Quantitative Biomarkers for Prediction of Epidermal Growth Factor Receptor Mutation in Non-Small Cell Lung Cancer

OBJECTIVES: To predict epidermal growth factor receptor (EGFR) mutation status using quantitative radiomic biomarkers and representative clinical variables. METHODS: The study included 180 patients diagnosed as of non-small cell lung cancer (NSCLC) with their pre-therapy computed tomography (CT) scans. Using a radiomic method, 485 features that reflect the heterogeneity and phenotype of tumors were extracted. Afterwards, these radiomic features were used for predicting epidermal growth factor receptor (EGFR) mutation status by a least absolute shrinkage and selection operator (LASSO) based on multivariable logistic regression. As a result, we found that radiomic features have prognostic ability in EGFR mutation status prediction. In addition, we used radiomic nomogram and calibration curve to test the performance of the model. RESULTS: Multivariate analysis revealed that the radiomic features had the potential to build a prediction model for EGFR mutation. The area under the receiver operating characteristic curve (AUC) for the training cohort was 0.8618, and the AUC for the validation cohort was 0.8725, which were superior to prediction model that used clinical variables alone. CONCLUSION: Radiomic features are better predictors of EGFR mutation status than conventional semantic CT image features or clinical variables to help doctors to decide who need EGFR tyrosine kinase inhibitor (TKI) treatment.     

Disturbance,seeds, restoration,and the importance of experiments and long‐term observations: the Editors' Award for 2005

Question: Can the geographic patterning of endemic plant species inform reserve selection in a region of high endemism? Location: The Southeastern Coastal Plain of North America, focusing primarily on the imperiled longleaf pine (Pinus palustris P. Miller) ecosystem. Methods: We documented the high level of plant endemism in the region, and characterized the endemic taxa into distributional subregions. Results: A total of 1630 plant taxa are endemic to the Coastal Plain, a large proportion of which are endemic to phytogeographical subregions within the Coastal Plain, with particularly large numbers of narrow endemics occurring in the East Gulf Coastal Plain and Florida Peninsula. Conclusions: This pattern of local endemism presents challenges in conserving the full biota of the region: a reserve system focusing on few and large conservation areas has theoretical benefits for long‐term management and viability, but will fail to capture many local endemics. We propose that the dispersed distribution of endemic species will require a mixture of large core reserves and smaller satellite reserves.     

关于提高物种划分合理性的意见

正这是我在The Flora of Pan-Himalaya(泛喜马拉雅植物志)第二次全体国内作者会议上关于物种划分问题的发言的结尾部分。我认为物种划分是分类学(狭义)的核心内容,所以我以辐冠参属(Pseudocodon)的鸡蛋参复合群(Pseudocodon convolvulaceus complex)和芍药属(Paeonia)的滇牡丹复合群(Paeonia delavayi complex)为例,重点陈述了我处理物种划分的思路和做法。发言后,不少听众很关注我的十点看法,更有些同事希望我发表出来。我感谢同事们的好意。物种是生物多样性的基本单元,所以我把发言稍加修改后在《生物多样性》发表,表达我对物种划分的观点。我是把这十点意见作为讨论和点评的靶子发表的,希望能引起同行的关注、讨论和点评。     

White-Tailed Deer Foraging Habitat in Intensively Established Loblolly Pine Plantations

ABSTRACT Stand establishment techniques involving multiple herbicide applications are commonly used on industrial pine (Pinus spp.) plantations, raising concern over potential effects on white-tailed deer (Odocoileus virginianus) forage production. We tested effects of stand establishment intensity on deer forage in 1–5-year-old loblolly pine (Pinus taeda) plantations (n = 4) in the East Gulf Coastal Plain of Mississippi using forage biomass and 4 measures of nutritional carrying capacity that reflected crude protein or digestible energy requirements for body maintenance and lactation. We also assessed whether forage biomass combined with a deer use rating effectively indexed nutritional carrying capacity. Treatments were combinations of mechanical site preparation, chemical site preparation (CSP), and herbaceous weed control (HWC). Total forage biomass and forage biomass of grasses and forbs were reduced by broadcast HWC. Forage biomass of vines was reduced both by CSP and by multiple broadcast HWC applications. Maintenance-level carrying capacity estimates were reduced by broadcast HWC; lactation-level estimates were higher in moderate-intensity treatments. We believe the inherently low fertility of this region makes high-quality forage production a more important management priority than increasing forage quantity. Chemical or chemical and mechanical site preparation combined with banded HWC provided the best option for providing both forage quality and quantity in open-canopied, intensively managed pine plantations. Biomass-based indices may be suitable for indexing protein-based maintenance-level carrying capacity in this region, but our results indicated they were not useful for indexing other carrying capacity estimates.     

Assessing Ecoregional-Scale Habitat Suitability Index Models for Priority Landbirds

ABSTRACT Emerging methods in habitat and wildlife population modeling promise new horizons in conservation but only if these methods provide robust population-habitat linkages. We used Breeding Bird Survey (BBS) data to verify and validate newly developed habitat suitability index (HSI) models for 40 priority landbird species in the Central Hardwoods and West Gulf Coastal Plain/Ouachitas Bird Conservation Regions. We considered a species’ HSI model verified if there was a significant rank correlation between mean predicted HSI score and mean observed BBS abundance across the 88 ecological subsections within these Bird Conservation Regions. When we included all subsections, correlations verified 37 models. Models for 3 species were unverified. Rank correlations for an additional 5 species were not significant when analyses included only subsections with BBS abundance >0. To validate models, we developed generalized linear models with mean observed BBS abundance as the response variable and mean HSI score and Bird Conservation Region as predictor variables. We considered verified models validated if the overall model was an improvement over an intercept-only null model and the coefficient on the HSI variable in the model was >0. Validation provided a more rigorous assessment of model performance than verification, and models for 12 species that we verified failed validation. Species whose models failed validation were either poorly sampled by BBS protocols or associated with woodland and shrubland habitats embedded within predominantly open landscapes. We validated models for 25 species. Habitat specialists and species reaching their highest densities in predominantly forested landscapes were more likely to have validated models. In their current form, validated models are useful for conservation planning of priority landbirds and offer both insight into limiting factors at ecoregional scales and a framework for monitoring priority landbird populations from readily available national data sets.     

干旱年份三江平原沼泽甲烷(CH4)排放及影响因子

为了研究淡水沼泽CH4排放的影响因子及其机制,在中国东北部的三江平原样地观测了CH4排放通量以及部分影响因子.结果表明,在2003年4～10月生长季内,毛果苔草沼泽CH4通量平均值为3.30 mg·m-2·h-1(最小值为0.65 mg·m-2·h-1,最大值为13.47 mg·m-2·h-1),低于小叶章沼泽化草甸CH4通量平均值4.91 mg·m-2·h-1(最小值为-0.12 mg·m-2·h-1,最大值为16.25 mg·m-2·h-1).在不同阶段,两种类型沼泽CH4通量有明显的变化,控制因子也不一样.4月份低温限制了CH4通量,两种类型沼泽差异很小.5～7月下旬,小叶章沼泽化草甸CH4通量显著高于毛果苔草沼泽CH4通量(P＜0.01),这种差异是由融冻作用造成的.8月份,植株密度和剖面中活性有机碳的浓度成为主要的影响因子,毛果苔草沼泽CH4通量比小叶章沼泽化草甸高.     

气候变化背景下中国农业气候资源变化Ⅳ.黄淮海平原半湿润暖温麦-玉两熟灌溉农区农业气候资源时空变化特征

基于中国黄淮海平原半湿润暖温麦-玉两熟灌溉农区66个气象台站1961-2007年的气候资料,比较分析了该区域内1961-1980年和1981-2007年2个时段喜凉作物和喜温作物温度生长期长度以及温度生长期内的活动积温、日照时数、降水量、参考作物蒸散量和干燥度等农业气候资源的时空变化特征.结果表明： 随着气候变暖,与1961-1980年的平均状况相比,1981-2007年研究区域喜凉作物和喜温作物温度生长期均呈延长趋势,分别延长了7.4和6.9 d;≥0 ℃和≥10 ℃积温总体表现为增加趋势,其气候倾向率分别为4.0～137.0和1.0～142.0 ℃·d·(10 a)^-1;喜凉作物和喜温作物温度生长期日照时数均呈显著下降趋势;全区仅安徽省北部和河南省东南部喜凉作物和喜温作物温度生长期内降水量呈增加趋势,其他地区均呈减少趋势,且以河北省、山东省北部的减幅最明显;全区大部分区域喜凉作物和喜温作物温度生长期内参考作物蒸散量呈下降趋势,干燥度呈增加趋势.     

三江平原农田土壤跳虫多尺度空间自相关性

土壤动物多尺度空间自相关性特征是土壤动物空间异质性和空间共存格局研究的重要基础。以土壤跳虫为研究对象,以中国科学院三江平原沼泽湿地生态实验站为研究区,于2011年8月和10月,选取具30 a以上耕作历史的旱地为实验样地,以5 m为步长设置一个50 m×50 m的实验样地,采用地统计中的全局Moran's I指数和局部Moran's I指数相结合的方法,研究土壤跳虫多尺度空间自相关性特征。全局空间自相关结果表明,土壤跳虫群落总密度和多数跳虫种类存在显著的多尺度空间自相关特征,多数为显著的正的空间自相关性,形成明显的空间集群。局部空间自相关结果表明,土壤跳虫群落总密度和所有跳虫种类均存在显著的局部空间自相关性,在局部地区形成"高—高"和/或"低—低"的空间集群,并和"高—低"和/或"低—高"的空间孤立区相伴发生,即形成"斑块"和"孔隙"相间分布的水平镶嵌格局;这种镶嵌格局具一定的时间动态特征,从夏季到秋季斑块大小和空间分布范围略有变化。研究表明,土壤跳虫具有明显的多尺度空间自相关性;空间集群是土壤跳虫的常见空间分布格局,在样地内形成"斑块"和"孔隙"相间分布的水平镶嵌格局,这种格局具年内时间变异性。     

Life beneath the surface of the central Texan Balcones Escarpment: genus Anillinus Casey, 1918 (Coleoptera,Carabidae, Bembidiini): new species,a key to the Texas species,and notes about their way of life and evolution

The Texas fauna of the genus Anillinus Casey, 1918 includes three previously described species (A. affabilis (Brues), 1902, A. depressus (Jeannel), 1963 and A. sinuatus (Jeannel), 1963) and four new species here described: A. acutipennis Sokolov & Reddell, sp. n. (type locality: Fort Hood area, Bell County, Texas); A. comalensis Sokolov & Kavanaugh, sp. n. (type locality: 7 miles W of New Braunfels, Comal County, Texas); A. forthoodensis Sokolov & Reddell, sp. n. (type locality: Fort Hood area, Bell County, Texas); A. wisemanensis Sokolov & Kavanaugh, sp. n. (type locality: Wiseman Sink, Hays County, Texas). A key for identification of adults of these species is provided. The fauna includes both soil- and cave-inhabiting species restricted to the Balcones Fault Zone and Lampasas Cut Plain and adjacent areas underlain by the Edwards-Trinity Aquifer. Based on morphological and distributional data, we hypothesize that four lineages of endogean Anillinus species extended their geographical ranges from a source area in the Ouachita-Ozark Mountains to the Balconian region in central Texas. There the cavernous Edwards-Trinity aquifer system provided an excellent refugium as the regional climate in the late Tertiary and early Quaternary became increasingly drier, rendering life at the surface nearly impossible for small, litter-inhabiting arthropods. Isolated within the Edwards-Trinity aquifer system, these anilline lineages subsequently differentiated, accounting for the currently known diversity. The paucity of specimens and difficulty in collecting them suggest that additional undiscovered species remain to be found in the region.