A multidisciplinary systematic review of the use of diagrams as a means of collecting data from research subjects: application, benefits and recommendations

BACKGROUND: In research, diagrams are most commonly used in the analysis of data and visual presentation of results. However there has been a substantial growth in the use of diagrams in earlier stages of the research process to collect data. Despite this growth, guidance on this technique is often isolated within disciplines. METHODS: A multidisciplinary systematic review was performed, which included 13 traditional healthcare and non-health-focused indexes, non-indexed searches and contacting experts in the field. English-language articles that used diagrams as a data collection tool and reflected on the process were included in the review, with no restriction on publication date. RESULTS: The search identified 2690 documents, of which 80 were included in the final analysis. The choice to use diagrams for data collection is often determined by requirements of the research topic, such as the need to understand research subjects' knowledge or cognitive structure, to overcome cultural and linguistic differences, or to understand highly complex subject matter. How diagrams were used for data collection varied by the degrees of instruction for, and freedom in, diagram creation, the number of diagrams created or edited and the use of diagrams in conjunction with other data collection methods. Depending on how data collection is structured, a variety of options for qualitative and quantitative analysis are available to the researcher. The review identified a number of benefits to using diagrams in data collection, including the ease with which the method can be adapted to complement other data collection methods and its ability to focus discussion. However it is clear that the benefits and challenges of diagramming depend on the nature of its application and the type of diagrams used. DISCUSSION/CONCLUSION: The results of this multidisciplinary systematic review examine the application of diagrams in data collection and the methods for analyzing the unique datasets elicited. Three recommendations are presented. Firstly, the diagrammatic approach should be chosen based on the type of data needed. Secondly, appropriate instructions will depend on the approach chosen. And thirdly, the final results should present examples of original or recreated diagrams. This review also highlighted the need for a standardized terminology of the method and a supporting theoretical framework

Network Models of TEM β-Lactamase Mutations Coevolving under Antibiotic Selection Show Modular Structure and Anticipate Evolutionary Trajectories

Understanding how novel functions evolve (genetic adaptation) is a critical goal of evolutionary biology. Among asexual organisms, genetic adaptation involves multiple mutations that frequently interact in a non-linear fashion (epistasis). Non-linear interactions pose a formidable challenge for the computational prediction of mutation effects. Here we use the recent evolution of β-lactamase under antibiotic selection as a model for genetic adaptation. We build a network of coevolving residues (possible functional interactions), in which nodes are mutant residue positions and links represent two positions found mutated together in the same sequence. Most often these pairs occur in the setting of more complex mutants. Focusing on extended-spectrum resistant sequences, we use network-theoretical tools to identify triple mutant trajectories of likely special significance for adaptation. We extrapolate evolutionary paths (n = 3) that increase resistance and that are longer than the units used to build the network (n = 2). These paths consist of a limited number of residue positions and are enriched for known triple mutant combinations that increase cefotaxime resistance. We find that the pairs of residues used to build the network frequently decrease resistance compared to their corresponding singlets. This is a surprising result, given that their coevolution suggests a selective advantage. Thus, β-lactamase adaptation is highly epistatic. Our method can identify triplets that increase resistance despite the underlying rugged fitness landscape and has the unique ability to make predictions by placing each mutant residue position in its functional context. Our approach requires only sequence information, sufficient genetic diversity, and discrete selective pressures. Thus, it can be used to analyze recent evolutionary events, where coevolution analysis methods that use phylogeny or statistical coupling are not possible. Improving our ability to assess evolutionary trajectories will help predict the evolution of clinically relevant genes and aid in protein design

Changes in Body Weight and Psychotropic Drugs: A Systematic Synthesis of the Literature

<div><h3>Introduction</h3><p>Psychotropic medication use is associated with weight gain. While there are studies and reviews comparing weight gain for psychotropics within some classes, clinicians frequently use drugs from different classes to treat psychiatric disorders.</p> <h3>Objective</h3><p>To undertake a systematic review of all classes of psychotropics to provide an all encompassing evidence-based tool that would allow clinicians to determine the risks of weight gain in making both intra-class and interclass choices of psychotropics.</p> <h3>Methodology and Results</h3><p>We developed a novel hierarchical search strategy that made use of systematic reviews that were already available. When such evidence was not available we went on to evaluate randomly controlled trials, followed by cohort and other clinical trials, narrative reviews, and, where necessary, clinical opinion and anecdotal evidence. The data from the publication with the highest level of evidence based on our hierarchical classification was presented. Recommendations from an expert panel supplemented the evidence used to rank these drugs within their respective classes. Approximately 9500 articles were identified in our literature search of which 666 citations were retrieved. We were able to rank most of the psychotropics based on the available evidence and recommendations from subject matter experts. There were few discrepancies between published evidence and the expert panel in ranking these drugs.</p> <h3>Conclusion</h3><p>Potential for weight gain is an important consideration in choice of any psychotropic. This tool will help clinicians select psychotropics on a case-by-case basis in order to minimize the impact of weight gain when making both intra-class and interclass choices.</p> </div

Behavioural and Developmental Interventions for Autism Spectrum Disorder: A Clinical Systematic Review

Background: Much controversy exists regarding the clinical efficacy of behavioural and developmental interventions for improving the core symptoms of autism spectrum disorders (ASD). We conducted a systematic review to summarize the evidence on the effectiveness of behavioural and developmental interventions for ASD. Methods and Findings: Comprehensive searches were conducted in 22 electronic databases through May 2007. Further information was obtained through hand searching journals, searching reference lists, databases of theses and dissertations, and contacting experts in the field. Experimental and observational analytic studies were included if they were written in English and reported the efficacy of any behavioural or developmental intervention for individuals with ASD. Two independent reviewers made the final study selection, extracted data, and reached consensus on study quality. Results were summarized descriptively and, where possible, meta-analyses of the study results were conducted. One-hundred-and-one studies at predominantly high risk of bias that reported inconsistent results across various interventions were included in the review. Meta-analyses of three controlled clinical trials showed that Lovaas treatment was superior to special education on measures of adaptive behaviour, communication and interaction, comprehensive language, daily living skills, expressive language, overall intellectual functioning and socialization. High-intensity Lovaas was superior to low-intensity Lovaas on measures of intellectual functioning in two retrospective cohort studies. Pooling the results of two randomized controlle

On the Role of Enthalpic and Entropic Contributions to the Conformational Free Energy Landscape of MIL‐101(Cr) Secondary Building Units

The thermo‐structural behavior of metal‐organic framework (MOF) precursors is responsible for regulating the introduction of defects in MOF structures during synthesis. In this paper, factors affecting the flexibility of MIL‐101(Cr) half‐secondary building units (half‐SBUs) are evaluated in solution using enhanced sampling methods. In particular, entropic and enthalpic contributions to the conformational free energy landscape of isolated MIL‐101(Cr) half‐SBUs are calculated in water, in the presence and absence of ionic species (Na^{+} and F^{−}), and in N, N‐dimethylformamide (DMF). This analysis leads to the observation that the interplay between enthalpy and entropy determines the most probable conformational state for half‐SBUs. This observation extends to the most relevant SBU intermediate, in which conformational entropy plays a key role in stabilizing configurations that differ from those found in the MIL‐101(Cr) crystal structure. The findings highlight the importance of explicitly considering entropic effects, associated with finite‐temperature sampling when estimating the relative stability of different conformers of SBUs

Molecular level understanding of the free energy landscape in early stages of MOF nucleation

The assembly mechanism of hierarchical materials controlled by the choice of solvent and presence of spectator ions. In this paper, we use enhanced sampling molecular dynamics methods to investigate these effects on the configurational landscape of metal-linker interactions in the early stages of synthesis, using MIL-101(Cr) as a prototypical example. Microsecond-long well-tempered metadynamics (WTmetaD) uncover a complex free energy structural landscape, with distinct crystal (C) and non-crystal (NC) like configurations and their equilibrium population. In presence of ions (Na+, F-), we observe a complex effect on the crystallinity of secondary building units (SBUs), by encouraging/ suppressing salt bridges between C configurations and consequently controlling the percentage of defects. Solvent effects are assessed by introducing N, N-dimethylformamide (DMF) instead of water, where SBU adducts are appreciably more stable and compact. These results shed light on how solvent nature and ionic strength impact the free energy of nucleation phenomena that ultimately control materials synthesis and defect formation

Wildlife crime : The problems of enforcement

Environmental and wildlife crime appear recently to be benefitting from an increasing profile amongst those agencies tasked with their control, as well as receiving growing criminological attention. Despite this, those with responsibilities in this area report that it remains marginalised, receiving limited resources and suffering from a lack of political impetus to push such problems higher up the agenda. This is particularly so for those agencies, such as the police, that may be seen to have many more pressing objectives. This discussion paper considers the problems of relying on an enforcement approach to controlling such offences, taking, as an example, those activities that may be termed ‘wildlife crime’, focusing on the situation in England and Wales. Firstly, the legislative framework that criminalises harm or exploitation of wildlife is presented, alongside the main enforcement methods used. Next, the problems facing an enforcement approach are critically considered, the key issues being: under-resourcing and marginalisation, the large ‘dark figure’ of wildlife crime, the possibility of corruption, the lack of seriousness with which such crimes are viewed, and the lack of deterrent effect. Finally, responses to the problems of enforcement are presented, categorised as either methods to improve enforcement or, as the author advocates, methods which are alternatives to enforcement (such as adopting a crime prevention approach). The paper concludes with suggestions for future research in this field