Search results for: k-means clustering

Authors: Pomozova Kseniia, Gorlachev Gennadiy, Chernyaev Aleksandr, Golanov Andrey

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In clinical practice, and especially in stereotactic radiosurgery planning, the significance of diffusion-weighted imaging (DWI) is growing. This makes the existence of software capable of quickly processing and reliably visualizing diffusion data, as well as equipped with tools for their analysis in terms of different tasks. We are developing the «MRDiffusionImaging» software on the standard C++ language. The subject part has been moved to separate class libraries and can be used on various platforms. The user interface is Windows WPF (Windows Presentation Foundation), which is a technology for managing Windows applications with access to all components of the .NET 5 or .NET Framework platform ecosystem. One of the important features is the use of a declarative markup language, XAML (eXtensible Application Markup Language), with which you can conveniently create, initialize and set properties of objects with hierarchical relationships. Graphics are generated using the DirectX environment. The MRDiffusionImaging software package has been implemented for processing diffusion magnetic resonance imaging (dMRI), which allows loading and viewing images sorted by series. An algorithm for "masking" dMRI series based on T2-weighted images was developed using a deformable surface model to exclude tissues that are not related to the area of interest from the analysis. An algorithm of distortion correction using deformable image registration based on autocorrelation of local structure has been developed. Maximum voxel dimension was 1,03 ± 0,12 mm. In an elementary brain's volume, the diffusion tensor is geometrically interpreted using an ellipsoid, which is an isosurface of the probability density of a molecule's diffusion. For the first time, non-parametric intensity distributions, neighborhood correlations, and inhomogeneities are combined in one segmentation of white matter (WM), grey matter (GM), and cerebrospinal fluid (CSF) algorithm. A tool for calculating the coefficient of average diffusion and fractional anisotropy has been created, on the basis of which it is possible to build quantitative maps for solving various clinical problems. Functionality has been created that allows clustering and segmenting images to individualize the clinical volume of radiation treatment and further assess the response (Median Dice Score = 0.963 ± 0,137). White matter tracts of the brain were visualized using two algorithms: deterministic (fiber assignment by continuous tracking) and probabilistic using the Hough transform. The proposed algorithms test candidate curves in the voxel, assigning to each one a score computed from the diffusion data, and then selects the curves with the highest scores as the potential anatomical connections. White matter fibers were visualized using a Hough transform tractography algorithm. In the context of functional radiosurgery, it is possible to reduce the irradiation volume of the internal capsule receiving 12 Gy from 0,402 cc to 0,254 cc. The «MRDiffusionImaging» will improve the efficiency and accuracy of diagnostics and stereotactic radiotherapy of intracranial pathology. We develop software with integrated, intuitive support for processing, analysis, and inclusion in the process of radiotherapy planning and evaluating its results.

Keywords: diffusion-weighted imaging, medical imaging, stereotactic radiosurgery, tractography

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Authors: Anzal Abbas Jaffari, Wajiha Javed, Naseem Salahuddin

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Rationale: Rabies, a vaccine preventable disease, continues to be a critical public health issue as it kills around 2000-5000 people annually in Pakistan. Along with the disease spread among animals, the dog population remains a victim of brutal culling practices by the local authorities, which adversely affects ecosystem (sinking of poison in the soil – affecting vegetation & contaminating water) and the disease spread. The dog population has been exponentially rising primarily because a lack of a consolidated nationwide Animal Birth Control program and awareness among the local communities in general and children in particular. This is reflected in Pakistan’s low SARE score - 1.5, which makes the country trails behind other developing countries like Bangladesh (2.5) and Philippines (3.5).According to an estimate, the province of Sindh alone is home to almost 2.5 million dogs. The clustering of dogs in Peri-Urban areas and inner cities localities leads to an increase of reported dog bite cases in these areas specifically. Objective: Rabies Free Pakistan (RFP), which is a joint venture of Getz Pharma Private Limited and Indus Hospital & Health Network (IHHN); it was established in 2018 to eliminate Rabies from Pakistan by 2030 using the One Health Approach. Methodology: The RFP team is actively working on advocacy and policy front with both the Federal & Provincial government to ensure that all stakeholders currently involved in dog culling in Pakistan have a paradigm shift towards humane methods of vaccination and ABC. Along with the federal government, RFP aims to declare Rabies as a notifiable disease. Whereas RFP closely works with the provincial government of Sindh to initiate a province wide Rabies Control Program.RFP program follows international standards and WHO approved protocols for this program in Pakistan.RFP team has achieved various milestones in the fight against Rabies after successfully scaling up project operations and has vaccinated more than 30,000 dogs and neutered around 7,000 dogs since 2018. Recommendations: Effective implementation of Rabies program (MDV and ABC) requires a concentrated effort to address a variety of structural and policy challenges. This essentially demands a massive shift in the attitude of individuals towards rabies. The two most significant challenges in implementing a standard policy at the structural level are lack of institutional capacity, shortage of vaccine, and absence of inter-departmental coordination among major stakeholders: federal government, provincial ministry of health, livestock, and local bodies (including local councils). The lack of capacity in health care workers to treat dog bite cases emerges as a critical challenge at the clinical level. Conclusion: Pakistan can learn from the successful international models of Sri Lanka and Mexico as they adopted the One Health Approach to eliminate rabies like RFP. The WHO advised One Health approach provides the policymakers with an interactive and cross-sectoral guide, which involves all the essential elements of the eco system (including animals, humans, and other components).

Keywords: animal birth control, dog population, mass dog vaccination, one health, rabies elimination

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Authors: Evgenia Iakovleva, Juha Koivisto, Pasi Karppinen, J. Inkinen, Mikko Alava

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Preventing the spread of infectious diseases throughout the worldwide is one of the most important tasks of modern health care. Infectious diseases not only account for one fifth of the deaths in the world, but also cause many pathological complications for the human health. Touch surfaces pose an important vector for the spread of infections by varying microorganisms, including antimicrobial resistant organisms. Further, antimicrobial resistance is reply of bacteria to the overused or inappropriate used of antibiotics everywhere. The biggest challenges in bacterial detection by existing methods are non-direct determination, long time of analysis, the sample preparation, use of chemicals and expensive equipment, and availability of qualified specialists. Therefore, a high-performance, rapid, real-time detection is demanded in rapid practical bacterial detection and to control the epidemiological hazard. Among the known methods for determining bacteria on the surfaces, Hyperspectral methods can be used as direct and rapid methods for microorganism detection on different kind of surfaces based on fluorescence without sampling, sample preparation and chemicals. The aim of this study was to assess the relevance of such systems to remote sensing of surfaces for microorganisms detection to prevent a global spread of infectious diseases. Bacillus subtilis and Escherichia coli with different concentrations (from 0 to 10x8 cell/100µL) were detected with hyperspectral camera using different filters as visible visualization of bacteria and background spots on the steel plate. A method of internal standards was applied for monitoring the correctness of the analysis results. Distances from sample to hyperspectral camera and light source are 25 cm and 40 cm, respectively. Each sample is optically imaged from the surface by hyperspectral imaging system, utilizing a JAI CM-140GE-UV camera. Light source is BeamZ FLATPAR DMX Tri-light, 3W tri-colour LEDs (red, blue and green). Light colors are changed through DMX USB Pro interface. The developed system was calibrated following a standard procedure of setting exposure and focused for light with λ=525 nm. The filter is ThorLabs KuriousTM hyperspectral filter controller with wavelengths from 420 to 720 nm. All data collection, pro-processing and multivariate analysis was performed using LabVIEW and Python software. The studied human eye visible and invisible bacterial stains clustered apart from a reference steel material by clustering analysis using different light sources and filter wavelengths. The calculation of random and systematic errors of the analysis results proved the applicability of the method in real conditions. Validation experiments have been carried out with photometry and ATP swab-test. The lower detection limit of developed method is several orders of magnitude lower than for both validation methods. All parameters of the experiments were the same, except for the light. Hyperspectral imaging method allows to separate not only bacteria and surfaces, but also different types of bacteria, such as Gram-negative Escherichia coli and Gram-positive Bacillus subtilis. Developed method allows skipping the sample preparation and the use of chemicals, unlike all other microbiological methods. The time of analysis with novel hyperspectral system is a few seconds, which is innovative in the field of microbiological tests.

Keywords: Escherichia coli, Bacillus subtilis, hyperspectral imaging, microorganisms detection

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Authors: Chau-Kuang Chen, Juanita Buford, Colette Davis, Raisha Allen, John Hughes, James Tyus, Dexter Samuels

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During the post-Civil War era, the city of Nashville, Tennessee, had the highest mortality rate in the country. The elevated death and disease among ex-slaves were attributable to the unavailability of healthcare. To address the paucity of healthcare services, the College, an institution with the mission of educating minority professionals and serving the under served population, was established in 1876. This study was designed to assess if the College has accomplished its mission of serving under served communities and contributed to the elimination of health disparities in the United States. The study objective was to quantify the impact of socioeconomic status and adverse health outcomes on primary care professionals serving disadvantaged communities, which, in turn, was significantly associated with a health professional shortage score partly designated by the U.S. Department of Health and Human Services. Various statistical methods were used to analyze the alumni data in years 1975 – 2013. K-means cluster analysis was utilized to identify individual medical and dental graduates into the cluster groups of the practice communities (Disadvantaged or Non-disadvantaged Communities). Discriminant analysis was implemented to verify the classification accuracy of cluster analysis. The independent t test was performed to detect the significant mean differences for clustering and criterion variables between Disadvantaged and Non-disadvantaged Communities, which confirms the “content” validity of cluster analysis model. Chi-square test was used to assess if the proportion of cluster groups (Disadvantaged vs Non-disadvantaged Communities) were consistent with that of practicing specialties (primary care vs. non-primary care). Finally, the partial least squares (PLS) path model was constructed to explore the “construct” validity of analytics model by providing the magnitude effects of socioeconomic status and adverse health outcome on primary care professionals serving disadvantaged community. The social ecological theory along with statistical models mentioned was used to establish the relationship between medical and dental graduates (primary care professionals serving disadvantaged communities) and their social environments (socioeconomic status, adverse health outcome, health professional shortage score). Based on social ecological framework, it was hypothesized that the impact of socioeconomic status and adverse health outcomes on primary care professionals serving disadvantaged communities could be quantified. Also, primary care professionals serving disadvantaged communities related to a health professional shortage score can be measured. Adverse health outcome (adult obesity rate, age-adjusted premature mortality rate, and percent of people diagnosed with diabetes) could be affected by the latent variable, namely socioeconomic status (unemployment rate, poverty rate, percent of children who were in free lunch programs, and percent of uninsured adults). The study results indicated that approximately 83% (3,192/3,864) of the College’s medical and dental graduates from 1975 to 2013 were practicing in disadvantaged communities. In addition, the PLS path modeling demonstrated that primary care professionals serving disadvantaged community was significantly associated with socioeconomic status and adverse health outcome (p < .001). In summary, the majority of medical and dental graduates from the College provide primary care services to disadvantaged communities with low socioeconomic status and high adverse health outcomes, which demonstrate that the College has fulfilled its mission.

Keywords: disadvantaged community, K-means cluster analysis, PLS path modeling, primary care

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Authors: Marit D. Murry, Amy K. Marks

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The transition to college is a critical period that affords abundant opportunities for growth in conjunction with novel challenges for emerging adults. During this time, emerging adults are garnering experiences and acquiring hosts of new information that they are required to synthesize and use to inform life-shaping decisions. This stage is characterized by instability and exploration, which necessitates a diverse set of coping skills to successfully navigate and positively adapt to their evolving environment. However, important sociocultural factors result in differences that occur developmentally for minority emerging adults (i.e., emerging adults with an identity that has been or is marginalized). While the transition to college holds vast potential, not all are afforded the same chances, and many individuals enter into this stage at varying degrees of readiness. Understanding the nuance and diversity of student preparedness for college and contextualizing these factors will better equip systems to support incoming students. Emerging adulthood for ethnic, racial minority students presents itself as an opportunity for growth and resiliency in the face of systemic adversity. Ethnic, racial identity (ERI) is defined as an identity that develops as a function of one’s ethnic-racial group membership. Research continues to demonstrate ERI as a resilience factor that promotes positive adjustment in young adulthood. Adaptive coping responses (e.g., engaging in help-seeking behavior, drawing on personal and community resources) have been identified as possible mechanisms through which ERI buffers youth against stressful life events, including discrimination. Additionally, trait mindfulness has been identified as a significant predictor of general psychological health, and mindfulness practice has been shown to be a self-regulatory strategy that promotes healthy stress responses and adaptive coping strategy selection. The current study employed a person-centered approach to explore emerging patterns across ethnic identity development and psychological well-being criterion variables among college freshmen. Data from 283 incoming college freshmen at Northeastern University were analyzed. The Brief COPE Acceptance and Emotional Support scales, the Five Factor Mindfulness Questionnaire, and MIEM Exploration and Affirmation measures were used to inform the cluster profiles. The TwoStep auto-clustering algorithm revealed an optimal three-cluster solution (BIC = 848.49), which classified 92.6% (n = 262) of participants in the sample into one of the three clusters. The clusters were characterized as ‘Mixed Adjustment’, ‘Lowest Adjustment’, and ‘Moderate Adjustment.’ Cluster composition varied significantly by ethnicity X² (2, N = 262) = 7.74 (p = .021) and gender X² (2, N = 259) = 10.40 (p = .034). The ‘Lowest Adjustment’ cluster contained the highest proportion of students of color, 41% (n = 32), and male-identifying students, 44.2% (n = 34). Follow-up analyses showed higher ERI exploration in ‘Moderate Adjustment’ cluster members, also reported higher levels of psychological distress, with significantly elevated depression scores (p = .011), psychological diagnoses of depression (p = .013), anxiety (p = .005) and psychiatric disorders (p = .025). Supporting prior research, students engaging with identity exploration processes often endure more psychological distress. These results indicate that students undergoing identity development may require more socialization and different services beyond normal strategies.

Keywords: adjustment, coping, college, emerging adulthood, ethnic-racial identity, psychological well-being, resilience

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Authors: C. Bel, J. Nevado, F. Ciceri, M. Ropacki, T. Hoffmann, P. Lapunzina, C. Buesa

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Background: The Phelan-McDermid syndrome (PMS) is a genetic disorder caused by the deletion of the terminal region of chromosome 22 or mutation of the SHANK3 gene. Shank3 disruption in mice leads to dysfunction of synaptic transmission, which can be restored by epigenetic regulation with both Lysine Specific Demethylase 1 (LSD1) inhibitors. PMS subjects result in a variable degree of intellectual disability, delay or absence of speech, autistic spectrum disorders symptoms, low muscle tone, motor delays and epilepsy. Vafidemstat is an LSD1 inhibitor in Phase II clinical development with a well-established and favorable safety profile, and data supporting the restoration of memory and cognition defects as well as reduction of agitation and aggression in several animal models and clinical studies. Therefore, vafidemstat has the potential to become a first-in-class precision medicine approach to treat PMS patients. Aims: The goal of this research is to perform an observational trial to psychometrically characterize individuals carrying deletions in SHANK3 and build a foundation for subsequent precision psychiatry clinical trials with vafidemstat. Methodology: This study is characterizing the clinical profile of 20 to 40 subjects, > 16-year-old, with genotypically confirmed PMS diagnosis. Subjects will complete a battery of neuropsychological scales, including the Repetitive Behavior Questionnaire (RBQ), Vineland Adaptive Behavior Scales, Escala de Observación para el Diagnostico del Autismo (Autism Diagnostic Observational Scale) (ADOS)-2, the Battelle Developmental Inventory and the Behavior Problems Inventory (BPI). Results: By March 2021, 19 patients have been enrolled. Unsupervised hierarchical clustering of the results obtained so far identifies 3 groups of patients, characterized by different profiles of cognitive and behavioral scores. The first cluster is characterized by low Battelle age, high ADOS and low Vineland, RBQ and BPI scores. Low Vineland, RBQ and BPI scores are also detected in the second cluster, which in contrast has high Battelle age and low ADOS scores. The third cluster is somewhat in the middle for the Battelle, Vineland and ADOS scores while displaying the highest levels of aggression (high BPI) and repeated behaviors (high RBQ). In line with the observation that female patients are generally affected by milder forms of autistic symptoms, no male patients are present in the second cluster. Dividing the results by gender highlights that male patients in the third cluster are characterized by a higher frequency of aggression, whereas female patients from the same cluster display a tendency toward higher repetitive behavior. Finally, statistically significant differences in deletion sizes are detected comparing the three clusters (also after correcting for gender), and deletion size appears to be positively correlated with ADOS and negatively correlated with Vineland A and C scores. No correlation is detected between deletion size and the BPI and RBQ scores. Conclusions: Precision medicine may open a new way to understand and treat Central Nervous System disorders. Epigenetic dysregulation has been proposed to be an important mechanism in the pathogenesis of schizophrenia and autism. Vafidemstat holds exciting therapeutic potential in PMS, and this study will provide data regarding the optimal endpoints for a future clinical study to explore vafidemstat ability to treat shank3-associated psychiatric disorders.

Keywords: autism, epigenetics, LSD1, personalized medicine

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Authors: Mohamed Gazzeh, Bradley Null, Fethi Tlili, Hichem Besbes

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The burgeoning global ownership of personal vehicles has posed a significant strain on urban infrastructure, notably parking facilities, leading to traffic congestion and environmental concerns. Effective parking management systems (PMS) are indispensable for optimizing urban traffic flow and reducing emissions. The most commonly deployed systems nowadays rely on computer vision technology. This paper explores the integration of radar sensors and simulation in the context of smart parking management. We concentrate on radar sensors due to their versatility and utility in automotive applications, which extends to PMS. Additionally, radar sensors play a crucial role in driver assistance systems and autonomous vehicle development. However, the resource-intensive nature of radar data collection for algorithm development and testing necessitates innovative solutions. Simulation, particularly the monoDrive simulator, an internal development tool used by NI the Test and Measurement division of Emerson, offers a practical means to overcome this challenge. The primary objectives of this study encompass simulating radar sensors to generate a substantial dataset for algorithm development, testing, and, critically, assessing the transferability of models between simulated and real radar data. We focus on occupancy detection in parking as a practical use case, categorizing each parking space as vacant or occupied. The simulation approach using monoDrive enables algorithm validation and reliability assessment for virtual radar sensors. It meticulously designed various parking scenarios, involving manual measurements of parking spot coordinates, orientations, and the utilization of TI AWR1843 radar. To create a diverse dataset, we generated 4950 scenarios, comprising a total of 455,400 parking spots. This extensive dataset encompasses radar configuration details, ground truth occupancy information, radar detections, and associated object attributes such as range, azimuth, elevation, radar cross-section, and velocity data. The paper also addresses the intricacies and challenges of real-world radar data collection, highlighting the advantages of simulation in producing radar data for parking lot applications. We developed classification models based on Support Vector Machines (SVM) and Density-Based Spatial Clustering of Applications with Noise (DBSCAN), exclusively trained and evaluated on simulated data. Subsequently, we applied these models to real-world data, comparing their performance against the monoDrive dataset. The study demonstrates the feasibility of transferring models from a simulated environment to real-world applications, achieving an impressive accuracy score of 92% using only one radar sensor. This finding underscores the potential of radar sensors and simulation in the development of smart parking management systems, offering significant benefits for improving urban mobility and reducing environmental impact. The integration of radar sensors and simulation represents a promising avenue for enhancing smart parking management systems, addressing the challenges posed by the exponential growth in personal vehicle ownership. This research contributes valuable insights into the practicality of using simulated radar data in real-world applications and underscores the role of radar technology in advancing urban sustainability.

Keywords: autonomous vehicle simulator, FMCW radar sensors, occupancy detection, smart parking management, transferability of models

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Authors: Reza Nematirad, Anil Pahwa, Balasubramaniam Natarajan

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Time series data consist of successive data points collected over a period of time. Accurate prediction of future values is essential for informed decision-making in several real-world applications, including electricity load demand forecasting, lifetime estimation of industrial machinery, traffic planning, weather prediction, and the stock market. Due to their critical relevance and wide application, there has been considerable interest in time series forecasting in recent years. However, the proliferation of sensors and IoT devices, real-time monitoring systems, and high-frequency trading data introduce significant intricate temporal variations, rapid changes, noise, and non-linearities, making time series forecasting more challenging. Classical methods such as Autoregressive integrated moving average (ARIMA) and Exponential Smoothing aim to extract pre-defined temporal variations, such as trends and seasonality. While these methods are effective for capturing well-defined seasonal patterns and trends, they often struggle with more complex, non-linear patterns present in real-world time series data. In recent years, deep learning has made significant contributions to time series forecasting. Recurrent Neural Networks (RNNs) and their variants, such as Long short-term memory (LSTMs) and Gated Recurrent Units (GRUs), have been widely adopted for modeling sequential data. However, they often suffer from the locality, making it difficult to capture local trends and rapid fluctuations. Convolutional Neural Networks (CNNs), particularly Temporal Convolutional Networks (TCNs), leverage convolutional layers to capture temporal dependencies by applying convolutional filters along the temporal dimension. Despite their advantages, TCNs struggle with capturing relationships between distant time points due to the locality of one-dimensional convolution kernels. Transformers have revolutionized time series forecasting with their powerful attention mechanisms, effectively capturing long-term dependencies and relationships between distant time points. However, the attention mechanism may struggle to discern dependencies directly from scattered time points due to intricate temporal patterns. Lastly, Multi-Layer Perceptrons (MLPs) have also been employed, with models like N-BEATS and LightTS demonstrating success. Despite this, MLPs often face high volatility and computational complexity challenges in long-horizon forecasting. To address intricate temporal variations in time series data, this study introduces Times2D, a novel framework that parallelly integrates 2D spectrogram and derivative heatmap techniques. The spectrogram focuses on the frequency domain, capturing periodicity, while the derivative patterns emphasize the time domain, highlighting sharp fluctuations and turning points. This 2D transformation enables the utilization of powerful computer vision techniques to capture various intricate temporal variations. To evaluate the performance of Times2D, extensive experiments were conducted on standard time series datasets and compared with various state-of-the-art algorithms, including DLinear (2023), TimesNet (2023), Non-stationary Transformer (2022), PatchTST (2023), N-HiTS (2023), Crossformer (2023), MICN (2023), LightTS (2022), FEDformer (2022), FiLM (2022), SCINet (2022a), Autoformer (2021), and Informer (2021) under the same modeling conditions. The initial results demonstrated that Times2D achieves consistent state-of-the-art performance in both short-term and long-term forecasting tasks. Furthermore, the generality of the Times2D framework allows it to be applied to various tasks such as time series imputation, clustering, classification, and anomaly detection, offering potential benefits in any domain that involves sequential data analysis.

Keywords: derivative patterns, spectrogram, time series forecasting, times2D, 2D representation

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