Tag: statistics

Bioinformatics. 2023 Mar 21:btad138. doi: 10.1093/bioinformatics/btad138. Online ahead of print.

ABSTRACT

MOTIVATION: Deep learning attained excellent results in Digital Pathology recently. A challenge with its use is that high quality, representative training data sets are required to build robust models. Data annotation in the domain is labor intensive and demands substantial time commitment from expert pathologists. Active Learning (AL) is a strategy to minimize annotation. The goal is to select samples from the pool of unlabeled data for annotation that improves model accuracy. However, AL is a very compute demanding approach. The benefits for model learning may vary according to the strategy used, and it may be hard for a domain specialist to fine tune the solution without an integrated interface.

RESULTS: We developed a framework that includes a friendly user interface along with run-time optimizations to reduce annotation and execution time in AL in digital pathology. Our solution implements several AL strategies along with our Diversity-Aware Data Acquisition (DADA) acquisition function, which enforces data diversity to improve the prediction performance of a model. In this work, we employed a model simplification strategy (Network Auto-Reduction (NAR)) that significantly improves AL execution time when coupled with DADA. NAR produces less compute demanding models, which replace the target models during the AL process to reduce processing demands. An evaluation with a Tumor-Infiltrating Lymphocytes (TILs) classification application shows that: (i) DADA attains superior performance compared to state-of-the-art AL strategies for different Convolutional Neural Networks (CNNs), (ii) NAR improves the AL execution time by up to 4.3 ×, and (iii) target models trained with patches/data selected by the NAR reduced versions achieve similar or superior classification quality to using target CNNs for data selection.

AVAILABILITY: Source code: https://github.com/alsmeirelles/DADA.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PMID:36943380 | DOI:10.1093/bioinformatics/btad138

Rheumatology (Oxford). 2023 Mar 21:kead121. doi: 10.1093/rheumatology/kead121. Online ahead of print.

ABSTRACT

OBJECTIVES: To examine the effect of pre-course e-learning on residents’ practical performance in musculoskeletal ultrasound (MSUS).

METHODS: Multicentre, randomized controlled study following the CONSORT statement. Residents with no or little MSUS experience were randomized to either an e-learning group or a traditional group. One week before a 2-day face-to-face MSUS course, the e-learning group received access to an interactive platform consisting of online lectures, assignments, and practical instruction videos aligned with the content of the course. The traditional group only received standard pre-course information (program, venue, and time). All participants performed a pre- and post-course practical MSUS examination and were assessed by two individual raters, blinded to the group allocation, using the validated Objective Structured Assessment of Ultrasound skills (OSAUS) tool.

RESULTS: Twenty-eight participants completed the study. There were no statistically significant differences in the pre- or post-course practical MSUS performance between the e-learning group and the traditional group; the mean pre-course OSAUS score (±SD) in the e-learning group was 5.4 ± 3.7 compared with 5.2 ± 2.4 in the traditional group, p= 0.8, whereas the post-course OSAUS score in the e-learning group was 11.1 ± 2.8 compared with 10.9 ± 2.4 in the traditional group, p= 0.8. There was a significant difference between the mean pre- and post-course scores (5.74-point p< 0.001). The OSAUS assessment tool demonstrated good inter-rater reliability (ICC = 0.84).

CONCLUSION: We found no significant impact of pre-course e-learning on novices’ acquisition of practical MSUS skills. Hands-on training is of utmost importance and improves MSUS performance significantly. The OSAUS assessment tool is an applicable tool with high interrater reliability.

TRIAL REGISTRATION: https://clinicaltrials.gov/ NCT04959162.

PMID:36943374 | DOI:10.1093/rheumatology/kead121

Health Educ Res. 2023 Mar 21:cyad014. doi: 10.1093/her/cyad014. Online ahead of print.

ABSTRACT

In 2021, guidelines for early childhood education and care were released recommending children are provided access to outdoor areas during all free play sessions to reduce the risk of coronavirus disease of 2019 transmission, aligning with the existing recommendations to increase children’s physical activity. There is a need to understand how to disseminate guidelines in this setting as dissemination is a prerequisite of adoption and implementation. This randomized controlled trial explored the impact of a video-based strategy to disseminate guidelines on family day care educators’ intentions to adopt outdoor free play guidelines. Educators (N = 255) were randomized to receive a video (intervention) or text-based (usual care) resource via email describing recommendations. Educators were invited to participate in a post-intervention survey at 5-week follow-up assessing intentions to adopt guidelines. The secondary outcomes included knowledge, beliefs about capabilities, beliefs about consequences, social/professional role and identity, goals, implementation of guidelines, acceptability of resource and intervention reach. There was no statistically significant difference between groups in intentions to adopt guidelines [ß = 0.01 (95% confidence interval -0.50 to 0.52), P = 0.97], nor for any secondary outcomes. Further investigation is needed to identify effective dissemination strategies in the family day care setting to increase the adoption of public health guidelines.

PMID:36943373 | DOI:10.1093/her/cyad014

Bioinformatics. 2023 Mar 21:btad139. doi: 10.1093/bioinformatics/btad139. Online ahead of print.

ABSTRACT

MOTIVATION: Accurate power and sample size estimation is crucial to the design and analysis of genetic association studies. When analyzing a binary trait via logistic regression, important covariates such as age and sex are typically included in the model. However, their effects are rarely properly considered in power or sample size computation during study planning. Unlike when analyzing a continuous trait, the power of association testing between a binary trait and a genetic variant depends, explicitly, on covariate effects, even under the assumption of gene-environment independence. Earlier work recognizes this hidden factor but the implemented methods are not flexible.

METHOD: We thus propose and implement a generalized method for estimating power and sample size for (discovery or replication) association studies of binary traits that a) accommodates different types of non-genetic covariates E, b) deals with different types of G-E relationships, and c) is computationally efficient.

RESULTS: Extensive simulation studies show that the proposed method is accurate and computationally efficient for both prospective and retrospective sampling designs with various covariate structures. A proof-of-principle application focused on the understudied African sample in the UK Biobank data. Results show that, in contrast to studying the continuous blood pressure trait, when analyzing the binary hypertension trait ignoring covariate effects of age and sex leads to overestimated power and underestimated replication sample size.

AVAILABILITY: The simulated datasets can be found on the online web-page of this manuscript, and the UK Biobank application data can be accessed at https://www.ukbiobank.ac.uk. The R package SPCompute that implements the proposed method is available at CRAN. The genome-wide association studies are carried out using the software PLINK 2.0 (Purcell et al., 2007).

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PMID:36943372 | DOI:10.1093/bioinformatics/btad139

Mil Med. 2023 Mar 21:usad081. doi: 10.1093/milmed/usad081. Online ahead of print.

ABSTRACT

INTRODUCTION: Cervical spine immobilization in a low-resource environment is difficult secondary to limited equipment, prolonged transportation, and secondary complications. A structural aluminum malleable (SAM) splint is commonly utilized because of its availability and multipurpose intention. A one-step spray-on foam immobilization technique (Fast Cast) has been shown to be effective in lower-extremity splinting. The aim of this study was to demonstrate the ability of the Fast Cast to effectively immobilize the cervical spine in a head-to-head comparison against the SAM splint. We hypothesized that there would be no difference in surgeon scoring between Fast Cast and SAM splints for the immobilization of the cervical spine.

METHODS: This was a cadaveric experimental comparative study that compared a SAM splint versus Fast Cast for the immobilization of an unstable cervical spine. Each of the three cadaveric specimens had a corpectomy without fixation performed. A board-certified emergency medicine physician specialized in disaster medicine performed all SAM immobilizations. An orthopedic surgeon performed Fast Cast immobilizations. Each method of immobilization was done on each cadaver. Lateral fluoroscopic imaging was taken before and after immobilization and after log roll/gravity stress. Five board-certified orthopedic surgeons served as graders to independently score each splint. A 5-point Likert scale based on 10 splinting criteria (50 total points possible) was utilized to evaluate cervical spine immobilization. The lead statistical analyst was blinded to the immobilization groups. The statistical significance was assessed via a Wilcoxon signed-rank test and chi-square Fisher’s exact test with significance between groups set at α < .05. Inter-rater reliability of the Likert scale results was assessed with the interclass correlation coefficient.

RESULTS: Inter-rater reliability for the current Likert scale in the evaluation of cervical spine stabilization was good (interclass correlation coefficient = 0.76). For the cumulative Likert scale score, Fast Cast (32 [28-34]) exhibited a higher total score than SAM (44 [42-47]; P < .01). Likewise, Fast Cast exhibited a greater likelihood of higher Likert scores within each individual question as compared to SAM (P ≤ 0.04). In 100% of cases, raters indicated that Fast Cast passed the gravity stress examination without intrinsic loss of reduction or splinting material, whereas 33% of SAM passed (P < .01). In 100% of cases, raters indicated that Fast Cast passed the initial radiographic alignment following immobilization, whereas 66% of SAM passed (P = .04). In 100% of cases, raters indicated that Fast Cast passed radiographic alignment after the gravity stress examination, whereas 47% of SAM passed (P < .01).

CONCLUSION: The Fast Cast exceeded our expectations and was shown to be rated not equivalent but superior to SAM splint immobilization for the cervical spine. This has significant clinical implications as the single-step spray-on foam is easy to transport and has multifaceted applications. It also eliminates pressure points and circumferential wrapping and obstruction to airway/vascular access while immobilizing the cervical spine and allowing for radiographic examination. Further studies are needed for human use and application.

PMID:36943370 | DOI:10.1093/milmed/usad081

JMIR Form Res. 2023 Mar 21;7:e44666. doi: 10.2196/44666.

ABSTRACT

BACKGROUND: Early triage of patients with mushroom poisoning is essential for administering precise treatment and reducing mortality. To our knowledge, there has been no established method to triage patients with mushroom poisoning based on clinical data.

OBJECTIVE: The purpose of this work was to construct a triage system to identify patients with mushroom poisoning based on clinical indicators using several machine learning approaches and to assess the prediction accuracy of these strategies.

METHODS: In all, 567 patients were collected from 5 primary care hospitals and facilities in Enshi, Hubei Province, China, and divided into 2 groups; 322 patients from 2 hospitals were used as the training cohort, and 245 patients from 3 hospitals were used as the test cohort. Four machine learning algorithms were used to construct the triage model for patients with mushroom poisoning. Performance was assessed using the area under the receiver operating characteristic curve (AUC), decision curve, sensitivity, specificity, and other representative statistics. Feature contributions were evaluated using Shapley additive explanations.

RESULTS: Among several machine learning algorithms, extreme gradient boosting (XGBoost) showed the best discriminative ability in 5-fold cross-validation (AUC=0.83, 95% CI 0.77-0.90) and the test set (AUC=0.90, 95% CI 0.83-0.96). In the test set, the XGBoost model had a sensitivity of 0.93 (95% CI 0.81-0.99) and a specificity of 0.79 (95% CI 0.73-0.85), whereas the physicians’ assessment had a sensitivity of 0.86 (95% CI 0.72-0.95) and a specificity of 0.66 (95% CI 0.59-0.73).

CONCLUSIONS: The 14-factor XGBoost model for the early triage of mushroom poisoning can rapidly and accurately identify critically ill patients and will possibly serve as an important basis for the selection of treatment options and referral of patients, potentially reducing patient mortality and improving clinical outcomes.

PMID:36943366 | DOI:10.2196/44666

JMIR Form Res. 2023 Mar 21;7:e44725. doi: 10.2196/44725.

ABSTRACT

BACKGROUND: Electronic paper (E-paper) screens use electrophoretic ink to provide paper-like low-power displays with advanced networking capabilities that may potentially serve as an alternative to traditional whiteboards and television display screens in hospital settings. E-paper may be leveraged in the emergency department (ED) to facilitate communication. Providing ED patient status updates on E-paper screens could improve patient satisfaction and overall experience and provide more equitable access to their health information.

OBJECTIVE: We aimed to pilot a patient-facing digital whiteboard using E-paper to display relevant orienting and clinical information in real time to ED patients. We also sought to assess patients’ satisfaction after our intervention and understand our patients’ overall perception of the impact of the digital whiteboards on their stay.

METHODS: We deployed a 41-inch E-paper digital whiteboard in 4 rooms in an urban, tertiary care, and academic ED and enrolled 110 patients to understand and evaluate their experience. Participants completed a modified Hospital Consumer Assessment of Health Care Provider and Systems satisfaction questionnaire about their ED stay. We compared responses to a matched control group of patients triaged to ED rooms without digital whiteboards. We designed the digital whiteboard based on iterative feedback from various departmental stakeholders. After establishing IT infrastructure to support the project, we enrolled patients on a convenience basis into a control and an intervention (digital whiteboard) group. Enrollees were given a baseline survey to evaluate their comfort with technology and an exit survey to evaluate their opinions of the digital whiteboard and overall ED satisfaction. Statistical analysis was performed to compare baseline characteristics as well as satisfaction.

RESULTS: After the successful prototyping and implementation of 4 digital whiteboards, we screened 471 patients for inclusion. We enrolled 110 patients, and 50 patients in each group (control and intervention) completed the study protocol. Age, gender, and racial and ethnic composition were similar between groups. We saw significant increases in satisfaction on postvisit surveys when patients were asked about communication regarding delays (P=.03) and what to do after discharge (P=.02). We found that patients in the intervention group were more likely to recommend the facility to family and friends (P=.04). Additionally, 96% (48/50) stated that they preferred a room with a digital whiteboard, and 70% (35/50) found the intervention “quite a bit” or “extremely” helpful in understanding their ED stay.

CONCLUSIONS: Digital whiteboards are a feasible and acceptable method of displaying patient-facing data in the ED. Our pilot suggested that E-paper screens coupled with relevant, real-time clinical data and packaged together as a digital whiteboard may positively impact patient satisfaction and the perception of the facility during ED visits. Further study is needed to fully understand the impact on patient satisfaction and experience.

TRIAL REGISTRATION: ClinicalTrials.gov NCT04497922; https://clinicaltrials.gov/ct2/show/NCT04497922.

PMID:36943360 | DOI:10.2196/44725

J Public Health Manag Pract. 2023 Mar 17. doi: 10.1097/PHH.0000000000001701. Online ahead of print.

ABSTRACT

OBJECTIVE: To adapt an existing surveillance system to monitor the collateral impacts of the COVID-19 pandemic on health outcomes in New York City across 6 domains: access to care, chronic disease, sexual/reproductive health, food/economic insecurity, mental/behavioral health, and environmental health.

DESIGN: Epidemiologic assessment. Public health surveillance system.

SETTING: New York City.

PARTICIPANTS: New York City residents.

MAIN OUTCOME MEASURES: We monitored approximately 30 indicators, compiling data from 2006 to 2022. Sources of data include clinic visits, surveillance surveys, vital statistics, emergency department visits, lead and diabetes registries, Medicaid claims, and public benefit enrollment.

RESULTS: We observed disruptions across most indicators including more than 50% decrease in emergency department usage early in the pandemic, which rebounded to prepandemic levels by late 2021, changes in reporting levels of probable anxiety and depression, and worsening birth outcomes for mothers who identified as Asian/Pacific Islander or Black. Data are processed in SAS and analyzed using the R Surveillance package to detect possible inflections. Data are updated monthly to an internal Tableau Dashboard and shared with agency leadership.

CONCLUSIONS: As the COVID-19 pandemic continues into its third year, public health priorities are returning to addressing non-COVID-19-related diseases and conditions, their collateral impacts, and postpandemic recovery needs. Substantial work is needed to return even to a suboptimal baseline across multiple health topic areas. Our surveillance framework offers a valuable starting place to effectively allocate resources, develop interventions, and issue public communications.

PMID:36943341 | DOI:10.1097/PHH.0000000000001701

Int J Syst Evol Microbiol. 2023 Mar;73(3). doi: 10.1099/ijsem.0.005724.

ABSTRACT

We isolated and analysed a Gram-negative, facultatively thermophilic, xylan-degrading bacterium that we designated as strain DA-C8^T. The strain was isolated from compost from Ishigaki Island, Japan, by enrichment culturing using beech wood xylan as the sole carbon source. The strain showed high xylan degradation ability under anaerobic growth conditions. The isolate grew at 37-60 °C (optimum, 55 °C) and pH 4.0-11.0 (optimum, pH 9.0). As well as xylan, strain DA-C8^T could use polysaccharides such as arabinoxylan and galactan as carbon sources. Comparison of 16S rRNA gene sequences indicated that strain DA-C8^T was most closely related to Paenibacillus cisolokensis LC2-13A^T (93.9 %) and Paenibacillus chitinolyticus HSCC596 (93.5 %). In phylogenetic analysis, strain DA-C8^T belonged to the same lineage as Xylanibacillus composti K13^T (92.5 %), but there was less statistical support for branching (70 %). Digital DNA-DNA hybridization, average nucleotide identity values and average amino acid sequence identity between strain DA-C8^T and P. cisolokensis LC2-13A^T were 21.8, 68.3 and 58.2 %, respectively. Those between strain DA-C8^T and X. composti K13 were 23.7, 67.7 and 57.6 %, respectively. The whole-genome DNA G+C content of strain DA-C8^T was 52.3 mol%. The major cellular fatty acids were C_{16 : 0} (42.9 %), anteiso-C_{15 : 0} (20.0 %) and anteiso-C_{17 : 0} (16.7 %), the major quinone was menaquinone 7, and the major polar lipids were unidentified glycolipids. On the basis of phenotypic, chemotaxonomic and phylogenetic evidence, a novel genus is proposed-Insulambacter gen. nov.-for the novel species Insulambacter thermoxylanivorax sp. nov. The type strain is DA-C8^T (=JCM 34211^T=DSM 111723^T).

PMID:36943336 | DOI:10.1099/ijsem.0.005724

J Neurol Phys Ther. 2023 Apr 1;47(2):63. doi: 10.1097/NPT.0000000000000434.

NO ABSTRACT

PMID:36943323 | DOI:10.1097/NPT.0000000000000434