MicroRNAs (miRNAs) play important roles in post-transcriptional processes and regulate major cellular functions. The abnormal regulation of expression of miRNAs has been linked to numerous human diseases such as respiratory diseases, cancer, and neurodegenerative diseases. Latest miRNA-disease associations are predominantly found in unstructured biomedical literature.
View Article and Find Full Text PDFDeep neural networks (DNN) have fundamentally revolutionized the artificial intelligence (AI) field. The transformer model is a type of DNN that was originally used for the natural language processing tasks and has since gained more and more attention for processing various kinds of sequential data, including biological sequences and structured electronic health records. Along with this development, transformer-based models such as BioBERT, MedBERT, and MassGenie have been trained and deployed by researchers to answer various scientific questions originating in the biomedical domain.
View Article and Find Full Text PDFAdverse drug events constitute a major challenge for the success of clinical trials. Several computational strategies have been suggested to estimate the risk of adverse drug events in preclinical drug development. While these approaches have demonstrated high utility in practice, they are at the same time limited to specific information sources.
View Article and Find Full Text PDFIEEE J Biomed Health Inform
September 2023
In situations like the COVID-19 pandemic, healthcare systems are under enormous pressure as they can rapidly collapse under the burden of the crisis. Machine learning (ML) based risk models could lift the burden by identifying patients with a high risk of severe disease progression. Electronic Health Records (EHRs) provide crucial sources of information to develop these models because they rely on routinely collected healthcare data.
View Article and Find Full Text PDFMotivation: Epilepsy is a multifaceted complex disorder that requires a precise understanding of the classification, diagnosis, treatment and disease mechanism governing it. Although scattered resources are available on epilepsy, comprehensive and structured knowledge is missing. In contemplation to promote multidisciplinary knowledge exchange and facilitate advancement in clinical management, especially in pre-clinical research, a disease-specific ontology is necessary.
View Article and Find Full Text PDFWe report an updated analysis from a phase I study of the spleen tyrosine kinase (SYK) and FMS-like tyrosine kinase 3 inhibitor mivavotinib, presenting data for the overall cohort of lymphoma patients, and the subgroup of patients with diffuse large B-cell lymphoma (DLBCL; including an expanded cohort not included in the initial report). Patients with relapsed/refractory lymphoma for which no standard treatment was available received mivavotinib 60-120 mg once daily in 28-day cycles until disease progression/unacceptable toxicity. A total of 124 patients with lymphoma, including 89 with DLBCL, were enrolled.
View Article and Find Full Text PDFThe COVID-19 pandemic has highlighted the lack of preparedness of many healthcare systems against pandemic situations. In response, many population-level computational modeling approaches have been proposed for predicting outbreaks, spatiotemporally forecasting disease spread, and assessing as well as predicting the effectiveness of (non-) pharmaceutical interventions. However, in several countries, these modeling efforts have only limited impact on governmental decision-making so far.
View Article and Find Full Text PDFObjective: Healthcare data such as clinical notes are primarily recorded in an unstructured manner. If adequately translated into structured data, they can be utilized for health economics and set the groundwork for better individualized patient care. To structure clinical notes, deep-learning methods, particularly transformer-based models like , have recently received much attention.
View Article and Find Full Text PDFPrediction and understanding of virus-host protein-protein interactions (PPIs) have relevance for the development of novel therapeutic interventions. In addition, virus-like particles open novel opportunities to deliver therapeutics to targeted cell types and tissues. Given our incomplete knowledge of PPIs on the one hand and the cost and time associated with experimental procedures on the other, we here propose a deep learning approach to predict virus-host PPIs.
View Article and Find Full Text PDFClin Pharmacol Drug Dev
September 2022
The pharmacokinetics (PK) and safety of ofatumumab and bendamustine alone and in combination were evaluated in patients with treatment-naive or relapsed indolent B-cell non-Hodgkin lymphoma (iNHL). Patients were randomly assigned to ofatumumab and bendamustine or ofatumumab alone. Ofatumumab PK concentration profiles and parameters were similar, alone or in combination with bendamustine.
View Article and Find Full Text PDFBackground: Health care records provide large amounts of data with real-world and longitudinal aspects, which is advantageous for predictive analyses and improvements in personalized medicine. Text-based records are a main source of information in mental health. Therefore, application of text mining to the electronic health records - especially mental state examination - is a key approach for detection of psychiatric disease phenotypes that relate to treatment outcomes.
View Article and Find Full Text PDFDengue is a serious public health concern worldwide, with ∼3 billion people at risk of contracting dengue virus (DENV) infections, with some suffering severe consequences of disease and leading to death. Currently, there is no broad use vaccine or drug available for the prevention or treatment of dengue, which leaves only anti-mosquito strategies to combat the dengue menace. The present study is an extension of our earlier study aimed at determining the and protective effects of a plant-derived phytopharmaceutical drug for the treatment of dengue.
View Article and Find Full Text PDFBackground: Indatuximab ravtansine (BT062) is an antibody-drug conjugate that binds to CD138 and synergistically enhances the antitumor activity of lenalidomide in preclinical models of multiple myeloma. This phase 1/2a study was done to determine the safety, activity, and pharmacokinetics of indatuximab ravtansine in combination with immunomodulatory drugs in patients with relapsed or refractory multiple myeloma.
Methods: This open-label, phase 1/2a study took place at nine hospital sites in the USA.
Stud Health Technol Inform
May 2021
During the current COVID-19 pandemic, the rapid availability of profound information is crucial in order to derive information about diagnosis, disease trajectory, treatment or to adapt the rules of conduct in public. The increased importance of preprints for COVID-19 research initiated the design of the preprint search engine preVIEW. Conceptually, it is a lightweight semantic search engine focusing on easy inclusion of specialized COVID-19 textual collections and provides a user friendly web interface for semantic information retrieval.
View Article and Find Full Text PDFMotivation: The COVID-19 pandemic has prompted an impressive, worldwide response by the academic community. In order to support text mining approaches as well as data description, linking and harmonization in the context of COVID-19, we have developed an ontology representing major novel coronavirus (SARS-CoV-2) entities. The ontology has a strong scope on chemical entities suited for drug repurposing, as this is a major target of ongoing COVID-19 therapeutic development.
View Article and Find Full Text PDFBackground: Recent studies have suggested comorbid association between Alzheimer's disease (AD) and type 2 diabetes mellitus (T2DM) through identification of shared molecular mechanisms. However, the inference is pre-dominantly literature-based and lacks interpretation of pre-disposed genomic variants and transcriptomic measurables.
Objective: In this study, we aim to identify shared genetic variants and dysregulated genes in AD and T2DM and explore their functional roles in the comorbidity between the diseases.
Driven by the use cases of PubChemRDF and SCAIView, we have developed a first community-based clinical trial ontology (CTO) by following the OBO Foundry principles. CTO uses the Basic Formal Ontology (BFO) as the top level ontology and reuses many terms from existing ontologies. CTO has also defined many clinical trial-specific terms.
View Article and Find Full Text PDFTranscriptomic approaches can give insight into molecular mechanisms underlying chemical toxicity and are increasingly being used as part of toxicological assessments. To aid the interpretation of transcriptomic data, we have developed a systems toxicology method that relies on a computable biological network model. We created the first network model describing cardiotoxicity in zebrafish larvae-a valuable emerging model species in testing cardiotoxicity associated with drugs and chemicals.
View Article and Find Full Text PDFStud Health Technol Inform
June 2020
Clinical and medical knowledge evolve and this causes changes in concepts and terms that describe them. The objective of this work is to formally present an ontology-based standard architecture that will be used in the scenario of neurodegeneration research to maintain terminologies and their relations updated and coherent over the time. The proposed structure is composed by three elements that will allow the user to do a list of operations on the terminology resources explicitly contemplated by the Common Terminology Service Release 2 (CTS2).
View Article and Find Full Text PDFPurpose: TAK-659 is an investigational, dual SYK/FLT3 inhibitor with preclinical activity in B-cell malignancy models. This first-in-human, dose-escalation/expansion study aimed to determine the safety, tolerability, MTD/recommended phase II dose (RP2D), and preliminary efficacy of TAK-659 in relapsed/refractory solid tumors and B-cell lymphomas.
Patients And Methods: Patients received continuous, once-daily oral TAK-659, 60-120 mg in 28-day cycles, until disease progression or unacceptable toxicity.