Development of growth selection system and pocket engineering of d-amino acid oxidase to enhance selective deamination activity toward d-phosphinothricin.

D-amino acid oxidase (DAAO)-catalyzed selective oxidative deamination is a very promising process for synthesizing l-amino acids including l-phosphinothricin ( l-PPT, a high-efficiency and broad-spectrum herbicide). However, the wild-type DAAO's low activity toward unnatural substrates like d-phosphinothricin ( d-PPT) hampers its application. Herein, a DAAO from Caenorhabditis elegans (CeDAAO) was screened and engineered to improve the catalytic potential on d-PPT. First, we designed a novel growth selection system, taking into account the intricate relationship between the growth of Escherichia coli (E. coli) and the catalytic mechanism of DAAO. The developed system was used for high-throughput screening of gene libraries, resulting in the discovery of a variant (M6) with significantly increased catalytic activity against d-PPT. The variant displays different catalytic properties on substrates with varying hydrophobicity and hydrophilicity. Analysis using Alphafold2 modeling and molecular dynamic simulations showed that the reason for the enhanced activity was the substrate-binding pocket with enlarged size and suitable charge distribution. Further QM/MM calculations revealed that the crucial factor for enhancing activity lies in reducing the initial energy barrier of the reductive half reaction. Finally, a comprehensive binding-model index to predict the enhanced activity of DAAO toward d-PPT, and an enzymatic deracemization approach was developed, enabling the efficient synthesis of l-PPT with remarkable efficiency.

Association between prenatal exposure to per- and polyfluoroalkyl substances and neurodevelopment in children: Evidence based on birth cohort.

BACKGROUND: Although numerous studies have examined the effect of prenatal per- and polyfluoroalkyl substances (PFAS) exposure on neurodevelopment in children, findings have been inconsistent. OBJECTIVE: To better understand the effects of PFAS exposure during pregnancy on offspring neurodevelopment, we conducted a systematic review of prenatal exposure to different types of PFAS and neurodevelopment in children. METHODS: A comprehensive search was conducted in the PubMed, Web of Science, and EMBASE electronic databases up to March 2023. Only birth cohort studies that report a specific association between PFAS exposure during pregnancy and neurodevelopment were included in this review. RESULTS: 31 birth cohort studies that met the inclusion criteria were qualitatively integrated. Among these, 14 studies investigated the impact of PFAS exposure during pregnancy on cognition, 13 on neurobehavior, and 4 on both cognition and neurobehavior. Additionally, 4 studies explored the influence of PFAS on children's comprehensive development. CONCLUSION: Prenatal PFAS exposure was associated with poor neurodevelopment in children, including psychomotor development, externalizing behavior, and comprehensive development. However, conclusive evidence regarding its effects on other neurological outcomes remains limited. In addition, sex-specific effects on social behavior and sleep problems were identified.

[Three-Dimensional Nonlinear Finite Element Modeling and Analysis of Concomitant Atlanto-Occipital Fusion and Atlantoaxial Joint Dislocation].

OBJECTIVE: To establish, with finite element technology, a three-dimensional nonlinear finite element model of the normal occipital bone, atlas and axis and a three-dimensional nonlinear finite element model of concomitant atlanto-occipital fusion and atlantoaxial dislocation, providing a biomechanical method for clinical research on the upper cervical spine. METHODS: Finite element analysis was conducted with the CT data of a 27-year-old male volunteer, and a three-dimensional nonlinear finite element model, i.e., the normal model, of the normal occipital bone, atlas and axis was established accordingly. Finite element analysis was conducted with the CT data of a 35-year-old male patient with concomitant atlanto-occipital fusion and atlantoaxial dislocation. Then, the ideal state of a simple ligament rupture under high load was generated by computer simulation, and a three-dimensional nonlinear finite element model of concomitant atlanto-occipital fusion and atlantoaxial dislocation was established, i.e., the atlanto-occipital fusion with atlantoaxial dislocation model. For both models, a vertical upward torque of 1.5 N·m was applied on the upper surface of the occipital bone. Through comparative analysis of the two models under stress, the data of the range of motion (ROM) for flexion, extension, lateral bending, and rotation were examined. In addition, stress and deformation analysis with 1.5 N·m torque load was conducted to validate the effectiveness of the two three-dimensional nonlinear finite element models established in the study. RESULTS: When the normal model established in the study was under 1.5 N·m torque load, it exhibited a maximum ROM for each unit of flexion, extension, and the ROM approximated the experimental measurement results of human mechanics, confirming the validity of the simulation. The stress and deformation results of the model were consistent with the basic principles of mechanics. The moment-angular displacement of the model showed obvious nonlinear characteristics. Compared with the normal model, the atlanto-occipital fusion with atlantoaxial dislocation model showed reduced ROM of the atlanto-occipital joint under a torque of 1.5 N·m, while the ROM of the C1-C2 joint for the four conditions of flexion, posterior extention, lateral bending, and rotation under load, with the exception of rotating motion, was greatly increased compared with that of the normal model, which was in line with the actual clinical performance of the patient. CONCLUSION: The atlanto-occipital fusion with atlantoaxial dislocation model and the three-dimensional nonlinear finite element model of the normal occipital bone, atlas and axis were successfully established by finite element technology. The models had valid simulation and reliable kinematic characteristics, and could be used as a reliable tool to simulate clinical diseases.

Time-to-event estimation by re-defining time.

The primary goal of a time-to-event estimation model is to accurately infer the occurrence time of a target event. Most existing studies focus on developing new models to effectively utilize the information in the censored observations. In this paper, we propose a model to tackle the time-to-event estimation problem from a completely different perspective. Our model relaxes a fundamental constraint that the target variable, time, is a univariate number which satisfies a partial order. Instead, the proposed model interprets each event occurrence time as a time concept with a vector representation. We hypothesize that the model will be more accurate and interpretable by capturing (1) the relationships between features and time concept vectors and (2) the relationships among time concept vectors. We also propose a scalable framework to simultaneously learn the model parameters and time concept vectors. Rigorous experiments and analysis have been conducted in medical event prediction task on seven gene expression datasets. The results demonstrate the efficiency and effectiveness of the proposed model. Furthermore, similarity information among time concept vectors helped in identifying time regimes, thus leading to a potential knowledge discovery related to the human cancer considered in our experiments.

Caspase-1 Inflammasome Activation Mediates Homocysteine-Induced Pyrop-Apoptosis in Endothelial Cells.

RATIONALE: Endothelial injury is an initial mechanism mediating cardiovascular disease. OBJECTIVE: Here, we investigated the effect of hyperhomocysteinemia on programed cell death in endothelial cells (EC). METHODS AND RESULTS: We established a novel flow-cytometric gating method to define pyrotosis (Annexin V(-)/Propidium iodide(+)). In cultured human EC, we found that: (1) homocysteine and lipopolysaccharide individually and synergistically induced inflammatory pyroptotic and noninflammatory apoptotic cell death; (2) homocysteine/lipopolysaccharide induced caspase-1 activation before caspase-8, caspase-9, and caspase-3 activations; (3) caspase-1/caspase-3 inhibitors rescued homocysteine/lipopolysaccharide-induced pyroptosis/apoptosis, but caspase-8/caspase-9 inhibitors had differential rescue effect; (4) homocysteine/lipopolysaccharide-induced nucleotide-binding oligomerization domain, and leucine-rich repeat and pyrin domain containing protein 3 (NLRP3) protein caused NLRP3-containing inflammasome assembly, caspase-1 activation, and interleukin (IL)-1ß cleavage/activation; (5) homocysteine/lipopolysaccharide elevated intracellular reactive oxygen species, (6) intracellular oxidative gradient determined cell death destiny as intermediate intracellular reactive oxygen species levels are associated with pyroptosis, whereas high reactive oxygen species corresponded to apoptosis; (7) homocysteine/lipopolysaccharide induced mitochondrial membrane potential collapse and cytochrome-c release, and increased B-cell lymphoma 2-associated X protein/B-cell lymphoma 2 ratio which were attenuated by antioxidants and caspase-1 inhibitor; and (8) antioxidants extracellular superoxide dismutase and catalase prevented homocysteine/lipopolysaccharide -induced caspase-1 activation, mitochondrial dysfunction, and pyroptosis/apoptosis. In cystathionine ß-synthase-deficient (Cbs(-/-)) mice, severe hyperhomocysteinemia-induced caspase-1 activation in isolated lung EC and caspase-1 expression in aortic endothelium, and elevated aortic caspase-1, caspase-9 protein/activity and B-cell lymphoma 2-associated X protein/B-cell lymphoma 2 ratio in Cbs(-/-) aorta and human umbilical vein endothelial cells. Finally, homocysteine-induced DNA fragmentation was reversed in caspase-1(-/-) EC. Hyperhomocysteinemia-induced aortic endothelial dysfunction was rescued in caspase-1(-/-) and NLRP3(-/-) mice. CONCLUSIONS: Hyperhomocysteinemia preferentially induces EC pyroptosis via caspase-1-dependent inflammasome activation leading to endothelial dysfunction. We termed caspase-1 responsive pyroptosis and apoptosis as pyrop-apoptosis.

A robust data scaling algorithm to improve classification accuracies in biomedical data.

BACKGROUND: Machine learning models have been adapted in biomedical research and practice for knowledge discovery and decision support. While mainstream biomedical informatics research focuses on developing more accurate models, the importance of data preprocessing draws less attention. We propose the Generalized Logistic (GL) algorithm that scales data uniformly to an appropriate interval by learning a generalized logistic function to fit the empirical cumulative distribution function of the data. The GL algorithm is simple yet effective; it is intrinsically robust to outliers, so it is particularly suitable for diagnostic/classification models in clinical/medical applications where the number of samples is usually small; it scales the data in a nonlinear fashion, which leads to potential improvement in accuracy. RESULTS: To evaluate the effectiveness of the proposed algorithm, we conducted experiments on 16 binary classification tasks with different variable types and cover a wide range of applications. The resultant performance in terms of area under the receiver operation characteristic curve (AUROC) and percentage of correct classification showed that models learned using data scaled by the GL algorithm outperform the ones using data scaled by the Min-max and the Z-score algorithm, which are the most commonly used data scaling algorithms. CONCLUSION: The proposed GL algorithm is simple and effective. It is robust to outliers, so no additional denoising or outlier detection step is needed in data preprocessing. Empirical results also show models learned from data scaled by the GL algorithm have higher accuracy compared to the commonly used data scaling algorithms.

Structured feature selection using coordinate descent optimization.

BACKGROUND: Existing feature selection methods typically do not consider prior knowledge in the form of structural relationships among features. In this study, the features are structured based on prior knowledge into groups. The problem addressed in this article is how to select one representative feature from each group such that the selected features are jointly discriminating the classes. The problem is formulated as a binary constrained optimization and the combinatorial optimization is relaxed as a convex-concave problem, which is then transformed into a sequence of convex optimization problems so that the problem can be solved by any standard optimization algorithm. Moreover, a block coordinate gradient descent optimization algorithm is proposed for high dimensional feature selection, which in our experiments was four times faster than using a standard optimization algorithm. RESULTS: In order to test the effectiveness of the proposed formulation, we used microarray analysis as a case study, where genes with similar expressions or similar molecular functions were grouped together. In particular, the proposed block coordinate gradient descent feature selection method is evaluated on five benchmark microarray gene expression datasets and evidence is provided that the proposed method gives more accurate results than the state-of-the-art gene selection methods. Out of 25 experiments, the proposed method achieved the highest average AUC in 13 experiments while the other methods achieved higher average AUC in no more than 6 experiments. CONCLUSION: A method is developed to select a feature from each group. When the features are grouped based on similarity in gene expression, we showed that the proposed algorithm is more accurate than state-of-the-art gene selection methods that are particularly developed to select highly discriminative and less redundant genes. In addition, the proposed method can exploit any grouping structure among features, while alternative methods are restricted to using similarity based grouping.

Interleukin-35 Inhibits Endothelial Cell Activation by Suppressing MAPK-AP-1 Pathway.

Vascular response is an essential pathological mechanism underlying various inflammatory diseases. This study determines whether IL-35, a novel responsive anti-inflammatory cytokine, inhibits vascular response in acute inflammation. Using a mouse model of LPS-induced acute inflammation and plasma samples from sepsis patients, we found that IL-35 was induced in the plasma of mice after LPS injection as well as in the plasma of sepsis patients. In addition, IL-35 decreased LPS-induced proinflammatory cytokines and chemokines in the plasma of mice. Furthermore, IL-35 inhibited leukocyte adhesion to the endothelium in the vessels of lung and cremaster muscle and decreased the numbers of inflammatory cells in bronchoalveolar lavage fluid. Mechanistically, IL-35 inhibited the LPS-induced up-regulation of endothelial cell (EC) adhesion molecule VCAM-1 through IL-35 receptors gp130 and IL-12Rß2 via inhibition of the MAPK-activator protein-1 (AP-1) signaling pathway. We also found that IL-27, which shares the EBI3 subunit with IL-35, promoted LPS-induced VCAM-1 in human aortic ECs and that EBI3-deficient mice had similar vascular response to LPS when compared with that of WT mice. These results demonstrated for the first time that inflammation-induced IL-35 inhibits LPS-induced EC activation by suppressing MAPK-AP1-mediated VCAM-1 expression and attenuates LPS-induced secretion of proinflammatory cytokines/chemokines. Our results provide insight into the control of vascular inflammation by IL-35 and suggest that IL-35 is an attractive novel therapeutic reagent for sepsis and cardiovascular diseases.

Inhibition of Caspase-1 Activation in Endothelial Cells Improves Angiogenesis: A NOVEL THERAPEUTIC POTENTIAL FOR ISCHEMIA.

Deficient angiogenesis may contribute to worsen the prognosis of myocardial ischemia, peripheral arterial disease, ischemic stroke, etc. Dyslipidemic and inflammatory environments attenuate endothelial cell (EC) proliferation and angiogenesis, worsening the prognosis of ischemia. Under these dyslipidemic and inflammatory environments, EC-caspase-1 becomes activated and induces inflammatory cell death that is defined as pyroptosis. However, the underlying mechanism that correlates caspase-1 activation with angiogenic impairment and the prognosis of ischemia remains poorly defined. By using flow cytometric analysis, enzyme and receptor inhibitors, and hind limb ischemia model in caspase-1 knock-out (KO) mice, we examined our novel hypothesis, i.e. inhibition of caspase-1 in ECs under dyslipidemic and inflammatory environments attenuates EC pyroptosis, improves EC survival mediated by vascular endothelial growth factor receptor 2 (VEGFR-2), angiogenesis, and the prognosis of ischemia. We have made the following findings. Proatherogenic lipids induce higher caspase-1 activation in larger sizes of human aortic endothelial cells (HAECs) than in smaller sizes of HAECs. Proatherogenic lipids increase pyroptosis significantly more in smaller sizes of HAECs than in larger sizes of the cells. VEGFR-2 inhibition increases caspase-1 activation in HAECs induced by lysophosphatidylcholine treatment. Caspase-1 activation inhibits VEGFR-2 expression. Caspase-1 inhibition improves the tube formation of lysophosphatidylcholine-treated HAECs. Finally, caspase-1 depletion improves angiogenesis and blood flow in mouse hind limb ischemic tissues. Our results have demonstrated for the first time that inhibition of proatherogenic caspase-1 activation in ECs improves angiogenesis and the prognosis of ischemia.

Early hyperlipidemia promotes endothelial activation via a caspase-1-sirtuin 1 pathway.

OBJECTIVE: The role of receptors for endogenous metabolic danger signals-associated molecular patterns has been characterized recently as bridging innate immune sensory systems for danger signals-associated molecular patterns to initiation of inflammation in bone marrow-derived cells, such as macrophages. However, it remains unknown whether endothelial cells (ECs), the cell type with the largest numbers and the first vessel cell type exposed to circulating danger signals-associated molecular patterns in the blood, can sense hyperlipidemia. This report determined whether caspase-1 plays a role in ECs in sensing hyperlipidemia and promoting EC activation. APPROACH AND RESULTS: Using biochemical, immunologic, pathological, and bone marrow transplantation methods together with the generation of new apoplipoprotein E (ApoE)(-/-)/caspase-1(-/-) double knockout mice, we made the following observations: (1) early hyperlipidemia induced caspase-1 activation in ApoE(-/-) mouse aorta; (2) caspase-1(-/-)/ApoE(-/-) mice attenuated early atherosclerosis; (3) caspase-1(-/-)/ApoE(-/-) mice had decreased aortic expression of proinflammatory cytokines and attenuated aortic monocyte recruitment; and (4) caspase-1(-/-)/ApoE(-/-) mice had decreased EC activation, including reduced adhesion molecule expression and cytokine secretion. Mechanistically, oxidized lipids activated caspase-1 and promoted pyroptosis in ECs by a reactive oxygen species mechanism. Caspase-1 inhibition resulted in accumulation of sirtuin 1 in the ApoE(-/-) aorta, and sirtuin 1 inhibited caspase-1 upregulated genes via activator protein-1 pathway. CONCLUSIONS: Our results demonstrate for the first time that early hyperlipidemia promotes EC activation before monocyte recruitment via a caspase-1-sirtuin 1-activator protein-1 pathway, which provides an important insight into the development of novel therapeutics for blocking caspase-1 activation as early intervention of metabolic cardiovascular diseases and inflammations.

Association between pyrethroid exposure and risk of depressive symptoms in the general US adults.

This study aimed to investigate the association between pyrethroid exposure and the risk of depressive symptoms in adults in the USA. Data of participants aged ≥20 years (n = 6455) from the National Health and Nutrition Examination Survey (NHANES, 2007-2014) were included. 3-Phenoxybenzoic acid (3-PBA), an adequately detected pyrethroid metabolite, was used as a biomarker to assess pyrethroid exposure. Depressive symptoms were defined as the Patient's Health Questionnaire (PHQ-9) total score ≥10 or use of antidepressant. Multivariable logistic regression analyses were performed to examine the association between urinary 3-PBA levels and the risk of depressive symptoms. In this study, 1150 participants (weighted frequency, 18.45%) developed depressive symptoms. Participants in the highest tertile have a higher risk of depressive symptoms than those in the lowest tertile of urinary 3-PBA and weighted OR of 1.28 (95% CI, 1.00-1.63, P=0.019). There was a nonlinear association between urinary 3-PBA and depressive symptoms (P for nonlinearity = 0.034). Mediation analysis showed the mediating effect of trouble sleeping on the association of urinary 3-PBA with depressive symptoms was 28.8% (P = 0.006). Our findings indicate that pyrethroid exposure is associated with the increased risk of depressive symptoms, and trouble sleeping may mediated this association. Further studies should be conducted to validate our findings and elucidate their underlying mechanisms.

Identification of methylation-regulated genes modulating microglial phagocytosis in hyperhomocysteinemia-exacerbated Alzheimer's disease.

BACKGROUND: Hyperhomocysteinemia (HHcy) has been linked to development of Alzheimer's disease (AD) neuropathologically characterized by the accumulation of amyloid ß (Aß). Microglia (MG) play a crucial role in uptake of Aß fibrils, and its dysfunction worsens AD. However, the effect of HHcy on MG Aß phagocytosis remains unstudied. METHODS: We isolated MG from the cerebrum of HHcy mice with genetic cystathionine-ß-synthase deficiency (Cbs-/-) and performed bulk RNA-seq. We performed meta-analysis over transcriptomes of Cbs-/- mouse MG, human and mouse AD MG, MG Aß phagocytosis model, human AD methylome, and GWAS AD genes. RESULTS: HHcy and hypomethylation conditions were identified in Cbs-/- mice. Through Cbs-/- MG transcriptome analysis, 353 MG DEGs were identified. Phagosome formation and integrin signaling pathways were found suppressed in Cbs-/- MG. By analyzing MG transcriptomes from 4 AD patient and 7 mouse AD datasets, 409 human and 777 mouse AD MG DEGs were identified, of which 37 were found common in both species. Through further combinatory analysis with transcriptome from MG Aß phagocytosis model, we identified 130 functional-validated Aß phagocytic AD MG DEGs (20 in human AD, 110 in mouse AD), which reflected a compensatory activation of Aß phagocytosis. Interestingly, we identified 14 human Aß phagocytic AD MG DEGs which represented impaired MG Aß phagocytosis in human AD. Finally, through a cascade of meta-analysis of transcriptome of AD MG, functional phagocytosis, HHcy MG, and human AD brain methylome dataset, we identified 5 HHcy-suppressed phagocytic AD MG DEGs (Flt1, Calponin 3, Igf1, Cacna2d4, and Celsr) which were reported to regulate MG/MΦ migration and Aß phagocytosis. CONCLUSIONS: We established molecular signatures for a compensatory response of Aß phagocytosis activation in human and mouse AD MG and impaired Aß phagocytosis in human AD MG. Our discoveries suggested that hypomethylation may modulate HHcy-suppressed MG Aß phagocytosis in AD.

Switching the Cofactor Preference of Formate Dehydrogenase to Develop an NADPH-Dependent Biocatalytic System for Synthesizing Chiral Amino Acids.

Efficient formate dehydrogenase (FDH)-based cofactor regeneration systems are widely used for biocatalytic processes due to their ready availability, low reduction potential, and production of only benign byproducts. However, FDHs are usually specific to NAD+, and NADPH regeneration with formate is challenging. Herein, an FDH with a preference for NAD+ from Azospirillum palustre (ApFDH) was selected owing to its high activity. By static and dynamic structural analyses, a beneficial substitution, D222Q, was identified for cofactor-preference switching. However, its total activity was substantially decreased by 90% owing to the activity-specificity trade-off. Subsequently, a semirational library was designed and screened, which yielded a variant ApFDHD222Q+A199G+H380S with satisfactory activity and NADP+ specificity. Our analysis of dynamical cross-correlations revealed a substitution combination that brought balance to the dynamical correlation network. This combination successfully overcame the activity-specificity-stability trade-off and resulted in a beneficial outcome. The substitution combination (D222Q-A199G/H380S-C256A/C146S) enabled the simultaneous improvement of activity, specificity, and stability and was successfully applied to other 17 FDHs. Finally, by employing engineered ApFDH, an NADPH regeneration system was developed, optimized, and utilized for the asymmetric biosynthesis of l-phosphinothricin.

Novel Knowledge-Based Transcriptomic Profiling of Lipid Lysophosphatidylinositol-Induced Endothelial Cell Activation.

To determine whether pro-inflammatory lipid lysophosphatidylinositols (LPIs) upregulate the expressions of membrane proteins for adhesion/signaling and secretory proteins in human aortic endothelial cell (HAEC) activation, we developed an EC biology knowledge-based transcriptomic formula to profile RNA-Seq data panoramically. We made the following primary findings: first, G protein-coupled receptor 55 (GPR55), the LPI receptor, is expressed in the endothelium of both human and mouse aortas, and is significantly upregulated in hyperlipidemia; second, LPIs upregulate 43 clusters of differentiation (CD) in HAECs, promoting EC activation, innate immune trans-differentiation, and immune/inflammatory responses; 72.1% of LPI-upregulated CDs are not induced in influenza virus-, MERS-CoV virus- and herpes virus-infected human endothelial cells, which hinted the specificity of LPIs in HAEC activation; third, LPIs upregulate six types of 640 secretomic genes (SGs), namely, 216 canonical SGs, 60 caspase-1-gasdermin D (GSDMD) SGs, 117 caspase-4/11-GSDMD SGs, 40 exosome SGs, 179 Human Protein Atlas (HPA)-cytokines, and 28 HPA-chemokines, which make HAECs a large secretory organ for inflammation/immune responses and other functions; fourth, LPIs activate transcriptomic remodeling by upregulating 172 transcription factors (TFs), namely, pro-inflammatory factors NR4A3, FOS, KLF3, and HIF1A; fifth, LPIs upregulate 152 nuclear DNA-encoded mitochondrial (mitoCarta) genes, which alter mitochondrial mechanisms and functions, such as mitochondrial organization, respiration, translation, and transport; sixth, LPIs activate reactive oxygen species (ROS) mechanism by upregulating 18 ROS regulators; finally, utilizing the Cytoscape software, we found that three mechanisms, namely, LPI-upregulated TFs, mitoCarta genes, and ROS regulators, are integrated to promote HAEC activation. Our results provide novel insights into aortic EC activation, formulate an EC biology knowledge-based transcriptomic profile strategy, and identify new targets for the development of therapeutics for cardiovascular diseases, inflammatory conditions, immune diseases, organ transplantation, aging, and cancers.

Influence of medical domain knowledge on deep learning for Alzheimer's disease prediction.

BACKGROUND AND OBJECTIVE: Alzheimer's disease (AD) is the most common type of dementia that can seriously affect a person's ability to perform daily activities. Estimates indicate that AD may rank third as a cause of death for older people, after heart disease and cancer. Identification of individuals at risk for developing AD is imperative for testing therapeutic interventions. The objective of the study was to determine could diagnostics of AD from EMR data alone (without relying on diagnostic imaging) be significantly improved by applying clinical domain knowledge in data preprocessing and positive dataset selection rather than setting naïve filters. METHODS: Data were extracted from the repository of heterogeneous ambulatory EMR data, collected from primary care medical offices all over the U.S. Medical domain knowledge was applied to build a positive dataset from data relevant to AD. Selected Clinically Relevant Positive (SCRP) datasets were used as inputs to a Long-Short-Term Memory (LSTM) Recurrent Neural Network (RNN) deep learning model to predict will the patient develop AD. RESULTS: Risk scores prediction of AD using the drugs domain information in an SCRP AD dataset of 2,324 patients achieved high out-of-sample score - 0.98-0.99 Area Under the Precision-Recall Curve (AUPRC) when using 90% of SCRP dataset for training. AUPRC dropped to 0.89 when training the model using less than 1,500 cases from the SCRP dataset. The model was still significantly better than when using naïve dataset selection. CONCLUSION: The LSTM RNN method that used data relevant to AD performed significantly better when learning from the SCRP dataset than when datasets were selected naïvely. The integration of qualitative medical knowledge for dataset selection and deep learning technology provided a mechanism for significant improvement of AD prediction. Accurate and early prediction of AD is significant in the identification of patients for clinical trials, which can possibly result in the discovery of new drugs for treatments of AD. Also, the contribution of the proposed predictions of AD is a better selection of patients who need imaging diagnostics for differential diagnosis of AD from other degenerative brain disorders.

Pleiotropic effects of neutrophils on myocyte apoptosis and left ventricular remodeling during early volume overload.

Most of the available evidence on the role of neutrophils on pathological cardiac remodeling has been pertained after acute myocardial infarction. However, whether neutrophils directly contribute to the pathogenesis of cardiac remodeling after events other than acute myocardial infarction remains unknown. Here we show that acute eccentric hypertrophy induced by aorto-caval fistula (ACF) in the rats induced an increase in the inflammatory response characterized by activation of the STAT pathway and increased infiltration of neutrophils in the myocardium. This early inflammation was associated with a decrease in interstitial collagen accumulation and an increase in myocyte apoptosis. Neutrophil infiltration blockade attenuated MMP activation, ECM degradation, and myocyte apoptosis induced by ACF at 24 hours and attenuated the development of eccentric hypertrophy induced by ACF at 2 and 3 weeks, suggesting a causal relationship between neutrophils and the ACF-induced cardiac remodeling. In contrast, sustained neutrophil depletion over 4 weeks resulted in adverse cardiac remodeling with further increase in cardiac dilatation and macrophage infiltration, but with no change in myocyte apoptosis level. These data support a functional role for neutrophils in MMP activation, ECM degradation, and myocyte apoptosis during eccentric cardiac hypertrophy and underscore the adverse effects of chronic anti-neutrophil therapy on cardiac remodeling induced by early volume overload.

HDL subclass proteomic analysis and functional implication of protein dynamic change during HDL maturation.

Recent clinical trials reported that increasing high-density lipoprotein-cholesterol (HDL-C) levels does not improve cardiovascular outcomes. We hypothesize that HDL proteome dynamics determine HDL cardioprotective functions. In this study, we characterized proteome profiles in HDL subclasses and established their functional connection. Mouse plasma was fractionized by fast protein liquid chromatography, examined for protein, cholesterial, phospholipid and trigliceride content. Small, medium and large (S/M/L)-HDL subclasseses were collected for proteomic analysis by mass spectrometry. Fifty-one HDL proteins (39 in S-HDL, 27 in M-HDL and 29 in L-HDL) were identified and grouped into 4 functional categories (lipid metabolism, immune response, coagulation, and others). Eleven HDL common proteins were identified in all HDL subclasses. Sixteen, 3 and 7 proteins were found only in S-HDL, M-HDL and L-HDL, respectively. We established HDL protein dynamic distribution in S/M/L-HDL and developed a model of protein composition change during HDL maturation. We found that cholesterol efflux and immune response are essential functions for all HDL particles, and amino acid metabolism is a special function of S-HDL, whereas anti-coagulation is special for M-HDL. Pon1 is recruited into M/L-HDL to provide its antioxidative function. ApoE is incorporated into L-HDL to optimize its cholesterial clearance function. Next, we acquired HDL proteome data from Pubmed and identified 12 replicated proteins in human and mouse HDL particle. Finally, we extracted 3 shared top moleccular pathways (LXR/RXR, FXR/RXR and acute phase response) for all HDL particles and 5 top disease/bio-functions differentially related to S/M/L-HDL subclasses, and presented one top net works for each HDL subclass. We conclude that beside their essencial functions of cholesterol efflux and immune response, HDL aquired antioxidative and cholesterol clearance functions by recruiting Pon1 and ApoE during HDL maturation.

The Natural History of Labyrinthine Hemorrhage in Patients With Sudden Sensorineural Hearing Loss.

To investigate the application of inner ear 3-dimensional fluid-attenuated inversion recovery (3D-FLAIR) magnetic resonance imaging (MRI) in patients with sudden sensorineural hearing loss (SSNHL) accompanied by inner ear hemorrhage. A total of 1252 SSNHL patients who were admitted from January 2010 to April 2018 were included in the study. The patients' clinical features, complete blood counts, coagulation profiles, audiometry data, and MRI scans were retrospectively reviewed. Twenty-four patients had high labyrinth signals on inner ear 3D-FLAIR MRI (24/1252, 1.9%) that were diagnosed as inner ear hemorrhage. One patient had endolymphatic hydrops on the contralesional side. In the 24 patients, pure tone audiometry curves revealed profound deafness (19/24) and flat moderate hearing loss (5/24); most patients had associated vertigo (23/24) and tinnitus (19/24). Patients with SSNHL (N = 24) were treated. Sixteen patients had invalid improvement, 3 patients were markedly improved, 4 patients had effective treatment, and only 1 patient was cured, for a therapeutic efficacy of 33.3% (8/24). Follow-up 3D-FLAIR MRI in patients showed absorbance of labyrinthine hemorrhage and disappearance of the high signal intensity in the inner ear within 2 weeks to 4 months. Inner ear 3D-FLAIR MRI indicate that most cases of inner ear hemorrhage are spontaneous and that high labyrinth signals are absorbed within 4 months. The site of labyrinth hemorrhage is irregular and independent of hearing loss. Conventional treatment is not very effective, and an appropriate therapy for SSNHL requires further investigation.

Anti-depression mechanism of Zuojin Pills:based on UHPLC-TOF-MS, network pharmacology, and experimental verification / 中国中药杂志

This study aims to explore the anti-depression mechanism of Zuojin Pills based on the plasma constituents, network pharmacology, and experimental verification. UHPLC-TOF-MS was used for qualitative analysis of Zuojin Pills-containing serum. Targets of the plasma constituents and the disease were retrieved from PharmMapper and GeneCards. Then the protein-protein interaction(PPI) network was constructed and core targets were screened for GO term enrichment and KEGG pathway enrichment. Cytoscape 3.7.2 was employed construct the "compound-target-pathway" network and the targets and signaling pathways of Zuojin Pills against depression were predicted. CUMS-induced depression mouse model was established to verify the key targets. The results showed that a total of 21 constituents migrating to blood of Zuojin Pills were identified, which were mainly alkaloids. A total of 155 common targets of the constituents and the disease and 67 core targets were screened out. KEGG enrichment and PPI network analysis showed that Zuojin Pills may play a role in the treatment of depression through AMPK/SIRT1, NLRP3, insulin and other targets and pathways. Furthermore, the results of animal experiments showed that Zuojin Pills could significantly improve the depression behaviors of depression, reduce the levels of IL-1β, IL-6 and TNF-α in hippocampus and serum, activate AMPK/SIRT1 signaling, and reduce the protein expression of NLRP3. In conclusion, Zuojin Pills may play a role in the treatment of depression by activating AMPK/SIRT1 signaling pathway, and inhibiting NLRP3 activation and neuroinflammation in the hippocampus of mice.

Exome Sequencing Identifies TENM4 as a Novel Candidate Gene for Schizophrenia in the SCZD2 Locus at 11q14-21.

Schizophrenia is a complex psychiatric disorder with high genetic heterogeneity, however, the contribution of rare mutations to the disease etiology remains to be further elucidated. We herein performed exome sequencing in a Han Chinese schizophrenia family and identified a missense mutation (c.6724C>T, p.R2242C) in the teneurin transmembrane protein 4 (TENM4) gene in the SCZD2 locus, a region previously linked to schizophrenia at 11q14-21. The mutation was confirmed to co-segregate with the schizophrenia phenotype in the family. Subsequent investigation of TENM4 exons 31, 32, and 33 adjacent to the p.R2242C mutation revealed two additional missense mutations in 120 sporadic schizophrenic patients. Residues mutated in these mutations, which are predicted to be deleterious to protein function, were highly conserved among vertebrates. These rare mutations were not detected in 1000 Genomes, NHLBI Exome Sequencing Project databases, or our in-house 1136 non-schizophrenic control exomes. Analysis of RNA-Seq data showed that TENM4 is expressed in the brain with high abundance and specificity. In line with the important role of TENM4 in central nervous system development, our findings suggested that increased rare variants in TENM4 could be associated with schizophrenia, and thus TENM4 could be a novel candidate gene for schizophrenia in the SCZD2 locus.