Thermo-msf-parser: an open source Java library to parse and visualize Thermo Proteome Discoverer msf files

The Thermo Proteome Discoverer program integrates both peptide identification and quantification into a single workflow for peptide-centric proteomics. Furthermore, its close integration with Thermo mass spectrometers has made it increasingly popular in the field. Here, we present a Java library to parse the msf files that constitute the output of Proteome Discoverer. The parser is also implemented as a graphical user interface allowing convenient access to the information found in the msf files, and in Rover, a program to analyze and validate quantitative proteomics information. All code, binaries, and documentation is freely available at http://thermo-msf-parser.googlecode.com.     

天津地区归一化植被指数时间动态及其与气候因子的关系

利用1982—2003年8 km×8 km的NASA/GIMMS半月合成的归一化植被指数(NDVI)和气候数据,研究了天津年平均及逐月NDVI变化趋势以及降水和气温对其影响。结果表明：1982—2003年,年平均NDVI呈现波动性的微弱降低趋势;生长季中,不同月份的年际变化存在明显差异;春季和秋季NDVI呈增加趋势,其中10月达到显著性水平（P<0.05）,而夏季NDVI是降低的,6月下降达到极显著水平（P<0.01）;逐月NDVI与同期月平均气温及月降水量的回归分析表明,NDVI与温度和降水均有很好的非线性正相关关系（P<0.001）,证实温度和降水对NDVI的影响有很强的季节性;降水和气温对生长季不同月份的植被NDVI影响明显不同,同时呈现一定的滞后性。     

NDVI as an indicator for changes in water availability to woody vegetation

Barrier islands shrub thickets, the dominant woody community of many Atlantic coast barrier islands, are very sensitive to changes in the freshwater lens and thus, constitute a strong indicator of summer drought. NDVI was computed from airborne images and multispectral images on Hog Island (VA, USA) to evaluate summer growing season changes in woody communities for better predictions of climate change effects. Patterns of NDVI were compared year to year and monthly relative to precipitation and water table depth at the appropriate temporal scale. The highest absolute values of NDVI as well as the larger surface covered by woody vegetation (NDVI > 0.5) occurred in the wet year (2004) with a bimodal distribution of NDVI values (around 0.65 and 0.9) while both dry years (2007 and 2008) showed similar values in maximum, mean and standard deviation and unimodal distributions (around 0.75) of NDVI values. Positive linear adjustments were obtained between maximum (r² > 0.9) and mean NDVI (r² > 0.87) and the accumulated rainfall in the hydrological year and the mean water table depth from the last rainfall event till the date of the image acquisition. The spatial variations revealed that water table depth behaved different in wet and dry years. In dry years there was a remarkable increase in mean and maximum values linearly related to water table depth. The highest slope of the adjustment in 2007 indicated a sharp response of vegetation in the driest year. Monthly series of NDVI showed the major role of lack of precipitation through July and August in 2007 with missing classes of NDVI above 0.8 and unimodal distributions in mid-late summer. Best linear fits (r² close to 1) were obtained with rainfall at different temporal scales: accumulated rainfall in the hydrological year 2004 and accumulated rainfall in the last month previous to the date of 2007 image. Thus, in dry years productivity is closely related to water available from recent past as opposed to over the year for wet years. Good fits (r² values higher than 0.88) were obtained between monthly decrease in water table depth and NDVI variables just in the dry year. These results demonstrate the important feedback between woody vegetation response to changes in the freshwater lens using empirical data and could apply to other systems with strong directional gradients in resources.     

An NDVI analysis of vegetation trends in an Andean watershed

We performed a Landsat 5-TM derived normalized difference vegetation index (NDVI) analysis in a semi-arid watershed (2700 km²) in the Andes of southern Peru from 1985 to 2010. There, pastoralists rely on wetlands (bofedales) particularly during dry season months and in drought. We calculated annual dry season NDVI for 20 of the 26 years from 1985 to 2010 and used the mean to delineate wetlands in the watershed. To investigate the trends in NDVI, a multiple regression model with the covariates precipitation, temperature, Julian day, and year of image acquisition was performed on each cell (three million individual regressions). Results indicate there is a modest increase in NDVI for the majority of cells (81 %) in the watershed. Approximately 30 % of wetland areas display a decrease in NDVI. Dry season NDVI is moderately correlated with wet season precipitation (R ² = 0.56, p < 0.05) but absent a trend in precipitation, NDVI trends are not explained by this variable. Changes in land management may result in more intensive use of wetlands, causing the decreasing vegetation trends in some locations.     

基于SPOT-VGT NDVI的陕北植被覆盖时空变化

利用1998-2010年SPOT-VGT NDVI影像对陕北地区植被的时空变化进行分析.结果表明:研究期间,陕北地区归一化植被指数(NDVI)的季相变化明显,月均最高值出现在8月、最小值出现在1月,月均值的变化幅度在0.14 ～0.46,NDVI月均值为0.28,其年均值总体呈上升趋势;在空间上,植被改善地区集中于陕北中南部,生态环境退化区域集中在长城以北风沙区;气温和降水是影响植被变化的重要气候因子,其与NDVI变化的相关系数分别为0.72和0.58;植被改善明显的区域主要位于坡度15° ～25°的地区,反映出国家退耕还林还草工程对陕北地区生态环境的恢复和改善起到了巨大作用.     

基于MODIS/NDVI的陕北地区植被动态监测与评价

陕北地区从1999年退耕还林试点工程实施以来,区域植被发生很大变化,退耕前后植被动态变化监测成为退耕还林工程评价任务之一,而当前植被恢复监测评价的难点在于如何确定哪些是由于退耕而引起的植被变化。针对此问题,选取适合陕北地区植被变化监测的MODIS/NDVI数据,利用均值变化及趋势分析方法,从不同土地利用/覆被类型和不同坡度植被指数动态变化两方面分析退耕还林对植被动态变化的影响。结论如下:(1)陕北地区平均NDVI从2000-2008年呈现较明显的增长趋势,坡耕地和草地NDVI增长速度相对较快;(2)趋势分析结果显示,陕北绝大部分地区植被恢复良好,植被指数呈明显改善的面积占整个地区面积的64.96%,中度改善占18.58%,其中又以坡耕地、草地植被明显改善面积分别占陕北地区明显改善面积的45.43%和17.10%,坡耕地对陕北地区植被明显改善面积贡献最大;(3)7 15°、15 25°及25 35°坡度植被明显改善面积分别占总改善面积的39.91%、25.81%、2.28%,其中7 25°坡度植被明显改善面积占总面积的65.72%;(4)基于陕北地区近年气候呈暖干化发展趋势,同期降雨并未呈现显著变化,说明非气候因子中退耕还林等人为因素是引起NDVI增长的主要因素,退耕还林对于陕北地区植被恢复有明显促进作用。     

1982-2003年东北林区森林植被NDVI与水热条件的相关分析

以气象站点为研究单元,将1982—2003年东北林区森林植被月平均、季平均和年平均NDVI数据与其对应的水热条件(温度和降水)进行相关、偏相关和复相关分析。结果表明:温度是影响东北林区森林植被NDVI的最主要气候因子。春季、秋季不同森林植被平均NDVI与温度和降水呈极显著相关(P<0.01),其与温度的相关性高于其与降水的相关性。寒温带针叶林NDVI在生长季与温度和降水呈极显著相关(P<0.01),其与降水的相关性略高于其与温度的相关性,而全年温度对寒温带针叶林生长的影响高于降水。寒温带针叶林NDVI在4月份与降水的时滞偏相关性高于其他月份,相关系数达-0.385。温带针阔叶混交林NDVI在4—7月与温度的时滞偏相关性较高,相关系数分别为0.581,0.490,-0.266和-0.297。暖温带落叶阔叶林NDVI在4月份与温度的时滞偏相关性高于其他月份,相关系数为0.571;在7月份与降水时滞偏相关性高于其他月份,相关系数为-0.367。森林植被生长增长阶段NDVI受综合水热条件(温度和降水)的滞后影响显著。     

四川森林植被碳储量的时空变化

利用平均木法建立森林生物量与蓄积量模型,结合四川森林资源二类调查数据,研究了森林碳密度和碳储量的时空变化.结果表明 四川森林碳储量从1974年的300.02 Tg增加到2004年的469.96 Tg,年均增长率1.51%,表明其是CO2的"汇".由于人工林面积的增加,森林植被的平均碳密度从49.91 Mg·hm-2减少到37.39 Mg·hm-2.四川森林碳储量存在空间差异性,表现为川西北高山峡谷区＞川西南山区＞盆周低山区＞盆地丘陵区＞川西平原区.森林碳密度由东南向西北呈现逐渐增加趋势,即盆地丘陵区＜川西平原区＜川西南山区＜盆周低山区＜川西北高山峡谷区.通过分区森林经营与管理将提高四川森林的碳吸存能力.     

Spatial and temporal variation in the sediment properties of an intertidal mangrove forest: implications for sampling

Studies of the structure or functioning of intertidal soft sediments often involves collection of biogeochemical data over tidal, diel and seasonal time-scales. Little effort has, however, been made to quantify accurately the time-scales at which these properties vary. Many previous studies collected samples from different sites at different times, potentially resulting in the confounding of spatial and temporal variation. This experiment was designed to determine if time of day or time within the exposure period had any significant effect on measurements of 7 different properties of sediments. Samples of sediment were collected using contact cores at the beginning, middle and end of tidal emersion at each of 9 a.m., 12 p.m. and 3 p.m., with two replicate days of each condition, from mangrove forests fringing Glades Bay, Sydney, Australia. These samples were analysed for water-content, pigments, carbohydrates, grain-size and loss on ignition (LOI), to determine the potential effects of time of day and time within the tidal cycle on these properties of the sediments.Whilst both time of day and time within the tidal cycle were found to occasionally have a significant effect upon the measured properties, most of the variation occurred among sites and between replicate days of each set of conditions. The minimal influence of time of day and time within the tidal cycle show that sampling effort should be preferentially placed into replicating days of sampling and sites because these are the scales with the greatest variation. Differences in the patterns found also depended on whether the data were expressed as content or concentration, the consequences of which are briefly described.     

中国东北地区植被NDVI对气候变化的响应

结合1982—2003年GIMMS-NDVI数据集和GIS技术,应用基于像元的相关分析方法,分析了东北地区植被NDVI对气候变化的响应。结果表明：1）1982—2003年,东北地区年平均气温呈上升趋势,而年降水量呈下降趋势;东北地区植被NDVI与年平均气温呈显著正相关的像元占12.84%,主要分布在松嫩平原南部、三江平原中部和西辽河平原,植被类型为农田、阔叶林、草原。植被NDVI与年平均气温几乎不存在显著负相关性;植被NDVI与年降水呈显著和极显著正相关的像元比例为4.55%,主要植被类型为草原和农田;植被NDVI与年降水量呈显著负相关的像元比例为7.52%,主要植被类型为针叶林和阔叶林。2）东北地区植被与生长季气温显著正相关和显著负相关的比例分别为3.96%和4.35%;植被与生长季降水显著正相关和显著负相关的比例分别为8.81%和8.54%。3）东北地区58.21%的植被像元与春季气温显著或极显著正相关,主要分布在大兴安岭中部、小兴安岭、长白山及完达山-张广才岭等地区,主要植被类型为阔叶林、农田、针叶林和草甸;植被NDVI与春季气温几乎不存在显著负相关性。植被NDVI与春季降水呈显著正相关和显著负相关的比例分别为4.81%和1.67%。4）东北地区植被NDVI与夏季气温和降水呈显著相关的比例明显少于春季,与夏季气温正相关的比例为7.61%,与夏季降水显著负相关的比例为6.29%。秋季气温和降水对东北地区植被NDVI影响较小,其中植被NDVI与秋季气温显著正相关的像元占植被像元总数的6.05%,几乎不存在与秋季气温显著负相关的植被像元;植被NDVI与秋季降水显著负相关的比例为5.43%,几乎不存在与秋季降水显著正相关的植被像元。     

Monitoring temporal dynamics of Great Artesian Basin wetland vegetation,Australia, using MODIS NDVI

The Great Artesian Basin springs (Australia) are unique groundwater dependent wetland ecosystems of great significance, but are endangered by anthropogenic water extraction from the underlying aquifers. Relationships have been established between the wetland area associated with individual springs and their discharge, providing a potential means of monitoring groundwater flow using measurements of vegetated wetland area. Previous attempts to use this relationship to monitor GAB springs have used aerial photography or high resolution satellite images and gave sporadic temporal information. These “snapshot” studies need to be placed within a longer and more regular context to better assess changes in response to aquifer draw-downs. In this study we test the potential of 8 years of Moderate Resolution Imaging Spectroradiometer Normalised Difference Vegetation Index data as a long-term tracer of the temporal dynamics of wetland vegetation at the Dalhousie Springs Complex of the Great Artesian Basin. NDVI time series were extracted from MODIS images and phenologies of the main wetland vegetation species defined. Photosynthetic activity within wetlands could be discriminated from surrounding land responses in this medium resolution imagery. The study showed good correlation between wetland vegetated area and groundwater flow over the 2002–2010 period, but also the important influence of natural species phenologies, rainfall, and anthropogenic activity on the observed seasonal and inter-annual vegetation dynamics. Declining trends in the extent (km²) of vegetated wetland areas were observed between 2002 and 2009 followed by a return of wetland vegetation since 2010. This study underlines the need to continue long-term medium resolution satellite studies of the GAB to fully understand variability and trends in the spring-fed wetlands. The MODIS record allows a good understanding of variability within the wetlands, and gives a high temporal-frequency context for less frequent higher spatial resolution studies, therefore providing a strong baseline for assessment of future changes.     

苏干湖湿地植被覆盖度时空变化格局

植被覆盖度是反映群落外貌特征和影响植被生态系统稳定性的重要因子,其时空异质性演化规律研究有助于认识湿地群落的结构功能及其环境响应机制。采用湿地群落学调查和遥感技术相结合的方法,分析了苏干湖内陆盐沼湿地近30年植被覆盖度的时空变化及其影响因素。结果表明:像元二分模型在内陆盐沼湿地植被覆盖度研究方面具有较高的模拟精度;苏干湖湿地的植被覆盖度在1987—2017年间总体呈上升趋势,年际增幅为0.162%/5a,与气温和降水呈正相关关系;在空间上植被覆盖度与地下水位埋深呈正相关,与土壤全盐量呈负相关,但不同等级植被覆盖度与地下水位埋深、土壤全盐量间的相关性各有差异。苏干湖湿地植被覆盖度受地下水位埋深、土壤全盐量空间异质性的影响,呈现出斑块状镶嵌分布。     

India takes an open source approach to drug discovery

Open source software may have been around for 17 years, but using an open source model to speed up drug discovery is a relatively new idea. This month, India is launching a new open source initiative for developing drugs to treat diseases such as tuberculosis, malaria, and HIV.     

Closed forest or open woodland as natural vegetation in the surroundings of Linearbandkeramik settlements?

Deciduous woodland can be reconstructed as the potential vegetation cover of most parts of the Chernozem (black earth) loess areas settled by the early Neolithic farmers of the Bandkeramik culture in the sixth millennium b.c. The character of the woodland as closed, with few light-demanding plants, or more open is very important for the potential of an agricultural system. Botanical results are not able to indicate the composition of the woods quantitatively, but they can give indirect hints. It is discussed whether these archaeobotanical results, in combination with the characteristics of the wild and domesticated herbivores identified, can be interpreted with regard to the density of the woodland cover in Neolithic times. The use of the floodplains as pasture is interpreted from pollen analytical results.     

Impacts of temporal variation on apparent competition and coexistence in open ecosystems

The natural world is variable both in space and in time, but little ecological theory has been explicitly devoted to analyzing the consequences of both kinds of variability operating simultaneously. This issue is examined relative to the indirect interaction of apparent competition, which can limit the membership of prey communities. One limiting case that provides a useful starting point is to imagine that a local community is influenced by coupling with an external source landscape, but has little reciprocal influence on that landscape. There usually will be some rate of input of a locally inferior species that suffices to 'swamp' a superior species and drive it to extinction. We use simple models of apparent competition to show that when one superimposes upon this scenario temporal fluctuations, mediated through shifts in parameter values, such variation can either magnify the importance of the external input, or reduce it, depending on which component of the system experiences variation. We examine this in the case of both slow variation (for which we suggest a protocol that may be useful in a wide range of ecological models), and fast variation. The theoretical studies presented here provide examples of the rich range of outcomes that may arise due to temporal variability in spatially heterogeneous landscapes.     

Species distribution models predict temporal but not spatial variation in forest growth

Bioclimate envelope models have been widely used to illustrate the discrepancy between current species distributions and their potential habitat under climate change. However, the realism and correct interpretation of such projections has been the subject of considerable discussion. Here, we investigate whether climate suitability predictions correlate to tree growth, measured in permanent inventory plots and inferred from tree‐ring records. We use the ensemble classifier RandomForest and species occurrence data from ~200,000 inventory plots to build species distribution models for four important European forestry species: Norway spruce, Scots pine, European beech, and pedunculate oak. We then correlate climate‐based habitat suitability with volume measurements from ~50‐year‐old stands, available from ~11,000 inventory plots. Secondly, habitat projections based on annual historical climate are compared with ring width from ~300 tree‐ring chronologies. Our working hypothesis is that habitat suitability projections from species distribution models should to some degree be associated with temporal or spatial variation in these growth records. We find that the habitat projections are uncorrelated with spatial growth records (inventory plot data), but they do predict interannual variation in tree‐ring width, with an average correlation of .22. Correlation coefficients for individual chronologies range from values as high as .82 or as low as ?.31. We conclude that tree responses to projected climate change are highly site‐specific and that local suitability of a species for reforestation is difficult to predict. That said, projected increase or decrease in climatic suitability may be interpreted as an average expectation of increased or reduced growth over larger geographic scales.     

三江平原植被水分利用效率时空变化及其对气象因子变化的响应

水分利用效率(water use efficiency,WUE)是陆地生态系统响应全球变化的重要参数,分析区域生态系统WUE的变化特征及其与气象因子之间的响应关系,对于区域生态系统碳水循环研究以及水资源的科学管理具有重要意义。本文以三江平原为研究区,基于MODIS GPP和ET遥感数据、气象数据以及2000年、2014年土地覆盖数据,分析2000—2014年间植被WUE的时空变化特征以及植被WUE与关键气象因子之间的响应关系,并分析了土地覆盖变化下各植被类型WUE的变化特征。结果表明:三江平原WUE年均值变化呈波动式减少趋势,多年平均植被WUE为1.44 g C·kg^-1H₂O; WUE年内变化均近似呈"单峰型"曲线,1—3月及11、12月,WUE均处于最低值,在植被生长季(5—9月)期间,WUE均较高;季节WUE均值由高到低依次为夏季>秋季>春季>冬季;各植被类型WUE年内变化呈"双峰型"曲线,峰值主要分布在4—6月和9月;不同植被类型的年均WUE值从大到小依次为:混交林>针叶林>阔叶林>草地>耕地...     

黄龙山森林植被地上碳储量时空变化及驱动力

快速准确地估计植被地上碳储量及其动态变化,对评估森林固碳能力具有重要意义。以陕西省黄龙林区森林为研究对象,基于样地实测和卫星遥感数据,建立黄龙山林区植被地上碳储量模型,实现研究区2000-2021年长时间序列的森林植被地上碳储量的反演及时空分异研究。结果表明：（1）黄龙山森林植被地上碳储量平均值总体呈波动上升趋势,碳储量高于全省平均水平。（2）研究区东部、南部、中部及西北部是植被地上碳储量高值分布地区,且呈增加趋势;而东北部、西部和西南部植被地上碳储量较低,且呈减少趋势,研究区22年间森林植被地上部分固碳量增加,生产力提升。（3）年均温、年蒸散发量、年降水量和海拔是2000-2021年影响研究区森林植被地上碳储量空间分异主要因素;任意两个因子间的交互作用对黄龙山森林地上碳储量影响都大于单个因子,表明黄龙山森林植被地上碳储量在不同时间的空间分布受多种因素共同作用。年降水量对其空间分布影响逐渐减小,森林稳定性提高。研究在信息有限的基础上提出了快速估算地区植被地上碳储量的方法,了解了地区森林植被地上碳储量时空分异情况及其驱动因素,为掌握地区植被地上碳储量信息、评估森林固碳能力提供了重要依据。     

浙江省植被NDVI动态及其对气候的响应

利用GIMMS和MODIS两种归一化植被指数(NDVI)资料反演了1982—2010年浙江植被覆盖状况,结合同期研究区63个气象站点的气温、降水和湿润指数等气候指标,分析了该地区植被年际变化、月际变化及其对气候要素的响应特征。结果表明:(1)研究期间,浙江气候总体呈暖干化趋势,植被覆盖缓慢下降,主要是由于森林植被遭破坏,农业生产活动受抑制影响所致,其中NDVI显著减少的地区约占全省陆域面积的29.1%,主要发生在6—11月;(2)降水量及干湿程度对浙江植被NDVI年变化起着决定性作用。植被与气候要素年变化相关分析发现,NDVI与湿润指数关系较降水、气温更为密切,两者相关及偏相关系数均通过0.05水平的置信度检验,这表明在年际尺度上,湿度的增加增大了植被的生长势,有利于植被生长;(3)植被与气候要素月变化分析表明冬季的热量供给是影响浙江植被生长的重要因子,而植被变化对夏季降水和干湿程度的最大响应为滞后两个月;(4)农业生产水平的提高使得农作物种植区NDVI有所增加,人类活动对浙江植被覆盖的影响不可忽视。