The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

I have developed "tennis elbow" from lugging this book around the past four weeks, but it is worth the pain, the effort, and the aspirin. It is also worth the (relatively speaking) bargain price. Including appendixes, this book contains 894 pages of text. The entire panorama of the neural sciences is surveyed and examined, and it is comprehensive in its scope, from genomes to social behaviors. The editors explicitly state that the book is designed as "an introductory text for students of biology, behavior, and medicine," but it is hard to imagine any audience, interested in any fragment of neuroscience at any level of sophistication, that would not enjoy this book. The editors have done a masterful job of weaving together the biologic, the behavioral, and the clinical sciences into a single tapestry in which everyone from the molecular biologist to the practicing psychiatrist can find and appreciate his or

Principles of Neural Science

Neurons in the brain communicate by short electrical pulses, the so-called action potentials or spikes. How can we understand the process of spike generation? How can we understand information transmission by neurons? What happens if thousands of neurons are coupled together in a seemingly random network? How does the network connectivity determine the activity patterns? And, vice versa, how does the spike activity influence the connectivity pattern? These questions are addressed in this 2002 introduction to spiking neurons aimed at those taking courses in computational neuroscience, theoretical biology, biophysics, or neural networks. The approach will suit students of physics, mathematics, or computer science; it will also be useful for biologists who are interested in mathematical modelling. The text is enhanced by many worked examples and illustrations. There are no mathematical prerequisites beyond what the audience would meet as undergraduates: more advanced techniques are introduced in an elementary, concrete fashion when needed.

/pdf/spiking-neuron-models-single-neurons-populations-plasticity-58gzrd6ih6.pdf

Spiking Neuron Models: Single Neurons, Populations, Plasticity

中枢神経系疾患の治療は正常細胞（ニューロン）の機能維持を目的とするが，脳血管障害のように機能障害の原因が細胞の死滅に基づくことは多い．一方，脳腫瘍の治療においては薬物療法や放射線療法といった腫瘍細胞の死滅を目標とするものが大きな位置を占める．いずれの場合にも，細胞死の機序を理解することは各種病態や治療法の理解のうえで重要である．現在のところ最も研究の進んでいる細胞死の型はアポトーシスである．そのなかで重要な位置を占めるミトコンドリアにおける反応および抗アポトーシス因子について概要を紹介する．

Neuroscience 細胞死：最近の知見

Hebbian models of development and learning require both activity-dependent synaptic plasticity and a mechanism that induces competition between different synapses. One form of experimentally observed long-term synaptic plasticity, which we call spike-timing-dependent plasticity (STDP), depends on the relative timing of pre- and postsynaptic action potentials. In modeling studies, we find that this form of synaptic modification can automatically balance synaptic strengths to make postsynaptic firing irregular but more sensitive to presynaptic spike timing. It has been argued that neurons in vivo operate in such a balanced regime. Synapses modifiable by STDP compete for control of the timing of postsynaptic action potentials. Inputs that fire the postsynaptic neuron with short latency or that act in correlated groups are able to compete most successfully and develop strong synapses, while synapses of longer-latency or less-effective inputs are weakened.

/pdf/competitive-hebbian-learning-through-spike-timing-dependent-17innjp0ag.pdf

Competitive Hebbian learning through spike-timing-dependent synaptic plasticity

This work describes a novel mechanism of laminar flow control of straight and backward swept wings with a comb-like leading edge device. It is inspired by the leading-edge comb on owl feathers and the special design of its barbs, resembling a cascade of complex 3D-curved thin finlets. The details of the geometry of the barbs from an owl feather were used to design a generic model of the comb for experimental and numerical flow studies with the comb attached to the leading edge of a flat plate. Due to the owls demonstrating a backward sweep of the wing during gliding and flapping from live recordings, our examinations have also been carried out at differing sweep angles. The results demonstrate a flow turning effect in the boundary layer inboards, which extends downstream in the chordwise direction over distances of multiples of the barb lengths. The inboard flow-turning effect described here, counter-acts the outboard directed cross-span flow typically appearing for backward swept wings. This flow turning behavior is also shown on SD7003 airfoil using precursory LES investigations. From recent theoretical studies on a swept wing, such a way of turning the flow in the boundary layer is known to attenuate crossflow instabilities and delay transition. A comparison of the comb-induced cross-span velocity profiles with those proven to delay laminar to turbulent transition in theory shows excellent agreement, which supports the laminar flow control hypothesis. Thus, the observed effect is expected to delay transition in owl flight, contributing to a more silent flight.

https://iopscience.iop.org/article/10.1088/1748-3190/abc6b4/pdf

Flow turning effect and laminar control by the 3D curvature of leading edge serrations from owl wing

Barn owls do not immediately approach a source after they hear a sound, but wait for a second sound before they strike. This represents a gain in striking behavior by avoiding responses to random incidents. However, the first stimulus is also expected to change the threshold for perceiving the subsequent second sound, thus possibly introducing some costs. We mimicked this situation in a behavioral double-stimulus paradigm utilizing saccadic head turns of owls. The first stimulus served as an adapter, was presented in frontal space, and did not elicit a head turn. The second stimulus, emitted from a peripheral source, elicited the head turn. The time interval between both stimuli was varied. Data obtained with double stimulation were compared with data collected with a single stimulus from the same positions as the second stimulus in the double-stimulus paradigm. Sound-localization performance was quantified by the response latency, accuracy, and precision of the head turns. Response latency was increased with double stimuli, while accuracy and precision were decreased. The effect depended on the inter-stimulus interval. These results suggest that waiting for a second stimulus may indeed impose costs on sound localization by adaptation and this reduces the gain obtained by waiting for a second stimulus.

Influence of double stimulation on sound-localization behavior in barn owls.

Barn owls move their heads in very particular motions, compensating for the quasi-immovability of their eyes. These efficient predators often perform peering side-to-side head motions when scanning their surroundings and seeking prey. In this work, we use the head movements of barn owls as a model to bridge between biological active vision and machine vision. The biomotions are measured and used to actuate a specially built robot equipped with a depth camera for scanning. We hypothesize that the biomotions improve scan accuracy of static objects. Our experiments show that barn owl biomotion-based trajectories consistently improve scan accuracy when compared to intuitive scanning motions. This constitutes proof-of-concept evidence that the vision of robotic systems can be enhanced by bio-inspired viewpoint manipulation. Such biomimetic scanning systems can have many applications, e.g. manufacturing inspection or in autonomous robots.

https://iopscience.iop.org/article/10.1088/1748-3190/aa7728/pdf

From biokinematics to a robotic active vision system.

We have investigated the orientational behavior of a series of novel oligophenylenevinylenes which carry a sequence of hyperpolarizable and dipolar donor−acceptor (DA) pairs, designed to allow for a free rotation of the DA orientation in a plane perpendicular to the long molecular axis. The studies include both the measurement of effective dipole moments, which are relevant for the degree of polar ordering required for second-harmonic generation, and the assessment of the time scales involved in the orientational motion of the effective dipole moment. The comparison between calculated dipole moments and those measured for different oligomers in toluene solution and in a polystyrene matrix confirm that a DA-pair separation of ≈10 A along the oligomer leads to a high chromophore concentration in the sample, yet without the unfavorable effect of aggregation or antiparallel alignment of neighboring dipole pairs. Both the bulkiness of the oligomer molecules and the electrostatic coupling of adjacent dipoles gi...

Orientation and Dynamics of Chainlike Dipole Arrays: Donor-Acceptor-Substituted Oligophenylenevinylenes in a Polymer Matrix

Comparative neuroethological research emphasizes that brains of animals have been shaped by the specific demands and constraints imposed by the ecological niche that a species occupies. Since avian species have developed very diverse life styles and occupy extreme ecological niches, bird brains should show many specializations, which may be revealed in species that have survived under high ecological pressures. In this paper, we will give several examples of adaptations, in which we are able to correlate structural and physiological spe­cializations to the specific ecological demands: adaptations found to nocturnal hunting in barn owls, the characteristics of bird song and its underlying neurobiological correlates, retinopetal projections and their relation to peripheral attentional switching, looming detection, and adaptations related to memory capacities of food-storing birds. We stress especially that the analysis of the animal’s ecological situation is important in understanding the factors that shaped both behavior and the neuronal substrate.

Hermann Wagner

Papers

Flow turning effect and laminar control by the 3D curvature of leading edge serrations from owl wing

Influence of double stimulation on sound-localization behavior in barn owls.

From biokinematics to a robotic active vision system.

Orientation and Dynamics of Chainlike Dipole Arrays: Donor-Acceptor-Substituted Oligophenylenevinylenes in a Polymer Matrix

Effect of ecological pressures on brains : examples from avian neuroethology and general meanings