Tag: statistics

Int Health. 2022 Apr 8:ihac015. doi: 10.1093/inthealth/ihac015. Online ahead of print.

ABSTRACT

BACKGROUND: Gestational trophoblastic diseases (GTDs) may follow any form of pregnancy or a pregnancy loss. Early detection of GTDs is important, as some benign forms of the disease may progress into a chemoresistant and metastatic disease. This study aimed at determining the frequency of GTDs among women experiencing first trimester pregnancy loss and the associated patients’ characteristics.

METHODS: This was a cross-sectional study that included 200 conveniently sampled women who experienced first trimester pregnancy loss from January to December 2019 at a Regional Referral Hospital in central Tanzania. The specimen obtained from products of conception were collected, formalin-fixed and paraffin-embedded and submitted for histopathological evaluation, for which haematoxylin and eosin stain was used. Data were analysed using SPSS version 23.0. The χ2 test was used to determine the association between categorical variables. p-Values ˂0.05 were considered statistically significant.

RESULTS: Among 200 study participants, the overall frequency of GTDs was 42 (21%). Among those with GTDs, the most common histopathological diagnosis was partial hydatidiform mole (18 [42.9%]), followed by complete hydatidiform mole (17 [40.5%]) and choriocarcinoma (7 [16.5%]). In the studied participants, only increased human chorionic gonadotropin hormone levels were found to be statistically significantly associated with GTDs (p=0.000).

CONCLUSIONS: Results from this study suggest that routine histopathological evaluation of the products of conception is recommended in order to allow early detection of GTDs, including choriocarcinoma, which usually carries a poor prognosis. The histopathological reporting of choriocarcinoma among first trimester products of conception from Tanzania is novel.

PMID:35394041 | DOI:10.1093/inthealth/ihac015

Bioinformatics. 2022 Apr 8:btac199. doi: 10.1093/bioinformatics/btac199. Online ahead of print.

ABSTRACT

MOTIVATION: Single cell technologies play a crucial role in revolutionizing biological research over the past decade, which strengthens our understanding in cell differentiation, development, and regulation from a single-cell level perspective. Single-cell RNA sequencing (scRNA-seq) is one of the most common single cell technologies, which enables probing transcriptional states in thousands of cells in one experiment. Identification of cell types from scRNA-seq measurements is a fundamental and crucial question to answer. Most previous studies directly take gene expression as input while ignoring the comprehensive gene-gene interactions.

RESULTS: We propose scGraph, an automatic cell identification algorithm leveraging gene interaction relationships to enhance the performance of the cell type identification. ScGraph is based on a graph neural network to aggregate the information of interacting genes. In a series of experiments, we demonstrate that scGraph is accurate and outperforms eight comparison methods in the task of cell type identification. Moreover, scGraph automatically learns the gene interaction relationships from biological data and the pathway enrichment analysis shows consistent findings with previous analysis, providing insights on the analysis of regulatory mechanism.

AVAILABILITY: scGraph is freely available at https://github.com/QijinYin/scGraph and https://figshare.com/articles/software/scGraph/17157743.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PMID:35394015 | DOI:10.1093/bioinformatics/btac199

Huan Jing Ke Xue. 2022 Apr 8;43(4):2115-2123. doi: 10.13227/j.hjkx.202108038.

ABSTRACT

In order to study the current status of heavy metal pollution, the accumulation capacity of farmland Sphagnum for heavy metals and the source of heavy metal pollution in the soil near Gaozhai Reservoir in Maojian Tea Town, Duyun City, Guizhou Province were assessed. Sphagnum and topsoil near this area were selected as the research object to measure the content of heavy metals. Spatial analysis and multivariate statistical analysis methods were used to conduct pollution evaluation and source analysis of heavy metals. The results showed that the heavy metal content in topsoil and farmland Sphagnum were V>Zn>Cr>Pb>Cu>Ni>As>Cd>Hg and Zn>Cr>Ni>Cu>Pb>V>As>Cd>Hg, respectively. The dominant species of Sphagnum in the study area were Sphagnum palustre L. ssp. palustre and Sphagnum ovatum Hamp.C.Muell, both of which had a strong ability to accumulate soil Cd, Ni, Cu, and Zn; however, the S. ovatum enrichment capacity of soil heavy metals was generally higher than that of the latter. Both the single pollution index (C_f) and the geo-accumulation index (I_geo) indicated that the Cd and Hg content in soil were at the highest levels, and the average comprehensive pollution index RI was 87.75, which indicates a slight ecological risk. The sources of heavy metals in soil and Sphagnum included transportation, domestic sewage, agricultural activities, and natural soil-forming processes.

PMID:35393835 | DOI:10.13227/j.hjkx.202108038

Huan Jing Ke Xue. 2022 Apr 8;43(4):2081-2093. doi: 10.13227/j.hjkx.202109024.

ABSTRACT

Carbonatite and basalt are widely distributed in southwest China, and potentially toxic elements (PTEs) are associated with the naturally high background properties. It is important to carry out ecological risk assessments and identify potential sources of PTEs. A total of 3180 soil samples (0-20 cm) were collected in Hezhang county, a typical high background area of PTEs with the parent lithology of carbonatite and basalt. Samples were obtained from 18 large lead-zinc mines, which belong to a multi-ecological risk superimposed area with high ecological risk. The concentration of PTEs (Cd, Cr, As, Hg, Pb, Cu, Zn, and Ni) in the topsoil were analyzed, and statistical analysis (SA), geographic information system (GIS), enrichment factor (EF), potential ecological risk index (RI), and positive matrix factorization (PMF) methods were used to assess the ecological risk and quantify sources of PTEs. The mean values of PTEs concentrations in topsoil were 24.55, 2.25, 176.40, 89.60, 0.19, 64.20, 102.00, and 257.00 mg·kg^-1 for As, Cd, Cr, Cu, Hg, Ni, Pb, and Zn, respectively, which were remarkably higher than the average background value (ABV) of soils in Guizhou Province. The average concentrations of Cd, Cr, Cu, Ni, Pb, and Zn exceeded the screening values specified for the soil contamination risk in agricultural land (GB 15618-2018) by 7.50, 1.18, 1.79, 1.07, 1.40, and 1.29 times, respectively. The EF showed that Cd had a large area of moderate pollution; Pb, Zn, and Cu had a small area of slight pollution; the EFs values of Hg, Cr, Ni, and As were near the baseline value (EF≈1), and contaminations were slight or nonexistent. The PMF indicated that there were five sources, namely pyrite mines, lead-zinc mines, natural sources of basalt and carbonatite, and agricultural activities; the risk contribution ratios were 5.25%, 27.37%, 28.94%, 17.91%, and 20.53%, respectively. The most toxic coefficients of Hg and Cd were mainly natural sources, with contribution ratios of 86.3% and 72.7%, respectively. The soil samples in the mining areas expectedly contained high ratios of Zn/Cd and Pb/Cd, which confirmed that PTEs in the soil were mainly derived from the smelting wastes. The contents of metal oxides such as Fe, Mn, and Si were the influencing factors of PTEs enrichment. On the contrary, soil samples exhibited much lower Zn/Cd and Pb/Cd ratios in non-mining areas, indicating that the main origin of these metals in soil was the smelting flue gas dusts and geological background.

PMID:35393832 | DOI:10.13227/j.hjkx.202109024

Huan Jing Ke Xue. 2022 Apr 8;43(4):1898-1907. doi: 10.13227/j.hjkx.202107187.

ABSTRACT

As an important food production area in the north of China, the Hetao plain is extremely vulnerable to nitrate pollution caused by agricultural production activities and additional factors. Thus, it is of great significance for the environmental protection and rational use of groundwater to detect the current situation of groundwater nitrate pollution, temporal and spatial evolution characteristics, and main influencing factors in the Hetao irrigation district. We selected the Wualte irrigation area as the study area, and the characteristics of temporal and spatial changes in groundwater nitrate concentration and the main influencing factors in this area were explored. We used statistical analysis to analyze the nitrogen content of groundwater in the study area, and the Piper three-line diagram was used to explore the characteristics of chemical composition and evolution; furthermore, we used ion ratio and correlation analysis methods to explore the source of NO₃^–-N in groundwater. The results showed that NO₃^–-N was the main existing form of nitrogen in the Wulate irrigation area, and its concentration varied from 0.01 to 60.00 mg·L^-1, with an exceeding standard rate of 10.50%. In terms of time, the characteristic of time change was that the NO₃^–-N concentration in August of groundwater was the highest (average 6.61 mg·L^-1), followed by that in October (6.22 mg·L^-1) and November (6.25 mg·L^-1), and that in March (average value of 1.77 mg·L^-1) was the lowest. With the influence of rainfall and irrigation, the NO₃^–-N in the soil was infiltrated into the groundwater, showing the characteristic that wet season and concentrated irrigation periods were higher than those in other periods. Spatially, it appeared as southwest (8.87 mg·L^-1)>northwest (4.25 mg·L^-1)>east (0.89 mg·L^-1), mainly due to the original geological conditions, land use, and domestic waste stacking. In addition, the concentration of NO₃^–-N of groundwater in the study area was closely related to the depth of groundwater and redox conditions but was relatively less affected by the concentration of water chemical ions. Therefore, identifying the temporal and spatial distribution characteristics and main sources of groundwater nitrogen pollution can provide a scientific basis for scientific fertilization, groundwater nitrate pollution control, and water safety.

PMID:35393813 | DOI:10.13227/j.hjkx.202107187

Huan Jing Ke Xue. 2022 Apr 8;43(4):2018-2029. doi: 10.13227/j.hjkx.202107040.

ABSTRACT

Rainfall runoff is one of the important sources of urban river pollution. In order to understand the pollution characteristics of rainfall runoff, the synchronous sampling and monitoring of rainfall runoff in the old urban area of Nanning were carried out; the pollution condition, initial scouring effect, and pollution contribution ratio of different underlying surfaces under different rainfall conditions were analyzed; and the calculation method and influence factor analysis of initial scouring of runoff pollution were discussed. According to the underlying surface of the vegetable market in the old urban area, the selection standard and necessity of the underlying surface of rainfall runoff were discussed. The results showed that the average concentration (EMC) of COD and TSS in roads and vegetable markets were greater than those in green spaces and roofs in the runoff pollution of the old urban area of Nanning, and the EMC values of nutrient pollutants in field rainfall runoff were ranked in decreasing order as vegetable markets, green spaces, roofs, and roads. Under the condition of heavy rain, each underlying surface had an obvious initial scouring effect, the average value of initial scouring coefficient (b) was 0.67, and there were many pollutants transported by roads and green spaces at the initial stage. Under light rain and moderate rain conditions, there was no obvious initial scouring effect, and the average b values were 0.83 and 0.94, respectively. The b value calculated by the whole process was preferred for evaluating the scouring effect. Based on multivariate statistical analysis, the EMC value of TSS in road runoff was significantly positively correlated with the total rainfall duration (RD), and the EMC value of TN in green land runoff was significantly negatively correlated with the average rainfall intensity (ARI). Whether the vegetable market was considered as the underlying surface had a great impact on the calculation results of nutrient pollution load but had little impact on the calculation results of COD and TSS load. The difference percentage of nutrient pollution load under heavy rain reached 80%. Under this condition, the difference percentage of pollutant EMC between the road and vegetable market reached 1012%.

PMID:35393825 | DOI:10.13227/j.hjkx.202107040

Huan Jing Ke Xue. 2022 Apr 8;43(4):1885-1897. doi: 10.13227/j.hjkx.202108254.

ABSTRACT

In order to serve the water resources management of the Xiaohuangni River basin, this study explored the hydrochemical composition characteristics and ion sources of surface water in the basin. Samples of main stream and tributary river water and mine water were systematically collected. By means of a Piper diagram, Gibbs diagram, ion ratio coefficient, and mathematical statistical analysis, we analyzed the hydrochemical composition, spatial distribution characteristics, and main control factors of the Xiaohuangni River and evaluated the solute contribution rates of different sources. The results showed that the pH of the Xiaohuangni River basin ranged between 7.17 to 9.14, with an average of 8.00, which is generally considered weakly alkaline. Additionally, the total dissolved solids ranged between 154 mg·L^-1 to 460 mg·L^-1, with an average of 257.39 mg·L^-1, which was equivalent to that of the main stream of the Xijiang River. The dominant cation was Ca²⁺, accounting for 69% of the total cations; the dominant anions were HCO₃^– and SO₄^2-, accounting for 65% and 30% of the total anions, respectively. The main chemical type of the main stream was HCO₃-Ca. Affected by mining activities, the tributaries transitioned from HCO₃-Ca to HCO₃·SO₄-Ca and HCO₃·SO₄-Ca·Na type. River water solute was mainly controlled by the weathering of carbonate rock and silicate rock, with the participation of sulfuric and carbonic acid. The contribution rate of carbonate weathering to river water solute was 63%, and that of silicate weathering was 16.33%. Meanwhile, human activities contributed markedly to the dissolved solutes of the Xiaohuangni River basin, in which the contribution rate of mining activities was 13.4%, and the contribution rate of agricultural activities and domestic sewage was 4%.

PMID:35393812 | DOI:10.13227/j.hjkx.202108254

ESC Heart Fail. 2022 Apr 8. doi: 10.1002/ehf2.13926. Online ahead of print.

ABSTRACT

AIMS: The current study explores whether degree of inflammation, reflected by C-reactive protein (CRP) level, modifies the effect of intravenous (IV) corticosteroid administered in the emergency department (ED) on clinical outcomes in patients with acute heart failure (AHF).

METHODS AND RESULTS: We selected patients diagnosed with AHF in the ED, with confirmed N-terminal pro-B-type natriuretic peptide > 300 pg/mL and CRP > 5 mg/L in the ED from the Epidemiology of Acute Heart Failure in the Emergency Departments (EAHFE) registry. In these 1109 patients, 121 were treated by corticosteroid. The corticosteroid therapy hazard ratio (HR) for 30 day all-cause mortality was 1.26 [95% confidence interval (CI) 0.75-2.09, P = 0.38]. Although not statistically significant, HRs tended to decrease with increasing CRP level, with point estimates favouring corticosteroid at CRP levels above 20. In patients with CRP > 40 mg/L, with adjusted HRs of 0.56 (95% CI 0.20-1.55, P = 0.27) for 30 day all-cause mortality, 0.92 (95% CI 0.52-1.62, P = 0.78) for 30 day post-discharge ED revisit, hospitalization, or death, and adjusted odds ratio of 0.61 (95% CI 0.17-2.14, P = 0.44) for in-hospital all-cause mortality.

CONCLUSIONS: The present analysis suggests that corticosteroids might have the potential to improve outcomes in AHF patients with inflammatory activation. Larger, prospective studies of anti-inflammatory therapy should be considered to assess potential benefit in patients with the highest degree of inflammation.

PMID:35393762 | DOI:10.1002/ehf2.13926

Mol Inform. 2022 Apr 7. doi: 10.1002/minf.202100315. Online ahead of print.

ABSTRACT

Blood-brain-barrier permeability (BBBP) is an important property that is used to establish the drug-likeness of a molecule, as it establishes whether the molecule can cross the BBB when desired. It also eliminates those molecules which are not supposed to cross the barrier, as doing so would lead to toxicity. BBBP can be measured in vivo, in vitro or in silico. With the advent and subsequent rise of in silico methods for virtual drug screening, quite a bit of work has been done to predict this feature using statistical machine learning (ML) and deep learning (DL) based methods. In this work a mixed DL-based model, consisting of a Multi-layer Perceptron (MLP) and Convolutional Neural Network layers, has been paired with Mol2vec. Mol2vec is a convenient and unsupervised machine learning technique which produces high-dimensional vector representations of molecules and its molecular substructures. These succinct vector representations are utilized as inputs to the mixed DL model that is used for BBBP predictions. Several well-known benchmarks incorporating BBBP data have been used for supervised training and prediction by our mixed DL model which demonstrates superior results when compared to existing ML and DL techniques used for predicting BBBP.

PMID:35393777 | DOI:10.1002/minf.202100315

Biomed Chromatogr. 2022 Apr 7:e5381. doi: 10.1002/bmc.5381. Online ahead of print.

ABSTRACT

This research developed and validated a highly sensitive and selective UPLC-MS/MS approach using a triple quadrupole mass spectrometer for quantifying favipiravir (FAV). Moreover, we introduced a study evaluating bioequivalence using two drugs, favibrivix and avigan- containing favipiravir. Lean Six Sigma verified the capacity and performance of the process. Protein precipitation extraction was utilized to extract FAV from the collected human matrices. We used an ACQUITY UPLCr BEH HILIC column and valproic acid as an internal standard (IS). Furthermore, we conducted the procedure using an isocratic elution comprising acetonitrile and 0.005% ammonia in water (75:25, v/v), a flow rate of 0.25ml/min, a temperature-controlled at 10 ⁰ C, and an injection volume of 1.0μl. Our UPLC-MS/MS process has a broad range (50-10,000) ng/ml with a determination coefficient (r² ) of 0.9980. We validated the method in line with the FDA. The findings revealed that the test, favibrivix 200mg/tablet, and the reference, avigan® 200mg/tablet, were statistically bioequivalent regarding healthy Egyptian participants.

PMID:35393721 | DOI:10.1002/bmc.5381