doi: 10.5061/dryad.797kg
Juveniles of the cooperatively-breeding cichlid fish Neolamprologus pulcher either consistently provide help in form of alloparental egg care ('cleaners') or consistently abstain from helping ('non-cleaners'). These phenotypes are not based on heritable genetic differences. Instead they arise during ontogeny, which should lead to differences in brain structure or physiology, a currently untested prediction. We compared brain gene expression profiles of cleaners and non-cleaners in two experimental conditions, a helping opportunity and a control condition. We aimed to identify (i) expression differences between cleaners and non-cleaners in the control, (ii) changes in gene expression induced by the opportunity, and (iii) differences in plasticity of gene expression between cleaners and non-cleaners. Control cleaners and non-cleaners differed in the expression of a single gene, irx2, which regulates neural differentiation. During the opportunity, cleaners and non-cleaners had three up-regulated genes in common, which were implicated in neuroplasticity, hormonal signalling, and cell proliferation. Thus, the stimulus in the opportunity was sufficiently salient. Cleaners also showed higher expression of seven additional genes that were unique to the opportunity. One of these cleaner-specific genes is implicated in neuropeptide metabolism, indicating that this process is associated with cleaning performance. This suggests that the two types employed different pathways to integrate social information, preparing them for accelerated reaction to future opportunities. Interestingly, three developmental genes were down-regulated between the control and the opportunity in cleaners only. Our results indicate that the two behavioural types responded differently to the helping opportunity, and that only cleaners responded by down-regulating developmental genes. Read count matrix and treatment information on individualsRead count matrix from RNA-seq experiment of two distinct helper types in the cooperatively breeding cichlid fish Neolamprologus pulcher. 48 individuals in a 2x2 full-factorial design of cleaners and non-cleaners in control and opportunity. 38,2425 genes expressed in the telencephalon 45 min after the onset of the cooperation opportunity.data_Kasper_cichlid_helping_transcriptome.xlsx
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doi: 10.5061/dryad.37jg4
Entrainment of neural oscillations on multiple time scales is important for the perception of speech. Musical rhythms, and in particular the perception of a regular beat in musical rhythms, is also likely to rely on entrainment of neural oscillations. One recently proposed approach to studying beat perception in the context of neural entrainment and resonance (the “frequency-tagging” approach) has received an enthusiastic response from the scientific community. A specific version of the approach involves comparing frequency-domain representations of acoustic rhythm stimuli to the frequency-domain representations of neural responses to those rhythms (measured by electroencephalography, EEG). The relative amplitudes at specific EEG frequencies are compared to the relative amplitudes at the same stimulus frequencies, and enhancements at beat-related frequencies in the EEG signal are interpreted as reflecting an internal representation of the beat. Here, we show that frequency-domain representations of rhythms are sensitive to the acoustic features of the tones making up the rhythms (tone duration, onset/offset ramp duration); in fact, relative amplitudes at beat-related frequencies can be completely reversed by manipulating tone acoustics. Crucially, we show that changes to these acoustic tone features, and in turn changes to the frequency-domain representations of rhythms, do not affect beat perception. Instead, beat perception depends on the pattern of onsets (i.e., whether a rhythm has a simple or complex metrical structure). Moreover, we show that beat perception can differ for rhythms that have numerically identical frequency-domain representations. Thus, frequency-domain representations of rhythms are dissociable from beat perception. For this reason, we suggest caution in interpreting direct comparisons of rhythms and brain signals in the frequency domain. Instead, we suggest that combining EEG measurements of neural signals with creative behavioral paradigms is of more benefit to our understanding of beat perception. single participant behavioral data files.mat files for single participants. README.txt file in each zipped folder describes columnsdryad_data.zip
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doi: 10.34973/b5sq-jy51
We know how age affects the brain during lab-based tasks, but what about situations truer to everyday life, such as watching movies? We measured fMRI activity while participants (N=577) from the Cambridge Centre for Ageing and Neuroscience (www.cam-can.com) watched a movie. Watching the same movie induces significant inter-subject synchronization of brain activity across participants. These cross-subject correlations suggest that viewers are processing incoming information in a similar (or shared) way. We show that with advancing age, synchrony is preserved in some areas, including the language network, but decreased in others, including the medial prefrontal cortex, medial temporal lobe and fronto-parietal network. Synchrony declines were driven by more idiosyncratic responding in older adults and were associated with regionally-distinct temporal profiles and functional connectivity patterns, as well as declines in white matter integrity. These findings suggest that areas involved in language processing remain intact with age, while regions involved in attentional control and memory may show age-related declines, even in situations similar to daily life.
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Certain holographic states of matter with a global U(1) symmetry support a sound mode at zero temperature, caused neither by spontaneous symmetry breaking of the global U(1) nor by the emergence of a Fermi surface in the infrared. In this work, we show that such a mode is also found in zero density holographic quantum critical states. We demonstrate that in these states, the appearance of a zero temperature sound mode is the consequence of a mixed `t Hooft anomaly between the global U(1) symmetry and an emergent higher-form symmetry. At non-zero temperatures, the presence of a black hole horizon weakly breaks the emergent symmetry and gaps the collective mode, giving rise to a sharp Drude-like peak in the electric conductivity. A similar gapped mode arises at low temperatures for non-zero densities when the state has an emergent Lorentz symmetry, also originating from an approximate anomalous higher-form symmetry. However, in this case the collective excitation does not survive at zero temperature where, instead, it dissolves into a branch cut. We comment on the relation between our results and the application of the Luttinger theorem to compressible holographic states of matter.
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doi: 10.5061/dryad.8405j
Comparative studies have revealed that vasopressin-oxytocin pathways are associated with both pair bonding and grouping behaviour. However, the relationship between pair bonding and grouping behaviourremains unclear.In this study,our aim was to identify whether two species that differ in grouping behaviourdisplay a corresponding difference in their pair bonds, and in the underlying vasopressin-oxytocinhormonal pathways. Using two species of cichlid fishes, the highly social Neolamprologuspulcher and the non-social Telmatochromis temporalis, we measuredproximity of pairs during pair bond formation, and then measured social behaviors (proximity, aggression, submission,affiliation)and brain gene expression of isotocin and arginine vasotocin (the teleost homologues of oxytocin and vasopressin, respectively), as well as their receptors, after a temporary separation and subsequent reunion of the bonded pairs. Pairs of the social species spent more time in close proximity relative to the non-social species. Rates of aggression increased in both species following the separation and reunion treatment, relative to controls that were not separated.Overall, whole brain expression of isotocin was higher in the social species relative to the non-social species, and correlated with proximity, submission, and affiliation, but only in the social species. Our results suggest that both a social and a non-social cichlid species have similar behavioural responses to a temporary separation from a mate, and we found no differencein the brain gene expression of measured hormones and receptors based on our separation-reunion treatment. However, our results highlight the importance of isotocin in mediating submissive and affiliativebehaviourin cichlid fishes, and demonstrate thatisotocinhas species-specific correlations with socially relevantbehaviours. Cichlid pair bonding IT AVT dataRT-qPCR values and behavioral scores
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For foveated animals, visual tracking of moving stimuli requires the synergy between saccades and smooth pursuit eye movements. Deciding to trigger a catch-up saccade during pursuit influences the quality of visual input. This decision is a trade-off between tolerating sustained position error when no saccade is triggered or a transient loss of vision during the saccade due to saccadic suppression. Although catch-up saccades have been extensively investigated, it remains unclear how the trigger decision is made by the brain. de Brouwer et al (2002) demonstrated that catch-up saccades were less likely to occur when the expected time to foveate a target using pursuit alone is between 40 and 180ms into the future, referred to as the smooth zone. However, this descriptive result lacks a mechanistic explanation for how the trigger decision is made. More recently, we proposed a decision model (Coutinho et al., 2018) that relies on a probabilistic estimation of predicted position error (PEpred) during visual tracking. To test the model predictions, we investigated how human participants combined predicted position error, retinal slip, and the uncertainty in those estimates to make trigger decisions. We found a significant effect of the pre-saccadic magnitude of PEpred on trigger time and occurrence of catch-up saccades. To test the role of uncertainty, we blurred the moving target which led to longer and more variable saccade trigger times and more smooth pursuit trials, consistent with model predictions. As predicted by our model, large PEpred (>10deg) produced early saccades regardless of the level of uncertainty while saccades preceded by small PEpred (<10deg) were significantly modulated by high uncertainty. Our model also predicted increased signal dependent noise as retinal slip increases, which resulted in longer saccade trigger times and more smooth trials. In conclusion, the data supports our hypothesized role of PEpred in deciding when to trigger a catch-up saccade during smooth pursuit while taking into account uncertainty in sensory estimates. RawRaw double-step ramp eye-tracking data of 15 subjects from EyeLink 1000 and Matlab.LabeledS1-S5Labeled data file for subjects 1-5LabeledS7-S11Labeled data for subjects 7-11LabeledS12-S16Labeled data for subjects 12-16Data Collection Log
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We introduce Sleep, a new Python open-source graphical user interface (GUI) dedicated to visualization, scoring and analyses of sleep data. Among its most prominent features are: (1) Dynamic display of polysomnographic data, spectrogram, hypnogram and topographic maps with several customizable parameters, (2) Implementation of several automatic detection of sleep features such as spindles, K-complexes, slow waves, and rapid eye movements (REM), (3) Implementation of practical signal processing tools such as re-referencing or filtering, and (4) Display of main descriptive statistics including publication-ready tables and figures. The software package supports loading and reading raw EEG data from standard file formats such as European Data Format, in addition to a range of commercial data formats. Most importantly, Sleep is built on top of the VisPy library, which provides GPU-based fast and high-level visualization. As a result, it is capable of efficiently handling and displaying large sleep datasets. Sleep is freely available (http://visbrain.org/sleep) and comes with sample datasets and an extensive documentation. Novel functionalities will continue to be added and open-science community efforts are expected to enhance the capacities of this module.
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doi: 10.5061/dryad.72dk5
Infants recovering from anesthesia are at risk of life threatening Postoperative Apnea (POA). POA events are rare, and so the study of POA requires the analysis of long cardiorespiratory records. Manual scoring is the preferred method of analysis for these data, but it is limited by low intra- and inter-scorer repeatability. Furthermore, recommended scoring rules do not provide a comprehensive description of the respiratory patterns. This work describes a set of manual scoring tools that address these limitations. These tools include: (i) a set of definitions and scoring rules for 6 mutually exclusive, unique patterns that fully characterize infant respiratory inductive plethysmography (RIP) signals; (ii) RIPScore, a graphical, manual scoring software to apply these rules to infant data; (iii) a library of data segments representing each of the 6 patterns; (iv) a fully automated, interactive formal training protocol to standardize the analysis and establish intra- and inter-scorer repeatability; and (v) a quality control method to monitor scorer ongoing performance over time. To evaluate these tools, three scorers from varied backgrounds were recruited and trained to reach a performance level similar to that of an expert. These scorers used RIPScore to analyze data from infants at risk of POA in two separate, independent instances. Scorers performed with high accuracy and consistency, analyzed data efficiently, had very good intra- and inter-scorer repeatability, and exhibited only minor confusion between patterns. These results indicate that our tools represent an excellent method for the analysis of respiratory patterns in long data records. Although the tools were developed for the study of POA, their use extends to any study of respiratory patterns using RIP (e.g., sleep apnea, extubation readiness). Moreover, by establishing and monitoring scorer repeatability, our tools enable the analysis of large data sets by multiple scorers, which is essential for longitudinal and multicenter studies. Original and pre-processed data, and analysis resultsData acquired from infants at risk of Postoperative Apnea (in MATLAB *.mat format). Also, results of the analysis of these data by 4 scorers using the RIPScore manual scoring tool.StudyData.zip
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Example code for the analysis pipeline used to create the structural template and quantitative myelin water imaging atlases for An atlas for human brain myelin content throughout the adult life span https://www.nature.com/articles/s41598-020-79540-3
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doi: 10.5061/dryad.797kg
Juveniles of the cooperatively-breeding cichlid fish Neolamprologus pulcher either consistently provide help in form of alloparental egg care ('cleaners') or consistently abstain from helping ('non-cleaners'). These phenotypes are not based on heritable genetic differences. Instead they arise during ontogeny, which should lead to differences in brain structure or physiology, a currently untested prediction. We compared brain gene expression profiles of cleaners and non-cleaners in two experimental conditions, a helping opportunity and a control condition. We aimed to identify (i) expression differences between cleaners and non-cleaners in the control, (ii) changes in gene expression induced by the opportunity, and (iii) differences in plasticity of gene expression between cleaners and non-cleaners. Control cleaners and non-cleaners differed in the expression of a single gene, irx2, which regulates neural differentiation. During the opportunity, cleaners and non-cleaners had three up-regulated genes in common, which were implicated in neuroplasticity, hormonal signalling, and cell proliferation. Thus, the stimulus in the opportunity was sufficiently salient. Cleaners also showed higher expression of seven additional genes that were unique to the opportunity. One of these cleaner-specific genes is implicated in neuropeptide metabolism, indicating that this process is associated with cleaning performance. This suggests that the two types employed different pathways to integrate social information, preparing them for accelerated reaction to future opportunities. Interestingly, three developmental genes were down-regulated between the control and the opportunity in cleaners only. Our results indicate that the two behavioural types responded differently to the helping opportunity, and that only cleaners responded by down-regulating developmental genes. Read count matrix and treatment information on individualsRead count matrix from RNA-seq experiment of two distinct helper types in the cooperatively breeding cichlid fish Neolamprologus pulcher. 48 individuals in a 2x2 full-factorial design of cleaners and non-cleaners in control and opportunity. 38,2425 genes expressed in the telencephalon 45 min after the onset of the cooperation opportunity.data_Kasper_cichlid_helping_transcriptome.xlsx
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doi: 10.5061/dryad.37jg4
Entrainment of neural oscillations on multiple time scales is important for the perception of speech. Musical rhythms, and in particular the perception of a regular beat in musical rhythms, is also likely to rely on entrainment of neural oscillations. One recently proposed approach to studying beat perception in the context of neural entrainment and resonance (the “frequency-tagging” approach) has received an enthusiastic response from the scientific community. A specific version of the approach involves comparing frequency-domain representations of acoustic rhythm stimuli to the frequency-domain representations of neural responses to those rhythms (measured by electroencephalography, EEG). The relative amplitudes at specific EEG frequencies are compared to the relative amplitudes at the same stimulus frequencies, and enhancements at beat-related frequencies in the EEG signal are interpreted as reflecting an internal representation of the beat. Here, we show that frequency-domain representations of rhythms are sensitive to the acoustic features of the tones making up the rhythms (tone duration, onset/offset ramp duration); in fact, relative amplitudes at beat-related frequencies can be completely reversed by manipulating tone acoustics. Crucially, we show that changes to these acoustic tone features, and in turn changes to the frequency-domain representations of rhythms, do not affect beat perception. Instead, beat perception depends on the pattern of onsets (i.e., whether a rhythm has a simple or complex metrical structure). Moreover, we show that beat perception can differ for rhythms that have numerically identical frequency-domain representations. Thus, frequency-domain representations of rhythms are dissociable from beat perception. For this reason, we suggest caution in interpreting direct comparisons of rhythms and brain signals in the frequency domain. Instead, we suggest that combining EEG measurements of neural signals with creative behavioral paradigms is of more benefit to our understanding of beat perception. single participant behavioral data files.mat files for single participants. README.txt file in each zipped folder describes columnsdryad_data.zip
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doi: 10.34973/b5sq-jy51
We know how age affects the brain during lab-based tasks, but what about situations truer to everyday life, such as watching movies? We measured fMRI activity while participants (N=577) from the Cambridge Centre for Ageing and Neuroscience (www.cam-can.com) watched a movie. Watching the same movie induces significant inter-subject synchronization of brain activity across participants. These cross-subject correlations suggest that viewers are processing incoming information in a similar (or shared) way. We show that with advancing age, synchrony is preserved in some areas, including the language network, but decreased in others, including the medial prefrontal cortex, medial temporal lobe and fronto-parietal network. Synchrony declines were driven by more idiosyncratic responding in older adults and were associated with regionally-distinct temporal profiles and functional connectivity patterns, as well as declines in white matter integrity. These findings suggest that areas involved in language processing remain intact with age, while regions involved in attentional control and memory may show age-related declines, even in situations similar to daily life.
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Certain holographic states of matter with a global U(1) symmetry support a sound mode at zero temperature, caused neither by spontaneous symmetry breaking of the global U(1) nor by the emergence of a Fermi surface in the infrared. In this work, we show that such a mode is also found in zero density holographic quantum critical states. We demonstrate that in these states, the appearance of a zero temperature sound mode is the consequence of a mixed `t Hooft anomaly between the global U(1) symmetry and an emergent higher-form symmetry. At non-zero temperatures, the presence of a black hole horizon weakly breaks the emergent symmetry and gaps the collective mode, giving rise to a sharp Drude-like peak in the electric conductivity. A similar gapped mode arises at low temperatures for non-zero densities when the state has an emergent Lorentz symmetry, also originating from an approximate anomalous higher-form symmetry. However, in this case the collective excitation does not survive at zero temperature where, instead, it dissolves into a branch cut. We comment on the relation between our results and the application of the Luttinger theorem to compressible holographic states of matter.
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