easySTORM: a robust, lower-cost approach to localisation and TIRF microscopy

TIRF and STORM microscopy are super-resolving fluorescence imaging modalities for which current implementations on standard microscopes can present significant complexity and cost. We present a straightforward and low-cost approach to implement STORM and TIRF taking advantage of multimode optical fibres and multimode diode lasers to provide the required excitation light. Combined with open source software and relatively simple protocols to prepare samples for STORM, including the use of Vectashield for non-TIRF imaging, this approach enables TIRF and STORM imaging of cells labelled with appropriate dyes or expressing suitable fluorescent proteins to become widely accessible at low cost

A Faster Implementation of Online Run-Length Burrows-Wheeler Transform

Run-length encoding Burrows-Wheeler Transformed strings, resulting in Run-Length BWT (RLBWT), is a powerful tool for processing highly repetitive strings. We propose a new algorithm for online RLBWT working in run-compressed space, which runs in $O(n\lg r)$ time and $O(r\lg n)$ bits of space, where $n$ is the length of input string $S$ received so far and $r$ is the number of runs in the BWT of the reversed $S$. We improve the state-of-the-art algorithm for online RLBWT in terms of empirical construction time. Adopting the dynamic list for maintaining a total order, we can replace rank queries in a dynamic wavelet tree on a run-length compressed string by the direct comparison of labels in a dynamic list. The empirical result for various benchmarks show the efficiency of our algorithm, especially for highly repetitive strings.Comment: In Proc. IWOCA201

Bounds of concurrence and their relation with fidelity and frontier states

The bounds of concurrence in [F. Mintert and A. Buchleitner, Phys. Rev. Lett. 98 (2007) 140505] and [C. Zhang \textit{et. al.}, Phys. Rev. A 78 (2008) 042308] are proved by using two properties of the fidelity. In two-qubit systems, for a given value of concurrence, the states achieving the maximal upper bound, the minimal lower bound or the maximal difference upper-lower bound are determined analytically

From quantum fusiliers to high-performance networks

Our objective was to design a quantum repeater capable of achieving one million entangled pairs per second over a distance of 1000km. We failed, but not by much. In this letter we will describe the series of developments that permitted us to approach our goal. We will describe a mechanism that permits the creation of entanglement between two qubits, connected by fibre, with probability arbitrarily close to one and in constant time. This mechanism may be extended to ensure that the entanglement has high fidelity without compromising these properties. Finally, we describe how this may be used to construct a quantum repeater that is capable of creating a linear quantum network connecting two distant qubits with high fidelity. The creation rate is shown to be a function of the maximum distance between two adjacent quantum repeaters.Comment: 2 figures, Comments welcom

Rescaling Egocentric Vision: Collection, Pipeline and Challenges for EPIC-KITCHENS-100

This paper introduces the pipeline to extend the largest dataset in egocentric vision, EPIC-KITCHENS. The effort culminates in EPIC-KITCHENS-100, a collection of 100 hours, 20M frames, 90K actions in 700 variable-length videos, capturing long-term unscripted activities in 45 environments, using head-mounted cameras. Compared to its previous version (Damen in Scaling egocentric vision: ECCV, 2018), EPIC-KITCHENS-100 has been annotated using a novel pipeline that allows denser (54% more actions per minute) and more complete annotations of fine-grained actions (+128% more action segments). This collection enables new challenges such as action detection and evaluating the “test of time”—i.e. whether models trained on data collected in 2018 can generalise to new footage collected two years later. The dataset is aligned with 6 challenges: action recognition (full and weak supervision), action detection, action anticipation, cross-modal retrieval (from captions), as well as unsupervised domain adaptation for action recognition. For each challenge, we define the task, provide baselines and evaluation metrics.Published versionResearch at Bristol is supported by Engineering and Physical Sciences Research Council (EPSRC) Doctoral Training Program (DTP), EPSRC Fellowship UMPIRE (EP/T004991/1). Research at Catania is sponsored by Piano della Ricerca 2016-2018 linea di Intervento 2 of DMI, by MISE - PON I&C 2014-2020, ENIGMA project (CUP: B61B19000520008) and by MIUR AIM - Attrazione e Mobilita Internazionale Linea 1 - AIM1893589 - CUP E64118002540007

Regulation of cell protrusions by small GTPases during fusion of the neural folds.

Epithelial fusion is a crucial process in embryonic development, and its failure underlies several clinically important birth defects. For example, failure of neural fold fusion during neurulation leads to open neural tube defects including spina bifida. Using mouse embryos, we show that cell protrusions emanating from the apposed neural fold tips, at the interface between the neuroepithelium and the surface ectoderm, are required for completion of neural tube closure. By genetically ablating the cytoskeletal regulators Rac1 or Cdc42 in the dorsal neuroepithelium, or in the surface ectoderm, we show that these protrusions originate from surface ectodermal cells and that Rac1 is necessary for the formation of membrane ruffles which typify late closure stages, whereas Cdc42 is required for the predominance of filopodia in early neurulation. This study provides evidence for the essential role and molecular regulation of membrane protrusions prior to fusion of a key organ primordium in mammalian development

Partial change in EphA4 knockout mouse phenotype: Loss of diminished GFAP upregulation following spinal cord injury

In a previous study we found that the EphA4 receptor inhibits regeneration following spinal cord injury by blocking regrowth of axons and regulation of astrocyte reactivity. In our original studies using EphA4 null mice [Goldshmit et al., J. Neurosci., 2004] we found attenuated astrocyte reactivity following spinal cord injury. Several other studies have now supported the role of EphA4 in regulating neural regeneration but a recent study [Herrmann et al., Exp. Neurol., 2010] did not find an effect of EphA4 on astrocyte reactivity. Re-examination of astrocytic gliosis following injury in our current cohort of EphA4 null mice revealed that they no longer showed attenuation of astrocyte reactivity, however other EphA4 null mouse phenotypes, such as decreased size of the dorsal funiculus were unaltered. We hypothesised that long-term breeding on the C57Bl/6 background may influence the EphA4-mediated astrocyte phenotype and compared astrocytic gliosis at 4 days following spinal cord injury in wildtype and EphA4 null mice on the C57Bl/6 background and backcrossed C57Bl/6×129Sv(F2) mice, as well as wildtype 129Sv mice. 129Sv mice had increased GFAP expression and increased numbers of reactive GFAP astrocytes compared to C57Bl/6 mice. There was no significant effect of EphA4 deletion on GFAP expression in C57Bl/6 mice or the F2 crosses other than a moderately decreased number of EphA4 null astrocytes in C57Bl/6 mice using one of two antibodies. Therefore, there has been an apparent change in EphA4-mediated astroglial phenotype associated with long term breeding of the EphA4 colony but it does not appear to be influenced by background mouse strain