FocusStack and StimServer: a new open source MATLAB toolchain for visual stimulation and analysis of two-photon calcium neuronal imaging data

Two-photon calcium imaging of neuronal responses is an increasingly accessible technology for probing population responses in cortex at single cell resolution, and with reasonable and improving temporal resolution. However, analysis of two-photon data is usually performed using ad-hoc solutions. To date, no publicly available software exists for straightforward analysis of stimulus-triggered two-photon imaging experiments. In addition, the increasing data rates of two-photon acquisition systems imply increasing cost of computing hardware required for in-memory analysis. Here we present a Matlab toolbox, FocusStack, for simple and efficient analysis of two-photon calcium imaging stacks on consumer-level hardware, with minimal memory footprint. We also present a Matlab toolbox, StimServer, for generation and sequencing of visual stimuli, designed to be triggered over a network link from a two-photon acquisition system. FocusStack is compatible out of the box with several existing two-photon acquisition systems, and is simple to adapt to arbitrary binary file formats. Analysis tools such as stack alignment for movement correction, automated cell detection and peri-stimulus time histograms are already provided, and further tools can be easily incorporated. Both packages are available as publicly-accessible source-code repositories

A new mini-navigation tool allows accurate component placement during anterior total hip arthroplasty.

Introduction: Computer-assisted navigation systems have been explored in total hip arthroplasty (THA) to improve component positioning. While these systems traditionally rely on anterior pelvic plane registration, variances in soft tissue thickness overlying anatomical landmarks can lead to registration error, and the supine coronal plane has instead been proposed. The purpose of this study was to evaluate the accuracy of a novel navigation tool, using registration of the anterior pelvic plane or supine coronal plane during simulated anterior THA. Methods: Measurements regarding the acetabular component position, and changes in leg length and offset were recorded. Benchtop phantoms and target measurement values commonly seen in surgery were used for analysis. Measurements for anteversion and inclination, and changes in leg length and offset were recorded by the navigation tool and compared with the known target value of the simulation. Pearson\u27s Results: The device accurately measured cup position and leg length measurements to within 1° and 1 mm of the known target values, respectively. Across all simulations, there was a strong, positive relationship between values obtained by the device and the known target values ( Conclusion: The preliminary findings of this study suggest that the novel navigation tool tested is a potentially viable tool to improve the accuracy of component placement during THA using the anterior approach

Cell Therapy for Type 1 Diabetes

Acknowledgements The work described in this review was supported by a grant from the MRC. K.R.M. is supported by a fellowship from the Scottish Translational Medicines and Therapeutics Initiative through the Wellcome Trust.Peer reviewedPublisher PD

Growing communities through nature: research report

This is the final version.Growing Communities Through Nature was designed to test models for community engagement in co-production and local innovation, following this up with co-designed and co-delivered maintenance, monitoring and evaluation activity. The research team investigated the impact of using three different institutional vehicles for bringing together communities around local activity. The project worked in three Cornish towns - Launceston, Helston and Newquay - to run workshops co-designing public open spaces in collaboration with a number of partners. The workshops aimed to bring people together to share ideas about an existing space and its potential improvement, discuss new designs for the site and how to maintain the space, as well as monitoring and evaluating its impact on biodiversity and the local community. In addition to the benefits of climate change mitigation, the development of deeper working relationships between the University, partner organisations and the public provides a blueprint for further integration between higher education institutions and communities. Experience of using co-design, co-delivery and co-monitoring methods and tools provides a foundation from which the partners can develop future place-based activities to respond to a range of needs and challenges (such as community development and housing schemes). This approach could also be scaled-up to other Cornish towns and villages via larger collaborative funding applications. This research report documents the project, peoples’ experiences and the wider implications.UKR

Anthrax lethal toxin induced lysosomal membrane permeabilization and cytosolic cathepsin release is Nlrp1b/Nalp1b-dependent.

NOD-like receptors (NLRs) are a group of cytoplasmic molecules that recognize microbial invasion or 'danger signals'. Activation of NLRs can induce rapid caspase-1 dependent cell death termed pyroptosis, or a caspase-1 independent cell death termed pyronecrosis. Bacillus anthracis lethal toxin (LT), is recognized by a subset of alleles of the NLR protein Nlrp1b, resulting in pyroptotic cell death of macrophages and dendritic cells. Here we show that LT induces lysosomal membrane permeabilization (LMP). The presentation of LMP requires expression of an LT-responsive allele of Nlrp1b, and is blocked by proteasome inhibitors and heat shock, both of which prevent LT-mediated pyroptosis. Further the lysosomal protease cathepsin B is released into the cell cytosol and cathepsin inhibitors block LT-mediated cell death. These data reveal a role for lysosomal membrane permeabilization in the cellular response to bacterial pathogens and demonstrate a shared requirement for cytosolic relocalization of cathepsins in pyroptosis and pyronecrosis

On representations of super coalgebras

The general structure of the representation theory of a $Z_2$-graded coalgebra is discussed. The result contains the structure of Fourier analysis on compact supergroups and quantisations thereof as a special case. The general linear supergroups serve as an explicit illustration and the simplest example is carried out in detail.Comment: 18 pages, LaTeX, KCL-TH-94-

Approximating a Wavefunction as an Unconstrained Sum of Slater Determinants

The wavefunction for the multiparticle Schr\"odinger equation is a function of many variables and satisfies an antisymmetry condition, so it is natural to approximate it as a sum of Slater determinants. Many current methods do so, but they impose additional structural constraints on the determinants, such as orthogonality between orbitals or an excitation pattern. We present a method without any such constraints, by which we hope to obtain much more efficient expansions, and insight into the inherent structure of the wavefunction. We use an integral formulation of the problem, a Green's function iteration, and a fitting procedure based on the computational paradigm of separated representations. The core procedure is the construction and solution of a matrix-integral system derived from antisymmetric inner products involving the potential operators. We show how to construct and solve this system with computational complexity competitive with current methods.Comment: 30 page

Concentrations of Polychlorinated Biphenyls (PCB’s), Chlorinated Pesticides, and Heavy Metals and Other Elements in Tissues of Belugas, Delphinapterus leucas, from Cook Inlet

Tissues from Cook Inlet beluga whales, Delphinapterus leucas, that were collected as part of the Alaska Marine Mammal Tissue Archival Project were analyzed for polychlorinated biphenyls (PCB’s), chlorinated pesticides, and heavy metals and other elements. Concentrations of total PCB’s (ΣPCB’s), total DDT (ΣDDT), chlordane compounds, hexachlorobenzene (HCB), dieldrin, mirex, toxaphene, and hexachlorocyclohexane (HCH) measured in Cook Inlet beluga blubber were compared with those reported for belugas from two Arctic Alaska locations (Point Hope and Point Lay), Greenland, Arctic Canada, and the highly contaminated stock from the St. Lawrence estuary in eastern Canada. The Arctic and Cook Inlet belugas had much lower concentrations (ΣPCB’s and ΣDDT were an order of magnitude lower) than those found in animals from the St. Lawrence estuary. The Cook Inlet belugas had the lowest concentrations of all (ΣPCB’s aver-aged 1.49 ± 0.70 and 0.79 ± 0.56 mg/kg wet mass, and ΣDDT averaged 1.35 ± 0.73 and 0.59 ± 0.45 mg/kg in males and females, respectively). Concentrations in the blubber of the Cook Inlet males were significantly lower than those found in the males of the Arctic Alaska belugas (ΣPCB’s and ΣDDT were about half). The lower levels in the Cook Inlet animals might be due to differences in contaminant sources, food web differences, or different age distributions among the animals sampled. Cook Inlet males had higher mean and median concentrations than did females, a result attributable to the transfer of these compounds from mother to calf during pregnancy and during lactation. Liver concentrations of cadmium and mercury were lower in the Cook Inlet belugas (most cadmium values were <1 mg/kg and mercury values were 0.704–11.42 mg/kg wet mass), but copper levels were significantly higher in the Cook Inlet animals (3.97–123.8 mg/kg wet mass) than in Arctic Alaska animals and similar to those reported for belugas from Hudson Bay. Although total mercury levels were the lowest in the Cook Inlet population, methylmercury concentrations were similar among all three groups of the Alaska animals examined (0.34–2.11 mg/kg wet mass). As has been reported for the Point Hope and Point Lay belugas, hepatic concentrations of silver were r

Alfalfa variety performance in central Texas

Last updated: 10/19/201