The System of Environmental and Economic Accounts—2003 and the Economic Relevance of Physical Flow Accounting

The international handbook on integrated environmental and economic accounting (SEEA-2003) provides a detailed overview of environmental accounting approaches that have been developed in parallel with the system of national (economic) accounts. In addition to natural resource stock accounts and environmental protection expenditure accounts, SEEA-2003 pays considerable attention to physical flow accounting. Expanding the national economic accounts with physical data sets facilitates the joint analysis of environmental and economic policy issues. This article discusses the main characteristics of national accounts-oriented physical flow accounting approaches and provides an overview of the kind of indicators they may put forward. Although this article is not an attempt to provide a comprehensive review of macrooriented physical flow accounting approaches, the analytical advantages of national accounts-oriented physical flow accounts are illustrated.     

Analysing Population Numbers of the House Sparrow in the Netherlands With a Matrix Model and Suggestions for Conservation Measures

The House Sparrow (Passer domesticus), formerly a common bird species, has shown a rapid decline in Western Europe over recent decades. In The Netherlands, its decline is apparent from 1990 onwards. Many causes for this decline have been suggested that all decrease the vital rates, i.e. survival and reproduction, but their actual impact remains unknown. Although the House Sparrow has been dominant in The Netherlands, data on life history characteristics for this bird species are scarce: data on reproduction are non-existent, and here we first present survival estimates based on live encounters and dead recoveries of marked individuals over the period 1976–2003, 14 years before and 14 years during the decline, reported to the Dutch Ringing Centre. We show that there is an indication that both juvenile and adult survival are lower during the period of decline. Secondly, to be able to analyse the relative impact of changes in the vital rates, we formulated a general matrix model based on a range of survival values between zero and one with a step size of 0.01 (both juvenile and adult yearly survival) and a range of realistic reproduction values (one, three or five fledglings per pair per year). With the matrix model, we calculated the finite rate of population change (λ) and applied elasticity analysis. To diagnose the cause of the decline in the Dutch House Sparrow, we parameterised the model with estimates of survival values before and during the decline and present the resulting λ. With the survival estimates from the declining period, λ < 1 only if reproduction is relatively low. We discuss this result within the light of available literature data on survival in the House Sparrow. Finally, we evaluate which of the suggested causes of population decline should be reversed to mitigate the decline and how this can be achieved.     

ribosort: a program for automated data preparation and exploratory analysis of microbial community fingerprints

ribosort is a computer package for convenient editing of automated ribosomal intergenic spacer analysis (ARISA) and terminal restriction fragment length polymorphism (TRFLP) data. It is designed to eliminate the labourious task of manually classifying community fingerprints in microbial ecology studies. This program automatically assigns detected fragments and their respective relative abundances to appropriate ribotypes. It permits simultaneous sorting of multiple profiles and facilitates direct workflow from TRFLP and ARISA output through to community analyses. ribosort also provides several options to merge repeat profiles of a sample into a single composite profile. By creating a 'ribotypes by samples' matrix ready for statistical analyses, use of the package saves time and simplifies the preparation of DNA fingerprint data sets for statistical analysis. In addition, ribosort performs exploratory analysis on the data by creating multidimensional scaling plots that compare the similarity of sample profiles using the statistical software r.     

GITAR: An Open Source Tool for Analysis and Visualization of Hi-C Data

Interactions between chromatin segments play a large role in functional genomic assays and developments in genomic interaction detection methods have shown interacting topological domains within the genome. Among these methods, Hi-C plays a key role. Here, we present the Genome Interaction Tools and Resources (GITAR), a software to perform a comprehensive Hi-C data analysis, including data preprocessing, normalization, and visualization, as well as analysis of topologically-associated domains (TADs). GITAR is composed of two main modules: (1) HiCtool, a Python library to process and visualize Hi-C data, including TAD analysis; and (2) processed data library, a large collection of human and mouse datasets processed using HiCtool. HiCtool leads the user step-by-step through a pipeline, which goes from the raw Hi-C data to the computation, visualization, and optimized storage of intra-chromosomal contact matrices and TAD coordinates. A large collection of standardized processed data allows the users to compare different datasets in a consistent way, while saving time to obtain data for visualization or additional analyses. More importantly, GITAR enables users without any programming or bioinformatic expertise to work with Hi-C data. GITAR is publicly available at http://genomegitar.org as an open-source software.     

A Generalization of the Intraclass Tau Correlation for Tied and Censored Data

Intraclass tau correlations and a corresponding asymptotic permutation test have already been derived by WHITFIELD (1949), though for continuous data only. WHITFIELD'S concepts are now generalized for use with tied and censored data and a suggestion is made for the application of the methods to arbitrary and varying group sizes. Special attention is given to their application to dichotomous data. Extensive simulations confirming the safe use of the asymptotic test even for samples of moderate size are reported and calculated examples with data from twin-births and kidney transplantations presented.     

The Thermometer and the Calorimeter,or the Best Choice for Data Acquisition in the Sampling of Biological Rhythms

The comparison between measurements effected by different apparati shows that a given class of instruments provides an integral set of measurements. This characteristic has a certain disadvantage: the modification of the spectral bandwidth is limited to an attenuation of 3 dB. However, it also has certain advantages. The integral measurement (or the counting measurement) makes it possible to satisfy Shannon's sampling criteria by avoiding the necessary anti-aliasing filtering which is commonly impossible to realize on measurements of a biological nature. A second advantage is linked to the reduction of the background noise on the band.     

The Thermometer and the Calorimeter, or the Best Choice for Data Acquisition in the Sampling of Biological Rhythms

The comparison between measurements effected by different apparati shows that a given class of instruments provides an integral set of measurements. This characteristic has a certain disadvantage: the modification of the spectral bandwidth is limited to an attenuation of 3 dB. However, it also has certain advantages. The integral measurement (or the counting measurement) makes it possible to satisfy Shannon's sampling criteria by avoiding the necessary anti-aliasing filtering which is commonly impossible to realize on measurements of a biological nature. A second advantage is linked to the reduction of the background noise on the band.     

Epithelial Cell Repopulation and Preparation of Rodent Extracellular Matrix Scaffolds for Renal Tissue Development

This protocol details the generation of acellular, yet biofunctional, renal extracellular matrix (ECM) scaffolds that are useful as small-scale model substrates for organ-scale tissue development. Sprague Dawley rat kidneys are cannulated by inserting a catheter into the renal artery and perfused with a series of low-concentration detergents (Triton X-100 and sodium dodecyl sulfate (SDS)) over 26 hr to derive intact, whole-kidney scaffolds with intact perfusable vasculature, glomeruli, and renal tubules. Following decellularization, the renal scaffold is placed inside a custom-designed perfusion bioreactor vessel, and the catheterized renal artery is connected to a perfusion circuit consisting of: a peristaltic pump; tubing; and optional probes for pH, dissolved oxygen, and pressure. After sterilizing the scaffold with peracetic acid and ethanol, and balancing the pH (7.4), the kidney scaffold is prepared for seeding via perfusion of culture medium within a large-capacity incubator maintained at 37 °C and 5% CO₂. Forty million renal cortical tubular epithelial (RCTE) cells are injected through the renal artery, and rapidly perfused through the scaffold under high flow (25 ml/min) and pressure (~230 mmHg) for 15 min before reducing the flow to a physiological rate (4 ml/min). RCTE cells primarily populate the tubular ECM niche within the renal cortex, proliferate, and form tubular epithelial structures over seven days of perfusion culture. A 44 µM resazurin solution in culture medium is perfused through the kidney for 1 hr during medium exchanges to provide a fluorometric, redox-based metabolic assessment of cell viability and proliferation during tubulogenesis. The kidney perfusion bioreactor permits non-invasive sampling of medium for biochemical assessment, and multiple inlet ports allow alternative retrograde seeding through the renal vein or ureter. These protocols can be used to recellularize kidney scaffolds with a variety of cell types, including vascular endothelial, tubular epithelial, and stromal fibroblasts, for rapid evaluation within this system.     

具有亲缘关系矩阵的混合模型的方差组分迭代估计——应用于计算BLUP的方差比值和遗传参数

论述的是来自非均街资料的混合模型中具有亲缘关系矩阵时利用迭代法估计方差组分问题。这篇文章表明计算程序是可行的,只要能够按照混合模型中固定效应的结构矩阵和Henderson方法3的固定效应的假设条件正确地计算二次型约化平方和,就可获得较为精确的方差组分估计值;而且表明方差初始比值k偏高或偏低,不影响迭代求解的最后结果,这是因为在迭代过程中可以通过结构矩阵x'x和x'x的控制而自行调整。这些方差组分不仅可应用于选种种畜用的BLUP计算,还可用来估计遗传参数。     

Explanatory Variables for per Capita Stocks and Flows of Copper and Zinc

A number of potential explanatory variables for the stocks and flows of copper and zinc in contemporary technological societies are co-analyzed with the tools of exploratory data analysis. A one-year analysis (circa 1994) is performed for 50 countries that comprise essentially all anthropogenic stocks and flows of the two metals. The results show that (1) The key explanatory variable for metal use is gross domestic product (GDP) per capita (purchasing power parity, PPP). By itself, GDP explains between one-third and one-half of the variance of per capita copper and zinc use. Other variables that were significantly correlated with copper and zinc use included stock of passenger cars and television sets (per 1, 000 people); two infrastructure variables, wired telephone connections, urban population, and value added inmanufacturing. The results do not provide evidence supporting the Kuznets curve hypothesis for these metals. (2) Metal use per capita can be estimated using multiple regression equations. For copper, the natural logarithm of use is related to the explanatory variables GDP (PPP), value added in manufacturing, and urban population. This model explains 80% of the variance among the different countries (r²= 0.79). The natural logarithm of zinc use is related to GDP (PPP) and value added in manufacturing with an r² of 0.75; (3) For both metals, rates of metal fabrication, use, net addition to stock, and discard in low-and high-income countries differ significantly from each other. Our statistical analyses thus provide a basis for estimating the potential development of metal use, net addition to stock, and discard, using data on explanatory variables that are available at the international level.     

A Web-Based Data Architecture for Problem-Solving Environments: Application of Distributed Authoring and Versioning to the Extensible Computational Chemistry Environment

Next-generation problem-solving environments (PSEs) promise significant advances over those now available. They will span scientific disciplines and incorporate collaboration capabilities. They will host feature-detection and other agents, allow data mining and pedigree tracking, and provide access from a wide range of devices. Fundamental changes in PSE architecture are required to realize these and other PSE goals. This paper focuses specifically on issues related to data management and recommends an approach based on open, metadata-driven repositories with loosely defined, dynamic schemas. Benefits of this approach are discussed, and the redesign of the Extensible Computational Chemistry Environment's (Ecce) data storage architecture to use such a repository is described, based on the distributed authoring and versioning (DAV) standard. The suitability of DAV for scientific data, the mapping of the Ecce schema to DAV, and promising initial results are presented.     

Data reconciliation of concentration estimates from mid‐infrared and dielectric spectral measurements for improved on‐line monitoring of bioprocesses

Real‐time data reconciliation of concentration estimates of process analytes and biomass in microbial fermentations is investigated. A Fourier‐transform mid‐infrared spectrometer predicting the concentrations of process metabolites is used in parallel with a dielectric spectrometer predicting the biomass concentration during a batch fermentation of the yeast Saccharomyces cerevisiae. Calibration models developed off‐line for both spectrometers suffer from poor predictive capability due to instrumental and process drifts unseen during calibration. To address this problem, the predicted metabolite and biomass concentrations, along with off‐gas analysis and base addition measurements, are reconciled in real‐time based on the closure of mass and elemental balances. A statistical test is used to confirm the integrity of the balances, and a non‐negativity constraint is used to guide the data reconciliation algorithm toward positive concentrations. It is verified experimentally that the proposed approach reduces the standard error of prediction without the need for additional off‐line analysis. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009