Question Answering for Electronic Health Records: Scoping Review of Datasets and Models.

Background: Question answering (QA) systems for patient-related data can assist both clinicians and patients. They can, for example, assist clinicians in decision-making and enable patients to have a better understanding of their medical history. Substantial amounts of patient data are stored in electronic health records (EHRs), making EHR QA an important research area.

Biphasic co-detection of melanoma aneuploid tumor cells and tumor endothelial cells in guidance of specifying the field cancerized surgical excision margin and administering immunotherapy.

An optimum safety excision margin (EM) delineated by precise demarcation of field cancerization along with reliable biomarkers that enable predicting and timely evaluating patients' response to immunotherapy significantly impact effective management of melanoma. In this study, optimized biphasic "immunofluorescence staining integrated with fluorescence insitu hybridization" (iFISH) was conducted along the diagnosis-metastasis-treatment-cellular MRD axis to longitudinally co-detect a full spectrum of intact CD31 aneuploid tumor cells (TCs), CD31 aneuploid tumor endothelial cells (TECs), viable and necrotic circulating TCs (CTCs) and circulating TECs (CTECs) expressing PD-L1, Ki67, p16 and Vimentin in unsliced specimens of the resected primary tumor, EM, dissected sentinel lymph nodes (SLNs) and peripheral blood in an early-stage melanoma patient. Numerous PD-L1 aneuploid TCs and TECs were detected at the conventional safety EM (2 cm), quantitatively indicating the existence of a field cancerized EM for the first time.

Data science competition for cross-site individual tree species identification from airborne remote sensing data.

Data on individual tree crowns from remote sensing have the potential to advance forest ecology by providing information about forest composition and structure with a continuous spatial coverage over large spatial extents. Classifying individual trees to their taxonomic species over large regions from remote sensing data is challenging. Methods to classify individual species are often accurate for common species, but perform poorly for less common species and when applied to new sites.

Current status of weight bias and stigma in pediatrics and the need for greater focus on populations at risk.

Purpose Of Review: Obesity is one of the most common pediatric chronic conditions in the United States, affecting approximately 20% of American youth and is more common amongst Black, Latino, and Indigenous and low socioeconomic populations. The condition places children and adolescents at increased risk of physical and mental health conditions partly mediated by the weight bias and stigmatization experienced during the potentially vulnerable periods of childhood and adolescence.

Recent Findings: Weight bias and the resulting stigma are pervasive in society.

Formation of Artificial Fermi Surfaces with a Triangular Superlattice on a Conventional Two-Dimensional Electron Gas.

Imposing an external periodic electrostatic potential to the electrons confined in a quantum well makes it possible to engineer synthetic two-dimensional band structures, with electronic properties different from those in the host semiconductor. Here we report the fabrication and study of a tunable triangular artificial lattice on a GaAs/AlGaAs heterostructure where it is possible to transform from the original GaAs band structure and a circular Fermi surface to a new band structure with multiple artificial Fermi surfaces simply by altering a gate bias. For weak electrostatic modulation magnetotransport measurements reveal multiple quantum oscillations and commensurability oscillations due to the electron scattering from the artificial lattice.

Case report: Post-therapeutic laryngeal carcinoma patient possessing a high ratio of aneuploid CTECs to CTCs rapidly developed malignancy in pancreas.

Effectively evaluating therapeutic efficacy, detecting minimal residual disease (MRD) after therapy completion, and predicting early occurrence of malignancy in cancer patients remain as unmet imperative clinical demands. This article presents a case of a laryngeal carcinoma patient who had a surgical resection and complete post-operative chemoradiotherapy in combination with the targeted therapy, then rapidly developed pancreatic adenocarcinoma. Detected by SE-iFISH, the patient had a substantial amount of 107 non-hematological aneuploid circulating rare cells including 14 circulating tumor cells (CTCs, CD31/CD45) and 93 circulating tumor endothelial cells (CTECs, CD31/CD45) with a high ratio of CTECs/CTCs > 5 upon finishing post-surgical combination regimens.

Nonhematogenic circulating aneuploid cells confer inferior prognosis and therapeutic resistance in gliomas.

Aneuploidy is the hallmark of malignancy. Our previous study successfully detected nonhematogenic circulating aneuploidy cells (CACs) in types of gliomas. The current prospective clinical study aims to further precisely subcategorize aneuploid CACs, including CD31 circulating tumor cells (CTCs) and CD31 circulating tumor endothelial cells, and thoroughly investigate the clinical utilities of these different subtypes of cells.

Analysis of the prognostic role and biological characteristics of circulating tumor cell-associated white blood cell clusters in non-small cell lung cancer.

Background: Recently, circulating tumor-cell-associated white blood cell (CTC-WBC) clusters have been reported to have prognostic value in some cancers. The prognostic role of CTC-WBC clusters in lung cancer has not yet been elucidated. Very little information is available about the biological characteristics of CTC-WBC clusters.

Aneuploid Circulating Tumor Cells as a Predictor of Response to Neoadjuvant Chemotherapy in Non-Small Cell Lung Cancer.

Purpose: This study aimed to explore the potential application of circulating tumor cells (CTCs) in predicting the therapeutic effect of neoadjuvant chemotherapy (NAC) in non-small-cell lung cancer (NSCLC).

Methods: Using integrated subtraction enrichment and immunostaining-fluorescence in situ hybridization, the serial CTCs of patients with NSCLC were detected in 7.5 mL of blood at baseline and after two cycles of cisplatin-based NAC, and all aneuploidies of chromosome 8 were examined in the enriched CTCs.

Identification and Comprehensive Co-Detection of Necrotic and Viable Aneuploid Cancer Cells in Peripheral Blood.

Aneuploid circulating tumor cells (CTCs, CD31) and circulating tumor endothelial cells (CTECs, CD31) exhibit an active interplay in peripheral blood, and play an essential role in tumorigenesis, neoangiogenesis, disease progression, therapy-resistant minimal residual disease (MRD), cancer metastasis and relapse. Currently, most CTC detection techniques are restricted to the indistinguishable quantification of circulating rare cells, including both necrotic and viable cells in cancer patients. Clinically imperative demands to distinguish and detect live and/or dead non-hematological aneuploid cancer cells in peripheral blood, which will assist in the rapid evaluation of therapeutic effects, real-time monitoring of treatment resistance longitudinally developed along with therapy and the effective detection of post-therapeutic MRD, have not yet been achieved.

Role of aneuploid circulating tumor cells and CD31 circulating tumor endothelial cells in predicting and monitoring anti-angiogenic therapy efficacy in advanced NSCLC.

Prognosticating the efficacy of anti-angiogenic therapy through longitudinal monitoring and early detection of treatment resistance in cancer patients remain highly challenging. In this study, co-detection and comprehensive phenotypic and karyotypic molecular characterization of aneuploid circulating tumor cells (CTCs) and circulating tumor endothelial cells (CTECs) were conducted on non-small cell lung cancer (NSCLC) patients receiving bevacizumab plus chemotherapy. Prognostic values of the cell-based significant univariate risk factors identified by Cox regression analyses were progressively investigated.

Dysregulated KRAS gene-signaling axis and abnormal chromatin remodeling drive therapeutic resistance in heterogeneous-sized circulating tumor cells in gastric cancer patients.

The mechanism by which heterogeneous-sized circulating tumor cells (CTCs) in gastric cancer (GC) patients are resistant to the targeted therapy and/or chemotherapy remains unclear. This study investigated prognostic value and genomic variations of size-heterogenous CTCs, in an attempt to unravel the molecular mechanisms underlying the therapeutic resistance, which is relevant to poor prognosis in GC. Aneuploid CTCs, detected in 111 advanced GC patients, were categorized into small (≤white blood cell [WBC], 25.

Using FHIR to Construct a Corpus of Clinical Questions Annotated with Logical Forms and Answers.

This paper describes a novel technique for annotating logical forms and answers for clinical questions by utilizing Fast Healthcare Interoperability Resources (FHIR). Such annotations are widely used in building the semantic parsing models (which aim at understanding the precise meaning of natural language questions by converting them to machine-understandable logical forms). These systems focus on reducing the time it takes for a user to get to information present in electronic health records (EHRs).

PD-L1 aneuploid circulating tumor endothelial cells (CTECs) exhibit resistance to the checkpoint blockade immunotherapy in advanced NSCLC patients.

Sustained angiogenesis and increased PD-L1 expression on endothelial and carcinoma cells contribute toward fostering an immunosuppressive microenvironment suitable for tumor growth. PD-L1 CTCs were reported to associate with poor prognosis in NSCLC patients. However, whether or not aneuploid circulating tumor endothelial cells (CTECs) express PD-L1, then serve as a surrogate biomarker to evaluate immunotherapy efficacy remains unknown.

Epithelial-type systemic breast carcinoma cells with a restricted mesenchymal transition are a major source of metastasis.

Carcinoma cells undergo epithelial-mesenchymal transition (EMT); however, contributions of EMT heterogeneity to disease progression remain a matter of debate. Here, we addressed the EMT status of ex vivo cultured circulating and disseminated tumor cells (CTCs/DTCs) in a syngeneic mouse model of metastatic breast cancer (MBC). Epithelial-type CTCs with a restricted mesenchymal transition had the strongest lung metastases formation ability, whereas mesenchymal-type CTCs showed limited metastatic ability.

A data science challenge for converting airborne remote sensing data into ecological information.

Ecology has reached the point where data science competitions, in which multiple groups solve the same problem using the same data by different methods, will be productive for advancing quantitative methods for tasks such as species identification from remote sensing images. We ran a competition to help improve three tasks that are central to converting images into information on individual trees: (1) crown segmentation, for identifying the location and size of individual trees; (2) alignment, to match ground truthed trees with remote sensing; and (3) species classification of individual trees. Six teams (composed of 16 individual participants) submitted predictions for one or more tasks.

Comparing clinical judgment with the MySurgeryRisk algorithm for preoperative risk assessment: A pilot usability study.

Background: Major postoperative complications are associated with increased cost and mortality. The complexity of electronic health records overwhelms physicians' abilities to use the information for optimal and timely preoperative risk assessment. We hypothesized that data-driven, predictive-risk algorithms implemented in an intelligent decision-support platform simplify and augment physicians' risk assessments.

Evolutionary Expression of HER2 Conferred by Chromosome Aneuploidy on Circulating Gastric Cancer Cells Contributes to Developing Targeted and Chemotherapeutic Resistance.

Previous human epidermal growth factor receptor-2 (HER2)-derived resistance studies were based on models, which could not mirror evolutionary expression of HER2 during therapy. To investigate dynamic expression of HER2 and its contribution to developing therapeutic resistance conferred by chromosome aneuploidy, both the HER2 phenotype and chromosome 8 (Chr 8) aneuploidy on circulating tumor cells (CTC) were coexamined in advanced gastric cancer (AGC) patients. A total of 115 AGC patients, including 56 of histopathologic HER2 (hHER2) subjects who received first-line HER2-targeted therapy plus chemotherapy, and 59 of hHER2 patients who received chemotherapy alone, were prospectively enrolled.

MySurgeryRisk: Development and Validation of a Machine-learning Risk Algorithm for Major Complications and Death After Surgery.

Objective: To accurately calculate the risk for postoperative complications and death after surgery in the preoperative period using machine-learning modeling of clinical data.

Background: Postoperative complications cause a 2-fold increase in the 30-day mortality and cost, and are associated with long-term consequences. The ability to precisely forecast the risk for major complications before surgery is limited.

Quantified postsurgical small cell size CTCs and EpCAM circulating tumor stem cells with cytogenetic abnormalities in hepatocellular carcinoma patients determine cancer relapse.

Detection of hepatocellular carcinoma circulating tumor cells performed with conventional strategies, is significantly limited due to inherently heterogeneous and dynamic expression of EpCAM, as well as degradation of cytokeratins during epithelial-to-mesenchymal transition, which inevitably lead to non-negligible false negative detection of such "uncapturable and invisible" CTCs. A novel SE-iFISH strategy, improved for detection of HCC CTCs in this study, was applied to comprehensively detect, in situ phenotypically and karyotypically characterize hepatocellular and cholangiocarcinoma CTCs (CD45/CD31) in patients subjected to surgical resection. Clinical significance of diverse subtypes of CTC was systematically investigated.

Comprehensive in situ co-detection of aneuploid circulating endothelial and tumor cells.

Conventional circulating tumor cell (CTC) detection strategies rely on cell surface marker EpCAM and intracellular cytokeratins (CKs) for isolation and identification, respectively. Application of such methods is considerably limited by inherent heterogeneous and dynamic expression or absence of EpCAM and/or CKs in CTCs. Here, we report a novel strategy, integrating antigen-independent subtraction enrichment and immunostaining-FISH (SE-iFISH), to detect a variety of aneuploid circulating rare cells (CRCs), including CTCs and circulating tumor endothelial cells (CECs).

Aneuploidy of chromosome 8 in circulating tumor cells correlates with prognosis in patients with advanced gastric cancer.

Objective: Previous work indicated that aneuploidy of chromosome 8 in circulating tumor cells (CTCs) correlated with therapeutic efficacy for advanced gastric cancer (AGC) patients. In this follow-up study performed on the same population of AGC patients, we investigated whether and how aneuploidy of chromosome 8 in CTCs correlates with patients' clinical prognosis.

Methods: The prospective study was performed on 31 patients with newly diagnosed AGC.

Anisotropic Pauli Spin Blockade of Holes in a GaAs Double Quantum Dot.

Electrically defined semiconductor quantum dots are attractive systems for spin manipulation and quantum information processing. Heavy-holes in both Si and GaAs are promising candidates for all-electrical spin manipulation, owing to the weak hyperfine interaction and strong spin-orbit interaction. However, it has only recently become possible to make stable quantum dots in these systems, mainly due to difficulties in device fabrication and stability.

Enhanced detection and comprehensive in situ phenotypic characterization of circulating and disseminated heteroploid epithelial and glioma tumor cells.

Conventional strategy of anti-EpCAM capture and immunostaining of cytokeratins (CKs) to detect circulating tumor cells (CTCs) is limited by highly heterogeneous and dynamic expression or absence of EpCAM and/or CKs in CTCs. In this study, a novel integrated cellular and molecular approach of subtraction enrichment (SE) and immunostaining-FISH (iFISH) was successfully developed. Both large or small size CTCs and circulating tumor microemboli (CTM) in various biofluid samples including cerebrospinal fluid (CSF) of cancer patients and patient-derived-xenograft (PDX) mouse models were efficiently enriched and comprehensively identified and characterized by SE-iFISH.

Comprehensive characterization of chemotherapeutic efficacy on metastases in the established gastric neuroendocrine cancer patient derived xenograft model.

The HuPrime® human gastric neuroendocrine carcinoma derived xenograft model GA0087 was established in this study. GA0087 PDX model showed high gene expression of vascular endothelial growth factors (VEGF)-A and B, and high potential of lung metastasis. Circulating tumor cells (CTCs) with either large or small size, circulating tumor microemboli (CTM) and lung metastatic lesions were detected in GA0087 PDX mice.