A model-based approach for the analysis of neuronal information transmission in multi-input and -output systems

We present a new method to characterize multi-input and output neuronal systems using information theory. To obtain a lower bound of transinformation we take three steps: (1) Estimation of the deterministic response to isolate components carrying stimulus information. The deviation of the original response from the deterministic estimate is defined as noise. (2) Coordinate transformation using PCA yields an uncorrelated representation. (3) Partial transinformation values are calculated independently either by Shannon's formula assuming normality or based on density estimation for arbitrary distributions. We investigate the performance of the algorithms using simulated data and discuss suitable parameter settings. The approach allows to evaluate the degree to which stimulus features are encoded. Its potential is illustrated by analyses of neuronal activity in cat primary visual cortex evoked by electrical retina stimulation.     

SK channel subtypes enable parallel optimized coding of behaviorally relevant stimulus attributes: A review

Ion channels play essential roles toward determining how neurons respond to sensory input to mediate perception and behavior. Small conductance calcium-activated potassium (SK) channels are found ubiquitously throughout the brain and have been extensively characterized both molecularly and physiologically in terms of structure and function. It is clear that SK channels are key determinants of neural excitability as they mediate important neuronal response properties such as spike frequency adaptation. However, the functional roles of the different known SK channel subtypes are not well understood. Here we review recent evidence from the electrosensory system of weakly electric fish suggesting that the function of different SK channel subtypes is to optimize the processing of independent but behaviorally relevant stimulus attributes. Indeed, natural sensory stimuli frequently consist of a fast time-varying waveform (i.e., the carrier) whose amplitude (i.e., the envelope) varies slowly and independently. We first review evidence showing how somatic SK2 channels mediate tuning and responses to carrier waveforms. We then review evidence showing how dendritic SK1 channels instead determine tuning and optimize responses to envelope waveforms based on their statistics as found in the organism's natural environment in an independent fashion. The high degree of functional homology between SK channels in electric fish and their mammalian orthologs, as well as the many important parallels between the electrosensory system and the mammalian visual, auditory, and vestibular systems, suggest that these functional roles are conserved across systems and species.     

On the Classes of Aminoacyl-tRNA Synthetases,Amino Acids and the Genetic Code

The division of the aminoacyl-tRNA synthetases in two classes is compared with a division of the amino acids in two classes, obtained from the AAIndex databank by a principal component analysis. The division of the enzymes in Classes I and II follows to a great extent a division in the chemical and biological properties of their cognate amino acids. Furthermore, the phylogenetic trees of Classes I and II enzymes are highly correlated with dendrograms obtained for their cognate amino acids by using the indices in the AAIndex database. We argue that the evolution of aminoacyl-tRNA synthetases was determined by the characteristics of their corresponding amino acids. We interpret these results considering models for the origin and evolution of the genetic code in which an initial version, containing fewer amino acids, was modified by the incorporation of new amino acids following duplication and divergence of previous synthetases and tRNA molecules.     

Multivariate analysis of the Vicia sativa L. aggregate

GIL, J. & CUBERO, J. I., 1993. Multivariate analysis of the Vicia sativa L. aggregate . The sativa group of species was studied by using multivariate analysis and karyological analysis. Thirty biometrical characters were studied by using 92 Vicia sativa L. accessions from a variety of geographical sources. The four main taxa analysed were: sativa, macrocarpa, cordata and angustifolia. Principal component analysis provided clear separation among sativa, cordata and angustifolia in terms of the first two components. Karyotype analysis confirmed the PCA results, and by combining both methods, misclassed specimens can be correctly determined. Cluster analyses using the characters which displayed the greatest loads over the first components were performed in order to identify the most valuable characters from the taxonomic point of view. These were flower length, calyx length, pod width, constriction of the pod between seeds, leaf length, leaflet width, seed length and seed width. Our results suggest an early separation of angustifolia from the ancestral stem. The taxon cordata may be useful in future plant breeding programmes not only for crossing with V. saliva to increase the leaflet size of this taxon, but also as a bridge species between sativa and angustifolia.     

Oligochaeta of the middle Po River (Italy): principal component analysis of the benthic data

The application of principal component analysis to two types of habitat (the benthos of macrophytes and of central river bed) enabled us to single out some of the factors that affect the dynamics and the structure of the oligochaete population and its various reactions to environmental conditions. As regards macrophytes, the distribution of the variables on the basis of the first component is correlated, to a certain extent, with a seasonal factor without any significant differences among sites. The largest population is most closely correlated with the summer months. In fact, we found that the Naididae and Tubificidae species generally develop in larger numbers at higher temperatures. For the Tubificidae, we could detect a precise seasonal cycle. In the central river bed habitat, the first component was correlated with the river discharge, which determines the granulometric characteristics of the sediment; we noticed a correlation among the sites that have the same characteristics, regardless of sampling site or date. The species which correlate most closely among themselves are the Tubificidae Limnodrilus hoffmeisteri, Tubifex tubifex, L. udekemianus and L. profundicola, which are very characteristic of environments that contain abundant organic matter. The second component is correlated with temperature, and hence with the availability of oxygen, which determines the presence and the abundance of more sensitive species.     

Assessment of NIR spectroscopy for nondestructive analysis of physical and chemical attributes of sulfamethazine bolus dosage forms

The goal of this study was to assess the utility of near infrared (NIR) spectroscopy for the determination of content uniformity, tablet crushing strength (tablet hardness), and dissolution rate in sulfamethazine veterinary bolus dosage forms. A formulation containing sulfamethazine, corn starch, and magnesium stearate was employed. The formulations were wet granulated with a 10% (wt/vol) starch paste in a high shear granulator and dried at 60°C in a convection tray dryer. The tablets were compressed on a Stokes B2 rotary tablet press running at 30 rpm. Each sample was scanned in reflectance mode in the wavelengths of the NIR region. Principal component analysis (PCA) of the NIR tablet spectra and the neat raw materials indicated that the scores of the first 2 principal components were highly correlated with the chemical and physical attributes. Based on the PCA model, the significant wavelengths for sulfamethazine are 1514, (1660–1694), 2000, 2050, 2150, 2175, 2225, and 2275 nm; for corn starch are 1974, 2100, and 2325 nm; and for magnesium stearate are 2325 and 2375 nm. In addition, the loadings show large negative peaks around the water band regions (≈1420 and 1940 nm), indicating that the partial least squares (PLS) models could be affected by product water content. A simple linear regression model was able to predict content uniformity with a correlation coefficient of 0.986 at 1656 nm; the use of a PLS regression model, with 3 factors, had anr ² of 0.9496 and a sandard error of calibration of 0.0316. The PLS validation set had anr ² of 0.9662 and a standard error of 0.0354. PLS calibration models, based on tablet absorbance data, could successfully predict tablet crushing strength and dissolution in spite of varying active pharmaceutical ingredient (API) levels. Prediction plots based on these PLS models yielded correlation coefficients of 0.84 and 0.92 on independent validation sets for crushing strength and Q₁₂₀ (percentage dissolved in 120 minutes), respectively. Published: September 20, 2005 The opinions expressed in this paper are of the authors' personal views. They do not necessarily reflect the views or policies of the FDA.     

Phytoplankton Distribution in the Coastal Area Subject to the Impact with the Tiber River Outfall

The taxonomic composition and geographical distribution of phytoplankton in the coastal zone surrounding the River Tiber mouth were investigated in twelve surveys from April 1978 to September 1979. Ninety phytoplankton species were identified from 168 samples. Diatoms were clearly the dominating species, accounting for more than 95 per cent of total phytoplankton.— Principal Component Analysis was utilized to analyse the total information obtained.—The direct impact on the coastal environment of River Tiber water and its considerable nutrient load were seen as providing a permanent potential for the development of less structured phytoplankton communities. Heterogeneity of local hydrological conditions and fluctuations in the river's impact, lead to a virtually constant instability in the neritic environment near the Tiber River outfall.     

矿质元素及pH值与栀子中栀子苷含量的相关性

为了探讨栀子苷含量与土壤及药材中的矿质元素的相关关系,用主成分分析方法对8个不同产地的栀子土壤中13种矿质元素及pH与药材中12种矿质元素进行了多因素分析.结果表明:Fe和Ni、Fe和Al、Mn和Co之间呈极显著正相关.影响栀子苷含量的Mg和pH贡献率分别为49.614%和20.826%,两者对栀子苷的变异贡献率最大.同时进行了栀子苷含量的变化与主成分的多元相关分析,证实了矿质元素与中药功效之间存在相关性.     

Analysis of the agglutinating activity from unicellular algae

Agglutinating activity often varies both between and within the algal species assayed. However, it is difficulty to interpret such variation without further analysis. We report a statistical analysis of agglutinating activities against human, cow, sheep, and pig erythrocytes, using cell extracts from 43 taxa (strains) of freshwater microalgae. Most of the extracts agglutinated erythrocytes from at least one of the sources, but pig erythrocytes appeared to be most suitable for the detection of agglutination reactions. Chlorella cell extracts preferentially agglutinated human erythrocytes, whereas extracts of other taxa were less active against mammalian erythrocytes. Cluster analysis generated four distinct subclusters of taxa, characterized by different specificities for antigens or carbohydrate receptors on the erythrocytes. Principal component analysis further separated the agglutination characteristics of Chlamydomonas from Chlorella on the first two components. Specificity for pig erythrocytes accounted for most of the clustering or grouping of algal taxa in multivariate analysis. However, clustering or grouping patterns of Chlorella species on haemagglutinating activity resembled that based on DNA sequences, revealing a possible genetic connection of agglutinins and their biochemical characteristics in algal cells. Variability of agglutination reactions among the algae investigated is simplified and interpreted most easily using multivariate analysis.     

非线性映射法用于鼠尾草属植物的分析鉴定

运用梯度洗脱测定鼠尾草鼠植物中9个主要成分含量的实验数据,对鼠尾草属13个种26个样本进行非线性映射分析鉴定。结合BASICA语言程序,采用主成分分析法给出二维平面上的初始坐标,并运用逐点迭代循环至误差函数E最小,得到各样本的最终坐标,映射到二维空间,进行直观分析。能够直观地将孤隔鼠尾草亚属与荔枝草亚属的样本分离开来,具有一定合理性与实用性。     

The principal motions involved in the coupling mechanism of the recovery stroke of the myosin motor

Muscle contraction is driven by a cycle of conformational changes in the myosin II head. After myosin binds ATP and releases from the actin fibril, myosin prepares for the next power stroke by rotating back the converter domain that carries the lever arm by 60 degrees . This recovery stroke is coupled to the activation of myosin ATPase by a mechanism that is essential for an efficient motor cycle. The mechanics of this coupling have been proposed to occur via two distinct and successive motions of the two helices that hold the converter domain: in a first phase a seesaw motion of the relay helix, followed by a piston-like motion of the SH1 helix in a second phase. To test this model, we have determined the principal motions of these structural elements during equilibrium molecular dynamics simulations of the crystallographic end states of the recovery-stroke by using principal component analysis. This reveals that the only principal motions of these two helices that make a large-amplitude contribution towards the conformational change of the recovery stroke are indeed the predicted seesaw and piston motions. Moreover, the results demonstrate that the seesaw motion of the relay helix dominates in the dynamics of the pre-recovery stroke structure, but not in the dynamics of the post-recovery stroke structure, and vice versa for the piston motion of the SH1 helix. This is consistent with the order of the proposed two-phase model for the coupling mechanism of the recovery stroke. Molecular movies of these principal motions are available at http://www.iwr.uni-heidelberg.de/groups/biocomp/fischer.     

Spawning and Brood Defense of Smallmouth Bass Under the Process of Invasion into a Novel Habitat

Smallmouth bass, Micropterus dolomieu, known as one of the world's most disastrous invasive species, was introduced into Lake Aoki, central Japan in the last 10 years and is of concern for the conservation of the native biodiversity. We investigated spawning and brood defense under novel conditions to devise measures to eradicate a local population of this species. Compared to their native habitat, the size distribution of nesting males was less skewed to the right in this invasive population but rather a skewed normal distribution probably due to prevention of younger cohorts entering the nesting stock. The number of offspring deposited in nests was not positively related to the size of the nesting male. These observations imply that a shortage of suitable nest sites leads to an escalation in male–male competition, followed by a relaxation of female mate choice based on male size. Further, when presented with a model of a potential predator of the offspring, nesting males reacted individually and the intensity of site tenacity was independent of the male size. We propose that the removal of cover accompanied by the use of native predators of young bass can effectively decelerate the expansion of invasive smallmouth bass.     

Investigating the accessibility of the closed domain conformation of citrate synthase using essential dynamics sampling

A molecular dynamics study of pig heart citrate synthase is presented that aims to directly address the question of whether, for this enzyme, the ligand-induced closed domain conformation is accessible to the open unliganded enzyme. The approach utilises the technique of essential dynamics sampling, which is used in two modes. In exploring mode, the enzyme is encouraged to explore domain conformations it might not normally sample in free molecular dynamics simulation. In targeting mode, the enzyme is encouraged to adopt the domain conformation of a target structure. Using both modes extensively, it has been found that when the enzyme is prepared from a crystallographic open-domain structure and is in the unliganded state, it is unable to adopt the crystallographic closed-domain conformation of the liganded enzyme. Likewise, when the enzyme is prepared from the crystallographic closed liganded conformation with the ligands removed, it is unable to adopt the crystallographic open domain conformation. Structural investigations point to a common structural difference that is the source of this energy barrier; namely, the shift of alpha-helix 328-341 along its own axis relative to the large domain. Without this shift, the domains are unable to close or open fully. The charged substrate, oxaloacetate, binds near the base of this helix in the large domain and the interaction of Arg329 at the base of the helix with oxaloacetate is one that is consistent with the shift of this helix in going from the crystallographic open to closed structure. Therefore, the results suggest that without the substrate the enzyme remains in a partially open conformation ready to receive the substrate. In this way, the efficiency of the enzyme should be increased over one that is closed part of the time, with its binding site inaccessible to the substrate.     

Assessing the Performance of Neural Encoding Models in the Presence of Noise

An analytical method is introduced for evaluating the performance of neural encoding models. The method addresses a critical question that arises during the course of the development and validation of encoding models: is a given model near optimal in terms of its accuracy in predicting the stimulus-elicited responses of a neural system, or can the predictive accuracy be improved significantly by further model development? The evaluation method is based on a derivation of the minimum mean-square error between actual responses and modeled responses. It is formulated as a comparison between the mean-square error of the candidate model and the theoretical minimum mean-square error attainable through an optimal model for the system. However, no a priori information about the nature of the optimal model is required. The theoretically minimum error is determined solely from the coherence function between pairs of system responses to repeated presentations of the same dynamic stimulus. Thus, the performance of the candidate model is judged against the performance of an optimal model rather than against that of an arbitrarily assumed model. Using this method, we evaluated a linear model for neural encoding by mechanosensory cells in the cricket cercal system. At low stimulus intensities, the best-fit linear model of encoding by single cells was found to be nearly optimal, even though the coherence between stimulus-response pairs (a commonly used measure of system linearity) was low. In this low-stimulus-intensity regime, the mean square error of the linear model was on the order of the power of the cell responses. In contrast, at higher stimulus intensities the linear model was not an accurate representation of neural encoding, even though the stimulus-response coherence was substantially higher than in the low-intensity regime.     

Investigation of the anti-fungal activity of coptisine on Candida albicans growth by microcalorimetry combined with principal component analysis

Aims:  This study investigated the anti-fungal activity of coptisine on Candida albicans growth.
Methods and Results:  The metabolic power-time curves of Candida albicans growth at 37°C affected by coptisine were measured by microcalorimetry using an LKB-2277 Bioactivity Monitor with stop-flow mode. Then, the diameter of inhibitory zones in the agar layer was observed using agar cup method, and the minimal inhibitory concentration (MIC) of coptisine on Candida albicans growth was determined by serial dilution method. From the principal component analysis on nine quantitative parameters obtained from the power-time curves, we could easily evaluate the anti-fungal activity of coptisine by analysing the change of values of the main two parameters, growth rate constant k and maximum power output in the log phase P _{m, log}. The results showed that coptisine had strong anti-fungal activity: at a low concentration (45  μ g ml⁻¹) began to inhibit the growth of Candida albicans and at a high concentration (500  μ g ml⁻¹) completely inhibited Candida albicans growth. Coptisine gave big inhibitory zones with diameters between 11 and 43 mm within test range, and the MIC of it was 1000  μ g ml⁻¹.
Conclusions:  Coptisine had strong anti-fungal activity on Candida albicans growth. The method of microcalorimetry applied for the assay of anti-fungal activity of coptisine was quantitative, sensitive and simple.
Significance and Impact of the Study:  This work will provide useful information for the development of chemical biology policy in the use of anti-microbials in food and drug production.     

Assessment of Heavy Metal Contamination in the Sediments of the Shuangtaizi Estuary Using Multivariate Statistical Techniques

In order to assess heavy metal pollution of sediment samples collected from Shuangtaizi estuary, contamination factor (CF) and multivariate statistical analyses, including principal component analysis (PCA), cluster analysis (CA) and correlation analysis, are carried out in this paper. CF confirms that Pb, Cu and Hg concentrations are very low and all fall within the range of background, while Zn and Cd demonstrate moderate contamination (in A10, A13, A15, A16 and A17 sites) and very high contamination (in A10, A13, A15 and A17 sites), respectively. The PCA indicates that four significant principal components (PCs) are extracted, explaining 88.959% of total variance, which suggests that Pb, Cu and Zn are mainly associated with organic carbon (OC). The result from CA is consistent with that obtained from PCA, classifying that the heavy metals in two clusters derive from different sources. Correlation analysis supports the conclusions from PCA and CA, elucidating the relationships between heavy metals and particle sizes of the sediments.     

适宜印度块菌生长的地形和土壤因子

在云南、四川和西藏印度块菌产区的9个地点进行调查和采样,选择地形因子和土壤因子为评价指标,采用主成分分析法对印度块菌生长适宜性进行综合评价,以确定印度块菌的生长与地形因子和土壤因子的关系.结果表明:1)地形因子和土壤因子15个指标中提取出的5个主成分,累计贡献率达到87.5％.地形因子中坡位对块菌生长的影响最大,坡位越高越不适宜块菌生长,以中坡和中下坡最佳.2)土壤因子中容重、粉粒含量、pH值、全氮含量、交换性钙镁含量是块菌生长的限制因子.容重为0.65～0.82 g· cm-3适宜块菌生长,而容重过高(＞1 g·cm-3)不利于块菌的生长;粉粒含量为30.0％、砂粒含量为55.0％左右适宜块菌的生长,而粘粒含量过高不利于块菌的生长.在土壤化学因子中,pH值在6.40左右、全氮为2.29 ～3.70 g·kg-1、交换性钙为22.91～37.17 cmol·kg-1、交换性镁含量为1.85～2.59 cmol·kg-1的环境条件适宜块菌生长.3)综合评价表明,在9个采集地点,云南省昆明市哨上村和西藏自治区林芝地区江色岗得分较高,其地形和土壤条件最适合块菌生长;而四川省攀枝花市二十九梁子和云南省楚雄州五顶山得分较低,其地形和土壤条件不太适宜印度块菌生长.     

Multivariate analysis of phyto-climatic patterns of the Croatian part of the eastern Adriatic coast

ABSTRACT

The present study analyses the climatic patterns of that part of the eastern Adriatic coast belonging to the Republic of Croatia and the narrow zone of the inlands. This area comprises a part of the Mediterranean phytogeographic region characterised by the Mediterranean climate type, and the transitional area towards the Eurosiberian phytogeographic region influenced by the continental climate type. The analysis was performed using multivariate numerical methods, cluster analysis following by the inertia analysis, and Principal Components Analysis with partitioning, considering the principal local climatic gradients in the data set. Six main climate classes were obtained. The results are biologically more interpretable than those obtained by using either numerical indices or the Walter climate diagram system. This suggests that multivariate numerical methods could be more efficient tools for detecting biologically significant climatic patterns on a small spatial scale.     

Vegetation classification of East China with multi-temporal NOAA-AVHRR data

East China lies in the subtropical monsoon climatic zone and is dominated by subtropical evergreen broad-leaved forests,a unique vegetation type mainly distributed in East Asia with the largest distnbution in China.It is important to be able to monitor and estimate forest biomass and production,regional carbon storage,and global climate change impacts on these important vegetation types.In this paper,we used coarse resolution remote sensing data to identify the vegetation types in East China and developed a map of the spatial distribution of vegetation types in this region.Nineteen maximum normalized difference vegetation index(NDVI)composite images(acquisition time span of 7 months from February to August),which were derived from 10 days National Oceanographic and Atmospheric Administration(NOAA)Advanced Very High Resolution Radiometer(AVHRR)channel 1 and channel 2 observations,an unsupervised classification method,and the ISODATA algorithm were employed to identify the vegetation types.To reduce the dimensions of the dataset resulted in a total of 28 spectral clusters of land-cover of which two clusters were urban/bare soil and water,the images were processed using principal component analysis(PCA).The 26 remaining spectral clusters were merged into six vegetation types using the Chinese vegetation taxonomy system:evergreen broad-leaved forest,coniferous forest,bamboo forest,shrub-grass,aquatic vegetation,and agricultural vegetation.The spatial distribution and areal extent for the coniferous forests,shrub-grass,evergreen broad-leaved forests,and agricultural vegetation were calculated and comscale.The spatial accuracy and the area accuracy for coniferous forests,shrub-grass,evergreen broad-leaved forests,and agricultural vegetation were 79.2%,91.3%,68.2% and 95.9% and 92.1%,95.9%,63.8% and 90.5%,respectively.The spatial accuracy and area accuracy of the bamboo forest were 28.7% and 96.5%,respectively;the spatial accuracy of aquatic vegetation was 69.6%,but there was a significant difference in its area accuracy because image acquisition did not cover the full year.Our study demonstrated the fea sibility of using NOAA-AVHRR to identify the different vegetation types in the subtropical evergreen broad-leaved forest zone in East China.The spatial location of the six identified vegetation types agreed with the actual geo graphical distribution of the vegetation types in East China.