Automaticity

The Gene Expression Omnibus (GEO) is a major open biomedical research repository for transcriptomics and other omics datasets. It currently contains millions of gene expression samples from tens of thousands of studies collected by many biomedical research laboratories from around the world. While users of the GEO repository can search the metadata describing studies for locating relevant datasets, there are currently no methods or resources that facilitate global search of GEO at the data level. To address this shortcoming, we developed RummaGEO, a webserver application that enables gene expression signature search of a large collection of human and mouse RNA-seq studies deposited into GEO...

We present a mechanically sheared image acquisition format for upright and open-top light-sheet microscopes that automatically places data in its proper spatial context. This approach, which reduces computational post-processing and eliminates unnecessary interpolation or duplication of the data, is demonstrated on an upright variant of Axially Swept Light-Sheet Microscopy (ASLM) that achieves a field of view, measuring 774 x 435 microns, that is 3.2-fold larger than previous models and a raw and isotropic resolution of ∼420 nm...

This paper aims to investigate the dynamic response characteristics of subway station under earthquakes. To this end, seismic waves are transformed into equivalent nodal loads on viscoelastic artificial boundaries using theories and methods of wave motion. The calculation formulas for equivalent nodal loads of SV waves incident at any angle are established, and ANSYS' APDL program compiles to automatically generate the viscoelastic artificial boundary and input the seismic loads. A finite element model of soil-subway station interaction was established, and the seismic response characteristics of a two-story three-span subway station under different incidence angles of SV waves were investigated using the above seismic input method...

BACKGROUND AND AIMS: This cohort study investigated associations of nonalcoholic fatty liver disease (NAFLD) and metabolic dysfunction-associated fatty liver disease (MAFLD) with risk of increase in arterial stiffness (AS), measured as brachial-ankle pulse wave velocity (baPWV). METHODS AND RESULTS: Participants who had health examinations between 2006 and 2019 were analyzed for fatty liver and increased baPWV using liver ultrasonography and automatic volume plethysmography device...

In this paper I discuss the main models that have tried to explain brain asymmetries for emotions. The first models, based on clinical observations, proposed either a general right hemisphere dominance for emotions (the'right hemisphere') model or a different specialization of the right hemisphere for negative and of the left hemisphere for positive emotions (the'valence' model). In more recent times new models, based on partly modified versions of the previous ones have been proposed. The revised version of the 'valence' model, labeled the 'approach-avoidance' model maintained that hemispheric asymmetries are not related to the valence of the emotional stimulus but to the motivational (approach vs avoidance) system that is engaged by that stimulus...

In recent years, there has been a surge in the publication of clinical trial reports, making it challenging to conduct systematic reviews. Automatically extracting Population, Intervention, Comparator, and Outcome (PICO) from clinical trial studies can alleviate the traditionally time-consuming process of manually scrutinizing systematic reviews. Existing approaches of PICO frame extraction involves supervised approach that relies on the existence of manually annotated data points in the form of BIO label tagging...

Consumer concerns over healthy diets are increasing as a result of the toxicity and persistence of pesticide residues in foodstuffs. Developing sensitive and high-throughput monitoring techniques for these trace residues is seen as an essential step in ensuring food safety. An automatic and sensitive multi-residue analytical method was developed and validated for the simultaneous determination of 230 compounds, including pesticides and their hazardous metabolites, in fermented soy products. The method included preparing the sample using on-line extraction and clean-up system based on accelerated solvent extraction (ASE), then determining the analytes using GC-MS/MS techniques...

Previous studies have shown that adults exhibit the strongest attentional bias toward neutral infant faces when viewing faces with different expressions at different attentional processing stages due to different stimulus presentation times. However, it is not clear how the characteristics of the temporal processing associated with the strongest effect change over time. Thus, we combined a free-viewing task with eye-tracking technology to measure adults' attentional bias toward infant and adult faces with happy, neutral, and sad expressions of the same face...

OBJECTIVE: Focal cortical dysplasias (FCD) are characterized by distinct interictal spike patterns and high frequency oscillations (HFOs; ripples: 80-250 Hz; fast ripples: 250-500 Hz) in the intra-operative electrocorticogram (ioECoG). We studied the temporal relation between intra-operative spikes and HFOs and their relation to resected tissue in people with FCD with a favorable outcome. METHODS: We included patients who underwent ioECoG-tailored epilepsy surgery with pathology confirmed FCD and long-term Engel 1A outcome...

Great efforts have been made over the years to identify novel drug pairs with synergistic effects. Although numerous computational approaches have been proposed to analyze diverse types of biological big data, the pharmacogenomic profiles, presumably the most direct proxy of drug effects, have been rarely used due to the data sparsity problem. In this study, we developed a composite deep-learning-based model that predicts the drug synergy effect utilizing pharmacogenomic profiles as well as molecular properties...

Cholestasis, characterized by the obstruction of bile flow, poses a significant concern in neonates and infants. It can result in jaundice, inadequate weight gain, and liver dysfunction. However, distinguishing between biliary atresia (BA) and non-biliary atresia in these young patients presenting with cholestasis poses a formidable challenge, given the similarity in their clinical manifestations. To this end, our study endeavors to construct a screening model aimed at prognosticating outcomes in cases of BA...

Accurately identifying cancer driver genes (CDGs) is crucial for guiding cancer treatment and has recently received great attention from researchers. However, the high complexity and heterogeneity of cancer gene regulatory networks limit the precition accuracy of existing deep learning models. To address this, we introduce a model called SCIS-CDG that utilizes Schur complement graph augmentation and independent subspace feature extraction techniques to effectively predict potential CDGs. Firstly, a random Schur complement strategy is adopted to generate two augmented views of gene network within a graph contrastive learning framework...

Visual symmetry activates a network of regions in the extrastriate cortex and generates an event-related potential (ERP) called the sustained posterior negativity (SPN). Previous work has found that the SPN is robust to experimental manipulations of task, spatial attention, and memory load. In the current study, we investigated whether the SPN is also robust to alcohol-induced changes in mental state. A pilot experiment (N = 13) found that alcohol unexpectedly increased SPN amplitude. We followed this unexpected result with two new experiments on separate groups, using an alcohol challenge paradigm...

BACKGROUND: During COVID-19 pandemic period, it was difficult for the patients regular and scheduled follow-up in outpatient department, especially when lock-down. However, early detection of patients with initial infection or other serious conditions after ocular surgeries, such as intravitreous injection (IVI) for age-related macular degeneration (AMD). OBJECTIVE: We accessed a postoperative care chatbot system (PCCS) in smartphone for patients to self-report postoperative symptoms/signs with an instant bidirectional feedback system...

BACKGROUND: Preoperative imaging evaluation of liver volume and hepatic steatosis for the donor affects transplantation outcomes. However, computed tomography (CT) for liver volumetry and magnetic resonance spectroscopy (MRS) for hepatic steatosis are time consuming. Therefore, we investigated the correlation of automated 3D-multi-echo-Dixon sequence magnetic resonance imaging (ME-Dixon MRI) and its derived proton density fat fraction (MRI-PDFF) with CT liver volumetry and MRS hepatic steatosis measurements in living liver donors...

BACKGROUND: Few studies have described the insights of frontline health care providers and patients on how the diagnostic process can be improved in the emergency department (ED), a setting at high risk for diagnostic errors. The authors aimed to identify the perspectives of providers and patients on the diagnostic process and identify potential interventions to improve diagnostic safety. METHODS: Semistructured interviews were conducted with 10 ED physicians, 15 ED nurses, and 9 patients/caregivers at two separate health systems...

Sudden cardiac death (SCD) represents the most severe complication of hypertrophic cardiomyopathy (HCM). However, the relationship between strain, strain rate, and risk factors in SCD risk stratification remains elusive. The study aimed to assess the attenuation of strain and strain rate in HCM by feature-tracking cardiac magnetic resonance (FT-CMR). All strain and strain rates were obtained automatically by FT, with manual adjustment of endocardial and epicardial borders. Strain indicators included left ventricular (LV) global longitudinal (GLS), circumferential (GCS), radial strain (GRS), peak diastolic-longitudinal (PD-LSR), circumferential (PD-CSR), and radial strain rate (PD-RSR)...

Rhythmic movement is the fundamental motion dynamics characterized by repetitive patterns. Precisely defining onsets in rhythmic movement is essential for a comprehensive analysis of motor functions. Our study introduces an automated method for detecting rat's forelimb foot-strike onsets using deep learning tools. This method demonstrates high accuracy of onset detection by combining two techniques using joint coordinates and behavioral confidence scale. The analysis extends to neural oscillatory responses in the rat's somatosensory cortex, validating the effectiveness of our combined approach...

The objectives of this study were to assess the effect of a reduced liner-open phase applied through flow-responsive pulsation (FRP), as a method to provide supplemental stimulation, on teat tissue conditions and milking characteristics in dairy cows. In 2 switch-back trials, 156 Holstein cows milked 3 times daily were assigned to the FRP or conventional (CON) group in alternating sequences. Trial I lasted for 35 d and was split into 5 alternating 1-week periods of FRP and CON. The duration of Trial II was 84 d, consisting of 4 alternating 3-week periods of FRP and CON...

Breast cancer, a highly formidable and diverse malignancy predominantly affecting women globally, poses a significant threat due to its intricate genetic variability, rendering it challenging to diagnose accurately. Various therapies such as immunotherapy, radiotherapy, and diverse chemotherapy approaches like drug repurposing and combination therapy are widely used depending on cancer subtype and metastasis severity. Our study revolves around an innovative drug discovery strategy targeting potential drug candidates specific to RTK signalling, a prominently targeted receptor class in cancer...