Non-breeding conditions induce carry-over effects on survival of migratory birds.

Identifying the processes that limit populations is a foundational objective of ecology and an urgent need for conservation. For migratory animals, researchers must study individuals throughout their annual cycles to determine how environmental conditions limit demographic rates within each period of the annual cycle and also between periods through carry-over effects and seasonal interactions.1,2,3,4,5,6 Our poor understanding of the rates and causes of avian migration mortality7 hinders the identification of limiting factors and the reversal of widespread avian population declines.8,9 Here, we implement new methods to estimate apparent survival (hereafter survival) during migration directly from automated telemetry data10 in Kirtland's Warblers (Setophaga kirtlandii) and indirectly from mark-recapture data in Black-throated Blue Warblers (S. caerulescens). Previous experimental and observational studies of our focal species and other migratory songbirds have shown strong effects of Caribbean precipitation and habitat quality on food availability,11,12,13,14 body condition,12,13,14,15,16,17,18,19 migration timing,11,12,15,16,20,21,22,23 natal dispersal,24,25 range dynamics,26 reproductive success,20,22,27 and annual survival.18,19,20,23,28,29,30,31 Building on this research, we test the hypotheses that environmental conditions during the non-breeding period affect subsequent survival during spring migration and breeding. We found that reduced precipitation and environmental productivity in the non-breeding period strongly influenced survival in both species, primarily by reducing survival during spring migration. Our results indicate that climate-driven environmental conditions can carry over to affect survival in subsequent periods and thus likely play an important role in year-round population dynamics. These lethal carry-over effects may be widespread and are likely magnified by intensifying climate change.

Hunting for Early Melanomas With a Maximum Clinical Surface Diameter up to 6 mm: A Prospective Study of Reflectance Confocal Microscopy Features in 68 Consecutive Cases.

BACKGROUND: Early diagnosis of melanoma and prompt effective therapy optimizes prognosis. Reflectance confocal microscopy (RCM) facilitates diagnosis by providing immediate 3D single cell resolution down into the papillary dermis. METHODS: Consecutive cases were examined using a Vivascope 1500 confocal microscope at a single referral medical practice in Sydney, Australia 2019-2023. Melanoma clinical surface diameters were recorded by 0.1 mm increments up to 6.0 mm. The RCM features recorded were: pagetoid single cells or nests, pleomorphic cell shape, atypical dendritic cells, non-edged papillae, variation in melanocyte size and confluent sheets of cells. All cases required diagnostic agreement by two dermatohistopathologists using hematoxylin and eosin staining followed by SOX 10 and/or PRAME stains if required. RESULTS: Total cases were 68: 38 males (mean age 57) and 30 females (mean age 64). Melanoma in situ (n = 65) compared to invasive melanoma (n = 3), all males, invasion depth (0.4-0.5 mm). Most frequent RCM features found in 50% or more of cases within all diameter increments were: pagetoid single cells n = 64/68 (94%), pleomorphic cell shape n = 63/68 (93%), epidermal disarray n = 58/68 (85%), and atypical dendritic cells n = 45/68 (66%). Non-edged dermal papillae were n = 42/68 (62%). CONCLUSION: Melanoma RCM features were found throughout the diameter ranges. Confocal examination may facilitate early melanoma recognition in these ranges.

Scale-dependent population drivers inform avian management in a declining saline lake ecosystem.

Shrinking saline lakes provide irreplaceable habitat for waterbird species globally. Disentangling the effects of wetland habitat loss from other drivers of waterbird population dynamics is critical for protecting these species in the face of unprecedented changes to saline lake ecosystems, ideally through decision-making frameworks that identify effective management options and their potential outcomes. Here, we develop a framework to assess the effects of hypothesized population drivers and identify potential future outcomes of plausible management scenarios on a saline lake-reliant waterbird species. We use 36 years of monitoring data to quantify the effects of environmental conditions on the population size of a regionally important breeding colony of American white pelicans (Pelecanus erythrorhynchos) at Great Salt Lake, Utah, US, then forecast colony abundance under various management scenarios. We found that low lake levels, which allow terrestrial predators access to the colony, are probable drivers of recent colony declines. Without local management efforts, we predicted colony abundance could likely decline approximately 37.3% by 2040, although recent colony observations suggest population declines may be more extreme than predicted. Results from our population projection scenarios suggested that proactive approaches to preventing predator colony access and reversing saline lake declines are crucial for the persistence of the Great Salt Lake pelican colony. Increasing wetland habitat and preventing predator access to the colony together provided the most effective protection, increasing abundance 145.4% above projections where no management actions are taken, according to our population projection scenarios. Given the importance of water levels to the persistence of island-nesting colonial species, proactive approaches to reversing saline lake declines could likely benefit pelicans as well as other avian species reliant on these unique ecosystems.

AC Zeeman effect in microfabricated surface traps.

Quantum processors and atomic clocks based on trapped ions often utilize an ion's hyperfine transition as the qubit state or frequency reference, respectively. These states are a good choice because they are insensitive in first order to magnetic field fluctuations, leading to long coherence times and stable frequency splittings. In trapped ions, however, these states are still subject to the second order AC Zeeman effect due to the necessary presence of an oscillating magnetic field used to confine the ions in a Paul trap configuration. Here, we measure the frequency shift of the 2S1/2 hyperfine transition of a 171Yb+ ion caused by the radio frequency (RF) electromagnetic field used to create confinement in several microfabricated surface trap designs. By comparing different trap designs, we show that two key design modifications significantly reduce the AC Zeeman effect experienced by the ion: (1) an RF ground layer routed directly below the entire RF electrode, and (2) a symmetric RF electrode. Both of these changes lead to better cancellation of the AC magnetic field and, thus, overall reduced frequency shifts due to the AC Zeeman effect and reduced variation across the device. These improvements enable a more homogeneous environment for quantum computing and can reduce errors for precision applications such as atomic clocks.

Can ChatGPT transform cardiac surgery and heart transplantation?

Artificial intelligence (AI) is a transformative technology with many benefits, but also risks when applied to healthcare and cardiac surgery in particular. Surgeons must be aware of AI and its application through generative pre-trained transformers (GPT/ChatGPT) to fully understand what this offers to clinical care, decision making, training, research and education. Clinicians must appreciate that the advantages and potential for transformative change in practice is balanced by risks typified by validation, ethical challenges and medicolegal concerns. ChatGPT should be seen as a tool to support and enhance the skills of surgeons, rather than a replacement for their experience and judgment. Human oversight and intervention will always be necessary to ensure patient safety and to make complex decisions that may require a refined understanding of individual patient circumstances.

Short communication: Accuracy of whole-genome sequence imputation in Angus cattle using within-breed and multi breed reference populations.

Genotype imputation is a standard approach used in the field of genetics. It can be used to fill in missing genotypes or to increase genotype density. Accurate imputed genotypes are required for downstream analyses. In this study, the accuracy of whole-genome sequence imputation for Angus beef cattle was examined using two different ways to form the reference panel, a within-breed reference population and a multi breed reference population. A stepwise imputation was conducted by imputing medium-density (50k) genotypes to high-density, and then to the whole genome sequence (WGS). The reference population consisted of animals with WGS information from the 1 000 Bull Genomes project. The within-breed reference panel comprised 396 Angus cattle, while an additional 2 380 Taurine cattle were added to the reference population for the multi breed reference scenario. Imputation accuracies were variant-wise average accuracies from a 10-fold cross-validation and expressed as concordance rates (CR) and Pearson's correlations (PR). The two imputation scenarios achieved moderate to high imputation accuracies ranging from 0.896 to 0.966 for CR and from 0.779 to 0.834 for PR. The accuracies from two different scenarios were similar, except for PR from WGS imputation, where the within-breed scenario outperformed the multi breed scenario. The result indicated that including a large number of animals from other breeds in the reference panel to impute purebred Angus did not improve the accuracy and may negatively impact the results. In conclusion, the imputed WGS in Angus cattle can be obtained with high accuracy using a within-breed reference panel.

Macro- and micro-genetic environmental sensitivity of yearling weight in Angus beef cattle.

Australian beef cattle experience variable conditions, which may give rise to genotype-by-environment interactions depending on the genotypes' macro- and/or micro-genetic environmental sensitivity (GES). Macro-GES gives rise to genotype-by-environment interactions across definable and shared environments, while micro-GES causes heritable variation of phenotypes, e.g., the performance of progeny from one sire may be more variable than other sires. Yearling weight (YW) is a key trait in Australian Angus cattle that may be impacted by both macro- and micro-GES. Current models for genetic evaluation of YW attempt to account for macro-GES by fitting sire-by-herd interactions (S × H). Variation in micro-GES had not yet been estimated for YW in Australian Angus. The aim of this study was to estimate genetic variation due to macro- and micro-GES in YW of Australian Angus cattle. A reaction norm with contemporary group effects as the environmental covariate was fitted either as an alternative to or in combination with a random S × H effect to account for macro-GES. Double hierarchical generalised linear models (DHGLM), fitted as sire models, were used to estimate the genetic variance of the dispersion as a measure of micro-GES. Variation due to both macro- and micro-GES were found in YW. The variance of the slope of the reaction norm was 0.02-0.03 (SEs 0.00), while the S × H variance accounted for 7% of the phenotypic variance in all models. Results showed that both a random S × H effect and a reaction norm should be included to account for both macro-GES and the additional variation captured by an S × H effect. The heritability of the dispersion on the measurement scale ranged from 0.06 to 0.10 (SEs 0.00) depending on which model was used. It should therefore be possible to alter both macro- and micro-GES of YW in Australian Angus through selection. However, care should be taken to ensure an appropriate data structure when including sire-by-herd interactions in the mean part of a DHGLM; otherwise, it can cause biased estimates of micro-GES.

Exploring genetic variation in potential indicators of resilience in sheep using fibre diameter measured along the wool staple.

Production animals are increasingly exposed to a wide variety of disturbances that can compromise their productivity, health and well-being. As a result, there is a growing need to be able to select animals that are more resilient to environmental disturbances. Fibre diameter variation measured along a wool staple is expected to contain information about how resilient sheep are to the disturbances of their internal and external environment. This study aimed to develop potential resilience indicators from fibre diameter variation, estimate their genetic parameters and assess whether these traits are genetically correlated across three age stages. The study used 6 140 Merino sheep from the Sheep Cooperative Research Centre Information Nucleus Flocks recorded at yearling, 2 years old, and adult ages. Eight potential traits were defined based on theory, literature and exploratory analysis, which were suggested to capture the animal's ability to resist, respond and recover from potential disturbances. Genetic evaluation of the traits was conducted using pedigree-based animal models. The traits were shown to be low to moderately heritable (0.01-0.33) when examined at each of the three age stages. The potential indicators were generally well correlated with one another within age stages. Further, the genetic correlation between the same trait measured at different age stages was moderate to high between yearling and 2 years old (0.35-0.94) and between 2 years old and adults (0.18-0.70), while slightly lower between yearling and adult estimates (0.09-0.62). These results suggest that selection for resilience indicators from fibre diameter is possible; however, further studies are warranted to refine the trait definitions and validate these indicators against other measures of health, fitness and productive performance.

Genomics-informed conservation units reveal spatial variation in climate vulnerability in a migratory bird.

Identifying genetic conservation units (CUs) in threatened species is critical for the preservation of adaptive capacity and evolutionary potential in the face of climate change. However, delineating CUs in highly mobile species remains a challenge due to high rates of gene flow and genetic signatures of isolation by distance. Even when CUs are delineated in highly mobile species, the CUs often lack key biological information about what populations have the most conservation need to guide management decisions. Here we implement a framework for CU identification in the Canada Warbler (Cardellina canadensis), a migratory bird species of conservation concern, and then integrate demographic modelling and genomic offset to guide conservation decisions. We find that patterns of whole genome genetic variation in this highly mobile species are primarily driven by putative adaptive variation. Identification of CUs across the breeding range revealed that Canada Warblers fall into two evolutionarily significant units (ESU), and three putative adaptive units (AUs) in the South, East, and Northwest. Quantification of genomic offset, a metric of genetic changes necessary to maintain current gene-environment relationships, revealed significant spatial variation in climate vulnerability, with the Northwestern AU being identified as the most vulnerable to future climate change. Alternatively, quantification of past population trends within each AU revealed the steepest population declines have occurred within the Eastern AU. Overall, we illustrate that genomics-informed CUs provide a strong foundation for identifying current and future regional threats that can be used to inform management strategies for a highly mobile species in a rapidly changing world.

Targeted amplification-based whole genome sequencing of Monkeypox virus in clinical specimens.

IMPORTANCE: We present a protocol to efficiently sequence genomes of the MPXV-causing mpox. This enables researchers and public health agencies to acquire high-quality genomic data using a rapid and cost-effective approach. Genomic data can be used to conduct surveillance and investigate mpox outbreaks. We present 91 mpox genomes that show the diversity of the 2022 mpox outbreak in Ontario, Canada.

Chromothripsis orchestrates leukemic transformation in blast phase MPN through targetable amplification of DYRK1A.

Chromothripsis, the process of catastrophic shattering and haphazard repair of chromosomes, is a common event in cancer. Whether chromothripsis might constitute an actionable molecular event amenable to therapeutic targeting remains an open question. We describe recurrent chromothripsis of chromosome 21 in a subset of patients in blast phase of a myeloproliferative neoplasm (BP-MPN), which alongside other structural variants leads to amplification of a region of chromosome 21 in ∼25% of patients ('chr21amp'). We report that chr21amp BP-MPN has a particularly aggressive and treatment-resistant phenotype. The chr21amp event is highly clonal and present throughout the hematopoietic hierarchy. DYRK1A , a serine threonine kinase and transcription factor, is the only gene in the 2.7Mb minimally amplified region which showed both increased expression and chromatin accessibility compared to non-chr21amp BP-MPN controls. We demonstrate that DYRK1A is a central node at the nexus of multiple cellular functions critical for BP-MPN development, including DNA repair, STAT signalling and BCL2 overexpression. DYRK1A is essential for BP-MPN cell proliferation in vitro and in vivo , and DYRK1A inhibition synergises with BCL2 targeting to induce BP-MPN cell apoptosis. Collectively, these findings define the chr21amp event as a prognostic biomarker in BP-MPN and link chromothripsis to a druggable target.

Informing the use of a supplementary immunisation programme for the management of a community cluster of invasive meningococcal disease, Yorkshire, 2022.

OBJECTIVES: To outline the management of a community cluster of serogroup B invasive meningococcal disease (IMD) cases, including key factors for decision making and the choice and implementation of control measures. STUDY DESIGN: Descriptive report of cluster management. METHODS: Subtyping of IMD cases identified a number of potentially linked cases in a defined geographical area. An Incident Management Team (IMT) was convened to coordinate the public health response. A case definition was developed in order to identify further cases within the cluster. RESULTS: Four cases of IMD met the case definition and were initially considered as part of this cluster. Three resided in the same small town, which was the focus for public health management. The IMT agreed that it would be proportionate to instigate additional control measures. The population at higher risk of infection were identified, and a supplementary vaccination programme was rolled out in the community. Over five clinics, 45.6% (639/1401) of the target cohort received at least one dose of the vaccine, with 34.7% (486/1401) receiving both doses. Inequalities in uptake were observed by sex, age and deprivation. CONCLUSIONS: Decision making for public health responses to IMD clusters is complex. Informed by epidemiological evidence, numerous partners engaged in collaborative decision making, which was critical for the effective implementation of the community response. Links between the local authority public health team and the community enabled the use of existing structures and relationships to maximise the number of vaccinations delivered. No further cases of IMD linked to this cluster were identified.

Deliberate foreign body ingestion in patients with underlying mental illness: A retrospective multicentre study.

OBJECTIVE: Deliberate foreign body ingestion (DFBI) is characterised by recurrent presentations among patients with mental health conditions, intellectual disabilities and in prisoners. We aimed to profile the characteristics and evaluate the care of such patients in this study. METHODS: Adult patients with an endoscopic record of attempted foreign body retrieval between January 2013 and September 2020 were identified at three Australian hospitals. Those with a documented mental health diagnosis were included and their standard medical records reviewed. Presentation history, demographics, comorbidities and endoscopic findings were recorded and described. RESULTS: A total of 166 admissions were accounted for by 35 patients, 2/3 of which had borderline personality disorder (BPD). Repetitive presentations occurred in more than half of the cohort. There was an increased trend of hospital admissions throughout the years. At least half of the cohort had a documented mental health review during their admission. An average of 3.3 (2.9) foreign bodies were ingested per single episode. Endoscopic intervention was performed in 76.5% of incidents. The combined Length of stay for all patients was 680 days. CONCLUSION: Deliberate foreign body ingestion in mental health patients is a common, recurring and challenging problem that is increasing in frequency and requires collaborative research to further guide holistic management.

Supplementing Ca salts of soybean oil via low-moisture molasses-based blocks to improve reproductive performance and overall productivity of beef cows.

This experiment evaluated reproductive and productive responses of beef cows receiving self-fed low-moisture blocks (LMB) enriched or not with Ca salts of soybean oil (CSSO) throughout the breeding season. Non-pregnant, suckled multiparous Angus-influenced cows were assigned to a fixed-time artificial insemination (AI) protocol (day -10 to 0) followed by natural service (day 15-70). Cows were managed in 12 groups (46 ± 4 cows/group) maintained in individual pastures, and groups received LMB enriched with 25 % (as-fed basis) of CSSO or ground corn (CON) from day - 10 to 100. Both treatments were designed to yield a daily LMB intake of 0.454 kg/cow (as-fed basis). Cows receiving CSSO had greater (P < 0.01) mean concentrations of ω-6 fatty acids in plasma samples collected on days 0 and 55. Cows receiving CSSO had greater (P = 0.05) pregnancy rate to fixed-time AI (67.2 vs. 59.3 %), whereas final pregnancy rate did not differ (P = 0.92) between treatments. Pregnancy loss was less (P = 0.03) in CSSO cows (4.50 vs. 9.04 %), which also calved earlier during the calving season (treatment × week; P = 0.04). Weaning rate tended to be greater (P = 0.09) in CSSO (84.8 vs. 79.4 %), although calf weaning age and weight did not differ (P ≥ 0.72) between treatments. Kilos of calf weaned/cow exposed was greater (P = 0.04) in CSSO cows (234 vs. 215 kg). Therefore, supplementing CSSO to beef cows via LMB during the breeding season improved their reproductive and overall productivity during a cow-calf cycle.

Anorexia in Medicare Fee-for-Service Beneficiaries: A Claims-Based Analysis of Epidemiology and Mortality.

OBJECTIVES: Loss of appetite in older adults can lead to malnutrition, weight loss, frailty, and death, but little is known about its epidemiology in the United States (US). The objective of this study was to estimate the annual prevalence and incidence of anorexia in older adults with Medicare fee-for-service (FFS) health insurance. DESIGN: Retrospective and observational analysis of administrative health insurance claims data. SETTING: This study included Medicare FFS claims from all settings (eg, hospital inpatient/outpatient, office, assisted living facility, skilled nursing facility, hospice, rehabilitation facility, home). PARTICIPANTS: This study included all individuals aged 65 to 115 years old with continuous Medicare FFS medical coverage (Parts A and/or B) for at least one 12-month period from October 1, 2015, to September 30, 2021 (ie, approximately 30 million individuals each year). INTERVENTION: Not applicable. MEASUREMENTS: Anorexia was identified using medical claims with the ICD-10 diagnosis code "R63.0: Anorexia". This study compared individuals with anorexia to a control group without anorexia with respect to demographics, comorbidities using the Charlson Comorbidity Index (CCI), Claims-based Frailty Index (CFI), and annual mortality. The annual prevalence and incidence of anorexia were estimated for each 12-month period from October 1, 2015, to September 30, 2021. RESULTS: The number of individuals with anorexia ranged from 317,964 to 328,977 per year, a mean annual prevalence rate of 1.1%. The number of individuals newly diagnosed with anorexia ranged from 243,391 to 281,071 per year, a mean annual incidence rate of 0.9%. Individuals with anorexia had a mean (±standard deviation) age of 80.5±8.7 years (vs 74.9±7.5 years without anorexia; p<.001), 64.4% were female (vs 53.8%; p<.001), and 78.4% were White (vs 83.2%; p<.001). The most common CCI comorbidities for those with anorexia were chronic pulmonary disease (39.4%), dementia (38.3%), and peripheral vascular disease (38.0%). Median (interquartile range [IQR]) CCI with anorexia was 4 [5] (vs 1 [3] without anorexia; p<.001). The annual mortality rate among those with anorexia was 22.3% (vs 4.1% without anorexia; relative risk 5.49 [95% confidence interval, 5.45-5.53]). CONCLUSION: Approximately 1% of all adults aged 65-115 years old with Medicare FFS insurance are diagnosed with anorexia each year based on ICD-10 codes reported in claims. These individuals have a higher comorbidity burden and an increased risk of annual mortality compared to those without a diagnosis of anorexia. Further analyses are needed to better understand the relationship between anorexia, comorbidities, frailty, mortality, and other health outcomes.

An ecologist's introduction to continuous-time multi-state models for capture-recapture data.

Recent technological advances have led to a rapid increase in the collection of capture-recapture data in continuous time. Unlike traditional capture-recapture data, the detection times from these technologies are themselves random variables and analysis of these data, therefore, requires models that properly account for stochasticity in both state transitions and detection times. Despite the ubiquity of continuously collected capture-recapture data, the mathematical concepts needed to fit continuous-time models remain unfamiliar to many ecologists. In this paper, I provide an introduction to continuous-time models, with a focus on multi-state capture-recapture data. After reviewing the basic structure of these models, I describe several variations, including constant parameters, temporal variation in state transition rates and autocorrelation in detections. To aid comprehension, each model is accompanied by code to simulate data and fit the model in Stan. Although the models presented in this guide are only a small subset of the variations that are possible to suit the needs of specific datasets or questions, the concepts and code will hopefully serve as a foundation for future analyses, allowing ecologists to develop new and creative approaches to continuous-time modelling.

Gastrointestinal aspects of Peutz-Jeghers syndrome.

There are two main problems in the clinical management of the gastrointestinal (GI) tract in patients with Peutz-Jeghers syndrome (PJS), namely long-term cancer risk and managing polyp related complications (of which the most important clinically is intussusception). Given the rarity of this condition, the evidence base upon which to make recommendations is small. Furthermore, controversies persist regarding the relationship between PJ polyps, cancer development and cancer risk. In this article we will explore some of these controversies, to put into context the recommendations for clinical management of these patients. We will provide an overview, particularly focusing on clinical data, and on the recommendations for clinical management and surveillance of the GI tract in PJS. We highlight knowledge gaps which need to be addressed by further research.

Fluorescence in situ hybridisation in Carnoy's fixed tonsil tissue.

Fluorescence in situ hybridisation (FISH) is a powerful molecular technique that enables direct visualisation of specific bacterial species. Few studies have established FISH protocols for tonsil tissue in Carnoy's fixative, accordingly limiting its application to investigate the pathogenesis of tonsillar hyperplasia. Tonsil tissue from 24 children undergoing tonsillectomy for either recurrent tonsillitis or sleep-disordered breathing were obtained during a previous study. The specificity of each of the five FISH probes (Fusobacterium spp., Bacteroides spp., Streptococcus spp., Haemophilus influenzae and Pseudomonas spp.) were successfully optimised using pure and mixed bacterial isolates, and in Carnoy's fixed tonsil tissue. Bacteroides spp. were present in 100% of patients with microcolonies. In comparison, the prevalence of Fusobacterium spp. was 93.8%, Streptococcus spp. 85.7%, H. influenzae 82.35% and Pseudomonas spp. 76.5%. Notable differences in the organisation of bacterial taxa within a single microcolony were also observed. This is the first study to establish a robust FISH protocol identifying multiple aerobic and anaerobic bacteria in Carnoy's fixed tonsil tissue. This protocol provides a strong foundation for combining histological and microbiological analyses of Carnoy's fixed tonsil samples. It may also have important implications on the analysis of microorganisms in other human tissues prepared using the same techniques.