Native prey, not landscape change or novel prey, drive cougar (Puma concolor) distribution at a boreal forest range edge.

Many large carnivores, despite widespread habitat alteration, are rebounding in parts of their former ranges after decades of persecution and exploitation. Cougars (Puma concolor) are apex predator with their remaining northern core range constricted to mountain landscapes and areas of western North America; however, cougar populations have recently started rebounding in several locations across North America, including northward in boreal forest landscapes. A camera-trap survey of multiple landscapes across Alberta, Canada, delineated a range edge; within this region, we deployed an array of 47 camera traps in a random stratified design across a landscape spanning a gradient of anthropogenic development relative to the predicted expansion front. We completed multiple hypotheses in an information-theoretic framework to determine if cougar occurrence is best explained by natural land cover features, anthropogenic development features, or competitor and prey activity. We predicted that anthropogenic development features from resource extraction and invading white-tailed deer (Odocoileus virgianius) explain cougar distribution at this boreal range edge. Counter to our predictions, the relative activity of native prey, predominantly snowshoe hare (Lepus americanus), was the best predictor of cougar occurrence at this range edge. Small-bodied prey items are particularly important for female and sub-adult cougars and may support breeding individuals in the northeast boreal forest. Also, counter to our predictions, there was not a strong relationship detected between cougar occurrence and gray wolf (Canis lupus) activity at this range edge. However, further investigation is recommended as the possibility of cougar expansion into areas of the multi-prey boreal system, where wolves have recently been controlled, could have negative consequences for conservation goals in this region (e.g. the recovery of woodland caribou [Rangifer tarandus caribou]). Our study highlights the need to monitor contemporary distributions to inform conservation management objectives as large carnivores recover across North America.

Plasmid partitioning driven by collective migration of ParA between nucleoid lobes.

The ParABS system is crucial for the faithful segregation and inheritance of many bacterial chromosomes and low-copy-number plasmids. However, despite extensive research, the spatiotemporal dynamics of the ATPase ParA and its connection to the dynamics and positioning of the ParB-coated cargo have remained unclear. In this study, we utilize high-throughput imaging, quantitative data analysis, and computational modeling to explore the in vivo dynamics of ParA and its interaction with ParB-coated plasmids and the nucleoid. As previously observed, we find that F-plasmid ParA undergoes collective migrations ("flips") between cell halves multiple times per cell cycle. We reveal that a constricting nucleoid is required for these migrations and that they are triggered by a plasmid crossing into the cell half with greater ParA. Using simulations, we show that these dynamics can be explained by the combination of nucleoid constriction and cooperative ParA binding to the DNA, in line with the behavior of other ParA proteins. We further show that these ParA flips act to equally partition plasmids between the two lobes of the constricted nucleoid and are therefore important for plasmid stability, especially in fast growth conditions for which the nucleoid constricts early in the cell cycle. Overall, our work identifies a second mode of action of the ParABS system and deepens our understanding of how this important segregation system functions.

Mid-cell migration of the chromosomal terminus is coupled to origin segregation in Escherichia coli.

Bacterial chromosomes are dynamically and spatially organised within cells. In slow-growing Escherichia coli, the chromosomal terminus is initially located at the new pole and must therefore migrate to midcell during replication to reproduce the same pattern in the daughter cells. Here, we use high-throughput time-lapse microscopy to quantify this transition, its timing and its relationship to chromosome segregation. We find that terminus centralisation is a rapid discrete event that occurs ~25 min after initial separation of duplicated origins and ~50 min before the onset of bulk nucleoid segregation but with substantial variation between cells. Despite this variation, its movement is tightly coincident with the completion of origin segregation, even in the absence of its linkage to the divisome, suggesting a coupling between these two events. Indeed, we find that terminus centralisation does not occur if origin segregation away from mid-cell is disrupted, which results in daughter cells having an inverted chromosome organisation. Overall, our study quantifies the choreography of origin-terminus positioning and identifies an unexplored connection between these loci, furthering our understanding of chromosome segregation in this bacterium.

A mixed-method survey to understand the role of dog welfare organisations in Ireland, including reported challenges and potential solutions.

BACKGROUND: This novel study forms part of a larger research programme seeking an improved understanding of aspects of the owned dog population in Ireland. Dog welfare organisations (DWOs) in Ireland are recognised as an instrumental pillar of the animal welfare sector with some receiving substantial public funding. We conducted a survey of DWOs in Ireland (n = 39) to gain a better understanding of their role and function, including their policies and procedures and the rehoming of dogs to other regions. In addition, we wanted to get a better understanding of the challenges experienced by DWOs in fulfilling their role and their perspectives on potential solutions to these challenges. The survey questions consisted of closed and open-ended items. Closed items were analysed quantitively; open-ended items were analysed thematically. RESULTS: Most DWOs (> 80%) had written protocols for important welfare actions including rehoming procedures, assessment of owner suitability and euthanasia. DWOs sent dogs to Northern Ireland (13%), Great Britain (38.5%) and to other countries outside the United Kingdom (36%, including Germany, Sweden, Italy, the Netherlands and Czechia). Reported challenges included a general lack of funding, limited public awareness of the importance of dog welfare and insufficient capacity to handle dog numbers. To address these challenges, the DWOs highlighted the potential contribution of subsidised programmes and access to resources to educate potential owners. In a further qualitative evaluation to capture perceptions of appropriate solutions by DWOs, several themes emerged, relating to legislation, education, an overwhelmed workforce, and funding. CONCLUSIONS: This study provides important insights into the roles and functions of DWOs and challenges they experience in Ireland. It is hoped that the findings from this research will inform future research investigating potential solutions to these challenges as well as the development of policy in Ireland.

Partition complex structure can arise from sliding and bridging of ParB dimers.

In many bacteria, chromosome segregation requires the association of ParB to the parS-containing centromeric region to form the partition complex. However, the structure and formation of this complex have been unclear. Recently, studies have revealed that CTP binding enables ParB dimers to slide along DNA and condense the centromeric region through the formation of DNA bridges. Using semi-flexible polymer simulations, we demonstrate that these properties can explain partition complex formation. Transient ParB bridges organize DNA into globular states or hairpins and helical structures, depending on bridge lifetime, while separate simulations show that ParB sliding reproduces the multi-peaked binding profile observed in Caulobacter crescentus. Combining sliding and bridging into a unified model, we find that short-lived ParB bridges do not impede sliding and can reproduce both the binding profile and condensation of the nucleoprotein complex. Overall, our model elucidates the mechanism of partition complex formation and predicts its fine structure.

☠Track: Inferred counting and tracking of replicating DNA loci.

Fluorescent microscopy is the primary method to study DNA organization within cells. However, the variability and low signal/noise commonly associated with live-cell time-lapse imaging challenges quantitative measurements. In particular, obtaining quantitative or mechanistic insight often depends on the accurate tracking of fluorescent particles. Here, we present ★Track, an inference method that determines the most likely temporal tracking of replicating intracellular particles such DNA loci while accounting for missing, merged, and spurious detections. It allows the accurate prediction of particle copy numbers as well as the timing of replication events. We demonstrate ★Track's abilities and gain new insight into plasmid copy number control and the volume dependence of bacterial chromosome replication initiation. By enabling the accurate tracking of DNA loci, ★Track can help to uncover the mechanistic principles of chromosome organization and dynamics across a range of systems.

A Qualitative Exploration of Challenges and Opportunities for Dog Welfare in Ireland Post COVID-19, as Perceived by Dog Welfare Organisations.

This novel qualitative study identifies challenges and opportunities to improve dog welfare in Ireland, as perceived by dog welfare organisations (DWOs), a previously underutilised stakeholder. This study sought the views of this predominantly voluntary sector of the next steps for policy and action in dog welfare, in light of the effects of the "puppy pandemic", increased costs and COVID-19 restrictions. An integrated online focus group and interview design involving DWOs was analysed using inductive thematic analysis. Thematic analysis identified 2 key themes: (1) Key challenges and solutions in general dog welfare and (2) Challenges and opportunities in the welfare organisation sector. DWOs perceived poor public awareness of appropriate dog-husbandry, inadequate legislation enforcement, negative impact of puppy farms, and increased financial and volunteer burden. DWOs helped construct a best practice rehoming pathway, identified how overall standards could be improved and recommendations to enhance dog welfare. The DWOs perceived an increased numbers of households acquiring dogs, difficulties in rehoming, and financial challenges as threatening their viability as organisations and Irish dog welfare. Greater enforcement of legislation, greater communication between organisations and the government, and more media awareness were seen as helpful by the DWOs to improve dog welfare standards and their organisations.

High-throughput imaging and quantitative analysis uncovers the nature of plasmid positioning by ParABS.

The faithful segregation and inheritance of bacterial chromosomes and low-copy number plasmids requires dedicated partitioning systems. The most common of these, ParABS, consists of ParA, a DNA-binding ATPase and ParB, a protein that binds to centromeric-like parS sequences on the DNA cargo. The resulting nucleoprotein complexes are believed to move up a self-generated gradient of nucleoid-associated ParA. However, it remains unclear how this leads to the observed cargo positioning and dynamics. In particular, the evaluation of models of plasmid positioning has been hindered by the lack of quantitative measurements of plasmid dynamics. Here, we use high-throughput imaging, analysis and modelling to determine the dynamical nature of these systems. We find that F plasmid is actively brought to specific subcellular home positions within the cell with dynamics akin to an over-damped spring. We develop a unified stochastic model that quantitatively explains this behaviour and predicts that cells with the lowest plasmid concentration transition to oscillatory dynamics. We confirm this prediction for F plasmid as well as a distantly-related ParABS system. Our results indicate that ParABS regularly positions plasmids across the nucleoid but operates just below the threshold of an oscillatory instability, which according to our model, minimises ATP consumption. Our work also clarifies how various plasmid dynamics are achievable in a single unified stochastic model. Overall, this work uncovers the dynamical nature of plasmid positioning by ParABS and provides insights relevant for chromosome-based systems.

Understanding the dog population in the Republic of Ireland: insight from existing data sources?

BACKGROUND: Reliable information about national pet dog populations is an important contributor to informed decision-making, both by governments and national dog welfare organisations. In some countries, there is an improved understanding of aspects of the national pet dog population, but as yet limited published information is available in Ireland. The current study reviews the utility of existing data to inform our understanding of recent changes to the pet dog population in Ireland, including both biological and organisational processes. RESULTS: Based on national data on dog licencing and microchipping registration, pet dog numbers have remained relatively stable in recent years (ie prior to the COVID-19 pandemic). Since 2015, there has been a substantial decrease in the number of dogs managed through dog control centres. Although the completeness of the data are likely variable, there appears to be substantial, and increasing, number of dogs moving from Ireland to other countries, including UK, Sweden, Italy, Germany and Singapore. We also note an increase (albeit much smaller) in the number of dogs being moved into Ireland. CONCLUSIONS: This study highlights the challenges faced when using existing national data to gain insights into the dog population of Ireland. The linking of existing national databases (individual dog identification, dog licencing, dog control statistics) has the potential to improve both the representativeness and accuracy of information about the Irish pet dog population. In the next phases of our work, we will focus on the work of dog welfare organisations, given both the increased role played by these organisations and the substantial public funding that has been committed in this sector.

Disentangled Representation Learning for OCTA Vessel Segmentation With Limited Training Data.

Optical coherence tomography angiography (OCTA) is an imaging modality that can be used for analyzing retinal vasculature. Quantitative assessment of en face OCTA images requires accurate segmentation of the capillaries. Using deep learning approaches for this task faces two major challenges. First, acquiring sufficient manual delineations for training can take hundreds of hours. Second, OCTA images suffer from numerous contrast-related artifacts that are currently inherent to the modality and vary dramatically across scanners. We propose to solve both problems by learning a disentanglement of an anatomy component and a local contrast component from paired OCTA scans. With the contrast removed from the anatomy component, a deep learning model that takes the anatomy component as input can learn to segment vessels with a limited portion of the training images being manually labeled. Our method demonstrates state-of-the-art performance for OCTA vessel segmentation.

Prevalence, Cost, and Variation in Cost of Pediatric Hospitalizations in Ontario, Canada.

Importance: Identifying conditions that could be prioritized for research based on health care system burden is important for developing a research agenda for the care of hospitalized children. However, existing prioritization studies are decades old or do not include data from both pediatric and general hospitals. Objective: To assess the prevalence, cost, and variation in cost of pediatric hospitalizations at all general and pediatric hospitals in Ontario, Canada, with the aim of identifying conditions that could be prioritized for future research. Design, Setting, and Participants: This population-based cross-sectional study used health administrative data from 165 general and pediatric hospitals in Ontario, Canada. Children younger than 18 years with an inpatient hospital encounter between April 1, 2014, and March 31, 2019, were included. Main Outcomes and Measures: Condition-specific prevalence, cost of pediatric hospitalizations, and condition-specific variation in cost per inpatient encounter across hospitals. Variation in cost was evaluated using (1) intraclass correlation coefficient (ICC) and (2) number of outlier hospitals. Costs were adjusted for inflation to 2018 US dollars. Results: Overall, 627 314 inpatient hospital encounters (44.8% among children younger than 30 days and 53.0% among boys) at 165 hospitals (157 general and 8 pediatric) costing $3.3 billion were identified. A total of 408 003 hospitalizations (65.0%) and $1.4 billion (43.8%) in total costs occurred at general hospitals. Among the 50 most prevalent and 50 most costly conditions (of 68 total conditions), the top 10 highest-cost conditions accounted for 55.5% of all costs and 48.6% of all encounters. The conditions with highest prevalence and cost included low birth weight (86.2 per 1000 encounters; $676.3 million), preterm newborn (38.0 per 1000 encounters; $137.4 million), major depressive disorder (20.7 per 1000 encounters; $78.3 million), pneumonia (27.3 per 1000 encounters; $71.6 million), other perinatal conditions (68.0 per 1000 encounters; $65.8 million), bronchiolitis (25.4 per 1000 encounters; $54.6 million), and neonatal hyperbilirubinemia (47.9 per 1000 encounters; $46.7 million). The highest variation in cost per encounter among the most costly medical conditions was observed for 2 mental health conditions (other mental health disorders [ICC, 0.28] and anxiety disorders [ICC, 0.19]) and 3 newborn conditions (intrauterine hypoxia and birth asphyxia [ICC, 0.27], other perinatal conditions [ICC, 0.17], and surfactant deficiency disorder [ICC, 0.17]). Conclusions and Relevance: This population-based cross-sectional study of hospitalized children identified several newborn and mental health conditions as having the highest prevalence, cost, and variation in cost across hospitals. Findings of this study can be used to develop a research agenda for the care of hospitalized children that includes general hospitals and to ultimately build a more substantial evidence base and improve patient outcomes.

Health-related out-of-pocket expenses for children living with rare diseases - tuberous sclerosis and mitochondrial disorders: A prospective pilot study in Australian families.

AIM: We aimed to describe health-related out-of-pocket (OOP) expenses incurred by Australian families living with children with chronic and complex diseases. METHODS: A prospective pilot study of OOP expenses in families with children with tuberous sclerosis (TS) or mitochondrial disorders (MD) in 2016-2017. An initial survey assessed the family's financial situation, child's health functioning and estimated previous 6 months' and lifetime OOP expenses. Thereafter, families completed a survey each month for 6 months, prospectively tracking OOP expenses. RESULTS: Initial surveys were completed by 13 families with 15 children; median age 7 years (range: 1-12); 5 with MD, 10 with TS. All families reported OOP expenses: 38% paid $2000 per annum, more than double the annual per-capita OOP costs reported for Australia by the Organisation for Economic Co-operation and Development. Eight families estimated $5000-$25 000 in OOP expenses over their child's lifetime and 62% of mothers reduced or stopped work due to caring responsibilities. Eleven families paid annual private health insurance premiums of $2000-$5122, but 72% said this was poor value-for-money. Prospective tracking by eight families (9 children) identified the median OOP expenditure was $863 (range $55-$1398) per family for 6 months. OOP spending was associated with visits to allied health professionals, non-prescription medicines, special foods, supplements and disposable items. Eight families paid for 91 prescription medications over 6 months. CONCLUSION: All families caring for children with TS or MD reported OOP expenses. A larger study is needed to explore the affordability of health care for children living with a broader range of chronic diseases.

Patient care standards for primary mitochondrial disease in Australia: an Australian adaptation of the Mitochondrial Medicine Society recommendations.

This document provides consensus-based recommendations for general physicians and primary care physicians who diagnose and manage patients with mitochondrial diseases (MD). It builds on previous international guidelines, with particular emphasis on clinical management in the Australian setting. This statement was prepared by a working group of medical practitioners, nurses and allied health professionals with clinical expertise and experience in managing Australian patients with MD. As new treatments and management plans emerge, these consensus-based recommendations will continue to evolve, but current standards of care are summarised in this document.

The quantitative basis for the redistribution of immobile bacterial lipoproteins to division septa.

The spatial localisation of proteins is critical for most cellular function. In bacteria, this is typically achieved through capture by established landmark proteins. However, this requires that the protein is diffusive on the appropriate timescale. It is therefore unknown how the localisation of effectively immobile proteins is achieved. Here, we investigate the localisation to the division site of the slowly diffusing lipoprotein Pal, which anchors the outer membrane to the cell wall of Gram-negative bacteria. While the proton motive force-linked TolQRAB system is known to be required for this repositioning, the underlying mechanism is unresolved, especially given the very low mobility of Pal. We present a quantitative, mathematical model for Pal relocalisation in which dissociation of TolB-Pal complexes, powered by the proton motive force across the inner membrane, leads to the net transport of Pal along the outer membrane and its deposition at the division septum. We fit the model to experimental measurements of protein mobility and successfully test its predictions experimentally against mutant phenotypes. Our model not only explains a key aspect of cell division in Gram-negative bacteria, but also presents a physical mechanism for the transport of low-mobility proteins that may be applicable to multi-membrane organelles, such as mitochondria and chloroplasts.

The CTPase activity of ParB determines the size and dynamics of prokaryotic DNA partition complexes.

ParB-like CTPases mediate the segregation of bacterial chromosomes and low-copy number plasmids. They act as DNA-sliding clamps that are loaded at parS motifs in the centromere of target DNA molecules and spread laterally to form large nucleoprotein complexes serving as docking points for the DNA segregation machinery. Here, we solve crystal structures of ParB in the pre- and post-hydrolysis state and illuminate the catalytic mechanism of nucleotide hydrolysis. Moreover, we identify conformational changes that underlie the CTP- and parS-dependent closure of ParB clamps. The study of CTPase-deficient ParB variants reveals that CTP hydrolysis serves to limit the sliding time of ParB clamps and thus drives the establishment of a well-defined ParB diffusion gradient across the centromere whose dynamics are critical for DNA segregation. These findings clarify the role of the ParB CTPase cycle in partition complex assembly and function and thus advance our understanding of this prototypic CTP-dependent molecular switch.

A simple, quantitative assay for the detection of viable but non-culturable (VBNC) bacteria.

This protocol determines the fraction of a bacterial population that is viable and culturable, viable and non-culturable, or non-viable (dead). Each population is detected by isolating colonies on agar plates, performing direct counts, and staining for live or dead cells. Its application is limited to bacteria that are stainable and when permissible growth conditions are known. The quantitative data extracted allow for the detection of a viable but non-culturable (alive and non-dividing) population from a liquid culture. For complete details on the use and execution of this protocol, please refer to Stott et al. (2015).

The long and winding road: perspectives of people and parents of children with mitochondrial conditions negotiating management after diagnosis.

BACKGROUND: The diagnostic odyssey for people with a rare disease is well known, but difficulties do not stop at diagnosis. Here we investigate the experience of people, or parents of children with a diagnosed mitochondrial respiratory chain disorder (MRCD) in the management of their disease. The work complements ongoing projects around implementation of consensus recommendations for management of people with MRCD. People with or caring for a child with a formally diagnosed MRCD were invited to take part in an hour-long focus group held via videoconference. Questions elicited experiences of receiving management advice or information specific to their MRCD in four areas drawn from the consensus recommendations: diet and supplements, exercise, access to social services, and mental health. Sessions were audio-recorded, transcribed and analysed using a combination of inductive and deductive coding. RESULTS: Focus groups were conducted with 20 participants from five Australian states in June-September 2020. Fourteen adults with a MRCD (three of whom also had a child with a MRCD), and six who cared for a child with a MRCD took part. The overarching finding was that of the need for ongoing negotiation to access the advice and service required to manage their condition. The nature of these negotiations varied across contexts but mostly related to joint decision-making, and more commonly, the need to advocate for their care with non-specialist services (e.g., dieticians, schools). The effort required for this self-advocacy was a prominent theme. While most participants reported receiving adequate advice around supplements, and to a lesser extent diet and exercise, the majority reported no formal advice around mental health or practical assistance accessing social services. CONCLUSION: These focus groups have revealed several gaps in the system for people with a MRCD, interacting with care providers after diagnosis. Focus group participants had to negotiate with a range of different stakeholders in order to secure appropriate advice or services. Notable was the gap in appropriate generalist services (e.g., dieticians) with sufficient knowledge of MRCD to support people with their day-to-day challenges.

A calibration equation between Δ48 values of carbonate and temperature.

RATIONALE: Information on the temperature of formation or alteration of carbonate minerals can be obtained by measuring the abundance of the isotopologues 47 and 48 (Δ47 and Δ48 values) of CO2 released during acid dissolution. The combination of these two proxies can potentially provide a greater insight into the temperature of formation, particularly if the carbonate minerals form by non-equilibrium processes. METHODS: We have precipitated calcium carbonates at seven temperatures between 5 and 65°C and measured their δ48 values using a Thermo-253 plus isotope ratio mass spectrometer. The values were transformed to Δ48 values in the conventional manner and then converted to the carbon dioxide equilibrium scale. RESULTS: Using the Δ48 values, we have established an empirical calibration between temperature and Δ48 values: [Formula: see text] CONCLUSIONS: The calibration line produced allows the determination of the temperature of natural carbonates using the Δ48 values and agrees with the measurements of the Δ47 and Δ48 values of some carbonates assumed to have formed under equilibrium conditions.

Pattern selection in reaction diffusion systems.

Turing's theory of pattern formation has been used to describe the formation of self-organized periodic patterns in many biological, chemical, and physical systems. However, the use of such models is hindered by our inability to predict, in general, which pattern is obtained from a given set of model parameters. While much is known near the onset of the spatial instability, the mechanisms underlying pattern selection and dynamics away from onset are much less understood. Here, we provide physical insight into the dynamics of these systems. We find that peaks in a Turing pattern behave as point sinks, the dynamics of which is determined by the diffusive fluxes into them. As a result, peaks move toward a periodic steady-state configuration that minimizes the mass of the diffusive species. We also show that the preferred number of peaks at the final steady state is such that this mass is minimized. Our work presents mass minimization as a potential general principle for understanding pattern formation in reaction diffusion systems far from onset.

Not really a smoker? A study on the prevalence of and attitudes to occasional social smoking in a third level institution in Ireland.

BACKGROUND: Occasional smoking is defined as any smoking occurring on a less than daily basis. Social smoking, i.e. smoking primarily in social contexts, is a sub-group of occasional smoking. Data on occasional cigarette smoking and the subset of social smoking among third level students are limited. OBJECTIVES: (1) To determine prevalence of occasional/social smoking among third level students in an Irish university; (2) to evaluate students' attitudes to occasional/social smoking, including perceived benefits and harm; (3) to explore when students commenced occasional/social smoking, their reasons and continued smoking habits; and (4) to determine any influence of other factors, e.g. alcohol consumption, on occasional/social smoking. METHODS: An anonymous online survey was distributed to undergraduates and postgraduates, using SurveyMonkey. Data were analysed in Microsoft Excel. RESULTS: Of 18,407 students surveyed, 1310 (7.1%) responded;1267 (96.7%) provided adequate data for analysis. Of the 1267 students, 423 (33.4%) self-reported as current smokers of whom 106/1267 (8.4%) self-classified as daily smokers and 317/1267 (25%) as occasional smokers. The 25% of occasional smokers comprised 266/1267 (21%) social smokers and 51/1267 (4%) non-social smokers. Occasional smokers tended to start smoking earlier and think less about quitting than daily smokers. Of 423 current smokers, 386 (97.2%) reported that alcohol increased their smoking habits. CONCLUSION: Prevalence of self-reported occasional smoking among university students was higher than daily smoking. Most occasional smokers primarily smoked in social contexts. All current smokers reported that alcohol increased cigarette intake. Effective intervention campaigns tailored to determinants of occasional/social smoking are needed as part of induction to third level.