Neurophysiological activity following gains and losses among young adults with non-suicidal self-injury: An ERP study.

OBJECTIVE: Non-suicidal self-injury (NSSI) is an increasingly concerning issue that is linked to a range of mental health problems. However, little is known about the potential neurophysiological mechanisms underlying risk decision-making in Major depressive disorder (MDD) patients with NSSI-the present study aimed to fill this important literature gap. METHODS: A total of 81 MDD patients (with NSSI: n = 40, without NSSI: n = 41) and 44 matched healthy controls (HC) underwent a modified version of the Iowa Gambling Task (IGT) while an electroencephalogram was recorded. Feedback-related negativity (FRN) and P300 were examined during the feedback stage of the risky decision-making process. RESULTS: Behavioural findings revealed that individuals diagnosed with MDD displayed a greater tendency to make risky decisions compared to the control group. Furthermore, MDD patients with NSSI demonstrated a significantly more negative ΔFN (i.e., the difference in neural response to losses compared to gains) than those without NSSI. Further, NSSI patients showed a larger difference ΔFN (loss minus gain), which was associated with enhanced impulsivity. CONCLUSIONS: Collectively, the findings suggest that there is an altered processing of risky decision-making in the electrophysiology of patients with MDD who engage in NSSI. The ΔFN may serve as a psychophysiological marker indicating risk for NSSI.

Plant growth-promoting rhizobacteria enhance active ingredient accumulation in medicinal plants at elevated CO2 and are associated with indigenous microbiome.

Introduction: Plant growth-promoting rhizobacteria (PGPR) and elevated CO2 (eCO2) have demonstrated their individual potential to enhance plant yield and quality through close interaction with rhizosphere microorganisms and plant growth. However, the efficacy of PGPR under eCO2 on rhizosphere microbiome and, ultimately, plant yield and active ingredient accumulation are not yet fully understood. Methods: This study investigated how the medicinal plant Pseudostellaria heterophylla (P. heterophylla) and its rhizosphere microbes respond to PGPR (Bacillus subtilis and Pseudomonas fluorescens) at eCO2 (1,000 ppm). Results and Discussion: It was found that the yield and active ingredient polysaccharides accumulation in the tuber of P. heterophylla were significantly increased by 38 and 253%, respectively. This promotion has been associated with increased root development and changes in the indigenous microbial community. Metagenomics analysis revealed a significant reduction in pathogenic Fusarium abundance in the rhizosphere. Potential biocontrol bacteria Actinobacteria and Proteobacteria were enriched, especially the genera Bradyrhizobium and Rhodanobacter. The reshaping of the rhizosphere microbiome was accompanied by the upregulation of biological pathways related to metabolite biosynthesis in the rhizosphere. These modifications were related to the promotion of the growth and productivity of P. heterophylla. Our findings highlighted the significant role played by PGPR in medicinal plant yield and active ingredient accumulation when exposed to eCO2.

Arginine-solubilized lipoic acid-induced ß-sheets of silk fibroin-strengthened hydrogel for postoperative rehabilitation of breast cancer.

Breast cancer is the most common cancer among women worldwide, and adjuvant radiotherapy (RT) following tumor removal is one of the most commonly used treatments for breast cancer. However, the high risk of tumor recurrence and inevitable radiation skin injury after RT remain fatal problems, seriously challenging the patient's postoperative rehabilitation. Herein, a multifunctional poly (lipoic acid)-based hydrogel is constructed through one-step heating the mixture of α-lipoic acid (LA)/arginine (Arg)/silk fibroin (SF), without introducing any non-natural molecules. The multiple synergistic interactions among LA, Arg, and SF not only enhance the solubilization of LA in aqueous systems but also stabilize poly(lipoic acid) through strong salt bridge hydrogen bonds and ionic hydrogen bonds. Intriguingly, the LA-based surfactant induced ß-sheet transformation of SF can further modulate the bulk strength of the hydrogel. Regulating the content of LA in hydrogels not only allows efficient control of hydrogel bioactivity but also enables the evolution of hydrogels from injectable forms to adhesive patches. Based on the different biological activities and forms of hydrogels, they can be implanted internally or applied externally on the mice's skin, achieving simultaneous prevention of tumor recurrence post-surgery and assistance in treating radiation-induced skin damage after radiotherapy.

Neuronal lipid droplets play a conserved and sex-biased role in maintaining whole-body energy homeostasis.

Lipids are essential for neuron development and physiology. Yet, the central hubs that coordinate lipid supply and demand in neurons remain unclear. Here, we combine invertebrate and vertebrate models to establish the presence and functional significance of neuronal lipid droplets (LD) in vivo. We find that LD are normally present in neurons in a non-uniform distribution across the brain, and demonstrate triglyceride metabolism enzymes and lipid droplet-associated proteins control neuronal LD formation through both canonical and recently-discovered pathways. Appropriate LD regulation in neurons has conserved and male-biased effects on whole-body energy homeostasis across flies and mice, specifically neurons that couple environmental cues with energy homeostasis. Mechanistically, LD-derived lipids support neuron function by providing phospholipids to sustain mitochondrial and endoplasmic reticulum homeostasis. Together, our work identifies a conserved role for LD as the organelle that coordinates lipid management in neurons, with implications for our understanding of mechanisms that preserve neuronal lipid homeostasis and function in health and disease.

Aberrant high-beta band functional connectivity during reward processing in melancholic major depressive disorder: An MEG study.

OBJECTIVE: To identify the spatial-temporal pattern variation of whole-brain functional connectivity (FC) during reward processing in melancholic major depressive disorder (MDD) patients, and to determine the clinical correlates of connectomic differences. METHODS: 61 MDD patients and 32 healthy controls were enrolled into the study. During magnetoencephalography (MEG) scanning, all participants completed the facial emotion recognition task. The MDD patients were further divided into two groups: melancholic (n = 31) and non-melancholic (n = 30), based on the Mini International Neuropsychiatric Interview (M.I.N.I.) assessment. Melancholic symptoms were examined by using the 6-item melancholia subscale from the Hamilton Depression Rating Scale (HAM-D6). The whole-brain orthogonalized power envelope connections in the high-beta band (20-35 Hz) were constructed in each period after the happy emotional stimuli (0-200 ms, 100-300 ms, 200-400 ms, 300-500 ms, and 400-600 ms). Then, the network-based statistic (NBS) was used to determine the specific abnormal connection patterns in melancholic MDD patients. RESULTS: The NBS identified a sub-network difference at the mid-late period (300-500 ms) in response to happy faces among the three groups (corrected P = 0.035). Then, the post hoc and correlation analyses found five FCs were decreased in melancholic MDD patients and were related to HAM-D6 score, including FCs of left fusiform gyrus-right orbital inferior frontal gyrus (r = -0.52, P < 0.001), left fusiform gyrus-left amygdala (r = -0.26, P = 0.049), left posterior cingulate gyrus-right precuneus (r = -0.32, P = 0.025), left precuneus-right precuneus (r = -0.27, P = 0.049), and left precuneus-left inferior occipital gyrus (r = -0.32, P = 0.025). CONCLUSION: In response to happy faces, melancholic MDD patients demonstrated a disrupted functional connective pattern (20-35 Hz, 300-500 ms), which involved brain regions in visual information processing and the limbic system. The aberrant functional connective pattern in reward processing might be a biomarker of melancholic MDD.

Neural responses to decision-making in suicide attempters with youth major depressive disorder.

An improved understanding of the factors associated with suicidal attempts in youth suffering from depression is crucial for the identification and prevention of future suicide risk. However, there is limited understanding of how neural activity is modified during the process of decision-making. Our study aimed to investigate the neural responses in suicide attempters with major depressive disorder (MDD) during decision-making. Electroencephalography (EEG) was recorded from 79 individuals aged 16-25 with MDD, including 39 with past suicide attempts (SA group) and 40 without (NSA group), as well as from 40 age- and sex- matched healthy controls (HCs) during the Iowa Gambling Task (IGT). All participants completed diagnostic interviews, self-report questionnaires. Our study examined feedback processing by measuring the feedback-related negativity (FRN), ΔFN (FRN-loss minus FRN-gain), and the P300 as electrophysiological indicators of feedback evaluation. The SA group showed poorest IGT performance. SA group and NSA group, compared with HC group, exhibited specific deficits in decision-making (i.e., exhibited smaller (i.e., blunted) ΔFN). Post hoc analysis found that the SA group was the least sensitive to gains and the most sensitive to losses. In addition, we also found that the larger the value of ΔFN, the better the decision-making ability and the lower the impulsivity. Our study highlights the link between suicide attempts and impaired decision-making in individuals with major depressive disorder. These findings constitute an important step in gaining a better understanding of the specific reward-related abnormalities that could contribute to the young MDD patients with suicide attempts.

MPRAVarDB: an online database and web server for exploring regulatory effects of genetic variants.

SUMMARY: Massively parallel reporter assay (MPRA) is an important technology for evaluating the impact of genetic variants on gene regulation. Here, we present MPRAVarDB, an online database and web server for exploring regulatory effects of genetic variants. MPRAVarDB harbors 18 MPRA experiments designed to assess the regulatory effects of genetic variants associated with GWAS loci, eQTLs, and genomic features, totaling 242 818 variants tested more than 30 cell lines and 30 human diseases or traits. MPRAVarDB enables users to query MPRA variants by genomic region, disease and cell line, or any combination of these parameters. Notably, MPRAVarDB offers a suite of pretrained machine-learning models tailored to the specific disease and cell line, facilitating the prediction of regulatory variants. The user-friendly interface allows users to receive query and prediction results with just a few clicks. AVAILABILITY AND IMPLEMENTATION: https://mpravardb.rc.ufl.edu.

Metabolism of Malus halliana Roots Provides Insights into Iron Deficiency Tolerance Mechanisms.

Iron (Fe) deficiency is one of the most common micronutrient imbalances limiting plant growth globally, especially in arid and saline alkali regions due to the decreased availability of Fe in alkaline soils. Malus halliana grows well in arid regions and is tolerant of Fe deficiency. Here, a physiological and metabolomic approach was used to analyze the short-term molecular response of M. halliana roots to Fe deficiency. On the one hand, physiological data show that the root activity first increased and then decreased with the prolongation of the stress time, but the change trend of root pH was just the opposite. The total Fe content decreased gradually, while the effective Fe decreased at 12 h and increased at 3 d. The activity of iron reductase (FCR) increased with the prolongation of stress. On the other hand, a total of 61, 73, and 45 metabolites were identified by GC-MS in three pairs: R12h (Fe deficiency 12 h) vs. R0h (Fe deficiency 0 h), R3d (Fe deficiency 3 d) vs. R0h, and R3d vs. R12h, respectively. Sucrose, as a source of energy, produces monosaccharides such as glucose by hydrolysis, while glucose accumulates significantly at the first (R12h vs. R0h) and third time points (R3d vs. R0h). Carbohydrates (digalacturonate, L-xylitol, ribitol, D-xylulose, glucose, and glycerol) are degraded into pyruvate through glycolysis and pentose phosphate, which participate in the TCA. Glutathione metabolism and the TCA cycle coordinate with each other, actively respond to Fe deficiency stress, and synthesize secondary metabolites at the same time. This study thoroughly examines the metabolite response to plant iron deficiency, highlighting the crucial roles of sugar metabolism, tricarboxylic acid cycle regulation, and glutathione metabolism in the short-term iron deficiency response of apples. It also lays the groundwork for future research on analyzing iron deficiency tolerance.

Higher Flower Hydraulic Safety, Drought Tolerance and Structural Resource Allocation Provide Drought Adaptation to Low Mean Annual Precipitation in Caragana Species.

Determining the differences in flower hydraulic traits and structural resource allocation among closely related species adapted to low mean annual precipitation (MAP) can provide insight into plant adaptation to arid environments. Here, we measured the maximum flower hydraulic conductance (Kmax-flower), water potential at induction 50% loss of Kmax-flower (P50-flower), flower pressure-volume parameters, dry mass of individual flowers and structural components (vexillum, wings, keels, stamens and sepals) of six Caragana species growing in regions ranging from 110 to 1400 mm MAP. Compared with species from high-MAP environments, those from low-MAP environments presented lower Kmax-flower, more negative P50-flower, osmotic potential at full turgor (πo) and turgor loss points (πtlp), and a greater bulk modulus of elasticity (ε). Consequently, a negative correlation between Kmax-flower (hydraulic efficiency) and P50-flower (hydraulic safety) was observed across Caragana species. Furthermore, the dry masses of individual flowers and structural components (vexillum, wings, keels, stamens and sepals) were greater in the species from the low-MAP environment than in those from the high-MAP environment. These findings suggest that greater flower hydraulic safety and drought tolerance combined with greater structural resource allocation promote drought adaptation in Caragana species to low-MAP environments.

Study on the Efficacy and Safety of the Huangqi Guizhi Wuwu Decoction in the Prevention and Treatment of Chemotherapy-Induced Peripheral Neuropathy: Meta-Analysis of 32 Randomized Controlled Trials.

Purpose: Chemotherapy-induced peripheral neuropathy (CIPN) still lacks efficient therapeutic drugs. This study aimed to systematically evaluate the effects of Huangqi Guizhi Wuwu Decoction (HGWD) alone or combined with positive drugs on CIPN prevention and treatment. Methods: The PubMed, Embase, Web of Science, Cochrane, China National Knowledge Infrastructure (CNKI), Wan Fang Data, China Science and Technology Journal (VIP) and Chinese Biomedical (CBM) databases were searched for randomized controlled trials (RCTs) of HGWD for CIPN prevention and treatment. The search time ranged from database establishment to October 17, 2023. The Cochrane risk-of-bias assessment tool was used for quality assessment, Review Manager 5.3 and STATA 12.0 were used for meta-analysis, and GRADEprofiler was used for evidence level assessment. Results: A total of 32 RCTs involving 1987 patients were included. The meta-analysis results revealed the following: 1. In terms of the total CIPN incidence, that in the HGWD group was lower than that in the blank control group. The incidence in both the HGWD and HGWD+positive drug groups was lower than that in the monotherapy-positive drug group. 2. In terms of the incidence of severe CIPN, that in the HGWD group was lower than that in the blank control and positive drug groups. There was no statistically significant difference between the HGWD+positive drug and positive drug groups. Sensitivity analysis revealed that the results of severe incidence in the HGWD group was lower than that in the positive drug group were unstable 3. HGWD did not increase the number of chemotherapy-related adverse events. Conclusion: HGWD can safely and effectively prevent CIPN, reduce symptoms, improve quality of life and reduce the impact of chemotherapy drugs on sensory nerve conduction. However, more high-quality RCTs are needed to compare the efficacy of HGWD with that of positive control drugs in preventing severe CIPN.

Comparison of single-shot, FOCUS single-shot, MUSE, and FOCUS MUSE diffusion weighted imaging for pulmonary lesions: A pilot study.

Rationale and objectives: To compare the performance of SS, FOCUS SS, MUSE, and FOCUS MUSE DWI for pulmonary lesions to obtain a better technique for pulmonary DWI imaging. Materials and methods: 44 patients with pulmonary lesions were recruited to perform pulmonary DWI using SS, FOCUS SS, MUSE, and FOCUS MUSE sequences. Then, two radiologists with 12 and 10 years of chest MRI experiences assessed the overall image quality while another two radiologists both with 3 years of experiences evaluated the SNR, DR, and ADC of pulmonary lesions. Using interclass correlation coefficient (ICC) and kappa statistics to assess consistency of readers, Friedman test and Dunn-Bonferroni post hoc were used to calculate the difference between sequences. Mann-Whitney test and ROC curve were used to distinguish malignant from benign lesions. Results: All the assessed variables of the four sequences presented good to excellent intra-/inter-observer consistency. Compared with SS, FOCUS SS and MUSE, FOCUS MUSE demonstrated better image quality, including significantly higher 5-point Likert scale score (P < 0.001) and smaller DR (P < 0.001). SNR was comparable among SS, FOCUS SS, and FOCUS MUSE (P > 0.05) while MUSE presented with significantly higher SNR over them (P < 0.01). ADC of malignant was significantly smaller than that of benign for all the four sequences (P < 0.05). ROC analysis showed relatively better diagnostic performance of FOCUS MUSE (AUC = 0.820) over SS (AUC = 0.748), FOCUS SS (AUC = 0.778), and MUSE (AUC = 0.729) in distinguishing malignant from benign lesions. Conclusion: FOCUS MUSE possessed sufficient SNR and was better over SS, FOUCS SS, and MUSE for characterizing pulmonary lesions.

Layered NaBa2M3Q3(Q2) (M = Cu or Ag; Q = S or Se) Chalcogenides and Local Ordering in Their Mixed-Anion Compositions.

Three new NaBa2M3Q3(Q2) (M = Ag or Cu; Q = S or Se) chalcogenides were prepared by using solid-state methods and structurally characterized by using single-crystal X-ray diffraction. NaBa2Ag3Se3(Se2) and NaBa2Cu3Se3(Se2) crystallize in monoclinic space group C2/m and have a two-dimensional structure composed of edge-sharing MSe4/4 tetrahedra separated by Na+ and Ba2+ cations, along with (Se2)2- dimers at the center of the spacings between [M3Se3]3- slabs. NaBa2Ag3S3(S2) adopts a related structure with space group C2/m but has additional, crystallographically distinct Ag atoms in the [Ag3S3]3- layer that are linearly coordinated. NaBa2Ag3Se3(Se2) and NaBa2Ag3S3(S2) have indirect band gaps measured to be 1.2 and 1.9 eV, respectively, which is supported by band structures calculated using density functional theory. Mixed-anion NaBa2Cu3Se5-xSx compositions were prepared to probe the presence of anion ordering and heteronuclear (S-Se)2- dimers. Structural analyses of the sulfoselenides indicate that selenium preferentially occupies the Q-Q dimer sites, while Raman spectroscopy reveals a mixture of (S2), (Se2), and heteronuclear (S-Se) units in the sulfur-rich products. The local ordering of the chalcogens is rationalized using simple bonding concepts and adds to a growing framework for understanding ordering phenomena in mixed-anion systems.

Electrophysiological predictors of early response to antidepressants in major depressive disorder.

BACKGROUND: Psychomotor retardation (PMR) is a core feature of major depressive disorder (MDD), which is characterized by abnormalities in motor control and cognitive processes. PMR in MDD can predict a poor antidepressant response, suggesting that PMR may serve as a marker of the antidepressant response. However, the neuropathological relationship between treatment outcomes and PMR remains uncertain. Thus, this study examined electrophysiological biomarkers associated with poor antidepressant response in MDD. METHODS: A total of 142 subjects were enrolled in this study, including 49 healthy controls (HCs) and 93 MDD patients. All participants performed a simple right-hand visuomotor task during magnetoencephalography (MEG) scanning. Patients who exhibited at least a 50 % reduction in disorder severity at the endpoint (>2 weeks) were considered to be responders. Motor-related beta desynchronization (MRBD) and inter- and intra-hemispheric functional connectivity were measured in the bilateral motor network. RESULTS: An increased MRBD and decreased inter- and intra-hemispheric functional connectivity in the motor network during movement were observed in non-responders, relative to responders and HCs. This dysregulation predicted the potential antidepressant response. CONCLUSION: Abnormal local activity and functional connectivity in the motor network indicate poor psychomotor function, which might cause insensitivity to antidepressant treatment. This could be regarded as a potential neural mechanism for the prediction of a patient's treatment response.

Proteomic predictors of individualized nutrient-specific insulin secretion in health and disease.

Population-level variation and mechanisms behind insulin secretion in response to carbohydrate, protein, and fat remain uncharacterized. We defined prototypical insulin secretion responses to three macronutrients in islets from 140 cadaveric donors, including those with type 2 diabetes. The majority of donors' islets exhibited the highest insulin response to glucose, moderate response to amino acid, and minimal response to fatty acid. However, 9% of donors' islets had amino acid responses, and 8% had fatty acid responses that were larger than their glucose-stimulated insulin responses. We leveraged this heterogeneity and used multi-omics to identify molecular correlates of nutrient responsiveness, as well as proteins and mRNAs altered in type 2 diabetes. We also examined nutrient-stimulated insulin release from stem cell-derived islets and observed responsiveness to fat but not carbohydrate or protein-potentially a hallmark of immaturity. Understanding the diversity of insulin responses to carbohydrate, protein, and fat lays the groundwork for personalized nutrition.

Discovery of sesquiterpene lactones with anti-inflammatory effect from Youngia japonica.

The preliminary study revealed that the ethyl acetate eluate of Youngia japonica (YJ-E) could inhibit the expression of key proteins of p-p65, p-IκBα, p-IKKα/ß, and p-AKT in LPS stimulated BV2 cell. Further phytochemical study led to the isolation of eight compounds from YJ-E, including one new sesquiterpene lactone. Their structures were elucidated by several spectroscopic data, and comparing the NMR data of known compound. In addition, all of the isolates were evaluated for the anti-inflammatory effect. As a result, compounds 3 and 4 distinctly attenuated the expressions of p-IκBα, p-p65, and p-AKT in LPS stimulated BV2 cell, respectively.

SFN promotes renal fibrosis via binding with MYH9 in chronic kidney disease.

Chronic kidney disease (CKD) is a clinical syndrome characterized by persistent renal function decline. Renal fibrosis is the main pathological process in CKD, but an effective treatment does not exist. Stratifin (SFN) is a highly-conserved, multi-function soluble acidic protein. Therefore, this study explored the effects of SFN on renal fibrosis. First, we found that SFN was highly expressed in patients with CKD, as well as in renal fibrosis animal and cell models. Next, transforming growth factor-beta 1 (TGF-ß1) induced injury and fibrosis in human renal tubule epithelial cells, and SFN knockdown reversed these effects. Furthermore, SFN knockdown mitigated unilateral ureteral obstruction (UUO)-induced renal tubular dilatation and renal interstitial fibrosis in mice. Liquid chromatography-tandem mass spectrometry/mass spectrometry (LC-MS/MS), co-immunoprecipitation (Co-IP), and immunofluorescence co-localization assays demonstrated that SFN bound the non-muscle myosin-encoding gene, myosin heavy chain 9 (MYH9), in the cytoplasm of renal tubular epithelial cells. MYH9 knockdown also reduced Col-1 and α-SMA expression, which are fibrosis markers. Finally, silencing SFN decreased MYH9 expression, alleviating renal fibrosis. These results suggest that SFN promotes renal fibrosis in CKD by interacting with MYH9. This study may provide potential strategies for the treatment of CKD.

Involvement of METTL3-mediated m6A methylation in the early development of porcine cloned embryos.

METTL3-mediated N6-methyladenosine (m6A) modification is critical for gametogenesis and early embryonic development. However, the function of METTL3-mediated m6A modification in the early development of somatic nuclear transfer embryos (SCNT) remains unclear. Here, we found that METTL3 mRNA and protein levels exhibit dynamic changes during the early development of porcine SCNT embryos. The levels of METTL3 mRNA and protein in SCNT embryos at specific developmental stages differ from those in parthenogenetic activation (PA) counterparts. SiRNA injection effectively reduced the levels of METTL3 mRNA and protein in 4-cell embryos and blastocysts. METTL3 knockdown significantly reduced the cleavage and blastocyst rates of SCNT embryos. METTL3 knockdown significantly reduced the number of total cells and trophectoderm (TE) cells in the resulting blastocysts and perturbed cell lineage allocation. In addition, METTL3 knockdown reduced the levels of m6A modification in 4-cell embryos and blastocysts. Importantly, METTL3 knockdown decreased the expression levels of CDX2, GATA3, NANOG and YAP, and increased the expression levels of SOX2 and OCT4. Taken together, these results demonstrate that METTL3-mediated m6A modification regulates early development and lineage differentiation of porcine SCNT embryos.

Effect and prognosis of endoscopic intracranial hematoma removal and hematoma puncture and drainage in patients with hypertensive intracerebral hemorrhage.

Introduction: Hypertensive intracerebral hemorrhage is one of the most serious complications of hypertension. The treatment focuses on reducing bleeding damage and promoting functional recovery. Aim: This study investigated the efficacy and prognosis of endoscopic intracranial hematoma removal (EIHR) and hematoma puncture and drainage (HPD) in treating hypertensive intracerebral hemorrhage (HICH). Material and methods: Ninety-two patients admitted to our hospital for EIHR and HPD between September 30, 2021 and September 30, 2022 were enrolled, including 14 cases of EIHR (endoscopy group) and 78 cases of HPD (puncture group). The efficacy of the two surgery modes in treating HICH patients was compared. Univariate logistic regression (ULR) and multivariate logistic regression (MLR) were employed to analyze the influences of different treatment methods on the prognosis of patients with HICH. Results: The average hematoma clearance rate (HCR) of all patients was 80.52%, and the patients in the endoscopy group had a higher HCR than those in the puncture group (73.00% vs. 86.00%) (p < 0.001). The good prognosis rate (GPR) shown by the Glasgow Outcome Scale (GOS) score in the endoscopy group was 69.23%, and that in the puncture group was 40.38%, a large but statistically non-significant difference (p > 0.05). Conclusions: The HCR of EIHR was greatly higher based on that of HPD, but showed no great difference in prognostic effect. The higher the GCS score on admission, the lower the likelihood of poor prognosis.

In silico generation and augmentation of regulatory variants from massively parallel reporter assay using conditional variational autoencoder.

Predicting the functional consequences of genetic variants in non-coding regions is a challenging problem. Massively parallel reporter assays (MPRAs), which are an in vitro high-throughput method, can simultaneously test thousands of variants by evaluating the existence of allele specific regulatory activity. Nevertheless, the identified labelled variants by MPRAs, which shows differential allelic regulatory effects on the gene expression are usually limited to the scale of hundreds, limiting their potential to be used as the training set for achieving a robust genome-wide prediction. To address the limitation, we propose a deep generative model, MpraVAE, to in silico generate and augment the training sample size of labelled variants. By benchmarking on several MPRA datasets, we demonstrate that MpraVAE significantly improves the prediction performance for MPRA regulatory variants compared to the baseline method, conventional data augmentation approaches as well as existing variant scoring methods. Taking autoimmune diseases as one example, we apply MpraVAE to perform a genome-wide prediction of regulatory variants and find that predicted regulatory variants are more enriched than background variants in enhancers, active histone marks, open chromatin regions in immune-related cell types, and chromatin states associated with promoter, enhancer activity and binding sites of cMyC and Pol II that regulate gene expression. Importantly, predicted regulatory variants are found to link immune-related genes by leveraging chromatin loop and accessible chromatin, demonstrating the importance of MpraVAE in genetic and gene discovery for complex traits.