bluuebunny/crossref_metadata_2025_split huggingface dataset:
Thresholds and alternative states in a Neotropical dry forest in response to fire severity
Authors: Peinetti H. Raúl , Bestelmeyer Brandon T. , Chirino Claudia C. , Vivalda Florencia L. , Kin Alicia G. 
Published: December 2023

AbstractNeotropical xerophytic forest ecosystems evolved with fires that shaped their resilience to disturbance events. However, it is unknown whether forest resilience to fires persists under a new fire regime influenced by anthropogenic disturbance and climate change. We asked whether there was evidence for a fire severity threshold causing an abrupt transition from a forest to an alternative shrub thicket state in the presence of typical postfire management. We studied a heterogeneous wildfire event to assess medium‐term effects (11 years) of varying fire severity in a xerophytic Caldén forest in central Argentina. We conducted vegetation surveys in patches that were exposed to low (LFS), medium (MFS), and high (HFS) fire severities but had similar prefire woody canopy cover. Satellite images were used to quantify fire severity using a delta Normalized Burning Ratio (dNBR) and to map prefire canopy cover. Postfire total woody canopy cover was higher in low and medium than high severity patches, but the understory woody component was highest in HFS patches. The density of woody plants was over three times higher under HFS than MFS and LFS due to the contribution of small woody plants to the total density. Unlike LFS and MFS patches, the small plants in HFS patches were persistent, multistem shrubs that resulted from the resprouting of top‐killed Prosopis caldenia trees and, more importantly, from young shrubs that probably established after the wildfire. Our results suggest that the Caldén forest is resilient to fires of low to moderate severities but not to high‐severity fires. Fire severities with dNBR values > ~600 triggered an abrupt transition to a shrub thicket state. Postfire grazing and controlled‐fire treatments likely contributed to shrub dominance after high‐severity wildfire. Forest to shrub thicket transitions enable recurring high‐severity fire events. We propose that repeated fires combined with grazing can trap the system in a shrub thicket state. Further studies are needed to determine whether the relationships between fire and vegetation structure examined in this case study represent general mechanisms of irreversible state changes across the Caldenal forest region and whether analogous threshold relationships exist in other fire‐prone woodland ecosystems.
Camouflage efficiency in a colour‐polymorphic predator is dependent on environmental variation and snow presence in the wild
Authors: Perrault Charlotte , Morosinotto Chiara , Brommer Jon E. , Karell Patrik 
Published: December 2023

AbstractColour polymorphism can be maintained by colour morph‐specific benefits across environmental conditions. Currently, the amount and the duration of snow cover during winter decrease especially in northern latitudes, which can alter the potential for camouflage of animals with light and dark morphs. Tawny owls, Strix aluco, are colour‐polymorphic avian predators with dark (brown) and light (grey) colour morphs, where the grey morph is presumed to enjoy camouflage benefits under snowy conditions. We studied the camouflage potential of morphs in two tawny owls potential using passerines' probability to mob in the wild during winter with and without snow. For comparison with other seasons, we also repeated the experiment during spring and autumn. We found that grey tawny owls have a lower probability of being mobbed than the brown tawny owls only during snowy winters. The two colour morphs therefore experience differential benefits across snow conditions, which may help to maintain colour morphs in the population, although further warming of winter climate will reduce the potential for camouflage for grey tawny owls in northern latitudes.
Testing foraging optimization models in brown bears: Time for a paradigm shift in nutritional ecology?
Authors: Mikkelsen Ashlee J. , Hobson Keith A. , Sergiel Agnieszka , Hertel Anne G. , Selva Nuria , Zedrosser Andreas 
Published: December 2023

AbstractHow organisms obtain energy to survive and reproduce is fundamental to ecology, yet researchers use theoretical concepts represented by simplified models to estimate diet and predict community interactions. Such simplistic models can sometimes limit our understanding of ecological principles. We used a polyphagous species with a wide distribution, the brown bear (Ursus arctos), to illustrate how disparate theoretical frameworks in ecology can affect conclusions regarding ecological communities. We used stable isotope measurements (δ13C, δ15N) from hairs of individually monitored bears in Sweden and Bayesian mixing models to estimate dietary proportions of ants, moose, and three berry species to compare with other brown bear populations. We also developed three hypotheses based on predominant foraging literature, and then compared predicted diets to field estimates. Our three models assumed (1) bears forage to optimize caloric efficiency (optimum foraging model), predicting bears predominately eat berries (~70% of diet) and opportunistically feed on moose (Alces alces) and ants (Formica spp. and Camponotus spp; ~15% each); (2) bears maximize meat intake (maximizing fitness model), predicting a diet of 35%–50% moose, followed by ants (~30%), and berries (~15%); (3) bears forage to optimize macronutrient balance (macronutrient model), predicting a diet of ~22% (dry weight) or 17% metabolizable energy from proteins, with the rest made up of carbohydrates and lipids (~49% and 29% dry matter or 53% and 30% metabolizable energy, respectively). Bears primarily consumed bilberries (Vaccinium myrtillus; 50%–55%), followed by lingonberries (V. vitis‐idaea; 22%–30%), crowberries (Empetrum nigrum; 8%–15%), ants (5%–8%), and moose (3%–4%). Dry matter dietary protein was lower than predicted by the maximizing fitness model and the macronutrient balancing model, but protein made up a larger proportion of the metabolizable energy than predicted. While diets most closely resembled predictions from optimal foraging theory, none of the foraging hypotheses fully described the relationship between foraging and ecological niches in brown bears. Acknowledging and broadening models based on foraging theories is more likely to foster novel discoveries and insights into the role of polyphagous species in ecosystems and we encourage this approach.
Weather influences survival probability in two coexisting mammals directly and indirectly via competitive asymmetry
Authors: Allison Austin Z. T. , Conway Courtney J. , Goldberg Amanda R. 
Published: December 2023

AbstractEcologists have studied the role of interspecific competition in structuring ecological communities for decades. Differential weather effects on animal competitors may be a particularly important factor contributing to the outcome of competitive interactions, though few studies have tested this hypothesis in free‐ranging animals. Specifically, weather might influence competitive dynamics by altering competitor densities and/or per‐capita competitive effects on demographic vital rates. We used a 9‐year data set of marked individuals to test for direct and interactive effects of weather and competitor density on survival probability in two coexisting mammalian congeners: Columbian ground squirrels (Urocitellus columbianus) and northern Idaho ground squirrels (Urocitellus brunneus). Ambient temperature and precipitation influenced survival probability in both species, but the effects of weather differed between the two species. Moreover, density of the larger Columbian ground squirrel negatively impacted survival probability in the smaller northern Idaho ground squirrel (but not vice versa), and the strength of the negative effect was exacerbated by precipitation. That is, cooler, wetter conditions benefited the larger competitor to the detriment of the smaller species. Our results suggest weather‐driven environmental variation influences the competitive equilibrium between ecologically similar mammals of differential body size. Whether future climate change leads to the competitive exclusion of either species will likely depend on the mechanism(s) explaining the coexistence of these competing species. Divergent body size and, hence, differences in thermal tolerance and giving up densities offer potential explanations for the weather‐dependent competitive asymmetry we documented, especially if the larger species competitively excludes the smaller species from habitat patches of shared preference via interference.
Introduction to special issue: Advancing disease ecology through eDNA monitoring of infectious agents
Authors: Childress Jasmine , Faust Christina L. , Deiner Kristy 
Published: December 2023

AbstractThis special issue focuses on the applications of environmental DNA (eDNA) sequencing for the detection and monitoring of disease‐causing agents, including viruses, bacteria, protozoans, myxozoans, fungi, trematodes, and arthropods. We explore the impact of eDNA technologies, such as metabarcoding and qPCR, in understanding the dynamics of pathogens in various environments as well as their implications for conservation, biosecurity, and veterinary and agricultural health under the “One Health” framework. This issue addresses how molecular sequencing provides innovative solutions to the challenges faced by conventional parasite and pathogen detection methods, enabling a more comprehensive understanding of the spatiotemporal dynamics of disease agents. Finally, we discuss the challenges in eDNA applications, such as primer development and taxonomic resolution, and the opportunities for future research in advancing eDNA methodologies for infectious disease studies. This issue highlights the growing importance of eDNA surveillance in understanding and managing the health of ecosystems and at‐risk species.
Metaverse: Trend, emerging themes, and future directions
Authors: To Wai‐Ming , Yu Billy T. W. , Chung Andy W. L. , Chung David W. K. 
Published: December 2023

AbstractMetaverse is going to change human life in a profound way because it offers an opportunity to merge our physical world with the digital/virtual worlds. Yet, how much effort has the research community across the world and disciplines contributed and what are the emerging themes of metaverse? The study aims to answer these important research questions using a bibliometric approach. Using a search of (“metaverse” OR “metaverses”) in “Article Title, Abstract, Keywords” and the date range up to 2022 on March 15, 2023 in Scopus, 1031 journal articles, reviews, and conference papers were identified. Among the 1031 identified documents, 816 (i.e., around 80%) were published in 2022. Feiyue Wang of the Institute of Automation, Chinese Academy of Sciences was found to be the most productive author with 17 metaverse publications, followed by Elif Ayiter of Sabancı Üniversitesi with 11 metaverse publications. The Chinese Academy of Sciences (with its Institute of Automation) was found to be the most productive affiliation with 29 publications. China, the United States, South Korea, and the United Kingdom were the most productive countries that contributed to over 58% of metaverse publications. Co‐occurrence of keywords analysis revealed that seven clusters were emerged. The clusters included “artificial intelligence and human perception,” “metaverses and blockchain,” “e‐learning and students,” “metaverse, avatar and immersive,” “virtual reality, virtual worlds, and Second Life,” “three dimensional computer graphics and deep learning,” and “augmented reality, mixed reality, and human computer interaction.” Implications and future directions are given.
Population structure, runs of homozygosity analysis and construction of single nucleotide polymorphism fingerprinting database of Longnan goat population
Authors: Ma Keyan , Li Dengpan , Qi Xingcai , Li Qiao , Wu Yi , Song Juanjuan , Zhang Yue , Yang Hai , Li Taotao , Ma Youji 
Published: December 2023

AbstractThe Longnan goat (LN) is a local breed discovered during the third census of China's livestock and poultry genetic resources. In order to thoroughly comprehend the population traits, this research examined a total of 70 animals from three different goat populations, namely the LN goat, Nanjiang Brown goat (NJ), and Boer goat (Boer). Specific‐Locus Amplified Fragment Sequencing was employed to analyze genetic diversity, population structure, and selective sweep patterns. Additionally, individual DNA fingerprints were generated to provide detailed genetic profiles for each subject. A total of 643,868 single nucleotide polymorphisms (SNPs) were detected, with a majority located in intergenic and intronic regions. Genetic diversity analysis uncovered lower diversity within the LN population compared to the other two populations. The analysis of population structure unveiled significant genetic distance between LN and both NJ and Boer populations, with distinct clustering patterns observed. Moreover, genetic differentiation coefficients (FST) of 0.1019 and 0.0854 were determined between LN and Boer, as well as LN and NJ, respectively, indicating substantial genetic differentiation. Selective sweep analysis, combining FST and π ratio, identified several genes associated with growth and development, reproduction, hair color, and immunity that may serve as valuable candidates for marker‐assisted breeding. Furthermore, identification of 47,541 runs of homozygosity (ROHs) revealed non‐uniform distribution across chromosomes, with the highest frequency on chromosome 1 and the lowest on chromosome 27. Correlations between different inbreeding coefficients varied, with the highest observed between FHOM and FGRM, and the lowest between FROH >1.5Mb and FROH <500kb. A total of 46 candidate genes were annotated within high‐frequency ROH islands, primarily associated with biological processes such as reproduction, growth and development, and immunity. Finally, a DNA fingerprint, consisting of 371 highly polymorphic SNPs, was generated and presented in the form of a two‐dimensional code for convenient access. Based on the population structure analysis, LN goats have been found to have a distant genetic distance and a higher degree of differentiation from both the Boer and NJ populations. Evaluation of genetic diversity parameters and ROH analysis indicates that the LN population exhibits lower genetic diversity and shows signs of inbreeding. Our findings offer theoretical support for the identification of genetic resources within this population.
Association between energy‐adjusted dietary inflammatory index and total immunoglobulin E: A cross‐sectional study
Authors: Su Liang , Wang Fang , Qin Cheng , Wang Zhimin , Yang Xuesong , Ye Jianzhou 
Published: December 2023

AbstractThe relationship between a pro‐inflammatory diet, assessed by the dietary inflammatory index (DII), and allergic diseases has attracted attention. However, the association between DII and immunoglobulin E (IgE) remains uncertain. We aim to investigate the association between energy‐adjusted DII (E‐DII) and total IgE. We analyzed data from the 2005 to 2006 National Health and Nutrition Examination Survey. The relationship between E‐DII and total IgE was assessed using linear regression and logistic regression analysis. Meanwhile, we conducted a subgroup analysis stratified by body mass index (BMI) and analyzed the mediating role of BMI. We included 3614 adult participants. After controlling for confounding factors, there was no statistical association between E‐DII and total IgE (β 0.023, 95% CI −0.01 to 0.057, p = .173) and the risk of high total IgE (OR 1.036, 95% CI 0.977 to 1.099, p = .233). We conducted subgroup analysis stratified by BMI. After controlling for confounding factors, only in overweight groups, E‐DII was statistically associated with total IgE (β 0.076, 95% CI 0.017 to 0.135, p = .012) and the risk of high total IgE (OR 1.124, 95% CI 1.015 to 1.246, p = .025). Generalized additive models and smooth curve fittings showed a positive linear relationship between E‐DII and total IgE in overweight participants. No statistical association was noted for the mediation effect of BMI on the association between E‐DII and total IgE in the overweight group (p = .23). Overweight participants with higher E‐DII were potentially at risk of elevated total IgE.
Successful treatment with enfortumab–vedotin of metastatic signet ring cell cancer expressing nectin‐4 and originating from the bladder
Authors: Aoki Maria , Naiki Taku , Naiki‐Ito Aya , Morikawa Toshiharu , Matsuyama Nayuka , Torii Koei , Kato Taiki , Maruyama Tetsuji , Inaguma Shingo , Yasui Takahiro 
Published: December 2023

IntroductionAs an aggressive adenocarcinoma phenotype, primary signet ring cell carcinoma of the urinary bladder is an extremely rare variant. The prognosis of metastatic signet ring cell carcinoma of the urinary bladder is extremely poor and the clinical course for its specific pathogenesis remains unelucidated.Case presentationA 64‐year‐old Japanese male patient was diagnosed with invasive urothelial carcinoma with glandular differentiation of a signet ring cell–type with pT4aN0M0, and he was eventually diagnosed with metastatic signet ring cell carcinoma of the urinary bladder. He was initially responsive to systemic combination induction chemotherapy of S‐1 and cisplatin followed by avelumab switch maintenance therapy; however, signet ring cell carcinoma of the urinary bladder relapse occurred in the pathological findings of a biopsy from the right thigh. Immunohistochemical analysis of this specimen identified strong positive staining for nectin‐4 and, following enfortumab–vedotin treatment, the patient showed a good response.ConclusionWe thus describe a rare case of metastatic signet ring cell carcinoma of the urinary bladder with nectin‐4 expression diagnosed by a biopsy of a metastatic site.
The possible role of nuclear factor erythroid‐2‐related factor 2 activators in the management of Covid‐19
Authors: Al‐kuraishy Hayder M. , Al‐Gareeb Ali I. , Eldahshan Omayma A. , Abdelkhalek Yasmine M. , El dahshan Magdy , Ahmed Eman A. , Sabatier Jean‐Marc , Batiha Gaber E.‐S. 
Published: December 2023

AbstractCOVID‐19 is caused by a novel SARS‐CoV‐2 leading to pulmonary and extra‐pulmonary manifestations due to oxidative stress (OS) development and hyperinflammation. COVID‐19 is primarily asymptomatic though it may cause acute lung injury (ALI), acute respiratory distress syndrome (ARDS), systemic inflammation, and thrombotic events in severe cases. SARS‐CoV‐2‐induced OS triggers the activation of different signaling pathways, which counterbalances this complication. One of these pathways is nuclear factor erythroid 2‐related factor 2 (Nrf2), which induces a series of cellular interactions to mitigate SARS‐CoV‐2‐mediated viral toxicity and OS‐induced cellular injury. Nrf2 pathway inhibits the expression of pro‐inflammatory cytokines and the development of cytokine storm in COVID‐19. Therefore, Nrf2 activators may play an essential role in reducing SARS‐CoV‐2 infection‐induced inflammation by suppressing NLRP3 inflammasome in COVID‐19. Furthermore, Nrf2 activators can attenuate endothelial dysfunction (ED), renin‐angiotensin system (RAS) dysregulation, immune thrombosis, and coagulopathy. Thus this mini‐review tries to clarify the possible role of the Nrf2 activators in the management of COVID‐19. Nrf2 activators could be an effective therapeutic strategy in the management of Covid‐19. Preclinical and clinical studies are recommended in this regard.
MPI‐parallelization of the grid inhomogeneous solvation theory calculation
Authors: Roe Daniel R. , Brooks Bernard R. 
Published: December 2023

AbstractThe grid inhomogeneous solvation theory (GIST) method requires the often time‐consuming calculation of water–water and water‐solute energy on a grid. Previous efforts to speed up this calculation include using OpenMP, GPUs, and particle mesh Ewald. This article details how the speed of this calculation can be increased by parallelizing it with MPI, where trajectory frames are divided among multiple processors. This requires very little communication between individual processes during trajectory processing, meaning the calculation scales well to large processor counts. This article also details how the entropy calculation, which must happen after trajectory processing since it requires information from all trajectory frames, is parallelized via MPI. This parallelized GIST method has been implemented in the freely‐available CPPTRAJ analysis software.
The management and clinical outcomes of pregnancies in women with urea cycle disorders: A review of the literature and results of an international survey
Authors: Stepien Karolina M. , Langendonk Janneke G. , Dao Myriam , Gomes Daniel Costa , Douillard Claire , Filipsson Karin , Glamuzina Emma , Haverkamp Jorien A. , Langeveld Mirjam , Lehman Anna , de Lonlay Pascale , Lund Allan M. , Oscarson Mikael , Peltenburg N. Chantal , Ramadža Danijela Petković , Ramachandran Radha , Reismann Peter , Shtylla Alboren , Tchan Michel , Tan Chong Yew , Wilson Callum , Woodall Alison , Murphy Elaine , Wagenmakers Margreet A. E. M. 
Published: December 2023

AbstractAn increasing number of women with urea cycle disorders (UCDs) are reaching child‐bearing age and becoming pregnant. Improved diagnostics and increased awareness of inherited metabolic diseases has also led to more previously undetected women being diagnosed with a UCD during or shortly after pregnancy. Pregnancy increases the risk of acute metabolic decompensation with hyperammonemia—which can occur in any trimester, and/or the postpartum period, and may lead to encephalopathy, psychosis, coma, and even death, if not diagnosed promptly and treated appropriately. There are also (theoretical) concerns that a maternal UCD, or its treatment, may cause potential risks for the unborn child. Currently evidence on management and outcome of pregnancies in UCDs is limited to case reports and there are no clear guidelines. In order to inform management and investigate outcomes of pregnancies in women with a UCD, we performed a retrospective review of published cases and analyzed data collected from an international online survey. We conclude that, although risk during the intra‐ and postpartum period exists, multidisciplinary management by an experienced team and a prospective plan usually result in successful pregnancy, labor, delivery, and postpartum period. No deaths were reported in mothers managed accordingly. With the exception of male neonates with Ornithine Transcarbamylase deficiency, the clinical outcome of children born to mothers with UCDs appears positive, although follow‐up is limited. The outcome for women presenting with a first acute metabolic decompensation during pregnancy or postpartum is less favorable. Deaths were associated with diagnostic delay/late management of hyperammonemia in previously undiagnosed women.