Using 3D point cloud and graph-based neural networks to improve the estimation of pulmonary function tests from chest CT.

Pulmonary function tests (PFTs) are important clinical metrics to measure the severity of interstitial lung disease for systemic sclerosis patients. However, PFTs cannot always be performed by spirometry if there is a risk of disease transmission or other contraindications. In addition, it is unclear how lung function is affected by changes in lung vessels. Therefore, convolution neural networks (CNNs) were previously proposed to estimate PFTs from chest CT scans (CNN-CT) and extracted vessels (CNN-Vessel). Due to GPU memory constraints, however, these networks used down-sampled images, which causes a loss of information on small vessels. Previous literature has indicated that detailed vessel information from CT scans can be helpful for PFT estimation. Therefore, this paper proposes to use a point cloud neural network (PNN-Vessel) and graph neural network (GNN-Vessel) to estimate PFTs from point cloud and graph-based representations of pulmonary vessel centerlines, respectively. After that, we combine different networks and perform multiple variable step-wise regression analysis to explore if vessel-based networks can contribute to the PFT estimation, in addition to CNN-CT. Results showed that both PNN-Vessel and GNN-Vessel outperformed CNN-Vessel, by 14% and 4%, respectively, when averaged across the intra-class correlation coefficient (ICC) scores of four PFTs metrics. In addition, compared to CNN-Vessel, PNN-Vessel used 30% of training time (1.1 h) and 7% parameters (2.1 M) and GNN-Vessel used only 7% training time (0.25 h) and 0.7% parameters (0.2 M). We combined CNN-CT, PNN-Vessel and GNN-Vessel with the weights obtained from multiple variable regression methods, which achieved the best PFT estimation accuracy (ICC of 0.748, 0.742, 0.836 and 0.835 for the four PFT measures respectively). The results verified that more detailed vessel information could provide further explanation for PFT estimation from anatomical imaging.

[4D-DIA proteomics reveals mechanism of Sanpian Decoction in treating chronic migraine in rats].

To explore the mechanism of the classic formula Sanpian Decoction in treating chronic migraine, this study employed the four-dimensional data-dependent acquisition(4D-DIA) proteomics to analyze the effect of the decoction on chronic migraine in rats and experimentally verified the key differentially expressed proteins. Firstly, SD male rats were randomly divided into groups and repeatedly injected with nitroglycerin to prepare a chronic migraine model. After 7 consecutive days of gavage, rat grimace scale(RGS) was employed to evaluate the treatment efficacy. The trigeminal ganglion was collected for 4D-DIA proteomics, on the basis of which the diffe-rentially expressed proteins between groups were screened. Multiple databases were used for the Gene Ontology(GO) and Kyoto Encyclopedia of Genes and Genomes(KEGG) enrichment of the differentially expressed proteins. STRING and Cytoscape were employed to establish the protein-protein interaction(PPI) network. Western blot was employed to determine the expression level of the key diffe-rentially expressed protein TRPV1. The results showed that there were 517 differentially expressed proteins between blank group and model group and 221 differentially expressed proteins between model group and medium-dose Sanpian Decoction group. The GO and KEGG enrichment results showed that these differentially expressed proteins were mainly related to inflammatory response, injurious sensory stimulation, triglyceride metabolism, immune regulation, etc., which mainly involved the inflammation-related TRP, AMPK, PI3K-Akt, and TGF-ß signaling pathways. The PPI network showed that the target proteins such as IGF, TOP2A, APOA1, CDK1, TTN, RYR1, and CSRP3 had high degrees. Compared with that in model group, the expression level of TRPV1 altered in medium-and high-dose Sanpian Decoction group(P<0.05). In conclusion, Sanpian Decoction may treat chronic migraine by regulating the inflammation-related pathways such as TRP, AMPK, and PI3K-Akt. It plays an important role in the regulation of TRPV1 protein and potentially modulates the perception of injurious stimuli, lipid metabolism, and immune responses.

An efficient labeled memory system for learned indexes.

The appearance and wide use of memory hardware bring significant changes to the conventional vertical memory hierarchy that fails to handle contentions for shared hardware resources and expensive data movements. To deal with these problems, existing schemes have to rely on inefficient scheduling strategies that also cause extra temporal, spatial and bandwidth overheads. Based on the insights that the shared hardware resources trend to be uniformly and hierarchically offered to the requests for co-located applications in memory systems, we present an efficient abstraction of memory hierarchies, called Label, which is used to establish the connection between the application layer and underlying hardware layer. Based on labels, our paper proposes LaMem, a labeled, resource-isolated and cross-tiered memory system by leveraging the way-based partitioning technique for shared resources to guarantee QoS demands of applications, while supporting fast and low-overhead cache repartitioning technique. Besides, we customize LaMem for the learned index that fundamentally replaces storage structures with computation models as a case study to verify the applicability of LaMem. Experimental results demonstrate the efficiency and efficacy of LaMem.

Central Mechanism of Acupuncture Treatment in Patients with Migraine: Study Protocol for Randomized Controlled Neuroimaging Trial.

Purpose: Acupuncture has been recognized as an effective and safe alternative therapy for migraine, but its central mechanism has not yet been adequately explained. Meanwhile, research into the clinical efficacy and central mechanism of true acupuncture (TA) and sham acupuncture (SA) is lacking. It is necessary to investigate whether TA has better efficacy than SA, and how they achieve different effects. This study aims to evaluate the efficacy of TA and SA, observe the brain response caused by TA and SA, and further investigate the central nervous mechanism of TA and SA treatment for patients with migraine. Patients and Methods: This is a randomized controlled neuroimaging trial combining acupuncture treatment with functional magnetic resonance imaging, with patients and outcome assessors blinded. A total of 60 patients with migraine will be randomly allocated to receive 12 sessions of either TA or SA treatments (three sessions per week for 4 weeks), and 30 healthy participants will be recruited as the healthy control (HC) group. Outcome assessment and neuroimaging will be conducted before and after the entire intervention. A headache diary and questionnaires of life quality and psychological properties will be used to evaluate clinical efficacy. Multimodal magnetic resonance imagining data analysis will be used to investigate the central mechanism of TA or SA in treating migraine. Pearson's correlation analysis will be used to reveal the relationship between the brain response and clinical improvements. Conclusion: The results of this study will reveal the brain response to TA and SA in patients with migraine and contribute to further expanding the knowledge of their central mechanism. Study Registration: This trial has been approved by the ethics committee of Dongzhimen Hospital affiliated to Beijing University of Chinese Medicine (DZMEC-KY-2020-38) and registered in the Chinese Clinical Trial Registry (registration number ChiCTR2000033995).

H2B gene family: A prognostic biomarker and correlates with immune infiltration in glioma.

The current prognosis of glioma is unfavorable and effective treatments remain limited. However, bioinformatics has created new opportunities for improving glioma treatment. Research indicates that H2B is involved in the pathological process of cancer. Thus, this study conducted bioinformatic analyses of the H2B gene family to evaluate whether these genes can play a role in predicting prognosis and are associated with immune infiltration. High expression of H2B genes was observed in cholangiocarcinoma, esophageal carcinoma, glioblastoma multiforme (GBM), head and neck squamous cell carcinoma, and other cancers. In addition, a rise in H2B gene expression was correlated with an increase in glioma grade. In the Cancer Genome Atlas (TCGA), the Chinese Glioma Genome Atlas (CGGA) database and multiple datasets from the Gene Expression Omnibus (GEO), high expression of H2B gene family members predicted poor prognosis of a variety of tumors including glioma. In particular, high H2BC5, H2BC9, H2BC11, and H2BC21 expression was associated with poor glioma prognosis. H2BC9, H2BC11, and H2BC12 expression were also positively correlated with both immune and stromal scores. Enrichment analysis indicated that H2B family genes may be involved in the pathological process of glioma using various pathways including the cell cycle and immune response. H2B-specific siRNAs were used to verify the role of H2BC5, H2BC9, H2BC11, and H2BC21 expression on cell cycle distribution. In summary, H2BC5, H2BC9, H2BC11, and H2BC21 were independent prognostic indicators of glioma, and H2BC9 and H2BC11 may correlate with tumor immunity.

[Effect of acupuncture on default mode network in patients with migraine based on functional Magnetic Resonance Imaging: a preliminary study].

OBJECTIVE: To investigate the effect of acupuncture on default mode network (DMN) in migraine patients without aura based on functional Magnetic Resonance Imaging (fMRI). METHODS: Fifteen patients with migraine were included and treated with acupuncture based on "root-knot" theory (Zuqiaoyin [GB 44] for shaoyang headache, Lidui [ST 45] for yangming headache, Zhiyin [BL 67] for taiyang headache, and ashi point), once every other day, three times a week for 4 weeks. The patients received fMRI scanning before and after acupuncture treatment, the effect of acupuncture on DMN in patients with migraine was observed; the frequency of migraine attack, visual analogue scale (VAS) score and the using of analgesic medication before and after treatment were recorded to evaluate the curative effect of acupuncture; the migraine-specific quality of life questionnaire (MSQ), self-rating anxiety scale (SAS) and self-rating depression scale (SDS) were used to evaluate the improvements of quality of life and emotional state. RESULTS: Compared before acupuncture, the functional connections of left parahippocampal cortex (PHC) and anterior medial prefrontal cortex (aMPFC), dorsal medial prefrontal cortex (dMPFC) and lateral temporal cortex (LTC) in DMN after acupuncture were weakened (P<0.05), and the functional connections of bilateral posterior cingulate cortex (PCC) and dMPFC were weakened (P<0.05). Compared before treatment, the frequency of migraine attack, VAS, SAS and SDS scores after treatment were decreased (P<0.05), and MSQ score was increased (P<0.05). CONCLUSION: Acupuncture shows good clinical efficacy for migraine without aura, and could adjust the functional connection of DMN.

Transcriptional expression of ZICs as an independent indicator of survival in gliomas.

The functional significance of the zinc-finger of the cerebellum (ZIC) gene family in gliomas remains to be elucidated. Clinical data from patients with gliomas, containing expression levels of ZIC genes, were extracted from CCLE, GEPIA2 and The Human Protein Atlas (HPA). Univariate survival analysis adjusted by Cox regression via OncoLnc was used to determine the prognostic significance of ZIC expression. We used cBioPortal to explore the correlation between gene mutations and overall survival (OS). ZIC expression was found to be related to immune cell infiltration in gliomas via TIMER analysis. GO term and KEGG pathway enrichment analyzes were performed with Metascape. PPI networks were constructed using STRING. The expression levels of ZIC1/3/4/5 in gliomas were significantly different from those in normal samples. High expression levels of ZIC1/5 were associated with poor OS in brain low-grade glioma (LGG) patients, while low ZIC3 expression combined was related to favorable OS in glioblastoma multiforme (GBM). ZIC alterations were associated with poor prognosis in LGG patients and related to favorable prognosis in GBM patients. We observed that the expression of ZICs was related to immune cell infiltration in glioma patients. ZICs were enriched in several pathways and biological processes involving Neuroactive ligand-receptor interaction (hsa04080). The PPI network revealed that some proteins coexpressed with ZICs played a role in the pathogenesis of gliomas. Differences in the expression levels of ZIC genes could provide a significant marker for predicting prognosis in gliomas.