DeepMHADTA: Prediction of Drug-Target Binding Affinity Using Multi-Head Self-Attention and Convolutional Neural Network

Drug-target interactions provide insight into the drug-side effects and drug repositioning. However, wet-lab biochemical experiments are time-consuming and labor-intensive, and are insufficient to meet the pressing demand for drug research and development. With the rapid advancement of deep learning, computational methods are increasingly applied to screen drug-target interactions. Many methods consider this problem as a binary classification task (binding or not), but ignore the quantitative binding affinity. In this paper, we propose a new end-to-end deep learning method called DeepMHADTA, which uses the multi-head self-attention mechanism in a deep residual network to predict drug-target binding affinity. On two benchmark datasets, our method outperformed several current state-of-the-art methods in terms of multiple performance measures, including mean square error (MSE), consistency index (CI), rm2, and PR curve area (AUPR). The results demonstrated that our method achieved better performance in predicting the drug–target binding affinity.     

大棚网纹甜瓜品种主要经济性状模糊综合评判

本文根据模糊数学的基本原理,对大棚栽培的13个网纹甜瓜品种,采用品质、产量和成熟期等11个经济性状,进行模糊综合评判．结果表明：Andes和Volga的综合经济性状较好;Earl’sSeine夏系I、Marchen、秋绿、Earl’s东海PF80,Heim,Earl’sSeine夏系Ⅱ、夏绿和Kyanaru次之;Bolero,JohnnyEarl’s和Earl’s东海S78较差．作者认为：Andes及Volga为大棚栽培的首选品种,其次选用Earl’sSeine夏系I、秋绿和Earl’s东海PF80等品种．     

Bacteriological and chemical changes occurring in Bunker-stored silage covered with biodegradable coating

AIMS: To evaluate the efficacy of a biodegradable silage coating for the ability to protect timothy (Phleum pratensa) type silage against spoilage and its quality under natural conditions. METHODS AND RESULTS: Triplicate mini-silos of silage were prepared for three treatments (1: uncoated; 2: coated with biodegradable coating and 3: sealed with plastic), two types of storage (unprotected or protected from rain) and 10 sampling times (0, 7, 14, 21, 28, 35, 42, 56, 63 and 70 days postensiling). Triplicate mini-silos were opened at each sampling time for microbiological (total aerobic bacteria, lactic acid bacteria, moulds and yeasts) and biochemical analyses [pH, dry matter (DM), water-soluble sugars (WSC), lactic (LA), acetic, propionic and butyric acids content]. The study showed that at day 70, counts of moulds and yeasts in silages protected against rain and coated with biodegradable coating were 5.98 log CFU g(-1) when compared with 5.92 and 3.62 log CFU g(-1) in samples from plastic-sealed silage and uncoated silage, respectively. The pH was low and stable pH (4.34) when compared with uncoated (7.17) and plastic sealed (8.34) silages (P < or = 0.05). A DM, WSC and LA content of 421.7, 13.4 and 20.9 g kg(-1) was, respectively, observed. For silage stored outdoors, a level of moulds and yeasts of 3.77 log CFU g(-1) of silage was also observed in silages coated with biodegradable coating after 28 days of storage. A stable pH showing a mean value of 4 was also observed. The pH, DM, WSC and LA content were, respectively, 4.18, 341.1, 13.34 and 31.8 g kg(-1) in these samples. After 70 days of storage, the level of moulds and yeasts on silage sealed with biodegradable coating was 7.73 log CFU g(-1). A DM, WSC and LA content of 291.9, 5.56 and 10.0 g kg(-1) was, respectively, observed. CONCLUSIONS: When compared with uncoated silage, the application of biodegradable coating can preserve the quality of silage for up to a month when exposed to rain and up to 70 days when protected from rain. SIGNIFICANCE AND IMPACT OF THE STUDY: Results emphasize the possibility of the use of a biodegradable coating as an alternative to plastic film for sealing horizontal bunker silos.     

长三角地区大棚避雨栽培下不同生态适应型葡萄的光合特性

研究了长江三角洲地区大棚避雨覆盖栽培下葡萄光合生理生态特性的变化规律.结果表明,不论是晴天还是阴天,避雨覆盖都显著削弱了大棚内的光合有效辐射（PFD）,但对气温（T_a）、大气水汽压（V_p）和蒸腾速率（T_r）无明显影响.避雨覆盖栽培使美人指与藤稔葡萄品种的叶片厚度分别下降了28.6%和18.4%、比叶鲜重分别下降了13.1%和11.6%、叶片总叶绿素(Chl)含量与表观量子效率（AQY）略有增加,但Chla、Chlb含量及Chla/Chlb比值与对照无显著差异.晴天时,避雨覆盖栽培使美人指和藤稔品种的净光合速率（P_n）日均值分别下降18.7%和13.1％、P_n日积分值分别下降17.2%和11.9％、水分利用效率（WUE）分别下降26%和36.9％、气孔导度（G_s）则分别增加76.8%和100.8%;阴天时,避雨覆盖栽培使美人指和藤稔品种的P_n日均值分别下降48.7%和33.5％、P_n日积分值分别下降34.0%和29.8％、WUE分别下降69.2%和67.7％、G_s分别增加178.0%和85.1%.美人指品种的生理、光合指标的变幅比藤稔品种大,且阴天条件下差异更显著,表明两品种的生态适应性有明显差异.     

Three-dimensional chromatin ensemble reconstruction via stochastic embedding

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Issues in using whole slide imaging for diagnostic pathology: “routine” stains,immunohistochemistry and predictive markers

The traditional microscope, together with the “routine” hematoxylin and eosin (H & E) stain, remains the “gold standard” for diagnosis of cancer and other diseases; remarkably, it and the majority of associated biological stains are more than 150 years old. Immunohistochemistry has added to the repertoire of “stains” available. Because of the need for specific identification and even measurement of “biomarkers,” immunohistochemistry has increased the demand for consistency of performance and interpretation of staining results. Rapid advances in the capabilities of digital imaging hardware and software now offer a realistic route to improved reproducibility, accuracy and quantification by utilizing whole slide digital images for diagnosis, education and research. There also are potential efficiencies in work flow and the promise of powerful new analytical methods; however, there also are challenges with respect to validation of the quality and fidelity of digital images, including the standard H & E stain, so that diagnostic performance by pathologists is not compromised when they rely on whole slide images instead of traditional stained tissues on glass slides.     

Observations on the biology of Leuciscus ‘svallize’ in the Kremasta reservoir (Greece)

The age, growth, feeding habits and reproductive biology of Leuciscus svallize in artificial lake Kremasta (Greece), are described. There is a considerable similarity in the feeding and reproductive characteristics between L. svallize and L. cephalus and also a similarity in the life span, growth patterns and age of maturation between L. svallize and some southern L. cephalus populations, which may suggest similar responses of closely related taxa to similar conditions.     

地膜覆盖和施氮量对旱作春玉米农田净温室效应的影响

以旱作雨养条件下的春玉米为试验对象,在长武黄土高原农业生态试验站进行田间试验,研究了地膜覆盖和施氮量对农田净温室效应和温室气体排放强度的影响.结果表明:采用地膜覆盖与增加施氮量都会影响净温室效应与温室气体排放强度,地膜覆盖条件下(FM),不同施氮量的春玉米产量为1643~16699 kg·hm-2,净温室效应(CO_2当量,下同)为595~4376 kg·hm^-2·a^-1,温室气体排放强度为213~358 kg·t^-1;无覆膜条件下(UM),不同施氮量的春玉米产量为956~8821 kg·hm-2,净温室效应为342~4004 kg·hm^-2·a^-1,温室气体排放强度为204~520 kg·t^-1.研究表明,对于旱作春玉米农田系统,地膜覆盖可以有效降低温室气体排放强度,增加作物产量,地膜覆盖下施氮250 kg·hm-2可以实现高产与降低环境代价的双赢.     

覆膜对春小麦农田微生物数量和土壤养分的影响

研究了黄绵土区不同覆膜时期对旱作麦田土壤微生物数量及其与土壤碳、氮、磷含量的关系。丰水的 1 999年 ,土壤微生物数量增长早 ,延续时间长 ,覆膜 60 d微生物数量最高 (3 3 .93 8× 1 0 6 /g dry soil) ,其次为全程覆膜 (3 2 .2 5 9× 1 0 6 ) ;干旱的 2 0 0 0年微生物平均数量只有 1 999年的 3 6.5 % ,在后期有一定降水后微生物数量才出现高峰 ,以全程覆膜数量最高(1 4.83 6× 1 0 6 ) ,覆膜 60 d次之 (1 1 .5 2 9× 1 0 6 )。 1 999年各类群微生物数量同土壤有机碳之间均呈显著或极显著负相关。2 0 0 0年相关系数几乎全面下降 ,氨化细菌、硝化细菌和反硝化细菌 ,甚至微生物总量同土壤有机碳之间都已不再显著相关。 1 999年土壤全氮同氨化细菌、硝化细菌、亚硝化细菌、解磷细菌及微生物总量均呈显著或极显著负相关 ,2 0 0 0年只与氨化细菌、亚硝化细菌、微生物总数显著负相关。土壤速效磷含量在 1 999年与解磷细菌显著负相关 ,而在 2 0 0 0年相关已不再显著。两年试验结束后 ,全程覆膜处理有机质下降 2 1 .2 % ,覆膜 60 d处理下降 1 7.2 % ,覆膜 3 0 d和不覆膜处理下降相对较小 (4 .3 %和 6.7% )。由于施用化肥 ,土壤全氮有明显升高。速效磷在 1 999生长季和随后的休闲期都有升高 ,在干旱的 2 0 0 0