Both Structural Variant and Single Nucleotide Polymorphism Load Impact Lifetime Fitness in a Threatened Bird Species.

The field of conservation genomics is becoming increasingly interested in whether, and how, structural variant (SV) genotype information can be leveraged in the management of threatened species. The functional consequences of SVs are more complex than for single nucleotide polymorphisms (SNPs), as SVs typically impact a larger proportion of the genome due to their size and thus may be more likely to contribute to load. While the impacts of SV-specific genetic load may be less consequential for large populations, the interplay between weakened selection and stochastic processes means that smaller populations, such as those of the threatened Aotearoa hihi/New Zealand stitchbird (Notiomystis cincta), may harbour a high SV load.

A deep learning based method for left ventricular strain measurements: repeatability and accuracy compared to experienced echocardiographers.

Background: Speckle tracking echocardiography (STE) provides quantification of left ventricular (LV) deformation and is useful in the assessment of LV function. STE is increasingly being used clinically, and every effort to simplify and standardize STE is important. Manual outlining of regions of interest (ROIs) is labor intensive and may influence assessment of strain values.

Demographic drivers of reproductive failure in a threatened bird: Insights from a decade of data.

Hatching failure affects up to 77% of eggs laid by threatened bird species, yet the true prevalence and drivers of egg fertilization failure versus embryo mortality as underlying mechanisms of hatching failure are unknown. Here, using ten years of data comprising 4,371 eggs laid by a population of a threatened bird, the hihi (, we investigate the relative importance of infertility and embryo death as drivers of hatching failure and explore population-level factors associated with them. We show that of the 1,438 eggs that failed to hatch (33% of laid eggs) between 2010 and 2020, 83% failed due to embryo mortality, with the majority failing in the early stages of embryonic development.

A high-density linkage map reveals broad- and fine-scale sex differences in recombination in the hihi (stitchbird; Notiomystis cincta).

Recombination, the process of DNA exchange between homologous chromosomes during meiosis, plays a major role in genomic diversity and evolutionary change. Variation in recombination rate is widespread despite recombination often being essential for progression of meiosis. One such variation is heterochiasmy, where recombination rates differ between sexes.

Differentiation of Myocardial Properties in Physiological Athletic Cardiac Remodeling and Mild Hypertrophic Cardiomyopathy.

Clinical differentiation between athletes' hearts and those with hypertrophic cardiomyopathy (HCM) can be challenging. We aimed to explore the role of speckle tracking echocardiography (STE) and cardiac magnetic resonance imaging (CMR) in the differentiation between athletes' hearts and those with mild HCM. We compared 30 competitive endurance elite athletes (7% female, age 41 ± 9 years) and 20 mild phenotypic mutation-positive HCM carriers (15% female, age 51 ± 12 years) with left ventricular wall thickness 13 ± 1 mm.

Deep learning for automated left ventricular outflow tract diameter measurements in 2D echocardiography.

Background: Measurement of the left ventricular outflow tract diameter (LVOTd) in echocardiography is a common source of error when used to calculate the stroke volume. The aim of this study is to assess whether a deep learning (DL) model, trained on a clinical echocardiographic dataset, can perform automatic LVOTd measurements on par with expert cardiologists.

Methods: Data consisted of 649 consecutive transthoracic echocardiographic examinations of patients with coronary artery disease admitted to a university hospital.

Parental breeding decisions and genetic quality predict social structure of independent offspring.

Across the animal kingdom, newly independent juveniles form social associations that influence later fitness, mate choice and gene flow, but little is known about the ontogeny of social environments, particularly in wild populations. Here we test whether associations among young animals form randomly or are influenced by environmental or genetic conditions established by parents. Parents' decisions determine natal birth sites, which could affect who independent young initially encounter; secondly, mate choice determines genetic condition (e.

Assembly of female and male hihi genomes (stitchbird; Notiomystis cincta) enables characterization of the W chromosome and resources for conservation genomics.

A high-quality reference genome can be a valuable resource for threatened species by providing a foundation to assess their evolutionary potential to adapt to future pressures such as environmental change. We assembled the genome of a female hihi (Notiomysits cincta), a threatened passerine bird endemic to Aotearoa New Zealand. The assembled genome is 1.

Early-life telomere length predicts life-history strategy and reproductive senescence in a threatened wild songbird.

Telomeres are well known for their associations with lifespan and ageing across diverse taxa. Early-life telomere length can be influenced by developmental conditions and has been shown positively affect lifetime reproductive success in a limited number of studies. Whether these effects are caused by a change in lifespan, reproductive rate or perhaps most importantly reproductive senescence is unclear.

Impact of exposure to urban air pollution on grey squirrel (Sciurus carolinensis) lung health.

The increased rate of global urbanisation has recently exacerbated the significant public health problem of traffic related air pollution. Despite the known significant impact on human health, little is known about the effects of air pollution on wildlife health. The lung is the primary target organ for the effects of exposure to air pollution, leading to lung inflammation, altering the lung epigenome, culminating in respiratory disease.

Genomic signatures of inbreeding depression for a threatened Aotearoa New Zealand passerine.

For small and isolated populations, the increased chance of mating between related individuals can result in a substantial reduction in individual and population fitness. Despite the increasing availability of genomic data to measure inbreeding accurately across the genome, inbreeding depression studies for threatened species are still scarce due to the difficulty of measuring fitness in the wild. Here, we investigate inbreeding and inbreeding depression for the extensively monitored Tiritiri Mātangi island population of a threatened Aotearoa New Zealand passerine, the hihi (Notiomystis cincta).

Systematic review of avian hatching failure and implications for conservation.

Avian hatching failure is a widespread phenomenon, affecting around 10% of all eggs that are laid and not lost to predation, damage, or desertion. Our understanding of hatching failure is limited in terms of both its underpinning mechanisms and its occurrence across different populations. It is widely acknowledged that rates of hatching failure are higher in threatened species and in populations maintained in captivity compared to wild, non-threatened species, but these differences have rarely been quantified and any broader patterns remain unexplored.

Disease progression rate is a strong predictor of ventricular arrhythmias in patients with cardiac laminopathies: a primary prevention cohort study.

Aims: Cardiac disease progression prior to first ventricular arrhythmia (VA) in LMNA genotype-positive patients is not described.

Methods And Results: We performed a primary prevention cohort study, including consecutive LMNA genotype-positive patients from our centre. Patients underwent repeated clinical, electrocardiographic, and echocardiographic examinations.

Variation in shape and consistency of selection between populations of the threatened Hihi (Notiomystis cincta).

The shape and intensity of natural selection can vary between years, potentially resulting in a chronic reduction of fitness as individuals need to track a continually changing optimum of fitness (i.e., a "lag load").

Genetic variance in fitness indicates rapid contemporary adaptive evolution in wild animals.

The rate of adaptive evolution, the contribution of selection to genetic changes that increase mean fitness, is determined by the additive genetic variance in individual relative fitness. To date, there are few robust estimates of this parameter for natural populations, and it is therefore unclear whether adaptive evolution can play a meaningful role in short-term population dynamics. We developed and applied quantitative genetic methods to long-term datasets from 19 wild bird and mammal populations and found that, while estimates vary between populations, additive genetic variance in relative fitness is often substantial and, on average, twice that of previous estimates.

Cardiac Structure and Function in Epilepsy Patients with Drug-Resistant Convulsive Seizures.

High frequency of convulsive seizures and long-lasting epilepsy are associated with an increased risk of sudden unexpected death in epilepsy (SUDEP). Structural changes in the myocardium have been described in SUDEP victims. It is speculated that these changes are secondary to frequent convulsive seizures and may predispose to SUDEP.

Who are you? A framework to identify and report genetic sample mix-ups.

Sample mix-ups occur when samples have accidentally been duplicated, mislabelled or swapped. When samples are subsequently genotyped or sequenced, this can lead to individual IDs being incorrectly linked to genetic data, resulting in incorrect or biased research results, or reduced power to detect true biological patterns. We surveyed the community and found that almost 80% of responding researchers have encountered sample mix-ups.

Physiological factors influencing female fertility in birds.

Fertility is fundamental to reproductive success, but not all copulation attempts result in a fertilized embryo. Fertilization failure is especially costly for females, but we still lack a clear understanding of the causes of variation in female fertility across taxa. Birds make a useful model system for fertility research, partly because their large eggs are easily studied outside of the female's body, but also because of the wealth of data available on the reproductive productivity of commercial birds.

The design and application of a 50 K SNP chip for a threatened Aotearoa New Zealand passerine, the hihi.

Next-generation sequencing has transformed the fields of ecological and evolutionary genetics by allowing for cost-effective identification of genome-wide variation. Single nucleotide polymorphism (SNP) arrays, or "SNP chips", enable very large numbers of individuals to be consistently genotyped at a selected set of these identified markers, and also offer the advantage of being able to analyse samples of variable DNA quality. We used reduced representation restriction-aided digest sequencing (RAD-seq) of 31 birds of the threatened hihi (Notiomystis cincta; stitchbird) and low-coverage whole genome sequencing (WGS) of 10 of these birds to develop an Affymetrix 50 K SNP chip.

Synthetic data for annotation and extraction of family history information from clinical text.

Background: The limited availability of clinical texts for Natural Language Processing purposes is hindering the progress of the field. This article investigates the use of synthetic data for the annotation and automated extraction of family history information from Norwegian clinical text. We make use of incrementally developed synthetic clinical text describing patients' family history relating to cases of cardiac disease and present a general methodology which integrates the synthetically produced clinical statements and annotation guideline development.

Genomic data of different resolutions reveal consistent inbreeding estimates but contrasting homozygosity landscapes for the threatened Aotearoa New Zealand hihi.

Inbreeding can lead to a loss of heterozygosity in a population and when combined with genetic drift may reduce the adaptive potential of a species. However, there is uncertainty about whether resequencing data can provide accurate and consistent inbreeding estimates. Here, we performed an in-depth inbreeding analysis for hihi (Notiomystis cincta), an endemic and nationally vulnerable passerine bird of Aotearoa New Zealand.

Neural classification of Norwegian radiology reports: using NLP to detect findings in CT-scans of children.

Background: With a motivation of quality assurance, machine learning techniques were trained to classify Norwegian radiology reports of paediatric CT examinations according to their description of abnormal findings.

Methods: 13.506 reports from CT-scans of children, 1000 reports from CT scan of adults and 1000 reports from X-ray examination of adults were classified as positive or negative by a radiologist, according to the presence of abnormal findings.

Two methods for modifed Doo-Sabin modeling of nonsmooth surfaces-applied to right ventricle modeling.

In recent years, there has been increased clinical interest in the right ventricle (RV) of the heart. RV dysfunction is an important prognostic marker for several cardiac diseases. Accurate modeling of the RV shape is important for estimating the performance.