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Mitigating the Multicollinearity Problem and Its Machine Learning Approach: A Review
Technologies have driven big data collection across many fields, such as genomics and business intelligence. This results in a significant increase in variables and data points (observations) collected and stored. Although this presents opportunities to better model the relationship between predictors and the response variables, this also causes serious problems during data analysis, one of which is the multicollinearity problem. The two main approaches used to mitigate multicollinearity are variable selection methods and modified estimator methods. However, variable selection methods may negate efforts to collect more data as new data may eventually be dropped from modeling, while recent studies suggest that optimization approaches via machine learning handle data with multicollinearity better than statistical estimators. Therefore, this study details the chronological developments to mitigate the effects of multicollinearity and up-to-date recommendations to better mitigate multicollinearity.
Journal Article
The Cult of the Apollonian and the Dionysian in Ancient Greek Religion as Reflected in Edith Wharton’s Novels
The two basic conflicting forces throughout Wharton’s tragic novels have a great affinity with the cult of the Apollonian and Dionysian in ancient Greek religion and in Nietzsche’s The Birth of Tragedy. On the one hand, it is the Apollonian ideal of civilized society and individual restraint, which is a beautiful illusion maintained in a bright appearance. When it encounters Dionysus, it is its defensive social rules, the social restrictions, and oppression it imposes on individuals; on the other hand, it is the awakening of Dionysian primitive passion, which tears off the social and individual protective veil of Apollo and reaches the Dionysian tragic cognition at the root of existence, requiring breaking social barriers and indulging the vitality of primitive nature. In this paper, the cult of the Apollonian and Dionysian in ancient Greek religion and as defined by Nietzsche in his The Birth of Tragedy is used to analyze the inner conflicts in the protagonists of Wharton’s tragic novels and the patterns of tragedy in each of her studied novels. Through such archetypal criticism of religious cults in Wharton’s major works, this paper attempts to refute most of the negative criticism of her novels.
Journal Article
Ferroptosis-Related Long Non-Coding RNA signature predicts the prognosis of Head and neck squamous cell carcinoma
: Head and neck squamous cell carcinoma (HNSCC) are head and neck cancers. On the other hand, ferroptosis is a novel iron-dependent and ROS reliant type of cell death observed various disease conditions.
: We constructed a prognostic multilncRNA signature based on ferroptosis-related differentially expressed lncRNAs in HNSCC.
: We identified 25 differently expressed lncRNAs associated with prognosis of HNSCC. Kaplan-Meier analyses revealed the high-risk lncRNAs signature associated with poor prognosis of HNSCC. Moreover, the AUC of the lncRNAs signature was 0.782, underscoring their utility in prediction HNSCC prognosis. Indeed, our risk assessment model was superior to traditional clinicopathological features in predicting HNSCC prognosis. GSEA revealed the immune and tumor-related pathways in the low risk group individuals. Moreover, TCGA revealed T cell functions including cytolytic activity, HLA, regulation of inflammationp, co-stimulation, co-inhibition and coordination of type II INF response were significantly different between the low-risk and high-risk groups. Immune checkpoints such as PDCD-1 (PD-1), CTLA4 and LAG3, were also expressed differently between the two risk groups.
A novel ferroptosis-related lncRNAs signature impacts on the prognosis of HNSCC.
Journal Article
Oxidative Stress in Radiation-Induced Cardiotoxicity
There is a distinct increase in the risk of heart disease in people exposed to ionizing radiation (IR). Radiation-induced heart disease (RIHD) is one of the adverse side effects when people are exposed to ionizing radiation. IR may come from various forms, such as diagnostic imaging, radiotherapy for cancer treatment, nuclear disasters, and accidents. However, RIHD was mainly observed after radiotherapy for chest malignant tumors, especially left breast cancer. Radiation therapy (RT) has become one of the main ways to treat all kinds of cancer, which is used to reduce the recurrence of cancer and improve the survival rate of patients. The potential cause of radiation-induced cardiotoxicity is unclear, but it may be relevant to oxidative stress. Oxidative stress, an accumulation of reactive oxygen species (ROS), disrupts intracellular homeostasis through chemical modification and damages proteins, lipids, and DNA; therefore, it results in a series of related pathophysiological changes. The purpose of this review was to summarise the studies of oxidative stress in radiotherapy-induced cardiotoxicity and provide prevention and treatment methods to reduce cardiac damage.
Journal Article
The role of ferroptosis in breast cancer patients: a comprehensive analysis
Breast cancer (BC) affects the breast tissue and is the second most common cause of mortalities among women. Ferroptosis is an iron-dependent cell death mode that is characterized by intracellular accumulation of reactive oxygen species (ROS). We constructed a prognostic multigene signature based on ferroptosis-associated differentially expressed genes (DEGs). Moreover, we comprehensively analyzed the role of ferroptosis-associated miRNAs, lncRNAs, and immune responses. A total of 259 ferroptosis-related genes were extracted. KEGG function analysis of these genes revealed that they were mainly enriched in the HIF-1 signaling pathway, NOD-like receptor signaling pathway, central carbon metabolism in cancer, and PPAR signaling pathway. Fifteen differentially expressed genes (ALOX15, ALOX15B, ANO6, BRD4, CISD1, DRD5, FLT3, G6PD, IFNG, NGB, NOS2, PROM2, SLC1A4, SLC38A1, and TP63) were selected as independent prognostic factors for BC patients. Moreover, T cell functions, including the CCR score, immune checkpoint, cytolytic activity, HLA, inflammation promotion, para-inflammation, T cell co-stimulation, T cell co-inhibition, and type II INF responses were significantly different between the low-risk and high-risk groups of the TCGA cohort. Immune checkpoints between the two groups revealed that the expressions of PDCD-1 (PD-1), CTLA4, LAG3, TNFSF4/14, TNFRSF4/8/9/14/18/25, and IDO1/2 among others were significantly different. A total of 1185 ferroptosis-related lncRNAs and 219 ferroptosis-related miRNAs were also included in this study. From the online database, we identified novel ferroptosis-related biomarkers for breast cancer prognosis. The findings of this study provide new insights into the development of new reliable and accurate cancer treatment options.
Journal Article
A meta-analysis of the impact of COVID-19 on liver dysfunction
Background
The novel coronavirus disease 2019 (COVID-19), which is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is leading to a worldwide pandemic. Except representative manifestation of pneumonia and acute respiratory symptoms, COVID-19 patients have also shown different levels of liver injury or liver dysfunction. The aim of our study was to explore the probable clinical severity and mortality of COVID-19 patients and their liver dysfunction.
Method
A combination of computer and manual retrieval was used to search in Medline through PubMed, EMBASE and Web of Science. Review Manager 5.3 software was used to examine the heterogeneity among the studies and to calculate the combined effect value (OR, 95CI). Subgroup analysis, sensitivity analysis, and publication bias test were also performed.
Results
We found a significant connection between liver dysfunction and mortality of COVID-19 patients with a pooled OR of 1.98 (95% CI 1.39–2.82;
P
= 0.0002). There was a significant association between AST and severity of COVID-19 with a pooled OR of 4.48 (95% CI 3.24–7.21;
P
< 0.001), and a pooled WMD of 3.35 (95% CI, 2.07 to 4.64;
P
< 0.001). In addition, there was a significant difference between TBIL and severity of COVID-19, with a pooled OR of 1.91 (95% CI 1.40–2.60;
P
< 0.001), and with a pooled WMD of 1.18 (95% CI, 0.78 to 1.58;
P
< 0.001)
.
Conclusion
The mortality and severity of COVID-19 patients are significantly associated with liver dysfunction. The non-survivors and severe COVID-19 patients have elevated serum AST levels than the survivors and non-severe COVID-19 patients. The results of this study form a basis for better clinical liver management of patients with COVID-19.
Journal Article
Practical Gods: Carl Dennis’s Secularized Religious Visions
This paper examines Carl Dennis’s secularized religious visions in his Pulitzer-winning poetry collection, Practical Gods (2001). Dennis’s secularized religious visions can be quite understandable in the context of the ascending trends of secularization, diversification, and globalization of religion in America, and they demonstrate affinities with literary predecessors such as Wallace Stevens, with his aestheticized religion under the influence of Nietzsche, as well as with the innovative religious thinking of William Blake, Kazantzakis, and Oscar Wilde, and with certain aspects of Taoism and Zen Buddhism. This paper addresses Dennis’s perception of theological controversies, such as the contradiction between the omnipotence of God and the existence of evil, theological determinism vs. human free will, theological view of history vs. New Historicism, divinity in man, aestheticized religion, and earthly paradise through the focused lens of Dennis’s “practical religion”. Despite the breadth of the theses in Dennis’s conceived practical religion as examined in this paper, they are all tied up with the core of the phenomenological study of religion: that religion is important to believers of the religion irrespective of the objective truth of the religion or the actual existence of God. In Dennis’s views, as accorded with the phenomenological study of religions, God maybe an idea and a fiction, but it is a necessary fiction for humans. Thus, Dennis humanizes gods with the flaws and fragility of humanity while deifying ordinary humanity in the contemporary context. Contrasting what he views as theological determinism with its view of linear history and the apocalypse of grand events, Dennis embraces human free will, a non-teleological, aestheticized living with necessary fiction, and a transient paradise on earth. Carl Dennis’s religious vision reveals a poststructuralist (even though he did not brand himself so) abolition of the absoluteness of a transcendent signifier as well as binary opposition (between God and man, good and evil, religious/historical truth and fictionality), and it manifests an affinity with New Historicism and the phenomenological study of religion.
Journal Article
Comprehensive analysis of the expression and prognosis for CDCAs in head and neck squamous cell carcinoma
Head and neck squamous cell carcinoma (HNSCC), a tumor included oral cavity, lips, larynx, oropharynx, and the nasopharynx et al. The cell division cycle-associated (CDCA) protein family (CDCA1-8) critical for normal cell function and cancer cell proliferation. We explored the mutation signatures and expression levels of various CDCAs in detail in HNSCC. A comprehensive bioinformatics analysis pipeline based on copy number and gene expressions data from patients with HNSCC in order to given new insights into the possible functions and distinct prognostics that underlie CDCAs regulation. We compared the transcriptional expression of CDCAs in HNSCC and found significantly elevated mRNA expression of CDCA1-8 in HNSCC tissues across multiple datasets. We also found CDCA5/6/8 are over-expressed both transcriptionally and translationally in patients with HNSCC. Our results suggested that that mRNA levels of CDCA1/2/4/7 related to the prognosis and can be used as a new useful biomarker for predicting the survival of HNSCC patients. The top 5 CDCAs neighboring gene alterations in HNSCCs were found in MYC, STAG1, RAD21, KLHL9 and NDC80. Multivariable Cox proportional hazard model also showed that CD8+ T cells were higher (P<0.05) in HNSCC-HPV-pos patients and that this was related to CDCA1/2/3/4/5/7. This study utilizes online tools to conduct specific gene analyses from free open databases, but our study requires more large-scale genomics research and basic research.
Journal Article
Alternative splicing events implicated in carcinogenesis and prognosis of thyroid gland cancer
Alternative splicing (AS), a critical post-transcriptional regulatory mechanism, expands gene expression patterns, thereby leading to increased protein diversity. Indeed, more than 95% of human genes undergo alternative splicing events (ASEs). In this study, we drew an all-around AS profile of thyroid cancer cells based on RNA-seq data. In total, there were 45,150 AS in 10,446 thyroid cancer cell genes derived from 506 patients, suggesting that ASEs is a common process in TC. Moreover, 1819 AS signatures were found to be significantly associated with the overall survival (OS) of TC patients. Kaplan–Meier survival analyses suggested that seven types of ASEs were associated with poor prognosis of TC (
P
< 0.05). Among them, exon skipping (ES) was the most common, with alternate promoter (AP) and alternate terminator (AT) coming second and third, respectively. Our results indicated that acceptor sites (AA) (AUC: 0.937), alternate donor sites (AD) (AUC: 0.965), AT (AUC: 0.964), ES (AUC: 0.999), mutually exclusive exons (ME) (AUC: 0.999), and retained intron (RI) (AUC: 0.837) exhibited an AUC greater than 0.6. In addition, age and risk score (All) were risk factors for TC patients. We also evaluated whether TC-ASEs are regulated by various splicing factors (SFs). We found that the expression of 90 SFs was associated with 469 ASEs and OS of TC patients. Our findings provide an insight into the role of spliceosomes in TC, which may offer novel perspectives in tumor research.
Journal Article