Adaptive MCMC for Bayesian Variable Selection in Generalised Linear Models and Survival Models.

Developing an efficient computational scheme for high-dimensional Bayesian variable selection in generalised linear models and survival models has always been a challenging problem due to the absence of closed-form solutions to the marginal likelihood. The Reversible Jump Markov Chain Monte Carlo (RJMCMC) approach can be employed to jointly sample models and coefficients, but the effective design of the trans-dimensional jumps of RJMCMC can be challenging, making it hard to implement. Alternatively, the marginal likelihood can be derived conditional on latent variables using a data-augmentation scheme (e.g., Pólya-gamma data augmentation for logistic regression) or using other estimation methods. However, suitable data-augmentation schemes are not available for every generalised linear model and survival model, and estimating the marginal likelihood using a Laplace approximation or a correlated pseudo-marginal method can be computationally expensive. In this paper, three main contributions are presented. Firstly, we present an extended Point-wise implementation of Adaptive Random Neighbourhood Informed proposal (PARNI) to efficiently sample models directly from the marginal posterior distributions of generalised linear models and survival models. Secondly, in light of the recently proposed approximate Laplace approximation, we describe an efficient and accurate estimation method for marginal likelihood that involves adaptive parameters. Additionally, we describe a new method to adapt the algorithmic tuning parameters of the PARNI proposal by replacing Rao-Blackwellised estimates with the combination of a warm-start estimate and the ergodic average. We present numerous numerical results from simulated data and eight high-dimensional genetic mapping data-sets to showcase the efficiency of the novel PARNI proposal compared with the baseline add-delete-swap proposal.

The dynamics of pattern matching in camouflaging cuttlefish.

Many cephalopods escape detection using camouflage1. This behaviour relies on a visual assessment of the surroundings, on an interpretation of visual-texture statistics2-4 and on matching these statistics using millions of skin chromatophores that are controlled by motoneurons located in the brain5-7. Analysis of cuttlefish images proposed that camouflage patterns are low dimensional and categorizable into three pattern classes, built from a small repertoire of components8-11. Behavioural experiments also indicated that, although camouflage requires vision, its execution does not require feedback5,12,13, suggesting that motion within skin-pattern space is stereotyped and lacks the possibility of correction. Here, using quantitative methods14, we studied camouflage in the cuttlefish Sepia officinalis as behavioural motion towards background matching in skin-pattern space. An analysis of hundreds of thousands of images over natural and artificial backgrounds revealed that the space of skin patterns is high-dimensional and that pattern matching is not stereotyped-each search meanders through skin-pattern space, decelerating and accelerating repeatedly before stabilizing. Chromatophores could be grouped into pattern components on the basis of their covariation during camouflaging. These components varied in shapes and sizes, and overlay one another. However, their identities varied even across transitions between identical skin-pattern pairs, indicating flexibility of implementation and absence of stereotypy. Components could also be differentiated by their sensitivity to spatial frequency. Finally, we compared camouflage to blanching, a skin-lightening reaction to threatening stimuli. Pattern motion during blanching was direct and fast, consistent with open-loop motion in low-dimensional pattern space, in contrast to that observed during camouflage.

Polyphasic circadian neural circuits drive differential activities in multiple downstream rhythmic centers.

Circadian clocks align various behaviors such as locomotor activity, sleep/wake, feeding, and mating to times of day that are most adaptive. How rhythmic information in pacemaker circuits is translated to neuronal outputs is not well understood. Here, we used brain-wide, 24-h in vivo calcium imaging in the Drosophila brain and searched for circadian rhythmic activity among identified clusters of dopaminergic (DA) and peptidergic neurosecretory (NS) neurons. Such rhythms were widespread and imposed by the PERIOD-dependent clock activity within the ∼150-cell circadian pacemaker network. The rhythms displayed either a morning (M), evening (E), or mid-day (MD) phase. Different subgroups of circadian pacemakers imposed neural activity rhythms onto different downstream non-clock neurons. Outputs from the canonical M and E pacemakers converged to regulate DA-PPM3 and DA-PAL neurons. E pacemakers regulate the evening-active DA-PPL1 neurons. In addition to these canonical M and E oscillators, we present evidence for a third dedicated phase occurring at mid-day: the l-LNv pacemakers present the MD activity peak, and they regulate the MD-active DA-PPM1/2 neurons and three distinct NS cell types. Thus, the Drosophila circadian pacemaker network is a polyphasic rhythm generator. It presents dedicated M, E, and MD phases that are functionally transduced as neuronal outputs to organize diverse daily activity patterns in downstream circuits.

A pleiotropic chemoreceptor facilitates the production and perception of mating pheromones.

Optimal mating decisions depend on the robust coupling of signal production and perception because independent changes in either could carry a fitness cost. However, since the perception and production of mating signals are often mediated by different tissues and cell types, the mechanisms that drive and maintain their coupling remain unknown for most animal species. Here, we show that in Drosophila, behavioral responses to, and the production of, a putative inhibitory mating pheromone are co-regulated by Gr8a, a member of the Gustatory receptor gene family. Specifically, through behavioral and pheromonal data, we found that Gr8a independently regulates the behavioral responses of males and females to a putative inhibitory pheromone, as well as its production in the fat body and oenocytes of males. Overall, these findings provide a relatively simple molecular explanation for how pleiotropic receptors maintain robust mating signaling systems at the population and species levels.

Circadian pacemaker neurons display cophasic rhythms in basal calcium level and in fast calcium fluctuations.

Circadian pacemaker neurons in the Drosophila brain display daily rhythms in the levels of intracellular calcium. These calcium rhythms are driven by molecular clocks and are required for normal circadian behavior. To study their biological basis, we employed genetic manipulations in conjunction with improved methods of in vivo light-sheet microscopy to measure calcium dynamics in individual pacemaker neurons over complete 24-h durations at sampling frequencies as high as 5 Hz. This technological advance unexpectedly revealed cophasic daily rhythms in basal calcium levels and in high-frequency calcium fluctuations. Further, we found that the rhythms of basal calcium levels and of fast calcium fluctuations reflect the activities of two proteins that mediate distinct forms of calcium fluxes. One is the inositol trisphosphate receptor (ITPR), a channel that mediates calcium fluxes from internal endoplasmic reticulum calcium stores, and the other is a T-type voltage-gated calcium channel, which mediates extracellular calcium influx. These results suggest that Drosophila molecular clocks regulate ITPR and T-type channels to generate two distinct but coupled rhythms in basal calcium and in fast calcium fluctuations. We propose that both internal and external calcium fluxes are essential for circadian pacemaker neurons to provide rhythmic outputs and thereby, regulate the activities of downstream brain centers.

Sex differences in the intrinsic reading neural networks of Chinese children.

Sex differences in reading performance have been considered a relatively stable phenomenon. However, there is no general agreement about their neural basis, which might be due to that sex differences are largely influenced by age. This paper focuses on the sex differences in the reading-related neural network of Chinese children and its interaction with age. We also attempt to predict reading abilities based on neural network. Fifty-three boys and 56 girls (8.2-14.6 years of age) were recruited. We collected their resting-state fMRI and behavioural data. Restricted sex differences were found in the resting-state reading neural network compared to extensive age by sex interaction effect. Specifically, the interactions between sex and age indicated that with increasing age, girls showed greater connectivity strength between visual orthographic areas and other brain areas within the reading network, while boys showed an opposite trend. After controlling age, the prediction models of reading performance for the girls mainly included interhemispheric connections, while the intrahemispheric connections (particularly the phonological route) mainly contributed to predicting the reading ability for boys. Taken together, these findings suggest that sex differences in reading neural networks are modulated by age. Partialling out age, boys and girls also show the stable sex differences in relationship between reading neural circuit and reading behaviour.

Geo-inspired crystallization engineering: multifunctional materials design and fabrication at nanoscale and beyond.

Crystallization engineering aims to design and develop solutions for the optimum conversion of natural resources for use by humans, by using crystallization. Crystallization is a cross-scale process, from atoms, ions and molecules in microscale to bulk crystals in macroscale. Fabricating nanomaterials with desired performances is an open issue with multiscale challenges during crystallization. For innovation in crystallization engineering, geology may provide various sources of inspiration such as structures, compositions and formation conditions, if mineral materials can be regarded as novel artificial materials. This review shows us some geo-inspirations that enable people to create and engineer novel materials with satisfactory performance.

Ce(OH)3 as a novel negative electrode material for supercapacitors.

Novel electrode materials with desired specific capacitances are needed for supercapacitors. Rare-earth (RE)-based materials are fascinating in the field of catalysis and energy. Herein, a series of hydroxides including La, Ce, Pr and Nd was synthesized via in situ precipitation. Interestingly, only Ce(OH)3 showed a redox peak in both positive and negative ranges. The other RE hydroxides exhibited a redox peak only in the positive range. Therefore, in order to certify that Ce(OH)3 can be used as a negative electrode, symmetrical supercapacitors consisting of Ce(OH)3 as both positive and negative electrodes were assembled, and showed a voltage window of 1.3 V. Moreover, asymmetrical supercapacitors were successfully fabricated, in which the positive electrode was composed of La(OH)3, Pr(OH)3 or Nd(OH)3. These results may pave the way to novel negative electrode materials.

Multifunctional inorganic nanomaterials for energy applications.

Our society has been facing more and more serious challenges towards achieving highly efficient utilization of energy. In the field of energy applications, multifunctional nanomaterials have been attracting increasing attention. Various energy applications, such as energy generation, conversion, storage, saving and transmission, are strongly dependent upon the electrical, thermal, mechanical, optical and catalytic functions of materials. In the nanoscale range, thermoelectric, piezoelectric, triboelectric, photovoltaic, catalytic and electrochromic materials have made major contributions to various energy applications. Inorganic nanomaterials' unique properties, such as excellent electrical and thermal conductivity, large surface area and chemical stability, make them highly competitive in energy applications. In this review, the latest research and development of multifunctional inorganic nanomaterials in energy applications were summarized from the perspective of different energy applications. Furthermore, we also illustrated the unique functions of inorganic nanomaterials to improve their performances and the combination of the functions of nanomaterials into a device. However, challenges may be traced back to the limitations set by scaling the relations between multifunctional inorganic nanomaterials and energy devices.

Electronegativity principles in metal oxides based supercapacitors.

To meet growing demands for energy consumptions in modern society, it is necessary to develop different energy sources. Renewable energy such as wind and solar sources are intermittent, therefore, energy storage devices become more and more important to store energy for use when no wind or no light. Supercapacitors play a key role in energy storage, mainly due to their high power density and long cycling life. However, supercapacitors are facing the obstacle of low energy density, one of the most intensive approaches is to rationally design new electrode materials. In this review, we focus on metal oxides-based materials and present an electronegativity criterion for the design and appropriate selection of new electrode chemical compositions. Metal elements with proper electronegativity scale have the potential to transfer electron for energy storage. Suitable positive and negative electrodes matching can enhance many properties of supercapacitors, which may overcome many related obstacles. Furthermore, electronegativity scale may also help people to find novel metal oxides based supercapacitors.

Morning and Evening Circadian Pacemakers Independently Drive Premotor Centers via a Specific Dopamine Relay.

Many animals exhibit morning and evening peaks of locomotor behavior. In Drosophila, two corresponding circadian neural oscillators-M (morning) cells and E (evening) cells-exhibit a corresponding morning or evening neural activity peak. Yet we know little of the neural circuitry by which distinct circadian oscillators produce specific outputs to precisely control behavioral episodes. Here, we show that ring neurons of the ellipsoid body (EB-RNs) display spontaneous morning and evening neural activity peaks in vivo: these peaks coincide with the bouts of locomotor activity and result from independent activation by M and E pacemakers. Further, M and E cells regulate EB-RNs via identified PPM3 dopaminergic neurons, which project to the EB and are normally co-active with EB-RNs. These in vivo findings establish the fundamental elements of a circadian neuronal output pathway: distinct circadian oscillators independently drive a common pre-motor center through the agency of specific dopaminergic interneurons.

A Series of Suppressive Signals within the Drosophila Circadian Neural Circuit Generates Sequential Daily Outputs.

We studied the Drosophila circadian neural circuit using whole-brain imaging in vivo. Five major groups of pacemaker neurons display synchronized molecular clocks, yet each exhibits a distinct phase of daily Ca2+ activation. Light and neuropeptide pigment dispersing factor (PDF) from morning cells (s-LNv) together delay the phase of the evening (LNd) group by ∼12 hr; PDF alone delays the phase of the DN3 group by ∼17 hr. Neuropeptide sNPF, released from s-LNv and LNd pacemakers, produces Ca2+ activation in the DN1 group late in the night. The circuit also features negative feedback by PDF to truncate the s-LNv Ca2+ wave and terminate PDF release. Both PDF and sNPF suppress basal Ca2+ levels in target pacemakers with long durations by cell-autonomous actions. Thus, light and neuropeptides act dynamically at distinct hubs of the circuit to produce multiple suppressive events that create the proper tempo and sequence of circadian pacemaker neuronal activities.

Functional PDF Signaling in the Drosophila Circadian Neural Circuit Is Gated by Ral A-Dependent Modulation.

The neuropeptide PDF promotes the normal sequencing of circadian behavioral rhythms in Drosophila, but its signaling mechanisms are not well understood. We report daily rhythmicity in responsiveness to PDF in critical pacemakers called small LNvs. There is a daily change in potency, as great as 10-fold higher, around dawn. The rhythm persists in constant darkness and does not require endogenous ligand (PDF) signaling or rhythmic receptor gene transcription. Furthermore, rhythmic responsiveness reflects the properties of the pacemaker cell type, not the receptor. Dopamine responsiveness also cycles, in phase with that of PDF, in the same pacemakers, but does not cycle in large LNv. The activity of RalA GTPase in s-LNv regulates PDF responsiveness and behavioral locomotor rhythms. Additionally, cell-autonomous PDF signaling reversed the circadian behavioral effects of lowered RalA activity. Thus, RalA activity confers high PDF responsiveness, providing a daily gate around the dawn hours to promote functional PDF signaling.

Importin-7 mediates memory consolidation through regulation of nuclear translocation of training-activated MAPK in Drosophila.

Translocation of signaling molecules, MAPK in particular, from the cytosol to nucleus represents a universal key element in initiating the gene program that determines memory consolidation. Translocation mechanisms and their behavioral impact, however, remain to be determined. Here, we report that a highly conserved nuclear transporter, Drosophila importin-7 (DIM-7), regulates import of training-activated MAPK for consolidation of long-term memory (LTM). We show that silencing DIM-7 functions results in impaired LTM, whereas overexpression of DIM-7 enhances LTM. This DIM-7-dependent regulation of LTM is confined to a consolidation time window and in mushroom body neurons. Image data show that bidirectional alteration in DIM-7 expression results in proportional changes in the intensity of training-activated MAPK accumulated within the nuclei of mushroom body neurons during LTM consolidation. Such DIM-7-regulated nuclear accumulation of activated MAPK is observed only in the training specified for LTM induction and determines the amplitude, but not the time course, of memory consolidation.

Synchronous Drosophila circadian pacemakers display nonsynchronous Ca²âº rhythms in vivo.

In Drosophila, molecular clocks control circadian rhythmic behavior through a network of ~150 pacemaker neurons. To explain how the network's neuronal properties encode time, we performed brainwide calcium imaging of groups of pacemaker neurons in vivo for 24 hours. Pacemakers exhibited daily rhythmic changes in intracellular Ca(2+) that were entrained by environmental cues and timed by molecular clocks. However, these rhythms were not synchronous, as each group exhibited its own phase of activation. Ca(2+) rhythms displayed by pacemaker groups that were associated with the morning or evening locomotor activities occurred ~4 hours before their respective behaviors. Loss of the receptor for the neuropeptide PDF promoted synchrony of Ca(2+) waves. Thus, neuropeptide modulation is required to sequentially time outputs from a network of synchronous molecular pacemakers.