Learning the Structure of Deep Sparse Graphical Models

Deep belief networks are a powerful way to model complex probability distributions. However, learning the structure of a belief network, particularly one with hidden units, is difficult. The Indian buffet process has been used as a nonparametric Bayesian prior on the directed structure of a belief network with a single infinitely wide hidden layer. In this paper, we introduce the cascading Indian buffet process (CIBP), which provides a nonparametric prior on the structure of a layered, directed belief network that is unbounded in both depth and width, yet allows tractable inference. We use the CIBP prior with the nonlinear Gaussian belief network so each unit can additionally vary its behavior between discrete and continuous representations. We provide Markov chain Monte Carlo algorithms for inference in these belief networks and explore the structures learned on several image data sets.

Tree-Structured Stick Breaking Processes for Hierarchical Data

Many data are naturally modeled by an unobserved hierarchical structure. In this paper we propose a flexible nonparametric prior over unknown data hierarchies. The approach uses nested stick-breaking processes to allow for trees of unbounded width and depth, where data can live at any node and are infinitely exchangeable. One can view our model as providing infinite mixtures where the components have a dependency structure corresponding to an evolutionary diffusion down a tree. By using a stick-breaking approach, we can apply Markov chain Monte Carlo methods based on slice sampling to perform Bayesian inference and simulate from the posterior distribution on trees. We apply our method to hierarchical clustering of images and topic modeling of text data.

Low power all-optical switch in a passive InGaAsP multiple quantum well waveguide

We demonstrate the use of resonant bandfilling nonlinearity in an InGaAsP/InGaAsP Multiple Quantum Well (MQW) waveguide due to photogenerated carriers to obtain switching at pulse powers, which can readily be obtained from an erbium amplified diode laser source. In order to produce gating a polarisation rotation gate was used, which relies on an asymmetry in the nonlinear refraction on the principle axes of the waveguide.

Differential effects of ageing on the EEG during pentobarbital and ketamine anaesthesia

Background and objectives: Pentobarbital and ketamine are commonly used in animal experiments, including studies on the effects of ageing on the central nervous system. The electroencephalogram is a sensitive measure of brain activity. The present study i

Nutritive value of fishes of Lake Tanganyika: II. Mineral composition

The composition of the minerals in three economically important fish species of Lake Tanganyika was determined. From the analyses there does not appear to be significant difference in the composition for the three species. Beside the major elements: Ca, P, K, Na, Mg, Cl, Fe, Al and Zn, eighteen trace elements were determined. The presence of the bones in the fish is especially nutritionally important for the following elements: Ca, P, Br, Sr, Mn and Mg.

The Gaussian process density sampler

We present the Gaussian Process Density Sampler (GPDS), an exchangeable generative model for use in nonparametric Bayesian density estimation. Samples drawn from the GPDS are consistent with exact, independent samples from a fixed density function that is a transformation of a function drawn from a Gaussian process prior. Our formulation allows us to infer an unknown density from data using Markov chain Monte Carlo, which gives samples from the posterior distribution over density functions and from the predictive distribution on data space. We can also infer the hyperparameters of the Gaussian process. We compare this density modeling technique to several existing techniques on a toy problem and a skullreconstruction task.

The search for the IFN-gamma receptor in fish: Functional and expression analysis of putative binding and signalling chains in rainbow trout Oncorhynchus mykiss

Interferons (IFNs), consisting of three major subfamilies, type I, type II (gamma) and type III (lambda) IFN, activate vertebrate antiviral defences once bound to their receptors. The three IFN subfamilies bind to different receptors, IFNAR1 and IFNAR2 for type I IFNs, IFN gamma R1 and IFN gamma R2 for type II IFN, and IL-28R1 and IL-10R2 for type III IFNs. In fish, although many types I and II IFN genes have been cloned, little is known about their receptors. In this report, two putative IFN-gamma receptor chains were identified and sequenced in rainbow trout (Oncorhynchus mykiss), and found to have many common characteristics with mammalian type II IFN receptor family members. The presented gene synteny analysis, phylogenetic tree analysis and ligand binding analysis all suggest that these molecules are the authentic IFN gamma Rs in fish. They are widely expressed in tissues, with IFN gamma R1 typically more highly expressed than IFN gamma R2. Using the trout RTG-2 cell line it was possible to show that the individual chains could be differentially modulated, with rIFN-gamma and rIL-1 beta down regulating IFN gamma R1 expression but up regulating IFN gamma R2 expression. Overexpression of the two receptor chains in RTG-2 cells revealed that the level of IFN gamma R2 transcript was crucial for responsiveness to rIFN-gamma, in terms of inducing gamma IP expression. Transfection experiments showed that the two putative receptors specifically bound to rIFN-gamma. These findings are discussed in the context of how the IFN gamma R may bind IFN-gamma in fish and the importance of the individual receptor chains to signal transduction. (c) 2009 Elsevier Ltd. All rights reserved.

Avoiding pathologies in very deep networks

Choosing appropriate architectures and regularization strategies of deep networks is crucial to good predictive performance. To shed light on this problem, we analyze the analogous problem of constructing useful priors on compositions of functions. Specifically, we study the deep Gaussian process, a type of infinitely-wide, deep neural network. We show that in standard architectures, the representational capacity of the network tends to capture fewer degrees of freedom as the number of layers increases, retaining only a single degree of freedom in the limit. We propose an alternate network architecture which does not suffer from this pathology. We also examine deep covariance functions, obtained by composing infinitely many feature transforms. Lastly, we characterize the class of models obtained by performing dropout on Gaussian processes.

Contractile and mechanical properties of epithelia with perturbed actomyosin dynamics.

Mechanics has an important role during morphogenesis, both in the generation of forces driving cell shape changes and in determining the effective material properties of cells and tissues. Drosophila dorsal closure has emerged as a reference model system for investigating the interplay between tissue mechanics and cellular activity. During dorsal closure, the amnioserosa generates one of the major forces that drive closure through the apical contraction of its constituent cells. We combined quantitation of live data, genetic and mechanical perturbation and cell biology, to investigate how mechanical properties and contraction rate emerge from cytoskeletal activity. We found that a decrease in Myosin phosphorylation induces a fluidization of amnioserosa cells which become more compliant. Conversely, an increase in Myosin phosphorylation and an increase in actin linear polymerization induce a solidification of cells. Contrary to expectation, these two perturbations have an opposite effect on the strain rate of cells during DC. While an increase in actin polymerization increases the contraction rate of amnioserosa cells, an increase in Myosin phosphorylation gives rise to cells that contract very slowly. The quantification of how the perturbation induced by laser ablation decays throughout the tissue revealed that the tissue in these two mutant backgrounds reacts very differently. We suggest that the differences in the strain rate of cells in situations where Myosin activity or actin polymerization is increased arise from changes in how the contractile forces are transmitted and coordinated across the tissue through ECadherin-mediated adhesion. Altogether, our results show that there is an optimal level of Myosin activity to generate efficient contraction and suggest that the architecture of the actin cytoskeleton and the dynamics of adhesion complexes are important parameters for the emergence of coordinated activity throughout the tissue.

PULSED ELECTRICAL OPERATION OF 1.5-MU-M VERTICAL-CAVITY SURFACE-EMITTING LASERS

Vertical cavity surface emitting lasers operating in the 1.3- and 1.5-mu m wavelength ranges are highly attractive for telecommunications applications. However, they are far less well-developed than devices operating at shorter wavelengths. Pulsed electrically-injected lasing at 1.5 mu m, at temperatures up to 240 K, is demonstrated in a vertical-cavity surface-emitting laser with one epitaxial and one dielectric reflector. This is an encouraging result in the development of practical sources for optical fiber communications systems.

亚历山大藻对海产贝类胚胎和蒙古裸腹溞的影响及致毒机制研究

本文研究了典型有毒赤潮藻——亚历山大藻(Alexandrium)对海湾扇贝(Argopecten irradians Lamarck)、文蛤(Meretrix meretrix Linnaeus)和太平洋牡蛎(Ostrea gigas Thunberg)受精卵孵化的影响和致毒机制以及对蒙古裸腹溞(Moina mongolica Daday)生命活动的影响。此外，还针对我国赤潮发生特点，模拟研究了我国东海大规模赤潮对菲律宾蛤仔（Ruditapes philippinarum (Adams et Reeve)）受精卵孵化和蒙古裸腹溞种群数量的影响。 结果发现：8株产PSP毒素的亚历山大藻：塔玛亚历山大藻( ATHK, AT5-1, AT5-3, ATCI02, ATCI03)，链状亚历山大藻, A. lusitanicum、微小亚历山大藻和2株不产PSP毒素的相关亚历山藻(AC-1, AS-1)对海湾扇贝受精卵的孵化均有显著抑制作用，说明在亚历山大藻属中，这种抑制作用具有一定的普遍性，并与PSP毒素的产生无直接关系，表明存在非PSP毒素的其它毒性物质。一种PSP标准毒素STX也没有这种抑制作用，进一步证明该抑制作用与PSP毒素不直接相关。 相关亚历山大藻AC-1对海湾扇贝、文蛤和太平洋牡蛎受精卵孵化的有显著的毒害作用，其藻液、重悬液、去藻液和内容物均显著影响受精卵的孵化。相关亚历山大藻AC-1对海湾扇贝、文蛤和太平洋牡蛎担轮幼虫细胞的超微结构有显著破坏作用，破坏膜结构和胞内结构，影响细胞内的功能器官如溶酶体的稳定性，使卵黄颗粒萎缩变形；对文蛤和太平洋牡蛎的受精卵显示出极强的毒害作用： 3000cells•ml-1时，使二者胚胎完全溶掉消失；在2000cells•ml-1的藻液中培养2h后，担轮幼虫的外膜发生溶解，整个幼体呈葡萄串样。相关亚历山大藻AC-1产生的这种毒性物质可能对贝类胚胎细胞的结构和功能有影响。 亚历山大藻对蒙古裸腹溞的毒性效应与不同藻种/藻株密切有关：塔玛亚历山大藻（AT-6, ATCI02）、链状亚历山大藻、A. lusitanicum和微小亚历山大藻不影响蒙古裸腹溞的存活，而塔玛亚历山大藻（ATHK、ATCI03和AT5-1）和相关亚历山大藻(AC-1, AS-1)有显著影响。蒙古裸腹溞能摄食塔玛亚历山大藻(AT-6, ATHK, ATCI02, ATCI03, AT5-1)，链状亚历山大藻, A. lusitanicum和微小亚历山大藻，很少或基本不摄食相关亚历山大藻。亚历山大藻影响蒙古裸腹溞的RNA/DNA比值和蛋白质含量以及Na+,K+-ATP酶活性。相关亚历山大藻AC-1对蒙古裸腹溞的存活有极强的毒性作用，藻液、重悬液、内容物和碎片均有显著影响；即使与3×106cells•ml-1小球藻混合，10和50cells•ml-1的相关亚历山大藻AC-1仍能使蒙古裸腹溞的产幼数和存活时间显著下降。亚历山大藻对蒙古裸腹溞生命活动的影响不仅与PSP毒素有关，还与非PSP毒素有关；蒙古裸腹溞可能也是研究有害藻急性和慢性毒性的一种理想生物。 应用菲律宾蛤仔胚胎和蒙古裸腹溞评价我国东海特大规模赤潮对海洋生物资源的潜在危害时发现：单种链状亚历山大藻对菲律宾蛤仔受精卵的孵化和蒙古裸腹溞的种群增长均有显著不利影响；单种东海原甲藻（1~10×104cells•ml-1）对菲律宾蛤仔受精卵的孵化没有影响；较低密度的东海原甲藻能维持蒙古裸腹溞（2~5×104cells•ml-1）的种群增长；较高密度的东海原甲藻对蒙古裸腹溞（10×104cells•ml-1）种群有显著的抑制作用。两种藻以赤潮密度混合后，适当密度的东海原甲藻能在一定程度上减轻链状亚历山大藻对菲律宾蛤仔受精卵和蒙古裸腹溞的毒性。可见，东海连年爆发的大规模赤潮不仅对浮游生态系统有不利影响，若同时爆发亚历山大藻赤潮，则对海洋浮游生态系统和贝类资源的恢复产生更加不利的影响。

海洋经济动物精子超低温保存的研究

从1949年以来经过近五十年的发展，超低温保存种质细胞技术已经趋于成熟，特别是在家畜推广良种化的过程中发挥重要作用。对海洋动物种质细胞保存研究的范围主要集中在鲑鳟鱼类和牡蛎等少数几种海洋生物上。本研究结合“国家自然科学基金”研究项目，进行了三种贝类和两种鱼类精子的超低温保存实验，得到了它们在液氮（－196 ℃）条件下的适宜保存条件。栉孔扇贝（Chlamys farreri）冻精解冻后复苏比例、受精率和孵化率最高可达到49.39％、42.06％和12.15睦栉孔扇贝精子超低温保存时发生冷冻伤害的温度范围在－30 ℃～－60 ℃；其低温保存的最适降温速率为20 ℃／min；使用抗冻剂二甲基亚砜（DMSO）的最适浓度为5 ℃，其保存效果优于甘油；样品保存的最佳体积为0.6ml～1ml；解冻精子的最适水温为35 ℃，50 ℃次之，20 ℃最差；用自然海水激活解冻后精子的效果好于低盐度溶液；在0 ℃进行预处理平衡时间不宜太长；在抗冻液中加入蛋黄对保存效果没有改善，并且会对冻精的孵化率有抑制作用；用20 ℃／min和5％DMSO冷冻精子，液氮中保存栉孔扇贝精子55天后其复苏比例达到42.17％。超低温保存紫贻贝（Mytilus galloprovincialis Lamarck）精子，解冻后其复苏比例、受精率和孵化率最高可达到41.63％、69.52％和54.74％。保存紫贻贝精子最适降温速率为5 ℃／min，发生冻伤的温度范围是－20 ℃～－60 ℃；使用抗冻剂DMSO的保存效果好于甘油，且使用抗冻剂DMSO的最适浓度为15％；利用自然海水激活冻精效果好于低盐度或高pH值的溶液；样品体积（在0.2～1ml之间）对保存效果没有影响；采用15％DMSO和5 ℃／min的降温速率处理精子，液氮中保存90天后复苏比例仍达到41.8％。保存菲律宾蛤仔（Ruditapes philippinarum （Adams and Reeve））精子的最适降温速率为5 ℃／min，发生冻伤的温度范围是－30 ℃～－60 ℃；抗冻剂DMSO的保存效果好于甘油，也用DMSO与甘油混合使用，使用抗冻剂DMSO的最适浓度为10％；利用自然海水激活冻精效果好于低盐度或高pH的溶液；样品体积（在0.2％～1.6ml之间）对保存效果有显著影响。冷冻保存后精子复苏比例、受精率和孵化率最高达到40.84％、68.87％和47.17％；以最适降温速率和抗冻剂浓度处理精子，并在液氮中保存36天后冻精复苏比例仍可以达到38.54％。黑鲷（Sparus macrocephalus）精子经过超低温保存后复苏率、存活率最高可以达到61.37％和61.4。保存黑鲷精子时发生冷冻伤害的温度范围是－20 ℃～－60 ℃，适宜的降温速率为20 ℃／min；使用抗冻剂DMSO的适宜浓度为20％；样品体积对保存效果有相关性；利用自然海水激活冻精效果好于低盐度或高pH值的溶液；使用20％DMSO和20 ℃／min降温速率处理，在液氮中保存黑鲷精子66天后解冻，其复苏率和存活率分别为59.81％和58.45％。在液氮中保存真鲷（Pagrosomus major）精子时发生冷冻伤害的温域为－30 ℃～－60 ℃，适宜的降温速率为20 ℃／min；使用抗冻剂DMSO的适宜浓度为20％；采用低盐度或高pH值的溶液激活冻精的效果不如自然海水。真鲷冻精的复苏率和存活率最高可达到50.73％和62.5；以20 ℃／min和20％DMSO处理真鲷精子，保存在液氮中46天后冻精复苏率和存活率为50.63％和61.02％。通过对多种贝类和鱼类精子的超低温保存实验，不仅获得超低温保存基本条件，并且通过显微镜观察结合前人的研究，对产生冻伤的原因和保护的机理提出了一个模式。

Taxonomic study on the family Mitridae (Mollusca : Gastropoda : Neogastropoda) from the China's Seas. Subfamilies: Imbricariinae and Cylindromitrinae

Ninteen species of subfamilies Imbricariinae and Cylindromitrinae, family Mitridae, are recorded from the China's seas. Of which, one genus and six species are recorded for the first time from China's seas, i.e., genus Ziba Adams H and Adams A, Cancilla (Cancilla) carnicolor, Ziba duplilirata, Z. insculpta, Neocancilla circula, Scabricola (Scabricola) desetangsii, Scabricola (Swainsonia) ocellata ocellata.