Exploring the Clinical Characteristics of COVID-19 Clusters Identified Using Factor Analysis of Mixed Data-Based Cluster Analysis.
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ABSTRACT:
SUBMITTER: Han L
PROVIDER: S-EPMC8323882 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:PurposeAsthma is a heterogeneous disease characterized by various types of airway inflammation and obstruction. Therefore, it is classified into several subphenotypes, such as early-onset atopic, obese non-eosinophilic, benign, and eosinophilic asthma, using cluster analysis. A number of asthmatics frequently experience exacerbation over a long-term follow-up period, but the exacerbation-prone subphenotype has rarely been evaluated by cluster analysis. This prompted us to identify clusters reflecting asthma exacerbation.MethodsA uniform cluster analysis method was applied to 259 adult asthmatics who were regularly followed-up for over 1 year using 12 variables, selected on the basis of their contribution to asthma phenotypes. After clustering, clinical profiles and exacerbation rates during follow-up were compared among the clusters.ResultsFour subphenotypes were identified: cluster 1 was comprised of patients with early-onset atopic asthma with preserved lung function, cluster 2 late-onset non-atopic asthma with impaired lung function, cluster 3 early-onset atopic asthma with severely impaired lung function, and cluster 4 late-onset non-atopic asthma with well-preserved lung function. The patients in clusters 2 and 3 were identified as exacerbation-prone asthmatics, showing a higher risk of asthma exacerbation.ConclusionsTwo different phenotypes of exacerbation-prone asthma were identified among Korean asthmatics using cluster analysis; both were characterized by impaired lung function, but the age at asthma onset and atopic status were different between the two.
| S-EPMC5603476 | biostudies-literature
Project description:BACKGROUND:Personal recovery is associated with many significant health-related factors, but studies exploring associations between activity factors and personal recovery among service users are scarce. The aims of this study were hence to; 1) investigate if various aspects of activity may mediate change in recovery while also acknowledging clinical, sociodemographic and well-being factors; 2) explore the effects of two activity-based interventions, Balancing Everyday Life (BEL) or standard occupational therapy (SOT), on personal recovery among service users. METHODS:Two-hundred-and-twenty-six service users were included in a cluster RCT, 133 from BEL units and 93 from SOT units. Participants commonly had a diagnosis of mood disorder and the mean age was 40. Instruments used targeted activity, mastery and functioning. A mixed-model regression analysis was employed. RESULTS:The model tested was whether selected variables could be used to mediate the change in recovery from the start to a six-month follow-up after intervention. Participants' personal recovery increased after treatment and increased further at the follow-up. The general level of recovery was negatively related to a diagnosis of depression/anxiety, both before and after treatment, but depressed/anxious service users still increased their recovery. There were no significant relations between recovery and sex or age. The interactions between change in recovery and changes in depression/anxiety, satisfaction with activities, sex, and age were all non-significant. All possible treatment mediators included were related to change in recovery, the strongest being occupational engagement and mastery, followed by activity satisfaction and symptoms. Mediation was shown by the decrease in the effect of the time factor (from intervention start to completion) when the covariates were introduced. In all cases the time variable was still significant. When testing a model with all variables simultaneously as covariates, occupational engagement and mastery were strongly significant. There was no difference between interventions regarding recovery improvement. CONCLUSION:The treatments were equally beneficial and were effective regardless of gender, age and diagnosis. Those who gained most from the treatment also gained in feelings of mastery and activity engagement. Activity engagement also moderated the level of recovery. To enhance recovery, interventions should facilitate meaningful activities and gaining control in life. TRIAL REGISTRATION:The study was registered with ClinicalTrials.gov . Reg. No. NCT02619318 . Retrospectively registered: December 2, 2015.
| S-EPMC7602343 | biostudies-literature
Project description:BackgroundThe Japanese age-standardised death rate of suicide (SDR) had decreased during 2009-2019, but increased in 2020-2021, during the COVID-19 pandemic.MethodsThis study aimed to explain the trend change in the SDR during the pandemic, disaggregated by prefecture, gender, suicide method and household, as compared to predicted SDR derived from pre-pandemic data, using linear mixed-effect and hierarchical linear regression models with robust standard error analyses.FindingsThe SDR was lower during March-June 2020 (during the first wave of the pandemic), but higher during July-December 2020 than the predicted SDR. In 2021, males' SDR was nearly equal to the predicted SDR, whereas females' SDR in the metropolitan-region (17.5%: 95% confidence interval: 13.9-21.2%) and non-metropolitan-region (24.7%: 95% confidence interval: 22.8-26.7%) continued to be higher than the predicted SDR. These gender- and region-dependent temporal fluctuations of SDR were synchronised with those of SDRs caused by hanging, at home and single-person-households. Additionally, the rising number of infected patients with the SARS-CoV-2 and polymerase chain reaction (PCR) diagnostic examinations were positively (β = 0.024) and negatively (β =-0.002) related to the SDR during the pandemic, respectively.InterpretationJapanese suicide statistics have previously established that the predominant method and place of suicide were by hanging and at the individual's home, respectively. The present findings suggest that transformed lifestyles during the pandemic, increasing time spent at home, enhanced the suicide risk of Japanese people by hanging and at home.FundingRegional Suicide Countermeasures Emergency Enhancement Fund of Mie Prefecture (2021-40).
| S-EPMC9160839 | biostudies-literature
Project description:Cluster randomized trials involving participants nested within intact treatment and control groups are commonly performed in various educational, psychological, and biomedical studies. However, recruiting and retaining intact groups present various practical, financial, and logistical challenges to evaluators and often, cluster randomized trials are performed with a low number of clusters (~20 groups). Although multilevel models are often used to analyze nested data, researchers may be concerned of potentially biased results due to having only a few groups under study. Cluster bootstrapping has been suggested as an alternative procedure when analyzing clustered data though it has seen very little use in educational and psychological studies. Using a Monte Carlo simulation that varied the number of clusters, average cluster size, and intraclass correlations, we compared standard errors using cluster bootstrapping with those derived using ordinary least squares regression and multilevel models. Results indicate that cluster bootstrapping, though more computationally demanding, can be used as an alternative procedure for the analysis of clustered data when treatment effects at the group level are of primary interest. Supplementary material showing how to perform cluster bootstrapped regressions using R is also provided.
| S-EPMC5965657 | biostudies-literature
Project description:BackgroundOsteoarthritis (OA) is a chronic, disabling, and prevalent disorder. As there is no cure for OA, long-term self-management is paramount. Support groups (SGs) can facilitate self-management among people living with OA. Understanding preferences in design and features of SGs, including online SGs (OSGs), among people with OA can inform future development of SG interventions for this condition.ObjectiveThe objective of this study was to investigate health care- and health information-seeking behavior, digital literacy, and preferences for the design of SGs in people with OA. The study also explored the perceived barriers and enablers to being involved in OSGs.MethodsAn online survey study was conducted with a mixed method design (quantitative and qualitative). Individuals aged ≥45 years with knee, hip, or back pain for ≥3 months were recruited from an extant patient database of the Institute of Bone and Joint Research via email invitations. Quantitative elements of the survey included questions about sociodemographic background; health care- and health information-seeking behavior; digital literacy; and previous participation in, and preferences for, SGs and OSGs. Respondents were classified into 2 groups (Yes-SG and No-SG) based on previous participation or interest in an SG. Group differences were assessed with Chi-square tests (significance level set at 5%). Responses to free-text questions relating to preferences regarding OSG engagement were analyzed qualitatively using an inductive thematic analysis.ResultsA total of 415 people with OA completed the survey (300/415, 72.3% females; 252/415, 61.0% lived in a major city). The Yes-SG group included 307 (307/415, 73.9%) participants. Between the Yes-SG and No-SG groups, there were no differences in sociodemographic characteristics, health care- and health information-seeking behavior, and digital literacy. An online format was preferred by 126/259 (48.7%) of the Yes-SG group. Trained peer facilitators were preferred, and trustworthiness of advice and information were highly prioritized by the respondents. Qualitative analysis for OSG participation revealed 5 main themes. Lack of time and motivation were the main barriers identified. The main enablers were related to accessibility, enjoyment of the experience, and the content of the discussed information.ConclusionsThese findings highlight the preferences in design features and content of SGs and OSGs and may assist in the further development of such groups.
| S-EPMC6918205 | biostudies-literature
Project description:BackgroundCoronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread around the world and reports of children during early epidemic period showed features of family clusters. The aim of this study is to assess clinical profiles of COVID-19 in family clusters with children.MethodsWe performed a systematic literature review of English database (PubMed, Web of Science) and Chinese database (" www.cnki.net ", " www.cqvip.com " and " www.Wanfangdata.com.cn ") to identify papers on family clusters of COVID-19 with children and their family members.ResultsEighteen studies involving 34 children and 98 adults from 28 families were included. Fever, cough and ground-grass opacity change of chest computed tomography (CT) were the dominant features, whereas proportion of asymptomatic infections for children was higher than adults with statistical significance (32.4% and 13.3%, respectively, P < 0.05). Median time of longer incubation period (10 days) and shorter duration of pharyngeal swab nucleic acid test positive period (11 days) were seen in children than adults (7 and 17 days, respectively) with statistical significance (P < 0.05). There were statistically significant differences in lymphopenia, increased C-reactive protein and abnormal chest CT between children and adult patients (P < 0.05). Twenty-seven families reported adults as first case of COVID-19 in family clusters.ConclusionsThe same virus strain can cause milder disease in children compared with their caregivers. Children of COVID-19 were infected by adults in family during the early epidemic period. Asymptomatic patients can transmit the virus.
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Project description:BACKGROUND: Phylogenetic comparison of bacteriophages requires whole genome approaches such as dotplot analysis, genome pairwise maps, and gene content analysis. Currently mycobacteriophages, a highly studied phage group, are categorized into related clusters based on the comparative analysis of whole genome sequences. With the recent explosion of phage isolation, a simple method for phage cluster prediction would facilitate analysis of crude or complex samples without whole genome isolation and sequencing. The hypothesis of this study was that mycobacteriophage-cluster prediction is possible using comparison of a single, ubiquitous, semi-conserved gene. Tape Measure Protein (TMP) was selected to test the hypothesis because it is typically the longest gene in mycobacteriophage genomes and because regions within the TMP gene are conserved. RESULTS: A single gene, TMP, identified the known Mycobacteriophage clusters and subclusters using a Gepard dotplot comparison or a phylogenetic tree constructed from global alignment and maximum likelihood comparisons. Gepard analysis of 247 mycobacteriophage TMP sequences appropriately recovered 98.8% of the subcluster assignments that were made by whole-genome comparison. Subcluster-specific primers within TMP allow for PCR determination of the mycobacteriophage subcluster from DNA samples. Using the single-gene comparison approach for siphovirus coliphages, phage groupings by TMP comparison reflected relationships observed in a whole genome dotplot comparison and confirm the potential utility of this approach to another widely studied group of phages. CONCLUSIONS: TMP sequence comparison and PCR results support the hypothesis that a single gene can be used for distinguishing phage cluster and subcluster assignments. TMP single-gene analysis can quickly and accurately aid in mycobacteriophage classification.
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Project description:BackgroundThe epidemiological importance of asymptomatic individuals who would never develop illness, compared to those who eventually develop symptoms, has yet to be fully clarified.MethodsThe very first cluster data in Tokyo and Kanagawa (n = 36) were analyzed. Movement of all close contact was restricted for 14 days and they underwent laboratory testing with polymerase chain reaction. The reproduction numbers of symptomatic and asymptomatic cases were estimated.ResultsThe reproduction number for symptomatic cases was estimated to be 1.2 (95% confidence interval (CI): 0.5-2.9). The relative infectiousness of asymptomatically infected cases was estimated to be 0.27 (95% CI: 0.03-0.81) of symptomatic cases.ConclusionThe relative transmissibility of asymptomatic cases is limited. Observing clusters starting with symptomatic transmission might be sufficient for the control.
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Project description:BACKGROUND: There are a number of different methods for generation of trees and algorithms for phylogenetic analysis in the study of bacterial taxonomy. Genotypic information, such as SSU rRNA gene sequences, now plays a more prominent role in microbial systematics than does phenotypic information. However, the integration of genotypic and phenotypic information for polyphasic studies is necessary for the classification and identification of microbes. Thus, we devised an algorithm that objectively identifies discriminative characteristics for focused clusters on generated trees from a dataset composed of coded data, such as phenotypic information. Moreover, this algorithm has been integrated into the polyphasic analysis software, InforBIO. RESULTS: We developed a differential-character-finding algorithm based on information measures and used this algorithm to identify the characteristic that best discriminates operational taxonomic unit clusters. For all characteristics in a dataset, the algorithm estimates commonality in focused clusters and diversity among clusters by scoring based on Shannon's and relative entropies. All the characteristics selected for scoring are equally weighted. Thresholds for the scores are defined to identify discriminative characteristics for clusters efficiently from a database. The unique feature of the algorithm, which is implemented in the InforBIO software, is that it can identify the phenotypic characteristics that discriminate and are associated with the clusters of a phylogenetic tree. We successfully applied this algorithm to the study of phylogenetic clusters of Pseudomonas species. CONCLUSION: The algorithm in the InforBIO software is a novel and useful approach for microbial polyphasic studies. The algorithm can also be applied to diverse cluster analyses. The InforBIO software is available from the download site http://wdcm.nig.ac.jp/inforbio/. This software is free for personal but not commercial use.
| S-EPMC1973088 | biostudies-other
Project description:BACKGROUND:Interpretation of gene expression microarray data in the light of external information on both columns and rows (experimental variables and gene annotations) facilitates the extraction of pertinent information hidden in these complex data. Biologists classically interpret genes of interest after retrieving functional information from a subset of genes of interest. Transcription factors play an important role in orchestrating the regulation of gene expression. Their activity can be deduced by examining the presence of putative transcription factors binding sites in the gene promoter regions. RESULTS:In this paper we present the multivariate statistical method RLQ which aims to analyze microarray data where additional information is available on both genes and samples. As an illustrative example, we applied RLQ methodology to analyze transcription factor activity associated with the time-course effect of steroids on the growth of primary human lung fibroblasts. RLQ could successfully predict transcription factor activity, and could integrate various other sources of external information in the main frame of the analysis. The approach was validated by means of alternative statistical methods and biological validation. CONCLUSIONS:RLQ provides an efficient way of extracting and visualizing structures present in a gene expression dataset by directly modeling the link between experimental variables and gene annotations.
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