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1.
Anal Chem ; 95(18): 7186-7194, 2023 05 09.
Artículo en Inglés | MEDLINE | ID: mdl-37103881

RESUMEN

The emergence of the coronavirus disease 2019 (COVID-19) pandemic prompted researchers to develop portable biosensing platforms, anticipating to detect the analyte in a label-free, direct, and simple manner, for deploying on site to prevent the spread of the infectious disease. Herein, we developed a facile wavelength-based SPR sensor built with the aid of a 3D printing technology and synthesized air-stable NIR-emitting perovskite nanocomposites as the light source. The simple synthesis processes for the perovskite quantum dots enabled low-cost and large-area production and good emission stability. The integration of the two technologies enabled the proposed SPR sensor to exhibit the characteristics of lightweight, compactness, and being without a plug, just fitting the requirements of on-site detection. Experimentally, the detection limit of the proposed NIR SPR biosensor for refractive index change reached the 10-6 RIU level, comparable with that of state-of-the-art portable SPR sensors. In addition, the bio-applicability of the platform was validated by incorporating a homemade high-affinity polyclonal antibody toward the SARS-CoV-2 spike protein. The results demonstrated that the proposed system was capable of discriminating between clinical swab samples collected from COVID-19 patients and healthy subjects because the used polyclonal antibody exhibited high specificity against SARS-CoV-2. Most importantly, the whole measurement process not only took less than 15 min but also needed no complex procedures or multiple reagents. We believe that the findings disclosed in this work can open an avenue in the field of on-site detection for highly pathogenic viruses.


Asunto(s)
Técnicas Biosensibles , COVID-19 , Nanocompuestos , Humanos , Resonancia por Plasmón de Superficie/métodos , SARS-CoV-2 , COVID-19/diagnóstico , Técnicas Biosensibles/métodos , Anticuerpos
2.
J Exp Bot ; 73(15): 5264-5278, 2022 09 03.
Artículo en Inglés | MEDLINE | ID: mdl-35641129

RESUMEN

Waterlogging severely affects the growth, development, and yield of crops. Accurate high-throughput phenotyping is important for exploring the dynamic crop waterlogging response in the field, and the genetic basis of waterlogging tolerance. In this study, a multi-model remote sensing phenotyping platform based on an unmanned aerial vehicle (UAV) was used to assess the genetic response of rapeseed (Brassica napus) to waterlogging, by measuring morphological traits and spectral indices over 2 years. The dynamic responses of the morphological and spectral traits indicated that the rapeseed waterlogging response was severe before the middle stage within 18 d after recovery, but it subsequently decreased partly. Genome-wide association studies identified 289 and 333 loci associated with waterlogging tolerance in 2 years. Next, 25 loci with at least nine associations with waterlogging-related traits were defined as highly reliable loci, and 13 loci were simultaneously identified by waterlogging tolerance coefficients of morphological traits, spectral indices, and common factors. Forty candidate genes were predicted in the regions of 13 overlapping loci. Our study provides insights into the understanding of the dynamic process and genetic basis of rapeseed waterlogging response in the field by a high-throughput UAV phenotyping platform. The highly reliable loci identified in this study are valuable for breeding waterlogging-tolerant rapeseed cultivars.


Asunto(s)
Brassica napus , Brassica rapa , Brassica rapa/genética , Estudio de Asociación del Genoma Completo , Fitomejoramiento , Dispositivos Aéreos No Tripulados
3.
Artículo en Inglés | MEDLINE | ID: mdl-33782006

RESUMEN

The Clinical and Laboratory Standards Institute (CLSI) revised the fluoroquinolone MIC breakpoints for Enterobacterales in 2019, based on pharmacokinetic/pharmacodynamic analyses. However, clinical evidence supporting these breakpoint revisions is limited. A retrospective study was conducted at 3 hospitals in Taiwan between January 2017 and March 2019. Patients treated with levofloxacin for bacteremia caused by members of the Enterobacterales with high MICs (1 or 2 µg/ml; levofloxacin susceptible by pre-2019 CLSI breakpoints) were compared with those with low-MIC bacteremia (≤0.5 µg/ml; levofloxacin susceptible by 2019 CLSI breakpoints) to assess therapeutic effectiveness by multivariable logistic regression. The primary outcome was 30-day mortality, and the secondary outcome was the emergence of levofloxacin-resistant isolates within 90 days after levofloxacin initiation. A total of 308 patients were eligible for the study. Kaplan-Meier analysis showed that patients infected with high-MIC isolates (n = 63) had a significantly lower survival rate than those infected with low-MIC isolates (n = 245) (P = 0.001). Multivariable logistic regression revealed that high levofloxacin MIC was a predictor of 30-day mortality (odds ratio [OR], 6.05; 95% confidence interval [CI], 1.51 to 24.18; P = 0.011). We consistently found similar results in a propensity score-matched cohort (OR, 5.38; 95% CI, 1.06 to 27.39; P = 0.043). The emergence of levofloxacin-resistant isolates was more common in the high-MIC group than the low-MIC group (25.0% versus 7.5%; P = 0.065). An estimated area under the concentration-time curve/MIC ratio of ≥87 was significantly associated with better survival (P = 0.002). In conclusion, patients infected with isolates with levofloxacin MICs within the pre-2019 CLSI susceptible range of 1 or 2 µg/ml exhibited higher mortality than those infected with isolates with MICs of ≤0.5 µg/ml.


Asunto(s)
Bacteriemia , Levofloxacino , Antibacterianos/uso terapéutico , Bacteriemia/tratamiento farmacológico , Humanos , Laboratorios , Levofloxacino/uso terapéutico , Pruebas de Sensibilidad Microbiana , Estudios Retrospectivos , Taiwán
4.
Sensors (Basel) ; 21(2)2021 Jan 19.
Artículo en Inglés | MEDLINE | ID: mdl-33477949

RESUMEN

Timely and accurate crop growth monitoring and yield estimation are important for field management. The traditional sampling method used for estimation of ramie yield is destructive. Thus, this study proposed a new method for estimating ramie yield based on field phenotypic data obtained from unmanned aerial vehicle (UAV) images. A UAV platform carrying RGB cameras was employed to collect ramie canopy images during the whole growth period. The vegetation indices (VIs), plant number, and plant height were extracted from UAV-based images, and then, these data were incorporated to establish yield estimation model. Among all of the UAV-based image data, we found that the structure features (plant number and plant height) could better reflect the ramie yield than the spectral features, and in structure features, the plant number was found to be the most useful index to monitor the yield, with a correlation coefficient of 0.6. By fusing multiple characteristic parameters, the yield estimation model based on the multiple linear regression was obviously more accurate than the stepwise linear regression model, with a determination coefficient of 0.66 and a relative root mean square error of 1.592 kg. Our study reveals that it is feasible to monitor crop growth based on UAV images and that the fusion of phenotypic data can improve the accuracy of yield estimations.


Asunto(s)
Boehmeria , Tecnología de Sensores Remotos
5.
Int J Mol Sci ; 22(2)2021 Jan 13.
Artículo en Inglés | MEDLINE | ID: mdl-33451024

RESUMEN

DC-SIGN, a C-type lectin mainly expressed in dendritic cells (DCs), has been reported to mediate several viral infections. We previously reported that DC-SIGN mediated H5N1 influenza A virus (AIVs) infection, however, the important DC-SIGN interaction with N-glycosylation sites remain unknown. This study aims to identify the optimal DC-SIGN interacting N-glycosylation sites in HA proteins of H5N1-AIVs. Results from NetNGlyc program analyzed the H5 hemagglutinin sequences of isolates during 2004-2020, revealing that seven and two conserved N-glycosylation sites were detected in HA1 and HA2 domain, respectively. A lentivirus pseudotyped A/Vietnam/1203/04 H5N1 envelope (H5N1-PVs) was generated which displayed an abundance of HA5 proteins on the virions via immuno-electron microscope observation. Further, H5N1-PVs or reverse-genetics (H5N1-RG) strains carrying a serial N-glycosylated mutation was generated by site-directed mutagenesis assay. Human recombinant DC-SIGN (rDC-SIGN) coated ELISA showed that H5N1-PVs bound to DC-SIGN, however, mutation on the N27Q, N39Q, and N181Q significantly reduced this binding (p < 0.05). Infectivity and capture assay demonstrated that N27Q and N39Q mutations significantly ameliorated DC-SIGN mediated H5N1 infection. Furthermore, combined mutations (N27Q&N39Q) significantly waned the interaction on either H5N1-PVs or -RG infection in cis and in trans (p < 0.01). This study concludes that N27 and N39 are two essential N-glycosylation contributing to DC-SIGN mediating H5N1 infection.


Asunto(s)
Moléculas de Adhesión Celular/metabolismo , Susceptibilidad a Enfermedades , Glicoproteínas Hemaglutininas del Virus de la Influenza/metabolismo , Subtipo H5N1 del Virus de la Influenza A/fisiología , Gripe Humana/inmunología , Gripe Humana/virología , Lectinas Tipo C/metabolismo , Receptores de Superficie Celular/metabolismo , Sustitución de Aminoácidos , Células Dendríticas/inmunología , Células Dendríticas/metabolismo , Glicosilación , Glicoproteínas Hemaglutininas del Virus de la Influenza/genética , Glicoproteínas Hemaglutininas del Virus de la Influenza/inmunología , Humanos , Subtipo H3N2 del Virus de la Influenza A , Subtipo H5N1 del Virus de la Influenza A/clasificación , Subtipo H5N1 del Virus de la Influenza A/genética , Subtipo H5N1 del Virus de la Influenza A/ultraestructura , Mutación , Filogenia
6.
BMC Bioinformatics ; 16: 302, 2015 Sep 21.
Artículo en Inglés | MEDLINE | ID: mdl-26390997

RESUMEN

BACKGROUND: Studies regarding coxsackievirus (CV) tend to focus on epidemic outbreaks, an imbalanced topology is considered to be an indication of acute infection with partial cross-immunity. In enteroviruses, a clear understanding of the characteristics of tree topology, transmission, and its demographic dynamics in viral succession and circulation are essential for identifying prevalence trends in endemic pathogens such as coxsackievirus B2 (CV-B2). This study applied a novel Bayesian evolutionary approach to elucidate the phylodynamic characteristics of CV-B2. A dataset containing 51 VP1 sequences and a dataset containing 34 partial 3D(pol) sequencing were analyzed, where each dataset included Taiwan sequences isolated during 1988-2013. RESULTS: Four and five genotypes were determined based on the 846-nucleotide VP1 and 441-nucleotide 3D(pol) (6641-7087) regions, respectively, with spatiotemporally structured topologies in both trees. Some strains with tree discordance indicated the occurrence of recombination in the region between the VP1 and 3D(pol) genes. The similarities of VP1 and 3D(pol) gene were 80.0%-96.8% and 74.7%-91.9%, respectively. Analyses of population dynamics using VP1 dataset indicated that the endemic CV-B2 has a small effective population size. The balance indices, high similarity, and low evolutionary rate in the VP1 region indicated mild herd immunity selection in the major capsid region. CONCLUSIONS: Phylodynamic analysis can reveal demographic trends and herd immunity in endemic pathogens.


Asunto(s)
Infecciones por Coxsackievirus/transmisión , Infecciones por Coxsackievirus/virología , Demografía , Enterovirus/fisiología , Filogenia , Teorema de Bayes , Niño , Preescolar , Infecciones por Coxsackievirus/epidemiología , Brotes de Enfermedades , Enterovirus/aislamiento & purificación , Genotipo , Humanos , Lactante , Filogeografía , ARN Viral/genética , Taiwán/epidemiología , Proteínas Virales/genética
7.
Clin Lab ; 60(11): 1895-901, 2014.
Artículo en Inglés | MEDLINE | ID: mdl-25648032

RESUMEN

BACKGROUND: Because of the high cost of commercially available quantitative PCR kits, we developed a beacon- based real-time PCR (B-rt-PCR) for Cytomegalovirus (CMV) viral load determination. METHODS: A total of 197 samples from 60 immunocompromised patients, who were bone marrow transplantation recipients or had hematological malignancies, were tested using B-rt-PCR, COBAS Amplicor CMV Monitor test (Amplicor CMV test), and conventional CMV PCR. The correlation results among these 3 assays were calculated. RESULTS: In these 197 samples, the CMV viral load determined by B-rt-PCR for positive specimens ranged from 19.8 to 4148.7 copies/10(5) peripheral blood mononuclear cells (PBMCs). When any positive result of B-rt-PCR, the Amplicor CMV test, or conventional PCR was considered as "CMV positive" for the 56 specimens tested by all three methods, we found that the positive and negative predictive values, respectively, were 100% and 98.6% for B-rt-PCR, 100% and 46.2% for the Amplicor CMV test, and 100% and 89.4% for conventional PCR. These three methods had good specificity (all 100%). However, the sensitivity rate of B-rt-PCR (96.3%) was higher compared to the Amplicor CMV test (46.2%) and conventional PCR (89.4%). CONCLUSIONS: The B-rt-PCR is evaluated to be a sensitive method for CMV detection in immunocompromised patients.


Asunto(s)
Infecciones por Citomegalovirus/diagnóstico , Citomegalovirus/genética , ADN Viral/genética , Huésped Inmunocomprometido , Reacción en Cadena en Tiempo Real de la Polimerasa , Infecciones por Citomegalovirus/inmunología , Infecciones por Citomegalovirus/virología , Humanos , Valor Predictivo de las Pruebas , Reproducibilidad de los Resultados , Estudios Retrospectivos , Carga Viral
8.
Front Pharmacol ; 14: 1237234, 2023.
Artículo en Inglés | MEDLINE | ID: mdl-37614310

RESUMEN

Background: Janus kinase (JAK) inhibitors have emerged as a progressively utilized therapeutic approach for the management of rheumatoid arthritis (RA). However, the complete determination of their cardiovascular safety remains inconclusive. Hence, the primary objective of this network meta-analysis is to meticulously assess and juxtapose the cardiovascular risks linked to distinct JAK inhibitors employed in RA patients. Methods: A systematic review and network meta-analysis were meticulously conducted, encompassing a collection of randomized controlled trials (RCTs) that focused on investigating the incidence of major adverse cardiovascular events (MACE) and all-cause mortality associated with Janus kinase (JAK) inhibitors administered to patients with rheumatoid arthritis (RA). Extensive exploration was performed across multiple electronic databases, incorporating studies published until March 2023. To be included in this analysis, the RCTs were required to involve adult participants diagnosed with RA who received treatment with JAK inhibitors. To ensure accuracy, two authors independently undertook the selection of eligible RCTs and meticulously extracted aggregate data. In order to examine the outcomes of MACE and all-cause mortality, a frequentist graph theoretical approach within network meta-analyses was employed, utilizing random-effects models. Third study has been registered on PROSPERO under the reference CRD42022384611. Findings: A specific selection encompassing a total of 14 meticulously chosen randomized controlled trials was undertaken, wherein 13,524 patients were assigned randomly to distinct treatment interventions. The analysis revealed no notable disparity in the occurrence of major adverse cardiovascular events (MACE) between the interventions and the placebo group. However, in comparison to adalimumab, the employment of JAK inhibitors exhibited an association with higher rates of all-cause mortality [odds ratio (OR): 1.7, 95% confidence interval (CI): 1.02-2.81]. This observed increase in risk primarily stemmed from the usage of tofacitinib (OR: 1.9, 95% CI: 1.12-3.23). None of the other JAK inhibitors exhibited a statistically significant variance in all-cause mortality when compared to adalimumab. Interpretation: Our study suggests that JAK inhibitors may not increase the risk of MACE in RA patients but may be associated with a higher risk of all-cause mortality compared to adalimumab, primarily due to tofacitinib use. Rheumatologists should carefully consider the cardiovascular risks when prescribing JAK inhibitors, particularly tofacitinib, for RA patients. Systematic Review Registration: https://www.crd.york.ac.uk/PROSPERO/display_record.php?RecordID=384611, CRD42022384611.

9.
IEEE Trans Vis Comput Graph ; 28(1): 718-726, 2022 01.
Artículo en Inglés | MEDLINE | ID: mdl-34587088

RESUMEN

One of the fundamental tasks in visualization is to compare two or more visual elements. However, it is often difficult to visually differentiate graphical elements encoding a small difference in value, such as the heights of similar bars in bar chart or angles of similar sections in pie chart. Perceptual laws can be used in order to model when and how we perceive this difference. In this work, we model the perception of Just Noticeable Differences (JNDs), the minimum difference in visual attributes that allow faithfully comparing similar elements, in charts. Specifically, we explore the relation between JNDs and two major visual variables: the intensity of visual elements and the distance between them, and study it in three charts: bar chart, pie chart and bubble chart. Through an empirical study, we identify main effects on JND for distance in bar charts, intensity in pie charts, and both distance and intensity in bubble charts. By fitting a linear mixed effects model, we model JND and find that JND grows as the exponential function of variables. We highlight several usage scenarios that make use of the JND modeling in which elements below the fitted JND are detected and enhanced with secondary visual cues for better discrimination.

10.
Virus Genes ; 42(2): 178-88, 2011 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-21369829

RESUMEN

To investigate the molecular epidemiology of Taiwanese Echovirus 30 (E-30) strains, we analyzed the 876 bp sequence of the VP1 gene from 32 Taiwanese strains isolated in 1988-2008, 498 reference sequences, and one Echovirus 21 strain as the out-group. Phylogenetic analysis detected six E-30 genotypes (designated GI-GVI) that had circulated globally during the past five decades. The genotypes varied widely in geographic distribution and circulation half-life. The GI, GII, and GV were ancient genotypes in which the first strains emerged in the 1950s. The GIII was a reemerging genotype, in which strains had first appeared in Colombia in 1995 before reemerging in the New Independent States (NIS) in 2003. The GIV, an emerging genotype that recently appeared in Asia in 2003, was closely related to the ancient genotypes. The GVI was the circulating genotype, which included eight clusters (A-H) that had circulated since 1967. No GVI-A, C, D, or E strains have been identified during the past 10 years. The GVI-B first appeared in China in 1984 and later in Russia and Asia in the 2000s. The GVI-F, G, and H strains, which comprised the prevalent clusters, had been dominant in Asia Pacific area, globally, and Europe, respectively. Taiwanese strains were classified into GVI-D (1988-1989), GVI-F (1993-2004), and GVI-G (1993-2008). The quiescence period of E-30 is longer in Taiwan (5-8 years) than in other countries (3-5 years).


Asunto(s)
Infecciones por Echovirus/epidemiología , Enterovirus Humano B/genética , Secuencia de Aminoácidos , Sustitución de Aminoácidos , Niño , Preescolar , Femenino , Genes Virales , Humanos , Masculino , Epidemiología Molecular , Datos de Secuencia Molecular , Filogenia , ARN Viral/genética , Taiwán/epidemiología
11.
Biomedicines ; 10(1)2021 Dec 30.
Artículo en Inglés | MEDLINE | ID: mdl-35052750

RESUMEN

The isolation of a virus using cell culture to observe its cytopathic effects (CPEs) is the main method for identifying the viruses in clinical specimens. However, the observation of CPEs requires experienced inspectors and excessive time to inspect the cell morphology changes. In this study, we utilized artificial intelligence (AI) to improve the efficiency of virus identification. After some comparisons, we used ResNet-50 as a backbone with single and multi-task learning models to perform deep learning on the CPEs induced by influenza, enterovirus, and parainfluenza. The accuracies of the single and multi-task learning models were 97.78% and 98.25%, respectively. In addition, the multi-task learning model increased the accuracy of the single model from 95.79% to 97.13% when only a few data of the CPEs induced by parainfluenza were provided. We modified both models by inserting a multiplexer and de-multiplexer layer, respectively, to increase the correct rates for known cell lines. In conclusion, we provide a deep learning structure with ResNet-50 and the multi-task learning model and show an excellent performance in identifying virus-induced CPEs.

12.
J Int Med Res ; 48(8): 300060520936415, 2020 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-32762484

RESUMEN

OBJECTIVE: To investigate if hydrogen-rich saline (HRS), which has been shown to have antioxidant and anti-inflammatory properties, could mitigate cardiac remodelling and reduce the incidence of atrial fibrillation (AF) in the rat model of cardiac hypertrophy. METHODS: Pressure overload was induced in rats by abdominal aortic constriction (AAC). The animals were separated into four groups: sham; AAC group; AAC plus low dose HRS (LHRS); AAC plus high dose HRS (HHRS). The sham and AAC groups received normal saline intraperitoneally and the LHRS and HHRS groups received 3 or 6 ml/kg HRS daily for six weeks, respectively. In vitro research was also performed using cardiotrophin-1 (CT-1)-induced hypertrophy of cultured neonatal rat cardiomyocytes. RESULTS: Cardiac hypertrophy was successfully induced by AAC and low and high dose HRS mitigated the pressure overload as shown by lower heart and atrial weights in these treatment groups. AF incidence and duration of the HRS groups were also significantly lower in the HRS groups compared with the AAC group. Atrial fibrosis was also reduced in the HRS groups and the JAK-STAT signalling pathway was down-regulated. In vitro experiments showed that hydrogen-rich medium mitigated the CT-1-induced cardiomyocyte hypertrophy with a similar effect as the JAK specific antagonists AG490. CONCLUSIONS: HRS was found to mitigate cardiac hypertrophy induced by pressure overload in rats and reduce atrial fibrosis and AF which was possibly achieved via inhibition of the JAK-STAT signalling pathway.


Asunto(s)
Fibrilación Atrial , Animales , Fibrilación Atrial/tratamiento farmacológico , Cardiomegalia/tratamiento farmacológico , Cardiomegalia/etiología , Modelos Animales de Enfermedad , Hidrógeno , Miocitos Cardíacos , Ratas , Ratas Sprague-Dawley , Solución Salina
13.
Diagnostics (Basel) ; 10(5)2020 May 21.
Artículo en Inglés | MEDLINE | ID: mdl-32455796

RESUMEN

Coronavirus disease 2019 (COVID-19), the current uncontrolled outbreak of infectious disease, has caused significant challenges throughout the world. A reliable rapid diagnostic test for COVID-19 is demanded worldwide. The real-time reverse transcriptase polymerase chain was one of the most quickly established methods in the novel viral pandemic and was considered as the gold standard for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this report, we illustrate our experience of applying a protocol from the Taiwan CDC and achieving assay optimization in the immediate circumstances to meet the urgent medical and public health needs.

14.
Medicine (Baltimore) ; 99(46): e22773, 2020 Nov 13.
Artículo en Inglés | MEDLINE | ID: mdl-33181649

RESUMEN

Nasopharyngeal carcinoma (NPC) has a distinctive geographical distribution in China, especially southern China. There are several risk factors for NPC, such as Epstein-Barr virus, genetics, and environmental exposures. Although the incidence of eye metastasis (EM) is lower than metastasis in other body parts, it often indicates poor prognosis.We assessed several serum biomarkers for their ability to predict EM in NPC. Patients with NPC were selected (n = 963), and were separated into two groups, EM and no eye metastasis. Ten factors were analyzed in both groups including triglyceride (TG), high-density lipoprotein, low-density lipoprotein, alkaline phosphatase, alpha fetoprotein, carbohydrate antigen-199, cancer antigen-153, apolipoproteins AI, apolipoprotein B, and cytokeratin fragment 19 (CYFRA21-1). Independent t tests, binary logistic regression, and receiver operating characteristic curves were used to assess the data.The EM group had significantly higher CYFRA21-1 and lower TG compared with the no eye metastasis group. Areas under the curve for CYFRA21-1, TG and CYFRA21-1/TG were 0.966, 0.771, and 0.976, respectively. The corresponding cut-off values were 12.12 ng/ml, 0.41 mmol/L, and 13.5. The sensitivity and specificity of CYFRA21-1/TG were 100% and 92.2%, respectively.The increased ratio of CYFRA21-1 to TG can be an accurate method to detect EM in patients with NPC.


Asunto(s)
Antígenos de Neoplasias/análisis , Neoplasias del Ojo/etiología , Queratina-19/análisis , Neoplasias Nasofaríngeas/genética , Metástasis de la Neoplasia/diagnóstico , Tiroglobulina/análisis , Adulto , Antígenos de Neoplasias/sangre , Biomarcadores de Tumor/análisis , China/epidemiología , Neoplasias del Ojo/epidemiología , Neoplasias del Ojo/genética , Femenino , Humanos , Queratina-19/sangre , Modelos Logísticos , Masculino , Persona de Mediana Edad , Neoplasias Nasofaríngeas/epidemiología , Metástasis de la Neoplasia/diagnóstico por imagen , Metástasis de la Neoplasia/fisiopatología , Factores de Riesgo , Sensibilidad y Especificidad , Tiroglobulina/sangre
15.
Dis Markers ; 2020: 8850873, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-33376560

RESUMEN

PURPOSE: Liver metastasis is the final stage of cancer progression and is associated with poor prognosis. Although numerous indicators have been identified as having prognostic value for lung cancer and liver metastasis, liver metastases are still not diagnosed by imaging in many patients. To provide a more accurate method for clinical prediction of liver metastasis, we analyzed multiple factors to identify potential predictive factors for liver metastasis of lung cancer. METHODS: Patients first diagnosed with lung cancer between 2002 and 2016 (n = 1746) were divided into two groups, with and without liver metastasis. Serum concentrations of calcium, carcinoembryonic antigen (CEA), cancer antigen-125 (CA125), cancer antigen-153 (CA153), carbohydrate antigen-199 (CA199), cytokeratin fraction 21-1 (CYFRA21-1), total prostate-specific antigen (TPSA), and neuron-specific enolase (NSE) were analyzed in both patient groups. RESULTS: There was no significant difference in age or sex between the two groups. CA125 and NSE were significantly associated with liver metastasis. Compared with CA125, NSE was more specific, while it was less sensitive (P < 0.001). Further analysis of NSE concentrations was conducted in patients with non-small-cell lung cancer and indicated that NSE concentration differed significantly between those with and without liver metastasis (P = 0.023). We conducted analysis with NSE and CA125 combined, resulting in acceptable sensitivity (51.2%), specificity (72.6%), and area under the curve (0.64) values; sensitivity and area under the curve values were higher than those for individual factors, while specificity was higher than that for CA125. CONCLUSIONS: The combination of CA125 and NSE can assist prediction of liver metastasis of lung cancer, providing improved diagnostic accuracy.


Asunto(s)
Biomarcadores de Tumor/sangre , Antígeno Ca-125/sangre , Neoplasias Hepáticas/diagnóstico , Neoplasias Hepáticas/secundario , Neoplasias Pulmonares/patología , Fosfopiruvato Hidratasa/sangre , Anciano , Antígenos de Neoplasias/sangre , Antígeno Carcinoembrionario/sangre , Femenino , Proteínas Ligadas a GPI/sangre , Humanos , Queratina-19/sangre , Masculino , Persona de Mediana Edad , Pronóstico
16.
Front Plant Sci ; 11: 617, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-32587594

RESUMEN

Rapeseed is an important oil crop in China. Timely estimation of rapeseed stand count at early growth stages provides useful information for precision fertilization, irrigation, and yield prediction. Based on the nature of rapeseed, the number of tillering leaves is strongly related to its growth stages. However, no field study has been reported on estimating rapeseed stand count by the number of leaves recognized with convolutional neural networks (CNNs) in unmanned aerial vehicle (UAV) imagery. The objectives of this study were to provide a case for rapeseed stand counting with reference to the existing knowledge of the number of leaves per plant and to determine the optimal timing for counting after rapeseed emergence at leaf development stages with one to seven leaves. A CNN model was developed to recognize leaves in UAV-based imagery, and rapeseed stand count was estimated with the number of recognized leaves. The performance of leaf detection was compared using sample sizes of 16, 24, 32, 40, and 48 pixels. Leaf overcounting occurred when a leaf was much bigger than others as this bigger leaf was recognized as several smaller leaves. Results showed CNN-based leaf count achieved the best performance at the four- to six-leaf stage with F-scores greater than 90% after calibration with overcounting rate. On average, 806 out of 812 plants were correctly estimated on 53 days after planting (DAP) at the four- to six-leaf stage, which was considered as the optimal observation timing. For the 32-pixel patch size, root mean square error (RMSE) was 9 plants with relative RMSE (rRMSE) of 2.22% on 53 DAP, while the mean RMSE was 12 with mean rRMSE of 2.89% for all patch sizes. A sample size of 32 pixels was suggested to be optimal accounting for balancing performance and efficiency. The results of this study confirmed that it was feasible to estimate rapeseed stand count in field automatically, rapidly, and accurately. This study provided a special perspective in phenotyping and cultivation management for estimating seedling count for crops that have recognizable leaves at their early growth stage, such as soybean and potato.

17.
Sci Rep ; 8(1): 8821, 2018 06 11.
Artículo en Inglés | MEDLINE | ID: mdl-29891869

RESUMEN

Coxsackievirus (CV)-B5 is a common human enterovirus reported worldwide; swine vesicular disease virus (SVDV) is a porcine variant of CV-B5. To clarify the transmission dynamics and molecular basis of host switching between CV-B5 and SVDV, we analysed and compared the VP1 and partial 3Dpol gene regions of these two viruses. Spatiotemporal dynamics of viral transmission were estimated using a Bayesian statistical inference framework. The detected selection events were used to analyse the key molecules associated with host switching. Analyses of VP1 sequences revealed six CV-B5 genotypes (A1-A4 and B1-B2) and three SVDV genotypes (I-III). Analyses of partial 3Dpol revealed five clusters (A-E). The genotypes evolved sequentially over different periods, albeit with some overlap. The major hub of CV-B5 transmission was in China whereas the major hubs of SVDV transmission were in Italy. Network analysis based on deduced amino acid sequences showed a diverse extension of the VP1 structural protein, whereas most sequences were clustered into two haplotypes in the partial 3Dpol region. Residue 178 of VP1 showed four epistatic interactions with residues known to play essential roles in viral host tropism, cell entry, and viral decoating.


Asunto(s)
Infecciones por Coxsackievirus/veterinaria , Infecciones por Coxsackievirus/virología , Enterovirus Humano B/clasificación , Enterovirus Humano B/genética , Evolución Molecular , Animales , Proteínas de la Cápside/genética , China/epidemiología , Análisis por Conglomerados , Infecciones por Coxsackievirus/epidemiología , ARN Polimerasas Dirigidas por ADN/genética , Enterovirus Humano B/aislamiento & purificación , Variación Genética , Genotipo , Humanos , Italia/epidemiología , Filogenia , Análisis de Secuencia de ADN , Análisis Espacio-Temporal , Porcinos , Enfermedades de los Porcinos/epidemiología , Enfermedades de los Porcinos/virología , Proteínas Virales/genética
18.
PLoS One ; 11(8): e0160672, 2016.
Artículo en Inglés | MEDLINE | ID: mdl-27529556

RESUMEN

Recent phylodynamic studies have focused on using tree topology patterns to elucidate interactions among the epidemiological, evolutionary, and demographic characteristics of infectious agents. However, because studies of viral phylodynamics tend to focus on epidemic outbreaks, tree topology signatures of tissue-tropism pathogens might not be clearly identified. Therefore, this study used a novel Bayesian evolutionary approach to analyze the A24 variant of coxsackievirus (CV-A24v), an ocular-tropism agent of acute hemorrhagic conjunctivitis. Analyses of the 915-nucleotide VP1 and 690-nt 3Dpol regions of 21 strains isolated in Taiwan and worldwide during 1985-2010 revealed a clear chronological trend in both the VP1 and 3Dpol phylogenetic trees: the emergence of a single dominant cluster in each outbreak. The VP1 sequences included three genotypes: GI (prototype), GIII (isolated 1985-1999), and GIV (isolated after 2000); no VP1 sequences from GII strains have been deposited in GenBank. Another five genotypes identified in the 3Dpol region had support values >0.9. Geographic and demographic transitions among CV-A24v clusters were clearly identified by Bayes algorithm. The transmission route was mapped from India to China and then to Taiwan, and each prevalent viral population declined before new clusters emerged. Notably, the VP1 and 3Dpol genes had high nucleotide sequence similarities (94.1% and 95.2%, respectively). The lack of co-circulating lineages and narrow tissue tropism affected the CV-A24v gene pool.


Asunto(s)
Enterovirus Humano C/fisiología , Filogenia , Tropismo Viral , Secuencia de Bases , Teorema de Bayes , Proteínas de la Cápside/genética , Enterovirus Humano C/genética , Evolución Molecular , Genotipo , Método de Montecarlo , Análisis Espacio-Temporal
19.
PLoS One ; 10(5): e0127377, 2015.
Artículo en Inglés | MEDLINE | ID: mdl-25992619

RESUMEN

An outbreak of adenovirus has been surveyed in Taiwan in 2011. To better understand the evolution and epidemiology of adenovirus in Taiwan, full-length sequence of hexon and fiber coapsid protein was analyzed using series of phylogenetic and dynamic evolution tools. Six different serotypes were identified in this outbreak and the species B was predominant (HAdV-3, 71.50%; HAdV-7, 15.46%). The most frequent diagnosis was acute tonsillitis (54.59%) and bronchitis (47.83%). Phylogenetic analysis revealed that hexon protein gene sequences were highly conserved for HAdV-3 and HAdV-7 circulation in Taiwan. However, comparison of restriction fragment length polymorphism (RFLP) analysis and phylogenetic trees of fiber gene in HAdV-7 clearly indicated that the predominant genotype in Taiwan has shifted from 7b to 7d. Several positive selection sites were observed in hexon protein. The estimated nucleotide substitution rates of hexon protein of HAdV-3 and HAdV-7 were 0.234×10-3 substitutions/site/year (95% HPD: 0.387~0.095×10-3) and 1.107×10-3 (95% HPD: 0. 541~1.604) respectively; those of the fiber protein of HAdV-3 and HAdV-7 were 1.085×10-3 (95% HPD: 1.767~0.486) and 0.132×10-3 (95% HPD: 0.283~0.014) respectively. Phylodynamic analysis by Bayesian skyline plot (BSP) suggested that using individual gene to evaluate the effective population size might possibly cause miscalculation. In summary, the virus evolution is ongoing, and continuous surveillance of this virus evolution will contribute to the control of the epidemic.


Asunto(s)
Infecciones por Adenovirus Humanos/virología , Adenovirus Humanos/clasificación , Bronquitis/epidemiología , Proteínas de la Cápside/genética , Tonsilitis/epidemiología , Infecciones por Adenovirus Humanos/epidemiología , Adenovirus Humanos/genética , Bronquitis/virología , Niño , Preescolar , Brotes de Enfermedades , Femenino , Genoma Viral , Humanos , Lactante , Masculino , Tasa de Mutación , Filogenia , Estudios Retrospectivos , Taiwán/epidemiología , Tonsilitis/virología
20.
PLoS One ; 10(6): e0129272, 2015.
Artículo en Inglés | MEDLINE | ID: mdl-26053872

RESUMEN

The infectious activity of coxsackievirus B1 (CV-B1) in Taiwan was high from 2008 to 2010, following an alarming increase in severe neonate disease in the United States (US). To examine the relationship between CV-B1 strains isolated in Taiwan and those from other parts of the world, we performed a phylodynamic study using VP1 and partial 3Dpol (414 nt) sequences from 22 strains of CV-B1 isolated in Taiwan (1989-2010) and compared them to sequences from strains isolated worldwide. Phylogenetic trees were constructed by neighbor-joining, maximum likelihood, and Bayesian Monte Carlo Markov Chain methods. Four genotypes (GI-IV) in the VP1 region of CV-B1 and three genotypes (GA-C) in the 3Dpol region of enterovirus B were identified and had high support values. The phylogenetic analysis indicates that the GI and GIII strains in VP1 were geographically distributed in Taiwan (1993-1994) and in India (2007-2009). On the other hand, the GII and GIV strains appear to have a wider spatiotemporal distribution and ladder-like topology A stair-like phylogeny was observed in the VP1 region indicating that the phylogeny of the virus may be affected by different selection pressures in the specified regions. Further, most of the GI and GII strains in the VP1 tree were clustered together in GA in the 3D tree, while the GIV strains diverged into GB and GC. Taken together, these data provide important insights into the population dynamics of CV-B1 and indicate that incongruencies in specific gene regions may contribute to spatiotemporal patterns of epidemicity for this virus.


Asunto(s)
Infecciones por Coxsackievirus/transmisión , Infecciones por Coxsackievirus/virología , Enterovirus Humano B/fisiología , Infecciones por Coxsackievirus/epidemiología , Enterovirus Humano B/clasificación , Variación Genética , Genotipo , Humanos , Tipificación de Secuencias Multilocus , Filogenia , Vigilancia de la Población , ARN Viral , Recombinación Genética , Taiwán/epidemiología
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