cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.70rxwdbxw
title: External validation of EPIC’s Risk of Unplanned Readmission model, the LACE+ index and SQLape® as predictors of unplanned hospital readmissions: A monocentric, retrospective, diagnostic cohort study in Switzerland

description: Introduction: Readmissions after an acute care hospitalization are
 relatively common, costly to the health care system, and are associated
 with significant burden for patients. As one way to reduce costs and
 simultaneously improve quality of care, hospital readmissions receive
 increasing interest from policy makers. It is only relatively recently
 that strategies were developed with the specific aim of reducing unplanned
 readmissions using prediction models to identify patients at risk. EPIC’s
 Risk of Unplanned Readmission model promises superior performance.
 However, it has only been validated for the US setting. Therefore, the
 main objective of this study is to externally validate the EPIC’s Risk of
 Unplanned Readmission model and to compare it to the internationally,
 widely used LACE+ index, and the SQLAPE® tool, a Swiss national quality of
 care indicator. Methods: A monocentric, retrospective, diagnostic cohort
 study was conducted. The study included inpatients, who were discharged
 between the 1st of January 2018 and the 31st of December 2019 from the
 Lucerne Cantonal Hospital, a tertiary-care provider in Central
 Switzerland. The study endpoint was an unplanned 30-day readmission.
 Models were replicated using the original intercept and beta coefficients
 as reported. Otherwise, score generator provided by the developers were
 used. For external validation, discrimination of the scores under
 investigation were assessed by calculating the area under the receiver
 operating characteristics curves (AUC). Calibration was assessed with the
 Hosmer-Lemeshow X2 goodness-of-fit test This report adheres to
 the TRIPOD statement for reporting of prediction models. Results: At least
 23,116 records were included. For discrimination, the EPIC´s prediction
 model, the LACE+ index and the SQLape® had AUCs of 0.692 (95% CI
 0.676-0.708), 0.703 (95% CI 0.687-0.719) and 0.705 (95% CI 0.690-0.720).
 The Hosmer-Lemeshow X2 tests had values of p&lt;0.001.
 Conclusion: In summary, the EPIC´s model showed less favorable performance
 than its comparators. It may be assumed with caution that the EPIC´s model
 complexity has hampered its wide generalizability - model updating is
 warranted.
DOI: 10.5061/dryad.f7m0cfxwh
title: Effects of released farmed mallards on species richness of breeding waterbirds and amphibians in natural, restored, and constructed wetlands

description: Common practices in current game management are wetland restoration and
 creation, as well as releases of quarry species. We studied the impact of
 releases of mallard ducklings on species richness of wild waterbirds and
 amphibians on three types of wetlands: natural, constructed and restored.
 Data on species richness, macrophyte cover and water characteristics
 (total phosphorous and pH) were collected at 32 sites in an agricultural
 landscape in southern Sweden. In total, 14 species of waterbirds were
 recorded, ranging from zero to seven per wetland and survey. Amphibians
 were present in 24 of the 32 wetlands; in total five species were found,
 ranging from zero to three per wetland. By using generalized linear
 modelling we found that wetland type best predicted waterbird species
 richness. Constructed wetlands had significantly more waterbird species,
 regardless of whether they were used for mallard releases or not. There
 were breeding amphibians in 62% of natural, 100% of restored and 77% of
 constructed wetlands. Breeding amphibians were present in 84% of wetlands
 without, and in 62% of wetlands with releases. However, included variables
 did not explain amphibian species richness in the wetlands. Releasing
 large numbers of mallards on a wetland and providing food ad libitum is
 likely to affect water quality, nutrient availability and predation
 pressure. Indeed, phosphorous levels were significantly higher in release
 wetlands, but no differences were found between wetland types.This means
 that mallard releases may increase nutrient loads in environments that are
 already eutrophied. However, in our study system releases did not
 influence species richness of waterbirds and amphibians locally.
 Constructing wetlands for mallard releases can thus have positive local
 effects on species richness.
description: Bird and amphibian surveys and water samples.
DOI: 10.5061/dryad.q83bk3jj2
title: Civil war is associated with longer escape distances among Sri Lankan birds - flight-initiation distances of Sri Lankan birds

description: War influences wildlife in a variety of ways but may influence their
 escape responses to approaching threats, including humans, because of its
 effect on human populations and behaviour, and landscape change. We
 collected 1,400 Flight-Initiation Distances (FIDs) from 157 bird species
 in the dry zone of Sri Lanka, where civil war raged for 26 years, ending
 in 2009. Accounting for factors known to influence FIDs (phylogeny,
 starting distance of approaches, body mass, prevailing human density,
 group size and location), we found birds have longer FIDs in the part of
 the dry zone which experienced civil war. Larger birds, often preferred by
 human hunters, showed greater increases in FID in the war zone, consistent
 with the idea that war was associated with greater hunting pressure, that
 larger birds experienced longer-lasting trauma, or had more plastic escape
 behaviour, than smaller species. While the mechanisms linking the war and
 avian escape responses remain ambiguous, wars evidently leave legacies
 which extend to behavioural responses in birds.
description: Please see the read_me file, manuscript, the code, and the
 phylogeny. 
description: Please see the read_me file, manuscript, the code, and the
 phylogeny.
DOI: 10.5061/dryad.dncjsxm09
title: Transmissible cancer influences immune gene expression in an endangered marsupial, the Tasmanian devil (Sarcophilus harrisii)

description: Understanding wildlife diseases’ effects on populations requires insight
 into local environmental conditions, host defence mechanisms, host
 life-history trade-offs, pathogen population dynamics, and their
 interactions. The survival of Tasmanian devils (Sarcophilus harrisii) is
 challenged by a novel, fitness limiting pathogen, Tasmanian devil facial
 tumour disease (DFTD), a clonally transmissible, contagious cancer. In
 order to understand the devils’ capacity to respond to DFTD, it is crucial
 to gain information on factors influencing the devils’ immune system. By
 using RT-qPCR, we investigated how DFTD infection in association with
 intrinsic (sex and age) and environmental (season) factors influences the
 expression of 10 immune genes in Tasmanian devil blood. Our study showed
 that the expression of immune genes (both innate and adaptive) differed
 across seasons, a pattern that was altered when infected with DFTD. The
 expression of immunogbulins IgE and IgM:IgG showed downregulation in
 colder months in DFTD infected animals. We also observed strong positive
 association between the expression of an innate immune gene, CD16, and
 DFTD infection. Our results demonstrate that sampling across seasons, age
 groups and environmental conditions are beneficial when deciphering the
 complex eco-evolutionary interactions of not only conventional
 host-parasite systems, but also of host and diseases with high mortality
 rates, such as transmissible cancers.
DOI: 10.5061/dryad.83bk3j9rw
title: Amphibian resistance to chytridiomycosis increases following low virulence chytrid fungal infection or drug-mediated clearance

description: Amphibian biodiversity is experiencing ongoing declines due in part to the
 infectious disease, chytridiomycosis. Efforts to mitigate the effects of
 the causal agent of chytridiomycosis, Batrachochytrium dendrobatidis (Bd),
 in the wild have not been wholly effective. Translocations are an
 important management tool for amphibians, and immunizations represent a
 possible strategy for preparing amphibians for release across a landscape
 where Bd exists. We evaluated the utility of using an isolate of Bd that
 was shown to be hypovirulent to the relict leopard frog (Rana onca) as a
 transmissible inoculum for promoting chytridiomycosis-resistance. We
 conducted a cohousing experiment to determine if the isolate we used could
 be passed between R. onca without increasing in virulence. We then
  followed with an experiment where frogs that were exposed to the
 hypovirulent isolate were then challenged with a virulent Bd isolate. In
 other experiments, we evaluated whether Bd infections followed by
 clearance with itraconazole (an antifungal) could increase resistance to
 chytridiomycosis in R. onca and Rana pipiens (northern leopard frog). We
 found that our hypovirulent Bd inoculation was transmissible between
 hosts, did not cause chytridiomycosis, and was effective at increasing
 chytridiomycosis-resistance. Rana onca inoculated with the hypovirulent Bd
 isolate had lower pathogen burdens and were 55 times more likely to
 survive infections by a virulent Bd isolate than non-inoculated frogs. For
 both species, prior exposure to Bd followed by infection clearance with
 itraconazole resulted in significantly increased survivorship and lower
 pathogen burdens as compared to controls that had no prior Bd exposure.
 Rana onca that were previously exposed to Bd were more than 15 times more
 likely to survive infections. Previously exposed R. pipiens survived in
 higher proportions than controls, but with weaker statistical support.
  
description: The data is predominately qPCR data generated from skin swabs
 collected weekly during our challenge studies. Outputs are measured in
 zoospore equivalents (ZE). This is a measure we have determined using DNA
 standards of a known amount of Bd zoospores. We also have some ancillary
 data included in these files (mass, SVL, and survivorship).
description: All missing values are frogs that had developed fatal disease and
 thus no longer contributed data to the experiment. These are noted as
 "null" in each dataset.
DOI: 10.5061/dryad.931zcrjkg
title: Mesozoic origin and out-of-India radiation of ricefishes (Adrianichthyidae)

description: The Indian subcontinent has an origin geologically different from Eurasia,
 but many terrestrial animal and plant species on it have congeneric or
 sister species in other parts of Asia, especially in the Southeast. This
 faunal and floral similarity between India and Southeast Asia is explained
 by either of the two biogeographic scenarios, ‘into-India’ or
 ‘out-of-India.’ Phylogenies based on complete
 mitochondrial genome and five nuclear genes were undertaken for ricefishes
 (Adrianichthyidae) to examine which of these two
 biogeographic scenarios fits better. We
 found that Oryzias setnai, the only
 adrianichthyid distributed in and endemic to the Western Ghats, a mountain
 range running parallel to the western coast of the Indian subcontinent, is
 sister to all other adrianichthyids from eastern India and Southeast–East
 Asia. Divergence time estimates and ancestral area reconstructions reveal
 that this western Indian species diverged in the late Mesozoic during the
 northward drift of the Indian subcontinent. These findings indicate that
 adrianichthyids dispersed eastward ‘out of India’ after the collision of
 the Indian subcontinent with Eurasia, and subsequently diversified in
 Southeast–East Asia. A review of geographic distributions of
 ‘out-of-India’ taxa reveals that they may have largely fuelled or modified
 the biodiversity of Eurasia.
DOI: 10.5061/dryad.wpzgmsbnc
title: Environmental and seasonal correlates of capercaillie movement traits in a Swedish wind farm

description: Animals continuously interact with their environment through behavioural
 decisions, rendering the appropriate choice of movement speed and
 directionality an important phenotypic trait. Anthropogenic activities may
 alter animal behaviour, including movement. A detailed understanding of
 movement decisions is therefore of great relevance for science and
 conservation alike. The study of movement decisions in relation to
 environmental and seasonal cues requires continuous observation of
 movement behaviour, recently made possible by high-resolution telemetry.
 We studied movement traits of 13 capercaillie (Tetrao urogallus), a mainly
 ground-moving forest bird species of conservation interest, over two
 summer seasons in a Swedish windfarm using high-resolution GPS tracking
 data (5-minute sampling interval). We filtered and removed unreliable
 movement steps using accelerometer data and step characteristics. We
 explored variation in movement speed and directionality in relation to
 environmental and seasonal covariates using Generalized Additive Mixed
 Models (GAMMs). We found evidence for clear daily and seasonal variation
 in speed and directionality of movement that reflected behavioural
 adjustments to biological and environmental seasonality. Capercaillie
 moved slower when more turbines were visible and faster close to turbine
 access roads. Movement speed and directionality were highest on open bogs,
 lowest on recent clear-cuts (&lt;5 y.o.) and intermediate in all types
 of forest. Our results provide novel insights into the seasonal and
 environmental correlates of capercaillie movement patterns and supplement
 previous behavioural observations on lekking behaviour and wind turbine
 avoidance with a more mechanistic understanding.
description: Please see the associated manuscript and the ReadMe file.
description: We would appreciate if you would notfiy
 joy.coppes[at]forst.bwl.de when using this dataset.
DOI: 10.5061/dryad.r4xgxd2ct
title: The interplay of wind and uplift facilitates over-water flight in facultative soaring birds

description: Flying over the open sea is energetically costly for terrestrial birds.
 Despite this, over-water journeys of many birds, sometimes hundreds of
 kilometers long, are uncovered by bio-logging technology. To understand
 how these birds afford their flights over the open sea, we investigated
 the role of atmospheric conditions, specifically wind and uplift, in
 subsidizing over-water flight at the global scale. We first established
 that ∆T, the temperature difference between sea surface and air, is a
 meaningful proxy for uplift over water. Using this proxy, we showed that
 the spatio-temporal patterns of sea-crossing in terrestrial migratory
 birds is associated with favorable uplift conditions. We then analyzed
 route selection over the open sea for five facultative soaring species,
 representing all major migratory flyways. The birds maximized wind support
 when selecting their sea-crossing routes and selected higher uplift when
 suitable wind support was available. They also preferred routes with low
 long-term uncertainty in wind conditions. Our findings suggest that, in
 addition to wind, uplift may play a key role in the energy seascape for
 bird migration that in turn determines strategies and associated costs for
 birds crossing ecological barriers such as the open sea.
description: The R scripts needed to reproduce the results are included in the
 repository: https://github.com/mahle68/global_seascape_public
DOI: 10.5061/dryad.f7m0cfxwj
title: Ecological inference using data from accelerometers needs careful protocols

description: 1. Accelerometers in animal-attached tags have proven to be powerful tools
 in behavioural ecology, being used to determine behaviour and provide
 proxies for movement-based energy expenditure. Researchers are collecting
 and archiving data across systems, seasons and device types. However, in
 order to use data repositories to draw ecological inference, we need to
 establish the error introduced according to sensor type and position on
 the study animal and establish protocols for error assessment and
 minimization. 2. Using laboratory trials, we examine the absolute accuracy
 of tri-axial accelerometers and determine how inaccuracies impact
 measurements of dynamic body acceleration (DBA) in human participants,
 with DBA as the main acceleration-based proxy for energy expenditure. We
 then examine how tag type and placement affect the acceleration signal in
 birds, using (i) pigeons Columba livia flying in a wind tunnel, with tags
 mounted simultaneously in two positions, and (ii) back- and tail-mounted
 tags deployed on wild kittiwakes Rissa tridactyla. Finally, we (iii)
 present a case study where two generations of tag were deployed using
 different attachment procedures on red-tailed tropicbirds Phaethon
 rubricauda foraging in different seasons. 3. Bench tests showed that
 individual acceleration axes required a two-level correction to eliminate
 measurement error. This resulted in DBA differences of up to 5% between
 calibrated and uncalibrated tags for humans walking at a range of speeds.
 Device position was associated with greater variation in DBA, with upper-
 and lower back-mounted tags varying by 9% in pigeons, and tail- and
 back-mounted tags varying by 13% in kittiwakes. The largest variation
 occurred between tropicbirds tagged in different seasons, where DBA varied
 by 25%, which may be due to tag attachment procedures. In general, the
 tropicbird study highlights the difficulties of attributing changes in
 signal amplitude to a single factor, when confounding influences tend to
 covary. 4. Accelerometer accuracy, tag placement, and attachment
 critically affect the signal amplitude and thereby the ability of the
 system to detect biologically meaningful phenomena. We propose a simple
 method to calibrate accelerometers that can be executed under field
 conditions. This should be used prior to deployments and archived with
 resulting data. We also suggest a way that researchers can assess accuracy
 in previously collected data, and caution that variable tag placement and
 attachment can increase sensor noise and even generate trends that have no
 biological meaning.
DOI: 10.6084/m9.figshare.31113140
title: Impact of polycystic kidney disease on outcomes after renal transplantation: systematic review and meta-analysis

description: Polycystic kidney disease (PKD) represents one of the most prevalent inherited renal disorders and constitutes the fourth leading etiology of end-stage kidney disease (ESKD). While renal transplantation remains the optimal therapeutic intervention for ESKD, existing evidence regarding post-transplant survival rates and graft loss in PKD recipients remains contentious. This systematic review incorporated studies from PubMed, Scopus, and Embase databases, with a preregistered protocol on PROSPERO (CRD420251002570). We evaluated the impact of PKD on post-transplant outcomes through comparative analyses of patient survival and graft survival at 1-, 5-, and 10-year intervals between PKD and non-PKD cohorts. Secondary outcomes included complication profiles. Methodological quality was appraised using the ROBINS-I tool for non-randomized studies. From 1,187 screened records, 23 studies were eligible for inclusion. Meta-analysis demonstrated superior 1-year patient survival in PKD kidney transplant recipients (OR 1.30, 95% CI: 1.08–1.56; 19 studies, I<sup>2</sup>=0.0%) and enhanced 10-year graft survival (OR 1.60, 95% CI: 1.52–1.62; 20 studies, I<sup>2</sup>=73.5%) compared to non-PKD counterparts. Subgroup analyses revealed amplified survival advantages in retrospective studies (OR 1.67, 95% CI: 1.35–2.07; 7 studies, I<sup>2</sup>=23.6%) and cohorts with unspecified donor types (OR 1.27, 95% CI: 1.05–1.53; 13 studies, I<sup>2</sup>=0.0%). Notably, PKD recipients exhibited higher incidence of post-transplant diabetes mellitus (OR 1.61, 95% CI: 1.40–1.81; I<sup>2</sup>=85.4%), while acute rejection episodes, infectious complications, and malignancy rates showed no intergroup divergence. PKD kidney transplant recipients demonstrate favorable short-term survival and long-term graft retention compared to non-PKD patients. However, residual confounding from donor characteristics, sample size heterogeneity, and methodological variations necessitate cautious interpretation.
DOI: 10.6084/m9.figshare.31113140.v1
title: Impact of polycystic kidney disease on outcomes after renal transplantation: systematic review and meta-analysis

description: Polycystic kidney disease (PKD) represents one of the most prevalent inherited renal disorders and constitutes the fourth leading etiology of end-stage kidney disease (ESKD). While renal transplantation remains the optimal therapeutic intervention for ESKD, existing evidence regarding post-transplant survival rates and graft loss in PKD recipients remains contentious. This systematic review incorporated studies from PubMed, Scopus, and Embase databases, with a preregistered protocol on PROSPERO (CRD420251002570). We evaluated the impact of PKD on post-transplant outcomes through comparative analyses of patient survival and graft survival at 1-, 5-, and 10-year intervals between PKD and non-PKD cohorts. Secondary outcomes included complication profiles. Methodological quality was appraised using the ROBINS-I tool for non-randomized studies. From 1,187 screened records, 23 studies were eligible for inclusion. Meta-analysis demonstrated superior 1-year patient survival in PKD kidney transplant recipients (OR 1.30, 95% CI: 1.08–1.56; 19 studies, I<sup>2</sup>=0.0%) and enhanced 10-year graft survival (OR 1.60, 95% CI: 1.52–1.62; 20 studies, I<sup>2</sup>=73.5%) compared to non-PKD counterparts. Subgroup analyses revealed amplified survival advantages in retrospective studies (OR 1.67, 95% CI: 1.35–2.07; 7 studies, I<sup>2</sup>=23.6%) and cohorts with unspecified donor types (OR 1.27, 95% CI: 1.05–1.53; 13 studies, I<sup>2</sup>=0.0%). Notably, PKD recipients exhibited higher incidence of post-transplant diabetes mellitus (OR 1.61, 95% CI: 1.40–1.81; I<sup>2</sup>=85.4%), while acute rejection episodes, infectious complications, and malignancy rates showed no intergroup divergence. PKD kidney transplant recipients demonstrate favorable short-term survival and long-term graft retention compared to non-PKD patients. However, residual confounding from donor characteristics, sample size heterogeneity, and methodological variations necessitate cautious interpretation.