bluuebunny/crossref_metadata_2025_split huggingface dataset:
Profiling and Bioinformatics Analyses of Differential Circular RNA Expression in Glioblastoma Multiforme Cells under Hypoxia
Authors: Chen Zheng , Su Shaohua , Yang Min , Wang Fei , Chen Ming 
Published: July 2022

Abstract
Background
The hypoxia microenvironment is highly associated with GBM’s malignant phenotypes. CircRNAs were reported involved in GBM’s biological characteristics and regulated by HIF-1α. However, the differential expression profile and role of circRNAs in GBM cells under hypoxia are still unclear.
Methods
The expression profiles of circRNAs in LN229 and T98G under hypoxia were explored via circRNA sequencing analysis. Those circRNAs significantly dysregulated both in LN229 and T98G, and could be found in circBase were selected and validated by qRT-PCR, RNase R digestion reaction and Sanger sequencing. Normal cell line and fresh GBM tissues were also used for qRT-PCR validation. The roles of differentially expressed circRNAs were evaluated by bioinformatics analyses.
Results
There were 672 dysregulated circRNAs in LN229 and 698 dysregulated circRNAs in T98G. GO analysis indicated that the alteration of circRNAs expression related to GBM cell’s biogenesis and metabolism. KEGG analysis demonstrated that TGF-β signaling pathway, HIF-1 signaling pathway and metabolism related signaling pathway were closely associated with differentially expressed circRNAs under hypoxia. These results were confirmed by GSEA analysis. The 6 selected and dysregulated circRNAs both in LN229 and T98G including hsa_circ_0000745, hsa_circ_0020093, hsa_circ_0020094, hsa_circ_0000943, hsa_circ_0004874 and hsa_circ_0002359 were validated by qRT-PCR. Inhibition of hsa_circ_0000745 inhibited GBM cell’s proliferation, migration and invasion. HIF-1α centered circRNA-miRNA-mRNA networks analysis showed that the 6 validated circRNAs could cross-talk with 11 related miRNAs.
Conclusion
The circRNA expressions are dysregulated in GBM cell under hypoxia. The 6 validated circRNAs could participate in GBM’s development and progression when hypoxia occurs. They might be the candidates for prognostic markers and adjuvant therapeutics of GBM in the future.
A New hydrocarbon Prospect Determination Through Seismic Interpretation and Petrophysical Evaluation of Bahariya Reservoir in Nader field, North Western Desert, Egypt
Authors: Metwalli Farouk I. , Basheer Alhussein Adham , Amin Ahmed Taha , El-Dabaa Shaimaa A. 
Published: July 2022

Abstract
The goal of this research is to carry out a subsurface and petrophysical investigation to estimate the petroleum potential of the Bahariya reservoir in the Nader Field of the Khalda Ridge concession in Egypt's northwestern desert. This study depends on using the composite logs for four wells, Nader-1, Nader-2, Nader-4, and Nader-8, and twenty (2D) seismic lines. The Bahariya Formation unconformably underlies and overlies the Abu Roash and Kharita formations, respectively. The Upper and Lower Bahariya formations were evaluated as the petroleum sandstone reservoirs in the studied field. Seismic interpretations were used to clarify the structural settings on the tops of these formations. These formations' time-and-depth-structure maps reveal a variety of structural features which aid in prospect identification and hydrocarbon potential in the area. The petrophysical evaluation involves lithology identification, reservoir pressure measurements, and determinations of petrophysical parameters such as effective porosity (PHIE), net-pay thickness, water saturation (Sw), shale content (Vsh), and hydrocarbon saturation (Sh). The results of this study revealed three new proposed locations to the southeast and north of the investigated Nader field. These locations are located on appropriate structures and on four- or three-way dip structural closures that are suitable for petroleum accumulations. They also have a decrease in Vsh and Sw, and an increase in net pay, PHIE, and Sh for the Upper and Lower Bahariya reservoirs. As a result, it is advised to concentrate exploration efforts on new promising locations for more economical petroleum discoveries.
Development and Validation of a Hypoxia - Related Prognostic Signature for Uveal melanoma
Authors: Lin Kunxia , Zheng Mi , Xu Nuo 
Published: July 2022

Abstract
Background: Uveal melanoma (UM) is the most common ocular malignancy in adults. Increasing evidence suggests that the hypoxic microenvironment is closely associated with tumor. However, there are few studies on the correlation between hypoxia-related genes and UM patient’s prognosis. Our study aimed to identify the prognostic hypoxia-related genes and construct a prognostic model to predict the prognosis overall survival of UM patients. Method: We obtained 80 UM patients from The Cancer Genome Atlas (TCGA) with RNA sequence data and from UCSC Xena with corresponding clinical information. Protein-protein interaction (PPI)network and regression analysis were conducted to identify prognostic genes and develop the prognostic hypoxia-related model. The accuracy of the model was assessed by the receiver operating characteristic (ROC) curve and K-M survival curve. The GSE22138 dataset was downloaded from GEO as a validation.Results: We identified 2 prognostic hypoxia-related genes, including ENO3 and PFKP. The prognostic model composed of 2 hypoxia-related genes had high accuracy and independence in predicting the prognosis of UM patient’s prognosis. Additionally, GSEA showed that biological processes related with tumor cell growth, energy metabolism, invasion and diffusion were remarkably activated enriched in the high-risk subgroup, including hypoxia, β-TGF, angiogenesis, glycolysis, apoptosis, etc. Further immune infiltration analysis revealed that the hypoxia risk score was related with immunosuppression and high-risk patients had higher immune scores and lower tumor purity compared with the low-risk patients.Conclusions: We constructed a hypoxia-related model, which had independent prognostic value for the overall survival of UM patients.
Vibration suppression mechanism of ultrasonic field energy
Authors: Lianjun Sun , Liao Wenhe , Kan Zheng , Song Dong , Tian Wei , Zhenwen Sun , Jing Shu , Feng Xue 
Published: July 2022

Abstract
For complex systems, the inhibition of self-excited vibration has always been a difficulty in engineering field. Currently, ultrasonic field energy as a special field energy could suppress vibration significantly. Unfortunately, vibration suppression mechanism has not been elucidated and intrinsic association with vibration field is still ambiguous. Here, we clarify coupling mechanism of ultrasonic field energy and unsteady vibration field energy firstly from the perspective of energy transfer and distribution. We find that it realizes spatially controllable redistribution of vibration field by changing distribution law of excitation waves, which makes vibration frequency migrate across scales. On this basis, we establish a relationship model between ultrasonic field energy and vibration field energy innovatively to accomplish precise vibration suppression. These insights generate important significance for active vibration suppression, which have broad applicability in flexible precision manufacturing, vibration inhibition of aircraft or satellite solar array, high-precision medical equipment and rail traffic stability control.
Compositional properties and codon usage pattern of mitochondrial cytochrome c oxidase I gene among Potamidids
Authors: Shabani Zulfa I. , Mfilinge Prosper L. , Mpenda Fulgence N. 
Published: July 2022

Abstract
Codon usage bias refers to the phenomenon where there is unequal occurrence of specific synonymous codons in a genome, the frequency of which varies within and among species. Molecular evolutionary researches suggest that CUB studies are significant in interpreting evolutionary trends of species or genes. A number of studies on codon usage bias are emerging in different organisms. However, such information remained unclear for organisms in the family Potamididae. This study systematically examined compositional features and codon usage patterns in MT-COI gene among potamidids to identify factors shaping codon usage bias. Quantification of codon usage bias and the identification of causative factors was performed by assessing various parameters such as nucleotide composition, effective number of codons (ENC), relative synonymous codon usage (RSCU), parity rule (PR2) analysis, neutrality plot analysis as well as a multivariate statistical approach of correspondence analysis (CoA). The results from neutrality plot suggested that natural selection is the dominant evolutionary factor for CUB in MT-COI gene among the different genera of potamidids. Correspondence analysis (CoA), parity plot and ENC analyses indicated the existence of mutational pressure with minor contribution. Nucleotide composition investigations indicated that, most codons are AT rich, with T nucleotides count being highly presented. Thus, compositional restraint was shown as among the reasons behind the pattern of codon usage in MT-COI gene of species in the family Potamididae.
Molecular Docking and In-vitro Evaluation of Apoptotic Effect of Novel Synthetic Organocopper Derivative in Human Breast Cancer Cell line as Anticancer Agent
Authors: Darwish Noura M , Saleh Abdulrahman M. , Hemdan Shimaa Badawy , Abdallah Ahmned Alamir Mahmoud 
Published: July 2022

Abstract
Conventional therapies have low effectiveness to fulfill results in breast cancer mortality. Organo-copper compounds exhibit cytotoxic activity against a variety of cancer cell lines. we investigated the anti-proliferative effect of the supramolecular coordination polymer (SCP) [CuCN./ Me3SnCN./pyz] (pyz./pyrazine ] in two breast cancer cell lines (T-47D: Breast ductal carcinoma and MDA-MB-231: breast cancer). the in vitro cytotoxic activity was evaluated using the MTT assay. To examine the possible relation between the cytotoxic activity of the SCP and oxidative stress, we measured ROS levels in both human breast cell lines. Changes in apoptotic gene expression were detected by RT-PC R and confirmed using western blot analysis. We did the molecular docking to evaluate and know how SCP interacts with the selected target, the target selection was based on the common essential pharmacophoric features between the crystal ligand, doxorubicin, and SCP. SCP manifested anti-proliferative activities in both T-47D cells and MDA-MB-231 cells. The antitumor activity of SCP was studied at concentrations of IC50. Analysis revealed decreased Bcl2 and increased P53 mRNA, suggesting that SCP exerts its regulatory action on apoptotic genes at the level of transcription. SCP-induced tumor cell apoptosis was attributed to activation of both caspase-3 and caspase-9 regulated pathways. Furthermore, based on the resulted data obtained from the molecular docking, SCP more interacting and binding with the target pocket compared with the crystal ligand and doxorubicin. the supramolecular coordination polymer (SCP) showed an antitumor effect and could be a promising candidate for the management of breast cancer patients.
Long-term prognostic role of elevated soluble suppression of tumorigenicity 2 in acute myocardial infarction: A meta-analysis including 11387 patients
Authors: Chen Jing , Ji Hai-gang , Jiang Wen-bo 
Published: July 2022

Abstract
The soluble suppression of tumorigenicity 2 (sST2) can be used to predict the long-term prognosis of acute myocardial infarction (AMI). However, the prognostic role of sST2 in AMI is unclear. This meta-analysis aimed to evaluate the association between sST2 and long-term clinical outcomes of AMI patients. Relevant literature was retrieved from PubMed, Embase, the Cochrane Library, and Web of Science databases. Meta-analysis was performed using hazard ratio (HR) and 95% confidence intervals (CIs) as effect measures. Thirteen studies with 11571 patients were finally included in the meta-analysis. Elevated sST2 predicted a poor outcome for all-cause mortality with a combined HR of 2.40 (95% CI: 1.64–3.51, P < 0.001) and major adverse cardiac events (MACEs) with the combined HR of 2.57 (95% CI: 1.56–4.24, P < 0.001). Subgroup analysis revealed that elevated sST2 was positively correlated with all-cause mortality and MACEs in the STEMI, NSTEMI, and unselected AMI subgroups. These results suggest that elevated sST2 can predict long-term prognosis for AMI patients.
Subsequence and Distant Supervision based Active Learning for Relation Extraction of Chinese Medical Texts
Authors: Ye Qi , Cai Tingting , Ruan Tong , Zheng Hong 
Published: July 2022

Abstract
Background: In recent years, relation extraction from unstructured texts has become an important task in medical research. However, relation extraction requires a large amount of labeled corpus, manually annotating sequences is time consuming and expensive. Therefore, efficient and economical methods for annotating sequences are required to ensure the performance of relational extraction. Methods: This paper proposes a method of subsequence and distant supervision based active learning. The method is annotated by selecting information-rich subsequences as a sampling unit instead of the full sentences in traditional active learning. Additionally, the method saves the labeled subsequence texts and their corresponding labels in a dictionary which is continuously updated and maintained, and pre-labels the unlabeled set through text matching based on the idea of distant supervision. Finally, the method combines a BERT-CRF model for relation extraction in Chinese medical texts. Results: Experimental results test on the CMeIE dataset that it achieves the best results compared to existing methods. And the best F1 values are obtained in different sampling strategies, which are 52.65%, 52.55% and 51.37% respectively.
Characterizing microbial community viability with RNA-based high-throughput sequencing
Authors: Wang Ya , Thompson Kelsey N. , Yan Yan , Short Meghan I. , Zhang Yancong , Franzosa Eric A. , Shen Jiaxian , Hartmann Erica M. , Huttenhower Curtis 
Published: July 2022

Abstract
BackgroundCharacterization of microbial viability is essential to the understanding of the basic biology of microbial communities, as the function of a microbiome is defined by its biochemically active (“viable”) community members. Current sequence-based technologies can rarely differentiate microbial viability, due to their inability to distinguish live and dead sourced DNA. As a result, our understanding of microbial community structures and the potential mechanisms of transmission between humans and our surrounding environments remains incomplete. As a potential solution, 16S rRNA transcript-based amplicon sequencing (16S-RNA-seq) has been proposed as a reliable methodology to characterize the viable components of a microbiome, but its efficacy has not been evaluated systematically. Here, we present our work to benchmark RNA-based amplicon sequencing for viability assessment in synthetic and environmentally-sourced microbial communities. ResultsIn synthetic mixtures of living and heat-killed Escherichia coli and Streptococcus sanguinis, 16S-RNA-seq successfully reconstructed the viable compositions of the communities. However, in the realistic environmental samples no significant compositional differences were observed in RNA (“actively transcribed - viable”) vs. DNA (“whole” communities) spiked with E. coli viability controls, suggesting that this methodology is not appropriate for viability assessment in complex communities. The results were slightly different when validated in environmental samples of similar origins (i.e., from Boston subway systems), where samples were differentiated both by environment type as well as by library type, though compositional dissimilarities between DNA and RNA samples remained low (Bray-Curtis distance median: 0.34-0.49). To improve the interpretation of 16S-RNA-seq results, we compared our results with previous studies and found that 16S-RNA-seq suggests taxon-wise viability trends (i.e. specific taxa are universally more or less likely to be viable compared to others) in samples of similar origins. ConclusionsThis study provides a comprehensive evaluation of 16S-RNA-seq for viability assessment in synthetic and complex microbial communities. The results found that while 16S-RNA-seq was able to semi-quantify microbial viability in relatively simple communities, it only suggests a taxon-dependent “relative” viability in realistic communities.
Cost-Effective Library Preparation for Whole Genome Sequencing with Feather DNA
Authors: Schweizer Teia M. , DeSaix Matthew G. 
Published: July 2022

Abstract
Samples from avian species of high conservation concern are often low in total genomic DNA (gDNA). Feathers are collected more frequently than blood, yet they contain low total gDNA which can present challenges in using them for genomics. Whole Genome Sequencing (WGS) can provide many insights that can be used to aid in species conservation, but current methods for working with feathers are cost prohibitive for population level genomic analyses. Thus, there is a need for a cost-effective method of preparing WGS libraries from feathers. To bridge the gap between sampling techniques commonly used in avian conservation genetics that yield low total gDNA and the powerful tool of WGS, we developed a method that successfully produces WGS libraries from feather gDNA with as low input as 0.48 ng of DNA and an average final library size of 300–500 base pairs. Sequencing results suggest high sequencing quality using our protocol with feather DNA. We conclude that our method will facilitate high-throughput WGS on low total gDNA samples, like feathers, thus expanding the power of genomic tools in critical avian conservation research.
On improving Cheng’s backpropagation for fully connectedcascade networks
Authors: Mizutani Eiji , Kubota Naoyuki , Truong Tam 
Published: July 2022

Abstract
In this journal, Cheng has proposed a backpropagation (BP) procedure calledBPFCC for deep L-stage fully connected cascaded (FCC) neural network learning in comparisonwith a neuron-by-neuron (NBN) algorithm of Wilamowski and Yu; yet, Cheng apparentlyneglected two major points of the NBN algorithm: (1) the merit of NBN is emphasizedon the multiple q-output (q > 1) case; and (2) NBN is described for a q-outputFCC different in structure from Cheng’s FCC type. In nonlinear regression (for minimizingthe sum of squared residuals), NBN employs forward passes only on the q-output FCC toevaluate the Gauss-Newton (approximate Hessian) matrix ∇rT∇r, the cross product of theJacobian matrix ∇r of the residual vector r. Notably, both BPFCC and NBN are designedto reduce the cost for evaluating (q rows per datum of) the Jacobian matrix ∇r rather thanthe dominant cost for forming the cross product ∇rT∇r by rank updates. The purpose ofthis paper is to present a new BP procedure that exploits the special FCC network structureof Cheng’s type for reducing the dominant cost (with no rows of ∇r explicitly), evaluatingthe Gauss-Newton matrix efficiently in a block arrow matrix form when q > 1.
Pricing American Options under Irrational Behavior with Numerical Approach
Authors: Rohi Mohammad Saber , Azari Hossein , Heidari Saghar 
Published: July 2022

Abstract
In this paper, we consider the pricing problem of American options under an irrational exercise strategy with a rationality parameter. Irrational behavior of option holders as reactions to market movements can lead to an exercising option strategy at a time that might not be an optimal time. Under the irrational exercising time strategy, the pricing problem of the American-style option results in the overvalued option price. A common way to study the irrational behavior of option holders and its impact on the American option pricing problem is to consider intensity-based models with stochastic intensity parameters. Under these models, the option pricing problem leads to a nonlinear parabolic partial differential equation (PDE) with an additional term to the PDE of the American option under rational strategy (classical American option with optimal exercise strategy) due to the intensity functions of models. Although the solution converges to the solution of the classical American option price when the parameter tends to infinity, the classical boundary conditions cannot apply to finite values of the parameter. For this, we propose a finite element method to solve the resulted PDE with a numerical approach. We also present numerical results to show the accuracy of the proposed method.
Variability of polyteny of giant chromosomes in Drosophila melanogaster salivary glands
Authors: Strashnyuk Volodymyr Yu. , Shakina Lubov A. , Skorobagatko Daria A. 
Published: July 2022

Abstract
Polyteny is an effective mechanism for accelerating growth and enhancing gene expression in eukaryotes. The purpose of investigation was to study the genetic variability of polyteny degree of giant chromosomes in the salivary glands of Drosophila melanogaster Meig. in relation to the differential fitness of different genotypes. 16 strains, lines and hybrids of fruit flies were studied. This study demonstrates the significant influence of hereditary factors on the level of polytenization of giant chromosomes in Drosophila. This is manifested in the differences between strains and lines, the effect of inbreeding, chromosome isogenization, hybridization, adaptively significant selection, sexual differences, and varying degrees of individual variability of a trait in different strains, lines, and hybrids. The effect size of the genotype on the degree of chromosome polyteny in Drosophila salivary glands was 45.3%, the effect size of sex was 9.5%. The data obtained allow us to conclude that the variations in the level of polyteny should be considered as a manifestation of the structural and functional polymorphism of giant chromosomes, which is an essential factor in the differential fitness of flies and has a selective value.
Rare Dizziness, Syncope, Loss of Consciousness, Seizure, and Risk of Falling after Vaccination
Authors: Ricke Darrell O. 
Published: July 2022

Abstract
Some individuals experience dizziness, syncope (temporary loss of consciousness caused by a fall in blood pressure), seizure, and similar rare adverse events after vaccination. Sudden impacts to alertness, consciousness, ability to talk, vision, or balance may pose rare risks for some vaccinees for a few days post vaccination. Herein, the Vaccine Adverse Event Reporting System (VAERS) database is examined for relevant adverse events. These adverse events exhibit a consistent pattern of onset soon after vaccination consistent with other reported reactogenicity adverse events. The onset of these adverse events soon after vaccination provides supportive evidence to reject the hypothesis that the majority of these adverse events represent background occurrences. The immediate onset timing of these adverse events represent a pattern that warrants further study. The observed onset pattern for multiple unrelated vaccines are consistent with the possible etiology of innate immune responses to vaccination as causative for these observed adverse events. Cautionary avoidance of some activities immediately following vaccination may reduce accidental injuries.