Vicente Galiano | Universidad Miguel Hernandez (original) (raw)

Papers by Vicente Galiano

Research paper thumbnail of On the use of deep learning and parallelism techniques to significantly reduce the HEVC intra-coding time

The Journal of Supercomputing

It is well-known that each new video coding standard significantly increases in computational com... more It is well-known that each new video coding standard significantly increases in computational complexity with respect to previous standards, and this is particularly true for the HEVC and VVC video coding standards. The development of techniques for reducing the required complexity without affecting the rate/distortion (R/D) performance is therefore always a topic of intense research interest. In this paper, we propose a combination of two powerful techniques, deep learning and parallel computing, to significantly reduce the complexity of the HEVC encoding engine. Our experimental results show that a combination of deep learning to reduce the CTU partitioning complexity with parallel strategies based on frame partitioning is able to achieve speedups of up to 26$$\\times$$ × when 16 threads are used. The R/D penalty in terms of the BD-BR metric depends on the video content, the compression rate and the number of OpenMP threads, and was consistently between 0.35 and 10% for the video s...

Research paper thumbnail of On the use of deep learning and parallelism techniques to significantly reduce the HEVC intra-coding time

The Journal of Supercomputing

It is well-known that each new video coding standard significantly increases in computational com... more It is well-known that each new video coding standard significantly increases in computational complexity with respect to previous standards, and this is particularly true for the HEVC and VVC video coding standards. The development of techniques for reducing the required complexity without affecting the rate/distortion (R/D) performance is therefore always a topic of intense research interest. In this paper, we propose a combination of two powerful techniques, deep learning and parallel computing, to significantly reduce the complexity of the HEVC encoding engine. Our experimental results show that a combination of deep learning to reduce the CTU partitioning complexity with parallel strategies based on frame partitioning is able to achieve speedups of up to 26$$\times$$ × when 16 threads are used. The R/D penalty in terms of the BD-BR metric depends on the video content, the compression rate and the number of OpenMP threads, and was consistently between 0.35 and 10% for the video s...

Research paper thumbnail of Distributing SystemC structures in parallel simulations

spring simulation multiconference, Mar 22, 2009

This paper deals with the most popular attempts of distributing SystemC simulations. SystemC is b... more This paper deals with the most popular attempts of distributing SystemC simulations. SystemC is becoming a popular framework for System-On-Chip (SoC) design and verification. Innovation in processor design does not come easily. Smaller features, faster speeds, and intricate digital logic require more simulation resources to accurately gauge the worth of a new design. In order to provide these resources, distributed

Research paper thumbnail of Quick and Accurate Strategy for Calculating the Solutions of the Photovoltaic Single-Diode Model Equation

IEEE Journal of Photovoltaics, 2022

Research paper thumbnail of Frame-Based and Subpicture-Based Parallelization Approaches of the HEVC Video Encoder

Applied Sciences, 2018

The most recent video coding standard, High Efficiency Video Coding (HEVC), is able to significan... more The most recent video coding standard, High Efficiency Video Coding (HEVC), is able to significantly improve the compression performance at the expense of a huge computational complexity increase with respect to its predecessor, H.264/AVC. Parallel versions of the HEVC encoder may help to reduce the overall encoding time in order to make it more suitable for practical applications. In this work, we study two parallelization strategies. One of them follows a coarse-grain approach, where parallelization is based on frames, and the other one follows a fine-grain approach, where parallelization is performed at subpicture level. Two different frame-based approaches have been developed. The first one only uses MPI and the second one is a hybrid MPI/OpenMP algorithm. An exhaustive experimental test was carried out to study the performance of both approaches in order to find out the best setup in terms of parallel efficiency and coding performance. Both frame-based and subpicture-based approaches are compared under the same hardware platform. Although subpicture-based schemes provide an excellent performance with high-resolution video sequences, scalability is limited by resolution, and the coding performance worsens by increasing the number of processes. Conversely, the proposed frame-based approaches provide the best results with respect to both parallel performance (increasing scalability) and coding performance (not degrading the rate/distortion behavior).

Research paper thumbnail of Qué son los supercomputadores

Research paper thumbnail of Performance Overview of the Latest Video Coding Proposals: HEVC, JEM and VVC

Journal of Imaging, 2021

The audiovisual entertainment industry has entered a race to find the video encoder offering the ... more The audiovisual entertainment industry has entered a race to find the video encoder offering the best Rate/Distortion (R/D) performance for high-quality high-definition video content. The challenge consists in providing a moderate to low computational/hardware complexity encoder able to run Ultra High-Definition (UHD) video formats of different flavours (360°, AR/VR, etc.) with state-of-the-art R/D performance results. It is necessary to evaluate not only R/D performance, a highly important feature, but also the complexity of future video encoders. New coding tools offering a small increase in R/D performance at the cost of greater complexity are being advanced with caution. We performed a detailed analysis of two evolutions of High Efficiency Video Coding (HEVC) video standards, Joint Exploration Model (JEM) and Versatile Video Coding (VVC), in terms of both R/D performance and complexity. The results show how VVC, which represents the new direction of future standards, has, for th...

Research paper thumbnail of Comment on “Parameter extraction of single‐diode photovoltaic module using experimental current–voltage data”

International Journal of Circuit Theory and Applications, 2021

Research paper thumbnail of Aggregation of 25-hydroxycholesterol in a complex biomembrane. Differences with cholesterol

Biochimica et Biophysica Acta (BBA) - Biomembranes, 2020

25-Hydroxycholesterol (25HC), one of the most important oxysterol molecules, can be used by cells... more 25-Hydroxycholesterol (25HC), one of the most important oxysterol molecules, can be used by cells to fight bacterial and viral infections but the mechanism that defines its biological effects are unknown. Using molecular dynamics, we have aimed to describe the orientation and location of 25HC in the membrane as well as the interactions it might have with lipids. We have studied two complex model membrane systems, one similar to the late endosome membrane and the other one to the plasma membrane. Our results reinforce that 25HC is inserted in the membrane in a relative stable location similar to but not identical to cholesterol. 25HC fluctuates in the membrane to a much greater degree than cholesterol, but the effect of 25HC on the phospholipid order parameters is not significantly different. One of the most notable facts about 25HC is that, unlike cholesterol, this molecule tends to aggregate, forming dimers, trimers and higher-order aggregates. These aggregates are formed spontaneously through the formation of hydrogen bonds between the two 25HC atoms, the formation of hydrogen bonds being independent of the studied system. Remarkably, no contacts or hydrogen bonds are observed between 25HC and cholesterol molecules, as well as between cholesterol molecules themselves at any time. It would be conceivable that 25HC, by forming high order aggregates without significantly altering the membrane properties, would modify the way proteins interact with the membrane and henceforth form a true innate antiviral molecule.

Research paper thumbnail of Heterogeneous CPU plus GPU approaches for HEVC

The Journal of Supercomputing, 2018

Research paper thumbnail of Feasibility study of portable microwave microstrip open-loop resonator for non-invasive blood glucose level sensing: proof of concept

Medical & Biological Engineering & Computing, 2019

Research paper thumbnail of Two-Step Linear Least-Squares Method For Photovoltaic Single-Diode Model Parameters Extraction

IEEE Transactions on Industrial Electronics, 2018

In this paper a new method to calculate the five parameters of the single-diode model of a photov... more In this paper a new method to calculate the five parameters of the single-diode model of a photovoltaic cell or panel is presented. This new method takes into account the intrinsic properties of the model equation and the technique of linear least-squares fitting, so, the computational complexity and costs are very low. Moreover, the proposed method, named Two-Step Linear Least-Squares (TSLLS) method, is able to work absolutely blindly with any kind of I-V curve. It does not need initial guesses at all and, consequently, it is not necessary to know previously any information of any parameter. The proposed method provides the parameters of the singlediode model just using the coordinates of N points (N≥5) of the I-V curve. The results provided by this method in a first stage have the same order of accuracy of the best documented methods in the field of parameters extraction, but, furthermore, in a second stage the best accuracy documented until now is obtained in two important case studies usually used in the literature as well as in a largescale I-V curve repository with more than one million of curves.

Research paper thumbnail of A highly scalable parallel encoder version of the emergent JEM video encoder

The Journal of Supercomputing, 2018

Research paper thumbnail of Discovery of nonnucleoside inhibitors of polymerase from infectious pancreatic necrosis virus (IPNV)

Drug design, development and therapy, 2018

Infectious pancreatic necrosis virus (IPNV) causes serious losses in several fish species of comm... more Infectious pancreatic necrosis virus (IPNV) causes serious losses in several fish species of commercial interest. IPNV is a non-enveloped double-stranded RNA virus with a genome consisting of two segments A and B. Segment B codes for the VP1 protein, a non-canonical RNA-dependent RNA polymerase that can be found both in its free form and linked to the end of genomic RNA, an essential enzyme for IPNV replication. We take advantage of the knowledge over the allosteric binding site described on the surface of the thumb domain of Hepatitis C virus (HCV) polymerase to design new non-nucleoside inhibitors against the IPNV VP1 polymerase. Molecular docking techniques have been used to screen a chemical library of 23,760 compounds over a defined cavity in the surface of the thumb domain. Additional ADMET (absorption, distribution, metabolism, excretion, and toxicity) filter criteria has been applied. We select two sets of 9 and 50 inhibitor candidates against the polymerases of HCV and IPNV...

Research paper thumbnail of Spontaneous membrane insertion of a dengue virus NS2A peptide

Archives of Biochemistry and Biophysics, 2017

Non-structural NS2A protein of Dengue virus is essential for viral replication but poorly charact... more Non-structural NS2A protein of Dengue virus is essential for viral replication but poorly characterized because of its high hydrophobicity. We have previously shown experimentally that NS2A possess a segment, peptide dens25, known to insert into membranes and interact specifically with negativelycharged phospholipids. To characterize its membrane interaction we have used two types of molecular dynamics membrane model systems, a highly mobile membrane mimetic (HMMM) and an endoplasmic reticulum (ER) membrane-like model. Using the HMMM system, we have been able of demonstrating the spontaneous binding of dens25 to the negatively-charged phospholipid 1,2-divalerylsn-glycero-3-phosphate containing membrane whereas no binding was observed for the membrane containing the zwitterionic one 1,2-divaleryl-sn-glycero-3-phosphocholine. Using the ER-like membrane model system, we demonstrate the spontaneous insertion of dens25 into the middle of the membrane, it maintained its three-dimensional structure and presented a nearly parallel orientation with respect to the membrane surface. Both charged and hydrophobic amino acids, presenting an interfacial/hydrophobic pattern characteristic of a membrane-proximal segment, are responsible for membrane binding and insertion. Dens25 might control protein/membrane interaction and be involved in membrane rearrangements critical for the viral cycle. These data should help us in the development of inhibitor molecules that target NS2A segments involved in membrane reorganisation.

Research paper thumbnail of GPU-based HEVC intra-prediction module

The Journal of Supercomputing, 2016

The HEVC video coding standard requires nearly 70 % more time than H.264/AVC to encode a video se... more The HEVC video coding standard requires nearly 70 % more time than H.264/AVC to encode a video sequence. Manycore architectures can considerably help to reduce the coding time. In this paper, we propose the use of GPUs to perform the intra-picture prediction without any R/D loss. We have evaluated our proposal and compared the results with the ones obtained when running on a CPU. The results show that a time reduction of up to 85 % can be obtained without any R/D loss.

Research paper thumbnail of An Updated Review on Marine Anticancer Compounds: The Use of Virtual Screening for the Discovery of Small-Molecule Cancer Drugs

Molecules (Basel, Switzerland), Jan 23, 2017

Marine secondary metabolites are a promising source of unexploited drugs that have a wide structu... more Marine secondary metabolites are a promising source of unexploited drugs that have a wide structural diversity and have shown a variety of biological activities. These compounds are produced in response to the harsh and competitive conditions that occur in the marine environment. Invertebrates are considered to be among the groups with the richest biodiversity. To date, a significant number of marine natural products (MNPs) have been established as antineoplastic drugs. This review gives an overview of MNPs, both in research or clinical stages, from diverse organisms that were reported as being active or potentially active in cancer treatment in the past seventeen years (from January 2000 until April 2017) and describes their putative mechanisms of action. The structural diversity of MNPs is also highlighted and compared with the small-molecule anticancer drugs in clinical use. In addition, this review examines the use of virtual screening for MNP-based drug discovery and reveals th...

Research paper thumbnail of Shared Memory Tile-Based vs Hybrid Memory GOP-Based Parallel Algorithms for HEVC Encoder

Algorithms and Architectures for Parallel Processing, 2016

After the emergence of the new High Efficiency Video Coding standard, several strategies have bee... more After the emergence of the new High Efficiency Video Coding standard, several strategies have been followed in order to take advantage of the parallel features available in it. Many of the parallelization approaches in the literature have been performed in the decoder side, aiming at achieving real-time decoding. However, the most complex part of the HEVC codec is the encoding side. In this paper, we perform a comparative analysis of two parallelization proposals. One of them is based on tiles, employing shared memory architectures and the other one is based on Groups Of Pictures, employing distributed shared memory architectures. The results show that good speed-ups are obtained for the tile-based proposal, especially for high resolution video sequences, but the scalability decreases for low resolution video sequences. The GOP-based proposal outperforms the tile-based proposal when the number of processes increases. This benefit grows up when low resolution video sequences are compressed.

Research paper thumbnail of Looking for inhibitors of the dengue virus NS5 RNA-dependent RNA-polymerase using a molecular docking approach

Drug Design, Development and Therapy, 2016

The dengue virus (DENV) nonstructural protein 5 (NS5) contains both an N-terminal methyltransfera... more The dengue virus (DENV) nonstructural protein 5 (NS5) contains both an N-terminal methyltransferase domain and a C-terminal RNA-dependent RNA polymerase domain. Polymerase activity is responsible for viral RNA synthesis by a de novo initiation mechanism and represents an attractive target for antiviral therapy. The incidence of DENV has grown rapidly and it is now estimated that half of the human population is at risk of becoming infected with this virus. Despite this, there are no effective drugs to treat DENV infections. The present in silico study aimed at finding new inhibitors of the NS5 RNA-dependent RNA polymerase of the four serotypes of DENV. We used a chemical library comprising 372,792 nonnucleotide compounds (around 325,319 natural compounds) to perform molecular docking experiments against a binding site of the RNA template tunnel of the virus polymerase. Compounds with high negative free energy variation (∆G −10.5 kcal/mol) were selected as putative inhibitors. Additional filters for favorable druggability and good absorption, distribution, metabolism, excretion, and toxicity were applied. Finally, after the screening process was completed, we identified 39 compounds as lead DENV polymerase inhibitor candidates. Potentially, these compounds could act as efficient DENV polymerase inhibitors in vitro and in vivo.

Research paper thumbnail of Location of the bioactive pentacyclic triterpene ursolic acid in the membrane. A molecular dynamics study

Journal of Biomolecular Structure and Dynamics, 2016

Research paper thumbnail of On the use of deep learning and parallelism techniques to significantly reduce the HEVC intra-coding time

The Journal of Supercomputing

It is well-known that each new video coding standard significantly increases in computational com... more It is well-known that each new video coding standard significantly increases in computational complexity with respect to previous standards, and this is particularly true for the HEVC and VVC video coding standards. The development of techniques for reducing the required complexity without affecting the rate/distortion (R/D) performance is therefore always a topic of intense research interest. In this paper, we propose a combination of two powerful techniques, deep learning and parallel computing, to significantly reduce the complexity of the HEVC encoding engine. Our experimental results show that a combination of deep learning to reduce the CTU partitioning complexity with parallel strategies based on frame partitioning is able to achieve speedups of up to 26$$\\times$$ × when 16 threads are used. The R/D penalty in terms of the BD-BR metric depends on the video content, the compression rate and the number of OpenMP threads, and was consistently between 0.35 and 10% for the video s...

Research paper thumbnail of On the use of deep learning and parallelism techniques to significantly reduce the HEVC intra-coding time

The Journal of Supercomputing

It is well-known that each new video coding standard significantly increases in computational com... more It is well-known that each new video coding standard significantly increases in computational complexity with respect to previous standards, and this is particularly true for the HEVC and VVC video coding standards. The development of techniques for reducing the required complexity without affecting the rate/distortion (R/D) performance is therefore always a topic of intense research interest. In this paper, we propose a combination of two powerful techniques, deep learning and parallel computing, to significantly reduce the complexity of the HEVC encoding engine. Our experimental results show that a combination of deep learning to reduce the CTU partitioning complexity with parallel strategies based on frame partitioning is able to achieve speedups of up to 26$$\times$$ × when 16 threads are used. The R/D penalty in terms of the BD-BR metric depends on the video content, the compression rate and the number of OpenMP threads, and was consistently between 0.35 and 10% for the video s...

Research paper thumbnail of Distributing SystemC structures in parallel simulations

spring simulation multiconference, Mar 22, 2009

This paper deals with the most popular attempts of distributing SystemC simulations. SystemC is b... more This paper deals with the most popular attempts of distributing SystemC simulations. SystemC is becoming a popular framework for System-On-Chip (SoC) design and verification. Innovation in processor design does not come easily. Smaller features, faster speeds, and intricate digital logic require more simulation resources to accurately gauge the worth of a new design. In order to provide these resources, distributed

Research paper thumbnail of Quick and Accurate Strategy for Calculating the Solutions of the Photovoltaic Single-Diode Model Equation

IEEE Journal of Photovoltaics, 2022

Research paper thumbnail of Frame-Based and Subpicture-Based Parallelization Approaches of the HEVC Video Encoder

Applied Sciences, 2018

The most recent video coding standard, High Efficiency Video Coding (HEVC), is able to significan... more The most recent video coding standard, High Efficiency Video Coding (HEVC), is able to significantly improve the compression performance at the expense of a huge computational complexity increase with respect to its predecessor, H.264/AVC. Parallel versions of the HEVC encoder may help to reduce the overall encoding time in order to make it more suitable for practical applications. In this work, we study two parallelization strategies. One of them follows a coarse-grain approach, where parallelization is based on frames, and the other one follows a fine-grain approach, where parallelization is performed at subpicture level. Two different frame-based approaches have been developed. The first one only uses MPI and the second one is a hybrid MPI/OpenMP algorithm. An exhaustive experimental test was carried out to study the performance of both approaches in order to find out the best setup in terms of parallel efficiency and coding performance. Both frame-based and subpicture-based approaches are compared under the same hardware platform. Although subpicture-based schemes provide an excellent performance with high-resolution video sequences, scalability is limited by resolution, and the coding performance worsens by increasing the number of processes. Conversely, the proposed frame-based approaches provide the best results with respect to both parallel performance (increasing scalability) and coding performance (not degrading the rate/distortion behavior).

Research paper thumbnail of Qué son los supercomputadores

Research paper thumbnail of Performance Overview of the Latest Video Coding Proposals: HEVC, JEM and VVC

Journal of Imaging, 2021

The audiovisual entertainment industry has entered a race to find the video encoder offering the ... more The audiovisual entertainment industry has entered a race to find the video encoder offering the best Rate/Distortion (R/D) performance for high-quality high-definition video content. The challenge consists in providing a moderate to low computational/hardware complexity encoder able to run Ultra High-Definition (UHD) video formats of different flavours (360°, AR/VR, etc.) with state-of-the-art R/D performance results. It is necessary to evaluate not only R/D performance, a highly important feature, but also the complexity of future video encoders. New coding tools offering a small increase in R/D performance at the cost of greater complexity are being advanced with caution. We performed a detailed analysis of two evolutions of High Efficiency Video Coding (HEVC) video standards, Joint Exploration Model (JEM) and Versatile Video Coding (VVC), in terms of both R/D performance and complexity. The results show how VVC, which represents the new direction of future standards, has, for th...

Research paper thumbnail of Comment on “Parameter extraction of single‐diode photovoltaic module using experimental current–voltage data”

International Journal of Circuit Theory and Applications, 2021

Research paper thumbnail of Aggregation of 25-hydroxycholesterol in a complex biomembrane. Differences with cholesterol

Biochimica et Biophysica Acta (BBA) - Biomembranes, 2020

25-Hydroxycholesterol (25HC), one of the most important oxysterol molecules, can be used by cells... more 25-Hydroxycholesterol (25HC), one of the most important oxysterol molecules, can be used by cells to fight bacterial and viral infections but the mechanism that defines its biological effects are unknown. Using molecular dynamics, we have aimed to describe the orientation and location of 25HC in the membrane as well as the interactions it might have with lipids. We have studied two complex model membrane systems, one similar to the late endosome membrane and the other one to the plasma membrane. Our results reinforce that 25HC is inserted in the membrane in a relative stable location similar to but not identical to cholesterol. 25HC fluctuates in the membrane to a much greater degree than cholesterol, but the effect of 25HC on the phospholipid order parameters is not significantly different. One of the most notable facts about 25HC is that, unlike cholesterol, this molecule tends to aggregate, forming dimers, trimers and higher-order aggregates. These aggregates are formed spontaneously through the formation of hydrogen bonds between the two 25HC atoms, the formation of hydrogen bonds being independent of the studied system. Remarkably, no contacts or hydrogen bonds are observed between 25HC and cholesterol molecules, as well as between cholesterol molecules themselves at any time. It would be conceivable that 25HC, by forming high order aggregates without significantly altering the membrane properties, would modify the way proteins interact with the membrane and henceforth form a true innate antiviral molecule.

Research paper thumbnail of Heterogeneous CPU plus GPU approaches for HEVC

The Journal of Supercomputing, 2018

Research paper thumbnail of Feasibility study of portable microwave microstrip open-loop resonator for non-invasive blood glucose level sensing: proof of concept

Medical & Biological Engineering & Computing, 2019

Research paper thumbnail of Two-Step Linear Least-Squares Method For Photovoltaic Single-Diode Model Parameters Extraction

IEEE Transactions on Industrial Electronics, 2018

In this paper a new method to calculate the five parameters of the single-diode model of a photov... more In this paper a new method to calculate the five parameters of the single-diode model of a photovoltaic cell or panel is presented. This new method takes into account the intrinsic properties of the model equation and the technique of linear least-squares fitting, so, the computational complexity and costs are very low. Moreover, the proposed method, named Two-Step Linear Least-Squares (TSLLS) method, is able to work absolutely blindly with any kind of I-V curve. It does not need initial guesses at all and, consequently, it is not necessary to know previously any information of any parameter. The proposed method provides the parameters of the singlediode model just using the coordinates of N points (N≥5) of the I-V curve. The results provided by this method in a first stage have the same order of accuracy of the best documented methods in the field of parameters extraction, but, furthermore, in a second stage the best accuracy documented until now is obtained in two important case studies usually used in the literature as well as in a largescale I-V curve repository with more than one million of curves.

Research paper thumbnail of A highly scalable parallel encoder version of the emergent JEM video encoder

The Journal of Supercomputing, 2018

Research paper thumbnail of Discovery of nonnucleoside inhibitors of polymerase from infectious pancreatic necrosis virus (IPNV)

Drug design, development and therapy, 2018

Infectious pancreatic necrosis virus (IPNV) causes serious losses in several fish species of comm... more Infectious pancreatic necrosis virus (IPNV) causes serious losses in several fish species of commercial interest. IPNV is a non-enveloped double-stranded RNA virus with a genome consisting of two segments A and B. Segment B codes for the VP1 protein, a non-canonical RNA-dependent RNA polymerase that can be found both in its free form and linked to the end of genomic RNA, an essential enzyme for IPNV replication. We take advantage of the knowledge over the allosteric binding site described on the surface of the thumb domain of Hepatitis C virus (HCV) polymerase to design new non-nucleoside inhibitors against the IPNV VP1 polymerase. Molecular docking techniques have been used to screen a chemical library of 23,760 compounds over a defined cavity in the surface of the thumb domain. Additional ADMET (absorption, distribution, metabolism, excretion, and toxicity) filter criteria has been applied. We select two sets of 9 and 50 inhibitor candidates against the polymerases of HCV and IPNV...

Research paper thumbnail of Spontaneous membrane insertion of a dengue virus NS2A peptide

Archives of Biochemistry and Biophysics, 2017

Non-structural NS2A protein of Dengue virus is essential for viral replication but poorly charact... more Non-structural NS2A protein of Dengue virus is essential for viral replication but poorly characterized because of its high hydrophobicity. We have previously shown experimentally that NS2A possess a segment, peptide dens25, known to insert into membranes and interact specifically with negativelycharged phospholipids. To characterize its membrane interaction we have used two types of molecular dynamics membrane model systems, a highly mobile membrane mimetic (HMMM) and an endoplasmic reticulum (ER) membrane-like model. Using the HMMM system, we have been able of demonstrating the spontaneous binding of dens25 to the negatively-charged phospholipid 1,2-divalerylsn-glycero-3-phosphate containing membrane whereas no binding was observed for the membrane containing the zwitterionic one 1,2-divaleryl-sn-glycero-3-phosphocholine. Using the ER-like membrane model system, we demonstrate the spontaneous insertion of dens25 into the middle of the membrane, it maintained its three-dimensional structure and presented a nearly parallel orientation with respect to the membrane surface. Both charged and hydrophobic amino acids, presenting an interfacial/hydrophobic pattern characteristic of a membrane-proximal segment, are responsible for membrane binding and insertion. Dens25 might control protein/membrane interaction and be involved in membrane rearrangements critical for the viral cycle. These data should help us in the development of inhibitor molecules that target NS2A segments involved in membrane reorganisation.

Research paper thumbnail of GPU-based HEVC intra-prediction module

The Journal of Supercomputing, 2016

The HEVC video coding standard requires nearly 70 % more time than H.264/AVC to encode a video se... more The HEVC video coding standard requires nearly 70 % more time than H.264/AVC to encode a video sequence. Manycore architectures can considerably help to reduce the coding time. In this paper, we propose the use of GPUs to perform the intra-picture prediction without any R/D loss. We have evaluated our proposal and compared the results with the ones obtained when running on a CPU. The results show that a time reduction of up to 85 % can be obtained without any R/D loss.

Research paper thumbnail of An Updated Review on Marine Anticancer Compounds: The Use of Virtual Screening for the Discovery of Small-Molecule Cancer Drugs

Molecules (Basel, Switzerland), Jan 23, 2017

Marine secondary metabolites are a promising source of unexploited drugs that have a wide structu... more Marine secondary metabolites are a promising source of unexploited drugs that have a wide structural diversity and have shown a variety of biological activities. These compounds are produced in response to the harsh and competitive conditions that occur in the marine environment. Invertebrates are considered to be among the groups with the richest biodiversity. To date, a significant number of marine natural products (MNPs) have been established as antineoplastic drugs. This review gives an overview of MNPs, both in research or clinical stages, from diverse organisms that were reported as being active or potentially active in cancer treatment in the past seventeen years (from January 2000 until April 2017) and describes their putative mechanisms of action. The structural diversity of MNPs is also highlighted and compared with the small-molecule anticancer drugs in clinical use. In addition, this review examines the use of virtual screening for MNP-based drug discovery and reveals th...

Research paper thumbnail of Shared Memory Tile-Based vs Hybrid Memory GOP-Based Parallel Algorithms for HEVC Encoder

Algorithms and Architectures for Parallel Processing, 2016

After the emergence of the new High Efficiency Video Coding standard, several strategies have bee... more After the emergence of the new High Efficiency Video Coding standard, several strategies have been followed in order to take advantage of the parallel features available in it. Many of the parallelization approaches in the literature have been performed in the decoder side, aiming at achieving real-time decoding. However, the most complex part of the HEVC codec is the encoding side. In this paper, we perform a comparative analysis of two parallelization proposals. One of them is based on tiles, employing shared memory architectures and the other one is based on Groups Of Pictures, employing distributed shared memory architectures. The results show that good speed-ups are obtained for the tile-based proposal, especially for high resolution video sequences, but the scalability decreases for low resolution video sequences. The GOP-based proposal outperforms the tile-based proposal when the number of processes increases. This benefit grows up when low resolution video sequences are compressed.

Research paper thumbnail of Looking for inhibitors of the dengue virus NS5 RNA-dependent RNA-polymerase using a molecular docking approach

Drug Design, Development and Therapy, 2016

The dengue virus (DENV) nonstructural protein 5 (NS5) contains both an N-terminal methyltransfera... more The dengue virus (DENV) nonstructural protein 5 (NS5) contains both an N-terminal methyltransferase domain and a C-terminal RNA-dependent RNA polymerase domain. Polymerase activity is responsible for viral RNA synthesis by a de novo initiation mechanism and represents an attractive target for antiviral therapy. The incidence of DENV has grown rapidly and it is now estimated that half of the human population is at risk of becoming infected with this virus. Despite this, there are no effective drugs to treat DENV infections. The present in silico study aimed at finding new inhibitors of the NS5 RNA-dependent RNA polymerase of the four serotypes of DENV. We used a chemical library comprising 372,792 nonnucleotide compounds (around 325,319 natural compounds) to perform molecular docking experiments against a binding site of the RNA template tunnel of the virus polymerase. Compounds with high negative free energy variation (∆G −10.5 kcal/mol) were selected as putative inhibitors. Additional filters for favorable druggability and good absorption, distribution, metabolism, excretion, and toxicity were applied. Finally, after the screening process was completed, we identified 39 compounds as lead DENV polymerase inhibitor candidates. Potentially, these compounds could act as efficient DENV polymerase inhibitors in vitro and in vivo.

Research paper thumbnail of Location of the bioactive pentacyclic triterpene ursolic acid in the membrane. A molecular dynamics study

Journal of Biomolecular Structure and Dynamics, 2016