Identify and mitigate bias in electronic phenotyping: A comprehensive study from computational perspective.

Electronic phenotyping is a fundamental task that identifies the special group of patients, which plays an important role in precision medicine in the era of digital health. Phenotyping provides real-world evidence for other related biomedical research and clinical tasks, e.g., disease diagnosis, drug development, and clinical trials, etc. With the development of electronic health records, the performance of electronic phenotyping has been significantly boosted by advanced machine learning techniques. In the healthcare domain, precision and fairness are both essential aspects that should be taken into consideration. However, most related efforts are put into designing phenotyping models with higher accuracy. Few attention is put on the fairness perspective of phenotyping. The neglection of bias in phenotyping leads to subgroups of patients being underrepresented which will further affect the following healthcare activities such as patient recruitment in clinical trials. In this work, we are motivated to bridge this gap through a comprehensive experimental study to identify the bias existing in electronic phenotyping models and evaluate the widely-used debiasing methods' performance on these models. We choose pneumonia and sepsis as our phenotyping target diseases. We benchmark 9 kinds of electronic phenotyping methods spanning from rule-based to data-driven methods. Meanwhile, we evaluate the performance of the 5 bias mitigation strategies covering pre-processing, in-processing, and post-processing. Through the extensive experiments, we summarize several insightful findings from the bias identified in the phenotyping and key points of the bias mitigation strategies in phenotyping.

A Murine Commensal Protozoan Influences Host Glucose Homeostasis by Facilitating Free Choline Generation.

Recent progress indicates that the gut microbiota plays important role in regulating the host's glucose homeostasis. However, the mechanisms remain unclear. Here, we reported that one integral member of the murine gut microbiota, the protozoan Tritrichomonas musculis could drive the host's glucose metabolic imbalance. Using metabolomics analysis and in vivo assays, we found that mechanistically this protozoan influences the host glucose metabolism by facilitating the production of a significant amount of free choline. Free choline could be converted sequentially by choline-utilizing bacteria and then the host to a final product trimethylamine N-oxide, which promoted hepatic gluconeogenesis. Together, our data reveal a previously underappreciated gut eukaryotic microorganism by working together with other members of microbiota to influence the host's metabolism. Our study underscores the importance and prevalence of metabolic interactions between the gut microbiota and the host in modulating the host's metabolic health. IMPORTANCE Blood glucose levels are important for human health and can be influenced by gut microbes. However, its mechanism of action was previously unknown. In this study, researchers identify a unique member of the gut microbes in mice that can influence glucose metabolism by promoting the host's ability to synthesis glucose by using nonglucose materials. This is because of its ability to generate the essential nutrient choline, and choline, aided by other gut bacteria and the host, is converted to trimethylamine N-oxide, which promotes glucose production. These studies show how gut microbes promote metabolic dysfunction and suggest novel approaches for treating patients with blood glucose abnormality.

Distributed Fiber-Optic Strain Sensing of an Innovative Reinforced Concrete Beam-Column Connection.

Distributed fiber-optic sensing (DFOS) technologies have been used for decades to detect damage in infrastructure. One recent DFOS technology, Optical Frequency Domain Reflectometry (OFDR), has attracted attention from the structural engineering community because its high spatial resolution and refined accuracy could enable new monitoring possibilities and new insight regarding the behavior of reinforced concrete (RC) structures. The current research project explores the ability and potential of OFDR to measure distributed strain in RC structures through laboratory tests on an innovative beam-column connection, in which a partial slot joint was introduced between the beam and the column to control damage. In the test specimen, fiber-optic cables were embedded in both the steel reinforcement and concrete. The specimen was tested under quasi-static cyclic loading with increasing displacement demand at the structural laboratory of the Pacific Earthquake Engineering Research (PEER) Center of UC Berkeley. Different types of fiber-optic cables were embedded both in the concrete and the rebar. The influence of the cable coating and cable position are discussed. The DFOS results are compared with traditional measurements (DIC and LVDT). The high resolution of DFOS at small deformations provides new insights regarding the mechanical behavior of the slotted RC beam-column connection, including direct measurement of beam curvature, rebar deformation, and slot opening and closing. A major contribution of this work is the quantification of the performance and limitations of the DFOS system under large cyclic strains. Performance is quantified in terms of non-valid points (which occur in large strains when the DFOS analyzer does not return a strain value), maximum strain that can be reliably measured, crack width that causes cable rupture, and the effect of the cable coating on the measurements. Structural damage indices are also proposed based on the DFOS results. These damage indices correlate reasonably well with the maximum sustained drift, indicating the potential of using DFOS for RC structural damage assessment. The experimental data set is made publicly available.

Strain Transfer Mechanisms and Mechanical Properties of Optical Fiber Cables.

Understanding the strain transfer mechanism is required to interpret strain sensing results for fiber optic cables. The strain transfer mechanism for fiber optic cables embedded in cementitious materials has yet to be thoroughly investigated experimentally. Interpretation of fiber optic sensing results is of particular concern when there is a displacement discontinuity. This study investigates the strain transfer mechanism for different types of fiber optic cables while embedded in concrete cubes, sustaining a boundary condition which features a displacement discontinuity. The strain transfer mechanisms for different cables are compared under increasing strain levels. Under cyclic loading, the nonlinear behavior of the force-displacement relation and of the strain distribution in the fiber optic cable are discussed. The mechanical properties of the fiber optic cables are presented and discussed. A parameter is proposed to quantify the strain transfer length. The results of this study will assist researchers and engineers to select appropriate cables for strain sensing and interpret the fiber optic sensing results.

Thermodynamic Analysis and Crystallographic Properties of MFe2O4, MCr2O4 and MAl2O4 (M = Fe, Ni, Zn) Formed on Structural Materials in Pressurized Water Reactor Primary Circuit under Zinc and Zinc-aluminum Water Chemistry.

Zinc injection technology (zinc water chemistry, ZWC) was widely applied in pressurized water reactor (PWR) primary circuits to reduce radiation buildup and improve corrosion resistance of structural materials. The simultaneous injection of zinc-aluminium (ZAWC) is a novel implement created to replace part of Zn2+ by Al3+. It was reported ZAWC can improve further corrosion resistance of carbon steels and stainless steels. However, ZAWC sometimes showed even negative effects on Nickel-alloys. In this study, mechanism of formation of oxide film on metals was investigated. The reactions of Fe2+ Ni2+ in oxide films replaced by Zn2+, or Fe3+ replaced by Al3+ in ZAWC were analysed. The thermodynamic data and solubility of mixed oxides (ZnFe2O4, ZnCr2O4, and ZnAl2O4), the products of replace reactions, were calculated. According to the Gibbs free energy difference between products and reactants, ΔGθ(T) values of the formation reaction of ZnFe2O4, ZnCr2O4, and ZnAl2O4 are extremely negative. Solubility of ZnAl2O4 is the lowest among mixed oxide products, which implies the oxide film composites of ZnAl2O4 may show a lower corrosion rate. In addition, the preferential formation of NiAl2O4 on Ni-based-alloy, under ZAWC, was discussed based on crystallographic properties of spinel, which was considered as the cause of negative effects of ZAWC on corrosion resistance of Nickel-alloys. This research provides an analytical basis for the study of thermodynamic stability of oxide films under different chemical chemistry and a theoretical basis for improving corrosion resistance of different metals and optimizing the chemical conditions of PWR primary circuit.

LIGHT (TNFSF14) inhibits glucose uptake of adipocytes by downregulating GLUT4 expression via AKT signaling pathway.

Glucose homeostasis of adipocytes could be regulated by immune-adipose crosstalk. In order to investigate the effects of Lymphotoxin-like inducible protein that competes with glycoprotein D for herpesvirus entry on T cells (LIGHT) on glucose metabolism, we performed the present study. Our results showed that LIGHT deficiency improved glucose tolerance and enhanced glucose consumption of inguinal white adipose tissue (iWAT) under high fat diet. Consistently, Light overexpression could inhibit glucose uptake during the process of white adipogenesis. Mechanistically, LIGHT interacted with lymphotoxin-ß receptor (LTßR) to attenuate AKT pathway leading to downregulation of glucose transporter-4 (GLUT4) expression, which resulted in glucose uptake inhibition. In summary, our findings revealed LIGHT-LTßR-AKT-GLUT4 axis as a regulator of glucose uptake in adipose tissue, which suggested the pivotal role of LIGHT in maintaining glucose homeostasis.

Facile Fabrication of Multifunctional Metal-Organic Framework Hollow Tubes To Trap Pollutants.

Pollutant treatment is critical in modern society and often requires tedious workup and expensive facilities. By virtue of structural diversity and tunability, metal-organic frameworks (MOFs) have shown promise in pollutant control. We herein report a powerful templated freeze-drying protocol for the fabrication of multifunctional MOF hollow tubular structures for both air and liquid contaminants filtration. Various hollow tube systems (e.g., "Janus", "coaxial" and "cellular") are produced. Specially, a multilayer coaxial MOF hollow tube is prepared for highly efficient capture of mixed inorganic-organic liquid contaminants with >94% filtration efficiency. Further, a "cellular" hollow tube with low pressure-drop (12 Pa, 10 cm s-1) is applied in particulate matter filtration with high efficiency (>92%). Given the rich structural and functional diversities, this protocol might bring MOFs into industrial applications to remediate environmental problems.

Shaping of Metal-Organic Frameworks: From Fluid to Shaped Bodies and Robust Foams.

The applications of metal-organic frameworks (MOFs) toward industrial separation, catalysis, sensing, and some sophisticated devices are drastically affected by their intrinsic fragility and poor processability. Unlike organic polymers, MOF crystals are insoluble in any solvents and are usually not thermoplastic, which means traditional solvent- or melting-based processing techniques are not applicable for MOFs. Herein, a continuous phase transformation processing strategy is proposed for fabricating and shaping MOFs into processable fluids, shaped bodies, and even MOF foams that are capable of reversible transformation among these states. Based on this strategy, a cup-shaped Cu-MOF composite and hierarchically porous MOF foam were developed for highly efficient catalytic C-H oxidation (conv. 76% and sele. 93% for cup-shaped Cu-MOF composite and conv. 92% and sele. 97% for porous foam) with ease of recycling and dramatically improved kinetics. Furthermore, various MOF-based foams with low densities (<0.1 g cm(-3)) and high MOF loadings (up to 80 wt %) were obtained via this protocol. Imparted with hierarchically porous structures and fully accessible MOFs uniformly distributed, these foams presented low energy penalty (pressure drop <20 Pa, at 500 mL min(-1)) and showed potential applications as efficient membrane reactors.

A Solvent-Free Hot-Pressing Method for Preparing Metal-Organic-Framework Coatings.

Metal-organic frameworks (MOFs), with their well-defined pores and rich structural diversity and functionality, have drawn a great deal of attention from across the scientific community. However, industrial applications are hampered by their intrinsic fragility and poor processability. Stable and resilient MOF devices with tunable flexibility are highly desirable. Herein, we present a solvent- and binder-free approach for producing stable MOF coatings by a unique hot-pressing (HoP) method, in which temperature and pressure are applied simultaneously to facilitate the rapid growth of MOF nanocrystals onto desired substrates. This strategy was proven to be applicable to carboxylate-based, imidazolate-based, and mixed-metal MOFs. We further successfully obtained superhydrophobic and "Janus" MOF films through layer-by-layer pressing. This HoP method can be scaled up in the form of roll-to-roll production and may push MOFs into unexplored industrial applications.

Effects of zinc-aluminium injection on corrosion behaviour and semiconductor properties of carbon steel in the PHT system of PHWR.

Carbon steel is widely used as the piping of the primary heat transport system (PHT) in pressurized heavy water reactors (PHWR). Effects of zinc/aluminum treatment and simultaneous injection of zinc and aluminum on corrosion behavior and semiconductor properties of oxide films formed on carbon steels were characterized by the gravimetric method, potentiodynamic polarization scan, EIS, Mott-Schottky test, SEM, EDS mapping, XPS analysis and photocurrent response measurement. The results showed that all the metal cation ions treatment can improve the corrosion resistance of oxide films in varying degrees. 20 ppb Zn2+ had the greatest enhancement in corrosion resistance, followed by 20 ppb Zn2+ + 20 ppb Al3+. ZnFe2O4, FeAl2O4 and ZnAl2O4 were detected to be new spinel phases generated in oxide films. The oxide films on the surface of carbon steel all demonstrated n-type semiconductor properties. It was worth noting that the total content of manganese and zinc in the oxide film played an important role in the corrosion resistance of carbon steel.

The HVEM-BTLA Immune Checkpoint Restrains Murine Chronic Cholestatic Liver Injury by Regulating the Gut Microbiota.

The herpes virus entry mediator (HVEM) is an immune checkpoint molecule regulating immune response, but its role in tissue repair remains unclear. Here, we reported that HVEM deficiency aggravated hepatobiliary damage and compromised liver repair after 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC)-induced injury. A similar phenotype was observed in B and T lymphocyte attenuator (BTLA)-deficient mice. These were correlated with impairment of neutrophil accumulation in the liver after injury. The hepatic neutrophil accumulation was regulated by microbial-derived secondary bile acids. HVEM-deficient mice had reduced ability to deconjugate bile acids during DDC-feeding, suggesting a gut microbiota defect. Consistently, both HVEM and BTLA deficiency had dysregulated intestinal IgA responses targeting the gut microbes. These results suggest that the HVEM-BTLA signaling may restrain liver injury by regulating the gut microbiota.

A tyrosine catabolic intermediate 4-hydroxyphenylpyruate attenuates murine endotoxic shock by blocking NLRP3 inflammasome activation.

The metabolic alterations of amino acid metabolism are closely associated with inflammatory response. However, relatively little is known about the roles of phenylalanine (Phe)/tyrosine (Tyr) catabolites during inflammation. Nitisinone (NTBC) is an orphan drug used to treat hereditary tyrosinemia type I potentially by changing Phe/Tyr metabolic flow. In this study, we used NTBC as a tool to investigate the potential role of the Phe/Tyr catabolic pathway in inflammatory responses. We found that NTBC was effective in tempering the bacterial endotoxin lipopolysaccharide (LPS)-induced septic shock in mice. Mechanistically, the protective effect was related to the accumulation of a Phe/Tyr catabolic intermediate, 4-hydroxyphenylpyruvate (4-HPP), induced by the NTBC treatment. 4-HPP could inhibit NLRP3 inflammasome priming and activation processes and therefore reduce IL-1ß release and pyroptosis. Like NTBC, 4-HPP was also effective in attenuating endotoxic shock in mice. Our results suggest the Phe/Tyr catabolic pathway as a potential immunoregulatory hub that may be exploited therapeutically to alleviate inflammation.

FAM96A is essential for maintaining organismal energy balance and adipose tissue homeostasis in mice.

The iron (Fe) metabolism plays important role in regulating systemic metabolism and obesity development. The Fe inside cells can form iron-sulfur (Fe-S) clusters, which are usually assembled into target proteins with the help of a conserved cluster assembly machinery. Family with sequence similarity 96A (FAM96A; also designated CIAO2A) is a cytosolic Fe-S assembly protein involved in the regulation of cellular Fe homeostasis. However, the biological function of FAM96A in vivo is still incompletely defined. Here, we tested the role of FAM96A in regulating organismal Fe metabolism, which is relevant to obesity and adipose tissue homeostasis. We found that in mice genetically lacking FAM96A globally, intracellular Fe homeostasis was interrupted in both white and brown adipocytes, but the systemic Fe level was normal. FAM96A deficiency led to adipocyte hypertrophy and organismal energy expenditure reduction even under nonobesogenic normal chow diet-fed conditions. Mechanistically, FAM96A deficiency promoted mechanistic target of rapamycin (mTOR) signaling in adipocytes, leading to an elevation of de novo lipogenesis and, therefore, fat mass accumulation. Furthermore, it also caused mitochondrial defects, including defects in mitochondrial number, ultrastructure, redox activity, and metabolic function in brown adipocytes, which are known to be critical for the control of energy balance. Moreover, adipocyte-selective FAM96A knockout partially phenocopied global FAM96A deficiency with adipocyte hypertrophy and organismal energy expenditure defects but the mice were resistant to high-fat diet-induced weight gain. Thus, FAM96A in adipocytes may autonomously act as a critical gatekeeper of organismal energy balance by coupling Fe metabolism to adipose tissue homeostasis.

Low temperature NH3-SCR performance and mechanism of Mn and Fe supported CeCO3F-monazite catalysts.

The group has shown that Baiyun Ebo rare earth concentrate has excellent performance in NH3-SCR denitrification when used as a carrier, where rare earth elements are mainly present in cerium fluorocarbon ore (CeCO3F) and monazite (CePO4) mineral phases. In this paper, a new low-temperature NH3-SCR catalyst of Mn-Fe/CeCO3F-monazite was prepared by an impregnation method, using synthetic CeCO3F and purified monazite as carriers. By exploring its denitrification performance and mechanistic analysis, it provides theoretical guidance for the use of rare earth concentrates as low-temperature NH3-SCR catalysts. Our previous studies have determined the optimum loading of Fe, so this paper needs to be investigated for the optimum doping ratio of the active substance Mn. The results of the activity tests, XRD and BET have determined that the best denitrification rate and catalytic performance was achieved at a ratio of Mn : Ce of 1 : 5. The denitrification activity of the different catalysts was investigated by loading Fe, Mn and Fe and Mn together. The results obtained by means of experimental analyses such as XRD, SEM, BET and activity tests showed that the composite catalyst loaded with Fe and Mn at the same time, had the highest activity and its denitrification rate could reach 94.8% at 250 °C. This is mainly attributed to the fact that the interaction of Fe, Mn can promote the dispersion of each other on the carrier surface, which greatly improves the specific surface area of the catalyst. The introduction of Fe and Mn increases the acidic sites and the amount of acid on the catalyst surface, which results in the formation of a large number of oxygen vacancies and the presence of more oxygen species on the catalyst surface, which facilitate the migration of oxygen. The new catalyst was investigated by Fourier transform infrared (FTIR) spectroscopy to characterise the adsorption and transformation behaviour of the reactive species on the surface of the catalyst, and to investigate the reaction mechanism. The results showed that the entire reaction process followed the L-H mechanism, with the gaseous NO adsorption and activation on the catalyst surface generating bidentate nitrate, bridging nitrate species and NH3/NH4 + species as the main intermediate species involved in the reaction, both of which underwent redox reactions on the catalyst surface to produce N2 and H2O. The above results indicated that the CeCO3F-monazite carrier has excellent performance, and provided a theoretical basis for the high-value utilization of rare earth concentrates.

Dual Pathway for Promotion of Stem Cell Neural Differentiation Mediated by Gold Nanocomposites.

The neural differentiation of embryonic stem cells (ESCs) is of great value in the treatment of neurodegenerative diseases. On the basis of the two related signaling pathways that direct the neural differentiation of ESCs, we used gold nanoparticles (GNP) as a means of combining chemical and physical cues to trigger the neurogenic differentiation of stem cells. Neural differentiation-related functional units (glyco and sulfonate units on glycosaminoglycans, GAG) were anchored on the GNP surface and were then transferred to the cell membrane surface via GNP-membrane interactions. The functional units were able to activate the GAG-related signaling pathway, in turn promoting differentiation and maturation of stem cells into neuronal lineages. In addition, using the photothermal effect of GNP, the differentiation-inducing factor retinoic acid (RA), could be actively delivered into cells via laser irradiation. The RA-related intracellular signaling pathway was thereby further triggered, resulting in strong promotion of neurogenesis with a 300-fold increase in mature neural marker expression. The gold nanocomposites developed in this work provide the basis for a new strategy directing ESCs differentiation into nerve cells with high efficiency and high purity by acting on two related signaling pathways.

Roll-to-Roll Production of Metal-Organic Framework Coatings for Particulate Matter Removal.

A powerful roll-to-roll hot-pressing strategy for mass production of metal-organic framework (MOF)-based filters (MOFilters) using various MOF systems with ranges of substrates is presented. Thus-obtained MOFilters show superior particulate matter removal efficiency under desired working temperatures. Such versatile MOFilters can be scaled up and purposely designed, which endows MOFilters with great potentials in both residential and industrial pollution control.

Photocurrent response and semiconductor characteristics of Ce-Ce2O3-CeO2-modified TiO2 nanotube arrays.

We reported Ce and its oxide-modified TiO2 nanotube arrays (TNTs) and their semiconductor properties. The TNTs were prepared by anodic oxidation on pure Ti and investigated by electrochemical photocurrent response analysis. Then, the TNT electrodes were deposited of Ce by cathodic reduction of Ce(NO3)3 6H2O. After deposition, the TNT electrodes were fabricated by anodic oxidation at E = 1.0 V(SCE) for various electricity as Ce-Ce2O3-CeO2 modification. The Ce-deposited TNTs (band gap energy Eg = 2.92 eV) exhibited enhanced photocurrent responses under visible light region and indicated more negative flat band potential (Efb) compared with the TNTs without deposition. After anodic oxidation, the mixed Ce and its oxide (Ce2O3-CeO2)-modified TNT photoelectrodes exhibited higher photocurrent responses under both visible and UV light regions than the TNTs without deposition. The photocurrent responses and Efb were found to be strongly dependent on the contents of Ce2O3 and CeO2 deposited on TNTs. A new characteristic of Eg = 2.1 ± 0.1 eV was investigated in the Ce2O3- and CeO2-modified photoelectrodes. X-ray diffraction (XRD), scanning electron microscopy (SEM), and X-ray photoelectron spectroscopy (XPS) were also employed to characterize various modified TNTs photoelectrodes.