Publications by authors named "Yongpeng Zhang"

19 Publications

  • Page 1 of 1

Deployment of a bioabsorbable plate as the rigid buttress for skull base repair after endoscopic pituitary surgery.

Gland Surg 2021 Mar;10(3):1010-1017

Department of Neurosurgery, Qilu Hospital of Shandong University, Jinan, China.

Background: Bioresorbable alloplastic implants have become desirable as a rigid buttress for reconstructing skull base defects. This study aimed to describe the use of a biodegradable plate (PolyMax RAPID) in skull base repair of endoscopic endonasal pituitary surgery and to investigate the clinical outcome and safety of this novel method.

Methods: Between January 2019 and January 2020, 22 patients with pituitary adenomas who underwent endoscopic skull base repair with a Polymax RAPID plate were included. After endonasal transsphenoidal surgery, a trimmed bioresorbable plate was placed in the position between the dura and the bone of the skull base to reconstruct the sellar floor and buttress the pituitary gland and sellar packing. The patient demographics, radiologic imaging, and postoperative outcomes were carefully reviewed. All patients were followed up by a routine nasal endoscopic assessment and radiologic examinations.

Results: The present study comprised 10 (45.5%) males and 12 (54.4%) females with an average age of 51.9 years. There were 7 (31.8%) growth hormone (GH) secreting adenomas, 2 (9.1%) thyroid stimulating hormone (TSH) secreting adenomas, and 13 (59.1%) non-functioning adenomas. Enlarged sellar floor and paranasal sinusitis were seen in 13 (59.1%) and 11 (50.0%) cases shown by preoperative computed tomography (CT) or magnetic resonance imaging (MRI), respectively. There were 6 (27.3%) grade-1 and 16 (72.7%) grade-0 cases by intraoperative cerebrospinal fluid (CSF) leak grading. None of these patients received lumbar drains postoperatively and no postoperative CSF rhinorrhea was detected in our series. The PolyMax RAPID plates which could be clearly identified on postoperative CT or sagittal T1-weighted MRI were shown to provide an ideal rigid buttress for sellar repair.

Conclusions: The Polymax RAPID plate can be an optimal implant to achieve rigid repair of sellar floor defects after endonasal transsphenoidal pituitary surgery.
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http://dx.doi.org/10.21037/gs-20-642DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8033064PMC
March 2021

Deep learning-based detection and stage grading for optimising diagnosis of diabetic retinopathy.

Diabetes Metab Res Rev 2021 May 13;37(4):e3445. Epub 2021 Mar 13.

Department of Ophthalmology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.

Aims: To establish an automated method for identifying referable diabetic retinopathy (DR), defined as moderate nonproliferative DR and above, using deep learning-based lesion detection and stage grading.

Materials And Methods: A set of 12,252 eligible fundus images of diabetic patients were manually annotated by 45 licenced ophthalmologists and were randomly split into training, validation, and internal test sets (ratio of 7:1:2). Another set of 565 eligible consecutive clinical fundus images was established as an external test set. For automated referable DR identification, four deep learning models were programmed based on whether two factors were included: DR-related lesions and DR stages. Sensitivity, specificity and the area under the receiver operating characteristic curve (AUC) were reported for referable DR identification, while precision and recall were reported for lesion detection.

Results: Adding lesion information to the five-stage grading model improved the AUC (0.943 vs. 0.938), sensitivity (90.6% vs. 90.5%) and specificity (80.7% vs. 78.5%) of the model for identifying referable DR in the internal test set. Adding stage information to the lesion-based model increased the AUC (0.943 vs. 0.936) and sensitivity (90.6% vs. 76.7%) of the model for identifying referable DR in the internal test set. Similar trends were also seen in the external test set. DR lesion types with high precision results were preretinal haemorrhage, hard exudate, vitreous haemorrhage, neovascularisation, cotton wool spots and fibrous proliferation.

Conclusions: The herein described automated model employed DR lesions and stage information to identify referable DR and displayed better diagnostic value than models built without this information.
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http://dx.doi.org/10.1002/dmrr.3445DOI Listing
May 2021

Effect of the Characteristic Size and Content of Graphene on the Crack Propagation Path of Alumina/Graphene Composite Ceramics.

Materials (Basel) 2021 Jan 28;14(3). Epub 2021 Jan 28.

School of Mechanical and Automotive Engineering, Qilu University of Technology (Shandong Academyof Sciences), Jinan 250353, China.

In this paper, the Voronoimosaic model and the cohesive element method were used to simulate crack propagation in the microstructure of alumina/graphene composite ceramic tool materials. The effects of graphene characteristic size and volume content on the crack propagation behavior of microstructure model of alumina/graphene composite ceramics under different interfacial bonding strength were studied. When the phase interface is weak, the average energy release rate is the highest as the short diameter of graphene is 10-50 nm and the long diameter is 1600-2000 nm. When the phase interface is strong, the average energy release rate is the highest as the short diameter of graphene is 50-100 nm and the long diameter is 800-1200 nm. When the volume content of graphene is 0.50 vol.%, the average energy release rate reaches the maximum. When the velocity load is 0.005 m s, the simulation result is convergent. It is proven that the simulation results are in good agreement with the experimental phenomena.
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http://dx.doi.org/10.3390/ma14030611DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7865948PMC
January 2021

An Entropic Approach to Estimating the Instability Criterion of People in Floodwaters.

Entropy (Basel) 2021 Jan 6;23(1). Epub 2021 Jan 6.

Beijing Key Laboratory of Urban Hydrological Cycle and Sponge City Technology, College of Water Sciences, Beijing Normal University, Beijing 100875, China.

People are always susceptible to a loss of stability in urban floodwaters that leads to serious casualties. Thus, the safety criterion for the instability of people in floodwaters must be determined. In this study, the hydrodynamic criterion of the instability of people in floodwaters in terms of the incipient velocity and water depth is derived using the probability method based on Shannon entropy theory. The derived model can characterize variations in the incipient velocity of people in floodwaters with respect to the inundating water depth. Furthermore, a comparison with seven experimental datasets available in the literature shows the validity of the proposed entropy-based model considering data scattering. A sensitivity analysis of the derived model to some of the incorporated parameters was performed, and the qualitative results are in accordance with our understanding of the physical mechanism of the instability of people in floodwaters. Taking the physical parameters (height and mass) of Chinese adults and children as a representative example, this study also showed the vulnerability degree of Chinese adults and children subject to floodwaters. These findings could provide a reference for administrators and stakeholders for flood hazard mitigation and flood strategy management. This study shows that an entropy-based method could be a valuable addition to existing deterministic models for characterizing the instability criterion of people in an urban flooding event.
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http://dx.doi.org/10.3390/e23010074DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7825550PMC
January 2021

Cryptotanshinone ameliorates cardiac injury and cardiomyocyte apoptosis in rats with coronary microembolization.

Drug Dev Res 2020 Dec 19. Epub 2020 Dec 19.

Department of Cardiovascular Medicine, Pingxiang People's Hospital, Pingxiang, Jiangxi, China.

Coronary microembolization (CME) is a prevalent cardiovascular disease, especially nowadays when percutaneous coronary intervention is widely applied. However, neither cardio-protective agents nor devices for distal protection could effectively prevent the occurrence of CME. Therefore, we aimed to develop a new drug for CME. Rats were orally administrated with different doses of Cryptotanshinone (CTS, 5, 15, 45 mg/kg) daily for 2 weeks, respectively, following CME surgery. Then cardiac function and cardiac injury were evaluated in CME rats as well as measuring oxidative stress and apoptosis in cardiomyocytes. Compared to sham group, CME operation induced cardiac dysfunction, cardiac injury, the activation of platelet and endothelium, cardiomyocyte apoptosis and oxidative stress, all of which could be dose-dependently restored by CTS pretreatment. Moreover, NF-κB signaling pathway participated in the development of CME and also in the preventive process of CTS against CME. CTS might serve as a potential and promising candidate drug to prevent the occurrence of CME.
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http://dx.doi.org/10.1002/ddr.21777DOI Listing
December 2020

Effect of Cryptotanshinone on Measures of Rat Cardiomyocyte Oxidative Stress and Gene Activation Associated with Apoptosis.

Cardiorenal Med 2021 16;11(1):18-26. Epub 2020 Dec 16.

College of Traditional Chinese Medicine, Hebei North University, Zhangjiakou, China,

Background: Oxidative stress is a key factor that results in cardiomyocyte apoptosis and cardiovascular diseases. Cryptotanshinone (CTS), one of the major bioactive constitutes extracted from the root of the plant Salvia miltiorrhizaBunge, has been widely studied for various disease treatments. However, the roles of CTS on cardiomyocytes remain unclear.

Methods: In the present study, neonatal rat cardiomyocytes were pretreated with CTS for 4 h before being exposed to H2O2. Cell viability for the cells with or without pretreatment with CTS before exposure to H2O2 was evaluated by the MTT assay. Production of lactate dehydrogenase (LDH), nitric oxide (NO), prostaglandin E2 (PGE2), malondialdehyde (MDA), superoxide dismutase (SOD), catalase (CAT), and glutathione peroxides (GSH-Px) was quantified by corresponding detection kits. The mRNA levels of Bcl-2 antiapoptotic and Bax-like proapoptotic genes were quantified with RT-PCR. Production of reactive oxygen species (ROS) was qualified and quantified with a dichlorofluorescein diacetate cellular ROS detection assay kit. The extracellular signal-related kinase (ERK) phosphorylation and nuclear factor κB (NF-κB) activation were measured by Western blot.

Results: Our results revealed that the CTS pretreatment could enhance cell viability and promote Bcl-2 antiapoptotic gene expression. Additionally, CTS could abolish the H2O2-induced production of NO, LDH, and PGE2. Consistent with these findings, CTS could inhibit ROS and MDA production and promote SOD, CAT, and GSH-Px activities. Mechanistically, CTS may achieve these processes by inhibiting ERK and NF-κB signal pathways.

Conclusion: CTS protects cardiomyocytes against the H2O2-induced cellular injuries through ERK and NF-κB inactivation and ROS scavenging. Therefore, CTS is a promising reagent against ROS-induced cardiomyopathy.
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http://dx.doi.org/10.1159/000507184DOI Listing
December 2020

Deciphering of antibiotic resistance genes (ARGs) and potential abiotic indicators for the emergence of ARGs in an interconnected lake-river-reservoir system.

J Hazard Mater 2021 May 12;410:124552. Epub 2020 Nov 12.

Environmental Science and Engineering School, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai 200240, China. Electronic address:

This study aimed to decipher the patterns of antibiotic resistance genes (ARGs) and linkages of key abiotic indicators with ARGs in an interconnected lake-river-reservoir system. The results showed that seasonal variations in the relative abundance of ARGs and mobile gene elements (MGEs) were significant (KW, p < 0.05). ARGs representative of fecal pollution and natural environment were primarily distributed in the river and reservoir, respectively. The lake, river, and reservoir shared 54.5% of ARGs subtypes, most of which are multidrug resistance genes encoding for efflux pumps. Network results showed that ARGs conferring resistance to aminoglycoside frequently co-occurred with class 1 integrons and Limnohabitans. The resistance risks were low and associated with non-corresponding ARGs, and the highest resistance risk was caused by enrofloxacin in the Dianshan Lake. Fluorescence indices derived from two methods exhibited consistent positive correlations with abundance of individual genes (i.e. aada1 and aadA2-03) as well as total aminoglycoside resistance genes (Pearson, p < 0.05). Moreover, ARGs indicators of human and animal fecal pollution showed linkages with humic-like and fulvic-like indices (Pearson, p < 0.05). The results provide novel insights into the roles of abiotic factors on indicating dynamics of ARGs in aquatic environment impacted by anthropogenic activities.
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http://dx.doi.org/10.1016/j.jhazmat.2020.124552DOI Listing
May 2021

Real-Time Evacuation Strategy Based on Cell-Inspired Simulation Model.

IEEE Trans Nanobioscience 2021 Apr 31;20(2):202-211. Epub 2021 Mar 31.

During the evacuation process in an emergency, the route conditions usually change instantaneously, which makes routing selection a challenging work. To describe dynamic changes in the evacuation environment, this work proposes a real-time evacuation strategy based on a comprehensive route constraint in the framework of a cell-inspired simulation model, intelligence decision P system (IDPS). In our model, the comprehensive route constraint is formed to describe more complex road condition information including the total distance, congestion state, and unreliability of the route. Meanwhile, the IDPS model has been further improved in both the knowledge base description and the decision-making ability. Experiments are conducted to simulate five different scenarios in a fire evacuation. The results show that the evacuation strategy with a comprehensive route constraint has a significant improvement in the evacuation efficiency and has higher robustness. Which kind of route condition should be emphasized more in different evacuation scenarios is also analyzed.
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http://dx.doi.org/10.1109/TNB.2020.3039992DOI Listing
April 2021

DOM as an indicator of occurrence and risks of antibiotics in a city-river-reservoir system with multiple pollution sources.

Sci Total Environ 2019 Oct 3;686:276-289. Epub 2019 Jun 3.

Shanghai Academy of Environmental Sciences, Shanghai 200233, China.

Multiple sources contribute to the presence of antibiotic residues in water environments, and the environmental risks caused by antibiotics were paid more and more attention. This work aims to establish a relationship between optical properties of dissolved organic matter (DOM) and sources and risks of antibiotics. Occurrence of antibiotics and DOM in a city-river-reservoir freshwater system containing distinct antibiotic sources was investigated during three seasons using LC-MS and fluorescence excitation-emission matrix coupled with parallel factor analysis (EEM-PARAFAC), respectively. The results showed that antibiotics and DOM in the water had trends of increasing levels from the upstream to the midstream in the system. Five classes of antibiotics had statistically significant correlations with the humic-like component (C3) in the water (Pearson, p < 0.05). Especially, norfloxacin (NFX), which was dominant in the aquaculture source, significantly increased the fluorescence of C3 according to the fluorescence titration (R = 0.86, p < 0.01). Furthermore, fluorescence signature in the aquaculture pond posed broad humic acid-like peaks with relatively higher abundances compared to other areas. These results suggested that C3 could be recognized as an indicator of NFX from aquaculture sources. Meanwhile, C3 can largely account for ecological risks of tetracyclines according to the results of redundancy analysis. This work highlights the roles of EEM-PARAFAC on tracing the source of antibiotics and the correlations between environmental risks of antibiotics and DOM in the aquatic environment.
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http://dx.doi.org/10.1016/j.scitotenv.2019.05.439DOI Listing
October 2019

Elevated Level of miR-551b-5p is Associated With Inflammation and Disease Progression in Patients With Severe Acute Pancreatitis.

Ther Apher Dial 2018 Dec 10;22(6):649-655. Epub 2018 Jul 10.

Department of Emergency, People's Hospital of Dongying, Dongying, Shandong, China.

Circulating microRNAs have the potential to be noninvasive biomarkers for assessing disease progression. MicroRNA-551b-5p (miR-551b-5p) was previously reported to be differentially expressed in pancreatic patients. The serum miR-551b-5p level was measured in patients with mild acute pancreatitis (MAP), severe acute pancreatitis (SAP), and healthy controls using quantitative real-time polymerase chain reaction (RT-PCR) analysis to evaluate its impact on inflammatory response. Acute Physiology and Chronic Health Evaluation II (APACHE II), Multiple Organ Dysfunction Score (MODS), Sequential Organ Assessment Score (SOFA), and Ranson's scores were recorded. Inflammatory cytokines, IL-6, IL-17, IL-1β, and Tumor Necrosis Factor-α (TNF-α), were detected in serum samples obtained from MAP and SAP patients on admission day 1, day 3, and day 5 using Enzyme Linked Immunosorbent Assay (ELISA). Inflammatory cytokines were analyzed in peripheral blood mononuclear cells (PBMCs), which were transfected with miR-551b-5p-negative controls and inhibitors. The serum miR-551b-5p level was significantly higher in MAP and SAP patients compared to controls (P < 0.001). An elevated miR-551b-5p level is positively associated with APACHE II, MODS, SOFA, and Ranson's scores (P < 0.001). Serum cytokines levels were significantly elevated in MAP and SAP patients compared to controls (P < 0.05). In addition, the level of these inflammatory cytokines was increased in PBMCs of SAP patients in comparison with those of healthy controls (P < 0.05), and this rise was significantly reduced with the addition of an miR-551b-5p inhibitor. In conclusion, serum miR-551b-5p is elevated in patients with MAP and SAP and is involved in the regulation of inflammatory response. It may be a useful biomarker for assessing the severity of SAP.
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http://dx.doi.org/10.1111/1744-9987.12720DOI Listing
December 2018

Variation pattern of terrestrial antibiotic resistances and bacterial communities in seawater/freshwater mixed microcosms.

Chemosphere 2018 Jun 21;200:201-208. Epub 2018 Feb 21.

School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China; School of Marine Science and Technology, Tianjin University, Tianjin 300072, China. Electronic address:

The ocean is the final place where pollutants generated by human activities are deposited. As a result, the long-range transport of the ocean can facilitate the diffusion of terrestrial contaminants, including ARGs. However, to our knowledge, little research has been devoted to discussing the content change of terrestrial ARGs and the reason for the change in coastal area. This study established various microcosms, in which seawater and freshwater were mixed at different ratio to simulate the environmental conditions of different regions in coastal areas. Four ARGs were quantified, and 16S pyrosequencing was conducted. The results showed that the terrestrial ARGs influenced the concentration of the corresponding ARGs in coastal areas, and the content change pattern of each ARG was distinct. The influence of salinity on the ARG content was limited in most cases. Moreover, most dominant bacteria from freshwater had significant positive correlation (p < 0.05) with selected ARGs, except for bla. The dominant bacteria in freshwater diminished dramatically in microcosms with a high proportion of seawater. Freshwater may have a strong impact on the bacteria composition of seawater, and the materials from freshwater may prompt the growth of some bacteria (include potential hosts of ARGs) in coastal area.
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http://dx.doi.org/10.1016/j.chemosphere.2018.02.119DOI Listing
June 2018

Occurrence of intracellular and extracellular antibiotic resistance genes in coastal areas of Bohai Bay (China) and the factors affecting them.

Environ Pollut 2018 May;236:126-136

School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, China.

Coastal areas are the transition zones between ocean and land where intracellular antibiotic resistance genes (iARGs) and extracellular antibiotic resistance genes (eARGs) could spread among marine organisms, and between humans and marine organisms. However, little attention has been paid to the combined research on iARGs and eARGs in marine environment. In this context, we collected water and sediment samples from the coastal areas of the Bohai Bay in China and performed molecular and chemical analyses. The results of quantitative real-time PCR (qPCR) showed that the relative abundance of eARGs was up to 4.3 ± 1.3 × 10 gene copies/16S rRNA copies in the water samples and 2.6 ± 0.3 × 10 gene copies/16S rRNA copies in the sediment samples. Also, the abundance of eARGs was significantly higher than that of iARGs. Furthermore, the average abundances of antibiotic resistance genes (ARGs, include iARGs and eARGs) were the highest in both the water and sediment samples from the estuaries. The results of liquid chromatography-mass spectrometry showed that the concentrations of antibiotics in estuaries and areas near the mariculture site were higher than that in the other sites. The class 1 integron gene (int1) and sul1 in the intracellular DNA were significantly correlated in the water samples. Moreover, significant correlation between int1 and sul2 in the extracellular DNA was also found in the sediment samples. The combination of sulfamerazine and tetracycline as well as the combination of sulfamethazine and dissolved oxygen can both explain the abundance of ARGs, implying the combined effects of multiple stresses on ARGs.
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http://dx.doi.org/10.1016/j.envpol.2018.01.033DOI Listing
May 2018

Light-weight reference-based compression of FASTQ data.

BMC Bioinformatics 2015 Jun 9;16:188. Epub 2015 Jun 9.

College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, 518060, China.

Background: The exponential growth of next generation sequencing (NGS) data has posed big challenges to data storage, management and archive. Data compression is one of the effective solutions, where reference-based compression strategies can typically achieve superior compression ratios compared to the ones not relying on any reference.

Results: This paper presents a lossless light-weight reference-based compression algorithm namely LW-FQZip to compress FASTQ data. The three components of any given input, i.e., metadata, short reads and quality score strings, are first parsed into three data streams in which the redundancy information are identified and eliminated independently. Particularly, well-designed incremental and run-length-limited encoding schemes are utilized to compress the metadata and quality score streams, respectively. To handle the short reads, LW-FQZip uses a novel light-weight mapping model to fast map them against external reference sequence(s) and produce concise alignment results for storage. The three processed data streams are then packed together with some general purpose compression algorithms like LZMA. LW-FQZip was evaluated on eight real-world NGS data sets and achieved compression ratios in the range of 0.111-0.201. This is comparable or superior to other state-of-the-art lossless NGS data compression algorithms.

Conclusions: LW-FQZip is a program that enables efficient lossless FASTQ data compression. It contributes to the state of art applications for NGS data storage and transmission. LW-FQZip is freely available online at: http://csse.szu.edu.cn/staff/zhuzx/LWFQZip.
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http://dx.doi.org/10.1186/s12859-015-0628-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4459677PMC
June 2015

A novel nonsense mutation in BBS4 gene identified in a Chinese family with Bardet-Biedl syndrome.

Chin Med J (Engl) 2014 ;127(24):4190-6

Beijing Tongren Eye Center, Beijing Key Laboratory of Ophthalmology and Visual Science, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China; Beijing Institute of Ophthalmology, Beijing Key Laboratory of Ophthalmology and Visual Science, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China.

Background: Bardet-Biedl syndrome (BBS) is a genetically heterogeneous disease, and information about BBS in Chinese populations is very limited. The purpose of the present study was to determine the genetic cause of BBS in a Chinese Han family.

Methods: Clinical data were recorded for the 4-year-old female proband and the available family members. The proband was screened for mutation by Sanger sequencing for a total of 142 exons of the 12 BBS-causing genes (BBS1-BBS12). The variants detected in the proband were further confirmed in the other family members.

Results: We identified a novel homozygous nonsense mutation (c.70A>T, p.K24X) in the BBS4 gene exon 2 in the proband. Such mutant allele was predicted to cause a premature truncation in the N-terminal of the BBS4 protein, and probably induced the nonsense-mediated decay of BBS4 messenger RNAs. The proband's parents and brother were heterozygous for the nonsense mutant allele. It was absent in 50 Chinese control subjects. An additional rare heterozygous missense single nucleotide polymorphism (SNP) named rs200718870 in BBS10 gene was also detected in the proband, her father and her brother. Some manifestations of the proband including atypical retinitis pigmentosa, choroidal sclerosis, high myopia, and early onset of obesity might be associated with this mutation in BBS4 gene. The proband's father also reported surgical removal of an extra finger during childhood.

Conclusions: The present study described a novel nonsense mutation in BBS4 gene in a Chinese family. This homozygous mutation was predicted to completely abolish the synthesis of the BBS4 protein. We also detected a rare heterozygous missense SNP in BBS10 gene in the family, but did not find sufficient evidence to support the triallelic inheritance.
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August 2015

CompMap: a reference-based compression program to speed up read mapping to related reference sequences.

Bioinformatics 2015 Feb 4;31(3):426-8. Epub 2014 Oct 4.

College of Computer Science and Software Engineering, Shenzhen University, Shenzhen 518060, China and Infectious Disease Initiative, The Broad Institute, Cambridge, MA 02142, USA.

Summary: Exhaustive mapping of next-generation sequencing data to a set of relevant reference sequences becomes an important task in pathogen discovery and metagenomic classification. However, the runtime and memory usage increase as the number of reference sequences and the repeat content among these sequences increase. In many applications, read mapping time dominates the entire application. We developed CompMap, a reference-based compression program, to speed up this process. CompMap enables the generation of a non-redundant representative sequence for the input sequences. We have demonstrated that reads can be mapped to this representative sequence with a much reduced time and memory usage, and the mapping to the original reference sequences can be recovered with high accuracy.

Availability And Implementation: CompMap is implemented in C and freely available at http://csse.szu.edu.cn/staff/zhuzx/CompMap/.

Contact: xiaoyang@broadinstitute.org

Supplementary Information: Supplementary data are available at Bioinformatics online.
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http://dx.doi.org/10.1093/bioinformatics/btu656DOI Listing
February 2015

High-throughput DNA sequence data compression.

Brief Bioinform 2015 Jan 3;16(1):1-15. Epub 2013 Dec 3.

The exponential growth of high-throughput DNA sequence data has posed great challenges to genomic data storage, retrieval and transmission. Compression is a critical tool to address these challenges, where many methods have been developed to reduce the storage size of the genomes and sequencing data (reads, quality scores and metadata). However, genomic data are being generated faster than they could be meaningfully analyzed, leaving a large scope for developing novel compression algorithms that could directly facilitate data analysis beyond data transfer and storage. In this article, we categorize and provide a comprehensive review of the existing compression methods specialized for genomic data and present experimental results on compression ratio, memory usage, time for compression and decompression. We further present the remaining challenges and potential directions for future research.
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http://dx.doi.org/10.1093/bib/bbt087DOI Listing
January 2015

A new optimal sliding mode controller design using scalar sign function.

ISA Trans 2014 Mar 10;53(2):267-79. Epub 2013 Oct 10.

Department of Engineering Technology, Prairie View A & M University, Prairie View, TX 77446, United States.

This paper presents a new optimal sliding mode controller using the scalar sign function method. A smooth, continuous-time scalar sign function is used to replace the discontinuous switching function in the design of a sliding mode controller. The proposed sliding mode controller is designed using an optimal Linear Quadratic Regulator (LQR) approach. The sliding surface of the system is designed using stable eigenvectors and the scalar sign function. Controller simulations are compared with another existing optimal sliding mode controller. To test the effectiveness of the proposed controller, the controller is implemented on an aluminum beam with piezoceramic sensor and actuator for vibration control. This paper includes the control design and stability analysis of the new optimal sliding mode controller, followed by simulation and experimental results. The simulation and experimental results show that the proposed approach is very effective.
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http://dx.doi.org/10.1016/j.isatra.2013.09.007DOI Listing
March 2014

Real-time random delay compensation with prediction-based digital redesign.

ISA Trans 2011 Apr 30;50(2):207-12. Epub 2010 Dec 30.

Engineering Technology Department, Prairie View A&M University, Prairie View, TX 77446, United States.

Today's technological demands require challenging control solutions such as real-time applications of Networked Control System (NCS). However, due to communication protocol and shared data bus, NCS experiences uncertain and unpredictable time delays in both input and output channels. These delays cause asynchronization between the controller and the plant thereby degrading the performance of closed-loop control systems. To address this problem, this paper proposes to utilize digital redesign technique to provide real-time random delay compensation.
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http://dx.doi.org/10.1016/j.isatra.2010.11.009DOI Listing
April 2011