Predicting Secondary Structures, Contact Numbers, and Residue-wise Contact Orders of Native Protein Structure from Amino Acid Sequence by Critical Random Networks

Prediction of one-dimensional protein structures such as secondary structures and contact numbers is useful for the three-dimensional structure prediction and important for the understanding of sequence-structure relationship. Here we present a new machine-learning method, critical random networks (CRNs), for predicting one-dimensional structures, and apply it, with position-specific scoring matrices, to the prediction of secondary structures (SS), contact numbers (CN), and residue-wise contact orders (RWCO). The present method achieves, on average, $Q_3$ accuracy of 77.8% for SS, correlation coefficients of 0.726 and 0.601 for CN and RWCO, respectively. The accuracy of the SS prediction is comparable to other state-of-the-art methods, and that of the CN prediction is a significant improvement over previous methods. We give a detailed formulation of critical random networks-based prediction scheme, and examine the context-dependence of prediction accuracies. In order to study the nonlinear and multi-body effects, we compare the CRNs-based method with a purely linear method based on position-specific scoring matrices. Although not superior to the CRNs-based method, the surprisingly good accuracy achieved by the linear method highlights the difficulty in extracting structural features of higher order from amino acid sequence beyond that provided by the position-specific scoring matrices.Comment: 20 pages, 1 figure, 5 tables; minor revision; accepted for publication in BIOPHYSIC

Litosol: suas características e provável gênese

Some of the characteristics peculiar to Litosois are discussed based on data published on Litosois occurring in the States of São Paulo and Paraná. Litosois are the first stages of development of a soil. Litosois probably originate through the exposure of the rockbed caused by an excessive relief. Rock weathering processes are intensive, prevailing those of chemical nature rather than those processes in which physical phenomena dominate. The A horizon has a high organic matter content (2% to 10%). Silt and clay amount to approximately 50% of the fine earth in the A horizon, with the exception of Litosois originated from sandstone and granite. The SiO2/Al2O3 relationship of the soil's colloidal complex and the clay's cation exchange capacity indicate that it is quite probable the presence of 2:1 type clay in Litosois derived from basic rocks

Fast and efficient critical state modelling of field-cooled bulk high-temperature superconductors using a backward computation method

Abstract: A backward computation method has been developed to accelerate modelling of the critical state magnetization current in a staggered-array bulk high-temperature superconducting (HTS) undulator. The key concept is as follows: (i) a large magnetization current is first generated on the surface of the HTS bulks after rapid field-cooling (FC) magnetization; (ii) the magnetization current then relaxes inwards step-by-step obeying the critical state model; (iii) after tens of backward iterations the magnetization current reaches a steady state. The simulation results show excellent agreement with the H -formulation method for both the electromagnetic and electromagnetic-mechanical coupled analyses, but with significantly faster computation speed. The simulation results using the backward computation method are further validated by the recent experimental results of a five-period Gd–Ba–Cu–O (GdBCO) bulk undulator. Solving the finite element analysis (FEA) model with 1.8 million degrees of freedom (DOFs), the backward computation method takes less than 1.4 h, an order of magnitude or higher faster than other state-of-the-art numerical methods. Finally, the models are used to investigate the influence of the mechanical stress on the distribution of the critical state magnetization current and the undulator field along the central axis

Mineralogia da fração argila de perfis de solos da série Ibitiruna

O presente trabalho teve por finalidade o estudo minera lógico, da fração argila, da série Ibitiruna (RANZANI et al. 9), pertencente a unidade de mapeamento Podzólico Vermelho Amarelo - variação Laras (COMISSÃO DE SOLOS 1). Foram coletados três perfis de solos, pertencente a série Ibitiruna, designados por perfis P1, P2 e P3. As amostras dos horizontes foram colhidas a partir da superfície do solo até a rocha. A fração argila foi separada por sedimentação, sendo posteriormente, dividida em duas subfrações (centrifugação): 2 a 0,2 mícron e menor que 0,2 mícron, argila grossa e fina respectivamente. O material obtido nestas duas frações, sofreu determinações químicas (capacidade de troca de cátions) e determinações de raio-X (obtenção de difratogramas, com o auxílio do contador Geiger, e filmes, pelo método do pó). Através dêstes resultados, foi efetuado o reconhecimento dos minerais de argila assim como estimativa semiquantitativa. A análise mineralógica das frações argila grossa e fina, referentes à natureza e à quantidade dos minerais de argila indica o seguinte: a caolinita é o mineral dominante nas duas frações argila, com teores sempre acima de 40%; a montmorilonita e os minerais do grupo de 14 Anormalmente ocorrem com valôres inferiores a 10%.The purpose of this work was to study mineralogically the clay fraction of the Ibitiruna series (RANZANI e_t jal. 9). These soils belong to the Great Soil Group Red - Yellow Podzolic, Laras variety. Three profiles were collected within the areas where Ibitiruna series occur; these were labeled profiles P1, P2 and P3. The soil horizons were sampled individually in each profile from the surface down to the rock bed. The clay fraction was subdevided by centrifugation in coarce and fine clay with 0,2 micron as their limit of separation. The identification of clay minerals in the two fractions and a semiquantitative analysis was done by interpretation of the results obtained from chemical analysis (cation exchange capacity) and X-ray analysis (difratogram using a Geiger counter and films using the powder method). The mineralogical study of the two clay fractions, relative to the nature and quantity of clay minerals, indicate the following: kaolinita is the mineral that occur in greater quantit in the two clay fractions with a content always highter then 40%; the montmorilonite and the 14 A minerals normally occur values lower than 10%

Mineralogia da fração argila de perfis de solos da série Piracicaba

The purpose of this work was to study mineralogically the clay fraction of the Piracicaba series (RANZANI et al. 9). These soils belong to the Great Soil Group Red-Yellow Podzolic, Piracicaba variety. Four profiles were collected within the areas where Piracicaba series occur; these were labeled profiles P1 through P4. The soil horizons were sampled individually in each profile from the surface down to the rock bed. The clay fraction was subdevided by centrifugation in coarse and fine clay with 0,2 micron as their limit of separation. The identification of clay minerals in the two fractions and a semiquantitative analysis was done by interpretation of the results obtained from chemical analysis (% of K2O and cation exchange capacity) and X-ray analysis (difratogram using a Geiger counter and films using the powder method). The mineralogical analysis of the solo clay fractions, relative to the nature and quantity of clay minerals, indicate the following: the content of illite in the coarse clay fraction is always higher than 10% and in certain horizons shows a content of 30% or even 40%. The montmorilonite and the 14 A minerals normally occur with values lower than 10%, Kaolinite is the mineral that occur in greater quantity in the two clay fractions with a content always higher than 40%.O presente trabalho teve por finalidade o estudo mineralógico, da fração argila, da série Piracicaba (RANZANI et al. 9), pertencente à unidade de mapeamento Podzólico Vermelho Amarelo - variação Piracicaba (COMISSÃO DE SOLOS, 2). Foram coletados, na área de ocorrência da série Piracicaba, quatro perfis de solos, designados por perfis P1, P2, P3 e P4. As amostras dos horizontes foram colhidas a partir da superfície do solo até a rocha. A fração argila foi separada por sedimentação, sendo posteriormente, dividida em duas subfrações (centrifugação): 2 a 0,2 mícron e menor que 0,2 mícron, argila grossa e fina, respectivamente. O material obtido nestas duas frações, sofreu determinações químicas (% de K2O e capacidade de troca de cátions) e determinações de raio - X (obtenção de difratogramas, com auxílio do contador Geiger, e filmes, pelo método do pó). Através destes resultados, foi efetuado o reconhecimento dos minerais de argila assim como estimativa semiquantitativa. A análise mineralógica das frações argila grossa e fina, referentes à natureza e à quantidade dos minerais de argila indica o seguinte: o teor de ilita, na fração argila grossa é sempre maior do que 10%, sendo que, em certos horizontes, apresenta teor de 30% e mesmo 40%. A montmorilonita e os minerais de 14 A normalmente ocorrem com valores inferiores a 10%. A caolinita é o mineral dominante nas duas frações argila, com teores sempre acima de 40%

Cellulose mill liquid alkaline waste and gypsum as a substitute for lime in soils

Alkaline liquid effluent from cellulose factories was used in an experimental study to appraise the feasibility of utilizing this material with industrial gypsum (residual material from superphosphate production) for the correction of soil acidity. A soil + gypsum column was prepared and leached with the sodium rich industrial waste. Soil pH was raised but the amont of material needed bring it to 6.5 was found to vary with soil chemical composition and soil acidity buffering capacity. The soil leachate was richer in Na when gypsum was presented. Results obtained show that industrial gypsum combined with alkaline waste neutralizes soil acidity, increases soil calcium content and prevents sodium accumulation in the soil.Foram coletados vários efluentes alcalinos da fábrica de celulose a fim de estudar a utilização destes junto com fosfogesso na correção da acidez do solo. Avaliou-se o poder de neutralização dos efluentes e a lixiviação de sódio na presença de fosfogesso numa coluna de terra. A aplicação do efluente eleva o pH do solo e o volume de efluente necessário para atingir pH 6,5 depende da sua composição química e o poder tampão de acidez do solo. A lixiviação de sódio é maior quando o fosfogesso é incorporado ao solo. A combinação do efluente com o fosfogesso corrige a acidez do solo, aumenta o teor de cálcio e, ao mesmo tempo, reduz o acúmulo de sódio no solo

Release of magnesium from vermiculite by acid dissolution

The vermiculite from Paulistânia, State of Piauí, was used to study a release of magnesium by acid dissolution. The material was ground and sieved to separate two fractions: 0.50 to 0.15mm and < 0.10mm. Each fraction was divided into three parts, two of which were heated respectively to 550°C and 950°C in a muffle furnace for one hour. These vermiculites were treated with concentrated sulfuric acid and concentrated phosphoric acid in order to evaluate their efficiency in acid dissolution of vermiculite. A release of magnesium in relation to a quantity of sulfuric acid added and a amount of calcium carbonate necessary to neutralize a residual acidity of the product were also investigated. The sulfuric acid was just as effective as phosphoric acid in the dissolution of vermiculites and the release of magnesium. The particle-size and heat treatment of vermiculite had no influence on the amount of magnesium released by acid dissolution. The addiction of sulfuric acid to vermiculite in equal amount released more than 80% of magnesium. A quantity of calcium carbonate necessary to neutralize the residual acidity of the product was about one half the weight of the vermiculite.Estudou-se a liberação de magnésio estrutural da vermiculita procedente de Paulistânia, Estado de Piauí. O material foi triturado e peneirado para obter duas frações de 0,50 a l,15mm e de < 0,10mm. Cada fração de vermiculita foi dividida em três partes. As duas partes foram aquecidas num forno mufla às temperaturas de 550 e 950°C, respectivamente, durante uma hora. As vermiculitas, assim preparadas, foram tratadas com ácido sulfúrico conc. e ácido fosfórico conc. para avaliar a eficiência dos ácidos na liberação de magnésio. Em seguida, estudou-se a liberação de magnésio em função da quantidade de ácido sulfúrico e a necessidade de carbonato de cálcio para neutralizar a acidez residual do produto. Não houve diferença entre o ácido sulfúrico e o ácido fosfórico quanto a extração de magnésio da vermiculita. A granulometria e o aquecimento não influiram na liberação de magnésio pelos ácidos. A adição de ácido sulfúrico à vermiculita em quantidades iguais liberou mais que 80% de magnésio. A quantidade de carbonato de cálcio necessária para neutralizar a acidez residual do produto foi aproximadamente a metade do peso da vermiculita

Inverse analysis of critical current density in a bulk high-temperature superconducting undulator

In order to optimise the design of undulators using high-temperature superconductor (HTS) bulks we have developed a method to estimate the critical current density (Jc) of each bulk from the overall measured magnetic field of an undulator. The vertical magnetic field was measured along the electron-beam axis in a HTS bulk-based undulator consisting of twenty Gd-Ba-Cu-O (GdBCO) bulks inserted in a 12-T solenoid. The Jc values of the bulks were estimated by an inverse analysis approach in which the magnetic field was calculated by the forward simulation of the shielding currents in each HTS bulk with a given Jc. Subsequently the Jc values were iteratively updated using the pre-calculated response matrix of the undulator magnetic field to Jc. We demonstrate that it is possible to determine the Jc of each HTS bulk with sufficient accuracy for practical application within around 10 iterations. The pre-calculated response matrix, created in advance, enables the inverse analysis to be performed within a practically short time, on the order of several hours. The measurement error, which destroys the uniqueness of the solution, was investigated and the points to be noted for future magnetic field measurements were clarified. The results show that this inverse-analysis method allows the estimation of the Jc of each bulk comprising an HTS bulk undulator.CHART (Swiss Accelerator Research and Technology Collaboration); EPSRC Early Career Fellowship, EP/P020313/

Composite structural motifs of binding sites for delineating biological functions of proteins

Most biological processes are described as a series of interactions between proteins and other molecules, and interactions are in turn described in terms of atomic structures. To annotate protein functions as sets of interaction states at atomic resolution, and thereby to better understand the relation between protein interactions and biological functions, we conducted exhaustive all-against-all atomic structure comparisons of all known binding sites for ligands including small molecules, proteins and nucleic acids, and identified recurring elementary motifs. By integrating the elementary motifs associated with each subunit, we defined composite motifs which represent context-dependent combinations of elementary motifs. It is demonstrated that function similarity can be better inferred from composite motif similarity compared to the similarity of protein sequences or of individual binding sites. By integrating the composite motifs associated with each protein function, we define meta-composite motifs each of which is regarded as a time-independent diagrammatic representation of a biological process. It is shown that meta-composite motifs provide richer annotations of biological processes than sequence clusters. The present results serve as a basis for bridging atomic structures to higher-order biological phenomena by classification and integration of binding site structures.Comment: 34 pages, 7 figure