The brainstem reticular formation is a small-world, not scale-free, network

Recently, it has been demonstrated that several complex systems may have simple graph-theoretic characterizations as so-called ‘small-world’ and ‘scale-free’ networks. These networks have also been applied to the gross neural connectivity between primate cortical areas and the nervous system of Caenorhabditis elegans. Here, we extend this work to a specific neural circuit of the vertebrate brain—the medial reticular formation (RF) of the brainstem—and, in doing so, we have made three key contributions. First, this work constitutes the first model (and quantitative review) of this important brain structure for over three decades. Second, we have developed the first graph-theoretic analysis of vertebrate brain connectivity at the neural network level. Third, we propose simple metrics to quantitatively assess the extent to which the networks studied are small-world or scale-free. We conclude that the medial RF is configured to create small-world (implying coherent rapid-processing capabilities), but not scale-free, type networks under assumptions which are amenable to quantitative measurement

Phosphorylation site sequence of smooth muscle myosin light chain (Mr = 20 000)

AbstractThe amino terminal sequence of the myosin light chain (Mr = 20 000) isolated from chicken gizzards was found to be acetyl-Ser-Ser-Lys-Arg-Ala-Lys-Ala-Lys-Thr-Thr-Lys-Lys-Arg-Pro-Gln-Arg-Ala-Thr-Ser(P)-Asn-Val-Phe. This sequence assignment differs from that reported by Maita et al. [(1981) European J. Biochem. 117, 417] in the order of the tryptic peptides. The revised amino acid sequence exhibits greater homology with the phosphorylation site sequences of the regulatory light chains from cardiac and skeletal muscle. Moreover it is now apparent why synthetic peptides corresponding to the previously reported sequence were very poor substrates for the myosin light chain kinase

Namib Desert dune/interdune transects exhibit habitat-specific edaphic bacterial communities.

The sand dunes and inter-dune zones of the hyper-arid central Namib Desert represent heterogeneous soil habitats. As little is known about their indigenous edaphic bacterial communities, we aimed to evaluate their diversity and factors of assembly and hypothesized that soil physicochemistry gradients would strongly shape dune/interdune communities. We sampled a total of 125 samples from 5 parallel dune/interdune transects and characterized 21 physico-chemical edaphic parameters coupled with 16S rRNA gene bacterial community fingerprinting using T-RFLP and 454 pyrosequencing. Multivariate analyses of T-RFLP data showed significantly different bacterial communities, related to physico-chemical gradients, in four distinct dune habitats: the dune top, slope, base and interdune zones. Pyrosequencing of 16S rRNA gene amplicon sets showed that each dune zone presented a unique phylogenetic profile, suggesting a high degree of environmental selection. The combined results strongly infer that habitat filtering is an important factor shaping Namib Desert dune bacterial communities, with habitat stability, soil texture and mineral and nutrient contents being the main environmental drivers of bacterial community structures

Schemes for Parallel Quantum Computation Without Local Control of Qubits

Typical quantum computing schemes require transformations (gates) to be targeted at specific elements (qubits). In many physical systems, direct targeting is difficult to achieve; an alternative is to encode local gates into globally applied transformations. Here we demonstrate the minimum physical requirements for such an approach: a one-dimensional array composed of two alternating 'types' of two-state system. Each system need be sensitive only to the net state of its nearest neighbors, i.e. the number in state 1 minus the number in state 2. Additionally, we show that all such arrays can perform quite general parallel operations. A broad range of physical systems and interactions are suitable: we highlight two potential implementations.Comment: 12 pages + 3 figures. Several small corrections mad

Fast Quantum Search Algorithms in Protein Sequence Comparison - Quantum Biocomputing

Quantum search algorithms are considered in the context of protein sequence comparison in biocomputing. Given a sample protein sequence of length m (i.e m residues), the problem considered is to find an optimal match in a large database containing N residues. Initially, Grover's quantum search algorithm is applied to a simple illustrative case - namely where the database forms a complete set of states over the 2^m basis states of a m qubit register, and thus is known to contain the exact sequence of interest. This example demonstrates explicitly the typical O(sqrt{N}) speedup on the classical O(N) requirements. An algorithm is then presented for the (more realistic) case where the database may contain repeat sequences, and may not necessarily contain an exact match to the sample sequence. In terms of minimizing the Hamming distance between the sample sequence and the database subsequences the algorithm finds an optimal alignment, in O(sqrt{N}) steps, by employing an extension of Grover's algorithm, due to Boyer, Brassard, Hoyer and Tapp for the case when the number of matches is not a priori known.Comment: LaTeX, 5 page

Groundwater : meltwater interaction in a proglacial aquifer

Groundwater plays a significant role in the hydrology of active glacial catchments, with evidence that it may buffer changes in meltwater river flow and partially compensate for glacial loss. However, to date there has been little direct research into the hydrogeology and groundwater dynamics of proglacial aquifers. Here we directly investigate the three dimensional nature of a proglacial sandur (floodplain) aquifer in SE Iceland, using hydrogeological, geophysical, hydrological and stable isotopic techniques, and provide evidence of groundwater-melt water dynamics over three years. We show that the proglacial sandur forms a thick (at least 50-100 m), high permeability (transmissivity up to 2500 m2/day) aquifer, extending over an area of approximately 6 km2. At least 35 million m3 of groundwater is stored in the aquifer, equivalent to ~23-28% of total annual river flow through the catchment. The volume of mean annual groundwater flow through the aquifer is at least 0.1-1 m3/sec, equivalent to ~10-20% of mean annual river flow. Groundwater across the aquifer is actively recharged from local precipitation and strongly influenced by individual rainfall events and seasonal precipitation. Glacial meltwater influence on groundwater also occurs in a zone extending from 20-500 m away from the meltwater river, for at least 3km down-sandur, and to at least 15 m deep. Within this zone summer recharge from the river to groundwater occurs when meltwater river flows are high, maintaining high summer groundwater levels compared to winter levels; and groundwater temperature and chemistry are strongly influenced by meltwater. Beyond this zone there is no substantial meltwater influence on groundwater. From ~2 km down-sandur there is extensive groundwater discharge via springs, supporting semi-perennial streams that form distinct local ecosystems, and providing baseflow to the main meltwater river. This research indicates that predicted continued climate change-related reductions in glacier coverage and increases in precipitation are likely to increase the significance of groundwater storage as a water resource, and of groundwater discharges in maintaining environmental river flows in glacier catchments

Micron-sized atom traps made from magneto-optical thin films

We have produced magnetic patterns suitable for trapping and manipulating neutral atoms on a $1 \mu$m length scale. The required patterns are made in Co/Pt thin films on a silicon substrate, using the heat from a focussed laser beam to induce controlled domain reversal. In this way we draw lines and "paint" shaped areas of reversed magnetization with sub-micron resolution. These structures produce magnetic microtraps above the surface that are suitable for holding rubidium atoms with trap frequencies as high as ~1 MHz.Comment: 6 pages, 7 figure

Parvalbumin, calbindin, or calretinin in cortically projecting and GABAergic, cholinergic, or glutamatergic basal forebrain neurons of the rat

The basal forebrain (BF) plays an important role in modulating cortical activity and facilitating processes of attention, learning, and memory. This role is subserved by cholinergic neurons but also requires the participation of other noncholinergic neurons. Noncholinergic neurons include gamma-amino butyric acidergic (GABAergic) neurons, some of which project in parallel with the cholinergic cells to the cerebral cortex, others of which project caudally or locally. With the original aim of distinguishing different subgroups of GABAergic neurons, we examined immunostaining for the calcium binding proteins (CBPs) parvalbumin (Parv), calbindin (Calb), and calretinin (Calret) in the rat. Although the CBP(+) cell groups were distributed in a coextensive manner with the GABAergic cells, they were collectively more numerous. Of cells retrogradely labeled with cholera toxin (CT) from the prefrontal or parietal cortex, Parv(+) and Calb(+) cells, but not Calret(+) cells, represented substantial proportions ( approximately 35-45% each) that collectively were greater than that of GABAergic projection neurons. From dual immunostaining for the CBPs and glutamic acid decarboxylase (GAD), it appeared that the vast majority (>90%) of the Parv(+) group was GAD(+), whereas only a small minority (40%) and Calret(+) (>80%) neurons were immunopositive for phosphate-activated glutaminase, the synthetic enzyme for transmitter glutamate. The results suggested that, whereas Calret(+) cells predominantly comprise caudally or locally projecting, possibly glutamatergic BF neurons, Parv(+) cells likely comprise the cortically projecting GABAergic BF neurons and Calb(+) cells the cortically projecting, possibly glutamatergic BF neurons that would collectively participate with the cholinergic cells in the modulation of cortical activity. Copyright 2003 Wiley-Liss, Inc

An NMR-based nanostructure switch for quantum logic

We propose a nanostructure switch based on nuclear magnetic resonance (NMR) which offers reliable quantum gate operation, an essential ingredient for building a quantum computer. The nuclear resonance is controlled by the magic number transitions of a few-electron quantum dot in an external magnetic field.Comment: 4 pages, 2 separate PostScript figures. Minor changes included. One reference adde

Adiabatic creation of entangled states by a bichromatic field designed from the topology of the dressed eigenenergies

Preparation of entangled pairs of coupled two-state systems driven by a bichromatic external field is studied. We use a system of two coupled spin-1/2 that can be translated into a three-state ladder model whose intermediate state represents the entangled state. We show that this entangled state can be prepared in a robust way with appropriate fields. Their frequencies and envelopes are derived from the topological properties of the model.Comment: 10 pages, 9 figure