深圳城市生态大数据智慧管理和服务平台技术集成与应用研究

生态环境是人类赖以生存和发展的基础,城市生态大数据智慧管理和服务平台建设是生态城市和美丽城市建设的需要。以深圳市为例,借助物联网、移动互联网、计算机、数据库和网络地理信息系统技术,以及时空地理大数据整合和共享、大数据挖掘分析和云端一体化业务协同等关键技术,结合城市生态系统评估分析决策模型/方法/对策库,在实现深圳市“空-地-网-统计-众源”等多源异构生态大数据有效集成的基础上,搭建了 “数据采集-信息提取-知识发现-决策生成-快速服务”全流程、一体化的深圳市生态大数据智慧管理和服务平台,构建了面向业务部门和科研人员等专业用户的生态野外数据调查采集系统和城市生态监测与评估管理决策分析系统,以及面向社会大众的深圳生态大调查APP。平台首次揭示了深圳市1979年以来不同生态系统的格局、构成、过程、服务和健康状况的变化,提升了深圳市生态环境综合决策科学化、生态环境监管精准化、生态环境公共服务便民化水平。平台有效降低了用户数据收集与处理和操作专业模型的难度,突破了原始数据应用的瓶颈和难点,提高了专业模型在业务部门中的使用率。未来,依靠“生态大数据+生态专业模型”的技术方案实现从数据到知识的挖掘,是实现城市生态大数据智慧化和专业化管理的关键,也是全面提高城市生态环境保护信息化服务水平的重要途径。     

医疗大数据应用需求分析与平台建设构想

医疗大数据的应用对于临床医学研究、科学管理和医疗服务模式转型发展都具有重要意义。文章介绍了国内外医疗大数据应用现状，以及作者所在单位在医疗数据利用方面的做法经验，并从医务人员、患者、管理人员和科研人员的角度，分析了医疗大数据的应用需求。最后，结合已有实践，提出了医疗大数据应用平台的建设构想和步骤方法等。     

Survival and detectability bias of avian fence collision surveys in sagebrush steppe

We used female ring-necked pheasant (Phasianus colchicus) carcasses as surrogates for greater sage-grouse (Centrocercus urophasianus) to study factors influencing survival and detection bias associated with avian fence collision surveys in southern Idaho, USA, during spring 2009. We randomly placed 50 pheasant carcasses on each of 2 study areas, estimated detection probability during fence-line surveys, and monitored survival and retention of carcasses and their associated sign over a 31-day period. Survival modeling suggested site and habitat features had little impact on carcass survival, and constant survival models were most supported by the data. Model averaged carcass daily survival probability was low on both study areas and ranged from 0.776 to 0.812. Survival of all carcass sign varied strongly by location, and the top sign survival model included a site effect parameter. Model averaged daily survival probability for collision sign on the 2 study sites ranged from 0.863 to 0.988 and varied between sites. Logistic regression modeling indicated detection probability of carcasses during fence-line surveys for avian collision victims was influenced by habitat type and microsite shrub height at the carcass location. Carcasses located in big sagebrush (Artemisia tridentata) habitats were detected at a lower rate (0.36) than carcasses in little (A. arbuscula) and black sagebrush (A. nova) habitats (0.71). Increasing shrub height at the carcass location from the little sagebrush mean of 16.5 cm to the big sagebrush mean of 36.0 cm reduced detection probability by approximately 30%. Avian fence collision surveys in sagebrush-steppe habitats should be conducted at ≤2-week sampling intervals to reduce the impact of survival bias on collision rate estimates. Two-week sampling intervals may be too long in areas with low carcass and sign survival, therefore survival rates should be estimated on all study areas to determine the appropriate sampling interval duration. Researchers should be aware of the effects of local vegetation on detection probabilities, and methods to correct detection probabilities based on collision site attributes should be applied to ensure more accurate collision rate estimates. Additionally, caution should be used when aggregating or comparing uncorrected collision data from areas with differing vegetation, as detection probabilities are likely different between sites. © 2011 The Wildlife Society.     

不同蒿属植物对光强的适应性差异研究

对中国四种蒿属植物(毛莲蒿、蒙古蒿、牡蒿和灰苞蒿)的光合响应曲线进行了研究。结果表明:牡蒿具有高光饱点(411.0μmol·m-2·s-1)和最大光合速率(18.627μmol·m-2·s-1),以及较低的光补偿点(17.867μmol·m-2·s-1),对高光的适应能力最强;灰苞蒿的暗呼吸速率(0.353μmol·m-2·s-1)和表观量子效率(0.038)最低,说明该种对弱光的适应能力较差,且在弱光条件下只能维持较低的生长速率;灰苞蒿水分利用效率随光强的变化趋势与其他三种蒿属植物一致,但总体上维持在一个较高的水平,可能与其对干旱生境的适应有关。光合响应曲线各个拟合指标在种间呈现出了较大的变异,其中光补偿点(L cpμmol·m-2·s-1)和暗呼吸速率(R dayμmol·m-2·s-1)差异达到了显著水平。说明植物功能性状与植物对环境长期适应密切相关,并且这种适应性是稳定可遗传的。     

大数据时代的大脑科学——绘制智力的蓝图

在很多"之歌"中,我非常喜欢《长江之歌》,歌中唱道"你从远古走来,……你是无穷的源泉".正值《生物化学与生物物理进展》创刊40周年的日子,我愿意唱一首心中的歌——"脑之歌".人类大脑就好比是一条历史长河,它从远古流到了今天,又将从今天流向未来,是自然通过漫长进化所产生的最精细、最复杂、最优美和最成功的器官,是智力演化的最伟大奇迹,是人类智力产生的源泉,是人类灵性的家园.人脑以其非凡的能力造就了人类知识和文明的社会传承.可是到如今,我们还不知道人脑在整体上是如何工作的.脑功能神经组学或许是破解脑的奥秘的钥匙.     

Extrachromosomal DNA isolated from tomato big bud and Candidatus Phytoplasma australiense phytoplasma strains

The nucleotide sequences of two extrachromosomal elements from tomato big bud (TBB) and one extrachromosomal element from Candidatus Phytoplasma australiense (Ca. P. australiense) phytoplasmas were determined. Both TBB plasmids (3319 and 4092 bp) contained an open reading frame ( approximately 570 bp) with homology to the rolling circle replication initiator protein (Rep). This gene was shorter than the rep genes identified from other phytoplasma plasmids, geminiviruses and bacterial plasmids. Both TBB extrachromosomal DNAs (eDNAs) encoded a putative DNA primase (dnaG) gene, a chromosomal gene required for DNA replication and which contains the conserved topoisomerase/primase domain. We speculate that the replication mechanism for the TBB phytoplasma eDNA involves the dnaG gene instead of the rep gene. The Ca. P. australiense eDNA (3773 bp) was shown to be circular and contained four open reading frames. The rep gene was encoded on ORF 1 and had homology to both plasmid (pLS1) and geminivirus-like domains.     

The Impact of Annual and Seasonal Rainfall Patterns on Growth and Phenology of Emergent Tree Species in Southeastern Amazonia,Brazil

Understanding tree growth in response to rainfall distribution is critical to predicting forest and species population responses to climate change. We investigated inter‐annual and seasonal variation in stem diameter by three emergent tree species in a seasonally dry tropical forest in southeast Pará, Brazil. Annual diameter growth rates by Swietenia macrophylla demonstrated strong positive correlation with annual rainfall totals during 1997–2009; Hymenaea courbaril growth rates demonstrated weak positive correlation, whereas Parkia pendula exhibited weak negative correlation. For both Swietenia and Hymenaea, annual diameter growth rates correlated positively and significantly with rainfall totals during the first 6 mo of the growing year (July to December). Vernier dendrometer bands monitored at 4‐wk intervals during 3–5 yr confirmed strong seasonal effects on stem diameter expansion. Individuals of all three species expanded in unison during wet season months and were static or even contracted during dry season months. Stems of the deciduous Swietenia contracted as crowns were shed during the early dry season, expanded slightly as new crowns were flushed, and then contracted further during 3–5 wk flowering periods in the late dry season by newly mature crowns. The three species’ physiographic distribution patterns at the study site may partially underlie observed differences in annual and seasonal growth. With most global circulation models predicting conditions becoming gradually drier in southeast Amazonia over the coming decades, species such as Swietenia that perform best on the ‘wet end’ of current conditions may experience reduced growth rates. However, population viability will not necessarily be threatened if life history and ecophysiological responses to changing conditions are compensatory.     

机器学习在微生物组宿主表型预测中的应用

随着大数据时代的到来,如何将生物组学海量数据转化为易理解及可视化的知识是当前生物信息学面临的重要挑战之一。为了处理复杂、高维的微生物组数据,目前机器学习算法已被应用于人体微生物组研究,以揭示疾病背后的复杂机制。本文首先简述了微生物组数据处理方法及常用的机器学习算法,如支持向量机(SVM)、随机森林(RF)和人工神经网络(ANN)等,然后对机器学习的工作流程及其要点进行阐述,并探讨了机器学习算法在基于微生物组数据预测宿主表型方面的应用。最后以唾液微生物组数据预测口腔异味为例,实现了机器学习算法的模型构建与评估分析,并提供了可用于微生物组研究实践的R/Python代码(https://github.com/LiLabZSU/microbioML)。     

Long-term automatic trap data reveal factors affecting diurnal flight patterns of the Mediterranean Fruit fly

Mediterranean Fruit Fly (medfly), Ceratitis capitata (Wiedemann), is considered to be one of the most destructive fruit insect pests throughout the world. In recent years, the temporal dynamics of the medfly have been extensively studied by season, and, to a lesser extent, on a daily basis. We exploited, for the first time, a sequential automatic medfly male trapping system, in combination with climate data, to characterize diel flight patterns of male medflies trapped. The process was carried out in four commercial citrus fields over three growing seasons. Results showed that throughout the year, medfly flight activity began 4–6 hr after sunrise and peaked up to 2 to 3 hr before sunset. Generalized additive models (GAM) of the 934 days sampled revealed that in the fall, the diurnal flight activity was unimodal, that is, it began increasing at noon, peaking in the afternoon. By contrast, in the spring and summer, the diurnal flight activity exhibited a bimodal pattern, decreasing at midday. GAMs also revealed that hour after sunrise and temperature influenced medfly captures, with the former the more dominant factor. Thus, photophase significantly impacted the medfly's diurnal flight activity in each season. This study demonstrated that automatic traps that timestamp each capture are a primary research tool in insect flight activity studies that contributes to understanding diurnal insect activity within the growing season.     

Greater sage-grouse winter habitat use on the eastern edge of their range

Greater sage-grouse (Centrocercus urophasianus) at the western edge of the Dakotas occur in the transition zone between sagebrush and grassland communities. These mixed sagebrush (Artemisia sp.) and grasslands differ from those habitats that comprise the central portions of the sage-grouse range; yet, no information is available on winter habitat selection within this region of their distribution. We evaluated factors influencing greater sage-grouse winter habitat use in North Dakota during 2005–2006 and 2006–2007 and in South Dakota during 2006–2007 and 2007–2008. We captured and radio-marked 97 breeding-age females and 54 breeding-age males from 2005 to 2007 and quantified habitat selection for 98 of these birds that were alive during winter. We collected habitat measurements at 340 (177 ND, 163 SD) sage-grouse use sites and 680 random (340 each at 250 m and 500 m from locations) dependent sites. Use sites differed from random sites with greater percent sagebrush cover (14.75% use vs. 7.29% random; P < 0.001), percent total vegetation cover (36.76% use vs. 32.96% random; P ≤ 0.001), and sagebrush density (2.12 plants/m² use vs. 0.94 plants/m² random; P ≤ 0.001), but lesser percent grass cover (11.76% use vs. 16.01% random; P ≤ 0.001) and litter cover (4.34% use vs. 5.55% random; P = 0.001) and lower sagebrush height (20.02 cm use vs. 21.35 cm random; P = 0.13) and grass height (21.47 cm use vs. 23.21 cm random; P = 0.15). We used conditional logistic regression to estimate winter habitat selection by sage-grouse on continuous scales. The model sagebrush cover + sagebrush height + sagebrush cover × sagebrush height ( = 0.60) was the most supported of the 13 models we considered, indicating that percent sagebrush cover strongly influenced selection. Logistic odds ratios indicated that the probability of selection by sage-grouse increased by 1.867 for every 1% increase in sagebrush cover (95% CI = 1.627–2.141) and by 1.041 for every 1 cm increase in sagebrush height (95% CI = 1.002–1.082). The interaction between percent sagebrush canopy cover and sagebrush height (β = −0.01, SE ≤ 0.01; odds ratio = 0.987 [95% CI = 0.983–0.992]) also was significant. Management could focus on avoiding additional loss of sagebrush habitat, identifying areas of critical winter habitat, and implementing management actions based on causal mechanisms (e.g., soil moisture, precipitation) that affect sagebrush community structure in this region. Published 2012. This article is a U.S. Government work and is in the public domain in the USA.