bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distance learning in clinical medical education amid COVID-19 pandemic in Jordan: current situation, challenges, and perspectives
Authors: Al-Balas Mahmoud , Al-Balas Hasan Ibrahim , Jaber Hatim M. , Obeidat Khaled , Al-Balas Hamzeh , Aborajooh Emad A. , Al-Taher Raed , Al-Balas Bayan 
Published: October 2020

Abstract
Background
As COVID-19 has been declared as a pandemic disease by the WHO on March 11th, 2020, the global incidence of COVID-19 disease increased dramatically. In response to the COVID-19 situation, Jordan announced the emergency state on the 19th of March, followed by the curfew on 21 March. All educational institutions have been closed as well as educational activities including clinical medical education have been suspended on the 15th of March. As a result, Distance E-learning emerged as a new method of teaching to maintain the continuity of medical education during the COVID-19 pandemic related closure of educational institutions. Distance E-Learning is defined as using computer technology to deliver training, including technology-supported learning either online, offline, or both. Before this period, distance learning was not considered in Jordanian universities as a modality for education. This study aims to explore the situation of distance E-learning among medical students during their clinical years and to identify possible challenges, limitations, satisfaction as well as perspectives for this approach to learning.

Methods
This cross-sectional study is based on a questionnaire that was designed and delivered to medical students in their clinical years. For this study, the estimated sample size (n = 588) is derived from the online Raosoft sample size calculator.

Results
A total of 652 students have completed the questionnaire, among them, 538 students (82.5%) have participated in distance learning in their medical schools amid COVID-19 pandemic. The overall satisfaction rate in medical distance learning was 26.8%, and it was significantly higher in students with previous experience in distance learning in their medical schools as well as when instructors were actively participating in learning sessions, using multimedia and devoting adequate time for their sessions. The delivery of educational material using synchronous live streaming sessions represented the major modality of teaching and Internet streaming quality and coverage was the main challenge that was reported by 69.1% of students.

Conclusion
With advances in technologies and social media, distance learning is a new and rapidly growing approach for undergraduate, postgraduate, and health care providers. It may represent an optimal solution to maintain learning processes in exceptional and emergency situations such as COVID-19 pandemic. Technical and infrastructural resources reported as a major challenge for implementing distance learning, so understanding technological, financial, institutional, educators, and student barriers are essential for the successful implementation of distance learning in medical education.
Researchers’ views on, and experiences with, the requirement to obtain informed consent in research involving human participants: a qualitative study
Authors: Xu Antonia , Baysari Melissa Therese , Stocker Sophie Lena , Leow Liang Joo , Day Richard Osborne , Carland Jane Ellen 
Published: October 2020

Abstract
Background
Informed consent is often cited as the “cornerstone” of research ethics. Its intent is that participants enter research voluntarily, with an understanding of what their participation entails. Despite agreement on the necessity to obtain informed consent in research, opinions vary on the threshold of disclosure necessary and the best method to obtain consent. We aimed to investigate Australian researchers’ views on, and their experiences with, obtaining informed consent.

Methods
Semi-structured interviews were conducted with 23 researchers from NSW institutions, working in various fields of research. Interviews were analysed and coded to identify themes.

Results
Researchers reported that consent involved information disclosure, understanding and a voluntary decision. They emphasised the variability of consent interactions, which were dependent on potential participants’ abilities and interests, study complexity and context. All researchers reported providing written information to potential participants, yet questioned the readability and utility of this information. The majority reported using signed consent forms to ‘operationalise’ consent and reported little awareness of, and lack of support in implementing more dynamic informed consent procedures, such as verbal informed consent, that was fit for the purposes of their studies. Views on Human Research Ethics Committees (HRECs) varied. Some reported inconsistent, arduous inputs on the information form and consent process. Others expressed reliance on HRECs for guidance, viewing them as institutional safeguards.

Conclusions
This study highlights the importance of transparent relationships, both between researchers and participants, and between researchers and HRECs. Where the relationship with study participants was reported as more robust, researchers felt that they were better able to ensure participants made better, more informed decisions. Where the relationship with HRECs was reported as more robust, researchers were more likely to view them as institutional safeguards, rather than as bureaucratic hindrances. Conscientious and mindful researchers are paramount to ensuring the procedure accommodates individual requirements. This study advocates that when designing ethical informed consent practices, researchers should be integrated as autonomous players with a positive input on the process, rather than, in the worst case, predatory recruiters to be curtailed by information forms and oversight.
Ada-WHIPS: explaining AdaBoost classification with applications in the health sciences
Authors: Hatwell Julian , Gaber Mohamed Medhat , Atif Azad R. Muhammad 
Published: October 2020

AbstractBackgroundComputer Aided Diagnostics (CAD) can support medical practitioners to make critical decisions about their patients’ disease conditions. Practitioners require access to the chain of reasoning behind CAD to build trust in the CAD advice and to supplement their own expertise. Yet, CAD systems might be based on black box machine learning models and high dimensional data sources such as electronic health records, magnetic resonance imaging scans, cardiotocograms, etc. These foundations make interpretation and explanation of the CAD advice very challenging. This challenge is recognised throughout the machine learning research community. eXplainable Artificial Intelligence (XAI) is emerging as one of the most important research areas of recent years because it addresses the interpretability and trust concerns of critical decision makers, including those in clinical and medical practice.MethodsIn this work, we focus on AdaBoost, a black box model that has been widely adopted in the CAD literature. We address the challenge – to explain AdaBoost classification – with a novel algorithm that extracts simple, logical rules from AdaBoost models. Our algorithm,Adaptive-Weighted High Importance Path Snippets(Ada-WHIPS), makes use of AdaBoost’s adaptive classifier weights. Using a novel formulation, Ada-WHIPS uniquely redistributes the weights among individual decision nodes of the internal decision trees of the AdaBoost model. Then, a simple heuristic search of the weighted nodes finds a single rule that dominated the model’s decision. We compare the explanations generated by our novel approach with the state of the art in an experimental study. We evaluate the derived explanations with simple statistical tests of well-known quality measures, precision and coverage, and a novel measurestabilitythat is better suited to the XAI setting.ResultsExperiments on 9 CAD-related data sets showed that Ada-WHIPS explanations consistently generalise better (mean coverage 15%-68%) than the state of the art while remaining competitive for specificity (mean precision 80%-99%). A very small trade-off in specificity is shown to guard against over-fitting which is a known problem in the state of the art methods.ConclusionsThe experimental results demonstrate the benefits of using our novel algorithm for explaining CAD AdaBoost classifiers widely found in the literature. Our tightly coupled, AdaBoost-specific approach outperforms model-agnostic explanation methods and should be considered by practitioners looking for an XAI solution for this class of models.
Endothelin receptor antagonist improves donor lung function in an ex vivo perfusion system
Authors: Walweel K. , Skeggs K. , Boon A. C. , See Hoe L. E. , Bouquet M. , Obonyo N. G. , Pedersen S. E. , Diab S. D. , Passmore M. R. , Hyslop K. , Wood E. S. , Reid J. , Colombo S. M. , Bartnikowski N. J. , Wells M. A. , Black D. , Pimenta L. P. , Stevenson A. K. , Bisht K. , Marshall L. , Prabhu D. A. , James L. , Platts D. G. , Macdonald P. S. , McGiffin D. C. , Suen J. Y. , Fraser J. F. 
Published: October 2020

Abstract
Background
A lung transplant is the last resort treatment for many patients with advanced lung disease. The majority of donated lungs come from donors following brain death (BD). The endothelin axis is upregulated in the blood and lung of the donor after BD resulting in systemic inflammation, lung damage and poor lung graft outcomes in the recipient. Tezosentan (endothelin receptor blocker) improves the pulmonary haemodynamic profile; however, it induces adverse effects on other organs at high doses. Application of ex vivo lung perfusion (EVLP) allows the development of organ-specific hormone resuscitation, to maximise and optimise the donor pool. Therefore, we investigate whether the combination of EVLP and tezosentan administration could improve the quality of donor lungs in a clinically relevant 6-h ovine model of brain stem death (BSD).

Methods
After 6 h of BSD, lungs obtained from 12 sheep were divided into two groups, control and tezosentan-treated group, and cannulated for EVLP. The lungs were monitored for 6 h and lung perfusate and tissue samples were processed and analysed. Blood gas variables were measured in perfusate samples as well as total proteins and pro-inflammatory biomarkers, IL-6 and IL-8. Lung tissues were collected at the end of EVLP experiments for histology analysis and wet-dry weight ratio (a measure of oedema).

Results
Our results showed a significant improvement in gas exchange [elevated partial pressure of oxygen (P = 0.02) and reduced partial pressure of carbon dioxide (P = 0.03)] in tezosentan-treated lungs compared to controls. However, the lungs hematoxylin–eosin staining histology results showed minimum lung injuries and there was no difference between both control and tezosentan-treated lungs. Similarly, IL-6 and IL-8 levels in lung perfusate showed no difference between control and tezosentan-treated lungs throughout the EVLP. Histological and tissue analysis showed a non-significant reduction in wet/dry weight ratio in tezosentan-treated lung tissues (P = 0.09) when compared to control.

Conclusions
These data indicate that administration of tezosentan could improve pulmonary gas exchange during EVLP.
Quantitative CT-based image registration metrics provide different ventilation and lung motion patterns in prone and supine positions in healthy subjects
Authors: Shin Kyung Min , Choi Jiwoong , Chae Kum Ju , Jin Gong Yong , Eskandari Ali , Hoffman Eric A. , Hall Chase , Castro Mario , Lee Chang Hyun 
Published: October 2020

Abstract
Background
Previous studies suggested that the prone position (PP) improves oxygenation and reduces mortality among patients with acute respiratory distress syndrome (ARDS). However, the mechanism of this clinical benefit of PP is not completely understood. The aim of the present study was to quantitatively compare regional characteristics of lung functions in the PP with those in the supine position (SP) using inspiratory and expiratory computed tomography (CT) scans.

Methods
Ninety subjects with normal pulmonary function and inspiration and expiration CT images were included in the study. Thirty-four subjects were scanned in PP, and 56 subjects were scanned in SP. Non-rigid image registration-based inspiratory-expiratory image matching assessment was used for regional lung function analysis. Tissue fractions (TF) were computed based on the CT density and compared on a lobar basis. Three registration-derived functional variables, relative regional air volume change (RRAVC), volumetric expansion ratio (J), and three-dimensional relative regional displacement (s*) were used to evaluate regional ventilation and deformation characteristics.

Results
J was greater in PP than in SP in the right middle lobe (P = 0 .025), and RRAVC was increased in the upper and right middle lobes (P < 0.001). The ratio of the TF on inspiratory and expiratory scans, J, and RRAVC at the upper lobes to those at the middle and lower lobes and that ratio at the upper and middle lobes to those at the lower lobes of were all near unity in PP, and significantly higher than those in SP (0.98–1.06 vs 0.61–0.94, P < 0.001).

Conclusion
We visually and quantitatively observed that PP not only induced more uniform contributions of regional lung ventilation along the ventral-dorsal axis but also minimized the lobar differences of lung functions in comparison with SP. This may help in the clinician’s search for an understanding of the benefits of the application of PP to the patients with ARDS or other gravitationally dependent pathologic lung diseases.

Trial registration
Retrospectively registered.
MsrR is a thiol-based oxidation-sensing regulator of the XRE family that modulates C. glutamicum oxidative stress resistance
Authors: Si Meiru , Chen Can , Zhong Jingyi , Li Xiaona , Liu Yang , Su Tao , Yang Ge 
Published: October 2020

Abstract
Background
Corynebacterium glutamicum thrives under oxidative stress caused by the inevitably extreme environment during fermentation as it harbors antioxidative stress genes. Antioxidant genes are controlled by pathway-specific sensors that act in response to growth conditions. Although many families of oxidation-sensing regulators in C. glutamicum have been well described, members of the xenobiotic-response element (XRE) family, involved in oxidative stress, remain elusive.

Results
In this study, we report a novel redox-sensitive member of the XER family, MsrR (multiple stress resistance regulator). MsrR is encoded as part of the msrR-3-mst (3-mercaptopyruvate sulfurtransferase) operon; msrR-3-mst is divergent from multidrug efflux protein MFS. MsrR was demonstrated to bind to the intergenic region between msrR-3-mst and mfs. This binding was prevented by an MsrR oxidation-mediated increase in MsrR dimerization. MsrR was shown to use Cys62 oxidation to sense oxidative stress, resulting in its dissociation from the promoter. Elevated expression of msrR-3-mst and mfs was observed under stress. Furthermore, a ΔmsrR mutant strain displayed significantly enhanced growth, while the growth of strains lacking either 3-mst or mfs was significantly inhibited under stress.

Conclusion
This report is the first to demonstrate the critical role of MsrR-3-MST-MFS in bacterial stress resistance.
Overexpression of microRNA-367 inhibits angiogenesis in ovarian cancer by downregulating the expression of LPA1
Authors: Zheng Qingling , Dai Xin , Fang Wei , Zheng Yan , Zhang Jin , Liu Yanxiang , Gu Donghua 
Published: October 2020

AbstractBackgroundCompelling evidences reported the role of microRNAs (miRNAs) in ovarian cancer. However, little was known regarding the molecular mechanism of miR-367 in ovarian cancer. This study intended to investigate the role and regulatory mechanism of miR-367 in ovarian cancer involving lysophosphatidic acid receptor-1 (LPA1).MethodsPotentially regulatory miRNAs in ovarian cancer were obtained from bioinformatics analysis. RT-qPCR was used to detect miR-367 expression in both ovarian cancer tissues and relevant adjacent normal tissues. Relationship between miR-367 and LPA1 was predicted by miRNA database and further verified using dual luciferase reporter gene assay and RIP. EdU and Transwell assay were used to measure the proliferation and invasion ability of cells. Moreover, tube formation and chick chorioallantois membrane (CAM) assay were performed to determine angiogenesis of human umbilical vein endothelial cells (HUVECs). Finally, the roles of LPA1 in tumor growth was also studied using nude mice xenograft assay.ResultsHigh expression of LPA1 and low expression of miR-367 were observed in ovarian cancer tissues and cells. Overexpressed miR-367 downregulated LPA1 expression to inhibit proliferation, invasion, and angiogenesis of cancer cells. Low expression of LPA1 suppressed tumor formation and repressed angiogenesis in ovarian in vivo.ConclusionAll in all, overexpression of miR-367 downregulated LPA1 expression to inhibit ovarian cancer progression, which provided a target for the cancer treatment.
Evaluation of the potential role of long non-coding RNA LINC00961 in luminal breast cancer: a case–control and systems biology study
Authors: Mehrpour Layeghi Sepideh , Arabpour Maedeh , Esmaeili Rezvan , Naghizadeh Mohammad Mehdi , Tavakkoly Bazzaz Javad , Shakoori Abbas 
Published: October 2020

AbstractBackgroundLuminal subtype is the most common subgroup of breast cancer (BC), accounting for more than 70% of this cancer. Long non-coding RNAs (lncRNAs) are a group of RNAs which play critical roles in diverse cellular processes. It is proved that dysregulation of them can contribute to the development of various cancers, including BC. LINC00961 was reported to be downregulated in several cancers, however, its expression level in BC remains largely unknown. The purpose of the present study was to investigate the possible role of LINC00961 in luminal A and B subtypes of BC.MethodsTo obtain novel lncRNAs associated with different cancers and differentially expressed lncRNAs (DElncRNAs) between BC tumor and normal tissues, Lnc2Cancer and GDC databases were used, respectively. After performing literature review, the expression level of the selected lncRNA (LINC00961) was evaluated in 79 luminal A and B BC specimens and adjacent non-cancerous tissues by Quantitative Reverse Transcription PCR (qRT-PCR). LINC00961 expression was also evaluated in two luminal A BC cell lines, compared to a normal breast cell line. The comparison of the differences between tumor and adjacent non-tumor samples was performed by paired sample t-test. Moreover, correlation analysis between LINC00961 expression and clinicopathological features was performed using the chi-square, fisher exact, and independent t-test. In order to investigate the possible roles of LINC00961 in luminal A and B BC, different bioinformatics analyses such as functional annotation of the LINC00961 co-expressed genes and protein–protein interaction (PPI) networks construction were also performed.ResultsLINC00961 was selected as a significant DElncRNA which had not been studied in BC. According to q-RT PCR assay, LINC00961 was downregulated in luminal BC tissues and cell lines. Its expression was correlated with smoking status and the age of menarche in luminal BC patients. Also, the results of the bioinformatics analysis were consistent with the data obtained from q-RT PCR assay. The final results indicated that LINC00961 might be involved in multiple cancer-associated pathways such as chemokine, Ras and PI3K–Akt signaling pathways, GPCR ligand binding, and signal transduction in luminal subtypes of BC. CDH5, GNG11, GNG8, SELL, S1PR1, CCL19, FYN, ACAN, CD3E, ACVRL1, CAV1, and PPARGC1A were identified as the top hub genes of the PPI networks across luminal subgroup.ConclusionOur findings suggested that LINC00961 was significantly downregulated in luminal A and B subtypes of BC. Moreover, bioinformatics analysis provided a basis for better identification of the potential role of LINC00961 in luminal subtype of BC.
Micelles self-assembled by 3-O-β-d-glucopyranosyl latycodigenin enhance cell membrane permeability, promote antibiotic pulmonary targeting and improve anti-infective efficacy
Authors: Zhang Man , Ye Lili , Huang Hao , Cheng Dandan , Liu Kaixin , Wu Wenbo , Shen Fukui , Jiang Zhihong , Hou Yuanyuan , Bai Gang 
Published: October 2020

Abstract
Background
Nanoparticle-based pulmonary drug delivery systems are commonly developed and applied for drug-targeted delivery. They exhibit significant advantages compared to traditional pulmonary drug delivery systems. However, developing the formulation of each drug is a time-consuming and laborious task.

Results
In this study, a universal lung-targeting nanoparticle was designed and constructed. The self-assembled micelles were composed of a platycodon secondary saponin, 3-O-β-d-glucopyranosyl platycodigenin 682 (GP-682), based on its specific amphiphilic structure. The GP-682 micelles exhibited a relatively stable zeta potential with a particle size between 60 and 90 nm, and the critical micelle concentration (CMC) value was approximately 42.3 μg/mL. Preincubation of GP-682 micelles markedly enhanced their cell membrane permeability and improved drug uptake in vitro. The results were visualized using fluorescent dye tracing, transmission electron microscopy (TEM) observations and the lactate dehydrogenase (LDH) release assay. The obtained benefits enhanced the distribution of levofloxacin (Lev) in mouse lung tissue and reduced antibiotics overdosing. The acute lung injury mouse model induced by the Pseudomonas aeruginosa PA 14 strain demonstrated that preinjection of GP-682 micelles before antibiotic administration resulted in a higher survival rate and anti-infective efficacy in vivo. It also caused reductions in pulmonary injury, bacterial invasion and cytokine expression compared with treatment with Lev alone.

Conclusions
GP-682 micelles are another nanoparticle-based pulmonary drug delivery system and provide a new lung-targeting therapy option.