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Vertebrate genomes are partitioned into contact domains defined by enhanced internal contact frequency and formed by two principal mechanisms: compartmentalization of transcriptionally active and inactive domains, and stalling of chromosomal loop-extruding cohesin by CTCF bound at domain boundaries. While Drosophila has widespread contact domains and CTCF, it is currently unclear whether CTCF-dependent domains exist in flies. We genetically ablate CTCF in Drosophila and examine impacts on genome folding and transcriptional regulation in the central nervous system. We find that CTCF is required to form a small fraction of all domain boundaries, while critically controlling expression patterns of certain genes and supporting nervous system function. We also find that CTCF recruits the pervasive boundary-associated factor Cp190 to CTCF-occupied boundaries and co-regulates a subset of genes near boundaries together with Cp190. These results highlight a profound difference in CTCF-requirement for genome folding in flies and vertebrates, in which a large fraction of boundaries are CTCF-dependent and suggest that CTCF has played mutable roles in genome architecture and direct gene expression control during metazoan evolution. Although the Drosophila genome has widespread contact domains and CTCF, it remains unclear whether CTCF-dependent domains exist in flies. Here, the authors ablate CTCF in Drosophila and find that CTCF is required to form a small fraction of all domain boundaries, suggesting differences in the role of CTCF for genome folding in flies and vertebrates.

The three-dimensional arrangement of the human genome comprises a complex network of structural and regulatory chromatin loops important for coordinating changes in transcription during human development. To better understand the mechanisms underlying context-specific 3D chromatin structure and transcription during cellular differentiation, we generated comprehensive in situ Hi-C maps of DNA loops during human monocyte-to-macrophage differentiation. We demonstrate that dynamic looping events are regulatory rather than structural in nature and uncover widespread coordination of dynamic enhancer activity at preformed and acquired DNA loops. Enhancer-bound loop formation and enhancer-activation of preformed loops represent two distinct modes of regulation that together form multi-loop activation hubs at key macrophage genes. Activation hubs connect 3.4 enhancers per promoter and exhibit a strong enrichment for Activator Protein 1 (AP-1) binding events, suggesting multi-loop activation hubs driven by cell-type specific transcription factors may represent an important class of regulatory chromatin structures for the spatiotemporal control of transcription.

Enhancers are key drivers of gene regulation thought to act via 3D physical interactions with the promoters of their target genes. However, genome-wide depletions of architectural proteins such as cohesin result in only limited changes in gene expression, despite a loss of contact domains and loops. Consequently, the role of cohesin and 3D contacts in enhancer function remains debated. Here, we developed CRISPRi of regulatory elements upon degron operation (CRUDO), a novel approach to measure how changes in contact frequency impact enhancer effects on target genes by perturbing enhancers with CRISPRi and measuring gene expression in the presence or absence of cohesin. We systematically perturbed all 1,039 candidate enhancers near five cohesin-dependent genes and identified 34 enhancer-gene regulatory interactions. Of 26 regulatory interactions with sufficient statistical power to evaluate cohesin dependence, 18 show cohesin-dependent effects. A decrease in enhancer-promoter contact frequency upon removal of cohesin is frequently accompanied by a decrease in the regulatory effect of the enhancer on gene expression, consistent with a contact-based model for enhancer function. However, changes in contact frequency and regulatory effects on gene expression vary as a function of distance, with distal enhancers (e.g., >50Kb) experiencing much larger changes than proximal ones (e.g., <50Kb). Because most enhancers are located close to their target genes, these observations can explain how only a small subset of genes - those with strong distal enhancers - are sensitive to cohesin. Together, our results illuminate how 3D contacts, influenced by both cohesin and genomic distance, tune enhancer effects on gene expression.

The Encyclopedia of DNA elements (ENCODE) project is a collaborative effort to create a comprehensive catalog of functional elements in the human genome. The current database comprises more than 19000 functional genomics experiments across more than 1000 cell lines and tissues using a wide array of experimental techniques to study the chromatin structure, regulatory and transcriptional landscape of the and genomes. All experimental data, metadata, and associated computational analyses created by the ENCODE consortium are submitted to the Data Coordination Center (DCC) for validation, tracking, storage, and distribution to community resources and the scientific community. The ENCODE project has engineered and distributed uniform processing pipelines in order to promote data provenance and reproducibility as well as allow interoperability between genomic resources and other consortia. All data files, reference genome versions, software versions, and parameters used by the pipelines are captured and available the ENCODE Portal. The pipeline code, developed using Docker and Workflow Description Language (WDL; https://openwdl.org/) is publicly available in GitHub, with images available on Dockerhub (https://hub.docker.com), enabling access to a diverse range of biomedical researchers. ENCODE pipelines maintained and used by the DCC can be installed to run on personal computers, local HPC clusters, or in cloud computing environments Cromwell. Access to the pipelines and data the cloud allows small labs the ability to use the data or software without access to institutional compute clusters. Standardization of the computational methodologies for analysis and quality control leads to comparable results from different ENCODE collections - a prerequisite for successful integrative analyses.

EndoC-βH1 is emerging as a critical human beta cell model to study the genetic and environmental etiologies of beta cell function, especially in the context of diabetes. Comprehensive knowledge of its molecular landscape is lacking yet required to fully take advantage of this model. Here, we report extensive chromosomal (spectral karyotyping), genetic (genotyping), epigenetic (ChIP-seq, ATAC-seq), chromatin interaction (Hi-C, Pol2 ChIA-PET), and transcriptomic (RNA-seq, miRNA-seq) maps of this cell model. Integrated analyses of these maps define known (e.g., PDX1, ISL1) and putative (e.g., PCSK1, mir-375) beta cell-specific chromatin interactions and transcriptional cis-regulatory networks, and identify allelic effects on cis-regulatory element use and expression. Importantly, comparative analyses with maps generated in primary human islets/beta cells indicate substantial preservation of chromatin looping, but also highlight chromosomal heterogeneity and fetal genomic signatures in EndoC-βH1. Together, these maps, and an interactive web application we have created for their exploration, provide important tools for the broad community in the design and success of experiments to probe and manipulate the genetic programs governing beta cell identity and (dys)function in diabetes.

EndoC- H1 is emerging as a critical human beta cell model to study the genetic and environmental etiologies of beta cell function, especially in the context of diabetes. Comprehensive knowledge of its molecular landscape is lacking yet required to fully take advantage of this model. Here, we report extensive chromosomal (spectral karyotyping), genetic (genotyping), epigenetic (ChIP-seq, ATAC-seq), chromatin interaction (Hi-C, Pol2 ChIA-PET), and transcriptomic (RNA-seq, miRNA-seq) maps of this cell model. Integrated analyses of these maps define known (e.g., PDX1, ISL1) and putative (e.g., PCSK1, mir-375) beta cell-specific chromatin interactions and transcriptional cis-regulatory networks, and identify allelic effects on cis-regulatory element use and expression. Importantly, comparative analyses with maps generated in primary human islets/beta cells indicate substantial preservation of chromatin looping, but also highlight chromosomal heterogeneity and fetal genomic signatures in EndoC- H1. Together, these maps, and an interactive web application we have created for their exploration, provide important tools for the broad community in the design and success of experiments to probe and manipulate the genetic programs governing beta cell identity and (dys)function in diabetes.

Early illness detection enables medical professionals to deliver the best care and increases the likelihood of a full recovery. In this work, we show that computer-aided design (CAD) systems are capable of using chest X-ray (CXR) medical imaging modalities for the identification of respiratory system disorders. At present, the COVID-19 pandemic is the most well-known illness. We propose a system based on explainable artificial intelligence to detect COVID-19 from CXR images by using several cutting-edge convolutional neural network (CNN) models, as well as the Vision of Transformer (ViT) models. The proposed system also visualizes the infected areas of the CXR images. This gives doctors and other medical professionals a second option for supporting their decision. The proposed system uses some preprocessing of the images, which includes the segmentation of the region of interest using a UNet model and rotation augmentation. CNN employs pixel arrays, while ViT divides the image into visual tokens; therefore, one of the objectives is to compare their performance in COVID-19 detection. In the experiments, a publicly available dataset (COVID-QU-Ex) is used. The experimental results show that the performances of the CNN-based models and the ViT-based models are comparable. The best accuracy was 99.82%, obtained by the EfficientNetB7 (CNN-based) model, followed by the SegFormer (ViT-based). In addition, the segmentation and augmentation enhanced the performance.

Background Due to the differences in size and invasiveness when compared to non-giant macroadenomas (nGPAs), giant pituitary adenomas (GPAs) are considerably harder to resect. This study aimed to differentiate GPAs from nGPAs, based on the presenting complaints, surgical approaches, peri- and postoperative outcomes. Methods We retrospectively analyzed cases of pituitary macroadenomas that underwent surgical resection at a tertiary care hospital. GPAs were tumors greater than 4 cm in the largest dimension, while nGPAs were tumors smaller than 4 cm. 55 GPA patients and 70 nGPA patients from 2006 to 2017 were included. Demographic, perioperative, and post-operative outcomes were evaluated. Group comparisons for continuous variables were made using an independent t-test/Mann Whitney U test and categorical data was analyzed on Chi-square/Fisher exact test; a p-value of < 0.05 was considered significant. Results Visual deterioration was the most common complaint, reported by 61.4% of nGPA patients and 81.8% of GPA patients. The mean extent of gross total resection was 47.1% in nGPA patients and 18.2% in GPA patients (p = 0.001). After surgery, tumor recurrence was seen in 1.4% of nGPA patients and 18.2% of GPA patients (p = 0.001). First re-do surgery was required in 5.7% of nGPA patients and 25.5% of GPA patients (p = 0.004). Conclusion Compared to nGPAs, GPAs are more likely to present with a higher number of preoperative symptoms, and lesser chances of gross total tumor resection. GPAs are also associated with a higher rate of recurrence, which results in more follow-up procedures. Larger, multi-center longitudinal studies need to be done to validate these findings.

This study presents the single-step synthesis of a variety of 3-phenylimidazo[1,2- a ]pyridine derivatives 1–24 by reacting different phenacyl bromides with 2-aminopyridine in the presence of DABCO (1,4-diazabicyclo[2.2.2]octane) as a base. Compounds were characterized by spectroscopic techniques to confirm their structures. All synthetic derivatives were evaluated against important metabolic drug targets, including human carbonic anhydrase I and II, α -glucosidase, and α -amylase enzymes. Pertinent to mention that all the synthetic analogs revealed potent inhibitory strength with K i values in the range of 104.36—439.41 nM against hCA-I and 119.46—472.35 nM against hCA-II in comparison with the standard acetazolamide K i  = 466.53 ± 41.22 nM (for hCA-I) and K i  = 481.18 ± 33.05 nM (for hCA-II). All compounds showed potent inhibitory activity against α -glucosidase enzyme with IC 50 value 247.50—784.32 nM, compared to the standard acarbose = 22,800 nM. In addition, compounds were also identified as potent inhibitors of α -amylase with an IC 50 value of 342.67–1011.53 nM compared to the standard acarbose = 10,000 nM. In silico studies of the potential compounds 8 , 13 , 15 , 19 , 20 , and 21 against hCA-I, hCA-II, α -glycosidase, and α -amylase were performed to assess the enzyme–ligand interactions with the residues of the active-site target enzymes.

Background Competencies-based education has gained global recognition, emphasizing the need for educators to align educational outcomes with healthcare system requirements. However, limited literature exists on competency frameworks and Entrustable Professional Activities (EPAs) specific to health professions educationists, hindering the development of tailored Master’s programs. Aim This study aimed to develop a competency framework outlining the roles and functions for Master’s learners in Health Professions Education (MHPE) and identify the key EPAs that form the foundation of a task-based MHPE curriculum, along with the expected levels of entrustment. Methods An international Delphi study was conducted involving three rounds of surveys and qualitative discussions with an expert panel of health professions educationists from diverse contexts ( n  = 29). The Delphi technique, including open-ended and quantitative rating scales, was employed to reach consensus on the EPAs and their levels of entrustment. The final list of EPAs was validated using the EQual rubric. Results A total of 16 EPAs were identified and validated, mapped to core and potential roles and functions of health professions educationists. There is less agreement on the level of entrustment that should be attained at the master level, resulting in EPAs that must be fully entrusted before graduation and others which need further development afterwards. Conclusion The study presents a comprehensive competency framework and a set of EPAs tailored for MHPE programs, providing a structured approach to curriculum design and learner assessment. The findings underscore the importance of incorporating context-specific considerations and aligning educational objectives with the evolving roles and responsibilities of health professions educationists.