bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hidden diversity – DNA metabarcoding reveals hyper-diverse benthic invertebrate communities
Authors: Gleason Jennifer Erin , Hanner Robert H. , Cottenie Karl 
Published: March 2022

AbstractFreshwater ecosystems, such as streams, are facing increasing pressures from agricultural land use. Aquatic insects and other macroinvertebrates have historically been used as indicators of ecological condition and water quality in freshwater biomonitoring programs; however, many of these protocols use coarse taxonomic resolution (e.g., family) when identifying macroinvertebrates. The use of family-level identification can mask species-level diversity, as well as patterns in community composition in response to environmental variables. Recent literature stresses the importance of robust biomonitoring to detect trends in insect decline globally, though most of these studies are carried out in terrestrial habitats. Here, we incorporate molecular identification (DNA metabarcoding) into a stream biomonitoring sampling design to explore the diversity and variability of aquatic macroinvertebrate communities at small spatial scales. We sampled twenty southern Ontario streams in an agricultural landscape for aquatic macroinvertebrates and, using DNA metabarcoding, revealed incredibly rich benthic communities which were largely comprised of rare taxa detected only once per stream despite multiple biological replicates. In addition to numerous rare taxa, our species pool estimates indicated that after 240 samples from twenty streams, there was a large proportion of taxa present which remained undetected by our sampling regime. When comparing different levels of taxonomic resolution, we observed that using OTUs revealed over ten times more taxa than family-level identification. A single insect family, the Chironomidae, contained over one third of the total number of OTUs detected in our study. Within-stream dissimilarity estimates were consistently high for all taxonomic groups (invertebrate families, invertebrate OTUs, chironomid OTUs), indicating stream communities are very dissimilar at small spatial scales. While we predicted that increased land use would homogenize benthic communities, this was not supported as within-stream dissimilarity was unrelated to land use.
Visual Perception of 3D Space and Shape in Time - Part II: 3D Space Perception with Holographic Depth
Authors: Bustanoby Isabella , Krupien Andrew , Afifa Umaima , Asdell Benjamin , Bacani Michaela , Boudreau James , Carmona Javier , Chandrashekar Pranav , Diamond Mark , Espino Diego , Gangal Arnav , Kittur Chandan , Li Yaochi , Mann Tanvir , Matamoros Christian , McCarthy Trevor , Mills Elizabeth , Nazareth Stephen , Nguyen Justin , Ochoa Kenya , Robbins Sophie , Sparakis Despoina , Ta Brian , Trengove Kian , Xu Tyler , Yamaguchi Natsuko , Yang Christine , Zafran Eden , Blaisdell Aaron P. , Arisaka Katsushi 
Published: March 2022

AbstractVisual perception plays a critical role in navigating 3D space and extracting semantic information crucial to survival. Even though visual stimulation on the retina is fundamentally 2D, we seem to perceive the world around us in vivid 3D effortlessly. This reconstructed 3D space is allocentric and faithfully represents the external 3D world. How can we recreate stable 3D visual space so promptly and reliably?To solve this mystery, we have developed new concepts MePMoS (Memory-Prediction-Motion-Sensing) and NHT (Neural Holography Tomography). These models state that visual signal processing must be primarily top-down, starting from memory and prediction. Our brains predict and construct the expected 3D space holographically using traveling alpha brainwaves. Thus, 3D space is represented by the three time signals in three directions.To test this hypothesis, we designed reaction time (RT) experiments to observe predicted space-to-time conversion, especially as a function of distance. We placed LED strips on a horizontal plane to cover distances from close up to 2.5 m or 5 m, either using a 1D or a 2D lattice. Participants were instructed to promptly report observed LED patterns at various distances. As expected, stimulation at the fixation cue location always gave the fastest RT. Additional RT delays were proportional to the distance from the cue. Furthermore, both covert attention (without eye movements) and overt attention (with eye movements) created the same RT delays, and both binocular and monocular views resulted in the same RTs. These findings strongly support our predictions, in which the observed RT-depth dependence is indicative of the spatiotemporal conversion required for constructing allocentric 3D space. After all, we perceive and measure 3D space by time as Einstein postulated a century ago.
Early Tactile Stimulation Influences the Development of Alzheimer Disease in Gestationally Stressed APPNL-G-FAdult OffspringNL-G-F/NL-G-Fmice
Authors: Hossain Shakhawat R. , Karem Hadil , Jafari Zahra , Kolb Bryan E. , Mohajerani Majid H. 
Published: March 2022

AbstractAlzheimer Disease (AD) is associated with cerebral plaques and tangles, reduced synapse number, and shrinkage in several brain areas and these morphological effects are associated with the onset of compromised cognitive, motor, and anxiety-like behaviours. The focus of this study was to examine the effect of neonatal tactile stimulation on AD-like behavioural and neurological symptoms on APPNL-G-F/NL-G-Fmice, a mouse model of AD. Our findings indicate that neonatal tactile stimulation improves cognition, motor skills, and anxiety-like symptoms in both gestationally stressed and non-stressed adult APP mice and that these alterations are associated with reduced Aβ plaque formation. Thus, tactile stimulation appears to be a promising non-invasive preventative strategy for slowing the onset of dementia in aging animals.
Genomic resolution of cryptic species diversity in chipmunks
Authors: Herrera Nathanael D. , Bell Kayce C. , Callahan Colin M. , Nordquist Erin , Sarver Brice A. J. , Sullivan Jack , Demboski John R. , Good Jeffrey M. 
Published: March 2022

ABSTRACTDiscovery of cryptic species is essential to understanding the process of speciation and assessing the impacts of anthropogenic stressors. Here, we used genomic data to test for cryptic species diversity within an ecologically well-known radiation of North American rodents, western chipmunks (Tamias). We assembled a de novo reference genome for a single species (Tamias minimus) combined with new and published targeted sequence-capture data for 21,551 autosomal and 493 X-linked loci sampled from 121 individuals spanning 22 species. We identified at least two cryptic lineages corresponding with an isolated subspecies of least chipmunk (T. minimus grisescens) and with a restricted subspecies of the yellow-pine chipmunk (T. amoenus cratericus) known only from around the extensive Craters of the Moon lava flow. Additional population-level sequence data revealed that the so-called Crater chipmunk is a distinct species that is abundant throughout the coniferous forests of southern Idaho. This cryptic lineage does not appear to be most closely related to the ecologically and phenotypically similar yellow-pine chipmunk but does show evidence for recurrent hybridization with this and other species.
Transcranial random noise stimulation of the primary visual cortex but not retina modulates visual contrast sensitivity
Authors: Potok Weronika , Post Alain , Bächinger Marc , Kiper Daniel , Wenderoth Nicole 
Published: March 2022

AbstractTranscranial random noise stimulation (tRNS) has been shown to significantly improve visual perception. Previous studies demonstrated that tRNS delivered over cortical areas acutely enhances visual contrast detection of stimuli when tRNS intensity is optimized for the individual. However, it is currently unknown whether tRNS-induced signal enhancement could be achieved within different neural substrates along the retino-cortical pathway and whether the beneficial effect of optimal tRNS intensities can be reproduced across sessions.In 3 experimental sessions, we tested whether tRNS applied to the primary visual cortex (V1) and/or to the retina improves visual contrast detection. We first measured visual contrast detection threshold (VCT; N=24, 16 females) during tRNS delivery separately over V1 (no tRNS, 0.75, 1, 1.5mA) and over the retina (no tRNS, 0.1, 0.2, 0.3mA), determined the optimal tRNS intensities for each individual (ind-tRNS), and retested the effects of ind-tRNS within the sessions. We further investigated whether we could reproduce the ind-tRNS-induced modulation on a different session (N=19, 14 females). Finally, we tested whether the simultaneous application of ind-tRNS to the retina and V1 causes additive effects.We found that at the group level tRNS of 0.75mA decreases VCT compared to baseline when delivered to the V1. Beneficial effects of ind-tRNS could be replicated when retested within the same experimental session but not when retested in a separate session. Applying tRNS to the retina did not cause a systematic reduction of VCT, irrespective of whether the individually optimized intensity was considered or not. We also did not observe consistent additive effects of V1 and retina stimulation.Our findings demonstrate that V1 seems to be more sensitive than the retina to tRNS-induced modulation of visual contrast processing.Significance statementOur findings confirm previous evidence showing acute online benefits of tRNS of V1 on visual contrast detection in accordance with the stochastic resonance phenomenon. We further extend it, demonstrating that the optimal tRNS intensity varies among participants, but when individually tailored it can improve visual processing when re-tested within the experimental session. The tRNS-induced enhancement in visual sensitivity seems to be specific for cortical contrast processing as stimulation of the retina did not lead to systematic effects.
Social media mining and photo-identification detects the shift of long-term seasonal foraging habitat for a juvenile loggerhead sea turtle
Authors: Papafitsoros Kostas 
Published: March 2022

AbstractAnimal imagery uploaded on social media has been identified as an important tool in wildlife research and conservation and has been used in a variety of recent studies. Here a case study is presented, where a detailed analysis of social media content revealed a shift of a long-term foraging habitat for a juvenile loggerhead sea turtle (Caretta caretta) in Greece. In particular, this individual was a long term resident of Zakynthos island, Greece, from 2016 until 2020 (5 consecutive summer seasons), regularly foraging on a nearshore reef, with no observations of it being made during the 2021 season. However regular social media image mining combined with photo-identification, detected this individual foraging in the Gulf of Corinth in August 2021, more that 200km away from his previous foraging habitat. This case study (i) shows the possibility for juvenile loggerheads to shift their foraging site even after long term use, with implications in capture-mark-recapture studies and (ii) once more highlights the usefulness of social media mining and citizen science in diverse aspects of sea turtle studies.
Genomic patterns of divergence in the early and late steps of speciation of the deep-sea vent thermophilic worms of the genusAlvinella
Authors: Thomas–Bulle Camille , Bertrand Denis , Nagarajan Niranjan , Copley Richard , Corre Erwan , Hourdez Stéphane , Bonnivard Éric , Claridge-Chang Adam , Jollivet Didier 
Published: March 2022

AbstractBackgroundThe transient and fragmented nature of the deep-sea hydrothermal environment made of ridge subduction, plate collision and the emergence of new rifts is currently acting to the separation of vent populations, local adaptation and is likely to promote bursts of speciation and species specialization. The tube-dwelling wormsAlvinella pompejanacalled the Pompeii worm and its sister speciesA. caudatalive syntopically on the hottest part of deep-sea hydrothermal chimneys along the East Pacific Rise. They are exposed to extreme thermal and chemical gradients, which vary greatly in space and time, and thus represent ideal candidates for understanding the evolutionary mechanisms at play in the vent fauna evolution.ResultsIn the present study, we explored genomic patterns of divergence in the early and late steps of speciation of these emblematic worms using transcriptome assemblies and the first draft genome to better understand the relative role of geographic isolation and habitat preference in their genome evolution. Analyses were conducted on allopatric populations ofAlvinella pompejana(early stage of separation) and betweenA. pompejanaand its syntopic speciesAlvinella caudata(late stage of speciation). We first identified divergent genomic regions and targets of selection as well as their position in the genome over collections of orthologous genes and, then, described the speciation dynamics by documenting the annotation of the most divergent and/or positively selected genes involved in the isolation process. Gene mapping clearly indicated that divergent genes associated with the early stage of speciation, although accounting for nearly 30% of genes, are highly scattered in the genome without any island of divergence and not involved in gamete recognition or mito-nuclear incompatibilities. By contrast, genomes ofA. pompejanaandA. caudataare clearly separated with nearly all genes (96%) exhibiting high divergence. This congealing effect however seems to be linked to habitat specialization and still allows positive selection on genes involved in gamete recognition, as a possible long-duration process of species reinforcement.ConclusionOur analyses pointed out the non-negligible role of natural selection on both the early and late stages of speciation in the emblematic thermophilic worms living on the walls of deep-sea hydrothermal chimneys. They shed ligth on the evolution of gene divergence during the process of speciation and species specialization over a very long period of time.
A tale of two connectivities: intra- and inter-subject functional connectivity jointly enable better prediction of social abilities
Authors: Xie Hua , Redcay Elizabeth 
Published: March 2022

AbstractNaturalistic functional magnetic resonance imaging (fMRI) paradigms, such as movie viewing, are attracting increased attention, given their ability to mimic the real-world cognitive demands on attention and multimodal sensory integration. Moreover, naturalistic paradigms allow for characterizing brain network responses associated with dynamic social cognition in a model-free manner using inter-subject functional connectivity (ISFC). While intra-subject functional connectivity (FC) characterizes the individual’s brain functional architecture, ISFC characterizes the neural coupling driven by time-locked extrinsic dynamic stimuli across individuals. Here, we hypothesized that ISFC and FC provide distinct and complementary information about individual differences in social cognition. To test this hypothesis, we examined a public movie-viewing fMRI dataset with 32 healthy adults and 90 typically developing children. Building three partial least squares regression (PLS) models to predict social abilities using FC and/or ISFC, we compared predictive performance to determine whether combining two connectivity measures could improve the prediction accuracy of individuals’ social-cognitive abilities measured by a Theory of Mind (ToM) assessment. Our results indicated that the joint model (ISFC+FC) yielded the highest predictive accuracy and significantly predicted individuals’ social cognitive abilities (rho = 0.34, p < 0.001). We also confirmed that the improved accuracy was not due to the increased feature dimensionality. In conclusion, we demonstrated that intra-/inter-subject connectivity encodes unique information about social abilities, and a joint investigation could help us gain a more complete understanding of the complex processes supporting social cognition.
LIN-35 is necessary in both the soma and germline for preserving fertility in Caenorhabditis elegans under moderate temperature stress
Authors: Mikeworth Brian P. , Compere Frances V. , Quaglia Kristen , Petrella Lisa N. 
Published: March 2022

ABSTRACTMaintenance of germline function under stress conditions is crucial for species survival. The germline across many species is especially sensitive to elevated temperature stress. We have investigated the role that the pocket protein LIN-35 plays in preserving fertility in C. elegans under moderate high temperature stress. Here we show that lin-35 mutants have a number of temperature sensitive germline defects. The decreased brood size seen at elevated temperatures is more severe in lin-35 mutants than wild type. This loss of fertility under temperature stress is primarily due to loss of zygotic but not maternal LIN-35. Additionally, we have found that expression of LIN-35 is necessary in both the germline and soma for the preserving fertility at elevated temperature. Specifically, germline expressed LIN-35 is primarily what is important for maintaining fertility in hermaphrodites, but broad somatic expression of LIN-35 is also necessary for oocyte formation and/or function at elevated temperatures. Additionally, we found that overexpression of LIN-35 in the germline only can stabilize the formation of P granules in primordial germ cells. Our data adds to the emerging critical role that LIN-35 plays in buffering tissues against stress.
Regional variation in cholinergic terminal activity determines the non-uniform occurrence of cortical slow-wave activity during REM sleep
Authors: Nazari Mojtaba , Abadchi Javad Karimi , Naghizadeh Milad , Bermudez-Contreras Edgar J. , McNaughton Bruce L. , Tatsuno Masami , Mohajerani Majid H. 
Published: March 2022

AbstractSleep consists of two basic stages: non-rapid eye movement (NREM) and rapid eye movement (REM) sleep. NREM sleep is characterized by slow high-amplitude cortical EEG signals, while REM sleep is characterized desynchronized cortical rhythms. While, until recently, it has been widely believed that cortical activity during REM sleep is globally desynchronized, recent electrophysiological studies showed slow waves (SW) in some cortical areas during REM sleep. Electrophysiological techniques, however, have been unable to resolve the regional structure of these activities, due to relatively sparse sampling. We mapped functional gradients in cortical activity during REM sleep using mesoscale imaging in mice, and observed local SW patterns occurring mainly in somatomotor and auditory cortical regions, with minimum presence within the default mode network. The role of the cholinergic system in local desynchronization during REM sleep was also explored by calcium imaging of cholinergic terminal activity within the mouse cortex. Terminal activity was weaker in regions exhibiting SW activity more frequently during REM sleep. We also analyzed Allen Mouse Brain Connectivity dataset and found that these regions have weaker cholinergic projections from the basal forebrain.
Environmental thresholds in the functional mycobiome of global drylands
Authors: Egidi Eleonora , Delgado-Baquerizo Manuel , Berdugo Miguel , Guirado Emilio , Albanese Davide , Singh Brajesh K. , Coleine Claudia 
Published: March 2022

AbstractFungi are major drivers of ecosystem functions. Increases in aridity are known to negatively impact fungal communities in dryland ecosystems globally, however, much less is known on the potential influence of other environmental drivers. To fill this knowledge gap, we reanalyzed fungal data from 912 soil samples, providing the largest and most complete fungal community dataset from global drylands. We used machine learning tools to examine geographical patterns in community composition and spatial, edaphic, and climatic factors driving them. Further, we determined critical thresholds of community turnover along those gradients. Our analysis identifies UV index, climate seasonality, and sand content as the most important environmental predictors of community shifts, harbouring greatest association with the richness of putative plant pathogens and saprobes. Important nonlinear relationships existed with each of these fungal guilds, with increases in UV and temperature seasonality above 7.5 and 900 SD, respectively, being associated with an increased probability of plant pathogens and unspecified saprotrophs occurrence. Conversely, these environmental parameters had a negative relationship with litter and soil saprotrophs richness. Consequently, these functional groups might be differentially sensitive to environmental changes, which might result in an inevitable disturbance of current plant-soil dynamics in drylands.
Retinal neuroblast migration and laminar organization requires the cytoskeletal-interacting protein Mllt11
Authors: Blommers Marley , Stanton-Turcotte Danielle , Iulianella Angelo 
Published: March 2022

ABSTRACTBackgroundThe vertebrate retina is an organized laminar structure comprised of distinct cell types populating three nuclear layers. During development, each retinal cell type follows a stereotypical temporal order of genesis, differentiation, and migration, giving rise to its stratified organization. Once born, the precise positioning of cells along the apico-basal (radial) axis of the retina is critical for subsequent connections to form, relying on orchestrated migratory processes. While these processes are critical for visual function to arise, the regulators of cellular migration and retinal lamination remain largely unexplored.ResultsWe report a role for a microtubule-interacting protein, Mllt11 (Myeloid/lymphoid or mixed-lineage leukemia; translocated to chromosome 11/All1 Fused Gene From Chromosome 1q) in mammalian retinal cell migration during retinogenesis. We show that Mllt11 loss-of-function in mouse retinal neuroblasts affected the migration of ganglion and amacrine cells into the ganglion cell layer, and led to their ectopic accumulation in the inner plexiform layer.ConclusionsWe demonstrate that Mllt11 plays a critical role in the migration and lamination of neurons in the retina, and its loss impacted formation of the basal-most retinal layers.
Symbiosis with rhizobia limits range expansion only in polyploid legumes
Authors: Parshuram Zoe A. , Harrison Tia L. , Simonsen Anna K. , Stinchcombe John R. , Frederickson Megan E. 
Published: March 2022

SummaryBoth mutualism and polyploidy are thought to influence invasion success in plants but few studies have tested their joint effects. Mutualism can limit range expansion when plants cannot find a compatible partner in a novel habitat, or facilitate range expansion when mutualism increases a plant’s niche breadth. Polyploids are also expected to have greater niche breadth because of greater self-compatibility and phenotypic plasticity, increasing invasion success.For 839 legume species, we compiled data from published sources to estimate ploidy, symbiotic status with rhizobia, specificity on rhizobia, and the number of introduced ranges.We found that diploid species have had limited spread around the globe regardless of whether they are symbiotic or how many partners of rhizobia they can host. Polyploids, in contrast, have been successfully introduced to many new ranges, but interactions with rhizobia constrain their range expansion. In a hidden state model of trait evolution, we also found evidence of a high rate of re-diploidization in symbiotic legume lineages, suggesting that symbiosis and ploidy may interact at macroevolutionary scales.Overall, our results suggest that symbiosis with rhizobia affects range expansion only in polyploid legumes.