bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of extracellular matrix stiffness on genomic heterogeneity in MYCN-amplified neuroblastoma cell line
Authors: López-Carrasco Amparo , Martín-Vañó Susana , Burgos-Panadero Rebeca , Monferrer Ezequiel , Berbegall Ana P , Fernández-Blanco Beatriz , Navarro Samuel , Noguera Rosa 
Published: October 2020

Abstract
Background: Increased tissue stiffness is a common feature of malignant solid tumors, often associated with metastasis and poor patient outcomes. Vitronectin, as an extracellular matrix anchorage glycoprotein related to a stiff matrix, is present in a particularly increased quantity and specific distribution in high-risk neuroblastoma. Furthermore, as cells can sense and transform the proprieties of the extracellular matrix into chemical signals through mechanotransduction, genotypic changes related to stiffness are possible.Methods: We applied high density SNPa and NGS techniques to in vivo and in vitro models (orthotropic xenograft vitronectin knock-out mice and 3D bioprinted hydrogels with different stiffness) using two representative neuroblastoma cell lines (the MYCN-amplified SK-N-BE(2) and the ALK -mutated SH-SY5Y), to discern how tumor genomics patterns and clonal heterogeneity of the two cell lines are affected. Results: We describe a remarkable subclonal selection of genomic aberrations in SK-N-BE(2) cells grown in knock-out vitronectin xenograft mice that also emerged when cultured for long times in stiff hydrogels. In particular, we detected an enlarged subclonal cell population with chromosome 9 aberrations in both models. Similar abnormalities were found in human high-risk neuroblastoma with MYCN amplification. The genomics of the SH-SY5Y cell line remained stable when cultured in both models. Conclusions: Focus on heterogeneous intratumor segmental chromosome aberrations and mutations, as a mirror image of tumor microenvironment, is a vital area of future research.
Cytotype Distribution and Chloroplast Phylogeography of Actinidia Chinensis Complex
Authors: Wang Zhi , Zhong Caihong , Li Dawei , Yan Chunlin , Yao Xiaohong , Li Zuozhou 
Published: October 2020

Abstract
Background: Previous plant phylogeography in subtropical China mostly focused on rare and endangered species, whereas few studies conducted on the taxa with relatively wide distribution, especially for polyploid species. We used Actinidia chinensis complex, a widespread geographically woody liana of variable ploidy in subtropical China, to investigate its cytotype and haplotype distribution pattern based on three chloroplast fragments (ndhF-rpl132, ps16-trnQ and trnE-trnT). Macroevolutionary, microevolutionary and niche modeling tools were also combined to disentangle the origin and the demographic history of the species or cytotypes. Results: The ploidy levels of 3569 individuals from 128 populations sampled throughout the species distribution range were estimated using flow cytometry. The widespread cytotypes were diploids followed by tetraploids and hexaploids, while triploids and octaploids occasionally occurred in a few populations. Thirty-one chloroplast haplotypes were detected and the genetic diversity and genetic structure were great differences between the var. chinensis and var. deliciosa. Our results also revealed these two varieties (or ploidy races) inhabit significantly different climatic niche spaces. Ecological niche models (ENMs) indicate that all varieties’ ranges contracted during the Last Interglacial (LIG), and expanded eastward or northward during the Last Glacial Maximum (LGM). Conclusions: Pliocene and Plio-Pleistocene climatic fluctuations and vicariance may have played key roles in shaping the current population structure and historical demography in the A. chinensis complex. The polyploidization process also played an important role in the historical demography of the A. chinensis complex through improving their adaptability to environmental changes.
Combined effects of low-dose gambogic acid and NaI131 in drug-resistant non-small-cell lung cancer cells
Authors: Huang Jing , Ding Ming , Wu Ying , Han Shuhua , Xie Yan , Yang Sufang , Zhu Xiaoli , Chen Pingsheng 
Published: October 2020

Abstract
Background

Radioactive seed is a method for treating drug-resistant, late-stage non-small cell lung cancer (NSCLC), but has undesirable side effects. Gambogic acid (GA), an ingredient of traditional Chinese medicine, exerts broad-spectrum antitumour activities via several pathways. This study aimed to elucidate the mechanism involved in the combined effect of low-dose GA and NaI131 to sensitize the antitumour activity of NaI131 in drug-resistant NSCLC cells.
Methods

Human NSCLC cell line A549 and drug-resistant cell lines A549/DDP and A549/Taxol were treated with NaI131, low-dose GA or a combination of both; control group of each cell line was treated with phosphate-buffered saline. Following treatment, cell proliferation, apoptosis, cell cycle, and levels of expression of apoptosis-related proteins namely CDK1, Cyclin B, mtp53, HSP90, and Bax, Bcl-2 respectively, and P-glycoprotein 1 (P-gp) known to confer resistance to chemotherapy, were detected using western blotting and immunofluorescence. mRNA levels of mtp53 and HSP90 were measured using qRT-PCR.
Results

Compared to the control group, A549, A549/DDP, and A549/Taxol cells treated with NaI131, GA or combination of drugs exhibited G2/M arrest, increased percentage of total apoptotic cells, significantly reduced protein levels of CDK1, Cyclin B, mtp53, HSP90, Bcl-2 and P-gp, increased protein levels of Bax and decreased mRNA levels of mtp53 and HSP90. The changes in the combination group were significantly different from the other groups.
Conclusion

In NSCLC cell lines, low-dose GA could enhance the effect of NaI131 on G2/M arrest, promote cell apoptosis, reduce drug-resistance and hence could be explored as a potential radionuclide sensitizer.
Comparison of the efficacy of five front-of-pack nutrition labels in helping the Brazilian consumer make a healthier choice
Authors: Blom Wendy A.M. , Goenee Chantal , Juliano Lucia , de Groene Els M. , Martins Fernanda de Oliveira 
Published: October 2020

Abstract
Background:
We tested, in an online survey, how well five different front-of-pack (FOP) labels helped Brazilian consumers make a healthier choice between two food or beverage products as compared to a no FOP label control.
Methods:
All 1072 respondents were randomly assigned to one of six groups 1) no FOP label (control), 2) ABIA label, 3) GGALIii Nutrient Profile label, 4) IdeC label, 5) Hybrid label or 6) Nutri-Score label and were all shown 9 food stimuli consisting of two products. The nutrient profile of the ABIA and Hybrid labels take into account the serving size of the food, while the other three labels score per 100 g. Respondents were asked which of the two products they thought was the healthier choice.
Results:
Overall, the Hybrid and ABIA labels performed best, resulting in a statistically significantly higher percentage of correct answers compared to the control for 9/9 and 8/9 of the food stimuli, respectively. Nutri-Score performed reasonably well and outperformed the control in 6/9 cases. The IdeC and GGALIii NP warning labels were the least useful, performing only one and two times better, respectively, than the control group.
Conclusion:
The Hybrid and the ABIA FOP labels, two interpretative traffic light labels that use colours and provide nutritional information per serving, were best suited to help Brazilian consumers choose the healthier product. They especially outperformed the other FOP labels when serving sizes differed significantly or when deeper consideration of nutritional information was needed to make an informed decision.
Predictors of Caregiver Burden in Aged Caregivers of Demented Older Patients
Authors: Tsai Chia-Fen , Hwang Wei-Shen , Lee Jun-Jun , Wang Wen-Fu , Huang Ling-Chun , Huang Li-Kai , Lee Wei-Ju , Sung Pi-Shan , Liu Yi-Chien , Hsu Chih-Cheng , Fuh Jong-Ling 
Published: October 2020

Abstract
BackgroundDementia in the oldest-old is projected to increase exponentially as is the burden of their caregivers who may experience unique challenges and suffering. Thus, we aim to investigate which factors are associated with older caregivers’ burden in caring demented outpatients in a multicenter cohort.MethodsPatients and their caregivers, both aged ≧65 years, in the National Dementia Registry Study in Taiwan (T-NDRS) were included in this study. Caregiver burden was measured with the short version of the Zarit Burden Interview (ZBI). The correlations between the ZBI scores and characteristics of caregivers and patients, including severity of dementia, physical comorbidities, instrumental activities of daily living (IADL), neuropsychiatric symptoms assessed by the Neuropsychiatric Inventory (NPI), and family monthly income, were analyzed.ResultsWe recruited 328 aged informal caregiver-patient dyads. The mean age of caregivers was 73.7± 7.0 years, with female predominance (66.8%), and the mean age of patients was 78.8±6.9 years, with male predominance (61.0%). Multivariable linear regression showed that IADLs (β=0.83, p<0.001) and NPI subscores of apathy (β=3.83, p<0.001)and irritability (β=4.25, p<0.001) were positively associated with ZBI scores. The highest family monthly income (β= -10.92, p=0.001) and caregiver age (β= -0.41, p=0.001) were negatively correlated with ZBI scores.ConclusionsOlder caregivers of older demented patients experience a higher care burden when patients had greater impaired functional autonomy and the presence of NPI symptoms of apathy and irritability. Our findings provide the direction to identify risky older caregivers, and we should pay more attention to and provide support for these exhausted caregivers.
Tubularized Urethral Reconstruction Using Everted Saphenous Vein Graft in A Beagle Model
Authors: Li Dan , Shen Zhou , Xu Yujie 
Published: October 2020

Abstract
Background: The repair of anterior urethral stricture and hypospadias require urethral reconstruction. We conduct the study to investigate the efficacy of anterior urethral reconstruction using everted saphenous vein graft in tubular fashion. Methods: Twelve male beagles were randomly divided into three groups: experimental group( n=5), control group( n=5) and normal group( n=2). A 3 cm defect in anterior urethra was created. Autologous saphenous vein graft was harvested. In experimental group, urethral defect was replaced by everted saphenous vein graft in tubular fashion. In control group, urethral reconstruction was performed using uneverted saphenous vein graft. At 6 months postoperatively, beagles in all groups received retrograde urethrography to evaluate urethral patency and were killed for histological examination. Results: Retrograde urethrography showed the urethral caliber of beagles in experimental group were similar to those of normal. Ether urethral stricture or fistula were detected in all animals in control group. In experimental group, the everted saphenous vein graft completely integrated into the urethra. The reconstructed urethra had a wide lumen and was completely covered by urothelium. The subepithelial collagen and muscle fibers were well formed and highly organized. Everted saphenous vein graft had a high ability of neovascularization. In control group, the reconstructed segment had a fibrotic urethral lumen in which urothelium was not intact. And there were few newly formed capillaries. Conclusions: Everted saphenous vein graft can be used as tubular substitute material for anterior urethral strictures and hypospadias.
Development of A Nomogram to Predict Survival Outcome Among Epithelial Ovarian Cancer Patients With Site-Distant Metastases: A Population-Based Study
Authors: Wang Bo , Wang Shixuan , Ren Wu 
Published: October 2020

Abstract
Objective. The incidence of initial diagnosis with distant metastasis in patients with epithelial ovarian cancer is not rare, for which the available prognostic evaluation criteria is absent. This study aimed to develop a nomogram score to predict long-term prognosis.Methods. This study analyzed patients with epithelial ovarian cancer from the Surveillance, Epidemiology, and End Results (SEER) database between 1975 and 2016. Multivariable logistic and Cox regression were performed to identify survival trajectories. A nomogram score was used to predict long-term survival probability. Results. A total of 131050 patients were included, 18.2%, 7.8% and 66.1% had localized, regional and distant metastases, respectively. Metastases were inversely associated with high probability of 5-year overall survival outcome, localized (OR, 4.62; 95%CI, 4.45-4.80), regional (OR, 2.47; 95%CI, 2.36-2.59) compared with distant metastases. Survival was poorer among regional (HR, 1.72; 95%CI, 1.65-1.79) and distant (HR, 3.39; 95%CI, 3.29-3.49) metastases at diagnosis. For incidence, 0.9%, 6.7%, 5.8% and 0.2% had bone, liver, lung and brain metastases in the all-cause mortality cohort respectively, 1.6%, 9.9%, 8.8% and 0.3% had bone, liver, lung and brain metastases in the cancer-specific mortality cohort respectively. The median survival among the all-cause mortality cohort was 21.0 months, cancer-specific mortality cohort was 15.0 months. Organ-specific metastases were independently associated with survival prognosis.Conclusions. Nomogram score in estimating the long-term prognosis is feasible, for which contribute to directing clinical treatment and prognosis assessment in patient harboring site-distant metastases.
Extracting Knowledge Networks from Plant Scientific Literature: Potato Tuber Flesh Color as an Exemplary Trait
Authors: Singh Gurnoor , Papoutsoglou Evangelia , Keijts-Lalleman Frederique , Vencheva Bilyana , Rice Mark , Visser Richard G.F. , Bachem Christian , Finkers Richard 
Published: October 2020

Abstract
Background: Scientiﬁc literature carries a wealth of information crucial for research, but only a fraction of it is present as structured information in databases and therefore can be analyzed using traditional data analysis tools. Natural language processing (NLP) is often and successfully employed to support humans by distilling relevant information from large corpora of free text and structuring it in a way that lends itself to further computational analyses. For this pilot, we developed a pipeline that uses NLP on biological literature to produce knowledge networks. We focused on the ﬂesh color of potato, a well-studied trait with known associations, and we investigated whether these knowledge networks can assist us in formulating new hypotheses on the underlying biological processes. Results: We trained an NLP model based on a manually annotated corpus of 34 full-text potato articles, to recognize relevant biological entities and relationships between them in text (genes, proteins, metabolites and traits). This model detected the number of biological entities with a precision of 97.65% and a recall of 88.91% on the training set. We conducted a time series analysis on 4023 PubMed abstract of plant genetics-based articles which focus on 4 major Solanaceous crops (tomato, potato, eggplant and capsicum), to determine that the networks contained both previously known and contemporaneously unknown leads to subsequently discovered biological phenomena relating to ﬂesh color. Analysis of these networks indicates a connection between our trait and a candidate gene (zeaxanthin epoxidase) already two years prior to explicit statements of that connection in the literature. Conclusions: Our time-based analysis indicates that network-assisted hypothesis generation shows promise for knowledge discovery, data integration and hypothesis generation in scientiﬁc research.
High Body Mass Index Was Related to Favorable Therapeutic Efficacy of Epidermal Growth Factor Receptor Targeted Therapy in Advanced Non-Small Cell Lung Cancer
Authors: Chen Yue-Yun , Yin Xu-De , Xie Ke , Wang Pei-Pei , Fu Yang , Li Qing , Liu Bi-Sheng , Liu Ting , Ding Zhen-Yu 
Published: October 2020

Abstract
BackgroundIt’s widely accepted that Obesity is closely associated with the elevated risk of various cancers. However, there’s no consensus regarding the impact of body mass index (BMI) on the outcome of targeted therapy targeted-therapy efficacy in lung cancer. MethodsTreatment-naive advanced NSCLC patients harboring EGFR mutation prescribed TKI were screened and enrolled from 3 referral centers. Patients enrolled from West China Hospital were set as the training group, and the others as validation group. Both the demographic features including mutation status and BMI, and therapeutic effects including objective response rate (ORR), progression-free survival (PFS), and overall survival (OS) were collected.ResultsIn the training group, patients were dichotomized according to their BMI. Those with higher BMI (>22.5) achieved a prolonged PFS compared with those with lower BMI (13.8 and 10.9 mon, HR: 0.68; 95% CI: 0.54-0.86; P = 0.001), and the priority persisted irrespective of different cut-off values. Besides, the favorable association of high BMI with long PFS was confirmed in the validation cohort (14.0 and 11.6 mon, P=0.089) and whole cohort (13.7 and 11.3 mon, P=0.004). In the multivariate analysis, BMI was an independent favorable factor of PFS, together with gender, albumin, and performance. By integration of these factors, a nomogram to predict to 1-,3-year PFS was established. Finally, higher BMI was associated with better objective response rate (ORR, 74% and 69%) and longer overall survival (OS, 41.4 and 33.5 mon, P=0.011). ConclusionHigh BMI was independently associated with efficacy of EGFR-TKI treatment in advanced NSCLC patients.
Family Health Climate: A Qualitative Exploration of Everyday Family Life and Health
Authors: Wäsche Hagen , Niermann Christina , Bezold Jelena , Woll Alexander 
Published: October 2020

Abstract
Background The family is an important social environment for children’s, adolescents’ and adults’ health. However, studies mostly focused on dyadic and unidirectional influences of parents on their children. Studies addressing influences arising from daily family life and including family level influences are rare and the existing studies solely focus on the relevance for children’s health or health-related behaviors. We use a qualitative approach to explore how daily family life and its inherent health-related cues affect family members’ physical activity and eating behavior. Methods Semi-structured interviews utilizing an interview guide were conducted. Since we aimed to examine family life, we analyzed both parents’ and their children’s views on health-related interaction patterns and family environmental influences on individuals’ health-related behavior. Twenty-two members of seven families were interviewed. Transcripts of the interviews were systematically analyzed following Grounded Theory principles.Results The interviews revealed that various individual as well as environmental factors shape health-related aspects of daily family life. A model was developed that organizes these influencing factors on family life with regard to health-related interactions and the emergence of the Family Health Climate (FHC) – reflecting shared perceptions and cognitions regarding a healthy lifestyle within families – and its consequences. Family interactions and family time, often realized through shared family meals, are key factors for families’ health with regard to nutrition and physical activity. The FHC showed to affect various aspects related to health behavior of individual family members.Conclusions The model allows to gain knowledge on underlying processes and mechanisms of family life that influences individuals’ health-related behavior. Based on a better understanding of the association between family life and individual health behavior the development of family-based interventions can be informed. Furthermore, the insights can help to guide further research focusing on families as a system.
BSR-Seq Analysis Provides Insights into Cold Stress in Actinidia Arguta F1 Populations
Authors: Lin Miao miao , Sun Shihang , Fang Jinbao , Qi Xiujuan , Sun Leiming , Zhong Yunpeng , Sun Yanxiang , Hong Gu , Wang Ran 
Published: October 2020

Abstract
BackgroundThe freezing injury, which is one of the important abiotic stresses in horticultural crops, can influences the growth and development and the production area of kiwifruit (Actinidia Lind1). Actinidia arguta has excellent cold resistance in Actinidia species, but knowledge relevant to molecular mechanisms is still limited so far. Understanding the mechanism of cold resistance in kiwifruit is important for cold-resistant breeding. ResultsIn our study, a cross of ‘Ruby-3’×‘Kuilv’ male was built for the A. arguta hardiness study, and 20 cold-tolerant and 20 cold-sensitive populations were selected from 492 populations according to LT50. Then, we performed Bulked segregant RNA-seq combined with single-molecule real-time sequencing to identify differentially expressed genes with cold hardiness. We found that the content of soluble sucrose and the activity of β-amylase were higher in the cold tolerant population pool than in the cold sensitive population pool. Upon -30°C low temperature treatment, 126 differentially expressed genes were found, and 59 genes were upregulated and 67 genes were downregulated when comparing the tolerant and sensitive pools, respectively. KEGG pathway analysis showed that the DEGs mainly belonged to starch and sucrose metabolism and amino sugar and nucleotide sugar metabolism. There were main 10 key enzyme encoding genes and two regulatory genes were up regulated in tolerant pool, regulated genes of CBF pathway were found to be different expressed, especially, 14-3-3 gene was down regulated and EBF gene was up regulated. To validate the BSR-Seq results, 24 DEGs were determined by qRT-PCR, and the results were consistent with BSR-Seq.ConclusionOur research provides valuable insights into the mechanism related to cold resistance in Actinidia and identified potential genes that are important for cold resistance in kiwifruit.
Integrative Bioinformatics Analysis Identified Hub Genes in Association with Development of Lung Adenocarcinoma
Authors: Hu Xilin , Xu Hanlin , Jiao Wenjie , Tian Kaihua 
Published: October 2020

Abstract
Background: Cancer-related death is mainly caused by lung adenocarcinoma (LUAD), an aggressive malignant tumor. Therefore, the identification of important LUAD-related genes and the further analysis of its prognostic significance are critical for the survival of LUAD patients.Methods: Weighted Gene Co-expression Network Analysis (WGCNA) and differential gene expression analysis methods were adopted to screen out TCGA-LUAD database and the gene expression profiles of GSE32863 from GEO. Functional annotation analysis and protein-protein interaction (PPI) network were conducted on differential co-expression genes. Furthermore, survival analysis was carried out on twelve hub genes that were identified by applying the CytoHubba plugin of Cytoscape. Finally, we validated the protein level of survival-related gene in HPA database.Results: A total of 358 differential co-expression genes were extracted from the database of TCGA and GEO. These genes were mainly enriched in extracellular structure organization, cell−substrate adhesion and response to acid chemical (biological process), cell−cell junction and collagen−containing extracellular matrix (cellular component), DNA−binding transcription activator activity, glycosaminoglycan binding, and growth factor binding (molecular function). In the KEGG analysis, the main pathways were Drug metabolism−cytochrome P450. Moreover, in a PPI network, the 12 hub genes (GNG11, ADRB2, ADCY4, TGFBR2, IL6, GPC3, VIPR1, GRK5, CAV1, RAMP3, RAMP2, and CALCRL) were identified. The expression level of ADCY4, VIPR1, and TGFBR2 was corresponded with clinical stages and overall survival (OS) in LUAD patients. Finally, the protein level of ADCY4 and VIPR1 was down-regulated consistently with mRNA levels in LUAD samples.Conclusion: Perhaps, ADCY4, VIPR1 and TGFBR2 play important role in tumorigenesis, so they will serve as prognostic biomarkers and therapeutic targets of LUAD in the future.