Synapses in digital medium: computational investigations of neural basis of anticipation

Anticipation is an emerging concept that can provide a bridge between the deepest philosophical theories about the nature of life and cognition on one hand and the empirical biological sciences steeped in reductionist and Newtonian conception of causality. Three conceptions of anticipation have been emerging from the literature that may be operationalised in a way leading to a viable empirical programme. The discussion of the research into a novel dynamical concept of anticipating synchronisation lends credence to such a possibility and suggests further links between the three anticipation paradigms. A careful progress mindful to the deep philosophical concerns but also respecting empirical evidence will ultimately lead towards unifying theoretical and empirical biological sciences and may offer progress where reductionist science have been so far faltering.

Chemistry and structure by design: ordered CuNi(CN)4 sheets with copper(II) in a square-planar environment

Layered copper–nickel cyanide, CuNi(CN)4, a 2-D negative thermal expansion material, is one of a series of copper(II)-containing cyanides derived from Ni(CN)2. In CuNi(CN)4, unlike in Ni(CN)2, the cyanide groups are ordered generating square-planar Ni(CN)4 and Cu(NC)4 units. The adoption of square-planar geometry by Cu(II) in an extended solid is very unusual.

Global patterns of plant root colonization intensity by mycorrhizal fungi explained by climate and soil chemistry

Aim Most vascular plants on Earth form mycorrhizae, a symbiotic relationship between plants and fungi. Despite the broad recognition of the importance of mycorrhizae for global carbon and nutrient cycling, we do not know how soil and climate variables relate to the intensity of colonization of plant roots by mycorrhizal fungi. Here we quantify the global patterns of these relationships. Location Global. Methods Data on plant root colonization intensities by the two dominant types of mycorrhizal fungi world-wide, arbuscular (4887 plant species in 233 sites) and ectomycorrhizal fungi (125 plant species in 92 sites), were compiled from published studies. Data for climatic and soil factors were extracted from global datasets. For a given mycorrhizal type, we calculated at each site the mean root colonization intensity by mycorrhizal fungi across all potentially mycorrhizal plant species found at the site, and subjected these data to generalized additive model regression analysis with environmental factors as predictor variables. Results We show for the first time that at the global scale the intensity of plant root colonization by arbuscular mycorrhizal fungi strongly relates to warm-season temperature, frost periods and soil carbon-to-nitrogen ratio, and is highest at sites featuring continental climates with mild summers and a high availability of soil nitrogen. In contrast, the intensity of ectomycorrhizal infection in plant roots is related to soil acidity, soil carbon-to-nitrogen ratio and seasonality of precipitation, and is highest at sites with acidic soils and relatively constant precipitation levels. Main conclusions We provide the first quantitative global maps of intensity of mycorrhizal colonization based on environmental drivers, and suggest that environmental changes will affect distinct types of mycorrhizae differently. Future analyses of the potential effects of environmental change on global carbon and nutrient cycling via mycorrhizal pathways will need to take into account the relationships discovered in this study.

Moderating mycorrhizas: arbuscular mycorrhizas modify rhizosphere chemistry and maintain plant phosphorus status within narrow boundaries

Pastures often experience a pulse of phosphorus (P) when fertilized. We examined the role of arbuscular mycorrhizal fungi (AMF) in the uptake of P from a pulse. Five legumes (Kennedia prostrata, Cullen australasicum, Bituminaria bituminosa, Medicago sativa and Trifolium subterraneum) were grown in a moderate P, sterilized field soil, either with (+AMF) or without (−AMF) addition of unsterilized field soil. After 9–10 weeks, half the pots received 15 mg P kg−1 of soil. One week later, we measured: shoot and root dry weights; percentage of root length colonized by AMF; plant P, nitrogen and manganese (Mn) concentrations; and rhizosphere carboxylates, pH and plant-available P. The P pulse raised root P concentration by a similar amount in uncolonized and colonized plants, but shoot P concentration increased by 143% in uncolonized plants and 53% in colonized plants. Inoculation with AMF decreased the amount of rhizosphere carboxylates by 52%, raised rhizosphere pH by ∼0.2–0.7 pH units and lowered shoot Mn concentration by 38%. We conclude that AMF are not simply a means for plants to enhance P uptake when P is limiting, but also act to maintain shoot P within narrow boundaries and can affect nutrient uptake through their influence on rhizosphere chemistry.

Freezing skeletal muscle tissue does not affect its decomposition in soil: Evidence from temporal changes in tissue mass, microbial activity and soil chemistry based on excised samples

The study of decaying organisms and death assemblages is referred to as forensic taphonomy, or more simply the study of graves. This field is dominated by the fields of entomology, anthropology and archaeology. Forensic taphonomy also includes the study of the ecology and chemistry of the burial environment. Studies in forensic taphonomy often require the use of analogues for human cadavers or their component parts. These might include animal cadavers or skeletal muscle tissue. However, sufficient supplies of cadavers or analogues may require periodic freezing of test material prior to experimental inhumation in the soil. This study was carried out to ascertain the effect of freezing on skeletal muscle tissue prior to inhumation and decomposition in a soil environment under controlled laboratory conditions. Changes in soil chemistry were also measured. In order to test the impact of freezing, skeletal muscle tissue (Sus scrofa) was frozen (−20 °C) or refrigerated (4 °C). Portions of skeletal muscle tissue (∼1.5 g) were interred in microcosms (72 mm diameter × 120 mm height) containing sieved (2 mm) soil (sand) adjusted to 50% water holding capacity. The experiment had three treatments: control with no skeletal muscle tissue, microcosms containing frozen skeletal muscle tissue and those containing refrigerated tissue. The microcosms were destructively harvested at sequential periods of 2, 4, 6, 8, 12, 16, 23, 30 and 37 days after interment of skeletal muscle tissue. These harvests were replicated 6 times for each treatment. Microbial activity (carbon dioxide respiration) was monitored throughout the experiment. At harvest the skeletal muscle tissue was removed and the detritosphere soil was sampled for chemical analysis. Freezing was found to have no significant impact on decomposition or soil chemistry compared to unfrozen samples in the current study using skeletal muscle tissue. However, the interment of skeletal muscle tissue had a significant impact on the microbial activity (carbon dioxide respiration) and chemistry of the surrounding soil including: pH, electroconductivity, ammonium, nitrate, phosphate and potassium. This is the first laboratory controlled study to measure changes in inorganic chemistry in soil associated with the decomposition of skeletal muscle tissue in combination with microbial activity.

Molecular insights of p47phox phosphorylation dynamics in the regulation of NADPH oxidase activation and superoxide production

Phagocyte superoxide production by a multicomponent NADPH oxidase is important in host defense against microbial invasion. However inappropriate NADPH oxidase activation causes inflammation. Endothelial cells express NADPH oxidase and endothelial oxidative stress due to prolonged NADPH oxidase activation predisposes many diseases. Discovering the mechanism of NADPH oxidase activation is essential for developing novel treatment of these diseases. The p47phox is a key regulatory subunit of NADPH oxidase; however, due to the lack of full protein structural information, the mechanistic insight of p47phox phosphorylation in NADPH oxidase activation remains incomplete. Based on crystal structures of three functional domains, we generated a computational structural model of the full p47phox protein. Using a combination of in silico phosphorylation, molecular dynamics simulation and protein/protein docking, we discovered that the C-terminal tail of p47phox is critical for stabilizing its autoinhibited structure. Ser-379 phosphorylation disrupts H-bonds that link the C-terminal tail to the autoinhibitory region (AIR) and the tandem Src homology 3 (SH3) domains, allowing the AIR to undergo phosphorylation to expose the SH3 pocket for p22phox binding. These findings were confirmed by site-directed mutagenesis and gene transfection of p47phox_/_ coronary microvascular cells. Compared with wild-type p47phoxcDNAtransfected cells, the single mutation of S379A completely blocked p47phox membrane translocation, binding to p22phox and endothelial O2 . production in response to acute stimulation of PKC. p47phox C-terminal tail plays a key role in stabilizing intramolecular interactions at rest. Ser-379 phosphorylation is a molecular switch which initiates p47phox conformational changes and NADPH oxidase-dependent superoxide production by cells.

Surface chemistry of alanine on Ni{111}

The adsorption of L-alanine on Ni{111} has been studied as a 10 model of enantioselective heterogeneous catalysts. Synchrotron-based X-ray 11 photoelectron spectroscopy and near-edge X-ray absorption fine structure 12 (NEXAFS) spectroscopy were used to determine the chemical state, bond 13 coordination, and out-of-plane orientation of the molecule on the surface. 14 Alanine adsorbs in anionic and zwitterionic forms between 250 and ≈320 K. 15 NEXAFS spectra exhibit a strong angular dependence of the π* resonance 16 associated with the carboxylate group, which is compatible with two distinct 17 orientations with respect to the surface corresponding to the bidentate and 18 tridentate binding modes. Desorption and decomposition begin together at 19 ≈300 K, with decomposition occurring in a multistep process up to ≈450 K. Comparison with previous studies of amino acid 20 adsorption on metal surfaces shows that this is among the lowest decomposition temperatures found so far and lower than typical 21 temperatures used for hydrogenation reactions where modified Ni catalysts are used.

Using problem-based learning in a chemistry practical class for pharmacy students and engaging them with feedback

Objective: To introduce a new approach to problem based learning (PBL) used in the context of medicinal chemistry practical class teaching pharmacy students. Design: The described chemistry practical is based on independent studies by small groups of undergraduate students (4-5), who design their own practical work taking relevant professional standards into account. Students are carefully guided by feedback and acquire a set of skills important to their future profession as healthcare professionals. This model has been tailored to the application of PBL in a chemistry practical class setting for a large student cohort (150 students). Assessment: The achievement of learning outcomes is based on the submission of relevant documentation including a certificate of analysis, in addition to peer assessment. Some of the learning outcomes are also assessed in the final written examination at the end of the academic year. Conclusion: The described design of a novel PBL chemistry laboratory course for pharmacy students has been found to be successful. Self-reflective learning and engagement with feedback were encouraged, and students enjoyed the challenging learning experience. Skills that are highly essential for the students’ future careers as healthcare professionals are promoted.

Layered oxychalcogenides: structural chemistry and thermoelectric properties

Layered oxychalcogenides have recently emerged as promising thermoelectric materials. The alternation of ionic oxide and covalent chalcogenide layers found in these materials often results in interesting electronic properties, and also facilitates the tuning of their properties via chemical substitution at both types of layers. This review highlights some common structure types found for layered oxychalcogenides and their interrelationships. This review pays special attention to the potential of these materials for thermoelectric applications, and provides an overview of the thermoelectric properties of materials of current interest, including BiCuSeO.

Exploiting thermally-reversible chemistry for controlling the crosslinking of polymer networks

High explosives are highly sensitive to accidental detonation by impact, fire, shrapnel and small arms fire. This sensitivity can be reduced by storing the energetic material within a rubbery polymer matrix and are known as plastic bonded explosives (PBX). The current procedure used to manufacture PBX involves mixing the energetic material with a hydroxy-functionalised aliphatic polymer. Upon the addition of an isocyanate crosslinker an immediate polymerisation occurs and thus the rapidly curing mixture must be used to fill the missile or shells, referred to as ‘stores’. This process can lead to poor distribution of the crosslinker resulting in the formation of an inhomogeneously crosslinked matrix and the formation of voids. One solution to this problem involves containing the crosslinker within polyurethane microcapsules that are uniformly dispersed in the explosive-polymer mixture. Upon the application of a stimulus the crosslinker can be released from the microcapsules and the formation of a uniformly crosslinked PBX achieved. Herein is reported the design and synthesis of polyurethane microcapsules that release isocyanate crosslinkers when desired using a thermal stimulus. This has been achieved by exploiting the thermally-reversible nature of oxime-urethane and Diels-Alder adducts that have been incorporated into the shell wall of the microcapsules. An alternative approach to controlling the polymerisation of PBX materials has also been achieved using thermally-reversible blocked isocyanates that regenerate the isocyanate crosslinker when exposed to heat.

Chemistry in Eriocaulaceae

Eriocaulaceae is a pantropical family that comprises about 1100 species distributed in 11 genera. The infrafamilial relationships are still unsatisfactorily resolved, because of the tiny flowers and generalized morphology, which makes the taxonomy very difficult. Flavonoid and naphthopyranone profiles have proved to be important in order to contribute to the alignment of genera into the family. We here present a survey of the chemical data of Eriocaulaceae with a discussion about their contribution to the taxonomy of Eriocaulaceae.

Population and Computational Analysis of the MGEA6 P521A Variation as a Risk Factor for Familial Idiopathic Basal Ganglia Calcification (Fahr`s Disease)

Familial idiopathic basal ganglia calcification, also known as ""Fahr`s disease"" (FD), is a neuropsychiatric disorder with autosomal dominant pattern of inheritance and characterized by symmetric basal ganglia calcifications and, occasionally, other brain regions. Currently, there are three loci linked to this devastating disease. The first one (IBGC1) is located in 14q11.2-21.3 and the other two have been identified in 2q37 (IBGC2) and 8p21.1-q11.13 (IBGC3). Further studies identified a heterozygous variation (rs36060072) which consists in the change of the cytosine to guanine located at MGEA6/CTAGE5 gene, present in all of the affected large American family linked to IBGC1. This missense substitution, which induces changes of a proline to alanine at the 521 position (P521A), in a proline-rich and highly conserved protein domain was considered a rare variation, with a minor allele frequency (MAF) of 0.0058 at the US population. Considering that the population frequency of a given variation is an indirect indicative of potential pathogenicity, we screened 200 chromosomes in a random control set of Brazilian samples and in two nuclear families, comparing with our previous analysis in a US population. In addition, we accomplished analyses through bioinformatics programs to predict the pathogenicity of such variation. Our genetic screen found no P521A carriers. Polling these data together with the previous study in the USA, we have now a MAF of 0.0036, showing that this mutation is very rare. On the other hand, the bioinformatics analysis provided conflicting findings. There are currently various candidate genes and loci that could be involved with the underlying molecular basis of FD etiology, and other groups suggested the possible role played by genes in 2q37, related to calcium metabolism, and at chromosome 8 (NRG1 and SNTG1). Additional mutagenesis and in vivo studies are necessary to confirm the pathogenicity for variation in the P521A MGEA6.

A psychophysical and computational analysis of the spatio-temporal mechanisms underlying the flash-lag effect

Several accounts put forth to explain the flash-lag effect (FLE) rely mainly on either spatial or temporal mechanisms. Here we investigated the relationship between these mechanisms by psychophysical and theoretical approaches. In a first experiment we assessed the magnitudes of the FLE and temporal-order judgments performed under identical visual stimulation. The results were interpreted by means of simulations of an artificial neural network, that wits also employed to make predictions concerning the F LE. The model predicted that a spatio-temporal mislocalisation would emerge from two, continuous and abrupt-onset, moving stimuli. Additionally, a straightforward prediction of the model revealed that the magnitude of this mislocalisation should be task-dependent, increasing when the use of the abrupt-onset moving stimulus switches from a temporal marker only to both temporal and spatial markers. Our findings confirmed the model`s predictions and point to an indissoluble interplay between spatial facilitation and processing delays in the FLE.

Black-box decomposition approach for computational hemodynamics: One-dimensional models

Increasing efforts exist in integrating different levels of detail in models of the cardiovascular system. For instance, one-dimensional representations are employed to model the systemic circulation. In this context, effective and black-box-type decomposition strategies for one-dimensional networks are needed, so as to: (i) employ domain decomposition strategies for large systemic models (1D-1D coupling) and (ii) provide the conceptual basis for dimensionally-heterogeneous representations (1D-3D coupling, among various possibilities). The strategy proposed in this article works for both of these two scenarios, though the several applications shown to illustrate its performance focus on the 1D-1D coupling case. A one-dimensional network is decomposed in such a way that each coupling point connects two (and not more) of the sub-networks. At each of the M connection points two unknowns are defined: the flow rate and pressure. These 2M unknowns are determined by 2M equations, since each sub-network provides one (non-linear) equation per coupling point. It is shown how to build the 2M x 2M non-linear system with arbitrary and independent choice of boundary conditions for each of the sub-networks. The idea is then to solve this non-linear system until convergence, which guarantees strong coupling of the complete network. In other words, if the non-linear solver converges at each time step, the solution coincides with what would be obtained by monolithically modeling the whole network. The decomposition thus imposes no stability restriction on the choice of the time step size. Effective iterative strategies for the non-linear system that preserve the black-box character of the decomposition are then explored. Several variants of matrix-free Broyden`s and Newton-GMRES algorithms are assessed as numerical solvers by comparing their performance on sub-critical wave propagation problems which range from academic test cases to realistic cardiovascular applications. A specific variant of Broyden`s algorithm is identified and recommended on the basis of its computer cost and reliability. (C) 2010 Elsevier B.V. All rights reserved.