bluuebunny/crossref_metadata_2025_split huggingface dataset:
Socioeconomic-related inequalities in oral hygiene behaviors: a cross-sectional analysis of the PERSIAN cohort study
Authors: Soofi Moslem , Pasdar Yahya , Karami Matin Behzad , Hamzeh Behrooz , Rezaei Satar , Kazemi Karyani Ali , Moradi Nazar Mehdi , Soltani Shahin , Hajizadeh Mohammad , Salimi Yahya , Zangeneh Alireza , Poustchi Hossein , Sharafkhah Maryam , Haghdoust Ali Akbar , Shirzad Ahoodashti Mahboobeh , Mohammadkarimi Vahid , Aghazadeh-Attari Javad , Mansour-Ghanaei Fariborz , Yazdanbod Abbas , Eftekhar Ebrahim , Rahimi Zahra , Bahramali Ehsan , Moslem Alireza , Jamalizadeh Ahmad , Ardakani Fatemeh Ezoddini , Zanganeh Mehdi , Ahmadi Ali , Ostadrahimi Alireza , Tohidinezhad Fariba , Rahimi Kazerooni Salar , Najafi Farid 
Published: February 2020

Abstract
Background
Socioeconomic-related inequality in oral hygiene behaviors in Iran is poorly understood. This study aims to measure and decompose socioeconomic-related inequalities in oral hygiene behaviors among middle-aged and elderly adults in Iran.

Methods
A cross-sectional analysis was performed using data from the Prospective Epidemiological Research Studies in IrAN (PERSIAN), a large national cohort study. A total of 130,016 individuals aged 35 years and above from 17 cohort centers in Iran were included in the study. The normalized concentration index (Cn) was used to measure the magnitude of inequality in oral hygiene behaviors, i.e. brushing at least twice and flossing once daily, among middle-aged and elderly Iranian adults included in the cohort centers. Decomposition analysis was performed to quantify the contribution of each determinant to the observed inequality in oral hygiene behaviors.

Results
Totally, 65.5% of middle-aged and elderly adults brushed their teeth twice a day or more, 7.6% flossed at least once a day and 3.48% had both habits. The estimated Cn of the two habits combined, i.e. tooth brushing and dental flossing, for all provinces taken part in the PERSIAN cohort study was 0.399 (95% confidence interval [CI]: 0.383 to 0.417), indicating that the prevalence of the two habits combined is more concentrated among individuals with higher socioeconomic status. Inequality in oral hygiene behaviors was pro-rich in all cohort centers. The decomposition results suggested socioeconomic status as the main factor contributing to the overall inequality, followed by the level of education, and the province of residence.

Conclusion
A low prevalence of oral hygiene behaviors among middle-aged and elderly Iranian adults was observed. There was also a pro-rich inequality in oral hygiene behaviors among middle-aged and elderly adults in all cohort centers. These results suggest an urgent need for targeted policy interventions to increase the prevalence of preventive oral hygiene behaviors among the poor and less-educated middle-aged and elderly adults in Iran.
Relative contributions of non-essential Sec pathway components and cell envelope-associated proteases to high-level enzyme secretion by Bacillus subtilis
Authors: Neef Jolanda , Bongiorni Cristina , Schmidt Brian , Goosens Vivianne J. , van Dijl Jan Maarten 
Published: February 2020

Abstract
Background
Bacillus subtilis is an important industrial workhorse applied in the production of many different commercially relevant proteins, especially enzymes. Virtually all of these proteins are secreted via the general secretion (Sec) pathway. Studies from different laboratories have demonstrated essential or non-essential contributions of various Sec machinery components to protein secretion in B. subtilis. However, a systematic comparison of the impact of each individual Sec machinery component under conditions of high-level protein secretion was so far missing.

Results
In the present study, we have compared the contributions of non-essential Sec pathway components and cell envelope-associated proteases on the secretion efficiency of three proteins expressed at high level. This concerned the α-amylases AmyE from B. subtilis and AmyL from Bacillus licheniformis, and the serine protease BPN’ from Bacillus amyloliquefaciens. We compared the secretion capacity of mutant strains in shake flask cultures, and the respective secretion kinetics by pulse-chase labeling experiments. The results show that secDF, secG or rasP mutations severely affect AmyE, AmyL and BPN’ secretion, but the actual effect size depends on the investigated protein. Additionally, the chaperone DnaK is important for BPN’ secretion, while AmyE or AmyL secretion are not affected by a dnaK deletion. Further, we assessed the induction of secretion stress responses in mutant strains by examining AmyE- and AmyL-dependent induction of the quality control proteases HtrA and HtrB. Interestingly, the deletion of certain sip genes revealed a strong differential impact of particular signal peptidases on the magnitude of the secretion stress response.

Conclusions
The results of the present study highlight the importance of SecDF, SecG and RasP for protein secretion and reveal unexpected differences in the induction of the secretion stress response in different mutant strains.
Long non-coding RNA FER1L4 inhibits prostate cancer progression via sponging miR-92a-3p and upregulation of FBXW7
Authors: Huo Wei , Qi Fei , Wang Kaichen 
Published: February 2020

Abstract
Background
Dysregulation of long non-coding RNAs (lncRNAs) is involved in development of prostate cancer. However, the molecular mechanisms of many lncRNAs in prostate cancer have not been studied yet.

Methods
The lncRNA Fer-1-like protein 4 (FER1L4) expression was explored in prostate tumors and normal prostate tissues by RT-qPCR and bioinformatic analysis. Overexpression of FER1L4 was performed to evaluate its role in prostate cancer cell proliferation and survival. The molecular mechanism of FER1L4 was investigated by dual luciferase reporter assay, RNA pull down assay, western blotting and RT-qPCR.

Results
It was found that FER1L4 was lower in prostate cancer tissues than normal tissues. Higher expression of FER1L4 was associated with prostate cancer tissues of early stage (AJCC stage I/II). Overexpression of FER1L4 inhibited cell proliferation and promoted cell apoptosis in prostate cancer cells. Bioinformatic analysis, RT-qPCR, RNA pull down assay and dual luciferase assay showed that FER1L4 upregulated F-box/WD repeat-containing protein 7 (FBXW7) tumor suppressor via sponging miR-92a-3p. Silencing of FBXW7 reversed the cell phenotypes caused by FER1L4 overexpression in prostate cancer cells.

Conclusion
The data demonstrated that FER1L4, a downregulated lncRNA in prostate cancer, was pivotal for cell proliferation and survival of prostate cancer. The study provided new sights into understanding of the signaling network in prostate cancer and implied that FER1L4 might be a biomarker for patients with prostate cancer.
CircMUC16 promotes autophagy of epithelial ovarian cancer via interaction with ATG13 and miR-199a
Authors: Gan Xiaoling , Zhu Hongtao , Jiang Xingwei , Obiegbusi Samuel C. , Yong Min , Long Xingtao , Hu Jianguo 
Published: February 2020

Abstract
Background
Circular RNA (circRNA) has been proven to play a significant role in multiple types of cancer. However, the expression and role of circRNAs in epithelial ovarian cancer (EOC) remains elusive.

Methods
CircRNA and mRNA expression profiles of EOC were screened with sequencing analysis. Gene silencing and over-expression were used to study circRNA function. Cell proliferation and Matrigel invasion assays were used to detect cell proliferation and invasion, respectively. The expression of circRNAs, mRNAs and miRNAs was detected using qPCR. The location of circRNAs was detected using FISH. The expression of proteins was detected using western blot and immunohistochemistry.

Results
CircMUC16 had increased expression in EOC tissues as compared to healthy ovarian tissues. The expression of circMUC16 was linked to the progression in stage and grade of EOC. Hence, silencing circMUC16 suppressed autophagy flux of SKOV3 cells. In contrast, ectopic expression of circMUC16 promoted autophagy flux of A2780 cells. CircMUC16-mediated autophagy exacerbated EOC invasion and metastasis. Mechanistically, circMUC16 could directly bind to miR-199a-5p and relieve suppression of target Beclin1 and RUNX1. In turn, RUNX1 elevated the expression of circMUC16 via promotion of its transcription. CircMUC16 could directly bind to ATG13 and promote its expression.

Conclusion
This study demonstrated that circMUC16 regulated Beclin1 and RUNX1 by sponging miR-199a-5p. The data suggested that circMUC16 could be a potential target for EOC diagnosis and therapy.
Surface chemistry modified upconversion nanoparticles as fluorescent sensor array for discrimination of foodborne pathogenic bacteria
Authors: Yin Mingyuan , Jing Chuang , Li Haijie , Deng Qiliang , Wang Shuo 
Published: February 2020

Abstract
Background
The identification of foodborne pathogenic bacteria types plays a crucial role in food safety and public health. In consideration of long culturing times, tedious operations and the desired specific recognition elements in conventional methods, the alternative fluorescent sensor arrays can offer a high-effective approach in bacterial identification by using multiple cross-reactive receptors. Herein, we achieve this goal by constructing an upconversion fluorescent sensor array based on anti-stokes luminogens featuring a series of functional lanthanide-doped upconversion nanoparticles (UCNPs) with phenylboronic acid, phosphate groups, or imidazole ionic liquid. The prevalent spotlight effect of microorganism and the electrostatic interaction between UCNPs and bacteria endow such sensor array an excellent discrimination property.

Results
Seven common foodborne pathogenic bacteria including two Gram-positive bacteria (Staphylococcus aureus and Listeria monocytogenes) and five Gram-negative bacteria (Escherichia coli, Salmonella, Cronobacter sakazakii, Shigella flexneri and Vibrio parahaemolyticus) are precisely identified with 100% accuracy via linear discriminant analysis (LDA). Furthermore, blends of bacteria have been identified accurately. Bacteria in real samples (tap water, milk and beef) have been effectively discriminated with 92.1% accuracy.

Conclusions
Current fluorescence sensor array is a powerful tool for high-throughput bacteria identification, which overcomes the time-consuming bacteria culture and heavy dependence of specific recognition elements. The high efficiency of whole bacterial cell detection and the discrimination capability of life and death bacteria can brighten the application of fluorescence sensor array.
Economic evaluation of dapagliflozin versus metformin in Chinese patients whose diabetes is inadequately controlled with diet and exercise
Authors: Nian Hua , Wan Xu , Ma Jing , Jie Fu , Wu Bin 
Published: February 2020

Abstract
Background
To investigate the long-term economic outcome of dapagliflozin versus metformin in Chinese patients with type 2 diabetes mellitus (T2DM) whose diet and exercise have not provided sufficient glycemic control.

Methods
An economic analysis of dapagliflozin versus metformin was conducted by using the Chinese Outcomes Model for T2DM with a time horizon of lifetime, which was developed and validated based on the Chinese population. The efficacy data of lowering HbA1c of dapagliflozin and metformin was derived from a network meta-analysis. Other clinical, cost and utility inputs were obtained from published sources. Lifetime discounted quality-adjusted life-years, cost, and incremental cost-effectiveness ratio were measured. The uncertainty was facilitated by one-way and probabilistic sensitivity analyses.

Results
The comparison of metformin and dapagliflozin in Chinese patients with insufficient glycemic control by diet and exercise showed that dapagliflozin was more costly and produced fewer health benefits in our simulated cohort. The sensitivity analyses indicated that the results were robust.

Conclusions
Dapagliflozin is not likely to be cost-effective compared with metformin for Chinese patients with T2DM inadequately controlled with diet and exercise.
Role of STAT3 signaling pathway in breast cancer
Authors: Ma Jia-hui , Qin Li , Li Xia 
Published: February 2020

AbstractBreast cancer has grown to be the second leading cause of cancer-related deaths in women. Only a few treatment options are available for breast cancer due to the widespread occurrence of chemoresistance, which emphasizes the need to discover and develop new methods to treat this disease. Signal transducer and activator of transcription 3 (STAT3) is an early tumor diagnostic marker and is known to promote breast cancer malignancy. Recent clinical and preclinical data indicate the involvement of overexpressed and constitutively activated STAT3 in the progression, proliferation, metastasis and chemoresistance of breast cancer. Moreover, new pathways comprised of upstream regulators and downstream targets of STAT3 have been discovered. In addition, small molecule inhibitors targeting STAT3 activation have been found to be efficient for therapeutic treatment of breast cancer. This systematic review discusses the advances in the discovery of the STAT3 pathways and drugs targeting STAT3 in breast cancer.
NoncoRNA: a database of experimentally supported non-coding RNAs and drug targets in cancer
Authors: Li Lulu , Wu Pengfei , Wang Zhenyu , Meng Xiangqi , Zha Caijun , Li Ziwei , Qi Tengfei , Zhang Yangong , Han Bo , Li Shupeng , Jiang Chuanlu , Zhao Zheng , Cai Jinquan 
Published: February 2020

AbstractNoncoRNA (http://www.ncdtcdb.cn:8080/NoncoRNA/) is a manually curated database of experimentally supported non-coding RNAs (ncRNAs) and drug target associations that aim to potentially provide a high-quality data resource for exploring drug sensitivity/resistance-related ncRNAs in various human cancers. ncRNA are RNA molecular that do not encode proteins, but are involved in gene regulation and cellular functions in variety of human diseases, including neurodegenerative diseases and cancers. Here, we developed NoncoRNA which contained 8233 entries between 5568 ncRNAs and 154 drugs in 134 cancers. Each entry in the NoncoRNA contains detailed information on the ncRNAs, drugs, and cancers, the ncRNA expression pattern and experimental detection techniques, drug response and other targets, literature references, and other information. NoncoRNA offers a user-friendly, open access web interface to easily browse, search, and download data. NoncoRNA also provides a submission page for researchers to submit newly validated ncRNA-drug-cancer associations. NoncoRNA might serve as an immeasurable resource for understanding the roles of ncRNAs in cancer therapy.
Chronic whipworm infection exacerbates Schistosoma mansoni egg-induced hepatopathology in non-human primates
Authors: Le Loc , Khatoon Sabiha , Jiménez Paola , Peterson Christopher , Kernen Rebecca , Zhang Weidong , Molehin Adebayo J. , Lazarus Samra , Sudduth Justin , May Jordan , Karmakar Souvik , Rojo Juan U. , Ahmad Gul , Torben Workineh , Carey David , Wolf Roman F. , Papin James F. , Siddiqui Afzal A. 
Published: February 2020

Abstract
Background
Schistosomiasis continues to inflict significant morbidity and mortality in the tropical and subtropical regions of the world. The disease endemicity overlaps with the transmission of other parasitic diseases. Despite the ubiquity of polyparasitism in tropical regions, particularly in rural communities, little is known about the impact of multiple helminth infections on disease progression. In this pilot study, we describe the influence of chronic Trichuris trichiura infection on Schistosoma mansoni egg-induced hepatopathology in infected baboons.

Methods
Baboons with or without underlying whipworm infection were challenged with S. mansoni cercariae to establish schistosomiasis. Adult S. mansoni worms were recovered by perfusion and enumerated, hepatic granulomas were quantified via light microscopy, and transcriptional profiling of tissues were completed using RNA sequencing technologies.

Results
Co-infection with both S. mansoni and T. trichiura resulted in higher female schistosome worm burden and significantly larger liver granuloma sizes. Systems biology analyses of peripheral blood mononuclear cells (PBMC) revealed pathways associated with increased liver damage in co-infected baboons.

Conclusions
Underlying chronic whipworm infection intensified schistosome egg-induced liver pathology in infected baboons. RNA-Seq analysis provided insight into pathways associated with increased liver damage, corroborating histological findings.
Single-cell transcriptome analysis reveals TOX as a promoting factor for T cell exhaustion and a predictor for anti-PD-1 responses in human cancer
Authors: Kim Kyungsoo , Park Seyeon , Park Seong Yong , Kim Gamin , Park Su Myeong , Cho Jae-Won , Kim Da Hee , Park Young Min , Koh Yoon Woo , Kim Hye Ryun , Ha Sang-Jun , Lee Insuk 
Published: February 2020

Abstract
Background
T cells exhibit heterogeneous functional states in the tumor microenvironment. Immune checkpoint inhibitors (ICIs) can reinvigorate only the stem cell-like progenitor exhausted T cells, which suggests that inhibiting the exhaustion progress will improve the efficacy of immunotherapy. Thus, regulatory factors promoting T cell exhaustion could serve as potential targets for delaying the process and improving ICI efficacy.

Methods
We analyzed the single-cell transcriptome data derived from human melanoma and non-small cell lung cancer (NSCLC) samples and classified the tumor-infiltrating (TI) CD8+ T cell population based on PDCD1 (PD-1) levels, i.e., PDCD1-high and PDCD1-low cells. Additionally, we identified differentially expressed genes as candidate factors regulating intra-tumoral T cell exhaustion. The co-expression of candidate genes with immune checkpoint (IC) molecules in the TI CD8+ T cells was confirmed by single-cell trajectory and flow cytometry analyses. The loss-of-function effect of the candidate regulator was examined by a cell-based knockdown assay. The clinical effect of the candidate regulator was evaluated based on the overall survival and anti-PD-1 responses.

Results
We retrieved many known factors for regulating T cell exhaustion among the differentially expressed genes between PDCD1-high and PDCD1-low subsets of the TI CD8+ T cells in human melanoma and NSCLC. TOX was the only transcription factor (TF) predicted in both tumor types. TOX levels tend to increase as CD8+ T cells become more exhausted. Flow cytometry analysis revealed a correlation between TOX expression and severity of intra-tumoral T cell exhaustion. TOX knockdown in the human TI CD8+ T cells resulted in downregulation of PD-1, TIM-3, TIGIT, and CTLA-4, which suggests that TOX promotes intra-tumoral T cell exhaustion by upregulating IC proteins in cancer. Finally, the TOX level in the TI T cells was found to be highly predictive of overall survival and anti-PD-1 efficacy in melanoma and NSCLC.

Conclusions
We predicted the regulatory factors involved in T cell exhaustion using single-cell transcriptome profiles of human TI lymphocytes. TOX promoted intra-tumoral CD8+ T cell exhaustion via upregulation of IC molecules. This suggested that TOX inhibition can potentially impede T cell exhaustion and improve ICI efficacy. Additionally, TOX expression in the TI T cells can be used for patient stratification during anti-tumor treatments, including anti-PD-1 immunotherapy.
Comprehensive characterization of cell-free tumor DNA in plasma and urine of patients with renal tumors
Authors: Smith Christopher G. , Moser Tina , Mouliere Florent , Field-Rayner Johanna , Eldridge Matthew , Riediger Anja L. , Chandrananda Dineika , Heider Katrin , Wan Jonathan C. M. , Warren Anne Y. , Morris James , Hudecova Irena , Cooper Wendy N. , Mitchell Thomas J. , Gale Davina , Ruiz-Valdepenas Andrea , Klatte Tobias , Ursprung Stephan , Sala Evis , Riddick Antony C. P. , Aho Tevita F. , Armitage James N. , Perakis Samantha , Pichler Martin , Seles Maximilian , Wcislo Gabriel , Welsh Sarah J. , Matakidou Athena , Eisen Tim , Massie Charles E. , Rosenfeld Nitzan , Heitzer Ellen , Stewart Grant D. 
Published: February 2020

AbstractBackgroundCell-free tumor-derived DNA (ctDNA) allows non-invasive monitoring of cancers, but its utility in renal cell cancer (RCC) has not been established.MethodsHere, a combination of untargeted and targeted sequencing methods, applied to two independent cohorts of patients (n = 91) with various renal tumor subtypes, were used to determine ctDNA content in plasma and urine.ResultsOur data revealed lower plasma ctDNA levels in RCC relative to other cancers of similar size and stage, with untargeted detection in 27.5% of patients from both cohorts. A sensitive personalized approach, applied to plasma and urine from select patients (n = 22) improved detection to ~ 50%, including in patients with early-stage disease and even benign lesions. Detection in plasma, but not urine, was more frequent amongst patients with larger tumors and in those patients with venous tumor thrombus.With data from one extensively characterized patient, we observed that plasma and, for the first time, urine ctDNA may better represent tumor heterogeneity than a single tissue biopsy. Furthermore, in a subset of patients (n = 16), longitudinal sampling revealed that ctDNA can track disease course and may pre-empt radiological identification of minimal residual disease or disease progression on systemic therapy. Additional datasets will be required to validate these findings.ConclusionsThese data highlight RCC as a ctDNA-low malignancy. The biological reasons for this are yet to be determined. Nonetheless, our findings indicate potential clinical utility in the management of patients with renal tumors, provided improvement in isolation and detection approaches.
Perspectives in fluid biomarkers in neurodegeneration from the 2019 biomarkers in neurodegenerative diseases course—a joint PhD student course at University College London and University of Gothenburg
Authors: Obrocki Pawel , Khatun Ayesha , Ness Deborah , Senkevich Konstantin , Hanrieder Jörg , Capraro Federica , Mattsson Niklas , Andreasson Ulf , Portelius Erik , Ashton Nicholas J. , Blennow Kaj , Schöll Michael , Paterson Ross W. , Schott Jonathan M. , Zetterberg Henrik 
Published: February 2020

AbstractUntil relatively recently, a diagnosis of probable Alzheimer’s disease (AD) and other neurodegenerative disorders was principally based on clinical presentation, with post-mortem examination remaining a gold standard for disease confirmation. This is in sharp contrast to other areas of medicine, where fluid biomarkers, such as troponin levels in myocardial infarction, form an integral part of the diagnostic and treatment criteria. There is a pressing need for such quantifiable and easily accessible tools in neurodegenerative diseases.In this paper, based on lectures given at the 2019 Biomarkers in Neurodegenerative Diseases Course, we provide an overview of a range of cerebrospinal fluid (CSF) and blood biomarkers in neurodegenerative disorders, including the ‘core’ AD biomarkers amyloid β (Aβ) and tau, as well as other disease-specific and general markers of neuroaxonal injury. We then highlight the main challenges in the field, and how those could be overcome with the aid of new methodological advances, such as assay automation, mass spectrometry and ultrasensitive immunoassays.As we hopefully move towards an era of disease-modifying treatments, reliable biomarkers will be essential to increase diagnostic accuracy, allow for earlier diagnosis, better participant selection and disease activity and treatment effect monitoring.