The relationship between Comprehensive Geriatric Assessment parameters and depression in elderly patients

BackgroundDepression is common and serious among elderly patients. The treatment of elderly depression is often delayed owing to insufficient diagnosis, which eventually leads to adverse consequences.AimsTo explore the association between the parameters of the Comprehensive Geriatric Assessment and depression in elderly patients.MethodsA cross-sectional study of 211 outpatients and inpatients aged ≥ 65 years from the Comprehensive Geriatric Assessment database was conducted. A Comprehensive Geriatric Assessment inventory was prepared by compiling and screening general characteristics, chronic diseases (cardiovascular disease, diabetes, and peptic ulcer disease), nutritional status, daily living ability, anthropometric measurements (body mass index (BMI), upper arm circumference, and calf circumference), and blood biochemical indicators (hemoglobin, albumin, prealbumin, triglycerides, and low-density lipoprotein cholesterol). The Geriatric Depression Scale was also conducted for each elderly patient to screen for depression. A multivariable logistic regression analysis was used to determine the association between the parameters of the Comprehensive Geriatric Assessment and geriatric depression.ResultsThere were 63 patients in the depression group with a median age of 84.00 years, and 148 patients in the non-depression group with a median age of 78.50 years. After controlling for confounders, the risk of depression in elderly patients with cardiovascular diseases was 6.011 times higher than that in those without cardiovascular diseases (p < 0.001); and the risk of depression in elderly patients with peptic ulcer diseases was 4.352 times higher than that in those without peptic ulcer diseases (p < 0.001); the risk of depression in elderly patients decreased by 22.6% for each 1-point increase in the Mini Nutritional Assessment (p < 0.001). The risk of depression in elderly patients decreased by 19.9% for each 1-point increase in calf circumference (p = 0.002), and by 13.0% for each 1-point increase in albumin (p = 0.014).ConclusionOur findings suggest that Comprehensive Geriatric Assessment parameters, such as cardiovascular disease, peptic ulcer disease, Mini Nutritional Assessment score, calf circumference, and albumin, were associated with depression. The Comprehensive Geriatric Assessment can assist in the early identification of depression in the elderly population

NCNet: Deep Learning Network Models for Predicting Function of Non-coding DNA

The human genome consists of 98.5% non-coding DNA sequences, and most of them have no known function. However, a majority of disease-associated variants lie in these regions. Therefore, it is critical to predict the function of non-coding DNA. Hence, we propose the NCNet, which integrates deep residual learning and sequence-to-sequence learning networks, to predict the transcription factor (TF) binding sites, which can then be used to predict non-coding functions. In NCNet, deep residual learning networks are used to enhance the identification rate of regulatory patterns of motifs, so that the sequence-to-sequence learning network may make the most out of the sequential dependency between the patterns. With the identity shortcut technique and deep architectures of the networks, NCNet achieves significant improvement compared to the original hybrid model in identifying regulatory markers

Digital-WGS: Automated, highly efficient whole-genome sequencing of single cells by digital microfluidics

单细胞全基因组测序(whole-genome sequencing, WGS)是表征细胞内DNA动态变化的关键手段，可为我们提供全面、深度的生物学信息，是生命科学领域研究的热点。然而，单细胞全基因组测序仍面临着诸如样品制备复杂、成本高、扩增偏置性强、误差大的挑战。杨朝勇教授课题组搭建了基于数字微流控的单细胞操控与纳升级全基因组测序平台Digital-WGS，可用于一体化、全自动的单细胞处理与分析。通过Digital-WGS方法制备的单细胞样本在不同测序深度下均展示出了高均一性、高覆盖率、高准确性的优势，解决了当前单细胞基因组测序操作复杂、成本高、均一性差、准确度低等问题，为单细胞基因组测序的广泛应用提供了新的思路。 本研究工作在化学化工学院杨朝勇教授的指导下完成，2015级iChEM直博生阮庆宇为第一作者。Single-cell whole-genome sequencing (WGS) is critical for characterizing dynamic intercellular changes in DNA. Current sample preparation technologies for single-cell WGS are complex, expensive, and suffer from high amplification bias and errors. Here, we describe Digital-WGS, a sample preparation platform that streamlines high-performance single-cell WGS with automatic processing based on digital microfluidics. Using the method, we provide high single-cell capture efficiency for any amount and types of cells by a wetted hydrodynamic structure. The digital control of droplets in a closed hydrophobic interface enables the complete removal of exogenous DNA, sufficient cell lysis, and lossless amplicon recovery, achieving the low coefficient of variation and high coverage at multiple scales. The single-cell genomic variations profiling performs the excellent detection of copy number variants with the smallest bin of 150 kb and single-nucleotide variants with allele dropout rate of 5.2%, holding great promise for broader applications of single-cell genomics.We thank the National Natural Science Foundation of China (21927806, 21735004, 21521004, and 21325522), the National Key R&D Program of China (2018YFC1602900, 2019YFA0905800), Innovative Research Team of High-Level Local Universities in Shanghai (SSMU-ZLCX20180701), and the Program for Changjiang Scholars and Innovative Research Team in University (IRT13036) for financial support. 研究工作得到了国家自然科学基金(21927806、21735004、21521004、21325522), 国家重点研发项目(2018YFC1602900、2019YFA0905800)和教育部“长江学者和创新团队发展计划” (IRT13036)的资助与支持

Source attribution of particulate matter pollution over North China with the adjoint method

We quantify the source contributions to surface PM2.5 (fine particulate matter) pollution over North China from January 2013 to 2015 using the GEOS-Chem chemical transport model and its adjoint with improved model horizontal resolution (1/4 degrees x 5/16 degrees) and aqueous-phase chemistry for sulfate production. The adjoint method attributes the PM2.5 pollution to emissions from different source sectors and chemical species at the model resolution. Wintertime surface PM2.5 over Beijing is contributed by emissions of organic carbon (27% of the total source contribution), anthropogenic fine dust (27%), and SO2 (14%), which are mainly from residential and industrial sources, followed by NH3 (13%) primarily from agricultural activities. About half of the Beijing pollution originates from sources outside of the city municipality. Adjoint analyses for other cities in North China all show significant regional pollution transport, supporting a joint regional control policy for effectively mitigating the PM2.5 air pollution.China's National Basic Research Program [2014CB441303]; National Natural Science Foundation of China [41205103, 41475112]SCI(E)[email protected]

Air pollution–aerosol interactions produce more bioavailable iron for ocean ecosystems

It has long been hypothesized that acids formed from anthropogenic pollutants and natural emissions dissolve iron (Fe) in airborne particles, enhancing the supply of bioavailable Fe to the oceans. However, field observations have yet to provide indisputable evidence to confirm this hypothesis. Single-particle chemical analysis for hundreds of individual atmospheric particles collected over the East China Sea shows that Fe-rich particles from coal combustion and steel industries were coated with thick layers of sulfate after 1 to 2 days of atmospheric residence. The Fe in aged particles was present as a “hotspot” of (insoluble) iron oxides and throughout the acidic sulfate coating in the form of (soluble) Fe sulfate, which increases with degree of aging (thickness of coating). This provides the “smoking gun” for acid iron dissolution, because iron sulfate was not detected in the freshly emitted particles and there is no other source or mechanism of iron sulfate formation in the atmosphere

Directional Selection from Host Plants Is a Major Force Driving Host Specificity in Magnaporthe Species

One major threat to global food security that requires immediate attention, is the increasing incidence of host shift and host expansion in growing number of pathogenic fungi and emergence of new pathogens. The threat is more alarming because, yield quality and quantity improvement efforts are encouraging the cultivation of uniform plants with low genetic diversity that are increasingly susceptible to emerging pathogens. However, the influence of host genome differentiation on pathogen genome differentiation and its contribution to emergence and adaptability is still obscure. Here, we compared genome sequence of 6 isolates of Magnaporthe species obtained from three different host plants. We demonstrated the evolutionary relationship between Magnaporthe species and the influence of host differentiation on pathogens. Phylogenetic analysis showed that evolution of pathogen directly corresponds with host divergence, suggesting that host-pathogen interaction has led to co-evolution. Furthermore, we identified an asymmetric selection pressure on Magnaporthe species. Oryza sativa-infecting isolates showed higher directional selection from host and subsequently tends to lower the genetic diversity in its genome. We concluded that, frequent gene loss or gain, new transposon acquisition and sequence divergence are host adaptability mechanisms for Magnaporthe species, and this coevolution processes is greatly driven by directional selection from host plants

RMDAP: A Versatile, Ready-To-Use Toolbox for Multigene Genetic Transformation

Background: The use of transgenes to improve complex traits in crops has challenged current genetic transformation technology for multigene transfer. Therefore, a multigene transformation strategy for use in plant molecular biology and plant genetic breeding is thus needed. Methodology/Principal Findings: Here we describe a versatile, ready-to-use multigene genetic transformation method, named the Recombination-assisted Multifunctional DNA Assembly Platform (RMDAP), which combines many of the useful features of existing plant transformation systems. This platform incorporates three widely-used recombination systems, namely, Gateway technology, in vivo Cre/loxP and recombineering into a highly efficient and reliable approach for gene assembly. RMDAP proposes a strategy for gene stacking and contains a wide range of flexible, modular vectors offering a series of functionally validated genetic elements to manipulate transgene overexpression or gene silencing involved in a metabolic pathway. In particular, the ability to construct a multigene marker-free vector is another attractive feature. The built-in flexibility of original vectors has greatly increased the expansibility and applicability of the system. A proof-ofprinciple experiment was confirmed by successfully transferring several heterologous genes into the plant genome. Conclusions/Significance: This platform is a ready-to-use toolbox for full exploitation of the potential for coordinate regulation of metabolic pathways and molecular breeding, and will eventually achieve the aim of what we call ‘‘one-sto

Study of Heavy Gas Pollutants’ Dispersion in Street Canyon Terrain

This study focused on heavy gas dispersion under the terrain conditions of street canyons. The effects of street aspect ratio and height ratio were investigated, and the influence of environmental wind speed in the typical ideal street canyon terrain was explored. The results indicated that the surrounding flow field distributions in street terrains were dominated by higher buildings. In addition, when the building height was held constant, the flow field was affected by the joint influence of the two isolated buildings. The interception effect of the street canyon on upstream pollutants declined with the decrease in the street canyon’s aspect ratio. In addition, when the height ratios were different, a large quantity of upstream pollutants accumulated on the windward side of higher buildings. The relative concentration per unit area inside the canyon was affected by the air circulation inside and outside the canyon and the size of the dispersion space. The increase in the environmental wind speed promotes the entry of pollutants into the street while aggravating the overall dispersion of the pollutants. Therefore, the emergence of the most unsafe wind speeds caused most of the pollutants to gather in the street canyons