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PubMed2025

GRUMB: a genome-resolved metagenomic framework for monitoring urban microbiomes and diagnosing pathogen risk.

SUMMARY: Urban infrastructure hosts dynamic microbial communities that complicate biosurveillance and AMR monitoring. Existing tools rarely combine genome-resolved reconstruction with ecological modeling and batch-aware analytics tailored to infrastructure-scale studies. We present GRUMB (Genome-Resolved Urban Microbiome Biosurveillance), an open-source, SLURM-compatible pipeline that reconstructs high-quality metagenome-assembled genomes (MAGs) from shotgun sequencing reads and integrates taxonomic/functional annotation (CARD, VFDB), batch-aware normalization, ecological diagnostics and machine learning classification of environment types with uncertainty and risk scoring. GRUMB accepts either SRA project accessions or paired-end FASTQ files with metadata, and produces assemblies, MAGs, taxonomic and functional profiles, ecological outputs and risk-informed classification. Its modular design enables reproducible, infrastructure-scale biosurveillance across diverse environments. AVAILABILITY AND IMPLEMENTATION: GRUMB is freely available under the MIT License at: https://github.com/SuleimanAminu/genome-resolved-urban-microbiome-biosurveillance; Zenodo DOI: https://doi.org/10.5281/zenodo.15505402. Requirements: Linux (Ubuntu 20.04+), Python 3.11, R 4.2+, SLURM. Issues and feature requests are tracked on GitHub.

Microbiota↗
PubMed2026

Minimizing Off-Target Effects of CRISPR-Cas9 With Optimized sgRNA: Evaluation of Efficiency and Specificity in the Tumor Protein 53 (TP53) Region.

CRISPR-Cas9 is a widely used genetic tool with therapeutic potential in molecular biology. CRISPR-Cas9 enables precise genome editing by its ability to target specific DNA sequence. After off-target and on-target regions are identified, CRISPR-Cas9 is applied to these regions based on the match between the guide RNA (gRNA) and target DNA sequence. This study points to the off-target impact of mismatches between the gRNA and target DNA on exon regions of the TP53 gene, which are involved in regulating multiple genes and cellular functions. Off-target positions are typically evaluated using scoring methods. In this study, we have used latent class analysis to reveal subclasses of off-target positions. Thus, we have created the levels of off-target positions and evaluated the effects of mismatching positions within these classes using machine learning classifiers. The results revealed that mismatching positions could be categorized into three levels: low, middle, and high off-target positions. We have improved a computational framework to minimize off-target effects and to identify the PAM sequences in the gRNA design. Thus, carefully designed gRNAs will ensure that desired genetic edits are performed and target variants are achieved. This work will avail the future research aimed at optimizing genome editing by customizing CRISPR-Cas9 to target specific protospacer DNA through gRNA.

CRISPR-Cas Systems↗
PubMed1991

The introduction of a new system of care delivery into a surgical ward in Sweden.

Action research is used to implement a change in the system of care delivery on a surgical ward in Sweden. Couched within a Lewinian framework the stages of change, the problems faced by staff and their solutions are described. The effects of the change to a system of care more closely resembling the Loeb model of primary nursing, in which accountability is for the duration of the shift, were closely monitored. Observation of registered nurses showed a three-fold increase in the time spent giving direct patient care. A significant increase in scores on a measure of "Intrinsic Job Satisfaction" was also found (P less than 0.01) together with increased scores on a measure of "Patient Focus" (P less than 0.001). These findings were sustained over time. The problems of evaluating a system of care which is based on a different philosophy are addressed.

Humans↗
PubMed2006

Classification of patients with pain based on neuropathic pain symptoms: comparison of an artificial neural network against an established scoring system.

Wider use of pain assessment tools that are specifically designed for certain types of pain--such as neuropathic pain--contribute an increasing amount of information which in turn offers the opportunity to employ advanced methods of data analysis. In this manuscript, we present the results of a study where we employed artificial neural networks (ANNs) in an analysis of pain descriptors with the goal of determining how an approach that uses a specific symptoms-based tool would perform with data from the real world of clinical practice. We also used traditional statistics approaches in the form of established scoring systems as well as logistic regression analysis for the purpose of comparison. Our results confirm the clinical experience that groups of pain descriptors rather than single items differentiate between patients with neuropathic and non-neuropathic pain. The accuracy obtained by ANN analysis was only slightly higher than that of the traditional approaches, indicating the absence of nonlinear relationships in this dataset. Data analysis with ANNs provides a framework that extends what current approaches offer, especially for dynamic data, such as the rating of pain descriptors over time.

Adult↗
PubMed2002

Fatigue as a predictor of work disability.

The objective of this study was to assess the predictive value of fatigue for work disability on medical grounds within the framework of a large prospective cohort study. Analyses were carried out on the data of 10 927 employees with a follow up of 32 months. We found that fatigue, as measured with the Checklist Individual Strength, was a strong predictor of subsequent permanent work disability. The for age, gender, presence of a chronic medical condition, and educational level adjusted relative risks were, for the 2nd, 3rd, and 4th fatigue score quartile against the first, respectively: 2.17 (1.17-4.03), 3.30 (1.67-6.52), and 12.8 (5.14-32.1).

Adolescent↗
PubMed1995

Multi-attribute health status classification systems. Health Utilities Index.

In this article, multi-attribute approaches to the assessment of health status are reviewed with a special focus on 2 recently developed systems, the Health Utilities Index (HUI) Mark II and Mark III systems. The Mark II system consists of 7 attributes: sensation, mobility, emotion, cognition, self-care, pain and fertility. The Mark III system contains 8 attributes: vision, hearing, speech, ambulation, dexterity, emotion, cognition and pain. Each attribute consists of multiple levels of functioning. A combination of levels across the attributes constitutes a health state. The HUI systems are deliberately focused on the fundamental core attributes of health status, and on the capacity of individuals to function with respect to these attributes. Thus, the measure obtained constitutes a pure description of health status, uncontaminated by differential opportunity or preference. Multi-attribute systems provide a compact but comprehensive framework for describing health status for use in population health and programme evaluation studies. An important advantage of such systems is their ability to simultaneously provide detail on an attribute-by-attribute basis and to capture combinations of deficits among attributes. An additional advantage is their compatibility with multi-attribute preference functions, which provide a method for computing a summary health-related quality-of-life score for each health state.

Canada↗
PubMedDate not supplied

Comparison of two methods for teaching advanced arrhythmias to nurses.

An experimental study to compare the effectiveness of assisted self-directed learning (ASD) and traditional lecture methods (TLM) in acquiring competency for electrocardiogram interpretation was conducted within a conceptual framework of developmental and adult learning theory (Erickson, Tomlin & Swain, 1983; Knowles, 1980). After two teaching units were designed and an EKG posttest was constructed (r = .75) from actual patient records, registered nurse volunteers (N = 19) were randomly assigned to groups for simultaneous instruction. Because of the small sample size, statistical procedures were used to determine the effectiveness of randomization and to justify statistical procedures. EKG post-test scores for the experimental group (ASD, M = 81) and the control group (TLM, M = 71) were significantly different (one-tailed t = 1.79; p = .045); however, participants' prior knowledge of basic arrhythmias was not independent of method (ANCOVA, F[1, 16] = 21.373, p = .0003, covariate; F[1.16] = 2.312, p = .1479, main effects). EKG post-test scores were not related to critical care experience, cardiac monitoring experience, education level, or course satisfaction. While both methods are effective, ASD had higher mean scores and is more cost- and time-efficient.

Arrhythmias, Cardiac↗
PubMed1995

In pursuit of computer literacy in health management education.

Computer literacy skills are essential tools students must possess to do well in computer-related and quantitative courses, and to be effective health managers. Many health management education programs are faced with the challenge of finding an ideal framework for teaching computer literacy courses. Recently, Austin and Malec (1990) proposed an instructional method for teaching computer literacy. This method was used for three consecutive semesters to teach the computer literacy course offered at Sangamon State University. A case analysis technique was utilized to assess of the effectiveness of this method. A pre-test and post-test design was used in the study. Post-test scores were found to be significantly higher than pre-test scores. Improvements in students' attitudes toward computers were noticed in the areas pertaining to how they view their competency levels. Overall, the data for this study suggest that this instructional method is effective for teaching computer literacy to adult students who have had limited exposure to computers.

Attitude to Computers↗
PubMedDate not supplied

Patient comprehension of gastroenterology (GI) educational materials.

The purpose of this study was to describe patient comprehension of discharge instruction materials used by one gastroenterology department. Two conceptual frameworks, Orem's self-care model of nursing and Klare's reading comprehension model, were used to guide research design and to explain study findings. A descriptive correlational design was used to explore the relationship between years of schooling, word recognition, and reading comprehension. The study participants (n = 30) included 10 male and 20 female patients. Mean years of schooling was post-high school; mean word recognition score was high school level. Findings included moderate correlation between years of schooling and word recognition scores (r = .64) and strong correlation between word recognition and reading comprehension scores (r = .77-.82). Reading comprehension scores for the majority of participants (60%) were at the frustration comprehension level. Findings suggest that word recognition ability and educational level may be insufficient to ensure comprehension.

Adult↗
PubMed2004

Molecular systematics and biogeography of the southern South american freshwater "crabs" Aegla (decapoda: Anomura: Aeglidae) using multiple heuristic tree search approaches.

Recently new heuristic genetic algorithms such as Treefinder and MetaGA have been developed to search for optimal trees in a maximum likelihood (ML) framework. In this study we combined these methods with other standard heuristic approaches such as ML and maximum parsimony hill-climbing searches and Bayesian inference coupled with Markov chain Monte Carlo techniques under homogeneous and mixed models of evolution to conduct an extensive phylogenetic analysis of the most abundant and widely distributed southern South American freshwater"crab,"the Aegla(Anomura: Aeglidae). A total of 167 samples representing 64 Aegla species and subspecies were sequenced for one nuclear (28S rDNA) and four mitochondrial (12S and 16S rDNA, COI, and COII) genes (5352 bp total). Additionally, six other anomuran species from the genera Munida,Pachycheles, and Uroptychus(Galatheoidea), Lithodes(Paguroidea), and Lomis(Lomisoidea) and the nuclear 18S rDNA gene (1964 bp) were included in preliminary analyses for rooting the Aegla tree. Nonsignificantly different phylogenetic hypotheses resulted from all the different heuristic methods used here, although the best scored topologies found under the ML hill-climbing, Bayesian, and MetaGA approaches showed considerably better likelihood scores (Delta> 54) than those found under the MP and Treefinder approaches. Our trees provided strong support for most of the recognized Aegla species except for A. cholchol,A. jarai,A. parana,A. marginata, A. platensis, and A. franciscana, which may actually represent multiple species. Geographically, the Aegla group was divided into a basal western clade (21 species and subspecies) composed of two subclades with overlapping distributions, and a more recent central-eastern clade (43 species) composed of three subclades with fairly well-recognized distributions. This result supports the Pacific-Origin Hypothesis postulated for the group; alternative hypotheses of Atlantic or multiple origins were significantly rejected by our analyses. Finally, we combined our phylogenetic results with previous hypotheses of South American paleodrainages since the Jurassic to propose a biogeographical framework of the Aegla radiation.

Animals↗
PubMed2006

Development of a measure to assess invalidating childhood environments in the eating disorders.

OBJECTIVE: The role of childhood abuse is well recognised within the eating disorders. However, the impact of parental invalidation of the child's emotional needs has not been investigated. Such invalidation is potentially important because it appears to be associated with the difficulties in tolerating distress that are often seen in adults with eating disorders. This study aims to develop a measure of childhood invalidating environments (Invalidating Childhood Environments Scale; ICES). It also investigated the relationship between childhood experiences, levels of distress tolerance and eating pathology. METHOD: Seventy-three eating-disordered women and 62 non-eating-disordered women completed a newly developed measure of invalidating environments (ICES), the Eating Disorders Inventory, and a Distress Tolerance Scale. RESULTS: The ICES had acceptable psychometric and clinical validity. Women who scored highly on the ICES had greater levels of eating disturbance. Within the clinical sample, the data were compatible with a model where difficulties in tolerating distress partially mediate the relationship between perceived invalidation by the father and eating pathology. CONCLUSIONS: Parental invalidation is a potentially important construct in the eating disorders. This paper demonstrates that the ICES is a valid measure of that construct. This study suggests a clear framework for working with patients, where evidence of an invalidating childhood environment indicates a need to work with patients on their capacity to tolerate distress.

Adaptation, Psychological↗
PubMed2004

What respondents recall about walking and what self-report items elicit about walking.

BACKGROUND: Research on the cognitive processing of survey questions suggests that the distribution of walking bouts (e.g., mean, skew) may influence retrospective self-report responses. METHODS: Undergraduate women (N = 209) kept a weekly log of their walking behavior, then responded to four different self-report measures of walking [National Health Interview Survey (NHIS), Context, Fuzzy-Typical, and Fuzzy-Maximum]. The logs were evaluated to determine which walking characteristics best summarized their walking behavior. Principal components analysis yielded three components of walking behaviors: Frequency, Duration, and Maximum. Multiple regression was used to determine if the walking components differentially predicted the four self-report measures of walking. RESULTS: The Maximum walking component was a significant predictor of all self-report measures of walking. The Context score was also predicted by the Frequency Component. The Frequency and Duration walking components did not predict the NHIS or Fuzzy self-report measures independently of Maximum walking. CONCLUSIONS: Frequency-by-duration self-report measures of walking appear to be more sensitive to the maximum rather than the frequency or duration of walking behavior. Measurement of the frequency of bouts may be best accomplished by providing a framework of recall cues around which walks of different types occur.

Adult↗
PubMed1996

Subject-verb agreement in Spanish and English: differences in the role of conceptual constraints.

This paper reports studies of subject-verb agreement errors with speakers of Spanish and English; we used a sentence completion task, first introduced by Bock and Miller (1991). In a series of four experiments, we assessed the role of semantic information carried by the sentential subject in the induction of subject-verb agreement errors. For Spanish speakers, a sentence preamble such as la etiqueta score las botellas (the label on the bottles), which is usually interpreted to denote several labels, induced more agreement errors than preambles that normally denote a single entity. This finding replicates previous research with Italian (Vigliocco et al., 1995). English speakers, on the other hand, were not sensitive to this semantic dimension, as was found earlier by Bock and Miller (1991). This cross-linguistic difference is discussed in the framework of a modified version of the computational model of grammatical encoding proposed by Kempen and Hoenkamp (1987). In this version of the model agreement is computed through a unification operation instead of feature-copying, allowing for an independent retrieval of agreement features from the conceptual representation for the subject and the verb. We propose that languages differ in the extent to which the selection of the verb is controlled by features on the subject and features from the conceptual representation.

Adult↗
PubMed2004

Assessment of post-stroke quality of life in cost-effectiveness studies: the usefulness of the Barthel Index and the EuroQoL-5D.

Stroke is a major cause of death and long-term disability in Western societies and constitutes a major claim on health care budgets. We address the problem of estimating quality adjusted life years (QALYs) for use in cost-effectiveness studies of stroke interventions. In the acute phase after stroke--at stroke onset and during rehabilitation--many patients are physically or mentally not able to (self-)report their quality of life. Missing values may obviously bias cost-effectiveness results. We have examined the direct relationship between a conventional clinical scale of functional status that is suited for proxy-assessment (Barthel Index (BI)) and a measure of health related quality of life (EuroQoL-5D). Based on data collected within the framework of an evaluation of three stroke-service experiments in The Netherlands (n = 598, 6 month follow-up), we established a plausible and significant relationship between the measures. Health related quality of life (HRQoL) is -0.25 for patients with a BI of 0, and with each additional point HRQoL increases with 0.05. Independent patients (BI 20) get a HRQoL is 0.75, which corresponds to the general population reference score for our sample. BI scores may be used as proxy for HRQoL in case of missing values on EuroQoL-5D.

Activities of Daily Living↗
PubMed2004

On the selective relation of frontal cortical asymmetry and anger-out versus anger-control.

The model of anterior asymmetry and emotion proposes an asymmetric representation of approach and withdrawal systems in the left and right anterior brain regions. Within this framework, 3 different concepts have been related to anterior asymmetry: affective valence, motivational direction, and behavioral activation. The aim of the present study was an empirical investigation into the relation between anterior cortical activity and questionnaire measures related to the 3 dimensions positive versus negative affect, approach versus withdrawal motivation, and behavioral activation versus inhibition. Subjects with relative greater left than right frontal cortical activity showed higher anger-out scores and lower anger-control scores. These results support the hypothesis that motivational direction is related to frontal asymmetry (approach-left and withdrawal-right). Furthermore, subjects with greater bilateral (left and right) frontal cortical activity showed higher behavioral activation scores. This finding might suggest that behavioral activation is related to approach and withdrawal motivation.

Adult↗
PubMed1998

Beneficial and harmful effects of augmented feedback on physicians' clinical-teaching performances.

PURPOSE: To evaluate whether clinical-teaching skills could be improved by providing teachers with augmented student feedback. METHOD: A randomized, controlled trial in 1994 included 42 attending physicians and 39 residents from the Department of Medicine at the Indiana University School of Medicine who taught 110 students on medicine ward rotations for one-month periods. Before teaching rotations, intervention group teachers received norm-referenced, graphic summaries of their teaching performances as rated by students. At mid-month, intervention group teachers received students' ratings augmented by individualized teaching-effectiveness guidelines based on the Stanford Faculty Development Program framework. Linear models were used to analyze the students' mean ratings of teaching behaviors at mid-month and end-of-month. Independent variables included performance ratings, intervention status, teacher status, teaching experience, and interactions with baseline ratings. RESULTS: Complex interactions with baseline performance were found for most teaching categories at mid-month and end-of-month. The intervention-group teachers who had high baseline performance scores had higher student ratings than did the control group teachers with similar baseline scores; the intervention group teachers who had low baseline performance scores were rated lower than were the control group teachers with comparable baseline scores. The residents who had medium or high baseline scores were rated higher than were the attending physicians with comparable baseline scores; the performance of the residents who had low baseline scores was similar to that of the attending physicians with comparable baseline scores. CONCLUSION: Baseline performance is important for targeting those teachers most likely to benefit from augmented student feedback. Potential deterioration in teaching performance warrants a reconsideration of distributing students' ratings to teachers with low baseline performance scores.

Clinical Clerkship↗
PubMed1998

Effects of an irritable bowel syndrome educational class on health-promoting behaviors and symptoms.

OBJECTIVE: The degree to which patient education in the areas of diet, exercise, and stress management can improve symptoms of irritable bowel syndrome (IBS) through healthier lifestyle behaviors is unknown. The aim of this study was to determine the effects of outpatient education on the short and long term outcomes, and the association between health-promoting behaviors and symptoms. METHODS: Pender's Health Promotion Model provided the theoretical framework. The study had a prospective longitudinal design. A consecutive sample of 52 adult outpatients with IBS attended a structured class that taught health-promoting modifications of lifestyle. Participants completed the Health-Promoting Lifestyle Profile (HPLP) and selected items from a Bowel Disease Questionnaire (BDQ) before the class and 1 month and 6 months later. Spearman rank correlations were used to assess the association between HPLP and symptom scores. Wilcoxon rank sum tests compared changes in scores versus their baseline values. RESULTS: Response rates at 1 and 6 months were 75% and 83%, respectively. Results revealed significant 1- and 6 month-improvements in pain and Manning symptoms (p < 0.01) and in some HPLP scores (exercise at 1 month, p < 0.05; stress management at 6 months, p < 0.01). Significant associations were found between some, but not all, HPLP and symptom scores over time. CONCLUSION: A structured IBS educational class for patients with IBS improved symptoms and some health-promoting behaviors. However, relationships among specific behaviors and specific symptoms did not consistently correspond with this improvement.

Adult↗
PubMed1991

Determinants of 2-year outcome after coronary angioplasty in patients with multivessel disease on the basis of comprehensive preprocedural evaluation. Implications for patient selection. The Multivessel Angioplasty Prognosis Study Group.

BACKGROUND: To assess the likelihood of intermediate-term event-free survival (freedom from death, coronary artery bypass surgery, and myocardial infarction) in patients with multivessel coronary disease undergoing coronary angioplasty, 350 consecutive patients from four clinical sites were carefully evaluated and followed for 22 +/- 10 months. METHODS AND RESULTS: Eight clinical variables were evaluated at the clinical sites, and 23 angiographic variables describing the number, morphology, and topography of coronary stenoses were evaluated at a core angiographic laboratory. Most patients had Canadian Cardiovascular Society class III or IV angina (72%), two-vessel coronary disease (68%), and well-preserved left ventricular function (mean ejection fraction, 58 +/- 12%; range, 18-85%). Follow-up was complete in 99% of patients. At 2 years, event-free survival was 72%, overall survival was 96%, freedom from bypass surgery was 82%, and freedom from nonfatal myocardial infarction without surgery was 96%. Sequential Cox proportional hazards regression analyses allowing stepwise entry of variables prospectively coded as simple, as of intermediate complexity, or as complex found event-free survival to be independently predicted by low Canadian Cardiovascular Society angina class, no diabetes, no proximal left anterior descending stenoses, and the sum of stenosis simplified risk-territory scores of 15 or less. In the absence of class IV angina and these risk factors, 2-year event-free survival was 87% and overall survival was 100%. In the presence of two or more of these risk factors, event-free survival was less than 50%. CONCLUSIONS: Recognition of risk factors for poor long-term outcome in this setting may improve clinical decision making and provide a framework on which to base meaningful subgroup analyses in randomized trials assessing the efficacy of coronary angioplasty.

Angioplasty, Balloon, Coronary↗