One of the main challenges in metagenomics is the identification of microorganisms in clinical and environmental samples. While an extensive and heterogeneous set of computational tools is available ...to classify microorganisms using whole-genome shotgun sequencing data, comprehensive comparisons of these methods are limited.
In this study, we use the largest-to-date set of laboratory-generated and simulated controls across 846 species to evaluate the performance of 11 metagenomic classifiers. Tools were characterized on the basis of their ability to identify taxa at the genus, species, and strain levels, quantify relative abundances of taxa, and classify individual reads to the species level. Strikingly, the number of species identified by the 11 tools can differ by over three orders of magnitude on the same datasets. Various strategies can ameliorate taxonomic misclassification, including abundance filtering, ensemble approaches, and tool intersection. Nevertheless, these strategies were often insufficient to completely eliminate false positives from environmental samples, which are especially important where they concern medically relevant species. Overall, pairing tools with different classification strategies (k-mer, alignment, marker) can combine their respective advantages.
This study provides positive and negative controls, titrated standards, and a guide for selecting tools for metagenomic analyses by comparing ranges of precision, accuracy, and recall. We show that proper experimental design and analysis parameters can reduce false positives, provide greater resolution of species in complex metagenomic samples, and improve the interpretation of results.
Abstract
As police records expand with big data analytics, so too has the range of non-conviction information seeping into the public domain through criminal background checks. Numerous studies have ...documented the negative effects of background checks for those with criminal convictions, but less understood are the effects of non-conviction records. We draw on 8 focus groups and 52 interviews to understand how the release of non-conviction records are: (1) creating new institutional risk management pressures for police institutions, (2) expanding the role of employers as arbiters of risk, (3) redefining understandings of ‘the risky subject’ to include victims, those with mental health challenges and other innocent individuals subject to police contact and (4) raising critical legal questions about privacy and presumptions of innocence.
Meanings of risk in criminal justice assessment continue to evolve, making it critical to understand how particular compositions of risk are mediated, resisted and re-configured by experts and ...practitioners. Criminal justice organizations are working with computer scientists, software engineers and private companies that are skilled in big data analytics to produce new ways of thinking about and managing risk. Little is known, however, about how criminal justice systems, social justice organizations and individuals are shaping, challenging and redefining conventional actuarial risk episteme(s) through the use of big data technologies. The use of such analytics is shifting organizational risk practices, challenging social science methods of assessing risk, producing new knowledge about risk and consequently new forms of algorithmic governance. This article explores how big data reconfigure risk by producing a new form of algorithmic risk—a form of risk which is posited as different from the social science (psychologically) informed risk techniques already in use in many justice sectors. It also shows that new experts are entering the risk game, including technologists who make data public and accessible to a range of stakeholders. Finally, it demonstrates that big data analytics can be used to produce forms of usable knowledge that constitute types of ‘information activism’. This form of activism produces alternative risk narratives, which are focused on ‘criminogenic structures’ or ‘criminogenic policy’.
This paper discusses the concerns associated with the introduction of, and increased reliance on, actuarial risk tools in sentencing in order to: (1) stimulate cross-disciplinary dialog and research ...about the impact of incorporating actuarial risk logic into sentencing processes and (2) identify questions requiring further empirical examination. In this article, I recognize that actuarial risk logic offers managerial and organizational benefits, but I also demonstrate that the application of actuarial risk when sentencing offenders is not without important consequences. First, I provide a brief outline of the emergence, logic, and entrenchment of probabilistic reasoning within criminal justice decision-making, and the more recent extension and application of actuarial risk logic to sentencing. Then, I use the following themes to define the limits of using risk sciences in sentencing: (1) the logical structure of risk; (2) the slippage between risk prediction and individual causation; (3) current methodological limits of risk science; (4) the potential for gender and race discrimination; (5) the legal relevance and transparency of risk-based sentencing; and (6) the jurisprudential and organizational impact of various risk technologies. Importantly, the nature and severity of these complications will vary by, and within, the jurisdiction (or sentencing regime) because current sentencing practices are influenced by local jurisdictional needs and sentencing laws.
The complete genome sequence of the radiation-resistant bacterium Deinococcus radiodurans R1 is composed of two chromosomes (2,648,638 and 412,348 base pairs), a megaplasmid (177,466 base pairs), and ...a small plasmid (45,704 base pairs), yielding a total genome of 3,284,156 base pairs. Multiple components distributed on the chromosomes and megaplasmid that contribute to the ability of D. radiodurans to survive under conditions of starvation, oxidative stress, and high amounts of DNA damage were identified. Deinococcus radiodurans represents an organism in which all systems for DNA repair, DNA damage export, desiccation and starvation recovery, and genetic redundancy are present in one cell.
Recent calls for 'evidence-based' approaches have firmly positioned risk assessment as a promising path towards more efficient, unbiased, and empirically based offender management, in custody and in ...the community. Simultaneously, sociological and critical legal scholars have questioned the focus on individual needs at the expense of wider structural factors'. I will demonstrate the need to reconceptualise risk/need logics and the use of 'evidence'. I will argue that various criminal justice processes are themselves dynamic criminogenic risks that produce systemic conditions for recidivism and which, if modified, could make a measurable difference in recidivism and other correctional efficiencies. Finally, I will argue that the logic of dynamic risk is transferable to an analysis of socio-structural factors, and that this characterisation can alter the framing of penal subjects, governmental responsibilities, and potentially interrupt the systemically produced criminogenic pathways that perpetuate criminal involvement and marginalisation.
Arabidopsis thaliana (Arabidopsis) is unique among plant model organisms in having a small genome (130-140 Mb), excellent physical and genetic maps, and little repetitive DNA. Here we report the ...sequence of chromosome 2 from the Columbia ecotype in two gap-free assemblies (contigs) of 3.6 and 16 megabases (Mb). The latter represents the longest published stretch of uninterrupted DNA sequence assembled from any organism to date. Chromosome 2 represents 15% of the genome and encodes 4,037 genes, 49% of which have no predicted function. Roughly 250 tandem gene duplications were found in addition to large-scale duplications of about 0.5 and 4.5 Mb between chromosomes 2 and 1 and between chromosomes 2 and 4, respectively. Sequencing of nearly 2 Mb within the genetically defined centromere revealed a low density of recognizable genes, and a high density and diverse range of vestigial and presumably inactive mobile elements. More unexpected is what appears to be a recent insertion of a continuous stretch of 75% of the mitochondrial genome into chromosome 2.
Expressions of masculinity in prison are most often characterized as being structured in response to an environment that encourages displays of stoicism, bravery, physical prowess and ...violence/aggression. However, we found that the antagonistic, precarious and risk-prone environment of the prison shapes prisoners’ behaviours and the constitution of ‘normative’ and hegemonic masculinities in more nuanced ways than prior research suggests. Drawing on in-depth interviews with 56 male parolees, we explored how these men perceived and responded to risk while incarcerated, as well as how prison masculinities are linked with experiences and management of risk to their personal (legal, physical and emotional) safety. In this article, we focus on how prisoners mobilized and negotiated their masculine subjectivities to handle the uncertainty of imprisonment and the various risks they encountered in prison. We argue that penal risks and prison masculinities are mutually constitutive; risk is linked to perceptions of physical and emotional vulnerability, which shape prisoners’ masculine embodiment. Simultaneously, prisoners try to respond to uncertainty and perceived risk in ways that present their masculinity as empowered rather than submissive. Our findings advance the conceptualization of prison and hegemonic masculinities, penal environments and risk/uncertainty.
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