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Background: Cancer pathology shows disease development and associated molecular features. It provides extensive phenotypic information that is cancer-predictive and has potential implications for planning treatment. Based on the exceptional performance of computational approaches in the field of digital pathogenic, the use of rich phenotypic information in digital pathology images has enabled us to identify low-level gliomas (LGG) from high-grade gliomas (HGG). Because the differences between the textures are so slight, utilizing just one feature or a small number of features produces poor categorization results., Methods: In this work, multiple feature extraction methods that can extract distinct features from the texture of histopathology image data are used to compare the classification outcomes. The successful feature extraction algorithms GLCM, LBP, multi-LBGLCM, GLRLM, color moment features, and RSHD have been chosen in this paper. LBP and GLCM algorithms are combined to create LBGLCM. The LBGLCM feature extraction approach is extended in this study to multiple scales using an image pyramid, which is defined by sampling the image both in space and scale. The preprocessing stage is first used to enhance the contrast of the images and remove noise and illumination effects. The feature extraction stage is then carried out to extract several important features (texture and color) from histopathology images. Third, the feature fusion and reduction step is put into practice to decrease the number of features that are processed, reducing the computation time of the suggested system. The classification stage is created at the end to categorize various brain cancer grades. We performed our analysis on the 821 whole-slide pathology images from glioma patients in the Cancer Genome Atlas (TCGA) dataset. Two types of brain cancer are included in the dataset: GBM and LGG (grades II and III). 506 GBM images and 315 LGG images are included in our analysis, guaranteeing representation of various tumor grades and histopathological features., Results: The fusion of textural and color characteristics was validated in the glioma patients using the 10-fold cross-validation technique with an accuracy equals to 95.8%, sensitivity equals to 96.4%, DSC equals to 96.7%, and specificity equals to 97.1%. The combination of the color and texture characteristics produced significantly better accuracy, which supported their synergistic significance in the predictive model. The result indicates that the textural characteristics can be an objective, accurate, and comprehensive glioma prediction when paired with conventional imagery., Conclusion: The results outperform current approaches for identifying LGG from HGG and provide competitive performance in classifying four categories of glioma in the literature. The proposed model can help stratify patients in clinical studies, choose patients for targeted therapy, and customize specific treatment schedules., (© 2024. The Author(s).)

Background: Using next-generation sequencing technologies, scientists can sequence complex microbial communities directly from the environment. Significant insights into the structure, diversity, and ecology of microbial communities have resulted from the study of metagenomics. The assembly of reads into longer contigs, which are then binned into groups of contigs that correspond to different species in the metagenomic sample, is a crucial step in the analysis of metagenomics. It is necessary to organize these contigs into operational taxonomic units (OTUs) for further taxonomic profiling and functional analysis. For binning, which is synonymous with the clustering of OTUs, the tetra-nucleotide frequency (TNF) is typically utilized as a compositional feature for each OTU., Results: In this paper, we present AFIT, a new l-mer statistic vector for each contig, and AFITBin, a novel method for metagenomic binning based on AFIT and a matrix factorization method. To evaluate the performance of the AFIT vector, the t-SNE algorithm is used to compare species clustering based on AFIT and TNF information. In addition, the efficacy of AFITBin is demonstrated on both simulated and real datasets in comparison to state-of-the-art binning methods such as MetaBAT 2, MaxBin 2.0, CONCOT, MetaCon, SolidBin, BusyBee Web, and MetaBinner. To further analyze the performance of the purposed AFIT vector, we compare the barcodes of the AFIT vector and the TNF vector., Conclusion: The results demonstrate that AFITBin shows superior performance in taxonomic identification compared to existing methods, leveraging the AFIT vector for improved results in metagenomic binning. This approach holds promise for advancing the analysis of metagenomic data, providing more reliable insights into microbial community composition and function., Availability: A python package is available at: https://github.com/SayehSobhani/AFITBin ., (© 2024. The Author(s).)

Background: In bioinformatics, interactions are modelled as networks, based on graph models. Generally, these support a single-layer structure which incorporates a specific entity (i.e., node) and only one type of link (i.e., edge). However, real-world biological systems consisting of biological objects belonging to heterogeneous entities, and these operate and influence each other in multiple contexts, simultaneously. Usually, node similarities are investigated to assess the relatedness between biological objects in a network of interest, and node embeddings are widely used for studying novel interaction from a topological point of view. About that, the state-of-the-art presents several methods for evaluating the node similarity inside a given network, but methodologies able to evaluate similarities between pairs of nodes belonging to different networks are missing. The latter are crucial for studies that relate different biological networks, e.g., for Network Alignment or to evaluate the possible evolution of the interactions of a little-known network on the basis of a well-known one. Existing methods are ineffective in evaluating nodes outside their structure, even more so in the context of multilayer networks, in which the topic still exploits approaches adapted from static networks. In this paper, we presented pyMulSim, a novel method for computing the pairwise similarities between nodes belonging to different multilayer networks. It uses a Graph Isomorphism Network (GIN) for the representative learning of node features, that uses for processing the embeddings and computing the similarities between the pairs of nodes of different multilayer networks., Results: Our experimentation investigated the performance of our method. Results show that our method effectively evaluates the similarities between the biological objects of a source multilayer network to a target one, based on the analysis of the node embeddings. Results have been also assessed for different noise levels, also through statistical significance analyses properly performed for this purpose., Conclusions: PyMulSim is a novel method for computing the pairwise similarities between nodes belonging to different multilayer networks, by using a GIN for learning node embeddings. It has been evaluated both in terms of performance and validity, reporting a high degree of reliability., (© 2024. The Author(s).)

Background: Drug design is a challenging and important task that requires the generation of novel and effective molecules that can bind to specific protein targets. Artificial intelligence algorithms have recently showed promising potential to expedite the drug design process. However, existing methods adopt multi-objective approaches which limits the number of objectives., Results: In this paper, we expand this thread of research from the many-objective perspective, by proposing a novel framework that integrates a latent Transformer-based model for molecular generation, with a drug design system that incorporates absorption, distribution, metabolism, excretion, and toxicity prediction, molecular docking, and many-objective metaheuristics. We compared the performance of two latent Transformer models (ReLSO and FragNet) on a molecular generation task and show that ReLSO outperforms FragNet in terms of reconstruction and latent space organization. We then explored six different many-objective metaheuristics based on evolutionary algorithms and particle swarm optimization on a drug design task involving potential drug candidates to human lysophosphatidic acid receptor 1, a cancer-related protein target., Conclusion: We show that multi-objective evolutionary algorithm based on dominance and decomposition performs the best in terms of finding molecules that satisfy many objectives, such as high binding affinity and low toxicity, and high drug-likeness. Our framework demonstrates the potential of combining Transformers and many-objective computational intelligence for drug design., (© 2024. The Author(s).)

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., (© 2024. The Author(s).)

Background: Classification of binary data arises naturally in many clinical applications, such as patient risk stratification through ICD codes. One of the key practical challenges in data classification using machine learning is to avoid overfitting. Overfitting in supervised learning primarily occurs when a model learns random variations from noisy labels in training data rather than the underlying patterns. While traditional methods such as regularization and early stopping have demonstrated effectiveness in interpolation tasks, addressing overfitting in the classification of binary data, in which predictions always amount to extrapolation, demands extrapolation-enhanced strategies. One such approach is hybrid mechanistic/data-driven modeling, which integrates prior knowledge on input features into the learning process, enhancing the model's ability to extrapolate., Results: We present NoiseCut, a Python package for noise-tolerant classification of binary data by employing a hybrid modeling approach that leverages solutions of defined max-cut problems. In a comparative analysis conducted on synthetically generated binary datasets, NoiseCut exhibits better overfitting prevention compared to the early stopping technique employed by different supervised machine learning algorithms. The noise tolerance of NoiseCut stems from a dropout strategy that leverages prior knowledge of input features and is further enhanced by the integration of max-cut problems into the learning process., Conclusions: NoiseCut is a Python package for the implementation of hybrid modeling for the classification of binary data. It facilitates the integration of mechanistic knowledge on the input features into learning from data in a structured manner and proves to be a valuable classification tool when the available training data is noisy and/or limited in size. This advantage is especially prominent in medical and biomedical applications where data scarcity and noise are common challenges. The codebase, illustrations, and documentation for NoiseCut are accessible for download at https://pypi.org/project/noisecut/ . The implementation detailed in this paper corresponds to the version 0.2.1 release of the software., (© 2024. The Author(s).)

Background: Text summarization is a challenging problem in Natural Language Processing, which involves condensing the content of textual documents without losing their overall meaning and information content, In the domain of bio-medical research, summaries are critical for efficient data analysis and information retrieval. While several bio-medical text summarizers exist in the literature, they often miss out on an essential text aspect: text semantics., Results: This paper proposes a novel extractive summarizer that preserves text semantics by utilizing bio-semantic models. We evaluate our approach using ROUGE on a standard dataset and compare it with three state-of-the-art summarizers. Our results show that our approach outperforms existing summarizers., Conclusion: The usage of semantics can improve summarizer performance and lead to better summaries. Our summarizer has the potential to aid in efficient data analysis and information retrieval in the field of biomedical research., (© 2024. The Author(s).)

Background: Blood test is extensively performed for screening, diagnoses and surveillance purposes. Although it is possible to automatically evaluate the raw blood test data with the advanced deep self-supervised machine learning approaches, it has not been profoundly investigated and implemented yet., Results: This paper proposes deep machine learning algorithms with multi-dimensional adaptive feature elimination, self-feature weighting and novel feature selection approaches. To classify the health risks based on the processed data with the deep layers, four machine learning algorithms having various properties from being utterly model free to gradient driven are modified., Conclusions: The results show that the proposed deep machine learning algorithms can remove the unnecessary features, assign self-importance weights, selects their most informative ones and classify the health risks automatically from the worst-case low to worst-case high values., (© 2024. The Author(s).)

Deep Self-Attention Network (Transformer) is an encoder-decoder architectural model that excels in establishing long-distance dependencies and is first applied in natural language processing. Due to its complementary nature with the inductive bias of convolutional neural network (CNN), Transformer has been gradually applied to medical image processing, including kidney image processing. It has become a hot research topic in recent years. To further explore new ideas and directions in the field of renal image processing, this paper outlines the characteristics of the Transformer network model and summarizes the application of the Transformer-based model in renal image segmentation, classification, detection, electronic medical records, and decision-making systems, and compared with CNN-based renal image processing algorithm, analyzing the advantages and disadvantages of this technique in renal image processing. In addition, this paper gives an outlook on the development trend of Transformer in renal image processing, which provides a valuable reference for a lot of renal image analysis., (© 2024. The Author(s).)

Background: Dynamic Contrast Enhanced Magnetic Resonance Imaging (DCE-MRI) plays an important role in the diagnosis and treatment of breast cancer. However, obtaining complete eight temporal images of DCE-MRI requires a long scanning time, which causes patients' discomfort in the scanning process. Therefore, to reduce the time, the multi temporal feature fusing neural network with Co-attention (MTFN) is proposed to generate the eighth temporal images of DCE-MRI, which enables the acquisition of DCE-MRI images without scanning. In order to reduce the time, multi-temporal feature fusion cooperative attention mechanism neural network (MTFN) is proposed to generate the eighth temporal images of DCE-MRI, which enables DCE-MRI image acquisition without scanning., Methods: In this paper, we propose multi temporal feature fusing neural network with Co-attention (MTFN) for DCE-MRI Synthesis, in which the Co-attention module can fully fuse the features of the first and third temporal image to obtain the hybrid features. The Co-attention explore long-range dependencies, not just relationships between pixels. Therefore, the hybrid features are more helpful to generate the eighth temporal images., Results: We conduct experiments on the private breast DCE-MRI dataset from hospitals and the multi modal Brain Tumor Segmentation Challenge2018 dataset (BraTs2018). Compared with existing methods, the experimental results of our method show the improvement and our method can generate more realistic images. In the meanwhile, we also use synthetic images to classify the molecular typing of breast cancer that the accuracy on the original eighth time-series images and the generated images are 89.53% and 92.46%, which have been improved by about 3%, and the classification results verify the practicability of the synthetic images., Conclusions: The results of subjective evaluation and objective image quality evaluation indicators show the effectiveness of our method, which can obtain comprehensive and useful information. The improvement of classification accuracy proves that the images generated by our method are practical., (© 2024. The Author(s).)

Copy-number variations (CNVs), which refer to deletions and duplications of chromosomal segments, represent a significant source of variation among individuals, contributing to human evolution and being implicated in various diseases ranging from mental illness and developmental disorders to cancer. Despite the development of several methods for detecting copy number variations based on next-generation sequencing (NGS) data, achieving robust detection performance for CNVs with arbitrary coverage and amplitude remains challenging due to the inherent complexity of sequencing samples. In this paper, we propose an alternative method called OTSUCNV for CNV detection on whole genome sequencing (WGS) data. This method utilizes a newly designed adaptive sequence segmentation algorithm and an OTSU-based CNV prediction algorithm, which does not rely on any distribution assumptions or involve complex outlier factor calculations. As a result, the effective detection of CNVs is achieved with lower computational complexity. The experimental results indicate that the proposed method demonstrates outstanding performance, and hence it may be used as an effective tool for CNV detection., (© 2024. The Author(s).)

Background: Since AI algorithms can analyze patient data, medical records, and imaging results to suggest treatment plans and predict outcomes, they have the potential to support pathologists and clinicians in the diagnosis and treatment of oral and maxillofacial pathologies, just like every other area of life in which it is being used. The goal of the current study was to examine all of the trends being investigated in the area of oral and maxillofacial pathology where AI has been possibly involved in helping practitioners., Methods: We started by defining the important terms in our investigation's subject matter. Following that, relevant databases like PubMed, Scopus, and Web of Science were searched using keywords and synonyms for each concept, such as "machine learning," "diagnosis," "treatment planning," "image analysis," "predictive modelling," and "patient monitoring." For more papers and sources, Google Scholar was also used., Results: The majority of the 9 studies that were chosen were on how AI can be utilized to diagnose malignant tumors of the oral cavity. AI was especially helpful in creating prediction models that aided pathologists and clinicians in foreseeing the development of oral and maxillofacial pathology in specific patients. Additionally, predictive models accurately identified patients who have a high risk of developing oral cancer as well as the likelihood of the disease returning after treatment., Conclusions: In the field of oral and maxillofacial pathology, AI has the potential to enhance diagnostic precision, personalize care, and ultimately improve patient outcomes. The development and application of AI in healthcare, however, necessitates careful consideration of ethical, legal, and regulatory challenges. Additionally, because AI is still a relatively new technology, caution must be taken when applying it to this industry., (© 2024. The Author(s).)

Objectives: In this paper, a uniformly convergent numerical scheme is proposed for solving a singularly perturbed Fredholm integro-differential equation with an integral initial condition. The equation involves a left boundary layer which makes it difficult to solve it using the standard numerical methods. A fitted operator finite difference method is used to approximate the differential part of the equation and the composite Simpson [Formula: see text] rule is used for the integral parts of the equation and the initial condition., Result: The stability bound and error estimation of the approximated solution are performed, to show the uniform convergence of the scheme with order one in the maximum norm. Numerical test examples are provided to calculate the maximum absolute errors, thrgence, and the uniform error for a couple of examples to support theoretical analysis., (© 2024. The Author(s).)

The integration of biology, computer science, and statistics has given rise to the interdisciplinary field of bioinformatics, which aims to decode biological intricacies. It produces extensive and diverse features, presenting an enormous challenge in classifying bioinformatic problems. Therefore, an intelligent bioinformatics classification system must select the most relevant features to enhance machine learning performance. This paper proposes a feature selection model based on the fractal concept to improve the performance of intelligent systems in classifying high-dimensional biological problems. The proposed fractal feature selection (FFS) model divides features into blocks, measures the similarity between blocks using root mean square error (RMSE), and determines the importance of features based on low RMSE. The proposed FFS is tested and evaluated over ten high-dimensional bioinformatics datasets. The experiment results showed that the model significantly improved machine learning accuracy. The average accuracy rate was 79% with full features in machine learning algorithms, while FFS delivered promising results with an accuracy rate of 94%., (© 2024. The Author(s).)

A colored de Bruijn graph (also called a set of k-mer sets), is a set of k-mers with every k-mer assigned a set of colors. Colored de Bruijn graphs are used in a variety of applications, including variant calling, genome assembly, and database search. However, their size has posed a scalability challenge to algorithm developers and users. There have been numerous indexing data structures proposed that allow to store the graph compactly while supporting fast query operations. However, disk compression algorithms, which do not need to support queries on the compressed data and can thus be more space-efficient, have received little attention. The dearth of specialized compression tools has been a detriment to tool developers, tool users, and reproducibility efforts. In this paper, we develop a new tool that compresses colored de Bruijn graphs to disk, building on previous ideas for compression of k-mer sets and indexing colored de Bruijn graphs. We test our tool, called ESS-color, on various datasets, including both sequencing data and whole genomes. ESS-color achieves better compression than all evaluated tools and all datasets, with no other tool able to consistently achieve less than 44% space overhead. The software is available at http://github.com/medvedevgroup/ESSColor. [ABSTRACT FROM AUTHOR]

Purpose: String indexes such as the suffix array (sa) and the closely related longest common prefix (lcp) array are fundamental objects in bioinformatics and have a wide variety of applications. Despite their importance in practice, few scalable parallel algorithms for constructing these are known, and the existing algorithms can be highly non-trivial to implement and parallelize. Methods: In this paper we present caps-sa, a simple and scalable parallel algorithm for constructing these string indexes inspired by samplesort and utilizing an LCP-informed mergesort. Due to its design, caps-sa has excellent memory-locality and thus incurs fewer cache misses and achieves strong performance on modern multicore systems with deep cache hierarchies. Results: We show that despite its simple design, caps-sa outperforms existing state-of-the-art parallel sa and lcp-array construction algorithms on modern hardware. Finally, motivated by applications in modern aligners where the query strings have bounded lengths, we introduce the notion of a bounded-context sa and show that caps-sa can easily be extended to exploit this structure to obtain further speedups. We make our code publicly available at https://github.com/jamshed/CaPS-SA. [ABSTRACT FROM AUTHOR]

Background: We study the problem of finding maximal exact matches (MEMs) between a query string Q and a labeled graph G. MEMs are an important class of seeds, often used in seed-chain-extend type of practical alignment methods because of their strong connections to classical metrics. A principled way to speed up chaining is to limit the number of MEMs by considering only MEMs of length at least κ (κ -MEMs). However, on arbitrary input graphs, the problem of finding MEMs cannot be solved in truly sub-quadratic time under SETH (Equi et al., TALG 2023) even on acyclic graphs. Results: In this paper we show an O (n · L · d L - 1 + m + M κ , L) -time algorithm finding all κ -MEMs between Q and G spanning exactly L nodes in G, where n is the total length of node labels, d is the maximum degree of a node in G, m = | Q | , and M κ , L is the number of output MEMs. We use this algorithm to develop a κ -MEM finding solution on indexable Elastic Founder Graphs (Equi et al., Algorithmica 2022) running in time O (n H 2 + m + M κ) , where H is the maximum number of nodes in a block, and M κ is the total number of κ -MEMs. Our results generalize to the analysis of multiple query strings (MEMs between G and any of the strings). Additionally, we provide some experimental results showing that the number of graph MEMs is an order of magnitude smaller than the number of string MEMs of the corresponding concatenated collection. Conclusions: We show that seed-chain-extend type of alignment methods can be implemented on top of indexable Elastic Founder Graphs by providing an efficient way to produce the seeds between a set of queries and the graph. The code is available in https://github.com/algbio/efg-mems. [ABSTRACT FROM AUTHOR]

Background: Reviews on Down syndrome do not or only marginally address the issue of kidney and urogenital tract abnormalities, and lower urinary tract dysfunctions. Hence, we performed a meta-analysis of the literature. Methods: A literature search was undertaken in the Library of Medicine, Web of Science and Excerpta Medica. The search algorithm combined various keywords: (Down syndrome OR trisomy 21 OR mongolism) AND (kidney OR urinary tract OR bladder) AND (malformation OR dysfunction OR anomaly OR abnormality OR size). The Preferred Reporting Items for Systematic Reviews and Meta-Analyses statement was used. Results: Eight case-control studies were retained for the final analysis. Three studies addressed the prevalence of kidney and urogenital tract abnormalities: an increased pooled relative risk of 5.49 (95%-CI: 1.78–16.93) was observed in Down syndrome. Penile malformations, obstructive malformations (including urethral valves), dilated urinary tract system, and kidney hypodysplasia were especially common. Three reports addressed the prevalence of lower urinary tract dysfunction: an increased pooled relative risk of 2.95 (95%-CI: 1.15–7.56) was observed. Finally, an autoptic study and an ultrasound study disclosed a reduced kidney size in Down syndrome. Conclusions: This meta-analysis indicates that abnormalities of the kidney and urogenital tract, lower urinary tract dysfunctions, and a reduced kidney size present with an increased frequency in individuals with Down syndrome. [ABSTRACT FROM AUTHOR]

Digital data processing has revolutionized medical documentation and enabled the aggregation of patient data across hospitals. Initiatives such as those from the AO Foundation about fracture treatment (AO Sammelstudie, 1986), the Major Trauma Outcome Study (MTOS) about survival, and the Trauma Audit and Research Network (TARN) pioneered multi-hospital data collection. Large trauma registries, like the German Trauma Registry (TR-DGU) helped improve evidence levels but were still constrained by predefined data sets and limited physiological parameters. The improvement in the understanding of pathophysiological reactions substantiated that decision making about fracture care led to development of patient's tailored dynamic approaches like the Safe Definitive Surgery algorithm. In the future, artificial intelligence (AI) may provide further steps by potentially transforming fracture recognition and/or outcome prediction. The evolution towards flexible decision making and AI-driven innovations may be of further help. The current manuscript summarizes the development of big data from local databases and subsequent trauma registries to AI-based algorithms, such as Parkland Trauma Mortality Index and the IBM Watson Pathway Explorer. [ABSTRACT FROM AUTHOR]

Background: Mortality rate estimation in small areas can be difficult due the low number of events/exposure (i.e. stochastic error). If the death records are not completed, it adds a systematic uncertainty on the mortality estimates. Previous studies in Brazil have combined demographic and statistical methods to partially overcome these issues. We estimated age- and sex-specific mortality rates for all 5,565 Brazilian municipalities in 2010 and forecasted probabilistic mortality rates and life expectancy between 2010 and 2030. Methods: We used a combination of the Tool for Projecting Age-Specific Rates Using Linear Splines (TOPALS), Bayesian Model, Spatial Smoothing Model and an ad-hoc procedure to estimate age- and sex-specific mortality rates for all Brazilian municipalities for 2010. Then we adapted the Lee-Carter model to forecast mortality rates by age and sex in all municipalities between 2010 and 2030. Results: The adjusted sex- and age-specific mortality rates for all Brazilian municipalities in 2010 reveal a distinct regional pattern, showcasing a decrease in life expectancy in less socioeconomically developed municipalities when compared to estimates without adjustments. The forecasted mortality rates indicate varying regional improvements, leading to a convergence in life expectancy at birth among small areas in Brazil. Consequently, a reduction in the variability of age at death across Brazil's municipalities was observed, with a persistent sex differential. Conclusion: Mortality rates at a small-area level were successfully estimated and forecasted, with associated uncertainty estimates also generated for future life tables. Our approach could be applied across countries with data quality issues to improve public policy planning. [ABSTRACT FROM AUTHOR]

Background: Optimizing transitional care by practicing family-centered care might reduce unplanned events for patients who undergo major abdominal cancer surgery. However, it remains unknown whether involving family caregivers in patients' healthcare also has negative consequences for patient safety. This study assessed the safety of family involvement in patients' healthcare by examining the cause of unplanned events in patients who participated in a family involvement program (FIP) after major abdominal cancer surgery. Methods: This is a secondary analysis focusing on the intervention group of a prospective cohort study conducted in the Netherlands. Data were collected from April 2019 to May 2022. Participants in the intervention group were patients who engaged in a FIP. Unplanned events were analyzed, and root causes were identified using the medical version of a prevention- and recovery-information system for monitoring and analysis (PRISMA) that analyses unintended events in healthcare. Unplanned events were compared between patients who received care from family caregivers and patients who received professional at-home care after discharge. A Mann-Whitney U test was used to analyze data. Results: Of the 152 FIP participants, 68 experienced an unplanned event and were included. 112 unplanned events occurred with 145 root causes since some unplanned events had several root causes. Most root causes of unplanned events were patient-related factors (n = 109, 75%), such as patient characteristics and disease-related factors. No root causes due to inadequate healthcare from the family caregiver were identified. Unplanned events did not differ statistically (interquartile range 1–2) (p = 0.35) between patients who received care from trained family caregivers and those who received professional at-home care after discharge. Conclusion: Based on the insights from the root-cause analysis in this prospective multicenter study, it appears that unplanned emergency room visits and hospital readmissions are not related to the active involvement of family caregivers in surgical follow-up care. Moreover, surgical follow-up care by trained family caregivers during hospitalization was not associated with increased rates of unplanned adverse events. Hence, the concept of active family involvement by proficiently trained family caregivers in postoperative care appears safe and feasible for patients undergoing major abdominal surgery. [ABSTRACT FROM AUTHOR]

Background: Kenya aims to achieve universal health coverage (UHC) by 2030 and has selected the National Health Insurance Fund (NHIF) as the 'vehicle' to drive the UHC agenda. While there is some progress in moving the country towards UHC, the availability and accessibility to NHIF-contracted facilities may be a barrier to equitable access to care. We estimated the spatial access to NHIF-contracted facilities in Kenya to provide information to advance the UHC agenda in Kenya. Methods: We merged NHIF-contracted facility data to the geocoded inventory of health facilities in Kenya to assign facility geospatial locations. We combined this database with covariates data including road network, elevation, land use, and travel barriers. We estimated the proportion of the population living within 60- and 120-minute travel time to an NHIF-contracted facility at a 1-x1-kilometer spatial resolution nationally and at county levels using the WHO AccessMod tool. Results: We included a total of 3,858 NHIF-contracted facilities. Nationally, 81.4% and 89.6% of the population lived within 60- and 120-minute travel time to an NHIF-contracted facility respectively. At the county level, the proportion of the population living within 1-hour of travel time to an NHIF-contracted facility ranged from as low as 28.1% in Wajir county to 100% in Nyamira and Kisii counties. Overall, only four counties (Kiambu, Kisii, Nairobi and Nyamira) had met the target of having 100% of their population living within 1-hour (60 min) travel time to an NHIF-contracted facility. On average, it takes 209, 210 and 216 min to travel to an NHIF-contracted facility, outpatient and inpatient facilities respectively. At the county level, travel time to an NHIF-contracted facility ranged from 10 min in Vihiga County to 333 min in Garissa. Conclusion: Our study offers evidence of the spatial access estimates to NHIF-contracted facilities in Kenya that can inform contracting decisions by the social health insurer, especially focussing on marginalised counties where more facilities need to be contracted. Besides, this evidence will be crucial as the country gears towards accelerating progress towards achieving UHC using social health insurance as the strategy to drive the UHC agenda in Kenya. [ABSTRACT FROM AUTHOR]

Background: Staffing ratios in nursing homes vary among the federal states of Germany, but there are no rational grounds for these variations. In a previous study, a new instrument for the standardized calculation of staffing requirements in nursing homes was developed (Algorithm1.0). The development was based on a new empirical data collection method that derives actual and target values for the time and number of care interventions provided. Algorithm1.0 found an increased requirement of 36% of staff in German nursing homes. Based on these results, the German legislature has commissioned a model program to trial and evaluate a complex intervention comprising increased staffing combined with strategies for organizational development. Methods: The mixed-methods study consists of (i) developing a concept for restructuring the work organization, (ii) the application of this concept combined with increased staffing in 10 nursing homes (complex intervention), and the further development of the concept using a participatory and iterative formal evaluation process. The intervention consists of (a) quantitative measures of increased staffing based on a calculation using Algorithm1.0 and (b) qualitative measures regarding organizational development. The intervention will be conducted over one year. The effects of the intervention on job satisfaction and quality of care will be evaluated in (iii) a comprehensive prospective, controlled summative evaluation. The results will be compared with ten matched nursing homes as a control group. Finally, (iv) prototypical concepts for qualification-oriented work organization, a strategy for the national rollout, and the further development of Algorithm1.0 into Algorithm 2.0 will be derived. Discussion: In Germany, there is an ongoing dynamic legislation process regarding further developing the long-term care sector. The study, which is the subject of the study protocol presented here, generates an evidence-based strategy for the staffing requirements for nursing homes. Ethics and dissemination. This study was approved by the Ethics Committee of the German Association of Nursing Science (Deutsche Gesellschaft für Pflegewissenschaft) on 02.08.2023 (amended on 20.09.2023). Research findings are disseminated through presentations at national and international conferences and publications in peer-reviewed scientific journals. Trial registration number: German Clinical Trails Register DRKS00031773 (Date of registration 09.11.2023). [ABSTRACT FROM AUTHOR]

The application of network formulaology and network pharmacology has significantly advanced the scientific understanding of traditional Chinese medicine (TCM) treatment mechanisms in disease. The field of herbal biology is experiencing a surge in data generation. However, researchers are encountering challenges due to the fragmented nature of the data and the reliance on programming tools for data analysis. We have developed TCMNPAS, a comprehensive analysis platform that integrates network formularology and network pharmacology. This platform is designed to investigate in-depth the compatibility characteristics of TCM formulas and their potential molecular mechanisms. TCMNPAS incorporates multiple resources and offers a range of functions designed for automated analysis implementation, including prescription mining, molecular docking, network pharmacology analysis, and visualization. These functions enable researchers to analyze and obtain core herbs and core formulas from herbal prescription data through prescription mining. Additionally, TCMNPAS facilitates virtual screening of active compounds in TCM and its formulas through batch molecular docking, allowing for the rapid construction and analysis of networks associated with "herb-compound-target-pathway" and disease targets. Built upon the integrated analysis concept of network formulaology and network pharmacology, TCMNPAS enables quick point-and-click completion of network-based association analysis, spanning from core formula mining from clinical data to the exploration of therapeutic targets for disease treatment. TCMNPAS serves as a powerful platform for uncovering the combinatorial rules and mechanism of TCM formulas holistically. We distribute TCMNPAS within an open-source R package at GitHub (https://github.com/yangpluszhu/tcmnpas), and the project is freely available at http://54.223.75.62:3838/. [ABSTRACT FROM AUTHOR]

Background: Treatment variation from observational data has been used to estimate patient-specific treatment effects. Causal Forest Algorithms (CFAs) developed for this task have unknown properties when treatment effect heterogeneity from unmeasured patient factors influences treatment choice – essential heterogeneity. Methods: We simulated eleven populations with identical treatment effect distributions based on patient factors. The populations varied in the extent that treatment effect heterogeneity influenced treatment choice. We used the generalized random forest application (CFA-GRF) to estimate patient-specific treatment effects for each population. Average differences between true and estimated effects for patient subsets were evaluated. Results: CFA-GRF performed well across the population when treatment effect heterogeneity did not influence treatment choice. Under essential heterogeneity, however, CFA-GRF yielded treatment effect estimates that reflected true treatment effects only for treated patients and were on average greater than true treatment effects for untreated patients. Conclusions: Patient-specific estimates produced by CFAs are sensitive to why patients in real-world practice make different treatment choices. Researchers using CFAs should develop conceptual frameworks of treatment choice prior to estimation to guide estimate interpretation ex post. [ABSTRACT FROM AUTHOR]

Background: Pre-operative risk assessment can help clinicians prepare patients for surgery, reducing the risk of perioperative complications, length of hospital stay, readmission and mortality. Further, it can facilitate collaborative decision-making and operational planning. Objective: To develop effective pre-operative risk assessment algorithms (referred to as Patient Optimizer or POP) using Machine Learning (ML) that predict the development of post-operative complications and provide pilot data to inform the design of a larger prospective study. Methods: After institutional ethics approval, we developed a base model that encapsulates the standard manual approach of combining patient-risk and procedure-risk. In an automated process, additional variables were included and tested with 10-fold cross-validation, and the best performing features were selected. The models were evaluated and confidence intervals calculated using bootstrapping. Clinical expertise was used to restrict the cardinality of categorical variables (e.g. pathology results) by including the most clinically relevant values. The models were created with logistic regression (LR) and extreme gradient-boosted trees using XGBoost (Chen and Guestrin, 2016). We evaluated performance using the area under the receiver operating characteristic curve (AUROC) and the area under the precision-recall curve (AUPRC). Data was obtained from a metropolitan university teaching hospital from January 2015 to July 2020. Data collection was restricted to adult patients undergoing elective surgery. Results: A total of 11,475 adult admissions were included. The performance of XGBoost and LR was very similar across endpoints and metrics. For predicting the risk of any post-operative complication, kidney failure and length-of-stay (LOS), POP with XGBoost achieved an AUROC (95%CI) of 0.755 (0.744, 0.767), 0.869 (0.846, 0.891) and 0.841 (0.833, 0.847) respectively and AUPRC of 0.651 (0.632, 0.669), 0.336 (0.282, 0.390) and 0.741 (0.729, 0.753) respectively. For 30-day readmission and in-patient mortality, POP with XGBoost achieved an AUROC (95%CI) of 0.610 (0.587, 0.635) and 0.866 (0.777, 0.943) respectively and AUPRC of 0.116 (0.104, 0.132) and 0.031 (0.015, 0.072) respectively. Conclusion: The POP algorithms effectively predicted any post-operative complication, kidney failure and LOS in the sample population. A larger study is justified to improve the algorithm to better predict complications and length of hospital stay. A larger dataset may also improve the prediction of additional specific complications, readmission and mortality. [ABSTRACT FROM AUTHOR]

Background: Stroke is a leading cause of mortality and disability with ischemic stroke being the most common type of stroke. Salvianolic acid C (SalC), a polyphenolic compound found in Salviae Miltiorrhizae Radix et Rhizoma, has demonstrated therapeutic potential in the recovery phase of ischemic stroke. However, its pharmacological effects and underlying mechanisms during the early stages of ischemic stroke remain unclear. This study aimed to examine the potential mechanism of action of SalC during the early phase of ischemic stroke using network pharmacology strategies and RNA sequencing analysis. Methods: SalC effects on infarct volume, neurological deficits, and histopathological changes were assessed in a mouse model of transient middle cerebral artery occlusion (tMCAO). By integrating RNA sequencing data with a cerebral vascular disease (CVD)-related gene database, a cerebral ischemic disease (CID) network containing dysregulated genes from the tMCAO model was constructed. Network analysis algorithms were applied to evaluate the key nodes within the CID network. In vivo and in vitro validation of crucial targets within the identified pathways was conducted. Results: SalC treatment significantly reduced infarct volume, improved neurological deficits, and reversed pathological changes in the tMCAO mouse model. The integration of RNA sequencing data revealed an 80% gene reversion rate induced by SalC within the CID network. Among the reverted genes, 53.1% exhibited reversion rates exceeding 50%, emphasizing the comprehensive rebalancing effect of SalC within the CID network. Neuroinflammatory-related pathways regulated by SalC, including the toll-like-receptor 4 (TLR4)- triggering receptor expressed on myeloid cells 1 (TREM1)-nuclear factor kappa B (NF-κB) pathway, were identified. Further in vivo and in vitro experiments confirmed that TLR4-TREM1-NF-κB pathway was down-regulated by SalC in microglia, which was essential for its anti-inflammatory effect on ischemic stroke. Conclusions: SalC attenuated cerebral ischemic injury by inhibiting neuroinflammation mediated by microglia, primarily through the TLR4-TREM1-NF-κB pathway. These findings provide valuable insights into the potential therapeutic benefits of SalC in ischemic stroke. [ABSTRACT FROM AUTHOR]

Background: Liver cirrhosis is a chronic liver disease with hepatocyte necrosis and lesion. As one of the TCM formulas Wuling Powder (WLP) is widely used in the treatment of liver cirrhosis. However, it's key functional components and action mechanism still remain unclear. We attempted to explore the Key Group of Effective Components (KGEC) of WLP in the treatment of Liver cirrhosis through integrative pharmacology combined with experiments. Methods: The components and potential target genes of WLP were extracted from published databases. A novel node importance calculation model considering both node control force and node bridging force is designed to construct the Function Response Space (FRS) and obtain key effector proteins. The genetic knapsack algorithm was employed to select KGEC. The effectiveness and reliability of KGEC were evaluated at the functional level by using gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Finally, the effectiveness and potential mechanism of KGEC were confirmed by CCK-8, qPCR and Western blot. Results: 940 effective proteins were obtained in FRS. KEGG pathways and GO terms enrichments analysis suggested that effective proteins well reflect liver cirrhosis characteristics at the functional level. 29 components of WLP were defined as KGEC, which covered 100% of the targets of the effective proteins. Additionally, the pathways enriched for the KGEC targets accounted for 83.33% of the shared genes between the targets and the pathogenic genes enrichment pathways. Three components scopoletin, caryophyllene oxide, and hydroxyzinamic acid from KGEC were selected for in vivo verification. The qPCR results demonstrated that all three components significantly reduced the mRNA levels of COL1A1 in TGF-β1-induced liver cirrhosis model. Furthermore, the Western blot assay indicated that these components acted synergistically to target the NF-κB, AMPK/p38, cAMP, and PI3K/AKT pathways, thus inhibiting the progression of liver cirrhosis. Conclusion: In summary, we have developed a new model that reveals the key components and potential mechanisms of WLP for the treatment of liver cirrhosis. This model provides a reference for the secondary development of WLP and offers a methodological strategy for studying TCM formulas. [ABSTRACT FROM AUTHOR]

Background: Dento-maxillofacial deformities are common problems. Orthodontic–orthognathic surgery is the primary treatment but accurate diagnosis and careful surgical planning are essential for optimum outcomes. This study aimed to establish and verify a machine learning–based decision support system for treatment of dento-maxillofacial malformations. Methods: Patients (n = 574) with dento-maxillofacial deformities undergoing spiral CT during January 2015 to August 2020 were enrolled to train diagnostic models based on five different machine learning algorithms; the diagnostic performances were compared with expert diagnoses. Accuracy, sensitivity, specificity, and area under the curve (AUC) were calculated. The adaptive artificial bee colony algorithm was employed to formulate the orthognathic surgical plan, and subsequently evaluated by maxillofacial surgeons in a cohort of 50 patients. The objective evaluation included the difference in bone position between the artificial intelligence (AI) generated and actual surgical plans for the patient, along with discrepancies in postoperative cephalometric analysis outcomes. Results: The binary relevance extreme gradient boosting model performed best, with diagnostic success rates > 90% for six different kinds of dento-maxillofacial deformities; the exception was maxillary overdevelopment (89.27%). AUC was > 0.88 for all diagnostic types. Median score for the surgical plans was 9, and was improved after human–computer interaction. There was no statistically significant difference between the actual and AI- groups. Conclusions: Machine learning algorithms are effective for diagnosis and surgical planning of dento-maxillofacial deformities and help improve diagnostic efficiency, especially in lower medical centers. [ABSTRACT FROM AUTHOR]

Artificial intelligence (AI) has been integrated into dentistry for improvement of current dental practice. While many studies have explored the utilization of AI in various fields, the potential of AI in dentistry, particularly in low-middle income countries (LMICs) remains understudied. This scoping review aimed to study the existing literature on the applications of artificial intelligence in dentistry in low-middle income countries. A comprehensive search strategy was applied utilizing three major databases: PubMed, Scopus, and EBSCO Dentistry & Oral Sciences Source. The search strategy included keywords related to AI, Dentistry, and LMICs. The initial search yielded a total of 1587, out of which 25 articles were included in this review. Our findings demonstrated that limited studies have been carried out in LMICs in terms of AI and dentistry. Most of the studies were related to Orthodontics. In addition gaps in literature were noted such as cost utility and patient experience were not mentioned in the included studies. [ABSTRACT FROM AUTHOR]

Background: Smoking is a risk factor for many chronic diseases. Multiple smoking status ascertainment algorithms have been developed for population-based electronic health databases such as administrative databases and electronic medical records (EMRs). Evidence syntheses of algorithm validation studies have often focused on chronic diseases rather than risk factors. We conducted a systematic review and meta-analysis of smoking status ascertainment algorithms to describe the characteristics and validity of these algorithms. Methods: The Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines were followed. We searched articles published from 1990 to 2022 in EMBASE, MEDLINE, Scopus, and Web of Science with key terms such as validity, administrative data, electronic health records, smoking, and tobacco use. The extracted information, including article characteristics, algorithm characteristics, and validity measures, was descriptively analyzed. Sources of heterogeneity in validity measures were estimated using a meta-regression model. Risk of bias (ROB) in the reviewed articles was assessed using the Quality Assessment of Diagnostic Accuracy Studies-2 tool. Results: The initial search yielded 2086 articles; 57 were selected for review and 116 algorithms were identified. Almost three-quarters (71.6%) of algorithms were based on EMR data. The algorithms were primarily constructed using diagnosis codes for smoking-related conditions, although prescription medication codes for smoking treatments were also adopted. About half of the algorithms were developed using machine-learning models. The pooled estimates of positive predictive value, sensitivity, and specificity were 0.843, 0.672, and 0.918 respectively. Algorithm sensitivity and specificity were highly variable and ranged from 3 to 100% and 36 to 100%, respectively. Model-based algorithms had significantly greater sensitivity (p = 0.006) than rule-based algorithms. Algorithms for EMR data had higher sensitivity than algorithms for administrative data (p = 0.001). The ROB was low in most of the articles (76.3%) that underwent the assessment. Conclusions: Multiple algorithms using different data sources and methods have been proposed to ascertain smoking status in electronic health data. Many algorithms had low sensitivity and positive predictive value, but the data source influenced their validity. Algorithms based on machine-learning models for multiple linked data sources have improved validity. [ABSTRACT FROM AUTHOR]

Background: In the classification of bruxism patients based on electroencephalogram (EEG), feature extraction is essential. The method of using multi-channel EEG fusing electrocardiogram (ECG) and Electromyography (EMG) signal features has been proved to have good performance in bruxism classification, but the classification performance based on single channel EEG signal is still understudied. We investigate the efficacy of single EEG channel in bruxism classification. Methods: We have extracted time-domain, frequency-domain, and nonlinear features from single EEG channel to classify bruxism. Five common bipolar EEG recordings from 2 bruxism patients and 4 healthy controls during REM sleep were analyzed. The time domain (mean, standard deviation, root mean squared value), frequency domain (absolute, relative and ratios power spectral density (PSD)), and non-linear features (sample entropy) of different EEG frequency bands were analyzed from five EEG channels of each participant. Fine tree algorithm was trained and tested for classifying sleep bruxism with healthy controls using five-fold cross-validation. Results: Our results demonstrate that the C4P4 EEG channel was most effective for classification of sleep bruxism that yielded 95.59% sensitivity, 98.44% specificity, 97.84% accuracy, and 94.20% positive predictive value (PPV). Conclusions: Our results illustrate the feasibility of sleep bruxism classification using single EEG channel and provides an experimental foundation for the development of a future portable automatic sleep bruxism detection system. [ABSTRACT FROM AUTHOR]

The last decade of phylogenetics has seen the development of many methods that leverage constraints plus dynamic programming. The goal of this algorithmic technique is to produce a phylogeny that is optimal with respect to some objective function and that lies within a constrained version of tree space. The popular species tree estimation method ASTRAL, for example, returns a tree that (1) maximizes the quartet score computed with respect to the input gene trees and that (2) draws its branches (bipartitions) from the input constraint set. This technique has yet to be used for parsimony problems where the input are binary characters, sometimes with missing values. Here, we introduce the clade-constrained character parsimony problem and present an algorithm that solves this problem for the Dollo criterion score in O (| Σ | 3.726 (n + k) + | Σ | 1.726 n k) time, where n is the number of leaves, k is the number of characters, and Σ is the set of clades used as constraints. Dollo parsimony, which requires traits/mutations to be gained at most once but allows them to be lost any number of times, is widely used for tumor phylogenetics as well as species phylogenetics, for example analyses of low-homoplasy retroelement insertions across the vertebrate tree of life. This motivated us to implement our algorithm in a software package, called Dollo-CDP, and evaluate its utility for analyzing retroelement insertion presence / absence patterns for bats, birds, toothed whales as well as simulated data. Our results show that Dollo-CDP can improve upon heuristic search from a single starting tree, often recovering a better scoring tree. Moreover, Dollo-CDP scales to data sets with much larger numbers of taxa than branch-and-bound while still having an optimality guarantee, albeit a more restricted one. Lastly, we show that our algorithm for Dollo parsimony can easily be adapted to Camin-Sokal parsimony but not Fitch parsimony. [ABSTRACT FROM AUTHOR]

Background: Determination of batch-to-batch consistency of botanical drugs (BDs) has long been the bottleneck in quality evaluation primarily due to the chemical diversity inherent in BDs. This diversity presents an obstacle to achieving comprehensive standardization for BDs. Basically, a single detection mode likely leads to substandard analysis results as different classes of structures always possess distinct physicochemical properties. Whereas representing a workaround for multi-target standardization using multi-modal data, data processing for information from diverse sources is of great importance for the accuracy of classification. Methods: In this research, multi-modal data of 78 batches of Guhong injections (GHIs) consisting of 52 normal and 26 abnormal samples were acquired by employing HPLC-UV, -ELSD, and quantitative 1H NMR (q1HNMR), of which data obtained was then individually used for Pearson correlation coefficient (PCC) calculation and partial least square-discriminant analysis (PLS-DA). Then, a mid-level data fusion method with data containing qualitative and quantitative information to establish a support vector machine (SVM) model for evaluating the batch-to-batch consistency of GHIs. Results: The resulting outcomes showed that datasets from one detection mode (e.g., data from UV detectors only) are inadequate for accurately assessing the product's quality. The mid-level data fusion strategy for the quality evaluation enabled the classification of normal and abnormal batches of GHIs at 100% accuracy. Conclusions: A quality assessment strategy was successfully developed by leveraging a mid-level data fusion method for the batch-to-batch consistency evaluation of GHIs. This study highlights the promising utility of data from different detection modes for the quality evaluation of BDs. It also reminds manufacturers and researchers about the advantages of involving data fusion to handle multi-modal data. Especially when done jointly, this strategy can significantly increase the accuracy of product classification and serve as a capable tool for studies of other BDs. [ABSTRACT FROM AUTHOR]