Effects of spatial variability in vegetation phenology, climate, landcover, biodiversity, topography, and soil property on soil respiration across a coastal ecosystem.

Coastal terrestrial-aquatic interfaces (TAIs) are crucial contributors to global biogeochemical cycles and carbon exchange. The soil carbon dioxide (CO2) efflux in these transition zones is however poorly understood due to the high spatiotemporal dynamics of TAIs, as various sub-ecosystems in this region are compressed and expanded by complex influences of tides, changes in river levels, climate, and land use. We focus on the Chesapeake Bay region to (i) investigate the spatial heterogeneity of the coastal ecosystem and identify spatial zones with similar environmental characteristics based on the spatial data layers, including vegetation phenology, climate, landcover, diversity, topography, soil property, and relative tidal elevation; (ii) understand the primary driving factors affecting soil respiration within sub-ecosystems of the coastal ecosystem. Specifically, we employed hierarchical clustering analysis to identify spatial regions with distinct environmental characteristics, followed by the determination of main driving factors using Random Forest regression and SHapley Additive exPlanations. Maximum and minimum temperature are the main drivers common to all sub-ecosystems, while each region also has additional unique major drivers that differentiate them from one another. Precipitation exerts an influence on vegetated lands, while soil pH value holds importance specifically in forested lands. In croplands characterized by high clay content and low sand content, the significant role is attributed to bulk density. Wetlands demonstrate the importance of both elevation and sand content, with clay content being more relevant in non-inundated wetlands than in inundated wetlands. The topographic wetness index significantly contributes to the mixed vegetation areas, including shrub, grass, pasture, and forest. Additionally, our research reveals that dense vegetation land covers and urban/developed areas exhibit distinct soil property drivers. Overall, our research demonstrates an efficient method of employing various open-source remote sensing and GIS datasets to comprehend the spatial variability and soil respiration mechanisms in coastal TAI. There is no one-size-fits-all approach to modeling carbon fluxes released by soil respiration in coastal TAIs, and our study highlights the importance of further research and monitoring practices to improve our understanding of carbon dynamics and promote the sustainable management of coastal TAIs.

Passive eDNA sampling facilitates biodiversity monitoring and rare species detection.

Environmental DNA (eDNA) technology has revolutionized biomonitoring, but challenges remain regarding water sample processing. The passive eDNA sampler (PEDS) represents a viable alternative to active, water filtration-based eDNA enrichment methods, but the effectiveness of PEDS for surveying biodiverse and complex natural water bodies is unknown. Here, we collected eDNA using filtration and glass fiber filter-based PEDS (submerged in water for 1 d) from 27 sites along the final reach of the Yangtze River and the coast of the Yellow Sea, followed by eDNA metabarcoding analysis of fish biodiversity and quantitative PCR (qPCR) for a critically endangered aquatic mammal, the Yangtze finless porpoise. We ultimately detected 98 fish species via eDNA metabarcoding. Both eDNA sampling methods captured comparable local species richness and revealed largely similar spatial variation in fish assemblages and community partitions between the river and sea sites. Notably, the Yangtze finless porpoise was detected only in the metabarcoding of eDNA collected by PEDS at five sites. Also, species-specific qPCR revealed that the PEDS captured porpoise eDNA at more sites (7 vs. 2), in greater quantities, and with a higher detection probability (0.803 vs. 0.407) than did filtration. Our results demonstrate the capacity of PEDS for surveying fish biodiversity, and support that continuous eDNA collection by PEDS can be more effective than instantaneous water sampling at capturing low abundance and ephemeral species in natural waters. Thus, the PEDS approach can facilitate more efficient and convenient eDNA-based biodiversity surveillance and rare species detection.

Yclon: Ultrafast clustering of B cell clones from high-throughput immunoglobulin repertoire sequencing data.

MOTIVATION: The next-generation sequencing technologies have transformed our understanding of immunoglobulin (Ig) profiles in various immune states. Clonotyping, which groups Ig sequences into B cell clones, is crucial in investigating the diversity of repertoires and changes in antigen exposure. Despite its importance, there is no widely accepted method for clonotyping, and existing methods are computationally intensive for large sequencing datasets. RESULTS: To address this challenge, we introduce YClon, a fast and efficient approach for clonotyping Ig repertoire data. YClon uses a hierarchical clustering approach, similar to other methods, to group Ig sequences into B cell clones in a highly sensitive and specific manner. Notably, our approach outperforms other methods by being more than 30 to 5000 times faster in processing the repertoires analyzed. Astonishingly, YClon can effortlessly handle up to 2 million Ig sequences on a standard laptop computer. This enables in-depth analysis of large and numerous antibody repertoires. AVAILABILITY AND IMPLEMENTATION: YClon was implemented in Python3 and is freely available on GitHub.

Developing a cluster-based approach for deciphering complexity in individuals with neurodevelopmental differences.

Objective: Individuals with neurodevelopmental disorders such as global developmental delay (GDD) present both genotypic and phenotypic heterogeneity. This diversity has hampered developing of targeted interventions given the relative rarity of each individual genetic etiology. Novel approaches to clinical trials where distinct, but related diseases can be treated by a common drug, known as basket trials, which have shown benefits in oncology but have yet to be used in GDD. Nonetheless, it remains unclear how individuals with GDD could be clustered. Here, we assess two different approaches: agglomerative and divisive clustering. Methods: Using the largest cohort of individuals with GDD, which is the Deciphering Developmental Disorders (DDD), characterized using a systematic approach, we extracted genotypic and phenotypic information from 6,588 individuals with GDD. We then used a k-means clustering (divisive) and hierarchical agglomerative clustering (HAC) to identify subgroups of individuals. Next, we extracted gene network and molecular function information with regard to the clusters identified by each approach. Results: HAC based on phenotypes identified in individuals with GDD revealed 16 clusters, each presenting with one dominant phenotype displayed by most individuals in the cluster, along with other minor phenotypes. Among the most common phenotypes reported were delayed speech, absent speech, and seizure. Interestingly, each phenotypic cluster molecularly included several (3-12) gene sub-networks of more closely related genes with diverse molecular function. k-means clustering also segregated individuals harboring those phenotypes, but the genetic pathways identified were different from the ones identified from HAC. Conclusion: Our study illustrates how divisive (k-means) and agglomerative clustering can be used in order to group individuals with GDD for future basket trials. Moreover, the result of our analysis suggests that phenotypic clusters should be subdivided into molecular sub-networks for an increased likelihood of successful treatment. Finally, a combination of both agglomerative and divisive clustering may be required for developing of a comprehensive treatment.

Data-driven studies in face identity processing rely on the quality of the tests and data sets.

There is growing interest in how data-driven approaches can help understand individual differences in face identity processing (FIP). However, researchers employ various FIP tests interchangeably, and it is unclear whether these tests 1) measure the same underlying ability/ies and processes (e.g., confirmation of identity match or elimination of identity match) 2) are reliable, 3) provide consistent performance for individuals across tests online and in laboratory. Together these factors would influence the outcomes of data-driven analyses. Here, we asked 211 participants to perform eight tests frequently reported in the literature. We used Principal Component Analysis and Agglomerative Clustering to determine factors underpinning performance. Importantly, we examined the reliability of these tests, relationships between them, and quantified participant consistency across tests. Our findings show that participants' performance can be split into two factors (called here confirmation and elimination of an identity match) and that participants cluster according to whether they are strong on one of the factors or equally on both. We found that the reliability of these tests is at best moderate, the correlations between them are weak, and that the consistency in participant performance across tests and is low. Developing reliable and valid measures of FIP and consistently scrutinising existing ones will be key for drawing meaningful conclusions from data-driven studies.

Automatic generation of pseudoknotted RNAs taxonomy.

BACKGROUND: The ability to compare RNA secondary structures is important in understanding their biological function and for grouping similar organisms into families by looking at evolutionarily conserved sequences such as 16S rRNA. Most comparison methods and benchmarks in the literature focus on pseudoknot-free structures due to the difficulty of mapping pseudoknots in classical tree representations. Some approaches exist that permit to cluster pseudoknotted RNAs but there is not a general framework for evaluating their performance. RESULTS: We introduce an evaluation framework based on a similarity/dissimilarity measure obtained by a comparison method and agglomerative clustering. Their combination automatically partition a set of molecules into groups. To illustrate the framework we define and make available a benchmark of pseudoknotted (16S and 23S) and pseudoknot-free (5S) rRNA secondary structures belonging to Archaea, Bacteria and Eukaryota. We also consider five different comparison methods from the literature that are able to manage pseudoknots. For each method we clusterize the molecules in the benchmark to obtain the taxa at the rank phylum according to the European Nucleotide Archive curated taxonomy. We compute appropriate metrics for each method and we compare their suitability to reconstruct the taxa.

Definition of High-Risk Motion Patterns for Female ACL Injury Based on Football-Specific Field Data: A Wearable Sensors Plus Data Mining Approach.

The aim of the present study was to investigate if the presence of anterior cruciate ligament (ACL) injury risk factors depicted in the laboratory would reflect at-risk patterns in football-specific field data. Twenty-four female footballers (14.9 ± 0.9 year) performed unanticipated cutting maneuvers in a laboratory setting and on the football pitch during football-specific exercises (F-EX) and games (F-GAME). Knee joint moments were collected in the laboratory and grouped using hierarchical agglomerative clustering. The clusters were used to investigate the kinematics collected on field through wearable sensors. Three clusters emerged: Cluster 1 presented the lowest knee moments; Cluster 2 presented high knee extension but low knee abduction and rotation moments; Cluster 3 presented the highest knee abduction, extension, and external rotation moments. In F-EX, greater knee abduction angles were found in Cluster 2 and 3 compared to Cluster 1 (p = 0.007). Cluster 2 showed the lowest knee and hip flexion angles (p < 0.013). Cluster 3 showed the greatest hip external rotation angles (p = 0.006). In F-GAME, Cluster 3 presented the greatest knee external rotation and lowest knee flexion angles (p = 0.003). Clinically relevant differences towards ACL injury identified in the laboratory reflected at-risk patterns only in part when cutting on the field: in the field, low-risk players exhibited similar kinematic patterns as the high-risk players. Therefore, in-lab injury risk screening may lack ecological validity.

Machine learning identifies pathophysiologically and prognostically informative phenotypes among patients with mitral regurgitation undergoing transcatheter edge-to-edge repair.

AIMS: Patients with mitral regurgitation (MR) present with considerable heterogeneity in cardiac damage depending on underlying aetiology, disease progression, and comorbidities. This study aims to capture their cardiopulmonary complexity by employing a machine-learning (ML)-based phenotyping approach. METHODS AND RESULTS: Data were obtained from 1426 patients undergoing mitral valve transcatheter edge-to-edge repair (MV TEER) for MR. The ML model was developed using 609 patients (derivation cohort) and validated on 817 patients from two external institutions. Phenotyping was based on echocardiographic data, and ML-derived phenotypes were correlated with 5-year outcomes. Unsupervised agglomerative clustering revealed four phenotypes among the derivation cohort: Cluster 1 showed preserved left ventricular ejection fraction (LVEF; 56.5 ± 7.79%) and regular left ventricular end-systolic diameter (LVESD; 35.2 ± 7.52 mm); 5-year survival in Cluster 1, hereinafter serving as a reference, was 60.9%. Cluster 2 presented with preserved LVEF (55.7 ± 7.82%) but showed the largest mitral valve effective regurgitant orifice area (0.623 ± 0.360 cm2) and highest systolic pulmonary artery pressures (68.4 ± 16.2 mmHg); 5-year survival ranged at 43.7% (P-value: 0.032). Cluster 3 was characterized by impaired LVEF (31.0 ± 10.4%) and enlarged LVESD (53.2 ± 10.9 mm); 5-year survival was reduced to 38.3% (P-value: <0.001). The poorest 5-year survival (23.8%; P-value: <0.001) was observed in Cluster 4 with biatrial dilatation (left atrial volume: 312 ± 113 mL; right atrial area: 46.0 ± 8.83 cm2) although LVEF was only slightly reduced (51.5 ± 11.0%). Importantly, the prognostic significance of ML-derived phenotypes was externally confirmed. CONCLUSION: ML-enabled phenotyping captures the complexity of extra-mitral valve cardiac damage, which does not necessarily occur in a sequential fashion. This novel phenotyping approach can refine risk stratification in patients undergoing MV TEER in the future.

PTGAC Model: A machine learning approach for constructing phylogenetic tree to compare protein sequences.

This work proposes a machine learning-based phylogenetic tree generation model based on agglomerative clustering (PTGAC) that compares protein sequences considering all known chemical properties of amino acids. The proposed model can serve as a suitable alternative to the Unweighted Pair Group Method with Arithmetic Mean (UPGMA), which is inherently time-consuming in nature. Initially, principal component analysis (PCA) is used in the proposed scheme to reduce the dimensions of 20 amino acids using seven known chemical characteristics, yielding 20 TP (Total Points) values for each amino acid. The approach of cumulative summing is then used to give a non-degenerate numeric representation of the sequences based on these 20 TP values. A special kind of three-component vector is proposed as a descriptor, which consists of a new type of non-central moment of orders one, two, and three. Subsequently, the proposed model uses Euclidean Distance measures among the descriptors to create a distance matrix. Finally, a phylogenetic tree is constructed using hierarchical agglomerative clustering based on the distance matrix. The results are compared with the UPGMA and other existing methods in terms of the quality and time of constructing the phylogenetic tree. Both qualitative and quantitative analysis are performed as key assessment criteria for analyzing the performance of the proposed model. The qualitative analysis of the phylogenetic tree is performed by considering rationalized perception, while the quantitative analysis is performed based on symmetric distance (SD). On both criteria, the results obtained by the proposed model are more satisfactory than those produced earlier on the same species by other methods. Notably, this method is found to be efficient in terms of both time and space requirements and is capable of dealing with protein sequences of varying lengths.

The Evolution of Artificial Intelligence in Biomedicine: Bibliometric Analysis.

BACKGROUND: The utilization of artificial intelligence (AI) technologies in the biomedical field has attracted increasing attention in recent decades. Studying how past AI technologies have found their way into medicine over time can help to predict which current (and future) AI technologies have the potential to be utilized in medicine in the coming years, thereby providing a helpful reference for future research directions. OBJECTIVE: The aim of this study was to predict the future trend of AI technologies used in different biomedical domains based on past trends of related technologies and biomedical domains. METHODS: We collected a large corpus of articles from the PubMed database pertaining to the intersection of AI and biomedicine. Initially, we attempted to use regression on the extracted keywords alone; however, we found that this approach did not provide sufficient information. Therefore, we propose a method called "background-enhanced prediction" to expand the knowledge utilized by the regression algorithm by incorporating both the keywords and their surrounding context. This method of data construction resulted in improved performance across the six regression models evaluated. Our findings were confirmed through experiments on recurrent prediction and forecasting. RESULTS: In our analysis using background information for prediction, we found that a window size of 3 yielded the best results, outperforming the use of keywords alone. Furthermore, utilizing data only prior to 2017, our regression projections for the period of 2017-2021 exhibited a high coefficient of determination (R2), which reached up to 0.78, demonstrating the effectiveness of our method in predicting long-term trends. Based on the prediction, studies related to proteins and tumors will be pushed out of the top 20 and become replaced by early diagnostics, tomography, and other detection technologies. These are certain areas that are well-suited to incorporate AI technology. Deep learning, machine learning, and neural networks continue to be the dominant AI technologies in biomedical applications. Generative adversarial networks represent an emerging technology with a strong growth trend. CONCLUSIONS: In this study, we explored AI trends in the biomedical field and developed a predictive model to forecast future trends. Our findings were confirmed through experiments on current trends.

Monitoring COVID-19 Cases and Vaccination in Indian States and Union Territories Using Unsupervised Machine Learning Algorithm.

The worldwide spread of the novel coronavirus originating from Wuhan, China led to an ongoing pandemic as COVID-19. The disease being a contagion transmitted rapidly in India through the people having travel histories to the affected countries, and their contacts that tested positive. Millions of people across all states and union territories (UT) were affected leading to serious respiratory illness and deaths. In the present study, two unsupervised clustering algorithms namely k-means clustering and hierarchical agglomerative clustering are applied on the COVID-19 dataset in order to group the Indian states/UTs based on the pandemic effect and the vaccination program from the period of March, 2020 to early June, 2021. The aim of the study is to observe the plight of each state and UT of India combating the novel coronavirus infection and to monitor their vaccination status. The research study will be helpful to the government and to the frontline workers coping to restrict the transmission of the virus in India. Also, the results of the study will provide a source of information for future research regarding the COVID-19 pandemic in India.

PEG-induced physiological drought for screening winter wheat genotypes sensitivity - integrated biochemical and chlorophyll a fluorescence analysis.

This study aimed to screen different winter wheat genotypes at the onset of metabolic changes induced by water deficit to comprehend possible adaptive features of photosynthetic apparatus function and structure to physiological drought. The drought treatment was the most influential variable affecting plant growth and relative water content, and genotype variability determined with what intensity varieties of winter wheat seedlings responded to water deficit. PEG-induced drought, as expected, changed phenomenological energy fluxes and the efficiency with which an electron is transferred to final PSI acceptors. Based on the effect size, fluorescence parameters were grouped to represent photochemical parameters, that is, the donor and acceptor side of PSII (PC1); the thermal phase of the photosynthetic process, or the electron flow around PSI, and the chain of electrons between PSII and PSI (PC2); and phenomenological energy fluxes per cross-section (PC3). Furthermore, four distinct clusters of genotypes were discerned based on their response to imposed physiological drought, and integrated analysis enabled an explanation of their reactions' specificity. The most reliable JIP-test parameters for detecting and comparing the drought impact among tested genotypes were the variable fluorescence at K, L, I step, and PITOT. To conclude, developing and improving screening methods for identifying and evaluating functional relationships of relevant characteristics that are useful for acclimation, acclimatization, and adaptation to different types of drought stress can contribute to the progress in breeding research of winter wheat drought-tolerant lines.

Classification of air quality zones and fine particulate matter sensitive areas by risk assessment approach.

Many studies have shown that fine particulate matter can cause health problems. Thus, effectively controlling fine particulate matter concentration is an important issue around the world. The Taiwan Environmental Protection Administration (TWEPA) divides Taiwan into seven air quality zones based on counties and cities for managing air quality and analyzing pollution transmission. However, this artificial division by administrative areas relatively poorly match natural conditions and topographical and geographic factors and hence poorly represent air quality characteristics. This study proposes an air quality sensitive map analysis framework, which uses hierarchical agglomerative clustering with empirical orthogonal function and analysis of variance methods, to provide more detailed, reasonable, and township-level air quality zones incorporating the different spatial-temporal characteristics over the region. The risk concept is introduced to evaluate PM2.5 risk sensitivity for each administrative district, combining three aspects: hazard (PM2.5 exceedance probability), exposure (population density of sensitive groups), and vulnerability (average wind speed). Considering air quality spatial-temporal characteristics, Taiwan can be optimally divided into 14 air quality zones. PM2.5 risk is highest for western inland towns than western coastal towns, with eastern regions exhibiting least risk. Adopting the proposed air quality zones and clarifying high risk areas allows PM2.5 causes to be identified for different air quality zones. This allows a targeted control strategy for high risk areas to effectively improve domestic air quality. The proposed model also provides powerful reference for environmental management and environmental impact assessment for future construction and development.

Hybrid learning method based on feature clustering and scoring for enhanced COVID-19 breath analysis by an electronic nose.

Breath pattern analysis based on an electronic nose (e-nose), which is a noninvasive, fast, and low-cost method, has been continuously used for detecting human diseases, including the coronavirus disease 2019 (COVID-19). Nevertheless, having big data with several available features is not always beneficial because only a few of them will be relevant and useful to distinguish different breath samples (i.e., positive and negative COVID-19 samples). In this study, we develop a hybrid machine learning-based algorithm combining hierarchical agglomerative clustering analysis and permutation feature importance method to improve the data analysis of a portable e-nose for COVID-19 detection (GeNose C19). Utilizing this learning approach, we can obtain an effective and optimum feature combination, enabling the reduction by half of the number of employed sensors without downgrading the classification model performance. Based on the cross-validation test results on the training data, the hybrid algorithm can result in accuracy, sensitivity, and specificity values of (86 ± 3)%, (88 ± 6)%, and (84 ± 6)%, respectively. Meanwhile, for the testing data, a value of 87% is obtained for all the three metrics. These results exhibit the feasibility of using this hybrid filter-wrapper feature-selection method to pave the way for optimizing the GeNose C19 performance.

Clusters of COVID-19 Indicators in India: Characterization, Correspondence and Change Analysis.

We conduct a long-term epidemiology study of COVID-19 in India from Mar 2020 to May 2021 using a number of indicators such as active cases, daily new cases, and deaths, on a micro (district level, per capita) and macro level (state level). Our automated shape-based cluster discovery of the per capita daily new cases (case rate) during the first wave in India (between Mar 2020 and Jan 2021) revealed four distinct shape patterns: sharp-rise and decline, steady-rise and decline, plateau and multiple relatively high peaks. These clusters exhibit a strong geographical correlation. To determine the correspondence between clusters obtained by different indicators, we design a novel metric for determining edge-weights in their intersection graph. This is used for comparative analysis and to develop informative hierarchical cartographic visualizations. We then perform dynamic cluster analysis for different time windows to answer some pertinent questions. Is the second wave similar to or different from the first wave? How has the relative ranking (on micro- and macro-level indicators) of the states varied over the last one year? How much medical resources have been stressed during the peak? We demonstrate that using multiple indicators, we can assess the impact of the epidemic holistically in a particular geography. Our analysis techniques and insights obtained can help the local and state governments in monitoring and managing COVID-19 situation and fine-tuning the ongoing vaccination drive in India.

Image-level trajectory inference of tau pathology using variational autoencoder for Flortaucipir PET.

PURPOSE: Alzheimer's disease (AD) studies revealed that abnormal deposition of tau spreads in a specific spatial pattern, namely Braak stage. However, Braak staging is based on post mortem brains, each of which represents the cross section of the tau trajectory in disease progression, and numerous studies were reported that do not conform to that model. This study thus aimed to identify the tau trajectory and quantify the tau progression in a data-driven approach with the continuous latent space learned by variational autoencoder (VAE). METHODS: A total of 1080 [18F]Flortaucipir brain positron emission tomography (PET) images were collected from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database. VAE was built to compress the hidden features from tau images in latent space. Hierarchical agglomerative clustering and minimum spanning tree (MST) were applied to organize the features and calibrate them to the tau progression, thus deriving pseudo-time. The image-level tau trajectory was inferred by continuously sampling across the calibrated latent features. We assessed the pseudo-time with regard to tau standardized uptake value ratio (SUVr) in AD-vulnerable regions, amyloid deposit, glucose metabolism, cognitive scores, and clinical diagnosis. RESULTS: We identified four clusters that plausibly capture certain stages of AD and organized the clusters in the latent space. The inferred tau trajectory agreed with the Braak staging. According to the derived pseudo-time, tau first deposits in the parahippocampal and amygdala, and then spreads to the fusiform, inferior temporal lobe, and posterior cingulate. Prior to the regional tau deposition, amyloid accumulates first. CONCLUSION: The spatiotemporal trajectory of tau progression inferred in this study was consistent with Braak staging. The profile of other biomarkers in disease progression agreed well with previous findings. We addressed that this approach additionally has the potential to quantify tau progression as a continuous variable by taking a whole-brain tau image into account.

Automatic Quasi-Clique Merger Algorithm - a Hierarchical Clustering Based on Subgraph-Density.

The Automatic Quasi-clique Merger algorithm is a new algorithm adapted from early work published under the name QCM (introduced by Ou and Zhang in 2007). The AQCM algorithm performs hierarchical clustering in any data set for which there is an associated similarity measure quantifying the similarity of any data i and data j. Importantly, the method exhibits two valuable performance properties: 1) the ability to automatically return either a larger or smaller number of clusters depending on the inherent properties of the data rather than on a parameter. 2) the ability to return a very large number of relatively small clusters automatically when such clusters are reasonably well defined in a data set. In this work we present the general idea of a quasi-clique agglomerative approach, provide the full details of the mathematical steps of the AQCM algorithm, and explain some of the motivation behind the new methodology. The main achievement of the new methodology is that the agglomerative process now unfolds adaptively according to the inherent structure unique to a given data set, and this happens without the time-costly parameter adjustment that drove the previous QCM algorithm. For this reason we call the new algorithm automatic. We provide a demonstration of the algorithm's performance at the task of community detection in a social media network of 22,900 nodes.

A Clustering-Enhanced Memetic Algorithm for the Quadratic Minimum Spanning Tree Problem.

The quadratic minimum spanning tree problem (QMSTP) is a spanning tree optimization problem that considers the interaction cost between pairs of edges arising from a number of practical scenarios. This problem is NP-hard, and therefore there is not a known polynomial time approach to solve it. To find a close-to-optimal solution to the problem in a reasonable time, we present for the first time a clustering-enhanced memetic algorithm (CMA) that combines four components, i.e., (i) population initialization with clustering mechanism, (ii) a tabu-based nearby exploration phase to search nearby local optima in a restricted area, (iii) a three-parent combination operator to generate promising offspring solutions, and (iv) a mutation operator using Lévy distribution to prevent the population from premature. Computational experiments are carried on 36 benchmark instances from 3 standard sets, and the results show that the proposed algorithm is competitive with the state-of-the-art approaches. In particular, it reports improved upper bounds for the 25 most challenging instances with unproven optimal solutions, while matching the best-known results for all but 2 of the remaining instances. Additional analysis highlights the contribution of the clustering mechanism and combination operator to the performance of the algorithm.

Subphenotyping of Patients With Aortic Stenosis by Unsupervised Agglomerative Clustering of Echocardiographic and Hemodynamic Data.

OBJECTIVES: The aim of this retrospective analysis was to categorize patients with severe aortic stenosis (AS) according to clinical presentation by applying unsupervised machine learning. BACKGROUND: Patients with severe AS present with heterogeneous clinical phenotypes, depending on disease progression and comorbidities. METHODS: Unsupervised agglomerative clustering was applied to preprocedural data from echocardiography and right heart catheterization from 366 consecutively enrolled patients undergoing transcatheter aortic valve replacement for severe AS. RESULTS: Cluster analysis revealed 4 distinct phenotypes. Patients in cluster 1 (n = 164 [44.8%]), serving as a reference, presented with regular cardiac function and without pulmonary hypertension (PH). Accordingly, estimated 2-year survival was 90.6% (95% CI: 85.8%-95.6%). Clusters 2 (n = 66 [18.0%]) and 4 (n = 91 [24.9%]) both comprised patients with postcapillary PH. Yet patients in cluster 2 with preserved left and right ventricular structure and function showed a similar survival as those in cluster 1 (2-year survival 85.8%; 95% CI: 76.9%-95.6%), whereas patients in cluster 4 with dilatation of all heart chambers and a high prevalence of mitral and tricuspid regurgitation (12.5% and 14.8%, respectively) died more often (2-year survival 74.9% [95% CI: 65.9%-85.2%]; HR for 2-year mortality: 2.8 [95% CI: 1.4-5.5]). Patients in cluster 3, the smallest (n = 45 [12.3%]), displayed the most extensive disease characteristics (ie, left and right heart dysfunction together with combined pre- and postcapillary PH), and 2-year survival was accordingly reduced (77.3% [95% CI: 65.2%-91.6%]; HR for 2-year mortality: 2.6 [95% CI: 1.1-6.2]). CONCLUSIONS: Unsupervised machine learning aids in capturing complex clinical presentations as observed in patients with severe AS. Importantly, structural alterations in left and right heart morphology, possibly due to genetic predisposition, constitute an equally sensitive indicator of poor prognosis compared with high-grade PH.

Pharmacological treatment profiles in the FACE-BD cohort: Treatment description and complete data for bipolar subtypes.

In the current study, we provide the list of pharmacological interventions applied during the one-year follow-up period of the Pharmacological treatment profiles in the FACE-BD cohort study. These data show the treatments used in the new clusters formed in this previous study and also in usual bipolarity subtypes. The proportion of each treatment used during the follow-up was calculated. Days on each treatment were also included in this dataset. The complete clinical and paraclinical data analyzed for clusters and bipolar subtypes were included in this dataset. Socio-demographic self-administered and clinician-administered scales, clinical evaluation during the follow-up, psychiatric and somatic comorbidities, and blood tests are shown in this material.