bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of potential core genes as potential biomarkers for predicting progress and prognosis in glioblastoma
Authors: Zeng Jianping , Hua Shushan , Liu Jing , Mungur Rajneesh , He Yongsheng , Feng Jiugeng 
Published: April 2022

Abstract
Background
Glioblastoma is a common malignant neuroepithelial neoplasm with poor clinical outcome and limited treatment options. It is extremely important to search and confirm diverse hub genes that are effective in the advance and prediction of glioblastoma.
Methods
We analyzed three microarray datasets (GSE50161, GSE4290, GSE68848), which was derived from the GEO database. GO function and KEGG pathway enrichment analysis for Differentially Expressed Genes (DEGs) were performed using the DAVID. PPI network of these DEGs was analyzed based on the Search Tool for the Retrieval of Interacting Genes database and visualized by Cytoscape software. Hub genes were identified through PPI network and Robust Rank Aggregation method. The Cancer Genome Atlas (TCGA) and Oncomine database were used to perform the validation of hub genes. In addition, the survival curve analysis was also conducted to verify the correlation between the expression of hub genes and prognosis. The human glioblastoma cells and normal cells were collected and then RT-PCR, Western-blot and immunofluorescence were conducted to validate the expression of NDC80. A Cell Counting Kit-8 (CCK-8) assay were used to detect the proliferative of glioma cells. The effects of NDC80 on migration and invasion of GBM cell lines were evaluated by conducting scratch assay and transwell assay.
Results
A total of 716 overlapping genes were in the common region, containing 188 upregulated DEGs and 528 downregulated DEGs. Furthermore, we also found among the overlapping DEGs, ten hub genes with a high degree of connectivity. The expression of ten hub genes in TCGA and Oncomine database were significantly overexpressed in glioblastoma compared with normal ones. Besides, the survival analysis showed that the patients with low expression of six genes (BIR5C, CDC20, NDC80, CDK1, TOP2A and MELK) had a significant favorable prognosis (P < 0.01). We firstly discovered that NDC80, an important molecule in other cancers, also plays an important role in malignant gliomas. The RT-PCR, western blot and immunofluorescence results showed that the expression level of NDC80 was significantly higher in human glioblastoma cells than in normal cells. Moreover, we identified that NDC80 up-regulates the proliferation and invasion abilities of human glioblastoma cells.
Conclusions
The distinguished six genes may be utilized to form a board of progressive and predictive biomarkers of glioblastoma for clinical purpose. Especially, NDC80 was discovered that may play an important role in glioblastoma.
Atmospheric Muography for Imaging and Monitoring Mesoscale Convective Systems
Authors: Tanaka Hiroyuki K.M. , Gluyas Jon , Holma Marko , Joutsenvaara Jari , Kuusiniemi Pasi , Leone Giovanni , Presti Domenico Lo , Matsushima Jun , Oláh László , Poluianov Stepan , Steigerwald Sara , Thompson Lee F. , Usoskin Ilya , Varga Dezső , Yokota Yusuke 
Published: April 2022

Abstract
Large-scale solid bodies on Earth such as volcanoes and man-made pyramids have been visualized with solid earth muography, and the recently invented technique, acqueous muography, has already demonstrated its capability to visualize ocean tides and tsunami. In this work, atmospheric muography, a technique to visualize and monitor the vertical profile of tropic cyclones (TCs) is presented for the first time. The density distribution and time-dependent behavior of several TCs which had approached Kagoshima, Japan, has been investigated with muography. The resultant time-sequential images captured their warm cores, and their movements were consistent with the TC trails and barometric pressure variations observed at meteorological stations. By combining multidirectional muographic images with barometric data, we anticipate that muography will become a useful tool to monitor the three-dimensional density distribution of a targeted mesoscale convective system.
Intraoperative visual field assessment in parietal gliomas resection and the role of virtual reality headset-based mapping
Authors: Diego Molina-Botello , J. Garza-Cruz Karla , Simran Mangwani-Mordani , E. Tello-Mara Isaac , G. Mondragón-Soto Michel , O. Santellán-Hernández José , M. Aguilar-Hidalgo Keren , I. Mejía-Pérez Sonia 
Published: April 2022

Abstract
The aim of this literature review is to summarize techniques used to prevent postoperative visual pathway complications during parietal glioma resection involving optic radiations (OR), focusing on the use of virtual reality (VR) headset during awake patient surgery. We searched the Medline database for literature between the years of 1970 and 2021. Only results that included the use of AC for sensory mapping were included for evaluation. The search was limited to studies published in English and humans as subjects. Only studies that reported patient groups treated with either parietal glioma surgery under general anesthesia or awake conditions were included. Articles describing deep brain stimulation as the therapy were excluded. The variables initially selected for analysis included the length of surgery, length of hospital stay, extent of resection, cost, mortality, and neurological morbidity. Cost was later removed from the studied variables because too few studies reported it. No commentaries or reviews were included. Gliomas are the most common primary brain tumors located mainly in the cerebral cortex. 17% are found in the parietal lobe, which is a convergence area for multiple stimulus integration. After surgical resection of this lobe, patients may develop postoperative verbal, linguistic and visual field deficits. The gold standard treatment for these tumors is surgical resection. The main technique to preserve functional pathways is by intraoperative monitoring, for which different tools have been developed in the past years. Surgeons can test and preserve important tracts, such as the visual pathway. Intraoperative ultrasound has shown to be an excellent, accessible, and affordable intraoperative monitoring tool. Magnetic resonance imaging-based tractography and reality-based brain mapping allow not only intraoperative monitoring, but also create a preoperative plan by demarcating the structures and margins of the tumor prior to and during surgery, increasing success rate in maximum resection.
QSAR of SARS-CoV-2 Main Protease Inhibitors Utilizing Theoretical Molecular Descriptors
Authors: Nandi Sisir , Kumar Mohit , Saxena Anil Kumar 
Published: April 2022

Abstract
The COVID-19 caused by novel strain of severe acute respiratory syndrome coronaviruses (SARS-CoV-2), has caused fatalities around the world since the end of 2019 due to its high virulence and quick multiplicity in the human body. Hence there has been an exigency to develop effective remedial measures to mitigate the mortalities. Scientists have been able to develop few corona vaccines to provide immunity, but there are no specific small molecule chemotherapeutics to combat the novel coronavirus which has spread to the whole world due to its contagiousness. In the viral genome exploration, it has been found that the main protease also known as chymotrypsin-like cysteine protease ([Mpro] or 3C-like protease [3CLpro]) is responsible for the novel corona virus replication, transcription and host immunity destruction. Therefore, the main protease has been selected as one of the major targets for the design of new inhibitors. The protein crystallographic and molecular docking studies on SARS-CoV-2 Mpro inhibitors and some QSAR studies have been carried out on SARS-CoV main protease inhibitors to get some lead molecules for SARS-CoV-2 inhibition. But there is hardly any QSAR done on the diverse data of SARS-CoV-2 main protease inhibitors. In view of it, QSAR studies have been attempted on SARS-CoV-2 Mpro inhibitors utilizing theoretical molecular descriptors solely computed from the structures of novel corona viral main protease inhibitors. The developed best QSAR model showing R2, Q2Loo and R2pred values of 0.7389, 0.6666, and 0.6453 respectively has been further validated on external data set where a good correlation (r = 0.787) has been found. Therefore, this model may be useful for the design of new SARS-CoV-2 main protease inhibitors.
Characterization of replication and variations of genomic segments of a bat reovirus, BatMRV/B19-02 by RNA-seq in the infected Vero-E6 cells
Authors: Lo Van Thi , Yoon Sun-Woo , Noh Ji Yeong , Jang Seong Sik , Na Woonsung , Song Daesub , Jeong Dae Gwin , Kim Hye Kwon 
Published: April 2022

Abstract
Mammalian Orthoreoviruses have been isolated from a wide variety of mammalian species that can cause enteric, respiratory and encephalitis infections. We report a novel MRV type 1 detected in Miniopterus schreibersii may have resulted from reassortment events. Using next-generation sequencing RNA-seq, we found that the ratios of relative abundances in RNA levels of the ten reovirus segments are constant during the late stages of infection in infected cells. We also discovered that the related RNA abundance level of each gene differed. Remarkably, the relative abundances of total RNA of M2 (coding µ1 protein) and S4 (coding σ3 protein) genes were higher than others throughout infection time. In addition, massive junctions were defined. These are evidence to support the hypothesis of generating defective genome segments and cross-family recombination mechanisms. These findings may support further the study of gene function, viral replication and virus evolution in the host.
Effect of MTHFR C677T gene polymorphism on folic acid intervention in Chinese hypertensive patients：a multicentered, randomized, double-blind, clinical trial
Authors: Zou JianF , Zhang Yan , Tang Lei , Shi XiuL , Chen GuiM , Zhang Xu , Xu YaP , Zhang RuS , Wang Rui , Wu Qian , Tang GenF 
Published: April 2022

Abstract
Objectives To describe the changes in serum folate concentration and assess the influence of individual methylenetetrahydrofolate reductase (MTHFR) C677T on the changes of serum folate concentration that resulted from 8 weeks of supplementation with folic acid in Chinese hypertensive patients.Methods We conducted a multicenter, randomized, double-blind controlled clinical trial of different dosages folate supplementation in Chinese hypertensive patients.A total of 1657 patients with mild or moderate essential hypertension were randomly assigned to one of eight treatment groups corresponding to eight different doses of folic acid, ranging from 0 mg to 2.4 mg,once daily for 8 weeks. Individual serum folate levels were measured at baseline, and at 4 and 8 weeks posttreatment.Results compared with patients with 677CC genotype, those with TT genotype had significantly lower folate concentrations at baseline.After 4 or 8 weeks of treatment, increases in serum folate were seen across all genotypes and FA dosage groups. At 8 weeks posttreatment ,there was no statistically significant difference in folate levels between groups according genotypes,and patients with CC genotype showed an attenuated response compared with those with TT genotype.( CC,0.45 vs. TT,0.56 ,P< 0.05).Conclusion We demonstrated that MTHFR C677T polymorphisms affected folate levels at the baseline and the therapeutic response of folic acid intervention. Patients with TT genotype benefited more after folic acid supplementation in Chinese hypertensive population.
Dynamics of mitochondrial nucleoid proteins involved in development of cotyledon mitochondria during mung bean seed germination
Authors: Cheng Ning , Lo Yih-Shan , Lin Na-Sheng , Dai Hwa 
Published: April 2022

Abstract
Mitochondrial DNA (mtDNA) protein complexes, called mitochondrial-nucleoids (mt-nucleoids), are dynamic and redistribute during mitochondria propagation and gene expression. These proteins involve in mtDNA replication, transcription, maintenance and repair. In this study, we analyzed mt-nucleoid proteins in isolated mt-nucleoids from cotyledons at different developmental ages. We aimed to understand the changes in mt-nucleoids associated protein during cotyledon development. We found that some transcription/translation factors pre-exist in nucleoids of dormant seed mitochondria. High numbers of metabolic proteins co-purified with mtDNA appeared in dormant seeds and developmental cotyledon mitochondria. This report provides some idea about the dynamic of mt-nucleoid proteins along with cotyledon mitochondrial development during seed germination.
High-Density Individually Addressable Platinum Nanoelectrodes for Neuroscience Applications
Authors: Raj Vidur , Gopakumar Aswani , Vaidya Gayatri , Scott John , Toth Milos , Jagadish Chennupati , Gautam Vini 
Published: April 2022

Abstract
3-D vertical nanoelectrode arrays (NEAs) have found application in several biomedical and sensing applications, including high-resolution neuronal excitation and measurement and single-molecule electrochemical biosensing. There have been several reports on high-density nanoelectrodes in recent years, with the filling ratio of electrodes close to 0.002 (assuming the electrode diameter of 200 nm and pitch of 4 µm). Still, it is well below the nanowire filling ratio required to form interconnected neuronal networks, i.e, more than 0.14 (assuming the electrode diameter of 200 nm and pitch of 1.5µm). Here, we employ a multi-step, large-area electron beam lithography procedure along with a targeted, focused ion beam based metal deposition technique to realize an individually addressable, 60-channel nanoelectrode chip with a filling ratio as high as 0.16, which is well within the limit required for the formation of interconnected neuronal networks. Moreover, we have designed the NEA chip to be compatible with the commercially available MEA2100-System, which can in the future enable the chip to be readily used for obtaining data from individual electrodes. We also perform an in-depth electrochemical impedance spectroscopy characterization to show that the electrochemical behavior and the charge transfer mechanism in the array are significantly influenced by changing the thickness of the SU-8 planarization layer (i.e., the thickness of exposed platinum surface). In addition to neural signal excitation and measurement, we propose that these NEA chips have the potential for other future applications, such as high-resolution single-molecule level electrochemical and bio-analyte sensing.
Molecular and morphological evidences for hybrid origin of Kushui Rose
Authors: Zhang Hui , Zhao Fan , Wang Ying , Zhang Yu-jie , Sun Kun , Da Ling-Ling 
Published: April 2022

Abstract
Natural hybridization plays a significant role in evolution of the genus of Rosa, e.g., Kushui Rose (R. Sertate x R. Rugosa) is always considered as a natural hybrid of R. sertata and the cultivated rose R. rugosa. In order to test the hybrid origin of Kushui Rose, we conducted molecular sequences analysis and morphological traits examination in its related taxa in the genus. Although Principal component analysis (PCA) of Morphological characteristics revealed Kushui Rose was intermediate between R. rugosa and R. willmottiae, and also and R. sertata, but the unambiguous sequence additivities of nuclear DNAs (ITS and GAPDH) as well as the incongruence between nuclear and chloroplast gene trees revealed the hybrid origin of Kushui Rose from R. rugosa and R. willmottiae rather than R. sertata. Further, the cluster relationships in concatenated chloroplast (cpDNA) trees (psbA-trnH, trnL-F, and trnS-G) implied that R. willmottiae and R. rugosa respectively acted as its maternal parent and paternal parent during its homoploidization speciation. Here our study could provide a more reasonable orientation for further study in conservation biology of the hybrid species as well as in its agronomy traits with heterosis effect.
A feature selection based parallelized CNN-BiGRU network for speech emotion recognition in Odia language
Authors: Maji Bubai , Swain Monorama , Panda Rutuparna 
Published: April 2022

Abstract
Emotion recognition from speech is an integral part of human interaction. This paper represents work that includes the creation and evaluation of speech emotion recognition on the Odia database. Previous research in this field implemented several benchmark datasets. In this work, we use two benchmark datasets for cross-validation with our own created Odia dataset name as SITB-OSED. Initially, the spectral, prosodic, and voice quality features are extracted from a raw audio file; secondly, a Gradient Boost Decision Tree (GBDT) feature selection method is used to remove all the redundant features and select the potential features. Here, two distinct series of experiments are performed. Firstly, the baseline model, which takes all the combined selected features, is chosen as input (spectral, prosodic, and voice quality features). Secondly, the proposed model processes all the selected features through two separate channels, the Convolutional neural network (CNN) and Bi-directional gated recurrent units (Bi-GRU). Specifically, the proposed method achieved 6.67%, 6.03%, and 5.55% higher accuracy than the baseline model on the Ryerson Audio-Visual Database of Emotional Speech and Song (RAVDESS) Interactive Emotional Dyadic Motion Capture (IEMOCAP) and SITB-OSED datasets. We also report that the proposed parallelized CNN-BiGRU model outperforms the recent state-of-the-art methods with an accuracy of 82.29% and 78.54% on the RAVDESS and IEMOCAP datasets, respectively. For our SITB-OSED dataset, the overall recognition accuracy of 84.02% is achieved.
Free-field soil response to bidirectional horizontal non-uniform ground motion from multi-point shaking table tests
Authors: Han Junyan , Guo Zhike , Zhong Zilan , Naggar M.Hesham El , Miao Huiquan , Du Xiuli 
Published: April 2022

Abstract
This paper assesses the dynamic nonlinear free-field soil response under bidirectional horizontal non-uniform excitation through a series of multi-point 1g shaking table tests. The soil bed was enclosed in an innovative soil box supported by an array of three shake tables and was subjected to uniform and non-uniform ground motions in one and two horizontal directions. The soil response to bidirectional and unidirectional excitations, both uniform and non-uniform, were compared and discussed in terms of acceleration time history and Fourier spectra, acceleration amplification factor and soil settlement, as well as shear stress-shear strain behavior. The comparison of soil responses to bidirectional and unidirectional shakings demonstrated that the trends of peak acceleration amplification factors are similar along soil depth, but the response difference to bidirectional and unidirectional shaking is increasingly higher along the soil profile towards the ground surface, especially for uniform excitation. The variations of soil settlement, shear stress-strain and damping curves under bidirectional excitation were similar to that under longitudinal excitation; however, they were much different than those observed under transverse excitation. The soil damping in Y-direction under non-uniform excitation was larger than that under uniform excitation. These different site response characteristics under bidirectional non-uniform excitation should be properly considered in the seismic design of extended infrastructure.
Depression in an over-55 years old community-dwelling elderly healthy population: from prevalence to social-economic state, lifestyle and Nutrients – A population-based study
Authors: Moghadam Mohammad Reza Shadmand Foumani , Etemadi Sharif , Jandari Sajedeh , Rashidipour Mina , Bakhshipour Reyhane , Amushahi Mohammad , Pezeshki Parnian , Hosseini Zohreh 
Published: April 2022

Abstract
Background: The older adults are increasing and depression is commonly observed within this community. This study is one of the first that assessed depression and its risk factors in a healthy well-nourished over-55 years old population. Method: Beck Depression Inventory-13 (BDI-13) was used to determine depression in 766 individuals. a full report of socioeconomic factors was gathered. Lifestyle and physical activity were assessed using Health Survey Questionnaire 36-Item Short-Form and International Physical Activity Questionnaire, respectively. The dietary nutrient intake was recorded using an adjusted dietary recall analyzed using the USDA Food Ingredients Database. Result: The prevalence of depression was 31.5% (62.5±6.6 years old). One hundred and thirty-two (17.2%), 93 (12.1%), and 19 (2.5%) individuals had mild, moderate, or severe depression. Males, higher age, not working, higher education, inactivity, living alone, lower-income, divorced, and widows had a higher odd-ratio (OR) of depression. lifestyle shows a 1% higher quality of life score in any component can have 3.8-1.1% significantly lower OR of depression. Trance fatty acids, starch, iron, and copper that are generally increased during oil reheating showed a higher OR for having depression. The correlation of quality of lifestyle components with the severity of depression (BDI-13 score) was the strongest and negative while the weakest correlation was for nutrients with BDI-13 score. Conclusion: The risk of depression in healthy populations is high. Active lifestyle and healthy diet with the presence of family can reduce OR of depression in elderly populations. Food processes can be more important than diet.
Supraclavicular irradiation is a risk factor of lymphedema in breast cancer patients treated with axillary lymph node dissection and taxane-containing regimens
Authors: Horisawa Nanae , Yoshimura Akiyo , Oze Isao , Sawaki Masataka , Hattori Masaya , Haruru Kotani , Kataoka Ayumi , Ozaki Yuri , Nozawa Kazuki , Endo Yuka , Takatsuka Daiki , Isogai Ayaka , Iwata Hiroji 
Published: April 2022

Abstract
Purpose: Breast cancer-related lymphedema (LE) significantly impairs the patients’ quality of life. Axillary lymph node dissection (ALND) is a strong risk factor for LE in breast cancer surgery. In addition, postoperative administration of docetaxel (DTX) has been reported to be a risk factor for LE in patients who undergo ALND. Herein, we performed a secondary analysis of the risk of objective LE after ALND using data from our previous study.Methods: Patients who visited the medical follow-up clinic between 12 November 2018 and 11 January 2019 and at least one year postoperatively were eligible for this study. Objective LE was defined as a difference of at least 2 cm between the affected and unaffected arms or when therapeutic intervention had already been performed for LE. The risk factors for objective LE according to taxane-containing regimen, radiation therapy, and body mass index and the effects of a taxane-containing regimen followed by supraclavicular irradiation on LE were examined.Results: Objective LE was observed in 52 patients (24%). Univariate and multivariate analyses showed that supraclavicular field irradiation was a statistically significant risk factor for objective LE. The sequential use of taxane-containing regimen and supraclavicular RT was more likely to be a risk factor for LE than ALND alone.Conclusion: The risk for LE was more likely to be higher with the sequential use of taxane-containing chemotherapy and supraclavicular field irradiation. Therefore, management of LE is important these cases.