Integrating network analysis with differential expression to uncover therapeutic and prognostic biomarkers in esophageal squamous cell carcinoma.

Introduction: Esophageal squamous cell carcinoma (ESCC) accounts for over 90% of all esophageal tumors. However, the molecular mechanism underlying ESCC development and prognosis remains unclear, and there are still no effective molecular biomarkers for diagnosing or predicting the clinical outcome of patients with ESCC. Here, we used bioinformatics analysis to identify potential biomarkers and therapeutic targets for ESCC. Methodology: Differentially expressed genes (DEGs) between ESCC and normal esophageal tissue samples were obtained by comprehensively analyzing publicly available RNA-seq datasets from the TCGA and GTEX. Gene Ontology (GO) annotation and Reactome pathway analysis identified the biological roles of the DEGs. Moreover, the Cytoscape 3.10.1 platform and subsidiary tools such as CytoHubba were used to visualize the DEGs' protein-protein interaction (PPI) network and identify hub genes, Furthermore our results are validated by using Single-cell RNA analysis. Results: Identification of 2524 genes exhibiting altered expression enriched in pathways including keratinization, epidermal cell differentiation, G alpha(s) signaling events, and biological process of cell proliferation and division, extracellular matrix (ECM) disassembly, and muscle function. Moreover, upregulation of hallmarks E2F targets, G2M checkpoints, and TNF signaling. CytoHubba revealed 20 hub genes that had a valuable influence on the progression of ESCC in these patients. Among these, the high expression levels of four genes, CDK1 MAD2L1, PLK1, and TOP2A, were associated with critical dependence for cell survival in ESCC cell lines, as indicated by CRISPR dependency scores, gene expression data, and cell line metadata. We also identify the molecules targeting these essential hub genes, among which GSK461364 is a promising inhibitor of PLK1, BMS265246, and Valrubicin inhibitors of CDK1 and TOP2A, respectively. Moreover, we identified that elevated expression of MMP9 is associated with worse overall survival in ESCC patients, which may serve as potential prognostic biomarker or therapeutic target for ESCC. The single-cell RNA analysis showed MMP9 is highly expressed in myeloid, fibroblast, and epithelial cells, but low in T cells, endothelial cells, and B cells. This suggests MMP9's role in tumor progression and matrix remodeling, highlighting its potential as a prognostic marker and therapeutic target. Discussion: Our study identified key hub genes in ESCC, assessing their potential as therapeutic targets and biomarkers through detailed expression and dependency analyses. Notably, MMP9 emerged as a significant prognostic marker with high expression correlating with poor survival, underscoring its potential for targeted therapy. These findings enhance our understanding of ESCC pathogenesis and highlight promising avenues for treatment.

Advance computational tools for multiomics data learning.

The burgeoning field of bioinformatics has seen a surge in computational tools tailored for omics data analysis driven by the heterogeneous and high-dimensional nature of omics data. In biomedical and plant science research multi-omics data has become pivotal for predictive analytics in the era of big data necessitating sophisticated computational methodologies. This review explores a diverse array of computational approaches which play crucial role in processing, normalizing, integrating, and analyzing omics data. Notable methods such similarity-based methods, network-based approaches, correlation-based methods, Bayesian methods, fusion-based methods and multivariate techniques among others are discussed in detail, each offering unique functionalities to address the complexities of multi-omics data. Furthermore, this review underscores the significance of computational tools in advancing our understanding of data and their transformative impact on research.

Comparative transcriptomic analysis of the nodulation-competent zone and inference of transcription regulatory network in silicon applied Glycine max [L.]-Merr. Roots.

KEY MESSAGE: The study unveils Si's regulatory influence by regulating DEGs, TFs, and TRs. Further bHLH subfamily and auxin transporter pathway elucidates the mechanisms enhancing root development and nodulation. Soybean is a globally important crop serving as a primary source of vegetable protein for millions of individuals. The roots of these plants harbour essential nitrogen fixing structures called nodules. This study investigates the multifaceted impact of silicon (Si) application on soybean, with a focus on root development, and nodulation employing comprehensive transcriptomic analyses and gene regulatory network. RNA sequence analysis was utilised to examine the change in gene expression and identify the noteworthy differentially expressed genes (DEGs) linked to the enhancement of soybean root nodulation and root development. A set of 316 genes involved in diverse biological and molecular pathways are identified, with emphasis on transcription factors (TFs) and transcriptional regulators (TRs). The study uncovers TF and TR genes, categorized into 68 distinct families, highlighting the intricate regulatory landscape influenced by Si in soybeans. Upregulated most important bHLH subfamily and the involvement of the auxin transporter pathway underscore the molecular mechanisms contributing to enhanced root development and nodulation. The study bridges insights from other research, reinforcing Si's impact on stress-response pathways and phenylpropanoid biosynthesis crucial for nodulation. The study reveals significant alterations in gene expression patterns associated with cellular component functions, root development, and nodulation in response to Si.

Clinical Applications of Dual-Energy CT.

Dual-energy CT (DECT) provides insights into the material properties of tissues and can differentiate between tissues with similar attenuation on conventional single-energy imaging. In the conventional CT scanner, differences in the X-ray attenuation between adjacent structures are dependent on the atomic number of the materials involved, whereas in DECT, the difference in the attenuation is dependent on both the atomic number and electron density. The basic principle of DECT is to obtain two datasets with different X-ray energy levels from the same anatomic region and material decomposition based on attenuation differences at different energy levels. In this article, we discuss the clinical applications of DECT and its potential robust improvements in performance and postprocessing capabilities.

Evaluation of Pediatric Radiology Fellowship Website Content in USA and Canada.

PURPOSE: Prospective radiology fellows often rely on the internet to obtain valuable information regarding the application process as well as the unique qualities and aspects of different fellowship programs. The aim of this study was to analyze the content of Accreditation Council for Graduate Medical Education (ACGME) Pediatric Radiology Fellowship websites within the USA and Canadian Accredited Pediatric Radiology Fellowship program websites. METHODS: All active ACGME Pediatric Radiology fellowship websites as of October 2018 were evaluated using 26 criteria in the following domains: application process, recruitment, program structure, education, research, clinical care, and incentives. Fellowships without websites were excluded from the study. Canadian programs were compiled from a list obtained as of October 2018 from the Canadian Association of Radiologists fellowship directory. Each fellowship program was evaluated using the same 26 criteria as the US programs. RESULTS: 45 active ACGME Pediatric Radiology fellowship programs and 9 Canadian programs were identified. 43 of the US fellowships (96%), and 8 of the Canadian fellowships (89%) had dedicated fellowship websites available for analysis. For US data, websites on average contained 8 out of the 26 data points (31%). Whereas, in Canada, websites on average contained 11 out of the 26 data points (41%). CONCLUSION: Most fellowship websites demonstrate several information deficiencies. This presents an actionable opportunity for individual programs to better inform trainees, promote Pediatric Radiology, and attract the highest quality applicants.

An Evaluation of the Content of Canadian and American Nuclear Medicine Fellowship Websites.

BACKGROUND: Radiology trainees frequently use the Internet to research potential fellowship programs across all subspecialties. For a field like nuclear medicine, which has multiple training pathways, program websites can be an essential resource for potential applicants. This study aimed to analyze the online content of Canadian and American Nuclear Medicine fellowship websites. MATERIALS AND METHODS: The content of all active Canadian and American Nuclear Medicine fellowship websites was evaluated using 26 criteria in the following subdivisions: application, recruitment, education, research, clinical work, and incentives. Fellowships without websites were excluded from the study. Scores were summed per program and compared by geographic region and ranking. RESULTS: A total of 42 active Canadian and American Nuclear Medicine fellowship programs were identified, of which 39 fellowships had dedicated fellowship websites available for the analysis. On average, fellowship websites contained 34.4% (9 ± 3.3) of the 26 criteria. Programs did not score differently on the criteria by geographical distribution (P = .08) nor by ranking (P = .18). CONCLUSION: Most Canadian and American Nuclear Medicine fellowship websites are lacking content relevant to prospective fellows. Addressing inadequacies in online content may support programs to inform and recruit residents into fellowship programs.

Canadian and American Emergency Radiology Fellowship Websites: An Evaluation of Content.

PURPOSE: The internet is commonly employed by Radiology trainees to investigate and learn about potential fellowship programs. As a new and emerging subspecialty, Emergency Radiology requires strong internet presence and training program website content. This is vital to ensure good exposure of the fellowship programs to inform medical students, radiology trainees, and program directors, highlight unique aspects of a fellowship and raise awareness of the discipline at large. METHODS: To assess the standard and depth of information available online, Canadian and American Radiology fellowship websites were evaluated for content. Thirty-six criteria related to application process and recruitment, departmental structure, incentives, education, and research and clinical training were evaluated for presence or absence. RESULTS: Sixteen Emergency Radiology fellowship program websites were assessed from the United States and Canada for 36 criteria across 5 individual areas; application process and recruitment, departmental structure, incentives, education and research, and clinical training. Overall there was an absence of information found across all 5 areas. In particular areas for improvement were identified in education and research, and incentives both with median values of 12.5% of criteria present. CONCLUSION: Most Emergency Radiology fellowship program websites demonstrate several information deficiencies. This relative lack of comprehensive information represents an actionable opportunity for individual programs and the field to better educate trainees, program directors and the public about the unique training of Emergency Radiologists.

How well do we represent ourselves: an analysis of musculoskeletal radiology fellowships website content in Canada and the USA.

OBJECTIVE: Radiology residents review information available on fellowship program websites for shortlisting programs and for applying for fellowships. The aim of this study was to evaluate the comprehensiveness of musculoskeletal (MSK) fellowship program websites. METHODS: The content of US and Canadian MSK fellowship program websites was evaluated using 25 distinct criteria in the following domains: application, recruitment, research, clinical, education, clinical work, benefits. Programs without websites were excluded from analysis. RESULTS: In Canada and the USA, there were 100 MSK fellowship programs, 90 of them having dedicated websites. The average score across all programs was 9.5/25 or 38%. The most comprehensive program included 18/25 items or 72%. The least comprehensive program included only 1/25 items or 4%. The median score across all programs was 9/25 or 36%.More programs included information on the application process (65.5/90, 72.8%; SD 24.7%) than in education/research (24/90, 26.7%; SD 17.3%) or incentives (12.5/90, 13.9%; SD 7.8%).Mean scores amongst US schools did not differ based on geographical distribution (p = 0.32), although they did by rank; schools ranked in the bottom tier scored lower than the unranked, middle, and top tier schools (p < 0.05). CONCLUSION: The majority of MSK fellowship program websites are not comprehensive. Areas that needed the most improvement include incentives, education/research, clinical teaching, and recruitment information. Addressing these insufficiencies can help programs in easing the application process for prospective fellows and enhance recruitment.

Dual-Energy CT: A Paradigm Shift in Acute Traumatic Abdomen.

Abdominal trauma, one of the leading causes of death under the age of 45, can be broadly classified into blunt and penetrating trauma, based on the mechanism of injury. Blunt abdominal trauma usually results from motor vehicle collisions, fall from heights, assaults, and sports and is more common than penetrating abdominal trauma, which is usually seen in firearm injuries and stab wounds. In both blunt and penetrating abdominal trauma, an optimized imaging approach is mandatory to exclude life-threatening injuries. Easy availability of the portable ultrasound in the emergency department and trauma bay makes it one of the most commonly used screening imaging modalities in the abdominal trauma, especially to exclude hemoperitoneum. Evaluation of the visceral and vascular injuries in a hemodynamically stable patient, however, warrants intravenous contrast-enhanced multidetector computed tomography scan. Dual-energy computed tomography with its postprocessing applications such as iodine selective imaging and virtual monoenergetic imaging can reliably depict the conspicuity of traumatic solid and hollow visceral and vascular injuries.

Unravelling the Mysteries of Traumatic Diaphragmatic Injury: An Up-to-Date Review.

Traumatic diaphragmatic injury (TDI) is an underdiagnosed condition that has recently increased in prevalence due to its association with automobile collisions. The initial injury is often obscured by concurrent thoracic and abdominal injuries. Traumatic diaphragmatic injury itself is rarely lethal at initial presentation, however associated injuries and complications of untreated TDI such as herniation and strangulation of abdominal viscera have serious clinical consequences. There are 2 primary mechanisms of TDIs: penetrating TDI which tend to be smaller, more difficult to detect, and result in fewer complications; and blunt TDIs which are larger and have higher overall mortality due to associated injuries or delayed complications. The anatomy of thoracic and abdominal cavities distinguishes the epidemiology, pathophysiology, symptoms, treatment, and prognosis of right versus left TDI. Although there is no definitive radiologic sign for diagnosing TDI, many signs have been introduced in the literature and the concurrent presence of multiple signs increases the sensitivity of TDI detection. Conservative versus surgical management depends on mechanism of TDI, side, and most importantly the associated injuries.

Changes in Approach to Solid Organ Injury: What the Radiologist Needs to Know.

This review aims to examine the challenges facing radiologists interpreting trauma computed tomography (CT) images in this era of a changing approach to management of solid organ trauma. After reviewing the pearls and pitfalls of CT imaging protocols for detection of traumatic solid organ injuries, we describe the key changes in the 2018 American Association for the Surgery of Trauma Organ Injury Scales for liver, spleen, and kidney and their implications for management strategies. We then focus on the important imaging findings in observed in patients who undergo nonoperative management and patients who are imaged post damage control surgery.

A Comparative Evaluation of Cardiothoracic Radiology Fellowship Website Content.

PURPOSE: Prospective radiology fellows often rely on the internet to obtain information with regard to the application process for and the unique qualities of different fellowship programs. The aim of this study was to analyze the content of websites of the United States' and Canadian cardiothoracic radiology fellowships. METHODS: All active Cardiothoracic Radiology fellowship websites as of July 2019 were evaluated and compared using 25 criteria in the following domains: Application, Recruitment, Clinical Training, Education/Research, and Incentives. Program website information availability was compared by geographic region. RESULTS: There were 60 active cardiothoracic radiology fellowships, and 59 of these fellowships had a dedicated fellowship website. Websites, on average, had 9.3 of the 25 criteria (37.2%). The mean number of schools that satisfied the criterion in the "Incentives" domain ([7.75/59] 10.5%±2.8%) was significantly lower than that for the "Application Process" domain ([40.50/59]; 68.7%±40.6%) (P=0.01). There was no significant difference in the information content of programs in different geographic regions (P=0.246). CONCLUSION: Most cardiothoracic radiology fellowship websites were lacking content relevant to prospective fellows. Provision of more relevant and easily accessible online content may support programs to better inform and recruit residents and to promote the specialty of cardiothoracic radiology.

An Evaluation of the Content of Canadian Radiology Fellowship Websites.

PURPOSE: Prospective radiology fellows utilize the internet to apply for radiology fellowship programs. The aim of this study was to analyze the online content of Canadian radiology fellowship websites. METHODS: The content of all active Canadian radiology fellowship websites were evaluated using 30 criteria in the following domains: application, recruitment, education and research, clinical work and benefits. Fellowships without websites were excluded from the study. The prevalence of assessed elements was compared to geography and Canadian medical school ranking. RESULTS: We identified 107 active Canadian radiology fellowship programmes, of which 102 university fellowships (95.3%) had dedicated fellowship websites available for analysis. Of these 102 programs, the median score was 13/30 (43.0%). Websites of fellowship programs affiliated with top ranked medical schools contained more of the assessed criteria than middle and lower ranked schools (17.0 vs 13.0 vs 9.0, p < 0.0001)). Geographical difference was identified across Canada with Atlantic and Central Canada fellowship programs having significantly more criteria than Western programs (15.5 vs 16.0 vs 10.0, p < 0.001). CONCLUSIONS: Most Canadian radiology fellowship websites are devoid of content pertinent to prospective radiology fellows. Addressing deficiencies in online content may assist programs to inform and recruit residents into radiology fellowship programs.