pathCLIP: Detection of Genes and Gene Relations From Biological Pathway Figures Through Image-Text Contrastive Learning.

In biomedical literature, biological pathways are commonly described through a combination of images and text. These pathways contain valuable information, including genes and their relationships, which provide insight into biological mechanisms and precision medicine. Curating pathway information across the literature enables the integration of this information to build a comprehensive knowledge base.

Iterative Prompt Refinement for Mining Gene Relationships from ChatGPT.

ChatGPT has demonstrated its potential as a surrogate knowledge graph. Trained on extensive data sources, including open-access publications, peer-reviewed research articles and biomedical websites, ChatGPT extracted information on gene relationships and biological pathways. However, a major challenge is model hallucination, i.

Rural populations facilitated early SARS-CoV-2 evolution and transmission in Missouri, USA.

In the United States, rural populations comprise 60 million individuals and suffered from high COVID-19 disease burdens. Despite this, surveillance efforts are biased toward urban centers. Consequently, how rurally circulating SARS-CoV-2 viruses contribute toward emerging variants remains poorly understood.

An alternative processing approach to increase CD138 intensity in flow cytometric analysis of plasma cells.

Background: Surface median immunofluorescence intensity (MFI) of plasma cells antigens, particularly CD138, by flow cytometry underestimates plasma cell populations when compared with that estimated by morphological assessment on Wright's-stained slides. CD138 MFI using traditional sample preparation methods for flow cytometric analysis is often dim and difficult to interpret due to multiple factors. This becomes critical when diagnosing and accurately classifying plasma cell dyscrasias.

pathCLIP: Detection of Genes and Gene Relations from Biological Pathway Figures through Image-Text Contrastive Learning.

In biomedical literature, biological pathways are commonly described through a combination of images and text. These pathways contain valuable information, including genes and their relationships, which provide insight into biological mechanisms and precision medicine. Curating pathway information across the literature enables the integration of this information to build a comprehensive knowledge base.

Applications of cutting-edge artificial intelligence technologies in biomedical literature and document mining.

The biomedical literature is a vast and invaluable resource for biomedical research. Integrating knowledge from the literature with biomedical data can help biological studies and the clinical decision-making process. Efforts have been made to gather information from the biomedical literature and create biomedical knowledge bases, such as KEGG and Reactome.

Dipeptidylpeptidase 4 promotes survival and stemness of acute myeloid leukemia stem cells.

Leukemic-stem-cell-specific targeting may improve the survival of patients with acute myeloid leukemia (AML) by avoiding the ablative effects of standard regimens on normal hematopoiesis. Herein, we perform an unbiased screening of compounds targeting cell surface proteins and identify clinically used DPP4 inhibitors as strong suppressors of AML development in both murine AML models and primary human AML cells xenograft model. We find in retrovirus-induced AML mouse models that DPP4-deficient AML cell-transplanted mice exhibit delay and reversal of AML development, whereas deletion of DPP4 has no significant effect on normal hematopoiesis.

Immune-Related Gene Signatures to Predict the Effectiveness of Chemoimmunotherapy in Triple-Negative Breast Cancer Using Exploratory Subgroup Discovery.

Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer with limited therapeutic options. Although immunotherapy has shown potential in TNBC patients, clinical studies have only demonstrated a modest response. Therefore, the exploration of immunotherapy in combination with chemotherapy is warranted.

SARS-CoV-2 and influenza co-infection: A cross-sectional study in central Missouri during the 2021-2022 influenza season.

As SARS-CoV-2 and influenza viruses co-circulate, co-infections with these viruses generate an increasing concern to public health. To evaluate the prevalence and clinical impacts of SARS-CoV-2 and influenza A virus co-infections during the 2021-2022 influenza season, SARS-CoV-2-positive samples from 462 individuals were collected from October 2021 to January 2022. Of these individuals, 152 tested positive for influenza, and the monthly co-infection rate ranged from 7.

Adherence to guidelines-recommended diagnostic testing was associated with overall survival in patients with diffuse large B-cell lymphoma after rituximab-based treatment: an observational cohort study.

Purpose: This study assessed the impact of adherence to guidelines-recommended diagnostic testing on treatment selection and overall survival (OS) in patients with diffuse large B-cell lymphoma (DLBCL) initiated on rituximab-based first line of treatment (1-LOT).

Methods: This retrospective cohort study used a nationwide electronic health record-derived de-identified database, including diagnostic testing information on immunohistochemistry (IHC), fluorescence in situ hybridization (FISH) and karyotype analysis that were abstracted from pathology reports or clinical visit notes, where available. The study included patients above 18 years old who were diagnosed with DLBCL between January 2011 and December 2019 and initiated on rituximab-based 1-LOT.

Early expression of mature αβ TCR in CD4CD8 T cell progenitors enables MHC to drive development of T-ALL bearing NOTCH mutations.

During normal T cell development in mouse and human, a low-frequency population of immature CD4CD8 double-negative (DN) thymocytes expresses early, mature αβ T cell antigen receptor (TCR). We report that these early αβ TCR+ DN (EADN) cells are DN3b-DN4 stage and require CD3δ but not major histocompatibility complex (MHC) for their generation/detection. When MHC - is present, however, EADN cells can respond to it, displaying a degree of coreceptor-independent MHC reactivity not typical of mature, conventional αβ T cells.

Investigation of the Utility of Features in a Clinical De-identification Model: A Demonstration Using EHR Pathology Reports for Advanced NSCLC Patients.

Background: Electronic health record (EHR) systems contain a large volume of texts, including visit notes, discharge summaries, and various reports. To protect the confidentiality of patients, these records often need to be fully de-identified before circulating for secondary use. Machine learning (ML) based named entity recognition (NER) model has emerged as a popular technique of automatic de-identification.

SARS-CoV-2 show no infectivity at later stages in a prolonged COVID-19 patient despite positivity in RNA testing.

Inpatient coronavirus disease 2019 (COVID-19) cases present enormous costs to patients and health systems in the United States. Many hospitalized patients may continue testing COVID-19 positive even after the resolution of symptoms. Thus, a pressing concern for clinicians is the safety of discharging these asymptomatic patients if they have any remaining infectivity.

Rapid High-Throughput Whole-Genome Sequencing of SARS-CoV-2 by Using One-Step Reverse Transcription-PCR Amplification with an Integrated Microfluidic System and Next-Generation Sequencing.

The long-lasting global COVID-19 pandemic demands timely genomic investigation of SARS-CoV-2 viruses. Here, we report a simple and efficient workflow for whole-genome sequencing utilizing one-step reverse transcription-PCR (RT-PCR) amplification on a microfluidic platform, followed by MiSeq amplicon sequencing. The method uses Fluidigm integrated fluidic circuit (IFC) and instruments to amplify 48 samples with 39 pairs of primers, including 35 custom-designed primer pairs and four additional primer pairs from the ARTIC network protocol v3.

The Value of Artificial Intelligence in Laboratory Medicine.

Objectives: As laboratory medicine continues to undergo digitalization and automation, clinical laboratorians will likely be confronted with the challenges associated with artificial intelligence (AI). Understanding what AI is good for, how to evaluate it, what are its limitations, and how it can be implemented are not well understood. With a survey, we aimed to evaluate the thoughts of stakeholders in laboratory medicine on the value of AI in the diagnostics space and identify anticipated challenges and solutions to introducing AI.

Digital Tumor Board Solutions Have Significant Impact on Case Preparation.

Purpose: Multidisciplinary tumor boards (TBs) are the gold standard for decision-making in cancer care. Variability in preparation, conduction, and impact is widely reported. The benefit of digital technologies to support TBs is unknown.

Artificial Intelligence-Driven Structurization of Diagnostic Information in Free-Text Pathology Reports.

Background: Free-text sections of pathology reports contain the most important information from a diagnostic standpoint. However, this information is largely underutilized for computer-based analytics. The vast majority of NLP-based methods lack a capacity to accurately extract complex diagnostic entities and relationships among them as well as to provide an adequate knowledge representation for downstream data-mining applications.

A clinician's perspective on co-developing and co-implementing a digital tumor board solution.

Healthcare has entered the information age. This will deliver huge opportunities for healthcare providers to deliver more individualized treatments for patients, and as such improve outcomes. Nowhere is the prospect greater than in cancer care.

The utility of thromboelastography and tranexamic acid in plasminogen activator inhibitor deficiency during pregnancy: a rare case report.

: Complete plasminogen activator inhibitor-1 (PAI-1) deficiency is a very rare genetic disorder that is associated with an increased risk of bleeding diathesis. Patients with PAI-1 deficiency are also known to be at increased risk for massive postpartum hemorrhage. We discuss one such rare case of PAI-1 deficiency in a young pregnant patient at 22 weeks of gestation with history of prolonged bleeding.

Localized accumulation of kappa restricted Russell body-containing plasma cells in tonsil.

An abnormal clonal plasma cell proliferation with Russell bodies is rare in chronic inflammatory reactions in adult patients. We describe the first case of light chain restricted Russell body accumulation within germinal centers of lymphoid follicles of the tonsil in a child. This should not be confused with a neoplastic process.

mutation in a child with refractory macrocytic anemia and Down Syndrome.

Here we report a case of refractory macrocytic anemia with a spliceosomal point mutation involving the gene in a child with Down syndrome (DS). Such mutations have been shown to cause refractory macrocytic anemia and myelodysplastic syndrome (MDS) in elderly individuals. We report the hematological indices of a child with DS and a spliceosomal mutation.

Molecular Testing Strategies for Pulmonary Adenocarcinoma: An Optimal Approach With Cost Analysis.

Context.—: Molecular analysis of lung adenocarcinoma for therapeutically important genes is standard of practice, with multiple professional organizations recommending testing of all adenocarcinomas for mutations in , , and . Some organizations recommend analyzing these genes in association with a panel.