bluuebunny/crossref_metadata_2025_split huggingface dataset:
Low acclimation capacity of narrow‐ranging thermal specialists exposes susceptibility to global climate change
Authors: Markle Tricia M. , Kozak Kenneth H. 
Published: April 2018

AbstractThermal acclimation is hypothesized to offer a selective advantage in seasonal habitats and may underlie disparities in geographic range size among closely‐related species with similar ecologies. Understanding this relationship is also critical for identifying species that are more sensitive to warming climates. Here, we study North American plethodontid salamanders to investigate whether acclimation ability is associated with species’ latitudinal extents and the thermal range of the environments they inhabit. We quantified variation in thermal physiology by measuring standard metabolic rate (SMR) at different test and acclimation temperatures for 16 species of salamanders with varying latitudinal extents. A phylogenetically‐controlled Markov chain Monte Carlo generalized linear mixed model (MCMCglmm) was then employed to determine whether there are differences inSMRbetween wide‐ and narrow‐ranging species at different acclimation temperatures. In addition, we tested for a relationship between the acclimation ability of species and the environmental temperature ranges they inhabit. Further, we investigated if there is a trade‐off between critical thermal maximum (CTMax) and thermal acclimation ability.MCMCglmm results show a significant difference in acclimation ability between wide and narrow‐ranging temperate salamanders. Salamanders with wide latitudinal distributions maintain or slightly increaseSMRwhen subjected to higher test and acclimation temperatures, whereas several narrow‐ranging species show significant metabolic depression. We also found significant, positive relationships between acclimation ability and environmental thermal range, and between acclimation ability andCTMax. Wide‐ranging salamander species exhibit a greater capacity for thermal acclimation than narrow‐ranging species, suggesting that selection for acclimation ability may have been a key factor enabling geographic expansion into areas with greater thermal variability. Further, given that narrow‐ranging salamanders are found to have both poor acclimation ability and lower tolerance to warm temperatures, they are likely to be more susceptible to environmental warming associated with anthropogenic climate change.
Roads to isolation: Similar genomic history patterns in two species of freshwater crabs with contrasting environmental tolerances and range sizes
Authors: Tay Ywee Chieh , Ng Daniel Jia Jun , Loo Jun Bin , Huang Danwei , Cai Yixiong , Yeo Darren Chong Jinn , Meier Rudolf 
Published: April 2018

AbstractFreshwater species often show high levels of endemism and risk of extinction owing to their limited dispersal abilities. This is exemplified by the stenotopic freshwater crab, Johora singaporensis which is one of the world's 100 most threatened species, and currently inhabits less than 0.01 km2 of five low order hill streams within the highly urbanized island city‐state of Singapore. We compared populations of J. singaporensis with that of the non‐threatened, widespread, abundant, and eurytopic freshwater crab, Parathelphusa maculata, and found surprisingly high congruence between their population genomic histories. Based on 2,617 and 2,470 genome‐wide SNPs mined via the double‐digest restriction‐associated DNA sequencing method for ~90 individuals of J. singaporensis and P. maculata, respectively, the populations are strongly isolated (FST = 0.146–0.371), have low genetic diversity for both species (also for COI), and show signatures of recent genetic bottlenecks. The most genetically isolated populations for both species are separated from other populations by one of the oldest roads in Singapore. These results suggest that anthropogenic developments may have impacted stream‐dependent species in a uniform manner, regardless of ubiquity, habitat preference, or dispersal modes of the species. While signs of inbreeding were not detected for the critically endangered species, the genetic distinctiveness and low diversity of the populations call for genetic rescue and connecting corridors between the remaining fragments of the natural habitat.
ShapeRotator: An R tool for standardized rigid rotations of articulated three‐dimensional structures with application for geometric morphometrics
Authors: Vidal‐García Marta , Bandara Lashi , Keogh J. Scott 
Published: April 2018

AbstractThe quantification of complex morphological patterns typically involves comprehensive shape and size analyses, usually obtained by gathering morphological data from all the structures that capture the phenotypic diversity of an organism or object. Articulated structures are a critical component of overall phenotypic diversity, but data gathered from these structures are difficult to incorporate into modern analyses because of the complexities associated with jointly quantifying 3D shape in multiple structures. While there are existing methods for analyzing shape variation in articulated structures in two‐dimensional (2D) space, these methods do not work in 3D, a rapidly growing area of capability and research. Here, we describe a simple geometric rigid rotation approach that removes the effect of random translation and rotation, enabling the morphological analysis of 3D articulated structures. Our method is based on Cartesian coordinates in 3D space, so it can be applied to any morphometric problem that also uses 3D coordinates (e.g., spherical harmonics). We demonstrate the method by applying it to a landmark‐based dataset for analyzing shape variation using geometric morphometrics. We have developed an R tool (ShapeRotator) so that the method can be easily implemented in the commonly used R package geomorph and MorphoJ software. This method will be a valuable tool for 3D morphological analyses in articulated structures by allowing an exhaustive examination of shape and size diversity.
Assessing the impacts of imperfect detection on estimates of diversity and community structure through multispecies occupancy modeling
Authors: Benoit David , Jackson Donald A. , Ridgway Mark S. 
Published: April 2018

AbstractDetecting all species in a given survey is challenging, regardless of sampling effort. This issue, more commonly known as imperfect detection, can have negative impacts on data quality and interpretation, most notably leading to false absences for rare or difficult‐to‐detect species. It is important that this issue be addressed, as estimates of species richness are critical to many areas of ecological research and management. In this study, we set out to determine the impacts of imperfect detection, and decisions about thresholds for inclusion in occupancy, on estimates of species richness and community structure. We collected data from a stream fish assemblage in Algonquin Provincial Park to be used as a representation of ecological communities. We then used multispecies occupancy modeling to estimate species‐specific occurrence probabilities while accounting for imperfect detection, thus creating a more informed dataset. This dataset was then compared to the original to see where differences occurred. In our analyses, we demonstrated that imperfect detection can lead to large changes in estimates of species richness at the site level and summarized differences in the community structure and sampling locations, represented through correspondence analyses.
Do the fluorescent red eyes of the marine fish Tripterygion delaisi stand out? In situ and in vivo measurements at two depths
Authors: Harant Ulrike K. , Santon Matteo , Bitton Pierre‐Paul , Wehrberger Florian , Griessler Thomas , Meadows Melissa G. , Champ Connor M. , Michiels Nico K. 
Published: April 2018

AbstractSince the discovery of red fluorescence in fish, much effort has been invested to elucidate its potential functions, one of them being signaling. This implies that the combination of red fluorescence and reflection should generate a visible contrast against the background. Here, we present in vivo iris radiance measurements of Tripterygion delaisi under natural light conditions at 5 and 20 m depth. We also measured substrate radiance of shaded and exposed foraging sites at those depths. To assess the visual contrast of the red iris against these substrates, we used the receptor noise model for chromatic contrasts and Michelson contrast for achromatic calculations. At 20 m depth, T. delaisi iris radiance generated strong achromatic contrasts against substrate radiance, regardless of exposure, and despite substrate fluorescence. Given that downwelling light above 600 nm is negligible at this depth, we can attribute this effect to iris fluorescence. Contrasts were weaker in 5 m. Yet, the pooled radiance caused by red reflection and fluorescence still exceeded substrate radiance for all substrates under shaded conditions and all but Jania rubens and Padina pavonia under exposed conditions. Due to the negative effects of anesthesia on iris fluorescence, these estimates are conservative. We conclude that the requirements to create visual brightness contrasts are fulfilled for a wide range of conditions in the natural environment of T. delaisi.
Changes in intestinal microbiota across an altitudinal gradient in the lizard Phrynocephalus vlangalii
Authors: Zhang Wenya , Li Na , Tang Xiaolong , Liu Naifa , Zhao Wei 
Published: April 2018

AbstractHigh altitude is an important driving force in animal evolution. However, the effect of altitude on gut microbial communities in reptiles has not been examined in detail. Here, we investigated the intestinal microbiota of three populations of the lizard Phrynocephalus vlangalii living at different altitudes using 16S rRNA gene sequencing. Bacteroidetes, Firmicutes, and Proteobacteria were the most abundant phyla. Bacteroides, Odoribacter, and Parabacteroides were the most abundant genera. Significant differences in the intestinal microbiota composition were found among the three populations from different altitudes. The proportions of Verrucomicrobia and Akkermansia decreased, whereas Bacteroides increased significantly with altitude. Greater abundance of Bacteroides at higher altitude led to the fractional increase in the phylum Bacteroides relative to other phyla. Hypoxia may be the main factor that caused intestinal microbiota variation in P. vlangalii along the altitude gradient. Overall, our study suggested that the community composition and structure of intestinal microbiota of the lizard P. vlangalii varied along altitudes, and such differences likely play a certain role in highland adaptation. Our findings warrant a further study that would determine whether ambient and body temperatures play a key role in the modulation of intestinal microbiota in reptiles.
Chesson's coexistence theory
Authors: Barabás György , D'Andrea Rafael , Stump Simon Maccracken 
Published: April 2018

AbstractWe give a comprehensive review of Chesson's coexistence theory, summarizing, for the first time, all its fundamental details in one single document. Our goal is for both theoretical and empirical ecologists to be able to use the theory to interpret their findings, and to get a precise sense of the limits of its applicability. To this end, we introduce an explicit handling of limiting factors, and a new way of defining the scaling factors that partition invasion growth rates into the different mechanisms contributing to coexistence. We explain terminology such as relative nonlinearity, storage effect, and growth‐density covariance, both in a formal setting and through their biological interpretation. We review the theory's applications and contributions to our current understanding of species coexistence. While the theory is very general, it is not well suited to all problems, so we carefully point out its limitations. Finally, we critique the paradigm of decomposing invasion growth rates into stabilizing and equalizing components: we argue that these concepts are useful when used judiciously, but have often been employed in an overly simplified way to justify false claims.
Genetic variation determines which feedbacks drive and alter predator–prey eco‐evolutionary cycles
Authors: Cortez Michael H. 
Published: April 2018

AbstractEvolution can alter the ecological dynamics of communities, but the effects depend on the magnitudes of standing genetic variation in the evolving species. Using an eco‐coevolutionary predator–prey model, I identify how the magnitudes of prey and predator standing genetic variation determine when ecological, evolutionary, and eco‐evolutionary feedbacks influence system stability and the phase lags in predator–prey cycles. Here, feedbacks are defined by subsystems, i.e., the dynamics of a subset of the components of the whole system when the other components are held fixed; ecological (evolutionary) feedbacks involve the direct and indirect effects between population densities (species traits) and eco‐evolutionary feedbacks involve the direct and indirect effects between population densities and traits. When genetic variation is low in both species, ecological feedbacks and eco‐evolutionary feedbacks involving either the predator or the prey trait have the strongest effects on system stability, when genetic variation is high in one species, evolutionary and eco‐evolutionary feedbacks involving that species’ trait have the strongest effects, and, when genetic variation is high in both species, evolutionary feedbacks involving one or both traits and eco‐coevolutionary feedbacks involving both traits have the strongest effects. I present the biological conditions under which each feedback can destabilize the whole system and cause predator–prey cycles. Predator–prey cycles can also arise when all feedbacks are stabilizing. This counterintuitive outcome occurs when feedbacks involving many variables are more stabilizing than feedbacks involving fewer variables or vice versa. I also identify how the indirect effects of prey and predator density on the predator dynamics (mediated by evolutionary responses in one or both species) alter the phase lags in predator–prey cycles. I present conditions under which the trait‐mediated indirect effects introduce delays that cause the lag between prey and predator peaks to increase. This work explains and unifies empirical and theoretical studies on how predator–prey coevolution alters the dynamics of predator–prey systems and how those effects depend on the magnitudes of prey and predator standing genetic variation.
Unusual Heteronuclear Uranyl Clusters with Aliphatic Monocarboxylate Ligands and Coordination Modes of Crotonate, Butyrate, and Valerate Ions
Authors: Savchenkov Anton V. , Vologzhanina Anna V. , Pushkin Denis V. , Serezhkina Larisa B. 
Published: April 2018

AbstractInvited for the cover of this issue is Anton Savchenkov from Samara National Research University, Russian Federation. The cover image shows the heteronuclear uranyl clusters evolving from a typical mononuclear anionic complex unit with aliphatic monocarboxylate ligands.
In Vivo Recording of Ascorbate and Neural Excitability in Medial Vestibular Nucleus and Hippocampus Following Ice Water Vestibular Stimulation in Rats
Authors: Xin Ying , Song Yu , Xiao Tongfang , Zhang Yinghong , Li Lijuan , Li Tao , Zhang Ke , Liu Junxiu , Ma Furong , Mao Lanqun 
Published: April 2018

AbstractVertigo is a common clinical symptom; however, the chemical and electrophysiological processes involved in the pathological mechanism of vertigo remain to be fully understood. In this study, we used an online electrochemical system (OECS) and electrophysiological system to record the dynamics of ascorbate and the change in the neural excitability in medial vestibular nucleus (MVN) and hippocampus of rats following vertigo induced by vestibular ice water stimulation. The OECS employed for recording the dynamics of ascorbate consists of in vivo microdialysis and online selective electrochemical detection. We observed that the level of ascorbate in MVN increased to 155±14 % of the basal level after ice water vestibular stimulation. Whereas, the level of ascorbate in hippocampus decreased to 55±12 % of the basal level after ice water vestibular stimulation. To explore the neural excitability of MVN and hippocampus, we used an electrophysiological recording system and analyzed spontaneous firing rate (SFR) of the neuronal discharges in both nucleus. We found that, in MVN, the neural excitability began to increase during vestibular ice stimulation, remained to be elevated until 1 hour after stimulation. Whereas, in hippocampus, the neural excitability decreased soon after vestibular ice stimulation and recovered 1 hour after stimulation. Dynamics of ascorbate recorded with the OECS correlate with the change in the neural excitability, which may suggest the function of ascorbate as an antioxidant and possibly as a neuromodulator for glutamate‐mediated neurotransmission. The involvement of MVN and hippocampus for the dynamics of ascorbate observed here may be related to the vestibular compensation of vertigo.
A new method for microwave assisted ethanolic extraction of Mentha rotundifolia bioactive terpenoids
Authors: García‐Sarrió María Jesús , Sanz María Luz , Sanz Jesús , González‐Coloma Azucena , Cristina Soria Ana 
Published: April 2018

AbstractA new microwave‐assisted extraction (MAE) method using ethanol as solvent has been optimized by means of a Box‐Behnken experimental design for the enhanced extraction of bioactive terpenoids from Mentha rotundifolia leaves; 100°C, 5 min, 1.125 g dry sample: 10 mL solvent and a single extraction cycle were selected as optimal conditions. Improved performance of MAE method in terms of extraction yield and/or reproducibility over conventional solid‐liquid extraction and ultrasound assisted extraction was also previously assessed. A comprehensive characterization of MAE extracts was carried out by GC‐MS. A total of 46 compounds, mostly terpenoids, were identified; piperitenone oxide and piperitenone were the major compounds determined. Several neophytadiene isomers were also detected for the first time in MAE extracts. Different procedures (solid‐phase extraction and activated charcoal (AC) treatment) were also evaluated for clean‐up of MAE extracts, with AC providing the highest enrichment in bioactive terpenoids. Finally, the MAE method here developed is shown as a green, fast, efficient and reproducible liquid extraction methodology to obtain M. rotundifolia bioactive extracts for further application, among others, as food preservatives.
Spatial regression with an informatively missing covariate: Application to mapping fine particulate matter
Authors: Grantham Neal S. , Reich Brian J. , Liu Yang , Chang Howard H. 
Published: April 2018

The United States Environmental Protection Agency has established a large network of stations to monitor fine particulate matter of <2.5 µm (PM2.5) that is known to be harmful to human health. Unfortunately, the network has limited spatial coverage, and stations often only measure PM2.5 every few days. Satellite‐measured aerosol optical depth (AOD) is a low‐cost surrogate with greater spatiotemporal coverage, and spatial regression models have established that including AOD as a covariate improves the spatial interpolation of PM2.5. However, AOD is often missing, and our analysis reveals that the conditions that lead to missing AOD are also conducive to high AOD. Therefore, naïve interpolation that ignores informative missingness may lead to bias. We propose a joint hierarchical model for PM2.5 and AOD that accounts for informatively missing AOD. We conduct a simulation study of the effects of ignoring informative missingness in the covariate and evaluate the performance of the proposed model. We apply the method to map daily PM2.5 in the Southeastern United States. Our analysis reveals statistically significant informative missingness and relationships between PM2.5 and AOD in many seasons after accounting for meteorological and land‐use variables.
Real‐time hybrid simulation for an RC bridge pier subjected to both horizontal and vertical ground motions
Authors: Chae Yunbyeong , Lee Jinhaeng , Park Minseok , Kim Chul‐Young 
Published: April 2018

SummaryIt is well known that real‐time hybrid simulation (RTHS) is an effective and viable dynamic testing method. Numerous studies have been conducted for RTHS during the last 2 decades; however, the application of RTHS toward practical civil infrastructure is fairly limited. One of the major technical barriers preventing RTHS from being widely accepted in the testing community is the difficulty of accurate displacement control for axially stiff members. For such structures, a servo‐hydraulic actuator can generate a large force error due to the stiff oil column in the actuator even if there is a small axial displacement error. This difficulty significantly restricts the implementation of RTHS for structures such as columns, walls, bridge piers, and base isolators. Recently, a flexible loading frame system was developed, enabling a large‐capacity real‐time axial force application to axially stiff members. With the aid of the flexible loading frame system, this paper demonstrates an RTHS for a bridge structure with an experimental reinforced concrete pier, which is subjected to both horizontal and vertical ground motions. This type of RTHS has been a challenging task due to the lack of knowledge for satisfying the time‐varying axial force boundary condition, but the newly developed technology for real‐time force control and its incorporation into RTHS enabled a successful implementation of the RTHS for the reinforced concrete pier of this study.
A comprehensive review on beneficial dietary phytochemicals in common traditional Southern African leafy vegetables
Authors: Sivakumar Dharini , Chen Lingyun , Sultanbawa Yasmina 
Published: April 2018

AbstractRegular intake of sufficient amounts of certain dietary phytochemicals was proven to reduce the incidence of noncommunicable chronic diseases and certain infectious diseases. In addition, dietary phytochemicals were also reported to reduce the incidence of metabolic disorders such as obesity in children and adults. However, limited information is available, especially on dietary phytochemicals in the commonly available traditional leafy vegetables. Primarily, the review summarizes information on the major phytochemicals and the impact of geographical location, genotype, agronomy practices, postharvest storage, and processing of common traditional leafy vegetables. The review also briefly discusses the bioavailability and accessibility of major phytochemicals, common antinutritive compounds of the selected vegetables, and recently developed traditional leafy vegetable‐based food products for dietary diversification to improve the balanced diet for the consumers. The potential exists for better use of traditional leafy vegetables to sustain food security and to improve the health and well‐being of humans.
Application of Metal Foam as a Flow Field for PEM Fuel Cell Stack
Authors: Kim M. , Kim C. , Sohn Y. 
Published: April 2018

AbstractThe channel/rib structure, commonly used in proton‐exchange membrane fuel cells (PEMFC), has disadvantages of uneven pressure distribution, gas supply, and produced‐water management under “rib” portion. In recent years, porous metal foam has been studied as an alternative flow field. We determined that the application of porous metal foams improved the PEMFC performance by compensating for the drawback of the channel/rib‐type flow field owing to the unique properties of metal foams (e.g., high conductivity, high porosity, and ease‐of‐deformation). Thus, this study confirmed the difference in the PEMFC performance with metal foams depending on cell configurations. Furthermore, the actual 500 W class PEMFC stack was fabricated to confirm the possibility of the metal foam application in the stack scale.