Application of a variational autoencoder for clustering and analyzing in situ articular cartilage cellular response to mechanical stimuli.

In various biological systems, analyzing how cell behaviors are coordinated over time would enable a deeper understanding of tissue-scale response to physiologic or superphysiologic stimuli. Such data is necessary for establishing both normal tissue function and the sequence of events after injury that lead to chronic disease. However, collecting and analyzing these large datasets presents a challenge-such systems are time-consuming to process, and the overwhelming scale of data makes it difficult to parse overall behaviors. This problem calls for an analysis technique that can quickly provide an overview of the groups present in the entire system and also produce meaningful categorization of cell behaviors. Here, we demonstrate the application of an unsupervised method-the Variational Autoencoder (VAE)-to learn the features of cells in cartilage tissue after impact-induced injury and identify meaningful clusters of chondrocyte behavior. This technique quickly generated new insights into the spatial distribution of specific cell behavior phenotypes and connected specific peracute calcium signaling timeseries with long term cellular outcomes, demonstrating the value of the VAE technique.

The immune landscape of sepsis and using immune clusters for identifying sepsis endotypes.

Background: The dysregulated immune response to sepsis still remains unclear. Stratification of sepsis patients into endotypes based on immune indicators is important for the future development of personalized therapies. We aimed to evaluate the immune landscape of sepsis and the use of immune clusters for identifying sepsis endotypes. Methods: The indicators involved in innate, cellular, and humoral immune cells, inhibitory immune cells, and cytokines were simultaneously assessed in 90 sepsis patients and 40 healthy controls. Unsupervised k-means cluster analysis of immune indicator data were used to identify patient clusters, and a random forest approach was used to build a prediction model for classifying sepsis endotypes. Results: We depicted that the impairment of innate and adaptive immunity accompanying increased inflammation was the most prominent feature in patients with sepsis. However, using immune indicators for distinguishing sepsis from bacteremia was difficult, most likely due to the considerable heterogeneity in sepsis patients. Cluster analysis of sepsis patients identified three immune clusters with different survival rates. Cluster 1 (36.7%) could be distinguished from the other clusters as being an "effector-type" cluster, whereas cluster 2 (34.4%) was a "potential-type" cluster, and cluster 3 (28.9%) was a "dysregulation-type" cluster, which showed the lowest survival rate. In addition, we established a prediction model based on immune indicator data, which accurately classified sepsis patients into three immune endotypes. Conclusion: We depicted the immune landscape of patients with sepsis and identified three distinct immune endotypes with different survival rates. Cluster membership could be predicted with a model based on immune data.

Learning Consistency and Specificity of Cells From Single-Cell Multi-Omic Data.

Advancements in single-cell technologies concomitantly develop the epigenomic and transcriptomic profiles at the cell levels, providing opportunities to explore the potential biological mechanisms. Even though significant efforts have been dedicated to them, it remains challenging for the integration analysis of multi-omic data of single-cell because of the heterogeneity, complicated coupling and interpretability of data. To handle these issues, we propose a novel self-representation Learning-based Multi-omics data Integrative Clustering algorithm (sLMIC) for the integration of single-cell epigenomic profiles (DNA methylation or scATAC-seq) and transcriptomic (scRNA-seq), which the consistent and specific features of cells are explicitly extracted facilitating the cell clustering. Specifically, sLMIC constructs a graph for each type of single-cell data, thereby transforming omics data into multi-layer networks, which effectively removes heterogeneity of omic data. Then, sLMIC employs the low-rank and exclusivity constraints to separate the self-representation of cells into two parts, i.e., the shared and specific features, which explicitly characterize the consistency and diversity of omic data, providing an effective strategy to model the structure of cell types. Feature extraction and cell clustering are jointly formulated as an overall objective function, where latent features of data are obtained under the guidance of cell clustering. The extensive experimental results on 13 multi-omics datasets of single-cell from diverse organisms and tissues indicate that sLMIC observably exceeds the advanced algorithms regarding various measurements.

Investigating oral somatosensory perception and oral symptoms of head and neck cancer patients: insights on eating behaviour.

PURPOSE: Sensory alterations and oral manifestations are prevalent among head and neck cancer (HNC) patients. While taste and smell alterations have been thoroughly investigated, studies on their oral somatosensory perception remain limited. Building upon our previous publication that primarily focused on objective somatosensory measurements, the present work examined self-reported sensory perception, including somatosensation and oral symptoms, in HNC patients and evaluated their link with eating behaviour. METHODS: A cross-sectional study was conducted using self-reported questionnaires on sensory perception, oral symptoms, sensory-related food preference, and eating behaviour among HNC patients (n = 30). Hierarchical clustering analysis was performed to categorise patients based on their sensory perception. Correlations between oral symptoms score, sensory perception, sensory-related food preference, and eating behaviour were explored. RESULTS: Two distinct sensory profiles of patients were identified: no alteration (n = 14) and alteration (n = 16) group. The alteration group showed decreased preference towards several sensory modalities, especially the somatosensory. Concerning eating behaviour, more patients in the alteration group agreed to negatively connotated statements (e.g. having food aversion and eating smaller portions), demonstrating greater eating difficulties. In addition, several oral symptoms related to salivary dysfunction were reported. These oral symptoms were correlated with sensory perception, sensory-related food preference, and eating behaviour. CONCLUSION: This study presented evidence demonstrating that sensory alterations in HNC patients are not limited to taste and smell but cover somatosensory perception and are linked to various aspects of eating. Moreover, patients reported experiencing several oral symptoms. Those with sensory alterations and oral symptoms experienced more eating difficulties.

An inversion-based clustering approach for complex clusters.

BACKGROUND: The choice of an appropriate similarity measure plays a pivotal role in the effectiveness of clustering algorithms. However, many conventional measures rely solely on feature values to evaluate the similarity between objects to be clustered. Furthermore, the assumption of feature independence, while valid in certain scenarios, does not hold true for all real-world problems. Hence, considering alternative similarity measures that account for inter-dependencies among features can enhance the effectiveness of clustering in various applications. METHODS: In this paper, we present the Inv measure, a novel similarity measure founded on the concept of inversion. The Inv measure considers the significance of features, the values of all object features, and the feature values of other objects, leading to a comprehensive and precise evaluation of similarity. To assess the performance of our proposed clustering approach that incorporates the Inv measure, we evaluate it on simulated data using the adjusted Rand index. RESULTS: The simulation results strongly indicate that inversion-based clustering outperforms other methods in scenarios where clusters are complex, i.e., apparently highly overlapped. This showcases the practicality and effectiveness of the proposed approach, making it a valuable choice for applications that involve complex clusters across various domains. CONCLUSIONS: The inversion-based clustering approach may hold significant value in the healthcare industry, offering possible benefits in tasks like hospital ranking, treatment improvement, and high-risk patient identification. In social media analysis, it may prove valuable for trend detection, sentiment analysis, and user profiling. E-commerce may be able to utilize the approach for product recommendation and customer segmentation. The manufacturing sector may benefit from improved quality control, process optimization, and predictive maintenance. Additionally, the approach may be applied to traffic management and fleet optimization in the transportation domain. Its versatility and effectiveness make it a promising solution for diverse fields, providing valuable insights and optimization opportunities for complex and dynamic data analysis tasks.

Lung cancer clustering by identification of similarities and discrepancies of DNA copy numbers using maximal information coefficient.

Lung cancer is the second most diagnosed cancer and the first cause of cancer related death for men and women in the United States. Early detection is essential as patient survival is not optimal and recurrence rate is high. Copy number (CN) changes in cancer populations have been broadly investigated to identify CN gains and deletions associated with the cancer. In this research, the similarities between cancer and paired peripheral blood samples are identified using maximal information coefficient (MIC) and the spatial locations with substantially high MIC scores in each chromosome are used for clustering analysis. The results showed that a sizable reduction of feature set can be obtained using only a subset of locations with high MIC values. The clustering performance was evaluated using both true rate and normalized mutual information (NMI). Clustering results using the reduced feature set outperformed the performance of clustering using entire feature set in several chromosomes that are highly associated with lung cancer with several identified oncogenes.

Wildfires and climate justice: future wildfire events predicted to disproportionally impact socioeconomically vulnerable communities in North Carolina.

Wildfire events are becoming increasingly common across many areas of the United States, including North Carolina (NC). Wildfires can cause immediate damage to properties, and wildfire smoke conditions can harm the overall health of exposed communities. It is critical to identify communities at increased risk of wildfire events, particularly in areas with that have sociodemographic disparities and low socioeconomic status (SES) that may exacerbate incurred impacts of wildfire events. This study set out to: (1) characterize the distribution of wildfire risk across NC; (2) implement integrative cluster analyses to identify regions that contain communities with increased vulnerability to the impacts of wildfire events due to sociodemographic characteristics; (3) provide summary-level statistics of populations with highest wildfire risk, highlighting SES and housing cost factors; and (4) disseminate wildfire risk information via our online web application, ENVIROSCAN. Wildfire hazard potential (WHP) indices were organized at the census tract-level, and distributions were analyzed for spatial autocorrelation via global and local Moran's tests. Sociodemographic characteristics were analyzed via k-means analysis to identify clusters with distinct SES patterns to characterize regions of similar sociodemographic/socioeconomic disparities. These SES groupings were overlayed with housing and wildfire risk profiles to establish patterns of risk across NC. Resulting geospatial analyses identified areas largely in Southeastern NC with high risk of wildfires that were significantly correlated with neighboring regions with high WHP, highlighting adjacent regions of high risk for future wildfire events. Cluster-based analysis of SES factors resulted in three groups of regions categorized through distinct SES profiling; two of these clusters (Clusters 2 and 3) contained indicators of high SES vulnerability. Cluster 2 contained a higher percentage of younger (<5 years), non-white, Hispanic and/or Latino residents; while Cluster 3 had the highest mean WHP and was characterized by a higher percentage of non-white residents, poverty, and less than a high school education. Counties of particular SES and WHP-combined vulnerability include those with majority non-white residents, tribal communities, and below poverty level households largely located in Southeastern NC. WHP values per census tract were dispersed to the public via the ENVIROSCAN application, alongside other environmentally-relevant data.

Comprehensive analysis of human monocyte subsets using full-spectrum flow cytometry and hierarchical marker clustering.

Introduction: Exploring monocytes' roles within the tumor microenvironment is crucial for crafting targeted cancer treatments. Methods: This study unveils a novel methodology utilizing four 20-color flow cytometry panels for comprehensive peripheral immune system phenotyping, specifically targeting classical, intermediate, and non-classical monocyte subsets. Results: By applying advanced dimensionality reduction techniques like t-distributed stochastic neighbor embedding (tSNE) and FlowSom analysis, we performed an extensive profiling of monocytes, assessing 50 unique cell surface markers related to a wide range of immunological functions, including activation, differentiation, and immune checkpoint regulation. Discussion: This in-depth approach significantly refines the identification of monocyte subsets, directly supporting the development of personalized immunotherapies and enhancing diagnostic precision. Our pioneering panel for monocyte phenotyping marks a substantial leap in understanding monocyte biology, with profound implications for the accuracy of disease diagnostics and the success of checkpoint-inhibitor therapies. Key findings include revealing distinct marker expression patterns linked to tumor progression and providing new avenues for targeted therapeutic interventions.

High-risk space-time clusters of mortality in children 5 to 14 years of age in Mato Grosso state, Brazil. / Clusters Espaço-Temporais de Alto Risco da Mortalidade Infantojuvenil em Mato Grosso, Brasil.

The study aimed to detect high-risk areas for deaths of children and adolescents 5 to 14 years of age in the state of Mato Grosso, Brazil, from 2009 to 2020. This was an exploratory ecological study with municipalities as the units of analysis. Considering mortality data from the Mortality Information System (SIM) and demographic data from the Brazilian Institute of Geography and Statistics (IBGE), the study used multivariate statistics to identify space-time clusters of excess mortality risk in this age group. From 5 to 9 years of age, two clusters with high mortality risk were detected; the most likely located in the state's southern mesoregion (RR: 1.6; LRT: 8,53). Among the 5 clusters detected in the 10-14-year age group, the main cluster was in the state's northern mesoregion (RR: 2,26; LRT: 7,84). A reduction in mortality rates was observed in the younger age group and an increase in these rates in the older group. The identification of these clusters, whose analysis merits replication in other parts of Brazil, is the initial stage in the investigation of possible factors associated with morbidity and mortality in this group, still insufficiently explored, and for planning adequate interventions.

O objetivo deste estudo é detectar as áreas de maior risco para óbitos de crianças e adolescentes de 5 a 14 anos no estado de Mato Grosso entre os anos de 2009 e 2020. Estudo ecológico, tipo exploratório, cuja unidade de análise foram os municípios. Considerando dados de mortalidade do SIM e os demográficos do IBGE, o estudo utilizou a estatística multivariada para a identificação dos clusters espaço-temporais de sobrerrisco de mortalidade nesta faixa etária. Dos 5 aos 9 anos, dois clusters de alto risco de mortalidade foram detectados; o mais provável localizado na mesorregião sul (RR: 1,6; LRV: 8,53). Dentre os 5 clusters detectados na faixa etária dos 10 aos 14 anos, o principal foi localizado na mesorregião norte (RR: 2,26; LRV: 7,84). Foi identificada redução das taxas de mortalidade na faixa etária mais jovem e aumento destas taxas na faixa etária mais velha. A identificação destes clusters, cuja análise merece ser replicada a outras partes do território nacional, é a etapa inicial para a investigação de possíveis fatores associados à morbi-mortalidade deste grupo ainda pouco explorado e para o planejamento de intervenções adequadas.

Evaluation of a walking school bus program: a cluster randomized controlled trial.

BACKGROUND: The purpose of this study was to investigate the effects of a walking school bus intervention on children's active commuting to school. METHODS: We conducted a randomized controlled trial (RCT) in Houston, Texas (Year 1) and Seattle, Washington (Years 2-4) from 2012 to 2016. The study had a two-arm, cluster randomized design comparing the intervention (walking school bus and education materials) to the control (education materials) over one school year October/November - May/June). Twenty-two schools that served lower income families participated. Outcomes included percentage of days students' active commuting to school (primary, measured via survey) and moderate-to-vigorous physical activity (MVPA, measured via accelerometry). Follow-up took place in May or June. We used linear mixed-effects models to estimate the association between the intervention and outcomes of interest. RESULTS: Total sample was 418 students [Mage=9.2 (SD = 0.9) years; 46% female], 197 (47%) in the intervention group. The intervention group showed a significant increase compared with the control group over time in percentage of days active commuting (ß = 9.04; 95% CI: 1.10, 16.98; p = 0.015) and MVPA minutes/day (ß = 4.31; 95% CI: 0.70, 7.91; p = 0.02). CONCLUSIONS: These findings support implementation of walking school bus programs that are inclusive of school-age children from lower income families to support active commuting to school and improve physical activity. TRAIL REGISTRATION: This RCT is registered at clinicaltrials.gov (NCT01626807).

Exploring the mystery of colon cancer from the perspective of molecular subtypes and treatment.

The molecular categorization of colon cancer patients remains elusive. Gene set enrichment analysis (GSEA), which investigates the dysregulated genes among tumor and normal samples, has revealed the pivotal role of epithelial-to-mesenchymal transition (EMT) in colon cancer pathogenesis. In this study, we employed multi-clustering method for grouping data, resulting in the identification of two clusters characterized by varying prognostic outcomes. These two subgroups not only displayed disparities in overall survival (OS) but also manifested variations in clinical variables, genetic mutation, and gene expression profiles. Using the nearest template prediction (NTP) method, we were able to replicate the molecular classification effectively within the original dataset and validated it across multiple independent datasets, underscoring its robust repeatability. Furthermore, we constructed two prognostic signatures tailored to each of these subgroups. Our molecular classification, centered on EMT, hold promise in offering fresh insights into the therapy strategies and prognosis assessment for colon cancer.

Unsupervised machine learning for clustering forward head posture, protraction and retraction movement patterns based on craniocervical angle data in individuals with nonspecific neck pain.

OBJECTIVES: The traditional understanding of craniocervical alignment emphasizes specific anatomical landmarks. However, recent research has challenged the reliance on forward head posture as the primary diagnostic criterion for neck pain. An advanced relationship exists between neck pain and craniocervical alignment, which requires a deeper exploration of diverse postures and movement patterns using advanced techniques, such as clustering analysis. We aimed to explore the complex relationship between craniocervical alignment, and neck pain and to categorize alignment patterns in individuals with nonspecific neck pain using the K-means algorithm. METHODS: This study included 229 office workers with nonspecific neck pain who applied unsupervised machine learning techniques. The craniocervical angles (CCA) during rest, protraction, and retraction were measured using two-dimensional video analysis, and neck pain severity was assessed using the Northwick Park Neck Pain Questionnaire (NPQ). CCA during sitting upright in a comfortable position was assessed to evaluate the resting CCA. The average of midpoints between repeated protraction and retraction measures was considered as the midpoint CCA. The K-means algorithm helped categorize participants into alignment clusters based on age, sex and CCA data. RESULTS: We found no significant correlation between NPQ scores and CCA data, challenging the traditional understanding of neck pain and alignment. We observed a significant difference in age (F = 140.14, p < 0.001), NPQ total score (F = 115.83, p < 0.001), resting CCA (F = 79.22, p < 0.001), CCA during protraction (F = 33.98, p < 0.001), CCA during retraction (F = 40.40, p < 0.001), and midpoint CCA (F = 66.92, p < 0.001) among the three clusters and healthy controls. Cluster 1 was characterized by the lowest resting and midpoint CCA, and CCA during pro- and -retraction, indicating a significant forward head posture and a pattern of retraction restriction. Cluster 2, the oldest group, showed CCA measurements similar to healthy controls, yet reported the highest NPQ scores. Cluster 3 exhibited the highest CCA during protraction and retraction, suggesting a limitation in protraction movement. DISCUSSION: Analyzing 229 office workers, three distinct alignment patterns were identified, each with unique postural characteristics; therefore, treatments addressing posture should be individualized and not generalized across the population.

Identification of inflammatory clusters in long-COVID through analysis of plasma biomarker levels.

Mechanisms underlying long COVID remain poorly understood. Patterns of immunological responses in individuals with long COVID may provide insight into clinical phenotypes. Here we aimed to identify these immunological patterns and study the inflammatory processes ongoing in individuals with long COVID. We applied an unsupervised hierarchical clustering approach to analyze plasma levels of 42 biomarkers measured in individuals with long COVID. Logistic regression models were used to explore associations between biomarker clusters, clinical variables, and symptom phenotypes. In 101 individuals, we identified three inflammatory clusters: a limited immune activation cluster, an innate immune activation cluster, and a systemic immune activation cluster. Membership in these inflammatory clusters did not correlate with individual symptoms or symptom phenotypes, but was associated with clinical variables including age, BMI, and vaccination status. Differences in serologic responses between clusters were also observed. Our results indicate that clinical variables of individuals with long COVID are associated with their inflammatory profiles and can provide insight into the ongoing immune responses.

Temporal change in multimorbidity prevalence, clustering patterns, and the association with mortality: findings from the China Kadoorie Biobank study in Jiangsu Province.

Objectives: The characteristics of multimorbidity in the Chinese population are currently unclear. We aimed to determine the temporal change in multimorbidity prevalence, clustering patterns, and the association of multimorbidity with mortality from all causes and four major chronic diseases. Methods: This study analyzed data from the China Kadoorie Biobank study performed in Wuzhong District, Jiangsu Province. A total of 53,269 participants aged 30-79 years were recruited between 2004 and 2008. New diagnoses of 15 chronic diseases and death events were collected during the mean follow-up of 10.9 years. Yule's Q cluster analysis method was used to determine the clustering patterns of multimorbidity. A Cox proportional hazards model was used to estimate the associations of multimorbidity with mortalities. Results: The overall multimorbidity prevalence rate was 21.1% at baseline and 27.7% at the end of follow-up. Multimorbidity increased more rapidly during the follow-up in individuals who had a higher risk at baseline. Three main multimorbidity patterns were identified: (i) cardiometabolic multimorbidity (diabetes, coronary heart disease, stroke, and hypertension), (ii) respiratory multimorbidity (tuberculosis, asthma, and chronic obstructive pulmonary disease), and (iii) mental, kidney and arthritis multimorbidity (neurasthenia, psychiatric disorders, chronic kidney disease, and rheumatoid arthritis). There were 3,433 deaths during the follow-up. The mortality risk increased by 24% with each additional disease [hazard ratio (HR) = 1.24, 95% confidence interval (CI) = 1.20-1.29]. Compared with those without multimorbidity at baseline, both cardiometabolic multimorbidity and respiratory multimorbidity were associated with increased mortality from all causes and four major chronic diseases. Cardiometabolic multimorbidity was additionally associated with mortality from cardiovascular diseases and diabetes, with HRs of 2.64 (95% CI = 2.19-3.19) and 28.19 (95% CI = 14.85-53.51), respectively. Respiratory multimorbidity was associated with respiratory disease mortality, with an HR of 9.76 (95% CI = 6.22-15.31). Conclusion: The prevalence of multimorbidity has increased substantially over the past decade. This study has revealed that cardiometabolic multimorbidity and respiratory multimorbidity have significantly increased mortality rates. These findings indicate the need to consider high-risk populations and to provide local evidence for intervention strategies and health management in economically developed regions.

Unveiling Trichosporon austroamericanum sp. nov.: A Novel Emerging Opportunistic Basidiomycetous Yeast Species.

During an epidemiological survey, a potential novel species within the basidiomycetous yeast genus Trichosporon was observed. The clinical strain was obtained from a urine sample taken from a Brazilian kidney transplant recipient. The strain was molecularly identified using the intergenic spacer (IGS1) ribosomal DNA locus and a subsequent phylogenetic analysis showed that multiple strains that were previously reported by other studies shared an identical IGS1-genotype most closely related to that of Trichosporon inkin. However, none of these studies provided an in-depth characterization of the involved strains to describe it as a new taxon. Here, we present the novel clinically relevant yeast for which we propose the name Trichosporon austroamericanum sp. nov. (holotype CBS H-24937). T. austroamericanum can be distinguished from other siblings in the genus Trichosporon using morphological, physiological, and phylogenetic characters.

COVID-19 patient profiles over four waves in Barcelona metropolitan area: A clustering approach.

OBJECTIVES: Identifying profiles of hospitalized COVID-19 patients and explore their association with different degrees of severity of COVID-19 outcomes (i.e. in-hospital mortality, ICU assistance, and invasive mechanical ventilation). The findings of this study could inform the development of multiple care intervention strategies to improve patient outcomes. METHODS: Prospective multicentre cohort study during four different waves of COVID-19 from March 1st, 2020 to August 31st, 2021 in four health consortiums within the southern Barcelona metropolitan region. From a starting point of over 292 demographic characteristics, comorbidities, vital signs, severity scores, and clinical analytics at hospital admission, we used both clinical judgment and supervised statistical methods to reduce to the 36 most informative completed covariates according to the disease outcomes for each wave. Patients were then grouped using an unsupervised semiparametric method (KAMILA). Results were interpreted by clinical and statistician team consensus to identify clinically-meaningful patient profiles. RESULTS: The analysis included nw1 = 1657, nw2 = 697, nw3 = 677, and nw4 = 787 hospitalized-COVID-19 patients for each of the four waves. Clustering analysis identified 2 patient profiles for waves 1 and 3, while 3 profiles were determined for waves 2 and 4. Patients allocated in those groups showed a different percentage of disease outcomes (e.g., wave 1: 15.9% (Cluster 1) vs. 31.8% (Cluster 2) for in-hospital mortality rate). The main factors to determine groups were the patient's age and number of obese patients, number of comorbidities, oxygen support requirement, and various severity scores. The last wave is also influenced by the massive incorporation of COVID-19 vaccines. CONCLUSION: Our study suggests that a single care model at hospital admission may not meet the needs of hospitalized-COVID-19 adults. A clustering approach appears to be appropriate for helping physicians to differentiate patients and, thus, apply multiple care intervention strategies, as another way of responding to new outbreaks of this or future diseases.

Patterns of cognitive-emotional change after cognitive-behavioural treatment in emotional disorders: A 12-month longitudinal cluster analysis.

INTRODUCTION: The aim of this study was to use cluster analysis based on the trajectory of five cognitive-emotional processes (worry, rumination, metacognition, cognitive reappraisal and expressive suppression) over time to explore differences in clinical and performance variables in primary care patients with emotional symptoms. METHODS: We compared the effect of adding transdiagnostic cognitive-behavioural therapy (TD-CBT) to treatment as usual (TAU) according to cluster membership and sought to determine the variables that predicted cluster membership. 732 participants completed scales about cognitive-emotional processes, anxiety and depressive symptoms, functioning, and quality of life (QoL) at baseline, posttreatment, and at 12 months. Longitudinal cluster analysis and logistic regression analyses were carried out. RESULTS: A two-cluster solution was chosen as the best fit, named as "less" or "more" improvement in cognitive-emotional processes. Individuals who achieved more improvement in cognitive-emotional processes showed lower emotional symptoms and better QoL and functioning at all three time points. TAU+TD-CBT, income level, QoL and anxiety symptoms were significant predictors of cluster membership. CONCLUSIONS: These results underscore the value of adding TD-CBT to reduce maladaptive cognitive-emotional regulation strategies. These findings highlight the importance of the processes of change in therapy and demonstrate the relevance of the patient's cognitive-emotional profile in improving treatment outcomes.

Clustering of health behaviors and their associations with cardiometabolic risk factors among adults at high risk for type 2 diabetes in India: A latent class analysis.

BACKGROUND: We aimed to identify clusters of health behaviors and study their associations with cardiometabolic risk factors in adults at high risk for type 2 diabetes in India. METHODS: Baseline data from the Kerala Diabetes Prevention Program (n = 1000; age 30-60 years) were used for this study. Information on physical activity (PA), sedentary behavior, fruit and vegetable intake, sleep, and alcohol and tobacco use was collected using questionnaires. Blood pressure, waist circumference, 2-h plasma glucose, high-density lipoprotein and low-density lipoprotein cholesterol, and triglycerides were measured using standardized protocols. Latent class analysis was used to identify clusters of health behaviors, and multilevel mixed-effects linear regression was employed to examine their associations with cardiometabolic risk factors. RESULTS: Two classes were identified, with 87.4% of participants in class 1 and 12.6% in class 2. Participants in both classes had a high probability of not engaging in leisure-time PA (0.80 for class 1; 0.73 for class 2) and consuming <5 servings of fruit and vegetables per day (0.70 for class 1; 0.63 for class 2). However, participants in class 1 had a lower probability of sitting for >=3 h per day (0.26 vs 0.42), tobacco use (0.10 vs 0.75), and alcohol use (0.08 vs 1.00) compared to those in class 2. Class 1 had a significantly lower mean systolic blood pressure (ß = -3.70 mm Hg, 95% confidence interval [CI] -7.05, -0.36), diastolic blood pressure (ß = -2.45 mm Hg, 95% CI -4.74, -0.16), and triglycerides (ß = -0.81 mg/dL, 95% CI -0.75, -0.89). CONCLUSION: Implementing intervention strategies, tailored to cluster-specific health behaviors, is required for the effective prevention of cardiometabolic disorders among high-risk adults for type 2 diabetes.

Energy landscape analysis and time-series clustering analysis of patient state multistability related to rheumatoid arthritis drug treatment: The KURAMA cohort study.

Rheumatoid arthritis causes joint inflammation due to immune abnormalities, resulting in joint pain and swelling. In recent years, there have been considerable advancements in the treatment of this disease. However, only approximately 60% of patients achieve remission. Patients with multifactorial diseases shift between states from day to day. Patients may remain in a good or poor state with few or no transitions, or they may switch between states frequently. The visualization of time-dependent state transitions, based on the evaluation axis of stable/unstable states, may provide useful information for achieving rheumatoid arthritis treatment goals. Energy landscape analysis can be used to quantitatively determine the stability/instability of each state in terms of energy. Time-series clustering is another method used to classify transitions into different groups to identify potential patterns within a time-series dataset. The objective of this study was to utilize energy landscape analysis and time-series clustering to evaluate multidimensional time-series data in terms of multistability. We profiled each patient's state transitions during treatment using energy landscape analysis and time-series clustering. Energy landscape analysis divided state transitions into two patterns: "good stability leading to remission" and "poor stability leading to treatment dead-end." The number of patients whose disease status improved increased markedly until approximately 6 months after treatment initiation and then plateaued after 1 year. Time-series clustering grouped patients into three clusters: "toward good stability," "toward poor stability," and "unstable." Patients in the "unstable" cluster are considered to have clinical courses that are difficult to predict; therefore, these patients should be treated with more care. Early disease detection and treatment initiation are important. The evaluation of state multistability enables us to understand a patient's current state in the context of overall state transitions related to rheumatoid arthritis drug treatment and to predict future state transitions.

Biclustering analysis on tree-shaped time-series single cell gene expression data of Caenorhabditis elegans.

BACKGROUND: In recent years, gene clustering analysis has become a widely used tool for studying gene functions, efficiently categorizing genes with similar expression patterns to aid in identifying gene functions. Caenorhabditis elegans is commonly used in embryonic research due to its consistent cell lineage from fertilized egg to adulthood. Biologists use 4D confocal imaging to observe gene expression dynamics at the single-cell level. However, on one hand, the observed tree-shaped time-series datasets have characteristics such as non-pairwise data points between different individuals. On the other hand, the influence of cell type heterogeneity should also be considered during clustering, aiming to obtain more biologically significant clustering results. RESULTS: A biclustering model is proposed for tree-shaped single-cell gene expression data of Caenorhabditis elegans. Detailedly, a tree-shaped piecewise polynomial function is first employed to fit non-pairwise gene expression time series data. Then, four factors are considered in the objective function, including Pearson correlation coefficients capturing gene correlations, p-values from the Kolmogorov-Smirnov test measuring the similarity between cells, as well as gene expression size and bicluster overlapping size. After that, Genetic Algorithm is utilized to optimize the function. CONCLUSION: The results on the small-scale dataset analysis validate the feasibility and effectiveness of our model and are superior to existing classical biclustering models. Besides, gene enrichment analysis is employed to assess the results on the complete real dataset analysis, confirming that the discovered biclustering results hold significant biological relevance.