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1.
BMC Bioinformatics ; 22(1): 170, 2021 Mar 31.
Artículo en Inglés | MEDLINE | ID: mdl-33789571

RESUMEN

BACKGROUND: The most common measure of association between two continuous variables is the Pearson correlation (Maronna et al. in Safari an OMC. Robust statistics, 2019. https://login.proxy.bib.uottawa.ca/login?url=https://learning.oreilly.com/library/view/-/9781119214687/?ar&orpq&email=^u). When outliers are present, Pearson does not accurately measure association and robust measures are needed. This article introduces three new robust measures of correlation: Taba (T), TabWil (TW), and TabWil rank (TWR). The correlation estimators T and TW measure a linear association between two continuous or ordinal variables; whereas TWR measures a monotonic association. The robustness of these proposed measures in comparison with Pearson (P), Spearman (S), Quadrant (Q), Median (M), and Minimum Covariance Determinant (MCD) are examined through simulation. Taba distance is used to analyze genes, and statistical tests were used to identify those genes most significantly associated with Williams Syndrome (WS). RESULTS: Based on the root mean square error (RMSE) and bias, the three proposed correlation measures are highly competitive when compared to classical measures such as P and S as well as robust measures such as Q, M, and MCD. Our findings indicate TBL2 was the most significant gene among patients diagnosed with WS and had the most significant reduction in gene expression level when compared with control (P value = 6.37E-05). CONCLUSIONS: Overall, when the distribution is bivariate Log-Normal or bivariate Weibull, TWR performs best in terms of bias and T performs best with respect to RMSE. Under the Normal distribution, MCD performs well with respect to bias and RMSE; but TW, TWR, T, S, and P correlations were in close proximity. The identification of TBL2 may serve as a diagnostic tool for WS patients. A Taba R package has been developed and is available for use to perform all necessary computations for the proposed methods.


Asunto(s)
Correlación de Datos , Simulación por Computador , Humanos
2.
Int J Mol Sci ; 22(5)2021 Mar 05.
Artículo en Inglés | MEDLINE | ID: mdl-33807854

RESUMEN

We observed substantial differences in predicted Major Histocompatibility Complex II (MHCII) epitope presentation of SARS-CoV-2 proteins for different populations but only minor differences in predicted MHCI epitope presentation. A comparison of this predicted epitope MHC-coverage revealed for the early phase of infection spread (till day 15 after reaching 128 observed infection cases) highly significant negative correlations with the case fatality rate. Specifically, this was observed in different populations for MHC class II presentation of the viral spike protein (p-value: 0.0733 for linear regression), the envelope protein (p-value: 0.023), and the membrane protein (p-value: 0.00053), indicating that the high case fatality rates of COVID-19 observed in some countries seem to be related with poor MHC class II presentation and hence weak adaptive immune response against these viral envelope proteins. Our results highlight the general importance of the SARS-CoV-2 structural proteins in immunological control in early infection spread looking at a global census in various countries and taking case fatality rate into account. Other factors such as health system and control measures become more important after the early spread. Our study should encourage further studies on MHCII alleles as potential risk factors in COVID-19 including assessment of local populations and specific allele distributions.


Asunto(s)
/mortalidad , Antígenos de Histocompatibilidad Clase II/genética , Antígenos de Histocompatibilidad Clase II/inmunología , Proteínas Estructurales Virales/química , Inmunidad Adaptativa , Alelos , /transmisión , Biología Computacional/métodos , Correlación de Datos , Epítopos de Linfocito B/genética , Epítopos de Linfocito B/inmunología , Epítopos de Linfocito T/genética , Epítopos de Linfocito T/inmunología , Antígenos HLA/genética , Antígenos de Histocompatibilidad Clase I/genética , Antígenos de Histocompatibilidad Clase I/inmunología , Humanos , Mortalidad , Proteínas Estructurales Virales/inmunología
3.
Acta Med Indones ; 53(1): 13-17, 2021 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-33818402

RESUMEN

BACKGROUND: real-time RT-PCR was recommended by WHO for COVID-19 diagnosis. The cycle threshold (Ct) values were expected to have an association with clinical manifestation. However, the diagnostic modalities such as quantitative molecular detection and virus isolation were not yet available for the routine test. This study has been conducted to analyze the relationship between the Ct values of qualitative rRT-PCR and the clinical manifestation and to describe the factors determining the result. METHODS: from March to April 2020, specimens were sent to our laboratory from different healthcare centers in Jakarta. The patient's characteristic and clinical manifestation were extracted from the specimen's epidemiology forms. The specimens extracted and tested using rRT-PCR, and the Ct value were collected. The data were analyzed using the appropriate statistic test. RESULTS: from 339 positive results, the mild to moderate case was 176 (52%) and the severe cases was 163 (48%). Female was dominant in the mild to moderate cases (58%), while the male was prevalent in the severe cases (60%). The median age for mild to moderate case was 35 years old and severe cases was 49 years old. Statistical analysis found relationship between both group with gender (p = 0.001) and age (p < 0.001), but not with the Ct value. CONCLUSION: many variables in specimen sampling and processing could affect the Ct value result. In addition, the disease's severity was depended with the host immune response, regardless the number of virus. There was suggested no significant difference between the Ct values of mild-moderate and severe COVID-19, and thus should not be loosely interpreted.


Asunto(s)
Reacción en Cadena en Tiempo Real de la Polimerasa , Evaluación de Síntomas , Adulto , Factores de Edad , /epidemiología , /métodos , /estadística & datos numéricos , Correlación de Datos , Femenino , Humanos , Indonesia/epidemiología , Masculino , Persona de Mediana Edad , Variaciones Dependientes del Observador , Reacción en Cadena en Tiempo Real de la Polimerasa/métodos , Reacción en Cadena en Tiempo Real de la Polimerasa/estadística & datos numéricos , Reproducibilidad de los Resultados , Índice de Severidad de la Enfermedad , Factores Sexuales , Evaluación de Síntomas/métodos , Evaluación de Síntomas/estadística & datos numéricos , Carga Viral
4.
Medicine (Baltimore) ; 100(15): e25553, 2021 Apr 16.
Artículo en Inglés | MEDLINE | ID: mdl-33847684

RESUMEN

BACKGROUND: Acute myocardial infarction (AMI) is a common disease leading threat to human health around the world. Here we aimed to explore new biomarkers and potential therapeutic targets in AMI through adopting integrated bioinformatics tools. METHODS: The gene expression Omnibus (GEO) database was used to obtain genes data of AMI and no-AMI whole blood. Furthermore, differentially expressed genes (DEGs) were screened using the "Limma" package in R 3.6.1 software. Functional and pathway enrichment analyses of DEGs were performed via "Bioconductor" and "GOplot" package in R 3.6.1 software. In order to screen hub DEGs, the STRING version 11.0 database, Cytoscape and molecular complex detection (MCODE) were applied. Correlation among the hub DEGs was evaluated using Pearson's correlation analysis. RESULTS: By performing DEGs analysis, 289 upregulated and 62 downregulated DEGs were successfully identified from GSE66360, respectively. And they were mainly enriched in the terms of neutrophil activation, immune response, cytokine, nuclear factor kappa-B (NF-κB) signaling pathway, IL-17 signaling pathway, and tumor necrosis factor (TNF) signaling pathway. Based on the data of protein-protein interaction (PPI), the top 10 hub genes were ranked, including interleukin-8 (CXCL8), TNF, N-formyl peptide receptor 2 (FPR2), growth-regulated alpha protein (CXCL1), transcription factor AP-1 (JUN), interleukin-1 beta (IL1B), platelet basic protein (PPBP), matrix metalloproteinase-9 (MMP9), toll-like receptor 2 (TLR2), and high affinity immunoglobulin epsilon receptor subunit gamma (FCER1G). What's more, the results of correlation analysis demonstrated that there was positive correlation between the 10 hub DEGs. CONCLUSION: Ten DEGs were identified as potential candidate diagnostic biomarkers for patients with AMI in present study. However, further experiments are needed to confirm the functional pathways and hub genes associated with AMI.


Asunto(s)
Biología Computacional/métodos , Perfilación de la Expresión Génica/métodos , Infarto del Miocardio/genética , Biomarcadores/análisis , Correlación de Datos , Citocinas/metabolismo , Bases de Datos Genéticas , Humanos , Inmunidad/genética , Activación Neutrófila/genética , Mapas de Interacción de Proteínas/genética , Transducción de Señal/genética
5.
Zhongguo Zhong Yao Za Zhi ; 46(5): 1134-1140, 2021 Mar.
Artículo en Chino | MEDLINE | ID: mdl-33787107

RESUMEN

To establish the method for determining non-volatile ingredients of neochlorogenic acid, chlorogenic acid, cryptochlorogenic acid, caffeic acid, isochlorogenic acid A, rosmarinic acid, ferulic acid, rutin, luteoloside, isoquercitrin, hesperidin, diosmin, diosmetin, luteolin, acacetin and linarin in Menthae Haplocalycis Herba formula granules and traditional herbal pieces by UPLC-MS/MS, and analyze the correlation of non-volatile ingredients in Menthae Haplocalycis Herba formula granules and traditional herbal pieces. Shim-pack GIST C_(18) column(2.1 mm×100 mm, 2 µm) was adopted with acetonitrile-0.1% formic acid aqueous solution as the mobile phase for gradient elution at the flow rate of 0.4 mL·min~(-1). The column temperature was set at 35 ℃. The quantitative analysis was performed using the electrospray ionization source and the multiple reaction monitoring. The linear relationship, resolution, repeatability and recovery of the 16 chemical components all met the requirements. The 16 non-volatile ingredients in traditional herbal pieces of Menthae Haplocalycis Herba could be tracked in formula granules. There were certain differences of the 16 chemical components among Menthae Haplocalycis Herba formula granules of different manufacturers and traditional herbal pieces of different producing areas. The UPLC-MS/MS method was simple, rapid and accurate, and could be used for the quality control of non-volatile ingredients in Menthae Haplocalycis Herba formula granules and traditional herbal pieces.


Asunto(s)
Medicamentos Herbarios Chinos , Espectrometría de Masas en Tándem , Cromatografía Líquida de Alta Presión , Cromatografía Liquida , Correlación de Datos
6.
JAMA Netw Open ; 4(3): e214117, 2021 03 01.
Artículo en Inglés | MEDLINE | ID: mdl-33739433

RESUMEN

Importance: Deficient (ie, <20 ng/mL) or insufficient (ie, 20 to <30 ng/mL) 25-hydroxyvitamin D (also known as calcifediol) levels are more common in Black individuals than White individuals and are associated with increased coronavirus disease 2019 (COVID-19) risk. Whether COVID-19 risk is associated with differences in vitamin D levels of 30 ng/mL or greater is not known. Objective: To examine whether COVID-19 test results are associated with differences in vitamin D levels of 30 ng/mL or greater, including for White individuals and for Black individuals. Design, Setting, and Participants: This retrospective cohort study was conducted at an academic medical center in Chicago, Illinois. Participants included individuals with data on vitamin D level within 365 days before COVID-19 testing, which was conducted from March 3 to December 30, 2020. Data were analyzed from September 11, 2020, to February 5, 2021. Exposures: The last vitamin D level before COVID-19 testing was categorized as less than 20 ng/mL (ie, deficient), 20 to less than 30 ng/mL (ie, insufficient), 30 to less than 40 ng/mL, or 40 ng/mL or greater. Treatment was defined by vitamin D type and dose 14 days before COVID-19 testing and treatment changes after last vitamin D level. Main Outcomes and Measures: The main outcome was a positive result for COVID-19 in polymerase chain reaction testing. Multivariable analyses tested whether previously measured vitamin D level was associated with having test results positive for COVID-19 in White individuals and in Black individuals, controlling for months and treatment changes since the vitamin D level was measured, as well as demographic characteristics and comorbidity indicators. Results: A total of 4638 individuals (mean [SD] age 52.8 [19.5] years; 3205 [69%] women) had data for a vitamin D level within 1 year before COVID-19 testing, including 2288 (49%) Black individuals, 1999 (43%) White individuals, and 351 individuals (8%) who were another race/ethnicity (eg, Asian, Mideast Indian, >1 race). Stratified by vitamin D level, 1251 individuals (27%) had less than 20 ng/mL, 1267 individuals (27%) had 20 to less than 30 ng/mL, 1023 individuals (22%) had 30 to less than 40 ng/mL, and 1097 individuals (24%) had 40 ng/mL or greater. Lower vitamin D levels were more common in Black individuals (<20 ng/mL: 829 of 2288 Black individuals [36%]) than White individuals (<20 ng/mL: 315 of 1999 White individuals [16%]). A total of 333 individuals (7%) had test results positive for COVID-19, including 102 White individuals (5%) and 211 Black individuals (9%). Multivariate analysis controlling for time since last vitamin D level measurement was used to estimate the outcomes associated with levels 14 days before COVID-19 testing. A positive test result for COVID-19 was not significantly associated with vitamin D levels in White individuals but was associated with vitamin D levels in Black individuals (compared with ≥40 ng/mL: <20 ng/mL incidence rate ratio [IRR], 2.55 [95% CI, 1.26-5.15]; P = .009; 20 to <30 ng/mL IRR, 1.69 [95% CI, 0.75-3.84]; P = .21; 30 to <40 ng/mL IRR, 2.64 [95% CI, 1.24-5.66]; P = .01). Stratified by vitamin D level, estimated COVID-19 positivity rates in Black individuals were 9.72% (95% CI, 6.74%-13.41%) for individuals with a vitamin D level less than 20 ng/mL, 6.47% (95% CI, 3.33%-10.28%) for individuals with a vitamin D level of 20 to less than 30 ng/mL, 10.10% (95% CI, 6.00%-15.47%) for individuals with a vitamin D level of 30 to less than 40 ng/mL, and 3.82% (95% CI, 1.78%-6.68%) for individuals with a vitamin D level of 40 ng/mL or higher. Multivariate analysis in individuals with a vitamin D level of 30 ng/mL or greater found that the IRR of a positive COVID-19 test result was 0.97 (95% CI, 0.94-0.99; P = .008) per 1-ng/mL increase in vitamin D overall and 0.95 (95% CI, 0.91-0.98; P = .003) per 1-ng/mL increase in vitamin D in Black individuals. Conclusions and Relevance: In this single-center retrospective cohort study, COVID-19 risk increased among Black individuals with vitamin D level less than 40 ng/mL compared with those with 40 ng/mL or greater and decreased with increasing levels among individuals with levels greater than 30 ng/mL. No significant associations were noted for White individuals. Randomized clinical trials should examine whether increasing vitamin D level to greater than 40 ng/mL affects COVID-19 risk.


Asunto(s)
/estadística & datos numéricos , Deficiencia de Vitamina D , Vitamina D/análogos & derivados , Grupo de Ascendencia Continental Africana/estadística & datos numéricos , /diagnóstico , /prevención & control , Chicago/epidemiología , Estudios de Cohortes , Comorbilidad , Correlación de Datos , Grupo de Ascendencia Continental Europea/estadística & datos numéricos , Femenino , Humanos , Incidencia , Masculino , Persona de Mediana Edad , Estudios Retrospectivos , Medición de Riesgo/etnología , Vitamina D/análisis , Deficiencia de Vitamina D/sangre , Deficiencia de Vitamina D/diagnóstico , Deficiencia de Vitamina D/etnología
7.
JAMA Netw Open ; 4(3): e214302, 2021 03 01.
Artículo en Inglés | MEDLINE | ID: mdl-33749770

RESUMEN

Importance: Accumulating evidence suggests that children infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are more likely to manifest mild symptoms and are at a lower risk of developing severe respiratory disease compared with adults. It remains unknown how the immune response in children differs from that of adolescents and adults. Objective: To investigate the association of age with the quantity and quality of SARS-CoV-2 antibody responses. Design, Setting, and Participants: This cross-sectional study used 31 426 SARS-CoV-2 antibody test results from pediatric and adult patients. Data were collected from a New York City hospital from April 9 to August 31, 2020. The semiquantitative immunoglobin (Ig) G levels were compared between 85 pediatric and 3648 adult patients. Further analysis of SARS-CoV-2 antibody profiles was performed on sera from 126 patients aged 1 to 24 years. Main Outcomes and Measures: SARS-CoV-2 antibody positivity rates and IgG levels were evaluated in patients from a wide range of age groups (1-102 years). SARS-CoV-2 IgG level, total antibody (TAb) level, surrogate neutralizing antibody (SNAb) activity, and antibody binding avidity were compared between children (aged 1-10 years), adolescents (aged 11-18 years), and young adults (aged 19-24 years). Results: Among 31 426 antibody test results (19 797 [63.0%] female patients), with 1194 pediatric patients (mean [SD] age, 11.0 [5.3] years) and 30 232 adult patients (mean [SD] age, 49.2 [17.1] years), the seroprevalence in the pediatric (197 [16.5%; 95% CI, 14.4%-18.7%]) and adult (5630 [18.6%; 95% CI, 18.2%-19.1%]) patient populations was similar. The SARS-CoV-2 IgG level showed a negative correlation with age in the pediatric population (r = -0.45, P < .001) and a moderate but positive correlation with age in adults (r = 0.24, P < .001). Patients aged 19 to 30 years exhibited the lowest IgG levels (eg, aged 25-30 years vs 1-10 years: 99 [44-180] relative fluorescence units [RFU] vs 443 [188-851] RFU). In the subset cohort aged 1 to 24 years, IgG, TAb, SNAb and avidity were negatively correlated with age (eg, IgG: r = -0.51; P < .001). Children exhibited higher median (IQR) IgG levels, TAb levels, and SNAb activity compared with adolescents (eg, IgG levels: 473 [233-656] RFU vs 191 [82-349] RFU; P < .001) and young adults (eg, IgG levels: 473 [233-656] RFU vs 85 [38-150] RFU; P < .001). Adolescents also exhibited higher median (IQR) TAb levels, IgG levels, and SNAb activity than young adults (eg, TAb levels: 961 [290-2074] RFU vs 370 [125-697]; P = .006). In addition, children had higher antibody binding avidity compared with young adults, but the difference was not significant. Conclusions and Relevance: The results of this study suggest that SARS-CoV-2 viral specific antibody response profiles are distinct in different age groups. Age-targeted strategies for disease screening and management as well as vaccine development may be warranted.


Asunto(s)
Anticuerpos Neutralizantes/sangre , Anticuerpos Antivirales/sangre , Afinidad de Anticuerpos/inmunología , Formación de Anticuerpos/inmunología , Factores de Edad , /epidemiología , /métodos , Niño , Correlación de Datos , Estudios Transversales , Femenino , Humanos , Inmunoglobulina G/sangre , Masculino , Persona de Mediana Edad , Ciudad de Nueva York/epidemiología , /aislamiento & purificación
8.
Eur Rev Med Pharmacol Sci ; 25(5): 2409-2414, 2021 03.
Artículo en Inglés | MEDLINE | ID: mdl-33755980

RESUMEN

The COVID-19 (Corona Virus Disease 2019) outbreak, which seriously affected people's lives across the world, has not been effectively controlled. Previous studies have demonstrated that SARS-COV-2 (Severe acute respiratory syndrome coronavirus 2) infecting host cells mainly rely on binding to receptor proteins, namely ACE2 and TMPRSS2. COVID-19 transmission is faster than the severe acute respiratory syndrome (SARS) pneumonia outbreak in 2002. This is mainly attributed to the different pathways of virus-infected host cells, coupled with patients' atypical clinical characteristics. SARS-CoV-2 is mainly transmitted through respiratory droplets and contact, infecting lung tissues before damaging other body organs, such as the liver, brain, kidney and heart. The present study identified potential target genes for SARS-COV-2 receptors, ACE2 and TMPRSS2, in normal human lung tissue. The findings provide novel insights that will guide future drug development approaches for treatment of COVID-19.


Asunto(s)
/genética , Receptores Virales/genética , Serina Endopeptidasas/genética , /biosíntesis , /metabolismo , Correlación de Datos , Expresión Génica , Humanos , Receptores Virales/biosíntesis , Receptores Virales/metabolismo , /metabolismo , Serina Endopeptidasas/biosíntesis , Serina Endopeptidasas/metabolismo
9.
Zhonghua Shao Shang Za Zhi ; 37(3): 257-262, 2021 Mar 20.
Artículo en Chino | MEDLINE | ID: mdl-33706430

RESUMEN

Objective: To investigate the correlation of Staphylococcus aureus superantigens and human ear keloid formation. Methods: The retrospective case-control study method was used. The discarded keloid tissue was collected from 10 patients (9 females and 1 male, aged 19-59 years) with ear keloid after core excision of ear keloid, and the discarded normal skin tissue was collected from 3 female patients (aged 20-24 years) with pigmented nevus after operation, who were admitted to affiliated Hospital of Nantong University from June 2017 to March 2018. The exudation from ear keloid surface was collected for bacteria culture and identification. The keloid and normal skin tissue were collected to detect the protein expression of Staphylococcus aureus enterotoxin A+enterotoxin B+toxic shock syndrome toxin-1 (TSST-1) by Western blotting, and the keloid was divided into superantigen positive group and superantigen negative group according to the protein expression of Staphylococcus aureus enterotoxin A+enterotoxin B+TSST-1. The protein expressions of T cell receptor (TCR) V ß of keloid in 2 groups were detected by Western blotting. Collagen fibers formation and inflammatory cells infiltration in keloid dermis of 2 groups were observed by Masson and hematoxylin eosin staining, respectively. Enzyme-linked immunosorbent assay method was used to detect expression of Staphylococcus aureus enterotoxin A, enterotoxin B, and TSST-1 in keloids with superantigen positive. Data were statistically analyzed with paired sample t test. Results: Bacteria were cultured from the exudation on ear keloid surface, hemolysis was observed around the dominant bacteria after being cultured for 24 hours, and the colony was white or golden yellow, which was identified as Staphylococcus aureus. The protein expression of Staphylococcus aureus enterotoxin A+enterotoxin B+TSST-1 of normal skin was negative in 3 patients, and the protein expression was 0.267±0.016. The protein expression of Staphylococcus aureus enterotoxin A+enterotoxin B+TSST-1 of keloid was positive in 4 patients, with the protein expression of 0.472±0.016, which was included into superantigen positive group, and the protein expression of Staphylococcus aureus enterotoxin A+enterotoxin B+TSST-1 of keloid was negative in 6 patients, with the protein expression of 0.255±0.004, which was included into superantigen negative group. The protein expression of Staphylococcus aureus enterotoxin A+enterotoxin B+TSST-1 of keloid in superantigen positive group was obviously higher than that of keloid in superantigen negative group and that in normal skin (t=15.22, 8.63, P<0.01). The protein expression of TCR Vß in keloid of superantigen positive group was 0.389±0.023, which was significantly higher than 0.169±0.014 in superantigen negative group (t=8.62, P<0.01). Masson staining showed that a large number of collagen fibers existed in dermis of keloid in 2 groups. HE staining showed that there were a small number of inflammatory cells infiltration around the blood vessels of keloid dermis in superantigen negative group and a large number of inflammatory cells infiltration around the blood vessels of keloid in superantigen positive group. Among the 4 patients with superantigen positive keloid, Staphylococcus aureus enterotoxin A was positive in 2 patients, Staphylococcus aureus enterotoxin B was positive in 2 patients, and among that Staphylococcus aureus enterotoxin A and enterotoxin B were both positive in 1 patient, with no TSST-1 detected in any patient. Conclusions: The superantigen secreted by Staphylococcus aureus is one of the many causes of ear keloid, which may be related to the activation of keloid signal pathway by superantigen of Staphylococcus aureus.


Asunto(s)
Queloide , Staphylococcus aureus , Adulto , Estudios de Casos y Controles , Correlación de Datos , Femenino , Humanos , Masculino , Persona de Mediana Edad , Estudios Retrospectivos , Superantígenos , Adulto Joven
10.
Ecotoxicol Environ Saf ; 215: 112150, 2021 Jun 01.
Artículo en Inglés | MEDLINE | ID: mdl-33756290

RESUMEN

To estimate spatial distribution, source analysis and uncertainty of heavy metals (Pb, Cd, Cr, Hg, As, Cu, Zn, and Ni) based on geographic information system (GIS), positive matrix factorization model (PMF) and bootstrap (BS) using 382 soil samples collected from cultivated soils in Lanzhou. The mean contents of Cd, Hg, Cu, Zn and Ni were high as 1.7,1.7, 2.1, 1.5 and 1.3 times local background values, mean contents of Pb, Cr and As were lower than local background values. However, the mean contents of eight heavy metals were lower environmental quality risk control standard for soil contamination of agricultural soil. Proportions of four sources were identified: Cr was predominantly contributed by natural sources (29.14%), Cu, Zn and Ni was primarily from industrial sources (25.26%), Hg and As were mainly of agricultural sources (27.49%), Pb and Cd mainly came from traffic source and smelting-related activities (18.09%). Uncertainties analysis contained three aspects: bootstrap runs, factor contributions in the PMF solution, and coefficient of variation (CV) values. By combining the four pollution source factors with bootstrap runs, the accuracy of the four pollution source factors were reliable based on PMF model. The median values in the BS runs was considered the most true factor contribution, and the 5th-95th quartile interval represents the variability of each factor, Factor 4 (traffic source) R2 was 0.70 and lower variability. The highest CV value usually means a significantly deviation degree. In this study, the CV values of Cr in Factor 1, Cu, Zn, and Ni in Factor 2, Hg, and As in Factor 3, Pb, and Cd in Factor 4 were lower, indicates a lower deviation degree. and with the lowest content among heavy metals usually was also with the greatest uncertainties. In this study improves understanding of the reduction of heavy metal pollution in cultivated soil, and also serves as reference for pollution source apportionment in other regions.


Asunto(s)
Monitoreo del Ambiente , Metales Pesados/análisis , Contaminantes del Suelo/análisis , Agricultura , China , Correlación de Datos , Contaminación Ambiental/análisis , Sistemas de Información Geográfica , Industrias , Mercurio/análisis , Medición de Riesgo , Suelo , Incertidumbre
11.
BMC Bioinformatics ; 22(1): 116, 2021 Mar 10.
Artículo en Inglés | MEDLINE | ID: mdl-33691629

RESUMEN

BACKGROUND: Correlation network analysis has become an integral tool to study metabolite datasets. Networks are constructed by omitting correlations between metabolites based on two thresholds-namely the r and the associated p-values. While p-value threshold settings follow the rules of multiple hypotheses testing correction, guidelines for r-value threshold settings have not been defined. RESULTS: Here, we introduce a method that allows determining the r-value threshold based on an iterative approach, where different networks are constructed and their network topology is monitored. Once the network topology changes significantly, the threshold is set to the corresponding correlation coefficient value. The approach was exemplified on: (i) a metabolite and morphological trait dataset from a potato association panel, which was grown under normal irrigation and water recovery conditions; and validated (ii) on a metabolite dataset of hearts of fed and fasted mice. For the potato normal irrigation correlation network a threshold of Pearson's |r|≥ 0.23 was suggested, while for the water recovery correlation network a threshold of Pearson's |r|≥ 0.41 was estimated. For both mice networks the threshold was calculated with Pearson's |r|≥ 0.84. CONCLUSIONS: Our analysis corrected the previously stated Pearson's correlation coefficient threshold from 0.4 to 0.41 in the water recovery network and from 0.4 to 0.23 for the normal irrigation network. Furthermore, the proposed method suggested a correlation threshold of 0.84 for both mice networks rather than a threshold of 0.7 as applied earlier. We demonstrate that the proposed approach is a valuable tool for constructing biological meaningful networks.


Asunto(s)
Redes y Vías Metabólicas , Miocardio/metabolismo , Solanum tuberosum/metabolismo , Riego Agrícola , Animales , Correlación de Datos , Conjuntos de Datos como Asunto , Ratones
12.
Medicine (Baltimore) ; 100(12): e25326, 2021 Mar 26.
Artículo en Inglés | MEDLINE | ID: mdl-33761736

RESUMEN

ABSTRACT: Single-nucleotide polymorphisms (SNPs) in the transcription factor 7-like 2 (TCF7L2) gene have been identified to be associated with the susceptibility to type 2 diabetes mellitus (T2DM) in various populations worldwide, but the results in Chinese are conflicting, and no data are available about the Liannan Yao population. Therefore, this study aimed to investigate the association of the TCF7L2 gene polymorphisms (rs12255372, rs7903146, rs7901695, rs11196205, and rs7895340) with T2DM in the Yao population living in the rural areas in the Liannan Yao Autonomous County.This was a case-control study of 28 subjects with T2DM or prediabetes and 52 non-T2DM controls, all from the Chinese Yao population and recruited between January 2019 and June 2020. Patients with T2DM and prediabetes were grouped as the case group. The five SNPs (rs12255372, rs7903146, rs7901695, rs11196205, and rs7895340) were examined by polymerase chain reaction and direct genomic DNA sequencing in case and control groups.The subjects in case group were older than the controls (55±14 vs 48 ±â€Š15 years, P = .047), had higher FBG levels (9.31 ±â€Š5.43 vs 4.09 ±â€Š0.81, P < .001), higher TC (5.79 ±â€Š1.29 vs 5.13 ±â€Š1.18 mmol/L, P = .025), and higher triglycerides (2.94 ±â€Š2.04 vs 1.86 ±â€Š1.39 mmol/L, P = .003). The genotypic distribution for each of the SNPs was in agreement with the Hardy-Weinberg equilibrium. There were no statistically significant differences in the distributions of genotypes or alleles at all five SNPs of the TCF7L2 gene between the case and control groups (all P > .05).TCF7L2 SNPs were not associated with T2DM in the Liannan Yao population.


Asunto(s)
Diabetes Mellitus Tipo 2 , Proteína 2 Similar al Factor de Transcripción 7/genética , Glucemia/análisis , Estudios de Casos y Controles , China/epidemiología , Colesterol/sangre , Correlación de Datos , Diabetes Mellitus Tipo 2/sangre , Diabetes Mellitus Tipo 2/diagnóstico , Diabetes Mellitus Tipo 2/epidemiología , Diabetes Mellitus Tipo 2/genética , Femenino , Predisposición Genética a la Enfermedad , Humanos , Masculino , Persona de Mediana Edad , Polimorfismo de Nucleótido Simple , Triglicéridos/sangre
13.
Isr Med Assoc J ; 23(3): 153-159, 2021 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-33734627

RESUMEN

BACKGROUND: Immune cell counts in blood in severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection may be useful prognostic biomarkers of disease severity, mortality, and response to treatment. OBJECTIVES: To analyze sub-populations of lymphocytes at hospital admission in survivors and deceased from severe pneumonia due to coronavirus disease-2019 (COVID-19). METHODS: We conducted a cross-sectional study of healthcare workers confirmed with SARS-CoV-2 in convalescents (control group) and healthy controls (HC) diagnosed with severe COVID-19. Serum samples were taken at hospital admission and after recovery. Serum samples ≥ 25 days after onset of symptoms were analyzed for lymphocyte subpopulations through flow cytometry. Descriptive statistics, Kruskall-Wallis test, receiver operating characteristic curve, calculation of sensitivity, specificity, predictive values, and Kaplan-Meier analysis were performed. RESULTS: We included 337 patients: 120 HC, 127 convalescents, and 90 severe COVID-19 disease patients (50 survivors, 40 deceased). For T cells, total lymphocytes ≥ 800/µL, CD3+ ≥ 400/µL, CD4+ ≥ 180/µL, CD8+ ≥ 150/µL, B cells CD19+ ≥ 80/µL, and NK ≥ 34/µL subsets were associated with survival in severe COVID-19 disease patients. All subtypes of lymphocytes had higher concentrations in survivors than deceased, but similar between HC and convalescents. Leukocytes ≥ 10.150/µL or neutrophils ≥ 10,000/µL were associated with increased mortality. The neutrophil-to-lymphocyte ratio (NLR) ≥ 8.5 increased the probability of death in severe COVID-19 (odds ratio 11.68). CONCLUSIONS: Total lymphocytes; NLR; and levels of CD3+, CD4+, CD8+, and NK cells are useful as biomarkers of survival or mortality in severe COVID-19 disease and commonly reach normal levels in convalescents.


Asunto(s)
Linfocitos T CD4-Positivos/patología , Linfocitos T CD8-positivos/patología , Linfopenia , Neutrófilos/patología , Biomarcadores/sangre , /diagnóstico , /terapia , Correlación de Datos , Estudios Transversales , Femenino , Humanos , Estimación de Kaplan-Meier , Células Asesinas Naturales/patología , Recuento de Leucocitos/métodos , Linfopenia/sangre , Linfopenia/diagnóstico , Linfopenia/etiología , Masculino , México/epidemiología , Persona de Mediana Edad , Mortalidad , Valor Predictivo de las Pruebas , Evaluación de Síntomas/métodos
14.
BMC Cardiovasc Disord ; 21(1): 158, 2021 03 30.
Artículo en Inglés | MEDLINE | ID: mdl-33784966

RESUMEN

INTRODUCTION: The cause-and-effect relationship of QTc prolongation in Coronavirus disease 2019 (COVID-19) patients has not been studied well. OBJECTIVE: We attempt to better understand the relationship of QTc prolongation in COVID-19 patients in this study. METHODS: This is a retrospective, hospital-based, observational study. All patients with normal baseline QTc interval who were hospitalized with the diagnosis of COVID-19 infection at two hospitals in Ohio, USA were included in this study. RESULTS: Sixty-nine patients had QTc prolongation, and 210 patients continued to have normal QTc during hospitalization. The baseline QTc intervals were comparable in the two groups. Patients with QTc prolongation were older (mean age 67 vs. 60, P 0.003), more likely to have underlying cardiovascular disease (48% versus 26%, P 0.001), ischemic heart disease (29% versus 17%, P 0.026), congestive heart failure with preserved ejection fraction (16% versus 8%, P 0.042), chronic kidney disease (23% versus 10%, P 0.005), and end-stage renal disease (12% versus 1%, P < 0.001). Patients with QTc prolongation were more likely to have received hydroxychloroquine (75% versus 59%, P 0.018), azithromycin (18% vs. 14%, P 0.034), a combination of hydroxychloroquine and azithromycin (29% vs 7%, P < 0.001), more than 1 QT prolonging agents (59% vs. 32%, P < 0.001). Patients who were on angiotensin-converting enzyme inhibitors (ACEi) were less likely to develop QTc prolongation (11% versus 26%, P 0.014). QTc prolongation was not associated with increased ventricular arrhythmias or mortality. CONCLUSION: Older age, ESRD, underlying cardiovascular disease, potential virus mediated cardiac injury, and drugs like hydroxychloroquine/azithromycin, contribute to QTc prolongation in COVID-19 patients. The role of ACEi in preventing QTc prolongation in COVID-19 patients needs to be studied further.


Asunto(s)
/tratamiento farmacológico , Enfermedades Cardiovasculares/epidemiología , Electrocardiografía , Síndrome de QT Prolongado , Insuficiencia Renal Crónica/epidemiología , Factores de Edad , Anciano , /complicaciones , /fisiopatología , Comorbilidad , Correlación de Datos , Electrocardiografía/métodos , Electrocardiografía/estadística & datos numéricos , Femenino , Humanos , Síndrome de QT Prolongado/diagnóstico , Síndrome de QT Prolongado/epidemiología , Síndrome de QT Prolongado/etiología , Masculino , Persona de Mediana Edad , Evaluación de Procesos y Resultados en Atención de Salud , Medición de Riesgo/métodos , Análisis de Supervivencia , Estados Unidos/epidemiología
15.
Medicine (Baltimore) ; 100(12): e25277, 2021 Mar 26.
Artículo en Inglés | MEDLINE | ID: mdl-33761731

RESUMEN

ABSTRACT: Drug-resistant epilepsy (DRE) affects 7% to 20% of children with epilepsy. Although some risk factors for DRE have been identified, the results have not been consistent. Moreover, data regarding the risk factors for epilepsy and its seizure outcome in the first 2 years of life are limited.We analyzed data for children aged 0 to 2 years with epilepsy and neurodevelopmental disability from January, 2013, through December, 2017. These patients were followed up to compare the risk of DRE in patients with genetic defect (genetic group) with that without genetic defect (nongenetic group). Additionally, we conducted a meta-analysis to identify the pooled prevalence of genetic factors in children with DRE.A total of 96 patients were enrolled. A total of 68 patients were enrolled in the nongenetic group, whereas 28 patients were enrolled in the genetic group. The overall DRE risk in the genetic group was 6.5 times (95% confidence interval [CI], 2.15-19.6; p = 0.03) higher than that in the nongenetic group. Separately, a total of 1308 DRE patients were participated in the meta-analysis. The pooled prevalence of these patients with genetic factors was 22.8% (95% CI 17.4-29.3).The genetic defect plays a crucial role in the development of DRE in younger children with epilepsy and neurodevelopmental disability. The results can serve as a reference for further studies of epilepsy panel design and may also assist in the development of improved treatments and prevention strategies for DRE.


Asunto(s)
Aberraciones Cromosómicas/estadística & datos numéricos , Discapacidades del Desarrollo , Epilepsia Refractaria , Enfermedades Genéticas Congénitas , Medición de Riesgo/métodos , China/epidemiología , Correlación de Datos , Discapacidades del Desarrollo/diagnóstico , Discapacidades del Desarrollo/epidemiología , Epilepsia Refractaria/diagnóstico , Epilepsia Refractaria/epidemiología , Epilepsia Refractaria/genética , Femenino , Enfermedades Genéticas Congénitas/diagnóstico , Enfermedades Genéticas Congénitas/epidemiología , Humanos , Lactante , Recién Nacido , Masculino , Mutación , Canal de Sodio Activado por Voltaje NAV1.1/genética , Canal de Sodio Activado por Voltaje NAV1.6/genética , Prevalencia , Estudios Prospectivos , Factores de Riesgo , Proteína 2 del Complejo de la Esclerosis Tuberosa/genética
16.
BMJ Open Respir Res ; 8(1)2021 03.
Artículo en Inglés | MEDLINE | ID: mdl-33664125

RESUMEN

BACKGROUND: Air pollution may affect the risk of respiratory infection, though research has focused on uncommon infections or infections in children. Whether ambient air pollutants increase the risk of common acute respiratory infections among adults is uncertain, yet this may help understand whether pollutants influence spread of pandemic respiratory infections like COVID-19. OBJECTIVE: To estimate the association between ambient air pollutant exposures and respiratory infections in adults. METHODS: During five study examinations over 12 years, 6536 participants in the multiethnic study of atherosclerosis (MESA) reported upper respiratory tract infections, bronchitis, pneumonia or febrile illness in the preceding 2 weeks. Using a validated spatiotemporal model, we estimated residential concentrations of ambient PM2.5, NOx and NO2 for the 2-6 weeks (short-term) and year (long-term) prior to each examination. RESULTS: In this population aged 44-84 years at baseline, 10%-32% of participants reported a recent respiratory infection, depending on month of examination and study region. PM2.5, NOx and NO2 concentrations over the prior 2-6 weeks were associated with increased reporting of recent respiratory infection, with risk ratios (95% CIs) of 1.04 (1.00 to 1.09), 1.15 (1.10 to 1.20) and 1.21 (1.10 to 1.33), respectively, per increase from 25th to 75th percentile in residential pollutant concentration. CONCLUSION: Higher short-term exposure to PM2.5 and traffic-related pollutants are associated with increased risk of symptomatic acute respiratory infections among adults. These findings may provide an insight into the epidemiology of COVID-19.


Asunto(s)
Contaminación del Aire/efectos adversos , Contaminación del Aire/estadística & datos numéricos , Aterosclerosis/etnología , Aterosclerosis/epidemiología , /epidemiología , Comparación Transcultural , Grupos Étnicos/estadística & datos numéricos , Infecciones del Sistema Respiratorio/etnología , Infecciones del Sistema Respiratorio/epidemiología , Enfermedad Aguda , Adulto , Anciano , Anciano de 80 o más Años , Bronquitis/epidemiología , Bronquitis/etnología , Correlación de Datos , Estudios Transversales , Femenino , Fiebre/epidemiología , Fiebre/etnología , Humanos , Masculino , Persona de Mediana Edad , Oportunidad Relativa , Neumonía/epidemiología , Neumonía/etnología , Riesgo , Análisis Espacio-Temporal , Estados Unidos
17.
Artículo en Inglés | MEDLINE | ID: mdl-33669693

RESUMEN

The aerobic cost of running (CR), an important determinant of running performance, is usually measured during constant speed running. However, constant speed does not adequately reflect the nature of human locomotion, particularly competitive races, which include stochastic variations in pace. Studies in non-athletic individuals suggest that stochastic variations in running velocity produce little change in CR. This study was designed to evaluate whether variations in running speed influence CR in trained runners. Twenty competitive runners (12 m, VO2max = 73 ± 7 mL/kg; 8f, VO2max = 57 ± 6 mL/kg) ran four 6-minute bouts at an average speed calculated to require ~90% ventilatory threshold (VT) (measured using both v-slope and ventilatory equivalent). Each interval was run with minute-to-minute pace variation around average speed. CR was measured over the last 2 min. The coefficient of variation (CV) of running speed was calculated to quantify pace variations: ±0.0 m∙s-1 (CV = 0%), ±0.04 m∙s-1 (CV = 1.4%), ±0.13 m∙s-1(CV = 4.2%), and ±0.22 m∙s-1(CV = 7%). No differences in CR, HR, or blood lactate (BLa) were found amongst the variations in running pace. Rating of perceived exertion (RPE) was significantly higher only in the 7% CV condition. The results support earlier studies with short term (3s) pace variations, that pace variation within the limits often seen in competitive races did not affect CR when measured at running speeds below VT.


Asunto(s)
Consumo de Oxígeno , Carrera , Correlación de Datos , Humanos , Locomoción
18.
Behav Genet ; 51(2): 110-124, 2021 03.
Artículo en Inglés | MEDLINE | ID: mdl-33624124

RESUMEN

We investigated how the COVID-19 crisis and the extraordinary experience of lockdown affected young adults in England and Wales psychologically. One month after lockdown commenced (T2), we assessed 30 psychological and behavioural traits in more than 4000 twins in their mid-twenties and compared their responses to the same traits assessed in 2018 (T1). Mean changes from T1 to T2 were modest and inconsistent. Contrary to the hypothesis that major environmental changes related to COVID-19 would result in increased variance in psychological and behavioural traits, we found that the magnitude of individual differences did not change from T1 to T2. Twin analyses revealed that while genetic factors accounted for about half of the reliable variance at T1 and T2, they only accounted for ~ 15% of individual differences in change from T1 to T2, and that nonshared environmental factors played a major role in psychological and behavioural changes. Shared environmental influences had negligible impact on T1, T2 or T2 change. Genetic factors correlated on average .86 between T1 and T2 and accounted for over half of the phenotypic stability, as would be expected for a 2-year interval even without the major disruption of lockdown. We conclude that the first month of lockdown has not resulted in major psychological or attitudinal shifts in young adults, nor in major changes in the genetic and environmental origins of these traits. Genetic influences on the modest psychological and behavioural changes are likely to be the result of gene-environment correlation not interaction.


Asunto(s)
/genética , Enfermedades en Gemelos/genética , Genética Conductual , Adulto , Correlación de Datos , Enfermedades en Gemelos/psicología , Inglaterra , Femenino , Estudios de Seguimiento , Interacción Gen-Ambiente , Humanos , Individualidad , Masculino , Medio Social , Aislamiento Social , Gales , Adulto Joven
19.
Int J Biol Macromol ; 177: 204-210, 2021 Apr 30.
Artículo en Inglés | MEDLINE | ID: mdl-33582215

RESUMEN

BACKGROUND: Given the observed olfactory and gustatory dysfunctions in patients with COVID-19 and recent findings on taste receptors possible important activities in the immune system, we elected to estimate the correlation between COVID-19 mortality and polymorphism of a particular type of bitter taste receptor gene called TAS2R38, in a worldwide epidemiological point of view. METHODS: Pooled rate of each of the rs713598, rs1726866, rs10246939, and PAV/AVI polymorphisms of the TAS2R38 gene was obtained in different countries using a systematic review methodology and its relationship with the mortality of COVID-19. Data were analyzed by the comprehensive meta-analysis software and SPSS. RESULTS: There was only a significant reverse Pearson correlation in death counts and PAV/AVI ratio, p = 0.047, r = -0.503. Also, a significant reverse correlation of PAV/AVI ratio and death rate was seen, r = -0.572 p = 0.021. rs10246939 ratio had a significant positive correlation with death rate, r = 0.851 p = 0.031. Further analysis was not significant. Our results showed that the higher presence of PAV allele than AVI, and a higher rate of G allele than A in rs10246939 polymorphism in a country, could be associated with lower COVID-19 mortality. While assessing all three polymorphisms showed a huge diversity worldwide. CONCLUSION: Due to extraoral activities of bitter taste receptor genes, especially in mucosal immunity, this gene seems to be a good candidate for future studies on COVID-19 pathophysiology. Also, the high worldwide diversity of TAS2R38 genes polymorphism and its possible assassination with mortality raises concerns about the efficiency of vaccine projects in different ethnicities.


Asunto(s)
/genética , Polimorfismo de Nucleótido Simple , Receptores Acoplados a Proteínas G/genética , Gusto/genética , Alelos , Correlación de Datos , Bases de Datos Factuales , Estudios de Asociación Genética , Predisposición Genética a la Enfermedad , Genotipo , Humanos
20.
Medicine (Baltimore) ; 100(5): e24075, 2021 Feb 05.
Artículo en Inglés | MEDLINE | ID: mdl-33592861

RESUMEN

BACKGROUND: Hepatitis B virus-related acute-on-chronic liver failure (HBV-ACLF) is a life-threatening syndrome with high mortality. Biomarkers are urgently needed to predict the prognosis of HBV-ACLF. Recent evidence suggests a key role for immune system in the pathology of HBV-ACLF. Here, we analyzed the correlation between peripheral blood T lymphocytes and the severity and prognosis in HBV-ACLF patients. METHOD: Sixty-six patients with HBV-ACLF received conventional medical treatments for 4 weeks. Twenty-five healthy subjects and 20 HBV patients were enrolled for comparison. We determined white blood cell count, lymphocytes, CD3+, CD4+ and CD8+ T cells, and CD4+CD25+ Treg cells in the blood of all subjects. Their associations with laboratory parameters before or after treatments were statistically analyzed. RESULT: The results showed that compare normal subjects and chronic hepatitis B patients, HBV-ACLF patients had significantly increased white blood count, CD4+ T cells and decreased lymphocytes, CD3+ T cells, and Treg cells. Correlation analysis showed that white blood cell, lymphocytes, and peripheral T lymphocytes were correlated with prothrombin activity (PTA) and model for end-stage liver disease (MELD) scores. After treatment, white blood cell, lymphocytes, and peripheral T lymphocytes were also correlated with PTA and MELD scores. Additionally, total bilirubin (TBIL), alanine aminotransferase (ALT), international standard ratio (INR), MELD, and white blood cell count were potential prognostic criteria for HBV-ACLF patients. CONCLUSION: HBV-ACLF patients had depletion and dysfunction of immune system. Changes of peripheral T lymphocytes were closely related to the pathogenesis and prognosis of disease. Our results may contribute to predict the severity of HBV-ACLF, and provide a prognosis response to improve the treatment of HBV-ACLF.


Asunto(s)
Insuficiencia Hepática Crónica Agudizada , Linfocitos T CD4-Positivos/inmunología , Linfocitos T CD8-positivos/inmunología , Hepatitis B Crónica/complicaciones , Recuento de Linfocitos/métodos , Linfocitos T Reguladores/inmunología , Insuficiencia Hepática Crónica Agudizada/sangre , Insuficiencia Hepática Crónica Agudizada/diagnóstico , Insuficiencia Hepática Crónica Agudizada/etiología , Insuficiencia Hepática Crónica Agudizada/mortalidad , China/epidemiología , Correlación de Datos , Femenino , Humanos , Masculino , Persona de Mediana Edad , Valor Predictivo de las Pruebas , Pronóstico , Índice de Severidad de la Enfermedad
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