bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chloroplast phylogenomics and the dynamic evolution of Santalum (Santalaceae)
Authors: Liu Xiaojin , Xu Daping , Hong Zhou , Zhang Ningnan , Cui Zhiyi 
Published: February 2021

Abstract
Background

Santalum (Santalaceae, sandalwood) is a hemiparasitic genus including approximately 15 extant species. It is known for its aromatic heartwood oil, which is used in incense and perfume. Demand for sandalwood-based products has led to drastic over-harvesting, and wild Santalum populations are now threatened. Knowledge of the phylogenetic relationships and genetic diversity will be critical for the conservation and proper management of this genus. Here, we sequenced the chloroplast genome of 11 Santalum species. The data were then used to investigate the chloroplast genome evolutionary dynamics and relationships and divergence time within Santalum and related species.
Results

The Santalum chloroplast genome contains the typical quadripartite structures, ranging from 143,291 to 144,263 bp. The chloroplast genome contains 124 genes. The whole set of ndh genes and the infA gene were found to lose their function. Between 17 and 31 SSRs were found in the Santalum chloroplast genome, and mononucleotide simple sequence repeats (SSRs) were the major type. The P-distance among the Santalum species was 0.0003 to 0.00828. Three mutation hotspot regions, 14 small inversions, and 460 indels events were discovered in the Santalum chloroplast genome. Our phylogenomic assessment provides improved resolution compared to past analyses. Our divergence time analysis shows that the crown age of Santalum was 8.46 Mya, the first divergence occurred around 6.97 Mya, and diversification was complete within approximately 1 Mya.
Conclusions

By sequencing the 12 chloroplast genomes of Santalum, we gain insight into the evolution of its chloroplast genomes. The chloroplast genome sequences had sufficient polymorphic information to elucidate the evolutionary history of Santalum.
Coughing Children in Family Practice and Primary Care – A Systematic Review On Prevalence, Aetiology and Prognosis
Authors: Bergmann Milena , Haasenritter Jörg , Beidatsch Dominik , Schwarm Sonja , Bartsch Kaja , Bösner Stefan , Grevenrath Paula , Schmidt Laura , Viniol Annika , Donner-Banzhoff Norbert , Becker Annette 
Published: February 2021

Abstract
Background: For evidence-based decision-making general practitioners need setting specific knowledge on the pre-test probabilities of underlying diseases and a symptom’s course. We performed a systematic review on symptom evaluating studies in primary care to give evidence on the prevalence, aetiologies and prognosis of coughing children who consult primary care settings. Methods: Following a pre-defined algorithm and independent double reviewer ratings we searched MEDLINE and EMBASE. We included data from all quantitative original research articles in English, French or German assessing unselected study populations of children consulting for cough in primary care. We used the random effects model for meta-analysis in eligible subgroups if comprehensive in terms of heterogeneity. Results: We identified 14 eligible studies on prevalence, five on aetiology and one on prognosis. Prevalence estimates varied between 4.7% and 23.3% of all reasons for encounter or up to estimates of 60% when related to patients or consultations. Cough in children is more frequent than in adults with lowest prevalences in adolescents and in summer. Acute cough is mostly caused by upper respiratory tract infections (62.4%) and bronchitis (33.3%); subacute or chronic cough by recurrent respiratory tract infection (27.7%), asthma (3% in cough of all durations to 50.4% in more than 3 weeks cough), and pertussis (37.2%). Potentially serious diseases like croup, pneumonia or tuberculosis are scarce. In children with subacute and chronic cough the total duration of cough ranged from 24 to 192 days. About 62.3% of children suffering from prolonged cough are still coughing two months after the beginning of symptoms. We found strong heterogeneity across studies and only five studies with an overall low risk of bias. Conclusion: Cough is one of the most frequent reasons of encounter in primary care. Our findings on aetiologies and prognosis fit in with current guideline recommendations supporting a thoughtful wait-and-see approach in acute cough and a special awareness of asthma in chronic cough. There is a remarkable high pre-test probability of pertusssis in children with cough of more than two weeks’ duration. To develop primary-care cough guidelines symptom-evaluating studies assessing setting and age specific aetiologies and prognosis of cough are needed.
Effects of Consumption Frequency of 10 Food Groups on Activities of Daily Living in Elderly Japanese Women: A Longitudinal Cohort Study
Authors: Kojima Narumi , Kim Miji , Saito Kyoko , Yoshida Yuko , Hirano Hirohiko , Obuchi Shuichi , Shimada Hiroyuki , Suzuki Takao , Iwasa Hajime , Kim Hunkyung 
Published: February 2021

Abstract
Background

This study aimed to examine the effects of the consumption frequency of 10 food groups on activities of daily living (ADL) in elderly Japanese women.
Methods

This was a four-year longitudinal cohort study conducted in Itabashi Ward, Tokyo. Participants were 1,111 community-dwelling elderly women aged 75 to 85 years, without baseline ADL disability or missing values. The main outcome measures were the relationship between the baseline consumption frequency of 10 food groups and future incidence of ADL disability. The relationship between baseline consumption frequency of 10 food groups and change in ADL status was analyzed through logistic regression analyses.
Results

The incidence rate of ADL disability was 7.6%. The trend tests show that less-frequent consumption of soy products, colored vegetables, and fats/oils leads to a significantly higher odds ratio of ADL disability incidence whether adjusted or not (p < 0.005, p = 0.03, and p = 0.02, respectively, when adjusted).
Conclusions

Our results suggest that in community-dwelling elderly Japanese women, lower consumption frequency of soy products, colored vegetables, or fats/oils are risk factors for future incidence of ADL disability.
Influences of Tumor Size and Pleural Layer Invasion on the Prognosis of Patients with Stage IB Lung Adenocarcinoma
Authors: Sui Qihai , Liang Jiaqi , Hu Zhengyang , Xu Xinming , Chen Zhencong , Huang Yiwei , Zhao Mengnan , Bi Guoshu , Zhan Cheng , Lin Zongwu , Wang Qun , Wang Lin 
Published: February 2021

Abstract
Backgroud: Lung adenocarcinoma (ADC) at stage IB has its own prognostic characteristics. This study aimed to investigate the clinical factors that may affect the prognosis of patients with stage IB ADC.Methods: The data of ADC cases were selected from the Surveillance, Epidemiology, and End Results (SEER) database (2010-2016) and patients in Zhongshan Hospital Affliated to Fudan University (Department of Thoracic Surgery, 2015-2016). Kaplan-Meier method was used to obtain the overall survival (OS). Factors that significantly related to the prognosis were evaluated by univariate and multivariate analysis (UVA, MVA) using the Cox model. A nomogram was developed and validated to predict the 3-year OSs of those patients.Results: 7605 patients with stage IB ADC were included ultimately and were divided into 2 groups, a training cohort (n = 5,324) and a test cohort (n = 2,281). Besides, there was a validation cohort (n = 272) for the verification of the nomogram model. Those with significantly older age, male, the white race, lower grades of tumor differentiation, larger tumor size (31-40mm) without pleural layer (PL) invasion as well as receiving sublobectomy suffered from poorer survival (P < 0.001), which were identified as independent factors for stage IB ADC (P < 0.001), and according to which, a nomogram model was created.Conclusion: Age, sex, race, histological grade, surgery to the primary site, and tumor size combined with PL invasion were independent risk factors for stage IB ADC, based on which a nomogram was constructed to predict the prognosis.
Different Concentrations of C5a Affect Human Dental Pulp Mesenchymal Stem Cells Differentiation
Authors: Liu Jie , Wei Xiaoling , Hu Junlong , Tan Xiaohan , Kang Xiaocui , Gao Li , Li Ning , Shi Xin , Yuan Mengtong , Hu Weiping , Liu Mingyue 
Published: February 2021

Abstract
Background During the process of deep decay, when decay approaches the pulp, an immune response is triggered inside the pulp, which activates the complement cascade. The effect of complement component 5a (C5a) on the differentiation of dental pulp mesenchymal stem cells (DPSCs) is related to dentin reparation. The aim of the present study was to stimulate DPSCs with different concentrations of C5a and evaluate the differentiation of odontoblasts using dentin sialoprotein (DSP). Methods DPSCs were divided into the following six groups: i) Control; ii) DPSCs treated with 50 ng/ml C5a; iii) DPSCs treated with 100 ng/ml C5a; iv) DPSCs treated with 200 ng/ml C5a; v) DPSCs treated with 300 ng/ml C5a; and vi) DPSCs treated with 400 ng/ml C5a. Flow cytometry and multilineage differentiation potential were used to identify DPSCs. Mineralization induction, Real-time PCR and Western blot were conducted to evaluate the differentiation of odontoblast in the 6 groups.Result DPSCs can express mesenchymal stem cell markers, including CD105, CD90, CD73 and, a less common marker, mesenchymal stromal cell antigen-1. In addition, DPSCs can differentiate into adipocytes, neurocytes and osteoblasts. All six groups formed mineralized nodules after 28 days of culture. Reverse transcription-quantitative PCR and western blotting indicated that the high concentration C5a groups expressed higher DSP levels and promoted DPSC differentiation, whereas the low concentration C5a groups displayed an inhibitory effect.Conclusion In this study, the increasing concentration of C5a, which accompanies the immune process in the dental pulp, has demonstrated an enhancing effect on odontoblast differentiation at higher C5a concentrations in vitro.
Analysis of Spatial Distribution Characteristics of Human Echinococcosis at the Township Level in Sichuan Province, China
Authors: He Wei , Yu Wen-jie , Zhang Guang-jia , Liao Sha , Wang Qi , Li Rui-rui , Zhong Bo , Yang Liu , Yao Ren-xin , Liu Yang , Zeli Dan-ba , Qin Sheng-chao , Wang Shi-an , Wang Yan-xia , Huang Yan , Wang Qian 
Published: February 2021

Abstract
BackgroundEchinococcosis is a global zoonotic parasitic disease caused by the larvae of Echinococcus, which affects both humans and animals. In China, this disease is highly endemic in Sichuan Province. In this study, we investigated the prevalence and spatial distribution characteristics of human echinococcosis at the township level in Sichuan province, so as to provide a reference for the development of precise prevention and control strategies in the future.MethodsWe explored the prevalence of echinococcosis using the B-ultrasonography diagnostic method in Sichuan province between 2016 and 2019, where patients and transmission conditions had been identified in the past. All data were inputted using Epi-Info software, while SPSS software was used for statistical analysis. We then employed ArcGIS software to draw the spatial distribution map and perform trend surface analysis. Finally, Geoda software was used to analyze spatial autocorrelation and draw Lisa clustering map.ResultsA total of 2 542 135 people from 649 towns in 35 counties of Sichuan province were screened for echinococcosis, of which 11 743 echinococcosis patients were detected. The prevalence of echinococcosis in humans was 0.462%, among which the occurrence of cystic echinococcosis [CE] was 0.221%, while that of alveolar echinococcosis [AE] was 0.244%. We also observed that the predominance of echinococcosis in humans decreased gradually from west to east and from north to south based on the results of the spatial distribution map and trend surface analysis. The Global Moran's I index was 0.77 (Z = 32.07, P < 0.05), which indicated that the prevalence of echinococcosis in humans was spatially clustered, exhibiting a significant spatial positive correlation. Further, the findings of local spatial autocorrelation analysis revealed that the “high-high” concentration areas were primarily located in some townships in the northwest of Sichuan province. On the other hand, the “low-low” concentration areas were predominantly located in some townships in the southeast of Sichuan province. Conclusion﻿Our findings demonstrated that the prevalence of echinococcosis in humans of Sichuan province is following a downward trend, implying that the current prevention and control work has achieved some substantial outcomes. However, the prevalence in humans at the township level is widely distributed and differs greatly, with a clear clustering in space. Therefore in the future, precise prevention and control strategies should be formulated for clusters, particularly strengthening the “high-high” clusters at the township level.
Telocytes Reduce Oxidative Stress by Downregulating DUOX2 Expression in Inflamed Lungs of Mice
Authors: Liang Tao , Zhang Nu , Ju Huihui , Zhou Yile , Yang Yajie , Tang Haihong , Song Dongli , Fang Hao 
Published: February 2021

Abstract
Background: Telocytes (TCs), a newly identified interstitial cell type, have been found to participate in tissue protection and repair. This study investigated the antioxidative effects of TCs in inflamed lungs of mice.Methods: Acute respiratory distress syndrome mice were used as model of inflamed lungs of mice. Gene sequencing was used to screen for differentially expressed miRNAs in TCs after lipopolysaccharide (LPS) stimulation. AntagomiR-146a-5p-pretreated TCs were first injected into mice, and the antioxidant activity of TCs was estimated. TCs, RAW264.7 cells, and MLE-12 cells were collected for mRNA, miRNA, and protein measurements after LPS stimulation. Silencing miRNAs were delivered to examine the involved signaling pathways in the experiments. Oxidative stress was examined in cultured cells, supernatants, and lung tissue by measuring malondialdehyde (MDA) levels.Results: MiR-146a-5p and miR-21a-3p were upregulated in TCs after LPS stimulation. Compared with ARDS mice, TC-preinfused ARDS mice had reduced lung tissue injury scores, lung wet-dry ratios, white blood cell counts in alveolar lavage fluid and MDA concentrations in lung tissue. However, ARDS mice preinfused with antagomiR-146a-5p TCs did not exhibit any of the corresponding changes. DUOX2 was downregulated in TCs at both the gene and protein levels, and the concentration of MDA was decreased in TCs and their culture medium after LPS stimulation. DUOX2 expression was restored when TCs were treated with antagomiR-146a-5p. CREB1 was downregulated by miR-146a-5p, as confirmed by a dual-luciferase reporter assay, and the protein expression of DUOX2 was downregulated by CREB1, which was further confirmed by treating TCs with a specific CREB1 inhibitor.Conclusion: LPS stimulation increases miRNA-146a-5p expression in TCs, which downregulates the CREB1/DUOX2 pathway, resulting in a decrease in oxidative stress in cultured TCs. TCs reduce LPS-induced oxidative stress by decreasing DUOX2 expression in inflamed lungs of mice.
The Gut Microbiome as a Promising Biomarker of Cancer Progression Among Female Never-smokers With Lung Adenocarcinoma
Authors: Otoshi Takehiro , Nagano Tatsuya , Park Jonguk , Hosomi Koji , Yamashita Tomoya , Tachihara Motoko , Tabata Tokiko , Sekiya Reina , Tanaka Yugo , Kobayashi Kazuyuki , Mizuguchi Kenji , Itoh Tomoo , Maniwa Yoshimasa , Kunisawa Jun , Nishimura Yoshihiro 
Published: February 2021

Abstract
Background: The gut microbiome plays an important role in the immune system and has attracted attention as a new biomarker of various diseases, including cancer. As such, in this study, we examined the relationship between the gut microbiome and lung cancer progression. In addition, we assessed the correlation between the gut microbiome and epidermal growth factor receptor (EGFR) mutation status.Methods: Female never-smokers diagnosed with lung adenocarcinoma were consecutively enrolled between May 2018 and August 2019. Fecal samples were collected within 1 month before or after diagnosis and before administration of any lung cancer treatment. Principal coordinate analyses were performed using Bray-Curtis distance matrices to investigate the effects of clinical variables (age, body mass index, Tumor-Node-Metastasis stage, T category, N category, M category, primary tumor size, performance status, and EGFR mutation status) on the gut microbial community. A correlation analysis was also performed to determine the strength of association between the dominant taxonomy (comprising ≥1% of the relative abundance of bacterial DNA sequences) and clinical variables.Results: A total of 37 patients were enrolled. T category and primary tumor size were significantly correlated with the gut microbial community (p=0.018 and 0.041, respectively). At the genus level, a significant positive correlation was observed between the relative abundance of Faecalibacterium and both T category (correlation coefficient, R=0.51, p=0.0013) and primary tumor size (R=0.37, p=0.024), whereas a significant negative correlation was observed between the relative abundances of Fusicatenibacter and Bacteroides and T category (R=−0.35, p=0.034 and R=−0.32, p=0.05, respectively) and primary tumor size (R=−0.36, p=0.029 and R=−0.41, p=0.012, respectively). EGFR mutation status had no statistically significant effect on the gut microbial community (p=0.11). However, the relative abundances of Bifidobacterium and Faecalibacterium were significantly higher in EGFR mutation–negative patients than EGFR mutation–positive patients (p=0.012 and 0.041), whereas the relative abundance of Blautia was significantly lower in EGFR mutation–negative patients (p=0.036).Conclusions: This is the first study identifying the gut microbiome as a promising biomarker of lung cancer progression. Further elucidation of the role of the gut microbiome in lung cancer progression could facilitate development of new treatments for lung cancer.
Genome-wide Association Study of Individual Sugar Content and Sugar Conversion in Fruit of Japanese Pear (Pyrus spp.)
Authors: Nishio Sogo , Hayashi Takeshi , Shirasawa Kenta , Saito Toshihiro , Terakami Shingo , Takada Norio , Takeuchi Yukie , Moriya Shigeki , Itai Akihiko 
Published: February 2021

Abstract
Background: Sweetness is one of the most important traits determining fruit quality. Sweetness is controlled not only by the total sugar content but also by the contents of individual sugars. The major sugars in mature Rosaceae fruits are sucrose, fructose, glucose, and sorbitol, which have different levels of sweetness. Among these, sucrose and fructose have high sweetness, whereas glucose and sorbitol have low sweetness. The objective of this study was to identify the quantitative trait loci (QTLs) associated with fruit traits including individual sugar accumulation and conversion, to infer the candidate genes underlying the QTLs, and to assess the potential of genomic selection for breeding pear fruit traits.Results: We evaluated 10 fruit traits and conducted genome-wide association studies (GWAS) for 106 cultivars and 17 breeding populations (1112 F1 individuals) using 3484 tag single-nucleotide polymorphisms (SNPs) genotyped by double-digest restriction-site associated DNA sequencing (ddRAD-Seq). By implementing a mixed linear model and a Bayesian multiple-QTL model in GWAS, 56 SNPs associated with fruit traits were identified. Four loci were presumed to be associated with sugar conversion because the SNPs were significant for more than one individual sugar and the individual sugar contents associated with each SNP genotype were negatively correlated. In particular, a SNP located close to acid invertase gene PPAIV3 on chromosome 7 and a newly identified SNP on chromosome 11 had quite large effects on sugar conversion. We used ‘Golden Delicious’ doubled haploid (GDDH) 13, an apple reference genome to infer the candidate genes for the identified SNPs. In the region flanking the SNP on chromosome 11, there is a tandem repeat of early responsive to dehydration (ERD6)-like sugar transporter genes which might play a role in the phenotypes observed.Conclusions: SNPs associated with sugar accumulation and conversion were newly identified at several loci, and candidate genes underlying QTLs were inferred using advanced apple genome information. Several QTLs showed clear effects with more than 10% of phenotypic variance explained by those SNPs in the breeding populations. By combining the effects of multiple QTLs, breeders would be able to select seedlings that will later bear fruit with high sucrose and fructose content.
The value of D-dimer, ESR and CRP in the Diagnosis of Deep Vein Thrombosis of Lower Limbs After Hip and Knee Joint Replacement
Authors: Fan Xinchao , Zhang Kai , Sun Xilong , Duan Xiangrui , Wan Dadi , Yuan Ye , Zhou Yibin , Qiu Changmao , Li Wenyi , Li Xicheng 
Published: February 2021

Abstract
Objective: To investigate the diagnostic value of D-dimer, ESR and CRP in deep vein thrombosis (DVT) of lower extremity after hip and knee replacement.Methods: Clinical data of 216 patients who underwent hip and knee replacement in our hospital from January 2018 to November 2020 were retrospectively analyzed. Among them, there were 86 patients with lower extremity deep vein thrombosis and 130 patients without lower extremity deep vein thrombosis. Preoperative blood D-dimer, prothrombin time, fibrinogen content, erythrocyte sedimentation rate (ESR), C-reactive protein (CRP), albumin and hemoglobin levels were collected. Chi-square test was used to compare the rate of deep vein thrombosis in lower limbs. The PSM propensity score matching method was used to select 86 patients from 130 patients without lower extremity deep vein thrombosis (DVT) as control group. The levels of D-dimer, albumin and hemoglobin in 172 patients were compared, and the diagnostic efficacy of D-dimer, ESR and CRP in the diagnosis of lower extremity deep vein thrombosis after hip and knee replacement was analyzed by ROC curve.Results: ROC curve analysis results showed that: The optimal cut-off values of D-dimer, prothrombin time, ESR, CRP and age for the diagnosis of DVT of lower extremity after hip replacement were 1.745mg/L, 10.850s, 15.500mm/h, 2.375mg/L and 72 years old, respectively. The sensitivity was 71.8%, 66.7%, 61.5%, 94.9%, 71.8%, the specificity was 74.1%, 66.7%, 70.4%, 33.3%, 100%, and the area under the curve was 0.746, 0.683, 0.658, 0.651, 0.869. The optimal truncation value of D-dimer for the diagnosis of DVT of lower extremity after knee replacement was 0.285mg/L, the sensitivity was 78.7%, the specificity was 44.1%, and the area under the curve was 0.622.Conclusion: The diagnostic value of D-dimer in the formation of lower extremity DVT after knee arthroplasty is higher than that after hip arthroplasty, but the diagnostic value of prothrombin time, ESR, CRP and age in the formation of lower extremity DVT after hip arthroplasty is higher than that after knee arthroplasty.