A Review of the Statistical and Quantitative Methods Used to Study Alcohol-Attributable Crime

Modelling the relationship between alcohol consumption and crime generates new knowledge for crime prevention strategies. Advances in data, particularly data with spatial and temporal attributes, have led to a growing suite of applied methods for modelling. In support of alcohol and crime researchers we synthesized and critiqued existing methods of spatially and quantitatively modelling the effects of alcohol exposure on crime to aid method selection, and identify new opportunities for analysis strategies. We searched the alcohol-crime literature from 1950 to January 2014. Analyses that statistically evaluated or mapped the association between alcohol and crime were included. For modelling purposes, crime data were most often derived from generalized police reports, aggregated to large spatial units such as census tracts or postal codes, and standardized by residential population data. Sixty-eight of the 90 selected studies included geospatial data of which 48 used cross-sectional datasets. Regression was the prominent modelling choice (n = 78) though dependent on data many variations existed. There are opportunities to improve information for alcohol-attributable crime prevention by using alternative population data to standardize crime rates, sourcing crime information from non-traditional platforms (social media), increasing the number of panel studies, and conducting analysis at the local level (neighbourhood, block, or point). Due to the spatio-temporal advances in crime data, we expect a continued uptake of flexible Bayesian hierarchical modelling, a greater inclusion of spatial-temporal point pattern analysis, and shift toward prospective (forecast) modelling over small areas (e.g., blocks).     

Event Networks and the Identification of Crime Pattern Motifs

In this paper we demonstrate the use of network analysis to characterise patterns of clustering in spatio-temporal events. Such clustering is of both theoretical and practical importance in the study of crime, and forms the basis for a number of preventative strategies. However, existing analytical methods show only that clustering is present in data, while offering little insight into the nature of the patterns present. Here, we show how the classification of pairs of events as close in space and time can be used to define a network, thereby generalising previous approaches. The application of graph-theoretic techniques to these networks can then offer significantly deeper insight into the structure of the data than previously possible. In particular, we focus on the identification of network motifs, which have clear interpretation in terms of spatio-temporal behaviour. Statistical analysis is complicated by the nature of the underlying data, and we provide a method by which appropriate randomised graphs can be generated. Two datasets are used as case studies: maritime piracy at the global scale, and residential burglary in an urban area. In both cases, the same significant 3-vertex motif is found; this result suggests that incidents tend to occur not just in pairs, but in fact in larger groups within a restricted spatio-temporal domain. In the 4-vertex case, different motifs are found to be significant in each case, suggesting that this technique is capable of discriminating between clustering patterns at a finer granularity than previously possible.     

Addressing the Carbon‐Crime Blind Spot: A Carbon Footprint Approach

Governments estimate the social and economic impacts of crime, but its environmental impact is largely unacknowledged. Our study addresses this by estimating the carbon footprint of crime in England and Wales and identifies the largest sources of emissions. By applying environmentally extended input‐output analysis–derived carbon emission factors to the monetized costs of crime, we estimate that crime committed in 2011 in England and Wales gave rise to over 4 million tonnes of carbon dioxide equivalents. Burglary resulted in the largest proportion of the total footprint (30%), because of the carbon associated with replacing stolen/damaged goods. Emissions arising from criminal justice system services also accounted for a large proportion (21% of all offenses; 49% of police recorded offenses). Focus on these offenses and the carbon efficiency of these services may help reduce the overall emissions that result from crime. However, cutting crime does not automatically result in a net reduction in carbon, given that we need to take account of potential rebound effects. As an example, we consider the impact of reducing domestic burglary by 5%. Calculating this is inherently uncertain given that it depends on assumptions concerning how money would be spent in the absence of crime. We find the most likely rebound effect (our medium estimate) is an increase in emissions of 2%. Despite this uncertainty concerning carbon savings, our study goes some way toward informing policy makers of the scale of the environmental consequences of crime and thus enables it to be taken into account in policy appraisals.     

国内住区环境设计预防犯罪研究进展与反思

通过计量分析方法对近30年来住区环境设计预防犯罪领域的文献进行关键词共现分析、关键词时区分析以及关键词聚类分析等,总结了该领域在国内的研究进程及学科发展趋势。以CPTED理论为分析框架,简要梳理了该领域当前的研究方法、数据来源类型和研究发现,并结合现有城市居住区规划设计规范内容探讨其在犯罪环境预防方面的启示;在此基础上从数据来源、研究的地域性和案件类型的差异性以及研究成果的实践应用等方面对当前的研究进展进行剖析与反思。针对当前该领域实践与理论研究中存在的不足与瓶颈,对未来这一研究领域的发展和实践提出具体建议。     

Marriage Markets and Male Mating Effort: Violence and Crime Are Elevated Where Men Are Rare

The negative social outcomes in populations with male-biased sex ratios are a growing concern. In general, the expectation is of heightened violence as a result of excess men engaging in antisocial behavior and crime, thereby threatening societal stability. While intuitive, these claims are largely unsupported in the literature. Using mating market theory as our guide, we examine indicators of male mating effort, including (1) violent competition between men (homicide, aggravated assault) and (2) indicators of uncommitted sexual behavior (rape, sex offenses, and prostitution). Our unit of analysis is U.S. county-level data. We find that counties with more men have lower rates of crime and violent behavior. Our findings challenge conventional claims of male excess leading to elevated levels of violence. Instead, in support of mating market predictions, we find that criminal and violent behavior related to male mating effort is least common in male-biased sex ratios. We discuss the implications of our findings for public policy regarding incarceration and criminal behavior.     

How scale-free are biological networks.

The concept of scale-free network has emerged as a powerful unifying paradigm in the study of complex systems in biology and in physical and social studies. Metabolic, protein, and gene interaction networks have been reported to exhibit scale-free behavior based on the analysis of the distribution of the number of connections of the network nodes. Here we study 10 published datasets of various biological interactions and perform goodness-of-fit tests to determine whether the given data is drawn from the power-law distribution. Our analysis did not identify a single interaction network that has a nonzero probability of being drawn from the power-law distribution.     

Investigating meta-approaches for reconstructing gene networks in a mammalian cellular context

The output of state-of-the-art reverse-engineering methods for biological networks is often based on the fitting of a mathematical model to the data. Typically, different datasets do not give single consistent network predictions but rather an ensemble of inconsistent networks inferred under the same reverse-engineering method that are only consistent with the specific experimentally measured data. Here, we focus on an alternative approach for combining the information contained within such an ensemble of inconsistent gene networks called meta-analysis, to make more accurate predictions and to estimate the reliability of these predictions. We review two existing meta-analysis approaches; the Fisher transformation combined coefficient test (FTCCT) and Fisher's inverse combined probability test (FICPT); and compare their performance with five well-known methods, ARACNe, Context Likelihood or Relatedness network (CLR), Maximum Relevance Minimum Redundancy (MRNET), Relevance Network (RN) and Bayesian Network (BN). We conducted in-depth numerical ensemble simulations and demonstrated for biological expression data that the meta-analysis approaches consistently outperformed the best gene regulatory network inference (GRNI) methods in the literature. Furthermore, the meta-analysis approaches have a low computational complexity. We conclude that the meta-analysis approaches are a powerful tool for integrating different datasets to give more accurate and reliable predictions for biological networks.     

Iterative Cross-Correlation Analysis of Resting State Functional Magnetic Resonance Imaging Data

Seed-based cross-correlation analysis (sCCA) and independent component analysis have been widely employed to extract functional networks from the resting state functional magnetic resonance imaging data. However, the results of sCCA, in terms of both connectivity strength and network topology, can be sensitive to seed selection variations. ICA avoids the potential problems due to seed selection, but choosing which component(s) to represent the network of interest could be subjective and problematic. In this study, we proposed a seed-based iterative cross-correlation analysis (siCCA) method for resting state brain network analysis. The method was applied to extract default mode network (DMN) and stable task control network (STCN) in two independent datasets acquired from normal adults. Compared with the networks obtained by traditional sCCA and ICA, the resting state networks produced by siCCA were found to be highly stable and independent on seed selection. siCCA was used to analyze DMN in first-episode major depressive disorder (MDD) patients. It was found that, in the MDD patients, the volume of DMN negatively correlated with the patients'' social disability screening schedule scores.     

Network cohesion,group size and neocortex size in female-bonded Old World primates

Most primates are intensely social and spend a large amount of time servicing social relationships. In this study, we use social network analysis to examine the relationship between primate group size, total brain size, neocortex ratio and several social network metrics concerned with network cohesion. Using female grooming networks from a number of Old World monkey species, we found that neocortex size was a better predictor of network characteristics than endocranial volumes. We further found that when we controlled for group size, neocortex ratio was negatively correlated with network density, connectivity, relative clan size and proportional clan membership, while there was no effect of neocortex ratio on change in connectivity following the removal of the most central female in the network. Thus, in species with larger neocortex ratios, females generally live in more fragmented networks, belong to smaller grooming clans and are members of relatively fewer clans despite living in a closely bonded group. However, even though groups are more fragmented to begin with among species with larger neocortices, the removal of the most central individual does cause groups to fall apart, suggesting that social complexity may ultimately involve the management of highly fragmented social groups while at the same time maintaining overall social cohesion. These results emphasize a need for more detailed brain data on a wider sample of primate species.     

Multilayer network analyses as a toolkit for measuring social structure

The formalization of multilayer networks allows for new ways to measure sociality in complex social systems,including groups of animals.The same mathematical representation and methods are widely applicable across fields and study systems,and a network can represent drastically different types of data.As such,in order to apply analyses and interpret the results in a meaningful way the researcher must have a deep understanding of what their network is representing and what parts of it are being measured by a given analysis.Multilayer social networks can represent social structure with more detail than is often present in single layer networks,including multiple"types"of individuals,interactions,or relationships,and the extent to which these types are interdependent.Multilayer networks can also encompass a wider range of social scales,which can help overcome complications that are inherent to measuring sociality.In this paper,I dissect multilayer networks into the parts that correspond to different components of social structures.I then discuss common pitfalls to avoid across different stages of multilayer network analyses-some novel and some that always exist in social network analysis but are magnified in multi-layer representations.This paper serves as a primer for building a customized toolkit of multilayer network analyses,to probe components of social structure in animal social systems.     

Metabolic network discovery through reverse engineering of metabolome data

Reverse engineering of high-throughput omics data to infer underlying biological networks is one of the challenges in systems biology. However, applications in the field of metabolomics are rather limited. We have focused on a systematic analysis of metabolic network inference from in silico metabolome data based on statistical similarity measures. Three different data types based on biological/environmental variability around steady state were analyzed to compare the relative information content of the data types for inferring the network. Comparing the inference power of different similarity scores indicated the clear superiority of conditioning or pruning based scores as they have the ability to eliminate indirect interactions. We also show that a mathematical measure based on the Fisher information matrix gives clues on the information quality of different data types to better represent the underlying metabolic network topology. Results on several datasets of increasing complexity consistently show that metabolic variations observed at steady state, the simplest experimental analysis, are already informative to reveal the connectivity of the underlying metabolic network with a low false-positive rate when proper similarity-score approaches are employed. For experimental situations this implies that a single organism under slightly varying conditions may already generate more than enough information to rightly infer networks. Detailed examination of the strengths of interactions of the underlying metabolic networks demonstrates that the edges that cannot be captured by similarity scores mainly belong to metabolites connected with weak interaction strength.     

Reverse Engineering Boolean Networks: From Bernoulli Mixture Models to Rule Based Systems

A Boolean network is a graphical model for representing and analyzing the behavior of gene regulatory networks (GRN). In this context, the accurate and efficient reconstruction of a Boolean network is essential for understanding the gene regulation mechanism and the complex relations that exist therein. In this paper we introduce an elegant and efficient algorithm for the reverse engineering of Boolean networks from a time series of multivariate binary data corresponding to gene expression data. We call our method ReBMM, i.e., reverse engineering based on Bernoulli mixture models. The time complexity of most of the existing reverse engineering techniques is quite high and depends upon the indegree of a node in the network. Due to the high complexity of these methods, they can only be applied to sparsely connected networks of small sizes. ReBMM has a time complexity factor, which is independent of the indegree of a node and is quadratic in the number of nodes in the network, a big improvement over other techniques and yet there is little or no compromise in accuracy. We have tested ReBMM on a number of artificial datasets along with simulated data derived from a plant signaling network. We also used this method to reconstruct a network from real experimental observations of microarray data of the yeast cell cycle. Our method provides a natural framework for generating rules from a probabilistic model. It is simple, intuitive and illustrates excellent empirical results.     

Computational identification of cellular networks and pathways

In this article we highlight recent developments in computational functional genomics to identify networks of functionally related genes and proteins based on diverse sources of genomic data. Our specific focus is on statistical methods to identify genetic networks. We discuss integrated analysis of microarray datasets, methods to combine heterogeneous data sources, the analysis of high-dimensional phenotyping screens and describe efforts to establish a reliable and unbiased gold standard for method comparison and evaluation.     

Proximity data-loggers increase the quantity and quality of social network data

Social network analysis is an ideal quantitative tool for advancing our understanding of complex social behaviour. However, this approach is often limited by the challenges of accurately characterizing social structure and measuring network heterogeneity. Technological advances have facilitated the study of social networks, but to date, all such work has focused on large vertebrates. Here, we provide proof of concept for using proximity data-logging to quantify the frequency of social interactions, construct weighted networks and characterize variation in the social behaviour of a lek-breeding bird, the wire-tailed manakin, Pipra filicauda. Our results highlight how this approach can ameliorate the challenges of social network data collection and analysis by concurrently improving data quality and quantity.     

Graph-based methods for analysing networks in cell biology

Availability of large-scale experimental data for cell biology is enabling computational methods to systematically model the behaviour of cellular networks. This review surveys the recent advances in the field of graph-driven methods for analysing complex cellular networks. The methods are outlined on three levels of increasing complexity, ranging from methods that can characterize global or local structural properties of networks to methods that can detect groups of interconnected nodes, called motifs or clusters, potentially involved in common elementary biological functions. We also briefly summarize recent approaches to data integration and network inference through graph-based formalisms. Finally, we highlight some challenges in the field and offer our personal view of the key future trends and developments in graph-based analysis of large-scale datasets.     

Gene network inference and visualization tools for biologists: application to new human transcriptome datasets

Gene regulatory networks inferred from RNA abundance data have generated significant interest, but despite this, gene network approaches are used infrequently and often require input from bioinformaticians. We have assembled a suite of tools for analysing regulatory networks, and we illustrate their use with microarray datasets generated in human endothelial cells. We infer a range of regulatory networks, and based on this analysis discuss the strengths and limitations of network inference from RNA abundance data. We welcome contact from researchers interested in using our inference and visualization tools to answer biological questions.