Miracle-dz/UniFAR-FTUs huggingface dataset:
Lyophilized platelets inhibit platelet aggregation with simultaneous paradoxical promotion of platelet adhesion

Lyophilized platelets have been explored as a potential hemostatic agent due to their long-term ambient storage capabilities that make them readily available in various scenarios. Additionally, their high biocompatibility and the key role of platelet interactions in various clinical conditions make them a promising platform for drug delivery. To explore these applications and for wider clinical deployment, the interactions between lyophilized platelets and fresh platelets must be examined. This project characterized receptor expression on the lyophilized platelet surface and their ability to bind fibrinogen using flow cytometry. The effect of lyophilized platelets on aggregation of unaltered platelets was assessed using light transmission aggregometry while the effect on adhesion was evaluated using static and microfluidic assays. Lyophilized platelets maintained significant levels of GPIIb and GPVI receptors on their surface, though the expression was reduced from fresh platelets. Additionally, lyophilized platelets maintained GPIb expression similar to fresh platelets. Furthermore, 15.8% of the lyophilized platelets exhibited the active conformation of the GPIIb/IIIa receptor, indicating a significant increase over fresh platelets. Lyophilized platelets also exhibited an increase in exposed phosphatidylserine and fibrinogen binding. Despite the effect of lyophilized platelets in promoting the adhesion of fresh platelets on a collagen-coated surface, their net effect was inhibitory on platelet aggregation. This study demonstrates that lyophilized platelets can have paradoxical effects on platelet adhesion and aggregation, which could have an impact for clinical applications. Detailed characterization and engineering of these effects will be important for their continued development as a drug delivery platform.
Sex-specific association between inflammation and endothelial function relevant gene and vulnerable carotid plaque

Objectives: We aimed to explore sex-specific association between genes involved in inflammation and endothelial function and vulnerable carotid plaque, a subclinical precursor of ischemic stroke. Methods: Carotid plaque and plaque phenotype were assessed by carotid ultrasound in high-risk participants for stroke drawn from a multicenter, cross-sectional survey in southwestern China. We examined 18 single nucleotide polymorphisms (SNPs) in 10 genes related to inflammation and endothelial function. Sex differences in the genotype of the candidate SNPs and risk of vulnerable carotid plaques were assessed. Interaction tests were performed to identify the SNPs that might modify the association between the sex and vulnerable plaques. For SNPs with suggestive evidence for interaction with sex (p for interaction<0.05), stratification analysis by sex was performed to evaluate the sex-specific association between the SNP and vulnerable plaques. Results: 2,644 high-risk individuals were enrolled, comprising 1,202 (45.5%) men and 1,442 (54.5%) women. Vulnerable carotid plaques were detected in 425 (16.1%) participants. Among candidate SNPs, the genotype frequencies of 5 SNPs (TNFSF4 rs11811788, TNFSF4 rs1234313, IL6R rs4845625, VCAM1 rs2392221, and ITGA2 rs1991013) were significantly different between sex (all p < 0.05). Univariable and multivariable analyses suggested that male individuals had a significantly higher prevalence of vulnerable carotid plaques (20.0% vs. 12.8%, adjusted OR 1.72, 95% CI 1.12–2.66, p = 0.014), while none of the candidate SNPs was significantly associated with vulnerable plaques (all p > 0.05). Interaction tests found the association between sex and vulnerable plaques is affected by the genotype of IL6R rs4845625 (p for interaction = 0.031). Stratification analysis revealed a strong association between IL6R rs4845625 and vulnerable carotid plaque in man (dominant model TT vs. CT + CC: adjusted OR 1.52, 95% CI 1.12–2.07, p = 0.007; codominant model TT vs. CC: adjusted OR 1.50, 95% CI 1.00–2.25, p = 0.048) but not in women (p > 0.05 in all genetic models). Conclusion: The rs4845625 polymorphism in IL6R has sex-specific effects on vulnerable carotid plaque in Chinese Han high-risk individuals for stroke. Our findings provide a plausible genetic basis underlying the sex difference in carotid plaque vulnerability.
Integrative analyses of mRNA and microRNA expression profiles reveal the innate immune mechanism for the resistance to Vibrio parahaemolyticus infection in Epinephelus coioides

Vibrio parahaemolyticus, as one of the main pathogens of marine vibriosis, has brought huge losses to aquaculture. However, the interaction mechanism between V. parahaemolyticus and Epinephelus coioides remains unclear. Moreover, there is a lack of comprehensive multi-omics analysis of the immune response of grouper spleen to V. parahaemolyticus. Herein, E. coioides was artificially injected with V. parahaemolyticus, and it was found that the mortality was 16.7% in the early stage of infection, and accompanied by obvious histopathological lesions in the spleen. Furthermore, 1586 differentially expressed genes were screened by mRNA-seq. KEGG analysis showed that genes were significantly enriched in immune-related pathways, Acute-phase immune response, Apoptosis, Complement system and Cytokine-cytokine receptor interaction. As for miRNA-seq analysis, a total of 55 significantly different miRNAs were identified. Further functional annotation analysis indicated that the target genes of differentially expressed miRNAs were enriched in three important pathways (Phosphatidylinositol signaling system, Lysosome and Focal adhesions). Through mRNA-miRNA integrated analysis, 1427 significant miRNA–mRNA pairs were obtained and “p53 signaling pathway”, “Intestinal immune network for IgA production” were considered as two crucial pathways. Finally, miR-144-y, miR-497-x, novel-m0459-5p, miR-7133-y, miR-378-y, novel-m0440-5p and novel-m0084-3p may be as key miRNAs to regulate immune signaling pathways via the miRNA-mRNA interaction network. The above results suggest that the mRNA-miRNA integrated analysis not only sheds new light on the molecular mechanisms underlying the interaction between host and V. parahaemolyticus but also provides valuable and new insights into resistance to vibrio infection.
Innate immunity to malaria: The good, the bad and the unknown

Malaria is the cause of 600.000 deaths annually. However, these deaths represent only a tiny fraction of total malaria cases. Repeated natural infections with the causative agent, Plasmodium sp. parasites, induce protection from severe disease but not sterile immunity. Thus, immunity to Plasmodium is incomplete. Conversely, immunization with attenuated sporozoite stage parasites can induce sterile immunity albeit after multiple vaccinations. These different outcomes are likely to be influenced strongly by the innate immune response to different stages of the parasite lifecycle. Even small numbers of sporozoites can induce a robust proinflammatory type I interferon response, which is believed to be driven by the sensing of parasite RNA. Moreover, induction of innate like gamma-delta cells contributes to the development of adaptive immune responses. Conversely, while blood stage parasites can induce a strong proinflammatory response, regulatory mechanisms are also triggered. In agreement with this, intact parasites are relatively weakly sensed by innate immune cells, but isolated parasite molecules, notably DNA and RNA can induce strong responses. Thus, the innate response to Plasmodium parasite likely represents a trade-off between strong pro-inflammatory responses that may potentiate immunity and regulatory processes that protect the host from cytokine storms that can induce life threatening illness.
The combination of Lonicerae Japonicae Flos and Forsythiae Fructus herb-pair alleviated inflammation in liver fibrosis

Objective: To explore the active components and epigenetic regulation mechanism underlying the anti-inflammatory effects of Lonicerae Japonicae Flos and Forsythiae Fructus herb-pair (LFP) in carbon tetrachloride (CCl4)-induced rat liver fibrosis. Methods: The main active ingredients and disease-related gene targets of LFP were determined using TCMSP and UniProt, and liver fibrosis disease targets were screened in the GeneCards database. A network was constructed with Cytoscape 3.8. 0 and the STRING database, and potential protein functions were analyzed using bioinformatics analysis. Based on these analyses, we determined the main active ingredients of LFP and evaluated their effects in a CCl4-induced rat liver fibrosis model. Serum biochemical indices were measured using commercial kits, hepatocyte tissue damage and collagen deposition were evaluated by histopathological studies, and myofibroblast activation and inflammation were detected by reverse transcription-polymerase chain reaction (RT-PCR) and western blotting. High-performance liquid chromatography-mass spectrometry was performed to determine the levels of homocysteine, reduced glutathione, and oxidized glutathione, which are involved in inflammation and oxidative stress. Results: The main active components of LFP were quercetin, kaempferol, and luteolin, and its main targets were α-smooth muscle actin, cyclooxygenase-2, formyl-peptide receptor-2, prostaglandin-endoperoxide synthase 1, nuclear receptor coactivator-2, interleukinβ, tumor necrosis factor α, CXC motif chemokine ligand 14, and transforming growth factor β1. A combination of quercetin, kaempferol, and luteolin alleviated the symptoms of liver fibrosis. Conclusion: The results of this study support the role of LFP in the treatment of liver fibrosis, and reveal that LFP reduces collagen formation, inflammation, and oxidative stress. This study suggests a potential mechanism of action of LFP in the treatment of liver fibrosis.
Subjective perception of activity level: A prognostic factor for developing chronic dizziness after vestibular schwannoma resection?

Introduction A vestibular schwannoma (VS) resection causes an acute unilateral vestibular deafferentation resulting in acute postoperative symptoms. Despite the expected resolution of most of the symptoms, due to central vestibular compensation, more than one out of four patients develop chronic dizziness. Several predictive factors, such as age and tumor size, have been suggested. Despite its potential effect on the process of central vestibular compensation, the level of physical activity after VS resection was not yet considered. Therefore, the association between the level of physical activity and chronic dizziness after VS resection will be investigated. Methods This retrospective cohort study included 66 patients who underwent a retro-sigmoid VS resection between October 2001 and February 2007. Patients were assessed before surgery and at 9 weeks and 6 months postoperatively. At 9 weeks, patients were asked to report their level of physical activity (PA) during the past week by using a visual analogue scale and their balance performance was assessed by four standing balance conditions with eyes closed and the Timed Up and Go test (TUG). Based on the Dizziness Handicap Inventory (DHI) score at 6 months, patients were divided in a chronic dizziness group (DHI > 30) and non-chronic dizziness group (DHI-score ≤ 30). Age, sex, Koos classification, preoperative vestibular function, treatment group, balance performance, and level of PA were compared between both groups and used as independent variables in linear regression analyses with the DHI score at 6 months as dependent variable. Results The chronic dizzy patients revealed to have significantly lower levels of PA (p < 0.001) and worse static and dynamic balance performance (p = 0.023 and p = 0.041, respectively) 9 weeks after surgery. After elimination, the multiple regression analysis resulted in a model with two variables (PA level, TUG) which significantly predicted the DHI score (F2,42 = 6.581; R2 = 0.239; p = 0.003). Conclusion This study revealed associations between (1) the level of PA and balance performance in the subacute phase and (2) chronic dizziness after VS resection. Assessment of the level of PA and balance performance during the subacute phase, which can be performed in a non-invasive and non-time-consuming way, might therefore provide prognostic information after VS resection.
Experimental research on production law of multilayer heterogeneous reservoirs

In the development of multi-layer co-production heterogeneous reservoirs, problems such as serious inter-layer heterogeneity and interference always exist, resulting in an unclear understanding of inter-layer production. A clear understanding of the interference mechanism and influence of main controlling factors of multi-layer heterogeneous reservoirs on the production of small layers is the key to the effective development of the reservoirs. On the basis of clarifying the main controlling factors affecting the production of multi-layer heterogeneous reservoirs, this paper developed a multi-pipe parallel displacement experiment system to carry out indoor heterogeneous reservoir multi-layer water injection flooding experiments. Combined with dynamic and static parameters, the experiments simulated and evaluated the effects of factors such as permeability ratio, water cut, shutting down high permeability layers, production pressure difference, and change in crude oil viscosity in high permeability layers. The primary objective of this work is to reveal the mechanism of small-layer interference under different conditions, and clarify the influence of main control factors on the production of small-layer. The results show that the smaller the permeability ratio is, the weaker the difference in physical properties among layers along the vertical direction is. The reduction in the difference in seepage resistance decreases the dynamic interference among layers. The reduction in the water ratio among layers and shutting down high permeability layers can reduce the interlayer interference effectively. Increasing production pressure difference effectively improves the oil displacement efficiency of reservoirs with poor physical properties. A lower fluidity in the high permeability layers can effectively improve the oil displacement efficiency of other layers.
Analysis of Elymus nutans seed coat development elucidates the genetic basis of metabolome and transcriptome underlying seed coat permeability characteristics

The seed coat takes an important function in the life cycle of plants, especially seed growth and development. It promotes the accumulation of nutrients inside the seed and protects the seed embryo from mechanical damage. Seed coat permeability is an important characteristic of seeds, which not only affects seed germination, but also hinders the detection of seed vigor by electrical conductivity (EC) method. This research aimed to elucidate the mechanism of seed coat permeability formation through metabolome and transcriptome analysis of Elymus nutans. We collected the samples at 8, 18, and 28 days post-anthesis (dpa), and conducted a seed inclusion exosmosis experiment and observed the seed coat permeability. Moreover, we analyzed the changes in the metabolome and transcriptome during different development stages. Here, taking 8 dpa as control, 252 upregulated and 157 downregulated differentially expressed metabolites (DEMs) were observed and 886 upregulated unigenes and 1170 downregulated unigenes were identified at 18 dpa, while 4907 upregulated unigenes and 8561 downregulated unigenes were identified at 28 dpa. Meanwhile, we observed the components of ABC transporters, the biosynthesis of unsaturated fatty acids, and phenylalanine metabolism pathways. The key metabolites and genes affecting seed coat permeability were thiamine and salicylic acid. Furthermore, there were 13 and 14 genes with correlation coefficients greater than 0.8 with two key metabolites, respectively, and the —log2Fold Change— of these genes were greater than 1 at different development stages. Meanwhile, pathogenesis-related protein 1 and phenylalanine ammonia-lyase play an important role in regulating the formation of compounds. Our results outline a framework for understanding the development changes during seed growth of E. nutans and provide insights into the traits of seed coat permeability and supply a great significance value to seed production and quality evaluation.
Post hoc Explanations may be Ineffective for Detecting Unknown Spurious Correlation

We investigate whether three types of post hoc model explanations--feature attribution, concept activation, and training point ranking--are effective for detecting a model's reliance on spurious signals in the training data. Specifically, we consider the scenario where the spurious signal to be detected is unknown, at test-time, to the user of the explanation method. We design an empirical methodology that uses semi-synthetic datasets along with pre-specified spurious artifacts to obtain models that verifiably rely on these spurious training signals. We then provide a suite of metrics that assess an explanation method's reliability for spurious signal detection under various conditions. We find that the post hoc explanation methods tested are ineffective when the spurious artifact is unknown at test-time especially for non-visible artifacts like a background blur. Further, we find that feature attribution methods are susceptible to erroneously indicating dependence on spurious signals even when the model being explained does not rely on spurious artifacts. This finding casts doubt on the utility of these approaches, in the hands of a practitioner, for detecting a model's reliance on spurious signals.
HCMUS at MediaEval2021: PointRend with Attention Fusion Refinement for Polyps Segmentation

The Medico task in MediaEval 2021 explores the challenge of building accurate and high-performance algorithms to detect all types of polyps in endoscopic images. This paper introduces our approach for the automatic segmentation of polyp images. We employ a ResNeXt as an encoder backbone with a UNet decoder. Further, the addition of PointRend and Attention Fusion Refinement on the network improves our segmentation performance. The experimental results show the efficiency of the proposed method, which achieves a Jaccard index of 0.7572, an accuracy of 0.9634, and a dice score of 0.8326.
Estimating the energy saving potential of residential consumption in China based on decent living standards

The basic well-being of residents should be fully considered when making residential energy-saving policies. In this study, decent living standards for China were proposed. The provincial energy saving potential of Chinese residents were estimated from a lifetime perspective using environmental extended input–output analysis. The results show that, in 2017, the energy saving potential of Chinese residents constituted 32.74% of total energy consumption. The consumption categories of transportation, housing and cooking had the greatest energy saving potential of 1668.40, 3540.83 and 3229.75 trillion kJ, respectively, in which direct energy consumption accounted for 85% of total energy consumption. For food, clothing, water, health care and education, there was only energy saving potential from indirect consumption, of which food has the largest indirect energy consumption of 3159.25 trillion kJ. Moreover, the energy saving potential varied at the provincial level, coming from different consumption categories. Special attentions should be paid to the transportation in Beijing, housing in Liaoning, and cooking in Gansu, which have relatively greater energy saving potential with per capita energy saving potential of 207.38, 1002.16, and 4256.6 thousand kJ, respectively. The results verify the importance of differentiated and targeted energy policies for residential consumption in different provinces.
Genome-wide association analysis of anti-TNF-α treatment response in Chinese patients with psoriasis

Background: TNF-α inhibitors are effective biological agents for treating psoriasis, but the treatment responses differ across patients. This study aimed to identify genetic biomarkers of anti-TNF-α response in Chinese psoriasis patients using a genome-wide association approach. Methods: We recruited two independent cohorts of Chinese psoriasis patients administered etanercept biosimilar (with or without methotrexate). We identified 61 and 87 good responders (PASI improvement ≥75%), 19 and 10 poor responders (PASI improvement <50%) after 24 weeks treatment in the two cohorts, respectively. Then we performed genome-wide association studies (GWAS) on anti-TNF-α response in each cohort independently, followed by a fixed-effects inverse-variance meta-analysis in the 148 good and 29 poor responders. Results: We tested genetic associations with >3 million genetic variants in either cohort. Meta-analysis identified significant associations within seven loci at p < 10−5, which also showed consistent association evidence in the two cohorts. These seven loci include rs2431355 (OR = 6.65, p = 4.46 × 10−7, IQGAP2-F2RL2 on 5q13.3), rs11801616 (OR = 0.11, p = 1.75 × 10−6, SDC3 on 1p35.2), rs3754679 (OR = 0.17, p = 7.71 × 10−6, CNOT11 on 2q11.2), rs13166823 (OR = 0.09, p = 3.71 × 10−6, IRF1-AS1 on 5q31.1), rs10220768 (OR = 5.49, p = 1.48 × 10−6, NPAP1 on 15q11.2), rs4796752 (OR = 5.56, p = 1.49 × 10−6, KRT31 on 17q21.2), and rs13045590 (OR = 0.08, p = 9.67 × 10−7, CTSZ on 20q13.3). Of the seven SNPs, six SNPs showed significant eQTL effect (p < 1 × 10−6) for several genes in multiple tissues. Conclusion: These results suggest novel biological mechanisms and potential biomarkers for the response to anti-TNF therapies. These findings warrant further validation.
CX3CL1-induced CD16+ monocytes extravasation in myeloperoxidase-ANCA-associated vasculitis correlates with renal damage

Background Monocytes are involved in the pathogenesis of ANCA-associated vasculitis (AAV). Monocyte/macrophages are the dominant infiltrating cells in the glomeruli of patients with myeloperoxidase-AAV (MPO-AAV). However, how human monocyte subsets extravasate to the kidney in MPO-AAV with renal damage is unclear. Methods 30 MPO-AAV patients with renal damage and 22 healthy controls were enrolled in this study. Monocyte subsets and monocyte-related chemokines in the blood and kidneys of MPO-AAV patients were detected. The chemoattractant activity of the CX3CL1-CX3CR1 axis on CD16+ monocytes was observed. The effect of MPO-ANCA on the migration of CD16+ monocytes to human glomerular endothelial cells (HGECs) was detected by flow cytometry and transwell migration assay. Results Compared with controls, CD16+ monocytes were significantly decreased in the blood and increased in the glomeruli of MPO-AAV patients with renal damage. The level of CX3CL1, but not CCL2, was significantly increased in the plasma of MPO-AAV patients. CX3CL1 co-localized with glomerular endothelial cells in MPO-AAV patients with renal damage. Moreover, we initially found that MPO-ANCA promotes an increase of the chemokine CX3CL1 on HGECs, imposing recruitment on CD16+ monocytes. Finally, the percentage of CD16+ monocytes in the blood was found to be positively correlated with estimated glomerular filtration rate (eGFR) and negatively correlated with urinary protein creatinine ratio in MPO-AAV patients with renal damage. Furthermore, the urinary protein creatinine ratio was positively correlated with the infiltrating of CD14+ and CD16+ cells in the kidneys. Conclusion Enhanced extravasation of CD16+ monocytes to the kidney via the CX3CL1-CX3CR1 axis may be involved in renal damage in MPO-AAV.