bluuebunny/crossref_metadata_2025_split huggingface dataset:
Targeting influenza A virus by splicing inhibitor herboxidiene reveals the importance of subtype-specific signatures around splice sites
Authors: Han Yi-Ju , Lee Kuo-Ming , Wu Guan-Hong , Gong Yu-Nong , Dutta Avijit , Shih Shin-Ru 
Published: February 2023

Abstract
Background
The association between M segment splicing and pathogenicity remains ambiguous in human influenza A viruses. In this study, we aimed to investigate M splicing in various human influenza A viruses and characterize its physiological roles by applying the splicing inhibitor, herboxidiene.

Methods
We examined the M splicing of human H1N1 and H3N2 viruses by comparing three H1N1 and H3N2 strains, respectively, through reverse transcriptase-polymerase chain reaction (RT-PCR) analyses. We randomly selected M sequences of human H1N1, H2N2, and H3N2 viruses isolated from 1933 to 2020 and examined their phylogenetic relationships. Next, we determined the effects of single nucleotide variations on M splicing by generating mutant viruses harboring the 55C/T variant through reverse genetics. To confirm the importance of M2 splicing in the replication of H1N1 and H3N2, we treated infected cells with splicing inhibitor herboxidiene and analyzed the viral growth using plaque assay. To explore the physiological role of the various levels of M2 protein in pathogenicity, we challenged C57BL/6 mice with the H1N1 WSN wild-type strain, mutant H1N1 (55T), and chimeric viruses including H1N1 + H3wt and H1N1 + H3mut. One-tailed paired t-test was used for virus titer calculation and multiple comparisons between groups were performed using two-way analysis of variance.

Results
M sequence splice site analysis revealed an evolutionarily conserved single nucleotide variant C55T in H3N2, which impaired M2 expression and was accompanied by collinear M1 and mRNA3 production. Aberrant M2 splicing resulted from splice-site selection rather than a general defect in the splicing process. The C55T substitution significantly reduced both M2 mRNA and protein levels regardless of the virus subtype. Consequently, herboxidiene treatment dramatically decreased both the H1N1 and H3N2 virus titers. However, a lower M2 expression only attenuated H1N1 virus replication and in vivo pathogenicity. This attenuated phenotype was restored by M replacement of H3N2 M in a chimeric H1N1 virus, despite low M2 levels.

Conclusions
The discrepancy in M2-dependence emphasizes the importance of M2 in human influenza A virus pathogenicity, which leads to subtype-specific evolution. Our findings provide insights into virus adaptation processes in humans and highlights splicing regulation as a potential antiviral target.
Structure-function analysis of CYP719As involved in methylenedioxy bridge-formation in the biosynthesis of benzylisoquinoline alkaloids and its de novo production
Authors: Liu Xiuyu , Jiao Xiang , Cheng Yatian , Ma Ying , Bu Junling , Jin Baolong , Li Qishuang , Hu Zhimin , Tang Jinfu , Lai Changjiangsheng , Wang Jian , Cui Guanghong , Chen Yun , Guo Juan , Huang Luqi 
Published: February 2023

AbstractBenzylisoquinoline alkaloids (BIAs) are a type of secondary metabolite with clinical application value. (S)-stylopine is a special BIA which contains methylenedioxy bridge structures. CYP719As could catalyze the methylenedioxy bridge-formation on the A or D rings of protoberberine alkaloids, while displaying significant substrate regiospecificity. To explore the substrate preference of CYP719As, we cloned and identified five CyCYP719A candidates from Corydalis yanhusuo. Two CyCYP719As (CyCYP719A39 and CyCYP719A42) with high catalytic efficiency for the methylenedioxy bridge-formation on the D or A rings were characterized, respectively. The residues (Leu 294 for CyCYP719A42 and Asp 289 for CyCYP719A39) were identified as the key to controlling the regioselectivity of CYP719As affecting the methylenedioxy bridge-formation on the A or D rings by homology modeling and mutation analysis. Furthermore, for de novo production of BIAs, CyCYP719A39, CyCYP719A42, and their mutants were introduced into the (S)-scoulerine-producing yeast to produce 32 mg/L (S)-stylopine. These results lay a foundation for understanding the structure-function relationship of CYP719A-mediated methylenedioxy bridge-formation and provide yeast strains for the BIAs production by synthetic biology.
Molecular sensitization pattern to house dust mites is formed from the first years of life and includes group 1, 2, Der p 23, Der p 5, Der p 7 and Der p 21 allergens
Authors: Yuriev Serhii , Rodinkova Victoria , Mokin Vitalii , Varchuk Ilona , Sharikadze Olena , Marushko Yuriy , Halushko Bohdan , Kurchenko Andrii 
Published: February 2023

Abstract
Background
As the process and nature of developing sensitivity to house dust mites (HDMs) remain not fully studied, our goal was to establish the pattern, nature and timeframe of house dust mite (HDM) sensitization development in patients in Ukraine as well as the period when treatment of such patients would be most effective.

Methods
The data of the multiplex allergy test Alex2 was collected from 20,033 patients. To determine age specifics of sensitization, descriptive statistics were used. Bayesian Network analysis was used to build probabilistic patterns of individual sensitization.

Results
Patients from Ukraine were most often sensitized to HDM allergens of group 1 (Der p 1, Der f 1) and group 2 (Der p 2, Der f 2) as well as to Der p 23 (55%). A considerable sensitivity to Der p 5, Der p 7 and Der p 21 allergens was also observed. The overall nature of sensitization to HDM allergens among the population of Ukraine is formed within the first year of life. By this time, there is a pronounced sensitization to HDM allergens of groups 1 and 2 as well as to Der p 23. Significance of sensitization to Der p 5, Der p 7 and Der p 21 allergens grows starting from the age of 3–6. Bayesian Network data analysis indicated the leading role of sensitization to Der p 1 and Der f 2. While developing the sensitivity to group 5 allergens, the leading role may belong to Der p 21 allergen.

Conclusion
The results obtained indicate the importance of determining the sensitization profile using the multi-component approach. A more detailed study of the optimal age for AIT prescription is required as the pattern of sensitization to HDMs is formed during the first year of life.
All-in-one smart dressing for simultaneous angiogenesis and neural regeneration
Authors: Yuan Tiejun , Tan Minhong , Xu Yang , Xiao Qiyao , Wang Hui , Wu Chen , Li Fulun , Peng Lihua 
Published: February 2023

AbstractWound repair, along with skin appendage regeneration, is challenged by insufficient angiogenesis and neural regeneration. Therefore, promoting both proangiogenic and neuro-regenerative therapeutic effects is essential for effective wound repair. However, most therapeutic systems apply these strategies separately or ineffectively. This study investigates the performance of an all-in-one smart dressing (ASD) that integrates angiogenic functional materials and multiple biological factors within a light crosslinked hydrogel, forming a multi-functional dressing capable of facilitating simultaneous micro-vascularization and neural regeneration. The ASD uses a zeolite-imidazolate framework 67 with anchored vanadium oxide (VO2@ZIF-67) that allows for the on-demand release of Co2+ with fluctuations in pH at the wound site to stimulate angiogenesis. It can simultaneously release CXCL12, ligustroflavone, and ginsenoside Rg1 in a sustained manner to enhance the recruitment of endogenous mesenchymal stem cells, inhibit senescence, and induce neural differentiation to achieve in situ nerve regeneration. The ASD can stimulate rapid angiogenesis and nerve regeneration within 17 days through multiple angiogenic and neuro-regenerative cues within one dressing. This study provides a proof-of-concept for integrating functional nanomaterials and multiple complementary drugs within a smart dressing for simultaneous angiogenesis and neural regeneration.
“I feel like marijuana is the only drug that wouldn’t kill me”: perceptions of cannabis use in previously incarcerated Black men who have sex with other men
Authors: Flores Rey , Kerman Jared , Schneider John , Harawa Nina 
Published: February 2023

Abstract
Background
Fragmented state laws have impacted cannabis uptake and perceptions in the USA. Little research has explored the attitudes, beliefs, and social network influences of young Black men who have sex with men (BMSM) who have experienced incarceration and use cannabis. While problematic cannabis use is not well defined and understudied, scholars have found that a person’s social network can mediate problematic substance use and reduce recidivism rates by providing both tangible and emotional support. This analysis examines how social networks contribute to cannabis perceptions and use among BMSM with criminal legal system involvement in Chicago, IL, and Houston TX.

Methods
Researchers conducted interviews with 25 cis gender Black men informed by life course theory, with a focus on the role of social networks, incarceration, and other life experiences in substance use. All interviews were audio-recorded, de-identified, and transcribed; participants were compensated $50. A deductive-inductive thematic analysis was used to analyze all qualitative data collected.

Results
Twelve BMSM in Chicago and 13 BMSM in Houston (M = 26.6 years old, SD = 3.7) were interviewed. A majority identified as gay (56%), with 12 participants (48%) reporting having a high school diploma or equivalent; their average age of first substance use was 15.2 (SD = 2.9). Participants perceived cannabis usage to be categorically distinct from other intoxicating substance usage, with many describing it as not harmful and potentially beneficial. Three themes shaped their choices and attitudes regarding cannabis and “hard” drugs—social networks, need fulfillment, and knowledge of risk.

Conclusion
Participant descriptions of cannabis use emphasize their drug-use behavior as being produced by agent decision-making and risk assessment. Future work should expand on how these decisions are made, and how social networks can be leveraged to encourage non-harmful drug consumption behaviors.
Crk proteins activate the Rap1 guanine nucleotide exchange factor C3G by segregated adaptor-dependent and -independent mechanisms
Authors: Rodríguez-Blázquez Antonio , Carabias Arturo , Morán-Vaquero Alba , de Cima Sergio , Luque-Ortega Juan R. , Alfonso Carlos , Schuck Peter , Manso José Antonio , Macedo-Ribeiro Sandra , Guerrero Carmen , de Pereda José M. 
Published: February 2023

Abstract
Background
C3G is a guanine nucleotide exchange factor (GEF) that activates Rap1 to promote cell adhesion. Resting C3G is autoinhibited and the GEF activity is released by stimuli that signal through tyrosine kinases. C3G is activated by tyrosine phosphorylation and interaction with Crk adaptor proteins, whose expression is elevated in multiple human cancers. However, the molecular details of C3G activation and the interplay between phosphorylation and Crk interaction are poorly understood.

Methods
We combined biochemical, biophysical, and cell biology approaches to elucidate the mechanisms of C3G activation. Binding of Crk adaptor proteins to four proline-rich motifs (P1 to P4) in C3G was characterized in vitro using isothermal titration calorimetry and sedimentation velocity, and in Jurkat and HEK293T cells by affinity pull-down assays. The nucleotide exchange activity of C3G over Rap1 was measured using nucleotide-dissociation kinetic assays. Jurkat cells were also used to analyze C3G translocation to the plasma membrane and the C3G-dependent activation of Rap1 upon ligation of T cell receptors.

Results
CrkL interacts through its SH3N domain with sites P1 and P2 of inactive C3G in vitro and in Jurkat and HEK293T cells, and these sites are necessary to recruit C3G to the plasma membrane. However, direct stimulation of the GEF activity requires binding of Crk proteins to the P3 and P4 sites. P3 is occluded in resting C3G and is essential for activation, while P4 contributes secondarily towards complete stimulation. Tyrosine phosphorylation of C3G alone causes marginal activation. Instead, phosphorylation primes C3G lowering the concentration of Crk proteins required for activation and increasing the maximum activity. Unexpectedly, optimal activation also requires the interaction of CrkL-SH2 domain with phosphorylated C3G.

Conclusion
Our study revealed that phosphorylation of C3G by Src and Crk-binding form a two-factor mechanism that ensures tight control of C3G activation. Additionally, the simultaneous SH2 and SH3N interaction of CrkL with C3G, required for the activation, reveals a novel adaptor-independent function of Crk proteins relevant to understanding their role in physiological signaling and their deregulation in diseases.
Identification and validation of a novel survival prediction model based on the T-cell phenotype in the tumor immune microenvironment and peripheral blood for gastric cancer prognosis
Authors: Ma Jing , Li Jianhui , He Nan , Qian Meirui , Lu Yuanyuan , Wang Xin , Wu Kaichun 
Published: February 2023

Abstract
Background
The correlation and difference in T-cell phenotypes between peripheral blood lymphocytes (PBLs) and the tumor immune microenvironment (TIME) in patients with gastric cancer (GC) is not clear. We aimed to characterize the phenotypes of CD8+ T cells in tumor infiltrating lymphocytes (TILs) and PBLs in patients with different outcomes and to establish a useful survival prediction model.

Methods
Multiplex immunofluorescence staining and flow cytometry were used to detect the expression of inhibitory molecules (IMs) and active markers (AMs) in CD8+TILs and PBLs, respectively. The role of these parameters in the 3-year prognosis was assessed by receiver operating characteristic analysis. Then, we divided patients into two TIME clusters (TIME-A/B) and two PBL clusters (PBL-A/B) by unsupervised hierarchical clustering based on the results of multivariate analysis, and used the Kaplan–Meier method to analyze the difference in prognosis between each group. Finally, we constructed and compared three survival prediction models based on Cox regression analysis, and further validated the efficiency and accuracy in the internal and external cohorts.

Results
The percentage of PD-1+CD8+TILs, TIM-3+CD8+TILs, PD-L1+CD8+TILs, and PD-L1+CD8+PBLs and the density of PD-L1+CD8+TILs were independent risk factors, while the percentage of TIM-3+CD8+PBLs was an independent protective factor. The patients in the TIME-B group showed a worse 3-year overall survival (OS) (HR: 3.256, 95% CI 1.318–8.043, P = 0.006), with a higher density of PD-L1+CD8+TILs (P < 0.001) and percentage of PD-1+CD8+TILs (P = 0.017) and PD-L1+CD8+TILs (P < 0.001) compared to the TIME-A group. The patients in the PBL-B group showed higher positivity for PD-L1+CD8+PBLs (P = 0.042), LAG-3+CD8+PBLs (P < 0.001), TIM-3+CD8+PBLs (P = 0.003), PD-L1+CD4+PBLs (P = 0.001), and LAG-3+CD4+PBLs (P < 0.001) and poorer 3-year OS (HR: 0.124, 95% CI 0.017–0.929, P = 0.015) than those in the PBL-A group. In our three survival prediction models, Model 3, which was based on the percentage of TIM-3+CD8+PBLs, PD-L1+CD8+TILs and PD-1+CD8+TILs, showed the best sensitivity (0.950, 0.914), specificity (0.852, 0.857) and accuracy (κ = 0.787, P < 0.001; κ = 0.771, P < 0.001) in the internal and external cohorts, respectively.

Conclusion
We established a comprehensive and robust survival prediction model based on the T-cell phenotype in the TIME and PBLs for GC prognosis.
VEGF-A enhances the cytotoxic function of CD4+ cytotoxic T cells via the VEGF-receptor 1/VEGF-receptor 2/AKT/mTOR pathway
Authors: Chen Ziyi , Zhang Meng , Liu Yufeng , Chen Zhe , Wang Ling , Wang Wenjuan , Wang Jincheng , He Mingqian , Shi Bingyin , Wang Yue 
Published: February 2023

Abstract
Background
CD4+ cytotoxic T cells (CD4 CTLs) are CD4+ T cells with major histocompatibility complex-II-restricted cytotoxic function. Under pathologic conditions, CD4 CTLs hasten the development of autoimmune disease or viral infection by enhancing cytotoxicity. However, the regulators of the cytotoxicity of CD4 CTLs are not fully understood.

Methods
To explore the potential regulators of the cytotoxicity of CD4 CTLs, bulk RNA and single-cell RNA sequencing (scRNA-seq), enzyme-linked immunosorbent assay, flow cytometry, quantitative PCR, and in-vitro stimulation and inhibition assays were performed.

Results
In this study, we found that VEGF-A promoted the cytotoxicity of CD4 CTLs through scRNA-seq and flow cytometry. Regarding the specific VEGF receptor (R) involved, VEGF-R1/R2 signaling was activated in CD4 CTLs with increased cytotoxicity, and the VEGF-A effects were inhibited when anti-VEGF-R1/R2 neutralizing antibodies were applied. Mechanistically, VEGF-A treatment activated the AKT/mTOR pathway in CD4 CTLs, and the increases of cytotoxic molecules induced by VEGF-A were significantly reduced when the AKT/mTOR pathway was inhibited.

Conclusion
In conclusion, VEGF-A enhances the cytotoxicity of CD4 CTLs through the VEGF-R1/VEGF-R2/AKT/mTOR pathway, providing insights for the development of novel treatments for disorders associated with CD4 CTLs.
Hydrogen attenuates postoperative pain through Trx1/ASK1/MMP9 signaling pathway
Authors: Li Juan , Ruan Shirong , Jia Jinhui , Li Qian , Jia Rumeng , Wan Li , Yang Xing , Teng Peng , Peng Qilin , Shi Ya-dan , Yu Pan , Pan Yinbing , Duan Man-lin , Liu Wen-Tao , Zhang Li , Hu Liang 
Published: February 2023

Abstract
Background
Postoperative pain is a serious clinical problem with a poorly understood mechanism, and lacks effective treatment. Hydrogen (H2) can reduce neuroinflammation; therefore, we hypothesize that H2 may alleviate postoperative pain, and aimed to investigate the underlying mechanism.

Methods
Mice were used to establish a postoperative pain model using plantar incision surgery. Mechanical allodynia was measured using the von Frey test. Cell signaling was assayed using gelatin zymography, western blotting, immunohistochemistry, and immunofluorescence staining. Animals or BV-2 cells were received with/without ASK1 and Trx1 inhibitors to investigate the effects of H2 on microglia.

Results
Plantar incision surgery increased MMP-9 activity and ASK1 phosphorylation in the spinal cord of mice. MMP-9 knockout and the ASK1 inhibitor, NQDI-1, attenuated postoperative pain. H2 increased the expression of Trx1 in the spinal cord and in BV-2 cells. H2 treatment mimicked NQDI1 in decreasing the phosphorylation of ASK1, p38 and JNK. It also reduced MMP-9 activity, downregulated pro-IL-1β maturation and IBA-1 expression in the spinal cord of mice, and ameliorated postoperative pain. The protective effects of H2 were abolished by the Trx1 inhibitor, PX12. In vitro, in BV-2 cells, H2 also mimicked NQDI1 in inhibiting the phosphorylation of ASK1, p38, and JNK, and also reduced MMP-9 activity and decreased IBA-1 expression induced by LPS. The Trx1 inhibitor, PX12, abolished the protective effects of H2 in BV-2 cells.

Conclusions
For the first time, the results of our study confirm that H2 can be used as a therapeutic agent to alleviate postoperative pain through the Trx1/ASK1/MMP9 signaling pathway. MMP-9 and ASK1 may be the target molecules for relieving postoperative pain.
Blood tissue Plasminogen Activator (tPA) of liver origin contributes to neurovascular coupling involving brain endothelial N-Methyl-D-Aspartate (NMDA) receptors
Authors: Furon Jonathane , Yetim Mervé , Pouettre Elsa , Martinez de Lizarrondo Sara , Maubert Eric , Hommet Yannick , Lebouvier Laurent , Zheng Ze , Ali Carine , Vivien Denis 
Published: February 2023

Abstract
Background
Regulation of cerebral blood flow (CBF) directly influence brain functions and dysfunctions and involves complex mechanisms, including neurovascular coupling (NVC). It was suggested that the serine protease tissue-type plasminogen activator (tPA) could control CNV induced by whisker stimulation in rodents, through its action on N-methyl-d-Aspartate receptors (NMDARs). However, the origin of tPA and the location and mechanism of its action on NMDARs in relation to CNV remained debated.

Methods
Here, we answered these issues using tPANull mice, conditional deletions of either endothelial tPA (VECad-CreΔtPA) or endothelial GluN1 subunit of NMDARs (VECad-CreΔGluN1), parabioses between wild-type and tPANull mice, hydrodynamic transfection-induced deletion of liver tPA, hepatectomy and pharmacological approaches.

Results
We thus demonstrate that physiological concentrations of vascular tPA, achieved by the bradykinin type 2 receptors-dependent production and release of tPA from liver endothelial cells, promote NVC, through a mechanism dependent on brain endothelial NMDARs.

Conclusions
These data highlight a new mechanism of regulation of NVC involving both endothelial tPA and NMDARs.
An interpersonal neurobiology perspective on the mind and mental health: personal, public, and planetary well-being
Authors: Siegel Daniel J. , Drulis Chloe 
Published: February 2023

AbstractThis article outlines an Interpersonal Neurobiology (IPNB) perspective on the fundamental components that comprise mental health and promote well-being. The central aim of this paper is to answer essential but often overlooked questions related to the field of mental health, such as: What is the mind? What is the basis of well-being? What is the self and how does it develop? We will offer scientific support for the IPNB position that the mind is relational and embodied and that integration is the basis of mental health. It will also describe how the self extends beyond the individual, arising from and inextricably connected to the social, cultural and planetary systems in which we exist. IPNB is not a form of therapy; rather, it is a framework that focuses on deepening our understanding of the mind and human development across the lifespan. Drawing from interdisciplinary principles from a range of fields including physics, mathematics, neuroscience, and psychology, we will provide a practical view of the underlying basis of mental suffering and the scientific mechanisms of change to improve mental well-being. These core principles are building blocks of clinical evaluation and treatment that can be applied across multiple theoretical orientations and client populations. The special emphasis in this article is on the issue of psychache as an underlying cause of suicide and its relationship to personal, public and planetary health.