bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical quality in cancer research - Strategy to assess data integrity of germline variants inferred from tumor-only testing sequencing data
Authors: Ménard Timothé , Rolo Donato , Koneswarakantha Björn 
Published: August 2021

Abstract
In the majority of cancers, pathogenic variants are only found at the level of the tumor; however, an unusual number of cancers and/or diagnoses at an early age in a single family may suggest a genetic predisposition. Predisposition plays a major role in about 5 to 10% of adult cancers and in certain childhood tumors. As access to genomic testing for cancer patients continues to expand, the identification of Potential Germline Pathogenic Variants (PGPV) through tumor-DNA sequencing is also increasing. Statistical methods have been developed to infer the presence of a PGPV without the need of a matched normal sample. These methods are mainly used for exploratory research, for example in real-world Clinico-Genomic Databases/platforms (CGDB). These databases are being developed to support many applications such as targeted drug development, clinical trial optimization and post marketing studies. To ensure the integrity of data used for research, a quality management system should be established, and quality oversight activities should be conducted to assess and mitigate clinical quality risks (for patient safety and data integrity). As opposed to well-defined "good practice" quality guidelines (GxP) areas such as good clinical practice, there are no comprehensive instructions on how to assess the clinical quality of statistically derived variables from sequencing data such as PGPV. In this report, we aim to share our strategy and propose a possible set of tactics to assess the PGPV quality and to ensure data integrity in exploratory research.
Baseline Predictors of Attrition in a Randomised Controlled Trial of a New Group Psychological Intervention for People with Recurrent Binge Eating Episodes Associated to Overweight or Obesity
Authors: Mannan Haider , Palavras Marly Amorim , Hay Phillipa , Claudino Angelica 
Published: August 2021

Abstract
Purpose: Understanding the high rate of treatment attrition in trials of people with eating disorders is important as it can compromise the quality of the trials. In clinical practice, it may also contribute to illness chronicity, relapse, and costs. Thus, we investigated factors associated with treatment attrition to a new manualised psychotherapy HAPIFED compared to CBT-E, for individuals with Bulimia Nervosa or Binge Eating Disorder comorbid with overweight or obesity.Methods: In total, 98 participants were recruited with 50 randomised to HAPIFED and 48 to the control intervention CBT-E, all administered in groups of up to 10 participants. An investigator external to the site conducted the random allocation, which was concealed from the statistician involved in the analysis, and known only to the therapists until the finalization of the 12-month follow-up after the end of active treatment. Three scenarios in the timeline treatment of a total of 30 sessions were assessed: 33% or 60% or 75% of presence. Logistic regression analysis was performed to find the correlates of attrition.Results: None of the six variables - frequency of binge eating episodes, purging, eating disorder symptom severity, weight, illness duration and mental health-related quality of life - significantly predicted attrition at 33%, but longer illness duration predicted lower treatment attrition at both 60% and 75% presence of the interventions. Also for 75% presence, lower body weight predicted lower treatment attrition. Conclusions: Lower attrition due to late treatment completion was associated with longer binge eating illness length and a lower body weight. More research is needed to recognize factors that may interfere with engagement in treatments aiming to avoid early dropout.Trial registration: US National Institutes of Health clinical trial registration number NCT02464345, date of registration 1 June 2015.
MicroRNA-2392 Functions as a Tumor Suppressor Gene and Inhibits Malignant Progression of Hepatocellular Carcinoma via Directly Targeting JAG2
Authors: Liu Chunying , Sun Bin , Ji Weidan , Lin Xuejing , Chen Lei , Qian Haihua , Su Changqing 
Published: August 2021

Abstract
Background

Dysregulation of microRNA (miRNA) expression in various cancers and their vital roles in malignant progression of cancers are well investigated. Our previous studies have analyzed miRNAs that promote malignant progression of hepatocellular carcinoma (HCC), this study aim to systematically elucidate metastasis suppressor miRNAs in HCC.
Methods

High-throughput RNA sequencing analysis was used to identify anti-metastatic miRNAs of HCC. The relative expression levels of miRNAs were confirmed by qRT-PCR. The biological functions of miRNAs were studied by CCK8, wound-healing, transwell, colony formation in HCC cells. Circulating tumor cells were enriched from blood samples of HCC patients and cultured by three-dimensional (3D) system. The potential target mRNAs of miRNAs were analyzed by bioinformatics analysis and confirmed by luciferase reporter assay. Liver metastasis model via tail vein injection was further examined in nude mice. Kaplan-Meier and Cox regression were used to analyze the value of potential target mRNAs on overall survival.
Results

miR-2392 was significantly down-regulated in HCC. Overexpression of miR-2392 suppressed proliferation, mobility, spheroid formation and maintenance of cancer stem cells (CSC)-like characteristics in HCC cell lines, whereas down-regulation of miR-2392 led to the opposite results. CTCs from HCC patients with lower serum miR-2392 level had stronger cell spheroid formation ability. A negative correlation between the content of miR-2392 in serum and the number of CTC spheroids had been found. We identified Jagged2 (JAG2) as a direct target of miR-2392, miR-2392 inhibited the expression and nuclear accumulation of JAG2 by targeting 3’-UTR of JAG2. HCC cells were treated with LV-miR-2392 inhibitor and JAG2-siRNA to explore the mechanism of miR-2392 and JAG2 on HCC. Down-regulation of JAG2 inhibited the overexpression effects of miR-2392 in vitro and in vivo. JAG2 is highly expressed in HCC and is closely related to poor prognosis and survival of patients.
Conclusions

Our findings indicated a significant role of the miR-2392/JAG2 axis in suppressing HCC cell growth and aggressiveness, miR-2392 may play a role as a tumor suppressor gene to guide the individualized precise treatment of HCC.
Influence of Climate Change and Anthropogenic Activities on Groundwater Level in the Northern Huangqihai Basin, China
Authors: Jin Jing , Wang Zihe , Zhao Yiping , Ding Huijun , Chen Yufei 
Published: August 2021

Abstract
The variation in the groundwater level, which is an indicative factor that can reflect changes in both groundwater level and groundwater quantity, was selected as the factor to be analyzed. Rainfall and groundwater exploitation were chosen as the representative factors of climate change and anthropogenic activities, respectively. By applying the elastic coefficient method and other mathematical statistical methods, the influence of climate change and anthropogenic activities on groundwater was analyzed qualitatively and quantitatively. The northern Huangqihai basin was chosen as the study area. The rainfall in the study area showed an increasing trend from 1996–2020, while most variations in groundwater level were negative. This result indicated that the positive influence of rainfall on the variation in the groundwater level in the study area was not enough to offset the negative influence of groundwater exploitation. The correlation between anthropogenic activities and variations in the groundwater level was lower in wet years than in normal years but the highest in dry years. Based on the comparative method of the slope changing ratio of cumulative quantity and the elastic coefficient method, it was determined that the contribution rate of climate change to the variation in groundwater level was 22.08% and that of human activities was 77.92%. Thus, the sustainable development of the groundwater environment can be realized by positively guiding anthropogenic activities and minimizing negative influences.
Preparation and Characterization of Bio-Nitrogen-Doped Activated Carbon
Authors: ZHANG xingping , Li Haichao , Wang Guangle , Ji Qingsong , Liang Tian 
Published: August 2021

Abstract
Blood (livestock blood) is a cheap and readily available biomass material with a relatively high protein content.In this study, bio-nitrogen doped activated carbon (BN-AC) was prepared by chemical activation method with nitrogen-rich pig blood as raw material and magnesium chloride as activator.The specific surface area of BN-AC is 283.719 m2/g, and the pore volume is 0.128 cm3/g.The optimum conditions for the preparation of BN-AC were as follows: the mass impregnation ratio of activator to blood powder was 2:1, the impregnation time was 12 h, and the activation temperature was 600 ℃.The forms of biological nitrogen in activated carbon were studied by elemental analysis, Boehm titration, FTIR and XPS.The results showed that the total basicity of 0.720 mmol/g, and acidity of 0.313 mmol/g of the BN-AC.The surface of the precursor has only one Pyrrolic N, and the surface of BN-AC contains Pyridinic N, Pyrrolic N and Graphitic N, the N content of the precursor was successfully preserved.BN-AC has higher methylene blue and iodine adsorption values than ordinary activated carbon.
Effects of early-life exposure to topsoil on the muscle fiber characteristics and gene expression of weaned piglets
Authors: Wang Yongjie , Tsai Tsung Cheng , Morse Palika , Zhang Shilei , Maxwell Charles , Zhao Jiangchao , Huang Yan 
Published: August 2021

Abstract
The objective of this experiment was to investigate the influence of early exposure to topsoil on the muscle fiber characteristics and transcription related myogenesis, intramuscular fat metabolism, muscle fiber types, and mTOR signaling pathway of weaned pigs. A Total of 180 piglets were separately assigned to No soil, Antibacterial soil, and Normal soil group (each group, n=60), and were fed ad libitum with common antibiotic-free corn-soybean meal diets until day-31. Ten pigs from each group with similar body weight were selected to be slaughtered, and the longissimus dorsi (LD) muscle samples were collected for histological analysis and measurements of genes and proteins expression levels. In the present study, the muscle fiber diameter and the area of Normal soil and Antibacterial soil group were significantly higher than No soil group (P < 0.05). The Normal soil significantly upregulated the gene expression of MyoG compared to No soil and Antibacterial soil groups (P < 0.05). The gene expression of CD36 and CPT-1 of Normal soil group was significantly lower than No soil group (P < 0.05), while HSL expression of Normal soil group was significantly higher than Antibacterial and No soil groups (P < 0.05). The MyHC I of Normal soil group was significantly higher than No soil group (P < 0.05), but the expression MyHC IIa was lower than No soil group (P < 0.05). The protein expression expressed the similar result with gene expression. In addition, the Normal soil significantly increased the AMPK and mTOR phosphorylation compared to No soil and Antibacterial soil groups (P < 0.05). These data suggest that early exposure to topsoil regulates the muscle fiber growth, modulates the expression pattern related to myogenesis, muscle fiber type, intramuscular fat metabolism, and increases the phosphorylation of mTOR and AMPK pathways.
No Difference in the Incidence or Location of Deep Venous Thrombosis According to use of Pharmacological Prophylaxis Following Total Knee Arthroplasty
Authors: Itou Junya , Kuwashima Umito , Itoh Masafumi , Okazaki Ken 
Published: August 2021

Abstract
BackgroundThe incidence and characteristics of deep vein thrombosis (DVT) following total knee arthroplasty (TKA) without pharmacologic prophylaxis have not been fully investigated. This study aimed to determine whether there are any differences in the incidence, location, and characteristics of DVT following TKA with pharmacologic prophylaxis and without pharmacologic prophylaxis.MethodsIn total, 216 consecutive knees that underwent primary TKA were retrospectively evaluated. Enoxaparin was used postoperatively for pharmacologic prophylaxis. We excluded 60 knees because of use of antiplatelet agents or anticoagulants before surgery, history of venous thromboembolism, or bleeding risk. The remaining 156 knees were included in the analysis and divided into two groups: with pharmacologic prophylaxis (n = 79) and without pharmacologic prophylaxis (n = 77).ResultsThe overall incidence of DVT was 34% (54/156 knees). DVT was detected in 31.6% of knees in the group with pharmacologic prophylaxis and in 37.6% of knees in the group without pharmacologic prophylaxis; the difference was not statistically significant. Soleal vein thrombus was observed in 74.6% of the knees with DVT and non-floating thrombus was observed in 98.7%.ConclusionsNo differences were found in the incidence, location, or characteristics of DVT following TKA with or without pharmacological prophylaxis.
Investigation of Some Antibiotic Resistance Genes of Indigenous Lactobacilli Isolated From Traditional Yogurt In Zanjan Province of Iran
Authors: Moghimi Bahare , Dana Maryam Ghobadi , Shapouri Reza 
Published: August 2021

Abstract
Purpose: Given the increasing use of antibiotics on humans and livestock for treatment or as a growth stimulant, antibiotic resistance has become a general concern. The food chain and specially fermented foods could be a source of antibiotic-resistant bacteria and resistance genes. Lactic Acid Bacteria (LAB) and Lactobacilli are considered safe to use as starter culture or probiotic strains. Recently, however, antibiotic-resistant genes isolated from LABs showed the necessity of setting international regulations to reduce the risk of antibiotic resistance genes transmission via the food chain. The current study aimed to investigate the antibiotic resistance of Lactobacilli isolated from traditional yogurt samples from Zanjan province in Iran.Methods: Lactobacilli characterization and identification were carried out through biochemical and molecular methods. The disk diffusion method was applied to determine phenotype resistance using 13 antibiotic disks resistance genes presence were investigated in the isolates to determine transferability risk, respectively.Results: Based on biochemical and molecular methods, 24 isolates have been identified as Lactobacilli with multiple antibiotic-resistant phenotypes. Vancomycin resistance was a typical phenotype and genotype among isolates. On investigated Lactobacilli chromosome, Tetracycline resistance genes Chloramphenicol (cat), beta-lactam, aminoglycosides (aph (3’)-III), and aadA resistance genes have been detected. While the examined resistance genes have not been detected on the plasmids, they were all on the bacterial chromosome.Conclusion: The results showed that the investigated isolates did not carry the resistance genes on their plasmids. It, therefore, would be a good point since they probably do not transfer resistance genes to other bacteria, and they would be proper candidates to do more investigation for introducing new safe starter culture or probiotic strain to food industries.
Determination of Salt Tolerance of Oil Palm SUP-PSU 1 Using Cell Suspension Culture
Authors: Sukdee Thirasak , Te-chato Sompong , YENCHON SUREERAT 
Published: August 2021

Abstract
Oil palm is an oil crop that produces the highest oil yield throughout the year. Repeated application of fertilizer in oil palm orchard results in severe salinity of planting areas. Therefore, the objective of this study was to determine growth, physiochemistry and re-growth of calli as effected by sodium chloride (NaCl). The calli were cultured in liquid oil palm culture medium (OPCM) supplemented with different concentrations of NaCl (0, 50, 100, 150, 200, 300 and 400 mM), 0.1 mg/l dicamba and 200 mg/l ascorbic acid for 4, 8 and 12 weeks. The results showed that increase in concentrations of NaCl and exposure times decreased growth rate of cells in suspension culture. The concentration of NaCl which inhibited growth rate at 50 % (IC50) was 166.73 mM after culture for 12 weeks. Increase in concentrations of NaCl and exposure times increased electrolyte leakage (EL), changing of electrical conductivity (EC) medium and proline content. NaCl at concentration of 400 mM gave the highest EL, changing of EC medium and proline content at 82.22 %, 3.77 mS/cm and 64.93 µg/gFW, respectively. Over 200 mM NaCl oil palm cells cannot survive. After transfer treated callus clumps to OPCM without NaCl for 8 weeks, the clumps treated in 50 mM NaCl gave the highest fresh weight at 416.5 mg while 100 mM gave the highest average number of nodules per tube at 84 nodules. This result suggests that cells of oil palm in vitro could not stand to NaCl at concentration higher than 200 mM.
Preclinical Evaluation of Bone Marrow Mesenchymal Stem Cells Overexpressing MicroRNA-126 to Treat Critical Limb Ischemia
Authors: Nammian Pegah , Asadi-Yousefabad Seyedeh-Leili , Daneshi Sajad , Fallahi Jafar , Tabei Seyed Mohammad Bagher , Razban Vahid 
Published: August 2021

Abstract
Introduction: Critical limb ischemia (CLI) considered as the most severe form of peripheral artery disease (PAD). Current therapy for CLI are surgical reconstruction and endovascular therapy or limb amputation (for patients with no treatment options). Neovasculogenesis induced by stem cells including mesenchymal stem cells (MSCs) therapy is a promising approach to treat CLI. But this method of treatment faces challenges such as: MSCs survival and paracrine secretion. MicroRNAs are post transcriptional regulatory molecules that regulate many biological processes including VEGF pathway. MicroRNAs could be used to increase viability and angiogenic potential of MSCs. This study was conducted to reinforce and increase the angiogenic potential of BM-MSCs by using microRNA-126 and evaluate the effect of this stem cell gene therapy on treatment of ischemic tissues in CLI mouse models. Methods: BM-MSCs were isolated from male C57 BL/6 inbred mice and characterized by morphology, flow cytometry, differentiation to osteocyte and adipocyte. Transformed BM-MSCs containing miR-126 were produced by using lentiviral vector. Then femoral artery ligation and total excision of the femoral artery was performed on C57BL/6 mice to create CLI model. Animals were allocated to control, BM-MSCs, virus and BM-MSCs miR-126 groups and defined number of the cells and virus were injected 24 h after surgery. In order to determine in vitro and in vivo effects, the following tests were performed: wound healing assay, behavioral tests including: Tarlov, Ischemia, Modified ischemia, Function and the grade of limb necrosis scores, donor cell survival assay, real-time PCR and histological analysis. Results: Results indicated that during 28 days after transplantation, BM-MSCs and virus groups had an enhancing effect on angiogenesis. BM-MSCs miR-126 group had remarkable effect on endothelial cell migration, muscle restructure, functional improvements and neovascularization in ischemic tissues and led to more effective treatment. In vivo evaluation showed that miR-126 could increase BM-MSCs survival and paracrine secretion of angiogenic factors such as VEGF, and led to remarkable functional improvements and neovascularization in ischemic tissues. Conclusions: According to the obtained results, it could concluded that combination of BM-MSCs and miR-126 leads to more effective recovery from critical limb ischemia compared to using them alone. In fact, miR-126 can be used as a strong modifier to reinforce the angiogenic potential of BM-MSCs, leading to more effective treatment for CLI.
In Search for the Optimal Preprocessing Technique for Deep Learning Based Diabetic Retinopathy Stage Classification from Fundus Images
Authors: Mukherjee Nilarun , Sengupta Souvik 
Published: August 2021

Abstract
Background: Diabetic retinopathy (DR) is a complication of diabetes mellitus, which if left untreated may lead to complete vision loss. Early diagnosis and treatment is the key to prevent further complications of DR. Computer-aided diagnosis is a very effective method to support ophthalmologists, as manual inspection of pathological changes in retina images are time consuming and expensive. In recent times, Machine Learning and Deep Learning techniques have subsided conventional rule based approaches for detection, segmentation and classification of DR stages and lesions in fundus images. Method: In this paper, we present a comparative study of the different state-of-the-art preprocessing methods that have been used in deep learning based DR classification tasks in recent times and also propose a new unsupervised learning based retinal region extraction technique and new combinations of preprocessing pipelines designed on top of it. Efficacy of different existing and new combinations of the preprocessing methods are analyzed using two publicly available retinal datasets (EyePACS and APTOS) for different DR stage classification tasks, such as referable DR, DR screening, and five-class DR grading, using a benchmark deep learning model (ResNet-50). Results: It has been observed that the proposed preprocessing strategy composed of region of interest extraction through K-means clustering followed by contrast and edge enhancement using Graham’s method and z-score intensity normalization achieved the highest accuracy of 98.5%, 96.51% and 90.59% in DR-screening, referable-DR, and DR gradation tasks respectively and also achieved the best quadratic weighted kappa score of 0.945 in DR grading task. It achieved best AUC-ROC of 0.98 and 0.9981 in DR grading and DR screening tasks respectively. Conclusion: It is evident from the results that the proposed preprocessing pipeline composed of the proposed ROI extraction through K-means clustering, followed by edge and contrast enhancement using Graham’s method and then z-score intensity normalization outperforms all other existing preprocessing pipelines and has proven to be the most effective preprocessing strategy in helping the baseline CNN model to extract meaningful deep features.
Fabrication And Characterization of Cs0.33WO3 Nanorod Combined Within Dye Sensitized Solar Cells For Near-Infrared Light Absorption
Authors: Liu Bo-Tau , Hung Tai-Yuan , Gorji Nima E. 
Published: August 2021

Abstract
Near-infrared (NIR) light absorbing materials have been widely used in vehicle and building applications due to their transparent film structure with high absorption rate in NIR range and a high transmittance for the visible light. In this paper, Cesium-doped Tungstate (Cs0.33WO3) has been combined with dye-sensitized solar cell (DSSC) to convert the heat energy (absorbed from NIR light) into photocurrent. Cs0.33WO3 Nanorods were synthesized and used to prepare the active layer of the cell. The mesoporous Titanium dioxide (TiO2) on FTO has also been used as the electron transport layer (ETL). This simple structure of FTO/TiO2/Cs0.33WO3 resulted in a poor Fermi level alignment and a low voltage. However, a buffer layer made of Poly[(9,9-bis(3′-(N,N-dimethylamino)propyl)-2,7-fluorene)-alt-2,7-(9,9- dioctylfluorene)] (PFN-DOF) improved the Fermi level alignment and the quality of the interface in the modified structure of FTO/TiO2/PFN-DOF/Cs0.33WO3 which improved the initial Jsc from 0.38 μA/cm2 to 0.45 μA/cm2 for the NIR range. In addition, the Jsc of this modified structure improved from 18.84 μA/cm2 to 27.56 μA/cm2 for the visible light. Finally, by using a P25-doped TiO2 layer, the Jsc increased from 0.70 μA/cm2 to 31.12 μA/cm2 for both NIR and visible light, respectively.