Monogenic polynomials of four variables with binomial expansion

In the recent past one of the main concern of research in the field of Hypercomplex Function Theory in Clifford Algebras was the development of a variety of new tools for a deeper understanding about its true elementary roots in the Function Theory of one Complex Variable. Therefore the study of the space of monogenic (Clifford holomorphic) functions by its stratification via homogeneous monogenic polynomials is a useful tool. In this paper we consider the structure of those polynomials of four real variables with binomial expansion. This allows a complete characterization of sequences of 4D generalized monogenic Appell polynomials by three different types of polynomials. A particularly important case is that of monogenic polynomials which are simply isomorphic to the integer powers of one complex variable and therefore also called pseudo-complex powers.

Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases.

Mapping perturbed molecular circuits that underlie complex diseases remains a great challenge. We developed a comprehensive resource of 394 cell type- and tissue-specific gene regulatory networks for human, each specifying the genome-wide connectivity among transcription factors, enhancers, promoters and genes. Integration with 37 genome-wide association studies (GWASs) showed that disease-associated genetic variants-including variants that do not reach genome-wide significance-often perturb regulatory modules that are highly specific to disease-relevant cell types or tissues. Our resource opens the door to systematic analysis of regulatory programs across hundreds of human cell types and tissues (http://regulatorycircuits.org).

Ruminant rhombencephalitis-associated Listeria monocytogenes alleles linked to a multilocus variable-number tandem-repeat analysis complex

Listeria monocytogenes is among the most important food-borne pathogens and is well adapted to persist in the environment. To gain insight into the genetic relatedness and potential virulence of L. monocytogenes strains causing central nervous system (CNS) infections, we used multilocus variable-number tandem-repeat analysis (MLVA) to subtype 183 L. monocytogenes isolates, most from ruminant rhombencephalitis and some from human patients, food, and the environment. Allelic-profile-based comparisons grouped L. monocytogenes strains mainly into three clonal complexes and linked single-locus variants (SLVs). Clonal complex A essentially consisted of isolates from human and ruminant brain samples. All but one rhombencephalitis isolate from cattle were located in clonal complex A. In contrast, food and environmental isolates mainly clustered into clonal complex C, and none was classified as clonal complex A. Isolates of the two main clonal complexes (A and C) obtained by MLVA were analyzed by PCR for the presence of 11 virulence-associated genes (prfA, actA, inlA, inlB, inlC, inlD, inlE, inlF, inlG, inlJ, and inlC2H). Virulence gene analysis revealed significant differences in the actA, inlF, inlG, and inlJ allelic profiles between clinical isolates (complex A) and nonclinical isolates (complex C). The association of particular alleles of actA, inlF, and newly described alleles of inlJ with isolates from CNS infections (particularly rhombencephalitis) suggests that these virulence genes participate in neurovirulence of L. monocytogenes. The overall absence of inlG in clinical complex A and its presence in complex C isolates suggests that the InlG protein is more relevant for the survival of L. monocytogenes in the environment.

Wide QRS-complex tachycardia with variable VA-conduction: what is the mechanism?

We describe the case of a 16-year-old woman with a surgically corrected tetralogy of Fallot presenting with recurrent wide-QRS-complex tachycardia. The tachycardia could be induced and terminated with ventricular stimulation only. QRS morphology during sinus rhythm and tachycardia was identical and variable VA-conduction was observed. Mapping of the tachycardia showed that variations of HH intervals preceded VV intervals. Therefore, a mechanism involving re-entry within the bundle branches was suggested. However, detailed mapping showed cranial to caudal depolarization of the His bundle, leading to the diagnosis of atrioventricular node re-entrant tachycardia. The tachycardia was abolished by radiofrequency catheter ablation of the slow AV nodal pathway. We conclude that variable VA conduction can occur in patients with atrioventricular node re-entrant tachycardia. The atrial tissue is not always an integral part of the re-entrant circuit.

Increased spread and replication efficiency of Listeria monocytogenes in organotypic brain-slices is related to multilocus variable number of tandem repeat analysis (MLVA) complex.

BACKGROUND Listeria (L.) monocytogenes causes fatal infections in many species including ruminants and humans. In ruminants, rhombencephalitis is the most prevalent form of listeriosis. Using multilocus variable number tandem repeat analysis (MLVA) we recently showed that L. monocytogenes isolates from ruminant rhombencephalitis cases are distributed over three genetic complexes (designated A, B and C). However, the majority of rhombencephalitis strains and virtually all those isolated from cattle cluster in MLVA complex A, indicating that strains of this complex may have increased neurotropism and neurovirulence. The aim of this study was to investigate whether ruminant rhombencephalitis strains have an increased ability to propagate in the bovine hippocampal brain-slice model and can be discriminated from strains of other sources. For this study, forty-seven strains were selected and assayed on brain-slice cultures, a bovine macrophage cell line (BoMac) and a human colorectal adenocarcinoma cell line (Caco-2). They were isolated from ruminant rhombencephalitis cases (n = 21) and other sources including the environment, food, human neurolisteriosis cases and ruminant/human non-encephalitic infection cases (n = 26). RESULTS All but one L. monocytogenes strain replicated in brain slices, irrespectively of the source of the isolate or MLVA complex. The replication of strains from MLVA complex A was increased in hippocampal brain-slice cultures compared to complex C. Immunofluorescence revealed that microglia are the main target cells for L. monocytogenes and that strains from MLVA complex A caused larger infection foci than strains from MLVA complex C. Additionally, they caused larger plaques in BoMac cells, but not CaCo-2 cells. CONCLUSIONS Our brain slice model data shows that all L. monocytogenes strains should be considered potentially neurovirulent. Secondly, encephalitis strains cannot be conclusively discriminated from non-encephalitis strains with the bovine organotypic brain slice model. The data indicates that MLVA complex A strains are particularly adept at establishing encephalitis possibly by virtue of their higher resistance to antibacterial defense mechanisms in microglia cells, the main target of L. monocytogenes.

Two intertidal, non-calcifying macroalgae (Palmaria palmata and Saccharina latissima) show complex and variable responses to short-term CO2 acidification

Ocean acidification, the result of increased dissolution of carbon dioxide (CO2) in seawater, is a leading subject of current research. The effects of acidification on non-calcifying macroalgae are, however, still unclear. The current study reports two 1-month studies using two different macroalgae, the red alga Palmaria palmata (Rhodophyta) and the kelp Saccharina latissima (Phaeophyta), exposed to control (pHNBS = 8.04) and increased (pHNBS = 7.82) levels of CO2-induced seawater acidification. The impacts of both increased acidification and time of exposure on net primary production (NPP), respiration (R), dimethylsulphoniopropionate (DMSP) concentrations, and algal growth have been assessed. In P. palmata, although NPP significantly increased during the testing period, it significantly decreased with acidification, whereas R showed a significant decrease with acidification only. S. latissima significantly increased NPP with acidification but not with time, and significantly increased R with both acidification and time, suggesting a concomitant increase in gross primary production. The DMSP concentrations of both species remained unchanged by either acidification or through time during the experimental period. In contrast, algal growth differed markedly between the two experiments, in that P. palmata showed very little growth throughout the experiment, while S. latissima showed substantial growth during the course of the study, with the latter showing a significant difference between the acidified and control treatments. These two experiments suggest that the study species used here were resistant to a short-term exposure to ocean acidification, with some of the differences seen between species possibly linked to different nutrient concentrations between the experiments.

Second worldwide proficiency study on variable number of tandem repeats typing of Mycobacterium tuberculosis complex

Global Network for the Molecular Surveillance of Tuberculosis 2010: A. Miranda (Tuberculosis Laboratory of the National Institute of Health, Porto, Portugal)

Homomeric ring assemblies of eukaryotic Sm proteins have affinity for both RNA and DNA - Crystal structure of an oligomeric complex of yeast SmF

Sm and Sm-like proteins are key components of small ribonucleoproteins involved in many RNA and DNA processing pathways. In eukaryotes, these complexes contain seven unique Sm or Sm-like (Lsm) proteins assembled as hetero-heptameric rings, whereas in Archaea and bacteria six or seven-membered rings are made from only a single polypeptide chain. Here we show that single Sm and Lsm proteins from yeast also have the capacity to assemble into homo-oligomeric rings. Formation of homo-oligomers by the spliceosomal small nuclear ribonucleoprotein components SmE and SmF preclude hetero-interactions vital to formation of functional small nuclear RNP complexes in vivo. To better understand these unusual complexes, we have determined the crystal structure of the homomeric assembly of the spliceosomal protein SmF. Like its archaeal/bacterial homologs, the SmF complex forms a homomeric ring but in an entirely novel arrangement whereby two heptameric rings form a co-axially stacked dimer via interactions mediated by the variable loops of the individual SmF protein chains. Furthermore, we demonstrate that the homomeric assemblies of yeast Sm and Lsm proteins are capable of binding not only to oligo(U) RNA but, in the case of SmF, also to oligo(dT) single-stranded DNA.

Controlling the complex Lorenz equations by modulation

We demonstrate that a system obeying the complex Lorenz equations in the deep chaotic regime can be controlled to periodic behavior by applying a modulation to the pump parameter. For arbitrary modulation frequency and amplitude there is no obvious simplification of the dynamics. However, we find that there are numerous windows where the chaotic system has been controlled to different periodic behaviors. The widths of these windows in parameter space are narrow, and the positions are related to the ratio of the modulation frequency of the pump to the average pulsation frequency of the output variable. These results are in good agreement with observations previously made in a far-infrared laser system.

Phylogeny of the Sporobolus indicus complex, based on internal transcribed spacer (ITS) sequences

The entire internal transcribed spacer ( ITS) region, including the 5.8S subunit of the nuclear ribosomal DNA ( rDNA), was sequenced by direct double-stranded sequencing of polymerase chain reaction (PCR) amplified fragments. The study included 40 Sporobolus ( Family Poaceae, subfamily Chloridoideae) seed collections from 14 putative species ( all 11 species from the S. indicus complex and three Australian native species). These sequences, along with those from two out-group species [ Pennisetum alopecuroides ( L.) Spreng. and Heteropogon contortus ( L.) P. Beauv. ex Roemer & Schultes, Poaceae, subfamily Panicoideae], were analysed by the parsimony method (PAUP; version 4.0b4a) to infer phylogenetic relationships among these species. The length of the ITS1, 5.8S subunit and ITS2 region were 222, 164 and 218 base pairs ( bp), respectively, in all species of the S. indicus complex, except for the ITS2 region of S. diandrus P. Beauv. individuals, which was 217 bp long. Of the 624 characters included in the analysis, 245 ( 39.3%) of the 330 variable sites contained potential phylogenetic information. Differences in sequences among the members of the S. pyramidalis P. Beauv., S. natalensis (Steud.) Dur & Schinz and S. jacquemontii Kunth. collections were 0%, while differences ranged from 0 to 2% between these and other species of the complex. Similarly, differences in sequences among collections of S. laxus B. K. Simon, S. sessilis B. K. Simon, S. elongatus R. Br. and S. creber De Nardi were 0%, compared with differences of 1-2% between these four species and the rest of the complex. When comparing S. fertilis ( Steud.) Clayton and S. africanus (Poir.) Robyns & Tourney, differences between collections ranged from 0 to 1%. Parsimony analysis grouped all 11 species of the S. indicus complex together, indicating a monophyletic origin. For the entire data set, pair-wise distances among members of the S. indicus complex varied from 0.00 to 1.58%, compared with a range of 20.08-21.44% among species in the complex and the Australian native species studied. A strict consensus phylogenetic tree separated 11 species of the S. indicus complex into five major clades. The phylogeny, based on ITS sequences, was found to be congruent with an earlier study on the taxonomic relationship of the weedy Sporobolus grasses revealed from random amplified polymorphic DNA ( RAPD). However, this cladistic analysis of the complex was not in agreement with that created on past morphological analyses and therefore gives a new insight into the phylogeny of the S. indicus complex.

Gene expression regulation and lineage evolution: the North and South tale of the hybrid polyploid Squalius alburnoides complex

The evolution of hybrid polyploid vertebrates, their viability and their perpetuation over evolutionary time have always been questions of great interest. However, little is known about the impact of hybridization and polyploidization on the regulatory networks that guarantee the appropriate quantitative and qualitative gene expression programme. The Squalius alburnoides complex of hybrid fish is an attractive system to address these questions, as it includes a wide variety of diploid and polyploid forms, and intricate systems of genetic exchange. Through the study of genome-specific allele expression of seven housekeeping and tissue-specific genes, we found that a gene copy silencing mechanism of dosage compensation exists throughout the distribution range of the complex. Here we show that the allele-specific patterns of silencing vary within the complex, according to the geographical origin and the type of genome involved in the hybridization process. In southern populations, triploids of S. alburnoides show an overall tendency for silencing the allele from the minority genome, while northern population polyploids exhibit preferential biallelic gene expression patterns, irrespective of genomic composition. The present findings further suggest that gene copy silencing and variable expression of specific allele combinations may be important processes in vertebrate polyploid evolution.

Neural-network approach to modeling liquid crystals in complex confinement

Finding the structure of a confined liquid crystal is a difficult task since both the density and order parameter profiles are nonuniform. Starting from a microscopic model and density-functional theory, one has to either (i) solve a nonlinear, integral Euler-Lagrange equation, or (ii) perform a direct multidimensional free energy minimization. The traditional implementations of both approaches are computationally expensive and plagued with convergence problems. Here, as an alternative, we introduce an unsupervised variant of the multilayer perceptron (MLP) artificial neural network for minimizing the free energy of a fluid of hard nonspherical particles confined between planar substrates of variable penetrability. We then test our algorithm by comparing its results for the structure (density-orientation profiles) and equilibrium free energy with those obtained by standard iterative solution of the Euler-Lagrange equations and with Monte Carlo simulation results. Very good agreement is found and the MLP method proves competitively fast, flexible, and refinable. Furthermore, it can be readily generalized to the richer experimental patterned-substrate geometries that are now experimentally realizable but very problematic to conventional theoretical treatments.

Neural-network approach to modeling liquid crystals in complex confinement

Finding the structure of a confined liquid crystal is a difficult task since both the density and order parameter profiles are nonuniform. Starting from a microscopic model and density-functional theory, one has to either (i) solve a nonlinear, integral Euler-Lagrange equation, or (ii) perform a direct multidimensional free energy minimization. The traditional implementations of both approaches are computationally expensive and plagued with convergence problems. Here, as an alternative, we introduce an unsupervised variant of the multilayer perceptron (MLP) artificial neural network for minimizing the free energy of a fluid of hard nonspherical particles confined between planar substrates of variable penetrability. We then test our algorithm by comparing its results for the structure (density-orientation profiles) and equilibrium free energy with those obtained by standard iterative solution of the Euler-Lagrange equations and with Monte Carlo simulation results. Very good agreement is found and the MLP method proves competitively fast, flexible, and refinable. Furthermore, it can be readily generalized to the richer experimental patterned-substrate geometries that are now experimentally realizable but very problematic to conventional theoretical treatments.

Development of procedures for the simulation of atmospheric flows over complex terrain, using OpenFOAM

The main purpose of this work was the development of procedures for the simulation of atmospheric ows over complex terrain, using OpenFOAM. For this aim, tools and procedures were developed apart from this code for the preprocessing and data extraction, which were thereafter applied in the simulation of a real case. For the generation of the computational domain, a systematic method able to translate the terrain elevation model to a native OpenFOAM format (blockMeshDict) was developed. The outcome was a structured mesh, in which the user has the ability to de ne the number of control volumes and its dimensions. With this procedure, the di culties of case set up and the high computation computational e ort reported in literature associated to the use of snappyHexMesh, the OpenFOAM resource explored until then for the accomplishment of this task, were considered to be overwhelmed. Developed procedures for the generation of boundary conditions allowed for the automatic creation of idealized inlet vertical pro les, de nition of wall functions boundary conditions and the calculation of internal eld rst guesses for the iterative solution process, having as input experimental data supplied by the user. The applicability of the generated boundary conditions was limited to the simulation of turbulent, steady-state, incompressible and neutrally strati ed atmospheric ows, always recurring to RaNS (Reynolds-averaged Navier-Stokes) models. For the modelling of terrain roughness, the developed procedure allowed to the user the de nition of idealized conditions, like an uniform aerodynamic roughness length or making its value variable as a function of topography characteristic values, or the using of real site data, and it was complemented by the development of techniques for the visual inspection of generated roughness maps. The absence and the non inclusion of a forest canopy model limited the applicability of this procedure to low aerodynamic roughness lengths. The developed tools and procedures were then applied in the simulation of a neutrally strati ed atmospheric ow over the Askervein hill. In the performed simulations was evaluated the solution sensibility to di erent convection schemes, mesh dimensions, ground roughness and formulations of the k - ε and k - ω models. When compared to experimental data, calculated values showed a good agreement of speed-up in hill top and lee side, with a relative error of less than 10% at a height of 10 m above ground level. Turbulent kinetic energy was considered to be well simulated in the hill windward and hill top, and grossly predicted in the lee side, where a zone of ow separation was also identi ed. Despite the need of more work to evaluate the importance of the downstream recirculation zone in the quality of gathered results, the agreement between the calculated and experimental values and the OpenFOAM sensibility to the tested parameters were considered to be generally in line with the simulations presented in the reviewed bibliographic sources.