bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adaptation of Oxford Nanopore technology for hepatitis C whole genome sequencing and identification of within-host viral variants
Authors: Riaz Nasir , Leung Preston , Barton Kirston , Smith Martin A. , Carswell Shaun , Bull Rowena , Lloyd Andrew R. , Rodrigo Chaturaka 
Published: March 2021

Abstract
Background
Hepatitis C (HCV) and many other RNA viruses exist as rapidly mutating quasi-species populations in a single infected host. High throughput characterization of full genome, within-host variants is still not possible despite advances in next generation sequencing. This limitation constrains viral genomic studies that depend on accurate identification of hemi-genome or whole genome, within-host variants, especially those occurring at low frequencies. With the advent of third generation long read sequencing technologies, including Oxford Nanopore Technology (ONT) and PacBio platforms, this problem is potentially surmountable. ONT is particularly attractive in this regard due to the portable nature of the MinION sequencer, which makes real-time sequencing in remote and resource-limited locations possible. However, this technology (termed here ‘nanopore sequencing’) has a comparatively high technical error rate. The present study aimed to assess the utility, accuracy and cost-effectiveness of nanopore sequencing for HCV genomes. We also introduce a new bioinformatics tool (Nano-Q) to differentiate within-host variants from nanopore sequencing.

Results
The Nanopore platform, when the coverage exceeded 300 reads, generated comparable consensus sequences to Illumina sequencing. Using HCV Envelope plasmids (~ 1800 nt) mixed in known proportions, the capacity of nanopore sequencing to reliably identify variants with an abundance as low as 0.1% was demonstrated, provided the autologous reference sequence was available to identify the matching reads. Successful pooling and nanopore sequencing of 52 samples from patients with HCV infection demonstrated its cost effectiveness (AUD$ 43 per sample with nanopore sequencing versus $100 with paired-end short read technology). The Nano-Q tool successfully separated between-host sequences, including those from the same subtype, by bulk sorting and phylogenetic clustering without an autologous reference sequence (using only a subtype-specific generic reference). The pipeline also identified within-host viral variants and their abundance when the parameters were appropriately adjusted.

Conclusion
Cost effective HCV whole genome sequencing and within-host variant identification without haplotype reconstruction are potential advantages of nanopore sequencing.
Current knowledge of Chagas-related heart disease among pediatric cardiologists in the United States
Authors: Malhotra Sanchi , Masood Imran , Giglio Noberto , Pruetz Jay D. , Pannaraj Pia S. 
Published: March 2021

Abstract
Background
Chagas disease is a pathogenic parasitic infection with approximately 8 million cases worldwide and greater than 300,000 cases in the United States (U.S.). Chagas disease can lead to chronic cardiomyopathy and cardiac complications, with variable cardiac presentations in pediatrics making it difficult to recognize. The purpose of our study is to better understand current knowledge and experience with Chagas related heart disease among pediatric cardiologists in the U.S.

Methods
We prospectively disseminated a 19-question survey to pediatric cardiologists via 3 pediatric cardiology listservs. The survey included questions about demographics, Chagas disease presentation and experience.

Results
Of 139 responses, 119 cardiologists treat pediatric patients in the U.S. and were included. Most providers (87%) had not seen a case of Chagas disease in their practice; however, 72% also had never tested for it. The majority of knowledge-based questions about Chagas disease cardiac presentations were answered incorrectly, and 85% of providers expressed discomfort with recognizing cardiac presentations in children. Most respondents selected that they would not include Chagas disease on their differential diagnosis for presentations such as conduction anomalies, myocarditis and/or apical aneurysms, but would be more likely to include it if found in a Latin American immigrant. Of respondents, 87% agreed that they would be likely to attend a Chagas disease-related lecture.

Conclusions
Pediatric cardiologists in the U.S. have seen very few cases of Chagas disease, albeit most have not sent testing or included it in their differential diagnosis. Most individuals agreed that education on Chagas disease would be worth-while.
Is body mass index (BMI) or body adiposity index (BAI) a better indicator to estimate body fat and selected cardiometabolic risk factors in adults with intellectual disabilities?
Authors: Zwierzchowska Anna , Celebańska Diana , Rosołek Barbara , Gawlik Krystyna , Żebrowska Aleksandra 
Published: March 2021

Abstract
Background
The BMI index cannot always be used in people with intellectual disabilities due to neuromuscular coordination disorders and psychological barriers that may hinder conventional body weight measurement. The study aimed to assess the usefulness of BMI and BAI in estimating obesity and body fat in people with intellectual disabilities.

Methods
The first stage of the research involved 161 people with profound intellectual disabilities. Somatic parameters (BM, BH, WC, HC) were measured and BMI, BAI, WHR were calculated. Fifty seven persons with above-normal BMI and BAI were included in the second stage of the study and biochemical parameters were determined (TC, LDL-cholesterol, HDL-cholesterol, TG, GL).

Results
According to both BMI and BAI classifications, most people were overweight or obese. A high correlation of %BF with BMI and BAI indices was observed (r = 0.78). The sensitivity of both indices was 95.65%. In groups with above-normal BMI and BAI, an upward trend was found for mean values of TC, LDL, TG, and GL, with a simultaneous downward trend for HDL. Statistically significant intergroup differences were recorded for TG and GL (p < 0.05) for both indices (BMI and BAI).

Conclusions
Our research demonstrated that BAI is complementary to BMI and can be recommended for the estimation of body fat and cardiometabolic risks in people with intellectual disabilities. Due to the ease of measurement, BAI has high utility value.
Collision of Epstein–Barr virus-positive and -negative gastric cancer, diagnosed by molecular analysis: a case report
Authors: Miyabe Ken , Saito Motonobu , Koyama Kei , Umakoshi Michinobu , Ito Yukinobu , Yoshida Makoto , Kudo-Asabe Yukitsugu , Saito Katsuharu , Nanjo Hiroshi , Maeda Daichi , Matsusaka Keisuke , Goto Akiteru , Kono Koji 
Published: March 2021

Abstract
Background
Epstein–Barr virus (EBV)-positive gastric carcinoma (GC) is defined by the proliferation of GC cells with EBV infection. The co-existence of EBV-positive and -negative components in a single GC is rare. We report a case of GC with the co-existence of EBV-positive and EBV-negative components, in which we performed—for the first time—various molecular analyses to elucidate their histogenesis.

Case presentation
An 81-year-old man was diagnosed with GC based on the results of endoscopy and a pathological examination of the biopsy specimen. Systemic chemotherapy was performed, since lymph node and lung metastases were diagnosed based on computed tomography. Total gastrectomy and lymph node dissection were performed after chemotherapy, after confirming that the size of the metastatic lymph nodes had decreased and that the lung metastasis had disappeared. Grossly, a type 3 tumor was located in the middle posterior part of the stomach body. At the cut section, the tumor consisted of a white and solid part on the anal side of the tumor and a flat and elevated part on the oral side. Histologically, the former part consisted of GC with lymphoid stroma and the latter part was composed of poorly differentiated adenocarcinoma without prominent lymphocytic infiltration. The two histopathological components were clearly separated from each other. On EBV-encoded small RNA (EBER)-in situ hybridization (ISH), the part with the lymphoid stroma component was positive, while the other part was negative. Immunohistochemistry revealed that both components showed the overexpression of p53. Sequencing of TP53 using DNA extracted from the two components was conducted, and revealed different patterns. Targeted next generation sequencing revealed MYC amplification in the EBV-positive component of the tumor and HER2 amplification in the EBV-negative part. Immunohistochemistry revealed that the EBV-positive part was C-MYC( +)/HER2(−) and the EBV-negative part was C-MYC(−)/HER2( +). Correspondingly, chromogenic ISH and dual-color ISH showed amplification of C-MYC and no amplification of HER2 in the EBV-positive part, and no amplification of C-MYC and amplification of HER2 in the EBV-negative part.

Conclusion
We presented a case of collision of two different GCs composed of EBER-ISH ( +)/C-MYC ( +) and EBER-ISH (−)/HER2 ( +) cells.
Incidence and multidimensional predictors of occasional and recurrent falls among Malaysian community‐dwelling older persons
Authors: Ooi Theng Choon , Singh Devinder Kaur Ajit , Shahar Suzana , Rajab Nor Fadilah , Vanoh Divya , Sharif Razinah , Tan Maw Pin 
Published: March 2021

Abstract
Background
Falls incidence rate and comprehensive data on factors that predict occasional and repeated falls from large population-based studies are scarce. In this study, we aimed to determine the incidence of falls and identify predictors of occasional and recurrent falls. This was done in the social, medical, physical, nutritional, biochemical, cognitive dimensions among community-dwelling older Malaysians.

Methods
Data from 1,763 Malaysian community-dwelling older persons aged ≥ 60 years were obtained from the LRGS-TUA longitudinal study. Participants were categorized into three groups according to the presence of a single fall (occasional fallers), ≥two falls (recurrent fallers), or absence of falls (non-fallers) at an 18-month follow-up.

Results
Three hundred and nine (17.53 %) participants reported fall occurrences at an 18-month follow-up, of whom 85 (27.51 %) had two or more falls. The incidence rate for occasional and recurrent falls was 8.47 and 3.21 per 100 person-years, respectively. Following multifactorial adjustments, being female (OR: 1.57; 95 % CI: 1.04–2.36), being single (OR: 5.31; 95 % CI: 3.36–37.48), having history of fall (OR: 1.86; 95 % CI: 1.19–2.92) higher depression scale score (OR: 1.10; 95 % CI: 1.02–1.20), lower hemoglobin levels (OR: 0.90; 95 % CI: 0.81-1.00) and lower chair stand test score (OR: 0.93; 95 % CI: 0.87-1.00) remained independent predictors of occasional falls. While, having history of falls (OR: 2.74; 95 % CI: 1.45–5.19), being a stroke survivor (OR: 8.57; 95 % CI: 2.12–34.65), higher percentage of body fat (OR: 1.04; 95 % CI: 1.01–1.08) and lower chair stand test score (OR: 0.87; 95 % CI: 0.77–0.97) appeared as recurrent falls predictors.

Conclusions
Having history of falls and lower muscle strength were predictors for both occasional and recurrent falls among Malaysian community-dwelling older persons. Modifying these predictors may be beneficial in falls prevention and management strategies among older persons.
Exercise-induced muscle damage: multi-parametric MRI quantitative assessment
Authors: Lyu Xiaohong , Gao Yue , Liu Qiang , Zhao Heng , Zhou Huadong , Pan Shinong 
Published: March 2021

Abstract
Background
To explore the value of magnetic resonance quantitative analysis using diffusion tensor imaging, T2 mapping, and intravoxel incoherent motion in the evaluation of eccentric exercise-induced muscle damage and to compare the effects of various eccentric exercise modes at different time points in rats.

Methods
A total of 174 Sprague-Dawley male rats were randomly divided into five groups: control, once-only exercise, continuous exercise, intermittent exercise, and once-fatigue exercise groups. Each experimental group was divided into seven time-subgroups: 0.5 h, 24 h, 48 h, 72 h, 96 h, 120 h and 168 h after exercise. The quadriceps femoris muscles were then scanned using magnetic resonance imaging. The apparent diffusion coefficient and fractional anisotropy values of diffusion tensor imaging, T2 values of T2 mapping, D and D* values of intravoxel incoherent motion and optical density values of desmin were measured. Associations among different eccentric exercise programmes, magnetic resonance imaging findings, and histopathological results were evaluated. Dunnett’s test, two-way repeated measures analysis of variance, and Pearson correlation analysis were used for statistical analysis.

Results
Diffusion tensor imaging showed that the number of muscle fibre bundles decreased to varying degrees with different time points and eccentric exercises. Apparent diffusion coefficient values of the exercise groups showed a trend that first increased and then decreased, the opposite of fractional anisotropy. The specimens in all eccentric exercise programmes showed high signal T2 values after exercise, the highest among which was in the once-fatigue exercise group. D and D* in the experimental groups were significantly higher than those in the control group at 0.5–48 h after exercise. The apparent diffusion coefficient, fractional anisotropy, T2, D and D* values correlated with the optical density values of desmin.

Conclusions
Diffusion tensor imaging, T2 mapping, and intravoxel incoherent motion technology accurately reflect the degree of skeletal muscle damage and recovery associated with eccentric exercise. The degree of muscle damage was the lowest in the continuous exercise group and the highest in the once-fatigue exercise group, which may provide more information and guidance for the formulation of physical and athletic training programmes.
Long term follow-up of inguinal endometriosis
Authors: Mu BoRan , Zhang ZhiQiang , Liu Chongdong , Zhang Kunning , Li ShuHong , Leng JinHua , Li MengHui 
Published: March 2021

Abstract
Background
Inguinal endometriosis (IEM) is a rare extra pelvic endometriosis. Here, we study the clinical characteristics, management strategies, and long-term gynecological outcomes of IEM patients at Beijing Chaoyang Hospital.

Case presentation
Three patients presented with a total of four lesions (one on the left side, one on the right side, and one bilaterally). The diameters of the four lesions were 2 cm, 2 cm, 3.5 cm and 1.5 cm, respectively. Two patients were admitted with inguinal hernias. Two patients were admitted with endometrioses—one with ovarian endometriosis and one with pelvic endometriosis. The hernia sac was repaired concomitantly via excision of the round ligament in two patients. One patient underwent a concomitant laparoscopy for gynecologic evaluations, including an ablation to the peritoneal endometriosis, and resection of the left uterosacral ligament endometriosis and pelvic adhesiolysis. All lesions were located on the extraperitoneal portion of the round ligament and were diagnosed histologically. No recurrence was observed in the inguinal region. All patients diagnosed with adenomyosis were treated with medication alone without any complaints.

Conclusions
Inguinal endometriosis can occur simultaneously with pelvic endometriosis. In most cases, a concomitant hernia sac appears together with groin endometriosis. Clinical management should be individualized and performed in tandem with general practitioners and obstetrics & gynecology experts. Pelvic disease, in particular, should be followed-up by a gynecologist.
Collaborative care model for diabetes in primary care settings in Qatar: a qualitative exploration among healthcare professionals and patients who experienced the service
Authors: Abdulrhim Sara , Sankaralingam Sowndramalingam , Ibrahim Mohamed Izham Mohamed , Diab Mohammed Issam , Hussain Mohamed Abdelazim Mohamed , Al Raey Hend , Ismail Mohammed Thahir , Awaisu Ahmed 
Published: March 2021

Abstract
Background
Diabetes mellitus is highly prevalent and associated with huge economic burden globally. The conventional care and management of diabetes mellitus is highly fragmented and complex, warranting the need for a comprehensive Collaborative Care Model (CCM). Little is known about the perception of patients with diabetes and their healthcare providers about CCM, its barriers and facilitators. This study aimed to explore the value of CCM in diabetes care at a primary healthcare (PHC) setting from the perspective of patients with diabetes and healthcare professionals (HCPs), in an effort to expand our current knowledge on collaborative care in diabetes at primary care level for the purpose of quality improvement and service expansion.

Methods
Using an exploratory case study approach, semi-structured interviews were conducted among patients and HCPs who encountered CCM in Qatar during 2019 and 2020. The semi-structured interviews were transcribed verbatim and the data were analysed and interpreted using a deductive-inductive thematic analysis approach.

Results
Twelve patients and 12 HCPs at a diabetes clinic participated in one-to-one interviews. The interviews resulted in five different themes: the process and components of collaborative care model (four subthemes), current organizational support and resources (three subthemes), impact of collaborative care model on diabetes outcomes (three subthemes), enablers of collaborative care model (three subthemes), and barriers to collaborative care model (three subthemes). The participants indicated easy access to and communication with competent and pleasant HCPs. The patients appreciated the extra time spent with HCPs, frequent follow-up visits, and health education, which empowered them to self-manage diabetes. HCPs believed that successful CCM provision relied on their interest and commitment to care for patients with diabetes. Generally, participants identified barriers and facilitators that are related to patients, HCPs, and healthcare system.

Conclusions
The providers and users of CCM had an overall positive perception and appreciation of this model in PHC settings. Barriers to CCM such as undesirable attributes of HCPs and patients, unsupportive hospital system, and high workload must be addressed before implementing the model in other PHC settings.
A novel approach to thermographic images analysis of equine thoracolumbar region: the effect of effort and rider’s body weight on structural image complexity
Authors: Masko Malgorzata , Borowska Marta , Domino Malgorzata , Jasinski Tomasz , Zdrojkowski Lukasz , Gajewski Zdzislaw 
Published: March 2021

Abstract
Background
The horses’ backs are particularly exposed to overload and injuries due to direct contact with the saddle and the influence of e.g. the rider’s body weight. The maximal load for a horse’s back during riding has been suggested not to exceed 20% of the horses’ body weight. The common prevalence of back problems in riding horses prompted the popularization of thermography of the thoracolumbar region. However, the analysis methods of thermographic images used so far do not distinguish loaded horses with body weight varying between 10 and 20%.

Results
The superficial body temperature (SBT) of the thoracolumbar region of the horse’s back was imaged using a non-contact thermographic camera before and after riding under riders with LBW (low body weight, 10%) and HBW (high body weight, 15%). Images were analyzed using six methods: five recent SBT analyses and the novel approach based on Gray Level Co-Occurrence Matrix (GLCM) and Gray Level Run Length Matrix (GLRLM). Temperatures of the horse’s thoracolumbar region were higher (p < 0.0001) after then before the training, and did not differ depending on the rider’s body weight (p > 0.05), regardless of used SBT analysis method. Effort-dependent differences (p < 0.05) were noted for six features of GLCM and GLRLM analysis. The values of selected GLCM and GLRLM features also differed (p < 0.05) between the LBW and HBW groups.

Conclusion
The GLCM and GLRLM analyses allowed the differentiation of horses subjected to a load of 10 and 15% of their body weights while horseback riding in contrast to the previously used SBT analysis methods. Both types of analyzing methods allow to differentiation thermal images obtained before and after riding. The textural analysis, including selected features of GLCM or GLRLM, seems to be promising tools in considering the quantitative assessment of thermographic images of horses’ thoracolumbar region.
Inhibition of cancer cell-derived exosomal microRNA-183 suppresses cell growth and metastasis in prostate cancer by upregulating TPM1
Authors: Dai Yanping , Gao Xiaoqin 
Published: March 2021

Abstract
Background
Emerging evidence continues to highlight the significant role of microRNAs (miRNAs) in the regulation of cancer growth and metastasis. Herein, the current study aimed to elucidate the role of exosomal miR-183 in prostate cancer development.

Methods
Initially, public microarray-based gene expression profiling of prostate cancer was employed to identify differentially expressed miRNAs. The putative target gene TPM1 of miR-183 was subsequently predicted, followed by the application of a luciferase reporter assay and examination of the expression patterns in prostate cancer patients and cell lines. The effects of miR-183 and TPM1 on processes such as cell proliferation, invasion and migration were evaluated using in vitro gain- and loss-of-function experiments. The effect of PC3 cells-derived exosomal miR-183 was validated in LNCaP cells. In vivo experiments were also performed to examine the effect of miR-183 on prostate tumor growth.

Results
High expression of miR-183 accompanied with low expression of TPM1 was detected in prostate cancer. Our data indicated that miR-183 could target and downregulate TPM1, with the overexpression of miR-183 and exosomal miR-183 found to promote cell proliferation, migration, and invasion in prostate cancer. Furthermore, the tumor-promoting effect of exosome-mediated delivery of miR-183 was subsequently confirmed in a tumor xenograft model.

Conclusions
Taken together, the key findings of our study demonstrate that prostate cancer cell-derived exosomal miR-183 enhance prostate cancer cell proliferation, invasion and migration via the downregulation of TPM1, highlighting a promising therapeutic target against prostate cancer.