bluuebunny/crossref_metadata_2025_split huggingface dataset:
Co-Increasing Neuronal Noise and Beta Power in the Developing Brain
Authors: He Wei , Donoghue Thomas , Sowman Paul F , Seymour Robert A , Brock Jon , Crain Stephen , Voytek Bradley , Hillebrand Arjan 
Published: November 2019

ABSTRACTAccumulating evidence across species indicates that brain oscillations are superimposed upon an aperiodic 1/f- like power spectrum. Maturational changes in neuronal oscillations have not been assessed in tandem with this underlying aperiodic spectrum. The current study uncovers co-maturation of the aperiodic component alongside the periodic components (oscillations) in spontaneous magnetoencephalography (MEG) data. Beamformer-reconstructed MEG time-series allowed a direct comparison of power in the source domain between 24 children (8.0 ± 2.5 years, 17 males) and 24 adults (40.6 ± 17.4 years, 16 males). Our results suggest that the redistribution of oscillatory power from lower to higher frequencies that is observed in childhood does not hold once the age-related changes in the aperiodic signal are controlled for. When estimating both the periodic and aperiodic components, we found that power increases with age in the beta band only, and that the 1/fsignal is flattened in adults compared to children. These results suggest a pattern of co-maturing beta oscillatory power with the aperiodic 1/fsignal in typical childhood development.
DeepPheno: Predicting single gene loss-of-function phenotypes using an ontology-aware hierarchical classifier
Authors: Kulmanov Maxat , Hoehndorf Robert 
Published: November 2019

AbstractMotivationPredicting the phenotypes resulting from molecular perturbations is one of the key challenges in genetics. Both forward and reverse genetic screen are employed to identify the molecular mechanisms underlying phenotypes and disease, and these resulted in a large number of genotype–phenotype association being available for humans and model organisms. Combined with recent advances in machine learning, it may now be possible to predict human phenotypes resulting from particular molecular aberrations.ResultsWe developed DeepPheno, a neural network based hierarchical multi-class multi-label classification method for predicting the phenotypes resulting from complete loss-of-function in single genes. DeepPheno uses the functional annotations with gene products to predict the phenotypes resulting from a loss-of-function; additionally, we employ a two-step procedure in which we predict these functions first and then predict phenotypes. Prediction of phenotypes is ontology-based and we propose a novel ontology-based classifier suitable for very large hierarchical classification tasks. These methods allow us to predict phenotypes associated with any known protein-coding gene. We evaluate our approach using evaluation metrics established by the CAFA challenge and compare with top performing CAFA2 methods as well as several state of the art phenotype prediction approaches, demonstrating the improvement of DeepPheno over state of the art methods. Furthermore, we show that predictions generated by DeepPheno are applicable to predicting gene–disease associations based on comparing phenotypes, and that a large number of new predictions made by DeepPheno interact with a gene that is already associated with the predicted phenotype.Availabilityhttps://github.com/bio-ontology-research-group/deepphenoContactrobert.hoehndorf@kaust.edu.sa
BowSaw: inferring higher-order trait interactions associated with complex biological phenotypes
Authors: DiMucci Demetrius , Kon Mark , Segrè Daniel 
Published: November 2019

AbstractMachine learning is helping the interpretation of biological complexity by enabling the inference and classification of cellular, organismal and ecological phenotypes based on large datasets, e.g. from genomic, transcriptomic and metagenomic analyses. A number of available algorithms can help search these datasets to uncover patterns associated with specific traits, including disease-related attributes. While, in many instances, treating an algorithm as a black box is sufficient, it is interesting to pursue an enhanced understanding of how system variables end up contributing to a specific output, as an avenue towards new mechanistic insight. Here we address this challenge through a suite of algorithms, named BowSaw, which takes advantage of the structure of a trained random forest algorithm to identify combinations of variables (“rules”) frequently used for classification. We first apply BowSaw to a simulated dataset, and show that the algorithm can accurately recover the sets of variables used to generate the phenotypes through complex Boolean rules, even under challenging noise levels. We next apply our method to data from the integrative Human Microbiome Project and find previously unreported high-order combinations of microbial taxa putatively associated with Crohn’s disease. By leveraging the structure of trees within a random forest, BowSaw provides a new way of using decision trees to generate testable biological hypotheses.
Temperature and nutrient gradients correspond with lineage-specific microdiversification in the ubiquitous and abundant Limnohabitans freshwater genus
Authors: Props Ruben , Denef Vincent J. 
Published: November 2019

AbstractMost freshwater bacterial communities are characterized by a few dominant taxa, which are often ubiquitous across freshwater biomes worldwide. Our understanding of the genomic basis underlying this pattern is limited to a subset of taxa. Here, we investigated the genomic basis that enables Limnohabitans, a freshwater genus key in funneling carbon from primary producers to higher trophic levels, to achieve abundance and ubiquity. We reconstructed eight metagenome assembled genomes (MAGs) from this genus along broad environmental gradients existing in Lake Michigan, part of Earth’s largest surface freshwater system. De novo strain inference analysis resolved a total of 23 strains from these MAGs, which strongly partitioned into two habitat-specific clusters with co-occurring strains from different lineages. The largest number of strains belonged to the abundant LimB lineage, for which robust in situ strain-delineation had not previously been achieved. Our data show that temperature and nutrient levels may be two of the primary drivers of microdiversification within the Limnohabitans genus. Additionally, strains predominant in low and high phosphorus conditions had larger genomic divergence than strains abundant under different temperatures. Comparative genomics and gene expression analysis yielded evidence for the ability of LimB populations to exhibit cellular motility and chemotaxis, a phenotype not yet associated with cultured Limnohabitans strains. Our findings broaden historical marker gene-based surveys of Limnohabitans microdiversification, and provide in situ evidence of genome diversity and its functional implications across freshwater gradients.
Sounds are remapped across saccades
Authors: Szinte Martin , Aagten-Murphy David , Jonikaitis Donatas , Wollenberg Luca , Deubel Heiner 
Published: November 2019

AbstractTo achieve visual space constancy, our brain remaps eye-centered projections of visual objects across saccades. Here, we measured saccade trajectory curvature following the presentation of visual, auditory, and audiovisual distractors in a double-step saccade task to investigate if this stability mechanism also accounts for localized sounds. We found that saccade trajectories systematically curved away from the position at which either a light or a sound was presented, suggesting that both modalities are represented in eye-centered oculomotor centers. Importantly, the same effect was observed when the distractor preceded the execution of the first saccade. These results suggest that oculomotor centers keep track of visual, auditory and audiovisual objects by remapping their eye-centered representations across saccades. Furthermore, they argue for the existence of a supra-modal map which keeps track of multi-sensory object locations across our movements to create an impression of space constancy.
Identification of conserved gene regulatory networks that integrate environmental sensing and growth in the root cambium
Authors: Choe Goh , Van Hoang Nam , Zheng Yi , Aliaga Fandiño Ana Cecilia , Hur Jaeryung , Sung Inyoung , Ahn Hongryul , Kim Sun , Fei Zhangjun , Lee Ji-Young 
Published: November 2019

AbstractCambium drives lateral growth of stems and roots, contributing to diverse plant growth forms. Root crop is one outstanding example of the cambium-driven growth. To understand its molecular basis, we used radish to generate a compendium of root tissue- and stage-specific transcriptomes from two contrasting inbred lines in root growth. Expression patterns of key cambium regulators and hormone signaling components were validated. Clustering and GO enrichment analyses of radish datasets followed by comparative analysis against the newly established Arabidopsis early cambium data revealed evolutionary conserved stress-response transcription factors that might intimately control the cambium. Indeed, in vivo network made of selected stress-response and cambium regulators indicated ERF-1 as a potential key checkpoint of cambial activities, explaining how the cambium-driven growth is altered in response to environmental changes. Together, this study provides rich information about dynamic gene expression changes along the cambium-driven root growth with future engineering schemes for crop yields.
Actigraphy in brain-injured patients – A valid measurement for assessing circadian rhythms?
Authors: Angerer Monika , Schabus Manuel , Raml Marion , Pichler Gerald , Kunz Alexander B. , Scarpatetti Monika , Trinka Eugen , Blume Christine 
Published: November 2019

AbstractBackgroundActigraphy has received increasing attention in classifying rest-activity cycles. However, in patients with disorders of consciousness (DOC), actigraphy data may be considerably confounded by passive movements, such as nursing activities and therapies. Consequently, this study verified whether circadian rhythmicity is (still) visible in actigraphy data from patients with DOC after correcting for passive movements.MethodsWrist actigraphy was recorded over 7-8 consecutive days in patients with DOC (diagnosed with unresponsive wakefulness syndrome [UWS; n=19] and [exit] minimally conscious state [MCS/EMCS; n=11]). Presence and actions of clinical and research staff as well as visitors were indicated using a tablet in the patient’s room. Following removal and interpolation of passive movements, non-parametric rank-based tests were computed to identify differences between circadian parameters of uncorrected and corrected actigraphy data.ResultsUncorrected actigraphy data overestimated the interdaily stability and intradaily variability of patients’ activity and underestimated the deviation from a circadian 24h rhythm. Only 5/30 (17%) patients deviated more than 1h from 24h in the uncorrected data, whereas this was the case for 17/30 (57%) patients in the corrected data. When contrasting diagnoses based on the corrected dataset, stronger circadian rhythms and higher activity levels were observed in MCS/EMCS as compared to UWS patients. Day-to-night differences in activity were evident for both patient groups.ConclusionOur findings indicate that uncorrected actigraphy data overestimates the circadian rhythmicity of patients’ activity, as nursing activities, therapies, and visits by relatives follow a circadian pattern itself. Therefore, we suggest correcting actigraphy data from patients with reduced mobility.
Size, not temperature, drives cyclopoid copepod predation of invasive mosquito larvae
Authors: Russell Marie C. , Qureshi Alima , Wilson Christopher G. , Cator Lauren J. 
Published: November 2019

AbstractDuring range expansion, invasive species can experience new thermal regimes. Differences between the thermal performance of local and invasive species can alter species interactions, including predator-prey interactions. The Asian tiger mosquito,Aedes albopictus, is a known vector of several viral diseases of public health importance. It has successfully invaded many regions across the globe and currently threatens to invade regions of the UK where conditions would support seasonal activity. We assessed the functional response and predation efficiency (percentage of prey consumed) of the cyclopoid copepodsMacrocyclops albidusandMegacyclops viridisfrom South East England, UK against newly-hatched FrenchAe. albopictuslarvae across a relevant temperature range (15, 20, and 25°C). Predator-absent controls were included in all experiments to account for background prey mortality. We found that bothM. albidusandM. viridisdisplay type II functional response curves, and that both would therefore be suitable biocontrol agents in the event of anAe. albopictusinvasion in the UK. No significant effect of temperature on the predation interaction was detected by either type of analysis. However, the predation efficiency analysis did show differences due to predator species. The results suggest thatM. viridiswould be a superior predator against invasiveAe. albopictuslarvae due to the larger size of this copepod species, relative toM. albidus. Our work highlights the importance of size relationships in predicting interactions between invading prey and local predators.
Characterising shared space use networks using animal trapping data
Authors: Wanelik Klara M. , Farine Damien R. 
Published: November 2019

AbstractStudying the social behaviour of small or cryptic species often relies on constructing networks from sparse point-based observations of individuals (e.g. live trapping data). Such an approach assumes that individuals that have been asynchronously detected in the same trapping location will also be more likely to have interacted. However, there is very little guidance on how much data are required for making robust co-trapping networks. In this study, we propose that co-trapping networks broadly assume that co-trapping captures shared space use (and, subsequently, likelihood of interacting), and that it may be more parsimonious to directly model shared space use. We first use empirical data to highlight that characteristics of how animals use space can help us to establish new ways to model the potential for individuals to co-occur. We then show that a method that explicitly models individuals’ home ranges and subsequent overlap in space among individuals (spatial overlap networks) requires fewer data for inferring observed networks that are correlated with the true shared space use network (relative to co-trapping networks constructed from space sharing events). Further, we show that shared space use networks based on estimating spatial overlap are also more powerful for detecting biological effects present in the true shared space use network. Finally, we discuss when it is appropriate to make inferences about social interactions from shared space use. Our study confirms the potential for using sparse trapping data from cryptic species to address a range of important questions in ecology and evolution.Significance statementCharacterising animal social networks requires repeated (co-)observations of individuals. Collecting sufficient data to characterise the connections among individuals represents a major challenge when studying cryptic organisms—such as small rodents. This study draws from existing spatial mark-recapture data to inspire an approach that constructs networks by estimating space use overlap (representing the potential for interactions) from observations of individuals in the same location (e.g. a trap). We then use simulations to demonstrate that the method provides consistently higher correlations between inferred (or observed) networks and the true underlying network compared to current approaches, and requires fewer observations to reach higher correlations. We further demonstrate that these improvements translate to greater network accuracy and to more power for statistical hypothesis testing.
An information-theory approach to geometry for animal groups
Authors: Dahl Christoph D. , Ferrando Elodie , Zuberbühler Klaus 
Published: November 2019

AbstractOne of the hardest problems in studying animal behaviour is to quantify patterns of social interaction at the group level. Recent technological developments in global positioning system (GPS) devices have opened up new avenues for locating animals with unprecedented spatial and temporal resolution. Likewise, advances in computing power have enabled new levels of data analyses with complex mathematical models to address unresolved problems in animal behaviour, such as the nature of group geometry and the impact of group-level interactions on individuals. Here, we present an information theory-based tool for the analysis of group behaviour. We illustrate its affordances with GPS data collected from a freely interacting pack of 15 Siberian huskies (Canis lupus familiaris). We found that individual freedom in movement decisions was limited to about 4%, while a subject’s location could be predicted with 96% median accuracy by the locations of other group members, a pattern mediated by dominance, kin relations, sex, the relative time of the day and external events, such as feeding. We conclude that information theory-based approaches, coupled with state-of-the-art bio-logging technology, provide a powerful tool for future studies of animal social interactions beyond the dyadic level.
Environmental variables determining the distribution of an avian parasite: the case of thePhilornis torquanscomplex (Diptera: Muscidae) in South America
Authors: Cuervo Pablo F. , Percara Alejandro , Monje Lucas , Beldomenico Pablo M. , Quiroga Martín A. 
Published: November 2019

AbstractPhilornisflies are the major cause of myasis in altricial nestlings of neotropical birds. Its impact ranges from subtle to lethal, being of major concern in endangered bird species with geographically-restricted, fragmented and small-sized populations. In spite of its relevance for bird conservation, there is little information about the environmental dimensions determining their geographical range. We identified for the first time the macro-environmental variables constraining the abiotic niche of theP. torquanscomplex in South America, and provided a model map of its potential distribution based on environmental suitability. We used maximum entropy to model the ecological niche of theP. torquanscomplex, and to determine the contributing scenopoetic variables. We applied most of the recommendations to produce robust ecological niche models: accounting for sampling bias and spatial autocorrelation; using an accessible area for model calibration; testing multiple combinations of model parameters; using multiple statistical criteria; using a number of model replicates to determine consistency and uncertainty in geographical predictions. We identified the minimum temperature of the coldest month as the most relevant variable, associated with the largest decrease in habitat suitability in Brazil and northern South America. Furthermore, the mean temperature of the warmest quarter limited suitability mostly along the Andean range. In addition, humidity and moisture are influential factors in most of Argentina, northern Chile and coastal Peru. The geographical projection of the niche model suggests that environments in most of central-eastern Argentina, and in a broad area in central Chile, are suitable for the presence of theP. torquanscomplex. Besides of contributing to the knowledge of the ecology of the genus, this study is of relevance as a tool for bird conservation and represents a good reference for future work on the distribution of this parasite genus.
A mitochondria-targeted antioxidant affects the carotenoid-based plumage of red crossbills
Authors: Cantarero Alejandro , Mateo Rafael , Camarero Pablo , Alonso Daniel , Fernandez-Eslava Blanca , Alonso-Alvarez Carlos 
Published: November 2019

ABSTRACTThe mechanisms involved in the production of red carotenoid-based ornaments in vertebrates are still poorly understood. Those colours generated by red carotenoids often depend on the enzymatic production (ketolation) of these pigments from dietary yellow carotenoids. Recently, it has been proposed that this conversion takes place at the inner mitochondrial membrane (IMM). This implies that carotenoid ketolation and cell respiration could share the same biochemical pathways. Such a link would favour the evolution of red ketocarotenoid-based ornaments as reliable indices of individual quality under a sexual selection scenario. We exposed captive male red crossbills (Loxia curvirostraLinnaeus) to two different synthetic antioxidants designed to penetrate into the IMM: a synthetic ubiquinone (mitoQ) and a superoxide dismutase mimetic (mitoTEMPO). MitoQ decreased the blood levels of substrate yellow carotenoids and tocopherol. This could be attributed to the characteristics of the mitoQ molecule, which can distort the IMM structure, increasing free radical (superoxide) production and, potentially, antioxidant consumption. Contrarily, mitoTEMPO-treated birds increased the plasma levels of the second most abundant red ketocarotenoid of red crossbills (i.e. canthaxanthin). MitoTEMPO also increased plumage redness and total ketocarotenoid concentration in feathers among those birds exhibiting a redder plumage at the beginning of the study, rising the plasma values of the main red pigment (3-hydroxyechinenone) in paler birds. The results as a whole support the involvement of the mitochondrial antioxidant machinery in carotenoid biotransformation. The fact that the initial plumage redness determined the effect of mitoTEMPO suggests that the mitochondrial-based mechanism is intimately linked to individual quality.Summary statementAntioxidants designed to penetrate the mitochondrial membrane increased avian plumage redness but depending on pre-existing colouration. This supports mitochondrial involvement in the evolution of carotenoid-based ornaments as reliable quality signals.
Phylogenetic and metabolic diversity have contrasting effects on the ecological functioning of bacterial communities
Authors: Xenophontos Constantinos , Taubert Martin , Harpole W. Stanley , Küsel Kirsten 
Published: November 2019

AbstractQuantifying the relative contributions of microbial species to ecosystem functioning is challenging, because of the distinct mechanisms associated with microbial phylogenetic and metabolic diversity. We constructed bacterial communities with different diversity traits and employed exoenzyme activities (EEAs) and total available carbon (TAC) from substrates as proxies of bacterial functioning to test the independent effects of these two aspects of biodiversity. We expected that metabolic diversity, but not phylogenetic diversity would be associated with greater ecological function. Phylogenetically relatedness should intensify species interactions and coexistence, therefore amplifying the influence of metabolic diversity. We examined the effects of each diversity treatment using linear models, while controlling for the other, and found that phylogenetic diversity strongly influenced community functioning, positively and negatively. Metabolic diversity, however, exhibited negative or non-significant relationships with community functioning. When controlling for different substrates, EEAs increased along with phylogenetic diversity but decreased with metabolic diversity. The strength of diversity effects was related to substrate chemistry and the molecular mechanisms associated with each substrate’s degradation. EEAs of phylogenetically similar groups were strongly affected by within-genus interactions. These results highlight the unique flexibility of microbial metabolic functions that must be considered in further ecological theory development.