Reference curves for pediatric endocrinology: leveraging biomarker z-scores for clinical classifications

Context: Hormone reference intervals in pediatric endocrinology are traditionally partitioned by age and lack the framework for benchmarking individual blood test results as normalized z-scores and plotting sequential measurements onto a chart. Reference curve modeling is applicable to endocrine variables and represents a standardized method to account for variation with gender and age. Objective: We aimed to establish gender-specifc biomarker reference curves for clinical use and benchmark associations between hormones, pubertal phenotype, and body mass index (BMI). Methods: Using cross-sectional population sample data from 2139 healthy Norwegian children and adolescents, we analyzed the pubertal status, ultrasound measures of glandular breast tissue (girls) and testicular volume (boys), BMI, and laboratory measurements of 17 clinical biomarkers modeled using the established “LMS” growth chart algorithm in R. Results: Reference curves for puberty hormones and pertinent biomarkers were modeled to adjust for age and gender. Z-score equivalents of biomarker levels and anthropometric measurements were compiled in a comprehensive beta coeffcient matrix for each gender. Excerpted from this analysis and independently of age, BMI was positively associated with female glandular breast volume (β = 0.5, P < 0.001) and leptin (β = 0.6, P < 0.001), and inversely correlated with serum levels of sex hormone-binding globulin (SHBG) (β = −0.4, P < 0.001). Biomarker z-score profles differed signifcantly between cohort subgroups stratifed by puberty phenotype and BMI weight class. <p<Conclusion: Biomarker reference curves and corresponding z-scores provide an intuitive framework for clinical implementation in pediatric endocrinology and facilitate the application of machine learning classifcation and covariate precision medicine for pediatric patients

Cardiogenic Shock

Cardiogenic shock is a leading cause of mortality in critical care units globally, despite advances in research and medical management. This shock state is caused by an initial insult directly to the heart, including myocardial infarction, ventricular failure, or valve dysfunction. The purpose of this poster is to provide an overview of pathophysiology, signs and symptoms, clinical classifications, and management options for cardiogenic shock

Quantifying prediction of pathogenicity for within-codon concordance (PM5) using 7541 functional classifications of BRCA1 and MSH2 missense variants.

PURPOSE: Conditions and thresholds applied for evidence weighting of within-codon concordance (PM5) for pathogenicity vary widely between laboratories and expert groups. Because of the sparseness of available clinical classifications, there is little evidence for variation in practice. METHODS: We used as a truthset 7541 dichotomous functional classifications of BRCA1 and MSH2, spanning 311 codons of BRCA1 and 918 codons of MSH2, generated from large-scale functional assays that have been shown to correlate excellently with clinical classifications. We assessed PM5 at 5 stringencies with incorporation of 8 in silico tools. For each analysis, we quantified a positive likelihood ratio (pLR, true positive rate/false positive rate), the predictive value of PM5-lookup in ClinVar compared with the functional truthset. RESULTS: pLR was 16.3 (10.6-24.9) for variants for which there was exactly 1 additional colocated deleterious variant on ClinVar, and the variant under examination was equally or more damaging when analyzed using BLOSUM62. pLR was 71.5 (37.8-135.3) for variants for which there were 2 or more colocated deleterious ClinVar variants, and the variant under examination was equally or more damaging than at least 1 colocated variant when analyzed using BLOSUM62. CONCLUSION: These analyses support the graded use of PM5, with potential to use it at higher evidence weighting where more stringent criteria are met

Survival of esophageal cancer in China: A pooled analysis on hospital-based studies from 2000 to 2018

Background: Esophageal cancer (EC) causes more than 400 thousand deaths per year, and half of them occur in China. There are discrepancies regarding the survival of EC patients between population-based surveillance studies and hospital-based studies. Objectives: We aimed to synthesize the survival data from hospital-based EC studies in the Chinese population from 2000 to 2018 and to compare the survival rates between EC patients with different clinical classifications. Methods: The protocol of this systematic review was registered in PROSPERO (CRD-42019121559). We searched Embase, PubMed, CNKI, and Wanfang databases for studies published between January 1, 2000 and December 31, 2018. We calculated the pooled survival rates and 95% confidence intervals (CIs) by Stata software (V14.0). Results: Our literature search identified 933 studies, of which 331 studies with 79,777 EC patients met the inclusion criteria and were included in meta-analyses. The pooled survival rates were 74.1% (95% CI: 72.6–75.7%) for 1-year survival, 49.0% (95% CI: 44.2–53.8%) for 2-years survival, 46.0% (95% CI: 42.6–49.5%) for 3-years survival, and 40.1% (95% CI: 33.7–46.4%) for 5-years survival. An increased tendency toward EC survival was verified from 2000 to 2018. In addition, discrepancies were observed between EC patients with different clinical classifications (e.g., stages, histologic types, and cancer sites). Conclusions: Our findings showed a higher survival rate in hospital-based studies than population-based surveillance studies. Although this hospital-based study is subject to potential representability and publication bias, it offers insight into the prognosis of patients with EC in China

Improving Term Extraction with Terminological Resources

Studies of different term extractors on a corpus of the biomedical domain revealed decreasing performances when applied to highly technical texts. The difficulty or impossibility of customising them to new domains is an additional limitation. In this paper, we propose to use external terminologies to influence generic linguistic data in order to augment the quality of the extraction. The tool we implemented exploits testified terms at different steps of the process: chunking, parsing and extraction of term candidates. Experiments reported here show that, using this method, more term candidates can be acquired with a higher level of reliability. We further describe the extraction process involving endogenous disambiguation implemented in the term extractor YaTeA

Choosing the right cell line for breast cancer research

Breast cancer is a complex and heterogeneous disease. Gene expression profiling has contributed significantly to our understanding of this heterogeneity at a molecular level, refining taxonomy based on simple measures such as histological type, tumour grade, lymph node status and the presence of predictive markers like oestrogen receptor and human epidermal growth factor receptor 2 (HER2) to a more sophisticated classification comprising luminal A, luminal B, basal-like, HER2-positive and normal subgroups. In the laboratory, breast cancer is often modelled using established cell lines. In the present review we discuss some of the issues surrounding the use of breast cancer cell lines as experimental models, in light of these revised clinical classifications, and put forward suggestions for improving their use in translational breast cancer research

Machine Learning Modeling from Omics Data as Prospective Tool for Improvement of Inflammatory Bowel Disease Diagnosis and Clinical Classifications

Research of inflammatory bowel disease (IBD) has identified numerous molecular players involved in the disease development. Even so, the understanding of IBD is incomplete, while disease treatment is still far from the precision medicine. Reliable diagnostic and prognostic biomarkers in IBD are limited which may reduce efficient therapeutic outcomes. High-throughput technologies and artificial intelligence emerged as powerful tools in search of unrevealed molecular patterns that could give important insights into IBD pathogenesis and help to address unmet clinical needs. Machine learning, a subtype of artificial intelligence, uses complex mathematical algorithms to learn from existing data in order to predict future outcomes. The scientific community has been increasingly employing machine learning for the prediction of IBD outcomes from comprehensive patient data-clinical records, genomic, transcriptomic, proteomic, metagenomic, and other IBD relevant omics data. This review aims to present fundamental principles behind machine learning modeling and its current application in IBD research with the focus on studies that explored genomic and transcriptomic data. We described different strategies used for dealing with omics data and outlined the best-performing methods. Before being translated into clinical settings, the developed machine learning models should be tested in independent prospective studies as well as randomized controlled trials