bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative analysis of somatic variant calling on matched FF and FFPE WGS samples
Authors: Brienen Louise de Schaetzen van , Larmuseau Maarten , Eecken Kim Van der , De Ryck Frederic , Robbe Pauline , Schuh Anna , Fostier Jan , Ost Piet , Marchal Kathleen 
Published: March 2020

Abstract

Background. Research grade Fresh Frozen (FF) DNA material is not yet routinely collected in clinical practice. Many hospitals, however, collect and store Formalin Fixed Paraffin Embedded (FFPE) tumor samples. Consequently, the sample size of whole genome cancer cohort studies could be increased tremendously by including FFPE samples, although the presence of artefacts might obfuscate the variant calling. To assess whether FFPE material can be used for cohort studies, we performed an in-depth comparison of somatic SNVs called on matching FF and FFPE Whole Genome Sequence (WGS) samples extracted from the same tumor. Results. We first compared the calls between an FF and an FFPE sample from a metastatic prostate tumor, showing that on average 50% of the calls in the FF are recovered in the FFPE sample, with notable differences between variant callers. Combining the variants of the different callers using a simple heuristic, increases both the precision and the sensitivity of the variant calling. Validating the heuristic on nine additional matched FF-FFPE samples, resulted in an average F1-score of 0.58 and an outperformance of any of the individual callers. In addition, we could show that part of the discrepancy between the FF and the FFPE samples can be attributed to intra-tumor heterogeneity (ITH). Conclusion. This study illustrates that when using the correct variant calling strategy, the majority of clonal SNVs can be recovered in an FFPE sample with high precision and sensitivity. These results suggest that somatic variants derived from WGS of FFPE material can be used in cohort studies.
Prevalence of Generalized Joint Hypermobility in Children with Anxiety Disorders
Authors: javadi vadood , Modarres Shadi alsadat , Zahed Ghazal , Shiari Reza , Rahmani Khosro 
Published: March 2020

Abstract
Background: Concerning the high prevalence of anxiety disorders and joint hypermobility in children and the lack of related studies in this age group, we aimed to assess the association of hypermobility with anxiety disorders in children. Methods: In this case-control study, 93 children ages 8-15 years with anxiety disorders referring to the Child and Adolescent Psychiatry Clinic of Mofid Children’s Hospital, Tehran, Iran, during 2018, were enrolled. The control group consisted of 100 age and sex-matched children without anxiety disorders. Anxiety was evaluated using the Spence Children Anxiety Scale (SCAS). The diagnosis of generalized joint hypermobility was done based on Beighton and Shiari-Javadi criteria. Results: Based on Beighton’s diagnostic criteria 52.7% of the children in the case group and 16% of the children in the control group had generalized joint hypermobility. Moreover, based on Shiari-Javadi criteria, 49.5% and 13% of the children in the case and control groups had generalized joint hypermobility, respectively. Moreover, the internal correlation between the two criteria was 0.91 showing almost complete compatibility between the two (P<0.001). Age was a risk factor that could predict hypermobility in these children. Other variables such as sex, severity, and type of anxiety disorders, and ADHD, were not predictors of hypermobility syndrome. Conclusion: The prevalence of hypermobility was three times higher in children with anxiety disorders and only age was a predictor for the possibility to suffer from generalized joint hypermobility in these children.
Ultrasensitive wearable pressure sensors based on Silver nanowire-coated fabrics
Authors: Lian Yunlu , Yu He , Wang Mingyuan , Yang Xiaonan , Zhang Hefei 
Published: March 2020

Abstract
Flexible pressure sensors have attracted increasing attention due to their potential applications in wearable human health monitoring and care systems. Herein, we present a facile approach for fabricating all-textile-based piezoresistive pressure sensor with integrated Ag nanowire-coated fabrics. It fully takes advantage of the synergistic effect of the fiber/yarn/fabric multi-level contacts, leading to the ultrahigh sensitivity of 3.24×10 5 kPa −1 at 0–10 kPa and 2.16×10 4 kPa −1 at 10–100 kPa, respectively. Furthermore, the device achieved a fast response/relaxation time (32/24 ms), and a high stability (>1000 loading/unloading cycles). Thus, such all-textile pressure sensor with high performance is expected to be applicable in the fields of smart cloths, activity monitoring and healthcare device.
Insights into the care coordination needs of people living with rare diseases in Western Australia
Authors: Bauskis Alicia , Molster Caron 
Published: March 2020

Abstract
BackgroundPeople living with rare diseases face complex medical needs as well as a range of non-medical care needs. However, there is limited research on the experiences of care coordination for those living with a range of rare conditions. The paper addresses a research gap by capturing the views of both parents of children living with RD and adults living with rare diseases, and also explores some factors affecting people living in regional areas.Three focus groups were conducted with a total of sixteen participants who were adults living with a rare disease (and one carer) and parents of children living with rare diseases in Western Australia. Results were analysed using Braun and Clarke’s thematic analysis. ResultsThe study revealed that the participants in our study who were living with a rare disease (or their carers) (1) have complex care needs and a need to access multiple systems (2) have mixed experiences of care coordination (3) often go above and beyond to self-coordinate their care; and they (4) recognise opportunities for more systematic care coordination.ConclusionOur study has highlighted the complexity of care needs for many people living with a rare disease and the need for care coordination both within and across medical and non-medical domains. In exploring opportunities to provide more systematic care coordination, consideration should be given to European models of Centres of Expertise for Rare Diseases as well as complementary Resource Centres. Consideration of both models will help ensure patients receive holistic, well-integrated medical and non-medical care.
COX-2 gene rs689466 polymorphisms associated with increased risk of colorectal cancer among Caucasians
Authors: Zhao Hui , Chen Chen , Ali Mohammad Amzad 
Published: March 2020

Abstract
Background Several studies have reported the Cyclooxygenase 2 (COX-2) rs689466 polymorphism as a susceptibility locus of colorectal cancer (CRC), but their findings are inconsistent. Thus, this meta-analysis was performed to more accurately identify the effects of this polymorphism on CRC risk. Methods Potential case-control studies on EMBASE, Google of Scholar, Web of Science, Cochrane Library, and PubMed were searched. The strength of association was quantified by pooled odds ratio and 95% confidence interval. Totally 16 articles involving 8,998 cases and 11,917 controls were included. Results None of the five tested genetic models revealed any significant association between rs689466 polymorphism and CRC risk. Stratified analysis by ethnicity uncovered a significant association between this polymorphism and higher CRC risk in Caucasians, but not in Asians. In addition, we found high expression of COX-2 was associated with better overall survival for all CRC patients. Conclusion To sum up, the COX-2 rs689466 polymorphism may be related with susceptibility to CRC in Caucasians. This finding should be verified by larger-size studies with different ethnic groups.
Statistical and Bioinformatic Analysis of Hemimethylation Patterns in Lung Cancer
Authors: Sun Shuying , Zane Austin , Fulton Carolyn , Philipoom Jasmine 
Published: March 2020

Abstract
Background: DNA methylation is an epigenetic event involving the addition of a methyl-group to a cytosine-guanine base pair (i.e., CpG site). It is associated with different cancers. Our research focuses on studying lung cancer hemimethylation, which refers to methylation occurring on only one of the two DNA strands. Many studies often assume that methylation occurs on both DNA strands at a CpG site. However, recent publications show the existence of hemimethylation and its impact. It is important to identify cancer hemimethylation patterns. Methods: In this paper, we use the Wilcoxon signed rank test to identify hemimethylated CpG sites based on publicly available lung cancer methylation sequencing data. We then identify two types of hemimethylated CpG clusters, regular and polarity clusters, and genes with large numbers of hemimethylated sites. Highly hemimethylated genes are then studied for their biological interactions using available bioinformatics tools. Results: In this paper, we have conducted the first-ever in-depth investigation of hemimethylation for lung cancer. Our results show that hemimethylation does exist in lung cells either as singletons or clusters. Most clusters contain only 2 or 3 CpG sites. Polarity clusters are much shorter than regular clusters and appear less frequently. The majority of clusters found in tumor samples have no overlap with clusters found in normal samples, and vice versa. Several genes that are known to be associated with cancer are hemimethylated differently between the cancerous and normal samples. Furthermore, highly hemimethylated genes exhibit many different interactions with other genes that may be associated with cancer. Hemimethylation has diverse patterns and frequencies that are comparable between normal and tumorous cells. Therefore, hemimethylation may be related to both normal and tumor cell development. Conclusions: Our research has identified CpG clusters and genes that are hemimethylated in normal and lung tumor samples. Due to the potential impact of hemimethylation on gene expression and cell function, these clusters and genes may be important to advance our understanding of the development and progression of lung cancer.
Clinical characteristics and prognosis of elderly patients with colorectal cancer: comparison between surgical resection and supportive care
Authors: Kim Soohwan , Kim Dong Suk , Soh Jae Seung , Lim Sang-Woo , Lim Hyun , Kang Ho Suk , Kim Jong Hyeok 
Published: March 2020

Abstract
Background Elderly colorectal cancer (CRC) patients tend to avoid standard treatment, especially curative surgical resection, because of concerns about surgical complications or underlying diseases. This study is intended to compare clinical characteristics and prognosis between patients who had undergone surgical resection and received supportive care, and to evaluate the usefulness of surgical treatment in elderly patients. Methods A total of 114 patients aged ≥80 years who were diagnosed with CRC were analyzed retrospectively. Of these patients, 73 patients underwent surgical resection for malignancy and 41 patients received supportive care. Clinicopathological factors and overall survival (OS) rates were compared. Results The s urgical resection group had better Eastern Cooperative Oncology Group (ECOG) performance status, American Society of Anesthesiologists (ASA) physical status, and a lower stage than did the supportive-care group. The 3-year OS rate of the surgical group was significantly higher than that of the supportive-care group (60.7% vs. 9.1%, p < 0.001). In extremely elderly patients (age ≥85 years), the surgical group showed a better 3-year OS rate than did the supportive-care group (73.9% vs. 6.3%, p < 0.001), although ECOG performance status and ASA physical status were not different. The post-operative mortality rate was 4.1%. In the analysis of risk factors related to survival, surgical resection was a good prognostic factor. Conclusions Surgical treatment in elderly CRC patients showed a survival benefit, even in the extremely elderly patients. Surgical resection for CRC in elderly patients can be considered to improve survival.
Percutaneous kyphoplasty for osteoporotic vertebral compression fractures via unilateral versus bilateral approach
Authors: Yao Wenye , Zhang Bin , Lai Qi , Gao Song , Guo Runsheng 
Published: March 2020

Abstract
Objective To evaluate the efficacy of percutaneous kyphoplasty (PKP) for thoracolumbar osteoporotic vertebral compression fractures (OVCFs) via unilateral versus bilateral approach. Methods All patients who underwent PKP surgery for OVCFs in our hospital between June 2016 and December 2018 were included in this study. The pedicles were divided into two groups according to the manner of vertebral body puncture, which were as follows: unilateral pedicle puncture group (unilateral group, n=47) and bilateral pedicle puncture group (bilateral group, n=39).The operative time, amount of cement perfusion, correction angle of kyphosis, pain score before and after surgery, and leakage rate of bone cement were evaluated in all patients. The average follow-up was 19 months (range 13-34 months). Results The average age of patients who met the inclusion criteria, but not the exclusion criteria, was 76 years, and a total of 121 vertebral bodies were studied. There were 7 cases of postoperative bone cement leakage (unilateral group, 14.9%) and 6 cases of postoperative bone cement leakage (bilateral groups, 15.4%). There were differences in operative time and amount of cement perfusion between the two groups were statistically significant (P<0.05). There was no significant increase in age, body mass index, pain index during follow-up, treatment outcome, correction angle of kyphosis, and cement leakage rate between the two groups (P>0.05). Moreover, there was no significant difference in sex and bone cement leakage rate between the two groups by Pearson x 2 test (P>0.05). Conclusion Patients with OVCFs could obtain similar satisfactory clinical results via both unilateral and bilateral PKP approaches. However, the unilateral PKP approach is more advantageous as it has a shorter operative time, requires lesser cement volume, causes minimal trauma, is less costly, and results in lesser complications than the bilateral approach.
Deciphering the transcriptional regulatory networks that control size, color, and oil content in Brassica rapa seeds
Authors: Niu Yue , Wu Limin , Li Yanhua , Huang Hualei , Qian Mingchao , Sun Wei , Zhu Hong , Xu Yuanfang , Fan Yonghai , Mahmood Umer , Xu Benbo , Zhang Kai , Qu Cunmin , Li Jiana , Lu Kun 
Published: March 2020

Abstract
Background Brassica rapa is an important oilseed and vegetable crop species and is the A subgenome donor of two important oilseed Brassica crops, Brassica napus and Brassica juncea. Although seed size (SZ), seed color (SC), and oil content (OC) substantially affect seed yield and quality, the mechanisms regulating these traits in Brassica crops remain unclear. Results We collected seeds from a pair of B. rapa accessions with significantly different SZ, SC, and OC at seven seed developmental stages (every 7 days from 7 to 49 days after pollination), and identified 24,835 differentially expressed genes (DEGs) from seven pairwise comparisons between accessions at each developmental stage. K-means clustering identified a group of cell cycle-related genes closely connected to variation in SZ of B. rapa. A weighted correlation analysis using the WGCNA package in R revealed two important co-expression modules comprising genes whose expression was positively correlated with SZ increase and negatively correlated with seed yellowness, respectively. Upregulated expression of cell cycle-related genes in one module was important for the G2/M cell cycle transition, and the transcription factor Bra.A05TSO1 seemed to positively stimulate the expression of two CYCB1;2 genes to promote seed development. In the second module, a conserved complex regulated by the transcription factor TT8 appear to determine SC through downregulation of TT8 and its target genes TT3, TT18, and ANR. Further, upregulation of genes involved in triacylglycerol biosynthesis and storage in the seed oil body may increase OC. We further validated the accuracy of the transcriptome data by quantitative real-time PCR of 15 DEGs. Finally, we used our results to construct detailed models to clarify the regulatory mechanisms underlying variations in SZ, SC, and OC in B. rapa. Conclusions This study based on transcriptome comparison provides insight into the regulatory mechanisms underlying the variations of SZ, SC, and OC in plants. The findings hold great promise for improving seed yield, quality and OC through genetic engineering of critical genes in future molecular breeding.
Healthcare utilisation and out-of-pocket expenditure of type 2 diabetes patients with and without comorbidity: A study in primary care in Bhubaneswar, India.
Authors: Pati Sandipana , Swain Subhashisa , Akker Marjan van den , Schellevis F. (François) G. , Burgers Jako S. 
Published: March 2020

Abstract
Background

Globally, non-communicable diseases (NCD) necessitate increased healthcare expenditure. One NCD in particular, diabetes mellitus, is often associated with multiple, co-existing chronic conditions. In low- and middle-income countries where healthcare expenditure is mostly borne out of pocket, diabetes management may pose a significant economic burden.

Methods

A cross-sectional study was conducted in 17 urban primary healthcare facilities of Bhubaneswar to assess the healthcare utilisation and out-of-pocket expenditure among type 2 diabetes patients attending these facilities. Healthcare utilisation was determined by the number of visits to healthcare facilities in the last six months, and out-of-pocket expenditure was assessed by outpatient consultation fees, medicines, travels to health care facilities and diagnostic tests. Total out-of-pocket expenditure was defined as the sum of these costs.

Results

The median number of visits in 6 months for diabetes patients with any comorbidity was 4 and 5 for diabetes patients with more than 4 comorbidities. Among comorbidities, depression, stroke, auditory impairment and acid peptic disease were associated with higher healthcare utilisation. The total out-of-pocket expense was 2.3 times higher among diabetes patients with any comorbid condition compared to patients with diabetes only. The total median expenditure was higher for diabetes patients having stroke, heart diseases, kidney diseases and cancer compared to other comorbid conditions. The association of comorbidity in diabetes patients with health care utilization and out-of-pocket expenditure is statistically significant after adjustment for sociodemographic characteristics and diabetes duration.

Conclusion

Considerable expenditure is incurred by diabetes patients attending primary healthcare facilities for the management of diabetes and other chronic conditions. This is particularly painful for patients below the poverty line and with limited insurance cover. There is a need to increase the coverage of insurance schemes to address the chronic conditions management expenditure of outpatients.
pH-Dependent Nanodiamonds Enhance the Mechanical Properties of 3D-Printed Hyaluronic Acid Nanocomposite Hydrogels
Authors: Lim Dae Gon , Kang Eunah , Jeong Seong Hoon 
Published: March 2020

Abstract
Background: Nanocomposite hydrogels capable of undergoing manufacturing process have recently attracted attention in biomedical applications due to their desired mechanical properties and high functionality. Mechanically enhanced biomaterials composited with diverse nanophase inorganic particles are challenging because metastatic materials mimicking biological tissues require softness, biocompatibility, strength, and structurally compatible elasticity. Herein, nanodiamonds (NDs) have been chosen due to their hydrophilicity and pH-dependent surface functionality, along with their convenient chemical modalityResults: 3D printing nanocomposite hydrogels of hyaluronic acid (HA)/nanodiamond (ND) revealed that the addition of ND with the low weight ratio of 0.02 wt % resulted in higher compressive force and gel breaking point, compared with HA only nanocomposites. These HA nanocomposite hydrogels loaded with surface functionalized ND allowed for the enforced compressive stress to be tuned in a pH-dependent manner. HA nanocomposite hydrogels with ND-OH at pH 8 showed an increase of 1.40 fold (236.18 kPa) and 1.37 fold (616.72 kPa) the compressive stress at the composition of 0.02 wt % and 0.04 wt %, respectively, compared to those of ND-COOH (168.31, 449.59 kPa) at the same pH. Moreover, the compressive stress of HA/ND-OH (0.04 wt %) at pH 8 was mechanically enhanced 1.29 fold, compared to that of HA/ND-OH (0.04 wt %) at pH 7. These results indicate that the tunable buffering environment and interaction with the long chains of HA at the molecular level have a critical role in the dependency of the mechanical properties on pH. Conclusion: Due to the pH stability of the ND-OH nanophase, filament-based processing and layer-based deposition at microscale attained enforced mechanical properties of hydrogel. Fine surface tuning of the inorganic ND nanophase and controlled 3D printing leads to improved control over the pH-dependent mechanical properties of the nanocomposite hydrogels reported herein.
Circ_RPL23A acts as a miR-1233 sponge to suppress the progression of clear cell renal cell carcinoma by promoting ACAT2
Authors: Cheng Liang , Cao Huifeng , Xu Jianbo , Xu Mo , He Wenjie , Zhang Wenjing , Dong Longxin , Chen Dayin 
Published: March 2020

Abstract
Background

Clear cell renal cell carcinoma (CCRCC) is a prevalent urological carcinoma with high metastatic risk. Circular RNAs (circRNAs) have been identified as effective diagnostic and therapeutic biomarkers for CCRCC. This research aims to disclose the involvement of circRNA ribosomal protein L23a (circ_RPL23A) in CCRCC, and how it regulates carcinogenesis.

Methods

We performed quantitative real-time polymerase chain reaction (qRT-PCR) to examine circ_RPL23A, microRNA-1233 (miR-1233) and acetyl-coenzyme A acetyltransferase 2 (ACAT2). Cellular behavior detection included cell cycle, proliferation, apoptosis and metastasis, which were severally analyzed using propidium iodide (PI)-flow cytometry, 3-(4, 5-dimethylthiazol-2-y1)-2, 5-diphenyl tetrazolium bromide (MTT), Annexin V/PI-flow cytometry and transwell migration/invasion assays. ACAT2 and related proteins of cell cycle, epithelial-mesenchymal transition (EMT) were measured via western blot. Target relationship was analyzed via dual-luciferase reporter assay. A xenograft model was used to study circ_RPL23A action in mice.

Results

Both in CCRCC tissues and cells, circ_RPL23A had a down-regulated tendency. Explicitly, circ_RPL23A overexpression inhibited cell cycle, proliferation and metastasis but enhanced apoptosis of CCRCC cells, whereas these effects of circ_RPL23A were dependent on the suppression of its target miR-1233. Besides, miR-1233 could target ACAT2 and circ_RPL23A regulated ACAT2 by sponging miR-1233. Also importantly, miR-1233 was a pro-cancer gene in CCRCC via targeting ACAT2. CCRCC tumor growth was also decreased in vivo by circ_RPL23A through miR-1233/ACAT2 axis.

Conclusion

Altogether, the circ_RPL23A/miR-1233/ACAT2 axis in this report provides an in-depth cognition for CCRCC pathogenesis and circ_RPL23A may has pivotal value in diagnosing and treating CCRCC.