Datamining

Hyperspectral imaging (HSI) is a robust and nondestructive method that can detect foreign particles such as microbial, chemical, and physical contamination in food. This review summarizes the work done in the last two decades in this field with a highlight on challenges, risks, and research gaps. Considering the challenges of using HSI on complex matrices like food (e.g., the confounding and masking effects of background signals), application of machine learning and modeling approaches that have been successful in achieving better accuracy as well as increasing the detection limit have also been discussed here...

BACKGROUND: Idiopathic neck pain patients frequently experience oculomotor disfunctions with deficits in eye movement control between neutral and neck torsion position (SPNT test) being commonly investigated in clinical and research settings. OBJECTIVES: The aim of the study was to determine accuracy of SPNT test in classifying idiopathic neck pain patients. DESIGN: a datamining based diagnostic accuracy study. METHODS: The study was conducted on a referred sample of 38 chronic neck pain patients from orthopaedic outpatient clinic and 40 healthy controls...

Heveins and hevein-containing (hev-) lectins play important roles in stress and pathogenic responses in plants but cause health concerns in humans. Hev-hololectins contain multiple modular hev-peptide domains and are abundantly present in cereals and pseudocereals. However, it is unclear why some cereal hev-hololectins are presented as different forms of proteolytically processed proteoforms. Here we show the precursor architectures of hev-hololectins lead to different processing mechanisms to give either hololectins or hevein-like peptides...

Mechanisms underlying breast cancer brain metastasis (BCBM) are still unclear. In this study, we observed that extracellular vesicles (EVs) secreted from breast cancer cells with increased expression of tGLI1, a BCBM-promoting transcription factor, strongly activated astrocytes. EV-derived microRNA/miRNA microarray revealed tGLI1-positive breast cancer cells highly secreted miR-1290 and miR-1246 encapsulated in EVs. Genetic knockin/knockout studies established a direct link between tGLI1 and both miRNAs. Datamining and analysis of patient samples revealed that BCBM patients had more circulating EV-miRs-1290/1246 than those without metastasis...

Attenuated total reflectance-infrared spectroscopy (ATR-IR) coupled with partial least squares regression (PLSR) was evaluated as a rapid, label free and cost-effective tool to quantify water content in extracts obtained from spirulina wet biomass using a glucose glycerol natural deep eutectic solvent (NADES). NADESs are green, renewable and biodegradable solvents with unique properties outcompeting existing organic solvents, for instance, for plant or biomass extraction. The properties of NADESs depend critically on their water concentration, and therefore, it is essential to develop methods to monitor it, to ensure optimal extraction efficiency and experimental repeatability to achieve a better standardization of extraction protocols...

To help contain the spread of the COVID-19 pandemic and to protect front-line workers, new antiviral measures are required. Antiviral nanoparticles are one such possible measure. Metal nanoparticles made from a variety of metals including gold, silver, and copper can kill or disable viruses that cause significant health problems in humans (such as SARS-CoV-2, HIV, or influenza). To promote interaction between nanoparticles and viruses the stabilizing ligands on the nanoparticle surface should be optimized for docking with proteins...

Background: Over 80% people with Parkinson's disease (PD; PwP) live with chronic pain. Objective: Whether ethnic disparities in receipt of appropriate analgesia exist among PwP with chronic pain living in the United Kingdom (UK). Methods: A retrospective datamining of an existing King's PD Pain Questionnaire validation study dataset enrolling 300 PwP. Results: 69 PwP: 23 Black (57% female), 23 Asian (57% female) and 23 White (65% female) had similar pain burden on the King's PD Pain Scale...

The analytical stability of laboratory tests relies mostly on internal and external quality control procedures. Summarized patient data has in several studies been shown to be a good supplement for monitoring analytical stability. In our present investigation, we evaluate a datamining method for retrospective evaluation and assessment of analyte stability in whole blood. Results from the laboratory information system were used as the basis for the datamining approach. Blood tests were requested by the general practitioners and drawing of the blood sample was either at the general practitioner's or at the hospital outpatient clinics...

There are many difficulties in extracting and using knowledge for medical analytic and predictive purposes from Real-World Data, even when the data is already well structured in the manner of a large spreadsheet. Preparative curation and standardization or "normalization" of such data involves a variety of chores but underlying them is an interrelated set of fundamental problems that can in part be dealt with automatically during the datamining and inference processes. These fundamental problems are reviewed here and illustrated and investigated with examples...

Forming metallurgical phases has a critical impact on the performance of dissimilar materials joints. Here, we shed light on the forming mechanism of equilibrium and non-equilibrium intermetallic compounds (IMCs) in dissimilar aluminum/steel joints with respect to processing history (e.g., the pressure and temperature profiles) and chemical composition, where the knowledge of free energy and atomic diffusion in the Al-Fe system was taken from first-principles phonon calculations and data available in the literature...

The present brief survey is to alert developers in datamining, machine learning, inference methods, and other approaches in relation to diagnostic, predictive, and risk assessment medicine about a relatively new class of bioactive messaging peptides in which there is escalating interest. They provide patterns of communication and cross-chatter about states of health and disease within and, importantly, between cells (they also appear extracellularly in biological fluids). This chatter needs to be analyzed somewhat in the manner of the decryption of the Enigma code in the Second World War...

Cardio-oncology is an emerging field that transformed the medical management of patients with cancer. It encompasses the prevention and treatment of cardiovascular toxicities related to cancer treatments, aiming to reduce cardiac adverse events among cancer survivors. Cardiovascular toxicities related to cancer treatments are described through data collected during phase I to phase III therapeutic trials, and post-marketing surveillance (phase IV). Pharmacovigilance analyses, based on datamining from these extensive databases, allowed to understanding and identifying new adverse drug reactions, some recently made available, such as immunotherapy or inhibitor of Bruton tyrosine kinase (IBTK)...

The first step in the infection of fungal pathogens in humans is the adhesion of the pathogen to host tissue cells or abiotic surfaces such as catheters and implants. One of the main players involved in this are the expressed cell wall adhesins. Here, we review the Flo adhesin family and their involvement in the adhesion of these yeasts during human infections. Firstly, we redefined the Flo adhesin family based on the domain architectures that are present in the Flo adhesins and their functions, and set up a new classification of Flo adhesins...

INTRODUCTION: Joint damage in haemophilia often requires surgical correction. However, the surgery effect on bleeding rates and other clinical joint outcomes can be unclear. AIM: To investigate the effects of joint surgery on joint annualized bleeding rates (JABRs) and physical health outcomes in patients with haemophilia A undergoing N8-GP prophylaxis. METHODS: Patients in the pathfinder 2 trial received N8-GP prophylaxis, enrolling in the pathfinder 3 trial for indicated surgery...

While transcriptome- and proteome-wide technologies to assess processes in protein biogenesis are now widely available, we still lack global approaches to assay post-ribosomal biogenesis events, in particular those occurring in the eukaryotic secretory system. We here develop a method, SECRiFY, to simultaneously assess the secretability of >105 protein fragments by two yeast species, S. cerevisiae and P. pastoris, using custom fragment libraries, surface display and a sequencing-based readout. Screening human proteome fragments with a median size of 50-100 amino acids, we generate datasets that enable datamining into protein features underlying secretability, revealing a striking role for intrinsic disorder and chain flexibility...

PURPOSE/OBJECTIVE(S): Immune checkpoint inhibitor (ICI) therapy has emerged as the standard of care for patients with advanced non-small cell lung cancer (aNSCLC). Immuno-monotherapy (ImT) offers a better side effect profile than combination ICIs, but treatment response rates remain less than 25%. Predicting response to ImT could spare potential responders from adverse events and direct non-responders toward alternative treatments. Radiomics, a datamining technique that extracts patterns from medical imaging, has been incorporated into predictive models for many cancers...

Energetic metabolism controls key steps of kidney development, homeostasis, and epithelial repair following acute kidney injury (AKI). Hepatocyte nuclear factor-1β (HNF-1β) is a master transcription factor that controls mitochondrial function in proximal tubule (PT) cells. Patients with HNF1B pathogenic variant display a wide range of kidney developmental abnormalities and progressive kidney fibrosis. Characterizing the metabolic changes in PT cells with HNF-1β deficiency may help to identify new targetable molecular hubs involved in HNF1B-related kidney phenotypes and AKI...

Current understanding of functional characteristics and biochemical pathways in taste bud cells have been hindered due the lack of long-term cultured cells. To address this, we developed a holistic approach to fully characterise long term cultured bovine taste bud cells (BTBCs). Initially, cultured BTBCs were characterised using RT-PCR gene expression profiling, immunocytochemistry, flowcytometry and calcium imaging, that confirmed the cells were mature TBCs that express taste receptor genes, taste specific protein markers and capable of responding to taste stimuli, i...

Numerous studies have provided single-cell transcriptome profiles of host responses to SARS-CoV-2 infection. Critically lacking however is a datamine that allows users to compare and explore cell profiles to gain insights and develop new hypotheses. To accomplish this, we harmonized datasets from COVID-19 and other control condition blood, bronchoalveolar lavage, and tissue samples, and derived a compendium of gene signature modules per cell type, subtype, clinical condition, and compartment. We demonstrate approaches to probe these via a new interactive web portal (https://toppcell...

Since its identification in 2003, grapevine Pinot gris virus (GPGV, Trichovirus ) has now been detected in most grape-growing countries. So far, little is known about the epidemiology of this newly emerging virus. In this work, we used datamining as a tool to monitor in-silico the sanitary status of three vineyards in Italy. All data used in the study were recovered from a work that was already published and for which data were publicly available as SRA (Sequence Read Archive, NCBI) files. While incomplete, knowledge gathered from this work was still important, with evidence of differential accumulation of the virus in grapevine according to year, location, and variety-rootstock association...