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

WE experience the visual world as being three-dimensional. A major source of depth information derives from the slightly different views of each eye, leading to small variations in the retinal images ('disparities')' Neurons sensitive to visual disparities are thought to form the neural basis of stereo vision1–10. Barn owls2,3 as well as several mammalian species1,4–10 have neurons that are sensitive to visual disparities. But how visual disparities are represented in the brain has been a matter of discussion ever since the first disparity-sensitive neurons were found some 25 years ago. Here we adopt a new approach to this problem and study the neural computation of visual disparities with a paradigm borrowed from auditory research. The measurement of interaural time difference (ITD) has many similarities with the measurement of visual disparity on the formal, algorithmic level. We speculate that the similarities might extend to the level of neural computation. The neural representation of ITD is well understood11–18, and we have studied the representation of disparities with visual stimuli analogous to those successfully used in acoustic experiments. For example, ITD is converted in the brain to a pathlength on an axon that, owing to the finite conduction velocity in neurons, exactly matches the external ITD. This pathlength is called 'characteristic delay'12. Our results suggest that there is an analogue of the characteristic delay in stereo vision which we propose to call 'characteristic disparity'.

Disparity-sensitive cells in the owl have a characteristic disparity

Barn owl feathers at the leading edge of the wing are equipped with comb-like structures termed serrations on their outer vanes. Each serration is formed by one barb ending that separates and bends upwards. This structure is considered to play a role in air-flow control and noise reduction during flight. Hence, it has considerable potential for engineering applications, particularly in the aviation industry. Several publications have reported possible functions of serrations at artificial airfoils. However, only crude approximations of natural serrations have so far been investigated. We refer to these attempts as zero-order approximations of serrations. It was the goal of this study to present a quantitative three-dimensional characterization of natural serrations as first-order approximations (mean values) and second-order approximations (listed differences depending on the position of the serration along the leading edge). Confocal laser scanning microscopy was used for a three-dimensional reconstruction and investigation with high spatial resolution. Each serration was defined by its length, profile geometry and curvature. Furthermore, the orientation of the serrations at the leading edge was characterized by the inclination angle, the tilt angle and the separation distance of neighboring serrations. These data are discussed with respect to possible applications of serration-like structures for noise suppression and air-flow control.

The three-dimensional shape of serrations at barn owl wings: towards a typical natural serration as a role model for biomimetic applications

The eyes of barn owls (Tyto alba pratincola) display very little aberrations, and have thus excellent optical quality. In a series of behavioral experiments, we tested whether this presumably beneficial feature is also reflected at a perceptual level in this species. As fundamental indicators for visual performance, the spatial contrast sensitivity function (CSF) and grating acuity were measured in two barn owls with psychophysical techniques. Stimulus luminance was 2.7 cd/m(2). The CSF found here renders the typical band-limited, inverted U-shaped function, with a low maximum contrast sensitivity of 8-19 at a spatial frequency of 1 cyc/deg. Grating acuity was estimated from the CSF high frequency cut-off and yielded 3.0-3.7 cyc/deg. In a second experiment, in which contrast was held constant and spatial frequency was varied, grating acuity was measured directly (2.6-4.0 cyc/deg). These results put barn owls at the very low end of the visual acuity spectrum of birds, and demonstrate that visual resolution and sensitivity cannot be predicted by optical considerations alone.

https://www.experimental-ophthalmology.uni-bonn.de/publications/harmening/harmening-et-al._2009_spatial-contrast-sensitivity-and-grating-acuity-of-barn-owls.pdf

Spatial contrast sensitivity and grating acuity of barn owls.

Specific cues in a sound signal are naturally linked to certain parameters in acoustic space. In the barn owl, interaural time difference (ITD) varies mainly with azimuth, while interaural level difference (ILD) varies mainly with elevation. Previous data suggested that ITD is indeed the main cue for azimuthal sound localization in this species, while ILD is an important cue for elevational sound localization. The exact contributions of these parameters could be tested only indirectly because it was not possible to generate a stimulus that contained all relevant spatial information on the one hand, and allowed for a clean separation of these parameters on the other hand. Virtual auditory worlds offer this opportunity. Here we show that barn owls responded to azimuthal variations in virtual space in the same way as to variations in free-field stimuli. We interpret the increase of turning angle with sound-source azimuths (up to +/- 140 degrees) such that the owls did not experience front/back confusions with virtual stimuli. We then separated the influence of ITD from the influence of all other stimulus parameters by fixing the overall ITD in virtual stimuli to a constant value (+100 micros or +100 micros) while leaving all other sound characteristics unchanged. This manipulation influenced both azimuthal and elevational components of head arms. Since the owls' azimuthal head-turn amplitude always resembled the value signified by the ITD, these data demonstrated that azimuthal sound localization is influenced only by ITD both in the frontal hemisphere and in large parts of the rear hemisphere. ILDs did not have an influence on azimuthal components of head turns. While response latency to normal virtual stimuli was found to be largely independent of stimulus position, response delays of the head turns became longer if the ITD information pointed into a different hemisphere as the other cues of the sounds.

/pdf/sound-localization-experiments-with-barn-owls-in-virtual-34pxrf1pdy.pdf

Sound-localization experiments with barn owls in virtual space: influence of interaural time difference on head-turning behavior.

Computational maps are of central importance to a neuronal representation of the outside world. In a map, neighboring neurons respond to similar sensory features. A well studied example is the computational map of interaural time differences (ITDs), which is essential to sound localization in a variety of species and allows resolution of ITDs of the order of 10 μs. Nevertheless, it is unclear how such an orderly representation of temporal features arises. We address this problem by modeling the ontogenetic development of an ITD map in the laminar nucleus of the barn owl. We show how the owl's ITD map can emerge from a combined action of homosynaptic spike-based Hebbian learning and its propagation along the presynaptic axon. In spike-based Hebbian learning, synaptic strengths are modified according to the timing of pre- and postsynaptic action potentials. In unspecific axonal learning, a synapse's modification gives rise to a factor that propagates along the presynaptic axon and affects the properties of synapses at neighboring neurons. Our results indicate that both Hebbian learning and its presynaptic propagation are necessary for map formation in the laminar nucleus, but the latter can be orders of magnitude weaker than the former. We argue that the algorithm is important for the formation of computational maps, when, in particular, time plays a key role.

http://www.t35.physik.tu-muenchen.de/addons/publications/Kempter-2001a.pdf

Hermann Wagner

Papers

Disparity-sensitive cells in the owl have a characteristic disparity

The three-dimensional shape of serrations at barn owl wings: towards a typical natural serration as a role model for biomimetic applications

Spatial contrast sensitivity and grating acuity of barn owls.

Sound-localization experiments with barn owls in virtual space: influence of interaural time difference on head-turning behavior.

Formation of temporal-feature maps by axonal propagation of synaptic learning.