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1.
Front Pharmacol ; 15: 1349459, 2024.
Artículo en Inglés | MEDLINE | ID: mdl-38881867

RESUMEN

Background: Immune checkpoint inhibitors (ICIs) have revolutionized cancer treatment; however, a significant proportion of gastric cancer (GC) patients do not respond to this therapy. Consequently, there is an urgent need to elucidate the mechanisms underlying resistance to ICIs and identify robust biomarkers capable of predicting the response to ICIs at treatment initiation. Methods: In this study, we collected GC tissues from 28 patients prior to the administration of anti-programmed death 1 (PD-1) immunotherapy and conducted protein quantification using high-resolution mass spectrometry (MS). Subsequently, we analyzed differences in protein expression, pathways, and the tumor microenvironment (TME) between responders and non-responders. Furthermore, we explored the potential of these differences as predictive indicators. Finally, using machine learning algorithms, we screened for biomarkers and constructed a predictive model. Results: Our proteomics-based analysis revealed that low activity in the complement and coagulation cascades pathway (CCCP) and a high abundance of activated CD8 T cells are positive signals corresponding to ICIs. By using machine learning, we successfully identified a set of 10 protein biomarkers, and the constructed model demonstrated excellent performance in predicting the response in an independent validation set (N = 14; area under the curve [AUC] = 0.959). Conclusion: In summary, our proteomic analyses unveiled unique potential biomarkers for predicting the response to PD-1 inhibitor immunotherapy in GC patients, which may provide the impetus for precision immunotherapy.

2.
Sci Transl Med ; 16(752): eabq7074, 2024 Jun 19.
Artículo en Inglés | MEDLINE | ID: mdl-38896602

RESUMEN

Epidermal growth factor receptor inhibitors (EGFRis) are used to treat many cancers, but their use is complicated by the development of a skin rash that may be severe, limiting their use and adversely affecting patient quality of life. Most studies of EGFRi-induced rash have focused on the fully developed stage of this skin disorder, and early pathological changes remain unclear. We analyzed high-throughput transcriptome sequencing of skin samples from rats exposed to the EGFRi afatinib and identified that keratinocyte activation is an early pathological alteration in EGFRi-induced rash. Mechanistically, the induction of S100 calcium-binding protein A9 (S100A9) occurred before skin barrier disruption and led to keratinocyte activation, resulting in expression of specific cytokines, chemokines, and surface molecules such as interleukin 6 (Il6) and C-C motif chemokine ligand 2 (CCL2) to recruit and activate monocytes through activation of the Janus kinase (JAK)-signal transducers and activators of transcription (STAT) pathway, further recruiting more immune cells. Topical JAK inhibition suppressed the recruitment of immune cells and ameliorated the severity of skin rash in afatinib-treated rats and mice with epidermal deletion of EGFR, while having no effect on EGFRi efficacy in tumor-bearing mice. In a pilot clinical trial (NCT05120362), 11 patients with EGFRi-induced rash were treated with delgocitinib ointment, resulting in improvement in rash severity by at least one grade in 10 of them according to the MASCC EGFR inhibitor skin toxicity tool (MESTT) criteria. These findings provide a better understanding of the early pathophysiology of EGFRi-induced rash and suggest a strategy to manage this condition.


Asunto(s)
Receptores ErbB , Exantema , Inhibidores de las Cinasas Janus , Animales , Femenino , Humanos , Masculino , Ratones , Persona de Mediana Edad , Ratas , Administración Tópica , Afatinib/farmacología , Afatinib/uso terapéutico , Receptores ErbB/antagonistas & inhibidores , Receptores ErbB/metabolismo , Exantema/inducido químicamente , Exantema/patología , Inhibidores de las Cinasas Janus/farmacología , Inhibidores de las Cinasas Janus/uso terapéutico , Quinasas Janus/metabolismo , Quinasas Janus/antagonistas & inhibidores , Queratinocitos/efectos de los fármacos , Queratinocitos/metabolismo , Queratinocitos/patología , Inhibidores de Proteínas Quinasas/farmacología , Inhibidores de Proteínas Quinasas/uso terapéutico , Estudios Prospectivos
3.
Signal Transduct Target Ther ; 9(1): 108, 2024 May 06.
Artículo en Inglés | MEDLINE | ID: mdl-38705885

RESUMEN

Coinfusion of unrelated cord blood (UCB) units in haploidentical hematopoietic cell transplantation (haplo-HCT) (haplo-cord HCT) for hematopoietic malignancies showed promising results in previous reports, but the efficiency of haplo-cord HCT in acute myeloid leukemia (AML) still lacks sufficient evidence. This multicenter, randomized, phase 3 trial (ClinicalTrials.gov NCT03719534) aimed to assess the efficacy and safety of haplo-cord HCT in AML patients. A total of 268 eligible patients aged 18-60 years, diagnosed with measurable residual disease in AML (excluding acute promyelocytic leukemia), with available haploidentical donors and suitable for allotransplantation, were randomly allocated (1:1) to receive haplo-cord HCT (n = 134) or haplo-HCT (n = 134). The 3-year overall survival (OS) was the primary endpoint in this study. Overall median follow-up was 36.50 months (IQR 24.75-46.50). The 3-year OS of Haplo-cord HCT group was better than haplo-HCT group (80.5%, 95% confidence interval [CI]: 73.7-87.9 vs. 67.8% 95% CI 60.0-76.5, p = 0.013). Favorable progression-free survival (70.3%, 95% CI 62.6-78.8 vs. 57.6%, 95% CI 49.6-67.0, p = 0.012) and cumulative incidence of relapse (12.1%, 95% CI 12.0-12.2 vs. 30.3%, 95% CI 30.1-30.4, p = 0.024) were observed in haplo-cord HCT group. Grade 3-4 adverse events (AEs) within two years posttransplantation in the two groups were similar. Haplo-cord HCT patients exhibited a faster cumulative incidence of neutrophil recovery (p = 0.026) and increased T-cell reconstitution in the early period posttransplantation. Haplo-cord HCT can improve OS in AML patients without excessive AEs, which may exert additional benefits for recipients of haplo-HCT.


Asunto(s)
Trasplante de Células Madre de Sangre del Cordón Umbilical , Trasplante de Células Madre Hematopoyéticas , Leucemia Mieloide Aguda , Humanos , Adulto , Leucemia Mieloide Aguda/terapia , Masculino , Femenino , Persona de Mediana Edad , Adolescente , Trasplante Haploidéntico/efectos adversos , Adulto Joven
4.
PLoS One ; 19(1): e0296366, 2024.
Artículo en Inglés | MEDLINE | ID: mdl-38165910

RESUMEN

To explore the effects of cellulose and lignin on stimulating vegetation restoration and improving soil chemical properties in saline-alkali soil, a large area test was carried out, and 2 treatments were set up: T (cellulose and lignin+ Planted seeds) and CK (Planted seeds). In this study, the species, quantity, plant height, above-ground biomass, biodiversity of vegetation in the treated plots, the determination of soil chemical nutrient content, and the effect of cellulose and lignin on vegetation restoration in saline-alkali land were investigated. The results showed that: 1) Cellulose and lignin contributed to vegetation growth. Compared with CK treatment, plant height and aboveground biomass of T increased by 158.73% and 240.13%, respectively; 2) Cellulose and lignin improved soil structure, and soil porosity, and decreased soil compaction (21.95%); 3) Compared with CK treatment, T treatment decreased soil pH by 0.5 units, total salt content decreased by 30.95%, exchangeable Na+ decreased by 63.00%, and exchangeable sodium percentage (ESP) decreased by 61.51%. Furthermore, cellulose and lignin effectively improved the physical and chemical properties of saline-alkali soil, promoted the recovery of ecological environment in saline-alkali soil, and improved regional biodiversity, which will provide new methods for soil remediation and improvement in saline-alkali areas.


Asunto(s)
Álcalis , Suelo , Suelo/química , Lignina , Celulosa , Plantas , Sodio , Biodiversidad
5.
Front Endocrinol (Lausanne) ; 14: 1250865, 2023.
Artículo en Inglés | MEDLINE | ID: mdl-37780618

RESUMEN

Introduction: Snub-nosed monkeys are species in danger of extinction due to habitat fragmentation and human activities. Captivity has been suggested as an Auxiliary Conservation Area (ASA) strategy. However, little is known about the adaptation of different species of snub-nosed monkeys to captive environments. Methods: This study compared the gut microbiota between Rhinopithecus bieti, R. brelichi, and R. roxellana under identical captive conditions to provide insights for improving captive conservation strategies. Results: The results showed that these three Rhinopithecus species shared 80.94% of their Operational Taxonomic Unit (OTU), indicating high similarity in gut microbiota composition. The predominant phyla were Firmicutes and Bacteroidetes for all three Rhinopithecus species, but differences were observed in diversity, characteristic bacterial communities, and predicted function. Significant enrichment of cellulolytic families, including Ruminococcaceae, Clostridiales vadinBB60 group, Christensenellaceae, and Erysipelotrichaceae, and pathways involved in propionate and butyrate metabolism in the gut of R. bieti suggested that it may have a superior dietary fiber utilization capacity. In contrast, Bacteroidetes, Ruminoccaceae, and Trichospiraceae were more abundant in R. brelichi and R. roxellana, and were associated with saccharide and glycan metabolic pathways. Moreover, R. brelichi and R. roxellana also had higher similarity in microbiota composition and predicted function. Discussion: In conclusion, the results demonstrate that host species are associated with the composition and function of the gut microbiota in snub-nosed monkeys. Thus, host species should be considered when formulating nutritional strategies and disease surveillance in captive snub-nosed monkeys.


Asunto(s)
Colobinae , Microbioma Gastrointestinal , Presbytini , Animales , Humanos , Colobinae/microbiología , Ecosistema , Bacterias
6.
Front Chem ; 11: 1275448, 2023.
Artículo en Inglés | MEDLINE | ID: mdl-37829296

RESUMEN

In recent years, with the rapid development of the sports industry, the quality of sports training products on the market is uneven. Problems such as inaccurate detection of athletes' physical indicators, low comfort of sportswear, and reduced satisfaction with sports equipment often occur. To this end, this article proposes to apply conjugated materials with excellent optical, electrical, thermal and other properties to sports training and sports products, by summarizing the properties of conjugated materials and their applications in sports training, explores the potential of conjugated materials in improving athletes' training effects, monitoring sports status, and improving sports equipment. This article rates the application of conjugated materials in sports training products in terms of comfort, waterproofness, portability, lightness, aesthetics and breathability. The results showed that the average scores of the 20 sports participants on sportswear were 9.0475, 9.0075, 9.01, 9.025, 9.0325 and 9.04 respectively; the average scores on sports shoes were 9.035, 9.055, 9.02, 9.085, 9.0175 and 8.9975 respectively. Research shows that applying conjugated materials to sports training can improve athletes' performance and contribute to the better development of sports.

7.
Plants (Basel) ; 12(19)2023 Oct 04.
Artículo en Inglés | MEDLINE | ID: mdl-37836215

RESUMEN

A multitude of biotic and abiotic stress factors do harm to plants by bringing about diseases and inhibiting normal growth and development. As a pivotal signaling molecule, salicylic acid (SA) plays crucial roles in plant tolerance responses to both biotic and abiotic stresses, thereby maintaining plant normal growth and improving yields under stress. In view of this, this paper mainly discusses the role of SA in both biotic and abiotic stresses of plants. SA regulates the expression of genes involved in defense signaling pathways, thus enhancing plant immunity. In addition, SA mitigates the negative effects of abiotic stresses, and acts as a signaling molecule to induce the expression of stress-responsive genes and the synthesis of stress-related proteins. In addition, SA also improves certain yield-related photosynthetic indexes, thereby enhancing crop yield under stress. On the other hand, SA acts with other signaling molecules, such as jasmonic acid (JA), auxin, ethylene (ETH), and so on, in regulating plant growth and improving tolerance under stress. This paper reviews recent advances in SA's roles in plant stress tolerance, so as to provide theoretical references for further studies concerning the decryption of molecular mechanisms for SA's roles and the improvement of crop management under stress.

8.
Oncogenesis ; 12(1): 45, 2023 Sep 16.
Artículo en Inglés | MEDLINE | ID: mdl-37717015

RESUMEN

Neddylation is the writing of monomers or polymers of neural precursor cells expressed developmentally down-regulated 8 (NEDD8) to substrate. For neddylation to occur, three enzymes are required: activators (E1), conjugators (E2), and ligators (E3). However, the central role is played by the ubiquitin-conjugating enzymes E2M (UBE2M) and E2F (UBE2F), which are part of the E2 enzyme family. Recent understanding of the structure and mechanism of these two proteins provides insight into their physiological effects on apoptosis, cell cycle arrest and genome stability. To treat cancer, it is therefore appealing to develop novel inhibitors against UBE2M or UBE2F interactions with either E1 or E3. In this evaluation, we summarized the existing understanding of E2 interaction with E1 and E3 and reviewed the prospective of using neddylation E2 as a pharmacological target for evolving new anti-cancer remedies.

9.
Environ Sci Pollut Res Int ; 30(16): 47408-47421, 2023 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-36738414

RESUMEN

Satellite imagery time series change detection methods are effective in avoiding pseudochange due to vegetation phenology to a certain extent. Traditional time series change detection methods use thematic indexes (e.g., NDVI, RVI) to obtain time series information for corresponding change detection. However, change detection methods using several thematic index time series may not make full use of other spectral band information in remotely sensed images and may still suffer from over- and under-detections. To address this challenge, a temporal-spectral value and shape change detection method integrating thematic index information and spectral band information (TISB) is proposed. Possible clouds and cloud shadowing phenomena are removed according to the changes in the spectral values of the remotely sensed images to avoid the generation of pseudochanges in clouds. The spectral and time series information is used to obtain change information from the value perspective, and then, further possible enhanced change regions from a shape perspective to obtain the final change detection results through the expectation-maximization (EM) method. Experiments with Landsat images have shown that the TISB method improves detection results by approximately 1-4% compared to the comparison method.


Asunto(s)
Monitoreo del Ambiente , Imágenes Satelitales , Imágenes Satelitales/métodos , Monitoreo del Ambiente/métodos
10.
Int J Biol Macromol ; 230: 123219, 2023 Mar 01.
Artículo en Inglés | MEDLINE | ID: mdl-36642357

RESUMEN

Histone deacetylase 6 (HDAC6) is the only member of the HDAC family that resides primarily in the cytoplasm with two catalytic domains and a ubiquitin-binding domain. HDAC6 is highly expressed in various solid tumors and participates in a wide range of biological activities, including hormone receptors, the p53 signaling pathway, and the kinase cascade signaling pathway due to its unique structural foundation and abundant substrate types. Additionally, HDAC6 can function as an oncogenic factor in solid tumors, boosting tumor cell proliferation, invasion and metastasis, drug resistance, stemness, and lowering tumor cell immunogenicity, so assisting in carcinogenesis. Pan-HDAC inhibitors for cancer prevention are associated with potential cardiotoxicity in clinical investigations. It's interesting that HDAC6 silencing didn't cause any significant harm to normal cells. Currently, the use of HDAC6 specific inhibitors, individually or in combination, is among the most promising therapies in solid tumors. This review's objective is to give a general overview of the structure, biological functions, and mechanism of HDAC6 in solid tumor cells and in the immunological milieu and discuss the preclinical and clinical trials of selective HDAC6 inhibitors. These endeavors highlight that targeting HDAC6 could effectively kill tumor cells and enhance patients' immunity during solid tumor therapy.


Asunto(s)
Neoplasias , Humanos , Proliferación Celular , Histona Desacetilasa 6/metabolismo , Histona Desacetilasa 6/farmacología , Inhibidores de Histona Desacetilasas/farmacología , Inhibidores de Histona Desacetilasas/química , Inhibidores de Histona Desacetilasas/metabolismo , Neoplasias/tratamiento farmacológico
11.
Nat Plants ; 8(12): 1408-1422, 2022 12.
Artículo en Inglés | MEDLINE | ID: mdl-36396706

RESUMEN

Appropriate root system architecture (RSA) can improve maize yields in densely planted fields, but little is known about its genetic basis in maize. Here we performed root phenotyping of 14,301 field-grown plants from an association mapping panel to study the genetic architecture of maize RSA. A genome-wide association study identified 81 high-confidence RSA-associated candidate genes and revealed that 28 (24.3%) of known root-related genes were selected during maize domestication and improvement. We found that modern maize breeding has selected for a steeply angled root system. Favourable alleles related to steep root system angle have continuously accumulated over the course of modern breeding, and our data pinpoint the root-related genes that have been selected in different breeding eras. We confirm that two auxin-related genes, ZmRSA3.1 and ZmRSA3.2, contribute to the regulation of root angle and depth in maize. Our genome-wide identification of RSA-associated genes provides new strategies and genetic resources for breeding maize suitable for high-density planting.


Asunto(s)
Estudio de Asociación del Genoma Completo , Zea mays , Zea mays/genética , Fitomejoramiento , Alelos
12.
Psychol Res Behav Manag ; 15: 1721-1730, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-35855766

RESUMEN

Purpose: Research in the acculturation domain has noted the influence of parental attachment on depression among overseas students. However, an almost negligible effort has been made to investigate how it happens. This study aims to explore the relationship between parental attachment, basic psychological needs, career identity and depression of Chinese overseas students, while focusing on the mechanisms underlying such relationship. Methods: A total of 335 Chinese overseas students were asked to fill out a questionnaire, and the data of these samples were utilized to test the moderated mediation hypotheses through SPSS and AMOS. Results: The results indicate that parental attachment of Chinese overseas students has a negative effect on depression, while basic psychological needs play a part in mediating between parental attachment and depression. In addition, career identity moderates the mediating effect of basic psychological needs between parental attachment and depression. Conclusion: To the best of the authors' knowledge, this study has been one of the first attempts to reveal the influence mechanism of basic psychological needs and career identity on the relationship between parental attachment and depression of Chinese overseas students. It is expected that the preliminary findings of this study will encourage more research on the psychological mechanisms of Chinese overseas students, so as to provide a more comprehensive picture of the interaction between parental attachment and depression of overseas students studying in different countries with various backgrounds.

13.
Cell Mol Life Sci ; 79(8): 413, 2022 Jul 11.
Artículo en Inglés | MEDLINE | ID: mdl-35819633

RESUMEN

Cancer immunotherapy is a rapidly developing and effective method for the treatment of a variety of malignancies in recent years. As a significant immune checkpoint, programmed cell death 1 ligand 1 (PD-L1) and its receptor programmed cell death protein 1 (PD-1) play the most significant role in cancer immune escape and cancer immunotherapy. Though PD-L1 have become an important target for drug development and there have been various approved drugs and clinic trials targeting it, and various clinical response rate and adverse reactions prevent many patients from benefiting from it. In recent years, combination trials have become the main direction of PD-1/PD-L1 antibodies development. Here, we summarized PD-L1 biofunctions and key roles in various cancers along with the development of PD-L1 inhibitors. The regulators that are involved in controlling PD-L1 expression including post-translational modification, mRNA level regulation as well as degradation and exosome secretory pathway of PD-L1 were focused. This systematic summary may provide comprehensive understanding of different regulations on PD-L1 as well as a broad prospect for the search of the important regulator of PD-L1. The regulatory factors of PD-L1 can be potential targets for immunotherapy and increase strategies of immunotherapy in combination.


Asunto(s)
Antígeno B7-H1 , Neoplasias , Antígeno B7-H1/metabolismo , Humanos , Inmunoterapia/métodos , Neoplasias/metabolismo , Receptor de Muerte Celular Programada 1/metabolismo , Procesamiento Proteico-Postraduccional
14.
Life Sci ; 298: 120458, 2022 Jun 01.
Artículo en Inglés | MEDLINE | ID: mdl-35248525

RESUMEN

AIMS: Lysine-specific demethylase 5B (KDM5B) is an epigenetic regulator of chromatin that catalyzes the demethylation of histone 3 lysine 4. It is overexpressed in multiple cancer types and acts as a therapeutic target in cancer therapy. Nevertheless, its upstream regulatory pathway is not completely understood, prompting the search for the underlying biological factors driving KDM5B overexpression. MATERIALS AND METHODS: A comprehensive analysis was performed to examine the association between KDM5B overexpression and copy number variation (CNV), somatic mutation, mRNA expression, miRNA expression, and clinical characters from The Cancer Genome Atlas database. Coexpression and function enrichment analyses were performed with KDM5B-coexpressed genes. The gastric cancer (GC) cell line MKN45 was utilized to verify the regulation of KDM5B using the transcription factor (TF) Yin Yang 1 (YY1) and miR-29a-3p. KEY FINDINGS: KDM5B was overexpressed and associated with poor prognosis in GC. KDM5B upregulation was driven by CNV amplification and DNA hypomethylation rather than by KDM5B mutations. Enrichment analysis revealed that KDM5B-coexpressed genes were primarily related to the transmembrane transport function and the ubiquitin-mediated proteolysis signaling pathway. As a TF, YY1 might bind to the KDM5B promoter region to regulate KDM5B expression. In addition, miR-29a-3p might bind to and negatively regulate KDM5B expression. SIGNIFICANCE: Our results demonstrate that KDM5B expression is regulated via CNV amplification, DNA hypomethylation, and YY1 and miR-29a-3p; KDM5B expression regulation is associated with patient survival and tumor cell proliferation.


Asunto(s)
MicroARNs , Neoplasias Gástricas , Línea Celular Tumoral , Proliferación Celular/genética , ADN , Variaciones en el Número de Copia de ADN/genética , Regulación Neoplásica de la Expresión Génica , Humanos , Histona Demetilasas con Dominio de Jumonji/genética , Histona Demetilasas con Dominio de Jumonji/metabolismo , Lisina/metabolismo , MicroARNs/genética , Proteínas Nucleares/genética , Proteínas Represoras/genética , Neoplasias Gástricas/genética
15.
Mol Cancer ; 21(1): 75, 2022 03 16.
Artículo en Inglés | MEDLINE | ID: mdl-35296335

RESUMEN

BACKGROUND: Histone lysine-specific demethylase 1 (LSD1) expression has been shown to be significantly elevated in gastric cancer (GC) and may be associated with the proliferation and metastasis of GC. It has been reported that LSD1 repressed tumor immunity through programmed cell death 1 ligand 1 (PD-L1) in melanoma and breast cancer. The role of LSD1 in the immune microenvironment of GC is unknown. METHODS: Expression LSD1 and PD-L1 in GC patients was analyzed by immunohistochemical (IHC) and Western blotting. Exosomes were isolated from the culture medium of GC cells using an ultracentrifugation method and characterized by transmission electronic microscopy (TEM), nanoparticle tracking analysis (NTA), sucrose gradient centrifugation, and Western blotting. The role of exosomal PD-L1 in T-cell dysfunction was assessed by flow cytometry, T-cell killing and enzyme-linked immunosorbent assay (ELISA). RESULTS: Through in vivo exploration, mouse forestomach carcinoma (MFC) cells with LSD1 knockout (KO) showed significantly slow growth in 615 mice than T-cell-deficient BALB/c nude mice. Meanwhile, in GC specimens, expression of LSD1 was negatively correlated with that of CD8 and positively correlated with that of PD-L1. Further study showed that LSD1 inhibited the response of T cells in the microenvironment of GC by inducing the accumulation of PD-L1 in exosomes, while the membrane PD-L1 stayed constant in GC cells. Using exosomes as vehicles, LSD1 also obstructed T-cell response of other cancer cells while LSD1 deletion rescued T-cell function. It was found that while relying on the existence of LSD1 in donor cells, exosomes can regulate MFC cells proliferation with distinct roles depending on exosomal PD-L1-mediated T-cell immunity in vivo. CONCLUSION: LSD1 deletion decreases exosomal PD-L1 and restores T-cell response in GC; this finding indicates a new mechanism with which LSD1 may regulate cancer immunity in GC and provides a new target for immunotherapy against GC.


Asunto(s)
Antígeno B7-H1 , Neoplasias Gástricas , Animales , Histona Demetilasas/genética , Humanos , Ratones , Ratones Desnudos , Neoplasias Gástricas/genética , Linfocitos T , Microambiente Tumoral
16.
Comput Struct Biotechnol J ; 20: 1068-1076, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-35284049

RESUMEN

Sex differences are evident in the incidence and mortality of diverse cancers. With the development of personalized approaches in cancer treatment, the impact of sex differences has not been systematically incorporated into preclinical and clinical cancer research. The molecular mechanisms underlying sex differences in cancer have not been elucidated. Here, we developed the first database of Sex Differences in Cancer (SDC), a web-based public database that integrates resources from multiple databases, including The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression Project (GTEx), UCSC Xena, Broad Institute Cancer Cell Line Encyclopedia (CCLE), Genomics of Drug Sensitivity in Cancer (GDSC). SDC contains 27 types of cancers, 6 types of molecular data, more than 10,000 donors, 977 cancer cell lines were used to analyze sex differences among cancers. It provides five main modules: Survival and phenotype, Molecular differences, Signatures and pathways, Therapy response, Download. Users can download the all the visualized results and raw data after analysis. Collectively, SDC is the first integrated database to analyze sex differences in cancer on the web server, which will strengthen our understanding of the role of sex in cancers. It is implemented in Shiny-server and freely available for public use at http://sdc.anticancer.xyz.

17.
Genes (Basel) ; 13(2)2022 01 28.
Artículo en Inglés | MEDLINE | ID: mdl-35205226

RESUMEN

Roots are important plant organs for the absorption of water and nutrients. To date, there have been few genome-wide association studies of maize root system architecture (RSA) in the field. The genetic basis of maize RSA is poorly understood, and the maize RSA-related genes that have been cloned are very limited. Here, 421 maize inbred lines of an association panel were planted to measure the root systems at the maturity stage, and a genome-wide association study was performed. There was a strong correlation among eight RSA traits, and the RSA traits were highly correlated with the aboveground plant architecture traits (e.g., plant height and ear leaf length, r = 0.13-0.25, p < 0.05). The RSA traits of the stiff stalk subgroup (SS) showed lower values than those of the non-stiff stalk subgroup (NSS) and tropical/subtropical subgroup (TST). Using the RSA traits, the genome-wide association study identified 63 SNPs and 189 candidate genes. Among them, nine candidate genes co-localized between RSA and aboveground architecture traits. A further co-expression analysis identified 88 candidate genes having high confidence levels. Furthermore, we identified four highly reliable RSA candidate genes, GRMZM2G099797, GRMZM2G354338, GRMZM2G085042, and GRMZM5G812926. This research provides theoretical support for the genetic improvement of maize root systems, and it identified candidate genes that may act as genetic resources for breeding.


Asunto(s)
Estudio de Asociación del Genoma Completo , Zea mays , Fenotipo , Fitomejoramiento , Polimorfismo de Nucleótido Simple/genética , Zea mays/genética
18.
J Imaging ; 8(1)2022 Jan 14.
Artículo en Inglés | MEDLINE | ID: mdl-35049852

RESUMEN

Accurate morphological information on aortic valve cusps is critical in treatment planning. Image segmentation is necessary to acquire this information, but manual segmentation is tedious and time consuming. In this paper, we propose a fully automatic aortic valve cusps segmentation method from CT images by combining two deep neural networks, spatial configuration-Net for detecting anatomical landmarks and U-Net for segmentation of aortic valve components. A total of 258 CT volumes of end systolic and end diastolic phases, which include cases with and without severe calcifications, were collected and manually annotated for each aortic valve component. The collected CT volumes were split 6:2:2 for the training, validation and test steps, and our method was evaluated by five-fold cross validation. The segmentation was successful for all CT volumes with 69.26 s as mean processing time. For the segmentation results of the aortic root, the right-coronary cusp, the left-coronary cusp and the non-coronary cusp, mean Dice Coefficient were 0.95, 0.70, 0.69, and 0.67, respectively. There were strong correlations between measurement values automatically calculated based on the annotations and those based on the segmentation results. The results suggest that our method can be used to automatically obtain measurement values for aortic valve morphology.

19.
Bioinformatics ; 38(2): 527-529, 2022 01 03.
Artículo en Inglés | MEDLINE | ID: mdl-34323947

RESUMEN

SUMMARY: UCSC Xena platform provides huge amounts of processed cancer omics data from large cancer research projects (e.g. TCGA, CCLE and PCAWG) or individual research groups and enables unprecedented research opportunities. However, a graphical user interface-based tool for interactively analyzing UCSC Xena data and generating elegant plots is still lacking, especially for cancer researchers and clinicians with limited programming experience. Here, we present UCSCXenaShiny, an R Shiny package for quickly searching, downloading, exploring, analyzing and visualizing data from UCSC Xena data hubs. This tool could effectively promote the practical use of public data, and can serve as an important complement to the current Xena genomics explorer. AVAILABILITY AND IMPLEMENTATION: UCSCXenaShiny is an open source R package under GPLv3 license and it is freely available at https://github.com/openbiox/UCSCXenaShiny or https://cran.r-project.org/package=UCSCXenaShiny. The docker image is available at https://hub.docker.com/r/shixiangwang/ucscxenashiny. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Asunto(s)
Neoplasias , Programas Informáticos , Humanos , Genómica , Interpretación Estadística de Datos
20.
Environ Monit Assess ; 193(9): 589, 2021 Aug 20.
Artículo en Inglés | MEDLINE | ID: mdl-34415414

RESUMEN

To explore the pollution status of heavy metals and potential risks in the Yongding New River of Tianjin, China, a comparative study of concentrations of heavy metals (Cd, Cr, Cu, Pb, Zn, As, and Hg) in surface sediments from submerged areas (SA), fluctuant flooded district (FFD), and non-flooded district (NFD) was conducted. In the present study, a modified three-stage European Community Bureau of Reference sequential extraction procedure and EDTA-Na2 single extraction were used to determine the heavy metal distribution in different sediment samples. Results showed that Cd was the metal with the highest contamination level compared to a background value of Tianjin soils, particularly in SA, followed by As. The concentrations of Cr, Pb, Cu, and Zn were relatively higher in upstream. Cu and Pb had higher bioavailability when compared with the other metals, indicating the two metals were easier to be mobilized. The Pearson correlation coefficient is applied to assess the degree of correlation between heavy metals. As, Cu, Zn, and Hg had the strong correlation, implying they may have common sources. Human activity in the riparian such as agricultural production, vehicle, and burning coal increased inputs of heavy metals in the surface sediments and influenced their distribution spatially. Besides, we also calculated geo-accumulation indexes (Igeo) and eco-risk index to assess the degree of risk of heavy metals in sediments. The Igeo were higher in SA than in FFD and NFD. Based on Igeo and potential eco-risk index, Cd has the highest risk, followed by As and Hg.


Asunto(s)
Metales Pesados , Contaminantes Químicos del Agua , Monitoreo del Ambiente , Sedimentos Geológicos , Humanos , Metales Pesados/análisis , Medición de Riesgo , Ríos , Agua , Contaminantes Químicos del Agua/análisis
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