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

The recently observed possibility to suppress the β-relaxation intensity of o-terphenyl by annealing at temperatures below the glass transition guided us to ask, whether the absence of a dielectric β process in many glass-forming materials, e.g., salol (phenyl salicylate), is a matter of the slow cooling rates usually employed to enter the glassy state. In order to assess this issue, we have quenched liquid salol to well below Tg at a rate of dT/dt=−490 K/min. Opposed to the case of cooling rates around −5 K/min or slower, this highly quenched sample displays a symmetric dielectric relaxation peak near f=103 Hz with an appreciable relaxation strength, Δe=6×10−3. This novel feature of salol disappears irreversibly after a temperature excursion towards the glass transition at Tg=220 K.

Dielectric beta relaxations in the glassy state of salol

A model wing based on the geometry of the wing of a barn owl was designed, in which the feather structure of the barn-owl wing is approximated by a velvet-like surface. The first objective of this paper is to investigate the impact of artificial surface filaments on the overall flow field of a quasi-2D configuration of the model 3D wing. Two velvet-like surfaces are used and the velocity field is measured by particle-image velocimetry in a chord-length based Reynolds number range 20 , 000 ≤ R e c ≤ 60 , 000 at angles of attack 0 ° ≤ α ≤ 6 ° . An explanation of the mechanism that leads to the change in the near-wall flow field due to the surface structures is given. The second objective of the paper is the comparison of the 2D and the 3D results and the analysis of the impact of the three-dimensionality on the flow field. The first surface structure (“velvet 1”) mimics the length and density of the hairs and the softness of the natural owl-wing surface. It diminishes the size of the separation bubble or completely prevents separation. However, at three-dimensional flow the effect of the “velvet 1” surface is clearly reduced. The “velvet 2” surface consists of longer and thinner filaments than the “velvet 1” surface. At the lower Reynolds numbers ( R e c ≤ 40 , 000 ), the “velvet 2” surface structure does not alter the near-wall flow field significantly. However, at R e c > 40 , 000 the “velvet 2” surface structure serves as a distributed field of moving roughness elements such that the size of the separation bubble is reduced and becomes nearly independent of the angle of attack. When the three-dimensional flow field at the highest Reynolds number ( R e c = 60 , 000 ) is considered it is evident that the “velvet 2” surface yields the aerodynamically more stable flow field.

Surface structure and dimensional effects on the aerodynamics of an owl-based wing model

The neurophonic is a sound-evoked, frequency-following potential that can be recorded extracellularly in nucleus laminaris of the barn owl. The origin of the neurophonic, and thus the mechanisms th...

https://www.physiology.org/doi/pdf/10.1152/jn.00395.2010

On the origin of the extracellular field potential in the nucleus laminaris of the barn owl (Tyto alba).

Adaptive properties of "hard-wired" neuronal systems

Many organisms use multimodal maps to generate coherent neuronal representations that allow adequate responses to stimuli that excite several sensory modalities. During ontogeny of these maps, one modality typically acts as the dominant system the other modalities are aligned to. A well studied model for the alignment of sensory maps is the calibration of the auditory space map by the visual system in the optic tectum of the barn owl. However, a projection from the optic tectum to the site of plasticity in the auditory pathway that could deliver an instructive signal has not been found so far. We have analyzed the development of the connectivity between the bimodal (visual and auditory) map of space in the barn owl’s optic tectum and the auditory space map in the inferior colliculus with tracing methods and intracellular fills. Neurons in the tectal stratum griseum centrale were found to be suited to deliver an alignment signal from the visual midbrain to the auditory pathway. These neurons are presumably part of the efferent tectal projection pathway that mediates head saccades. The implications of a sensory alignment signal possibly being delivered by a (pre)motor command pathway are discussed.

https://www.jneurosci.org/content/jneuro/20/8/RC70.full.pdf

Hermann Wagner

Papers

Dielectric beta relaxations in the glassy state of salol

Surface structure and dimensional effects on the aerodynamics of an owl-based wing model

On the origin of the extracellular field potential in the nucleus laminaris of the barn owl (Tyto alba).

Adaptive properties of "hard-wired" neuronal systems

A candidate pathway for a visual instructional signal to the barn owl's auditory system.