Dictionary Learning and Sparse Coding-based Denoising for High-Resolution Task Functional Connectivity MRI Analysis

We propose a novel denoising framework for task functional Magnetic Resonance Imaging (tfMRI) data to delineate the high-resolution spatial pattern of the brain functional connectivity via dictionary learning and sparse coding (DLSC). In order to address the limitations of the unsupervised DLSC-based fMRI studies, we utilize the prior knowledge of task paradigm in the learning step to train a data-driven dictionary and to model the sparse representation. We apply the proposed DLSC-based method to Human Connectome Project (HCP) motor tfMRI dataset. Studies on the functional connectivity of cerebrocerebellar circuits in somatomotor networks show that the DLSC-based denoising framework can significantly improve the prominent connectivity patterns, in comparison to the temporal non-local means (tNLM)-based denoising method as well as the case without denoising, which is consistent and neuroscientifically meaningful within motor area. The promising results show that the proposed method can provide an important foundation for the high-resolution functional connectivity analysis, and provide a better approach for fMRI preprocessing.Comment: 8 pages, 3 figures, MLMI201

Long-term average spectral characteristics of Cantonese alaryngeal speech

Objective: In Hong Kong, esophageal (SE), tracheoesophageal (TE), electrolaryngeal (EL), and pneumatic artificial laryngeal (PA) speech are commonly used by laryngectomees as a means to regain verbal communication after total laryngectomy. While SE and TE speech has been studied to some extent, little is known regarding the EL and PA sound quality. The present study examined the sound quality associated with SE, TE, EL, and PA speech, and compared with that associated with laryngeal (NL) speech by using long-term average speech spectra (LTAS). Methods: Continuous speech samples of reading a 136-word passage were obtained from NL, SE, TE, EL, and PA speakers of Cantonese. The alaryngeal speakers were all superior speakers selected from the New Voice Club of Hong Kong, which is a self-help organization for the laryngectomees in Hong Kong. TE speakers were fitted with Provox valve, and EL speakers used Servox-type electrolarynx. Speech samples were digitized at 20 kHz and 16 bits/sample by using Praat, based on which LTAS contours were developed. First spectral peak (FSP), mean spectral energy (MSE), and spectral tilt (ST) derived from the LTAS contours associated with different speaker groups were compared. Results: Data revealed all speakers generally exhibited similar LTA contours. However, PA speakers exhibited the lowest average FSP value and the greatest average MSE value. NL phonation was associated with a significantly greater ST value than alaryngeal speech of Cantonese. Conclusion: The differences in FSP, MSE, and ST values in different speaker groups may be related to the different sound sources being used by the laryngectomees, and the difference in the way the sound source is coupled with the vocal tract system. © 2009 Elsevier Ireland Ltd. All rights reserved.postprin

Prevention of secondary caries by silver diamine fluoride

Purpose: This study aimed to investigate the use of 38% silver diamine fluoride (SDF) as a treatment for preventing secondary caries in glass ionomer cement (GIC) and composite resin (CR) restorations. Methods: Six extracted human sound premolars were collected. Four cavities (4 × 2 × 2 mm3) were prepared on each premolar and then allocated to the following restoration groups: group 1, SDF conditioning and GIC restoration; group 2, GIC restoration; group 3, SDF conditioning and CR restoration; and group 4, CR restoration. After thermal cycling and sterilisation, the teeth were soaked in a 5% sucrose solution containing Streptococcus mutans and Lactobacillus acidophilus for 28 days. Micro-computed tomography was used to study demineralisation. The outer lesion depth (OLD) and wall lesion depth (WLD) of the tooth–restoration interface were measured. The OLD and WLD were directly related to the extent of secondary caries. Two-way analysis of variance was used to analyse the effects of SDF conditioning and restorative materials on OLD. Results: The mean ± standard deviation OLD values were 156 ± 45 μm, 235 ± 33 μm, 153 ± 20 μm and 232 ± 24 μm for groups 1–4, respectively. The OLD was less in restorations with SDF conditioning (P < 0.001) than in those without SDF conditioning. No interaction effect on OLD was found between the restorative materials and SDF conditioning (P = 0.062). The WLD was detected only in groups 3 and 4. Clinical significance: Conditioning with 38% SDF can increase resistance of GIC and CR restorations to secondary caries.postprin

The Josephson heat interferometer

The Josephson effect represents perhaps the prototype of macroscopic phase coherence and is at the basis of the most widespread interferometer, i.e., the superconducting quantum interference device (SQUID). Yet, in analogy to electric interference, Maki and Griffin predicted in 1965 that thermal current flowing through a temperature-biased Josephson tunnel junction is a stationary periodic function of the quantum phase difference between the superconductors. The interplay between quasiparticles and Cooper pairs condensate is at the origin of such phase-dependent heat current, and is unique to Josephson junctions. In this scenario, a temperature-biased SQUID would allow heat currents to interfere thus implementing the thermal version of the electric Josephson interferometer. The dissipative character of heat flux makes this coherent phenomenon not less extraordinary than its electric (non-dissipative) counterpart. Albeit weird, this striking effect has never been demonstrated so far. Here we report the first experimental realization of a heat interferometer. We investigate heat exchange between two normal metal electrodes kept at different temperatures and tunnel-coupled to each other through a thermal `modulator' in the form of a DC-SQUID. Heat transport in the system is found to be phase dependent, in agreement with the original prediction. With our design the Josephson heat interferometer yields magnetic-flux-dependent temperature oscillations of amplitude up to ~21 mK, and provides a flux-to-temperature transfer coefficient exceeding ~ 60mK/Phi_0 at 235 mK [Phi_0 2* 10^(-15) Wb is the flux quantum]. Besides offering remarkable insight into thermal transport in Josephson junctions, our results represent a significant step toward phase-coherent mastering of heat in solid-state nanocircuits, and pave the way to the design of novel-concept coherent caloritronic devices.Comment: 4+ pages, 3 color figure

A framework for automatic semantic video annotation

The rapidly increasing quantity of publicly available videos has driven research into developing automatic tools for indexing, rating, searching and retrieval. Textual semantic representations, such as tagging, labelling and annotation, are often important factors in the process of indexing any video, because of their user-friendly way of representing the semantics appropriate for search and retrieval. Ideally, this annotation should be inspired by the human cognitive way of perceiving and of describing videos. The difference between the low-level visual contents and the corresponding human perception is referred to as the ‘semantic gap’. Tackling this gap is even harder in the case of unconstrained videos, mainly due to the lack of any previous information about the analyzed video on the one hand, and the huge amount of generic knowledge required on the other. This paper introduces a framework for the Automatic Semantic Annotation of unconstrained videos. The proposed framework utilizes two non-domain-specific layers: low-level visual similarity matching, and an annotation analysis that employs commonsense knowledgebases. Commonsense ontology is created by incorporating multiple-structured semantic relationships. Experiments and black-box tests are carried out on standard video databases for action recognition and video information retrieval. White-box tests examine the performance of the individual intermediate layers of the framework, and the evaluation of the results and the statistical analysis show that integrating visual similarity matching with commonsense semantic relationships provides an effective approach to automated video annotation

Small RNA Profile in Moso Bamboo Root and Leaf Obtained by High Definition Adapters

Moso bamboo (Phyllostachy heterocycla cv. pubescens L.) is an economically important fast-growing tree. In order to gain better understanding of gene expression regulation in this important species we used next generation sequencing to profile small RNAs in leaf and roots of young seedlings. Since standard kits to produce cDNA of small RNAs are biased for certain small RNAs, we used High Definition adapters that reduce ligation bias. We identified and experimentally validated five new microRNAs and a few other small non-coding RNAs that were not microRNAs. The biological implication of microRNA expression levels and targets of microRNAs are discussed

Promoter optimisation of lentiviral vectors for efficient insulin gene expression in canine mesenchymal stromal cells: potential surrogate beta cells.

BACKGROUND: The lack of an ideal cell type that can be easily acquired, modified to produce insulin, and re-implanted has been a limitation for ex vivo insulin gene therapy. Canine diabetes is currently treated with human insulin and is a good model for human diabetes. Mesenchymal stromal cells (MSCs) are a promising candidate cell type for gene therapy. In the present study, we optimised insulin production using lentiviral transduced canine MSCs (cMSCs), aiming to evaluate their ability for use as surrogate beta cells. METHODS: Canine MSCs were derived from bone marrow and validated by measuring the expression of MSC lineage specific markers. Lentivirus vectors encoding the proinsulin gene (with or without a Kozak sequence) under the control of spleen focus forming virus, cytomegalovirus, elongation factor 1α and simian virus 40 promotors were generated and used to transduce primary cMSCs and a hepatocyte cell line. The insulin-producing capacity of transduced primary cMSCs was assessed by measuring the concentration of C-peptide produced. RESULTS: Primary cMSC could be readily expanded in culture and efficiently transduced using lentiviral vectors encoding proinsulin. Increasing the multiplicity of infection from 3 to 20 led to an increase in C-peptide secretion (from 1700 to 4000 pmol/l). The spleen focus forming virus promoter conferred the strongest transcriptional ability. CONCLUSIONS: The results of the present study suggest that optimised lentiviral transduction of the insulin gene into primary cMSCs renders these cells capable of secreting insulin over both the short- and long-term, in sufficient quantities in vitro to support their potential use in insulin gene therapy.The study was funded by the Lollipop Trust. Work in the laboratory is supported by the Biomedical Research Centre.This is the final version of the article. It first appeared from Wiley via https://doi.org/10.1002/jgm.290

Genome wide association mapping of grain arsenic, copper, molybdenum and zinc in rice (Oryza sativa L.) grown at four international field sites

Peer reviewedPublisher PD

A Semi-Lagrangian scheme for a modified version of the Hughes model for pedestrian flow

In this paper we present a Semi-Lagrangian scheme for a regularized version of the Hughes model for pedestrian flow. Hughes originally proposed a coupled nonlinear PDE system describing the evolution of a large pedestrian group trying to exit a domain as fast as possible. The original model corresponds to a system of a conservation law for the pedestrian density and an Eikonal equation to determine the weighted distance to the exit. We consider this model in presence of small diffusion and discuss the numerical analysis of the proposed Semi-Lagrangian scheme. Furthermore we illustrate the effect of small diffusion on the exit time with various numerical experiments