LIDER: cell embedding based deep neural network classifier for supervised cell type identification

Background Automatic cell type identification has been an urgent task for the rapid development of single-cell RNA-seq techniques. Generally, the current approach for cell type identification is to generate cell clusters by unsupervised clustering and later assign labels to each cell cluster with manual annotation. Methods Here, we introduce LIDER (celL embeddIng based Deep nEural netwoRk classifier), a deep supervised learning method that combines cell embedding and deep neural network classifier for automatic cell type identification. Based on a stacked denoising autoencoder with a tailored and reconstructed loss function, LIDER identifies cell embedding and predicts cell types with a deep neural network classifier. LIDER was developed upon a stacked denoising autoencoder to learn encoder-decoder structures for identifying cell embedding. Results LIDER accurately identifies cell types by using stacked denoising autoencoder. Benchmarking against state-of-the-art methods across eight types of single-cell data, LIDER achieves comparable or even superior enhancement performance. Moreover, LIDER suggests comparable robust to batch effects. Our results show a potential in deep supervised learning for automatic cell type identification of single-cell RNA-seq data. The LIDER codes are available at https://github.com/ShiMGLab/LIDER

Association of antioxidants use with the risk of dementia among community-dwelling adults in the United Kingdom biobank

BackgroundData regarding the association between antioxidant supplementation and incident dementia are limited.MethodsWe included 494,632 adults (54.5% females) aged 40–71 years at baseline from the United Kingdom Biobank in the final analysis. Incident dementia was ascertained using hospital inpatient and death records up to January 2021.ResultsOver a median follow-up of 11.9 years, 7,128 new cases of all-cause dementia, 2,772 cases of Alzheimer’s disease, and 1,397 cases of vascular dementia were recorded. The hazard ratio (95% CI) for incident dementia associated with zinc supplementation was 0.84 (0.74–0.96), and the association remained significant after adjusting for all confounders (0.84 (0.74–0.96)). In the full model, zinc supplementation was associated with a reduced risk of Alzheimer’s disease [HR (95% CI): 0.71 (0.57–0.88)]. There was no significant association between zinc supplementation and the risk of vascular dementia. No significant associations with incident dementia were observed for other antioxidant supplementation. The association between zinc supplementation and incident dementia was significant among individuals with [HR (95% CI): 0.34 (0.15–0.77)] and without cataract [0.87 (0.77–0.99)] but it was stronger among those with cataract (p value for interaction = 0.0271).ConclusionOur findings suggest that zinc supplementation may help reduce the risk of all-cause dementia and Alzheimer’s disease in middle-aged or older adults, especially among those with cataracts

Diurnal Cycle Model of Lake Ice Surface Albedo : A Case Study of Wuliangsuhai Lake

Ice surface albedo is an important factor in various optical remote sensing technologies used to determine the distribution of snow or melt water on the ice, and to judge the formation or melting of lake ice in winter, especially in cold and arid areas. In this study, field measurements were conducted at Wuliangsuhai Lake, a typical lake in the semi-arid cold area of China, to investigate the diurnal variation of the ice surface albedo. Observations showed that the diurnal variations of the ice surface albedo exhibit bimodal characteristics with peaks occurring after sunrise and before sunset. The curve of ice surface albedo with time is affected by weather conditions. The first peak occurs later on cloudy days compared with sunny days, whereas the second peak appears earlier on cloudy days. Four probability density distribution functions—Laplace, Gauss, Gumbel, and Cauchy—were combined linearly to model the daily variation of the lake ice albedo on a sunny day. The simulations of diurnal variation in the albedo during the period from sunrise to sunset with a solar altitude angle higher than 5° indicate that the Laplace combination is the optimal statistical model. The Laplace combination can not only describe the bimodal characteristic of the diurnal albedo cycle when the solar altitude angle is higher than 5°, but also reflect the U-shaped distribution of the diurnal albedo as the solar altitude angle exceeds 15°. The scale of the model is about half the length of the day, and the position of the two peaks is closely related to the moment of sunrise, which reflects the asymmetry of the two peaks of the ice surface albedo. This study provides a basis for the development of parameterization schemes of diurnal variation of lake ice albedo in semi-arid cold regions

GWAS-by-subtraction reveals an IOP-independent component of primary open angle glaucoma

The etiology of primary open angle glaucoma is constituted by both intraocular pressure-dependent and intraocular pressure-independent mechanisms. However, GWASs of traits affecting primary open angle glaucoma through mechanisms independent of intraocular pressure remains limited. Here, we address this gap by subtracting the genetic effects of a GWAS for intraocular pressure from a GWAS for primary open angle glaucoma to reveal the genetic contribution to primary open angle glaucoma via intraocular pressure-independent mechanisms. Seventeen independent genome-wide significant SNPs were associated with the intraocular pressure-independent component of primary open angle glaucoma. Of these, 7 are located outside known normal tension glaucoma loci, 11 are located outside known intraocular pressure loci, and 2 are novel primary open angle glaucoma loci. The intraocular pressure-independent genetic component of primary open angle glaucoma is associated with glaucoma endophenotypes, while the intraocular pressure-dependent component is associated with blood pressure and vascular permeability. A genetic risk score for the intraocular pressure-independent component of primary open angle glaucoma is associated with 26 different retinal micro-vascular features, which contrasts with the genetic risk score for the intraocular pressure-dependent component. Increased understanding of these intraocular pressure-dependent and intraocular pressure-independent components provides insights into the pathogenesis of glaucoma

乌梁素海湖冰晴天反照率日变化特征的统计模型比较和分析

Based on the features of diurnal variation of ice surface albedo in the Lake Ulansuhai, the relationship between solar elevation angle and geographic coordinates and Julian days, together with normalized time, to express the diurnal variations of the ice albedo. Linear combinations of four probability density distribution functions with exponential forms, including Laplace, Gauss, Gumbel, and Cauchy equations, were used to simulate the diurnal variations in observed ice albedo from sunrise to sunset with solar elevation angle more than 5°. The results reveals that the Laplace combined statistical model is the best fit to the observations. It can not only clearly show the double-peak distribution in the diurnal variation in ice surface albedo when the elevation angle is greater than 5°, but also express the U-type distribution between the two peaks as the elevation angle is more than 15°. This model has advantages of simple form in expression and clear physical meaning. The length parameter is close to half day, and the peak location is associated with the time of sunrise, and the asymmetry of the two peaks can be also shown. It provides a solid foundation for the parameterization schemes on the diurnal variations in lake ice surface albedo in different regions. © 2020 by Journal of Lake Sciences.Peer reviewe

Persistent descending mesocolon as a vital risk factor for anastomotic failure and prolonged operative time for sigmoid colon and rectal cancers

Abstract Background The diagnostic criteria and effect of persistent descending mesocolon (PDM) on sigmoid and rectal cancers (SRCs) remain controversial. This study aims to clarify PDM patients' radiological features and short-term surgical results. Method From January 2020 to December 2021, radiological imaging data from 845 consecutive patients were retrospectively analyzed using multiplanar reconstruction (MRP) and maximum intensity projection (MIP). PDM is defined as the condition wherein the right margin of the descending colon is located medially to the left renal hilum. Propensity score matching (PSM) was used to minimize database bias. The anatomical features and surgical results of PDM patients were compared with those of non-PDM patients. Results Thirty-two patients with PDM and 813 patients with non-PDM were enrolled into the study who underwent laparoscopic resection. After 1:4 matching, patients were stratified into PDM (n = 27) and non-PDM (n = 105) groups. The lengths from the inferior mesenteric artery (IMA) to the inferior mesenteric vein (1.6 cm vs. 2.5 cm, p = 0.001), IMA to marginal artery arch (2.7 cm vs. 8.4 cm, p = 0.001), and IMA to the colon (3.3 cm vs. 10.2 cm, p = 0.001) were significantly shorter in the PDM group than those in the non-PDM group. The conversion to open surgery (11.1% vs. 0.9%, p = 0.008), operative time (210 min vs. 163 min, p = 0.001), intraoperative blood loss (50 ml vs. 30 ml, p = 0.002), marginal arch injury (14.8% vs. 0.9%, p = 0.006), splenic flexure free (22.2% vs. 3.8%, p = 0.005), Hartmann procedure (18.5% vs. 0.0%, p < 0.001) and anastomosis failure (18.5% vs. 0.9%, p = 0.001) were significantly higher in the PDM group. Moreover, PDM was an independent risk factor for prolonged operative time (OR = 3.205, p = 0.004) and anastomotic failure (OR = 7.601, p = 0.003). Conclusion PDM was an independent risk factor for prolonged operative time and anastomotic failure in SRCs surgery. Preoperative radiological evaluation using MRP and MIP can help surgeons better handle this rare congenital variant

EXAFS study on the local atomic structures around iron in glycosated haemoglobin

Samples with 5.1%, 9.8% and 15.3% HbA1c were extracted from normal subjects and patients with slight and serious diabetes respectively. Extended x-ray absorption fine structure spectra of Fe K absorption were collected at the EXAFS experimental station of the Beijing Synchrotron Radiation Facility. The step-by-step fluorescent mode was employed with a count time of 10 s per point. Several independent scans were averaged to eliminate the statistical noise. Reference backscattering amplitudes and phaseshifts were calculated using the curve wave theory (FEFF code) of EXAFS. Apart from the nitrogen neighbours around the central iron atom, oxygen neighbours are also found. The Fe-N bond length increases by about 0.02 Angstrom for the sample with 15.3% HbA1c compared with the others, but the Fe-O bond length is almost unchanged. With increasing of HbA1c concentration, the content of Hb increases and the content of HbO(2) decreases. This demonstrates that the glycosylation of haemoglobin will decrease its ability to carry oxygen