Computer program

Cellular composition and anatomical organization influence normal and aberrant organ functions. Emerging spatial single-cell proteomic assays such as Image Mass Cytometry (IMC) and Co-Detection by Indexing (CODEX) have facilitated the study of cellular composition and organization by enabling high-throughput measurement of cells and their localization directly in intact tissues. However, annotation of cell types and quantification of their relative localization in tissues remain challenging. To address these unmet needs for atlas-scale datasets like Human Pancreas Analysis Program (HPAP), we develop AnnoSpat (Annotator and Spatial Pattern Finder) that uses neural network and point process algorithms to automatically identify cell types and quantify cell-cell proximity relationships...

BACKGROUND AND OBJECTIVE: The morbidity of lung adenocarcinoma (LUAD) has been increasing year by year and the prognosis is poor. This has prompted researchers to study the survival of LUAD patients to ensure that patients can be cured in time or survive after appropriate treatment. There is still no fully valid model that can be applied to clinical practice. METHODS: We introduced struc2vec-based multi-omics data integration (SBMOI), which could integrate gene expression, somatic mutations and clinical data to construct mutation gene vectors representing LUAD patient features...

BACKGROUND: Interventions to prevent or attenuate cognitive decline and dementia in older adults are becoming increasingly important. Recently, cognitive training exercise can be via computer or mobile technology for independent or home use. Recent meta-analysis has reported that Computerized Cognitive Training (CCT) is effective at enhancing cognitive function in healthy older and Alzheimer's disease adults, although little is known about individual characteristics of each computerized program...

Insertion of active retroelements-L1s, Alu s, and SVAs-can disrupt proper genome function and lead to various disorders including cancer. However, the role of de novo retroelements (DNRTs) in birth defects and childhood cancers has not been well characterized due to the lack of adequate data and efficient computational tools. Here, we examine whole-genome sequencing data of 3,244 trios from 12 birth defect and childhood cancer cohorts in the Gabriella Miller Kids First Pediatric Research Program. Using an improved version of our tool xTea (x-Transposable element analyzer) that incorporates a deep-learning module, we identified 162 DNRTs, as well as 2 pseudogene insertions...

BACKGROUND AND AIM: Sarcopenia has gained considerable attention in the context of hepatocellular carcinoma, as it has been correlated with a poorer prognosis among patients undergoing sorafenib or lenvatinib treatment for hepatocellular carcinoma (HCC). The clinical significance of sarcopenia in first-line advanced HCC patients treated with lenvatinib and programmed death-1 (PD-1) inhibitors needs to be clarified. METHODS: Sarcopenia was diagnosed using CT (Computed tomography) or MRI (Magnetic Resonance Imaging), with the psoas muscle index (PMI) as the surrogate marker...

OBJECTIVE: The peculiar aim of this study is to discover and identify the most effective and potential inhibitors against the most influential target ERα receptor by in silico studies of 45 phytochemicals from six diverse ayurvedic medicinal plants. METHODS: The molecular docking investigation was carried out by the genetic algorithm program of AutoDock Vina. The molecular dynamic (MD) simulation investigations were conducted using the Desmond tool of Schrödinger molecular modelling...

This article presents a numerical and artificial intelligence (AI) based investigation on the web crippling performance of pultruded glass fiber reinforced polymers' (GFRP) rectangular hollow section (RHS) profiles subjected to interior-one-flange (IOF) loading conditions. To achieve the desired research objectives, a finite element based computational model was developed using one of the popular simulating software ABAQUS CAE. This model was then validated by utilizing the results reported in experimental investigation-based article of Chen and Wang...

INTRODUCTION: ; The present study aims to determine the frequency of vascular calcification in Takayasu arteritis (TA) and the risk factors for it and to evaluate its relation with atherosclerotic predictors such as metabolic syndrome (MS), left ventricular mass index (LVMI) and carotid intima-media thickness (CIMT). METHOD: A cross-sectional study was conducted in patients with TA; MS was defined according to the US National Cholesterol Education Program/Adult Treatment Panel III (NCEP/ATP III) criteria...

BACKGROUND: Adolescent mental health problems impose a significant burden. Exploring evolving social environments could enhance comprehension of their impact on mental health. We aimed to depict the trajectories of the neighborhood social exposome from middle to late adolescence and assess the intricate relationship between them and late adolescent mental health. METHODS: Participants (n = 3965) from the FinnTwin12 cohort with completed questionnaires at age 17were used...

BACKGROUND: Phthalate exposure may contribute to hypertensive disorders of pregnancy (HDP), including preeclampsia/eclampsia (PE/E), but epidemiologic studies are lacking. OBJECTIVES: To evaluate associations of pregnancy phthalate exposure with development of PE/E and HDP. METHODS: Using data from 3,430 participants in eight Environmental influences on Child Health Outcomes (ECHO) Program cohorts (enrolled from 1999 to 2019), we quantified concentrations of 13 phthalate metabolites (8 measured in all cohorts, 13 in a subset of four cohorts) in urine samples collected at least once during pregnancy...

Combinatorial optimization (CO) has a broad range of applications in various fields, including operations research, computer science, and artificial intelligence. However, many of these problems are classified as nondeterministic polynomial-time (NP)-complete or NP-hard problems, which are known for their computational complexity and cannot be solved in polynomial time on traditional digital computers. To address this challenge, continuous-time Ising machine solvers have been developed, utilizing different physical principles to map CO problems to ground state finding...

BACKGROUND: Postpartum depression (PPD) poses a significant maternal health challenge. The current approach to detecting PPD relies on in-person postpartum visits, which contributes to underdiagnosis. Furthermore, recognizing PPD symptoms can be challenging. Therefore, we explored the potential of using digital biomarkers from consumer wearables for PPD recognition. OBJECTIVE: The main goal of this study was to showcase the viability of using machine learning (ML) and digital biomarkers related to heart rate, physical activity, and energy expenditure derived from consumer-grade wearables for the recognition of PPD...

IMPORTANCE: The association of endovascular therapy (EVT) with outcomes is unclear for patients with very low Alberta Stroke Program Early Computed Tomography Score (ASPECTS) within 24 hours of stroke onset. OBJECTIVE: To explore the association of EVT with functional and safety outcomes among patients with ASPECTS of 0 to 2 scored with noncontrast computed tomography. DESIGN, SETTING, AND PARTICIPANTS: This cohort study used data from an ongoing, prospective, observational, nationwide registry including all patients treated at 38 stroke centers in China with an occlusion in the internal carotid artery or M1 or M2 segment of the middle cerebral artery within 24 hours of witnessed symptom onset...

Sequence similarity is of paramount importance in biology, as similar sequences tend to have similar function and share common ancestry. Scoring matrices, such as PAM or BLOSUM, play a crucial role in all bioinformatics algorithms for identifying similarities, but have the drawback that they are fixed, independent of context. We propose a new scoring method for amino acid similarity that remedies this weakness, being contextually dependent. It relies on recent advances in deep learning architectures that employ self-supervised learning in order to leverage the power of enormous amounts of unlabelled data to generate contextual embeddings, which are vector representations for words...

Neuronal loss in Alzheimer's disease has been reported to display features of apoptosis, pyroptosis (programmed necrosis), or necroptosis. This study thoroughly examines the production and characterization of MCM-41 based berberine (BBR)-loaded porous silica nanoparticles (MSNs) by a modified Stöber method, focusing on their possible role in inhibiting the apoptotic process. Particle size, polydispersity index, morphology, drug loading, zeta potential, entrapment efficiency, and drug release were examined...

INTRODUCTION AND IMPORTANCE: Multiple-choice questions (MCQs) offer a suitable means to assess the cognitive domain of learners with a high degree of objectivity. The study's objective is to formulate an equation for determining the ideal timing for MCQ examinations, thereby inspiring the development of a model to estimate the duration of these examinations. METHODS: The authors generated a specific computer program that integrated with the operating system of the examination...

Life activities, such as respiration, are accomplished through the continuous shape modulation of cells, tissues, and organs. Developing smart materials with shape-morphing capability is a pivotal step toward life-like systems and emerging technologies of wearable electronics, soft robotics, and biomimetic actuators. Drawing inspiration from cells, smart vesicular systems have been assembled to mimic the biological shape modulation. This would enable the understanding of cellular shape adaptation and guide the design of smart materials with shape-morphing capability...

Electronic circular dichroism (ECD) spectroscopy is a widely employed method for studying chiral analysis, requiring the presence of a chromophore close to a chiral centre. Porphyrinoids are found to be one of the best chromophoric systems serving for this purpose and enabling the application of ECD spectroscopy for chirality determination across diverse classes of organic compounds. Consequently, it is crucial to understand the induction mechanisms of ECD in the porphyrin-based complexes. The present study explores systematically the influence of secondary chromophores, bonded to an achiral zinc porphyrin or to chiral guest molecules, on the B-region of ECD spectra using the time-dependent density functional theory (TD-DFT) calculations...

Tolterodine tartrate (TOTA) is associated with adverse effect, high hepatic access, varied bioavailability, slight aqueous solubility, and short half-life after oral delivery. Hansen solubility parameters (HSP, HSPiP program), experimental solubility (T = 298.2 to 318.2 K and p = 0.1 MPa), computational (van't Hoff and Apelblat models), and thermodynamic models were used to the select solvent(s). HSPiP predicted PEG400 as the most suitable co-solvent based on HSP values (δd  = 17...

INTRODUCTION: Patients are often instructed to avoid weight bearing on the proximal tibia for 6 - 12 weeks post-surgery to avoid fracture fixation failure. However, delayed weight bearing leads to delayed mobility, causing difficulties in daily activities; problems such as pain, limited knee ROM, reduced quadriceps muscle strength, and impaired functional outcomes are reported in long-term follow-up. This study primarily aimed to evaluate the feasibility and explore the effect size...