bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of a Novel Prognostic Score Combining Clinicopathologic Variables, Gene Expression and Mutationprofiles for Lung Adenocarcinoma
Authors: Li Guofeng , Wang Guangsuo , Guo Yanhua , Li Shixuan , Zhang Youlong , Li Jialu , Peng Bin 
Published: June 2020

Abstract
Background: Integrating phenotypic and genotypicinformation to improve prognostic prediction is under active investigation for lung adenocarcinoma (LUAD). In this study, we developed a new prognostic model for event-free survival (EFS)and recurrence-free survival (RFS) based on the combination of clinicopathologic variables, gene expression and mutation data. Methods: We enrolled a total of 408 patients from the Cancer Genome Atlas Lung Adenocarcinoma (TCGA-LUAD) project for the study. We pre-selected gene expression or mutation features, and constructed 14 different input feature sets for predictivemodel development.We assessed model performance with multiple evaluation metrics including the distribution of C-index on testing dataset, risk score significance and time-dependent AUC under competing risks scenario.We stratified patients into higher and lower-risk subgroups by the final risk score, and further investigated underlying immune phenotyping variations associated with the differential risk.Results: The model integrating all three types of data achieved the bestprediction performance. The resultant risk score provided a higher-resolution risk stratification than other models within pathologically-definedsubgroups. The score could account for extra EFS-related variationsthat were not captured by clinicopathologic scores. Being validated forRFS prediction under a competing risks modeling framework, the score achieved a significantly higher time-dependent AUC as compared to that of the conventional clinicopathologic variables-based model (0.772 vs. 0.646, p-value< 0.001). The higher-risk patients were characterized with transcriptionalaberrations of multiple immune-related genes, and a significant depletion of mast cells and natural killer cells. Conclusions: We developed a novel prognostic risk score with improved prediction accuracy,using clinicopathologic variables, gene expression and mutation profiles as input, for LUAD. Such score was an significant predictor of both EFS and RFS.Trail registration: This study was based on public open data from TCGA and hence the study objects were retrospectively registered.
Study Protocol for Draup: De-implementation Ofroutine Chest Radiographs After Adoption of Ultrasound Guided Insertion and Confirmation of Central Venous Catheter Protocol, A Hybrid Implementation/effectiveness Study
Authors: Ablordeppey Enyo A. , Powell Byron J. , McKay Virginia R. , Keating Shannon M. , James Aimee S. , Carpenter Christopher R. , Kollef Marin H. , Griffey Richard T. 
Published: June 2020

Abstract
BACKGROUNDAvoiding low value medical practices is an important focus in current healthcare utilization. Despite advantages of point of care ultrasound (POCUS) over chest x-ray (CXR), including improved workflow and timeliness of results, POCUS-guided central venous catheter (CVC) position confirmation and exclusion of pneumothorax (PCEP) has had slow rate of adoption. This demonstrates a gap that is ripe for the development and application of de-implementation strategies that support substitution of POCUS for CXR after CVC insertion.METHODSDe-implementation of routine chest radiographs after adoption of ultrasound guided insertion and confirmation of central venous catheter protocol (DRAUP) will be created to de-implement an unnecessary imaging modality in the critical care environment. Guided by the Consolidated Framework for Implementation Research constructs, we will explore barriers and facilitators of POCUS for CVC PCEP in a single center, large tertiary, academic hospital via focus groups. The focus groups will inform the development and testing of strategies that address identified determinants of implementation and de-implementation.Operational use of the de-implementation strategies will be conceptualized using Morgan’s framework for understanding and reducing medical overuse. We will locally implement these strategies and assess them using Proctor’s outcomes (adoption, de-adoption, fidelity and penetration) in an observational study to demonstrate proof of concept, gaining valuable insights on our selected implementation and de-implementation strategies. Secondary outcomes will include POCUS-guided CVC PCEP efficacy measured by time and effectiveness measured by sensitivity and specificity of POCUS detection.DISCUSSIONWith limited data available to inform interventions that use concurrent implementation and de-implementation strategies to substitute CXR for POCUS using DRAUP, we propose that this primary implementation and secondary effectiveness pilot study will provide novel data that would expand the knowledge of replacing low value or unnecessary care in critically ill patients. Trial Registration: ClinicalTrials.gov Identifier, NCT04324762, Registered on 27 March 2020
Experimental evaluation of the shear behavior of large landslide slip zone using Multistage - Multiphase shearing method.
Authors: Getahun Ephrem , Qi Shengwen , Guo Songfeng , Shi Zhenming 
Published: June 2020

Abstract
Abstract
The study of shear behaviors comprises of the analysis of shear deformation characteristics and strength parameter determinations. Understanding the constitutive behaviour of shear zone soil samples is essential for evaluation of the critical shear behaviors of reactivated landslides, through considerate experimental tests. The experiment was carried out based on the multistage - multiphase shear technique via ring shear apparatus. The main advantage of this new method is to examine the same soil specimen for progressive loading and the continuous phases of shearing. The result shows that two major shear characteristics under the multiphase shear mode; the first is a post-peak shear weakening behavior of the soils on the last phase shear process, it indicated a decrease in friction resistance on fast rate effects, which enables to narrate with fastly moved coseismic landslide behaviors. The other one is a practical increase in friction coefficient values (hardening behavior) on the entire shear process as the rate increases. This shear resistance scenario can also be related with the stabilization mechanism of landslide slip surface soils against sliding.
Quantum dots as targeted doxorubicin drug delivery nanosystems in human lung cancer cells
Authors: Ruzycka Monika , Kowalik Patrycja , Kowalczyk Agata , Bujak Piotr , Nowicka Anna M. , Wojewódzka Maria , Kruszewski Marcin , Grudzinski Ireneusz P. 
Published: June 2020

Abstract
Background

Lung cancer is one of the most frequently diagnosed cancer all over the world and a leading cancer-related mortality. The therapy of lung cancer includes surgery, chemotherapy and radiatherapy and mailny depends on the type and stage of lung cancer characterized based on WHO guidelines. Althought the conventional chemotherapy is the main treatment option for small cell lung cancer (SCLC) and a common treatment for non-SCLC it is characterized with lack of specificity resulting to severe toxicities of normal cells and harmful side effects. Therefore, targeted drug delivery (TDD) systems have been used to reduce the systemic toxicity of some conventional chemotherapies in lung cancer. Quantum dots (QDs) are fascinating nanoscale crystals that can serve as nanocarriers in TDD due to their unique physicochemical properties. Therefore, in this paper, the as-desiged QDs, Ag-In-Zn-S-based nanoconjugates for selective doxorubicin (DOX) targeting to lung cancer cells were developed. The QD nanocrystals were modified with 11-mercaptoundecanoic acid (MUA), L-cysteine (Cys) and lipoic acid (LA) used as drug carriers for targeted delivery of DOX to A549 cells through conjugated folic acid (FA) a self-navigation molecule that docks to the folate receptors on cancer cells. The comprechensive physicochemical, cytotoxicity and genotoxicity studies were performed to characterise the novel QD-based nanocaries and their anticancer cargos.

Results

The results from FTIR, DLS and fluorescence quenching evidenced the successful attachment of FA to the QDs nanocrystals and DOX to the QDs-FA nanocarriers. UV-vis analysis determined the amount of FA and DOX covalently anchored to the QDs nanocrystal surface. Biological screeining revealed that QDs-FA-DOX nanoconjugates showed higher cytotoxicity in comparison to other forms of the synthesized QD samples, suggesting the cytotoxic effect of liberated DOX from the QD constructs. QD-MUA-FA-DOX occurred to be the most cytotoxic against A549 cells among nanoconjugates. In vitro scratch assay also revealed significant inhibition of A549 migration only due to treatment with QD-MUA-FA-DOX. Studies evidenced that all the nanoconjugates at IC 50 induced significantly more DNA breaks than that observed in non-treated cells. All in all, significant and the greatest cytotoxicity, genotoxicity together with inhibition of migratory potential of A549 cells was observed for QD-MUA-FA-DOX.

Conclusion

The studies show the therapeutic efficacy of DOX-loaded QD-based cargos suggesting their promising role as novel drug delivery systems navigating to folate receptors in lung cancer cells.
Machine Learning Model Demonstrates Stunting at Birth and Systemic Inflammatory Biomarkers as Predictors of Subsequent Infant Growth – A Four-year Prospective Study.
Authors: Harrison Elizabeth , Syed Sana , Ehsan Lubaina , Iqbal Najeeha T. , Sadiq Kamran , Umrani Fayyaz , Ahmed Sheraz , Rahman Najeeb , Jakhro Sadaf , Jennie Z. , Hughes Molly , Ali S. Asad 
Published: June 2020

Abstract
Background: Stunting affects up to one-third of children in low-to-middle income countries (LMICs) and has been correlated with cognitive decline and vaccine immunogenicity. Infants with stunting often have growth refractory to nutritional interventions. Early identification of at-risk infants is critical for early intervention and prevention of subsequent morbidity. The aim of this study was to investigate patterns of growth in infants up through 48 months of age, as well as potential predictors of growth.Methods: Height-for-age z-scores (HAZ) of children from Matiari (rural site in Pakistan) at birth, 18 months, and 48 months were obtained. Results of serum-based biomarkers collected at 6 and 9 months were recorded. A descriptive analysis of the population was followed by biomarker prediction assessment via machine learning methods; random forest classification bins of z-scores and random forest regression for continuous z-scores. Results: Of 107 children who were followed up to 48 months, about half were stunted (HAZ < -2) at birth which increased to 54% by 48 months of age. HAZ at 18 months had a positive linear correlation with HAZ at 48 months, while HAZ at birth was less strongly correlated with HAZ at either 18 or 48 months. Stunting status for the majority of children at 48 months was found to be the same as at 18 months. Most children with large gains started off stunted or severely stunted, while all of those with notably large losses were not stunted at birth. Random forest models identified HAZ at birth as the most important feature in predicting HAZ at 18 months. Of the biomarkers, AGP (Alpha- 1-acid Glycoprotein), CRP (C-Reactive Protein), and IL1 (interleukin-1) were assigned the highest importance rankings across both the classification and regressor models.Conclusion: We demonstrated that HAZ at birth is a strong predictor of subsequent growth in infants up through 48 months of age. Biomarkers of systemic inflammation, AGP, CRP, IL1, were also strong predictors of growth outcomes. These findings provide support for continued focus on interventions at birth and early infancy in children at risk for stunting who live in resource-constrained regions of the world.
Negative Regulation of Ptch1 by miR-342-5p and FoxO3 Induced Autophagy Involved in Renal Fibrosis
Authors: Tang Simin , Wang Yi , Xie Guiling , Li Wenjun , Chen Yanna , Liang Jinshu , Liu Pei , Song Fuhu , Zhou Jun 
Published: June 2020

Abstract
Background: The pathogenesis of renal fibrosis (RF) is not well understood. Here, we performed an integrative database analysis of miRNAs and mRNAs to discover the major regulatory pathway in RF.Methods: Putative miRNAs and mRNAs involved in RF in unilateral ureteral obstruction (UUO) model mice were extracted and analyzed using the Gene Expression Omnibus (GEO) database. The bioinformatics analysis suggested that Ptch1 expression is negatively regulated by miR-342-5p and FoxO3. Then real-time PCR, Western blot, Fluorescence in situ hybridization were done to confirm the hypothesis.Results: Sixty-three differentially expressed miRNAs (DE-miRNAs) in GSE118340, 141 DE-miRNAs in GSE42716, and 183 DE-mRNAs in GSE69101 were identified. Various bioinformatic analyses revealed miR-342-5p as a strong candidate regulator in RF. We also predicted that miR-342-5p targets Ptch1 and that FoxO3 is the transcription factor of Ptch1. We also observed that TGF-β1 upregulated the expression of miR-342-5p and inhibited the expression of FoxO3 and Ptch1 in TCMK-1 cells. Furthermore, downregulation of miR-342-5p or FoxO3 reversed the inhibitory effect of TGF-β1 on the expression of Ptch1 in TCMK-1 cells. Additionally, downregulation of Ptch1 increased TGF-β1-induced autophagy, as evidenced by an increase in the number of GFP-LC3 puncta and the increased protein expression of SOSTM1/p62 and LC3II/LC3I.Conclusion: Our findings showed that downregulation of Ptch1 induced autophagy in TGF-β1-stimulated TCMK-1 cells, and Ptch1 expression is negatively regulated by miR-342-5p and FoxO3. These findings will further our understanding of the molecular mechanisms of RF and provide useful novel therapeutic targets for RF.
Biopsy Quality is Essential for Preoperative Prognostication in Oral Tongue Cancer
Authors: Bello Ibrahim O , Wennerstrand Pia M. , Suleymanova Ilida , Siponen Maria , Qannam Ahmed , Nieminen Pentti , Leivo Ilmo , Almangush Alhadi , Salo Tuula 
Published: June 2020

Abstract
Background: A role for incisional biopsy in preoperative prognostication is increasingly being advocated in oral tongue squamous cell carcinomas (OTSCC). Biopsies at two locations were compared and prognostic factors in biopsies and their corresponding resections were evaluated. Methods: A total of 138 OTSCC biopsy slides from Finland and Saudi-Arabia were compared for size (horizontal and vertical) and invasive front. The Finnish cases were assessed for tumor stroma ratio (TSR) and tumor-infiltrating lymphocytes (TILs) using light microscopy and digital image analysis assessment and compared. Furthermore, TSR, TILs, and previously analyzed budding and depth of invasion (BD) score in biopsies were compared with their evaluation in the corresponding resections. Results: Finnish biopsies were deeper than Saudi-Arabian biopsies (59% versus 42%) while Saudi-Arabian biopsies were wider (98% versus 76%). Invasion fronts were more readily assessable in Finnish biopsies (72% versus 40%). There was 86.8% agreement between TSR and 75% agreement between TIL evaluation using light microscopy and digital assessment. Significant agreement was obtained on comparing the TSR (P=0.04) and BD (P<0.001) values in biopsies and resections. Conclusions: Biopsies of ≥5 mm depth from representative OTSCC areas are essential for prognostic information. Clinical pathologists are advised to assess BD score and TSR for prognostic features in such biopsies.
Does Sequential Balloon Expulsion Test improve the screening of Defecation Disorders?
Authors: Caetano Ana Célia , Costa Dalila , Gonçalves Raquel , Correia-Pinto Jorge , Rolanda Carla 
Published: June 2020

Abstract
Purpose
A Defecation Disorder (DD) is a difficulty in evacuation documented by physiological exams. However, this physiological evaluation can be cumbersome, inaccessible and costly. Three “low-cost” tools to evaluate DD – a clinical DD score, the balloon expulsion test (BET) and a digital rectal examination (DRE) score were evaluated as separate or combined tests for DD screening.
Methods
This prospective study occurred between January 2015 and March 2019 in the Gastroenterology Department of a tertiary hospital. Besides the gold standard physiological tests, constipated patients answered the clinical DD score and were evaluated by DRE and BET (standard and variable volume (vv)).
Results
From 98 constipated patients, 35 (38.9%) were diagnosed with DD according to Rome IV criteria, mainly female (n = 30, 86%) with a median age of 60 years old. The clinical DD score revealed an AUC of 0.417 (SE = 0.07, p = 0.191). The DRE score displayed an AUC of 0.56 (SE = 0.063, p = 0.301). The standard BET displayed a sensitivity of 86%, specificity of 58%, positive predictive value (PPV) of 57% and negative predictive value (NPV) of 86%. The sequential vvBET followed by standard BET improved the BET performance regarding the evaluation of DD, with a sensitivity of 86%, specificity of 67%, PPV of 63% and NPV of 87%. The sequential BET had an OR 8.942, p > 0.001, CI 3.18–25.14, revealing to be the most significant predictor for DD screening.
Conclusion
The sequential BET is a low cost, well-performing DD screening tool, appropriate to the Primary Care Setting.
CCBlock based on deep learning for diagnosis COVID-19 in chest x-ray image
Authors: Al-Bawi Ali , Al-Kaabi Karrar Ali , Jeryo Mohammed , Al-Fatlawi Ahmad 
Published: June 2020

Abstract
Purpose: COVID-19 pandemic continues to hit countries one after the other and has dramatically affected the health and well-being of the world's population. With the daily increase in the number of people with this disease, the impressive speed of spread and the delay in the results of PCR analysis, it may cause the disease to spread more broadly. Therefore it is necessary to consider finding alternative methods of detection and diagnosis COVID-19 to prohibit the spread of the disease among people. Convolutional Neural Network (CNN) automated detection systems have shown auspicious results in detecting patients with COVID-19 through radiography; thus, we suggest them as an alternative option to diagnose COVID-19.Method: In this study, an early screening model based on the enhancement of classical Visual Geometry Group Network (VGG) with Convolutional Covid Block (CCBlock) was proposed to detect and distinguish COVID-19 from Pneumonia, and healthy people using chest X-ray radiographs. The data set used for model testing is the x-ray images available on public platforms, which consist of 1,828 x-ray images, including 310 images for confirmed COVID-19 patients, 864 images for pneumonia patients, and 654 images for healthy people.Results: The experiment result of the dataset showed that the added enhancements to the classical VGG network with X-ray imaging provide the highest detection performance and overall accuracy of 98.52% for two classes and 95.34% accuracy for three classes.Conclusions: Considering the achievement results obtained, it was found that utilizing the enhanced VGG deep neural network helps radiologists automatically diagnose COVID-19 in X-ray images.
Healthy Lifestyle Behaviors Are Major Predictors of Mental Wellbeing During COVID-19 Pandemic Confinement: A Study on Adult Arabs in Higher Educational Institutions
Authors: Kilani Hashem , Bataineh Mo'ath F , Al-Nawayseh Ali , Atyat Khaled , Obeid Omar , Abu-Hilal Maher M. , Mansi Taiysir , Al-Kilani Maher , Al-Kitani Mahfooda , El-Saleh Majed , Jaber Ruba M. , Sweidan Ahmad , Himsi Mawaheb , Yousef Iyad , Alzeer Faten , Nasrallah Monther , Dhaheri Ayesha S Al , Al-Za’abi Abdulsalam , Allala Osama , Al-Kilani Laila , Alhasan Asma M , Ghieda Mohamed , Najah Yasir , Alsheekhly Saad , Alhaifi Ahmad , Shukri Raghda , Adwani Jamal Al , Waly Mostafa , Kilani Laila , Kilani Leen H. , Shareef Ahmad S al , Kilani Areej 
Published: June 2020

Abstract
Background: In previous times, infectious diseases affected the quality of human life during home confinement. This study investigated the influence of home confinement during the COVID-19 pandemic outbreak on lifestyle, mental wellbeing, nutritional status, and sleeping pattern. Method: An online multicategory questionnaire was distributed to collect Demographical information and combined the following tools: Food Frequency Questionnaire (FFQ), International Physical Activity Questionnaire (IPAQ), WHO-5 wellbeing score, and Pittsburgh Sleep Quality Index (PSQI). A snowball none-discriminate sampling procedure was followed to collect data from people attending or working at higher institution had covering the period between Mar/00/2020 and Apr/24/2020. A total of 1723 completed responses (917 Males 37.4 ±13.4 yrs. old and (806 Females 32.2 ± 11.5 yrs. old) were collected.Results: Female participants had significantly lower mental health scores as compared to males (53.9% vs 46.1%). on Mental wellbeing score was better among participants with medium and high Physical Activity Levels (p < 0.00). Additionally, mental wellbeing score was significantly improved by dietary quality and sleeping score (p < 0.001). However, physical activity was by far the major determinants of mental health score. Conclusion: Factors such as PA, Diet, sleeping patterns were associated with mental wellbeing during COVID-19 confinement among Arab participants.
Thermodynamics, kinetics, and isotherms for phenol removal from wastewater using red mud
Authors: Mandal Ashanendu , Dey Basab Brata , Das Sudip Kumar 
Published: June 2020

Abstract
The phenol removal through adsorption using industrial waste has been studied. The red mud generated as waste in the aluminum plants was used in this research. The surface characterizations of red mud were assessed. The batch experiment was investigated with pH (2–12), adsorption period (120–600 min), phenol content (40–200 mg/L), adsorbent dose (2–7 g/L), and temperature (30–50 °C). At the optimum operating condition, the percentage of phenol removal was 87.5%. The pseudo-second-order kinetic model (r2 = 0.98625–0.99994) fitted better than the pseudo-first-order kinetic model. The Freundlich isotherm model was best fitted (r2 = 0.99734–0.99955) among Langmuir, Dubinin–Radushkevich (D-R), and Temkin isotherms. The Langmuir monolayer adsorption capacity was 49.30966 mg/g at 30 °C. The adsorption mechanisms were supported by Reichenberg, Fick, Elovich, Furusawa, and Smith and Boyd models (r2 &gt; 0.8). The thermodynamics suggested endothermic, random, and spontaneous adsorption above 50 °C. The scale-up design using the Langmuir isotherm, and the disposal of used adsorbent after incineration, was established in this study. The research concludes that the red mud generated from the aluminum plant can be used to remove the phenol from wastewater.