bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comprehensive Analysis of the Prognostic Role and Mutational Characteristics of m6A-Related Genes in Lung Squamous Cell Carcinoma
Authors: Gu Chang , Shi Xin , Qiu Wenli , Huang Zhenyu , Yu Yan , Shen Feng , Chen Yumei , Pan Xufeng 
Published: March 2021

BackgroundThere have been limited treatment therapies for lung squamous cell carcinoma (LUSC). M6A-related genes may be the next therapeutic targets for LUSC. In this study, we explored the prognostic role and mutational characteristics of m6A-related genes in LUSC.MethodsLUSC gene expression data, mutational data, and corresponding clinical information were extracted from The Cancer Genome Atlas database. Differentially expressed genes (DEGs) were identified, and the mutation characteristics of LUSC patients were explored. Then, m6A-related genes were extracted and the correlations among the genes were detected. Finally, the prognostic roles of the genes were investigated and the nomogram model was developed. Besides, the protein–protein interaction (PPI) network was used to explore the potential interactions among the genes.ResultsIn total, there are 551 LUSC samples enrolled in our study, containing 502 LUSC tumor samples and 49 adjacent normal LUSC samples, respectively. There were 2970 upregulated DEGs and 1806 downregulated DEGs were further explored. IGF2BP1 and RBM15 had significant co-occurrence frequency (p &lt; 0.05). Besides, METTL14 and ZC3H13 or YTHDF3 also had significant co-occurrence frequency (p &lt; 0.05). All the m6A-related genes represent the positive correlation. WTAP was identified as a prognostic gene in the TCGA database while YTHDC1 and YTHDF1 were identified as prognostic genes. In multivariate Cox analysis, YTHDF1, age, pN stage, pTNM stage, and smoking were all identified as significant prognostic factors for OS.ConclusionWe investigated the expression patterns and mutational characteristics of LUSC patients and identified three potential independent prognostic m6A-related genes (WTAP, YTHDC1, and YTHDF1) for OS in LUSC patients.
Selective Pre-leaching of Tellurium From Telluride-Type Gold Concentrate
Authors: Yang Wei , Lan Xuechen , Wang Qian , Dong Ping , Wang Gang 
Published: March 2021

With a telluride-type gold ore flotation concentrate as the research object, the Na2S + NaOH collaborative leaching process was applied to selectively separate tellurium before the cyanide leaching of gold and silver. The effects of process parameters including the type of leaching agent, the amount of leaching agent, liquid-solid ratio, leaching temperature, and leaching time on the leaching rate of tellurium were investigated. The results showed that the tellurium leaching rate could reach 78.14% under the optimum conditions of −0.038 mm (95%) grinding fineness, 80 g/L Na2S concentration, 30 g/L NaOH concentration, 4:1 liquid-solid ratio, 80°C leaching temperature and 3 h′s leaching time. The kinetic analysis showed that the leaching process of tellurium from telluride-type gold concentrate was a mixed type of chemical reaction control and diﬀusion control. The grain parameter in the leaching process was 0.26263 and the apparent activation energy E = 17.12 kJ/mol. Tellurium could be pre-leached from the telluride-type gold flotation concentrate through the Na2S + NaOH alkaline leaching process to achieve the effective separation of tellurium from noble metals, which, when eliminating the adverse effects of telluride on the leaching of gold and silver, provides new ideas for the extraction of rare element tellurium.
The In Situ Observation of Phase Transformations During Intercritical Annealing of a Medium Manganese Advanced High Strength Steel by High Energy X-Ray Diffraction
Authors: Hu Xiaohua , Mueller Josh J. , Sun Xin , De Moor Emmanuel , Speer John G. , Matlock David K. , Ren Yang 
Published: March 2021

Microstructural changes during thermal processing of a medium manganese steel containing (in wt%) 0.19C and 4.39 Mn were evaluated in situ with a high energy X-ray diffraction system (HEXRD). Samples with an initial fully martensitic microstructure were heated to intercritical annealing (IA) temperatures of 600 or 650°C, held for 30 min, and cooled to room temperature. Diffraction data were analyzed to determine the variations in austenite and ferrite phase fractions and phase lattice constants throughout the ICA cycles. On heating, the 2 vol. pct of austenite present in the starting microstructure decomposed, and cementite precipitation then occurred. During isothermal holding, the austenite fraction increased, up to 20% for the sample annealed at 650°C. The measured austenite fractions were less than those calculated by Thermo-Calc for equilibrium conditions, indicating that the 30-min hold time was insufficient to achieve near-equilibrium conditions. Observed changes in lattice parameters during isothermal holding were interpreted to reflect composition changes due to redistribution of the C and Mn between austenite and ferrite. The results are discussed in relation to the potential for controlling austenite stability during ambient temperature deformation.
A Review on Structural Configurations of Magnetorheological Fluid Based Devices Reported in 2018–2020
Authors: Hua Dezheng , Liu Xinhua , Li Zengqiang , Fracz Pawel , Hnydiuk-Stefan Anna , Li Zhixiong 
Published: March 2021

Magnetorheological fluid (MRF) is a kind of smart materials with rheological behavior change by means of external magnetic field application, which has been widely adopted in many complex systems of different technical fields. In this work, the state-of-the-art MRF based devices are reviewed according to structural configurations reported from 2018 to 2020. Based on the rheological characteristic, the MRF has a variety of operational modes, such as flow mode, shear mode, squeeze mode and pinch mode, and has unique advantages in some special practical applications. With reference to these operational modes, improved engineering mechanical devices with MRF are summarized, including brakes, clutches, dampers, and mounts proposed over these 3 years. Furthermore, some new medical devices using the MRF are also investigated, such as surgical assistive devices and artificial limbs. In particular, some outstanding advances on the structural innovations and application superiority of these devices are introduced in detail. Finally, an overview of the significant issues that occur in the MRF based devices is reported, and the developing trends for the devices using the MRF are discussed.
Three-Dimensional CT for Quantification of Longitudinal Lung and Pneumonia Variations in COVID-19 Patients
Authors: Chen Qiuying , Chen Lv , Liu Shuyi , Chen Luyan , Li Minmin , Chen Zhuozhi , You Jingjing , Zhang Bin , Zhang Shuixing 
Published: March 2021

Objectives: Visual chest CT is subjective with interobserver variability. We aimed to quantify the dynamic changes of lung and pneumonia on three-dimensional CT (3D-CT) images in coronavirus disease 2019 (COVID-19) patients during hospitalization.Methods: A total of 110 laboratory-confirmed COVID-19 patients who underwent chest CT from January 3 to February 29, 2020 were retrospectively reviewed. Pneumonia lesions were classified as four stages: early, progressive, peak, and absorption stages on chest CT. A computer-aided diagnostic (CAD) system calculated the total lung volume (TLV), the percentage of low attenuation areas (LAA%), the volume of pneumonia, the volume of ground-glass opacities (GGO), the volume of consolidation plus the GGO/consolidation ratio. The CT score was visually assessed by radiologists. Comparisons of lung and pneumonia parameters among the four stages were performed by one-way ANOVA with post-hoc tests. The relationship between the CT score and the volume of pneumonia, and between LAA% and the volume of pneumonia in four stages was assessed by Spearman's rank correlation analysis.Results: A total of 534 chest CT scans were performed with a median interval of 4 days. TLV, LAA%, and the GGO/consolidation ratio were significantly decreased, while the volume of pneumonia, GGO, and consolidation were significantly increased in the progressive and peak stages (for all, P &lt; 0.05). The CT score was significantly correlated with the pneumonia volume in the four stages (r = 0.731, 0.761, 0.715, and 0.669, respectively, P &lt; 0.001).Conclusion: 3D-CT could be used as a useful quantification method in monitoring the dynamic changes of COVID-19 pneumonia.
ThermoScan: Semi-automatic Identification of Protein Stability Data From PubMed
Authors: Turina Paola , Fariselli Piero , Capriotti Emidio 
Published: March 2021

During the last years, the increasing number of DNA sequencing and protein mutagenesis studies has generated a large amount of variation data published in the biomedical literature. The collection of such data has been essential for the development and assessment of tools predicting the impact of protein variants at functional and structural levels. Nevertheless, the collection of manually curated data from literature is a highly time consuming and costly process that requires domain experts. In particular, the development of methods for predicting the effect of amino acid variants on protein stability relies on the thermodynamic data extracted from literature. In the past, such data were deposited in the ProTherm database, which however is no longer maintained since 2013. For facilitating the collection of protein thermodynamic data from literature, we developed the semi-automatic tool ThermoScan. ThermoScan is a text mining approach for the identification of relevant thermodynamic data on protein stability from full-text articles. The method relies on a regular expression searching for groups of words, including the most common conceptual words appearing in experimental studies on protein stability, several thermodynamic variables, and their units of measure. ThermoScan analyzes full-text articles from the PubMed Central Open Access subset and calculates an empiric score that allows the identification of manuscripts reporting thermodynamic data on protein stability. The method was optimized on a set of publications included in the ProTherm database, and tested on a new curated set of articles, manually selected for presence of thermodynamic data. The results show that ThermoScan returns accurate predictions and outperforms recently developed text-mining algorithms based on the analysis of publication abstracts.Availability: The ThermoScan server is freely accessible online at https://folding.biofold.org/thermoscan. The ThermoScan python code and the Google Chrome extension for submitting visualized PMC web pages to the ThermoScan server are available at https://github.com/biofold/ThermoScan.
Efficacy of Herbal Medicines Intervention for Colorectal Cancer Patients With Chemotherapy-Induced Gastrointestinal Toxicity — a Systematic Review and Meta-Analysis
Authors: Chen Yuanyuan , Cheng Chien-shan , Tan Hor-Yue , Tam Chi Wing , Wang Ning , Feng Yibin 
Published: March 2021

Purpose: Chemotherapy-induced gastrointestinal (CIGI) toxicity affects the quality of life of patients with colorectal cancer (CRC) and the clinical application of treatment drugs. This review aims to evaluate the efficacy of traditional herbal medicines (HMs) in alleviating symptoms of CIGI toxicity (including nausea and vomiting, anorexia, diarrhea, constipation, oral mucositis, abdominal pain, and abdominal distension), and to explore further individual herb or herbal combinations in alleviating the CIGI toxicity.Methods: Nine electronic databases were screened from 2010 to 2020. Twenty-two randomized controlled trials with a total of 1,995 patients evaluating the complementary efficacy of HMs with chemotherapy compared with chemotherapy-alone were included. Further, sensitivity analyses of orally administered multi-ingredient HM interventions were explored based on the composition of HM interventions.Results: The meta-analysis showed that HM treatment combined with chemotherapy significantly alleviated the overall CIGI toxicity (RR = 0.78 [0.72, 0.84], p &lt; 0.001, I2 = 44%), nausea and vomiting (RR = 0.74 [0.66, 0.82], p &lt; 0.001, I2 = 35%), diarrhea (P = 0.02, RR = 0.64, 95% CI = 0.44–0.93, I2 = 50%), oral mucositis (RR = 0.65 [0.48, 0.88], P = 0.005, I2 = 24%), and abdominal distension (RR = 0.36 [0.18, 0.73], P = 0.004, I2 = 0%). However, no statistically significant effects of HMs were shown in studies with a double-blind design for CIGI toxicity. Based on the ingredients of the HMs, further sensitivity analyses identified five herbs [Glycyrrhiza uralensis Fisch., Atractylodes macrocephala Koidz., Astragalus membranaceus (Fisch.) Bge., Codonopsis pilosula (Franch.) Nannf., and the pericarp of Citrus reticulata Blanco.] that were associated with significant reductions in CIGI toxicity.Conclusion: A statistically significant effect of HMs combined with chemotherapy on alleviating the overall CIGI toxicity, nausea and vomiting, diarrhea, oral mucositis, or abdominal distension is only shown in studies without a double-blind design. Further well-designed, double-blinded, large-scaled randomized controlled trials (RCTs) are warranted to comprehensively evaluate the treatment efficacy. Further clinical research that includes the five herbs with chemotherapy for patients, the safety of the combinations of these herbs, and the potential synergistic effects of these combinations of herbs should be conducted.
High-Throughput and Automated Acoustic Trapping of Extracellular Vesicles to Identify microRNAs With Diagnostic Potential for Prostate Cancer
Authors: Ku Anson , Fredsøe Jacob , Sørensen Karina D. , Borre Michael , Evander Mikael , Laurell Thomas , Lilja Hans , Ceder Yvonne 
Published: March 2021

Molecular profiling of extracellular vesicles (EVs) offers novel opportunities for diagnostic applications, but the current major obstacle for clinical translation is the lack of efficient, robust, and reproducible isolation methods. To bridge that gap, we developed a microfluidic, non-contact, and low-input volume compatible acoustic trapping technology for EV isolation that enabled downstream small RNA sequencing. In the current study, we have further automated the acoustic microfluidics-based EV enrichment technique that enables us to serially process 32 clinical samples per run. We utilized the system to enrich EVs from urine collected as the first morning void from 207 men referred to 10-core prostate biopsy performed the same day. Using automated acoustic trapping, we successfully enriched EVs from 199/207 samples (96%). After RNA extraction, size selection, and library preparation, a total of 173/199 samples (87%) provided sufficient materials for next-generation sequencing that generated an average of 2 × 106 reads per sample mapping to the human reference genome. The predominant RNA species identified were fragments of long RNAs such as protein coding and retained introns, whereas small RNAs such as microRNAs (miRNA) accounted for less than 1% of the reads suggesting that partially degraded long RNAs out-competed miRNAs during sequencing. We found that the expression of six miRNAs was significantly different (Padj &lt; 0.05) in EVs isolated from patients found to have high grade prostate cancer [ISUP 2005 Grade Group (GG) 4 or higher] compared to those with GG3 or lower, including those with no evidence of prostate cancer at biopsy. These included miR-23b-3p, miR-27a-3p, and miR-27b-3p showing higher expression in patients with GG4 or high grade prostate cancer, whereas miR-1-3p, miR-10a-5p, and miR-423-3p had lower expression in the GG4 PCa cases. Cross referencing our differentially expressed miRNAs to two large prostate cancer datasets revealed that the putative tumor suppressors miR-1, miR-23b, and miR-27a are consistently deregulated in prostate cancer. Taken together, this is the first time that our automated microfluidic EV enrichment technique has been found to be capable of enriching EVs on a large scale from 900 μl of urine for small RNA sequencing in a robust and disease discriminatory manner.
Case Report: A 3D-Printed Surgical Guide for Breast-Conserving Surgery After Neoadjuvant Chemotherapy
Authors: Wu Zhen-Yu , Kim Guk Bae , Lee Sangwook , Choi Seung Hyun , Kim Namkug , Ko BeomSeok 
Published: March 2021

BackgroundA challenging problem for patients undergoing breast-conserving surgery after neoadjuvant chemotherapy (NACT) is the accuracy of preoperative tumor localization. After chemotherapy, the original tumor is likely to shrink or scatter dramatically or even show complete remission. For breast-conserving surgery, the development of a guidance device to accurately estimate the resection area is imperative.Case PresentationWe produced a three-dimensional (3D)–printed breast surgical guide (BSG) based on prone and supine magnetic resonance imaging (MRI). This device was tested on a patient who underwent breast-conserving surgery after NACT. Both ultrasonography and MRI revealed that the tumor shrank substantially after NACT. Identifying the target tumor area using pre-NACT MRI was feasible, and the tumor was safely removed with clear resection margins.ConclusionThe BSG has several advantages over conventional methods for tumor localization after NACT. In particular, the BSG provided precise quantitative MRI information about the tumor area.
Case Report: Cutaneous Squamous Cell Carcinoma Arising From the Ulcer of the Lesions of Dupuytren’s Disease on the Palm
Authors: Sun Qingmiao , Fu Bin , Li Sheng , Fang Hong , Qiao Jianjun 
Published: March 2021

Dupuytren’s disease is a benign fibromatosis that mainly involves the fascia of the palm and digits. The relationship between Dupuytren’s disease and the evolution of cutaneous squamous cell carcinoma is still unclear. Here we report the case of a 52-year-old female with squamous cell carcinoma arising from the ulcer of the lesions of Dupuytren’s disease on the left palm. To our knowledge, this is the first reported case in the English literature of squamous cell carcinoma on the palm of someone with Dupuytren’s disease.
COVID-19 in Cancer Patients, Risk Factors for Disease and Adverse Outcome, a Population-Based Study From Norway
Authors: Johannesen Tom Børge , Smeland Sigbjørn , Aaserud Stein , Buanes Eirik Alnes , Skog Anna , Ursin Giske , Helland Åslaug 
Published: March 2021

BackgroundCancer has been suggested as a risk factor for severe outcome of SARS-CoV-2 infection. In this population-based study we aimed to identify factors associated with higher risk of COVID-19 and adverse outcome.MethodsData on all confirmed SARS-CoV-2 positive patients in the period January 1 to May 31, 2020 were extracted from the Norwegian Surveillance System for Communicable Diseases. Data on cancer and treatment was available from the Cancer Registry of Norway, the Norwegian Patient Registry and the Norwegian Prescription Database. Deaths due to COVID-19 were extracted from the Cause of Death Registry. From the Norwegian Intensive Care and Pandemic Registry we retrieved data on admittance to hospital and intensive care. We determined rates of COVID-19 disease in cancer patients and the rest of the population. We also ran multivariate analyses adjusting for age and gender.ResultsA total of 8 410 patients were diagnosed with SARS-CoV-2 infection in Norway during the study period, of which 547 (6.5%) were cancer patients. Overall, we found similar age adjusted rates of COVID-19 in the population with cancer as in the population without cancer. Unadjusted analysis showed that patients having undergone major surgery within the past 3 months had an increased risk of COVID-19 while we did not find increased Odds Ratio (OR) related to other oncological treatment modalities. No patients treated with stem cell or bone marrow transplant were diagnosed with COVID-19. The fatality rate of COVID-19 among cancer patients was 0.10. This was similar to non-cancer patients, when adjusting for age and sex with OR (95% CI) for death= 0.99 (0.68–1.42). Patients with distant metastases had significantly increased OR of death due to COVID-19 disease of 9.31 (95% CI 2.60–33.34). For the combined outcome death and/or admittance to hospital due to COVID-19, we found significant two-fold increased risk estimates for patients diagnosed with cancer less than one 1 year ago (OR 2.08, 95% CI 1.14–3.80), for those treated with anti-cancer drugs during the past 3 months (OR 1.80, 95% CI 1.07–3.01) and for patients undergoing major surgery during the past 3 months (OR 2.19, 95% CI 1.40–3.44).
miR-181d/RBP2/NF-κB p65 Feedback Regulation Promotes Chronic Myeloid Leukemia Blast Crisis
Authors: Zhou Minran , Yin Xiaolin , Zheng Lixin , Fu Yue , Wang Yue , Cui Zelong , Gao Zhenxing , Wang Xiaoming , Huang Tao , Jia Jihui , Chen Chunyan 
Published: March 2021

BackgroundChronic myeloid leukemia (CML) is a malignant clonal proliferative disease. Once it progresses into the phase of blast crisis (CML-BP), the curative effect is poor, and the fatality rate is extremely high. Therefore, it is urgent to explore the molecular mechanisms of blast crisis and identify new therapeutic targets.MethodsThe expression levels of miR-181d, RBP2 and NF-κB p65 were assessed in 42 newly diagnosed CML-CP patients and 15 CML-BP patients. Quantitative real-time PCR, Western blots, and cell proliferation assay were used to characterize the changes induced by overexpression or inhibition of miR-181d, RBP2 or p65. Luciferase reporter assay and ChIP assay was conducted to establish functional association between miR-181d, RBP2 and p65. Inhibition of miR-181d expression and its consequences in tumor growth was demonstrated in vivo models.ResultsWe found that miR-181d was overexpressed in CML-BP, which promoted leukemia cell proliferation. Histone demethylase RBP2 was identified as a direct target of miR-181d which downregulated RBP2 expression. Moreover, RBP2 inhibited transcriptional expression of NF-κB subunit, p65 by binding to its promoter and demethylating the tri/dimethylated H3K4 region in the p65 promoter locus. In turn, p65 directly bound to miR-181d promoter and upregulated its expression. Therefore, RBP2 inhibition resulting from miR-181d overexpression led to p65 upregulation which further forwarded miR-181d expression. This miR-181d/RBP2/p65 feedback regulation caused sustained NF-κB activation, which contributed to the development of CML-BP.ConclusionsTaken together, the miR-181d/RBP2/p65 feedback regulation promoted CML-BP and miR-181d may serve as a potential therapeutic target of CML-BP.