bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pair bond endurance promotes cooperative food defense and inhibits conflict in coral reef butterflyfishes
Authors: Nowicki Jessica P. , Walker Stefan P. W. , Coker Darren J. , Hoey Andrew S. , Nicolet Katia J. , Pratchett Morgan S. 
Published: November 2017

AbstractPair bonding is generally linked to monogamous mating systems, where the reproductive benefits of extended mate guarding and/or of bi-parental care are considered key adaptive functions. However, in some species, including coral reef butterflyfishes (f. Chaetodonitidae), pair bonding occurs in sexually immature and homosexual partners, and in the absence of parental care, suggesting there must be non-reproductive adaptive benefits of pair bonding. Here, we examined whether pair bonding butterflyfishes cooperate in defense of food, conferring direct benefits to one or both partners. Pairs ofChaetodon lunulatusandC. baronessause contrasting cooperative strategies. InC. lunulatus,both partners mutually defend their territory, while inC. baronessa,males prioritize territory defence; conferring improvements in feeding and energy reserves in both sexes relative to solitary counterparts. We further demonstrate that partner fidelity contributes to this function by showing that re-pairing invokes intra-pair conflict and inhibits cooperatively-derived feeding benefits, and that partner endurance is required for these costs to abate. Overall, our results suggest that in butterflyfishes, pair bonding enhances cooperative defense of prey resources, ultimately benefiting both partners by improving food resource acquisition and energy reserves.
Early-exposure to new sex pheromone blend alters mate preference in female butterflies and in their offspring
Authors: Dion Emilie , Pui Li Xian , Monteiro Antónia 
Published: November 2017

AbstractInsects use species-specific sex pheromone blends to attract members of the opposite sex which express the corresponding molecular receptors. Given this lock and key mechanism used for species identification and mate choice, it is currently not well understood how pheromone blends or receptor systems evolve. One possibility is that insects develop preferences for new sex pheromone blends via the process of learning, and that these learned preferences may be passed on to the next generation. We tested these hypotheses by exposing newly emerged Bicyclus anynana female butterflies to either wild type or to modified male sex pheromone blends. A few days later, we scored female mating outcome in a choice trial involving both male types. We also assessed the mating outcome of naïve offspring of females that underwent distinct odor learning trials to test for a potential inheritance of learned odor preferences. Naïve (parental) females mated preferentially with Wt-blend males, but females pre-exposed to new blends either shifted their preference to new-blend males, or mated equally with males of either blend type; the response depending on the new blend they were introduced to. Naïve daughters of females who were exposed to new-blend males behaved similarly to their experienced mothers. We demonstrate that females are able to learn preferences for novel pheromone blends in response to a short social experience, and pass that learned preference down to the next generation. This suggests that learning can be a key factor in the evolution of sex pheromone blend recognition and in chemosensory speciation.Significance statementWhile the diversity of sex pheromone communication systems across insects is well documented, the mechanisms that lead to such diversity are not well understood. Sex pheromones constitute a species-specific system of sexual communication that reinforces interspecific reproductive isolation. When odor blends evolve, the efficacy of male-female communication becomes compromised, unless preference for novel blends also evolves. We explore odor learning as a possible mechanism leading to changes in sex pheromone preferences. We show that preferences for new blends can develop following a short learning experience, and that these novel preferences can be transmitted to the next generation. To our knowledge, this is the first investigation of sex pheromone blend preference learning impacting mate choice and being inherited in an insect.
Temporal coupling of field potentials and action potentials in the neocortex
Authors: Watson Brendon O. , Ding Mingxin , Buzsáki György 
Published: November 2017

AbstractThe local field potential (LFP) is an aggregate measure of group neuronal activity and is often correlated with the action potentials of single neurons. In recent years investigators have found that action potential firing rates increase during elevations in power high-frequency band oscillations (50-200 Hz range). However action potentials also contribute to the LFP signal itself, making the spike–LFP relationship complex. Here we examine the relationship between spike rates and LFPs in varying frequency bands in rat neocortical recordings. We find that 50-180Hz oscillations correlate most consistently with high firing rates, but that other LFPs bands also carry information relating to spiking, including in some cases anti-correlations. Relatedly, we find that spiking itself and electromyographic activity contribute to LFP power in these bands. The relationship between spike rates and LFP power varies between brain states and between individual cells. Finally, we create an improved oscillation-based predictor of action potential activity by specifically utilizing information from across the entire recorded frequency spectrum of LFP. The findings illustrate both caveats and improvements to be taken into account in attempts to infer spiking activity from LFP.
B-1a cells acquire their unique characteristics by bypassing the pre-BCR selection stage
Authors: Wong Jason B , Hewitt Susannah L , Heltemes-Harris Lynn M , Mandal Malay , Johnson Kristen , Rajewsky Klaus , Koralov Sergei B , Clark Marcus R , Farrar Michael A , Skok Jane A 
Published: November 2017

SUMMARYB-1a cells are long-lived, self-renewing innate like B cells that predominantly inhabit the peritoneal and pleural cavities. In contrast to conventional B-2 cells they have a receptor repertoire that is biased towards bacterial and self-antigens, promoting a rapid response to infection and clearing of apoptotic cells. Although B-1a cells are known to primarily originate from fetal tissues the mechanisms by which they arise has been a topic of debate for many years. Here we show that in the fetal liver (FL) versus bone marrow (BM) environment, reduced IL-7R/STAT5 levels promote immunoglobulin kappa (Igk) recombination at the early pro-B cell stage. As a result, B cells can directly generate a mature B cell receptor (BCR) and bypass the requirement for a pre-BCR and pairing with surrogate light chain (SLC). This ‘alternate pathway’ of development enables the production of B cells with self reactive, skewed specificity receptors that are peculiar to the B-1a compartment. Together our findings connect seemingly opposing models of B-1a cell development and explain how these cells acquire their unique properties.
Network modelling unravels mechanisms of crosstalk between ethylene and salicylate signalling in potato
Authors: Ramšak Živa , Coll Anna , Stare Tjaša , Tzfadia Oren , Baebler Špela , Baebler Špela , Van de Peer Yves , Gruden Kristina 
Published: November 2017

ABSTRACTTo provide means for novel crop breeding strategies, it is crucial to understand the mechanisms underlying the interaction between plants and their pathogens. Network modelling represents a powerful tool that can unravel properties of complex biological systems. Here, we build on a reliable Arabidopsis (Arabidopsis thaliana L.) immune signalling model, extending it with the information from diverse publically available resources. The resulting prior knowledge network (20,012 nodes, 70,091 connections) was then translated to potato (Solanum tuberosum L.) and superimposed with an ensemble network inferred from potato time-resolved transcriptomics data. We used different network modelling approaches to generate specific hypotheses of potato immune signalling mechanisms. An interesting finding was the identification of a string of molecular events, illuminating the ethylene pathway modulation of the salicylic acid pathway through NPR1 gene expression. Functional validations confirmed this modulation, thus confirming the potential of our integrative network modelling approach for unravelling molecular mechanisms in complex systems.One-sentence summaryAnalysis of integrated prior knowledge and ensemble networks highlights a novel connection between ethylene and salicylic acid signalling modules in potato.
Addressing the reliability fallacy: Similar group effects may arise from unreliable individual effects
Authors: Fröhner Juliane H. , Teckentrup Vanessa , Smolka Michael N. , Kroemer Nils B. 
Published: November 2017

AbstractTo cast valid predictions of future behavior or diagnose disorders, the reliable measurement of a “biomarker” such as the brain activation to prospective reward is a prerequisite. Surprisingly, only a small fraction of functional magnetic resonance imaging (fMRI) studies report or cite the reliability of brain activation maps involved in group analyses. Here, using simulations and exemplary longitudinal data of 126 healthy adolescents performing an intertemporal choice task, we demonstrate that reproducing a group activation map over time is not a sufficient indication of reliable measurements at the individual level. Instead, selecting regions based on significant main effects at the group level may yield estimates that fail to reliably capture individual variance in the subjective evaluation of an offer. Collectively, our results call for more attention on the reliability of supposed biomarkers at the level of the individual. Thus, caution is warranted in employing brain activation patterns prematurely for clinical applications such as diagnosis or tailored interventions before their reliability has been conclusively established by large-scale studies. To facilitate assessing and reporting of the reliability of fMRI contrasts in future studies, we provide a toolbox that incorporates common measures of global and local reliability.
New Cell Fate Potentials and Switching Kinetics Uncovered in a Classic Bistable Genetic Switch
Authors: Fang Xiaona , Liu Qiong , Bohrer Christopher , Hensel Zach , Han Wei , Wang Jin , Xiao Jie 
Published: November 2017

AbstractBistable switches are common gene regulatory motifs directing two mutually exclusive gene expression states, and consequently distinct cell fates. Theoretical studies suggest that the simple circuitry of bistable switches is sufficient to encode more than two cell fates due to the non-equilibrium, heterogeneous cellular environment, allowing a high degree of adaptation and differentiation. However, new cell fates arising from a classic bistable switch without rewiring the circuitry have not been experimentally observed. By developing a new, dual single-molecule gene-expression reporting system in liveE. colicells, we investigated the expression dynamics of two mutually repressing transcription factors, CI and Cro, in the classic genetic switch of bacteriophage λ. We found that in addition to the two expected high-Cro and high-CI production states, there existed two new ones, in which neither CI nor Cro was produced, or both CI and Cro were produced. We constructed the corresponding potential landscape and mapped the transition kinetics between the four production states, providing insight into possible state-switching rates and paths. These findings uncover new cell fate potentials beyond the classical picture of λ switch, and open a new window to explore the genetic and environmental origins of the cell fate decision-making process in gene regulatory networks.
Resting-state functional brain connectivity best predicts the personality dimension of openness to experience
Authors: Dubois Julien , Galdi Paola , Han Yanting , Paul Lynn K. , Adolphs Ralph 
Published: November 2017

AbstractPersonality neuroscience aims to find associations between brain measures and personality traits. Findings to date have been severely limited by a number of factors, including small sample size and omission of out-of-sample prediction. We capitalized on the recent availability of a large database, together with the emergence of specific criteria for best practices in neuroimaging studies of individual differences. We analyzed resting-state functional magnetic resonance imaging data from 884 young healthy adults in the Human Connectome Project (HCP) database. We attempted to predict personality traits from the “Big Five”, as assessed with the NEO-FFI test, using individual functional connectivity matrices. After regressing out potential confounds (such as age, sex, handedness and fluid intelligence), we used a cross-validated framework, together with test-retest replication (across two sessions of resting-state fMRI for each subject), to quantify how well the neuroimaging data could predict each of the five personality factors. We tested three different (published) denoising strategies for the fMRI data, two inter-subject alignment and brain parcellation schemes, and three different linear models for prediction. As measurement noise is known to moderate statistical relationships, we performed final prediction analyses using average connectivity across both imaging sessions (1 h of data), with the analysis pipeline that yielded the highest predictability overall. Across all results (test/retest; 3 denoising strategies; 2 alignment schemes; 3 models), Openness to experience emerged as the only reliably predicted personality factor. Using the full hour of resting-state data and the best pipeline, we could predict Openness to experience (NEOFAC_O: r=0.24, R2=0.024) almost as well as we could predict the score on a 24-item intelligence test (PMAT24_A_CR: r=0.26, R2=0.044). Other factors (Extraversion, Neuroticism, Agreeableness and Conscientiousness) yielded weaker predictions across results that were not statistically significant under permutation testing. We also derived two superordinate personality factors (“α” and “β”) from a principal components analysis of the NEO-FFI factor scores, thereby reducing noise and enhancing the precision of these measures of personality. We could account for 5% of the variance in the β superordinate factor (r=0.27, R2=0.050), which loads highly on Openness to experience. We conclude with a discussion of the potential for predicting personality from neuroimaging data and make specific recommendations for the field.
Frontal eye field inactivation reduces saccade preparation in the superior colliculus, but does not alter how preparatory activity relates to saccade latency
Authors: Dash Suryadeep , Peel Tyler R. , Lomber Stephen G. , Corneil Brian D. 
Published: November 2017

AbstractA neural correlate for saccadic reaction times (SRTs) in the gap saccade task is the level of preparatory activity in the intermediate layers of the superior colliculus (iSC) just before visual target onset: greater levels of iSC preparatory activity precede shorter SRTs. The frontal eye fields (FEF) are one likely source of such iSC preparatory activity, since FEF preparatory activity is also inversely related to SRT. To better understand the FEF’s role in saccade preparation, and the way in which such preparation relates to SRT, in two male rhesus monkeys we examined iSC preparatory activity during unilateral reversible cryogenic inactivation of the FEF. FEF inactivation increased contralesional SRTs, and lowered ipsilesional iSC preparatory activity. FEF inactivation also reduced fixation-related activity in the rostral iSC. Importantly, the distributions of SRTs generated with or without FEF inactivation overlapped, enabling us to conduct a novel population-level analyses examining iSC preparatory activity just before generation of SRT-matched saccades. These analyses revealed no change during FEF inactivation in the relationship between iSC preparatory activity and SRT-matched saccades across a range of SRTs, even for the occasional express saccade. Thus, while our results emphasize that the FEF has an overall excitatory influence on preparatory activity in the iSC, the communication between the iSC and downstream oculomotor brainstem is unaltered for SRT-matched saccades, suggesting that the integration of preparatory and visual signals in the SC just before saccade initiation is largely independent of the FEF for saccades generated in this task.Significance statementHow does the brain decide when to move? Here, we investigate the role of two oculomotor structures, the superior colliculus (SC) and frontal eye fields (FEF), in dictating visually-guided saccadic reaction times (SRTs). In both structures, higher levels of preparatory activity precede shorter SRTs. Here, we show that FEF inactivation increases SRTs and decreases SC preparatory activity. Surprisingly, a population-level analysis of SC preparatory activity showed a negligible impact of FEF inactivation, providing one examines SRT-matched saccades. Thus, while the FEF is one source of preparatory input to the SC, it is not a critical source, and it is not involved in the integration of preparatory activity and visual signals that precedes saccade initiation in simple visually-guided saccade tasks.
Multifactorial Dynamics of White Matter Connectivity During Adolescence
Authors: Tunç Birkan , Parker Drew , Shinohara Russell T. , Elliott Mark A. , Ruparel Kosha , Gur Raquel E. , Gur Ruben C. , Verma Ragini 
Published: November 2017

AbstractStudying developmental changes in white matter connectivity is critical for understanding neurobiological substrates of cognition, learning, and neuropsychiatric disorders. This becomes especially important during adolescence when a rapid expansion of the behavioral repertoire occurs. Several factors such as brain geometry, genetic expression profiles, and higher level architectural specifications such as the presence of segregated modules have been associated with the observed organization of white matter connections. However, we lack understanding of the extent to which such factors jointly describe the brain network organization, nor have insights into how their contribution changes developmentally. We constructed a multifactorial model of white matter connectivity using Bayesian network analysis and tested it with diffusion imaging data from a large community sample. We investigated contributions of multiple factors in explaining observed connectivity, including architectural specifications, which promote a modular yet integrative organization, and brain’s geometric and genetic features. Our results demonstrated that the initially dominant geometric and genetic factors become less influential with age, whereas the effect of architectural specifications increases. The identified structural modules are associated with well-known functional systems, and the level of association increases with age. This integrative analysis provides a computational characterization of the normative evolution of structural connectivity during adolescence.
Calcimycocavitological Studies on Seashells from Beaches of North Goa, India
Authors: Dabolkar Sujata , Kamat Nandkumar 
Published: November 2017

ABSTRACTCalcimycocavitology deals with the study of hollowing out of spaces in hard calcareous seashells by the fungi called calcimycocavites. Endolithic fungi in the shells were first reported and named as the trace fossils in 1889 by Bornet and Flahault. Endolithic fungi bore inside the shell by the process of bioturbation by using organic acids (oxalic acid, citrate) and enzymes (proteases, dehydrogenases and oxidoreductases). Previous reports show the presence of tunnels formed by fungal hyphae in the shells. The present work reports preliminary results of calcimycocavitological studies on the seashells from beaches of north Goa, India. The calcareous sand samples were collected from Arambol, Ashvem, Morjim, Vagator, Anjuna, Baga and Miramar beaches by pool sampling method and were separated into different fractions by using standard sieves. Each fraction of sand was subjected to stereomicroscopic studies which revealed that the sand fraction between 150-250 μm included irregular shell fragments showing positive colonization by calcimycocavites. Hydrochloric acid treatment was used to dissolve the shells and release calcimycocavites biomass which was stained with Congo Red and tentatively identified as distinct microfungal forms. SEM studies of the calcareous shell fragments revealed the microtunneling behavior of the fungi. Digital analysis of SEM images using Mountain premium 7.2 software revealed the fine topography of calcimycocavites hyphae along with unidentified presumptive biomineral encrustations. The ecological, biological and biogeochemical implications of the findings are presented with respect to possible role of calcimycocavites in Calcium and Carbon cycling by breakdown of the calcareous shells and release of inorganic and organic components in the ecosystem.
DriverPower: Combined burden and functional impact tests for cancer driver discovery
Authors: Shuai Shimin , Gallinger Steven , Stein Lincoln ,   on behalf of the PCAWG Drivers and Functional Interpretation Group and the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Network
Published: November 2017

AbstractWe describe DriverPower, a software package that uses mutational burden and functional impact evidence to identify cancer driver mutations in coding and non-coding sites within cancer whole genomes. Using a total of 1,373 genomic features derived from public sources, DriverPower’s background mutation model explains up to 93% of the regional variance in the mutation rate across a variety of tumour types. By incorporating functional impact scores, we are able to further increase the accuracy of driver discovery. Testing across a collection of 2,583 cancer genomes from the Pan-Cancer Analysis of Whole Genomes (PCAWG) project, DriverPower identifies 217 coding and 95 non-coding driver candidates. Comparing to six published methods used by the PCAWG Drivers and Functional Interpretation Group, DriverPower has the highest F1-score for both coding and non-coding driver discovery. This demonstrates that DriverPower is an effective framework for computational driver discovery.
Correlated selection on amino acid deletion and replacement in mammalian protein sequences
Authors: Zheng Yichen , Graur Dan , Azevedo Ricardo B. R. 
Published: November 2017

AbstractA low ratio of nonsynonymous and synonymous substitution rates (dN/dS) at a codon is a sign of functional constraint caused by purifying selection. Intuitively, the functional constraint would also be expected to prevent such a codon from being deleted. Oddly, to the best of our knowledge, the correlation between the rates of deletion and substitution has never actually been estimated. Here, we use 8,595 protein coding-region sequences from 9 mammalian species to examine the relationship between deletion rate and dN/dS. We found significant positive correlations at both the level of sites and genes. We compared our data against controls consisting of simulated coding sequences evolving along identical phylogenetic trees, where the correlation is not included in the model a priori. A much weaker correlation was found in the corresponding simulated sequences, which is probably caused by alignment errors. In the real data, the correlations cannot be explained by alignment errors. Separate investigations on nonsynonymous (dN) and synonymous (dS) substitution rates indicate that the correlation is most likely due to a similarity in patterns of selection rather than mutation rates.