bluuebunny/crossref_metadata_2025_split huggingface dataset:
A guide to pre‐processing high‐throughput animal tracking data
Authors: Gupte Pratik Rajan , Beardsworth Christine E. , Spiegel Orr , Lourie Emmanuel , Toledo Sivan , Nathan Ran , Bijleveld Allert I. 
Published: October 2021

Abstract

Modern, high‐throughput animal tracking increasingly yields ‘big data’ at very fine temporal scales. At these scales, location error can exceed the animal's step size, leading to mis‐estimation of behaviours inferred from movement. ‘Cleaning’ the data to reduce location errors is one of the main ways to deal with position uncertainty. Although data cleaning is widely recommended, inclusive, uniform guidance on this crucial step, and on how to organise the cleaning of massive datasets, is relatively scarce.

A pipeline for cleaning massive high‐throughput datasets must balance ease of use and computationally efficiency, in which location errors are rejected while preserving valid animal movements. Another useful feature of a pre‐processing pipeline is efficiently segmenting and clustering location data for statistical methods while also being scalable to large datasets and robust to imperfect sampling. Manual methods being prohibitively time‐consuming, and to boost reproducibility, pre‐processing pipelines must be automated.

We provide guidance on building pipelines for pre‐processing high‐throughput animal tracking data to prepare it for subsequent analyses. We apply our proposed pipeline to simulated movement data with location errors, and also show how large volumes of cleaned data can be transformed into biologically meaningful ‘residence patches’, for exploratory inference on animal space use. We use tracking data from the Wadden Sea ATLAS system (WATLAS) to show how pre‐processing improves its quality, and to verify the usefulness of the residence patch method. Finally, with tracks from Egyptian fruit bats Rousettus aegyptiacus, we demonstrate the pre‐processing pipeline and residence patch method in a fully worked out example.

To help with fast implementation of standardised methods, we developed the R package atlastools, which we also introduce here. Our pre‐processing pipeline and atlastools can be used with any high‐throughput animal movement data in which the high data‐volume combined with knowledge of the tracked individuals' movement capacity can be used to reduce location errors. atlastools is easy to use for beginners while providing a template for further development. The common use of simple yet robust pre‐processing steps promotes standardised methods in the field of movement ecology and leads to better inferences from data.
Species interactions, environmental gradients and body size shape population niche width
Authors: Eloranta Antti P. , Finstad Anders G. , Sandlund Odd Terje , Knudsen Rune , Kuparinen Anna , Amundsen Per‐Arne 
Published: October 2021

Abstract

Competition for shared resources is commonly assumed to restrict population‐level niche width of coexisting species. However, the identity and abundance of coexisting species, the prevailing environmental conditions, and the individual body size may shape the effects of interspecific interactions on species’ niche width.

Here we study the effects of interspecific and intraspecific interactions, lake area and altitude, and fish body size on the trophic niche width and resource use of a generalist predator, the littoral‐dwelling large, sparsely rakered morph of European whitefish (Coregonus lavaretus; hereafter LSR whitefish). We use stable isotope, diet and survey fishing data from 14 subarctic lakes along an environmental gradient in northern Norway.

The isotopic niche width of LSR whitefish showed a humped‐shaped relationship with increasing relative abundance of sympatric competitors, suggesting widest population niche at intermediate intensity of interspecific interactions. The isotopic niche width of LSR whitefish tended to decrease with increasing altitude, suggesting reduced niche in colder, less productive lakes.

LSR whitefish typically shifted to a higher trophic position and increased reliance on littoral food resources with increasing body size, although between‐lake differences in ontogenetic niche shifts were evident. In most lakes, LSR whitefish relied less on littoral food resources than coexisting fishes and the niche overlap between sympatric competitors was most evident among relatively large individuals (>250 mm). Individual niche variation was highest among >200 mm long LSR whitefish, which likely have escaped the predation window of sympatric predators.

We demonstrate that intermediate intensity of interspecific interactions may broaden species’ niche width, whereas strong competition for limited resources and high predation risk may suppress niche width in less productive environments. Acknowledging potential humped‐shaped relationships between population niche width and interspecific interactions can help us understand species’ responses to environmental disturbance (e.g. climate change and species invasions) as well as the driving forces of niche specialization.
How wild bees find a way in European cities: Pollen metabarcoding unravels multiple feeding strategies and their effects on distribution patterns in four wild bee species
Authors: Casanelles‐Abella Joan , Müller Stefanie , Keller Alexander , Aleixo Cristiana , Alós Orti Marta , Chiron François , Deguines Nicolas , Hallikma Tiit , Laanisto Lauri , Pinho Pedro , Samson Roeland , Tryjanowski Piotr , Van Mensel Anskje , Pellissier Loïc , Moretti Marco 
Published: October 2021

Abstract

Urban ecosystems can sustain populations of wild bees, partly because of their rich native and exotic floral resources. A better understanding of the urban bee diet, particularly at the larval stage, is necessary to understand biotic interactions and feeding behaviour in urban ecosystems, and to promote bees by improving the management of urban floral resources.

We investigated the larval diet and distribution patterns of four solitary wild bee species with different diet specialization (i.e. Chelostoma florisomne, Osmia bicornis, Osmia cornuta and Hylaeus communis) along urban intensity gradients in five European cities (Antwerp, Paris, Poznan, Tartu and Zurich) using two complementary analyses. Specifically, using trap‐nests and pollen metabarcoding techniques, we characterized the species' larval diet, assessed diet consistency across cities and modelled the distribution of wild bees using species distribution models (SDMs).

Our results demonstrate that urban wild bees display different successful strategies to exploit existing urban floral resources: not only broad generalism (i.e. H. communis) but also intermediate generalism, with some degree of diet conservatism at the plant family or genus level (i.e. O. cornuta and O. bicornis), or even strict specialization on widely available urban pollen hosts (i.e. C. florisomne). Furthermore, we detected important diet variation in H. communis, with a switch from an herbaceous pollen diet to a tree pollen diet with increasing urban intensity.

Species distribution modelling indicated that wild bee distribution ranges inside urban ecosystems ultimately depend on their degree of specialization, and that broader diets result in less sensitivity to urban intensity.

Policy implications. Satisfying larval dietary requirements is critical to preserving and enhancing wild bee distributions within urban gradients. For high to intermediate levels of feeding specialization, we found considerable consistency in the preferred plant families or genera across the studied cities, which could be generalized to other cities where these bees occur. Identifying larval floral preferences (e.g. using pollen metabarcoding) could be helpful for identifying key plant taxa and traits for bee survival and for improving strategies to develop bee‐friendly cities.
Patient characteristics and treatment utilization in fatal stimulant‐involved overdoses in the United States Veterans Health Administration
Authors: Coughlin Lara N. , Zhang Lan , Bohnert Amy S. B. , Maust Donovan T. , Goldstick Jason , Lin Lewei ( Allison) 
Published: October 2021

AbstractBackground and AimsThis study aimed to (1) describe trends in stimulant‐alone and stimulant and other substance use overdose deaths from 2012 to 2018 and (2) measure patient and service use characteristics across stimulant‐related overdose death profiles.DesignRetrospective cohort study of patients who died from stimulant‐involved overdose between annual years 2012 and 2018.SettingUnited States Veterans Health Administration (VHA).A total of 3631 patients died from stimulant‐involved overdose, as identified through the National Death Index.MeasurementsStimulant‐involved overdose deaths were categorized by stimulant type (cocaine or methamphetamine/other) and other substance co‐involvement. Cause of death data were linked to patient characteristics, including demographic and treatment use preceding overdose from VHA administrative data. We examined trends over time and compared treatment use factors between the following mutually exclusive overdose profiles: cocaine alone, methamphetamine alone, cocaine + opioid, methamphetamine + opioid, any stimulant + other substance and cocaine + methamphetamine.FindingsThe rate of overdose death was 3.06 times higher in 2018 than 2012, with increases across all toxicology profiles. Compared with cocaine‐involved overdoses, methamphetamine‐involved overdoses were less likely in people who were older [adjusted odds ratio (aOR) = 0.22, 95% confidence interval (CI) = 0.06–0.87 aged 65+ versus 18–29] and more likely among those who lived in rural areas (aOR = 2.73, 95% CI = 1.43–5.23). People who died from stimulant + opioid overdoses had lower odds of a stimulant use disorder diagnosis compared with stimulant alone deaths (cocaine: aOR = 0.55, 95% CI = 0.41–0.75, methamphetamine: aOR = 0.44, 95% CI = 0.29–0.68).ConclusionsThe rate of deaths among US Veterans from stimulant‐related overdose was three times higher in 2018 than 2012. Key differences in characteristics of patients across overdose toxicology profiles, such as geographic location and health‐care use, point to distinct treatment needs based on stimulant use type.
CD103 integrin identifies a high IL‐10‐producing FoxP3+regulatory T‐cell population suppressing allergic airway inflammation
Authors: Tagkareli Sofia , Salagianni Maria , Galani Ioanna‐Evdokia , Manioudaki Maria , Pavlos Eleftherios , Thanopoulou Kalliopi , Andreakos Evangelos 
Published: October 2021

AbstractBackgroundAlthough FoxP3+regulatory T (Treg) cells constitute a highly heterogeneous population, with different regulatory potential depending on the disease context, distinct subsets or phenotypes remain poorly defined. This hampers the development of immunotherapy for allergic and autoimmune disorders. The present study aimed at characterizing distinct FoxP3+Treg subpopulations involved in the suppression of Th2‐mediated allergic inflammation in the lung.MethodsWe used an established mouse model of allergic airway disease based on ovalbumin sensitization and challenge to analyze FoxP3+Tregs during the induction and resolution of inflammation, and identify markers that distinguish their most suppressive phenotypes. We also developed a new knock‐in mouse model (Foxp3creCd103dtr) enabling the specific ablation of CD103+FoxP3+Tregs for functional studies.ResultsWe found that during resolution of allergic airway inflammation in mice >50% of FoxP3+Treg cells expressed the integrin CD103 which marks FoxP3+Treg cells of high IL‐10 production, increased expression of immunoregulatory molecules such as KLRG1, ICOS and CD127, and enhanced suppressive capacity for Th2‐mediated inflammatory responses. CD103+FoxP3+Tregs were essential for keeping allergic inflammation under control as their specific depletion inFoxp3creCd103dtrmice lead to severe alveocapillary damage, eosinophilic pneumonia, and markedly reduced lifespan of the animals. Conversely, adoptive transfer of CD103+FoxP3+Tregs effectively treated disease, attenuating Th2 responses and allergic inflammation in an IL‐10‐dependent manner.ConclusionsOur study identifies a novel regulatory T‐cell population, defined by CD103 expression, programmed to prevent exuberant type 2 inflammation and keep homeostasis in the respiratory tract under control. This has important therapeutic implications.
Open vs robot‐assisted radical cystectomy (BORARC): a double‐blinded, randomised feasibility study
Authors: Maibom Sophia L. , Røder Martin A. , Aasvang Eske K. , Rohrsted Malene , Thind Peter O. , Bagi Per , Kistorp Thomas , Poulsen Alicia M. , Salling Lisbeth N. , Kehlet Henrik , Brasso Klaus , Joensen Ulla N. 
Published: October 2021

ObjectiveTo examine surgical outcomes and feasibility of blinding patients and care providers to the surgical technique of radical cystectomy (RC).Patients and MethodsSingle‐centre, parallel‐group, double‐blinded, randomised feasibility study of open RC (ORC) vs robot‐assisted RC with intracorporeal urinary diversion (iRARC) in an ‘Enhanced Recovery After Surgery’ setup. A total of 50 patients aged ≥18 years with bladder cancer planned for RC with an ileal conduit were included. Patients with previous major abdominal/pelvic surgery, pelvic radiation or anaesthesiological contraindications were excluded. Primary outcomes were proportion of unblinded patients and success of blinding using Bang's Blinding Index. Secondary outcomes included length of stay (LOS), complication rates, blood loss, pain, and opioid consumption.ResultsA total of 26% of the patients were unblinded before discharge. We demonstrated that patients and doctors remained blinded for the allocated treatment, but nurses did not. Blood loss was greater in the ORC group as was operative time in the iRARC group. We found no difference in complication rate, LOS, or use of analgesics.ConclusionsThe present study demonstrates that blinding of surgical technique in RC is possible. The results of secondary outcomes are consistent with the findings of previous unblinded randomised controlled trials. Our study highlights that it is possible to perform a blinded phase III study to explore the optimal surgical technique in RC.
Peer pressure: The puzzle of aristocrats’ tax compliance in early nineteenth‐century Moscow
Authors: Korchmina Elena 
Published: October 2021

AbstractHow can developing countries successfully implement an income tax in the absence of a strong state? Recent theoretical research has suggested a possible solution: relying on voluntary compliance with tax demands can avoid the need for costly enforcement. This article provides empirical evidence for such a mechanism by investigating the introduction of the income tax in Russia in 1812. It uses a novel dataset to estimate the individual‐level tax compliance of Russian nobles. The dataset is constructed from self‐reported tax returns of all Russian aristocrats (around 4 000) who owned real estate in Moscow province. On the basis of both private narrative sources and state financial documents, findings show that the Russian nobility reliably declared their income: only 10 to 30 per cent of aristocrats evaded tax despite the limited legal repercussions of doing so. This surprisingly high level of tax compliance was achieved by the threat of public disclosure, whereby nobles had to declare their incomes to their peers. Nobles could face reputational risks from attempted evasion, particularly in the shadow of the looming Napoleonic invasion. Russia thus achieved its fiscal aims despite its low administrative capacity and without resorting to coercion.
Risk factors for 2‐year mortality in patients with prolonged disorders of consciousness: An international multicentre study
Authors: Estraneo Anna , Magliacano Alfonso , Fiorenza Salvatore , Formisano Rita , Grippo Antonello , Angelakis Efthymios , Cassol Helena , Thibaut Aurore , Gosseries Olivia , Lamberti Gianfranco , Noé Enrique , Bagnato Sergio , Edlow Brian L. , Chatelle Camille , Lejeune Nicolas , Veeramuthu Vigneswaran , Bartolo Michelangelo , Mattia Donatella , Toppi Jlenia , Zasler Nathan , Schnakers Caroline , Trojano Luigi 
Published: October 2021

AbstractBackground and purposePatients with prolonged disorders of consciousness (pDoC) have a high mortality rate due to medical complications. Because an accurate prognosis is essential for decision‐making on patients' management, we analysed data from an international multicentre prospective cohort study to evaluate 2‐year mortality rate and bedside predictors of mortality.MethodsWe enrolled adult patients in prolonged vegetative state/unresponsive wakefulness syndrome (VS/UWS) or minimally conscious state (MCS) after traumatic and nontraumatic brain injury within 3 months postinjury. At enrolment, we collected demographic (age, sex), anamnestic (aetiology, time postinjury), clinical (Coma Recovery Scale–Revised [CRS‐R], Disability Rating Scale, Nociception Coma Scale–Revised), and neurophysiologic (electroencephalogram [EEG], somatosensory evoked and event‐related potentials) data. Patients were followed up to gather data on mortality up to 24 months postinjury.ResultsAmong 143 traumatic (n = 55) and nontraumatic (n = 88) patients (VS/UWS, n = 68, 19 females; MCS, n = 75, 22 females), 41 (28.7%) died within 24 months postinjury. Mortality rate was higher in VS/UWS (42.6%) than in MCS (16%; p < 0.001). Multivariate regression in VS/UWS showed that significant predictors of mortality were older age and lower CRS‐R total score, whereas in MCS female sex and absence of alpha rhythm on EEG at study entry were significant predictors.ConclusionsThis study demonstrated that a feasible multimodal assessment in the postacute phase can help clinicians to identify patients with pDoC at higher risk of mortality within 24 months after brain injury. This evidence can help clinicians and patients' families to navigate the complex clinical decision‐making process and promote an international standardization of prognostic procedures for patients with pDoC.
Vitiligo Treatment Impact score (VITs): development and validation of a vitiligo burden of treatment questionnaire using the ComPaRe Vitiligo e‐cohort
Authors: Shourick J. , Seneschal J. , Andreu N. , Meurant J.‐M. , Pane I. , Ravaud P. , Tran V.‐T. , Ezzedine K. 
Published: October 2021

AbstractBackgroundVitiligo management is challenging and requires long‐term adherence of patients who often complain of the burden associated with treatment.ObjectiveTo develop and validate a patient reported measurement of the burden of treatment in vitiligo.MethodsThe study was nested within the ComPaRe Vitiligo e‐cohort, an online e‐cohort of vitiligo patients in France. Items were derived from a literature review and from the qualitative analysis of a survey using open‐ended questions of 204 patients with Vitiligo. Construct validity of the resulting instrument was assessed by comparing the instrument's score to the Dermatology Life Quality Index (DLQI), Vitiligo Impact Patient score (VIPs) and Treatment Burden Questionnaire (TBQ) scores. Reliability was assessed by test‐retest with 15 ± 10 days of interval between both assessments.ResultsIn total, 343 adult participants participated in the validation of the Vitiligo Treatment Impact score (VITs). The VITs is a 19‐item questionnaire assessing the burden of treatment in patients with vitiligo with results suggesting four domains (‘Finding a doctor’, ‘Phototherapy’, ‘Topical treatment’ and ‘Impact on outdoor activities and photoprotection’). The VITs total score was well correlated with the DLQI, VIP and TBQ scores. Agreement between test and retest was good (ICC 0.705, 95% CI 0.491–0.818).ConclusionsWe developed a patient reported measurement of the burden of treatment in vitiligo with good psychometric properties.
Conditional ablation of vasopressin‐synthesizing neurons in transgenic rats
Authors: Watanabe Jun , Takayanagi Yuki , Yoshida Masahide , Hattori Tatsuya , Saito Michiko , Kohno Kenji , Kobayashi Eiji , Onaka Tatsushi 
Published: October 2021

AbstractVasopressin‐synthesizing neurons are located in several brain regions, including the hypothalamic paraventricular nucleus (PVN), supraoptic nucleus (SON) and suprachiasmatic nucleus (SCN). Vasopressin has been shown to have various functions in the brain, including social recognition memory, stress responses, emotional behaviors and circadian rhythms. The precise physiological functions of vasopressin‐synthesizing neurons in specific brain regions remain to be clarified. Conditional ablation of local vasopressin‐synthesizing neurons may be a useful tool for investigation of the functions of vasopressin neurons in the regions. In the present study, we characterized a transgenic rat line that expresses a mutated human diphtheria toxin receptor under control of the vasopressin gene promoter. Under a condition of salt loading, which activates the vasopressin gene in the hypothalamic PVN and SON, transgenic rats were i.c.v. injected with diphtheria toxin. Intracerebroventricular administration of diphtheria toxin after salt loading depleted vasopressin‐immunoreactive cells in the hypothalamic PVN and SON, but not in the SCN. The number of oxytocin‐immunoreactive cells in the hypothalamus was not significantly changed. The rats that received i.c.v. diphtheria toxin after salt loading showed polydipsia and polyuria, which were rescued by peripheral administration of 1‐deamino‐8‐d‐arginine vasopressin via an osmotic mini‐pump. Intrahypothalamic administration of diphtheria toxin in transgenic rats under a normal hydration condition reduced the number of vasopressin‐immunoreactive neurons, but not the number of oxytocin‐immunoreactive neurons. The transgenic rat model can be used for selective ablation of vasopressin‐synthesizing neurons and may be useful for clarifying roles of vasopressin neurons at least in the hypothalamic PVN and SON in the rat.
Comparative analysis of Dipodomys species indicates that kangaroo rat hindlimb anatomy is adapted for rapid evasive leaping
Authors: Freymiller Grace A. , Whitford Malachi D. , Schwaner M. Janneke , McGowan Craig P. , Higham Timothy E. , Clark Rulon W. 
Published: October 2021

AbstractBody size is a key factor that influences antipredator behavior. For animals that rely on jumping to escape from predators, there is a theoretical trade‐off between jump distance and acceleration as body size changes at both the inter‐ and intraspecific levels. Assuming geometric similarity, acceleration will decrease with increasing body size due to a smaller increase in muscle cross‐sectional area than body mass. Smaller animals will likely have a similar jump distance as larger animals due to their shorter limbs and faster accelerations. Therefore, in order to maintain acceleration in a jump across different body sizes, hind limbs must be disproportionately bigger for larger animals. We explored this prediction using four species of kangaroo rats (Dipodomys spp.), a genus of bipedal rodent with similar morphology across a range of body sizes (40–150 g). Kangaroo rat jump performance was measured by simulating snake strikes to free‐ranging individuals. Additionally, morphological measurements of hind limb muscles and segment lengths were obtained from thawed frozen specimens. Overall, jump acceleration was constant across body sizes and jump distance increased with increasing size. Additionally, kangaroo rat hind limb muscle mass and cross‐sectional area scaled with positive allometry. Ankle extensor tendon cross‐sectional area also scaled with positive allometry. Hind limb segment length scaled isometrically, with the exception of the metatarsals, which scaled with negative allometry. Overall, these findings support the hypothesis that kangaroo rat hind limbs are built to maintain jump acceleration rather than jump distance. Selective pressure from single‐strike predators, such as snakes and owls, likely drives this relationship.