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OBJECTIVE: To describe the clinical features of Chinese patients with hydroxychloroquine (HCQ)-induced pigmentation and analyze the potential risk factors associated with HCQ-induced pigmentation. METHODS: A cross-sectional study was conducted over a duration of 7 months, during which patients who had received HCQ treatment for >6 months were included. Data was collected through a structured questionnaire that encompassed demographic and geographic characteristics, information on HCQ and concomitant medication usage, sun exposure characteristics, and hyperpigmentation-related characteristics. Univariate and multivariate analyses were employed to calculate the statistical association between HCQ-induced pigmentation and multiple variables. RESULTS: Out of 316 patients, 83 (26.3%) patients presented hyperpigmentation during HCQ treatment. Hyperpigmentation presented after a median duration of HCQ treatment of 12 months (interquartile range, 6.0 months-30.0 months) with a median cumulative dose of 108 g of HCQ (interquartile range, 36-288 g). The most frequently affected sites of pigmentation were the face (60.2%), lower limbs (36.1%), and hands (20.5%). There was a linear decrease in the incidence of pigmentation with increasing daily sun exposure time (p= 0.030). In the multivariate analysis, variables (cumulative HCQ dose and daily sun exposure time) were included in the final models. The results revealed an independent correlation between HCQ-induced pigmentation and daily sun exposure exceeding 1 h (OR: 0.431; 95%CI: 0.208-0.892; p= 0.023). CONCLUSIONS: The occurrence of HCQ-induced pigmentation is not uncommon, with an incidence rate of 26.3%. Daily sun exposure time exhibited a protective effect against HCQ-induced pigmentation.
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OBJECTIVE: A comprehensive immune landscape for HBV infection is pivotal to achieve HBV cure. DESIGN: We performed single-cell RNA sequencing of 2 43 000 cells from 46 paired liver and blood samples of 23 individuals, including six immune tolerant, 5 immune active (IA), 3 acute recovery (AR), 3 chronic resolved and 6 HBV-free healthy controls (HCs). Flow cytometry and histological assays were applied in a second HBV cohort for validation. RESULTS: Both IA and AR were characterised by high levels of intrahepatic exhausted CD8+ T (Tex) cells. In IA, Tex cells were mainly derived from liver-resident GZMK+ effector memory T cells and self-expansion. By contrast, peripheral CX3CR1+ effector T cells and GZMK+ effector memory T cells were the main source of Tex cells in AR. In IA but not AR, significant cell-cell interactions were observed between Tex cells and regulatory CD4+ T cells, as well as between Tex and FCGR3A+ macrophages. Such interactions were potentially mediated through human leukocyte antigen class I molecules together with their receptors CANX and LILRBs, respectively, contributing to the dysfunction of antiviral immune responses. By contrast, CX3CR1+GNLY+ central memory CD8+ T cells were concurrently expanded in both liver and blood of AR, providing a potential surrogate marker for viral resolution. In clinic, intrahepatic Tex cells were positively correlated with serum alanine aminotransferase levels and histological grading scores. CONCLUSION: Our study dissects the coordinated immune responses for different HBV infection phases and provides a rich resource for fully understanding immunopathogenesis and developing effective therapeutic strategies.
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Linfócitos T CD8-Positivos , Fígado , Humanos , Fígado/patologia , Antivirais , Linfócitos T Reguladores , Análise de Sequência de RNA , Vírus da Hepatite BRESUMO
3-Nitro-4-hydroxy-phenylarsonic acid (NHPA) as a veterinary drug can degraded into highly toxic inorganic arsenic and will be harmful to environment and food safety. Nanocomposites for the uptake of NHPA were obtained by efficiently immobilizing the nano-sized zirconium oxide onto hazelnut shell-based activated carbon using pyrolysis method. We found that the pyrolysis temperature played a crucial role in the adsorptive performances of the nanocomposites. The prepared nanocomposite at pyrolysis temperature of 600 °C with a mass ratio of ZrOCl2/activated carbon of 1:3 exhibited a fast adsorption equilibrium for NHPA within 5 min, excellent adsorption capacity of 825.7 mg g-1 and the higher adsorption capacity with the increase in temperature from 20 to 45 °C across a pH range of 4-6. 90% of the NHPA uptake was sustained in the NaNO3 solution of 0.7 mol L-1. The adsorption data were well simulated by the Langmuir and pseudo-second order equations. Thermodynamic parameters suggested that the uptake of the NHPA occurred spontaneously (ΔG0<0) with an endothermic characteristic (ΔH0>0). A synergetic effect of electrostatic attraction, As-O-Zr surface coordination and π-π interaction is the main adsorption mechanism of the nanocomposites for the removal of the NHPA.
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Corylus , Nanocompostos , Poluentes Químicos da Água , Adsorção , Carvão Vegetal , Concentração de Íons de Hidrogênio , Hidroxiácidos , Cinética , Termodinâmica , Água , Poluentes Químicos da Água/análise , ZircônioRESUMO
3-Nitro-4-hydroxy-phenylarsonic acid (3-NHPAA), an organic-arsenic compound, as one of widely used antibacterial veterinary drug, has greatly attracted the attention due to its potential threats on ecological environment. A series of the nanocomposites of zirconia nanoparticles with crystal phases (pure monoclinic, pure tetragonal and mixed phase (monoclinic + tetragonal)) anchored on reduced graphene oxide were produced through managing the concentration of triethanolamine solution and the reaction time. The effects of the crystal phases of the zirconia in the structure of the nanocomposites were played a key role in the adsorption performances of the 3-NHPAA. Experiment data identified the nanocomposites with monoclinic phase of zirconia excelled at the adsorption of the 3-NHPAA with a higher adsorption capacity up to 207.2 mg g-1. The uptake of the 3-NHPAA by the three nanocomposites was implemented within 60 min and highly pH-dependent which illustrated electrostatic attraction between them as a main mechanism during the adsorption process. A wider pH range (3.8-8.8) for the uptake of the 3-NHPAA by the nanocomposites with the monoclinic phase of zirconia was obtained compared with the nanocomposites containing tetragonal phase (3.8-5.9) or the mixed phase (3.8-7.1) of zirconia. The adsorption of the 3-NHPAA was well described by the pseudo-second order kinetic and Langmuir equations. The thermodynamic parameters suggested that the adsorption of the 3-NHPAA over the three nanocomposites was endothermic and spontaneous in nature. In summary, the nanocomposites of reduced graphene oxide and monoclinic phase of zirconia nanoparticles as an adsorbent were better to the adsorption of the 3-NHPAA.
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Arsênio , Grafite , Nanocompostos , Preparações Farmacêuticas , Poluentes Químicos da Água , Adsorção , Arsênio/análise , Concentração de Íons de Hidrogênio , Cinética , Poluentes Químicos da Água/análise , ZircônioRESUMO
To achieve the goal of carbon neutrality, the demand for energy saving by the residential sector has witnessed a soaring increase. As a promising paradigm to monitor and manage residential loads, the existing studies on non-intrusive load monitoring (NILM) either lack the scalability of real-world cases or pay unaffordable attention to identification accuracy. This paper proposes a high accuracy, ultra-sparse sample, and real-time computation based NILM method for residential appliances. The method includes three steps: event detection, feature extraction and load identification. A wavelet decomposition based standard deviation multiple (WDSDM) is first proposed to empower event detection of appliances with complex starting processes. The results indicate a false detection rate of only one out of sixteen samples and a time consumption of only 0.77 s. In addition, an essential feature for NILM is introduced, namely the overshoot multiple (which facilitates an average identification improvement from 82.1% to 100% for similar appliances). Moreover, the combination of modified weighted K-nearest neighbors (KNN) and overshoot multiples achieves 100% appliance identification accuracy under a sampling frequency of 6.25 kHz with only one training sample. The proposed method sheds light on highly efficient, user friendly, scalable, and real-world implementable energy management systems in the expectable future.
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Algoritmos , Análise por ConglomeradosRESUMO
A device of graphene nanoplatelet-based diffusion gradients in thin-films (G-DGT) was developed for in situ sampling of tetracycline (TC), oxytetracycline (OTC) and chlortetracycline (CTC) in aquatic environment. The accumulation of antibiotics in a synthetic solution by the proposed G-DGT was consistent with the theoretical curves predicted by the DGT equation. The values of the detection and quantification limits of G-DGT using high-performance liquid chromatography over the deployment time of 7 days were at the level of µg L-1 for the three antibiotics. The performance of the proposed G-DGT was unaffected by pH (3-9) and ionic strength (0.001-0.7 mol L-1 NaNO3). Fulvic acid did not significantly interfere with the performance of the proposed G-DGT device when the mass ratios between the three antibiotics and fulvic acid were within the range of 1:10-1:100. Humic acid had a significant effect on the performance of the proposed G-DGT for the sampling of the three antibiotics due to strong complexation and coprecipitation between the antibiotics and humic acid. The proposed G-DGT was used for the in situ sampling in spiked freshwaters and livestock culture wastewater and exhibited good precision and accuracy without notable interference from the matrices.
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Grafite , Poluentes Químicos da Água , Antibacterianos/análise , Monitoramento Ambiental , Águas Residuárias/análise , Poluentes Químicos da Água/análiseRESUMO
BACKGROUND: Several randomized controlled trials (RCTs) have compared the treatment of acute lung injury (ALI) with omega-3 fatty, yet the results remained inconsistent. Therefore, we attempted this meta-analysis to analyze the role of omega-3 fatty in the treatment of ALI patients. METHODS: We searched PubMed databases from inception date to October 31, 2019, for RCTs that compared the treatment of ALI with or without omega-3 fatty. Two authors independently screened the studies and extracted data from the published articles. Summary mean differences (MD) with 95% confidence intervals (CI) were calculated for each outcome by fixed- or random-effects model. RESULTS: Six RCTs with a total of 277 patients were identified, of whom 142 patients with omega-3 fatty acid treatment and 135 patients without omega-3 fatty treatment. Omega-3 fatty treatments significantly improve the PaO2 (MD = 13.82, 95% CI 8.55-19.09), PaO2/FiO2 (MD = 33.47, 95% CI 24.22-42.72), total protein (MD = 2.02, 95% CI 0.43-3.62) in ALI patients, and omega-3 fatty acid treatments reduced the duration of mechanical ventilation (MD = - 1.72, 95% CI - 2.84 to - 0.60) and intensive care unit stay (MD = - 1.29, 95% CI - 2.14 to - 0.43) in ALI patients. CONCLUSIONS: Omega-3 fatty can effectively improve the respiratory function and promote the recovery of ALI patients. Future studies focused on the long-term efficacy and safety of omega-3 fatty use for ALI are needed.
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Lesão Pulmonar Aguda , Ácidos Graxos Ômega-3 , Lesão Pulmonar Aguda/tratamento farmacológico , Ácidos Graxos Ômega-3/uso terapêutico , Humanos , Unidades de Terapia Intensiva , Prognóstico , Respiração ArtificialRESUMO
A reliable method for the determination of dissolved Cu2+ and Pb2+ species in water via a diffusive gradient in thin films (DGT) device using water-soluble carbon nanodots (CD) as the binding agent was developed (CD-DGT). The uptake of dissolved Cu2+ and Pb2+ species by CD-DGT increased linearly with a deployment time of over 120 h, while the uptake of Ca2+, Mg2+, Cd2+, Zn2+, Ni2+, and Co2+ by CD-DGT has no significant linear accumulation during the same deployment time. The concentrations of the dissolved Cu2+ and Pb2+ species measured using CD-DGT are in good agreement with the element concentrations spiked directly in a tested synthesis solution. The performance of CD-DGT for the determination of dissolved Cu2+ and Pb2+ species is found to be independent of ionic strength in the range of 0.001-0.05 mol L-1 and in the pH range from 5 to 8. The presence of fulvic acid and tannic acid has no significant influence on the uptake of dissolved Cu2+ and Pb2+ species by CD-DGT under the tested conditions. In different water samples, good agreement was observed between the dissolved Cu2+ and Pb2+ concentrations measured by CD-DGT, and diffusive equilibration in the thin film devices was found. Based on the results obtained, CD-DGT enables the selective and quantitative determination of dissolved Cu2+ and Pb2+ species in water.
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Lu2O3:RE3+ (RE3+ = Eu3+, Tb3+, Ho3+) nanoparticles have been successfully synthesized by a facile homogeneous precipitation method with subsequent sintering process. The crystal structure, morphology and luminescence properties of the as-prepared samples have been characterized by X-ray diffraction (XRD), transmission electron microscopy (TEM), Fourier transform infrared (FT-IR), thermogravimetric analysis (TGA), photoluminescence (PL) and cathodoluminescence (CL) spectra. Upon ultraviolet (UV) and low-voltage electron beam excitation, Lu2O3:RE3+ (RE3+ = Eu3+, Tb3+, Ho3+) nanoparticles show strong red (Eu3+,5D0 â 7F2), green (Tb3+,5D4 â 7F5), and green (Ho3+,5S2 â 5I8) emissions. They exhibit a good advantage of multicolor emissions in the visible region, and endow these kinds of materials with potential application in many fields, such as light display systems, optoelectronic devices and biological imaging.
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A new theoretical method was established for the combinatorial calculation of the dissociation rate constant (K-1) of the metal-organic complexes (MLs), the concentration of free ionic soil metals (CM), the labile concentration of soil metal-organic complexes (CML) based on diffusive gradients in thin-films (DGT) technique with a range of diffusive layer thicknesses (0.053-0.173â¯mm) in soils. The fitting results agreed well with the determined values. The values of K-1, CML and CM were calculated without other morphological analysis software and the fitting results agreed well with the determined values with some advantages such as the use of fewer hypothetical parameters, ease of calculation, the full embodiment of the contribution of MLs to the labile content. According to the results of model fitting, cation exchange capacity and soil organic matter were found to be the key environmental factors for K-1 values of Cd and Ni, respectively. The labile contents of Cd and Ni in soil were closely related with pH, soil organic matter and the total contents of heavy metals.
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Cádmio/análise , Monitoramento Ambiental/métodos , Níquel/análise , Poluentes do Solo/análise , Solo/química , Difusão , CinéticaRESUMO
Mg-Al layered double hydroxides (LDHs) adsorbent was synthesized in situ on γ-Al2O3 for the removal of Cr(VI) from aqueous solution. The material was characterized by X-ray diffraction (XRD), Fourier transform infrared spectroscopy, Raman spectroscopy, scanning electronic microscopy and thermogravimetry and differential thermal analysis. Compared to the LDHs powder, the calcined LDHs sorbent prepared in situ on γ-Al2O3 had higher specific surface area and was easy to recover and reuse. The adsorptive capacity for removing Cr(VI) from aqueous solution was resulting from the memory effect of LDHs based on the XRD results. Both the pseudo-second-order kinetic model and the Langmuir model fit the experimental data well. Furthermore, the adsorbent exhibits excellent sorption-regeneration performances.
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Óxido de Alumínio/química , Cromo/isolamento & purificação , Hidróxidos/síntese química , Adsorção , Hidróxidos/química , Cinética , Espectroscopia de Infravermelho com Transformada de Fourier , Análise Espectral Raman , Temperatura , Termogravimetria , Difração de Raios XRESUMO
We evaluated the possibility of sampling dissolved orthophosphate using the diffusive gradient in thin films (DGT) technique with a phosphate ion-imprinted polymer (PIP)-based adsorbent and assessed the effect of biofilm on the DGT measurement. The composition of biofilm formed on the DGT surface was analyzed, and the effect of biofouling on the diffusion coefficient of the analyte was investigated. The corrected diffusion coefficient for the biofouled DGT was estimated and used for the calculation of the DGT equation. PIP-binding gels had a higher adsorption affinity for orthophosphate than for the other anions, indicating its selectivity for orthophosphate. The concentrations predicted via DGT agreed well with the concentrations determined in the bulk solutions. Sampling of orthophosphate using PIP-DGT was consistent over a pH range of 3-9 and ionic strength range of 0.01-10â¯000 µM. Other P compounds cannot be measured using the PIP-DGT technique. The diffusion coefficient of the orthophosphate linearly decreased with increasing thickness of the biofilm. This sampling method performed predictably in freshwater when the biofilm was not formed or when value for the biofilm interference was reduced by using the corrected diffusion coefficient.
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Altered expression of miRNA-98 (miR-98) has been reported in osteoarthritis (OA) patients, while its role and underlying mechanisms remain elusive. In the present study, a rat model of OA was established using modified Hulth method, and the expression level of miR-98 and its effect on cartilage degradation and cell apoptosis in OA rats were examined. The results showed that up-regulated miR-98 was observed in OA rats, and knockdown of miR-98 in OA rats resulted in an inhibitory effect on cartilage degradation and chondrocyte apoptosis. Then the potential apoptosis associated genes regulated by miR-98 were screened and examined in cartilage tissues. The target gene of miR-98 was validated by luciferase reporter assay. The data showed that the increased miR-98 was accompanied with a reduced expression of Bcl-2 at both mRNA and protein levels. Furthermore, the silencing of miR-98 in OA rats prevented the down-regulation of Bcl-2 in cartilage tissues. Finally, the luciferase reporter assay validated that Bcl-2 was the target gene of miR-98. In this study, we found that miR-98 might promote chondrocyte apoptosis and cartilage degradation by down-regulating Bcl-2 expression in the pathogenesis of OA, suggesting that miR-98 can be a potential target for the treatment of OA.
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Apoptose/genética , Condrócitos/metabolismo , MicroRNAs/genética , Osteoartrite/genética , Proteínas Proto-Oncogênicas c-bcl-2/genética , Regiões 3' não Traduzidas/genética , Animais , Sequência de Bases , Western Blotting , Cartilagem Articular/metabolismo , Modelos Animais de Doenças , Regulação para Baixo , Feminino , Regulação da Expressão Gênica , Técnicas de Silenciamento de Genes , Células HEK293 , Humanos , Osteoartrite/metabolismo , Proteínas Proto-Oncogênicas c-bcl-2/metabolismo , Ratos Sprague-Dawley , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Homologia de Sequência do Ácido NucleicoRESUMO
Iodinated X-ray contrast media (ICM) was frequently detected in the aqueous environment. In this work, the applicability of three graphene-based nanomaterials (graphene nanosheets (GNS), graphene oxide (GO), and reduced graphene oxide (rGO)) for the adsorptive removal of the six ICMs including iohexol, iopamidol, iomeprol, iopromide, iodixanol and ioversol from aqueous solution was firstly evaluated by batch adsorption method. Among the three graphene-based nanomaterials, the GNS displayed the best adsorption performances for the adsorption of the six ICMs. The maximum uptakes of the six ICMs by the GNS (161.5 mg g-1 for iohexol, 267.2 mg g-1 for iodixanol, 197.7 mg g-1 for iopromide, 197.0 mg g-1 for iopamidol, 109.6 mg g-1 for iomeprol, and 168.2 mg g-1 for ioversol) can rapidly achieved within 10 min and indicate no dependence on pH in the range of 4-9. The results obtained from the calculations of isotherms, kinetics and thermodynamic supported the occurrence of a chemisorption of the GNS for the six ICMs. The π-π interactions between benzene ring of the ICMs and the sp2-hybridized two-dimensional sheet of GNS were deemed the predominant adsorption mechanism.
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Meios de Contraste , Grafite , Nanoestruturas , Poluentes Químicos da Água , Grafite/química , Meios de Contraste/química , Adsorção , Poluentes Químicos da Água/química , Nanoestruturas/química , Purificação da Água/métodos , Cinética , Termodinâmica , Iohexol/química , Iohexol/análogos & derivados , Raios XRESUMO
Although diffusion gradient in thin-film technique (DGT) has realized the in-situ sampling Sulfamethazine (SMT), the traditional DGT devices cannot be served as sensing devices but in-situ sampling devices. Here we report a recyclable surface enhanced Raman scattering (SERS) responsive DGT sensing device (recyclable SERS-DGT Sensing Device) capable of in-situ sensing of SMT in water. This is achieved by innovatively utilizing a recyclable SERS responsive liquid suspension of Au nanoparticles supported on g-C3N4 (Au@g-C3N4NS) as DGT binding phase. Au@g-C3N4NS is synthesized via in-situ growth method and embed in DGT binding phase, which exhibits good SERS activity, aqueous stability recyclable and adsorption performance. The SERS-DGT Sensing Device is valid for measuring SMT under a wide range of conditions (i.e., deployment time 24â¼180 h, concentrations range of 1.031â¼761.9 ng mL-1, pH 5â¼9, ionic strength 0.0001â¼0.05 mol L-1 NaCl, DOM concentrations 0â¼100 mg L-1, four recycles). Furthermore, substrate combined with DGT binding phase, can integrate the sampling, pretreatment and SERS detection of SMT, which can be recycled, improving the reliability and efficiency of environmental monitoring. In this article, recyclable SERS-DGT Sensing Device, a platform for recyclable in-situ sensing of antibiotics, holds great potential for environmental monitoring.
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Nanopartículas Metálicas , Poluentes Químicos da Água , Água , Sulfametazina , Ouro , Reprodutibilidade dos Testes , Monitoramento Ambiental/métodos , Difusão , Poluentes Químicos da Água/análiseRESUMO
Expanding the efficacy of immune checkpoint blockade (ICB) in colorectal cancer (CRC) presses for a comprehensive understanding of treatment responsiveness. Here, we analyze multiple sequential single-cell samples from 22 patients undergoing PD-1 blockade to map the evolution of local and systemic immunity of CRC patients. In tumors, we identify coordinated cellular programs exhibiting distinct response associations. Specifically, exhausted T (Tex) or tumor-reactive-like CD8+ T (Ttr-like) cells are closely related to treatment efficacy, and Tex cells show correlated proportion changes with multiple other tumor-enriched cell types following PD-1 blockade. In addition, we reveal the less-exhausted phenotype of blood-associated Ttr-like cells in tumors and find that their higher abundance suggests better treatment outcomes. Finally, a higher major histocompatibility complex (MHC) II-related signature in circulating CD8+ T cells at baseline is linked to superior responses. Our study provides insights into the spatiotemporal cellular dynamics following neoadjuvant PD-1 blockade in CRC.
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Linfócitos T CD8-Positivos , Neoplasias Colorretais , Imunoterapia , Análise de Célula Única , Humanos , Neoplasias Colorretais/imunologia , Neoplasias Colorretais/tratamento farmacológico , Neoplasias Colorretais/terapia , Neoplasias Colorretais/patologia , Análise de Célula Única/métodos , Linfócitos T CD8-Positivos/imunologia , Imunoterapia/métodos , Inibidores de Checkpoint Imunológico/farmacologia , Inibidores de Checkpoint Imunológico/uso terapêutico , Linfócitos do Interstício Tumoral/imunologia , Receptor de Morte Celular Programada 1/antagonistas & inibidores , Receptor de Morte Celular Programada 1/imunologia , Masculino , FemininoRESUMO
Objectives: Chronic obstructive pulmonary disease (COPD) is a prevalent respiratory disorder characterized by progressive airflow limitation. This meta-analysis aims to evaluate the effectiveness of respiratory muscle training (RMT) on key pulmonary function parameters, inspiratory muscle strength and quality of life in patients with stable COPD. Methods: A comprehensive search was conducted in the databases including PubMed, Cochrane, Web of Science, Embase, and ClinicalTrials.gov, from their inception to June 12, 2023. Randomized controlled trials (RCTs) evaluating the impact of RMT on stable COPD were included for meta-analysis. Results: In total, 12 RCTs involving 453 participants were included in the meta-analysis. RMT demonstrated a significant increase in maximal inspiratory pressure (PImax, MD, 95% CI: 14.34, 8.17 to 20.51, P < 0.001) but not on maximal expiratory pressure (PEmax). No significant improvement was observed in 6-Min walk test (6MWT), dyspnea, forced expiratory volume in 1 s (FEV1), forced vital capacity ratio (FVC) and quality of life between RMT and control groups. However, subgroup analysis revealed a significant negative effect of RMT alone on FEV1/FVC (MD, 95% CI: 2.59, -5.11 to -0.06, P = 0.04). When RMT was combined with other interventions, improvements in FEV1/FVC and FEV1 were found, although not statistically significant. Conclusion: RMT can effectively improve maximal inspiratory pressure in stable COPD patients, but the effect is slight in improving lung function, dyspnea and quality of life. It is recommended to combine with other treatment strategies to comprehensively improve the prognosis of COPD patients.
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BACKGROUND: Technical improvements have decreased sequencing costs and, as a result, the size and number of genomic datasets have increased rapidly. Because of the lower cost, large amounts of sequence data are now being produced by small to midsize research groups. Crossbow is a software tool that can detect single nucleotide polymorphisms (SNPs) in whole-genome sequencing (WGS) data from a single subject; however, Crossbow has a number of limitations when applied to multiple subjects from large-scale WGS projects. The data storage and CPU resources that are required for large-scale whole genome sequencing data analyses are too large for many core facilities and individual laboratories to provide. To help meet these challenges, we have developed Rainbow, a cloud-based software package that can assist in the automation of large-scale WGS data analyses. RESULTS: Here, we evaluated the performance of Rainbow by analyzing 44 different whole-genome-sequenced subjects. Rainbow has the capacity to process genomic data from more than 500 subjects in two weeks using cloud computing provided by the Amazon Web Service. The time includes the import and export of the data using Amazon Import/Export service. The average cost of processing a single sample in the cloud was less than 120 US dollars. Compared with Crossbow, the main improvements incorporated into Rainbow include the ability: (1) to handle BAM as well as FASTQ input files; (2) to split large sequence files for better load balance downstream; (3) to log the running metrics in data processing and monitoring multiple Amazon Elastic Compute Cloud (EC2) instances; and (4) to merge SOAPsnp outputs for multiple individuals into a single file to facilitate downstream genome-wide association studies. CONCLUSIONS: Rainbow is a scalable, cost-effective, and open-source tool for large-scale WGS data analysis. For human WGS data sequenced by either the Illumina HiSeq 2000 or HiSeq 2500 platforms, Rainbow can be used straight out of the box. Rainbow is available for third-party implementation and use, and can be downloaded from http://s3.amazonaws.com/jnj_rainbow/index.html.
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Genômica/métodos , Internet , Análise de Sequência/métodos , Software , Estatística como Assunto/métodos , Análise por Conglomerados , Humanos , Polimorfismo de Nucleotídeo Único/genéticaRESUMO
Non-convex relaxation methods have been widely used in tensor recovery problems, compared with convex relaxation methods, and can achieve better recovery results. In this paper, a new non-convex function, Minimax Logarithmic Concave Penalty (MLCP) function, is proposed, and some of its intrinsic properties are analyzed, among which it is interesting to find that the Logarithmic function is an upper bound of the MLCP function. The proposed function is generalized to tensor cases, yielding tensor MLCP and weighted tensor Lγ -norm. Consider that its explicit solution cannot be obtained when applying it directly to the tensor recovery problem. Therefore, the corresponding equivalence theorems to solve the such problem are given, namely, tensor equivalent MLCP theorem and equivalent weighted tensor Lγ -norm theorem. In addition, we propose two EMLCP-based models for classic tensor recovery problems, namely low-rank tensor completion (LRTC) and tensor robust principal component analysis (TRPCA), and design proximal alternate linearization minimization (PALM) algorithms to solve them individually. Furthermore, based on the Kurdyka-Åasiwicz property, it is proved that the solution sequence of the proposed algorithm has a finite length and converges to the critical point globally. Finally, extensive experiments show that the proposed algorithm achieves good results, and it is confirmed that the MLCP function is indeed better than the Logarithmic function in the minimization problem, which is consistent with the analysis of theoretical properties.