Multistability in Large Scale Models of Brain Activity

Noise driven exploration of a brain network’s dynamic repertoire has been hypothesized to be causally involved in cognitive function, aging and neurodegeneration. The dynamic repertoire crucially depends on the network’s capacity to store patterns, as well as their stability. Here we systematically explore the capacity of networks derived from human connectomes to store attractor states, as well as various network mechanisms to control the brain’s dynamic repertoire. Using a deterministic graded response Hopfield model with connectome-based interactions, we reconstruct the system’s attractor space through a uniform sampling of the initial conditions. Large fixed-point attractor sets are obtained in the low temperature condition, with a bigger number of attractors than ever reported so far. Different variants of the initial model, including (i) a uniform activation threshold or (ii) a global negative feedback, produce a similarly robust multistability in a limited parameter range. A numerical analysis of the distribution of the attractors identifies spatially-segregated components, with a centro-medial core and several well-delineated regional patches. Those different modes share similarity with the fMRI independent components observed in the “resting state” condition. We demonstrate non-stationary behavior in noise-driven generalizations of the models, with different meta-stable attractors visited along the same time course. Only the model with a global dynamic density control is found to display robust and long-lasting non-stationarity with no tendency toward either overactivity or extinction. The best fit with empirical signals is observed at the edge of multistability, a parameter region that also corresponds to the highest entropy of the attractors.     

AN ULTRASTRUCTURAL SURVEY OF CRYPTOMONAD PERIPLASTS USING QUICK-FREEZING FREEZE FRACTURE TECHNIQUES1

A quick-freezing technique for freeze fracturing was used to determine periplast plate types in 20 cryptomonads. With this technique cells are frozen so rapidly that major artifacts are eliminated. We propose that periplast plates are attached to the cell membrane by intramembrane particles (IMP's), consequently plate shapes are outlined by IMP distribution in fractured membranes. Round to oval, sometimes slightly angular, plates occur in Cryptomonas ovata, Cryptomonas tetrapyrenoidosa, Cryptomonas parapyrenoidifera, Cryptomonas obovata, Cryptomonas erosa and two unidentified species of Cryptomonas; large rectangular plates occur in Chroomonas pochmannii, Chroomonas coerulea and Hemiselmis sp.; small rectangular plates were found in Cryptomonas sp. (Strain SDB); square to slightly rounded plates occur in Cryptomonas chrysoidea and a single continuous plate or sheet, perforated by ejectisome pores, was observed in Cryptomonas caudata, Cryptomonas rostratiformis, Cryptomonas marssonii, Cryptomonas platyuris, Cryptomonas curvata, Cryptomonas ozolini, Chilomonas paramecium and Rhodomonas sp. Oval and square plates are described for the first time in Cryptomonas. Plate IMP's may be morphologically modified in size and shape, depending upon their location in relation to the plate, the plate ridges, and ejectisome chambers. Conformational changes in plate shapes, to form hexagons or polygons, may be induced when cells are subjected to fixation, desiccation, cryoprotectants or centrifugation.     

Quantitative Study of the Elastic Modulus of Loosely Attached Cells in AFM Indentation Experiments

When measuring the elastic (Young’s) modulus of cells using AFM, good attachment of cells to a substrate is paramount. However, many cells cannot be firmly attached to many substrates. A loosely attached cell is more compliant under indenting. It may result in artificially low elastic modulus when analyzed with the elasticity models assuming firm attachment. Here we suggest an AFM-based method/model that can be applied to extract the correct Young’s modulus of cells loosely attached to a substrate. The method is verified by using primary breast epithelial cancer cells (MCF-7) at passage 4. At this passage, approximately one-half of cells develop enough adhesion with the substrate to be firmly attached to the substrate. These cells look well spread. The other one-half of cells do not develop sufficient adhesion, and are loosely attached to the substrate. These cells look spherical. When processing the AFM indentation data, a straightforward use of the Hertz model results in a substantial difference of the Young’s modulus between these two types of cells. If we use the model presented here, we see no statistical difference between the values of the Young’s modulus of both poorly attached (round) and firmly attached (close to flat) cells. In addition, the presented model allows obtaining parameters of the brush surrounding the cells. The cellular brush observed is also statistically identical for both types of cells. The method described here can be applied to study mechanics of many other types of cells loosely attached to substrates, e.g., blood cells, some stem cells, cancerous cells, etc.     

From Schooling to Shoaling: Patterns of Collective Motion in Zebrafish (Danio rerio)

Animal groups on the move can take different configurations. For example, groups of fish can either be ‘shoals’ or ‘schools’: shoals are simply aggregations of individuals; schools are shoals exhibiting polarized, synchronized motion. Here we demonstrate that polarization distributions of groups of zebrafish (Danio rerio) are bimodal, showing two distinct modes of collective motion corresponding to the definitions of shoaling and schooling. Other features of the group''s motion also vary consistently between the two modes: zebrafish schools are faster and less dense than zebrafish shoals. Habituation to an environment can also alter the proportion of time zebrafish groups spend schooling or shoaling. Models of collective motion suggest that the degree and stability of group polarization increases with the group''s density. Examining zebrafish groups of different sizes from 5 to 50, we show that larger groups are less polarized than smaller groups. Decreased fearfulness in larger groups may function similarly to habituation, causing them to spend more time shoaling than schooling, contrary to most models'' predictions.     

Minibrain kinase and calcineurin coordinate activity-dependent bulk endocytosis through synaptojanin

Neurons use multiple modes of endocytosis, including clathrin-mediated endocytosis (CME) and activity-dependent bulk endocytosis (ADBE), during mild and intense neuronal activity, respectively, to maintain stable neurotransmission. While molecular players modulating CME are well characterized, factors regulating ADBE and mechanisms coordinating CME and ADBE activations remain poorly understood. Here we report that Minibrain/DYRK1A (Mnb), a kinase mutated in autism and up-regulated in Down’s syndrome, plays a novel role in suppressing ADBE. We demonstrate that Mnb, together with calcineurin, delicately coordinates CME and ADBE by controlling the phosphoinositol phosphatase activity of synaptojanin (Synj) during varying synaptic demands. Functional domain analyses reveal that Synj’s 5′-phosphoinositol phosphatase activity suppresses ADBE, while SAC1 activity is required for efficient ADBE. Consequently, Parkinson’s disease mutation in Synj’s SAC1 domain impairs ADBE. These data identify Mnb and Synj as novel regulators of ADBE and further indicate that CME and ADBE are differentially governed by Synj’s dual phosphatase domains.     

Analysing and meta-analysing time-series data of microbial growth and gene expression from plate readers

Responding to change is a fundamental property of life, making time-series data invaluable in biology. For microbes, plate readers are a popular, convenient means to measure growth and also gene expression using fluorescent reporters. Nevertheless, the difficulties of analysing the resulting data can be a bottleneck, particularly when combining measurements from different wells and plates. Here we present omniplate, a Python module that corrects and normalises plate-reader data, estimates growth rates and fluorescence per cell as functions of time, calculates errors, exports in different formats, and enables meta-analysis of multiple plates. The software corrects for autofluorescence, the optical density’s non-linear dependence on the number of cells, and the effects of the media. We use omniplate to measure the Monod relationship for the growth of budding yeast in raffinose, showing that raffinose is a convenient carbon source for controlling growth rates. Using fluorescent tagging, we study yeast’s glucose transport. Our results are consistent with the regulation of the hexose transporter (HXT) genes being approximately bipartite: the medium and high affinity transporters are predominately regulated by both the high affinity glucose sensor Snf3 and the kinase complex SNF1 via the repressors Mth1, Mig1, and Mig2; the low affinity transporters are predominately regulated by the low affinity sensor Rgt2 via the co-repressor Std1. We thus demonstrate that omniplate is a powerful tool for exploiting the advantages offered by time-series data in revealing biological regulation.     

Recognizing Sequences of Sequences

The brain''s decoding of fast sensory streams is currently impossible to emulate, even approximately, with artificial agents. For example, robust speech recognition is relatively easy for humans but exceptionally difficult for artificial speech recognition systems. In this paper, we propose that recognition can be simplified with an internal model of how sensory input is generated, when formulated in a Bayesian framework. We show that a plausible candidate for an internal or generative model is a hierarchy of ‘stable heteroclinic channels’. This model describes continuous dynamics in the environment as a hierarchy of sequences, where slower sequences cause faster sequences. Under this model, online recognition corresponds to the dynamic decoding of causal sequences, giving a representation of the environment with predictive power on several timescales. We illustrate the ensuing decoding or recognition scheme using synthetic sequences of syllables, where syllables are sequences of phonemes and phonemes are sequences of sound-wave modulations. By presenting anomalous stimuli, we find that the resulting recognition dynamics disclose inference at multiple time scales and are reminiscent of neuronal dynamics seen in the real brain.     

Attachment and Children’s Biased Attentional Processing: Evidence for the Exclusion of Attachment-Related Information

Research in both infants and adults demonstrated that attachment expectations are associated with the attentional processing of attachment-related information. However, this research suffered from methodological issues and has not been validated across ages. Employing a more ecologically valid paradigm to measure attentional processes by virtue of eye tracking, the current study tested the defensive exclusion hypothesis in late childhood. According to this hypothesis, insecurely attached children are assumed to defensively exclude attachment-related information. We hypothesized that securely attached children process attachment- related neutral and emotional information in a more open manner compared to insecurely attached children. Sixty-two children (59.7% girls, 8–12 years) completed two different tasks, while eye movements were recorded: task one presented an array of neutral faces including mother and unfamiliar women and task two presented the same with happy and angry faces. Results indicated that more securely attached children looked longer at mother’s face regardless of the emotional expression. Also, they tend to have more maintained attention to mother’s neutral face. Furthermore, more attachment avoidance was related to a reduced total viewing time of mother’s neutral, happy, and angry face. Attachment anxiety was not consistently related to the processing of mother’s face. Findings support the theoretical assumption that securely attached children have an open manner of processing all attachment-related information.     

How do changes to plate thickness, length, and face-connectivity affect femoral cancellous bone's density and surface area? An investigation using regular cellular models

Models of regular cellular-solids representing femoral head 'medial group' bone were used to (1) compare thickness data for plate-like and beam-like structures at realistic surface areas and densities; (2) test the validity of a standard formula for trabecular thickness (Tb.Th); and (3) study how systematic changes in cancellous bone thicknesses, spacing, and face-connectivity affect relative density and surface area. Models of different face-connectivities, produced by plate removal from the unit cell, were fitted to bone density and surface area data. The medial group bone was anisotropic: the supero-inferior (SI) direction was the principal direction for bone plate alignment and the plane normal to this had the largest number of bone/void intersections per unit line length (P(I)). A comparison of boundary perimeter per unit area data, in planes normal to SI, with surface area data placed the medial group bone between prismatic structures in which walls are parallel to one principal direction and isotropic structures. Selective removal of plates from a closed-cell model produced a similar result. For the same relative density and surface-area, plate-like models had significantly thinner cross-sections than beam-like models. The formula for Tb.Th produced overestimates of model plate thickness by up to 20% at realistic femoral cancellous densities. Trends in data on surface area to volume ratio and density observed on sampled medial group bone could be simulated by plate thickness changes on models of intermediate face-connectivity (approximately 1.5) or by plate removal from models with relatively thick and short (low aspect-ratio) plates. The latter mechanism is unrealistic for it resulted in beam-like structures at low 'medial group' densities, an architecture unlike the predominantly plate-like bone in the sample.     

Transverse stresses and modes of failure in tree branches and other beams

The longitudinal stresses in beams subjected to bending also set up transverse stresses within them; they compress the cross section when the beam''s curvature is being increased and stretch it when its curvature is being reduced. Analysis shows that transverse stresses rise to a maximum at the neutral axis and increase with both the bending moment applied and the curvature of the beam. These stresses can qualitatively explain the fracture behaviour of tree branches. Curved ‘hazard beams’ that are being straightened split down the middle because of the low transverse tensile strength of wood. By contrast, straight branches of light wood buckle when they are bent because of its low transverse compressive strength. Branches of denser wood break, but the low transverse tensile strength diverts the crack longitudinally when the fracture has only run half-way across the beam, to produce their characteristic ‘greenstick fracture’. The bones of young mammals and uniaxially reinforced composite beams may also be prone to greenstick fracture because of their lower transverse tensile strength.     

Fast and accurate specimen-specific simulation of trabecular bone elastic modulus using novel beam-shell finite element models

Elastic modulus and strength of trabecular bone are negatively affected by osteoporosis and other metabolic bone diseases. Micro-computed tomography-based beam models have been presented as a fast and accurate way to determine bone competence. However, these models are not accurate for trabecular bone specimens with a high number of plate-like trabeculae. Therefore, the aim of this study was to improve this promising methodology by representing plate-like trabeculae in a way that better reflects their mechanical behavior. Using an optimized skeletonization and meshing algorithm, voxel-based models of trabecular bone samples were simplified into a complex structure of rods and plates. Rod-like and plate-like trabeculae were modeled as beam and shell elements, respectively, using local histomorphometric characteristics. To validate our model, apparent elastic modulus was determined from simulated uniaxial elastic compression of 257 cubic samples of trabecular bone (4mm×4mm×4mm; 30μm voxel size; BIOMED I project) in three orthogonal directions using the beam-shell models and using large-scale voxel models that served as the gold standard. Excellent agreement (R(2)=0.97) was found between the two, with an average CPU-time reduction factor of 49 for the beam-shell models. In contrast to earlier skeleton-based beam models, the novel beam-shell models predicted elastic modulus values equally well for structures from different skeletal sites. It allows performing detailed parametric analyses that cover the entire spectrum of trabecular bone microstructures.     

Neurokernel: An Open Source Platform for Emulating the Fruit Fly Brain

We have developed an open software platform called Neurokernel for collaborative development of comprehensive models of the brain of the fruit fly Drosophila melanogaster and their execution and testing on multiple Graphics Processing Units (GPUs). Neurokernel provides a programming model that capitalizes upon the structural organization of the fly brain into a fixed number of functional modules to distinguish between these modules’ local information processing capabilities and the connectivity patterns that link them. By defining mandatory communication interfaces that specify how data is transmitted between models of each of these modules regardless of their internal design, Neurokernel explicitly enables multiple researchers to collaboratively model the fruit fly’s entire brain by integration of their independently developed models of its constituent processing units. We demonstrate the power of Neurokernel’s model integration by combining independently developed models of the retina and lamina neuropils in the fly’s visual system and by demonstrating their neuroinformation processing capability. We also illustrate Neurokernel’s ability to take advantage of direct GPU-to-GPU data transfers with benchmarks that demonstrate scaling of Neurokernel’s communication performance both over the number of interface ports exposed by an emulation’s constituent modules and the total number of modules comprised by an emulation.     

Dense chromatin plates in metaphase chromosomes

In a previous work we observed multilayered plate-like structures surrounding partially denatured HeLa chromosomes at metaphase ionic conditions. This unexpected finding has led us to carry out an extensive investigation of these structures. Our results show that plates can also be found in metaphase chromosomes from chicken lymphocytes. We have used atomic force microscopy (AFM) to image and investigate the mechanical properties of plates in aqueous solution. Plates are thin (~6.5 nm each layer) but compact and resistant to penetration by the AFM tip: their Young’s modulus is ~0.2 GPa and the stress required for surface penetration is ~0.03 GPa in the presence of Mg²⁺ (5–20 mM). Low-ionic strength conditions produce emanation of chromatin fibers from the edges of uncrosslinked plates. These observations and AFM results obtained applying high forces indicate that the chromatin filament is tightly tethered inside the plates. Images of metal-shadowed plates and cryo-electron microscopy images of frozen-hydrated plates suggest that nucleosomes are tilted with respect to the plate surface to allow an interdigitation between the successive layers and a thickness reduction compatible with the observed plate height. The similarities between denatured plates from chicken chromosomes and aggregates of purified chromatin from chicken erythrocytes suggest that chromatin has intrinsic structural properties leading to plate formation. Scanning electron micrographs and images obtained with the 200-kV transmission microscope show that plates are the dominant component of compact chromatids. We propose that metaphase chromosomes are formed by many stacked plates perpendicular to the chromatid axis.     

The Contribution of Qualitative CEUS to the Determination of Malignancy in Adnexal Masses,Indeterminate on Conventional US – A Multicenter Study

The aim of this study is to evaluate the efficacy of qualitative analysis of contrast-enhanced ultrasound (CEUS) in discrimination of adnexal masses which were undetermined by conventional ultrasound (US). A total of 120 patients underwent transabdominal CEUS. The initial enhancement time and intensity compared with the uterine myometrium, contrast agent distribution patterns and dynamic changes of enhancement were assessed. The sensitivity (Sen), specificity (Spe), positive predictive value (PPV), negative predictive value (NPV), accuracy (ACC) and Youden’s index were calculated for contrast variables. The gold standard was the histological diagnosis. There were 48 malignant tumors and 72 benign tumors. The enhancement features of malignant masses were different from benign ones. Earlier or simultaneous enhancement with inhomogeneous enhancement yielded the highest capability in differential diagnosis, and Sen, Spe, PPV, NPV, ACC, Youden’s index was 89.6%, 97.2%, 93.2%, 95.6%, 93.3%, and 0.88, respectively. The qualitative evaluation of CEUS is useful in the differential diagnosis of adnexal masses where conventional US is indeterminate.     

Structural Characteristics of Allomyrina Dichotoma Beetle＇s Hind Wings for Flapping Wing Micro Air Vehicle

In this study, we present a complete structural analysis ofAllomyrina dichotoma beetle＇s hind wings by investigating their static and dynamic characteristics. The wing was subjected to the static loading to determine its overall flexural stiffness. Dy- namic characteristics such as natural frequency, mode shape, and damping ratio of vibration modes in the operating frequency range were determined using a Bruel ＆ Kjaer fast Fourier transform analyzer along with a laser sensor. The static and dynamic characteristics of natural Allomyrina dichotoma beetle＇s hind wings were compared to those of a fabricated artificial wing. The results indicate that natural frequencies of the natural wing were significantly correlated to the wing surface area density that was defined as the wing mass divided by the hind wing surface area. Moreover, the bending behaviors of the natural wing and artificial wing were similar to that of a cantilever beam. Furthermore, the flexural stiffness of the artificial wing was a little higher than that of the natural one whereas the natural frequency of the natural wing was close to that of the artificial wing. These results provide important information for the biomimetic design of insect-scale artificial wings, with which highly ma- neuverable and efficient micro air vehicles can be designed.     

Development of a New Method to Track Multiple Honey Bees with Complex Behaviors on a Flat Laboratory Arena

A computer program that tracks animal behavior, thereby revealing various features and mechanisms of social animals, is a powerful tool in ethological research. Because honeybee colonies are populated by thousands of bees, individuals co-exist in high physical densities and are difficult to track unless specifically tagged, which can affect behavior. In addition, honeybees react to light and recordings must be made under special red-light conditions, which the eyes of bees perceive as darkness. The resulting video images are scarcely distinguishable. We have developed a new algorithm, K-Track, for tracking numerous bees in a flat laboratory arena. Our program implements three main processes: (A) The object (bee''s) region is detected by simple threshold processing on gray scale images, (B) Individuals are identified by size, shape and spatiotemporal positional changes, and (C) Centers of mass of identified individuals are connected through all movie frames to yield individual behavioral trajectories. The tracking performance of our software was evaluated on movies of mobile multi-artificial agents and of 16 bees walking around a circular arena. K-Track accurately traced the trajectories of both artificial agents and bees. In the latter case, K-track outperformed Ctrax, well-known software for tracking multiple animals. To investigate interaction events in detail, we manually identified five interaction categories; ‘crossing’, ‘touching’, ‘passing’, ‘overlapping’ and ‘waiting’, and examined the extent to which the models accurately identified these categories from bee''s interactions. All 7 identified failures occurred near a wall at the outer edge of the arena. Finally, K-Track and Ctrax successfully tracked 77 and 60 of 84 recorded interactive events, respectively. K-Track identified multiple bees on a flat surface and tracked their speed changes and encounters with other bees, with good performance.     

Chemical nanoprinting: a novel method for fabricating DNA microchips

We have developed a novel cost-effective procedure, namely ‘chemical nanoprinting’, for oligonucleotide or cDNA chips manufacture. In this thermo-controlled process, the oligonucleotides, covalently attached to a highly loaded ‘master-chip’ through disulfide bonds, are chemically transferred to the acrylamide layer mounted on a ‘print-chip’. It is demonstrated here that multiple identical print-chips can be produced from a single master-chip. This duplication process is a few hundreds of times faster than any existing methods and the speed of process and cost incurred are independent of the scale of the DNA chips.     

A Linear City Model with Asymmetric Consumer Distribution

The article analyzes a linear-city model where the consumer distribution can be asymmetric, which is important because in real markets this distribution is often asymmetric. The model yields equilibrium price differences, even though the firms’ costs are equal and their locations are symmetric (at the two endpoints of the city). The equilibrium price difference is proportional to the transportation cost parameter and does not depend on the good''s cost. The firms'' markups are also proportional to the transportation cost. The two firms’ prices will be equal in equilibrium if and only if half of the consumers are located to the left of the city’s midpoint, even if other characteristics of the consumer distribution are highly asymmetric. An extension analyzes what happens when the firms have different costs and how the two sources of asymmetry – the consumer distribution and the cost per unit – interact together. The model can be useful as a tool for further development by other researchers interested in applying this simple yet flexible framework for the analysis of various topics.     

Hybrid Epidemics—A Case Study on Computer Worm Conficker

Conficker is a computer worm that erupted on the Internet in 2008. It is unique in combining three different spreading strategies: local probing, neighbourhood probing, and global probing. We propose a mathematical model that combines three modes of spreading: local, neighbourhood, and global, to capture the worm’s spreading behaviour. The parameters of the model are inferred directly from network data obtained during the first day of the Conficker epidemic. The model is then used to explore the tradeoff between spreading modes in determining the worm’s effectiveness. Our results show that the Conficker epidemic is an example of a critically hybrid epidemic, in which the different modes of spreading in isolation do not lead to successful epidemics. Such hybrid spreading strategies may be used beneficially to provide the most effective strategies for promulgating information across a large population. When used maliciously, however, they can present a dangerous challenge to current internet security protocols.     

Cytokinesis in tobacco BY-2 and root tip cells: a new model of cell plate formation in higher plants

Cell plate formation in tobacco root tips and synchronized dividing suspension cultured tobacco BY-2 cells was examined using cryofixation and immunocytochemical methods. Due to the much improved preservation of the cells, many new structural intermediates have been resolved, which has led to a new model of cell plate formation in higher plants. Our electron micrographs demonstrate that cell plate formation consists of the following stages: (1) the arrival of Golgi-derived vesicles in the equatorial plane, (2) the formation of thin (20 +/- 6 nm) tubes that grow out of individual vesicles and fuse with others giving rise to a continuous, interwoven, tubulo-vesicular network, (3) the consolidation of the tubulo-vesicular network into an interwoven smooth tubular network rich in callose and then into a fenestrated plate-like structure, (4) the formation of hundreds of finger-like projections at the margins of the cell plate that fuse with the parent cell membrane, and (5) cell plate maturation that includes closing of the plate fenestrae and cellulose synthesis. Although this is a temporal chain of events, a developing cell plate may be simultaneously involved in all of these stages because cell plate formation starts in the cell center and then progresses centrifugally towards the cell periphery. The "leading edge" of the expanding cell plate is associated with the phragmoplast microtubule domain that becomes concentrically displaced during this process. Thus, cell plate formation can be summarized into two phases: first the formation of a membrane network in association with the phragmoplast microtubule domain; second, cell wall assembly within this network after displacement of the microtubules. The phragmoplast microtubules end in a filamentous matrix that encompasses the delicate tubulo-vesicular networks but not the tubular networks and fenestrated plates. Clathrin-coated buds/vesicles and multivesicular bodies are also typical features of the network stages of cell plate formation, suggesting that excess membrane material may be recycled in a selective manner. Immunolabeling data indicate that callose is the predominant lumenal component of forming cell plates and that it forms a coat-like structure on the membrane surface. We postulate that callose both helps to mechanically stabilize the early delicate membrane networks of forming cell plates, and to create a spreading force that widens the tubules and converts them into plate-like structures. Cellulose is first detected in the late smooth tubular network stage and its appearance seems to coincide with the flattening and stiffening of the cell plate.