The accurate diagnosis of idiopathic pulmonary fibrosis (IPF) is a major clinical challenge. We developed a model to diagnose IPF by applying Bayesian probit regression (BPR) modelling to gene ...expression profiles of whole lung tissue.
Whole lung tissue was obtained from patients with idiopathic pulmonary fibrosis (IPF) undergoing surgical lung biopsy or lung transplantation. Controls were obtained from normal organ donors. We performed cluster analyses to explore differences in our dataset. No significant difference was found between samples obtained from different lobes of the same patient. A significant difference was found between samples obtained at biopsy versus explant. Following preliminary analysis of the complete dataset, we selected three subsets for the development of diagnostic gene signatures: the first signature was developed from all IPF samples (as compared to controls); the second signature was developed from the subset of IPF samples obtained at biopsy; the third signature was developed from IPF explants. To assess the validity of each signature, we used an independent cohort of IPF and normal samples. Each signature was used to predict phenotype (IPF versus normal) in samples from the validation cohort. We compared the models' predictions to the true phenotype of each validation sample, and then calculated sensitivity, specificity and accuracy.
Surprisingly, we found that all three signatures were reasonably valid predictors of diagnosis, with small differences in test sensitivity, specificity and overall accuracy.
This study represents the first use of BPR on whole lung tissue; previously, BPR was primarily used to develop predictive models for cancer. This also represents the first report of an independently validated IPF gene expression signature. In summary, BPR is a promising tool for the development of gene expression signatures from non-neoplastic lung tissue. In the future, BPR might be used to develop definitive diagnostic gene signatures for IPF, prognostic gene signatures for IPF or gene signatures for other non-neoplastic lung disorders such as bronchiolitis obliterans.
Defining null expectations for animal site fidelity Picardi, Simona; Abrahms, Briana; Gelzer, Emily ...
Ecology letters,
January 2023, 2023-Jan, 2023-01-00, 20230101, Letnik:
26, Številka:
1
Journal Article
Recenzirano
Site fidelity—the tendency to return to previously visited locations—is widespread across taxa. Returns may be driven by several mechanisms, including memory, habitat selection, or chance; however, ...pattern‐based definitions group different generating mechanisms under the same label of ‘site fidelity’, often assuming memory as the main driver. We propose an operational definition of site fidelity as patterns of return that deviate from a null expectation derived from a memory‐free movement model. First, using agent‐based simulations, we show that without memory, intrinsic movement characteristics and extrinsic landscape characteristics are key determinants of return patterns and that even random movements may generate substantial probabilities of return. Second, we illustrate how to implement our framework empirically to establish ecologically meaningful, system‐specific null expectations for site fidelity. Our approach provides a conceptual and operational framework to test hypotheses on site fidelity across systems and scales.
Animals tend to exhibit site fidelity—returns to previously visited locations. But are all returns due to memory? We show that even without memory, simple movement mechanisms can result in frequent returns, which highlights the need for a null expectation. We introduce a framework to establish system‐, scale‐ and species‐specific null expectations for site fidelity.
Summary
1. Photographic mark–recapture is a cost‐effective, non‐invasive way to study populations. However, to efficiently apply photographic mark–recapture to large populations, computer software is ...needed for image manipulation and pattern matching.
2. We created an open‐source application for the storage, pattern extraction and pattern matching of digital images for the purposes of mark–recapture analysis. The resulting software package is a stand‐alone, multiplatform application implemented in Java. Our program employs the Scale Invariant Feature Transform (SIFT) operator that extracts distinctive features invariant to image scale and rotation.
3. We applied this system to a population of Masai giraffe (Giraffa camelopardalis tippelskirchi) in the Tarangire Ecosystem in northern Tanzania. Over 1200 images were acquired in the field during three primary sampling periods between September 2008 and December 2009. The pattern information in these images was extracted and matched resulting in capture histories for over 600 unique individuals.
4. Estimated error rates of the matching system were low based on a subset of test images that were independently matched by eye.
5. Encounter histories were subsequently analysed with open population models to estimate apparent survival rates and population size.
6. This new open‐access tool allowed photographic mark–recapture to be applied successfully to this relatively large population.
Mangrove forests store high amounts of carbon, protect communities from storms, and support fisheries. Mangroves exist in complex social-ecological systems, hence identifying socioeconomic conditions ...associated with decreasing losses and increasing gains remains challenging albeit important. The impact of national governance and conservation policies on mangrove conservation at the landscape-scale has not been assessed to date, nor have the interactions with local economic pressures and biophysical drivers. Here, we assess the relationship between socioeconomic and biophysical variables and mangrove change across coastal geomorphic units worldwide from 1996 to 2016. Globally, we find that drivers of loss can also be drivers of gain, and that drivers have changed over 20 years. The association with economic growth appears to have reversed, shifting from negatively impacting mangroves in the first decade to enabling mangrove expansion in the second decade. Importantly, we find that community forestry is promoting mangrove expansion, whereas conversion to agriculture and aquaculture, often occurring in protected areas, results in high loss. Sustainable development, community forestry, and co-management of protected areas are promising strategies to reverse mangrove losses, increasing the capacity of mangroves to support human-livelihoods and combat climate change.
Greater understanding of international cancer survival differences is needed. We aimed to identify predictors and consequences of cancer diagnosis through emergency presentation in different ...international jurisdictions in six high-income countries.
Using a federated analysis model, in this cross-sectional population-based study, we analysed cancer registration and linked hospital admissions data from 14 jurisdictions in six countries (Australia, Canada, Denmark, New Zealand, Norway, and the UK), including patients with primary diagnosis of invasive oesophageal, stomach, colon, rectal, liver, pancreatic, lung, or ovarian cancer during study periods from Jan 1, 2012, to Dec 31, 2017. Data were collected on cancer site, age group, sex, year of diagnosis, and stage at diagnosis. Emergency presentation was defined as diagnosis of cancer within 30 days after an emergency hospital admission. Using logistic regression, we examined variables associated with emergency presentation and associations between emergency presentation and short-term mortality. We meta-analysed estimates across jurisdictions and explored jurisdiction-level associations between cancer survival and the percentage of patients diagnosed as emergencies.
In 857 068 patients across 14 jurisdictions, considering all of the eight cancer sites together, the percentage of diagnoses through emergency presentation ranged from 24·0% (9165 of 38 212 patients) to 42·5% (12 238 of 28 794 patients). There was consistently large variation in the percentage of emergency presentations by cancer site across jurisdictions. Pancreatic cancer diagnoses had the highest percentage of emergency presentations on average overall (46·1% 30 972 of 67 173 patients), with the jurisdictional range being 34·1% (1083 of 3172 patients) to 60·4% (1317 of 2182 patients). Rectal cancer had the lowest percentage of emergency presentations on average overall (12·1% 10 051 of 83 325 patients), with a jurisdictional range of 9·1% (403 of 4438 patients) to 19·8% (643 of 3247 patients). Across the jurisdictions, older age (ie, 75–84 years and 85 years or older, compared with younger patients) and advanced stage at diagnosis compared with non-advanced stage were consistently associated with increased emergency presentation risk, with the percentage of emergency presentations being highest in the oldest age group (85 years or older) for 110 (98%) of 112 jurisdiction-cancer site strata, and in the most advanced (distant spread) stage category for 98 (97%) of 101 jurisdiction-cancer site strata with available information. Across the jurisdictions, and despite heterogeneity in association size (I2=93%), emergency presenters consistently had substantially greater risk of 12-month mortality than non-emergency presenters (odds ratio >1·9 for 112 100% of 112 jurisdiction-cancer site strata, with the minimum lower bound of the related 95% CIs being 1·26). There were negative associations between jurisdiction-level percentage of emergency presentations and jurisdiction-level 1-year survival for colon, stomach, lung, liver, pancreatic, and ovarian cancer, with a 10% increase in percentage of emergency presentations in a jurisdiction being associated with a decrease in 1-year net survival of between 2·5% (95% CI 0·28–4·7) and 7·0% (1·2–13·0).
Internationally, notable proportions of patients with cancer are diagnosed through emergency presentation. Specific types of cancer, older age, and advanced stage at diagnosis are consistently associated with an increased risk of emergency presentation, which strongly predicts worse prognosis and probably contributes to international differences in cancer survival. Monitoring emergency presentations, and identifying and acting on contributing behavioural and health-care factors, is a global priority for cancer control.
Canadian Partnership Against Cancer; Cancer Council Victoria; Cancer Institute New South Wales; Cancer Research UK; Danish Cancer Society; National Cancer Registry Ireland; The Cancer Society of New Zealand; National Health Service England; Norwegian Cancer Society; Public Health Agency Northern Ireland, on behalf of the Northern Ireland Cancer Registry; the Scottish Government; Western Australia Department of Health; and Wales Cancer Network.
Our understanding of ungulate migration is advancing rapidly due to innovations in modern animal tracking. Herein, we review and synthesize nearly seven decades of work on migration and other ...long-distance movements of wild ungulates. Although it has long been appreciated that ungulates migrate to enhance access to forage, recent contributions demonstrate that their movements are fine tuned to dynamic landscapes where forage, snow, and drought change seasonally. Researchers are beginning to understand how ungulates navigate migrations, with the emerging view that animals blend gradient tracking with spatial memory, some of which is socially learned. Although migration often promotes abundant populations-with broad effects on ecosystems-many migrations around the world have been lost or are currently threatened by habitat fragmentation, climate change, and barriers to movement. Fortunately, new efforts that use empirical tracking data to map migrations in detail are facilitating effective conservation measures to maintain ungulate migration.
Protected areas provide major benefits for humans in the form of ecosystem services, but landscape degradation by human activity at their edges may compromise their ecological functioning. Using ...multiple lines of evidence from 40 years of research in the Serengeti-Mara ecosystem, we find that such edge degradation has effectively "squeezed" wildlife into the core protected area and has altered the ecosystem's dynamics even within this 40,000-square-kilometer ecosystem. This spatial cascade reduced resilience in the core and was mediated by the movement of grazers, which reduced grass fuel and fires, weakened the capacity of soils to sequester nutrients and carbon, and decreased the responsiveness of primary production to rainfall. Similar effects in other protected ecosystems worldwide may require rethinking of natural resource management outside protected areas.
Context
Managers are faced with numerous methods for delineating wildlife movement corridors, and often must make decisions with limited data. Delineated corridors should be robust to different data ...and models.
Objectives
We present a multi-method approach for delineating and validating wildlife corridors using multiple data sources, which can be used conserve landscape connectivity. We used this approach to delineate and validate migration corridors for wildebeest (
Connochaetes taurinus
) in the Tarangire Ecosystem of northern Tanzania.
Methods
We used two types of locational data (distance sampling detections and GPS collar locations), and three modeling methods (negative binomial regression, logistic regression, and Maxent), to generate resource selection functions (RSFs) and define resistance surfaces. We compared two corridor detection algorithms (cost-distance and circuit theory), to delineate corridors. We validated corridors by comparing random and wildebeest locations that fell within corridors, and cross-validated by data type.
Results
Both data types produced similar RSFs. Wildebeest consistently selected migration habitat in flatter terrain farther from human settlements. Validation indicated three of the combinations of data type, modeling, and corridor detection algorithms (detection data with Maxent modeling, GPS collar data with logistic regression modeling, and GPS collar data with Maxent modeling, all using cost-distance) far outperformed the other seven. We merged the predictive corridors from these three data-method combinations to reveal habitat with highest probability of use.
Conclusions
The use of multiple methods ensures that planning is able to prioritize conservation of migration corridors based on all available information.
Migratory movement shapes infectious disease dynamics within migratory populations, but also impacts the disease dynamics of resident (non-migratory) species by transporting pathogens along migratory ...routes.Migratory animals often dominate local animal biomass and exert strong trophic effects on the resident species that they encounter. Many of these trophic effects could impact infectious disease transmission, yet very little is known about the role of migrant trophic effects in shaping resident disease dynamics.We propose mechanisms via which migrant trophic effects change the local infection risk for resident animals. We then describe a framework that captures the role of migration intensity and duration in modifying migrant transport and trophic effects that can be used to investigate the complex ecological interactions that determine resident parasite dynamics in nature.
Migratory animals can bring parasites into resident animal (i.e., non-migratory) home ranges (transport effects) and exert trophic effects that either promote or reduce parasite exposure to resident hosts. Here, we examine the importance of these transport and trophic effects and their interactions for resident parasite dynamics. We propose that migrant transport and trophic effects are impacted by the number of migratory animals entering a resident’s home range (migration intensity), the amount of time that migrants spend within a resident’s home range (migration duration), and the timing of migrant–resident interactions. We then incorporate migration intensity, duration, and timing into a framework for exploring the net impact of migrant trophic and transport effects on resident animal parasite prevalence.
Migratory animals can bring parasites into resident animal (i.e., non-migratory) home ranges (transport effects) and exert trophic effects that either promote or reduce parasite exposure to resident hosts. Here, we examine the importance of these transport and trophic effects and their interactions for resident parasite dynamics. We propose that migrant transport and trophic effects are impacted by the number of migratory animals entering a resident’s home range (migration intensity), the amount of time that migrants spend within a resident’s home range (migration duration), and the timing of migrant–resident interactions. We then incorporate migration intensity, duration, and timing into a framework for exploring the net impact of migrant trophic and transport effects on resident animal parasite prevalence.
Abstract
In Africa, livestock are important to local and national economies, but their productivity is constrained by infectious diseases. Comprehensive information on livestock movements and ...contacts is required to devise appropriate disease control strategies; yet, understanding contact risk in systems where herds mix extensively, and where different pathogens can be transmitted at different spatial and temporal scales, remains a major challenge. We deployed Global Positioning System collars on cattle in 52 herds in a traditional agropastoral system in western Serengeti, Tanzania, to understand fine-scale movements and between-herd contacts, and to identify locations of greatest interaction between herds. We examined contact across spatiotemporal scales relevant to different disease transmission scenarios. Daily cattle movements increased with herd size and rainfall. Generally, contact between herds was greatest away from households, during periods with low rainfall and in locations close to dipping points. We demonstrate how movements and contacts affect the risk of disease spread. For example, transmission risk is relatively sensitive to the survival time of different pathogens in the environment, and less sensitive to transmission distance, at least over the range of the spatiotemporal definitions of contacts that we explored. We identify times and locations of greatest disease transmission potential and that could be targeted through tailored control strategies.
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