Biostatistical Aspects of Whole Genome Sequencing Studies: Preprocessing and Quality Control.

Rapid advances in high-throughput DNA sequencing technologies have enabled large-scale whole genome sequencing (WGS) studies. Before performing association analysis between phenotypes and genotypes, preprocessing and quality control (QC) of the raw sequence data need to be performed. Because many biostatisticians have not been working with WGS data so far, we first sketch Illumina's short-read sequencing technology.

Are Macula or Optic Nerve Head Structures Better at Diagnosing Glaucoma? An Answer Using Artificial Intelligence and Wide-Field Optical Coherence Tomography.

Purpose: We wanted to develop a deep-learning algorithm to automatically segment optic nerve head (ONH) and macula structures in three-dimensional (3D) wide-field optical coherence tomography (OCT) scans and to assess whether 3D ONH or macula structures (or a combination of both) provide the best diagnostic power for glaucoma.

Methods: A cross-sectional comparative study was performed using 319 OCT scans of glaucoma eyes and 298 scans of nonglaucoma eyes. Scans were compensated to improve deep-tissue visibility.

Tritiated stainless steel (nano)particle release following a nuclear dismantling incident scenario: Significant exposure of freshwater ecosystem benthic zone.

Nuclear facilities continue to be developed to help meet global energy demands while reducing fossil fuel use. However, an incident during the dismantling of these facilities could accidentally release tritiated particles (e.g.

Calibrating machine learning approaches for probability estimation: A comprehensive comparison.

Statistical prediction models have gained popularity in applied research. One challenge is the transfer of the prediction model to a different population which may be structurally different from the model for which it has been developed. An adaptation to the new population can be achieved by calibrating the model to the characteristics of the target population, for which numerous calibration techniques exist.

Three-Dimensional Structural Phenotype of the Optic Nerve Head as a Function of Glaucoma Severity.

Importance: The 3-dimensional (3-D) structural phenotype of glaucoma as a function of severity was thoroughly described and analyzed, enhancing understanding of its intricate pathology beyond current clinical knowledge.

Objective: To describe the 3-D structural differences in both connective and neural tissues of the optic nerve head (ONH) between different glaucoma stages using traditional and artificial intelligence-driven approaches.

Design, Setting, And Participants: This cross-sectional, clinic-based study recruited 541 Chinese individuals receiving standard clinical care at Singapore National Eye Centre, Singapore, and 112 White participants of a prospective observational study at Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania.

scRNA-sequencing in chick suggests a probabilistic model for cell fate allocation at the neural plate border.

The vertebrate 'neural plate border' is a transient territory located at the edge of the neural plate containing precursors for all ectodermal derivatives: the neural plate, neural crest, placodes and epidermis. Elegant functional experiments in a range of vertebrate models have provided an in-depth understanding of gene regulatory interactions within the ectoderm. However, these experiments conducted at tissue level raise seemingly contradictory models for fate allocation of individual cells.

Tumor-Suppressive and Immunomodulating Activity of miR-30a-3p and miR-30e-3p in HNSCC Cells and Tumoroids.

Head and neck squamous cell carcinomas (HNSCCs) are heterogeneous tumors, well known for their frequent relapsing nature. To counter recurrence, biomarkers for early diagnosis, prognosis, or treatment response prediction are urgently needed. miRNAs can profoundly impact normal physiology and enhance oncogenesis.

Cost-effectiveness of a telemonitoring programme in patients with cardiovascular diseases compared with standard of care.

Objectives: The main aim of this work was to analyse the cost-effectiveness of an integrated care concept (NICC) that combines telemonitoring with the support of a care centre in addition to guideline therapy for patients. Secondary aims were to compare health utility and health-related quality of life (QoL) between NICC and standard of care (SoC).

Methods: The randomised controlled CardioCare MV Trial compared NICC and SoC in patients from Mecklenburg-West Pomerania (Germany) with atrial fibrillation, heart failure or treatment-resistant hypertension.

A gene regulatory network for neural induction.

During early vertebrate development, signals from a special region of the embryo, the organizer, can redirect the fate of non-neural ectoderm cells to form a complete, patterned nervous system. This is called neural induction and has generally been imagined as a single signalling event, causing a switch of fate. Here, we undertake a comprehensive analysis, in very fine time course, of the events following exposure of competent ectoderm of the chick to the organizer (the tip of the primitive streak, Hensen's node).

Medical Application of Geometric Deep Learning for the Diagnosis of Glaucoma.

Purpose: (1) To assess the performance of geometric deep learning in diagnosing glaucoma from a single optical coherence tomography (OCT) scan of the optic nerve head and (2) to compare its performance to that obtained with a three-dimensional (3D) convolutional neural network (CNN), and with a gold-standard parameter, namely, the retinal nerve fiber layer (RNFL) thickness.

Methods: Scans of the optic nerve head were acquired with OCT for 477 glaucoma and 2296 nonglaucoma subjects. All volumes were automatically segmented using deep learning to identify seven major neural and connective tissues.

A decision-support tool for funding health innovations at a tertiary academic medical center.

Objectives: To report the processes used to design and implement an assessment tool to inform funding decisions for competing health innovations in a tertiary hospital.

Methods: We designed an assessment tool for health innovation proposals with three components: "value to the institution," "novelty," and "potential for adoption and scaling." The "value to the institution" component consisted of twelve weighted value attributes identified from the host institution's annual report; weights were allocated based on a survey of the hospital's leaders.

Changes in the characteristics of patients treated for brain metastases with repeat stereotactic radiotherapy (SRT): a retrospective study of 184 patients.

Purpose: Brain metastases (BMs) are the leading cause of intracranial malignant neoplasms in adults. WHO, Karnofsky performance status (KPS), age, number of BMs, extracerebral progression (ECP), recursive partitioning analysis (RPA), diagnosis-specific graded prognostic assessment (Ds-GPA) are validated prognostic tools to help clinicians decide on treatment. No consensus exists for repeat stereotactic radiotherapy (SRT) for BMs.

Geometric Deep Learning to Identify the Critical 3D Structural Features of the Optic Nerve Head for Glaucoma Diagnosis.

Purpose: To compare the performance of 2 relatively recent geometric deep learning techniques in diagnosing glaucoma from a single optical coherence tomographic (OCT) scan of the optic nerve head (ONH); and to identify the 3-dimensional (3D) structural features of the ONH that are critical for the diagnosis of glaucoma.

Design: Comparison and evaluation of deep learning diagnostic algorithms.

Methods: In this study, we included a total of 2247 nonglaucoma and 2259 glaucoma scans from 1725 participants.

Comparison of telemonitoring combined with intensive patient support with standard care in patients with chronic cardiovascular disease - a randomized clinical trial.

Importance: Healthcare concepts for chronic diseases based on tele-monitoring have become increasingly important during COVID-19 pandemic.

Objective: To study the effectiveness of a novel integrated care concept (NICC) that combines tele-monitoring with the support of a call centre in addition to guideline therapy for patients with atrial fibrillation, heart failure, or treatment-resistant hypertension.

Design: A prospective, parallel-group, open-label, randomized, controlled trial.

Acute toxicities and cumulative dose to the brain of repeated sessions of stereotactic radiotherapy (SRT) for brain metastases: a retrospective study of 184 patients.

Background: Stereotactic radiation therapy (SRT) is a focal treatment for brain metastases (BMs); thus, 20 to 40% of patients will require salvage treatment after an initial SRT session, either because of local or distant failure. SRT is not exempt from acute toxicity, and the acute toxicities of repeated SRT are not well known. The objective of this study was to analyze the acute toxicities of repeated courses of SRT and to determine whether repeated SRT could lead to cumulative brain doses equivalent to those of whole-brain radiotherapy (WBRT).

AI-based clinical assessment of optic nerve head robustness superseding biomechanical testing.

Background/aims: To use artificial intelligence (AI) to: (1) exploit biomechanical knowledge of the optic nerve head (ONH) from a relatively large population; (2) assess ONH robustness (ie, sensitivity of the ONH to changes in intraocular pressure (IOP)) from a single optical coherence tomography (OCT) volume scan of the ONH without the need for biomechanical testing and (3) identify what critical three-dimensional (3D) structural features dictate ONH robustness.

Methods: 316 subjects had their ONHs imaged with OCT before and after acute IOP elevation through ophthalmo-dynamometry. IOP-induced lamina cribrosa (LC) deformations were then mapped in 3D and used to classify ONHs.

Comparison of calling pipelines for whole genome sequencing: an empirical study demonstrating the importance of mapping and alignment.

Rapid advances in high-throughput DNA sequencing technologies have enabled the conduct of whole genome sequencing (WGS) studies, and several bioinformatics pipelines have become available. The aim of this study was the comparison of 6 WGS data pre-processing pipelines, involving two mapping and alignment approaches (GATK utilizing BWA-MEM2 2.2.

Detection of m6A from direct RNA sequencing using a multiple instance learning framework.

RNA modifications such as m6A methylation form an additional layer of complexity in the transcriptome. Nanopore direct RNA sequencing can capture this information in the raw current signal for each RNA molecule, enabling the detection of RNA modifications using supervised machine learning. However, experimental approaches provide only site-level training data, whereas the modification status for each single RNA molecule is missing.

Discriminating Between Papilledema and Optic Disc Drusen Using 3D Structural Analysis of the Optic Nerve Head.

Background And Objectives: The distinction of papilledema from other optic nerve head (ONH) lesions mimicking papilledema, such as optic disc drusen (ODD), can be difficult in clinical practice. We aimed the following: (1) to develop a deep learning algorithm to automatically identify major structures of the ONH in 3-dimensional (3D) optical coherence tomography (OCT) scans and (2) to exploit such information to robustly differentiate among ODD, papilledema, and healthy ONHs.

Methods: This was a cross-sectional comparative study of patients from 3 sites (Singapore, Denmark, and Australia) with confirmed ODD, those with papilledema due to raised intracranial pressure, and healthy controls.

Guidelines of the French Society of ENT (SFORL): Drug-induced sleep endoscopy in adult obstructive sleep apnea syndrome.

Objectives: To determine the indications, anesthesiological and surgical procedure and interest of drug-induced sleep endoscopy in the treatment of adult obstructive sleep apnea syndrome.

Design: A redactional committee of 17 experts was set up. Conflicts of interest were disclosed and followed up throughout the process of drawing up the guidelines.

Sox8 remodels the cranial ectoderm to generate the ear.

The vertebrate inner ear arises from a pool of progenitors with the potential to contribute to all the sense organs and cranial ganglia in the head. Here, we explore the molecular mechanisms that control ear specification from these precursors. Using a multiomics approach combined with loss-of-function experiments, we identify a core transcriptional circuit that imparts ear identity, along with a genome-wide characterization of noncoding elements that integrate this information.

Ellipsoid calculations versus manual tumor delineations for glioblastoma tumor volume evaluation.

In glioblastoma, the response to treatment assessment is essentially based on the 2D tumor size evolution but remains disputable. Volumetric approaches were evaluated for a more accurate estimation of tumor size. This study included 57 patients and compared two volume measurement methods to determine the size of different glioblastoma regions of interest: the contrast-enhancing area, the necrotic area, the gross target volume and the volume of the edema area.

The genomic origins of the world's first farmers.

The precise genetic origins of the first Neolithic farming populations in Europe and Southwest Asia, as well as the processes and the timing of their differentiation, remain largely unknown. Demogenomic modeling of high-quality ancient genomes reveals that the early farmers of Anatolia and Europe emerged from a multiphase mixing of a Southwest Asian population with a strongly bottlenecked western hunter-gatherer population after the last glacial maximum. Moreover, the ancestors of the first farmers of Europe and Anatolia went through a period of extreme genetic drift during their westward range expansion, contributing highly to their genetic distinctiveness.