Non-coding RNAs: multi-tasking molecules in the cell

In the last years it has become increasingly clear that the mammalian transcriptome is highly complex and includes a large number of small non-coding RNAs (sncRNAs) and long noncoding RNAs (lncRNAs). Here we review the biogenesis pathways of the three classes of sncRNAs, namely short interfering RNAs (siRNAs), microRNAs (miRNAs) and PIWI-interacting RNAs (piRNAs). These ncRNAs have been extensively studied and are involved in pathways leading to specific gene silencing and the protection of genomes against virus and transposons, for example. Also, lncRNAs have emerged as pivotal molecules for the transcriptional and post-transcriptional regulation of gene expression which is supported by their tissue-specific expression patterns, subcellular distribution, and developmental regulation. Therefore, we also focus our attention on their role in differentiation and development. SncRNAs and lncRNAs play critical roles in defining DNA methylation patterns, as well as chromatin remodeling thus having a substantial effect in epigenetics. The identification of some overlaps in their biogenesis pathways and functional roles raises the hypothesis that these molecules play concerted functions in vivo, creating complex regulatory networks where cooperation with regulatory proteins is necessary. We also highlighted the implications of biogenesis and gene expression deregulation of sncRNAs and lncRNAs in human diseases like cancer.

A denoising approach for iterative side information creation in distributed video coding

In distributed video coding, motion estimation is typically performed at the decoder to generate the side information, increasing the decoder complexity while providing low complexity encoding in comparison with predictive video coding. Motion estimation can be performed once to create the side information or several times to refine the side information quality along the decoding process. In this paper, motion estimation is performed at the decoder side to generate multiple side information hypotheses which are adaptively and dynamically combined, whenever additional decoded information is available. The proposed iterative side information creation algorithm is inspired in video denoising filters and requires some statistics of the virtual channel between each side information hypothesis and the original data. With the proposed denoising algorithm for side information creation, a RD performance gain up to 1.2 dB is obtained for the same bitrate.

Design and performance of a novel low-density parity-check code for distributed video coding

Low-density parity-check (LDPC) codes are nowadays one of the hottest topics in coding theory, notably due to their advantages in terms of bit error rate performance and low complexity. In order to exploit the potential of the Wyner-Ziv coding paradigm, practical distributed video coding (DVC) schemes should use powerful error correcting codes with near-capacity performance. In this paper, new ways to design LDPC codes for the DVC paradigm are proposed and studied. The new LDPC solutions rely on merging parity-check nodes, which corresponds to reduce the number of rows in the parity-check matrix. This allows to change gracefully the compression ratio of the source (DCT coefficient bitplane) according to the correlation between the original and the side information. The proposed LDPC codes reach a good performance for a wide range of source correlations and achieve a better RD performance when compared to the popular turbo codes.

Sequencing of a 9.9 kb segment on the right arm of yeast chromosome VII reveals four open reading frames, including PFK1, the gene coding for succinyl-CoA synthetase (beta-chain) and two ORFs sharing homology with ORFs of the yeast chromosome VIII

A 9.9 kb DNA fragment from the right arm of chromosome VII of Saccharomyces cerevisiae has been sequenced and analysed. The sequence contains four open reading frames (ORFs) longer than 100 amino acids. One gene, PFK1, has already been cloned and sequenced and the other one is the probable yeast gene coding for the beta-subunit of the succinyl-CoA synthetase. The two remaining ORFs share homology with the deduced amino acid sequence (and their physical arrangement is similar to that) of the YHR161c and YHR162w ORFs from chromosome VIII.

10 kVp rule – An anthropomorphic pelvis phantom imaging study using a CR system: impact on image quality and effective dose using AEC and manual mode

Purpose - This study aims to investigate the influence of tube potential (kVp) variation in relation to perceptual image quality and effective dose (E) for pelvis using automatic exposure control (AEC) and non-AEC in a Computed Radiography (CR) system. Methods and materials - To determine the effects of using AEC and non-AEC by applying the 10 kVp rule in two experiments using an anthropomorphic pelvis phantom. Images were acquired using 10 kVp increments (60–120 kVp) for both experiments. The first experiment, based on seven AEC combinations, produced 49 images. The mean mAs from each kVp increment were used as a baseline for the second experiment producing 35 images. A total of 84 images were produced and a panel of 5 experienced observers participated for the image scoring using the two alternative forced choice (2AFC) visual grading software. PCXMC software was used to estimate E. Results - A decrease in perceptual image quality as the kVp increases was observed both in non-AEC and AEC experiments, however no significant statistical differences (p > 0.05) were found. Image quality scores from all observers at 10 kVp increments for all mAs values using non-AEC mode demonstrates a better score up to 90 kVp. E results show a statistically significant decrease (p = 0.000) on the 75th quartile from 0.37 mSv at 60 kVp to 0.13 mSv at 120 kVp when applying the 10 kVp rule in non-AEC mode. Conclusion - Using the 10 kVp rule, no significant reduction in perceptual image quality is observed when increasing kVp whilst a marked and significant E reduction is observed.

Image quality and dose analysis for a PA chest X-ray: comparison between AEC mode acquisition and manual mode using the 10 kVp ‘rule’

Purpose - To compare the image quality and effective dose applying the 10 kVp rule with manual mode acquisition and AEC mode in PA chest X-ray. Method - 68 images (with and without lesions) were acquired using an anthropomorphic chest phantom using a Wolverson Arcoma X-ray unit. These images were compared against a reference image using the 2 alternative forced choice (2AFC) method. The effective dose (E) was calculated using PCXMC software using the exposure parameters and the DAP. The exposure index (lgM provided by Agfa systems) was recorded. Results - Exposure time decreases more when applying the 10 kVp rule with manual mode (50%–28%) when compared with automatic mode (36%–23%). Statistical differences for E between several ionization chambers' combinations for AEC mode were found (p = 0.002). E is lower when using only the right AEC ionization chamber. Considering the image quality there are no statistical differences (p = 0.348) between the different ionization chambers' combinations for AEC mode for images with no lesions. Considering lgM values, it was demonstrated that they were higher when the AEC mode was used compared to the manual mode. It was also observed that lgM values obtained with AEC mode increased as kVp value went up. The image quality scores did not demonstrate statistical significant differences (p = 0.343) for the images with lesions comparing manual with AEC mode. Conclusion - In general the E is lower when manual mode is used. By using the right AEC ionising chamber under the lung the E will be the lowest in comparison to other ionising chambers. The use of the 10 kVp rule did not affect the visibility of the lesions or image quality.

10 kVp rule – An anthropomorphic pelvis phantom imaging study using a CR system: impact on image quality and effective dose using AEC and manual mode

Background - Pelvis and hip radiography are consistently found to be amongst the highest contributors to the collective effective dose (E) in all ten DOSE DATAMED countries in Europe, representing 2.8 to 9.4% of total collective dose (S) in the TOP 20 exams list. The level of image quality should provide all the diagnostic information in order not to jeopardise the diagnosis, but being able to provide the needed clinical information with the minimum dose. A recent study suggests further research to determine whether the “10 kVp rule” would have value for a range of examinations using Computed Radiography (CR) systems. As a “rule of thumb” increasing the kVp by 10 whilst halving the mAs is suggested to give a similar perceptual image quality when compared to the original exposure factors. Aims - In light of the 10kVp rule, this study aims to investigate the influence of tube potential (kVp) variation in relation to perceptual image quality and E for pelvis imaging using automatic exposure control (AEC) and non-AEC in a Computed Radiography (CR) system. Research questions - Does the 10kVp rule works for the pelvis in relation to image quality in a CR system? Does the image quality differs when the AEC is used instead of manual mode using the 10kVp rule and how this impacts on E?

A reliable M-mode ultrasound protocol for the assessment of diaphragm motion

Diaphragm is the principal inspiratory muscle. Different techniques have been used to assess diaphragm motion. Among them, M-mode ultrasound has gain particular interest since it is non-invasive and accessible. However it is operator-dependent and no objective acquisition protocol has been established. Purpose: to establish a reliable method for the assessment of the diaphragmatic motion via the M-mode ultrasound.

Image quality and dose analysis in PA chest x-ray: comparison between AEC and manual mode acquisition using the 10 kVp rule

Purpose: To compare image quality and effective dose when the 10 kVp rule is applied with manual and AEC mode in PA chest X-ray. Methods and Materials: A total of 68 images (with and without lesions) were acquired of an anthropomorphic chest phantom in a Wolverson Arcoma X-ray unit. The images were evaluated against a reference image using image quality criteria and the 2 alternative forced choice (2 AFC) method by five radiographers. The effective dose was calculated using PCXMC software using the exposure parameters and DAP. The exposure index (lgM) was recorded. Results: Exposure time decreases considerably when applying the 10 kVp rule in manual mode (50%-28%) compared to AEC mode (36%-23%). Statistical differences for effective dose between several AEC modes were found (p=0.002). The effective dose is lower when using only the right AEC ionization chamber. Considering image quality, there are no statistical differences (p=0.348) between the different AEC modes for images with no lesions. Using a higher kVp value the lgM values will also increase. The lgM values showed significant statistical differences (p=0.000). The image quality scores did not present statistically significant differences (p=0.043) for the images with lesions when comparing manual with AEC modes. Conclusion: In general, the dose is lower in the manual mode. By using the right AEC ionising chamber the effective dose will be the lowest in comparison to other ionising chambers. The use of the 10 kVp rule did not affect the detectability of the lesions.

Correlation modeling for a distributed scalable video codec based on the HEVC standard

The growing heterogeneity of networks, devices and consumption conditions asks for flexible and adaptive video coding solutions. The compression power of the HEVC standard and the benefits of the distributed video coding paradigm allow designing novel scalable coding solutions with improved error robustness and low encoding complexity while still achieving competitive compression efficiency. In this context, this paper proposes a novel scalable video coding scheme using a HEVC Intra compliant base layer and a distributed coding approach in the enhancement layers (EL). This design inherits the HEVC compression efficiency while providing low encoding complexity at the enhancement layers. The temporal correlation is exploited at the decoder to create the EL side information (SI) residue, an estimation of the original residue. The EL encoder sends only the data that cannot be inferred at the decoder, thus exploiting the correlation between the original and SI residues; however, this correlation must be characterized with an accurate correlation model to obtain coding efficiency improvements. Therefore, this paper proposes a correlation modeling solution to be used at both encoder and decoder, without requiring a feedback channel. Experiments results confirm that the proposed scalable coding scheme has lower encoding complexity and provides BD-Rate savings up to 3.43% in comparison with the HEVC Intra scalable extension under development. © 2014 IEEE.

H.264/AVC backward compatible Bit-Depth scalable video coding

As high dynamic range video is gaining popularity, video coding solutions able to efficiently provide both low and high dynamic range video, notably with a single bitstream, are increasingly important. While simulcasting can provide both dynamic range videos at the cost of some compression efficiency penalty, bit-depth scalable video coding can provide a better trade-off between compression efficiency, adaptation flexibility and computational complexity. Considering the widespread use of H.264/AVC video, this paper proposes a H.264/AVC backward compatible bit-depth scalable video coding solution offering a low dynamic range base layer and two high dynamic range enhancement layers with different qualities, at low complexity. Experimental results show that the proposed solution has an acceptable rate-distortion performance penalty regarding the HDR H.264/AVC single-layer coding solution.

Perceptually driven video error protection using a distributed source coding approach

In video communication systems, the video signals are typically compressed and sent to the decoder through an error-prone transmission channel that may corrupt the compressed signal, causing the degradation of the final decoded video quality. In this context, it is possible to enhance the error resilience of typical predictive video coding schemes using as inspiration principles and tools from an alternative video coding approach, the so-called Distributed Video Coding (DVC), based on the Distributed Source Coding (DSC) theory. Further improvements in the decoded video quality after error-prone transmission may also be obtained by considering the perceptual relevance of the video content, as distortions occurring in different regions of a picture have a different impact on the user's final experience. In this context, this paper proposes a Perceptually Driven Error Protection (PDEP) video coding solution that enhances the error resilience of a state-of-the-art H.264/AVC predictive video codec using DSC principles and perceptual considerations. To increase the H.264/AVC error resilience performance, the main technical novelties brought by the proposed video coding solution are: (i) design of an improved compressed domain perceptual classification mechanism; (ii) design of an improved transcoding tool for the DSC-based protection mechanism; and (iii) integration of a perceptual classification mechanism in an H.264/AVC compliant codec with a DSC-based error protection mechanism. The performance results obtained show that the proposed PDEP video codec provides a better performing alternative to traditional error protection video coding schemes, notably Forward Error Correction (FEC)-based schemes. (C) 2013 Elsevier B.V. All rights reserved.

Linear and sliding-mode control design for matrix converter-based unified power flow controllers

This paper presents the design and compares the performance of linear, decoupled and direct power controllers (DPC) for three-phase matrix converters operating as unified power flow controllers (UPFC). A simplified steady-state model of the matrix converter-based UPFC fitted with a modified Venturini high-frequency pulse width modulator is first used to design the linear controllers for the transmission line active (P) and reactive (Q) powers. In order to minimize the resulting cross coupling between P and Q power controllers, decoupled linear controllers (DLC) are synthesized using inverse dynamics linearization. DPC are then developed using sliding-mode control techniques, in order to guarantee both robustness and decoupled control. The designed P and Q power controllers are compared using simulations and experimental results. Linear controllers show acceptable steady-state behaviour but still exhibit coupling between P and Q powers in transient operation. DLC are free from cross coupling but are parameter sensitive. Results obtained by DPC show decoupled power control with zero error tracking and faster responses with no overshoot and no steady-state error. All the designed controllers were implemented using the same digital signal processing hardware.

10 kVp rule - An anthropomorphic pelvis phantom imaging study using a CR system: impact on image quality and effective dose using AEC and manual mode

Purpose: This study aims to investigate the influence of tube potential (kVp) variation in relation to perceptual image quality and effective dose for pelvis using automatic exposure control (AEC) and non-AEC in a computed radiography (CR) system. Methods and Materials: To determine the effects of using AEC and non-AEC by applying the 10 kVp rule in two experiments using an anthropomorphic pelvis phantom. Images were acquired using 10 kVp increments (60-120 kVp) for both experiments. The first experiment, based on seven AEC combinations, produced 49 images. The mean mAs from each kVp increment were used as a baseline for the second experiment producing 35 images. A total of 84 images were produced and a panel of 5 experienced observers participated for the image scoring using the 2 AFC visual grading software. PCXMC software was used to estimate the effective dose. Results: A decrease in perceptual image quality as the kVp increases was observed both in non-AEC and AEC experiments, however no significant statistical differences (p> 0.05) were found. Image quality scores from all observers at 10 kVp increments for all mAs values using non-AEC mode demonstrates a better score up to 90 kVp. Effective dose results show a statistical significant decrease (p=0.000) on the 75th quartile from 0.3 mSv at 60 kVp to 0.1 mSv at 120 kVp when applying the 10 kVp rule in non-AEC mode. Conclusion: No significant reduction in perceptual image quality is observed when increasing kVp whilst a marked and significant effective dose reduction is observed.

A PV panel simulator based on a two quadrant DC/DC power converter with a sliding mode controller

The use of a solar photovoltaic (PV) panel simulator can be a valued tool for the design and evaluation of the several components of a photovoltaic system. This simulator is based on power electronic converter controlled in such a way that will behave as a PV panel. Thus, in this paper a PV panel simulator based on a two quadrant DC/DC power converter is proposed. This topology will allow to achieve fast responses, like suddenly changes in the irradiation and temperature. To control the power converter it will be used a fast and robust sliding mode controller. Therefore, with the proposed system I-V curve simulation of a PV panel is obtained. Experimental results from a laboratory prototype are presented in order to confirm the theoretical operation.