Computer-based documentation

Health and disease are fundamentally influenced by microbial communities and their genes (the microbiome). An in-depth analysis of microbiome structure that enables the classification of individuals based on their health can be crucial in enhancing diagnostics and treatment strategies to improve the overall well-being of an individual. In this paper, we present a novel semi-supervised methodology known as Randomized Feature Selection based Latent Dirichlet Allocation (RFSLDA) to study the impact of the gut microbiome on a subject's health status...

This system paper documents the technical foundations for the extension of the Topology ToolKit (TTK) to distributed-memory parallelism with the Message Passing Interface (MPI). While several recent papers introduced topology-based approaches for distributed-memory environments, these were reporting experiments obtained with tailored, mono-algorithm implementations. In contrast, we describe in this paper a versatile approach (supporting both triangulated domains and regular grids) for the support of topological analysis pipelines, i...

The Electronic Personal Health Record (EPHR) provides an innovative service for citizens and professionals to manage health data, promoting patient-centred care. It enhances communication between patients and physicians and improves accessibility to documents for remote medical information management. The study aims to assess the prevalence of awareness and acceptance of the EPHR in northern Italy and define determinants and barriers to its implementation. In 2022, a region-wide cross-sectional study was carried out through a paper-based and online survey shared among adult citizens...

High-quality data is critical to deriving useful and reliable information. However, real-world data often contains quality issues undermining the value of the derived information. Most existing research on data quality management focuses on tabular data, leaving semi-structured data under-exploited. Due to the schema-less and hierarchical features of semi-structured data, discovering and fixing quality issues is challenging and time-consuming. To address the challenge, this paper presents JsonCurer, an interactive visualization system to assist with data quality management in the context of JSON data...

Stable chest pain is a common symptom with multiple potential causes. Non-invasive imaging has an important role in diagnosis and guiding management through the assessment of coronary stenoses, atherosclerotic plaque, myocardial ischaemia or infarction, and cardiac function. Computed tomography (CT) provides the anatomical evaluation of coronary artery disease (CAD) with the assessment of stenosis, plaque type and plaque burden, with additional functional information available from CT fractional flow reserve (FFR) or CT myocardial perfusion imaging...

Gigantol, a bibenzyl compound extracted from various medicinal plants, has shown a number of biological activities, making it an attractive candidate for potential medical applications. This systematic review aims to shed light on gigantol's promising role in inflammation treatment and its underlying mechanisms. Gigantol exhibits potential anti-inflammatory properties in pre-clinical pharmacological test systems. It effectively reduced the levels of pro-inflammatory markers and arachidonic acid metabolites through various pathways, such as NF-κB, AKT, PI3K, and JNK/cPLA2/12-LOX...

Germline cells are critical for transmitting genetic information to subsequent generations in biological organisms. While their differentiation from somatic cells during embryonic development is well-documented in most animals, the regulatory mechanisms initiating plant germline cells are not well understood. To thoroughly investigate the complex morphological transformations of their ultrastructure over developmental time, nanoscale 3D reconstruction of entire plant tissues is necessary, achievable exclusively through electron microscopy imaging...

In Chinese archaeological research, analyzing the evolution of motifs in ancient pottery is crucial for studying the spread and growth of cultures across various eras and regions. However, such analyses are often challenging due to the complexities of identifying motifs with evolutionary connections that may manifest concurrent changes in appearance, space, and time, compounded by ineffective documentation. We propose PM-Vis, a visual analytics system for tracing and analyzing the evolution of pottery motifs...

Correlation signal processing of optical three-dimensional (x, y, t) data can produce super-resolution images. The second order cross-correlation function XC 2 has been documented to produce super-resolution imaging with static and blinking emitters but not for diffusing emitters. Here, we both analytically and numerically demonstrate cross-correlation analysis for diffusing particles. We then expand our fluorescence correlation spectroscopy super-resolution optical fluctuation imaging (fcsSOFI) analysis to use cross-correlation as a post-processing computational technique to extract both dynamic and structural information of particle diffusion in nanoscale structures simultaneously...

BACKGROUND: This study examines the potential long-term joint association between smoking and diet quality as modifiable risk factors concerning cardiovascular diseases (CVDs) incidence and all-cause mortality among current and former smokers. METHODS: The study followed 955 smokers from the third and fourth examinations of the Tehran Lipid and Glucose Study to March 2018. Dietary data was collected using a food frequency questionnaire. Three diet quality indices (DQIs) were computed at baseline: DQI-international (DQI-I), DQI-revised (DQI-R), and Mediterranean-DQI (Med-DQI)...

A growing body of evidence makes plain that exposure to perceived racism-based events, particularly for Black emerging adults aged 18-29, represents a major public health concern in the United States given its widespread prevalence and documented association with adverse health outcomes. However, research on the prevalence and correlates of exposure to perceived racism-based police violence (RPV) for Black emerging adults is scant. The current study examines the prevalence and correlates of RPV exposure among a sample of 300 Black emerging adult college students, utilizing computer-assisted surveys...

MOTIVATION: Aging is intricately linked to diseases and mortality. It is reflected in molecular changes across various tissues which can be leveraged for the development of biomarkers of aging using machine learning models, known as aging clocks. Despite advancements in the field, a significant challenge remains: the lack of robust, Python-based software tools for integrating and comparing these diverse models. This gap highlights the need for comprehensive solutions that can handle the complexity and variety of data in aging research...

Amniotes feature two principal visual processing systems: the tectofugal and thalamofugal pathways. In most mammals, the thalamofugal pathway predominates, routing retinal afferents through the dorsolateral geniculate complex to the visual cortex. In most birds, the thalamofugal pathway often plays the lesser role with retinal afferents projecting to the principal optic thalami, a complex of several nuclei that resides in the dorsal thalamus. This thalamic complex sends projections to a forebrain structure called the Wulst, the terminus of the thalamofugal visual system...

MOTIVATION: Cosegregation analysis is a powerful tool for identifying pathogenic genetic variants, but its implementation remains challenging. Existing software is either limited in scope or too demanding for many end users. Moreover, current solutions lack methods for assessing the robustness of cosegregation evidence, which is important due to its reliance on uncertain estimates. RESULTS: We present shinyseg, a comprehensive web application for clinical cosegregation analysis...

Enrolling patients to the standard of care (SOC) arm in randomized clinical trials, especially for rare diseases, can be very challenging due to the lack of resources, restricted patient population availability, and ethical considerations. As the therapeutic effect for the SOC is often well documented in historical trials, we propose a Bayesian platform trial design with hybrid control based on the multisource exchangeability modelling (MEM) framework to harness historical control data. The MEM approach provides a computationally efficient method to formally evaluate the exchangeability of study outcomes between different data sources and allows us to make better informed data borrowing decisions based on the exchangeability between historical and concurrent data...

High-risk coronary plaques (HRP) are characterized in clinical radiological imaging by the presence of low plaque attenuation, a napkin-ring sign (NRS), spotty calcifications (SC) and a positive remodeling index (RI). To evaluate if these signs are detectable in postmortem imaging by a multi-phase postmortem CT angiography (MPMCTA), a retrospective study of a series of autopsy well-documented coronary plaques related to sudden cardiac death (SCD) was performed. Then correlations between histological and radiological findings were described...

SUMMARY: Recent technical advancements in single-cell chromatin accessibility sequencing (scCAS) have brought new insights to the characterization of epigenetic heterogeneity. As single-cell genomics experiments scale up to hundreds of thousands of cells, the demand for computational resources of downstream analysis grows intractably large and exceeds the capabilities of most researchers. Here, we propose EpiCarousel, a tailored Python package based on lazy loading, parallel processing, and community detection for memory- and time-efficient identification of metacells, i...

Over the past decade, information for precision disease medicine has accumulated in the form of textual data. To effectively utilize this expanding medical text, we proposed a multi-task learning-based framework based on hard parameter sharing for knowledge graph construction (MKG), and then used it to automatically extract gastric cancer (GC)-related biomedical knowledge from the literature and identify GC drug candidates. In MKG, we designed three separate modules, MT-BGIPN, MT-SGTF and MT-ScBERT, for entity recognition, entity normalization, and relation classification, respectively...

INTRODUCTION AND IMPORTANCE: Bipolar fractures involving segmental fractures of the lateral and proximal clavicles are exceptionally rare, with only isolated cases documented in the literature. Such fractures may easily be overlooked during the initial presentation. CASE PRESENTATION: We present the case of a 35-year-old male with deformation in the middle segment of the clavicle following a road traffic accident (RTA). On radiography, the injury was initially thought to be a lateral clavicle fracture combined with sternoclavicular joint dislocation but was later changed to a bipolar clavicle fracture intraoperatively...

BACKGROUND: To effectively address severe deformities at the fracture site in patients, meticulous preoperative preparation is essential. This involves ensuring the restoration of the normal structural force line of the affected area and prevention of any residual deformities. By utilizing E3D technology prior to surgery, creating models based on individual patient image data and performing osteotomy, the required surgical parameters can be measured, thereby reducing surgical risks and enhancing precision...