and 10 years (8 to 21), respectively. All 7 patients, who had homozygous or compound heterozygous mutations in the HSD3B7 , SRD5B1 , or CYP7B1 gene, are currently in good health without liver dysfunction. In the 5 patients with CDCA treatment, hepatic function gradually improved following initiation. No adverse effects were noted. Conclusions: We concluded that low-dose CDCA treatment is effective in 3β-HSD deficiency and 5β-reductase deficiency, as cholic acid has been in other countries. BASD carry a good prognosis following early diagnosis and initiation of long-term, low-dose CDCA treatment.
Novel de novo heterozygous mutation on SYNGAP1 from the Indian population
Authors: Verma Vijaya , Mandora Amit , Botre Abhijeet , Clement James Premdoss 
Published: January 2020

Abstract
Background : Exome sequencing is a prominent tool to identify novel and deleterious mutations which could be nonsense, frameshift, and canonical splice-site mutations in a specific gene. De novo mutations in SYNGAP1 , which codes for synaptic RAS-GTPase activating the protein, causes Intellectual disability (ID) and Autism Spectrum Disorder (ASD). SYNGAP1 related ASD/ID is one of the rare diseases that is detrimental to the normal neuronal developmental and disrupts the global development of a child. Results: We report a case of a child of 2-year old with global developmental delay, microcephaly subtle dysmorphism, absence seizures, disrupted sleep, delay in learning a language, and eating problems. Upon further validation, the child has a few traits of ASD. Here, based on focused exome sequencing, we report a de novo heterozygous mutation in SYNGAP1 exon 11 with c. 1861 C>T (p.arg612ter). Currently, the child is on atorvastatin and has shown considerable improvement in global behaviour and cognitive development. The long-term follow up of the child’s development would contribute to the already existing knowledge of the developmental trajectory in individuals with SYNGAP1 heterozygous mutation. Conclusion: In this report, we discuss the finding of a novel mutation in one of the genes, SYNGAP1 , implicated in ASD/ID. In addition, we discuss the current treatment prescribed to the patient and the progress of global developmental of the child.
Metagenomic Analysis of the Virome in Lung Tissues and Guts of Wild Mice
Authors: Yin Hai chang , Chen Hong yan , Zhao Li li , Lu Tao feng 
Published: January 2020

Abstract
Background Mice, as host animals of a variety of pathogens, can spread 60 kinds of human diseases including more than ten families of viruses including Poxviridae, Herpesviridae, and so on. Methods In this study, lung tissues and gut samples of 7-week-old mice from outdoor environments were sequenced using metagenomics, and an abundance of virome information was acquired. Results A total of 82 families of mammalian viruses, plant viruses, insect viruses, and phages were detected. Among the top 10 most abundant families were the RNA viruses Orthomyxoviridae, Picornaviridae, Bunyaviridae, and Arenaviridae, the DNA virus Herpesviridae, the insect viruses Nodaviridae and Baculoviridae, the plant virus Tombusviridae, and the phage Myoviridae. Except for Myoviridae, whose abundance in guts was higher than in lung tissues, the abundance of viruses in the lung tissues and guts showed no significant difference. Conclusions The data obtained in this study provided an overview of the viral community present in these mice samples, revealing some mouse-associated viruses closely related to known human or animal pathogens. Strengthening our understanding of unclassified viruses in mice in the natural environment could provide scientific guidance for the prevention and control of new viral outbreaks that can spread via rodents.
Identifying genetic variants and pathways associated with extreme levels of fetal hemoglobin in Sickle Cell Disease in Tanzania.
Authors: Nkya Siana , Mwita Liberata , Mgaya Josephine , Kumburu Happiness , Zwetselaar Marco van , Menzel Stephan , Mazandu Gaston Kuzamunu , Sangeda Raphael Z. , Chimusa Emile R. , Makani Julie 
Published: January 2020

Abstract
Background: Sickle cell disease (SCD) is a blood disorder caused by a point mutation on the beta globin gene resulting in the synthesis of abnormal hemoglobin. Fetal hemoglobin (HbF) reduces disease severity, but the levels vary from one individual to another. Most research has focused on common variants which differ across populations and hence do not fully account for HbF variation. Results: This study investigates rare and common genetic variants that influence HbF levels in SCD patients to elucidate variants and pathways in SCD patients with extreme HbF levels (≥7.7% for high HbF) and (≤2.5% for low HbF) in Tanzania. We performed targeted next generation sequencing (Illumina_Miseq) covering exonic and other significant fetal hemoglobin-associated loci, including BCL11A , MYB , HOXA9 , HBB , HBG1 , HBG2 , CHD4 , KLF1 , MBD3 , ZBTB7A and PGLYRP1 . Results revealed a range of genetic variants, including bi-allelic and multi-allelic SNPs, frameshift insertions and deletions, some of which have functional importance. Notably, there were significantly more deletions in individuals with high HbF levels (11% vs 0.9%). We identified frameshift deletion in individuals with high HbF levels and frameshift insertions in individuals with low HbF. CHD4 and MBD3 genes, interacting in the same sub-network, were identified to have a significant number of pathogenic or non-synonymous mutations in individuals with low HbF levels, suggesting an important role of epigenetic pathways in the regulation of HbF synthesis. Conclusion: This study provides new insights in selecting essential variants and identifying potential biological pathways associated with extreme HbF levels in SCD using multiple genomic variants associated with HbF in SCD.
Unmet supportive care needs and associated factors among young adult cancer patients in Japan
Authors: Okamura Masako , Fujimori Maiko , Sato Ayako , Uchitomi Yosuke 
Published: January 2020

Abstract
Background: Young adult cancer patients often face unique challenges and have potential unmet needs. This study aimed (1) to describe unmet supportive care needs among young adults with cancer in Japan, and (2) to identify its associated factors.Methods: In a cross-sectional web-based survey, 206 young adults with cancer were assessed for supportive care needs. Multiple regression analysis examined whether demographics, clinical variables and social support were associated with unmet supportive care needs.Results: A total of 206 patients (180 female) with a mean age of 33.7 years (SD=4.3, range: 22-39) participated. One hundred and fifty-eight participants (76.7%) reported at least one unmet supportive care needs. The top 20 unmet needs included 9 of the 10 psychological needs, 3 of the 5 physical and daily living needs, 8 of the 11 health system and information needs and 1 of the 5 sexuality needs. Multiple regression analysis revealed that perceived poorer PS, experience of change in work/school after a cancer diagnosis and poor social support were significantly associated with higher supportive care needs. The total score of supportive care needs was significantly associated with both psychological distress and QOL.Conclusions: More than 70% of young adult cancer survivors reported unmet supportive care needs and most of those were psychological needs. The findings suggest potential opportunities for intervention in addressing psychological needs rather than physical and information needs.
Comparative genome analysis and phylogenomic of Xanthomonas citri pv. viticola lead to new taxonomic insights about species of Xanthomonas
Authors: Farias Antonio Roberto Gomes de , Junior Wilson José da Silva , Junior José Bandeira do Nascimento , Balbino Valdir de Queiroz , Benko-Iseppon Ana Maria , Lima Nelson Bernardi , Gama Marco Aurélio Siqueira da , Souza Elineide Barbosa 
Published: January 2020

Abstract
Background Xanthomonas citri pv. viticola is one of the most critical grapevine diseases in the Northeast of Brazil, presenting a high risk to Brazilian and worldwide areas of grape production. The X.citri pv. viticola epithet was recently proposed to be changed from X. campestris pv. v iticola based on multilocus sequence analysis and whole-genome sequences. Besides, genomics has revolutionized the field of bacteriology, by associating genome sequencing with comparative analysis such as in silico analysis such as DNA-DNA hybridization, average nucleotide identity, distance between genomes, pan-genomic approach, and phylogenomic, providing valuable insights and knowledge about virulence factors and contributing to increase the understanding and clarifying the taxonomic relationship of Xanthomonas and others prokaryotic species.Results We used the whole-genome sequence of three Brazilian strains and the pathotype to characterize X.citri pv. viticola accessions plus 124 whole-genome sequences of Xanthomonas species available in NCBI, comprising 13 species and 15 pathovars. The whole-genome sequence structure of X. citri pv. viticola was shown presents a high level of conservation concerning other X. citri species. Pan-genomic approaches, average nucleotide identity analysis, and in silico DNA-DNA hybridization were carried out, allowing X.citri pv. viticola characterization and inferences on the phylogenetic relationships within Xanthomonas . The analysis of the sequence of the 128 genomes clustered the Xanthomonas strains in eight main groups according to the recently proposed classification in all approaches used. Also, the analysis revealed that X. hortorum and X. gardneri should be classified as a single species, and the strain 17 of X. campestris and XC01 of X. citri pv. mangiferaeindicae widely described in the literature are misclassified.Conclusions We performed the genomic characterization of three representative Brazilian strains of Xcv . The genomic approaches based in the pan-genome, average nucleotide identity, and in silico DNA-DNA hybridization support the proposed taxonomic position of X.citri pv. viticola and of the recently proposed Xanthomonas species and pathovars. In addition, we detected species delimitation of the misclassified Xanthomonas strains with extensive studies reported in the literature.
Antimalaria Activity of Cassia spectabilis DC Leaf and Its Inhibition Effect in Heme Detoxification
Authors: Ekasari Wiwied - , Basuki Dewi Resty , Arwati Heny - , Wahy Tutik Sri 
Published: January 2020

Abstract
Background In previous studies, Cassia spectabilis DC leaf has shown a good antimalarial activity. Therefore, this study is a follow-up study of leaf activity and mechanism of C. spectabilis DC as an antimalarial. Methods In vitro antimalarial activity testing using P. falciparum which was done with bioassay guide isolation in order to obtain the active compound. In vivo testing towards infected P. berghei mice was conducted to determine the effects of antimalarial prophylaxis and antimalarial activity in combination with artesunate. Whereas, heme detoxification inhibition testing as one of the antimalarial mechanisms was carried out using the Basilico method. Results The results showed that active antimalarial isolate obtained from C. spectabilis DC leaf had a structural pattern that was identical to (-)-7-hydroxyspectaline. Prophylactic test on infected P. berghei mice obtained the highest dose of inhibition percentage of 90% ethanol extract of C. spectabilis DC leaf was 68.61% while positive (doxycycline) control at 100 mg kg-1 was 73.54%. In antimalarial testing in combination with artesunate, it was found that administering 150 mg kg-1 (three times a day) of C. spectabilis DC (D0 − D2) + artesunate (D2) was better than the standard combination of amodiaquine + artesunate with 99.18% and 92.88% inhibition percentage. For the inhibitory activity of heme detoxification from ethanol extract 90%, C. spectabilis DC leaf had IC50 value of 0.375 mg mL-1 which was better than chloroquine diphosphate. Conclusion These results showed that C. spectabilis DC leaves possesses potent antimalarial activity and may offer a potential agent for effective and affordable antimalarial phytomedicine.
Orthodontic treatment effect on gingival recessions
Authors: Antanaviciene Guoste , Smailiene Dalia , Baseviciene Nomeda , Zasciurinskiene Egle 
Published: January 2020

Abstract
Background The occurrence of gingival recessions (GR) after orthodontic treatment (OT) is well described in the literature. However, there is a lack of information about changes to pre-existing GR during OT. Methods The aim of this retrospective study was to examine the change of GR before and after OT. Intraoral photographs of 993 patients treated with fixed appliances between 2005 and 2017 were evaluated. Patients who had at least one GR on the vestibular surface of maxillary/mandibular teeth mesial to first molars were included. GR was measured on good quality plaster models before and after OT. The change of GR (T0-T1) was categorised into the three groups: worsened, did not change and improved (this group consisted of GR, which became better but did not disappear, and fully healed, which disappeared after OT)). The change by ≥0.5 mm was recorded. Statistical analysis was performed using SPSS Statistics (Version 22.0. Armonk, NY). Results Fifty-one (5.1%) patient had ≥1 GR before OT. Of them, 37 (72.5%) patients were included in the final analysis according to the inclusion criteria. GR before OT was found on 114 buccal/labial surfaces. The mean GR improvement was 0.51 (95% CI: 0.40, 0.63) mm (p<0.001). GR improved in 71 teeth (62.3%), did not change in 37 (32.4%), and worsened in 6 (5.3%). Of the 71 GR, which improved, full healing was observed in 15 (21.1%) teeth. GR had a greater chance of improvement in cases with a thick/normal gingival biotype compared with the thin biotype (OR 2.4; 95% CI: 1.07; 5.28) (p=0.03). There was a lower chance for GR improvement in cases with pre-treatment open bite (OR 3.29; 95% CI: 1.10; 9.81) (p=0.03) and Class III patients (OR 2.79; 95% CI: 1.14; 6.83) (p=0.03). Conclusions Based on the results of this retrospective study, we conclude that orthodontic treatment may change and even influence the healing of GR.
Whole Exome Sequencing in Idiopathic Short Stature: Rare Mutations Affecting Growth
Authors: Khonsari Nami Mohammadian , Noorian Shahab , Rohani Farzaneh , Savad Sharham , Kabir Kourosh , Hakak-Zargar Benyamin , Ghanipour Nima , Gholami Mehri , Zaimkohan Hooshang 
Published: January 2020

Abstract
Introduction Evaluation of short stature is a challenge for pediatricians and in the process, idiopathic short stature (ISS) is an often diagnosis of exclusion. Non-pathogenetic mutations affecting height may present with phenotypes similar to the pathogenetic mutations. In this study, we aim to identify the underlying genetic cause of short stature in patients diagnosed with ISS and investigate potential treatments for them. Materials and Methods We identified 14 children in our practice who were under the age of 15 and were initially labelled as ISS. Then, we evaluated their plasma whole-exome sequencing (WES). Results Out of the 14 patients assessed with WES, five had normal results and correctly diagnosed with ISS. However, four of them had rare mutations that have not been extensively studied in the past. Due to the functions of these mutated genes and our patients’ phenotypes, we suspect that these mutations played a role in the short stature. Out of the remaining five patients, four had genetic mutations known to cause short stature and one had a mutation that was known not to affect height. Conclusion In patients who are initially diagnosed with ISS, WES can help to identify rare mutations that may play a role in short stature. Directing attention to these genes, may help with the correct diagnosis and choosing proper treatment for the patients.
Validity and Reliability of the Korean Anesthesia Surrendering Instrument
Authors: Lee Hanna , Han Jeongwon , Kang Jisoon 
Published: January 2020

Abstract
Background : In Korea, to reduce patients’ anxiety regarding anesthesia induction and to increase compliance, the nurses need a measurement for understanding of anesthesia surrendering. This study examined the reliability and validity of the Korean version of the anesthesia surrendering instrument (ASI), which was originally developed to measure anesthesia surrendering in Swedish adults. Methods: The study population consisted of 306 patients who received general anesthesia for abdominal, breast, knee, hip, lower back, or shoulder surgery in ten hospitals across five regions of Korea, from June to September 2019. We assessed the validity of the content, construct, and criterion used, as well as the reliability of the ASI. Results: The results showed that the instrument had appropriate content validity with the item-level content validity index ranging between 0.80 and 1.00 and a scale-level content validity index of 0.90. The construct validity test results showed that it comprised four sub-categories with a total of 26 items, and the internal consistency reliability tests showed Cronbach’s alpha values ranging between 0.71 and 0.88. In summary, the results confirmed that the Korean ASI had adequate reliability and validity. Conclusion: The study findings confirmed the applicability of this instrument for measuring anesthesia surrendering in Korean adults. Moreover, these results may be used in future studies on anesthesia surrendering in Korean adult patients.
Diammonium glycyrrhizinate lipid ligand ameliorates lipopolysaccharide-induced acute lung injury by modulating vascular endothelial barrier function
Authors: Liu Mei-Mei , Zhou Jin , Ji Dan , Yang Jun , Huang Yan-Ping , Wang Qi 
Published: January 2020

Abstract
Background: The present study investigated the attenuating effect of diammonium glycyrrhizinate lipid ligand (DGLL) on acute lung injury (ALI) and pulmonary edema induced by lipopolysaccharide (LPS) in rats.Methods: Rat ALI model was established by LPS (10 mg/kg) intraperitoneal injection, and DGLL (30, 60, 120 mg/kg) was administrated orall 1 hour before LPS infusion. Six hours after LPS stimulation, lung injury was evaluated by histological staining. Pulmonary edema was evaluated by lung wet-dry weight ratio, the protein concentration of bronchoalveolar lavage fluid (BALF), and the evans blue (EB) extravasation in lung tissues. The expression of cytokines and adhesion molecules in lung tissues were detected by ELISA method. The myeloperoxidase (MPO) expression was detected by immunohistochemical staining. Western blot was used to detect the expression changes of the proteins associated with pulmonary inflammation and microvascular permeability.Results: DGLL significantly inhibited LPS induced ALI, manifested as attenuation of MPO positive cells and TNF-α, IL-6, ICAM-1 expression in rat lung tissue. In addition, DGLL abrogated LPS-induced pulmonary edema, decreased the protein concentration in BALF and EB extravasation. Meanwhile, DGLL inhibited the degradation of vascular endothelial cadherin (VE-Cadherin) and tight junction protein, including ZO-1, Occludin, and JAM-1.Conclusions: DGLL has an inhibitory effect on LPS-induced rat ALI, which is related to the inhibition of inflammatory cell infiltration and microvascular barrier disruption. These results provide a theoretical basis for DGLL in the potential clinical treatment of ALI.
Screening and validation of candidate genes involved in the regulation of egg yolk deposition in chicken
Authors: Zhang Junnan , Duan Zhongyi , Wang Xiqiong , Li Fengning , Chen Jiajing , Lai Xingfu , Qu Liang , Sun Congjiao , Xu Guiyun 
Published: January 2020

Abstract
Background: The eggs with the same egg weight but may have wide differences in yolk weight. Eggs with a high proportion of yolk have richer nutritional value, more flavor and taste, and are more favourite by parts of consumers. However, large proportion of yolk means relatively much dry matters in eggs, which reduces the feed efficiency to some extent. To elucidation the genetic factors for the amounts of yolk in eggs is of scientific and practical significance.Results: Through RNA sequencing, we explored the transcriptome of ovarian tissue from twelve Wenchang chickens which includes six eggs with a high percentage of yolk (32%) and six low-percent eggs (25%).We identified 362 differential genes (P<0.01, log2foldchange<-1, log2foldchange>1), of which 220 were up-regulated and 142 were down-regulated in high-yolk percentage hens. According to GO term annotation and KEGG enrichment analysis, the differentially expressed genes (DEGs) were enriched into the regulation of various cell functions, cell differentiation and development. In addition, a large number of genes were associated with neuroactive ligand-receptor interactions, calcium signaling pathways and ubiquitin-mediated proteolysis. To further filter for genes that actually was involved in yolk accumulation, the chicken quantitative trait loci (QTL) database, genes within 100kb upstream and downstream of the yolk weight trait snp and intersection genes in protein interaction network diagrams were used for the detection of the genes that overlap with DEGs; we found that the 7 candidate genes in total, MNR2, AOX1, ANTXRL, GRAMD1C, EEF2, COMP, and JUND participate in affecting female reproductive performance and the growth and development of follicles, supporting cell transport, cell proliferation and differentiation, immune pathways, being combined with enzyme and cell secretion. All candidate genes and several random selected genes (a total of 24 genes) were verified by qRT-PCR and the trend was consistent with the results of RNA-Seq.Conclusions: In conclusion, investigating the molecular mechanism of high-yolk percentage traits provides a sight to optimize the breeding strategies to alter the proportion of yolk in chicken eggs.