Establishing a Gross Primary Productivity Model by SIF and PRI on the Rice Canopy.

Solar-induced chlorophyll fluorescence (SIF) has shown remarkable results in estimating vegetation carbon cycles, and combining it with the photochemical reflectance index (PRI) has great potential for estimating gross primary productivity (GPP). However, few studies have used SIF combined with PRI to estimate crop canopy GPP. Large temporal and spatial variability between SIF, PRI, and GPP has also been found in remote sensing observations, and the observed PRI and SIF are influenced by the ratio of different observed information (e.g., background, direct sunlit, and shaded leaves) and the physiological state of the vegetation. In this study, the PRI and SIF from a multi-angle spectrometer and the GPP from an eddy covariance system were used to assess the ability of the PRI to enhance the SIF-GPP estimation model. A semi-empirical kernel-driven Bidirectional Reflectance Distribution Function (BRDF) model was used to describe the hotspot PRI/SIF (PRIhs/SIFhs), and a modified two-leaf model was used to calculate the total canopy PRI/SIF (PRItot/SIFtot). We compared the accuracies of PRIhs/SIFhs and PRItot/SIFtot in estimating GPP. The results indicated that the PRItot+SIFtot-GPP model performed the best, with a correlation coefficient (R2) of the validation dataset of 0.88, a root mean square error (RMSE) of 3.74, and relative prediction deviation (RPD) of 2.71. The leaf area index (LAI) had a linear effect on the PRI/SIF estimation of GPP, but the temperature and vapor pressure differences had nonlinear effects. Compared with hotspot PRIhs/SIFhs, PRItot/SIFtot exhibited better consistency with GPP across different time series. Our research demonstrates that PRI is effective in enhancing SIF and PRI for estimating GPP on the rice canopy and also suggests that the two-leaf model would contribute to the vegetation index tracking the real-time crop productivity.

Graded diagnosis of Helicobacter pylori infection using hyperspectral images of gastric juice.

Helicobacter pylori is a potential underlying cause of many diseases. Although the Carbon 13 breath test is considered the gold standard for detection, it is high cost and low public accessibility in certain areas limit its widespread use. In this study, we sought to use machine learning and deep learning algorithm models to classify and diagnose H. pylori infection status. We used hyperspectral imaging system to gather gastric juice images and then retrieved spectral feature information between 400 and 1000 nm. Two different data processing methods were employed, resulting in the establishment of one-dimensional (1D) and two-dimensional (2D) datasets. In the binary classification task, the random forest model achieved a prediction accuracy of 83.27% when learning features from 1D data, with a specificity of 84.56% and a sensitivity of 92.31%. In the ternary classification task, the ResNet model learned from 2D data and achieved a classification accuracy of 91.48%.

Rest-Activity Rhythms Are Associated With Prevalent Cardiovascular Disease, Hypertension, Obesity, and Central Adiposity in a Nationally Representative Sample of US Adults.

BACKGROUND: Rest-activity rhythms (RARs), a measure of circadian rhythmicity in the free-living setting, are related to mortality risk, but evidence is limited on associations with cardiovascular disease (CVD) and its risk factors. METHODS AND RESULTS: Participants included 4521 adults from the 2013 to 2014 National Health and Nutrition Examination Survey physical activity monitoring examination. Wrist-worn ActiGraph GT3X+ data were used to estimate RARs. Multivariable logistic models evaluated associations of RARs with prevalent CVD, hypertension, obesity, and central adiposity. Participants (mean age, 49 years) in the highest versus lowest tertile of relative amplitude (greater circadian rhythmicity) had 39% to 62% lower odds of prevalent CVD, hypertension, obesity, and central adiposity. A more active wake period was associated with 19% to 72% lower CVD, hypertension, obesity, and central adiposity odds. Higher interdaily stability (regular sleep-wake and rest-activity patterns) was related to 52% and 23% lower CVD and obesity odds, respectively. In contrast, participants in the highest versus lowest tertile of intradaily variability (fragmented RAR and inefficient sleep) had >3-fold and 24% higher CVD and obesity odds, respectively. A later and less restful sleep period was associated with 36% to 2-fold higher CVD, hypertension, obesity, and central adiposity odds. A statistically significant linear trend was observed for all associations (P-trend<0.05). CONCLUSIONS: A robust, stable, and less fragmented RAR, an active wake period, and an earlier and more restful sleep period are associated with lower prevalent CVD, hypertension, obesity, and central adiposity, with evidence of a dose-response relationship. The magnitude, timing, and regularity of sleep-wake and rest-activity patterns may be important targets for reducing cardiovascular risk.

Genetic polymorphisms of very important pharmacogene variants in the Chinese Lisu population.

Aim: Interindividual and interethnic differences in drug efficacy drive the development and progress of pharmacogenomics and precision medicine. This study was performed to enrich the pharmacogenomic information for the Lisu population from China. Methods: 54 very important pharmacogene variants were selected from PharmGKB and genotyped in 199 Lisu individuals. The genotype distribution data of 26 populations were downloaded from the 1000 Genomes Project and analyzed with the χ2 test. Results: Among the 26 populations in the 1000 Genomes Project, African Caribbeans in Barbados; Esan in Nigeria; Gambian in Western Divisions, The Gambia; Luhya in Webuye, Kenya; Yoruba in Ibadan; Finnish in Finland; Toscani in Italy and Sri Lankan Tamil in the UK were the top eight nationalities with the most significant differences in genotype distribution from the Lisu population. The loci of CYP3A5 rs776746, KCNH2 rs1805123, ACE rs4291, SLC19A1 rs1051298 and CYP2D6 rs1065852 were significantly different in the Lisu. Conclusion: The results showed that there were substantial differences in SNPs of very important pharmacogene variants, which can provide a theoretical basis for individualized drug use for the Lisu.

NOTCH2, ATIC, MRI1, SLC6A13, ATP13A2 Genetic Variations are Associated with Ventricular Septal Defect in the Chinese Tibetan Population Through Whole-Exome Sequencing.

Background: Ventricular septal defect (VSD) is the most common congenital cardiac abnormality in children and the second most common in adults. This study aimed to explore the potentially causative genes in VSD patients in the Chinese Tibetan population, and to provide a theoretical basis for the genetic mechanism of VSD. Methods: Peripheral venous blood was collected from 20 VSD subjects, and whole-genome DNA was extracted. High-throughput sequencing was performed on qualified DNA samples using whole-exome sequencing (WES) technology. After filtering, detecting, and annotating qualified data, single nucleotide variations (SNVs) and insertion-deletion (InDel) markers were analyzed, and data processing software such as GATK, SIFT, Polyphen, and MutationTaster were used for comparative evaluation and prediction of pathogenic deleterious variants associated with VSD. Results: A total of 4793 variant loci, including 4168 SNVs, 557 InDels and 68 unknown loci and 2566 variant genes were obtained from 20 VSD subjects through bioinformatics analysis. According to the screening of the prediction software and database, the occurrence of VSD was predicted to be associated with five inherited pathogenic gene mutations, all of which were missense mutations, including NOTCH2 (c.1396C >A:p.Gln466Lys), ATIC (c.235C >T:p.Arg79Cys), MRI1 (c.629G >A:p.Arg210Gln), SLC6A13 (c.1138G >A:p.Gly380Arg), ATP13A2 (c.1363C >T:p.Arg455Trp). Conclusion: This study demonstrated that NOTCH2, ATIC, MRI1, SLC6A13, ATP13A2 gene variants were potentially associated with VSD in Chinese Tibetan population.

Whole-exome sequencing in searching for novel variants associated with the development of high altitude pulmonary edema.

BACKGROUND: High altitude pulmonary edema (HAPE) is a high-altitude idiopathic disease with serious consequences due to hypoxia at high altitude, and there is individual genetic susceptibility. Whole-exome sequencing (WES) is an effective tool for studying the genetic etiology of HAPE and can identify potentially novel mutations that may cause protein instability and may contribute to the development of HAPE. MATERIALS AND METHODS: A total of 50 unrelated HAPE patients were examined using WES, and the available bioinformatics tools were used to perform an analysis of exonic regions. Using the Phenolyzer program, disease candidate gene analysis was carried out. SIFT, PolyPhen-2, Mutation Taster, CADD, DANN, and I-Mutant software were used to assess the effects of genetic variations on protein function. RESULTS: The results showed that rs368502694 (p. R1022Q) located in NOS3, rs1595850639 (p. G61S) located in MYBPC3, and rs1367895529 (p. R333H) located in ITGAV were correlated with a high risk of HAPE, and thus could be regarded as potential genetic variations associated with HAPE. CONCLUSION: WES was used in this study for the first time to directly screen genetic variations related to HAPE. Notably, our study offers fresh information for the subsequent investigation into the etiology of HAPE.

Novel insights into source apportionment of dissolved organic matter in aquifer affected by anthropogenic groundwater recharge: Applicability of end-member mixing analysis based optical indices.

The composition and main sources of dissolved organic matter (DOM) in groundwater may change significantly under long-term anthropogenic groundwater recharge (AGR); however, the impact of AGR on quantitative sources of groundwater DOM has seldom been reported. This study evaluated the applicability of optical indices combined with mixing stable isotope analysis in R (MixSIAR) in end-member mixing analysis (EMMA) of groundwater DOM. Fluorescent indices, including C1%, C2%, and C3%, were more sensitive to AGR than other absorbance indices, as indicated by the significant difference between the dominant area of artificial groundwater recharged by surface water and the dominant area of natural groundwater recharged by atmospheric precipitation (NGRP). BIX-C1% was selected as the optimal dual index after the screening protocol of groundwater DOM for EMMA. Our results showed that DOM in the aquifer was mainly subject to autochthonous DOM and the contribution of background groundwater to AGRSW and NGRP groundwater accounted for 36.15% ± 32.41% and 55.46% ± 37.17% (p < 0.05), respectively. Therefore, AGR significantly changed the native DOM in the groundwater. In allochthonous sources of DOM, sewage and surface water contributed 29.54% ± 24.87% and 21.32% ± 28.08%, and 24.79% ± 15.56% and 15.21% ± 14.20% to AGRSW and NGRP groundwater, respectively. The contribution of surface water to AGRSW groundwater was significantly higher than that to NGRP groundwater (p < 0.05), indicating that AGR introduced significantly more DOM from surface water to groundwater. This study provides novel insights into the quantitative source apportionment of DOM in groundwater under long-term AGR, which will facilitate the environmental risk assessment of present AGR measures and the sustainable management of clean water.

Genome-Wide Association Study on the Hematological Phenotypic Characteristics of the Han Population from Northwest China.

Background: Hematological characteristics have positive reference value as clinical indicators in the evaluation of various diseases. The purpose of this study was to determine the gene loci associated with 20 hematological phenotypes in the Han population from northwest China. Methods: A genome-wide association study (GWAS) was conducted on hematological indicators of 1005 Han people from northwest China. Genotyping was performed with a GeneTitan multichannel instrument and Axiom Analysis Suite 6.0. Using the 1000 Genomes Project (phase 3) as a reference, haplotype imputation was performed with IMPUTE2. SNVs (single nucleotide variants) significantly associated with hematological phenotypes were identified. The top SNV (p < 5E-7) was then selected for replication detection. Results: Ninety genetic variations identified in the GWAS were significantly associated with hematological indicators. Among them, only rs35289401 (CCDC157) was significantly associated (genome-wide) with red blood cell distribution width (RDW) (p = 4.21E-08). The fourteen top SNVs were selected for replication verification and were significantly associated with hematological phenotypes. However, only HBS1 L-MYB rs1331309 was significantly associated with the mean hemoglobin content (p = 6.42E-07). We also found that the mean corpuscular hemoglobin (MCH) level in the rs1331309 GG/GT genotype was significantly higher than that in the TT genotype (p = 0.023). Conclusion: The GWAS identified a total of 90 genetic variants significantly associated with hematological phenotypic indicators. In particular, rs1331309 (HBS1 L-MYB) is expected to be a biomarker for monitoring the dynamics of MCH levels. This study provides a reference for related studies on the genetic structure of hematological characteristics. It provides a valuable reference for the clinical diagnosis or prediction of a variety of diseases.

CYP2S1 gene methylation among High-altitude pulmonary edema.

BACKGROUND: High altitude pulmonary edema (HAPE) is a fatal disease of fluid accumulation in the lungs resulting from acute exposure to high altitude and hypoxia. Now research has found that changes in DNA methylation are genetically related. We investigated the effects of hypermethylation and hypomethylation on HAPE. METHODS: We conducted an analysis of methylation in Chinese HAPE patients (53 patients and 53 controls). EpiTYPER of the Sequenom MassARRAY platform was used to detect DNA methylation at 43 CpG sites in CYP2S1. RESULTS: We used probability analysis to find that only five CPG sites were not methylated. CYP2S1_1_CpG_11, CYP2S1_2_CpG_11, CYP2S1_2_CpG_12, CYP2S1_2_CpG_13, and CYP2S1_3_CPG_11.12 in the case group were lower than those in the control group. Our results showed that, 12 CpG sites had different methylation levels in HAPE patients compared with healthy controls, and only CYP2S1_1_CPG_1.2.3 (OR = 2.920, 95 %Cl = 1.228-6.946, p = 0.015) had a higher risk of hypermethylation than hypomethylation. ROC curve analysis showed that the methylation level of CYP2S1 could effectively predict the risk of HAPE patients. CONCLUSION: Our results showed that several CpG sites in the promoter regions of CYP2S1 gene were abnormally methylated in HAPE patients.

Impacts of anthropogenic groundwater recharge (AGR) on nitrate dynamics in a phreatic aquifer revealed by hydrochemical and isotopic technologies.

Although anthropogenic groundwater recharge (AGR) can either elevate or decline the concentration of nitrate in the phreatic aquifer with high hydraulic conductivity, the long-term impact of AGR on nitrate dynamics in the phreatic aquifer and its reason is seldom disclosed. In this study, the hydrogen and oxygen stable isotopes (δ2H-H2O and δ18O-H2O) combined with mixing stable isotope analysis in R (MixSIAR) were used to group the study area into the dominant area of AGR by surface water (AGRSW) and the dominant area of natural groundwater recharged by precipitation (NGRP). Hydrochemical parameters and multiple stable isotopes, including δ2H-H2O, δ18O-H2O, δ15N-NO3-, δ18O-NO3-, and δ13C-DIC, were applied to explore the impacts of AGR on the concentration, biogeochemical processes, and main sources of nitrate. The results showed that AGR by surface water with low nitrate content can reduce nitrate pollution in groundwater. The characteristic of δ18O-NO3- value revealed that nitrification was the primary biogeochemical process of nitrogen in groundwater. AGR may enhance nitrification as indicated by the δ18O-NO3- value closer to the nitrification theoretical line. Dual nitrate stable isotopes and MixSIAR revealed that chemical fertilizer (CF), soil nitrogen (SN), and surface water (SW) contributed 10.88%, 49.92%, and 27.64% to nitrate in AGRSW groundwater, respectively, which was significantly different from their contributions to NGRP groundwater (p < 0.05). Notably, AGR significantly increased the contribution of SW but decreased the contribution of CF and SN in groundwater. This study provided a basis and guidance for groundwater quality assessment and pollution control in the phreatic aquifer with high hydraulic conductivity.

Genetic Polymorphisms of Very Important Pharmacogene Variants in the Blang Population from Yunnan Province in China.

BACKGROUND: We aimed to enrich the pharmacogenomic information of a Blang population (BP) from Yunnan Province in China. METHODS: We genotyped 55 very important pharmacogene (VIP) variants from the PharmGKB database and compared their genotype distribution (GD) in a BP with that of 26 populations by the χ 2 test. The minor allele frequency (MAF) distribution of seven significantly different single-nucleotide polymorphisms (SNPs) was conducted to compare the difference between the BP and 26 other populations. RESULTS: Compared with the GD of 55 loci in the BP, among 26 studied populations, GWD, YRI, GIH, ESN, MSL, TSI, PJL, ACB, FIN and IBS were the top-10 populations, which showed a significantly different GD >35 loci. CHB, JPT, CDX, CHS, and KHV populations had a significantly different GD <20 loci. A GD difference of 27-34 loci was found between the BP and 11 populations (LWK, CEU, ITU, STU, PUR, CLM, GBR, ASW, BEB, MXL and PEL). The GD of five loci (rs750155 (SULT1A1), rs4291 (ACE), rs1051298 (SLC19A1), rs1131596 (SLC19A1) and rs1051296 (SLC19A1)) were the most significantly different in the BP as compared with that of the other 26 populations. The genotype frequency of rs1800764 (ACE) and rs1065852 (CYP2D6) was different in all populations except for PEL and LWK, respectively. MAFs of rs1065852 (CYP2D6) and rs750155 (SULT1A1) showed the largest fluctuation between the BP and SAS, EUR, AFR and AMR populations. CONCLUSION: Our data can provide theoretical guidance for safe and efficacious personalized drug use in the Blang population.

Removal of lincomycin from aqueous solution by birnessite: kinetics, mechanism, and effect of common ions.

The removal of lincomycin (LIN) from aqueous solution by birnessite was investigated by batch experiments. When the dosage of birnessite is 500 mg L-1 and the initial concentration of LIN is 15.5 µmol L-1, more than 90% of LIN was removed within 240 min at pH 4.90. Under different conditions, the reactions were well fitted with the second-order model (R2 > 0.95). The removal kinetics and the reaction mechanism were described. The presence of cations (e.g., K+, Ca2+, Mg2+, Fe2+, and Mn2+) inhibited the removal of LIN by birnessite, following the order: Mn2+ > Fe2+ > Ca2+ > Mg2+ > K+ ≈ Na+, due to the sorption of cations on birnessite, companying with the electron transfer and precipitation of oxides (for Mn2+ and Fe2+). The addition of Cu2+, SO42-, or NO3- improved the reactions. The presence of Cu2+ could oxidize antibiotics, and the repulsion between SO42-or NO3- and birnessite might disperse the birnessite suspensions during the reactions. Mn(IV) and Mn(III) were the core Mn species that play an important role in LIN removal. These findings will help to understand the removal process of LIN and illustrate the influence of cations and anions on the removal of similar pollutants by birnessite.