Using deep learning to predict abdominal age from liver and pancreas magnetic resonance images

Estimation of the Global Equivalence Ratio of a Swirl Combustor from a Small Number of Absorption Spectra Using Machine Learning

A new optical diagnostic method that predicts the global fuel-air equivalence ratio of a swirl combustor using absorption spectra from only three optical paths is proposed here. Under normal operation, the global equivalence ratio and total flow rate determine the temperature and concentration fields of the combustor, which subsequently determine the absorption spectra of any combustion species. Therefore, spectra, as the fingerprint for a produced combustion field, were employed to predict the global equivalence ratio, one of the key operational parameters, in this study. Specifically, absorption spectra of water vapor at wavenumbers around 7444.36, 7185.6, and 6805.6 cm-1 measured at three different downstream locations of the combustor were used to predict the global equivalence ratio. As it is difficult to find analytical relationships between the spectra and produced combustion fields, a predictive model was a data-driven acquisition. The absorption spectra as an input were first feature-extracted through stacked convolutional autoencoders and then a dense neural network was used for regression prediction between the feature scores and the global equivalence ratio. The model could predict the equivalence ratio with an absolute error of ±0.025 with a probability of 96%, and a gradient-weighted regression activation mapping analysis revealed that the model leverages not only the peak intensities but also the variations in the shape of absorption lines for its predictions.

PYPE: A pipeline for phenome-wide association and Mendelian randomization in investigator-driven biobank scale analysis

Phenome-wide association studies (PheWASs) serve as a way of documenting the relationship between genotypes and multiple phenotypes, helping to uncover unexplored genotype-phenotype associations (known as pleiotropy). Secondly, Mendelian randomization (MR) can be harnessed to make causal statements about a pair of phenotypes by comparing their genetic architecture. Thus, approaches that automate both PheWASs and MR can enhance biobank-scale analyses, circumventing the need for multiple tools by providing a comprehensive, end-to-end tool to drive scientific discovery. To this end, we present PYPE, a Python pipeline for running, visualizing, and interpreting PheWASs. PYPE utilizes input genotype or phenotype files to automatically estimate associations between the chosen independent variables and phenotypes. PYPE can also produce a variety of visualizations and can be used to identify nearby genes and functional consequences of significant associations. Finally, PYPE can identify possible causal relationships between phenotypes using MR under a variety of causal effect modeling scenarios.

Proteomic analysis of serum extracellular vesicles reveals Fibulin-3 as a new marker predicting liver-related events in MASLD

BACKGROUND

There is a need for novel noninvasive markers for metabolic dysfunction-associated steatotic liver disease (MASLD) to stratify patients at high risk for liver-related events including liver cancer and decompensation. In the present study, we used proteomic analysis of proteins in extracellular vesicles (EVs) to identify new biomarkers that change with fibrosis progression and can predict the development of liver-related events.

METHODS

We analyzed serum EVs from 50 patients with MASLD assessed for liver fibrosis by biopsy and identified proteins that altered with advanced fibrosis. A further evaluation was conducted on another cohort of 463 patients with MASLD with biopsy.

RESULTS

Eight candidate proteins were identified by proteomic analysis of serum EVs. Among them, serum levels of Fibulin-3, Fibulin-1, and Ficolin 1 correlated with their EV levels. In addition, serum Fibulin-3 and serum Fibulin-1 levels changed significantly with advanced fibrosis. Using another cohort with biopsy, we found that the serum Fibulin-3 concentration was significantly greater in those with advanced fibrosis but that the serum Fibulin-1 concentration was not significantly different. Multivariate Cox proportional hazards analysis revealed that a higher Fibrosis-4 (FIB-4) index and higher serum Fibulin-3 concentration were independent risk factors for liver-related events. When the cutoff value for the serum Fibulin-3 concentration was 6.0 µg/mL according to the Youden index of AUROCs, patients with high serum Fibulin-3 significantly more frequently developed liver-related events than did other patients. Validation using another cohort of 226 patients with clinically diagnosed MASLD confirmed that high serum Fibulin-3 levels are associated with a greater frequency of liver-related events.

CONCLUSIONS

Serum Fibulin-3 was identified as a biomarker for predicting liver-related events in patients with MASLD.

Older Tissue Age Derived From Abdominal Computed Tomography Biomarkers of Muscle, Fat, and Bone Is Associated With Chronic Conditions and Higher Mortality

OBJECTIVE

To determine whether body composition derived from medical imaging may be useful for assessing biologic age at the tissue level because people of the same chronologic age may vary with respect to their biologic age.

METHODS

We identified an age- and sex-stratified cohort of 4900 persons with an abdominal computed tomography scan from January 1, 2010, to December 31, 2020, who were 20 to 89 years old and representative of the general population in Southeast Minnesota and West Central Wisconsin. We constructed a model for estimating tissue age that included 6 body composition biomarkers calculated from abdominal computed tomography using a previously validated deep learning model.

RESULTS

Older tissue age associated with intermediate subcutaneous fat area, higher visceral fat area, lower muscle area, lower muscle density, higher bone area, and lower bone density. A tissue age older than chronologic age was associated with chronic conditions that result in reduced physical fitness (including chronic obstructive pulmonary disease, arthritis, cardiovascular disease, and behavioral disorders). Furthermore, a tissue age older than chronologic age was associated with an increased risk of death (hazard ratio, 1.56; 95% CI, 1.33 to 1.84) that was independent of demographic characteristics, county of residency, education, body mass index, and baseline chronic conditions.

CONCLUSION

Imaging-based body composition measures may be useful in understanding the biologic processes underlying accelerated aging.

A high-speed microscopy system based on deep learning to detect yeast-like fungi cells in blood

Background: Blood-invasive fungal infections can cause the death of patients, while diagnosis of fungal infections is challenging. Methods: A high-speed microscopy detection system was constructed that included a microfluidic system, a microscope connected to a high-speed camera and a deep learning analysis section. Results: For training data, the sensitivity and specificity of the convolutional neural network model were 93.5% (92.7-94.2%) and 99.5% (99.1-99.5%), respectively. For validating data, the sensitivity and specificity were 81.3% (80.0-82.5%) and 99.4% (99.2-99.6%), respectively. Cryptococcal cells were found in 22.07% of blood samples. Conclusion: This high-speed microscopy system can analyze fungal pathogens in blood samples rapidly with high sensitivity and specificity and can help dramatically accelerate the diagnosis of fungal infectious diseases.

Brain structure ages-A new biomarker for multi-disease classification

Age is an important variable to describe the expected brain's anatomy status across the normal aging trajectory. The deviation from that normative aging trajectory may provide some insights into neurological diseases. In neuroimaging, predicted brain age is widely used to analyze different diseases. However, using only the brain age gap information (i.e., the difference between the chronological age and the estimated age) can be not enough informative for disease classification problems. In this paper, we propose to extend the notion of global brain age by estimating brain structure ages using structural magnetic resonance imaging. To this end, an ensemble of deep learning models is first used to estimate a 3D aging map (i.e., voxel-wise age estimation). Then, a 3D segmentation mask is used to obtain the final brain structure ages. This biomarker can be used in several situations. First, it enables to accurately estimate the brain age for the purpose of anomaly detection at the population level. In this situation, our approach outperforms several state-of-the-art methods. Second, brain structure ages can be used to compute the deviation from the normal aging process of each brain structure. This feature can be used in a multi-disease classification task for an accurate differential diagnosis at the subject level. Finally, the brain structure age deviations of individuals can be visualized, providing some insights about brain abnormality and helping clinicians in real medical contexts.

eXplainable Artificial Intelligence (XAI) in aging clock models

XAI is a rapidly progressing field of machine learning, aiming to unravel the predictions of complex models. XAI is especially required in sensitive applications, e.g. in health care, when diagnosis, recommendations and treatment choices might rely on the decisions made by artificial intelligence systems. AI approaches have become widely used in aging research as well, in particular, in developing biological clock models and identifying biomarkers of aging and age-related diseases. However, the potential of XAI here awaits to be fully appreciated. We discuss the application of XAI for developing the "aging clocks" and present a comprehensive analysis of the literature categorized by the focus on particular physiological systems.

Carbon Dioxide Concentration Estimation in Nonuniform Temperature Fields Based on Single-Pass Tunable Diode Laser Absorption Spectroscopy

We propose a novel technique to accurately predict carbon dioxide (CO2) concentrations even in flow fields with temperature gradients based on a single laser path absorption spectrum measurement and machine learning. Concentration measurements in typical tunable diode laser absorption spectroscopy are based on a ratio of two integrated absorbances, each from a spectral line with different temperature dependence. However, the inferred concentrations can deviate significantly from the actual concentrations in the presence of temperature gradients. Furthermore, it is also difficult to find an analytical expression to compensate for the effect of nonuniform temperature profiles on concentration measurements. In this study, the entire absorption feature was considered since its shape and peak intensities vary with temperature and concentration. Specifically, a predictive model is obtained in a data-driven manner that can identify and compensate for the effect of a nonuniform temperature field on the spectrum. Despite a very detailed understanding of the CO2 absorption spectrum, it is nearly impossible to collect sufficient spectra for model acquisition by varying all temperature gradient conditions. Therefore, the model was obtained using only simulated data, much like the concept of a "digital twin". Finally, the predictive performance of the acquired model was verified using experimental data. In all test cases, the predictive performance of the model was superior to that of the two-line method. Additionally, a gradient-weighted regression activation mapping analysis confirmed that the model utilizes both the peak intensities as well as the change in the shape of absorption lines for prediction.

Biomarkers of aging

Aging biomarkers are a combination of biological parameters to (i) assess age-related changes, (ii) track the physiological aging process, and (iii) predict the transition into a pathological status. Although a broad spectrum of aging biomarkers has been developed, their potential uses and limitations remain poorly characterized. An immediate goal of biomarkers is to help us answer the following three fundamental questions in aging research: How old are we? Why do we get old? And how can we age slower? This review aims to address this need. Here, we summarize our current knowledge of biomarkers developed for cellular, organ, and organismal levels of aging, comprising six pillars: physiological characteristics, medical imaging, histological features, cellular alterations, molecular changes, and secretory factors. To fulfill all these requisites, we propose that aging biomarkers should qualify for being specific, systemic, and clinically relevant.

Simultaneous measurement of carbon emission and gas temperature via laser-induced breakdown spectroscopy coupled with machine learning

A method, which can accurately measure carbon emission and gas temperature simultaneously in real-time from a laser-induced breakdown spectrum (LIBS) via machine learning, is proposed in this study. In typical, peak intensity ratios had been used to map species concentrations prior to plasma formation, after removing the broadband continuum of the spectrum; however, the dependence of these peak intensity ratios on the concentration changes with the change in gas density. Therefore, considering the fact that the strength and shape of this broadband continuum is a function of the gas density for a given optical setup, we attempted to collect a spectrum by shortening the time delay after the laser fire, such that the spectrum can contain some of the broadband continuum. Since the analytical quantification of this broadband continuum is not trivial, we employed a machine learning approach to acquire a model that simultaneously predicts the gas temperature and CO₂ concentration. The predictive performance of the model trained with spectra that contain the broadband continuum was much better than that without it; the gradient-weighted regression activation mapping (Grad-RAM) analysis revealed that the model utilizes the broadband spectrum for temperature prediction and correction of changes in peak intensity due to temperature changes in the concentration prediction process.

BMI-adjusted adipose tissue volumes exhibit depot-specific and divergent associations with cardiometabolic diseases

For any given body mass index (BMI), individuals vary substantially in fat distribution, and this variation may have important implications for cardiometabolic risk. Here, we study disease associations with BMI-independent variation in visceral (VAT), abdominal subcutaneous (ASAT), and gluteofemoral (GFAT) fat depots in 40,032 individuals of the UK Biobank with body MRI. We apply deep learning models based on two-dimensional body MRI projections to enable near-perfect estimation of fat depot volumes (R2 in heldout dataset = 0.978-0.991 for VAT, ASAT, and GFAT). Next, we derive BMI-adjusted metrics for each fat depot (e.g. VAT adjusted for BMI, VATadjBMI) to quantify local adiposity burden. VATadjBMI is associated with increased risk of type 2 diabetes and coronary artery disease, ASATadjBMI is largely neutral, and GFATadjBMI is associated with reduced risk. These results - describing three metabolically distinct fat depots at scale - clarify the cardiometabolic impact of BMI-independent differences in body fat distribution.

Association between smoking and non-alcoholic fatty liver disease in Southeast Asia

An estimated 8 million people die each year from tobacco smoking, with an increasing frequency recently being observed in Southeast Asian countries, which is a preventable risk factor for mortality. NAFLD, fibrosis, advancement of hepatocellular carcinoma, and prognosis for those with severe liver disease are all negatively influenced. NAFLD and cigarette usage seem to be a direct link. Oxidative stress and oncogenic signals have been implicated in cancer development in animal models and human clinical trials. The elevated risk of cardiovascular disease and malignancies in those with steatohepatitis and those who have had liver transplants is exacerbated by smoking. We found that smoking cessation may increase treatment response and fibrosis regression rates, decrease hepatocellular carcinoma incidence, and improve liver transplant outcomes. In the last segment, we'll look at electronic cigarettes, a hot subject in public health right now, as well as additional repercussions of smoking.