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1.
Small ; 20(24): e2307107, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38191832

RESUMO

Assembled gold nanoparticle (AuNP) superstructures can generate unique physicochemical characteristics and be used in various applications, thus becoming an attractive research field. Recently, several DNA-assisted gold nanoparticle assembly methods have been rigorously developed that typically require a non-catalytic equimolar molecular assembly to guarantee the designed assembly. Although efficient and accurate, exploring such non-catalytic nanoparticle assemblies in the complex cellular milieu under low trigger concentrations remains challenging. Therefore, developing a catalytic method that facilitates gold nanoparticle assemblies with relatively low DNA trigger concentrations is desirable. In this report, a catalytic method to program gold nanoparticle assemblies by DNAzyme circuits is presented, where only a small number of DNA triggers are able to induce the production of a large number of the desired nanoparticle assemblies. The feasibility of using logic DNAzyme circuits to control catalytic nanoparticle assemblies is experimentally verified. Additionally, catalytic AuNP assembly systems are established with cascading and feedback functions. The work provides an alternative research direction to enrich the tool library of nanoparticle assembly and their application in biosensing and nanomedicine.


Assuntos
DNA Catalítico , Ouro , Nanopartículas Metálicas , Ouro/química , DNA Catalítico/química , DNA Catalítico/metabolismo , Nanopartículas Metálicas/química , Catálise
2.
Chembiochem ; : e202400384, 2024 May 31.
Artigo em Inglês | MEDLINE | ID: mdl-38819745

RESUMO

Nanoparticles are a hot topic in the field of nanomaterial research due to their excellent physical and chemical properties. In recent years, DNA-directed nanoparticle self-assembly technology has been widely applied to the development of numerous complex nanoparticle superstructures. Due to the inherent stability and surface electric repulsion of nanoparticles, it is difficult to make nanoparticle superstructures respond to molecular signals in the external environment. In fact, enzyme-programmed molecular systems are developed to allow diverse functions, including logical operations, signal amplification, and dynamic assembly control. Therefore, combining enzyme-controlled DNA systems may endow nanoparticle assembly systems with more flexibility in program design, allowing them to respond to a variety of external signals. In this review, we summarize the basic principles of enzyme-controlled DNA/nanoparticle self-assembly and introduce its applications in heavy metal detection, gene expression, proteins inside living cells, cancer cell therapy, and drug delivery. With the continuous development of new nanoparticle materials and the increasing functionality of enzyme DNA circuits, enzyme-directed DNA/nanoparticle self-assembled probe technology is expected to see significant future development.

3.
Invest New Drugs ; 41(2): 254-266, 2023 04.
Artigo em Inglês | MEDLINE | ID: mdl-37036582

RESUMO

Despite remarkable initial responses of anaplastic lymphoma kinase (ALK) inhibitors in ALK-positive non-small cell lung cancer (NSCLC) patients, cancers eventually develop resistance within one to two years. This study aimed to compare the properties of iruplinalkib (WX­0593) with other ALK inhibitors and report the comprehensive characterization of iruplinalkib against the crizotinib resistance. The inhibitory effect of iruplinalkib on kinase activity was detected. A kinase screen was performed to evaluate the selectivity of iruplinalkib. The effect of iruplinalkib on related signal transduction pathways of ALK and c-ros oncogene 1 (ROS1) kinases was examined. The cellular and in vivo activities of ALK inhibitors were compared in engineered cancer-derived cell lines and in mice xenograft models, respectively. Human hepatocytes derived from three donors were used for evaluating hepatic enzyme inducing activity. HEK293 cell lines expressing transportors were used to invesigated the drug interaction potential mediated by several transporters. The results showed iruplinalkib potently inhibited the tyrosine autophosphorylation of wild-type ALK, ALKL1196M, ALKC1156Y and epidermal growth factor receptor (EGFR)L858R/T790M. The inhibitory effects of iruplinalkib in patient-derived xenograft and cell line-derived xenograft models were observed. Moreover, iruplinalkib showed robust antitumor effects in BALB/c nude mice xenograft models with ALK-/ROS1-positive tumors implanted subcutaneously, and the tumor suppressive effects in crizotinib-resistant model was significantly better than that of brigatinib. Iruplinalkib did not induce CYP1A2, CYP2B6 and CYP3A4 at therapeutic concentration, and was also a strong inhibitor of MATE1 and MATE2K transporters, as well as P-gp and BCRP. In conclusion, iruplinalkib, a highly active and selective ALK/ROS1 inhibitor, exhibited strong antitumor effects in vitro and in crizotinib-resistant models.


Assuntos
Carcinoma Pulmonar de Células não Pequenas , Neoplasias Pulmonares , Humanos , Animais , Camundongos , Carcinoma Pulmonar de Células não Pequenas/patologia , Crizotinibe/farmacologia , Crizotinibe/uso terapêutico , Inibidores de Proteínas Quinases/farmacologia , Inibidores de Proteínas Quinases/uso terapêutico , Proteínas Tirosina Quinases , Receptores ErbB/genética , Neoplasias Pulmonares/patologia , Camundongos Nus , Membro 2 da Subfamília G de Transportadores de Cassetes de Ligação de ATP , Células HEK293 , Receptores Proteína Tirosina Quinases , Quinase do Linfoma Anaplásico/metabolismo , Resistencia a Medicamentos Antineoplásicos , Piridinas/uso terapêutico , Mutação , Linhagem Celular Tumoral , Proteínas Proto-Oncogênicas , Proteínas de Neoplasias/metabolismo , Oncogenes
4.
Environ Res ; 216(Pt 2): 114513, 2023 01 01.
Artigo em Inglês | MEDLINE | ID: mdl-36208781

RESUMO

The rapid aerobic composting process has been used to reduce organic wastes, but the associated risks of antibiotic resistance genes (ARGs) need to evaluate in an efficient way. The primary objective of this work was to explore the underlying mechanism of initial adjustment in composting temperature on the variation of ARGs, mobile genetic elements (MGEs), and microbial composition during co-composting. The co-composting was initially externally heated (T2) for 5 days. The results showed that ARGs abundance in conventional composting (T1) was reduced by 49.36%, while multidrug was enriched by 86.16% after a period of 30 days. While in T2 ARGs were removed by 79.46% particularly the fraction of sulfonamide, multidrug, and vancomycin resistance genes were >90% without rebounding of any ARGs. Whereas, MGEs were reduced by 68.12% and 93.62% in T1 and T2, while the half-lives of ARGs and MGEs were lower in T2 compared to T1 (86.3%,86.7%). T2 also affected the metabolism function by regulating carbohydrate metabolism (9.62-10.39%) and amino acid metabolism (9.92-10.93%). Apart from this, the potential human pathogenic bacteria Pseudomonas was reduced by 90.6% in T2 and only 32.9% in T1 respectively. Network analysis showed that Ureibacillus, Weissella, Corynebacterium, Escherichia-Shigella, Acinetobacter were the main host of multiple genes. Structural equation models exhibited that bacterial communities were mainly responsible for the enrichment of ARGs in T1, whereas, it was directly affected by MGEs in T2. Similarly, ARGs variation was directly related to composting temperature. With this simple strategy, ARGs associated risk can be significantly reduced in composting.


Assuntos
Compostagem , Eliminação de Resíduos , Humanos , Suínos , Animais , Esterco/microbiologia , Antibacterianos , Temperatura , Alimentos , Genes Bacterianos , Resistência Microbiana a Medicamentos/genética , Bactérias/genética
5.
BMC Ophthalmol ; 23(1): 176, 2023 Apr 24.
Artigo em Inglês | MEDLINE | ID: mdl-37095443

RESUMO

BACKGROUND: To evaluate the prevalence and associated health and lifestyle factors of myopic maculopathy (MM) in a northern Chinese industrial city. METHODS: The cross-sectional Kailuan Eye Study included subjects who participated in the longitudinal Kailuan Study in 2016. Ophthalmologic and general examinations were performed on all the participants. MM was graded based on fundus photographs using the International Photographic Classification and Grading System. The prevalence of MM was evaluated. Univariate and multiple logistic regression were adopted to evaluated risk factors of MM. RESULTS: The study included 8330 participants with gradable fundus photographs for MM and ocular biometry data. The prevalence of MM was 1.11% (93/8330; 95% confidence interval [CI] 0.89-1.33%). Diffuse chorioretinal atrophy, patchy chorioretinal atrophy, macular atrophy, and plus lesions were observed in 72 (0.9%), 15 (0.2%), 6 (0.007%), and 32 eyes (0.4%), respectively. MM was more common in eyes with longer axial length (OR 4.517; 95%CI 3.273 to 6.235) and in participants with hypertension (OR 3.460; 95%CI 1.152 to 10.391), and older age (OR 1.084; 95%CI 1.036 to 1.134). CONCLUSIONS: The MM was present in 1.11% of the northern Chinese individuals 21 years or older and the associate factors include longer axial length, older age, and hypertension.


Assuntos
Degeneração Macular , Miopia Degenerativa , Degeneração Retiniana , Doenças Retinianas , Humanos , Acuidade Visual , Prevalência , Estudos Transversais , China/epidemiologia , Estilo de Vida , Atrofia
6.
J Environ Manage ; 343: 118073, 2023 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-37229868

RESUMO

Animal manure is known to harbor antibiotic resistance genes (ARGs). Aerobic composting is a prevalent cost-effective and sustainable method to treat animal waste. However, the effect of initially elevated temperature on antibiotic resistome during the composting process is unclear. In this study composting was subjected to initial external heating (EHC) for a period of 5 days compared to conventional composting (CC). After composting ARGs abundance was significantly reduced by 2.43 log in EHC and 1.95 log in CC. Mobile genetic elements (MGEs) also exhibited a reduction of 1.95 log in EHC and 1.49 log in CC. However, during the cooling phase, the genes resisting macrolide lincosamide and streptogramin B (MLSB) rebounded by 0.04 log in CC. The potential human pathogenic bacteria Pseudomonas (41.5-61.5%) and Actinobacteria (98.4-98.8%) were significantly reduced in both treatments and the bulk of targeted antibiotics were eliminated by 80.74% in EHC and 68.98% in CC. ARGs and N-functional genes (NFGs), mainly denitrification genes, were carried by the same microbial species, such as Corynebacterium sp. and Bacillus sp., of the dominant phylum. Redundancy analysis (RDA) revealed that CC microbial communities played a key role in the enrichment of ARGs while in EHC the variation of ARGs was attributed to the composting temperature. The number of high-risk ARGs was also lower in EHC (4) compared with CC (6) on day 30. These results provide insight into the effects of an initially enhanced temperature on ARGs removal and the relationship between ARGs and NFGs during the composting process.


Assuntos
Compostagem , Genes Bacterianos , Animais , Humanos , Antibacterianos/farmacologia , Temperatura , Resistência Microbiana a Medicamentos/genética , Bactérias/genética , Esterco
7.
Angew Chem Int Ed Engl ; 62(43): e202308797, 2023 Oct 23.
Artigo em Inglês | MEDLINE | ID: mdl-37691009

RESUMO

Programmable assembly of gold nanoparticle superstructures with precise spatial arrangement has drawn much attention for their unique characteristics in plasmonics and biomedicine. Bio-inspired methods have already provided programmable, molecular approaches to direct AuNP assemblies using biopolymers. The existing methods, however, predominantly use DNA as scaffolds to directly guide the AuNP interactions to produce intended superstructures. New paradigms for regulating AuNP assembly will greatly enrich the toolbox for DNA-directed AuNP manipulation and fabrication. Here, we developed a strategy of using a spatially programmable enzymatic nanorobot arm to modulate anisotropic DNA surface modifications and assembly of AuNPs. Through spatial controls of the proximity of the reactants, the locations of the modifications were precisely regulated. We demonstrated the control of the modifications on a single 15 nm AuNP, as well as on a rectangular DNA origami platform, to direct unique anisotropic AuNP assemblies. This method adds an alternative enzymatic manipulation to DNA-directed AuNP superstructure assembly.

8.
Graefes Arch Clin Exp Ophthalmol ; 260(3): 849-856, 2022 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-34591173

RESUMO

PURPOSE: The purpose of this study is to develop and validate the intelligent diagnosis of severe DR with lesion recognition based on color fundus photography. METHODS: The Kaggle public dataset for DR grading is used in the project, including 53,576 fundus photos in the test set, 28,101 in the training set, and 7,025 in the validation set. We randomly select 4,192 images for lesion annotation. Inception V3 structure is adopted as the classification algorithm. Both 299 × 299 pixel images and 896 × 896 pixel images are used as the input size. ROC curve, AUC, sensitivity, specificity, and their harmonic mean are used to evaluate the performance of the models. RESULTS: The harmonic mean and AUC of the model of 896 × 896 input are higher than those of the 299 × 299 input model. The sensitivity, specificity, harmonic mean, and AUC of the method with 896 × 896 resolution images as input for severe DR are 0.925, 0.907, 0.916, and 0.968, respectively. The prediction error mainly occurs in moderate NPDR, and cases with more hard exudates and cotton wool spots are easily predicted as severe cases. Cases with preretinal hemorrhage and vitreous hemorrhage are easily identified as severe cases, and IRMA is the most difficult lesion to recognize. CONCLUSIONS: We have studied the intelligent diagnosis of severe DR based on color fundus photography. This artificial intelligence-based technology offers a possibility to increase the accessibility and efficiency of severe DR screening.


Assuntos
Aprendizado Profundo , Diabetes Mellitus , Retinopatia Diabética , Algoritmos , Inteligência Artificial , Retinopatia Diabética/diagnóstico , Fundo de Olho , Humanos , Fotografação/métodos
9.
Retina ; 42(11): 2110-2119, 2022 11 01.
Artigo em Inglês | MEDLINE | ID: mdl-35839489

RESUMO

PURPOSE: To describe and analyze clinical characteristics of multifocal choroiditis with linear streaks (LSs). METHODS: Eight cases of multifocal choroiditis with LSs were retrospectively studied. Multimodal imaging was performed. Demographic data and spherical equivalent were collected. Axial length was measured. RESULTS: All cases are young myopic women with a mean age of 17.13 ± 3.64 years (range, 13-23 years), presenting with vision loss and distortion. Nine eyes with LSs were high myopia of -8.97 ± 2.69 D (range, -6.00 to 12.5 D; growing by 1.88 ± 0.61 D annually since wearing glasses), with mean axial length of 26.36 ± 1.71 mm. Vitreous cells were noted in seven eyes. LSs were located in the equator (eight eyes), around the optic disk (three eyes), and at the edge of the posterior pole (one eye). Angio-optical coherence tomography showed choroidal neovascularization in eight eyes, especially 2 to 3 choroidal neovascularizations in three eyes. The location of choroidal neovascularization were in subfovea (three eyes), parafovea (six eyes), and perifovea (two eyes). Swept source optical coherence tomography showed punched-out disruption of retinal pigment epithelium‒Bruch's membrane‒choriocapillaris complex at the LSs' sites. LSs showed fluorescence staining on late FA but hypofluorescence throughout all phases on ICGA. CONCLUSION: Multifocal choroiditis with LSs mostly occurs in young women with high myopia, especially occurring in eyes with rapid progression of myopia. LSs are mainly located in the midperiphery near the equator, being prone to concur with choroidal neovascularization. Based on our findings, we propose a new term called "streaky multifocal choroiditis" as a subtype of multifocal choroiditis.


Assuntos
Neovascularização de Coroide , Corioidite , Miopia , Feminino , Humanos , Adolescente , Adulto Jovem , Adulto , Coroidite Multifocal , Neovascularização de Coroide/diagnóstico , Corioidite/diagnóstico , Angiofluoresceinografia/métodos , Estudos Retrospectivos , Acuidade Visual , Tomografia de Coerência Óptica/métodos , Miopia/complicações , Miopia/diagnóstico
10.
BMC Ophthalmol ; 22(1): 104, 2022 Mar 05.
Artigo em Inglês | MEDLINE | ID: mdl-35248002

RESUMO

BACKGROUND: To report a case of herpetic uveitis caused by herpes simplex virus after cataract surgery in a patient without prior viral keratitis or uveitis. CASE PRESENTATION: A 70-year-old female was referred to our clinic with a 16-day history of acute blurry vision with painful redness in the right eye. She accepted cataract surgery for the right eye ten days before initial of ocular symptoms. There was significant inflammation in anterior chamber of the right eye. Retina exam showed moderate dense vitreous opacity but not necrotic or focal retinal lesion in the right eye. The aqueous humor collected from the right eye was positive for herpes simplex virus (HSV) DNA by PCR. The diagnosis of herpetic uveitis in the right eye was made due to clinical presentations and aqueous humor examination. CONCLUSION: Herpetic virus reactivation might occasionally occur after intraocular surgery in patients without prior ocular viral diseases, inducing atypical postoperative intraocular inflammation.


Assuntos
Catarata , Ceratite Herpética , Ceratite , Uveíte Anterior , Uveíte , Idoso , DNA Viral/análise , Feminino , Humanos , Ceratite Herpética/diagnóstico , Simplexvirus , Uveíte/diagnóstico , Uveíte Anterior/diagnóstico , Uveíte Anterior/etiologia
11.
Molecules ; 27(9)2022 Apr 20.
Artigo em Inglês | MEDLINE | ID: mdl-35566002

RESUMO

Quality control of animal-derived traditional Chinese medicines has improved dramatically as proteomics research advanced in the past few decades. However, it remains challenging to identify quality attributes with routine proteomics approaches since protein with fibrinolytic activity is rarely reported in pheretima, a typical animal-derived traditional medicine. A novel strategy based on bioinformatics combined with parallel reaction monitoring (PRM) was developed here to rapidly discover the marker peptides associated with a fibrinolytic effect. Potential marker peptides were found by lumbrokinase sequences' alignment and in silico digestion. The fibrinogen zymography was used to visually identify fibrinolytic proteins in pheretima. As a result, it was found that the fibrinolytic activity varied among different portions of pheretima. Fibrinolytic proteins were distributed regionally in the anterior and anterior-mid portion and there was no significant fibrinogenolytic activity observed in the mid-posterior and posterior portion. Finally, PRM experiments were deployed to validate and quantify selected marker peptides and a total of 11 peptides were identified as marker peptides, which could be potentially used in quality control of pheretima. This strategy provides a robust workflow to benefit the quality control of other animal-derived traditional medicines.


Assuntos
Biologia Computacional , Oligoquetos , Animais , Biomarcadores/metabolismo , Oligoquetos/metabolismo , Peptídeos/metabolismo , Peptídeos/farmacologia , Proteômica
12.
Diabetes Metab Res Rev ; 37(4): e3445, 2021 05.
Artigo em Inglês | MEDLINE | ID: mdl-33713564

RESUMO

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.


Assuntos
Aprendizado Profundo , Retinopatia Diabética , Retinopatia Diabética/diagnóstico , Humanos , Índice de Gravidade de Doença
13.
Drug Dev Res ; 82(4): 581-588, 2021 06.
Artigo em Inglês | MEDLINE | ID: mdl-33340142

RESUMO

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.


Assuntos
Doenças Cardiovasculares/tratamento farmacológico , Embolia/tratamento farmacológico , Fenantrenos/farmacologia , Administração Oral , Animais , Apoptose/efeitos dos fármacos , Doenças Cardiovasculares/cirurgia , Modelos Animais de Doenças , Embolia/cirurgia , Masculino , Miócitos Cardíacos/efeitos dos fármacos , NF-kappa B/metabolismo , Estresse Oxidativo/efeitos dos fármacos , Fenantrenos/administração & dosagem , Ratos , Ratos Sprague-Dawley , Transdução de Sinais/efeitos dos fármacos
14.
Entropy (Basel) ; 23(1)2021 Jan 06.
Artigo em Inglês | MEDLINE | ID: mdl-33419199

RESUMO

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.

15.
Brief Bioinform ; 16(1): 1-15, 2015 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-24300111

RESUMO

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.


Assuntos
Compressão de Dados/métodos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Dados de Sequência Molecular
16.
Bioinformatics ; 31(3): 426-8, 2015 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-25282641

RESUMO

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.


Assuntos
Compressão de Dados/métodos , Genoma Humano/genética , Sequenciamento de Nucleotídeos em Larga Escala , Alinhamento de Sequência/métodos , Análise de Sequência de DNA/métodos , Software , Biologia Computacional , Humanos , Valores de Referência
17.
BMC Bioinformatics ; 16: 188, 2015 Jun 09.
Artigo em Inglês | MEDLINE | ID: mdl-26051252

RESUMO

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.


Assuntos
Algoritmos , Compressão de Dados/métodos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Análise de Sequência de DNA/métodos , Software , Humanos
18.
Ophthalmologica ; 234(2): 67-72, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-26066478

RESUMO

BACKGROUND: The aim of this study was to determine whether pretreatment spectral-domain optical coherence tomographic (SD-OCT) features are associated with visual prognosis after treatment for idiopathic subfoveal choroidal neovascularization (ISCNV) with intravitreal ranibizumab. METHODS: We retrospectively evaluated SD-OCT images of eyes with ISCNV undergoing treatment with intravitreal ranibizumab with a mean follow-up of 7 months. RESULTS: This study included 22 patients (22 eyes) with a mean age of 32.7 ± 8.1 years. In univariate analysis, better final visual acuity expressed in logMAR units was significantly associated with a lower amount of pretreatment ellipsoid zone defects (p = 0.03; standardized correlation coefficient ß = 0.46) and a lower amount of pretreatment external limiting membrane (ELM) damage (p = 0.007; ß = 0.56). All other SD-OCT parameters were not significantly associated with final visual acuity. A higher improvement in visual acuity was marginally significantly associated with larger pretreatment ellipsoid zone defects (p = 0.049; ß = -0.43). CONCLUSIONS: The integrity of the outer retinal layers at baseline, in particular of the ELM, is of importance in predicting the final visual outcome in patients undergoing intravitreal medical therapy for ISCNV.


Assuntos
Inibidores da Angiogênese/uso terapêutico , Neovascularização de Coroide/diagnóstico , Neovascularização de Coroide/tratamento farmacológico , Ranibizumab/uso terapêutico , Acuidade Visual/fisiologia , Adolescente , Adulto , Neovascularização de Coroide/fisiopatologia , Feminino , Angiofluoresceinografia , Humanos , Injeções Intravítreas , Masculino , Pessoa de Meia-Idade , Prognóstico , Estudos Retrospectivos , Tomografia de Coerência Óptica , Fator A de Crescimento do Endotélio Vascular/antagonistas & inibidores , Adulto Jovem
19.
Retina ; 34(8): 1554-9, 2014 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-24667570

RESUMO

PURPOSE: To investigate changes in subfoveal choroidal thickness (SFCT) after intravitreal injections of ranibizumab for idiopathic subfoveal choroidal neovascularization (ISCNV). METHODS: The prospective consecutive case series study included 16 patients with unilateral ISCNV. All eyes with ISCNV were treated with a single intravitreal injection of 0.5 mg ranibizumab followed by as-needed dosing. Subfoveal choroidal thickness was measured using enhanced depth imaging optical coherence tomography. RESULTS: The mean total follow-up time was 4.9 ± 1.5 months, and the follow-up after the last intravitreal ranibizumab injection was 4.4 ± 1.3 months. In the treated eyes, the SFCT decreased significantly from 354 ± 84 µm at baseline to 328 ± 79 µm at 1 month later (P < 0.001) and reincreased (P = 0.02) to 342 ± 75 µm at the final visit (P = 0.15 versus baseline value). Change in SFCT was marginally (P = 0.11) associated with the change in retinal foveal thickness. In the contralateral unaffected eyes, the SFCT did not change significantly during follow-up (P = 0.76). CONCLUSION: In patients with unilateral ISCNV, intravitreal ranibizumab therapy was associated with a thinning of an abnormally thick subfoveal choroid, marginally in association with a parallel decrease in retinal foveal thickness. It remained elusive whether the choroidal thinning was due to a direct pharmacological effect of ranibizumab or whether it was secondary due to the foveal retinal thinning. In view of the significant differences in SFCT between affected eyes and unaffected contralateral eyes at baseline and in view of the significant therapy-associated decrease in SFCT, the potential role of SFCT as an additional marker for the diagnosis and follow-up of ISCNV and other neovascular maculopathies may be examined in future studies.


Assuntos
Inibidores da Angiogênese/uso terapêutico , Anticorpos Monoclonais Humanizados/uso terapêutico , Corioide/patologia , Neovascularização de Coroide/tratamento farmacológico , Adulto , Neovascularização de Coroide/diagnóstico , Feminino , Fóvea Central , Humanos , Injeções Intravítreas , Masculino , Tamanho do Órgão , Estudos Prospectivos , Ranibizumab , Tomografia de Coerência Óptica , Fator A de Crescimento do Endotélio Vascular/antagonistas & inibidores , Acuidade Visual/fisiologia , Adulto Jovem
20.
Ophthalmologica ; 231(4): 221-5, 2014.
Artigo em Inglês | MEDLINE | ID: mdl-24603209

RESUMO

PURPOSE: To evaluate choroidal thickness in patients with idiopathic choroidal neovascularization. METHODS: The observational case series study included patients who were consecutively diagnosed with idiopathic unilateral choroidal neovascularization as demonstrated by ophthalmoscopy, fluorescein angiography and enhanced depth imaging optical coherence tomography (EDI-OCT). Using EDI-OCT, choroidal thickness was measured at the fovea and at locations in a distance of 500, 1,000 and 1,500 µm temporal and nasal to the fovea. RESULTS: Mean subfoveal choroidal thickness was significantly (p = 0.002) thicker in the study group than in the control group (357 ± 99 vs. 316 ± 83 µm). In a parallel manner, the differences between the study group and the control group in choroidal thickness were significant for all other measurement points, except for the examination at 1,500 µm nasal to the fovea (p = 0.09). The results remained unchanged after adjusting for axial length and age. CONCLUSIONS: Idiopathic unilateral choroidal neovascularization is associated with a thickening of the choroid.


Assuntos
Corioide/patologia , Neovascularização de Coroide/complicações , Adolescente , Adulto , Neovascularização de Coroide/diagnóstico , Corantes , Feminino , Angiofluoresceinografia , Fóvea Central , Humanos , Verde de Indocianina , Masculino , Pessoa de Meia-Idade , Oftalmoscopia , Tamanho do Órgão , Estudos Prospectivos , Tomografia de Coerência Óptica , Acuidade Visual/fisiologia , Adulto Jovem
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