基于稀疏编码和SCG BPNN的鳞翅目昆虫图像识别

【目的】为了给林业、 农业或植物检疫等行业人员提供一种方便快捷的昆虫种类识别方法, 本文提出了一种新颖的鳞翅目昆虫图像自动识别方法。【方法】首先通过预处理对采集的昆虫标本图像去除背景, 分割出双翅, 并对翅图像的位置进行校正。然后把校正后的翅面分割成多个超像素, 用每个超像素的l, a, b颜色及x, y坐标平均值作为其特征数据。接下来用稀疏编码(SC)算法训练码本、 生成编码并汇集成特征向量训练量化共轭梯度反向传播神经网络（SCG BPNN）, 并用得到的BPNN进行分类识别。【结果】该方法对包含576个样本的昆虫图像的数据库进行了测试, 取得了高于99%的识别正确率, 并有理想的时间性能、 鲁棒性及稳定性。【结论】实验结果证明了本文方法在识别鳞翅目昆虫图像上的有效性。     

BCL::Fold—Protein topology determination from limited NMR restraints

When experimental protein NMR data are too sparse to apply traditional structure determination techniques, de novo protein structure prediction methods can be leveraged. Here, we describe the incorporation of NMR restraints into the protein structure prediction algorithm BCL::Fold. The method assembles discreet secondary structure elements using a Monte Carlo sampling algorithm with a consensus knowledge‐based energy function. New components were introduced into the energy function to accommodate chemical shift, nuclear Overhauser effect, and residual dipolar coupling data. In particular, since side chains are not explicitly modeled during the minimization process, a knowledge based potential was created to relate experimental side chain proton–proton distances to C_β–C_β distances. In a benchmark test of 67 proteins of known structure with the incorporation of sparse NMR restraints, the correct topology was sampled in 65 cases, with an average best model RMSD100 of 3.4 ± 1.3 Å versus 6.0 ± 2.0 Å produced with the de novo method. Additionally, the correct topology is present in the best scoring 1% of models in 61 cases. The benchmark set includes both soluble and membrane proteins with up to 565 residues, indicating the method is robust and applicable to large and membrane proteins that are less likely to produce rich NMR datasets. Proteins 2014; 82:587–595. © 2013 Wiley Periodicals, Inc.     

干旱区荒漠稀疏植被覆盖度提取及尺度扩展效应

选择线性混合像元分解模型、亚像元模型、最大三波段梯度差法模型以及修正的三波段梯度差法的2个变异模型来提取植被覆盖度,结合地面实测数据,探讨了提取干旱区荒漠稀疏植被覆盖度信息的适宜模型,并以简单平均法模拟了不同尺度的覆盖度影像,通过尺度上推检验了模型在MODIS尺度上的反演效应.结果表明：线性混合像元分解模型反演覆盖度的精度高于其他模型,适于稀疏植被地区,但端元的正确选取较难,从而影响其运用;亚像元分解模型是一个通用模型,植被分类图越精细,通过亚像元分解模型得到的覆盖度精度越高,但这也同时意味着该模型需要测定大量的输入参数;最大三波段梯度差法的算法简单、易于操作,其在农田等中高植被覆盖区及裸土区的预测值与实测值接近,但对干旱区稀疏植被的估计精度偏低;修正后的三波段最大梯度差法模型在稀疏植被覆盖区的预测值与实测值基本一致,在不同尺度上反演的覆盖度信息与实测值的一致性较好.该方法可有效提取干旱区低覆盖度植被信息.     

Measuring and modelling the radiation balance of a heterogeneous shrubland

The accurate quantification of the energy available for sensible and latent heat transfer from plant canopies is essential for the prediction of impacts of climate on vegetation water use and growth. Unlike agricultural fields and extensive forests of more humid zones, vegetation growing in semi‐arid climates is usually sparse creating a heterogeneous surface of shrubs, annuals and bare soil. Under these conditions many of the assumptions of the basic equations used in microclimatology, which assume a uniform vegetated surface, may be violated. It is proposed here that heterogeneous canopies may require a formulation of their energy balance that includes a measure of the canopy complexity in order to both interpret field measurements and be used in predictive models. This paper explores the need for a more complex formulation of the vegetation energy balance through a series of experiments on a sparse clumped shrubland of Retama sphaerocarpa in the Tabernas Desert, Almería, south‐east Spain. These experiments investigated the importance of the radiative properties of each surface on energy balance of soil, annuals and shrubs individually, and the surface as a whole. The study evaluated the use of the fractional vegetative cover (f) and the radiative characteristics of each surface (reflection coefficients and emissivities) for calculating net radiation partitioning between shrubs and bare soil. Results indicated that partitioning of net radiation between components could be accurately calculated from values of fractional vegetative cover, reflection coefficients and emissivities for both bare soil and plant surfaces. A sensitivity analysis showed the importance of specific radiation properties of each surface. Measurements of horizontal long‐wave fluxes between components showed that the location of a plant with respect to other plants made little difference to its long‐wave energy balance. The results also emphasized the importance of soil water content on the energy balance, through its influence on albedo and soil heat storage. This was particularly true when measurements of soil heat flux were used to measure the available energy for soil under shrubs and bare soil because of strong hysteresis cycles. These cycles were larger in the bare soil than in the substrate under shrubs.     

川东南杂交中稻超稀栽培对稻米整精米率和垩白粒率的影响

以‘II优7号’、‘汕优63’和‘香优2号’为材料,研究了超稀栽培与稻米整精米率和垩白粒率的关系及其作用原因,结果表明：栽秧密度与整精米率呈极显著负相关,与垩白粒率呈极显著正相关。在中高氮施肥水平条件下,当栽秧密度超稀到7.51万穴•hm-2时,在保证比传统高产栽培密度每公顷栽秧21.64万穴的对照不减产前提下,整精米率提高了15.69%～29.92%,垩白粒率降低了16.34%～21.22%。其原因在于,超稀植增加了每穗着粒数,降低了齐穗期的叶粒比,以致稻穗籽粒灌浆速率减慢而改善整精米率和垩白粒率。齐穗后20 d施氮可同时起到提高结实率和整精米率的双重效果。     

SNMDA: A novel method for predicting microRNA‐disease associations based on sparse neighbourhood

miRNAs are a class of small noncoding RNAs that are associated with a variety of complex biological processes. Increasing studies have shown that miRNAs have close relationships with many human diseases. The prediction of the associations between miRNAs and diseases has thus become a hot topic. Although traditional experimental methods are reliable, they could only identify a limited number of associations as they are time‐consuming and expensive. Consequently, great efforts have been made to effectively predict reliable disease‐related miRNAs based on computational methods. In this study, we present a novel approach to predict the potential microRNA‐disease associations based on sparse neighbourhood. Specifically, our method takes advantage of the sparsity of the miRNA‐disease association network and integrates the sparse information into the current similarity matrices for both miRNAs and diseases. To demonstrate the utility of our method, we applied global LOOCV, local LOOCV and five‐fold cross‐validation to evaluate our method, respectively. The corresponding AUCs are 0.936, 0.882 and 0.934. Three types of case studies on five common diseases further confirm the performance of our method in predicting unknown miRNA‐disease associations. Overall, results show that SNMDA can predict the potential associations between miRNAs and diseases effectively.     

Bayesian sparse‐based reconstruction in bioluminescence tomography improves localization accuracy and reduces computational time

Bioluminescence tomography (BLT) provides fundamental insight into biological processes in vivo. To fully realize its potential, it is important to develop image reconstruction algorithms that accurately visualize and quantify the bioluminescence signals taking advantage of limited boundary measurements. In this study, a new 2‐step reconstruction method for BLT is developed by taking advantage of the sparse a priori information of the light emission using multispectral measurements. The first step infers a wavelength‐dependent prior by using all multi‐wavelength measurements. The second step reconstructs the source distribution based on this developed prior. Simulation, phantom and in vivo results were performed to assess and compare the accuracy and the computational efficiency of this algorithm with conventional sparsity‐promoting BLT reconstruction algorithms, and results indicate that the position errors are reduced from a few millimeters down to submillimeter, and reconstruction time is reduced by 3 orders of magnitude in most cases, to just under a few seconds. The recovery of single objects and multiple (2 and 3) small objects is simulated, and the recovery of images of a mouse phantom and an experimental animal with an existing luminescent source in the abdomen is demonstrated. Matlab code is available at https://github.com/jinchaofeng/code/tree/master .      

Exploring the effects of sparse restraints on protein structure prediction

One of the main barriers to accurate computational protein structure prediction is searching the vast space of protein conformations. Distance restraints or inter‐residue contacts have been used to reduce this search space, easing the discovery of the correct folded state. It has been suggested that about 1 contact for every 12 residues may be sufficient to predict structure at fold level accuracy. Here, we use coarse‐grained structure‐based models in conjunction with molecular dynamics simulations to examine this empirical prediction. We generate sparse contact maps for 15 proteins of varying sequence lengths and topologies and find that given perfect secondary‐structural information, a small fraction of the native contact map (5%‐10%) suffices to fold proteins to their correct native states. We also find that different sparse maps are not equivalent and we make several observations about the type of maps that are successful at such structure prediction. Long range contacts are found to encode more information than shorter range ones, especially for α and αβ‐proteins. However, this distinction reduces for β‐proteins. Choosing contacts that are a consensus from successful maps gives predictive sparse maps as does choosing contacts that are well spread out over the protein structure. Additionally, the folding of proteins can also be used to choose predictive sparse maps. Overall, we conclude that structure‐based models can be used to understand the efficacy of structure‐prediction restraints and could, in future, be tuned to include specific force‐field interactions, secondary structure errors and noise in the sparse maps.     

基于多层次稀疏编码预测蛋白质亚细胞定位

文中提出了一种简单有效的蛋白质亚细胞区间定位预测方法,为进一步了解蛋白质的功能和性质提供理论基础。运用稀疏编码,结合氨基酸组成信息提取蛋白质序列特征,基于不同字典大小对得到的特征进行多层次池化整合,并送入支持向量机进行分类。经Jackknife检验,在数据集ZD98、CH317和Gram1253上的预测成功率分别达到95.9%、93.4%和94.7%。实验证明基于多层次稀疏编码的分类预测算法能显著提高蛋白质亚细胞区间定位的预测精度。     

Resolution-adapted recombination of structural features significantly improves sampling in restraint-guided structure calculation

Recent work has shown that NMR structures can be determined by integrating sparse NMR data with structure prediction methods such as Rosetta. The experimental data serve to guide the search for the lowest energy state towards the deep minimum at the native state which is frequently missed in Rosetta de novo structure calculations. However, as the protein size increases, sampling again becomes limiting; for example, the standard Rosetta protocol involving Monte Carlo fragment insertion starting from an extended chain fails to converge for proteins over 150 amino acids even with guidance from chemical shifts (CS-Rosetta) and other NMR data. The primary limitation of this protocol--that every folding trajectory is completely independent of every other--was recently overcome with the development of a new approach involving resolution-adapted structural recombination (RASREC). Here we describe the RASREC approach in detail and compare it to standard CS-Rosetta. We show that the improved sampling of RASREC is essential in obtaining accurate structures over a benchmark set of 11 proteins in the 15-25 kDa size range using chemical shifts, backbone RDCs and HN-HN NOE data; in a number of cases the improved sampling methodology makes a larger contribution than incorporation of additional experimental data. Experimental data are invaluable for guiding sampling to the vicinity of the global energy minimum, but for larger proteins, the standard Rosetta fold-from-extended-chain protocol does not converge on the native minimum even with experimental data and the more powerful RASREC approach is necessary to converge to accurate solutions.