Validity and reliability of the integrated palliative care outcome scale (IPOS) in Korea: a multicenter study of terminally ill cancer patients.

Background: The Integrated Palliative care Outcome Scale (IPOS) is a key tool for assessing the quality of palliative care using patient-reported outcomes. This study aimed to culturally adapt and translate the IPOS to Korean and verify its psychometric properties for use in palliative care settings.

Methods: The IPOS was translated and culturally adapted, followed by validation in 119 terminally ill cancer patients and 28 healthcare providers across six Hospice and Palliative Care Units from September 2023 to January 2024.

Asymmetrical evolution of promoter methylation of mammalian genes after duplication.

Even though gene duplication is a key source of new genes and evolutionary innovation, it is unclear how duplicates survive the period immediately following gene duplication, in which both copies are functionally redundant. In the absence of epigenetic silencing, the abundance of the gene product would double after gene duplication, which would often have deleterious effects. However, recent duplicates exhibit low expression levels, which could be at least partially explained by high levels of promoter methylation.

Disruption of the OsWRKY71 transcription factor gene results in early rice seed germination under normal and cold stress conditions.

Background: Early seed germination in crops can confer a competitive advantage against weeds and reduce the time to maturation and harvest. WRKY transcription factors regulate many aspects of plant development including seed dormancy and germination. Both positive and negative regulators of seed germination have been reported in many plants such as rice and Arabidopsis.

Genome wide clustering on integrated chromatin states and Micro-C contacts reveals chromatin interaction signatures.

We can now analyze 3D physical interactions of chromatin regions with chromatin conformation capture technologies, in addition to the 1D chromatin state annotations, but methods to integrate this information are lacking. We propose a method to integrate the chromatin state of interacting regions into a vector representation through the contact-weighted sum of chromatin states. Unsupervised clustering on integrated chromatin states and Micro-C contacts reveals common patterns of chromatin interaction signatures.

Inositol Hexaphosphate (InsP6) Activates the HDAC1/3 Epigenetic Axis to Maintain Intestinal Barrier Function.

HDACs (histone deacetylase) play a crucial role in regulating gene expression, and the inhibition of these enzymes is gaining attention as a promising therapeutic approach for cancer treatment. Despite their significant physiological and clinical importance, the mechanisms of HDAC activation remain poorly understood. This study reveals that inositol polyphosphate multikinase (IPMK) is essential for activating HDAC1 and HDAC3 in cell lines and mice.

Supervised learning of enhancer-promoter specificity based on genome-wide perturbation studies highlights areas for improvement in learning.

Motivation: Understanding the rules that govern enhancer-driven transcription remains a central unsolved problem in genomics. Now with multiple massively parallel enhancer perturbation assays published, there are enough data that we can utilize to learn to predict enhancer-promoter (EP) relationships in a data-driven manner.

Results: We applied machine learning to one of the largest enhancer perturbation studies integrated with transcription factor (TF) and histone modification ChIP-seq.

Intraoperative neuromonitoring during thyroidectomy does not decrease vocal cord palsy risk, but the cumulative experience of the surgeon may.

Purpose: To evaluate the influence of intraoperative neuromonitoring (IONM) on vocal cord palsy (VCP) rates and assess the temporal trends in VCP rates.

Methods: The subjects of this retrospective study were patients who underwent thyroidectomy for thyroid cancer between March, 2014 and June, 2022, at a university hospital in Korea. We compared VCP rates between the non-IONM and IONM groups and analyzed the risk factors for VCP and VCP rates over time.

Comparison of Speech Outcomes Between Speech Therapy Only and Double-Opposing Z-Plasty Combined With Speech Therapy in Patients With Submucous Cleft Palate.

The purpose of this study was to compare speech outcomes in patients with submucous cleft palate (SMCP) between speech therapy alone and double-opposing Z-plasty (DOZ) combined with speech therapy. The subjects were 67 patients with SMCP (overt type, 45 males, 22 females), who were divided into the observation group (n=18), the speech therapy group (n=24; duration, 17.8 mo), and the DOZ and speech therapy (DOZ-speech therapy) group (n=25; median age at DOZ, 5.

A comparison of RNA-Seq data preprocessing pipelines for transcriptomic predictions across independent studies.

Background: RNA sequencing combined with machine learning techniques has provided a modern approach to the molecular classification of cancer. Class predictors, reflecting the disease class, can be constructed for known tissue types using the gene expression measurements extracted from cancer patients. One challenge of current cancer predictors is that they often have suboptimal performance estimates when integrating molecular datasets generated from different labs.

Real-world Nationwide Outcomes of Minimally Invasive Surgery for Advanced Gastric Cancer Based on Korean Gastric Cancer Association-Led Survey.

Purpose: The study aimed to investigate real-world surgical outcomes of minimally invasive surgery (MIS) for advanced gastric cancer using Korean Gastric Cancer Association (KGCA)-led nationwide data.

Materials And Methods: A nationwide survey of patients who underwent surgical treatment for gastric cancer in 2019 was conducted by the KGCA. A total of 14,076 patients from 68 institutions underwent surgery, and 4,953 patients diagnosed with pathological stages IB-III gastric cancer were included.

Long-term Functional and Patient-reported Outcomes Between Intra-corporeal Delta-shaped Gastroduodenostomy and Gastrojejunostomy After Laparoscopic Distal Gastrectomy.

Purpose: This study aimed to compare the long-term functional and patient-reported outcomes between intra-corporeal delta-shaped gastroduodenostomy and gastrojejunostomy after laparoscopic distal gastrectomy for gastric cancer.

Materials And Methods: We retrospectively reviewed clinicopathological data from 616 patients who had undergone laparoscopic distal gastrectomy for stage I gastric cancer between January 2015 and September 2020. Among them, 232 patients who had undergone delta-shaped anastomosis and another 232 who had undergone Billroth II anastomosis were matched using propensity scores.

Feature Importance Analysis of a Deep Learning Model for Predicting Late Bladder Toxicity Occurrence in Uterine Cervical Cancer Patients.

(1) In this study, we developed a deep learning (DL) model that can be used to predict late bladder toxicity. (2) We collected data obtained from 281 uterine cervical cancer patients who underwent definitive radiation therapy. The DL model was trained using 16 features, including patient, tumor, treatment, and dose parameters, and its performance was compared with that of a multivariable logistic regression model using the following metrics: accuracy, prediction, recall, F1-score, and area under the receiver operating characteristic curve (AUROC).

Predicting factors associated with prolonged intensive care unit stay of patients with COVID-19.

Background: Predicting the length of stay (LOS) for coronavirus disease 2019 (COVID-19) patients in the intensive care unit (ICU) is essential for efficient use of ICU resources. We analyzed the clinical characteristics of patients with severe COVID-19 based on their clinical care and determined the predictive factors associated with prolonged LOS.

Methods: We included 96 COVID-19 patients who received oxygen therapy at a high-flow nasal cannula level or above after ICU admission during March 2021 to February 2022.

Prolonged patency of fully covered self-expandable metal stents with an externally anchored plastic stent in distal malignant biliary obstruction.

BACKGROUND : Fully covered self-expandable metal stents (FCSEMSs) are widely used for endoscopic treatment of distal malignant biliary obstruction (dMBO). We aimed to assess the efficacy of anchoring an external plastic stent to an FCSEMS in dMBO. METHODS : A multicenter retrospective cohort study was performed in patients with dMBO to compare stent patency between FCSEMSs and FCSEMSs with an externally anchored plastic stent (EPS).

Data supporting a saturation mutagenesis assay for Tat-driven transcription with the GigaAssay.

The data in this article are associated with the research paper "GigaAssay - an adaptable high-throughput saturation mutagenesis assay" [1]. The raw data are sequence reads of HIV-1 cDNA amplified from cellular genomic DNA in a new single-pot saturation mutagenesis assay designated the "GigaAssay". A bioinformatic pipeline and parameters used to analyze the data.

GigaAssay - An adaptable high-throughput saturation mutagenesis assay platform.

High-throughput assay systems have had a large impact on understanding the mechanisms of basic cell functions. However, high-throughput assays that directly assess molecular functions are limited. Herein, we describe the "GigaAssay", a modular high-throughput one-pot assay system for measuring molecular functions of thousands of genetic variants at once.

The essential but enigmatic regulatory role of HERVH in pluripotency.

Human specific endogenous retrovirus H (HERVH) is highly expressed in both naive and primed stem cells and is essential for pluripotency. Despite the proven relationship between HERVH expression and pluripotency, there is no single definitive model for the function of HERVH. Instead, several hypotheses of a regulatory function have been put forward including HERVH acting as enhancers, long noncoding RNAs (lncRNAs), and most recently as markers of topologically associating domain (TAD) boundaries.

Dynamic differential evolution schemes of WRKY transcription factors in domesticated and wild rice.

WRKY transcription factors play key roles in stress responses, growth, and development. We previously reported on the evolution of WRKYs from unicellular green algae to land plants. To address recent evolution events, we studied three domesticated and eight wild species in the genus Oryza, an ideal model due to its long history of domestication, economic importance, and central role as a model system.