Estimation of time-varying autocorrelation and its application to time-frequency analysis of nonstationary signals

This paper introduces a new method for adaptively estimating the time-varying autocorrelation (TV-AC) of nonstationary signals and studies its application to time-frequency analysis. The proposed method employs local estimation with a sliding window having a certain bandwidth to estimate the TV-AC locally. The window bandwidths are selected adaptively by a local plug-in rule to address the bias and variance tradeoff problem. Further, based on the proposed adaptive TV-AC estimation, a new time-frequency analysis method called adaptive windowed minimum variance spectral estimation (AWMVSE) is developed. Simulation results show that the proposed adaptive TV-AC estimation method and AWMVSE method have improved performances over conventional estimators with a fixed window. © 2013 IEEE.published_or_final_versio

Time-varying correlation coefficients estimation and its application to dynamic connectivity analysis of fMRI

Exploration of the dynamics of functional brain connectivity based on the correlation coefficients of functional magnetic resonance imaging (fMRI) data is important for understanding the brain mechanisms. Because fMRI data are time-varying in nature, the functional connectivity shows substantial fluctuations and dynamic characteristics. However, an effective method for estimating time-varying functional connectivity is lacking, which is mainly due to the difficulty in choosing an appropriate window to localize the time-varying correlation coefficients (TVCC). This paper introduces a novel method for adaptively estimating the TVCC of non-stationary signals and studies its application to infer dynamic functional connectivity of fMRI data in a visual task. The proposed method employs a sliding window having a certain bandwidth to estimate the TVCC locally and the window bandwidths are selected adaptively by a local plug-in rule to minimize the mean squared error. The results show that the functional connectivity changes in the visual task are transient, which suggests that simply assuming sustained connectivity changes during task period might not be sufficient to capture dynamic connectivity changes induced by tasks.published_or_final_versio

Broadband optical chaos for stimulated Brillouin scattering suppression in power over fiber

Broadband chaos generated in an optically injected semiconductor laser is applied for power-over-fiber transmission. By varying the injection power, period-one oscillation, period-two oscillation, and chaotic oscillation are observed in the injected slave laser, indicating a period-doubling route to chaos. Compared to the free-running output of the laser, its chaotic output has a drastically increased signal bandwidth, which leads to a 19 dB increase of the stimulated Brillouin scattering threshold. Using a chaos of 5:2GHz bandwidth, a maximum optical power of 27dBm is obtained after 20km transmission over fiber, which is applicable to optically powering some advanced communication networks. The approach uses the inherent nonlinear laser dynamics, which requires no modulation electronics or microwave signal sources. © 2011 Optical Society of America.published_or_final_versio

Fast and robust chromatic dispersion estimation based on temporal auto-correlation after digital spectrum superposition

We investigate and experimentally demonstrate a fast and robust chromatic dispersion (CD) estimation method based on temporal auto-correlation after digital spectrum superposition. The estimation process is fast, because neither tentative CD scanning based on CD compensation nor specific cost function calculations are used. Meanwhile, the proposed CD estimation method is robust against polarization mode dispersion (PMD), amplified spontaneous emission (ASE) noise and fiber nonlinearity. Furthermore, the proposed CD estimation method can be used for various modulation formats and digital pulse shaping technique. Only 4096 samples are necessary for CD estimation of single carrier either 112 Gbps DP-QPSK or 224 Gbps DP-16QAM signal with various pulse shapes. 8192 samples are sufficient for the root-raised-cosine pulse with roll-off factor of 0.1. As low as 50 ps/nm standard deviation together with a worst estimation error of about 160 ps/nm is experimentally obtained for 7 x 112 Gbps DP-QPSK WDM signal after the transmission through 480 km to 9120 km single mode fiber (SMF) loop using different launch powers

Transfer RNA-derived small RNAs in the cancer transcriptome

The cellular lifetime includes stages such as differentiation, proliferation, division, senescence and apoptosis.These stages are driven by a strictly ordered process of transcription dynamics. Molecular disruption to RNA polymerase assembly, chromatin remodelling and transcription factor binding through to RNA editing, splicing, post-transcriptional regulation and ribosome scanning can result in significant costs arising from genome instability. Cancer development is one example of when such disruption takes place. RNA silencing is a term used to describe the effects of post-transcriptional gene silencing mediated by a diverse set of small RNA molecules. Small RNAs are crucial for regulating gene expression and microguarding genome integrity.RNA silencing studies predominantly focus on small RNAs such as microRNAs, short-interfering RNAs and piwi-interacting RNAs. We describe an emerging renewal of inter-est in a‘larger’small RNA, the transfer RNA (tRNA).Precisely generated tRNA-derived small RNAs, named tRNA halves (tiRNAs) and tRNA fragments (tRFs), have been reported to be abundant with dysregulation associated with cancer. Transfection of tiRNAs inhibits protein translation by displacing eukaryotic initiation factors from messenger RNA (mRNA) and inaugurating stress granule formation.Knockdown of an overexpressed tRF inhibits cancer cell proliferation. Recovery of lacking tRFs prevents cancer metastasis. The dual oncogenic and tumour-suppressive role is typical of functional small RNAs. We review recent reports on tiRNA and tRF discovery and biogenesis, identification and analysis from next-generation sequencing data and a mechanistic animal study to demonstrate their physiological role in cancer biology. We propose tRNA-derived small RNA-mediated RNA silencing is an innate defence mechanism to prevent oncogenic translation. We expect that cancer cells are percipient to their ablated control of transcription and attempt to prevent loss of genome control through RNA silencing

Anti-inflammatory management for tendon injuries - friends or foes?

Acute and chronic tendon injuries are very common among athletes and in sedentary population. Most physicians prescribe anti-inflammatory managements to relieve the worst symptoms of swelling and pain, including non-steroidal anti-inflammatory drugs, corticosteroids and physical therapies. However, experimental research shows that pro-inflammatory mediators such as prostaglandins may play important regulatory roles in tendon healing. Noticeably nearly all cases of chronic tendon injuries we treat as specialists have received non-steroidal anti-inflammatory drugs by their physician, suggesting that there might be a potential interaction in some of these cases turning a mild inflammatory tendon injury into chronic tendinopathy in predisposed individuals. We are aware of the fact that non-steroidal anti-inflammatory drugs and corticosteroids may well have a positive effect on the pain control in the clinical situation whilst negatively affect the structural healing. It follows that a comprehensive evaluation of anti-inflammatory management for tendon injuries is needed and any such data would have profound clinical and health economic importance

Dynamics and Regulation of RecA Polymerization and De-Polymerization on Double-Stranded DNA

10.1371/journal.pone.0066712PLoS ONE86

MiR-637 maintains the balance between adipocytes and osteoblasts by directly targeting Osterix

Bone development is dynamically regulated by homeostasis, in which a balance between adipocytes and osteoblasts is maintained. Disruption of this differentiation balance leads to various bone-related metabolic diseases, including osteoporosis. In the present study, a primate-specific microRNA (miR-637) was found to be involved in the differentiation of human mesenchymal stem cells (hMSCs). Our preliminary data indicated that miR-637 suppressed the growth of hMSCs and induced S-phase arrest. Expression of miR-637 was increased during adipocyte differentiation (AD), whereas it was decreased during osteoblast differentiation (OS), which suggests miR-637 could act as a mediator of adipoosteogenic differentiation. Osterix (Osx), a significant transcription factor of osteoblasts, was shown to be a direct target of miR-637, which significantly enhanced AD and suppressed OS in hMSCs through direct suppression of Osx expression. Furthermore, miR-637 also significantly enhanced de novo adipogenesis in nude mice. In conclusion, our data indicated that the expression of miR-637 was indispensable for maintaining the balance of adipocytes and osteoblasts. Disruption of miR-637 expression patterns leads to irreversible damage to the balance of differentiation in bone marrow. © 2011 Zhang et al.published_or_final_versio

Functional Diversity and Structural Disorder in the Human Ubiquitination Pathway

The ubiquitin-proteasome system plays a central role in cellular regulation and protein quality control (PQC). The system is built as a pyramid of increasing complexity, with two E1 (ubiquitin activating), few dozen E2 (ubiquitin conjugating) and several hundred E3 (ubiquitin ligase) enzymes. By collecting and analyzing E3 sequences from the KEGG BRITE database and literature, we assembled a coherent dataset of 563 human E3s and analyzed their various physical features. We found an increase in structural disorder of the system with multiple disorder predictors (IUPred - E1: 5.97%, E2: 17.74%, E3: 20.03%). E3s that can bind E2 and substrate simultaneously (single subunit E3, ssE3) have significantly higher disorder (22.98%) than E3s in which E2 binding (multi RING-finger, mRF, 0.62%), scaffolding (6.01%) and substrate binding (adaptor/substrate recognition subunits, 17.33%) functions are separated. In ssE3s, the disorder was localized in the substrate/adaptor binding domains, whereas the E2-binding RING/HECT-domains were structured. To demonstrate the involvement of disorder in E3 function, we applied normal modes and molecular dynamics analyses to show how a disordered and highly flexible linker in human CBL (an E3 that acts as a regulator of several tyrosine kinase-mediated signalling pathways) facilitates long-range conformational changes bringing substrate and E2-binding domains towards each other and thus assisting in ubiquitin transfer. E3s with multiple interaction partners (as evidenced by data in STRING) also possess elevated levels of disorder (hubs, 22.90% vs. non-hubs, 18.36%). Furthermore, a search in PDB uncovered 21 distinct human E3 interactions, in 7 of which the disordered region of E3s undergoes induced folding (or mutual induced folding) in the presence of the partner. In conclusion, our data highlights the primary role of structural disorder in the functions of E3 ligases that manifests itself in the substrate/adaptor binding functions as well as the mechanism of ubiquitin transfer by long-range conformational transitions. © 2013 Bhowmick et al

Phytochemical screening and antimicrobial studies on the methanolic bulb extract of Allium sativum L.

Methanolic extract of the bulb of Allium sativum was screened for phytochemical and antimicrobial properties. The crude extract of A. sativum bulb showed positive results for carbohydrates, glycosides and proteins in high concentrations; alkaloids, saponins, reducing sugars, oils and steroids in medium concentrations, while flavonoids and acidic compounds were present in low amounts. Tannins, resins and terpenoids were however absent in the extract. All the six tested microorganisms exhibited varied susceptibility to the plant extract. The minimum inhibitory concentration (MIC) of the organisms were, 50 mg/ml for Salmonella paratyphi, 25 mg/ml for Bacillus subtilis, 100 mg/ml for Klebsiella pneumoniae, 12.5 mg/ml for Candida albicans, 3.12 mg/ml for Candida paralopsis and 6.25 mg/ml for Candida tropicalis. A. sativum showed both antifungal and antibacterial properties.Keywords: Phytochemical screening, antimicrobial activity, Allium sativum, bulb extractAfrican Journal of Biotechnology Vol. 12(14), pp. 1665-166