Repeatability of AI-based, automatic measurement of vertebral and cardiovascular imaging biomarkers in low-dose chest CT: the ImaLife cohort.

Objective: To evaluate the repeatability of AI-based automatic measurement of vertebral and cardiovascular markers on low-dose chest CT.

Methods: We included participants of the population-based Imaging in Lifelines (ImaLife) study with low-dose chest CT at baseline and 3-4 month follow-up. An AI system (AI-Rad Companion chest CT prototype) performed automatic segmentation and quantification of vertebral height and density, aortic diameters, heart volume (cardiac chambers plus pericardial fat), and coronary artery calcium volume (CACV).

CT-based airway changes after smoking cessation in the general population.

Purpose: Previous research has demonstrated improvements in CT-derived bronchial parameters in the first years after smoking cessation. This study investigates the association between longer smoking cessation duration and bronchial parameters in lung-healthy and lung-unhealthy ex-smokers from the general population.

Materials And Methods: We conducted a cross-sectional analysis using low-dose CT scans of ex-smokers from the general population with at least 10 pack-years from the ImaLife study, a sub study within the Lifelines cohort.

Pathophysiological processes underlying hidden hearing loss revealed in Kcnt1/2 double knockout mice.

Presbycusis is a prevalent condition in older adults characterized by the progressive loss of hearing due to age-related changes in the cochlea, the auditory portion of the inner ear. Many adults also struggle with understanding speech in noise despite having normal auditory thresholds, a condition termed "hidden" hearing loss because it evades standard audiological assessments. Examination of animal models and postmortem human tissue suggests that hidden hearing loss is also associated with age-related changes in the cochlea and may, therefore, precede overt age-related hearing loss.

Effect of emphysema on AI software and human reader performance in lung nodule detection from low-dose chest CT.

Background: Emphysema influences the appearance of lung tissue in computed tomography (CT). We evaluated whether this affects lung nodule detection by artificial intelligence (AI) and human readers (HR).

Methods: Individuals were selected from the "Lifelines" cohort who had undergone low-dose chest CT.

Functional, Morphological and Molecular Changes Reveal the Mechanisms Associated with Age-Related Vestibular Loss.

Age-related loss of vestibular function and hearing are common disorders that arise from the loss of function of the inner ear and significantly decrease quality of life. The underlying pathophysiological mechanisms are poorly understood and difficult to investigate in humans. Therefore, our study examined young (1.

Genome-Wide Scans and Transcriptomic Analyses Characterize Selective Changes as a Result of Chlorantraniliprole Resistance in .

Pesticide resistance in insects is an example of adaptive evolution occurring in pest species and is driven by the artificial introduction of pesticides. The diamondback moth (DBM), (Lepidoptera: Plutellidae), has evolved resistance to various insecticides. Understanding the genetic changes underpinning the resistance to pesticides is necessary for the implementation of pest control measures.

Transcriptome-Guided Identification of Drugs for Repurposing to Treat Age-Related Hearing Loss.

Age-related hearing loss (ARHL) or presbycusis is a prevalent condition associated with social isolation, cognitive impairment, and dementia. Age-related changes in the cochlea, the auditory portion of the inner ear, are the primary cause of ARHL. Unfortunately, there are currently no pharmaceutical approaches to treat ARHL.

Functional, Morphological, and Evolutionary Characterization of Hearing in Subterranean, Eusocial African Mole-Rats.

Naked mole-rats are highly vocal, eusocial, subterranean rodents with, counterintuitively, poor hearing. The causes underlying their altered hearing are unknown. Moreover, whether altered hearing is degenerate or adaptive to their unique lifestyles is controversial.

Tempo and Pattern of Avian Brain Size Evolution.

Relative brain sizes in birds can rival those of primates, but large-scale patterns and drivers of avian brain evolution remain elusive. Here, we explore the evolution of the fundamental brain-body scaling relationship across the origin and evolution of birds. Using a comprehensive dataset sampling> 2,000 modern birds, fossil birds, and theropod dinosaurs, we infer patterns of brain-body co-variation in deep time.

Sodium-activated potassium channels shape peripheral auditory function and activity of the primary auditory neurons in mice.

Potassium (K) channels shape the response properties of neurons. Although enormous progress has been made to characterize K channels in the primary auditory neurons, the molecular identities of many of these channels and their contributions to hearing in vivo remain unknown. Using a combination of RNA sequencing and single molecule fluorescent in situ hybridization, we localized expression of transcripts encoding the sodium-activated potassium channels K1.

Whole-genome resequencing reveals signatures of selection and timing of duck domestication.

Background: The genetic basis of animal domestication remains poorly understood, and systems with substantial phenotypic differences between wild and domestic populations are useful for elucidating the genetic basis of adaptation to new environments as well as the genetic basis of rapid phenotypic change. Here, we sequenced the whole genome of 78 individual ducks, from two wild and seven domesticated populations, with an average sequencing depth of 6.42X per individual.

Potential for bias and low precision in molecular divergence time estimation of the Canopy of Life: an example from aquatic bird families.

Uncertainty in divergence time estimation is frequently studied from many angles but rarely from the perspective of phylogenetic node age. If appropriate molecular models and fossil priors are used, a multi-locus, partitioned analysis is expected to equally minimize error in accuracy and precision across all nodes of a given phylogeny. In contrast, if available models fail to completely account for rate heterogeneity, substitution saturation and incompleteness of the fossil record, uncertainty in divergence time estimation may increase with node age.

The Fossil Calibration Database-A New Resource for Divergence Dating.

Fossils provide the principal basis for temporal calibrations, which are critical to the accuracy of divergence dating analyses. Translating fossil data into minimum and maximum bounds for calibrations is the most important-often least appreciated-step of divergence dating. Properly justified calibrations require the synthesis of phylogenetic, paleontological, and geological evidence and can be difficult for nonspecialists to formulate.

A multi-locus inference of the evolutionary diversification of extant flamingos (Phoenicopteridae).

Background: Modern flamingos (Phoenicopteridae) occupy a highly specialized ecology unique among birds and represent a potentially powerful model system for informing the mechanisms by which a lineage of birds adapts and radiates. However, despite a rich fossil record and well-studied feeding morphology, molecular investigations of the evolutionary progression among modern flamingos have been limited. Here, using three mitochondrial (mtDNA) markers, we present the first DNA sequence-based study of population genetic variation in the widely distributed Chilean Flamingo and, using two mtDNA and 10 nuclear (nDNA) markers, recover the species tree and divergence time estimates for the six extant species of flamingos.

Genome skimming identifies polymorphism in tern populations and species.

Background: Terns (Charadriiformes: Sterninae) are a lineage of cosmopolitan shorebirds with a disputed evolutionary history that comprises several species of conservation concern. As a non-model system in genetics, previous study has left most of the nuclear genome unexplored, and population-level studies are limited to only 15% of the world's species of terns and noddies. Screening of polymorphic nuclear sequence markers is needed to enhance genetic resolution because of supposed low mitochondrial mutation rate, documentation of nuclear insertion of hypervariable mitochondrial regions, and limited success of microsatellite enrichment in terns.

Synthesizing and databasing fossil calibrations: divergence dating and beyond.

Divergence dating studies, which combine temporal data from the fossil record with branch length data from molecular phylogenetic trees, represent a rapidly expanding approach to understanding the history of life. National Evolutionary Synthesis Center hosted the first Fossil Calibrations Working Group (3-6 March, 2011, Durham, NC, USA), bringing together palaeontologists, molecular evolutionists and bioinformatics experts to present perspectives from disciplines that generate, model and use fossil calibration data. Presentations and discussions focused on channels for interdisciplinary collaboration, best practices for justifying, reporting and using fossil calibrations and roadblocks to synthesis of palaeontological and molecular data.

Source-sink dynamics structure a common montane mammal.

Assessing the relative role of evolutionary processes on genetic diversity is critical for understanding species response to climatic change. However, many processes, independent of climate, can lead to the same genetic pattern. Because effective population size and gene flow are affected directly by abundance and dispersal, population ecology has the potential to profoundly influence patterns of genetic variation over microevolutionary timescales.

Fire and ice: genetic structure of the Uinta ground squirrel (Spermophilus armatus) across the Yellowstone hotspot.

The range of the Uinta ground squirrel, Spermophilus armatus, is centred over one of the most tectonically active regions today, the Yellowstone hotspot. We document the role of Quaternary tectonic and climatic history on the genetic structure of this species by screening museum and extant individuals throughout its range. Phylogeographic, divergence time, and demographic analyses of partial mitochondrial cytochrome b and control region DNA sequences yield insight into the cadence of evolution across three spatiotemporal scales: (i) a relatively deep intraspecific divergence of S.

The shifting baseline of northern fur seal ecology in the northeast Pacific Ocean.

Historical data provide a baseline against which to judge the significance of recent ecological shifts and guide conservation strategies, especially for species decimated by pre-20th century harvesting. Northern fur seals (NFS; Callorhinus ursinus) are a common pinniped species in archaeological sites from southern California to the Aleutian Islands, yet today they breed almost exclusively on offshore islands at high latitudes. Harvest profiles from archaeological sites contain many unweaned pups, confirming the presence of temperate-latitude breeding colonies in California, the Pacific Northwest, and the eastern Aleutian Islands.

Insertion events of CR1 retrotransposable elements elucidate the phylogenetic branching order in galliform birds.

Using standard phylogenetic methods, it can be hard to resolve the order in which speciation events took place when new lineages evolved in the distant past and within a short time frame. As an example, phylogenies of galliform birds (including well-known species such as chicken, turkey, and quail) usually show low bootstrap support values at short internal branches, reflecting the rapid diversification of these birds in the Eocene. However, given the key role of chicken and related poultry species in agricultural, evolutionary, general biological and disease studies, it is important to know their internal relationships.

Studying the effect of environmental change on biotic evolution: past genetic contributions, current work and future directions.

Evolutionary geneticists currently face a major scientific opportunity when integrating across the rapidly increasing amount of genetic data and existing biological scenarios based on ecology, fossils or climate models. Although genetic data acquisition and analysis have improved tremendously, several limitations remain. Here, we discuss the feedback between history and genetic variation in the face of environmental change with increasing taxonomic and temporal scale, as well as the major challenges that lie ahead.

Error in estimation of rate and time inferred from the early amniote fossil record and avian molecular clocks.

The best reconstructions of the history of life will use both molecular time estimates and fossil data. Errors in molecular rate estimation typically are unaccounted for and no attempts have been made to quantify this uncertainty comprehensively. Here, focus is primarily on fossil calibration error because this error is least well understood and nearly universally disregarded.