Towards Scientific Incident Response

A scientific incident analysis is one with a methodical, justifiable approach to the human decision-making process. Incident analysis is a good target for additional rigor because it is the most human-intensive part of incident response. Our goal is to provide the tools necessary for specifying precisely the reasoning process in incident analysis. Such tools are lacking, and are a necessary (though not sufficient) component of a more scientific analysis process. To reach this goal, we adapt tools from program verification that can capture and test abductive reasoning. As Charles Peirce coined the term in 1900, “Abduction is the process of forming an explanatory hypothesis. It is the only logical operation which introduces any new idea.” We reference canonical examples as paradigms of decision-making during analysis. With these examples in mind, we design a logic capable of expressing decision-making during incident analysis. The result is that we can express, in machine-readable and precise language, the abductive hypotheses than an analyst makes, and the results of evaluating them. This result is beneficial because it opens up the opportunity of genuinely comparing analyst processes without revealing sensitive system details, as well as opening an opportunity towards improved decision-support via limited automation

The reporting quality of natural language processing studies: systematic review of studies of radiology reports.

BACKGROUND: Automated language analysis of radiology reports using natural language processing (NLP) can provide valuable information on patients' health and disease. With its rapid development, NLP studies should have transparent methodology to allow comparison of approaches and reproducibility. This systematic review aims to summarise the characteristics and reporting quality of studies applying NLP to radiology reports. METHODS: We searched Google Scholar for studies published in English that applied NLP to radiology reports of any imaging modality between January 2015 and October 2019. At least two reviewers independently performed screening and completed data extraction. We specified 15 criteria relating to data source, datasets, ground truth, outcomes, and reproducibility for quality assessment. The primary NLP performance measures were precision, recall and F1 score. RESULTS: Of the 4,836 records retrieved, we included 164 studies that used NLP on radiology reports. The commonest clinical applications of NLP were disease information or classification (28%) and diagnostic surveillance (27.4%). Most studies used English radiology reports (86%). Reports from mixed imaging modalities were used in 28% of the studies. Oncology (24%) was the most frequent disease area. Most studies had dataset size > 200 (85.4%) but the proportion of studies that described their annotated, training, validation, and test set were 67.1%, 63.4%, 45.7%, and 67.7% respectively. About half of the studies reported precision (48.8%) and recall (53.7%). Few studies reported external validation performed (10.8%), data availability (8.5%) and code availability (9.1%). There was no pattern of performance associated with the overall reporting quality. CONCLUSIONS: There is a range of potential clinical applications for NLP of radiology reports in health services and research. However, we found suboptimal reporting quality that precludes comparison, reproducibility, and replication. Our results support the need for development of reporting standards specific to clinical NLP studies

A self-organized model for cell-differentiation based on variations of molecular decay rates

Systemic properties of living cells are the result of molecular dynamics governed by so-called genetic regulatory networks (GRN). These networks capture all possible features of cells and are responsible for the immense levels of adaptation characteristic to living systems. At any point in time only small subsets of these networks are active. Any active subset of the GRN leads to the expression of particular sets of molecules (expression modes). The subsets of active networks change over time, leading to the observed complex dynamics of expression patterns. Understanding of this dynamics becomes increasingly important in systems biology and medicine. While the importance of transcription rates and catalytic interactions has been widely recognized in modeling genetic regulatory systems, the understanding of the role of degradation of biochemical agents (mRNA, protein) in regulatory dynamics remains limited. Recent experimental data suggests that there exists a functional relation between mRNA and protein decay rates and expression modes. In this paper we propose a model for the dynamics of successions of sequences of active subnetworks of the GRN. The model is able to reproduce key characteristics of molecular dynamics, including homeostasis, multi-stability, periodic dynamics, alternating activity, differentiability, and self-organized critical dynamics. Moreover the model allows to naturally understand the mechanism behind the relation between decay rates and expression modes. The model explains recent experimental observations that decay-rates (or turnovers) vary between differentiated tissue-classes at a general systemic level and highlights the role of intracellular decay rate control mechanisms in cell differentiation.Comment: 16 pages, 5 figure

Reader and author gender and genre in Goodreads

This is an accepted manuscript of an article published by SAGE Publishing in Journal of Librarianship & Information Science on 01/05/2017, available online: https://doi.org/10.1177/0961000617709061 The accepted version of the publication may differ from the final published version.There are known gender differences in book preferences in terms of both genre and author gender but their extent and causes are not well understood. It is unclear whether reader preferences for author genders occur within any or all genres and whether readers evaluate books differently based on author genders within specific genres. This article exploits a major source of informal book reviews, the Goodreads.com website, to assess the influence of reader and author genders on book evaluations within genres. It uses a quantitative analysis of 201,560 books and their reviews, focusing on the top 50 user-specified genres. The results show strong gender differences in the ratings given by reviewers to books within genres, such as female reviewers rating contemporary romance more highly, with males preferring short stories. For most common book genres, reviewers give higher ratings to books authored by their own gender, confirming that gender bias is not confined to the literary elite. The main exception is the comic book, for which male reviewers prefer female authors, despite their scarcity. A word frequency analysis suggested that authors wrote, and reviewers valued, gendered aspects of books within a genre. For example, relationships and romance were disproportionately mentioned by women in mystery and fantasy novels. These results show that, perhaps for the first time, it is possible to get large scale evidence about the reception of books by typical readers, if they post reviews online

Domesticating the ‘troubled family’: Racialised sexuality and the postcolonial governance of family life in the UK

This article examines how the UK’s Troubled Families Programme (TFP) works as a strategy of domestication which produces and delimits certain forms of ‘family life’. Drawing upon critical geographies of home and empire, the article explores how the TFP works to manage the troubled family as part of a longer history of regulating unruly households in the name of national health and civilisation. Viewing the TFP as part of the production of heteronormative order, highlights how the policy remobilises and reconfigures older forms of colonial rule which work to demarcate between civility/savagery, the developable/undevelopable. In examining the postcolonial dimension of neoliberal social policy, the article stresses how the TFP relies on racializing and sexualised logics of socio-biological control borrowed from imperial eugenics. Reading the TFP in this way contributes to our understanding of neoliberal rule. That the troubled family can be either domesticated or destroyed (through benefit sanctions and eviction) equally reveals the extent to which domesticity works as a key site for the production of both ‘worthy’ and ‘surplus’ life

Chronic non-specific low back pain - sub-groups or a single mechanism?

Copyright 2008 Wand and O'Connell; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Background: Low back pain is a substantial health problem and has subsequently attracted a considerable amount of research. Clinical trials evaluating the efficacy of a variety of interventions for chronic non-specific low back pain indicate limited effectiveness for most commonly applied interventions and approaches. Discussion: Many clinicians challenge the results of clinical trials as they feel that this lack of effectiveness is at odds with their clinical experience of managing patients with back pain. A common explanation for this discrepancy is the perceived heterogeneity of patients with chronic non-specific low back pain. It is felt that the effects of treatment may be diluted by the application of a single intervention to a complex, heterogeneous group with diverse treatment needs. This argument presupposes that current treatment is effective when applied to the correct patient. An alternative perspective is that the clinical trials are correct and current treatments have limited efficacy. Preoccupation with sub-grouping may stifle engagement with this view and it is important that the sub-grouping paradigm is closely examined. This paper argues that there are numerous problems with the sub-grouping approach and that it may not be an important reason for the disappointing results of clinical trials. We propose instead that current treatment may be ineffective because it has been misdirected. Recent evidence that demonstrates changes within the brain in chronic low back pain sufferers raises the possibility that persistent back pain may be a problem of cortical reorganisation and degeneration. This perspective offers interesting insights into the chronic low back pain experience and suggests alternative models of intervention. Summary: The disappointing results of clinical research are commonly explained by the failure of researchers to adequately attend to sub-grouping of the chronic non-specific low back pain population. Alternatively, current approaches may be ineffective and clinicians and researchers may need to radically rethink the nature of the problem and how it should best be managed

Wind-Powered Wheel Locomotion, Initiated by Leaping Somersaults, in Larvae of the Southeastern Beach Tiger Beetle (Cicindela dorsalis media)

Rapid movement is challenging for elongate, soft-bodied animals with short or no legs. Leaping is known for only a few animals with this “worm-like” morphology. Wheel locomotion, in which the animal's entire body rolls forward along a central axis, has been reported for only a handful of animals worldwide. Here we present the first documented case of wind-powered wheel locomotion, in larvae of the coastal tiger beetle Cicindela dorsalis media. When removed from their shallow burrows, larvae easily can be induced to enter a behavioral sequence that starts with leaping; while airborne, larvae loop their body into a rotating wheel and usually either “hit the ground rolling” or leap again. The direction larvae wheel is closely related to the direction in which winds are blowing; thus, all our larvae wheeled up-slope, as winds at our study site consistently blew from sea to land. Stronger winds increased both the proportion of larvae wheeling, and the distance traveled, exceeding 60 m in some cases. In addition, the proportion of larvae that wheel and the distance traveled by wheeling larvae are significantly greater on smooth sandy beaches than on beach surfaces made rough and irregular by pedestrian, equestrian, and vehicular traffic. Like other coastal species of tiger beetles, C. dorsalis media has suffered major declines in recent years that are clearly correlated with increased human impacts. The present study suggests that the negative effects of beach traffic may be indirect, preventing larvae from escaping from predators using wheel locomotion by disrupting the flat, hard surface necessary for efficient wheeling

Adoption of practice guidelines and assessment tools in substance abuse treatment

<p>Abstract</p> <p>Background</p> <p>The gap between research and practice limits utilization of relevant, progressive and empirically validated strategies in substance abuse treatment.</p> <p>Methods</p> <p>Participants included substance abuse treatment programs from the Northeastern United States. Structural equation models were constructed with agency level data to explore two outcome variables: adoption of practice guidelines and assessment tools at two points in time; models also included organizational, staffing and service variables.</p> <p>Results</p> <p>In 1997, managed care involvement and provision of primary care services had the strongest association with increased use of assessment tools, which, along with provision of counseling services, were associated with a greater use of practice guidelines. In 2001, managed care involvement, counseling services and being a stand-alone drug treatment agency were associated with a greater use of assessment tools, which was in turn related to an increase in the use of practice guidelines.</p> <p>Conclusions</p> <p>This study provides managers, clinicians and policy-makers with a framework for understanding factors related to the adoption of new technologies in substance abuse treatment.</p

Surface Aggregation of Urinary Proteins and Aspartic Acid-Rich Peptides on the Faces of Calcium Oxalate Monohydrate Investigated by In Situ Force Microscopy

The growth of calcium oxalate monohydrate in the presence of Tamm-Horsfall protein (THP), osteopontin, and the 27-residue synthetic peptides (DDDS)6DDD and (DDDG)6DDD (D = aspartic acid, S = serine, and G = glycine) was investigated via in situ atomic force microscopy. The results show that these four growth modulators create extensive deposits on the crystal faces. Depending on the modulator and crystal face, these deposits can occur as discrete aggregates, filamentary structures, or uniform coatings. These proteinaceous films can lead to either the inhibition of or an increase in the step speeds (with respect to the impurity-free system), depending on a range of factors that include peptide or protein concentration, supersaturation, and ionic strength. While THP and the linear peptides act, respectively, to exclusively increase and inhibit growth on the \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\left( {\bar{1}01} \right)$$\end{document} face, both exhibit dual functionality on the (010) face, inhibiting growth at low supersaturation or high modulator concentration and accelerating growth at high supersaturation or low modulator concentration. Based on analyses of growth morphologies and dependencies of step speeds on supersaturation and protein or peptide concentration, we propose a picture of growth modulation that accounts for the observations in terms of the strength of binding to the surfaces and steps and the interplay of electrostatic and solvent-induced forces at the crystal surface