bluuebunny/crossref_metadata_2025_split huggingface dataset:
Incidence of Huntington disease in a northeastern Spanish region: A 13-year retrospective study at tertiary care centre
Authors: Bailo Paula Sienes , Lahoz Raquel , Marín Juan Pelegrín Sánchez , Álvarez Silvia Izquierdo 
Published: November 2020

Abstract
Background: Despite the progress in the knowledge of Huntington disease (HD) in recent years, the epidemiology continues uncertain, so the study of incidence becomes relevant. This is important since various factors (type of population, diagnostic criteria, disease-modifying factors, etc.) make these data highly variable. Therefore, the genetic diagnosis of these patients is important, since it unequivocally allows the detection of new cases.Methods: Descriptive retrospective study with 179 individuals. Incidence of HD was calculated from the ratio of number of symptomatic cases newly diagnosed per 100 000 inhabitants per year during the period 2007-2019 in Aragon (Spain).Results: 50 (27.9%) incident cases of HD (CAG repeat length ≥36) were identified from a total of 179 persons studied. The remaining 129/179 (73.4%) were HD negative (CAG repeat length <36). 29 (58.0%) females and 21 (42.0%) males were confirmed as HD cases. The overall incidence was 64.8 per 100 000 patient-years. 11/50 positive HD cases (22.0%) were identified by performing a predictive test, without clinical symptoms. The minimum number of CAG repeats found was 10 and the most common CAG length among HD negative individuals was 16.Conclusions: Our incidence lied within the range reported for other Caucasian populations. Implementation of new techniques has allowed to determine the exact number of CAG repeats, which is especially important in patients with triplet expansions in an HD intermediate and/or incomplete penetrance allele, both in diagnostic, predictive and prenatal tests.
Metatranscriptomic analyses reveal ruminal pH regulates fiber degradation and fermentation by shifting the microbial community and gene expression of carbohydrate-active enzymes
Authors: Li MengMeng , White Robin R. , Guan Le Luo , Harthan Laura , Hanigan Mark D. 
Published: November 2020

Abstract
Background: Volatile fatty acids (VFA) generated from ruminal fermentation by microorganisms provide up to 75% of total metabolizable energy in ruminants. Ruminal pH is an important factor affecting the profile and production of VFA by shifting the microbial community. However, how ruminal pH affects the microbial community and its relationship with expression of genes encoding carbohydrate-active enzyme (CAZyme) for fiber degradation and fermentation are not well investigated. To fill in this knowledge gap, six cannulated Holstein heifers were subjected to a continuous 10-day intraruminal infusion of distilled water or a dilute blend of hydrochloric and phosphoric acids to achieve a pH reduction of 0.5 units in a cross-over design. RNA-seq based transcriptome profiling was performed using total RNA extracted from ruminal liquid and solid fractions collected on day 9 of each period, respectively.Results: Metatranscriptomic analyses identified 19 bacterial phyla with 156 genera, 3 archaeal genera, 11 protozoal genera, and 97 CAZyme transcripts in sampled ruminal contents. Within these, 4 bacteria phyla (Proteobacteria, Firmicutes, Bacteroidetes, and Spirochaetes), 2 archaeal genera (Candidatus Methanomethylophilus and Methanobrevibacter), and 5 protozoal genera (Entodinium, Polyplastron, Isotricha, Eudiplodinium, and Eremoplastron) were considered as the core active microbes, and genes encoding for cellulase, endo-1,4-beta- xylanase, amylase, and alpha-N-arabinofuranosidase were the most abundant CAZyme transcripts distributed in the rumen. Rumen microbiota is not equally distributed throughout the liquid and solid phases of rumen contents, and ruminal pH significantly affect microbial ecosystem, especially for the liquid fraction. In total, 21 bacterial genera, 4 protozoal genera, and 6 genes encoding CAZyme were regulated by ruminal pH. Metabolic pathways participated in glycolysis, pyruvate fermentation to acetate, lactate, and propanoate were downregulated by low pH in the liquid fraction.Conclusions: The ruminal microbiome changed the expression of transcripts for biochemical pathways of fiber degradation and VFA production in response to reduced pH, and at least a portion of the shifts in transcripts was associated with altered microbial community structure.
LncRNA-SNHG6 promotes the progression of hepatocellular carcinoma by targeting miR-6509-5p and HIF1A
Authors: Fan Xiaoxi , Zhao Zhongwei , Song Jingjing , Zhang Dengke , Wu Fazong , Tu Jianfei , Xu Min , Ji Jiansong 
Published: November 2020

Abstract
Background: Accumulating evidences have been reported that long noncoding RNAs play crucial roles in the progression of hepatocellular carcinoma (HCC). SnoRNA host gene 6 (SNHG6) is believed to be involved in several human cancers, but the specific molecular mechanism of SNHG6 in HCC is not well studied. Methods: In this study, we experimentally down-regulated the SNHG6 in two hepatocellular carcinoma cell lines in vitro, and then measured the proliferation, migration and invasion abilities and the apoptotic levels. Also, we performed the xenograft assay to investigate the function of SNHG6 during the tumor growth in vivo. Results: We found SNHG6 was highly expressed in HCC tissues. Next, using Hep3B and Huh7 cells, we confirmed knockdown of SNHG6 reduced the proliferation, migration and invasion abilities in vitro. Also, by bioinformatics analysis, further molecular and cellular experiments, we found miR-6509-5p bound to SNHG6 directly, and the expression level of HIF1A was regulated through SNHG6/miR-6509-5p axis. Finally, we found that down-regulation of SNHG6 dramatically reduced the tumor growth ability of Huh7 cells in vivo. Conclusions: We concluded that SNHG6/miR-6509-5p/HIF1A axis functioned in the progression of hepatocellular carcinoma, and could be the promising therapeutic targets during the development of hepatocellular carcinoma drugs.
Assessment of irreducible aspects in developmental hip dysplasia by magnetic resonance imaging
Authors: Jia Huihui , Wang Liang , Chang Yan , Song Yongrui , Liu Yuqi , Zhang Fuyong , Feng Jie , Yang Xiaodong , Sheng Mao 
Published: November 2020

Abstract
Background: The developmental dysplasia of the hip (DDH) can cause a wide range of pathological changes, and often requires surgical treatment. Preoperative evaluation is very important for DDH. We aimed to assess the diagnostic capability of magnetic resonance imaging (MRI) for irreducible aspects preventing hip reduction in DDH. Methods: A total of 39 pediatric patients who received DDH evaluation in pediatric orthopedics from January 2015 to December 2019 were included. The samples included 4 cases of bilateral DDH and 35 cases of unilateral DDH, a total of 43 hip joint samples. All patients underwent surgical treatment, pathological examination and MRI of hip joint. Results: With pathological results or intraoperative findings as the gold standard, the sensitivity and specificity of MRI were 90.3% and 83.3% for the affected labrum, 92% and 83.3% for thickening of the round ligament, 90.0% and 91.3%for atrophy of the iliopsoas muscle, and 100% and 100% for fibrofatty pulvinar tissue and joint effusion, respectively. Conclutions: The MRI showed an extraordinary capability of detecting these irreducible factors and helped surgeon choose the appropriate treatment strategies.
Preconceptional and prenatal exposure to diurnal temperature variation increases the risk of childhood pneumonia
Authors: Zheng Xiangrong , Kuang Jian , Lu Chan , Deng Qihong , Wu Haiyu , Murithi Rachael Gakii , Johnson McSherry Brownel , Peng Wang , Wu Maolan 
Published: November 2020

Abstract
Background: Pneumonia is the leading cause of death and hospitalization among young children worldwide, but its risk factors remain unclear. Objective: To evaluate the effect of maternal exposure to diurnal temperature variation (DTV) during preconceptional and prenatal periods on childhood pneumonia. Methods: A retrospective cohort study by case-control design was conducted for pneumonia (N=699) and normal (N=811) children under age of 14 who were enrolled in XiangYa Hospital, Changsha, China from May 2017 to April 2019. Demographic data including gender, age, birth season, gestational age, parity, mode of delivery, and parental atopy were collected from the electronic medical records in the hospital system. We obtained the data of daily DTV in Changsha during 2003-2019 from China Meteorological Administration. Maternal exposure to DTV during preconceptional and prenatal periods was respectively calculated by the average of daily DTV during one year and three months before conception and entire pregnancy as well as the three trimesters. The association between maternal exposure to outdoor DTV and childhood pneumonia was analyzed by multiple logic regression model. Results: We found that childhood pneumonia was significantly associated with exposure to an increase in DTV during one year before conception and entire pregnancy, with ORs (95% CI) = 2.53 (1.56-4.10) and 1.85 (1.24-2.76). We further identified a significant risk of pneumonia due to DTV exposure during the first and second trimester of pregnancy. Sensitivity analysis showed that boys were more susceptible to the effect of prenatal exposure to outdoor DTV during pregnancy particularly in the first two trimesters compared to girls. Conclusions: Preconceptional and prenatal exposure to DTV plays an important role in development of childhood pneumonia, especially during the first and second trimesters of pregnancy.
New view on the organization and evolution of Palaeognathae mitogenomes poses the question on the ancestral gene rearrangement in Aves
Authors: Urantowka Adam Dawid , Kroczak Aleksandra , Mackiewicz Pawel 
Published: November 2020

Abstract
BackgroundBird mitogenomes differ from other vertebrates in gene rearrangement. The most common avian gene order, identified first in Gallus gallus, is considered ancestral for all Aves. However, other rearrangements including a duplicated control region and neighboring genes have been reported in many representatives of avian orders. The repeated regions can be easily overlooked due to inappropriate DNA amplification or genome sequencing. This raises a question about the actual prevalence of mitogenomic duplications and the validity of the current view on the avian mitogenome evolution. In this context, Palaeognathae is especially interesting because is sister to all other living birds, i.e. Neognathae. So far, a unique duplicated region has been found in one palaeognath mitogenome, that of Eudromia elegans. ResultsTherefore, we applied an appropriate PCR strategy to look for omitted duplications in other palaeognaths. The analyses revealed the duplicated control regions with adjacent genes in Crypturellus, Rhea and Struthio as well as ND6 pseudogene in three moas. The copies are very similar and were subjected to concerted evolution. Mapping the presence and absence of duplication onto the Palaeognathae phylogeny indicates that the duplication was an ancestral state for this avian group. This feature was inherited by early diverged lineages and lost two times in others. Comparison of incongruent phylogenetic trees based on mitochondrial and nuclear sequences showed that two variants of mitogenomes could exist in the evolution of palaeognaths. Data collected for other avian mitogenomes revealed that the last common ancestor of all birds and early diverging lineages of Neoaves could also possess the mitogenomic duplication.ConclusionsThe duplicated control regions with adjacent genes are more common in avian mitochondrial genomes than it was previously thought. These two regions could increase effectiveness of replication and transcription as well as the number of replicating mitogenomes per organelle. In consequence, energy production by mitochondria may be also more efficient. However, further physiological and molecular analyses are necessary to assess the potential selective advantages of the mitogenome duplications.
Propensity score-matched analysis of systemic chemotherapy versus salvage hysterectomy for persistent cervical cancer after definitive radiotherapy/concurrent chemoradiotherapy.
Authors: TAKEKUMA MUNETAKA , Takahashi Fumiaki , Mabuchi Seiji , Kudaka Wataru , Horie Koji , Ikeda Mariko , Shikama Ayumi , Mitsuhashi Akira , Nagao Shoji , Suzuki Shiro , Mizuno Mika , Nishio Shin , Tokunaga Hideki , Ota Yukinobu , Kasamatsu Takahiro , Kitagawa Ryo , Toita Takafumi , Kobayashi Hiroaki , Ishikawa Mitsuya , Yaegashi Nobuo 
Published: November 2020

Abstract
Background: The aim of the current study was to evaluate oncologic outcomes of patients who were treated with salvage hysterectomy (HT), compared to systemic chemotherapy (CT) for persistent cervical cancer after definitive radiotherapy (RT)/ concurrent chemoradiotherapy (CCRT).Methods: Patients with persistent cervical cancer treated with definitive RT/CCRT at 35 institutions from 2005–2014 were reviewed retrospectively (n = 317). Those who underwent a HT for persistent cervical cancer after definitive RT/CCRT were matched with propensity scores for patients who underwent systemic CT. Oncologic outcomes between the two groups using a propensity score matched–cohort analysis were compared.Results: A total of 142 patients with persistent cervical cancer after definitive RT/CCRT were included after matching (HT: 71, systemic CT: 71). All background factors between HT and CT groups were well balanced. Median overall survival was 3.8 and 1.5 years in the HT and CT groups, respectively (p= 0.00193, hazards ratio [HR] 0.41, 95% confidence interval [CI] 0.23–0.73), Increasing residual tumor size was significantly associated with a high incomplete resection rate (p = 0.016, Odds Ratio 1.11, 95%CI 1.02-1.22). Severe late adverse events occurred in 7 patients (9.9%) in the HT cohort.Conclusion: The current study demonstrated that, when compared to systemic CT, the adoption of salvage HT for patients with persistent cervical cancer after definitive RT/CCRT reduced mortality rate by about 60%. This indicates that salvage HT could be curative treatment for those patients. Further prospective clinical trials with regard to salvage HT after RT/CCRT are warranted.
Metabolic Engineering of Saccharomyces cerevisiae for High-Level Production of Gastrodin from Glucose
Authors: Yin Hua , Hu Tian Dong , Zhuang Yi Bin , Liu Tao 
Published: November 2020

Abstract
Background: The natural phenolic glycoside gastrodin is the major bioactive ingredient in the well-known Chinese herb Tianma and is widely used as a neuroprotective medicine in the clinic. Microbial production from sustainable resources is a promising method to replace plant extraction and chemical synthesis which were currently used in industrial gastrodin production. Saccharomyces cerevisiae is considered as an attractive host to produce natural plant products used in the food and pharmaceutical fields. In this work, we intended to explore the potential of S. cerevisiae as the host for high-level production of gastrodin from glucose.Results: Here, we first identified the plant-derived glucosyltransferase AsUGT to convert 4-hydroxybenzyl alcohol to gastrodin with high catalytic efficiency in yeast. Then, we engineered de novo production of gastrodin by overexpressing codon-optimized AsUGTsyn, the carboxylic acid reductase gene CARsyn from Nocardia species, the phosphopantetheinyl transferase gene PPTcg-1syn from Corynebacterium glutamicum, the chorismate pyruvate-lyase gene UbiCsyn from Escherichia coli, and the mutant ARO4K229L. Finally, we achieved an improved product titer by a chromosomal multiple-copy integration strategy and enhancement of metabolic flux toward the aglycon 4-hydroxybenzyl alcohol. The best optimized strain produced 2.1 g/L gastrodin in mineral medium with glucose as the sole carbon source by flask fermentation, which was 175 times higher than that of the original gastrodin-producing strain.Conclusions: The de novo high-level production of gastrodin was first achieved. Instead of chemical synthesis or plants extraction, our work provides an alternative strategy for the industrial production of gastrodin by microbial fermentation from a sustainable resource.
Linkage analysis, GWAS, transcriptome analysis to identify candidate genes for rice seedlings in response to high temperature stress
Authors: Wei Zhaoran , Yuan Qiaoling , Lin Hai , Li Xiaoxia , Zhang Chao , Gao Hongsheng , Zhang Bin , He Huiying , Liu Tianjiao , Zhang Jie , Gao Xu , Shi Shandang , Wang Bo , Gao Zhenyu , Kong Lingrang , Qian Qian , Shang Lianguang 
Published: November 2020

Abstract
Background: With the increase of global temperature, rice yield decline caused by the rising temperature is becoming more and more prominent. Mining heat-resistant genes and applying them to rice breeding is a feasible and effective way to solve the problem.Result: Three main biomass traits, including shoot length, dry weight, and fresh weight, changed after abnormally high temperature treatment in the seedling stage of a recombinant inbred line and natural groups. Based on a comparison of the results of linkage analysis and genome-wide association analysis, the presence of two sections with lengths of 57 kb and 69 kb in qDW7 and qFW6, respectively, was associated with the rice response to abnormally high temperatures in the seedling stage. Meanwhile, based on integrated transcriptome analysis, some genes are considered as candidate genes for subsequent research and analysis. Combining with reports of known genes and analysis of homologous genes, it was found that there are 8 genes in candidate genes that need to be focused in subsequent research.Conclusions: The results indicated several relevant loci, which would help researchers to further discover excellent heat-resistant genes that can be applied to rice heat-resistant breeding.
Peritumoral plasmacytoid dendritic cells predict a poor prognosis for intrahepatic cholangiocarcinoma after curative resection
Authors: Hu Zhi-Qiang , Zhou Zheng-Jun , Luo Chu-Bin , Xin Hao-Yang , Li Jia , Yu Song-Yang , Zhou Shao-Lai 
Published: November 2020

Abstract
Background: Plasmacytoid dendritic cells (pDCs) are present in various primary and metastatic human neoplasms; however, their clinical significance in intrahepatic cholangiocarcinoma is not clear. Methods: To evaluate pDCs’ distributions in and around tumors as well as their potential function and predictive value for prognosis in patients undergoing curative resection, we performed immunohistochemistry to examine the expression of pDC marker BDCA2, and CD3, CD4, CD8 and Foxp3 in intratumoral and peritumoral tissues from 359 patients with intrahepatic cholangiocarcinoma and compared with prognostic and clinicopathologic factors. Results: Results showed that patients with high numbers of BDCA2+ pDCs in peritumoral tissues were more likely to have elevated levels of carbohydrate antigen 19-9 and gamma-glutamyl transferase, larger and more tumors, advanced tumor-node-metastasis staging, more vascular/bile duct invasion, and lymphatic metastasis in association with greater chance of recurrence and shorter overall survival. Peritumoral tissues with larger numbers of pDCs also showed increased Foxp3+ regulatory T cell infiltration, both of which were found to be independent factors for predicting time to recurrence and overall survival. By contrast, patient outcomes were not associated with the presence of intratumoral pDCs. Conclusions: Peritumoral pDC infiltration may indicate an immune tolerogenic peritumor microenvironment and can be used to predict a poor prognosis for patients undergoing curative resection for intrahepatic cholangiocarcinoma.
Excessive Amounts of Salt Consumption and Atheroma Formation Among Patients Awaiting Coronary-Artery-Bypass-Grafting at A Tertiary Care Hospital in Sri Lanka
Authors: Amadoru Harischandra , Dias Ashini R , Wijesiri Nuwan , Gamage Pasan , Perera Thilini , Goonawardana Vas , Liyanage Nisansala , Malwatta Arunie , Anthonipille Ravikaran , Mahesh Buddhika , Alles Randara , Suriyarachchi Vasana , Siriwardana Sumudu , Jayasekara Prasanna , Jayatissa Renuka , Silva Rajitha De , Kapuruge Aruna 
Published: November 2020

Abstract
Background:Ischemic Heart Disease(IHD) characterized by atheroma formation, is a leading contributor for the rising disease burden of chronic non-communicable diseases in Sri Lanka. Even though excessive salt-consumption has been attributed with hypertension, documented literature is scarce on exploring its direct association with atheroma formation with primary data. Coronary-Artery- Bypass-Grafting(CABG) is done as a tertiary preventive measure for IHDs. The aim was to estimate the sodium-intake and to describe the association of salt consumption and atheroma formation among preoperative patients undergoing CABG at Sri Jayewardenepura General Hospital, Sri Lanka.MethodsA descriptive cross-sectional study was done on a calculated sample size of 213 participants who were awaiting CABG at SJGH. An interviewer-administered Additional file 1 was used, and dietary intake of sodium was calculated with food-frequency tables and web-based tools. A data extraction form was used and details regarding Coronary arterial segments with atheroma formation were obtained from angiogram reports. After exploring the normality, Spearman-correlation-coefficient and Mann-Whitney-U tests were used to explore associations of atheroma formation. Independent association of sodium-intake and Coronary arterial segments affected with atheroma was explored with multiple-logistic regression. ResultsThe sample was with a male preponderance(male to female ratio=3:1). Comorbidities were observed in a notable proportion: diabetes(47%), dyslipidemia(40%), hypertension(56%). The median(IQR) of BMI and waist circumference were 25.00(23.00-27.00)kg/m2 and 87.00(82.00-91.00)cm. The median(IQR) sodium-intake was 5875.50(4905.25-7091.25)mg. All participants (n=210) had a sodium intake of more than 2000mg/day. Sodium intake(rs=0.599,p<0.001) and BMI(rs=0.634,p=0.034) were significantly associated with atheroma segments whereas age, gender, diabetes, hypertension, dyslipidemia, waist circumference was not(p>0.05). Sodium intake was found to be an independent predictor of affecting “5 or more segments” when multiple logistic regression was applied(OR= 2.25,CI=1.41 to 3.61). Conclusions and RecommendationsThe daily intake of sodium by a regular person is more than the dietary recommendations in the study sample. Salt intake reflected by sodium intake seemingly increase the risk of atheroma formation in more coronary segments irrespective of age, sex as well as several known disease conditions and risk factors. More research must be promoted with analytical approaches in proving this hypothesis.
IL-17A in COVID-19: a meta-analysis
Authors: Fadlallah Sukayna , Eddin Marcel Shams , Rahal Elias 
Published: November 2020

Abstract
IL-17A is a proinflammatory cytokine attributed with homeostatic roles but that is also involved in autoimmune disease pathogenesis. While some studies have reported an increase in IL-17A in subjects affected by COVID-19, no significant associations were found by others. Hence, we undertook this meta-analysis to examine whether serum IL-17A increases in COVID-19 patients. We report here that IL-17A increases in COVID-19 subjects irrespective of disease severity. It is also higher in patients with moderate disease compared to controls as well as higher in patients with severe COVID-19. While the increase in serum levels in subjects with severe disease over those with moderate disease was statistically significant, the association was not as robust as the other comparisons. Hence, IL-17A may be of relevance when considering management approaches to COVID-19; however, therapeutic approaches that target IL-17A should consider whether alleviation of inflammation outweighs eliminating the possible anti-viral roles of this cytokine.