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PubMed2006

WholePathwayScope: a comprehensive pathway-based analysis tool for high-throughput data.

BACKGROUND: Analysis of High Throughput (HTP) Data such as microarray and proteomics data has provided a powerful methodology to study patterns of gene regulation at genome scale. A major unresolved problem in the post-genomic era is to assemble the large amounts of data generated into a meaningful biological context. We have developed a comprehensive software tool, WholePathwayScope (WPS), for deriving biological insights from analysis of HTP data. RESULT: WPS extracts gene lists with shared biological themes through color cue templates. WPS statistically evaluates global functional category enrichment of gene lists and pathway-level pattern enrichment of data. WPS incorporates well-known biological pathways from KEGG (Kyoto Encyclopedia of Genes and Genomes) and Biocarta, GO (Gene Ontology) terms as well as user-defined pathways or relevant gene clusters or groups, and explores gene-term relationships within the derived gene-term association networks (GTANs). WPS simultaneously compares multiple datasets within biological contexts either as pathways or as association networks. WPS also integrates Genetic Association Database and Partial MedGene Database for disease-association information. We have used this program to analyze and compare microarray and proteomics datasets derived from a variety of biological systems. Application examples demonstrated the capacity of WPS to significantly facilitate the analysis of HTP data for integrative discovery. CONCLUSION: This tool represents a pathway-based platform for discovery integration to maximize analysis power. The tool is freely available at http://www.abcc.ncifcrf.gov/wps/wps_index.php.

Computer Graphics↗

PubMed2006

Java GUI for InterProScan (JIPS): a tool to help process multiple InterProScans and perform ortholog analysis.

BACKGROUND: Recent, rapid growth in the quantity of available genomic data has generated many protein sequences that are not yet biochemically classified. Thus, the prediction of biochemical function based on structural motifs is an important task in post-genomic analysis. The InterPro databases are a major resource for protein function information. For optimal results, these databases should be searched at regular intervals, since they are frequently updated. RESULTS: We describe here a new program JIPS (Java GUI for InterProScan), a tool for tracking and viewing results obtained from repeated InterProScan searches. JIPS stores matches (in a local database) obtained from InterProScan searches performed with multiple versions of the InterPro database and highlights hits that have been added since the last search of the InterPro database. Results are displayed in an easy-to-use tabular format. JIPS also contains tools to assist with ortholog-based comparative studies of protein signatures. CONCLUSION: JIPS is an efficient tool for performing repeated InterProScans on large batches of protein sequences, tracking and viewing search results, and mining the collected data.

Algorithms↗

PubMed2006

The NeuARt II system: a viewing tool for neuroanatomical data based on published neuroanatomical atlases.

BACKGROUND: Anatomical studies of neural circuitry describing the basic wiring diagram of the brain produce intrinsically spatial, highly complex data of great value to the neuroscience community. Published neuroanatomical atlases provide a spatial framework for these studies. We have built an informatics framework based on these atlases for the representation of neuroanatomical knowledge. This framework not only captures current methods of anatomical data acquisition and analysis, it allows these studies to be collated, compared and synthesized within a single system. RESULTS: We have developed an atlas-viewing application ('NeuARt II') in the Java language with unique functional properties. These include the ability to use copyrighted atlases as templates within which users may view, save and retrieve data-maps and annotate them with volumetric delineations. NeuARt II also permits users to view multiple levels on multiple atlases at once. Each data-map in this system is simply a stack of vector images with one image per atlas level, so any set of accurate drawings made onto a supported atlas (in vector graphics format) could be uploaded into NeuARt II. Presently the database is populated with a corpus of high-quality neuroanatomical data from the laboratory of Dr Larry Swanson (consisting 64 highly-detailed maps of PHAL tract-tracing experiments, made up of 1039 separate drawings that were published in 27 primary research publications over 17 years). Herein we take selective examples from these data to demonstrate the features of NeuArt II. Our informatics tool permits users to browse, query and compare these maps. The NeuARt II tool operates within a bioinformatics knowledge management platform (called 'NeuroScholar') either as a standalone or a plug-in application. CONCLUSION: Anatomical localization is fundamental to neuroscientific work and atlases provide an easily-understood framework that is widely used by neuroanatomists and non-neuroanatomists alike. NeuARt II, the neuroinformatics tool presented here, provides an accurate and powerful way of representing neuroanatomical data in the context of commonly-used brain atlases for visualization, comparison and analysis. Furthermore, it provides a framework that supports the delivery and manipulation of mapped data either as a standalone system or as a component in a larger knowledge management system.

Anatomy, Artistic↗

PubMed2006

GenomeBlast: a web tool for small genome comparison.

BACKGROUND: Comparative genomics has become an essential approach for identifying homologous gene candidates and their functions, and for studying genome evolution. There are many tools available for genome comparisons. Unfortunately, most of them are not applicable for the identification of unique genes and the inference of phylogenetic relationships in a given set of genomes. RESULTS: GenomeBlast is a Web tool developed for comparative analysis of multiple small genomes. A new parameter called "coverage" was introduced and used along with sequence identity to evaluate global similarity between genes. With GenomeBlast, the following results can be obtained: (1) unique genes in each genome; (2) homologous gene candidates among compared genomes; (3) 2D plots of homologous gene candidates along the all pairwise genome comparisons; and (4) a table of gene presence/absence information and a genome phylogeny. We demonstrated the functions in GenomeBlast with an example of multiple herpesviral genome analysis and illustrated how GenomeBlast is useful for small genome comparison. CONCLUSION: We developed a Web tool for comparative analysis of small genomes, which allows the user not only to identify unique genes and homologous gene candidates among multiple genomes, but also to view their graphical distributions on genomes, and to reconstruct genome phylogeny. GenomeBlast runs on a Linux server with 4 CPUs and 4 GB memory. The online version of GenomeBlast is available to public by using a Web browser with the URL http://bioinfo-srv1.awh.unomaha.edu/genomeblast/.

Algorithms↗

PubMed2002

Bootstrap, Bayesian probability and maximum likelihood mapping: exploring new tools for comparative genome analyses.

BACKGROUND: Horizontal gene transfer (HGT) played an important role in shaping microbial genomes. In addition to genes under sporadic selection, HGT also affects housekeeping genes and those involved in information processing, even ribosomal RNA encoding genes. Here we describe tools that provide an assessment and graphic illustration of the mosaic nature of microbial genomes. RESULTS: We adapted the Maximum Likelihood (ML) mapping to the analyses of all detected quartets of orthologous genes found in four genomes. We have automated the assembly and analyses of these quartets of orthologs given the selection of four genomes. We compared the ML-mapping approach to more rigorous Bayesian probability and Bootstrap mapping techniques. The latter two approaches appear to be more conservative than the ML-mapping approach, but qualitatively all three approaches give equivalent results. All three tools were tested on mitochondrial genomes, which presumably were inherited as a single linkage group. CONCLUSIONS: In some instances of interphylum relationships we find nearly equal numbers of quartets strongly supporting the three possible topologies. In contrast, our analyses of genome quartets containing the cyanobacterium Synechocystis sp. indicate that a large part of the cyanobacterial genome is related to that of low GC Gram positives. Other groups that had been suggested as sister groups to the cyanobacteria contain many fewer genes that group with the Synechocystis orthologs. Interdomain comparisons of genome quartets containing the archaeon Halobacterium sp. revealed that Halobacterium sp. shares more genes with Bacteria that live in the same environment than with Bacteria that are more closely related based on rRNA phylogeny. Many of these genes encode proteins involved in substrate transport and metabolism and in information storage and processing. The performed analyses demonstrate that relationships among prokaryotes cannot be accurately depicted by or inferred from the tree-like evolution of a core of rarely transferred genes; rather prokaryotic genomes are mosaics in which different parts have different evolutionary histories. Probability mapping is a valuable tool to explore the mosaic nature of genomes.

Journal Article↗

PubMed2006

Tools for the identification of variable and potentially variable tandem repeats.

BACKGROUND: Tandem repeat arrays showing variation between sequences within a population, between strains or across species may have functional effects. The increasing availability of genomic sequence data makes routine description of observed variation possible, creating a need for tools to describe such variability. RESULTS: We present a set of programs that facilitate the identification of tandem repeats showing variation across multiple sequences or genomes, and the prediction of potentially polymorphic tandem repeats. The VNTRfinder (Variable Number of Tandem Repeats finder) program enables the detection of sequence length variation between arrays of inter-specific or intra-specific tandem repeats. In the absence of comparable sequences to explore observed variation, predictions are provided describing which tandem repeats are more likely to be variable, to help guide and focus further experimental evaluation. CONCLUSION: These tools represent a resource for researchers interested in tandem repeats in nucleotide sequences that are most likely to be of clinical and evolutionary interest. The tools are available at http://bioinformatics.rcsi.ie/vntrfinder/. Downloadable versions for UNIX/LINUX and WINDOWS which permit the consideration of longer and more numerous sequences are also available.

Algorithms↗

PubMed2006

A rapid screening tool for fatigue impact in multiple sclerosis.

BACKGROUND: Fatigue is a common complaint in multiple sclerosis (MS) and often interferes with daily functioning. Both clinicians and researchers may need to detect high levels of fatigue impact using a time and effort efficient tool. This study evaluates the psychometric properties of a rapid screening instrument for fatigue impact in multiple sclerosis. METHODS: Three visual analogue scales (VAS) for assessing the impact of fatigue were developed. Sixty two subjects with definite MS (mean age 52 +/- 10.5 years; 29 women) and 24 healthy controls (mean age 52 +/- 14 years; 13 women) completed all VAS scales (range 0-100), the Fatigue Severity Scale (FSS) (range 7-63), the Modified Fatigue Impact Scale (MFIS) (range 0-84) and the Guy's Neurological Disability Scale (GNDS) (range 0-5). All tests were repeated with an interval of maximum three days. To evaluate the reproducibility, intraclass correlations (ICC) were calculated, based on one-way analysis of variance for repeated measurements. Validity was considered by means of correlation coefficients. ROC analysis was used to determine the accuracy of the VAS scales. RESULTS: The ICC of the VAS scales ranged from 0.68 to 0.69. VAS scales showed low to moderate correlation with FSS, MFIS and GNDS (Kendall's tau 0.23-0.45) and were not related with physical or cognitive performance, or with depression. All VAS scales were able to discriminate between subjects with MS and controls. Twenty five subjects with MS had a Fatigue Severity Scale score of 36 or more and were classified into the "fatigue" group. ROC analysis showed that VAS_1 is most useful to classify subjects in the "fatigue" group. A cut-off value of VAS_1 of 59 displayed 76% sensitivity and 72% specificity. When using the MFIS score of 40 or more to classify the groups, VAS_1 remained the strongest tool, with 81% sensitivity and 77% specificity at a cut-off value of 59. CONCLUSION: The VAS for the impact of fatigue on daily life (VAS_1) is a moderately reliable, though valid and useful tool to screen rapidly for fatigue impact in multiple sclerosis. A cut-off value of 59 satisfactorily classifies individuals having severe fatigue with a high impact on daily life. In clinical practice, a more comprehensive assessment of fatigue and the impact on daily life is recommended.

Adult↗

PubMed2004

Computer simulation in conjunction with medical thermography as an adjunct tool for early detection of breast cancer.

BACKGROUND: Mathematical modelling and analysis is now accepted in the engineering design on par with experimental approaches. Computer simulations enable one to perform several 'what-if' analyses cost effectively. High speed computers and low cost of memory has helped in simulating large-scale models in a relatively shorter time frame. The possibility of extending numerical modelling in the area of breast cancer detection in conjunction with medical thermography is considered in this work. METHODS: Thermography enables one to see the temperature pattern and look for abnormality. In a thermogram there is no radiation risk as it only captures the infrared radiation from the skin and is totally painless. But, a thermogram is only a test of physiology, whereas a mammogram is a test of anatomy. It is hoped that a thermogram along with numerical modelling will serve as an adjunct tool. Presently mammogram is the 'gold-standard' in breast cancer detection. But the interpretation of a mammogram is largely dependent on the radiologist. Therefore, a thermogram that looks into the physiological changes in combination with numerical simulation performing 'what-if' analysis could act as an adjunct tool to mammography. RESULTS: The proposed framework suggested that it could reduce the occurrence of false-negative/positive cases. CONCLUSION: A numerical bioheat model of a female breast is developed and simulated. The results are compared with experimental results. The possibility of this method as an early detection tool is discussed.

Body Temperature↗

PubMed2006

Fluorophotometry as a diagnostic tool for the evaluation of dry eye disease.

BACKGROUND: Dry eye disease is a common debilitating ocular disease. Current diagnostic tests used in dry eye disease are often neither sensitive nor reproducible, making it difficult to accurately diagnose and determine end points for clinical trials, or evaluate the usefulness of different medications in the treatment of dry eye disease. The recently developed fluorophotometer can objectively detect changes in the corneal epithelium by quantitatively measuring its barrier function or permeability. The purpose of the study is to investigate the use of corneal fluorescein penetration measured by the fluorophotometer as a diagnostic tool in the evaluation of dry eye patients. METHODS: Dry eye patients (16 eyes), who presented with a chief complaint of ocular irritation corresponding with dry eye, low Schirmer's one test (<10 mm after 5 minutes) and corneal fluorescein staining score of more than two, were included in the study. Normal subjects (16 eyes), who came for refraction error evaluation, served as controls. Institutional Review Board (IRB) approved consent was obtained before enrolling the subjects in the study and all questions were answered while explaining the risks, benefits and alternatives. All Fluorophotometry of the central corneal epithelium was done utilizing the Fluorotron Master. Each eye had a baseline fluorescein scan performed, after which 50 l of 1% sodium fluorescein dye was instilled. Three minutes later, the fluorescein was washed with 50 ml of normal saline. Fluorescein scans were then started immediately after washing and were recorded at 10, 20, 40, and 60 minutes thereafter. The corneal peak values of fluorescein concentration were recorded within the central cornea in both dry eyes and in controls. RESULTS: Ten minutes after fluorescein installation, patients with dry eye disease averaged a five-fold increase in corneal tissue fluorescein concentration (mean = 375.26 +/- 202.67 ng/ml) compared with that of normal subjects (mean = 128.19 +/- 85.84 ng/ml). Sixty minutes after dye installation, patients with dry eye disease still revealed higher corneal tissue fluorescein concentration (mean = 112.87 +/- 52.83 ng/ml) compared with that of controls (mean = 40.64 +/- 7.96 ng/ml), averaging a three-fold increase. CONCLUSION: Patients with dry eye disease demonstrated an increased corneal permeability and a slower rate of elimination to topically administered fluorescein when measured by the fluorophotometer. This suggests that fluorophotometry may serve as a valuable quantitative and objective tool for the diagnosis of dry eye disease, and in following patients' response to new treatment modalities. Fluorophotometry may serve as an objective non-invasive tool for end-point analysis in clinical trials of new treatments for dry eye disease.

Adult↗

PubMed2006

Identification of similar regions of protein structures using integrated sequence and structure analysis tools.

BACKGROUND: Understanding protein function from its structure is a challenging problem. Sequence based approaches for finding homology have broad use for annotation of both structure and function. 3D structural information of protein domains and their interactions provide a complementary view to structure function relationships to sequence information. We have developed a web site http://www.sblest.org/ and an API of web services that enables users to submit protein structures and identify statistically significant neighbors and the underlying structural environments that make that match using a suite of sequence and structure analysis tools. To do this, we have integrated S-BLEST, PSI-BLAST and HMMer based superfamily predictions to give a unique integrated view to prediction of SCOP superfamilies, EC number, and GO term, as well as identification of the protein structural environments that are associated with that prediction. Additionally, we have extended UCSF Chimera and PyMOL to support our web services, so that users can characterize their own proteins of interest. RESULTS: Users are able to submit their own queries or use a structure already in the PDB. Currently the databases that a user can query include the popular structural datasets ASTRAL 40 v1.69, ASTRAL 95 v1.69, CLUSTER50, CLUSTER70 and CLUSTER90 and PDBSELECT25. The results can be downloaded directly from the site and include function prediction, analysis of the most conserved environments and automated annotation of query proteins. These results reflect both the hits found with PSI-BLAST, HMMer and with S-BLEST. We have evaluated how well annotation transfer can be performed on SCOP ID's, Gene Ontology (GO) ID's and EC Numbers. The method is very efficient and totally automated, generally taking around fifteen minutes for a 400 residue protein. CONCLUSION: With structural genomics initiatives determining structures with little, if any, functional characterization, development of protein structure and function analysis tools are a necessary endeavor. We have developed a useful application towards a solution to this problem using common structural and sequence based analysis tools. These approaches are able to find statistically significant environments in a database of protein structure, and the method is able to quantify how closely associated each environment is to a predicted functional annotation.

Computational Biology↗

PubMed2006

Wikis, blogs and podcasts: a new generation of Web-based tools for virtual collaborative clinical practice and education.

BACKGROUND: We have witnessed a rapid increase in the use of Web-based 'collaborationware' in recent years. These Web 2.0 applications, particularly wikis, blogs and podcasts, have been increasingly adopted by many online health-related professional and educational services. Because of their ease of use and rapidity of deployment, they offer the opportunity for powerful information sharing and ease of collaboration. Wikis are Web sites that can be edited by anyone who has access to them. The word 'blog' is a contraction of 'Web Log' - an online Web journal that can offer a resource rich multimedia environment. Podcasts are repositories of audio and video materials that can be "pushed" to subscribers, even without user intervention. These audio and video files can be downloaded to portable media players that can be taken anywhere, providing the potential for "anytime, anywhere" learning experiences (mobile learning). DISCUSSION: Wikis, blogs and podcasts are all relatively easy to use, which partly accounts for their proliferation. The fact that there are many free and Open Source versions of these tools may also be responsible for their explosive growth. Thus it would be relatively easy to implement any or all within a Health Professions' Educational Environment. Paradoxically, some of their disadvantages also relate to their openness and ease of use. With virtually anybody able to alter, edit or otherwise contribute to the collaborative Web pages, it can be problematic to gauge the reliability and accuracy of such resources. While arguably, the very process of collaboration leads to a Darwinian type 'survival of the fittest' content within a Web page, the veracity of these resources can be assured through careful monitoring, moderation, and operation of the collaborationware in a closed and secure digital environment. Empirical research is still needed to build our pedagogic evidence base about the different aspects of these tools in the context of medical/health education. SUMMARY AND CONCLUSION: If effectively deployed, wikis, blogs and podcasts could offer a way to enhance students', clinicians' and patients' learning experiences, and deepen levels of learners' engagement and collaboration within digital learning environments. Therefore, research should be conducted to determine the best ways to integrate these tools into existing e-Learning programmes for students, health professionals and patients, taking into account the different, but also overlapping, needs of these three audience classes and the opportunities of virtual collaboration between them. Of particular importance is research into novel integrative applications, to serve as the "glue" to bind the different forms of Web-based collaborationware synergistically in order to provide a coherent wholesome learning experience.

Audiovisual Aids↗

PubMed2004

An audit tool for assessing the appropriateness of carotid endarterectomy.

BACKGROUND: To update appropriateness ratings for carotid endarterectomy using the best clinical evidence and to develop a tool to audit the procedure's use. METHODS: A nine-member expert panel drawn from all the Canadian Specialist societies that are involved in the care of patients with carotid artery disease, used the RAND Appropriateness Methodology to rate scenarios where carotid endarterectomy may be performed. A 9-point rating scale was used that permits the categorization of the use of carotid endarterectomy as appropriate, uncertain, or inappropriate. A descriptive analysis was undertaken of the final results of the panel meeting. A database and code were then developed to rate all carotid endarterectomies performed in a Western Canadian Health region from 1997 to 2001. RESULTS: All scenarios for severe symptomatic stenosis (70-99%) were determined to be appropriate. The ratings for moderate symptomatic stenosis (50-69%) ranged from appropriate to inappropriate. It was never considered appropriate to perform endarterectomy for mild stenosis (0-49%) or for chronic occlusions. Endarterectomy for asymptomatic carotid disease was thought to be of uncertain benefit at best. The majority of indications for the combination of endarterectomy either prior to, or at time of coronary artery bypass grafting were inappropriate. The audit tool classified 98.0% of all cases. CONCLUSIONS: These expert panel ratings, based on the best evidence currently available, provide a comprehensive and updated guide to appropriate use of carotid endarterectomy. The resulting audit tool can be downloaded by readers from the Internet and immediately used for hospital audits of carotid endarterectomy appropriateness.

Algorithms↗

PubMed2005

Validating a Work Group Climate Assessment Tool for improving the performance of public health organizations.

BACKGROUND: This article describes the validation of an instrument to measure work group climate in public health organizations in developing countries. The instrument, the Work Group Climate Assessment Tool (WCA), was applied in Brazil, Mozambique, and Guinea to assess the intermediate outcomes of a program to develop leadership for performance improvement. Data were collected from 305 individuals in 42 work groups, who completed a self-administered questionnaire. METHODS: The WCA was initially validated using Cronbach's alpha reliability coefficient and exploratory factor analysis. This article presents the results of a second validation study to refine the initial analyses to account for nested data, to provide item-level psychometrics, and to establish construct validity. Analyses included eigenvalue decomposition analysis, confirmatory factor analysis, and validity and reliability analyses. RESULTS: This study confirmed the validity and reliability of the WCA across work groups with different demographic characteristics (gender, education, management level, and geographical location). The study showed that there is agreement between the theoretical construct of work climate and the items in the WCA tool across different populations. The WCA captures a single perception of climate rather than individual sub-scales of clarity, support, and challenge. CONCLUSION: The WCA is useful for comparing the climates of different work groups, tracking the changes in climate in a single work group over time, or examining differences among individuals' perceptions of their work group climate. Application of the WCA before and after a leadership development process can help work groups hold a discussion about current climate and select a target for improvement. The WCA provides work groups with a tool to take ownership of their own group climate through a process that is simple and objective and that protects individual confidentiality.

Journal Article↗

PubMed2004

Prediction of falls using a risk assessment tool in the acute care setting.

BACKGROUND: The British STRATIFY tool was previously developed to predict falls in hospital. Although the tool has several strengths, certain limitations exist which may not allow generalizability to a Canadian setting. Thus, we tested the STRATIFY tool with some modification and re-weighting of items in Canadian hospitals. METHODS: This was a prospective validation cohort study in four acute care medical units of two teaching hospitals in Hamilton, Ontario. In total, 620 patients over the age of 65 years admitted during a 6-month period. Five patient characteristics found to be risk factors for falls in the British STRATIFY study were tested for predictive validity. The characteristics included history of falls, mental impairment, visual impairment, toileting, and dependency in transfers and mobility. Multivariate logistic regression was used to obtain optimal weights for the construction of a risk score. A receiver-operating characteristic curve was generated to show sensitivities and specificities for predicting falls based on different threshold scores for considering patients at high risk. RESULTS: Inter-rater reliability for the weighted risk score indicated very good agreement (inter-class correlation coefficient = 0.78). History of falls, mental impairment, toileting difficulties, and dependency in transfer / mobility significantly predicted fallers. In the multivariate model, mental status was a significant predictor (P < 0.001) while history of falls and transfer / mobility difficulties approached significance (P = 0.089 and P = 0.077 respectively). The logistic regression model led to weights for a risk score on a 30-point scale. A risk score of 9 or more gave a sensitivity of 91% and specificity of 60% for predicting who would fall. CONCLUSION: Good predictive validity for identifying fallers was achieved in a Canadian setting using a simple-to-obtain risk score that can easily be incorporated into practice.

Accidental Falls↗

PubMed2003

Application of the Italian version of the Intensive Care Unit Memory tool in the clinical setting.

INTRODUCTION: The aims of the present study were to assess patients' memories of their stay in the intensive care unit (ICU) over time, using the Italian version of the ICU Memory (ICUM) tool, and to examine the relationship between memory and duration of ICU stay and infection. PATIENTS AND METHOD: Adult patients consecutively admitted to a four-bed ICU of a university hospital, whose stay in the ICU was at least 3 days, were prospectively studied. The ICUM tool was administered twice: face to face 1 week after ICU discharge to 93 patients (successfully in 87); and by phone after 3 months to 67 patients. Stability of memories over time was analyzed using Kappa statistics. RESULTS: Delusional memories appeared to be the most persistent recollections over time (minimum kappa value = 0.68), followed by feelings (kappa value > 0.7 in three out of six memories) and factual memories (kappa value > 0.7 in three out of 11 memories). The patients without a clear memory of their stay in the ICU reported a greater number of delusional memories than did those with a clear memory. Of patients without infection 35% had one or two delusional memories, and 60% of patients with infection had one to four delusional memories (P = 0.029). CONCLUSION: The ICUM tool is of value in a setting and language different from those in which it was created and used. Delusional memories are the most stable recollections, and are frequently associated both with lack of clear memory of ICU experience and with presence of infection during ICU stay.

Adult↗

PubMed2005

Artificial neural networks as prediction tools in the critically ill.

The past 25 years have witnessed the development of improved tools with which to predict short-term and long-term outcomes after critical illness. The general paradigm for constructing the best known tools has been the logistic regression model. Recently, a variety of alternative tools, such as artificial neural networks, have been proposed, with claims of improved performance over more traditional models in particular settings. However, these newer methods have yet to demonstrate their practicality and usefulness within the context of predicting outcomes in the critically ill.

Cohort Studies↗

PubMed2026

Effectiveness of a digi-physical tool and working method for paediatric obesity treatment in Abu Dhabi: a non-inferiority intervention study using an external historical comparator.

BACKGROUND: Effective paediatric obesity treatment requires high intensity, scalable interventions. A digi-physical tool for paediatric obesity treatment has shown positive results in Stockholm, Sweden. This study evaluates whether the same treatment method is effective in a different cultural setting. METHODS: This non-inferiority intervention study, using an external historical comparator, included 60 consecutively recruited children aged 6-15.9 years with obesity who initiated treatment at Sheikh Shakhbout Medical City in Abu Dhabi between June and December 2023. Patients were treated with Evira, a digi-physical tool and working method enabling high intensity individualized care, real-time monitoring, and interactive patient-clinician communication. The primary outcome was BMI z-score change at 26 weeks. Non-inferiority was assessed using a predefined margin of 0.10 BMI z-score, with outcomes compared to a prior published trial in Stockholm (n = 107). RESULTS: A total of 112 children were included in the analysis (Abu Dhabi cohort, n = 35; Stockholm cohort, n = 77). The adjusted mean change in BMI z-score was - 0.20 (95% CI: - 0.28, - 0.12) in the Abu Dhabi cohort and - 0.20 (- 0.26, - 0.14) in the Stockholm cohort (p = 0.88). Non-inferiority was confirmed, (predefined margin 0.10 was not exceeded). A clinically significant BMI z-score reduction (≥ 0.20 units) was achieved by 45.7% of participants in Abu Dhabi and 36.4% in Stockholm (p = 0.35). Non-retention rates at 26 weeks were 41.7% vs. 28.0%, respectively (p = 0.07). CONCLUSIONS: The findings provide promising evidence that treatment outcomes achieved with the digi-physical treatment tool were comparable in the Abu Dhabi and Stockholm cohorts, supporting its feasibility in a second cultural and healthcare setting.

Humans↗

PubMed2004

Development and preliminary assessment of the measurement properties of the Seating Identification Tool (SIT).

OBJECTIVE: To present and discuss the development and measurement properties of the Seating Identification Tool (SIT), a screening tool designed to identify the need for formal seating and wheelchair intervention among institutionalized elderly. Specifically, investigation of the inter-rater and test-retest reliability, sensitivity, specificity, the positive and negative predictive values of the SIT was conducted. DESIGN: A two-week retest design. SETTING: A long-term care facility in London, Ontario, Canada. SUBJECTS: Forty-two randomly selected residents with an average age of 83 years who had a disability and required the use of a wheelchair as their main mode of mobility. INTERVENTION: Two health care assistants from a long-term facility collected data using the SIT. One rater assessed all subjects two weeks later to evaluate test-retest reliability. Diagnostic properties (validity) were determined by having all subjects assessed by a seating therapist. MAIN MEASUREMENT: The SIT and formal evaluation by a therapist experienced in seating. RESULTS: The ICC for both test-retest and inter-rater reliability was 0.83. A cut-off score of 2 maximized the sensitivity (100%) and specificity (64% and 57% for raters 1 and 2 respectively) and the area under the receiver operating characteristics curve (0.855 and 0.862 for raters 1 and 2). The positive and negative predictive values ranged from 82 to 100%. CONCLUSION: The SIT is a quick, easy to use, reliable and valid screening tool that can be used to facilitate clinical referral for formal intervention. Other potential uses include population-based surveys to estimate the need for including seating intervention in strategic planning for the institutionalized elderly.

Aged↗