bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antelope space-use and behavioural responses to varying anthropogenic influences may permit long-term persistence in a highly human-dominated landscape
Authors: Jha Rohit Raj , Isvaran Kavita 
Published: September 2021

AbstractThe only means of conserving a species or a habitat in a human-dominated landscape is through promoting coexistence while minimizing conflict. To achieve this, it is vital to understand how wildlife are impacted by direct and indirect human activities. Such information is relatively rare from areas with high human densities. To investigate how animals respond to altered ecological conditions in human-dominated landscapes, we focussed on a wild herbivore of conservation concern in Krishnasaar Conservation Area (KrCA) in Nepal. Here, blackbuck Anticope cervicapra, a generalist grazer, lives in refugia located in a growing human population. We studied the impacts of humans on habitat-use and behaviour of blackbuck. We laid 250 × 250 m grid cells in the entire KrCA and carried out indirect sign surveys with three replications for habitat-use assessment. We observed herds of blackbuck for 89 hours in different possible habitat types, location and time of the day using scan sampling methods. Our habitat-use survey showed that habitats under intensive human use were hardly used by blackbuck, even when high-quality forage was available. In areas with low levels of human activity, natural risk factors, primarily habitat openness, was the major predictor of habitat-use. Interestingly, livestock presence positively influenced habitat-use by blackbuck. Blackbuck were substantially more vigilant when they were in forest than in grassland, again indicating an influence of risk. Overall, blackbuck appear to be sensitive to risk associated with both natural and anthropogenic factors. Our findings have direct implications for managing human-wildlife interactions in this landscape, specifically regarding strategies for livestock grazing in habitats highly used by blackbuck and concerning predictions of how changing land-use will impact long-term persistence of blackbuck. Our work suggests that wild herbivores may be able to persist in landscapes with high human densities so long as there are refuges where levels of human activity are relatively low.
Evaluating an internet-delivered fear conditioning and extinction protocol using response times and affective ratings
Authors: Björkstrand Johannes , Pine Daniel S. , Frick Andreas 
Published: September 2021

AbstractPavlovian fear conditioning is widely used to study mechanisms of fear learning, but high-throughput studies are hampered by the labor-intensive nature of examining participants in the lab. To circumvent this bottle-neck, fear conditioning tasks have been developed for remote delivery. Previous studies have examined remotely delivered fear conditioning protocols using expectancy and affective ratings. Here we replicate and extend these findings using an internet-delivered version of the Screaming Lady paradigm, evaluating the effects on negative affective ratings and response time to an auditory probe during stimulus presentations. In a sample of 80 adults, we observed clear evidence of both fear acquisition and extinction using affective ratings. Response times were faster when probed early, but not later, during presentation of stimuli paired with an aversive scream. The response time findings are at odds with previous lab-based studies showing slower responses to threat-predicting cues. The findings underscore the feasibility of employing remotely delivered fear conditioning paradigms with affective ratings as outcome, and highlight the need for further research examining optimal parameters for concurrent response time measures or alternate modes of non-verbal estimation of conditioned responses in Pavlovian conditioning protocols.
Diversity and Metabolic Potential of Microbial Communities in a Serpentinite-Hosted Spring at the Tablelands
Authors: Dart Emily , Brazelton William J. 
Published: September 2021

AbstractThe geochemical process of serpentinization releases energy and organic carbon: two of the basic requirements needed to support life. Sites of active serpentinization in the deep subsurface provide the intriguing possibility of a non-photosynthetically-supported biosphere. However, serpentinization also creates conditions, such as high pH and limited electron acceptors, which may limit microbial growth and diversity. Gaining an understanding of the identity and metabolic potential of microbes that thrive in these environments may provide insight as to whether serpentinization is sufficient to independently support life. Tablelands Ophiolite in Gros Morne National Park, Newfoundland, Canada is a continental site of serpentinization where serpentinite springs form surface pools. These pools provide easy sampling access to subsurface fluids and may allow for sampling of the subsurface microbial community. However, identification of members of the subsurface community in these pools is complicated by both surface contamination and contamination by organisms that inhabit the transition zone where hydrogen-rich subsurface fluids meet oxygen-rich surface fluids. This study was designed to distinguish among these potential sources of microorganisms by using a sampling technique that more effectively samples subsurface fluids. Community dissimilarity comparisons using environmental 16S rRNA gene sequencing indicate that the sampling design led to more direct access to subsurface fluids. These results are supported by metagenomic analyses that show metabolic pathways consistent with non-photosynthetic carbon fixation in the samples expected to represent subsurface fluids and that show hydrogen oxidation pathways in samples associated with the surface sources. These results provide a clearer picture of the diversity and metabolic potential of microbial communities potentially inhabiting subsurface, serpentinite-hosted habitats.
Variation in colour signals amongSarraceniapitcher plants and the potential role of areoles in the attraction of flying Hymenoptera
Authors: Dupont Corentin , Villemant Claire , Hatterman Tom , Pratviel Jeremie , Gaume Laurence , Gomez Doris 
Published: September 2021

AbstractSarraceniainsectivorous plants show a diversity of visual features in their pitchers but their perception by insects and their role in attraction, have received little attention. They also vary in prey composition, with some species trapping more flying Hymenoptera, such as bees. To test the hypothesis of a link between visual signal variability and prey segregation ability, and to identify which signal could attract flying Hymenoptera, we characterised, the colour patterns of 32 pitchers belonging to four taxa, modelled their perception by flying Hymenoptera, and examined the prey they trapped. The pitchers of the four taxa differed in colour patterns, with notably two long-leaved taxa displaying clear areoles, which contrasted strongly in colour and brightness with the vegetative background and with other pitcher areas in the eyes of flying Hymenoptera. These taxa trapped high proportion of flying hymenoptera. This suggests that contrasting areoles may act as a visual lure for flying Hymenoptera, making plants particularly visible to these insects. Prey capture also differed according to pitcher stage, morphology, season and visual characteristics. Further studies on prey visitation are needed to better understand the link between prey capture and attraction feature.
Principles governing the topological organization of object selectivities in ventral temporal cortex
Authors: Zhang Yiyuan , Zhou Ke , Bao Pinglei , Liu Jia 
Published: September 2021

SummaryTo achieve the computational goal of rapidly recognizing miscellaneous objects in the environment despite large variations in their appearance, our mind represents objects in a high-dimensional object space to provide separable category information and enable the extraction of different kinds of information necessary for various levels of the visual processing. To implement this abstract and complex object space, the ventral temporal cortex (VTC) develops different object-selective regions with certain topological organization as the physical substrate. However, the principle that governs the topological organization of object selectivities in the VTC remains unclear. Here, equipped with the wiring cost minimization principle constrained by the wiring length of neurons in human temporal lobe, we constructed a hybrid self-organizing map (SOM) model as an artificial VTC (VTC-SOM) to explain how the abstract and complex object space is faithfully implemented in the brain. In two in silico experiments with the empirical brain imaging and single-unit data, our VTC-SOM predicted the topological structure of fine-scale functional regions (face-, object-, body-, and place-selective regions) and the boundary (i.e., middle Fusiform Sulcus) in large-scale abstract functional maps (animate vs. inanimate, real-word large-size vs. small-size, central vs. peripheral), with no significant loss in functionality (e.g., categorical selectivity, a hierarchy of view-invariant representations). These findings illustrated that the simple principle utilized in our model, rather than multiple hypotheses such as temporal associations, conceptual knowledge, and computational demands together, was apparently sufficient to determine the topological organization of object-selectivities in the VTC. In this way, the high-dimensional object space is implemented in a two-dimensional cortical surface of the brain faithfully.
A novel, computationally tractable algorithm flags in big matrices every column associated in any way with others or a dependent variable, with much higher power when columns are linked like mutations in chromosomes
Authors: Antezana Marcos A. 
Published: September 2021

ABSTRACTWhen a data matrix DM has many independent variables IVs, it is not computationally tractable to assess the association of every distinct IV subset with the dependent variable DV of the DM, because the number of subsets explodes combinatorially as IVs increase. But model selection and correcting for multiple tests is complex even with few IVs.DMs in genomics will soon summarize millions of mutation markers and genomes. Searching exhaustively in such DMs for markers that alone or synergistically with others are associated with a trait is therefore computationally tractable only for 1- and 2-marker effects. Also population geneticists study mainly 2-marker combinations.I present a computationally tractable, fully parallelizable Participation in Association Score (PAS) that in a DM with markers detects one by one every column that is strongly associated in any way with others. PAS does not examine column subsets and its computational cost grows linearly with the number of columns, remaining reasonable even when DMs have millions of columns.PAS exploits how associations of markers in the rows of a DM cause associations of matches in the rows’ pairwise comparisons. For every such comparison with a match at a tested column, PAS computes the matches at other columns by modifying the comparison’s total matches (scored once per DM), yielding a distribution of conditional matches that reacts diagnostically to the associations of the tested column. Equally computationally tractable is dvPAS that flags DV-associated IVs by also probing the matches at the DV.P values for the scores are readily obtained by permutation and accurately Sidak-corrected for multiple tests, bypassing model selection. The P values of a column’s PASs for different orders of association are i.i.d. and readily turned into a single P value.Simulations show that i) PAS and dvPAS generate uniform-(0,1)-distributed type I error in null DMs and ii) detect randomly encountered binary and trinary models of significant n-column association and n-IV association with a binary DV, respectively, with power in the order of magnitude of exhaustive evaluation’s and false positives that are uniform-(0,1)-distributed or straightforwardly tuned to be so. Power to detect 2-way associations that extend over 100+ columns is non-parametrically ultimate but that to detect pure n-column associations and pure n-IV DV associations sinks exponentially as n increases.Important for geneticists, dvPAS power increases about twofold in trinary vs. binary DMs and by orders of magnitude with markers linked like mutations in chromosomes, specially in trinary DMs where furthermore dvPAS fine-maps with highest resolution.
abmR: an R package for agent-based model analysis of large-scale movements across taxa
Authors: Gochanour Benjamin , Fernández-López Javier , Contina Andrea 
Published: September 2021

AbstractAgent-based modeling (ABM) shows promise for animal movement studies. However, a robust, open-source, and spatially explicit ABM coding platform is currently lacking.We present abmR, an R package for conducting continental-scale ABM simulations across animal taxa. The package features two movement functions, each of which relies on the Ornstein-Uhlenbeck (OU) process.The theoretical background for abmR is discussed and the main functionalities are illustrated using example populations.Potential future additions to this open-source package may include the ability to specify multiple environmental variables or to model interactions between agents. Additionally, updates may offer opportunities for disease ecology and integration with other R movement modeling packages.
Intestinal epithelial IPMK protects mice from experimental colitis via governing colonic tuft cell development
Authors: Park Seung Eun , Jeong Jae Woong , Lee Su-Hyung , Park Seung Ju , Ryu Jaeseung , Oh Se Kyu , Fang Sungsoon , Kim Seyun 
Published: September 2021

ABSTRACTAs a pleiotropic signaling factor, inositol polyphosphate multikinase (IPMK) is involved in key biological events such as growth and innate immunity, acting either enzymatically to mediate the biosynthesis of inositol polyphosphates and phosphatidylinositol 3,4,5-trisphosphates, or noncatalytically to control key signaling target molecules. However, the functional significance of IPMK in regulating gut epithelial homeostasis remains largely unknown. Here we show that intestinal epithelial-specific deletion of IPMK aggravates dextran sulfate sodium (DSS)-induced colitis with higher clinical colitis scores and elevated epithelial barrier permeability. No apparent defects in PI3K-AKT signaling pathway and pro-inflammatory cytokine production were found in IPMK-deficient colons challenged by DSS treatment. RNA-sequencing and FACS analyses further revealed significantly decreased tuft cells in IPMK-deficient colons. Importantly, IPMK deletion in the gut epithelium was found to decrease choline acetyltransferase (ChAT) but not IL-25, suggesting selective loss of cholinergic signaling. Thus, these findings identify IPMK as a physiological determinant of tuft cell differentiation and highlight the critical function of IPMK in the control of gut homeostasis.
β-Catenin-NFκB-CFTR interactions in cholangiocytes regulate inflammation and fibrosis during ductular reaction
Authors: Hu Shikai , Russell Jacquelyn O. , Liu Silvia , Rai Ravi , Kosar Karis , Tao Junyan , Hurley Edward , Poddar Minakshi , Singh Sucha , Bell Aaron , Shin Donghun , Raeman Reben , Singhi Aatur D. , Nejak-Bowen Kari , Ko Sungjin , Monga Satdarshan P. 
Published: September 2021

AbstractExpansion of biliary epithelial cells (BECs) during ductular reaction (DR) is observed in liver diseases including cystic fibrosis (CF), and associated with inflammation and fibrosis, albeit without complete understanding of underlying mechanism. Using two different genetic knockouts of β-catenin, one with β-catenin loss is hepatocytes and BECs (KO1), and another with loss in only hepatocytes (KO2), we demonstrate disparate long-term repair after an initial injury by 2-week choline-deficient ethionine- supplemented diet. KO2 show gradual liver repopulation with BEC-derived β-catenin- positive hepatocytes, and resolution of injury. KO1 showed persistent loss of β-catenin, NF-κB activation in BECs, progressive DR and fibrosis, reminiscent of CF histology. We identify interactions of β-catenin, NFκB and CF transmembranous conductance regulator (CFTR) in BECs. Loss of CFTR or β-catenin led to NF-κB activation, DR and inflammation. Thus, we report a novel β-catenin-NFκB-CFTR interactome in BECs, and its disruption may contribute to hepatic pathology of CF.
MPTHub: an open-source software for characterizing the transport of particles in biorelevant media
Authors: Gabriel Leandro , Almeida Helena , Avelar Marta , Sarmento Bruno , das Neves José 
Published: September 2021

AbstractThe study of the transport of particles in different environments plays an essential role in understanding interactions with humans and other living organisms. Importantly, obtained data can be directly used for multiple applications in fields such as fundamental biology, toxicology or medicine. Particle movement in biorelevant media can be readily monitored using microscopy and converted into time-resolved trajectories using freely available tracking software. However, translation into tangible and meaningful parameters is time-consuming and not always intuitive. Thus, we developed a new software – MPTHub – as an open-access, stand-alone, user-friendly tool for the rapid and reliable analysis of particle trajectories extracted from video microscopy. The software was programmed using Python and allowed to import and analyze trajectory data, and export relevant data such as individual and ensemble time-averaged mean square displacements and effective diffusivity, and anomalous transport exponent. Data processing was reliable, fast (total processing time of less than 10 sec) and required minimal memory resources (up to a maximum of around 150 MB in RAM). Demonstration of software applicability was conducted by studying the transport of different polystyrene nanoparticles (100-200 nm) in mucus surrogates. Overall, MPTHub represents a freely available software tool that can be used even by unexperienced users for studying the transport of particles in biorelevant media.
Delayed implantation induced by letrozole in mice
Authors: Wang Fang , Li Shijie , Meng Lingshuai , Kuang Ye , Liu Zhonghua , Ma Xinghong 
Published: September 2021

AbstractImplantation timing is key for a successful pregnancy. Short delay in embryo implantation caused by targeted gene ablation produced a cascading problem in the later stages of the pregnancy. Although several delayed implantation models have been established in wild mice, almost none of them is suitable for investigating the delay on the late events of pregnancy. Here, we report a new delayed implantation model established by the intraperitoneally administration of letrozole at 5 mg/kg body weight on the day 3 of pregnancy. In these mice, initiation of implantation was induced at will by the injection of estradiol (E2). When the estradiol (3 ng) was injected on day 4 of pregnancy (i.e., without delay), the embryo implantation restarted, and the pregnancy continued normally. However, high dose of estrogen (25 ng) caused compromised implantation. We also found that only 67% of the female mice could be pregnant normally and finally gave birth when the injection of estradiol (3 ng) was on day 5 of pregnancy (i.e., one day delay). Most of the failed pregnancies had impaired decidualization, decreased plasma progesterone levels and compromised angiogenesis. Progesterone supplementation could rescue decidualization failure in the mice. Collectively, we established a new model of delayed implantation by letrozole, which can be easily used to study the effect and mechanisms of delay of embryo implantation on the progression of late pregnancy events.
The biogeography of the Mediterranean Taurus Mountains: Illustrating how complex topography and climatic conditions have shaped their biodiversity
Authors: Gür Hakan 
Published: September 2021

ABSTRACTClimate is well known as the main driver of species distributions. In this study, I focused on Geyik Mountains and surrounding areas to illustrate how complex topography and climatic conditions have shaped the distribution patterns of species/communities and therefore the biodiversity of the Mediterranean Taurus Mountains, one of the most biologically diverse areas in the Mediterranean Basin biodiversity hotspot. Accordingly, I used an ecological niche modelling approach, which has been widely used in recent biogeographic studies. I chose Taurus ground squirrels (Spermophilus taurensis) and coniferous forests as the representatives of high- and low-altitude species/communities, respectively. The results simply illustrate how complex topography and temperature and precipitation gradients have had a substantial role in shaping the distribution patterns of species/communities and therefore the biodiversity of the Mediterranean Taurus Mountains.
Viscous effects and complex local flow behaviors dominate hemolymph circulation in the living wings of locusts
Authors: Salcedo Mary K. , Jun Brian , Vlachos Pavlos , Mahadevan Lakshminarayanan , Combes Stacey A. 
Published: September 2021

ABSTRACTAn insects’ living systems – circulation, respiration, and a branching nervous system – extend from the body into the wing.1,2. Hemolypmh circulation in the wing is critical for hydrating tissues, such as the highly elastic resilin3 that enhances wing flexibility, and for supplying nutrients to living systems, including sensory organs such as scent-producing patches, sound-receiving tympana, and wind-sensing sensilla distributed across the wing.4–7During flight, the presence of hemolymph in the wings reduces aerodynamic instabilities like flutter8,9, and faster hemolymph flows are induced by flapping.10 Despite the critical role of hemolymph circulation in maintaining healthy wing function, wings are often considered “lifeless” cuticle, and most measurements remain qualitative or employ coarse, bulk-flow techniques. While pioneering work in the 1960s mapped hemolymph flow direction in 100 insect species,11 half a century later we still only have quantitative measurements of flow within the wings of a few insects. Here, we focused on the North American locust Schistocerca americana, a well-studied agricultural pest species, and performed a detailed, quantitative study of global and local hemolymph flows in the densely venated fore and hind wings, along with key regions in the body and pumping organs. Through high-speed fluorescent microscopy, we measured 800 individual trajectories of neutrally buoyant fluorescent particles that move in sync with hemolymph, in the wings and body of 8 live, resting locusts. Our data show that overall flow within the wings is circuitous, but local flow behavior is highly complex, with three distinct types of flow (pulsatile, continuous, and “leaky”) occurring in various combinations in different areas of the wing. We provide the first quantitative measurements of “leaky” flow into wing regions that act as sinuses, where hemolymph flows out of tubular veins and pools within thin membranous regions. We also calculate Péclet, Reynolds, and Womersley numbers, and find that viscous effects dominate flow regimes throughout the wing. Pumping organs and wing regions closest to the body display significantly faster flows and higher Reynolds numbers, but remain within the viscous flow regime. Given the central role of wings in sustaining ecologically important insect behaviors such as pollination, migration, and mating, along with the vast diversity of insect wings seen in nature, this first detailed, quantitative map of hemolymph flows across a wing provides a template for future studies investigating the dynamics of hemolymph flows critical to sustaining wing health among insects.