Measuring the sustainability of cities: An analysis of the use of local indicators

We analyze 17 studies of the use of urban sustainable development indicators (SDI) in developed western countries. The analysis reveals a lack of consensus not only on the conceptual framework and the approach favored, but also on the selection and optimal number of indicators. First, by performing different classifications and categorizations of SDI we identify problems inherent in territorial practices that use SDI. Second, we argue that the lack of consensus in several steps of the creation of SDI stems notably from the ambiguity in the definitions of sustainable development, objectives for the use of such indicators, the selection method and the accessibility of qualitative and quantitative data. Third, based on the reviewed studies, we propose a selection strategy for SDI through which we demonstrate the need to adopt a parsimonious list of SDI covering the sustainable development components and their constituent categories as broadly as possible while minimizing the number of indicators retained.     

Genetic diversity and models of viral evolution for the hepatitis C virus

In this review we discuss the application of theoretical frameworks to the interpretation of viral gene sequence data, with particular reference to the hepatitis C virus (HCV). The increasing availability of such data means that it is now possible (and necessary) to proceed from simple qualitative models of viral evolution, to more quantitative frameworks based on statistical inference, notably population genetics and molecular phylogenetics. We argue that these approaches are invaluable tools to the virologist and are essential for understanding the dynamics of viral infection and the outcome of therapeutic strategies. We use several recent HCV data-sets to illustrate the methods.     

Accessibility to greenspaces: GIS based indicators for sustainable planning in a dense urban context

The issue of accessibility to urban greenspaces is raising as one of the most debated in sustainable urban planning, especially in topics such as environmental justice and health inequalities. This is mainly due to the growing attention that is recognised today to health and well-being benefits from greenspaces. Different people interpret accessibility based on their individual needs and priorities, but it is generally acknowledged that access to greenspaces may be particularly beneficial for children, lower socioeconomic groups and for people with other mental/psychological illness. However, if accessibility is the measure of the ease of reaching valued destinations, clarifying its definition is an important pre-requisite for further analysis aimed at supporting urban planning choices on greenspaces.The following paper presents a set of accessibility indicators aimed at quantifying different measures of accessibility to existing open spaces for the city of Catania, south Italy, an urban context characterised by a general lack of greenspaces and high density of urban settlements.Proposed indicators are divided into two main categories: simple distance indicators (SIs) and proximity indicators (PIs). The first accounts for the number of people or users that can have access to a particular open space, while the second weights these people or users with the distance from their location to the open spaces. Indicators are calculated using different thresholds of Euclidean and network distances.Results show different scenarios in terms of rank of greenspaces accessibility, strongly influenced by chosen distance metric (Euclidean vs network) and thus emphasise a careful use of these indicators as planning support tools. Some practical implications of measuring accessibility for urban planning can be highlighted: for instance, specific land uses might be chosen for highly accessible open spaces, especially those characterised by a high proximity to residential settlements. Examples include allotment gardens, playgrounds and other informal green areas.     

Fuzzy rule‐based decision support system for evaluation of long‐established forest restoration projects

Although the importance of monitoring and evaluation of restoration actions is increasingly acknowledged, availability of accurate, quantitative monitoring data is very rare for most restoration areas, particularly for long‐established restoration projects. We propose using fuzzy rule‐based expert systems to evaluate the degree of success of restoration actions when available information on project results and impacts largely relies on expert‐based qualitative assessments and rough estimates of quantitative values. These systems use fuzzy logic to manage the uncertainty present in the data and to integrate qualitative and quantitative information. To illustrate and demonstrate the potential of fuzzy rule‐based systems for restoration evaluation, we applied this approach to seven forest restoration projects implemented in Spain between 1897 and 1952, using information compiled in the REACTION database on Mediterranean forest restoration projects. The information available includes both quantitative and expert‐based qualitative data, and covers a wide variety of indicators grouped into technical, structural, functional, and socioeconomic criteria. The fuzzy rule‐based system translates expert knowledge of restoration specialists and forest managers into a set of simple logic rules that integrate information on individual indicators into more general evaluation criteria. The rule‐based approach proposed here can be readily applicable to any kind of restoration project, provided that some information, even if vague and uncertain, is available for a variety of assessment indicators. The evaluation of long‐established forest restoration projects implemented in Spain revealed important asymmetries in the degree of restoration success between technical, structural, functional, and socioeconomic criteria.     

The measurement of skeletal maturity

A new approach to the measurement of skeletal maturity has been described. This was applied to the distal end of the femur in boys aged one month to four years. It is planned to extend this study to girls and to other ages and sites and to other bones in the knee area. The study began with the testing of reported indicators of skeletal maturity in respect of replicability, validity, discrimination and universality. As a result, seven qualitative graded indicators and three quantitative ratios were selected for further investigation. Maturity scores based on each qualitative indicator can be estimated using parameters from a simple probit analysis with chronological age as the independent variable. The statistical factors that influence the usefulness of these indicators have been discussed. The quantitative indicators investigated appear very useful as measures of maturity although some are redundant. The planned extension of the present study should allow the formulation of an appropriate model for the measurement of skeletal maturity by combining qualitative and quantitative data.     

Oral health and access to dental care: a qualitative investigation among older people in the community

doi:10.1111/j.1741‐2358.2009.00320.x
Oral health and access to dental care: a qualitative investigation among older people in the community Objective: The aim of this study was to explore older persons’ beliefs and attitudes towards oral health and access to and use of dental care services. Background: As the proportion of dentate older people increases, the need and demand for dental services will rise (J Public Health Dent, 60, 2000, 276). Design: Focus groups and semi‐structured interviews were used for data collection. Setting and subjects: The study participants included 63 older people in Perth, WA. Results: Five major themes emerged from the interviews – the need for information and knowledge; accessibility of services; cost and affordability of oral care; fear and anxiety regarding dental visits and relationships with dentists. Attitudes and behaviours were slow to change in this group. Conclusion: This investigation provided important perspectives regarding oral health and dental access for older people residing in the community and demonstrated the importance of understanding this group when considering provision and use of services.     

Scholarometer: A Social Framework for Analyzing Impact across Disciplines

The use of quantitative metrics to gauge the impact of scholarly publications, authors, and disciplines is predicated on the availability of reliable usage and annotation data. Citation and download counts are widely available from digital libraries. However, current annotation systems rely on proprietary labels, refer to journals but not articles or authors, and are manually curated. To address these limitations, we propose a social framework based on crowdsourced annotations of scholars, designed to keep up with the rapidly evolving disciplinary and interdisciplinary landscape. We describe a system called Scholarometer, which provides a service to scholars by computing citation-based impact measures. This creates an incentive for users to provide disciplinary annotations of authors, which in turn can be used to compute disciplinary metrics. We first present the system architecture and several heuristics to deal with noisy bibliographic and annotation data. We report on data sharing and interactive visualization services enabled by Scholarometer. Usage statistics, illustrating the data collected and shared through the framework, suggest that the proposed crowdsourcing approach can be successful. Secondly, we illustrate how the disciplinary bibliometric indicators elicited by Scholarometer allow us to implement for the first time a universal impact measure proposed in the literature. Our evaluation suggests that this metric provides an effective means for comparing scholarly impact across disciplinary boundaries.     

Modelling critical caribou summer ranges in West Greenland

Increasing tourism and mineral exploitation potentially affects the caribou range use. This fact requires identification of critical caribou areas to be able to avoid large effects on the population. We have applied resource selection functions using data from satellite tracking of caribou, satellite-based vegetation maps and a digital elevation model. Maps showing five levels of relative-probability-of-use for caribou during the summer in West Greenland were prepared. The maps clearly illustrate that the caribou are much more selective in choosing their feeding habitats in July than in late summer. Therefore, activities like tourism and mineral exploration would have least impact in September. We validated the results by comparing the models from the ARGOS-based locations with two models based on locations obtained during fieldwork. We therefore conclude that the method and satellite-based data used in this study are valuable tools for resource management in remote areas like West Greenland.     

Hydroxyl radical footprinting of fluorescently labeled DNA

Footprinting is one of the simplest and most accurate approaches to investigate structure and interaction of biopolymers. It is based on the more difficult accessibility of intra- and intermolecular contacts for external damaging agents. According to this method, one end of polymer molecules is labeled before a sample is incubated with a damaging agent. The distribution of split products is used to conclude on the accessibility of different polymer regions under specific conditions. A variety of enzymatic and chemical splitting agents are used for footprinting. Currently, the highest temporal and spatial resolution without profound specificity to a nucleotide sequence can be reached with the use of hydroxyl radicals. A new variant of this approach, which suggests the use of DNA fluorescent labeling together with the present-day quantitative analysis, will allow extending the method’s boundaries.     

Modeling large RNAs and ribonucleoprotein particles using molecular mechanics techniques.

There is a growing body of low-resolution structural data that can be utilized to devise structural models for large RNAs and ribonucleoproteins. These models are routinely built manually. We introduce an automated refinement protocol to utilize such data for building low-resolution three-dimensional models using the tools of molecular mechanics. In addition to specifying the positions of each nucleotide, the protocol provides quantitative estimates of the uncertainties in those positions, i.e., the resolution of the model. In typical applications, the resolution of the models is about 10-20 A. Our method uses reduced representations and allows us to refine three-dimensional structures of systems as big as the 16S and 23S ribosomal RNAs, which are about one to two orders of magnitude larger than nucleic acids that can be examined by traditional all-atom modeling methods. Nonatomic resolution structural data--secondary structure, chemical cross-links, chemical and enzymatic footprinting patterns, protein positions, solvent accessibility, and so on--are combined with known motifs in RNA structure to predict low-resolution models of large RNAs. These structural constraints are imposed on the RNA chain using molecular mechanics-type potential functions with parameters based on the quality of experimental data. Surface potential functions are used to incorporate shape and positional data from electron microscopy image reconstruction experiments into our models. The structures are optimized using techniques of energy refinement to get RNA folding patterns. In addition to providing a consensus model, the method finds the range of models consistent with the data, which allows quantitative evaluation of the resolution of the model. The method also identifies conflicts in the experimental data. Although our protocol is aimed at much larger RNAs, we illustrate these techniques using the tRNA structure as an example and test-bed.     

Surber and kick sampling: a comparison for the assessment of macroinvertebrate community structure in streams of south-western Australia

Macroinvertebrate community structure was compared in benthic samples taken by Surber and kick methods from a lotic system in south-western Australia. Eleven sites were sampled concurrently in winter, spring and summer 1987.Surber samples contained fewer individuals and more taxa, particularly those with a low frequency of occurrence. This was attributed to the lower surface area, but greater intensity of Surber sampling. It is proposed that the Surber method is more suited to taking cryptic and closely adherent taxa in sites with a highly heterogeneous substratum.Percentage similarity between paired Surber and kick samples was determined by Sorensen's and Czekanowski's coefficients, with mean values of 66% and 60% for June, 61% and 49% for September and 66% and 49% for December respectively. Ordination demonstrated a division of upland from lowland sites on axis 1, with a separation of paired-samples on axis 2. This pattern held across qualitative and quantitative datasets, with and without a downweighting on rare taxa. At each level of classification fewer paired-samples separated in qualitative than quantitative datasets.Kick sampling provided a substantial saving in costs over Surber sampling, particularly when qualitative data were utilised, making the method suitable for routine, biological monitoring. However, the initial use of replicated Surber sampling, particularly in areas that have not been previously sampled is recommended for environmental impact studies to detect rare taxa, that may be endangered.     

A Method for Serial Tissue Processing and Parallel Analysis of Aberrant Crypt Morphology,Mucin Depletion,and Beta-Catenin Staining in an Experimental Model of Colon Carcinogenesis

The use of architectural and morphological characteristics of cells for establishing prognostic indicators by which individual pathologies are assigned grade and stage is a well-accepted practice. Advances in automated micro- and macroscopic image acquisition and digital image analysis have created new opportunities in the field of prognostic assessment; but, one area in experimental pathology, animal models for colon cancer, has not taken advantage of these opportunities. This situation is primarily due to the methods available to evaluate the colon of the rodent for the presence of premalignant and malignant pathologies. We report a new method for the excision and processing of the entire colon of the rat and illustrate how this procedure permitted the quantitative assessment of aberrant crypt foci (ACF), a premalignant colon pathology, for characteristics consistent with progression to malignancy. ACF were detected by methylene blue staining and subjected to quantitative morphometric analysis. Colons were then restained with high iron diamine–alcian blue for assessment of mucin depletion using an image overlay to associate morphometric data with mucin depletion. The subsequent evaluation of ACF for beta-catenin staining is also demonstrated. The methods described are particularly relevant to the screening of compounds for cancer chemopreventive activity.     

染色质结构之美——染色质可及性

染色质可及性(chromatin accessibility)作为一种衡量染色质结合因子与染色质DNA结合能力高低的染色质属性,是评价染色质结构稳态的重要指标之一,在多种细胞核进程中扮演重要角色,包括基因转录调控以及DNA损伤修复等。该属性的异常调控与多种疾病的发生发展密切相关,包括肿瘤以及神经退行性疾病等。对于该属性探究已经成为生命科学与疾病领域的热点。伴随越来越多的新技术应运而生,例如染色质构象捕获技术、高通量测序技术以及两种技术的结合等。随着技术的进步,多种参与调控染色质可及性的因素被发现和总结,包括核小体占位、组蛋白修饰以及非编码RNA等。多项大规模的染色质组学数据绘制了多种疾病的染色质可及性图谱,为揭示疾病的发生发展与染色质可及性之间的关系提供了数据支持。同时,随着单细胞染色质可及性测序技术的发展,实现了对细胞类型染色质层面的划分,弥补了单纯依赖基因表达划分细胞类型的不足。本文将从染色质的组成与可及性、影响染色质可及性的因素、染色质可及性的检测方法,以及染色质可及性与癌症的关系等方面简要阐述染色质可及性的研究进展。     

Mapping indicator models: From intuitive problem structuring to quantified decision-making in sustainable forest management

Most commonly, sustainability indicator sets presented as lists do not take into account interactions among indicators in a systematic manner. Vice versa, existing environmental indicator systems do not provide a formalized approach for problem structuring and quantitative decision support. In this paper, techniques for considering indicator relationships are highlighted and a coupled approach between a qualitative and a quantitative method is analysed. Cognitive mapping (CM) is used for structuring indicators and three different causal maps are derived based on established sustainability concepts: (a) criteria and indicators (C&I hierarchy), (b) indicator network, and (c) Driving Force-Pressure-State-Impact-Response (DPSIR) system. These maps are transferred to the Analytic Network Process (ANP) to allow their application in multi-criteria decision analysis (MCDA).In an application example, Pan-European indicators for sustainable forest management (SFM) are utilized in an ANP-based assessment. The effects of the model structure on the overall evaluation result are demonstrated by means of three reporting periods on Austrian forestry.In a comparative analysis of CM and ANP it is tested whether their measures of indicator significance do correspond. Both centrality in CM and single limited priorities in ANP have been reported to identify key indicators that play an important role in networks. We found out that the correspondence between CM and ANP is the stronger the more rigidly cause-effect relationships are interpreted, which is the case for the DPSIR system of SFM indicators.It is demonstrated that using indicator sets without consideration of the indicator interactions will cause shortcomings for evaluation and assessment procedures in SFM. Given strict and consistent definition of causal indicator relationships, a coupled use of CM and ANP is recommendable for both enhancing the process of problem structuring as well as supporting preference-based evaluation of decision alternatives.     

Statistical tests for analysing directed movement of self-organising animal groups

We discuss some theory concerning directional data and introduce a suite of statistical tools that researchers interested in the directional movement of animal groups can use to analyse results from their models. We illustrate these tools by analysing the results of a model of groups moving under the duress of certain informed indistinguishable individuals, that arises in the context of honeybee (Apis mellifera) swarming behaviour. We modify an existing model of collective motion, based on inter-individual social interactions, allowing knowledgeable individuals to guide group members to the goal by travelling through the group in a direct line aligned with the goal direction.     

Local sequence patterns of hydrophobicity and solvent accessibility in soluble globular proteins

We examined the variation in the solvent accessibility and hydrophobicity of the amino acids along the sequences of 58 soluble globular proteins with known tertiary structure. We found that there is a significant tendency for the accessibilities to run in clusters along the sequence but that the hydrophobicities are distributed without such nonrandom clusters. Theseresults suggest severe limitations on the power of sequence analysis tools that use average hydrophobicity scores of overlapping subsequences to predict accessibility.     

Assessment of vulnerability to climate change using a multi-criteria outranking approach with application to heat stress in Sydney

Climate change vulnerability assessment is a complex form of risk assessment which accounts for both geophysical and socio-economic components of risk. In indicator-based vulnerability assessment (IBVA), indicators are used to rank the vulnerabilities of socio-ecological systems (SESs). The predominant aggregation approach in the literature, sometimes based on multi-attribute utility theory (MAUT), typically builds a global-scale, utility function based on weighted summation, to generate rankings. However, the corresponding requirement for additive independence and complete knowledge of system interactions by analyst are rarely if ever satisfied in IBVA.We build an analogy between the structures of Multi-Criteria Decision Analysis (MCDA) and IBVA problems and show that a set of techniques called Outranking Methods, developed in MCDA to deal with criteria incommensurability, data uncertainty and preference imprecision, offer IBVA a sound alternative to additive or multiplicative aggregation. We reformulate IBVA problems within an outranking framework, define thresholds of difference and use an outranking method, ELECTRE III, to assess the relative vulnerability to heat stress of 15 local government areas in metropolitan Sydney. We find that the ranking outcomes are robust and argue that an outranking approach is better suited for assessments characterized by a mix of qualitative, semi-quantitative and quantitative indicators, threshold effects and uncertainties about the exact relationships between indicators and vulnerability.     

Gated quenching of intrinsic fluorescence and phosphorescence of globular proteins. An extended model.

We present a theoretical model to account for the quenching data of macromolecular fluorescence and phosphorescence when the accessibility to the quencher is gated by a dynamic mechanism coupled to the fluctuation of the macromolecular matrix. We show that the model currently in use to interpret gated quenching processes gives only approximate results in both qualitative and quantitative terms, and it can be regarded as a specific case of the presented model. We show that the gating dynamics affect both the apparent accessibility (alpha obs) and Ksv values obtained by the modified Stern-Volmer plot. The effect of gating on alpha obs and Ksv depends upon the relative rate of gating compared to the excited state lifetime. The model allows us to predict the effect of viscosity on quenching if it takes place by a gated mechanism. The prediction can and is, in this case, compared to the existing data on glycerol effects on acrylamide quenching of the tryptophan fluorescence in RNAse T1. The result shows that a simple gated model is not compatible with the observed quenching behavior.     

Simultaneous and exact interval estimates for the contrast of two groups based on an extremely high dimensional variable: application to mass spec data

MOTIVATION: Analysis of high-throughput proteomic/genomic data, in particular, surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) data and microarray data, has led to a multitude of techniques aimed at identifying potential biomarkers. Most of the statistical techniques for comparing two groups are based on qualitative measures such as P-value. A quantitative way such as interval estimation for the contrasts of two groups is more appealing. RESULTS: We have devised a simultaneous confidence bands method capable of detecting potential biomarkers, while controlling for overall confidence coverage level, in high-dimensional datasets that discriminate two treatment groups using a permutation scheme. For example, for the SELDI-TOF MS data, we deal with the entire spectrum simultaneously and construct (1 - alpha) confidence bands for the mean differences between groups. Furthermore, peaks were identified based on the maximal differences between the groups as determined by the confidence bands. The analysis method herein described gives both qualitative (P-value) and quantitative data (magnitude of difference). The Clinical Proteomics Programs Databank's ovarian cancer dataset and data from in-house samples containing known spiked-in proteins were analyzed. We were able to identify potential biomarkers similar to those described in previous analysis of the ovarian cancer data, however, while these markers are highly significant between cancer and normal groups, our analysis indicated the absolute difference between the two groups was minimal. In addition, we found additional markers than those previously described with greater differences in average intensities. The proposed confidence bands method successfully detected the spiked-in peaks, as well as, secondary peaks generated by adducts and double-charged species. We also illustrate our method utilizing paired gene expression data from a prostate cancer microarray experiment by constructing confidence bands for the fold changes between cancer and normal samples. AVAILABILITY: R-package, 'seie.zip' (license: GNU GPL), is publiclly available at http://research2.dfci.harvard.edu/dfci/MS_spike-in_data/