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 tested how well barn owls can discriminate objects of different sizes. This ability may be important for the owls when catching prey. We performed a quantitative experiment in the laboratory and trained owls in a task in which the owls had to discriminate whether two rhombi presented simultaneously on a computer monitor were of the same or of different sizes. We obtained full data sets with two experienced owls and one data point with a third owl. For objects being sufficiently larger than the spatial resolution of the barn owl, the angular threshold was related to object size, implying that the discrimination followed Weber’s law. The range of Weber fractions we determined was between 0.026 and 0.09. For object sizes close to the spatial resolution, performance degraded. We conducted similar experiments with human subjects. Human thresholds showed the same dependence on object size, albeit down to smaller object sizes. Human performance resulted in a range of Weber fractions extending from 0.025 to 0.036. The differences between owls and humans could be explained by the much higher spatial acuity of humans compared with owls.

Size discrimination in barn owls as compared to humans

Whether owls can be trained to discriminate computer generated random-dot patterns purely on the basis of their figure-ground organisation is an open question. Here I investigate this question by (A) providing an operant shaping technique that prepared four barn owls for behavioural measurements employing a remote computer display (Experiment I) and (B) using the random-dot technique together with tests of discrimination-transfer (Experiment II). Tested were two functions of vision that are thought to be involved in figure-ground segregation: (1) texture perception and (2) motion perception. The computer displays consisted of patterns of randomly positioned black and grey dots, that differed either in their position, textural organisation, or common fate (motion). The rapidness with which the owls learned to discriminate varied between the different individuals and depended heavily on the visual function tested. The here described experiments have been instructive in four ways. First, Experiment I has provided an adequate operant shaping method that prepared barn owls to be behaviourally tested with random-dot patterns that were displayed on a CRT screen. Second, Experiment II provided behavioural data that clearly demonstrated that owls can abstract figure from ground in computer displays of random-dot patterns. Third, signal detection analysis of the measured psychometric curves revealed a consistent response criterion for stimuli above or near threshold level, indicating a high degree of stimulus control. Fourth, the transfer tests provided evidence for generalisation discrimination in owls. 40 On the Perceptual Identity of Depth Vision in the owl

On the perceptual identity of depth vision in the owl

Diese Dissertation ist auf den Internetseiten der Hochschulbibliothek online verfügbar.

Aspects of sound localization and spatial attention in barn owls and rats

The common technique of dielectric (epsilon) (t) measurements involves the application of a polarization invariant electric field to a capacitor filled with the material under study and the detection of the temporal evolution of the resulting current or charge flow. The counterpart condition of applying a given dielectric displacement and monitoring the electric field relates to the dielectric modulus M(t) with M((omega) ). Isothermal and thermally stimulated experimental techniques for directly accessing the relaxation M(t) are outlined and discussed as regards their relation to the dielectric retardation (epsilon) (t) and to dc-conductivity(sigma) dc. We also address several microscopic processes which are inherently linked to the dielectric modulus through their common feature of displaying a redistribution of charge.© (1997) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.

Hermann Wagner

Papers

Size discrimination in barn owls as compared to humans

On the perceptual identity of depth vision in the owl

Aspects of sound localization and spatial attention in barn owls and rats

Dielectric relaxation under constant charge conditions

Processing of auditory signals in the forebrain of the Barn Owl : neural mechanisms of across-frequency integration