Reliability-based cleaning of noisy training labels with inductive conformal prediction in multi-modal biomedical data mining

Accurately labeling biomedical data presents a challenge. Traditional semi-supervised learning methods often under-utilize available unlabeled data. To address this, we propose a novel reliability-based training data cleaning method employing inductive conformal prediction (ICP). This method capitalizes on a small set of accurately labeled training data and leverages ICP-calculated reliability metrics to rectify mislabeled data and outliers within vast quantities of noisy training data. The efficacy of the method is validated across three classification tasks within distinct modalities: filtering drug-induced-liver-injury (DILI) literature with title and abstract, predicting ICU admission of COVID-19 patients through CT radiomics and electronic health records, and subtyping breast cancer using RNA-sequencing data. Varying levels of noise to the training labels were introduced through label permutation. Results show significant enhancements in classification performance: accuracy enhancement in 86 out of 96 DILI experiments (up to 11.4%), AUROC and AUPRC enhancements in all 48 COVID-19 experiments (up to 23.8% and 69.8%), and accuracy and macro-average F1 score improvements in 47 out of 48 RNA-sequencing experiments (up to 74.6% and 89.0%). Our method offers the potential to substantially boost classification performance in multi-modal biomedical machine learning tasks. Importantly, it accomplishes this without necessitating an excessive volume of meticulously curated training data

The impact of different rose bengal formulations on corneal thickness and the efficacy of rose bengal/green light corneal cross-linking in the rabbit eye

PURPOSE:To examine central corneal thickness (CCT) changes during in vivo rose bengal-green light corneal cross-linking (RG-CXL) and compare the CXL efficacy of different rose bengal formulations. METHODS:After epithelium removal, the right eyes of rabbits were immersed in rose bengal solution prepared by different solvents (water, phosphate buffered saline, dextran, and hydroxypropyl methylcellulos [HPMC]) for 2 or 20 minutes, then the rose bengal distribution in the corneal stroma was analyzed by confocal fluorescence detection. During the RG-CXL process, the CCT was measured at seven time points. The left eyes served as the untreated control group. Corneal enzymatic resistance and corneal biomechanics were tested to compare the RG-CXL efficacy. RESULTS:The rose bengal infiltration depths were 120 and 200 µm for the 2- and 20-minute groups, respectively. CCT increased significantly after infiltration, then decreased significantly in the first 200 seconds of irradiation and decreased slowly for the next 400 seconds. The CCT of the 20-minute groups was significantly thicker than that of the 2-minute groups (P < .0001). All RG-CXL treatments improved the corneal enzymatic resistance and corneal biomechanics, with the effects being greater in the 20-minute groups. The inclusion of 1.1% HPMC in the rose bengal formulation helped to maintain CCT during irradiation while not affecting either the infiltration of rose bengal or the efficacy of RG-CXL. CONCLUSIONS:Within the range studied, RG-CXL efficacy increased with infiltration time. The incorporation of a 20-minute infiltration of 0.1% rose bengal-1.1% HPMC into the RG-CXL procedure may further improve the safety of the treatment and its prospects for clinical use

Is infants’ mutual exclusivity response based on preference to novelty or non-nameof an object?

Although “mutual exclusivity (ME)” is the term to refer to the behavior that infants map a novel label onto a novelobject rather than a familiar object, two studies, using preferential looking paradigm, aimed to investigate whether infants’ MEis based on preference to novelty or non-name of an object. In Study 1, 18-month-olds were tested on 2 conditions: familiar-object/novel-object trials with known label and familiar-object/novel-object trials with unknown label. The infants preferredto novel objects before naming but no naming effect found for both conditions. In Study 2, 18-month-olds in the same twoconditions as Study 1 were pre-familiarized to both of novel and familiar objects. The results showed that the naming effectswere found for both conditions, indicating that ME occurred. The findings of the present studies suggest that pre-familiarizationcould be used to validate if 18-month-olds’ ME response is based on non-name preference of an object

Analysis of prognostic value of lactate metabolism-related genes in ovarian cancer based on bioinformatics

Abstract Background Recent studies have provided evidence supporting the functional role and mechanism of lactate in suppressing anticancer immunity. However, there is no systematic analysis of lactate metabolism-related genes (LMRGs) and ovarian cancer (OV) prognosis. Results Six genes (CCL18, CCND1, MXRA5, NRBP2, OLFML2B and THY1) were selected as prognostic genes and a prognostic model was utilized. Kaplan-Meier (K-M) and Receiver Operating Characteristic (ROC) analyses were further performed and indicated that the prognostic model was effective. Subsequently, the neoplasm_cancer_status and RiskScore were determined as independent prognostic factors, and a nomogram was established with relatively accurate forecasting ability. Additionally, 2 types of immune cells (Central memory CD8 T cell and Immature B cell), 4 types of immune functions (APC co inhibition, DCs, Tfh and Th1 cells), 9 immune checkpoints (BTLA, CTLA4, IDO1, LAG3, VTCN1, CXCL10, CXCL9, IFNG, CD27) and tumor immune dysfunction and exclusion (TIDE) scores were significantly different between risk groups. The expression of 6 genes were verified by quantitative Real-Time Polymerase Chain Reaction (qRT-PCR) and the expression of 6 genes were higher in the high-grade serous carcinoma (HGSC) samples. Conclusion A prognostic model related to lactate metabolism was established for OV based on six genes (CCL18, CCND1, MXRA5, NRBP2, OLFML2B and THY1) that could provide new insights into therapy

Accelerated exacerbation of global extreme heatwaves under warming scenarios

It is generally believed that global warming drives an increase in heatwaves, but these changes vary regionally. Projected trends of heatwaves and comparisons between observed and projected heatwave trends are poorly understood. We selected multiple characteristics of global heatwave events, including indicators on heat-related health impacts under historical and future scenarios from the NASA Earth Exchange/Global Daily Downscaled Projections (NEX-GDDP) dataset. We quantified the trends in the frequency, intensity, duration and peak temperature of heatwave events and identified heatwave hotspots that respond dramatically to radiative forcing. Future simulations suggest a four-fold increase in the duration of heatwaves by 2050s, spatially concentrated in central Africa, northern South America and Southeast Asia, and the maximum duration of single heatwave event will be up to 44 days under a high emission scenario. Accelerated increasing trends are also detected in intensity, total duration and temperature of heatwaves with up to 2-fold, 8-fold and 9-fold larger than the trends of the baseline period under the high emission scenario. Considering socioeconomic exposure to extreme heatwaves, we identified some hotspot areas in western Europe, eastern North America and northern China that will face greater potential risks in the coming future and therefore need to urgently strengthen their adaptation capacity

Web-Based Data to Quantify Meteorological and Geographical Effects on Heat Stroke: Case Study in China

Heat stroke is a serious heat-related health outcome that can eventually lead to death. Due to the poor accessibility of heat stroke data, the large-scale relationship between heat stroke and meteorological factors is still unclear. This work aims to clarify the potential relationship between meteorological variables and heat stroke, and quantify the meteorological threshold that affected the severity of heat stroke. We collected daily heat stroke search index (HSSI) and meteorological data for the period 2013–2020 in 333 Chinese cities to analyze the relationship between meteorological variables and HSSI using correlation analysis and Random forest (RF) model. Temperature and relative humidity (RH) accounted for 62% and 9% of the changes of HSSI, respectively. In China, cases of heat stroke may start to occur when temperature exceeds 36°C and RH exceeds 58%. This threshold was 34.5°C and 79% in the north of China, and 36°C and 48% in the south of China. Compared to RH, the threshold of temperature showed a more evident difference affected by altitude and distance from the ocean, which was 35.5°C in inland cities and 36.5°C in coastal cities; 35.5°C in high-altitude cities and 36°C in low-altitude cities. Our findings provide a possible way to analyze the interaction effect of meteorological variables on heat-related illnesses, and emphasizes the effects of geographical environment. The meteorological threshold quantified in this research can also support policymaker to establish a better meteorological warning system for public health

Association between Offset of the Pupil Center from the Corneal Vertex and Wavefront Aberration

Purpose: To investigate the influence of offsets of the pupil center from the corneal vertex on wavefront aberrations in the anterior cornea and the whole eye. Methods: Both right and left eyes of 103 subjects were measured for the wavefront aberrations in the anterior cornea, along with the offset of the pupil center relative to the corneal vertex, using a Humphrey corneal topographer, and for the wavefront aberration in the whole eye using a WASCA wavefront sensor. Correlations of the pupil center offsets with the Zernike aberrations were tested. Results: X-axis shift of the pupil center from the corneal vertex was significantly correlated to horizontal coma for both the right (r = 0.54, P<0.0001) and left eyes (r=0.48, P<0.0001) in the cornea, but was weakly correlated to the coma in the whole eye (r=0.17, P=0.04 for OD; and r=0.17, P=0.05 for OS). Significant but weak correlations with the x-axis pupil center shift were also found for several other Zernike aberrations, including the oblique astigmatism, vertical trefoil and secondary astigmatism. Very few Zernike aberrations were significantly correlated to y-axis pupil center shift. Most Zernike aberrations were significantly correlated between the right and left eyes to produce bilateral symmetry in the cornea and the whole eye. Conclusions: The results suggest that offset of the pupil center from the corneal vertex plays an important role in determining horizontal coma and few other Zernike aberrations. Factors controlling bilateral symmetry of the wavefront aberrations between the two eyes could make important contributions to wavefront aberrations in the human eye

Association between COMT Polymorphism Val158Met and Opioid Consumption in Patients with Postoperative Pain: A Meta-Analysis

Background/Aims: Several factors influencing postoperative pain and the effect of opioid analgesics have been investigated on an individual level. The aim of this study was to clarify the impact of catecholamine-O-methyltransferase (COMT) gene Val158Met on opioid consumption in postoperative patients. Methods: A systematic review and meta-analysis of the literature up to September 30, 2017, were performed by using PubMed, Cochrane Library, ISI Web of Science, and Chinese National Knowledge Infrastructure (CNKI) database. The meta-analysis examined all studies involving the association between genetic polymorphisms of COMT Val158Met and opioid consumption during the acute postoperative period. Results: Of the 153 identified studies, 23 studies were retrieved for systematic review and 10 studies were retrieved for meta-analysis. However, it was impossible to conduct meta-analysis on the association between COMT Val158Met polymorphism and postoperative pain because of heterogeneity of the data. Overall, meta-analysis showed that COMT Val/Met carriers consumed less opioid for analgesia within the first 24 hours after surgery (SMD = 0.14, 95% CI = [0.03, 0.25], P = 0.01) but not within 48 hours (SMD = 0.14, 95% CI = [0.08, 0.36], P = 0.21). There was no significant difference in opioid consumption between Val/ Val and Met/Met patients. Conclusion: Patients with Val/Met but not Met/Met allele variant consumed less opioid, though larger and better-designed studies are required to obtain an exclusive conclusion about the correlation between postoperative pain and COMT Val158Met polymorphism