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1.
Neural Netw ; 176: 106327, 2024 Apr 18.
Artículo en Inglés | MEDLINE | ID: mdl-38692187

RESUMEN

Few-shot Event Detection (FSED) aims to identify novel event types in new domains with very limited annotated data. Previous PN-based (Prototypical Network) joint methods suffer from insufficient learning of token-wise label dependency and inaccurate prototypes. To solve these problems, we propose a span-based FSED model, called SpanFSED, which decomposes FSED into two subprocesses, including span extractor and event classifier. In span extraction, we convert sequential labels into a global boundary matrix that enables the span extractor to acquire precise boundary information irrespective of label dependency. In event classification, we align event types with an outside knowledge base like FrameNet and construct an enhanced support set, which injects more trigger information into the prototypical network of event prototypes. The superior performance of SpanFSED is demonstrated through extensive experiments on four event detection datasets, i.e., ACE2005, ERE, MAVEN and FewEvent. Access to our code and data is facilitated through the following link: .

2.
BMC Genomics ; 25(1): 68, 2024 Jan 17.
Artículo en Inglés | MEDLINE | ID: mdl-38233753

RESUMEN

BACKGROUND: Costaceae, commonly known as the spiral ginger family, consists of approximately 120 species distributed in the tropical regions of South America, Africa, and Southeast Asia, of which some species have important ornamental, medicinal and ecological values. Previous studies on the phylogenetic and taxonomic of Costaceae by using nuclear internal transcribed spacer (ITS) and chloroplast genome fragments data had low resolutions. Additionally, the structures, variations and molecular evolution of complete chloroplast genomes in Costaceae still remain unclear. Herein, a total of 13 complete chloroplast genomes of Costaceae including 8 newly sequenced and 5 from the NCBI GenBank database, representing all three distribution regions of this family, were comprehensively analyzed for comparative genomics and phylogenetic relationships. RESULT: The 13 complete chloroplast genomes of Costaceae possessed typical quadripartite structures with lengths from 166,360 to 168,966 bp, comprising a large single copy (LSC, 90,802 - 92,189 bp), a small single copy (SSC, 18,363 - 20,124 bp) and a pair of inverted repeats (IRs, 27,982 - 29,203 bp). These genomes coded 111 - 113 different genes, including 79 protein-coding genes, 4 rRNA genes and 28 - 30 tRNAs genes. The gene orders, gene contents, amino acid frequencies and codon usage within Costaceae were highly conservative, but several variations in intron loss, long repeats, simple sequence repeats (SSRs) and gene expansion on the IR/SC boundaries were also found among these 13 genomes. Comparative genomics within Costaceae identified five highly divergent regions including ndhF, ycf1-D2, ccsA-ndhD, rps15-ycf1-D2 and rpl16-exon2-rpl16-exon1. Five combined DNA regions (ycf1-D2 + ndhF, ccsA-ndhD + rps15-ycf1-D2, rps15-ycf1-D2 + rpl16-exon2-rpl16-exon1, ccsA-ndhD + rpl16-exon2-rpl16-exon1, and ccsA-ndhD + rps15-ycf1-D2 + rpl16-exon2-rpl16-exon1) could be used as potential markers for future phylogenetic analyses and species identification in Costaceae. Positive selection was found in eight protein-coding genes, including cemA, clpP, ndhA, ndhF, petB, psbD, rps12 and ycf1. Maximum likelihood and Bayesian phylogenetic trees using chloroplast genome sequences consistently revealed identical tree topologies with high supports between species of Costaceae. Three clades were divided within Costaceae, including the Asian clade, Costus clade and South American clade. Tapeinochilos was a sister of Hellenia, and Parahellenia was a sister to the cluster of Tapeinochilos + Hellenia with strong support in the Asian clade. The results of molecular dating showed that the crown age of Costaceae was about 30.5 Mya (95% HPD: 14.9 - 49.3 Mya), and then started to diverge into the Costus clade and Asian clade around 23.8 Mya (95% HPD: 10.1 - 41.5 Mya). The Asian clade diverged into Hellenia and Parahellenia at approximately 10.7 Mya (95% HPD: 3.5 - 25.1 Mya). CONCLUSION: The complete chloroplast genomes can resolve the phylogenetic relationships of Costaceae and provide new insights into genome structures, variations and evolution. The identified DNA divergent regions would be useful for species identification and phylogenetic inference in Costaceae.


Asunto(s)
Genoma del Cloroplasto , Filogenia , Teorema de Bayes , Genómica/métodos , ADN
3.
Int J Mol Sci ; 24(19)2023 Oct 09.
Artículo en Inglés | MEDLINE | ID: mdl-37834481

RESUMEN

Zingiberales includes eight families and more than 2600 species, with many species having important economic and ecological value. However, the backbone phylogenetic relationships of Zingiberales still remain controversial, as demonstrated in previous studies, and molecular dating based on chloroplast genomes has not been comprehensively studied for the whole order. Herein, 22 complete chloroplast genomes from 21 species in Zingiberales were sequenced, assembled, and analyzed. These 22 genomes displayed typical quadripartite structures, which ranged from 161,303 bp to 163,979 bp in length and contained 111-112 different genes. The genome structures, gene contents, simple sequence repeats, long repeats, and codon usage were highly conserved, with slight differences among these genomes. Further comparative analysis of the 111 complete chloroplast genomes of Zingiberales, including 22 newly sequenced ones and the remaining ones from the national center for biotechnology information (NCBI) database, identified three highly divergent regions comprising ccsA, psaC, and psaC-ndhE. Maximum likelihood and Bayesian inference phylogenetic analyses based on chloroplast genome sequences found identical topological structures and identified a strongly supported backbone of phylogenetic relationships. Cannaceae was sister to Marantaceae, forming a clade that was collectively sister to the clade of (Costaceae, Zingiberaceae) with strong support (bootstrap (BS) = 100%, and posterior probability (PP) = 0.99-1.0); Heliconiaceae was sister to the clade of (Lowiaceae, Strelitziaceae), then collectively sister to Musaceae with strong support (BS = 94-100%, and PP = 0.93-1.0); the clade of ((Cannaceae, Marantaceae), (Costaceae, Zingiberaceae)) was sister to the clade of (Musaceae, (Heliconiaceae, (Lowiaceae, Strelitziaceae))) with robust support (BS = 100%, and PP = 1.0). The results of divergence time estimation of Zingiberales indicated that the crown node of Zingiberales occurred approximately 85.0 Mya (95% highest posterior density (HPD) = 81.6-89.3 million years ago (Mya)), with major family-level lineages becoming from 46.8 to 80.5 Mya. These findings proved that chloroplast genomes could contribute to the study of phylogenetic relationships and molecular dating in Zingiberales, as well as provide potential molecular markers for further taxonomic and phylogenetic studies of Zingiberales.


Asunto(s)
Genoma del Cloroplasto , Zingiberales , Humanos , Filogenia , Zingiberales/genética , Teorema de Bayes , Genómica , Cloroplastos/genética
4.
Neural Netw ; 166: 344-353, 2023 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-37544091

RESUMEN

With weight-sharing and continuous relaxation strategies, the differentiable architecture search (DARTS) proposes a fast and effective solution to perform neural network architecture search in various deep learning tasks. However, unresolved issues, such as the inefficient memory utilization, and the poor stability of the search architecture due to channels randomly selected, which has even caused performance collapses, are still perplexing researchers and practitioners. In this paper, a novel efficient channel attention mechanism based on partial channel connection for differentiable neural architecture search, termed EPC-DARTS, is proposed to address these two issues. Specifically, we design an efficient channel attention module, which is applied to capture cross-channel interactions and assign weight based on channel importance, to dramatically improve search efficiency and reduce memory occupation. Moreover, only partial channels with higher weights in the mixed calculation of operation are used through the efficient channel attention mechanism, and thus unstable network architectures obtained by the random selection operation can also be avoided in the proposed EPC-DARTS. Experimental results show that the proposed EPC-DARTS achieves remarkably competitive performance (CIFAR-10/CIFAR-100: a test accuracy rate of 97.60%/84.02%), compared to other state-of-the-art NAS methods using only 0.2 GPU-Days.


Asunto(s)
Redes Neurales de la Computación
5.
Biotechnol Appl Biochem ; 70(3): 1109-1120, 2023 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-36480009

RESUMEN

To verify the inhibitory mechanism of ß-catenin-designed peptides in colorectal cancer(CRC) tumors, the following experiments were performed. In vitro colony formation, Transwell assays, and flow cytometry were performed to assess the biological effects of designed peptides (F18KD, F20A4-7k, F20A4-10k, and F20A3-9k + F20A4-10k + F20A5-9k) in HT-29 cells. In vivo xenograft experiments were performed and treated with peptides. Next, tumors were subjected to Hematoxylin and eosin staining (HE), immunohistochemical, and terminal deoxynucleotidyl transferase dUTP nick end labeling staining assays to evaluate the inhibitory effect of peptides on tumors. ß-Catenin levels were quantified via western blotting (WB) and quantitative real-time polymerase chain reaction, and ß-catenin was located using confocal laser scanning microscopy. T-cell factor-4 (TCF-4), C-myc, and CCND1 levels were quantified via WB. Results were obtained as following. First, the peptides reduced viability, migration, and invasion; promoted apoptosis; and stabilized the S phase of HT-29 cells. Second, peptides suppressed tumor growth and downregulated the expression of CD34, vascular endothelial growth factor, and ß-catenin in tumors. Furthermore, we found that peptides downregulated ß-catenin expression in both the cytoplasm and nucleus; TCF-4, C-myc, and CCND1 expression was also downregulated. Notably, ß-catenin-targeting peptides had a better inhibitory effect on CRC than non-ß-catenin-target peptides, and a combination of peptides exerted a more potent inhibitory effect on CRC than single peptides. It suggested that ß-Catenin-targeting peptides promote apoptosis in CRC tumors by inhibiting activation of the Wnt/ß-catenin pathway.


Asunto(s)
Neoplasias Colorrectales , Factor A de Crecimiento Endotelial Vascular , Humanos , Neoplasias Colorrectales/tratamiento farmacológico , Neoplasias Colorrectales/genética , Vía de Señalización Wnt , Apoptosis , Péptidos/farmacología , Péptidos/metabolismo , Proliferación Celular , Línea Celular Tumoral , Movimiento Celular , Regulación Neoplásica de la Expresión Génica
6.
IEEE Trans Cybern ; 53(4): 2685-2697, 2023 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-35687633

RESUMEN

The radial basis function (RBF) model and the Kriging model have been widely used in the surrogate-assisted evolutionary algorithms (SAEAs). Based on their characteristics, a global and local surrogate-assisted differential evolution algorithm (GL-SADE) for high-dimensional expensive problems is proposed in this article, in which a global RBF model is trained with all samples to estimate a global trend, and then its optima is used to significantly accelerate the convergence process. A local Kriging model prefers to select points with good predicted fitness and great uncertainty, which can effectively prevent the search from getting trapped into local optima. When the local Kriging model finds the best solution so far, a reward search strategy is executed to further exploit the local Kriging model. The experiments on a set of benchmark functions with dimensions varying from 30 to 200 are conducted to evaluate the performance of the proposed algorithm. The experimental results of the proposed algorithm are compared to four state-of-the-art algorithms to show its effectiveness and efficiency in solving high-dimensional expensive problems. Besides, GL-SADE is applied to an airfoil optimization problem to show its effectiveness.

7.
Cell Mol Biol Lett ; 27(1): 91, 2022 Oct 11.
Artículo en Inglés | MEDLINE | ID: mdl-36221069

RESUMEN

BACKGROUND: Long non-coding RNAs (lncRNAs) are critical regulators in lung adenocarcinoma (LUAD). M2-type tumor-associated macrophages (TAMs) also play oncogenic roles in LUAD. However, the involvement of lncRNAs in TAM activation is still largely unknown. METHODS: The expressions of LARRPM, LINC00240 and CSF1 were determined by RT-qPCR. The regulation of LINC00240 and CSF1 by LARRPM was investigated by RNA-protein pull-down, RNA immunoprecipitation, chromatin immunoprecipitation and bisulfite DNA sequencing. In vitro and in vivo gain- and loss-of-function assays were performed to investigate the roles of LARRPM. RESULTS: The lncRNA LARRPM was expressed at low levels in LUAD tissues and cells. The low expression of LARRPM was correlated with advanced stage and poor survival of patients with LUAD. Functional experiments revealed that LARRPM suppressed LUAD cell proliferation, migration and invasion, and promoted apoptosis. LARRPM also repressed macrophage M2 polarization and infiltration. Taken together, LARRPM significantly restricted LUAD progression in vivo. Mechanistically, LARRPM bound and recruited DNA demethylase TET1 to the promoter of its anti-sense strand gene LINC00240, leading to a decrease in DNA methylation level of the LINC00240 promoter and transcriptional activation of LINC00240. Functional rescue assays suggested that the lncRNA LINC00240 was responsible for the roles of LARRPM in the malignant behavior of LUAD cells. LARRPM decreased the binding of TET1 to the CSF1 promoter, resulting in increased DNA methylation of the CSF1 promoter and transcriptional repression of CSF1, which is responsible for the roles of LARRPM in macrophage M2 polarization and infiltration. The TAMs educated by LUAD cells exerted oncogenic roles, which was negatively regulated by LARRPM expressed in LUAD cells. CONCLUSIONS: LARRPM restricts LUAD progression through repressing both LUAD cell and macrophages. These data shed new insights into the regulation of LUAD progression by lncRNAs and provide data on the potential utility of LARRPM as a target for LUAD treatment.


Asunto(s)
Adenocarcinoma , Neoplasias Pulmonares , ARN Largo no Codificante , Adenocarcinoma/genética , Línea Celular Tumoral , Proliferación Celular , Regulación Neoplásica de la Expresión Génica , Humanos , Pulmón/metabolismo , Neoplasias Pulmonares/patología , Factor Estimulante de Colonias de Macrófagos , Macrófagos/metabolismo , Oxigenasas de Función Mixta/genética , Proteínas Proto-Oncogénicas/genética , ARN Largo no Codificante/genética , ARN Largo no Codificante/metabolismo
8.
Thorac Cancer ; 13(17): 2421-2428, 2022 09.
Artículo en Inglés | MEDLINE | ID: mdl-35866204

RESUMEN

BACKGROUND: Pazopanib is an approved multitarget anticancer agent for soft tissue sarcoma (STS) and renal cell carcinoma (RCC), which is also under clinical investigation for other malignancies, including small cell lung cancer (SCLC). However, the potential anti-SCLC mechanisms of pazopanib remain unclear. METHODS: Cell viability was evaluated by CCK-8, apoptotic cell detection was conducted using annexin V/PI staining followed by flow cytometry, and Western blot analysis was used to detect the apoptotic-related molecules and ER-stress pathway effectors. The intracellular reactive oxygen species (ROS) level was determined by DCFH-HA staining followed by flow cytometry. An NCI-H446 xenograft model was established to evaluate pazopanib on tumor suppression in vivo. Immunohistochemistry (IHC) was used to assess the proliferative activity of xenograft in NCI-H446 cell-bearing NOD-SCID mice. RESULTS: Pazopanib dose- and time-dependently inhibited SCLC cell proliferation induced significant apoptosis in SCLC cell lines, increased cleaved-caspase3 and Bax, and decreased Bcl-2. Moreover, the PERK-related ER-stress pathway was potently activated by pazopanib treatment, inhibiting ER-stress by salubrinal significantly reversing pazopanib-mediated apoptosis in SCLC cell lines. Furthermore, pazopanib-induced intracellular ROS levels increased, while inhibiting ROS by NAC significantly reversed pazopanib-induced apoptosis in SCLC cells. In addition, pazopanib significantly suppressed NCI-H446 xenograft growth and decreased Ki67 positive cells in the tumor. CONCLUSION: Our findings indicate that pazopanib induces SCLC cell apoptosis through the ER-stress process via upregulation of ROS levels. Further investigation of relevant biomarkers to accurately select patients for benefit from pazopanib should be further investigated.


Asunto(s)
Neoplasias Pulmonares , Carcinoma Pulmonar de Células Pequeñas , Animales , Apoptosis , Línea Celular Tumoral , Proliferación Celular , Estrés del Retículo Endoplásmico , Humanos , Indazoles , Neoplasias Pulmonares/patología , Ratones , Ratones Endogámicos NOD , Ratones SCID , Pirimidinas , Especies Reactivas de Oxígeno/metabolismo , Carcinoma Pulmonar de Células Pequeñas/tratamiento farmacológico , Sulfonamidas
11.
DNA Res ; 29(1)2022 Jan 28.
Artículo en Inglés | MEDLINE | ID: mdl-35137004

RESUMEN

Among relic species, genomic information may provide the key to inferring their long-term survival. Therefore, in this study, we investigated the genome of the Paleogene relic tree species, Bretschneidera sinensis, which is a rare endemic species within southeastern Asia. Specifically, we assembled a high-quality genome for B. sinensis using PacBio high-fidelity and high-throughput chromosome conformation capture reads and annotated it with long and short RNA sequencing reads. Using the genome, we then detected a trade-off between active and passive disease defences among the gene families. Gene families involved in salicylic acid and MAPK signalling pathways expanded as active defence mechanisms against disease, but families involved in terpene synthase activity as passive defences contracted. When inferring the long evolutionary history of B. sinensis, we detected population declines corresponding to historical climate change around the Eocene-Oligocene transition and to climatic fluctuations in the Quaternary. Additionally, based on this genome, we identified 388 single nucleotide polymorphisms (SNPs) that were likely under selection, and showed diverse functions in growth and stress responses. Among them, we further found 41 climate-associated SNPs. The genome of B. sinensis and the SNP dataset will be important resources for understanding extinction/diversification processes using comparative genomics in different lineages.


Asunto(s)
Polimorfismo de Nucleótido Simple , Árboles , Demografía , Genoma , Humanos , Análisis de Secuencia de ADN
12.
J Prosthodont Res ; 66(2): 279-287, 2022 Apr 27.
Artículo en Inglés | MEDLINE | ID: mdl-34588401

RESUMEN

PURPOSE: To evaluate the performance of polyetheretherketone (PEEK) versus titanium computer-aided designed and manufactured (CAD-CAM) framework for implant-supported fixed complete dentures (ISFCDs) with a follow-up for a duration of up to 5 years. METHODS: Consecutively edentulous patients who underwent ISFCDs with a PEEK framework or titanium framework at one dental specialist center were included in this retrospective study. Implant/prosthesis survival rates, mechanical/biological complications, and bone and soft tissue parameters were analyzed. Overall survival was analyzed using Kaplan-Meier survival curves and the log-rank test. RESULTS: Sixty ISFCDs (29 PEEK, 31 titanium) performed on 43 edentulous patients (331 implants) were included. An implant survival rate of 100% was obtained. There was no significant difference in the cumulative prosthesis survival rate between the PEEK (93.1%) and titanium groups (93.5%). The most common mechanical complications were fracture of the artificial veneer in both the PEEK (13.8%) and titanium (16.7%) groups. Bruxers had a higher prevalence of mechanical complications than non-bruxers (p<0.05). The biological complications included bleeding upon probing (13.8% for the PEEK group; 16.1% for the titanium group), soft tissue inflammation (3.4% for the PEEK group; 3.2% for the titanium group), and temporomandibular disorders (6.5% for the titanium group). The vertical bone loss was significantly lower in the PEEK group (0.70 mm) than in the titanium group (0.96 mm). Smokers had a significantly higher prevalence of biological complications than non-smokers. CONCLUSION: Within the limitations of this study, ISFCDs with PEEK frameworks can provide good prognosis for edentulous patients, still requiring longer-term validation.


Asunto(s)
Implantes Dentales , Titanio , Benzofenonas , Diseño Asistido por Computadora , Prótesis Dental de Soporte Implantado , Fracaso de la Restauración Dental , Dentadura Completa , Estudios de Seguimiento , Humanos , Polímeros , Falla de Prótesis , Estudios Retrospectivos
13.
IEEE Trans Cybern ; 52(12): 13472-13485, 2022 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-34236973

RESUMEN

This article presents a rough-to-fine evolutionary multiobjective optimization algorithm based on the decomposition for solving problems in which the solutions are initially far from the Pareto-optimal set. Subsequently, a tree is constructed by a modified k -means algorithm on N uniform weight vectors, and each node of the tree contains a weight vector. Each node is associated with a subproblem with the help of its weight vector. Consequently, a subproblem tree can be established. It is easy to find that the descendant subproblems are refinements of their ancestor subproblems. The proposed algorithm approaches the Pareto front (PF) by solving a few subproblems in the first few levels to obtain a rough PF and gradually refining the PF by involving the subproblems level-by-level. This strategy is highly favorable for solving problems in which the solutions are initially far from the Pareto set. Moreover, the proposed algorithm has lower time complexity. Theoretical analysis shows the complexity of dealing with a new candidate solution is O(M logN) , where M is the number of objectives. Empirical studies demonstrate the efficacy of the proposed algorithm.

15.
Cancer Sci ; 112(6): 2349-2360, 2021 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-33565687

RESUMEN

Reliable and noninvasive biomarkers for the early diagnosis of non-small-cell lung cancer (NSCLC) are an unmet need. This study aimed to screen and validate potential urinary biomarkers for the early diagnosis of NSCLC. Using protein mass spectrometry, urinary MDH2 was found to be abundant both in patients with lung cancer and lung cancer model mice compared with controls. Urine samples obtained as retrospective and prospective cohorts including 1091 NSCLC patients and 736 healthy controls were measured using ELISA. Patients with stage I NSCLC had higher urinary MDH2 compared with healthy controls. The area under the receiver-operating characteristic curve (AUC) for the urinary MDH2 was 0.7679 and 0.7234 in retrospective and prospective cohorts to distinguish stage I cases from controls. Urinary MDH2 levels correlated with gender and smoking history. MDH2 expression levels were elevated in lung cancer tissues. MDH2 knockdown using shRNA inhibited the proliferation of lung cancer cells. Our study demonstrated that urinary MDH2 concentration was higher in early-stage NSCLC patients compared with that in controls and that MDH2 could serve as a potential biomarker for early detection of NSCLC.


Asunto(s)
Biomarcadores de Tumor/orina , Carcinoma de Pulmón de Células no Pequeñas/diagnóstico , Neoplasias Pulmonares/diagnóstico , Malato Deshidrogenasa/orina , Regulación hacia Arriba , Células A549 , Animales , Área Bajo la Curva , Carcinoma de Pulmón de Células no Pequeñas/patología , Carcinoma de Pulmón de Células no Pequeñas/orina , Estudios de Casos y Controles , Línea Celular Tumoral , Detección Precoz del Cáncer , Regulación Neoplásica de la Expresión Génica , Humanos , Neoplasias Pulmonares/genética , Neoplasias Pulmonares/patología , Espectrometría de Masas , Ratones , Estadificación de Neoplasias , Trasplante de Neoplasias , Estudios Prospectivos , Estudios Retrospectivos
16.
IEEE Trans Cybern ; 51(6): 3238-3248, 2021 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-32167920

RESUMEN

Multiobjective multitasking optimization (MTO), which is an emerging research topic in the field of evolutionary computation, was recently proposed. MTO aims to solve related multiobjective optimization problems at the same time via evolutionary algorithms. The key to MTO is the knowledge transfer based on sharing solutions across tasks. Notably, positive knowledge transfer has been shown to facilitate superior performance characteristics. However, how to find more valuable transferred solutions for the positive transfer has been scarcely explored. Keeping this in mind, we propose a new algorithm to solve MTO problems. In this article, if a transferred solution is nondominated in its target task, the transfer is positive transfer. Furthermore, neighbors of this positive-transfer solution will be selected as the transferred solutions in the next generation, since they are more likely to achieve the positive transfer. Numerical studies have been conducted on benchmark problems of MTO to verify the effectiveness of the proposed approach. Experimental results indicate that our proposed framework achieves competitive results compared with the state-of-the-art MTO frameworks.

17.
IEEE Trans Cybern ; 51(11): 5546-5558, 2021 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-32559171

RESUMEN

When solving constrained multiobjective optimization problems (CMOPs), the most commonly used way of measuring constraint violation is to calculate the sum of all constraint violations of a solution as its distance to feasibility. However, this kind of constraint violation measure may not reflect the distance of an infeasible solution from feasibility for some problems, for example, when an infeasible solution closer to a feasible region does not have a smaller constraint violation than the one farther away from a feasible region. Unfortunately, no set of artificial benchmark problems focusing on this area exists. To remedy this issue, a set of CMOPs with deceptive constraints is introduced in this article. It is the first attempt to consider CMOPs with deceptive constraints (DCMOPs). Based on our previous work, which designed a set of directed weight vectors to solve CMOPs, this article proposes a cooperative framework with an improved version of directed weight vectors to solve DCMOPs. Specifically, the cooperative framework consists of two switchable phases. The first phase uses two subpopulations-one to explore feasible regions and the other to explore the entire space. The two subpopulations provide useful information about the optimal direction of objective improvement to each other. The second phase aims mainly at finding Pareto-optimal solutions. Then an infeasibility utilization strategy is used to improve the objective function values. The two phases are switchable based on the information found to date at any time in the evolutionary process. The experimental results show that this method significantly outperforms the algorithms with which it is compared on most of the DCMOPs, in terms of reliability and stability in finding a set of well-distributed optimal solutions.

18.
Evol Comput ; 29(1): 157-186, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-32567957

RESUMEN

An objective normalization strategy is essential in any evolutionary multiobjective or many-objective optimization (EMO or EMaO) algorithm, due to the distance calculations between objective vectors required to compute diversity and convergence of population members. For the decomposition-based EMO/EMaO algorithms involving the Penalty Boundary Intersection (PBI) metric, normalization is an important matter due to the computation of two distance metrics. In this article, we make a theoretical analysis of the effect of instabilities in the normalization process on the performance of PBI-based MOEA/D and a proposed PBI-based NSGA-III procedure. Although the effect is well recognized in the literature, few theoretical studies have been done so far to understand its true nature and the choice of a suitable penalty parameter value for an arbitrary problem. The developed theoretical results have been corroborated with extensive experimental results on three to 15-objective convex and non-convex instances of DTLZ and WFG problems. The article, makes important theoretical conclusions on PBI-based decomposition algorithms derived from the study.


Asunto(s)
Algoritmos , Evolución Biológica , Modelos Teóricos
19.
PLoS One ; 15(11): e0242591, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-33237925

RESUMEN

Abelmoschus is an economically and phylogenetically valuable genus in the family Malvaceae. Owing to coexistence of wild and cultivated form and interspecific hybridization, this genus is controversial in systematics and taxonomy and requires detailed investigation. Here, we present whole chloroplast genome sequences and annotation of three important species: A. moschatus, A. manihot and A. sagittifolius, and compared with A. esculentus published previously. These chloroplast genome sequences ranged from 163121 bp to 163453 bp in length and contained 132 genes with 87 protein-coding genes, 37 transfer RNA and 8 ribosomal RNA genes. Comparative analyses revealed that amino acid frequency and codon usage had similarity among four species, while the number of repeat sequences in A. esculentus were much lower than other three species. Six categories of simple sequence repeats (SSRs) were detected, but A. moschatus and A. manihot did not contain hexanucleotide SSRs. Single nucleotide polymorphisms (SNPs) of A/T, T/A and C/T were the largest number type, and the ratio of transition to transversion was from 0.37 to 0.55. Abelmoschus species showed relatively independent inverted-repeats (IR) boundary traits with different boundary genes compared with the other related Malvaceae species. The intergenic spacer regions had more polymorphic than protein-coding regions and intronic regions, and thirty mutational hotpots (≥200 bp) were identified in Abelmoschus, such as start-psbA, atpB-rbcL, petD-exon2-rpoA, clpP-intron1 and clpP-exon2.These mutational hotpots could be used as polymorphic markers to resolve taxonomic discrepancies and biogeographical origin in genus Abelmoschus. Moreover, phylogenetic analysis of 33 Malvaceae species indicated that they were well divided into six subfamilies, and genus Abelmoschus was a well-supported clade within genus Hibiscus.


Asunto(s)
Abelmoschus/genética , Cloroplastos/genética , ADN de Cloroplastos/genética , Genoma de Planta , Aminoácidos , Uso de Codones , Ontología de Genes , Genoma de Planta/genética , Malvaceae/clasificación , Malvaceae/genética , Anotación de Secuencia Molecular , Mutación , Filogenia , Hojas de la Planta/química , Plantas Medicinales/genética , Edición de ARN , Secuencias Repetitivas de Ácidos Nucleicos , Especificidad de la Especie
20.
J Cell Mol Med ; 24(10): 5751-5757, 2020 05.
Artículo en Inglés | MEDLINE | ID: mdl-32285549

RESUMEN

The aim of this study was to investigate in vitro magnetic resonance imaging (MRI) of PDAC using ENO1-targeted superparamagnetic iron oxide nanoparticles and xenograft models. Expression level and location of ENO1 protein in pancreatic cancer cell lines of CFPAC-1 and MiaPaCa-2 were detected by Western blotting, flow cytometry and confocal microscopy. Dex-g-PCL/SPIO nanoparticles targeting ENO1 were constructed with ENO1 antibody and characterized by MRI. In addition, ENO1-Dex-g-PCL/SPIO nanoparticles were tested to assess their efficacy on the detection of PDAC using in vitro and in vivo MRI. The results showed that ENO1 was expressed in both human PDAC cell lines of CFPAC-1 and MiaPaCa-2, demonstrating that the localization of cytoplasm and membrane was dominant. It was confirmed that ENO1 antibody was connected to the SPIO surface in ENO1-Dex-g-PCL/SPIO nanoparticles. The nanoparticles had satisfactory superparamagnetism and significantly enhance the detection of PDAC by in vivo and in vitro MRI. In conclusion, ENO1 can serve as a membrane protein expressed on human PDAC cell lines. ENO1-targeted SPIO nanoparticles using ENO1 antibody can increase the efficiency of detection of PDAC by in vitro and in vivo MRI.


Asunto(s)
Biomarcadores de Tumor/metabolismo , Proteínas de Unión al ADN/metabolismo , Nanopartículas Magnéticas de Óxido de Hierro/química , Imagen por Resonancia Magnética , Neoplasias Pancreáticas/diagnóstico por imagen , Neoplasias Pancreáticas/diagnóstico , Fosfopiruvato Hidratasa/metabolismo , Proteínas Supresoras de Tumor/metabolismo , Animales , Línea Celular Tumoral , Dextranos/química , Humanos , Nanopartículas Magnéticas de Óxido de Hierro/ultraestructura , Masculino , Ratones Endogámicos BALB C , Ratones Desnudos , Neoplasias Pancreáticas/patología , Poliésteres/química
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