基于机器学习的蛋白质编码区识别

针对DNA序列编码区的识别问题,本研究提出一个特征向量和逻辑回归的组合模型。首先对DNA序列进行数值处理转化为特征向量,并结合k字符相对频率技术提取特征向量的元素特征,之后利用二分类逻辑回归算法,对编码区和非编码区进行准确区分。选取了HMR195和BG570两个基准数据集进行五折交叉验证,结果表明,平均AUC(Area Under Curve)值分别为0.981 3和0.987 4,明显优于传统的贝叶斯判别法和VOSSDFT等方法。此外,本文提出的特征向量的维度很低,提高了运算效率。因此,本文组合模型能够较为高效准确地识别蛋白质编码区。     

Learning to represent visual input

One of the central problems in computational neuroscience is to understand how the object-recognition pathway of the cortex learns a deep hierarchy of nonlinear feature detectors. Recent progress in machine learning shows that it is possible to learn deep hierarchies without requiring any labelled data. The feature detectors are learned one layer at a time and the goal of the learning procedure is to form a good generative model of images, not to predict the class of each image. The learning procedure only requires the pairwise correlations between the activations of neuron-like processing units in adjacent layers. The original version of the learning procedure is derived from a quadratic ‘energy’ function but it can be extended to allow third-order, multiplicative interactions in which neurons gate the pairwise interactions between other neurons. A technique for factoring the third-order interactions leads to a learning module that again has a simple learning rule based on pairwise correlations. This module looks remarkably like modules that have been proposed by both biologists trying to explain the responses of neurons and engineers trying to create systems that can recognize objects.     

Genetically-based variation between two spider populations in foraging behavior

Summary Optimal foraging theory is based on the assumption that at least some aspects of foraging behavior are genetically determined (Pyke et al. 1977; Kamil and Sargent 1980; Pyke 1984). Nonetheless, very few studies have examined the role of genetics in foraging behavior. Here, we report on geographical differences in the foraging behavior of a spider (Agelenopsis aperta) and investigate whether these differences are genetically determined. Field studies were conducted on two different populations of A. aperta: one residing in a desert riparian habitat, and the other in a desert grassland habitat. Data from the spiders' natural encounters with prey demonstrated that grassland spiders exhibited a higher frequency of attack than riparian spiders towards 13 of 15 prey types, including crickets and ants. Grassland spiders also had shorter latencies to attack 12 of 15 prey types, including crickets and ants, than riparian spiders. Subsequently, we reared grassland and riparian spiders under controlled conditions in the laboratory and observed their interactions with prey to determine whether the populational differences we found in the field could be genetic. Again, grassland spiders showed a shorter latency to attack prey (crickets, ants) than riparian spiders. These latencies were not significantly affected by the hunger state or age of the spiders. Finally, we reared a second generation (F2) of grassland and riparian spiders in the laboratory and observed their interactions with prey to determine whether the populational differences in the previous generation were due to genetic effects or maternal effects. As before, grassland spiders exhibited a shorter latency to attack prey (crickets) than riparian spiders. We conclude that the foraging differences we observed between these two populations of A. aperta are genetically determined. These differences probably have resulted from either natural selection acting directly on attack frequency and the latency to attack prey, or natural selection acting on traits which are genetically correlated with these aspects of foraging behavior.     

Population Dynamics of the Root-Knot Nematode Meloidogyne Triticoryzae under Five Rice-Based Cropping Systems

Population dynamics of M. triticoryzae in five rice-based cropping systems have revealed that rice was the main host. Most of the population growth which contributed to the peak population density in September occurred in the rice crop. The other crops in the Rabi and summer seasons had a profound influence on the height of the peak in the succeeding rice crop. Some level of reproduction occurred in wheat, greengram and berseem in Rabi which contributed to relatively higher equilibrium densities. The potato variety Pusa Bahar increased the population density while Pusa Badshah decreased it. The lower temperature during the Rabi season also limited the rate of population growth. The incorporation of organic matter into the soil, either as crop residues of greengram or berseem, reduced the population growth of M. triticoryzae .     

Neuroendocrinology of context-dependent stress responses: vasotocin alters the effect of corticosterone on amphibian behaviors

The ability of an animal to respond with appropriate defensive behaviors when confronted with an immediate threat can affect its survival and reproductive success. In the roughskin newt (Taricha granulosa), exogenous corticosterone (CORT) rapidly blocks and vasotocin (VT) enhances reproductive behaviors (mainly clasping behavior). Electrophysiological studies have shown that pretreatment of male Taricha with VT counteracts the inhibitory effects of CORT on neuronal activity in the medulla. To test whether similar interactions between VT and CORT influence reproductive behaviors in Taricha, we recorded the time spent and incidence of clasping in males injected with VT or vehicle at 60 min and then CORT or vehicle at 5 min before presentation of a female. This study found that clasping behavior is suppressed in males that received vehicle and then CORT, but is not suppressed in males that received VT and then CORT. Considering these results and the possibility that the performance of clasping behaviors might cause increases in endogenous VT activity, we tested whether the suppressive effects of CORT administration on clasping behavior would occur in males that had recently clasped females. The study found that, in contrast to males that had been isolated from females, CORT administration did not suppress clasping behavior in males that had been allowed to clasp females for 60 min prior to the hormone injection. Our results suggest that, at least in this amphibian and perhaps in other animals, the neuroendocrine regulation of alternative behavioral responses to threats involves functional interactions between corticosteroids and VT-like peptides.     

From 'understanding the brain by creating the brain' towards manipulative neuroscience

Ten years have passed since the Japanese 'Century of the Brain' was promoted, and its most notable objective, the unique 'creating the brain' approach, has led us to apply a humanoid robot as a neuroscience tool. Here, we aim to understand the brain to the extent that we can make humanoid robots solve tasks typically solved by the human brain by essentially the same principles. I postulate that this 'Understanding the Brain by Creating the Brain' approach is the only way to fully understand neural mechanisms in a rigorous sense. Several humanoid robots and their demonstrations are introduced. A theory of cerebellar internal models and a systems biology model of cerebellar synaptic plasticity is discussed. Both models are experimentally supported, but the latter is more easily verifiable while the former is still controversial. I argue that the major reason for this difference is that essential information can be experimentally manipulated in molecular and cellular neuroscience while it cannot be manipulated at the system level. I propose a new experimental paradigm, manipulative neuroscience, to overcome this difficulty and allow us to prove cause-and-effect relationships even at the system level.     

Directional selectivities of near-field filiform hair mechanoreceptors on the crayfish tailfan (Crustacea: Decapoda)

Directional selectivities of mechanoreceptors that innervate filiform hairs on the crayfish tailfan were investigated with unidirectional, sinusoidal, water-motion stimuli. These recordings provide the first representative sample from filiform hair sensilla on the entire tailfan. The filiform hair receptors exhibit unimodal directional selectivity patterns that were well fitted by a cardioid function with a half-width of 122°. The preferred directions correspond to the major axis of hair motion, and are perpendicular to the orientation of lateral branches on the main hair shaft. Pooled plots of preferred directions demonstrate quadrimodal patterns on the telson and endopods which are associated with hair location, and a bimodal pattern on the exopods. For each appendage, the combination of the overall pattern of preferred directions with “coarse coding” of direction by individual receptors provides sensitivity to a full 0–360° range of water motion and the potential to discriminate the direction of water motion throughout this range. The results demonstrate several similarities to the wind-sensitive cercal receptor system in orthopteroid insects, and suggest that crustacean filiform hair receptors provide a sufficient sensory basis for behavioral orientation to water currents and shorelines. Accepted: 5 January 1998     

Deterrence coding by a larval Manduca chemosensory neurone mediating rejection of a non-host plant, Canna generalis L.

Abstract. The physiological basis of phagodeterrence was studied electrophy-siologically and behaviourally in the phytophagous caterpillars Manduca sexta and Manduca quinquemaculata. The model unacceptable non-host plant was the canna lily, Canna generalis. A strongly deterrent extract was obtained from fresh leaves of canna by extraction with hot ethanol or ethyl acetate in a blender. Behavioural rejection of these extracts was similar to that of fresh leaves, although less intense. In contrast, blender extracts using other solvents, as well as leaf surface rinses, were phagostimulant or neutral. Chromatographic fractionation of the deterrent ethanolic extract showed the active principles to be moderately polar and separable into two fractions. Previous ablation experiments had shown that the medial maxillary styloconica and epipharyngeal sensilla are the two most important chemosensory organs in mediating behavioural rejection of canna leaves; if only one of these organs is spared, the animal completely rejects canna. We investigated the neural responses of the medial styloconica and their contribution to the sensory coding responsible for this phagodeterrence. The active fractions of the deterrent ethanolic extract elicited a vigorous response from one chemosensory neurone in the medial styloconica. This neurone is distinguishable from others in the medial styloconica by its unique temporal response parameters and the characteristic shape changes of its action potentials. The response frequency of this neurone correlates with the degree of phagodeterrence in a dose-dependent manner. Threshold deterrence occurs at a concentration of extract (1%) that elicits firing in this neurone at a rate of c. 50 spikes/s peak instantaneous frequency and 30 total spikes in the first Is. We conclude that this is a ’deterrent neurone’ in the sense that vigorous response from this neurone is a sufficient sensory code for behavioural rejection of canna. Thus input from a single sensory neurone is capable of blocking feeding, since only one (unilateral) medial styloconicum is needed to mediate this rejection.     

Theodore H. Bullock: pioneer of integrative and comparative neurobiology

Theodore H. Bullock (1905–2005) was a pioneer of integrative and comparative neurobiology and one of the founders of neuroethology. His work—distinguished by the tremendous number of different research themes and animal taxa studied—provided the basis for a comprehensive analysis of brain evolution. Among his major achievements are: one of the first physiological analyses of rhythmic central pattern generators; the first simultaneous recording from both the presynaptic and postsynaptic region of a chemical synapse; the demonstration of intercellular communication through graded potentials; and the discovery of two novel sensory organs formed by infrared receptors in pit vipers and electroreceptors in electric fish. He was also one of the first who applied computational tools to the analysis of complex neural signals and to perform a comparative analysis of cognitive events. His two-volume treatise “Structure and function in the nervous system of invertebrates” (with G. Adrian Horridge) remains the most comprehensive, authoritative review of this topic ever written. In addition to his research merits, his legacy is particularly based on his cosmopolitan way of thinking and acting, his large, worldwide school of students, and his committed advocacy for comparative and systems-oriented neurobiology.     

Negatively correlated firing: the functional meaning of lateral inhibition within cortical columns

Lateral inhibition is a well documented aspect of neural architecture in the main sensory systems. Existing accounts of lateral inhibition focus on its role in sharpening distinctions between inputs that are closely related. However, these accounts fail to explain the functional role of inhibition in cortical columns, such as those in V1, where neurons have similar response properties. In this paper, we outline a model of position tracking using cortical columns of integrate-and-fire and Hodgkin-Huxley-type neurons which respond optimally to a particular location, to show that negatively correlated firing patterns arise from lateral inhibition in cortical columns and that this provides a clear benefit for population coding in terms of stability, accuracy, estimation time and neural resources.     

Performing Behavioral Tasks in Subjects with Intracranial Electrodes

Patients having stereo-electroencephalography (SEEG) electrode, subdural grid or depth electrode implants have a multitude of electrodes implanted in different areas of their brain for the localization of their seizure focus and eloquent areas. After implantation, the patient must remain in the hospital until the pathological area of brain is found and possibly resected. During this time, these patients offer a unique opportunity to the research community because any number of behavioral paradigms can be performed to uncover the neural correlates that guide behavior. Here we present a method for recording brain activity from intracranial implants as subjects perform a behavioral task designed to assess decision-making and reward encoding. All electrophysiological data from the intracranial electrodes are recorded during the behavioral task, allowing for the examination of the many brain areas involved in a single function at time scales relevant to behavior. Moreover, and unlike animal studies, human patients can learn a wide variety of behavioral tasks quickly, allowing for the ability to perform more than one task in the same subject or for performing controls. Despite the many advantages of this technique for understanding human brain function, there are also methodological limitations that we discuss, including environmental factors, analgesic effects, time constraints and recordings from diseased tissue. This method may be easily implemented by any institution that performs intracranial assessments; providing the opportunity to directly examine human brain function during behavior.