bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of water limitation and competition on tree carbon allocation in an Earth system modelling framework
Authors: Lichstein Jeremy W. , Zhang Tao , Weng Ensheng , Farrior Caroline E. , Dybzinski Ray , Malyshev Sergey , Shevliakova Elena , Birdsey Richard A. , Pacala Stephen W. 
Published: September 2024

Abstract

Earth system models (ESMs) have a limited capacity to represent plant functional diversity and shifts in trait distributions. Approaches to improving the representation of this complexity in ESMs include (i) optimality‐based approaches that predict trait–environment responses and (ii) explicitly modelling coexistence and community assembly. These approaches are expected to converge only when optimality‐based approaches identify competitively dominant strategies, which often differ from strategies that maximize ecosystem functioning or fitness components in monoculture.

We used two models, LM3‐PPA (a vegetation demographic model designed as an ESM component) and BiomeE (a computationally efficient analog for LM3‐PPA), to explore how water limitation affects carbon allocation strategies of canopy trees. We compared competitive allocation strategies and those that maximize biomass or productivity in monoculture. We did not explicitly model coexistence or community assembly. Rather, we used model experiments to identify competitive and maximizing strategies in a two‐dimensional trait space under different precipitation and mortality scenarios.

At 10 eastern US locations, we simulated historical, wet and dry climate scenarios, novel drought and three different mortality scenarios (low, medium or high sensitivity to water deficit). For each site and scenario, we identified the competitive strategy and three maximizing strategies (maximum biomass, productivity or drought‐tolerance).

Root: leaf ratios tended to increase and leaf area tended to decrease with increasing water stress (increasing water limitation and its effects on mortality). However, relative to maximizing strategies, competitive strategies shifted towards greater allocation to roots and leaves with increasing water stress.

Competitive overinvestments (greater allocation to roots and leaves by competitive strategies compared with maximizing strategies) were robust across different modelling contexts, including vegetation parameter sets (Acer vs. Populus), models (LM3‐PPA vs. BiomeE) and uncalibrated vsersus calibrated BiomeE versions.

Synthesis: The theoretical prediction that competitive and maximizing allocation strategies differ under water limitation is confirmed for a demographic model designed as an ESM component. Optimality‐based trait predictions can simplify representing trait diversity in ESMs but do not always correspond to competitive outcomes. Explicitly modelling coexistence and community assembly in ESMs is challenging but is likely the most general approach to representing trait diversity.
The test–retest reliability and validity of food photography and food diary analyses
Authors: Curtis Christopher , Hills Samuel P. , Arjomandkhah Nicola , Cooke Carlton , Ranchordas Mayur K. , Russell Mark 
Published: September 2024

AbstractAimsTo assess test–retest reliability of both food photography and food diary methods and validity of these data against known values derived from food labels.MethodsTest–retest reliability analyses of food diary and food photography were compared using single foodstuffs using intra‐class correlation coefficients, coefficients of variation, and limits of agreement. For food diaries, 24‐h test–retest reliability was also examined. Validity was assessed against weighed analyses. As part of habitual intake, a single foodstuff (randomly allocated from 14 common foods) was consumed by 26 participants over 24‐h. On two occasions (14 days apart), single‐blind dietary analyses allowed estimation of foodstuff‐specific energy and macronutrient content and 24‐h intakes.ResultsFor food diaries, test–retest reliability was acceptable (weight, energy, carbohydrate, protein, and fat: all intra‐class correlation coefficients: >0.990, coefficient of variation percentage: <0.1%, limits of agreements: <0.1 to <0.1, p > 0.05, and effect size: <0.01). For food photography, test–retest reliability was acceptable for weight, energy, carbohydrate, and protein (all intra‐class correlation coefficients: >0.898, coefficient of variation percentage: 3.6%–6.2%, limits of agreements: 1.1 to – 44.9, and effect size: 0.01–0.12). Food photography validity was worse than food diaries for all variables (percentage difference: 8.8%–15.3%, coefficient of variation percentage: 7.5%–13.8%, all p ≤ 0.05, and effect size: 0.001–0.11).ConclusionsGreater reliability and validity occurred in food diaries versus food photography. These findings suggest that using food photography may lead to an underestimation of energy and macronutrient content, which may have implications for dietary interventions and nutritional strategies.
A cross‐sectional study assessing the role of interventional radiology services in regional and remote Australia
Authors: Clements Warren , Zia Adil , Chang Kelvin , Brown Nicholas , Koukounaras Jim , Joseph Tim , Lukies Matthew W , Phan Tuan , Goh Gerard S , Varma Dinesh , Tomlinson Heath , Bolger Mark , Kavnoudias Helen 
Published: September 2024

AbstractIntroductionIt is estimated that 8% of hospitalised patients require treatment from Interventional Radiology (IR). However, little is known about the potential impact of IR on regional and remote Australians, including Indigenous patients. This study aimed to assess treatments performed by IRs on regional/remote patients to predict future IR workforce and governance needs.MethodsSingle‐centre cross‐sectional study at a tertiary Victorian hospital. Patients were identified when they had an advanced IR treatment between 1 January 2022 and 2024. Basic procedures such as biopsy and drain insertion were not included. The primary outcome was the type and volume of IR treatments performed on patients who were transferred from a regional or remote home location for treatment.ResultsOf 3485 advanced IR interventions, 908 procedures (26.0%) from patients who lived in a regional or remote location were included with 36.5% female, of mean age 55.6 years (SD 17.9). 1.4% identified as Indigenous which is similar to the Indigenous population incidence in Victoria of 1.0%. Of this group, 350 (38.5%) were either a day procedure, overnight elective admission, or simple inpatient procedure which could have been performed in a regional centre, which included 1.1% Indigenous patients.ConclusionThere is an unmet need for IR services in regional and remote Australia, with many patients being transferred to our metropolitan centre for treatment that could be performed in regional IR hubs. This data will be important to drive government and hospital planning including capital infrastructure, workforce modelling and future recognition of IR as a new specialty in Australia.
Bringing circuit theory into spatial occupancy models to assess landscape connectivity
Authors: Kervellec Maëlis , Couturier Thibaut , Bauduin Sarah , Chenesseau Delphine , Defos du Rau Pierre , Drouet‐Hoguet Nolwenn , Duchamp Christophe , Steinmetz Julien , Vandel Jean‐Michel , Gimenez Olivier 
Published: September 2024

Abstract

Occupancy models were originally developed to better understand species distribution while accounting for imperfect detection. Because species distribution is not only shaped by habitat quality but also by the ability of individuals to reach suitable habitats, spatial dynamic occupancy models have been proposed to extend the original framework by defining that site colonisation was a function of the Euclidean distance to occupied sites. However, not all sites in the landscape are equally accessible due to the presence of barriers, that of corridors, etc. To account for connectivity between sites, the Euclidean distance has recently been replaced by a least‐cost path distance, which explicitly accounts for landscape resistance, but assumes that individuals will follow the optimal route.

To relax this assumption, we first developed a new spatial occupancy model that incorporates commute‐time distance derived from circuit theory to model accessibility across sites. This distance has the advantage of modelling movement as a random walk and accounting for the fact that colonisation could be achieved from multiple paths. Our approach allows for the explicit estimation of landscape connectivity from detection/non‐detection data and a direct measure of connectivity uncertainty.

We implemented the model in the Bayesian framework using the nimble R package, which allows useful R connectivity functions to be called from within the model. Second, we carried out a simulation study to assess the performance of our model by considering four scenarios depicting an increasing level of landscape resistance. Third, to illustrate our new approach, we studied the recolonisation of two carnivores in France.

We quantified the degree to which rivers facilitate Eurasian otter (Lutra lutra) colonisation and highways impede Eurasian lynx (Lynx lynx) colonisation. Overall, spatial occupancy models provide a flexible framework to accommodate any distance metric designed to align with species dispersal ecology.
Bayesian estimation of spatially varying mortality risk using tagged animal data
Authors: Poulton Anna J. , Villegas‐Ríos David , Freitas Carla , Moland Even , Olsen Esben M. , Sethi Suresh A. , Ellner Stephen P. 
Published: September 2024

Abstract

The survival of animals is impacted by landscapes of spatially varying mortality factors including habitat type, predation risk or harvest risk, among others. Characterization of these spatial mortality processes is important for managing animal populations and their habitats, yet this information has proved challenging to capture. Advances in telemetry now make it possible to monitor tagged individuals' locations through time for a wide range of taxa, providing opportunity to assess movement and mortality simultaneously through spatial time‐to‐event data. Existing time‐to‐event modelling frameworks have largely ignored spatially varying mortality processes or have treated an animal's location as fixed at a regional level.

Here we present a general spatial survival model for analysing time‐to‐event data arising from animal telemetry. Our model has a flexible Cox regression form and can estimate the effects of conventional non‐spatial risk factors (size, seasonality, etc.), spatial covariates (e.g. habitat type) and spatial variation in risk not explained by covariates on mortality. We show how to fit our model using Bayesian methods and demonstrate applications of our model with several simulated examples and two animal telemetry case studies.

Our model produced consistent and unbiased parameter estimates throughout simulations with a variety of spatial and non‐spatial hazards. In the first case study, data from 147 tagged caribou in British Columbia, Canada, revealed a spatially heterogeneous mortality landscape with caribou survival varying by elevation, likely in response to space use by predators. Our second case study involved a dataset of 390 acoustically tagged Atlantic cod in a southern Norwegian fjord where a marine protected area (MPA) was established during the study. We found that the MPA led to a shift from mostly fishing mortality to mostly natural mortality within the fjord and that these risks had markedly different spatial hazard patterns.

Our spatial time‐to‐event model can make use of data from a variety of widely used telemetry technologies to characterize landscapes of mortality risks for different taxa. Our work provides new opportunities to inform the spatial ecology and management of fish and wildlife populations.
SQuID (subcutaneous insulin in diabetic ketoacidosis): Clinician acceptability
Authors: Griffey Richard T. , Schneider Ryan M. , Girardi Margo , LaRossa Gina , Yeary Julianne , Frawley Laura , Ancona Rachel , Kaser Taylor , Suarez Dan , Cruz‐Bravo Paulina 
Published: September 2024

AbstractBackgroundWe previously implemented the SQuID protocol (subcutaneous insulin in diabetic ketoacidosis [DKA]) demonstrating safe, effective treatment of low‐ to moderate‐severity DKA in a non–intensive care unit setting. Since success and sustainability of interventions rely on staff buy‐in, we assessed acceptability of SQuID among emergency department (ED) and inpatient clinicians.MethodsWe conducted a cross‐sectional study in an urban academic hospital (March 2023–November 2023), surveying ED nurses (RNs) and physicians (MDs) and floor RNs and MDs treating patients on SQuID via emailed survey links. Clinicians could only take the survey once. We used Sekhon's Theoretical Framework of Acceptability, validated for staff acceptability of a new intervention, assessing eight domains with 5‐point Likert responses. Clinicians were asked about prior experience with SQuID, and we assessed ED MD and RN preference (SQuID vs. intravenous [IV] insulin). Surveys included free‐text boxes for comments. We present descriptive statistics including proportions with 95% confidence interval and medians with interquartile ranges (IQRs) and conducted thematic analysis of free‐text comments.ResultsOur overall response rate (107/133) was 80% (34/42 ED RNs, 13/16 floor RNs, 47/57 ED MDs, 13/17 floor MDs), with first‐time users of SQuID ranging from 7.7% (hospitalist MDs) to 35.3% (ED RNs) of participants. ED clinicians preferred SQuID over IV insulin (67% vs. 12%, 21% no preference). Acceptability was high across all domains and clinician types (median 4, IQR 4–5). Overall percentage of positive responses (4s and 5s) across domains was 92% (ED RNs [89%], floor RNs [89%], ED MDs [97%], floor MDs [87%]). We identified several themes among participant comments.ConclusionsAcceptability was high across clinician types; 65% of ED clinicians preferred SQuID to IV insulin. Clinicians liked SQuID (affective attitude), found it easy to use (burden), were confident in its use (self‐efficacy), felt that it improved outcomes (perceived effectiveness), found that it was fair to patients (ethicality), found that it made sense (intervention coherence), and found that it did not interfere with other activities (opportunity cost).
Time to use the right classification to predict the severity of checkpoint inhibitor‐induced liver injury, as assessed for causality using the updated RUCAM
Authors: Hountondji Lina , Faure Stéphanie , Palassin Pascale , Viel Philine Witkowski Durand , Dupuy Marie , Larrey Dominique , Lamoureux Anouck , Coustal Cyrille , Pureur Dimitri , Lesage Candice , Assenat Éric , Rivière Benjamin , Faillie Jean‐Luc , Quantin Xavier , Pageaux Georges‐Philippe , Maria Alexandre Thibault Jacques , Meunier Lucy 
Published: September 2024

SummaryBackground and AimsWhile immune checkpoint inhibitors (ICIs) are revolutionising cancer therapy, checkpoint inhibitor‐induced liver injury is a significant immune‐related side effect of this immunotherapy. This study focuses on the severity classifications and characteristics of patients with checkpoint inhibitor‐induced hepatitis.MethodsA retrospective analysis of patients with severe Checkpoint Inhibitor‐induced hepatitis grade 3 and 4 according to the recommended Common Terminology Criteria for Adverse Events (CTCAE) classification was conducted. Data on clinicobiological characteristics, treatment and outcomes were collected from 3 university hospitals, and causality was assessed by using the updated Roussel Uclaf Causality Assessment Method. The severity of hepatitis was assessed using the Model for End‐stage Liver Disease score, the Drug‐Induced Liver Injury Network, and the Drug‐Induced Liver Injury International Expert Working Group classifications.ResultsWe retrospectively included 100 patients presenting various hepatitis patterns with a median time to onset of 20 days after checkpoint inhibitors. Severity grading varied significantly among the classifications used. A lower incidence of severe cases was observed when using the Drug‐Induced Liver Injury classifications instead of the recommended CCTCAE classification, and this was correlated with outcomes.ConclusionsThis retrospective study challenges the efficacy of the CTCAE classification in defining the severity of Checkpoint Inhibitor‐induced hepatitis and suggests that the traditional hepatology‐focused scores may be more relevant. The CTCAE classification is inconsistent and gives equal weight to jaundice and elevated transaminases, which leads to steroid overtreatment and limits the rechallenge of ICIs.
Integrated analysis of the Neogene–Quaternary Valdera‐Volterra Basin (Northern Apennines). Evidence for composite development of hinterland basins
Authors: Poneti Giovanni , Benvenuti Marco , Scarselli Nicola , Craig Jonathan , Sani Federico 
Published: September 2024

AbstractThe Neogene and Quaternary hinterland basins of the Northern Apennine have been the subject of different tectonic interpretations. Several studies considered these basins as the result of polyphase normal faulting framed in a continuous crustal extensional regime since the middle Miocene. On the contrary, geophysical and geological studies provided evidence of the important role played by out‐of‐sequence thrusts and backthrusts in the evolution of these basins during a prolongated and intense period of shortening. Here we present an integrated analysis of 2D stacked seismic reflection profiles, stratigraphic and geophysical data from deep exploration wells, gravity data, and published geological and biostratigraphic data for the Valdera‐Volterra basin (central Tuscany, Italy). The results support a polyphase and composite evolution of the basin, subdivided into three main phases. During the late Tortonian–Zanclean, the growth of major thrust‐related anticlines controlled the evolution of the sedimentary basin. The growth of a syncline determined the creation of accommodation space for the sediments. This main compressional deformation occurred during the Messinian and ended during the Late Zanclean. NE migration of the depocentre during the Early Zanclean was identified, likely possibly due to a differential activity growth between the bordering anticlines. During the Piacenzian, an extensional phase has been recognised, superposed to the previous compressive phase. During the Latest Piacenzian–Early Pleistocene (?), a final compressional phase took place resulting in the positive inversion of the Piacenzian WSW dipping main border fault.
Robust phylogenomics settles controversies of classification and reveals evolution of male embolic complex of the Laufeia clade (Araneae, Salticidae, Euophryini)
Authors: Yu Kun , Zhang Feng , Wang Yaozhuo , Maddison Wayne P. , Zhang Junxia 
Published: September 2024

AbstractThe Laufeia clade is a peculiar lineage of euophryine jumping spiders showing rapid divergence of male genital structures, especially the embolic complex that directly interacts with female genitalia during sperm transfer. With the rapid growth of species discovery and the perplexing morphology of male genitalia in the Laufeia clade, the controversy in its classification has become a crucial problem. In this study, we applied a phylogenomic approach using ultra‐conserved elements data to infer the phylogeny of the Laufeia clade with extensive taxon sampling. A comparative morphological study was performed to evaluate diagnostic characters and understand the evolution of the male embolic complex within the Laufeia clade. The evolution of microhabitats (foliage, tree trunk, rock and surface litter) was also investigated to uncover the potential link between the microhabitat shifts and male embolic complex divergence. The results provide a strongly supported phylogenetic framework and updated generic concepts for the Laufeia clade. The synapomorphies for the updated genera within the Laufeia clade were identified through character mapping on the phylogeny. Ancestral state reconstruction analyses revealed that the Type I embolic complex (characterized by a disc‐like embolic disc with a lamina as its outer edge) was ancestral and gradually evolved into the Type II (without lamina of embolic disc, base of embolic complex often modified into a functional “conductor”) and Type III (lacking lamina of embolic disc and base of embolic complex) embolic complex, and that some embolic shapes evolved multiple times independently in different lineages of the Laufeia clade. The shift from foliage‐dwelling to tree trunk‐dwelling in the common ancestor of the Laufeia clade may have facilitated the divergent evolution of male embolic complex in the Laufeia clade. This study provides a solid foundation for future studies of systematics and evolution of this group.
A Multi‐Center International Analysis of Lung Transplantation Outcomes in Patients With COVID‐19
Authors: Kashem Mohammed Abul , Loor Gabriel , Emtiazjoo Amir , Hartwig Matthew , Van Raemdonck Dirk , Calvelli Hannah , Leon Pena Andres , Salan‐Gomez Marcelo , Zhao Huaqing , Warnick Michael , Villavicencio Mauricio , Ius Fabio , Ghadimi Kamrouz , Salman Jawad , Chandrashekaran Satish , Machuca Tiago , Sanchez Pablo G. , Subramaniam Kathirvel , Neyrinck Arne , Huddleston Stephen , Ceulemans Laurens , Osho Asishana , D'Silva Ethan , Ramamurthy Uma , Shaffer Andrew , Langer Nathaniel , Toyoda Yoshiya 
Published: September 2024

ABSTRACTIntroductionLung transplantation has become increasingly utilized in patients with COVID‐19. While several single‐center and UNOS database studies have been published on lung transplants (LTs) for end‐stage lung disease (ESLD) from Coronavirus disease 2019 (COVID‐19), there is a lack of multi‐center and international data.MethodsThis is a multicenter analysis from 11 high‐volume lung transplant centers in the United States and Europe. Data were collected through the Multi‐Institutional ECLS Registry and stratified by ESLD due to COVID‐19 versus other etiologies. Demographics and clinical variables were compared using Chi‐square test and Fisher's exact test. Survival was assessed by Kaplan‐Meier curves and compared by log‐rank test with propensity score matching.ResultsOf 1606 lung transplant recipients, 46 (2.9%) were transplanted for ESLD from COVID‐19 compared to 1560 (97.1%) without a history of COVID‐19. Among COVID‐19 patients, 30 (65.2%) had COVID‐19‐associated ARDS and 16 (34.8%) had post‐COVID‐19 fibrosis. COVID‐19 patients had higher lung allocation scores (78.0 vs. 44.4, p < 0.0001), had severely limited functional status (37.0% vs. 2.9%, p < 0.0001), had higher preoperative ECMO usage (65.2% vs. 5.4%, p < 0.0001), and spent less time on the waitlist (32 vs. 137 days, p < 0.0001). A 30‐day survival was comparable between COVID‐19 and non‐COVID‐19 patients before (100% vs. 98.7%, p = 0.39) and after propensity matching (p = 0.15).ConclusionsPatients who received LTs due to COVID‐19 had short‐term survival comparable to that of patients without COVID‐19. Our findings support the idea that lung transplantation should be considered for select patients with ESLD due to COVID‐19.