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View article: The Importance of Patient Positioning in Radiography When Utilising Automatic Exposure Control
The Importance of Patient Positioning in Radiography When Utilising Automatic Exposure Control Open
Introduction Automatic exposure control (AEC) is a device used in radiographic practice which terminates a radiographic acquisition when a certain exposure threshold is reached. The AEC is commonly utilised for in‐bucky imaging, such as fo…
View article: Phasing single-molecule nano-NOMe-seq reveals chromatin state heterogeneity in the context of transcription and long-range interactions
Phasing single-molecule nano-NOMe-seq reveals chromatin state heterogeneity in the context of transcription and long-range interactions Open
A central challenge in molecular biology is determining how 3D chromatin architecture, particularly enhancer-promoter looping and insulating CTCF-mediated interactions, influences gene transcription in individual cells, which has significa…
View article: Epigenetic Changes Regulating Epithelial–Mesenchymal Plasticity in Human Trophoblast Differentiation
Epigenetic Changes Regulating Epithelial–Mesenchymal Plasticity in Human Trophoblast Differentiation Open
The phenotype of human placental extravillous trophoblast (EVT) at the end of pregnancy reflects both differentiation from villous cytotrophoblast (CTB) and later gestational changes, including loss of proliferative and invasive capacity. …
View article: Persistent chromatin alterations and gene expression reprogramming follow widespread DNA damage in glioblastoma
Persistent chromatin alterations and gene expression reprogramming follow widespread DNA damage in glioblastoma Open
DNA damage from routine cellular processes or exogenous insults can have a lasting impact on gene regulation beyond genetic mutations. The prevailing paradigm for the consequences of DNA damage repair revolves around restoration of the ori…
View article: mtgRNA-db: An annotated database of multi-target CRISPR-Cas9 guide-RNAs in the human genome
mtgRNA-db: An annotated database of multi-target CRISPR-Cas9 guide-RNAs in the human genome Open
CRISPR-Cas9 guide-RNA design tools can be used to identify guide-RNAs that target single human genomic loci. However, these approaches limit their effect to a single locus. Here, we generate a database of potential individual guide-RNAs th…
View article: A targetable developmental program co-regulates angiogenesis and immune evasion
A targetable developmental program co-regulates angiogenesis and immune evasion Open
Ultraviolet (UV)-induced DNA mutations produce genetic drivers of cutaneous melanoma initiation and numerous neoantigens that can trigger anti-tumor immune responses in the host. Consequently, melanoma cells must rapidly evolve to evade im…
View article: Colon Cancer Rates Among Asian Americans: A 2017–2021 Epidemiological Analysis
Colon Cancer Rates Among Asian Americans: A 2017–2021 Epidemiological Analysis Open
Colon cancer (CC) is a significant public health concern. With Asian Americans (AA) representing a rapidly growing demographic in the United States, our study examined CC prevalence among AA. The study merged 2017-2021 Medical Expenditure …
View article: The coordination between CTCF, cohesin and TFs impacts nucleosome repositioning and chromatin insulation to define state specific 3D chromatin folding
The coordination between CTCF, cohesin and TFs impacts nucleosome repositioning and chromatin insulation to define state specific 3D chromatin folding Open
CTCF-mediated chromatin folding plays a key role in gene regulation, however the mechanisms controlling chromatin organization across cell states are not fully elucidated. Comprehensive analyses reveal that CTCF binding stability and cohes…
View article: Brain and cancer associated binding domain mutations provide insight into CTCF’s relationship with chromatin and its ability to act as a chromatin organizer
Brain and cancer associated binding domain mutations provide insight into CTCF’s relationship with chromatin and its ability to act as a chromatin organizer Open
Although only a fraction of CTCF motifs are bound in any cell type, and approximately half of the occupied sites overlap cohesin, the mechanisms underlying cell-type specific attachment and ability to function as a chromatin organizer rema…
View article: Epigenetic changes regulating the epithelial-mesenchymal transition in human trophoblast differentiation
Epigenetic changes regulating the epithelial-mesenchymal transition in human trophoblast differentiation Open
The phenotype of human placental extravillous trophoblast (EVT) at the end of pregnancy reflects both first trimester differentiation from villous cytotrophoblast (CTB) and later gestational changes, including loss of proliferative and inv…
View article: Genetic Ethnicity and Hypertension Epistatic Interaction Underlying Racial Disparities in US Multiple Myeloma Susceptibility
Genetic Ethnicity and Hypertension Epistatic Interaction Underlying Racial Disparities in US Multiple Myeloma Susceptibility Open
Background Multiple myeloma (MM), a malignant plasma cell disorder, exhibits pronounced racial disparities in incidence and patient outcomes. The Centers for Disease Control and Prevention (CDC) reports that MM is twice as common in Black …
View article: Improving allele-specific epigenomic signal coverage by<i>10-fold</i>using Hidden Markov Modeling and Machine Learning
Improving allele-specific epigenomic signal coverage by<i>10-fold</i>using Hidden Markov Modeling and Machine Learning Open
Allele-specific epigenomic signals refer to differences in epigenomic patterns between the two copies, or “alleles,” of a DNA region inherited from each parent. Epigenomic patterns are defined as alterations of the DNA sequence (e.g., chem…
View article: A randomized trial of a wearable UV dosimeter for skin cancer prevention
A randomized trial of a wearable UV dosimeter for skin cancer prevention Open
Background Non-melanoma skin cancer (NMSC) is the most prevalent cancer in the United States. Despite guidelines on ultraviolet (UV) avoidance, it remains difficult for people to assess their exposure, as UV is invisible and the onset of U…
View article: Binding domain mutations provide insight into CTCF’s relationship with chromatin and its contribution to gene regulation
Binding domain mutations provide insight into CTCF’s relationship with chromatin and its contribution to gene regulation Open
Summary Here we used a series of CTCF mutations to explore CTCF’s relationship with chromatin and its contribution to gene regulation. CTCF’s impact depends on the genomic context of bound sites and the unique binding properties of WT and …
View article: R-loop landscapes in the developing human brain are linked to neural differentiation and cell-type specific transcription
R-loop landscapes in the developing human brain are linked to neural differentiation and cell-type specific transcription Open
Here, we construct genome-scale maps for R-loops, three-stranded nucleic acid structures comprised of a DNA/RNA hybrid and a displaced single strand of DNA, in the proliferative and differentiated zones of the human prenatal brain. We show…
View article: MethNet: a robust approach to identify regulatory hubs and their distal targets in cancer
MethNet: a robust approach to identify regulatory hubs and their distal targets in cancer Open
Aberrations in the capacity of DNA/chromatin modifiers and transcription factors to bind non-coding regions can lead to changes in gene regulation and impact disease phenotypes. However, identifying distal regulatory elements and connectin…
View article: Supplementary Data 3 from A New Biomarker That Predicts Colonic Neoplasia Outcome in Patients with Hyperplastic Colonic Polyps
Supplementary Data 3 from A New Biomarker That Predicts Colonic Neoplasia Outcome in Patients with Hyperplastic Colonic Polyps Open
PDF file - 132K
View article: Supplementary Data 4 from A New Biomarker That Predicts Colonic Neoplasia Outcome in Patients with Hyperplastic Colonic Polyps
Supplementary Data 4 from A New Biomarker That Predicts Colonic Neoplasia Outcome in Patients with Hyperplastic Colonic Polyps Open
PDF file - 203K
View article: Supplementary Data 2 from A New Biomarker That Predicts Colonic Neoplasia Outcome in Patients with Hyperplastic Colonic Polyps
Supplementary Data 2 from A New Biomarker That Predicts Colonic Neoplasia Outcome in Patients with Hyperplastic Colonic Polyps Open
PDF file - 174K
View article: Supplementary Data 4 from A New Biomarker That Predicts Colonic Neoplasia Outcome in Patients with Hyperplastic Colonic Polyps
Supplementary Data 4 from A New Biomarker That Predicts Colonic Neoplasia Outcome in Patients with Hyperplastic Colonic Polyps Open
PDF file - 203K
View article: Supplementary Data 1 from A New Biomarker That Predicts Colonic Neoplasia Outcome in Patients with Hyperplastic Colonic Polyps
Supplementary Data 1 from A New Biomarker That Predicts Colonic Neoplasia Outcome in Patients with Hyperplastic Colonic Polyps Open
PDF file - 145K
View article: Supplementary Data 3 from A New Biomarker That Predicts Colonic Neoplasia Outcome in Patients with Hyperplastic Colonic Polyps
Supplementary Data 3 from A New Biomarker That Predicts Colonic Neoplasia Outcome in Patients with Hyperplastic Colonic Polyps Open
PDF file - 132K
View article: Supplementary Data 1 from A New Biomarker That Predicts Colonic Neoplasia Outcome in Patients with Hyperplastic Colonic Polyps
Supplementary Data 1 from A New Biomarker That Predicts Colonic Neoplasia Outcome in Patients with Hyperplastic Colonic Polyps Open
PDF file - 145K
View article: Data from A New Biomarker That Predicts Colonic Neoplasia Outcome in Patients with Hyperplastic Colonic Polyps
Data from A New Biomarker That Predicts Colonic Neoplasia Outcome in Patients with Hyperplastic Colonic Polyps Open
The most frequently occurring lesions in the colon are the hyperplastic polyps. Hyperplastic polyps have long been considered as lesions with no malignant potential and colonoscopy for these patients is not recommended. However, recent wor…
View article: Data from A New Biomarker That Predicts Colonic Neoplasia Outcome in Patients with Hyperplastic Colonic Polyps
Data from A New Biomarker That Predicts Colonic Neoplasia Outcome in Patients with Hyperplastic Colonic Polyps Open
The most frequently occurring lesions in the colon are the hyperplastic polyps. Hyperplastic polyps have long been considered as lesions with no malignant potential and colonoscopy for these patients is not recommended. However, recent wor…
View article: Supplementary Data 2 from A New Biomarker That Predicts Colonic Neoplasia Outcome in Patients with Hyperplastic Colonic Polyps
Supplementary Data 2 from A New Biomarker That Predicts Colonic Neoplasia Outcome in Patients with Hyperplastic Colonic Polyps Open
PDF file - 174K