Temporal encoding in nervous systems: A rigorous definition

We propose a rigorous definition for the termtemporal encoding as it is applied to schemes for the representation of information withinpatterns of neuronal action potentials, and distinguish temporal encoding schemes from those based on window-averagedmean rate encoding. The definition relies on the identification of anencoding time window, defined as the duration of a neuron's spike train assumed to correspond to a single symbol in the neural code. The duration of the encoding time window is dictated by the time scale of the information being encoded. We distinguish between the concepts of theencoding time window and theintegration time window, the latter of which is defined as the duration of a stimulus signal that affects the response of the neuron. We note that the duration of the encoding and integration windows might be significantly different. We also present objective, experimentally assessable criteria for identifying neurons and neuronal ensembles that utilize temporal encoding to any significant extent. The definitions and criteria are made rigorous within the contexts of several commonly used analytical approaches, including thestimulus reconstruction analysis technique. Several examples are presented to illustrate the distinctions between and relative capabilities of rate encoding and temporal encoding schemes. We also distinguish our usage oftemporal encoding from the termtemporal coding, which is commonly used in reference to the representation of information about thetiming of events by rate encoding schemes.     

大脑中的抉择神经元

近年来神经科学领域的进展表明,大脑中不仅存在如位置神经元之类的特异性编码感觉信息的神经元,也存在能够特异性地反映动物思考过程的神经元。在一系列以侧内顶叶(LIP)为目标的猕猴电生理实验中,人们发现LIP神经元的动作电位发放率可以反映抉择思考的过程。抉择的研究为我们打开了一个研究大脑高级认知功能的窗口。抉择神经元的发现表明了大脑的高级认知功能是基于与感觉信息处理类似的神经计算原理。     

Intraspecies diversity of Coxiella burnetii as revealed by com1 and mucZ sequence comparison

Coxiella burnetii is classified within the γ subgroup of the Proteobacteria. All strains tested to date have an identical 16S rRNA sequence but 20 different genotypes have been determined by pulsed field gel electrophoresis (PFGE). In this study, intraspecies genetic diversity was investigated by sequence comparison of 715 bp of the Com1 encoding gene (com1) and 774 bp of the MucZ encoding gene (mucZ) in 37 strains isolated from animals and humans with acute or chronic Q fever in Europe, North America and Africa. Five and four groups were established from sequence analysis of com1 and mucZ, respectively. Neither relation of the defined groups to geographical distribution of the isolates was noted nor relation to disease form (acute/chronic). The same isolates were grouped together regardless of the gene being investigated. Comparison of the five proposed groups to previous groups, yielded after digestion by NotI PFGE, allowed for an intermediate classification of C. burnetii isolates between those obtained by using 16S rDNA (one group) and PFGE (20 groups).     

Proximity to an edge affects search strategy in adults and children

When searching for a hidden goal, search patterns are often defined according to one of two main search strategies: an absolute strategy, which usually involves searching at a fixed learned distance and direction from a particular reference point, or a relational strategy, which involves searching at a point that maintains the relationship between two or more other points. Past research has shown that humans tend to prefer a relational strategy whereas most non-humans prefer an absolute strategy. However, recent research (Hartley et al., 2004) used a simulated 3D environment to demonstrate that proximity to a boundary affects strategy. In particular, when searching close to an edge, human participants were more likely to use an absolute strategy whereas when searching at a central location, participants were more likely to use a relational strategy. The current studies extend the findings of Hartley et al. Experiment 1 showed that adult humans use different strategies based on the goal's proximity to the edge of a search space, and that strategies differed between males and females. Experiment 2 suggested that children also use different strategies based on the goal's proximity to a boundary, and that some goal locations may be harder to learn than others. Taken together, our results show that search strategies are flexible and context-specific.     

糖基转移酶基因双敲除对依博素生物合成的影响

以往研究已确定链霉菌胞外多糖依博素的生物合成基因簇(ste), ste15 和ste22 分别编码葡萄糖糖基转移酶和鼠李糖糖基转移酶。现通过基因同源重组双交换,在ste15基因缺失突变株Streptomyces sp. 139 (ste15-) 基础上,再进行ste22 基因阻断,经Southern 杂交验证,得到了ste15 和ste22 双基因缺失突变株Streptomyces sp. 139 (ste15-ste22-),并对该菌株进行了基因互补研究。双基因缺失株产生的胞外多糖与依博素相比,葡萄糖与鼠李糖含量明显降低,分子量下降,生物活性明显变弱。基因互补株产生的胞外多糖中葡萄糖与鼠李糖含量基本恢复至依博素水平,生物活性也显著提高。因此,进一步阐明了ste15和ste22基因参与了依博素生物合成中葡萄糖和鼠李糖重复单元序列的形成过程,在依博素的生物合成中起重要作用,变株产生的依博素新衍生物体内外生物学活性正在深入研究中。     

编码悬浮微块片上多组分并行免疫检测的方法

采用热压印光刻技术制备了一种多金属构成、带数字标识图形的悬浮微块,其中的镍层与金层可分别实现微块的磁控靶向与生物探针的联接。借助微块表面的数字微通孔标识符号,实现了微块的生物探针编码;用异硫氰酸荧光素荧光标记编码的悬浮微块,通过悬浮微块的多组分并行免疫荧光检测,实现了微块的生物探针解码及生物分子的定量检测。这种编码的地址数取决于微块表面的微通孔数,理论上可以成千上万。因此,表面经过生物探针修饰的悬浮微块是建立生物分子编码库的理想途径,可作为基于高通量悬浮阵列技术的免疫分析平台。     

Processing of calling songs by an L-shaped neuron in the prothoracic ganglion of the female cricket, Acheta domesticus

ABSTRACT. An L-shaped auditory intemeuron (LI) has been recorded from extracellularly and intracellularly, and identified morphologically (by Lucifer yellow or cobalt injection) in the prothoracic ganglion of mature female Acheta domesticus. The morphology of the LI is very similar to ascending, prothoracic acoustic interneurons that are most sensitive to higher carrier frequencies in both A. domesticus and other gryllid species. Its terminations in the brain are similar to ascending acoustic interneurons found in other gryllids. The LI neuron is most sensitive to 4–5 kHz model calling songs (CSs), the main carrier frequency of the natural call. Thresholds to high frequencies (8–15 kHz) are 15–20 dB higher. Increasing CS intensities of up to 15 dB above threshold at 4–5 kHz result in increased firing rates by the LI. More than 15 dB increase in intensity causes saturation with little increase in spiking rate until the intensity surpasses 80 dB. In response to 70 dB or higher stimulus intensities, the LI responds to the second and third CS syllables with one or two spikes, pauses, and then produces a burst of nerve impulses with the same or greater latency than for lower intensity stimuli. In response to CS syllables of changing duration (10–30 ms) this neuron responds with a rather constant duration burst of impulses. Syllable periods of the CS stimuli were accurately encoded by the LI. Progressively stronger injection of hyperpolarizing current reduces, and ultimately stops spiking of the LI in response to CS stimuli. More intense stimulation with reduced hyperpolarization shows an initial spike, pause and burst of spikes. Intracellular recording from axonal regions of the neuron shows large spikes, small EPSPs and a developing hyperpolarization through the response to a CS chirp. Inhibitory input to the LI is demonstrated at 4.5, 8 and 16 kHz. This probably explains the specialized response characteristics of the LI which enhanced its encoding of CS syllable period.     

基于分组码模型的DNA序列编码特性分析

基于差错控制原理,将遗传信息中由海量碱基构成的DNA序列看作经过编码而获得的具有某种编码特性的编码序列。在此基础上,将编码理论中分组码的分析方法用于对DNA序列进行分析,选用了（6,3）分组码对三种原核生物和两种真核生物DNA序列进行分析,在ORF起始端和结束端观察到明显的码间距离变化。证明该方法对DNA序列分析有较好的指导作用。     

基于光谱编码的血管内光声组分成像

光声成像突破了传统的光学成像和超声成像在生物组织成像领域的困境,该技术基于光声(Photoacoustic,PA)效应,脉冲激光激励下的生物组织产生超声信号,超声信号被接收后,通过反投影算法将其携带的时间信息和强度信息转化为能够反映生物组织吸收结构和分布的可视化图像。基于不同生物组织的光吸收差异,当激发光强度均匀且稳定时,光声成像反映的就是该物质对于该波长光的吸收特性。本文中,我们基于导管式的血管内光声断层扫描平台结合多波长激发的光声成像算法开发了基于光谱编码的血管内光声组分成像系统,实现了在离体血管斑块中脂质组分的定量成像,高分辨获得了脂质核心的大小形态和边界信息,表征了斑块内的脂质相对含量。     

Minute-encoding neurons in hippocampal-striatal circuits

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GlycoCT-a unifying sequence format for carbohydrates

As part of the EUROCarbDB project (www.eurocarbdb.org) we have carefully analyzed the encoding capabilities of all existing carbohydrate sequence formats and the content of publically available structure databases. We have found that none of the existing structural encoding schemata are capable of coping with the full complexity to be expected for experimentally derived structural carbohydrate sequence data across all taxonomic sources. This gap motivated us to define an encoding scheme for complex carbohydrates, named GlycoCT, to overcome the current limitations. This new format is based on a connection table approach, instead of a linear encoding scheme, to describe the carbohydrate sequences, with a controlled vocabulary to name monosaccharides, adopting IUPAC rules to generate a consistent, machine-readable nomenclature. The format uses a block concept to describe frequently occurring special features of carbohydrate sequences like repeating units. It exists in two variants, a condensed form and a more verbose XML syntax. Sorting rules assure the uniqueness of the condensed form, thus making it suitable as a direct primary key for database applications, which rely on unique identifiers. GlycoCT encompasses the capabilities of the heterogeneous landscape of digital encoding schemata in glycomics and is thus a step forward on the way to a unified and broadly accepted sequence format in glycobioinformatics.     

Re-orienting in space: do animals use global or local geometry strategies?

Here we compare whether birds encode surface geometry using principal axes, medial axes or local geometry. Birds were trained to locate hidden food in two geometrically identical corners of a rectangular arena and subsequently tested in an L-shaped arena. The chicks showed a primary local geometry strategy, and a secondary medial axes strategy, whereas the pigeons showed a medial axes strategy. Neither species showed behaviour supportive of the use of principal axes. This is, to our knowledge, the first study to directly examine these three current theories of geometric encoding.     

日本对虾(Marsupenaeys japonicus)HsP70基因cDNA的克隆与序列分析

根据中国明对虾(Fenneropenaeuschinensis)Hsp70的cDNA序列及日本对虾(Marsupenaeusjaponicus)Hsp70cDNA序列片段设计引物,用RT-PCR方法,从经热休克处理的日本对虾鳃总RNA中克隆到长1992bp的Hsp70cDNA序列,包括长1959bp的完整编码序列(CDS)。根据编码序列推导出相应的652个氨基酸,与其他真核生物Hsp70家族成员进行同源性比较,发现与凡纳滨对虾(Litopenaeusvannamei)、斑节对虾(PinaeusmonodonFabricius)、中国明对虾(Penaeuschinesis)的相似度分别为99.5%、99.4%、99.4%,与日本沼虾(Macrobrachiumnipponense)和罗氏沼虾(M.rosenbergii)的相似度分别为93.7%和92.9%,与虹鳟(Oncorhynchusmykiss)、原鸡(Callusgallus)、家鼠(Musmusculus)和人(Homosapiens)的相似度为89.2%、85.4%、88.3%和88.3%,表现出较高的保守性。分析表明所得到的日本对虾Hsp70是一种Dnak亚家族类型的细胞质Hsp70,拥有完整的N端ATP酶结构域(约45kDa)、底物肽结合结构域(18kDa)及C端结构域(10kDa)。以上结果说明我们所得到的序列是一条包含完整CDS的Hsp70基因序列。     

Spatiotemporal Content of Saccade Transients

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高等植物叶绿素生物合成的研究进展

叶绿素是植物叶绿体内参与光合作用的重要色素,其功能是捕获光能并驱动电子转移到反应中心.整个叶绿素生物合成过程(L-谷氨酰-tRNA→叶绿素a→叶绿素b)需要15步反应,涉及15种酶,迄今在模式植物拟南芥中已分离到27个编码这些酶的基因,完成了以拟南芥为代表的被子植物叶绿素生物合成全部基因的克隆.本文主要对近年来国内外有关植物叶绿素的生物合成过程及相关酶基因的克隆、生物合成途径中2个关键步骤(σ-氨基酮戊酸(ALA)合成和Mg离子插入原卟啉Ⅸ的调节)、影响叶绿素生物合成的主要因素(光、温度、营养元素等),以及叶绿素生物合成相关酶的其他生物学功能等的研究进展进行综述.     

Three-Dimensional Representation of Motor Space in the Mouse Superior Colliculus

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黑色素瘤相关抗原家族新基因restin的组织表达谱

Restin是从维甲酸诱导肿瘤分化细胞中克隆的一种黑色素瘤相关抗原家族(MAGE)的新成员.对该基因在不同组织、不同细胞系的表达水平进行研究,将有利于揭示其生物学功能.使用α3-2P-dCTP标记人restin编码区基因作为探针,针对12种不同成人组织mRNA的Multiple TissueNorthern(MTN)膜和含76种成人、胎儿及常用细胞系mRNA的Multiple Tissue Expression(MTE)Array膜进行杂交分析,同时利用地高辛标记探针对11种常见肿瘤组织进行原位杂交检测.结果显示,MTN膜杂交中,12种组织显示均一杂交条带,约1.8 kb,提示该基因可能不存在剪接变异体;MTE膜杂交中,正常组织中均有不同程度的表达,但在肿瘤细胞系中均低表达或者不表达;原位杂交的结果显示,在8种恶性肿瘤组织中均不表达,而在3种良性肿瘤组织中呈现较低的表达.结果提示,该基因在正常组织中的表达明显高于肿瘤组织和肿瘤细胞系,完全不同于其它MAGE-A、B、C的组织表达方式.结合该基因在维甲酸诱导分化的肿瘤细胞中高表达,推测restin可能与正常细胞的分化、增殖有关.     

植物NBS类抗病基因的进化

NBS(Nucleotide-binding site)类抗病基因是植物中最重要的一类抗病基因, 其进化模式、结构特点和功能调控一直是抗病基因研究领域的热点。这类基因具有保守的结构域, 广泛存在于植物基因组中, 在不同植物基因组中数目差异较大且具有较低的表达量。此外, 同源NBS类抗病基因之间通过频繁的序列交换产生广泛的序列多样性, 且抗病基因位点具有较差的线性。依据基因之间序列交换的频率, 抗病基因可分为TypeⅠ和TypeⅡ两类。文章从抗病基因的结构、数量、分布、序列多样性、进化模式以及表达调控等方面进行了综述, 旨在为后续NBS类抗病基因的相关研究提供参考。     

吡虫啉对水稻体内条纹病毒的胁迫效应

水稻条纹叶枯病为灰飞虱(SBPH)传播的一种病毒病,前些年在长江流域尤其江苏地区暴发成灾.为探讨杀虫剂吡虫啉对水稻体内条纹病毒(rice stripe virus,RSV)的胁迫效应,本研究模拟大面积生产上的用药方式,在灰飞虱传毒48 h后对稻苗分别施药1、2、3和4次(以B₁、B₂、B₃和B₄表示),以实时荧光定量PCR(real-time PCR)和蛋白免疫印痕(Western blotting, WB)等方法对稻苗中RSV NS3、CP、SP、NSvc4等4种基因的表达和CP、SP两种蛋白的含量进行分期检测.结果表明: 1)吡虫啉影响4种基因的表达,且其影响程度与施药强度及基因类型有关:有3个处理NS3基因表达水平上调,其中施药4次、接虫后16 d\[以(B₄, 16 d)表示,下同\]的表达水平最高,达10.86,其他处理的NS3基因表达都明显受到抑制.几乎所有B₂和B₃处理都使CP、SP和NSvc4基因的表达受到明显抑制,其相对表达水平为0～0.74;而B₁和B₄的一半处理明显促进其上调,其中(B₁, 16 d)和(B₄, 16 d)SP基因的表达量最高,分别为258.89和730.54.2)吡虫啉对CP、SP基因和CP、SP蛋白表达模式的胁迫效应不同,如(B₁, 19 d)CP基因几乎没有表达(0),但其相应的CP蛋白却明显上调(23.08)
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ECG Data Compression Using Modified Run Length Encoding of Wavelet Coefficients for Holter Monitoring

ObjectiveIn cardiac patient-care, compression of long-term ECG data is essential to minimize the data storage requirement and transmission cost. Hence, this paper presents a novel electrocardiogram data compression technique which utilizes modified run-length encoding of wavelet coefficients.MethodFirst, wavelet transform is applied to the ECG data which decomposes it and packs maximum energy to less number of transform coefficients. The wavelet transform coefficients are quantized using dead-zone quantization. It discards small valued coefficients lying in the dead-zone interval while other coefficients are kept at the formulated quantized output interval. Among all the quantized coefficients, an average value is assigned to those coefficients for which energy packing efficiency is less than 99.99%. The obtained coefficients are encoded using modified run-length coding. It offers higher compression ratio than conventional run-length coding without any loss of information.ResultsCompression performance of the proposed technique is evaluated using different ECG records taken from the MIT-BIH arrhythmia database. The average compression performance in terms of compression ratio, percent root mean square difference, normalized percent mean square difference, and signal to noise ratio are 17.18, 3.92, 6.36, and 28.27 dB respectively for 48 ECG records.ConclusionThe compression results obtained by the proposed technique is better than techniques recently introduced by others. The proposed technique can be utilized for compression of ECG records of Holter monitoring.