Inter-rater variability for the American Society of Anesthesiologists classification in patients undergoing hepato-pancreato-biliary surgery (MILESTONE-2): international survey among surgeons and anaesthesiologists.

Background: Patients undergoing hepato-pancreato-biliary surgery are typically preoperatively assessed using the American Society of Anesthesiologists (ASA) classification, which is also used for case-mix adjustment when comparing centre outcomes. Studies determining the inter-rater variability of the ASA classification within hepato-pancreato-biliary surgery are currently lacking.

Methods: An international survey was collected and a case-vignette study was performed (November 2022-April 2023) regarding the ASA classification in patients undergoing hepato-pancreato-biliary surgery among anaesthesiologists and surgeons from (inter)national societies.

ZNF143 is a transcriptional regulator of nuclear-encoded mitochondrial genes that acts independently of looping and CTCF.

Gene expression is orchestrated by transcription factors, which function within the context of a three-dimensional genome. Zinc-finger protein 143 (ZNF143/ZFP143) is a transcription factor that has been implicated in both gene activation and chromatin looping. To study the direct consequences of ZNF143/ZFP143 loss, we generated a ZNF143/ZFP143 depletion system in mouse embryonic stem cells.

ZNF143 binds DNA and stimulates transcription initiation to activate and repress direct target genes.

Transcription factors bind to sequence motifs and act as activators or repressors. Transcription factors interface with a constellation of accessory cofactors to regulate distinct mechanistic steps to regulate transcription. We rapidly degraded the essential and pervasively expressed transcription factor ZNF143 to determine its function in the transcription cycle.

Classifying the molecular functions of transcription factors beyond activation and repression.

Notch signaling is a highly conserved pathway activated by dynamic cellular interactions that initiates a molecular cascade that ultimately drives changes in gene expression. The Notch transcriptional complex (NTC) regulates genes that influence development and homeostasis. In this issue of , Rogers and colleagues (doi:10.

ZNF143 binds DNA and stimulates transcripstion initiation to activate and repress direct target genes.

Transcription factors bind to sequence motifs and act as activators or repressors. Transcription factors interface with a constellation of accessory cofactors to regulate distinct mechanistic steps to regulate transcription. We rapidly degraded the essential and ubiquitously expressed transcription factor ZNF143 to determine its function in the transcription cycle.

Epidemiology and survival factors of appendicular myxofibrosarcoma: a SEER-retrospective study.

Background: The low incidence of myxofibrosarcoma (MFS) makes high power studies difficult to perform. Demographic and prognostic factors for MFS and how they differ from all extremity soft tissue sarcomas (STS) are not well understood. The purpose of this study was to characterize a large cohort of patients with MFS and evaluate epidemiologic and survival factors when compared to all STS.

TRPS1 modulates chromatin accessibility to regulate estrogen receptor alpha (ER) binding and ER target gene expression in luminal breast cancer cells.

Common genetic variants in the repressive GATA-family transcription factor (TF) TRPS1 locus are associated with breast cancer risk, and luminal breast cancer cell lines are particularly sensitive to TRPS1 knockout. We introduced an inducible degron tag into the native TRPS1 locus within a luminal breast cancer cell line to identify the direct targets of TRPS1 and determine how TRPS1 mechanistically regulates gene expression. We acutely deplete over 80 percent of TRPS1 from chromatin within 30 minutes of inducing degradation.

The Androgen Receptor Does Not Directly Regulate the Transcription of DNA Damage Response Genes.

Unlabelled: The clinical success of combined androgen deprivation therapy (ADT) and radiotherapy (RT) in prostate cancer created interest in understanding the mechanistic links between androgen receptor (AR) signaling and the DNA damage response (DDR). Convergent data have led to a model where AR both regulates, and is regulated by, the DDR. Integral to this model is that the AR regulates the transcription of DDR genes both at a steady state and in response to ionizing radiation (IR).

TRPS1 modulates chromatin accessibility to regulate estrogen receptor (ER) binding and ER target gene expression in luminal breast cancer cells.

Breast cancer is the most frequently diagnosed cancer in women. The most common subtype is luminal breast cancer, which is typically driven by the estrogen receptor (ER), a transcription factor (TF) that activates many genes required for proliferation. Multiple effective therapies target this pathway, but individuals often develop resistance.

Correction of transposase sequence bias in ATAC-seq data with rule ensemble modeling.

Chromatin accessibility assays have revolutionized the field of transcription regulation by providing single-nucleotide resolution measurements of regulatory features such as promoters and transcription factor binding sites. ATAC-seq directly measures how well the Tn5 transposase accesses chromatinized DNA. Tn5 has a complex sequence bias that is not effectively scaled with traditional bias-correction methods.

ANKLE1 cleaves mitochondrial DNA and contributes to cancer risk by promoting apoptosis resistance and metabolic dysregulation.

Alleles within the chr19p13.1 locus are associated with increased risk of both ovarian and breast cancer and increased expression of the ANKLE1 gene. ANKLE1 is molecularly characterized as an endonuclease that efficiently cuts branched DNA and shuttles between the nucleus and cytoplasm.

Kinetic networks identify TWIST2 as a key regulatory node in adipogenesis.

Adipocytes contribute to metabolic disorders such as obesity, diabetes, and atherosclerosis. Prior characterizations of the transcriptional network driving adipogenesis have overlooked transiently acting transcription factors (TFs), genes, and regulatory elements that are essential for proper differentiation. Moreover, traditional gene regulatory networks provide neither mechanistic details about individual regulatory element-gene relationships nor temporal information needed to define a regulatory hierarchy that prioritizes key regulatory factors.

Intrinsic bias estimation for improved analysis of bulk and single-cell chromatin accessibility profiles using SELMA.

Genome-wide profiling of chromatin accessibility by DNase-seq or ATAC-seq has been widely used to identify regulatory DNA elements and transcription factor binding sites. However, enzymatic DNA cleavage exhibits intrinsic sequence biases that confound chromatin accessibility profiling data analysis. Existing computational tools are limited in their ability to account for such intrinsic biases and not designed for analyzing single-cell data.

Distinct MUNC lncRNA structural domains regulate transcription of different promyogenic factors.

Many lncRNAs have been discovered using transcriptomic data; however, it is unclear what fraction of lncRNAs is functional and what structural properties affect their phenotype. MUNC lncRNA (also known as eRNA) acts as an enhancer RNA for the Myod1 gene in cis and stimulates the expression of other promyogenic genes in trans by recruiting the cohesin complex. Here, experimental probing of the RNA structure revealed that MUNC contains multiple structural domains not detected by prediction algorithms in the absence of experimental information.

Oncological Outcomes in Patients with Appendicular Myxofibrosarcomas: A Retrospective Study.

Background: Myxofibrosarcoma (MFS) is notorious for its infiltrative growth pattern, making wide excisions difficult to achieve. Our objective was to assess the impact of surgical margins and other factors that affected rates of local recurrence (LR), distant metastasis (DM), and overall survival (OS) of individuals undergoing resection for MFS.

Methods: We retrospectively reviewed the medical records of 209 patients with appendicular soft tissue sarcomas between January 2012 and June 2018.

PEPPRO: quality control and processing of nascent RNA profiling data.

Nascent RNA profiling is growing in popularity; however, there is no standard analysis pipeline to uniformly process the data and assess quality. Here, we introduce PEPPRO, a comprehensive, scalable workflow for GRO-seq, PRO-seq, and ChRO-seq data. PEPPRO produces uniformly processed output files for downstream analysis and assesses adapter abundance, RNA integrity, library complexity, nascent RNA purity, and run-on efficiency.

A prospective observational cohort study to evaluate patients' experience during sequential cataract surgery under monitored anesthesia care and topical anesthesia.

Cataract surgery is the most common ambulatory surgery at our outpatient surgery center. Several studies have shown that patients with bilateral cataracts may experience different levels of anxiety, pain, and awareness during the first and second cataract extraction.A prospective observational cohort study was conducted at The Ohio State University Wexner Medical Center Eye and Ear Institute in order to compare anxiety, general comfort, awareness, and pain levels in patients undergoing sequential cataract surgeries.

Comparative interactomes of HSF1 in stress and disease reveal a role for CTCF in HSF1-mediated gene regulation.

Heat shock transcription factor 1 (HSF1) orchestrates cellular stress protection by activating or repressing gene transcription in response to protein misfolding, oncogenic cell proliferation, and other environmental stresses. HSF1 is tightly regulated via intramolecular repressive interactions, post-translational modifications, and protein-protein interactions. How these HSF1 regulatory protein interactions are altered in response to acute and chronic stress is largely unknown.

ARF-AID: A Rapidly Inducible Protein Degradation System That Preserves Basal Endogenous Protein Levels.

Inducible degron systems are widely used to specifically and rapidly deplete proteins of interest in cell lines and organisms. An advantage of inducible degradation is that the biological system under study remains intact and functional until perturbation, a feature that necessitates that the endogenous levels of the protein are maintained. However, endogenous tagging of genes with auxin-inducible degrons (AID) can result in chronic, auxin-independent proteasome-mediated degradation.

Responsible Return to Essential and Non-Essential Surgery During the COVID-19 Pandemic.

Non-essential surgery had largely been suspended during the COVID-19 Pandemic. Enormous amounts of resources were utilized to shift surgical practices to a "disaster footing" with most elective surgeons assuming new roles to offset the anticipated burden from surgical and medical personnel delivering acute care. As the number of COVID-19-infected patients began to plateau in the state of Ohio, a four-phase "Responsible Return to Surgery" approach was adopted in concert with the Ohio Department of Health and the Ohio Hospital Association.

Defining data-driven primary transcript annotations with primaryTranscriptAnnotation in R.

Summary: Nascent transcript measurements derived from run-on sequencing experiments are critical for the investigation of transcriptional mechanisms and regulatory networks. However, conventional mRNA gene annotations significantly differ from the boundaries of primary transcripts. New primary transcript annotations are needed to accurately interpret run-on data.

An improved auxin-inducible degron system preserves native protein levels and enables rapid and specific protein depletion.

Rapid perturbation of protein function permits the ability to define primary molecular responses while avoiding downstream cumulative effects of protein dysregulation. The auxin-inducible degron (AID) system was developed as a tool to achieve rapid and inducible protein degradation in nonplant systems. However, tagging proteins at their endogenous loci results in chronic auxin-independent degradation by the proteasome.

Ambulatory Surgery Center Medical Director: Visionary Leader.

The ambulatory surgery center medical director is a physician leader who recognizes the need to develop a culture that encourages communication and empowerment of employees and professional staff, leading to engagement that optimize care through patient selection, safety and satisfaction requires vision and guidance from the medical director and is central to success of the ASC. Innovative thinking further improves patient care and long-term success by leveraging advances in technology and sustainable practices.

Genetic and epigenetic determinants establish a continuum of Hsf1 occupancy and activity across the yeast genome.

Heat shock factor 1 is the master transcriptional regulator of molecular chaperones and binds to the same cis-acting heat shock element (HSE) across the eukaryotic lineage. In budding yeast, Hsf1 drives the transcription of ∼20 genes essential to maintain proteostasis under basal conditions, yet its specific targets and extent of inducible binding during heat shock remain unclear. Here we combine Hsf1 chromatin immunoprecipitation sequencing (seq), nascent RNA-seq, and Hsf1 nuclear depletion to quantify Hsf1 binding and transcription across the yeast genome.