bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quality analysis and metabolomic profiling of the effects of exogenous abscisic acid on rabbiteye blueberry
Authors: Han Tianyu , Li Weilin , Wu Wenlong , Shi Chong , Wang Xiaomin , Yang Haiyan , Xiong Zhenhao 
Published: March 2020

Abstract
Background: Blueberry is well known for its high content of bioactive metabolites, including anthocyanins, flavonols, and phenolic acids. This study aims to systematically study the effect of exogenous ABA application on ripening fruits in fruit growth, quality and anthocyanins content. The ripening process of blueberry fruit is divided into six stages for further analysis.Results: In this article, nontarget metabolomics were performed to demonstrate the effect on metabolites level. Basic results showed that 1000 mg/ml ABA significantly promoted fruit ripening, accelerated fruit colouration and increased soluble solid and anthocyanins content. At the same time, the fruit firmness and the content of some bioactive metabolites were also reduced. In metabolites level, a total of 1145 metabolites and 575 metabolites were detected and annotated in the positive model and the negative model, respectively. Principal component analysis and endogenous ABA content shows the exogenous ABA application is mainly concentrated on the green fruit turning into red fruit, after which the effect begins to decrease. The important metabolites of flavonoid pathway were detected and the result shows that anthocyanins synthesis was increased and parts of other bioactive metabolites were decreased. Conlusion: After comprehensive assessments, we believe that 1000 mg/ml exogenous ABA will have positive impacts on blueberry fruit quality and economic benefits. This finding provides a reference for different cultivation methods to improve the anthocyanin content of blueberry. Also, it provides a good research foundation for the next step of precise breeding for specific active compound of blueberry.
Association of surgical margins with local recurrence in patients undergoing breast-conserving surgery after neoadjuvant chemotherapy
Authors: Lin Joseph , Chen Sam Li-Sheng , Chen Dar-Ren , Lin Kuo-Juei , Wang Yu-Fen , Huang Ling-Hui 
Published: March 2020

Abstract
Background The aim of the current study was to report a single-institution experience using breast-conserving surgery after neoadjuvant chemotherapy (NACT), focusing on the association between microscopic resection margin status and locoregional recurrence (LRR). Methods Our institutional prospectively maintained database was reviewed to identify patients who were treated with NACT between January 2008 and April 2018. Results Among the main partial mastectomy specimens available for analysis (n = 161), 28 had margins < 1 mm, 21 had margin width of 1–2 mm and the remaining 112 had margins > 2 mm. LRR occurred in 16 patients (9.9%) and distant metastases were detected in 27 (16.8%) patients. There was no significant difference in the LRR between the > 2 mm margin group with a 60-month cumulative survival of 85.2% compared with 76.2% for the ≤ 2 mm group ( P = 0.335) in the Kaplan-Meier analysis. When we stratified patients by margin widths of ≥ 1 mm or < 1 mm, there was no LRR-free survival benefit observed for the ≥ 1 mm pathologic excision margin group in the univariate analysis (hazard ratio = 0.443; 95% confidence interval = 0.142–1.383; P = 0.161) with a 60-month cumulative LRR-free survival of 84.9% compared with 69.5% for the < 1 mm margin cohort ( P = 0.150). Conclusions In the absence of multiple scattered microscopic tumour foci, a negative margin of no ink on tumour maybe sufficient for stage I–III invasive breast cancer treated with NACT and breast-conserving surgery.
Clinical significance of skeletal muscle density and sarcopenia in patients with pancreatic cancer undergoing first-line chemotherapy: a retrospective observational study.
Authors: Kim In-Ho , Choi Moon Hyung , Lee In Seok , Hong Tae Ho , Lee Myung Ah 
Published: March 2020

Abstract
Background To investigate the clinical impact of sarcopenia and skeletal muscle density among patients with metastatic pancreatic adenocarcinoma who underwent palliative first line gemcitabine-based chemotherapy. Methods A total of 330 patients with metastatic pancreatic adenocarcinoma who were treated with palliative first line gemcitabine-based chemotherapy between January 2010 and March 2017 were included in this study. Sarcopenia and skeletal muscle density status were identified by L3 vertebra level skeletal muscle index in cm 2 /m 2 and muscle attenuation in Hounsfield units using computed tomography. Results A skeletal muscle index to skeletal muscle density comparison revealed a positive correlation (R 2 = 0.058, P<0.001). Kaplan–Meier analysis showed that low skeletal muscle density was associated with poor overall survival. Multivariate analysis using Cox regression showed that low skeletal muscle index and low skeletal muscle density were poor prognostic factors for overall survival, respectively. Co-presence of low skeletal muscle index and low skeletal muscle density had more powerful prognostic implication for overall survival. Grade 3 or higher toxicity of chemotherapy was more frequently observed in patients with low skeletal muscle index and low skeletal muscle density. Overall survival was not associated with skeletal muscle density status among patients who were chemotherapy responders (complete or partial responses). However, among non-responders (stable or progressive disease), low skeletal muscle density groups had significantly poorer overall survival than did the high skeletal muscle density groups. Conclusions Sarcopenia and skeletal muscle density status can be considered a prognostic factor in patients with metastatic pancreatic adenocarcinoma who receive palliative first line gemcitabine-based chemotherapy. Severe chemotherapy toxicity occurred in the sarcopenia and low skeletal muscle density groups. Our data suggest that comprehensive assessment of skeletal muscle parameters may be more useful prognostic factors.
Analysis of CCT7 Expression and Its Clinical Significance in Endometrial Cancer
Authors: Wang Liwen , Zhou Wei , Li Hui , Yang Hui , Shan Nianchun 
Published: March 2020

Abstract
Objective: Endometrial cancer (EC) is a common gynecologic malignancy; myometrial invasion (MI) is a typical approach of EC spreads and an important index to assess tumor metastasis and outcome of EC patients. CCT7 is a member of the TCP1 chaperone family, involved in cytoskeletal protein folding and unfolding. In this study, the role of CCT7 in EC development was investigated. Methods: Clinical data for 87 EC cases and expression of CCT7 were analyzed. CCT7 was knocked out using siRNA- CCT7 in Ishikawa and RL95-2 cells, and their function about proliferation, apoptosis and invasion were further tested. Bioinformatics methods were used to predict the potential pathways of CCT7 in EC development. Results: The rates of CCT7-positive cells in EC and adjacent normal endometrium tissues had significant difference (67.8% vs. 51.4%, p = 0.035), and the expression rate increased from low to high pathological stage (39.7% in the I/II stage, 71.4% in the III/IV stage, p = 0.029). Similar change was found in protein level. CCT7 expression differed significantly between the deep MI group (>1/2) and the superficial MI group (≤1/2) (P = 0.039). However, there were no differences with respect to age, pathological type and histological grade. CCT7 suppression induced a function-loss in in both Ishikawa and RL95-2 cells. Bioinformatics analysis demonstrated that EC patients with lower level CCT7 expression had better Overall survival (p= 0.0081). GO enrichment indicated that “RNA binding”, “Mitochondrion”, “Translation”, and “Spliceosome” were most significantly enriched potential pathways. Five hub genes, PSMA5, PSMD14, SNRPB, SNRPG and TXNL4 A, were all significantly upregulated in EC and had positive correlation with CCT7. Conclusions: CCT7 may be involved in EC development by excessively activating tumor cell function to promote MI or distant/nodal metastasis, which definitely impaired the prognosis of EC patients.
Maternal Risk Factors Associated with Poor Postpartum Healthcare Utilization
Authors: silverman michael e , Loudon Holly , Burgos Laudy 
Published: March 2020

Abstract
Objectives: Perceptions regarding the benefits of postpartum care among mothers and clinicians often differ. Clinicians generally perceive postpartum care as preventative, whereas pregnant and postpartum women often lack knowledge about its preventative benefits. As a result many women choose not to return for scheduled postpartum care visits. Methods: To examine if clinically relevant demographic and birth related factors are informative predictors for postpartum healthcare follow-up care, we conducted a population based cohort study of all women who delivered a child in 2012 – 2015 at the New York Mount Sinai Hospital Obstetrics and Gynecology Ambulatory Practice. Data was ascertained from electronic health records.Results: Of the 4,240 unique women who delivered between 2012-2015 at the Mount Sinai Hospital OB/GYN Ambulatory Practice, 1,685 (39.7%) did not return for their postpartum care follow-up appointment. The number of prenatal visits, maternal age, and parity were significantly associated with postpartum care follow-up. Conclusion for Practice: The purpose of this study was to determine identifiable factors associated with reduced postpartum healthcare follow-up utilization. Several clinically relevant variables were associated with the reduced likelihood for attending postpartum care visits. Because pregnant women represent a medically captured population, the results of this study point to the need to increase postpartum healthcare literacy during perinatal appointments especially among younger mothers, women who have had previous deliveries, and those with fewer prenatal visits.
Analyzing matched sets of microbiome data using the LDM and PERMANOVA
Authors: Zhu Zhengyi , Satten Glen , Mitchell Caroline , Hu Yi-Juan 
Published: March 2020

Abstract
Background: Matched-set data arise frequently in microbiome studies. For example, we may collect pre- and post-treatment samples from a set of individuals, or use important confounding variables to match data from case participants to one or more control participants. Thus, there is a need for statistical methods for data comprised of matched sets, to test hypotheses against traits of interest (e.g., clinical outcomes or environmental factors) at the community level and/or the OTU (operational taxonomic unit) level. Optimally, these methods should accommodate complex data such as those with unequal sample sizes cross sets, confounders varying within sets, as well as continuous traits of interest. Methods: PERMANOVA is a commonly used distance-based method for testing hypotheses at the community level. We have also developed the linear decomposition model (LDM) that unifies the community-level and OTU-level tests into one framework. Here we present a strategy that can be used with both PERMANOVA and the LDM for analyzing matched-set data. We propose to include an indicator variable for each set as covariates, so as to constrain comparisons between samples within a set, and also permute traits within each set, which can account for exchangeable sample correlations. The flexible nature of PERMANOVA and the LDM allows discrete or continuous traits or interactions to be tested, within-set confounders to be adjusted, and unbalanced data to be fully exploited. Results: Our simulations indicate that our proposed strategy outperformed alternative strategies in a wide range of scenarios. Using simulation, we also explored optimal designs for matched-set studies. The flexibility of PERMANOVA and the LDM for a variety of matched-set microbiome data is illustrated by the analysis of data from two real studies. Conclusions: Including set indicator variables and permuting within sets when analyzing matched-set data with PERMANOVA or the LDM is a strategy that performs well and is capable of handling the complex data structures that frequently occur in microbiome studies.
Zooming in on dynamics of marine microbial communities in the phycosphere of Akashiwo sanguinea (Dinophyta) blooms
Authors: Jung Seung Won , Park Joonsang , Kang Junsoo , Kim Hyun-Jung , Joo Hyung Min , Kang Donhyug , Seo Hyojeong , Kim Sunju , Jang Min-Chul , Lee Kyunwoo , Oh Seok Jin , Lee Sukchan , Lee Taek-Kyun 
Published: March 2020

Abstract
Background: Characterising ecological relationships between viruses, bacteria, and phytoplankton in the ocean are critical to understanding the ecosystem, yet these relationships are infrequently investigated together. To understand the dynamics of microbial communities and environmental factors in harmful algal blooms (HABs), we examined the environmental factors and microbial communities during Akashiwo sanguinea HABs in the Jangmok coastal waters of South Korea by metagenomics. Results: Specific bacterial communities showed synergistic and antagonistic relationships with A. sanguinea bloom. Endoparasitic dinoflagellate Amoebophrya sp. 1 controlled the bloom dynamics, as an increase in their abundance was correlated with HAB decline. In the nucleocytoplasmic large DNA viruses, abundance of Pandoraviridae increased following an increase in HAB. Operational taxonomic units and environmental factors associated with A. sanguinea were also visualized by network analysis: A. sanguinea-Amoebophrya sp. 1 (r=0.81, Time-lag: 2 day) and A. sanguinea-Pandoravirus dulcis (0.64, 0 day) relationships showed close association. A. sanguinea-dissolved organic carbon and -dissolved inorganic phosphorus relationships were also very closely correlated (each 0 day time-lag, respectively). Conclusions: Microbial communities and the environment dynamically and complexly changed in A. sanguinea bloom, and a rapid turnover of microorganisms could respond to ecological interactions. A. sanguinea bloom dramatically changes the environments through their exudation of dissolved carbohydrates by autotrophic processes, followed by changes in microbial communities involving host-specific viruses, bacteria, and parasitoids. Thus, microbial communities in HAB ecology are composed of various organisms and they interact in a complex way. Therefore, to interpret their ecosystem, the complex reactions among various microorganisms should be studied rather than studying a simple 1:1 reaction, such as a prey-predator interaction.
The effect of microbiota-based investigational drug RBX2660 on the gut microbiome and resistome revealed by a placebo-controlled clinical trial
Authors: Kwak Suryang , Choi JooHee , Hink Tiffany , Reske Kimberly A. , Blount Kenneth , Jones Courtney , Bost Margaret H. , Sun Xiaoqing , Burnham Carey-Ann D. , Dubberke Erik R. , Dantas Gautam 
Published: March 2020

Abstract
Background Intestinal microbiota restoration can be achieved by replacing a subject’s perturbed microbiota with that of a healthy donor. Recurrent Clostridioides difficile infection (rCDI) is one key application of such treatment. Another application of interest is depletion of antibiotic resistant genes (ARGs) and organisms (AROs). In this study, we investigated fecal specimens from a multicenter, randomized, double-blind, placebo-controlled phase 2b study of microbiota-based investigational drug RBX2660. Patients were administered either placebo, 1 dose of RBX2660 and 1 placebo, or 2 doses of RBX2660 via enema and longitudinally tracked for changes in their microbiome and antibiotic resistome. Results All patients exhibited significant recovery of gut microbiome diversity and decrease of ARG abundance during the first 7 days post-treatment. However, the microbiome and resistome shifts towards healthier configurations were more significant and longer lasting in RBX2660 recipients compared to placebo. We identified 18 taxa and 21 metabolic functions distinguishing the baseline microbiome of non-transplanted patients, and the majority of features were correlated to intrinsic vancomycin resistance. We also identified 7 patient-specific and 3 RBX2660-specific ARGs and tracked their dynamics post treatment. Whole genome sequencing of AROs cultured from RBX2660 product and patient samples indicate ARO eradication in patients via RBX2660 administration, but also, to a lesser extent, introduction of RBX2660-derived AROs. Conclusions By including a placebo group, we distinguished the effects of RBX2660 from baseline post-antibiotic microbiome dynamics. Antibiotic discontinuation alone resulted in significant recovery of gut microbial diversity and reduced ARG abundance, but RBX2660 administration more rapidly and completely changed the composition of patients’ microbiome, resistome, and ARO colonization by transplanting RBX2660 microbiota into the recipients. Although ARGs and AROs were transmitted through RBX2660, the resistome post-RBX2660 more closely resembled that of the administered product—a proxy for the donor—than an antibiotic perturbed state.
FVE-novel: Recovering Draft Genomes of Novel Viruses and Phages in Metagenomic Data
Authors: Tithi Saima Sultana , Aylward Frank O. , Jensen Roderick V. , Zhang Liqing 
Published: March 2020

Abstract
Background Despite the recent surge of viral metagenomic studies, recovering complete virus/phage genomes from metagenomic data is still extremely difficult and most viral contigs generated from de novo assembly programs are highly fragmented, posing serious challenges to downstream analysis and inference. Results Here we develop FVE-novel, a computational pipeline for reconstructing complete or near-complete viral draft genomes from metagenomic data. FVE-novel deploys FastViromeExplorer to efficiently map metagenomic reads to viral reference genomes or contigs, performs de novo assembly of the mapped reads to generate scaffolds, and extends the scaffolds via iterative assembly to produce final viral scaffolds. We applied FVE-novel to an ocean metagenomic sample and obtained 268 viral scaffolds that potentially come from novel viruses. Through manual examination and validation of the ten longest scaffolds, we successfully recovered four complete viral genomes, two are novel as they cannot be found in the existing databases and the other two are related to known phages. Conclusions The hybrid reference-based and de novo assembly approach used by FVE-novel represents a powerful new approach for exploring viral diversity in metagenomic data. FVE-novel is freely available at https://github.com/saima-tithi/FVE-novel .
Exosomal Transfer of MiR-500a-3p Confers Cisplatin Resistance and Stemness via Targeting FBXW7 in Gastric Cancer
Authors: Lin Hao , Zhang Caihua , Zhang Liang , liu pengpeng 
Published: March 2020

Abstract
Background Chemoresistance has become a major obstacle for gastric cancer (GC) therapy in clinical practice. MiRNAs have been reported to play critical roles in the development of chemoresistance in various tumors, including GC. However, the role of MiR-500a-3p within exosomes in cisplatin-resistant GC cells remains largely unknown. Materials and methods Cell proliferation and exosome delivery assays were performed using CCK-8 and transwell assays, respectively. CD63, CD81, β-tubulin, FBXW7, GAPDH, CD133, CD44 and SOX2 were detected by western blot and immunofluorescence assays. The expression levels of miR-500a-3p and FBXW7 mRNA were measured by real-time qRT-PCR. The interaction between miR-500a-3p and FBXW7 was predicted by bioinformatics software and confirmed by the dual-luciferase reporter. The mechanism of exosomal miR-500a-3p for cisplatin resistance was investigated in vitro and in vivo experiments. Results MiR-500a-3p level was upregulated in cisplatin-resistant GC cells and its downregulation enhanced cisplatin sensitivity. Moreover, extracellular miR-500a-3p could be incorporated into exosomes and transmitted to sensitive cells, thus disseminating cisplatin resistance. Additionally, exosomal miR-500a-3p promoted cisplatin resistance via targeting FBXW7 in vitro and in vivo . Clinically, higher expression of miR-500a-3p in the plasma exosomes of GC patients is correlated with DDP resistance and thereby results in poor progression-free prognosis. Conclusion Our finding highlights the potential of exosomal miR-500a-3p as an alternative modality for the prediction and treatment of GC with chemoresistance, providing a novel avenue for the treatment of GC.
Generalized anxiety disorder, depressive symptoms and sleep quality during COVID-19 epidemic in China: a web-based cross-sectional survey
Authors: Huang Yeen , Zhao Ning 
Published: March 2020

Abstract
Background

China has been severely affected by COVID-19 (Corona Virus Disease 2019) since December, 2019. This study aimed to assess the population mental health burden during the epidemic, and to explore the potential influence factors.

Methods

Using a web-based cross-sectional survey, we collected data from 7,236 self-selected volunteers assessed with demographic information, COVID-19 related knowledge, Generalized Anxiety Disorder-7 (GAD-7), Center for Epidemiology Scale for Depression (CES-D), and Pittsburgh Sleep Quality Index (PSQI). Logistic regressions were used to identify influence factors associated with mental health problem.

Results

Of the total sample analyzed, the overall prevalence of GAD, depressive symptoms, and sleep quality were 35.1%, 20.1%, and 18.2%, respectively. Young people reported a higher prevalence of GAD and depressive symptoms than older people ( P <0.001). Compared with other occupational group, healthcare workers have the highest rate of poor sleep quality ( P <0.001). Multivariate logistic regression showed that age (< 35 years) and times to focus on the COVID-19 (≥ 3 hours per day) were associated with GAD, and healthcare workers were associated with poor sleep quality.

Conclusions

Our study identified a major mental health burden of the public during COVID-19 epidemic in China. Young people, people who spent too much time on the epidemic, and healthcare workers were at high risk for mental illness. Continuous surveillance and monitoring of the psychological consequences for outbreaks should become routine as part of preparedness efforts worldwide.