Evaluation of a Bayesian inference network for ligand-based virtual screening

Background Bayesian inference networks enable the computation of the probability that an event will occur. They have been used previously to rank textual documents in order of decreasing relevance to a user-defined query. Here, we modify the approach to enable a Bayesian inference network to be used for chemical similarity searching, where a database is ranked in order of decreasing probability of bioactivity. Results Bayesian inference networks were implemented using two different types of network and four different types of belief function. Experiments with the MDDR and WOMBAT databases show that a Bayesian inference network can be used to provide effective ligand-based screening, especially when the active molecules being sought have a high degree of structural homogeneity; in such cases, the network substantially out-performs a conventional, Tanimoto-based similarity searching system. However, the effectiveness of the network is much less when structurally heterogeneous sets of actives are being sought. Conclusion A Bayesian inference network provides an interesting alternative to existing tools for ligand-based virtual screening

Exploring Differences in Pain Beliefs Within and Between a Large Nonclinical (Workplace) Population and a Clinical (Chronic Low Back Pain) Population Using the Pain Beliefs Questionnaire

BACKGROUND: Beliefs, cognitions, and behaviors relating to pain can be associated with a range of negative outcomes. In patients, certain beliefs are associated with increased levels of pain and related disability. There are few data, however, showing the extent to which beliefs of patients differ from those of the general population. OBJECTIVE: This study explored pain beliefs in a large nonclinical population and a chronic low back pain (CLBP) sample using the Pain Beliefs Questionnaire (PBQ) to identify differences in scores and factor structures between and within the samples. DESIGN: This was a cross-sectional study. METHODS: The samples comprised patients attending a rehabilitation program and respondents to a workplace survey. Pain beliefs were assessed using the PBQ, which incorporates 2 scales: organic and psychological. Exploratory factor analysis was used to explore variations in factor structure within and between samples. The relationship between the 2 scales also was examined. RESULTS: Patients reported higher organic scores and lower psychological scores than the nonclinical sample. Within the nonclinical sample, those who reported frequent pain scored higher on the organic scale than those who did not. Factor analysis showed variations in relation to the presence of pain. The relationship between scales was stronger in those not reporting frequent pain. LIMITATIONS: This was a cross-sectional study; therefore, no causal inferences can be made. CONCLUSIONS: Patients experiencing CLBP adopt a more biomedical perspective on pain than nonpatients. The presence of pain is also associated with increased biomedical thinking in a nonclinical sample. However, the impact is not only on the strength of beliefs, but also on the relationship between elements of belief and the underlying belief structur

Estimation of crown closure from AVIRIS data using regression analysis

Crown closure is one of the input parameters used for forest growth and yield modelling. Preliminary work by Staenz et al. indicates that imaging spectrometer data acquired with sensors such as the Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) have some potential for estimating crown closure on a stand level. The objectives of this paper are: (1) to establish a relationship between AVIRIS data and the crown closure derived from aerial photography of a forested test site within the Interior Douglas Fir biogeoclimatic zone in British Columbia, Canada; (2) to investigate the impact of atmospheric effects and the forest background on the correlation between AVIRIS data and crown closure estimates; and (3) to improve this relationship using multiple regression analysis

The chronic pain coping inventory: Confirmatory factor analysis of the French version

BACKGROUND: Coping strategies are among the psychosocial factors hypothesized to contribute to the development of chronic musculoskeletal disability. The Chronic Pain Coping Inventory (CPCI) was developed to assess eight behavioral coping strategies targeted in multidisciplinary pain treatment (Guarding, Resting, Asking for Assistance, Task Persistence, Relaxation, Exercise/Stretch, Coping Self-Statements and Seeking Social Support). The present study had two objectives. First, it aimed at measuring the internal consistency and the construct validity of the French version of the CPCI. Second, it aimed to verify if, as suggested by the CPCI authors, the scales of this instrument can be grouped according to the following coping families: Illness-focused coping and Wellness-focused coping. METHOD: The CPCI was translated into French with the forward and backward translation procedure. To evaluate internal consistency, Cronbach's alphas were computed. Construct validity of the inventory was estimated through confirmatory factor analysis (CFA) in two samples: a group of 439 Quebecois workers on sick leave in the sub-acute stage of low back pain (less than 84 days after the work accident) and a group of 388 French chronic pain patients seen in a pain clinic. A CFA was also performed to evaluate if the CPCI scales were grouped into two coping families (i.e. Wellness-focused and Illness-focused coping). RESULTS: The French version of the CPCI had adequate internal consistency in both samples. The CFA confirmed the eight-scale structure of the CPCI. A series of second-order CFA confirmed the composition of the Illness-focused family of coping (Guarding, Resting and Asking for Assistance). However, the composition of the Wellness-focused family of coping (Relaxation, Exercise/Stretch, Coping Self-Statements and Seeking Social Support) was different than the one proposed by the authors of the CPCI. Also, a positive correlation was observed between Illness and Wellness coping families. CONCLUSION: The present study indicates that the internal consistency and construct validity of the French version of the CPCI were adequate, but the grouping and labeling of the CPCI families of coping are debatable and deserve further analysis in the context of musculoskeletal and pain rehabilitation

Low-value clinical practices in injury care: a scoping review and expert consultation survey

BACKGROUND: Tests and treatments that are not supported by evidence and could expose patients to unnecessary harm, referred to here as low-value clinical practices, consume up to 30% of healthcare resources. Choosing Wisely and other organisations have published lists of clinical practices to be avoided. However, few apply to injury and most are based uniquely on expert consensus. We aimed to identify low-value clinical practices in acute injury care. METHODS: We conducted a scoping review targeting articles, reviews and guidelines that identified low-value clinical practices specific to injury populations. Thirty-six experts rated clinical practices on a 5-point Likert scale from clearly low-value to clearly beneficial. Clinical practices reported as low-value by at least one level I, II or III study and considered clearly or potentially low-value by at least 75% of experts were retained as candidates for low-value injury care. RESULTS: Of 50,695 citations, 815 studies were included and led to the identification of 150 clinical practices. Of these 63 were considered candidates for low-value injury care; 33 in the emergency room, 9 in trauma surgery, 15 in the intensive care unit and 5 in orthopaedics. We also identified 87 'grey zone' practices, which did not meet our criteria for low-value care. CONCLUSIONS: We identified 63 low-value clinical practices in acute injury care that are supported by empirical evidence and expert opinion. Conditional on future research, they represent potential targets for guidelines, overuse metrics and de-implementation interventions. We also identified 87 'grey zone' practices, which may be interesting targets for value-based decision-making. Our study represents an important step towards the de-implementation of low-value clinical practices in injury care. LEVEL OF EVIDENCE: III

What do we know and when do we know it?

Two essential aspects of virtual screening are considered: experimental design and performance metrics. In the design of any retrospective virtual screen, choices have to be made as to the purpose of the exercise. Is the goal to compare methods? Is the interest in a particular type of target or all targets? Are we simulating a ‘real-world’ setting, or teasing out distinguishing features of a method? What are the confidence limits for the results? What should be reported in a publication? In particular, what criteria should be used to decide between different performance metrics? Comparing the field of molecular modeling to other endeavors, such as medical statistics, criminology, or computer hardware evaluation indicates some clear directions. Taken together these suggest the modeling field has a long way to go to provide effective assessment of its approaches, either to itself or to a broader audience, but that there are no technical reasons why progress cannot be made

Morphological, physiological, and transcriptional responses of the freshwater diatom Fragilaria crotonensis to elevated pH conditions

Harmful algal blooms (HABs) caused by the toxin-producing cyanobacteria Microcystis spp., can increase water column pH. While the effect(s) of these basified conditions on the bloom formers are a high research priority, how these pH shifts affect other biota remains understudied. Recently, it was shown these high pH levels decrease growth and Si deposition rates in the freshwater diatom Fragilaria crotonensis and natural Lake Erie (Canada-US) diatom populations. However, the physiological mechanisms and transcriptional responses of diatoms associated with these observations remain to be documented. Here, we examined F. crotonensis with a set of morphological, physiological, and transcriptomic tools to identify cellular responses to high pH. We suggest 2 potential mechanisms that may contribute to morphological and physiological pH effects observed in F. crotonensis. Moreover, we identified a significant upregulation of mobile genetic elements in the F. crotonensis genome which appear to be an extreme transcriptional response to this abiotic stress to enhance cellular evolution rates–a process we have termed “genomic roulette.” We discuss the ecological and biogeochemical effects high pH conditions impose on fresh waters and suggest a means by which freshwater diatoms such as F. crotonensis may evade high pH stress to survive in a “basified” future

Low-value clinical practices in adult traumatic brain injury : an umbrella review protocol

Introduction Traumatic brain injury (TBI) leads to 50 000 deaths, 85 000 disabilities and costs $60 billion each year in the USA. Despite numerous interventions and treatment options, the outcomes of TBI have improved little over the last three decades. In a previous scoping review and expert consultation survey, we identified 13 potentially low-value clinical practices in acute TBI. The objective of this umbrella review is to synthesise the evidence on potentially low-value clinical practices in the care of acute TBI. Methods and analysis Using umbrella review methodology, we will search Cochrane Central Register of Controlled Trials, Embase, Epistemonikos, International Prospective Register of Systematic Reviews (PROSPERO) and PubMed to identify systematic reviews evaluating the effect of potential intrahospital low-value practices using tailored population, intervention, comparator, outcome and study design questions based on the results of a previous scoping review. We will present data on the methodological quality of these reviews (Assessing the Methodological Quality of Systematic Reviews-2), reported effect sizes and strength of evidence (Grading of Recommendations, Assessment, Development and Evaluation). Ethics and dissemination Ethics approval is not required as original data will not be collected. Knowledge users from five healthcare quality organisations and clinical associations are involved in the design and conduct of the study. Results will be disseminated in a peer-reviewed journal, at international scientific meetings and to clinical, healthcare quality and patient–partner associations. This work will support the development of metrics to measure the use of low-value practices, inform policy makers on potential targets for deimplementation and in the long term reduce the use of low-value clinical practices in acute TBI care

An interdisciplinary guideline development process: the Clinic on Low-back pain in Interdisciplinary Practice (CLIP) low-back pain guidelines

<p>Abstract</p> <p>Background</p> <p>Evaluation of low-back pain guidelines using Appraisal of Guidelines Research and Evaluation (AGREE) criteria has shown weaknesses, particularly in stakeholder involvement and applicability of recommendations. The objectives of this project were to: 1) develop a primary care interdisciplinary clinical practice guideline aimed at preventing prolonged disability from low-back pain, using a community of practice approach, and 2) assess the participants' impressions with the process, and evaluate the relationship between participant characteristics and their participation.</p> <p>Methods</p> <p>Ten stakeholder representatives recruited 136 clinicians to participate in this community of practice. Clinicians were drawn from the following professions: physiotherapists (46%), occupational therapists (37%), and family physicians (17%). Using previously published guidelines, systematic reviews, and meta-analyses, a first draft of the guidelines was presented to the community of practice. Four communication tools were provided for discussion and exchanges with experts: a web-based discussion forum, an anonymous comment form, meetings, and a symposium. Participants were prompted for comments on interpretation, clarity, and applicability of the recommendations. Clinical management recommendations were revised following these exchanges. At the end of the project, a questionnaire was sent to the participants to assess satisfaction towards the guidelines and the development process.</p> <p>Results</p> <p>Twelve clinical management recommendations on management of low-back pain and persistent disability were initially developed. These were discussed through 188 comments posted on the discussion forum and 103 commentary forms submitted. All recommendations were modified following input of the participants. A clinical algorithm summarizing the guidelines was also developed. A response rate of 75% was obtained for the satisfaction questionnaire. The majority of respondents appreciated the development process and agreed with the guideline content. Most participants thought recommendations improved between versions, and that participant comments contributed to this improvement. All stakeholders officially endorsed the guidelines.</p> <p>Conclusion</p> <p>The community of practice approach was a successful method to develop guidelines on low-back pain, with participants providing information to improve guideline recommendations. The information technology infrastructure that was developed remains for continuous interdisciplinary exchanges and updating of the guidelines.</p