A new Pennsylvanian Oriocrassatellinae from Brazil and the distribution of the genus Oriocrassatella in space and time

Oriocrassatella Etheridge Jr., 1907 is a long range crassatellid bivalve genus well recognized in shallow waters of epeiric seas throughout the upper part of Paleozoic. The first occurrences of this genus are recorded in the sedimentary successions of the Gondwana, both in Australia and South America. However, the geographic and age distribution of Oriocrassatella in Late Mississippian deposits of Australia and Argentina may indicate an earliest Visean or even a pre-Visean origin for the genus. Following its origin in Early Carboniferous a complex paleobiogeographic history from Southern to Northern Hemisphere took place in the Permian. During its initial dispersal phase from Late Carboniferous to the Early Permian the genus thrived in cold water environments associated to the Late Paleozoic Gondwana glaciation. Shallow-water bottoms of the warm waters of the central Gondwana fringe and Laurussia were colonized by Oriocrassatella only during Early Permian times when the genus became cosmopolitan. A new species of this genus is described herein, Oriocrassatella piauiensis n. sp., recorded from the Piaui Formation, Pennsylvanian of the Parnaiba Basin. This new species may represent an early adaptation to warm waters. However, based on available data, species of this genus seem to have adapted definitely to warm water environments probably related the Late Pennsylvanian interglacial phases. In these phases, climatic barrier were interrupted allowing the faunal interchange and larval dispersion following a South to North migration route through the eastern margins of Gondwana and the eastern Paleotethys.

Rates of description of Phytoseiidae mite species (Acari: Mesostigmata): space, time and body size variations

This study aims to analyse the degree of completeness of world inventory of the mite family Phytoseiidae and the factors that might determine the process of species description. The world data set includes 2,122 valid species described from 1839 to 2010. Species accumulation curves were analysed. The effect of localisation (latitude ranges) and body size on the species description patterns over space and time was assessed. A low proportion of species seems remain to be described, but this trend could be explained by a critical reduction in the number of specialists dedicated to the study of those mites. In addition, this trend refers to the areas where phytoseiids have been well studied around the world, and it may change considerably if the study of these mites would be intensified in some areas. The number of newly described species is lower near the tropics, and their body size is also smaller. Differences in body size were noted between the three sub-families of Phytoseiidae, the highest mean body lengths of adult females being observed for Amblyseiinae, the most diverse family. In the future, collections would have certainly to take into consideration such conclusions for instance in using more adequate optical equipment especially for field collections. The decrease in the number of phytoseiid mite described was confirmed and the factors that could explain such a trend are discussed. Information for improving further inventories is provided and discussed, especially in relation to sampling localization and study methods.

Identifying regulational alterations in gene regulatory networks by state space representation of vector autoregressive models and variational annealing

Background: In the analysis of effects by cell treatment such as drug dosing, identifying changes on gene network structures between normal and treated cells is a key task. A possible way for identifying the changes is to compare structures of networks estimated from data on normal and treated cells separately. However, this approach usually fails to estimate accurate gene networks due to the limited length of time series data and measurement noise. Thus, approaches that identify changes on regulations by using time series data on both conditions in an efficient manner are demanded. Methods: We propose a new statistical approach that is based on the state space representation of the vector autoregressive model and estimates gene networks on two different conditions in order to identify changes on regulations between the conditions. In the mathematical model of our approach, hidden binary variables are newly introduced to indicate the presence of regulations on each condition. The use of the hidden binary variables enables an efficient data usage; data on both conditions are used for commonly existing regulations, while for condition specific regulations corresponding data are only applied. Also, the similarity of networks on two conditions is automatically considered from the design of the potential function for the hidden binary variables. For the estimation of the hidden binary variables, we derive a new variational annealing method that searches the configuration of the binary variables maximizing the marginal likelihood. Results: For the performance evaluation, we use time series data from two topologically similar synthetic networks, and confirm that our proposed approach estimates commonly existing regulations as well as changes on regulations with higher coverage and precision than other existing approaches in almost all the experimental settings. For a real data application, our proposed approach is applied to time series data from normal Human lung cells and Human lung cells treated by stimulating EGF-receptors and dosing an anticancer drug termed Gefitinib. In the treated lung cells, a cancer cell condition is simulated by the stimulation of EGF-receptors, but the effect would be counteracted due to the selective inhibition of EGF-receptors by Gefitinib. However, gene expression profiles are actually different between the conditions, and the genes related to the identified changes are considered as possible off-targets of Gefitinib. Conclusions: From the synthetically generated time series data, our proposed approach can identify changes on regulations more accurately than existing methods. By applying the proposed approach to the time series data on normal and treated Human lung cells, candidates of off-target genes of Gefitinib are found. According to the published clinical information, one of the genes can be related to a factor of interstitial pneumonia, which is known as a side effect of Gefitinib.

Reduced platelet amyloid precursor protein ratio (APP ratio) predicts conversion from mild cognitive impairment to Alzheimer's disease

Studies have shown that platelet APP ratio (representing the percentage of 120-130 kDa to 110 kDa isoforms of the amyloid precursor protein) is reduced in patients with mild cognitive impairment (MCI) and Alzheimer's disease (AD). In the present study, we sought to determine if baseline APP ratio predicts the conversion from MCI to AD dementia after 4 years of longitudinal assessment. Fifty-five older adults with varying degrees of cognitive impairment (34 with MCI and 21 with AD) were assessed at baseline and after 4 years. MCI patients were re-classified according to the conversion status upon follow-up: 25 individuals retained the diagnostic status of MCI and were considered as stable cases (MCI-MCI); conversely, in nine cases the diagnosis of dementia due to AD was ascertained. The APP ratio (APPr) was determined by the Western blot method in samples of platelets collected at baseline. We found a significant reduction of APPr in MCI patients who converted to dementia upon follow-up. These individuals had baseline APPr values similar to those of demented AD patients. The overall accuracy of APPr to identify subjects with MCI who will progress to AD was 0.74 +/- A 0.10, p = 0.05. The cut-off of 1.12 yielded a sensitivity of 75 % and a specificity of 75 %. Platelet APPr may be a surrogate marker of the disease process in AD, with potential implications for the assessment of abnormalities in the APP metabolism in patients with and at risk for dementia. However, diagnostic accuracy was relatively low. Therefore, studies in larger samples are needed to determine whether APPr may warrant its use as a biomarker to support the early diagnosis of AD.

Divide to conquer: a complex pattern of biodiversity depicted by vertebrate components in the Brazilian Atlantic Forest

The identification of northern and southern components in different vertebrate species led researchers to accept a two-component hypothesis for the Brazilian Atlantic forest (BAF). Nevertheless, neither a formal proposal nor a meta-analysis to confirm this coincidence was ever made. Our main objective here was therefore to systematically test in how many vertebrate components the BAF could be divided by analysing existing empirical data. We used two approaches: (1) mapping and comparing the proposed areas of vertebrate endemism in the BAF and (2) analysing studies mentioning spatial subdivisions in distinct forest-dependent vertebrates within the biome, by the use of panbiogeography. The four large-scale endemism area components together with the six small-scale panbiogeographical ones allowed the definition of three BAF greater regions, subdivided into nine vertebrate components, latitudinally and longitudinally organized. Empirical time estimates of the diversification events within the BAF were also reviewed. Diversification of these vertebrates occurred not only in the Pleistocene but also throughout the Miocene. Our results confirm the BAF's complex history, both in space and time. We propose that future research should be small-scale and focused in the vertebrate components identified herein. Given the BAF's heterogeneity, studying via sections will be much more useful in identifying the BAF's historical biogeography. (c) 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 107, 39-55.

Closed-loop stable model predictive control of integrating systems with dead time

Model predictive control (MPC) applications in the process industry usually deal with process systems that show time delays (dead times) between the system inputs and outputs. Also, in many industrial applications of MPC, integrating outputs resulting from liquid level control or recycle streams need to be considered as controlled outputs. Conventional MPC packages can be applied to time-delay systems but stability of the closed loop system will depend on the tuning parameters of the controller and cannot be guaranteed even in the nominal case. In this work, a state space model based on the analytical step response model is extended to the case of integrating time systems with time delays. This model is applied to the development of two versions of a nominally stable MPC, which is designed to the practical scenario in which one has targets for some of the inputs and/or outputs that may be unreachable and zone control (or interval tracking) for the remaining outputs. The controller is tested through simulation of a multivariable industrial reactor system. (C) 2012 Elsevier Ltd. All rights reserved.

On the Deactivation Mechanisms of Adenine-Thymine Base Pair

In this contribution, the multiconfigurational second-order perturbation theory method based on a complete active space reference wave function (CASSCF/CASPT2) is applied to study all possible single and double proton/hydrogen transfers between the nucleobases in the adenine-thymine (AT) base pair, analyzing the role of excited states with different nature [localized (LE) and charge transfer (CT)] and considering concerted as well as step-wise mechanisms. According to the findings, once the lowest excited states, localized in adenine, are populated during UV irradiation of the Watson-Crick base pair, the proton transfer in the N-O bridge does not require high energy in order to populate a CT state. The latter state will immediately relax toward a crossing with the ground state, which will funnel the system to either the canonical structure or the imino-enol tautomer. The base pair is also capable of repairing itself easily since the imino-enol species is unstable to thermal conversion.

Permian non-marine bivalves of the Falkland Islands and their palaeoenvironmental significance

We describe the occurrence of non-marine bivalves in exposures of the Middle Permian (Capitanian) Brenton Loch Formation on the southern shore of Choiseul Sound, East Falklands. The bivalves are associated with ichnofossils and were collected from a bed in the upper part of the formation, within a 25 cm thick interval of dark siltstones and mudstones with planar lamination, overlain by massive sandstones. The shells are articulated, with the valves either splayed open or closed. At the top of the succession, mudstone beds nearly 1.5 m above the bivalve-bearing layers yielded well-preserved Glossopteris sp. cf. G. communis leaf fossils. The closed articulated condition of some shells indicates preservation under high sedimentation rates with low residence time of bioclasts at the sediment/water interface. However, the presence of specimens with splayed shells is usually correlated to the slow decay of the shell ligament in oxygen-deficient bottom waters. The presence of complete carbonized leaves of Glossopteris associated with the bivalve-bearing levels also suggests a possibly dysoxic-anoxic bottom environment. Overall, our data suggest that the bivalves were preserved by abrupt burial, possibly by distal sediment flows into a Brenton Loch lake, and may represent autochthonous to parautochthonous fossil accumulations. The shells resemble those of anthracosiids and are herein assigned to Palaeanodonta sp. aff. P. dubia, a species also found in the Permian succession of the Karoo Basin, South Africa. Our results confirm that (a) the true distributions in space and time of all Permian non-marine (freshwater) bivalves are not yet well known, and (b) there is no evidence for marine conditions in the upper part of the Brenton Loch Formation.

Spatial and Temporal Variation of Archaeal, Bacterial and Fungal Communities in Agricultural Soils

Background: Soil microbial communities are in constant change at many different temporal and spatial scales. However, the importance of these changes to the turnover of the soil microbial communities has been rarely studied simultaneously in space and time. Methodology/Principal Findings: In this study, we explored the temporal and spatial responses of soil bacterial, archaeal and fungal beta-diversities to abiotic parameters. Taking into account data from a 3-year sampling period, we analyzed the abundances and community structures of Archaea, Bacteria and Fungi along with key soil chemical parameters. We questioned how these abiotic variables influence the turnover of bacterial, archaeal and fungal communities and how they impact the long-term patterns of changes of the aforementioned soil communities. Interestingly, we found that the bacterial and fungal b-diversities are quite stable over time, whereas archaeal diversity showed significantly higher fluctuations. These fluctuations were reflected in temporal turnover caused by soil management through addition of N-fertilizers. Conclusions: Our study showed that management practices applied to agricultural soils might not significantly affect the bacterial and fungal communities, but cause slow and long-term changes in the abundance and structure of the archaeal community. Moreover, the results suggest that, to different extents, abiotic and biotic factors determine the community assembly of archaeal, bacterial and fungal communities.

An extension of the invariance principle for dwell-time switched nonlinear systems

In this paper, we propose an extension of the invariance principle for nonlinear switched systems under dwell-time switched solutions. This extension allows the derivative of an auxiliary function V, also called a Lyapunov-like function, along the solutions of the switched system to be positive on some sets. The results of this paper are useful to estimate attractors of nonlinear switched systems and corresponding basins of attraction. Uniform estimates of attractors and basin of attractions with respect to time-invariant uncertain parameters are also obtained. Results for a common Lyapunov-like function and multiple Lyapunov-like functions are given. Illustrative examples show the potential of the theoretical results in providing information on the asymptotic behavior of nonlinear dynamical switched systems. (C) 2012 Elsevier B.V. All rights reserved.

Identification of literary movements using complex networks to represent texts

The use of statistical methods to analyze large databases of text has been useful in unveiling patterns of human behavior and establishing historical links between cultures and languages. In this study, we identified literary movements by treating books published from 1590 to 1922 as complex networks, whose metrics were analyzed with multivariate techniques to generate six clusters of books. The latter correspond to time periods coinciding with relevant literary movements over the last five centuries. The most important factor contributing to the distinctions between different literary styles was the average shortest path length, in particular the asymmetry of its distribution. Furthermore, over time there has emerged a trend toward larger average shortest path lengths, which is correlated with increased syntactic complexity, and a more uniform use of the words reflected in a smaller power-law coefficient for the distribution of word frequency. Changes in literary style were also found to be driven by opposition to earlier writing styles, as revealed by the analysis performed with geometrical concepts. The approaches adopted here are generic and may be extended to analyze a number of features of languages and cultures.

Hydrochemical variability at the Upper Paraguay Basin and Pantanal wetland

Compartmentalization is a prerequisite to understand large wetlands that receive water from several sources. However, it faces the heterogeneity in space and time, resulting from physical, chemical and biological processes that are specific to wetlands. The Pantanal is a vast seasonally flooded continental wetland located in the centre of South America. The chemical composition of the waters that supply the Pantanal (70 rivers) has been studied in order to establish a compartmentalization of the wetland based on soil-water interactions. A PCA-based EMMA (End-Members Mixing Analysis) procedure shows that the chemistry of the rivers can be viewed as a mixture of 3 end-members, influenced by lithology and land use, and delimiting large regions. Although the chemical composition of the end-members changed between dry and wet seasons, their spatial distribution was maintained. The results were extended to the floodplain by simple tributary mixing calculation according to the hydrographical network and to the areas of influence for each river when in overflow conditions. The resulting map highlights areas of high geochemical contrast on either side of the river Cuiaba in the north, and of the rivers Aquidauana and Abobral in the south. The PCA-based treatment on a sampling conducted in the Nhecolandia, a large sub region of the Pantanal, allowed the identification and ordering of the processes that control the geochemical variability of the surface waters. Despite an enormous variability in electrical conductivity and pH, all data collected were in agreement with an evaporation process of the Taquari River water, which supplies the region. Evaporation and associated saline precipitations (Mg-calcite, Mg-silicates K-silicates) explained more than 77% of the total variability in the chemistry of the regional surface water sampling.

Complex, 3D strain patterns in a synkinematic tonalite batholith from the Aracuai Neoproterozoic orogen (Eastern Brazil): Evidence from combined magnetic and isotopic chronology studies

This work combines structural and geochronological data to improve our understanding of the mechanical behaviour of continental crust involving large amount of magma or partially melted material in an abnormally hot collisional belt. We performed a magnetic and geochronological (U/Pb) study on a huge tonalitic batholith from the Neoproterozoic Aracual belt of East Brazil to determine the strain distribution through space and time. Anisotropy of magnetic susceptibility, combined with rock magnetism investigations, supports that the magnetic fabric is a good proxy of the structural fabric. Field measurements together with the magnetic fabrics highlight the presence in the batholith of four domains characterized by contrasted magmatic flow patterns. The western part is characterized by a gently dipping, orogen-parallel (similar to NS) magmatic foliation that bears down-dip lineations, in agreement with westward thrusting onto the Sao Francisco craton. Eastward, the magmatic foliation progressively turns sub-vertical with a lineation that flips from sub-horizontal to sub-vertical over short distances. This latter domain involves an elongated corridor in which the magmatic foliation is sub-horizontal and bears an orogen-parallel lineation. Finally the fourth, narrow domain displays sub-horizontal lineations on a sub-vertical magmatic foliation oblique (similar to N150 degrees E) to the trend of the belt. U/Pb dating of zircons from the various domains revealed homogeneity in age for all samples. This, together with the lack of solid-state deformation suggests that: 1) the whole batholith emplaced during a magmatic event at similar to 580 Ma, 2) the deformation occurred before complete solidification. and 3) the various fabrics are roughly contemporaneous. The complex structural pattern mapped in the studied tonalitic batholith suggests a 3D deformation of a slowly cooling, large magmatic body and its country rock. We suggest that the development of the observed 3D flow field was promoted by the low viscosity of the middle crust that turned gravitational force as an active tectonic force combining with the East-West convergence between the Sao Francisco and Congo cratons. (C) 2012 Elsevier Ltd. All rights reserved.

Relating network rigidity, time scale hierarchies, and expression noise in gene networks

Fluctuation-dissipation theorems can be used to predict characteristics of noise from characteristics of the macroscopic response of a system. In the case of gene networks, feedback control determines the "network rigidity," defined as resistance to slow external changes. We propose an effective Fokker-Planck equation that relates gene expression noise to topology and to time scales of the gene network. We distinguish between two situations referred to as normal and inverted time hierarchies. The noise can be buffered by network feedback in the first situation, whereas it can be topology independent in the latter.

A new enrichment space for the treatment of discontinuous pressures in multi-fluid flows

In this work, a new enrichment space to accommodate jumps in the pressure field at immersed interfaces in finite element formulations, is proposed. The new enrichment adds two degrees of freedom per element that can be eliminated by means of static condensation. The new space is tested and compared with the classical P1 space and to the space proposed by Ausas et al (Comp. Meth. Appl. Mech. Eng., Vol. 199, 10191031, 2010) in several problems involving jumps in the viscosity and/or the presence of singular forces at interfaces not conforming with the element edges. The combination of this enrichment space with another enrichment that accommodates discontinuities in the pressure gradient has also been explored, exhibiting excellent results in problems involving jumps in the density or the volume forces. Copyright (c) 2011 John Wiley & Sons, Ltd.