Analysis and interpretation of high-throughput transcriptional and chromatin accessibility data at single-cell (sc) resolution are still open challenges in the biomedical field. The existence of countless bioinformatics tools, for the different analytical steps, increases the complexity of data interpretation and the difficulty to derive biological insights. In this article, we present SCALA, a bioinformatics tool for analysis and visualization of single-cell RNA sequencing (scRNA-seq) and Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq) datasets, enabling either independent or integrative analysis of the two modalities. SCALA combines standard types of analysis by integrating multiple software packages varying from quality control to the identification of distinct cell populations and cell states. Additional analysis options enable functional enrichment, cellular trajectory inference, ligand-receptor analysis, and regulatory network reconstruction. SCALA is fully parameterizable, presenting data in tabular format and producing publication-ready visualizations. The different available analysis modules can aid biomedical researchers in exploring, analyzing, and visualizing their data without any prior experience in coding. We demonstrate the functionality of SCALA through two use-cases related to TNF-driven arthritic mice, handling both scRNA-seq and scATAC-seq datasets. SCALA is developed in R, Shiny and JavaScript and is mainly available as a standalone version, while an online service of more limited capacity can be found at http://scala.pavlopouloslab.info or https://scala.fleming.gr.
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http://dx.doi.org/10.1016/j.csbj.2023.10.032 | DOI Listing |
BMC Public Health
December 2024
Department of English Language, Kotebe Metropoliatan University, Addis Ababa, Ethiopia.
Background: Community acceptance of Traditional birth attendants (TBAs) as professional birth attendant was reported as one of the bottlenecks that has been hindering facility childbirth care service use. Hence, the World Health Organization (WHO) recommended that all childbirths needed to be attended by professional skilled attendants who at least possessed midwifery skill through the safe motherhood initiative. However, many births in developing countries have been being attended by Traditional birth attendants (TBAs) mainly due to pregnant women and community acceptance for TBAs as sole birth attendants.
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December 2024
State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Sun Yat-Sen University, Guangzhou, 510060, China.
Background: Retinal microvascular abnormalities (RMA) reflect cumulative microvascular damage from systemic diseases and aging. However, little is known about the association between RMA and long-term survival outcomes. This study aimed to examine the relationships between RMA and the risk of all-cause and specific-cause mortality among U.
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December 2024
Department of Community Health and Clinical Sciences, Njala University, Bo, Sierra Leone.
Background: Bullying can have profound negative effects on nursing students who often contend with psychological trauma because of repeated acts of mistreatment. This study was done to explore the effects of bullying behaviours among nursing students with above average and below average academic performance in two nursing schools in Sierra Leone.
Methods: A qualitative exploratory study involved six rounds of data collection and analysis over a one month period.
BMC Nurs
December 2024
School of Nursing, Chengdu University of Traditional Chinese Medicine, No. 1166 Liutai Road, Wenjiang District, Chengdu city, Sichuan Province, 611137, China.
Background: Psychological capital (PsyCap) is a positive internal resource for individuals, playing a crucial role in mental health. Evaluating nurses' psychological capital is important for understanding their mental well-being, as they face unique occupational stressors. However, existing PsyCap questionnaires are developed for various other professions such as enterprise employees, teachers, patients, teenagers, and civil servants, making them less suitable for the nursing profession.
View Article and Find Full Text PDFBMC Med Educ
December 2024
Department of Conservative Dentistry and Endodontics, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, Tamil Nadu, 600077, India.
Introduction: This scoping review aimed to review the various challenges facing dental education. Dental education faces multiple institutional, student and faculty-based challenges. Institutional challenges include updating infrastructure resources, recruiting qualified faculty, and implementing administrative policies that enhance dental education.
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