bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of Proteomic Differences between Eutopic Endometrium and Ectopic Endometrium in Patients with Endometriosis
Authors: Chen Yongchang , Zhao Junbo , An Yuanyuan , Bi Fangfang 
Published: July 2020

Abstract
Objective

To analyze the difference in protein expression between eutopic endometrium and ectopic endometrium from a proteomic aspect, to investigate a preclinical research basis in the occurrence and development of endometriosis (EMT), and provide a theoretical basis for new diagnosis and treatment of EMT.
Methods

Eutopic and ectopic endometrium tissue were collected from 8 patients with an ovarian endometriotic cyst. The protein was extracted for the screening of differential proteins, database retrieval and bioinformatics. Functional classification of differential proteins was performed by gene ontology (GO), secondary annotation, and subcellular structure positioning. The functions of the proteins were analyzed by GO, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, and protein domain enrichments. Results were further validated by clustering analysis.
Results

Among a total of 6,233 identified proteins, 5,395 proteins had quantitative information, including 190 up-regulated proteins and 153 down-regulated proteins. Bioinformatics of differential proteins showed that the up-regulated proteins were primarily distributed in the nuclei and closely associated with conformation change of DNA and ribosome duplication, while the down-regulated proteins were predominantly distributed in the extracellular, cytoplasmic membrane and other positions and were related to the migration of endometrial tissues.
Conclusion

The differential expression of proteins in eutopic endometrium and ectopic endometrium plays an important role in the occurrence and development of EMT and its resultant infertility. The proteomic analysis provides a new basis for future research investigating the pathogenesis of EMT.
Gene Expression Profile of Active HE4 Stimulation in Epithelial Ovarian Cancer Cells: Microarray Study and Comprehensive Bioinformatics Analysis
Authors: Zhu Liancheng , Tan Mingzi , Xu Haoya , Lin Bei 
Published: July 2020

Abstract
Background.Human Epididymis Protein 4 (HE4) is a novel serum biomarker for diagnosis of epithelial ovarian cancer (EOC) with high specificity and sensitivity compared with CA125, and the increasing researches have been carried out on its roles in promoting carcinogenesis and chemoresistance in EOC in recent years, however, its underlying molecular mechanisms remain poorly understood. The aim of this study was to elucidate the molecular mechanisms of HE4 stimulation and to identify the key genes and pathways mediating carcinogenesis in EOC using microarray and bioinformatics analysis.Methods. We established a stable HE4-silence ES-2 ovarian cancer cell line labeled as “S”, and its active HE4 protein stimulated cells labeled as “S4”. Human whole genome microarray analysis was used to identify deferentially expressed genes (DEGs) from triplicate samples of S4 and S cells. “clusterProfiler” package in R, DAVID, Metascape, and Gene Set Enrichment Analysis (GSEA) were used to perform gene ontology (GO) and pathway enrichment analysis, and cBioPortal for WFDC2 coexpression analysis. GEO dataset (GSE51088) and quantitative real-time polymerase chain reaction (qRT-PCR) was applied for validation. The protein–protein interaction (PPI) network and modular analyses were performed using Metascape and Cytoscape. Results.In total, 713 DEGs were found (164 up regulated and 549 down regulated) and further analyzed by GO, pathway enrichment and PPI analyses. We found that MAPK pathway accounted for a significant portion of the enriched terms. WFDC2 coexpression analysis revealed ten WFDC2 coexpressed genes (TMEM220A, SEC23A, FRMD6, PMP22, APBB2, DNAJB4, ERLIN1, ZEB1, RAB6B, and PLEKHF1) that were also dramatically changed in S4 cells and validated by dataset GSE51088. Kaplan–Meier survival statistics revealed clinical significance for all of the 10 target genes. Finally, PPI was constructed, sixteen hub genes and eight molecular complex detections (MCODEs) were identified, the seeds of five most significant MCODEs were subjected to GO and KEGG enrichment analysis and their clinical significance was evaluated.Conclusions.By applying microarray and bioinformatics analyses, we identified DEGs and determined a comprehensive gene network of active HE4 stimulation in EOC cells. We offered several possible mechanisms and identified therapeutic and prognostic targets of HE4 in EOC.
Estimating the number of children in households with substance use disorders
Authors: Kraus Ludwig , Uhl Alfred , Atzendorf Josefine , Seitz Nicki-Nils 
Published: July 2020

Abstract
Background

Parental substance misuse is reported to endanger the health and psychological development of children and adolescents. The aim of the present study was to estimate the number of children currently affected by substance use disorders (SUDs) of any adult living in the same household.
Methods

Data came from the 2018 German Epidemiological Survey of Substance Abuse (ESA) among 18-64-year-olds (n = 9,267) and from population statistics. DSM-IV diagnostic criteria were used to assess SUD (abuse or dependence) related to tobacco, alcohol, cannabis, cocaine or amphetamine. Based on the number of household members, the number of children below the age 18 years and the information on SUD status of the respondent living in this household, the number of children in households with at least one member with SUD was estimated.
Results

In 2018, there were 13,597,428 children younger than 18 years living in Germany. Of these, 5.2–7.9% (686,482–696,279) were estimated to live in households where at least one adult had an alcohol-related disorder, 5.0–7.4% (674,065–690,792) in households where at least one adult was tobacco dependent and 0.38–1.05% (93,229–142,141) in households where at least one adult had a disorder related to the use of illicit drugs. The total number of children in close contact with SUD adults was estimated at 7.4–11.2% (1,000,725–1,522,667).
Conclusions

The large number of children affected by adults with SUD has implications for identification and prevention. Substantial variation in estimates, resulting from differences in methods, definition of exposure and exposure to whom, calls for international standardization in order to make estimates comparable.
High-throughput Sequencing Analysis of the Rhizosphere Arbuscular Mycorrhizal Fungi (AMF) Community Composition Associated with Ferula Sinkiangensis
Authors: Luo Yunfeng , He Yaling , Li Guifang , Lv Xinhua , Wang Zhongke , Zhuang Li 
Published: July 2020

Abstract
Background: Ferula sinkiangensis is an important and increasingly endangered medicinal plant. Arbuscular mycorrhiza fungi (AMF) are microbes that live in the soil and can enhance nutrient uptake, stress resistance, and pathogen defens in host plants. The composition of AMF communities associated with Ferula sinkiangensis and the relationship between these fungi and other pertinent abiotic factors, however, remains uncertain. Herein, we collected samples of rhizosphere and surrounding soil at a range of depths (0-20, 20-40, and 40-60 cm) and a range of slop positions (bottom, middle, top). These samples were then subjected to analyses of soil physicochemical properties and high-throughput sequencing (Illumina MiSeq), enabling us to examine AMF community composition and diversity, as well as the relationship between these parameters and other abiotic factors. Results: Through this analysis, we determined that Glomus and Diversispora were enriched in all samples. AMF diversity and richness varied significantly as a function of slope position, with this variation primarily being tied to differences in Glomus and Diversispora abundance. In contrast, no significant relationship between soil depth and overall AMF composition was noted, although some AMF were found to be sensitive to depth. Many factors were found to significantly affect AMF community composition, including organic matter (OM), TN (total nitrogen), TK (total potassium), AN (ammonium nitrogen), NN (nitrate nitrogen), AK (available potassium), TDS (total soluble salt), pH, SM (soil water content), and AE (slope position). We further found that Shannon diversity index values in these communities were positively correlated with TP (total phosphorus), NN, and pH values (p<0.05), while TP, TDS, and pH were positively correlated with Chao1 values (p<0.05). Conclusion: In summary, these findings reveal that Glomus and Diversispora are key AMF genera found within the rhizosphere soil of Ferula sinkiangensis. These fungi are closely associated with specific environmental and soil physicochemical properties. And The physical and chemical properties of soil were significantly different (p<0.05) because of slope position. Together, our results provide a novel understanding of the relationship between AMF species and Ferula sinkiangensis, providing a theoretical basis for further studies of their development.
Which combination is best for HbA1c, fasting plasma glucose, and 2-h post-challenge glucose for diagnosis of diabetes mellitus
Authors: Okada Junichi , Kashima Kohji , Yamada Eijiro , Nakajima Yasuyo , Okada Kazuya , Okada Shuichi , Yamada Masanobu 
Published: July 2020

Abstract
Background

We evaluated reliability among glycated hemoglobin (HbA1c), fasting plasma glucose (FPG), and a 75 g oral glucose tolerance test (75 g OGTT) where 2-h post-challenge glucose level (2hPG) in the diagnosis of diabetes and pre-diabetes to find out which parameter or combination of parameters is useful.
Methods

All the participants received 75 g OGTT and HbA1c measurements. For FPG, < 110 mg/dL was defined as “normal”, 110 ≤ FPG < 126 mg/dL was defined as “pre-diabetes”, and 126 mg/dL ≤ FPG was defined as “diabetes”. For 2hPG, < 140 mg/dL was defined as “normal”, 140 mg/dL ≤ 2hPG < 200 mg/dL was defined as “pre-diabetes”, and 200 mg/dL ≤ was defined as “diabetes”. For HbA1c, ≤ 6.2% was defined as “normal”, 6.2 < HbA1c < 6.5% was defined as “pre-diabetes”, and 6.5% ≤ was defined as “diabetes”. The prevalence of diabetes and pre-diabetes were estimated based on 7 different combinations as the following: “the combination of either HbA1c or FPG or 2hPG”, “the combination of either HbA1c or 2hPG”, “the combination of either HbA1c or FPG”, “HbA1c alone”, “the combination of either FPG or 2hPG”, “2hPG alone”, and “FPG alone”. Each diagnosed group were then divided into different age groups (40 s, 50 s, 60 s, 70 s, and 80 s) to consider the effect of age on results.
Results

For diagnosing “diabetes”, “the combination of either HbA1c or 2hPG” was almost as reliable as “the combination of either HbA1c or FPG or 2hPG” throughout all ages except for the 50 s. For diagnosing “pre-diabetes”, “the combination of either HbA1c or 2hPG” was almost as reliable as “the combination of either HbA1c or FPG or 2hPG” throughout all ages.
Discussion

Combining our results, measurement of HbA1c and 2hPG seems to be recommended for the diagnosis of diabetes and pre-diabetes. This means for an accurate diagnosis of diabetes and pre-diabetes, not only the measurement of HbA1c but also a 75 g OGTT is recommended. Unfortunately, screening by FPG alone is not recommended from this clinical study.
Conclusions

For accurate diagnosis of diabetes and pre-diabetes, the combination of HbA1c measurement and 75 g OGTT seemed to be a secure concept.
Marine Spatial Planning Connects Digital Technology, Excavation Equipment with Artificial Intelligence, Internet of Things for Underwater Heritage Investigation
Authors: Liao Victor Te Cheng 
Published: July 2020

Abstract
BackgroundUnderwater cultural heritage (UCH) as a time capsule had accumulated marine ecological biological resources for centuries since sinking until discovery, forming an ecosystem wildly involves multifaceted fields. ProblemThe convention on the United Nations Educational, Scientific, and Cultural Organization (UNESCO), coastal states claim UCH jurisdiction in situ protection. However, foreign countries demand UCH sovereignty to evolve an international political event. Consequently, underwater archaeology preservation and exploitation become a diplomatic intrigue although no human lives beneath the sea.Purpose The purpose of paper attempts to identify significant issues about UCH providing standard operating procedures (SOP), One-Stop service for a comprehensive investigation, and finds a way for international UCH disputes. MethodThe research collected relevant UCH issues from six participants' brainstorming, statistical analysis, and the Chi-Squared test. ResultsResults showed 13 issues about UCH with no significant difference but conversion into seven groups with a significant difference. Finding & ContributionThe top three groups, marine spatial planning (MSP), Digital Technology, Excavation Equipment were identified and contributed to better UCH investigation. The finding transnational, regional level regimes, community collaborative governance offers UCH better preservation.SuggestionFinally, suggestion MSP activating idle assets construct UCH research center through digital technology with excavation equipment and link artificial intelligence (AI), internet of things (IoT) to improve UCH investigation, and international collaboration.
Role of Medication Beliefs on Medication Adherence in Hypertensive Middle Eastern Refugees and Migrants in Australia
Authors: Shahin Wejdan , Kennedy Gerard A. , Cockshaw Wendell , Stupans Ieva 
Published: July 2020

Abstract
BackgroundAdherence to medication is essential in some patients for achieving treatment control in hypertension. Medication beliefs is one of the personal modifiable factors that has been recognised to influence medication adherence in different populations. However, there is no published research to confirm the relationship between medication beliefs and medication adherence in Middle Eastern refugees and migrants in Australia. These two different groups may develop different beliefs about their medications that lead to different medication taking behaviours. Understanding the possible differences in beliefs may have a significant impact on enhancing medication adherence in these groups.Design320 Middle Eastern refugees and migrants with hypertension were approached via various social groups in Australia and asked to complete Arabic versions of the Beliefs about Medicine Questionnaire (BMQ) and the Medication Adherence Questionnaire. BMQ scores (necessity and concerns scales) were classified as "accepting", "indifferent", "ambivalent" or "skeptical". Multiple mediation modelling was applied to examine the role of necessity and concerns scales as mediators between migration status and medication adherence.ResultsThere were significant associations between medication adherence and medication beliefs scores (necessity and concerns scales) (p = 0.0001). Necessity, and concern were mediators in the relationship between migration status and medication adherence. Significant differences were found between refugees and migrants for medication adherence and medication beliefs. Refugees were likely to have less necessity, and more concern beliefs than migrants. They were also less likely to adhere to medications. Almost 30% of refugees could be classified as skeptical and 40% as ambivalent. In contrast, 50% of migrants had accepting beliefs, and around 35% held ambivalent beliefs. Refugees and migrants with “accepting” beliefs reported the highest adherence to medication and those holding “skeptical” beliefs reported the lowest adherence.ConclusionMedication beliefs are potentially modifiable and are reasonable targets for clinical interventions designed to improve medication adherence. Understanding these beliefs and the likely differences between refugees and migrants is crucial to provide specific and targeted advice to each group independently in order to improve medication adherence and overall health.
Effect of COVID-19 on Liver Abnormalities: A Systematic review and Meta‐analysis
Authors: Bzeizi Khalid , Abdulla Maheeba , Mohammed Nafeesa , Alqamish Jehad , Jamshidi Negar , Broering Dieter 
Published: July 2020

Abstract
Emerging evidence suggest association of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection with development of many liver abnormalities. The overarching aim of this study was therefore to assess the available evidence on the clinical effects of SARS-CoV-2 on liver function laboratory tests and coagulation profile in affected individuals. We considered all study designs including epidemiological and observational that reported liver function test abnormalities in patients diagnosed with SARS-CoV-2 infection. Medline, Embase databases and Google Scholar as well as relevant reviews were searched to identify appropriate studies from inception to April 30th, 2020. We calculated pooled mean with 95% confidence intervals (95%CI) through a random-effect model meta-analysis. A total of 29 studies with 9991 participants were considered for the review from which 20 studies with sufficient quantitative data were included for the meta-analysis. The pooled mean for liver enzymes and coagulation parameters did not significantly change in patients affected by COVID-19 and remained within normal range. Our systematic review and meta-analysis findings of the available evidence suggest that COVID-19 did not have a significant impact on the liver enzymes or coagulation profile of patients with SARS-CoV-2 infection. Future studies need to adequately report all the liver function parameters with event rates.
Increasing use of linezolid in a tertiary NICU during a 10-year period: reasons and concerns for the future
Authors: Matrat Lucie , Plaisant Frank , Barreto Christine , Claris Olivier , Butin Marine 
Published: July 2020

Abstract
Background
Linezolid has been increasingly used in tertiary NICUs. The objectives of this study were to explore the indications of these linezolid prescriptions, to analyze a possible misuse and to provide solutions to avoid such misuse.
Methods
A monocentric retrospective cohort study included all neonates hospitalized in one tertiary NICU between January 1st, 2010 and December 31st, 2019 and who received at least one administration of linezolid. These data were confronted to epidemiological and antibiotic use data from the same NICU. Two independent pediatricians secondarily classified linezolid uses as adequate or not.
Results
During the study period, 66 infections in 57 patients led to linezolid use. Most patients were pre-term and 21 patients (37%) died. Infections were mainly related to methicillin-resistant coagulase negative staphylococci and were frequently either pneumoniae (35%) or isolated bacteremia (48%), including 25 persistent bacteremia (64% of the 39 bacteremia). Need for a better tissue distribution or first-line treatment failure were the main reasons to initiate linezolid. Linezolid was administered for a median duration of 7 [3;10] days. No side effects were reported. Twenty-two (33%) of the 66 linezolid prescriptions were retrospectively classified as inadequate.
Conclusions
A rapid increase in linezolid prescriptions has been observed in our tertiary NICU, from 2014 to 2019, with 33% inadequate uses. This worrisome trend should lead to search for therapeutic alternatives and to work on antibiotic stewardship to prevent the emergence of new antimicrobial bacterial resistance.
An Innovative Data Analysis Strategy For Accurate NGS Detection of Tumor mtDNA Mutations
Authors: Guo Shanshan , Zhou Kaixiang , Yuan Qing , Su Liping , Ji Xiaoying , Gu Xiwen , Guo Xu , Xing Jinliang 
Published: July 2020

Abstract
Background: Next generation sequencing (NGS) technology has been commonly applied to detect mtDNA mutations, which are reported to be strongly associated with cancers. However, several key challenges still exist in the bioinformatic analysis of mtDNA sequencing data, which greatly affect the detection accuracy of mtDNA mutations. Methods: Here, we systematically evaluated several key analysis procedures, including trimming, mapping and filtering, in mtDNA mutation detection of FFPE tissues, fresh tissues and plasma samples from cancer patients. Furthermore, the innovative bioinformatics pipeline integrating a newly-developed filtering algorithm was established.Results: We found that trimming procedure was essential for improving mtDNA mapping performance in plasma but not tissue samples. Mapping with rCRS-hg19 reference was strongly suggested for mtDNA mutation detection in plasma samples due to the extreme abundance of NUMTs. In addition, our results showed that the setting of 3 mismatches was most appropriate for mtDNA mutation calling. More importantly, we revealed the presence of a negative logarithmic relationship between mtDNA site sequencing depth and minimum detectable mutation frequency and thus build up an innovative and efficient filtering strategy to increase the accuracy and sensitivity of mutation detection. Finally, we verified that higher sequencing depth was required for PCR-based than capture-based enrichment strategy.Conclusions: Collectively, we established an innovative data analysis strategy, which is of great significance for improving the accuracy of mtDNA mutation detection for different types of tumor samples.
Immunohistochemical Markers and the Clinical Course of Adenosarcoma: a Series of Seven Cases
Authors: Omi Makiko , Tonooka Akiko , Chiba Tomohiro , Nomura Hidetaka , Kanao Hiroyuki , Takazawa Yutaka 
Published: July 2020

Abstract
Background: Uterine adenosarcoma, a rare subtype of uterine tumor, is a biphasic tumor consisting of epithelial and mesenchymal elements. There is no research comparing histopathological features of primary and recurrent tumors, including immunohistochemistry; furthermore, the relationship between pathology and the clinical course is unclear. We reviewed the pathology and immunohistochemical features of 7 adenosarcoma cases and investigated the relevance of the histomorphological features to the clinical course. We also compared immunohistochemical features of primary and recurrent tumors.Methods: Seven patients with adenosarcoma who underwent surgery in our hospital were evaluated. We performed immunohistochemical staining for the estrogen receptor (ER), progesterone receptor (PR), p53, and two SWI/SNF chromatin-remodeling proteins (SMARCA4, BCOR), which were recently developed for the diagnosis of undifferentiated sarcomas in addition to conventional staining methods. Results: All patients were International Federation of Gynecology and Obstetrics stage 1B to 1C. All tumors were polypoid, and every patient presented with abnormal uterine bleeding. Six patients were over 50 years old and were menopausal; 1 patient was under 50 years old and was non-menopausal (average age 59.1 years). Histologically, the sarcomatous components were homologous in 6 patients and heterogenous in 1 patient. Four patients were recurrent patients; 3 were non-recurrent. All 4 recurrent patients showed high-grade morphology with sarcomatous overgrowth and were negative for ER and PR. Three recurrences could be evaluated by imaging, showing recurrence only in a distant area; biopsy specimens from these tissues revealed the identical mesenchymal component found in the primary tumor without a benign epithelial component. Immunohistochemical staining results were also the same as for the original tumor, except for the p53 expression in 1 patient. At the primary site, p53 was overexpressed in 2 recurrent patients and had a wild-type level in 1 recurrent patient; however, all 3 recurrent tissues showed overexpression of p53. None of the 7 cases showed SMARCA4 loss, and BCOR expression was positive in 1 case.Conclusions: Initial pathological analysis of the adenosarcoma with appropriate immunohistochemical staining is vital for prognostic assessment. Expression of p53 might increase at recurrence. SMARCA4 and BCOR could be an index of malignancy, regardless of sarcomatous overgrowth.