A new physical accounting model for material flows in urban systems with application to the Stockholm Royal Seaport District

Sustainable urbanization requires streamlining of resource management in urban systems which in turn requires understanding of urban metabolism (UM). Even though various methods have been applied for UM analysis, to date there is no standardized method for comprehensive accounting of material flows in urban systems. Moreover, the accounting of material flows is rarely implemented with a bottom‐up approach that can provide a thorough analysis of UM. This article presents the Urban Accounting Model (UAM) which aims to allow comprehensive accounting of urban material flows based on a bottom‐up approach. The model comprises two interlinked sub‐models. The first was developed by integrating a new physical input output table (PIOT) framework for urban systems into a three‐dimensional structure. The second comprises a set of physical accounts for systematic accounting of material flows of each economic sector in the system in order to support the compilation of the PIOTs. The functions of the UAM were explored through its application to two urban neighborhoods in the Stockholm Royal Seaport district. The application highlighted that the UAM can describe the physical interactions between the urban system and the environment or other socioeconomic systems, and capture the intersectoral flows within the system. Moreover, its accounts provide information that allow an in‐depth analysis of the metabolism of specific sectors. Overall, the UAM can function as a useful tool for UM analysis as it systematizes data collection and at the same time depicts the physical reality of the urban system.     

Contribution of upper airway geometry to convective mixing

We investigated the axial dispersive effect of the upper airway structure (comprising mouth cavity, oropharynx, and trachea) on a traversing aerosol bolus. This was done by means of aerosol bolus experiments on a hollow cast of a realistic upper airway model (UAM) and three-dimensional computational fluid dynamics (CFD) simulations in the same UAM geometry. The experiments showed that 50-ml boluses injected into the UAM dispersed to boluses with a half-width ranging from 80 to 90 ml at the UAM exit, across both flow rates (250, 500 ml/s) and both flow directions (inspiration, expiration). These experimental results imply that the net half-width induced by the UAM typically was 69 ml. Comparison of experimental bolus traces with a one-dimensional Gaussian-derived analytical solution resulted in an axial dispersion coefficient of 200-250 cm(2)/s, depending on whether the bolus peak and its half-width or the bolus tail needed to be fully accounted for. CFD simulations agreed well with experimental results for inspiratory boluses and were compatible with an axial dispersion of 200 cm(2)/s. However, for expiratory boluses the CFD simulations showed a very tight bolus peak followed by an elongated tail, in sharp contrast to the expiratory bolus experiments. This indicates that CFD methods that are widely used to predict the fate of aerosols in the human upper airway, where flow is transitional, need to be critically assessed, possibly via aerosol bolus simulations. We conclude that, with all its geometric complexity, the upper airway introduces a relatively mild dispersion on a traversing aerosol bolus for normal breathing flow rates in inspiratory and expiratory flow directions.     

定量地层对比常用方法的比较和适用性分析

定量地层学以生物地层学原理为核心,将地层学信息定量化,运用数学模型进行地层对比,作为传统地层学对比的重要补充。传统的生物地层学根据经验选取标准化石来建立生物地层序列,但同时也丢失了大量的化石信息。定量地层学则能够利用所有的化石信息,在传统生物地层学的基础上得到更高分辨率的地层对比结果。现阶段定量地层对比常用的方法主要有图形对比法、约束最优化法和单元组合法三种,但对于这三种方法各自适应的数据情况方面,目前成果较少。本文对这三种方法的原理进行了简要的介绍和分析,并建立数据模型,从标准化石的可对比性、数据集的物种总数、剖面间共有物种和单延限分子的比例四个方面对三种方法的适用条件进行了讨论。其中图形对比法更适用于单延限分子较少、标准化石可对比性强的数据集。单元组合法对数据集中物种间相互关系的复杂程度较为敏感,共有物种较多的数据集有更好的对比结果,但数据集中物种总数的增加会对其产生一定的负面影响,需要依靠进一步的人工调整。约束最优化法则对数据集各方面的优化均有响应,对物种总数较大的数据集有较好的对比结果,且剖面间共有物种占比越大,对比结果越理想。     

Quantitative biochronology of Devonian ammonoids from Morocco and proposals for a refined unitary association method

Monnet, C., Klug, C., Goudemand, N., De Baets, K. & Bucher, H. 2011: Quantitative biochronology of Devonian ammonoids from Morocco and proposals for a refined unitary association method. Lethaia, Vol. 44, pp. 469–489. Based on a rich dataset, the biostratigraphy of the late Emsian and the Eifelian (Early–Middle Devonian) ammonoids from the Moroccan Tafilalt is re‐evaluated. We processed this dataset (comprising 53 species from 15 sections) with the unitary association method (UAM), by means of the UA‐graph freeware. This led to the construction of a sequence of 17 UAs (maximal sets of actually or virtually coexisting taxa), which are grouped into 10 laterally reproducible association zones. This biostratigraphical subdivision of this interval is in some parts finer than the classically used empirical stratigraphical scheme and than a previous graphic correlation analysis. It enabled us to measure regional ammonoid diversity of this interval in detail. The UAM is a powerful biochronological method, which benefits from complementary tools to analyse conflicting inter‐taxon stratigraphical relationships inherent to complex biostratigraphical datasets. In cases of under‐constrained superpositional relationships between the taxa, the UAM can yield results, which are not parsimonious in terms of reconstructed virtual coexistences. We suggest several additions to complement the algorithmic steps of the method. The most important is the exhaustive or heuristic reconstruction of possible solutions resolving the observed biostratigraphical contradictions (conflicting inter‐taxon superpositional relationships and cycles between maximal cliques) and the selection among the solutions of the most‐parsimonious one(s) in terms of reconstructed virtual coexistences. Multiple equivalent results may then be processed with standard consensus techniques. Finally, the robustness of the results can be tested by bootstrapping methods to provide confidence estimates on the ranges and associations of studied taxa. □Ammonites, Anti‐Atlas, biostratigraphy, correlation, zonation, diversity.     

Influence of Timber Harvesting Alternatives on Forest Soil Respiration and Its Biophysical Regulatory Factors over a 5-year Period in the Missouri Ozarks

We investigated the variability of soil respiration and several potential regulatory factors and modeled their interrelationships from May to August over a 5-year period in oak forests subjected to alternative harvesting treatments as part of the Missouri Ozark Forest Ecosystem Project (MOFEP). Treatments included even-aged management (EAM), uneven-aged management (UAM), and no-harvest management (NHM) and were implemented 7?C8?years prior to this study. Summer mean soil respiration did not differ among the treatments, possibly because of changes in treatment differences in the separate months and years that tended to cancel each other out when averaged. Summer mean soil respiration and soil moisture tended to be higher in wet years (2004, 2006, and 2008) and lower in dry years (2005 and 2007) in EAM and UAM than in NHM. Summer precipitation was assumed to be the primary driver of variability in summer mean soil respiration through its control on soil moisture and the normalized difference vegetation index (NDVI) in the harvested forests. Nonlinear models using soil temperature, soil moisture and day-of-the-year (DOY) were used to predict within-summer soil respiration for all the treatments. A sensitivity analysis of the model using 30?min interval data suggested that soil respiration was more sensitive to soil moisture in the EAM and UAM treatments than in NHM. We also found a change in the soil respiration?Csoil temperature relationship in the summer for all the treatments. Simulated data sets that removed the covariance structure between soil temperature and moisture suggested that the change in the respiration?Ctemperature relationship resulted from the combined effect of moisture stress and low temperature sensitivity at high temperatures during July and August. Simulations also showed the effect of moisture stress to be more limiting to soil respiration in the harvested forests than in the control at high temperatures, even resulting in a negative relationship at high temperatures.     

Environmental factors affectingin vitro nitrogenase activity of cyanobacteria isolated from rice-fields

The nitrogen-fixing capacity of four cyanobacterial strains was tested in relation to heterotrophic ability, tolerance to combined nitrogen and adaptive capacity to changes in light intensity and pH. Strains (Anabaena variabilis UAM 202;Calothrix marchica UAM 214;Nodularia spumigena UAM 204,Nostoc punctiforme UAM 205) were isolated from the rice-fields of Valencia (Spain).C. marchica, was the only strain able to grow and to fix dinitrogen under heterotrophic conditions, with fructose and glucose. Fructose was the best substrate supporting growth and dinitrogen fixation in mixotrophy (growth in the light under conditions where CO₂ and organic carbon are assimilated simultaneously), photoheterotrophy (growth in the light on an organic compound in the absence of net CO₂ fixation) and heterotrophy (growth on an organic compound in the dark). Ammonium repressed nitrogenase more than nitrate. Full repression was observed only at concentrations of combined nitrogen higher than those usually found in rice-fields. Carbohydrates had a protective effect on nitrogenase against ammonium inhibition inC. marchica. All four strains showed increased nitrogenase activity when the light intensity was increased during assays. Variations of pH normally occurring in rice fields led to no important changes in nitrogenase activity inC. marchica. This fact, together with its potential for heterotrophic growth and tolerance to combined nitrogen, make this the most suitable of the four strains for inoculation experiments in rice fields.     

A model of random mass-matching and its use for automated significance testing in mass spectrometric proteome analysis

A rapid and accurate method for testing the significance of protein identities determined by mass spectrometric analysis of protein digests and genome database searching is presented. The method is based on direct computation using a statistical model of the random matching of measured and theoretical proteolytic peptide masses. Protein identification algorithms typically rank the proteins of a genome database according to a score based on the number of matches between the masses obtained by mass spectrometry analysis and the theoretical proteolytic peptide masses of a database protein. The random matching of experimental and theoretical masses can cause false results. A result is significant only if the score characterizing the result deviates significantly from the score expected from a false result. A distribution of the score (number of matches) for random (false) results is computed directly from our model of the random matching, which allows significance testing under any experimental and database search constraints. In order to mimic protein identification data quality in large-scale proteome projects, low-to-high quality proteolytic peptide mass data were generated in silico and subsequently submitted to a database search program designed to include significance testing based on direct computation. This simulation procedure demonstrates the usefulness of direct significance testing for automatically screening for samples that must be subjected to peptide sequence analysis by e.g. tandem mass spectrometry in order to determine the protein identity.     

ASPMF: a new approach for identifying alternative splicing isoforms using peptide mass fingerprinting

Alternative splicing is generally accepted as a mechanism that explains the discrepancy between the number of genes and proteins. We used peptide mass fingerprinting with a theoretical database and scoring method to discover and identify alternative splicing isoforms. Our theoretical database was built using published alternative splicing databases such as ECgene, H-DBAS, and TISA. According to our theoretical database of 190,529 isoforms, 37% of human genes have multiple isoforms. The isoforms produced from a gene partially share common peptide fragments because they have common exons, making it difficult to distinguish isoforms. Therefore, we developed a new method that effectively distinguishes a true isoform among multiple isoforms in a gene. In order to evaluate our algorithm, we made test sets for 4226 protein isoforms extracted from our theoretical database randomly. Consequently, 94% of true isoforms were identified by our scoring algorithm.     

利用Poincare 散点图法检测t 波交替的指标研究

目的:利用Poincare散点图进行t波交替检测,不仅从形态上找到检测标准,进一步研究散点中有效的定量指标。方法:以European ST-T Database标准心电数据库和MIT-BIH心律失常数据库的心电信号作为检测对象,以128个连续心拍的t波中的7个点为检测数据,相邻心拍t波差分后组成新序列,并由差分序列作出散点图,观察散点形态。根据形态区别和t波交替的幅值变化特点,利用个散点到x+y=0直线的距离均值作为定量检测指标D0,为避免不同心电信号幅值影响,D0除以RQ峰值差为最终指标D,找出合适阈值判定是否存在t波交替,并与谱分析法的检测结果比较分析。结果:①从Poincare散点图形态上,存在t波交替的散点图与正常t波存在明显区别,存在t波交替则散点集中在以x+y=0为轴线的附近,形成类似椭圆的狭长形状;而正常t波形成的散点会以原点为中心均匀分布,散点形态为圆形。②由t波交替的特点和散点图形态可知,定量检测指标D越小,就越有可能存在t波交替。经过大量仿真测试和谱分析法的比较,规定检测标准为,当D<=35uv时,存在t波交替;指标D与谱分析法的结论相吻合,并且两种方法的判定结果由kappa一致性检验,一致性程度好,进一步说明D指标具有优越的敏感性,是t波交替检测的有效指标。结论:Poincare散点图的散点分布形态和散点到x+y=0轴线的距离均值分别是是t波交替有效的定性和定量检测指标。     

JenPep: a database of quantitative functional peptide data for immunology

MOTIVATION: The compilation of quantitative binding data underlies attempts to derive tools for the accurate prediction of epitopes in cellular immunology and is part of our concerted goal to develop practical computational vaccinology. RESULTS: JenPep is a family of relational databases supporting the growing community of immunoinformaticians. It contains quantitative data on peptide binding to Major Histocompatibility Complexes (MHCs) and to Transmembrane Peptide Transporter (TAP), as well as an annotated list of T-cell epitopes. AVAILABILITY: The database is available via the Internet. An HTML interface allowing searching of the database can be found at the following address: http://www.jenner.ac.uk/JenPep.     

Trichlorfon-Induced Inhibition of Nitrate and Ammonium Uptake in Cyanobacteria

The possibility that the primary effect of the toxic insecticidetrichlorfon is an inhibition of nitrate uptake in cyanobactenahas been investigated. A drastic reduction in the rate of uptakeis detected 3 h after the addition of the insecticide to batchcultures of nabaena PCC 7119. The dose-response curves indicatea relationship between the degree of inhibition of nitrate uptakeand the reduction of chlorophyll content and growth. Nitratereductase (ferredoxin : nitrate reductase, EC 1.7.99.4 [EC] ) activityis also lowered as a result of insecticide action. When AnabaenaPCC 7119 cells are grown with ammonium as a source of combinednitrogen, trichlorfon reduces the rate of ammonium uptake. Therate of uptake of both nitrate and ammonium is restored uponwashing the cells. Ultrastructural analysis of Anabaena nitrate-growncells shows that trichlorfon does not damage thylakoid membranes,but brings about the accumulation of enlarged cyanophycin granulesand the increase of carboxysome number. Nitrate uptake rateand chlorophyll and phycobiliprotein contents are also reducedby insecticide treatment in the cyanobacteria SynechococcusUAM 211, GloeothecePCC 6501, Plectonema calothricoides, NostocUAM 205 and Chlorogloeopsis PCC 6912. These results are consistentwith the inhibition of nitrate uptake due to weak adsorptionof trichlorfon to the plasmalemma being the main effect of theinsecticide on cyanobacterial metabolism. Key words: Nitrate uptake, cyanobacteria, Anabaena, ammonium uptake, trichlorfon     

PHYSIOLOGICAL DIFFERENCES BETWEEN TWO SPECIES OF CYANOBACTERIA IN RELATION TO PHOSPHORUS LIMITATION1

In order to gain a better understanding of the factors responsible for changes in cyanobacterial species composition in the Alberche River (central Spain), which is characterized by spatiotemporal N and P variability, we undertook P‐limitation studies on two isolated N₂‐fixing species that are well represented in the river: Calothrix elenkinii (Kosinskaja) UAM 225 and Nostoc punctiforme (Kützing) UAM 220. We examined differences in phosphorus‐storage capacity, phosphate uptake, and phosphatase activity between the two isolates grown under N₂‐fixing conditions. Although they shared a similar pattern of phosphate uptake, C. elenkinii cultures had a greater phosphorus storage capacity and greater phosphatase activity than those of N. punctiforme. The former showed a stronger response when cultured under low P concentrations. The two species showed specific differences in the rates of intracellular polyphosphate granule utilization and phosphatase activity. Our results suggest that C. elenkinii might be particularly well suited to river environments in which nutrient concentrations are generally low, but which experience episodic pulses of high P supply (inorganic and/or organic), favoring “luxury uptake” and storage strategies.     

A plant mutase that interconverts UDP-arabinofuranose and UDP-arabinopyranose

Plant cell walls constitute the bulk of the earth renewable source of energy and are a component in the diet of humans and herbivores. l-Arabinofuranosyl (Araf) residues are a quantifiably important constituent of these walls. Plants use uridine diphosphate (UDP)-l-arabinofuranose (UDP-Araf) to donate Araf residues in the biosynthesis of Araf-containing polysaccharides, proteoglycans, and glycoproteins. However, little is known about the formation of UDP-Araf. We now describe the purification and partial characterization of a rice UDP-arabinopyranose mutase (UAM) that catalyzes the formation of UDP-Araf from UDP-arabinopyranose (UDP-Arap). The reaction is reversible and at thermodynamic equilibrium the pyranose form is favored over the furanose form (90 : 10). Three related proteins that are encoded by rice gene loci Os03g40270, Os04g56520, and Os07g41360 were identified from partial amino acid sequences of UAM. These proteins have >80% sequence identity with polypeptides that are reversibly glycosylated in the presence of UDP-sugars. The rice mutase and two functionally active recombinant mutases were shown to be reversibly glycosylated in the presence of UDP-Glc. The cofactor, flavin-adenine-dinucleotide (FAD), is required for the catalytic activity of UDP-galactose mutases of prokaryotes, fungi, and protozoa. The plant mutases, which do not require a cofactor, must therefore have a different catalytic mechanism. Putative UAM-encoding genes are present in the green algae Chlamydomonas reinhardtii, the moss Physcomitrella patens, the gymnosperm Pinus taeda (loblolly pine), and in numerous dicots and monocots, indicating that UAMs are widespread in green plants.     

A decision support system for prediction of microbial spoilage in foods

Summary A method is developed to combine qualitative and quantitative information for the prediction of growth of microorganisms in foods. pH, water activity, temperature and oxygen availability of foods are coupled to growth characteristics of microorganisms. For that purpose, a database with characteristics of foods and a database of kinetic parameters of microorganisms are built. The first database has a tree structure, based on physical similarity of food products. This structure makes it possible to estimate information about a food product which is not listed by comparison with similar products at the same level of the tree or the level above. A method is developed to make an estimation of the microbial growth kinetics on the basis of models. This is done by introducing a growth factor, which can be calculated on the basis of readily available data from literature. Finally, qualitative knowledge is added. Since any bit of information can be changed, the system will give better predictions when more and more accurate information is added.     

The genetic differentiation at quantitative trait loci under local adaptation

Most adaptive traits are controlled by large number of genes that may all together be the targets of selection. Adaptation may thus involve multiple but not necessarily substantial allele frequency changes. This has important consequences for the detection of selected loci and implies that a quantitative genetics framework may be more appropriate than the classical 'selective sweep' paradigm. Preferred methods to detect loci involved in local adaptation are based on the detection of 'outlier' values of the allelic differentiation F(ST) . A quantitative genetics framework is adopted here to review theoretical expectations for how allelic differentiation at quantitative trait loci (F(STQ) ) relates to (i), neutral genetic differentiation (F(ST) ) and (ii), phenotypic differentiation (Q(ST) ). We identify cases where results of outlier-based methods are likely to be poor and where differentiation at selected loci conveys little information regarding local adaptation. A first case is when neutral differentiation is high, so that local adaptation does not necessitate increased differentiation. A second case is when local adaptation is reached via an increased covariance of allelic effects rather than via allele frequency changes, which is more likely under high gene flow when the number of loci is high and selection is recent. The comparison of theoretical predictions with observed data from the literature suggests that polygenic local adaptation involving only faint allele frequency changes are very likely in some species such as forest trees and for climate-related traits. Recent methodological improvements that may alleviate the weakness of F(ST) -based detection methods are presented.     

重组人睫状神经营养因子蛋白质定量检测方法的建立

采用ELISA双抗体夹心法,建立一种快速灵敏的定量检测rhCNTF成品蛋白含量的方法。结果显示,rhC-NTF抗原浓度在(0～25)ng范围内线性良好(r>0.99),灵敏度为0.3ng/ml,与其他重组细胞因子无交叉反应,样品的检测结果与理论含量相吻合,CV<15%,该方法检测速度快、重复性好、灵敏度高、特异性好。     

Phylogenetic information improves homology detection.

We present a database search method that is based on phylogenetic trees (treesearch). The method is used to search a protein sequence database for homologs to a protein family. In preparation for the search, a phylogenetic tree is constructed from a given multiple alignment of the family. During the search, each database sequence is temporarily inserted into the tree, thus adding a new edge to the tree. Homology between family and sequence is then judged from the length of this edge. In a comparison of our method to profiles (ISREC pfsearch), two implementations of hidden Markov models (HMMER hmmsearch and SAM hmmscore), and to the family pairwise search (FPS) method on 43 families from the SCOP database based on minimum false-positive counts (min-FPCs), we found a considerable gain in sensitivity. In 69% of the test cases, treesearch showed a min-FPC of at most 50, whereas the two second best methods (hmmsearch and FPS) showed this performance only in 53% cases. A similar impression holds for a large range of min-FPC thresholds. The results demonstrate that phylogenetic information can significantly improve the detection of distant homologies and justify our method as a useful alternative to existing methods.     

利用指骨弯曲程度推断化石人猿超科成员移动行为方式的新方法:以禄丰古猿为例

长久以来,指骨弯曲程度都被用来推断化石灵长类移动行为方式。此前已有一些方法被提出并用于定量化比较指骨弯曲程度,包括半径弯曲程度法（radius of curvature）、夹角法（included angle, IA）、标准化矩臂弯曲程度法（normalized curvature moment arm, NCMA）以及高精度多项式曲线拟合法（high-resolution polynomial curve fitting, HR-PCF）。然而,在对指骨弯曲程度进行定量化的过程中,这些方法都显示出了理论或技术上的局限性。因此,在运用这些方法之前,应当谨慎考虑其适用性和精确程度对分析结果所产生的影响。鉴于此,为了避免先前方法中存在的问题并更加精确地定量描述指骨弯曲程度,本文介绍了一种新方法作为替代。该方法基于对指骨侧视图背侧轮廓曲线几何形态测量学标志点数据的四阶多项式曲线拟合,称为几何形态测量学—多项式曲线拟合法（4th order polynomial curve fitting on geometric morphometric landmark data, GM-PCF）。它以标准化指骨曲线高度（normalized phalangeal curve height, NPCH）作为指骨弯曲程度的定量指标,并且可以将平均标准化指骨曲线进行可视化以用于其弯曲程度的直观对比。此外,它还可以提供在解释指骨弯曲程度的功能意义中非常关键的指骨（背侧轮廓曲线）长度比例信息。GM-PCF还能够分析化石中常见的不完整的指骨。为了检验新方法的适用性,我们从现生类人猿（anthropoids）中选取了15个涵盖灵长类大部分移动行为方式的类群作为参考样本,采用GM-PCF方法对其指骨弯曲程度进行了定量分析,结果表明标准化指骨曲线高度（NPCH）对灵长类移动行为方式有很好的指示意义,配合指骨曲线长度,还可以更进一步了解树栖四足行走（arboreal quadrupedalism）、悬垂（suspension）与摆荡（brachiation）等行为与灵长类体型大小的关系。作为个案,我们采用新方法对中国中新世的两种禄丰古猿（禄丰禄丰古猿Lufengpithecus lufengensis和蝴蝶禄丰古猿Lufengpithecus hudienensis）的指骨弯曲程度与参考样本进行了对比,并根据对比结果对其最为可能的移动行为方式偏好进行了推断。     

Virtual Expert Mass Spectrometrist: iTRAQ tool for database‐dependent search,quantitation and result storage

A frequent goal of MS‐based proteomics experiments nowadays is to quantify changes in the abundance of proteins across several biological samples. The iTRAQ labeling method is a powerful technique; when combined with LC coupled to MS/MS it allows relative quantitation of up to eight different samples simultaneously. Despite the usefulness of iTRAQ current software solutions have limited functionality and require the combined use of several software programs for analysis of the data from different MS vendors. We developed an integrated tool, now available in the virtual expert mass spectrometrist (VEMS) program, for database‐dependent search of MS/MS spectra, quantitation and database storage for iTRAQ‐labeled samples. VEMS also provides useful alternative report types for large‐scale quantitative experiments. The implemented statistical algorithms build on quantitative algorithms previously used in proposed iTRAQ tools as described in detail herein. We propose a new algorithm, which provides more accurate peptide ratios for data that show an intensity‐dependent saturation. The accuracy of the proposed iTRAQ algorithm and the performance of VEMS are demonstrated by comparing results from VEMS, MASCOT and PEAKS Q obtained by analyzing data from a reference mixture of six proteins. Users can download VEMS and test data from “ http://www.portugene.com/software.html ”.