bluuebunny/crossref_metadata_2025 huggingface dataset:
Transcriptional Response of Burkholderia cenocepacia H111 to Severe Zinc Starvation
Authors: Barnett James Paul
Published: September 2023

Burkholderia cenocepacia is an opportunistic pathogen that is primarily associated with severe respiratory infections in people with cystic fibrosis. These bacteria have significant intrinsic resistance to antimicrobial therapy, and there is a need for more effective treatments. Bacterial zinc uptake and homeostasis systems are attractive targets for new drugs, yet our understanding of how bacteria acquire and utilise zinc remains incomplete. Here we have used RNA-sequencing and differential gene expression analysis to investigate how B. cenocepacia H111 is able to survive in zinc poor environments, such as those expected to be encountered within the host. The data shows that 201 genes are significantly differentially expressed when zinc supply is severely limited. Included in the 85 upregulated genes, are genes encoding a putative ZnuABC high affinity zinc importer, two TonB-dependent outer membrane receptors that may facilitate zinc uptake across the outer cell membrane, and a COG0523 family zinc metallochaperone. Amongst the 116 downregulated genes, are several zinc-dependent enzymes suggesting a mechanism of zinc sparring to reduce the cells demand for zinc when bioavailability is low.
Tripterygium glycosides sensitizes cisplatin chemotherapeutic potency by modulating gut microbiota in epithelial ovarian cancer
Authors: Zhan Xinlu , Zuo Qi , Huang Genhua , Qi Zhanghua , Wang Yufan , Zhu Sihong , Zhong Yanying , Xiong Yifei , Chen Tingtao , Tan Buzhen
Published: September 2023

Epithelial ovarian cancer (EOC) is a fatal gynecological malignancy with limited therapeutic options. Previous research has demonstrated that Tripterygium glycosides (GTW) can enhance effectiveness of cisplatin (DDP) chemotherapy against EOC. However, the underlying mechanism of GTW alleviating EOC still remains unclear. In this article, an ID8 cell-derived xenograft mouse model was established to evaluate the anti-tumor efficacy of GTW combined with DDP. Consistent with previous findings, the results suggested that GTW combined with DDP can exhibit a stronger tumor suppressive effect than DDP alone. Additionally, GTW was found can further exert gastrointestinal protection against DDP by reducing pathological damage on colon tissue. Secondly, to verify whether gut microbiota play an instrumental role in GTW’s anticancer effect, we treated mice models with antibiotic to eliminate gut microbiota. And our experimental results indicated that all drug groups showed a weaker tumor suppressive effect and more severe gastrointestinal damage post antibiotic supplement. At genus level, the relative abundance of Lactobacillus was dramatically diminished by the antibiotic treatment, while combined treatment of GTW and DDP can significantly restore the level. Moreover, we performed Lactobacillus acidophilus transplantation and healthy mice fecal microbiota transplantation experiments to further investigate the link between the anticancer effect of GTW and gut microbiota. Our results suggested that both cisplatin-sensitizing and intestinal barrier-protecting effects of GTW can be recovered to a different extent. In conclusion, our results indicated that GTW is a promising chemosensitization and intestinal barrier repair drug for EOC, and the potential mechanism may corelate with the restoration of the compromised intestinal microbial balance.
Multiomics and bioinformatics identify differentially expressed effectors in the brain of Toxoplasma gondii infected masked palm civet
Authors: Yuan Hao , Jiang Tiantian , Zhang Wei-Dong , Yang Zipeng , Luo Shengjun , Wang Xiaohu , Zhu Xiaojing , Qi Shuting , Mahmmod Yasser S. , Zhang Xiu-Xiang , Yuan Zi-Guo
Published: September 2023

Introduction

The masked palm civet (Paguma larvata) serves as a reservoir in transmitting pathogens, such as Toxoplasma gondii, to humans. However, the pathogenesis of T. gondii infection in masked palm civets has not been explored. We studied the molecular changes in the brain tissue of masked palm civets chronically infected with T. gondii ME49.

Methods

The differentially expressed proteins in the brain tissue were investigated using iTRAQ and bioinformatics.

Results

A total of 268 differential proteins were identified, of which 111 were upregulated and 157 were downregulated. KEGG analysis identified pathways including PI3K-Akt signaling pathway, proteoglycans in cancer, carbon metabolism, T-cell receptor signaling pathway. Combing transcriptomic and proteomics data, we identified 24 genes that were differentially expressed on both mRNA and protein levels. The top four upregulated proteins were REEP3, REEP4, TEP1, and EEPD1, which was confirmed by western blot and immunohistochemistry. KEGG analysis of these 24 genes identified signaling cascades that were associated with small cell lung cancer, breast cancer, Toll-like receptor signaling pathway, Wnt signaling pathways among others. To understand the mechanism of the observed alteration, we conducted immune infiltration analysis using TIMER databases which identified immune cells that are associated with the upregulation of these proteins. Protein network analysis identified 44 proteins that were in close relation to all four proteins. These proteins were significantly enriched in immunoregulation and cancer pathways including PI3K-Akt signaling pathway, Notch signaling pathway, chemokine signaling pathway, cell cycle, breast cancer, and prostate cancer. Bioinformatics utilizing two cancer databases (TCGA and GEPIA) revealed that the four genes were upregulated in many cancer types including glioblastoma (GBM). In addition, higher expression of REEP3 and EEPD1 was associated with better prognosis, while higher expression of REEP4 and TEP1 was associated with poor prognosis in GBM patients.

Discussion

We identified the differentially expressed genes in the brain of T. gondii infected masked palm civets. These genes were associated with various cellular signaling pathways including those that are immune- and cancer-related.
Modeling and analyzing the action process of monoamine hormones in depression: a Petri nets-based intelligent approach
Authors: Wang Xuyue , Yu Wangyang , Zhang Chao , Wang Jia , Hao Fei , Li Jin , Zhang Jing
Published: September 2023

In contemporary society, the incidence of depression is increasing significantly around the world. At present, most of the treatment methods for depression are psychological counseling and drug therapy. However, this approach does not allow patients to visualize the logic of hormones at the pathological level. In order to better apply intelligence computing methods to the medical field, and to more easily analyze the relationship between norepinephrine and dopamine in depression, it is necessary to build an interpretable graphical model to analyze this relationship which is of great significance to help discover new treatment ideas and potential drug targets. Petri net (PN) is a mathematical and graphic tool used to simulate and study complex system processes. This article utilizes PN to study the relationship between norepinephrine and dopamine in depression. We use PN to model the relationship between the norepinephrine and dopamine, and then use the invariant method of PN to verify and analyze it. The mathematical model proposed in this article can explain the complex pathogenesis of depression and visualize the process of intracellular hormone-induced state changes. Finally, the experiment result suggests that our method provides some possible research directions and approaches for the development of antidepressant drugs.
High blood galectin-3 level associated with risk of frailty in aging
Authors: Ji Xueying , Jiang Zhaoshun , Qiu Yixuan , Yu Jiaming , Zhang Yan , Wang Jiaofeng , Ye Bo , Huang Yuxin , Gu Weidong , Huang Yiqin , Chen Jie , Bao Zhijun
Published: September 2023

Background

Frailty is one of the most problematic expressions of population aging, but its underlying mechanism has not been fully elucidated. Circulating galectin-3 (Gal-3) is involved in the pathogenesis of many age-related diseases. This study aims to explore the influence of circulating Gal-3 on the regulation of frailty and aging and to identify the potential mechanism further.

Methods

In this cross-sectional analysis, the Fried frailty phenotype (FP) was assessed among 149 community elderly residents in Shanghai. Peripheral blood mononuclear cells (PBMCs) were isolated by the Ficoll-Paque density gradient method, and differentially expressed genes (DEGs) encoding transcription factors in frailty were detected by Illumina and bioinformatics analyzed with R software. Gene Ontology (GO) enrichment analyses and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed to explore the functional roles of these DEGs and the target genes related to frailty phenotypes. The serum Gal-3 concentration was tested by enzyme-linked immunosorbent assay (ELISA). Mouse frailty phenotype was used to construct an in vivo model of frailty, after which the serum levels of circulating Gal-3 and its gene expression levels in mouse tissues were determined.

Results

Participants’ mean age was 72.04 ± 7.05 years. In total, 21.48% were frail and 36.91% were pre-frail. The mean serum Gal-3 concentration was 46.34 ± 17.99 ng/mL in frail participants, 32.30 ± 8.14 ng/mL in pre-frail participants, and 26.00 ± 5.87 ng/mL in non-frail individuals (p < 0.001). Significant positive correlations between serum Gal-3 level and FP score, SARC-F score, C-reactive protein (CRP), interleukin-6, etc., were observed. In addition, the KEGG pathway and GO enrichment analyses showed that 265 DEGs in PBMCs of frail participants were mainly related to inflammatory response, translation, RNA binding, protein binding, ribosome, and primary immunodeficiency. LGALS3 was identified as the overlapping gene between frailty-related DEGs and aging-related DEGs. The elevated serum Gal-3 concentration in the in vivo model of frailty was consistent with the results in participants.

Conclusion

In both community-dwelling older adults and aged mice, serum Gal-3 concentration was positively correlated with frailty. This circulating mediator may be a promising indicator of frailty.

Clinical trial registration

Chinese Clinical Trial Registry identifier, ChiCTR2000036399.
The roles of FGF21 and GDF15 in mediating the mitochondrial integrated stress response
Authors: Jena Jayashree , García-Peña Luis Miguel , Pereira Renata O.
Published: September 2023

Various models of mitochondrial stress result in induction of the stress-responsive cytokines fibroblast growth factor 21 (FGF21) and growth differentiation factor 15 (GDF15). This is an adaptive mechanism downstream of the mitochondrial integrated stress response frequently associated with improvements in systemic metabolic health. Both FGF21 and GDF15 have been shown to modulate energy balance and glucose homeostasis, and their pharmacological administration leads to promising beneficial effects against obesity and associated metabolic diseases in pre-clinical models. Furthermore, endogenous upregulation of FGF21 and GDF15 is associated with resistance to diet-induced obesity (DIO), improved glucose homeostasis and increased insulin sensitivity. In this review, we highlight several studies on transgenic mouse models of mitochondrial stress and will compare the specific roles played by FGF21 and GDF15 on the systemic metabolic adaptations reported in these models.
Mechanistic insights to drive catalytic hydrogenation of formamide intermediates to methanol via deaminative hydrogenation
Authors: Kothandaraman Jotheeswari , Heldebrant David J. , Lopez Johnny Saavedra , Dagle Robert A.
Published: September 2023

Amine-promoted hydrogenation of CO2 to methanol typically proceeds via a formamide intermediate when amines are used as additives or if the hydrogenation is performed in carbon capture solvents. The catalysts used for the hydrogenation of the formamide intermediate dictate the selectivity of the products formed: 1) Deoxygenative hydrogenation (C–O bond cleavage) resulting in N-methylation of amine and deactivation of the solvent, 2) Deaminative hydrogenation (C–N bond cleavage) resulting in formation of methanol and regeneration of the solvent. To date, catalytic reductions of CO2 with amine promoters suffer from poor selectively for methanol which we attribute to the limiting formamide intermediate, though to date, the conditions that favor C–N cleavage have yet to be fully understood. To better understand the reactivity of the formamide intermediates, a range of heterogenous catalysts were used to study the hydrogenation of formamide. Well-known gas phase CO2 hydrogenation catalysts catalyze the hydrogenation of formamide to N-methyl product via C–O bond cleavage. However, the selectivity can be readily shifted to selective C–N bond cleavage by addition of an additive with sufficient basicity for both homogenous and heterogeneous catalytic systems. The base additive shifts the selectivity by deprotonating a hemiaminal intermediate formed in situ during the formamide hydrogenation. This prevents dehydration process leading to N-methylated product, which is a key capture solvent deactivation pathway that hinders amine use in carbon capture, utilization, and storage (CCUS). The findings from this study provide a roadmap on how to improve the selectivity of known heterogenous catalysts, enabling catalytic reduction of captured CO2 to methanol.
Lessons learned from community and citizen science monitoring on the Elwha River restoration project
Authors: Eitzel M. V. , Meyer Ryan , Morley Sarah , Miller Ian , Shafroth Patrick B. , Behymer Chelsea , Jadallah Christopher , Parks David , Kagley Anna , Shaffer Anne , Ballard Heidi
Published: September 2023

Community and citizen science (CCS) projects – initiatives that involve public participation in scientific research – can both sustain and expand long-term monitoring of large dam removal projects. In this article, we discuss our perspectives on CCS associated with the Elwha River dam removals. We summarize how the public has been or could be involved in monitoring and distill lessons learned for other large dam removal projects. Much of the Elwha monitoring involved technical field work requiring training and incurring potential liability risks, guiding projects towards smaller-scale public involvement. Partnering with organizations that have capacity for volunteer management expanded CCS opportunities and provided logistical support to project managers committed to public engagement. We found that many projects engaged with students and/or with paid or unpaid interns; compensating participants in various ways can help to create reciprocal relationships that support long-term monitoring. In the future, other large dam removals could consider planning ahead for community involvement in dam removal monitoring to accommodate the technical and potentially hazardous nature of the work – broadening who may be able to participate. In addition, involving community members in setting research agendas could be an important first step in engaging them in long-term monitoring, in turn facilitating multi-generational research at the timescale of landscape-level changes. Finally, explicit relationship-building with Indigenous communities can enhance the benefits of community engagement in dam removal science for all involved.
MicroRNA-510 mediated negative regulation of Caveolin-1 in fibroblasts promotes aggressive tumor growth
Authors: King Brooke , Krisanits Bradley A. , Guo Qi J. , Blake Bobbie , Nogueira Lourdes M. , Jolly Gurbani , Satterwhite Arabia , Turner David P. , Hoffman Stanley , Evans-Knowell Ashley , Findlay Victoria J.
Published: September 2023

Introduction

In the US, despite the recent decline in breast cancer deaths, a persistent mortality disparity exists between black and white women with breast cancer, with black women having a 41% higher death rate. Several studies are now reporting that racial disparities can exist independent of socioeconomic and standard of care issues, suggesting that biological factors may be involved. Caveolin-1 (Cav1) loss in the tumor stromal compartment is a novel clinical biomarker for predicting poor outcome in breast cancer including triple negative subtype, however the mechanism of Cav1 loss is unknown. We previously identified miR-510-5p as a novel oncomir and propose here that the high levels observed in patients is a novel mechanism leading to stromal Cav1 loss and worse outcomes.

Methods

Cav1 was identified as a direct target of miR-510-5p through luciferase, western blot and qPCR assays. Stromal cross talk between epithelial cells and fibroblasts was assessed in vitro using transwell co-culture assays and in vivo using xenograft assays.

Results

We found that Cav1 is a direct target of miR-510-5p and that expression in fibroblasts results in an ‘activated’ phenotype. We propose that this could be important in the context of cancer disparities as we also observed increased levels of circulating miR-510-5p and reduced levels of stromal Cav1 in black women compared to white women with breast cancer. Finally, we observed a significant increase in tumor growth when tumor cells were co-injected with miR-510-5p expressing cancer associated fibroblasts in vivo.

Conclusion

We propose that miR-510-5p mediated negative regulation of Cav1 in fibroblasts is a novel mechanism of aggressive tumor growth and may be a driver of breast cancer disparity.
PLEKHA4 is a novel prognostic biomarker that reshapes the tumor microenvironment in lower-grade glioma
Authors: Zhi Wenqian , Wang Ye , Jiang Chenyu , Gong Yuqin , Chen Qiuyan , Mao Xiang , Deng Wensheng , Zhao Shasha
Published: September 2023

Background

Lower-grade glioma (LGG) is a primary intracranial tumor that carry a high risk of malignant transformation and limited therapeutic options. Emerging evidence indicates that the tumor microenvironment (TME) is a superior predictor for tumor progression and therapy response. PLEKHA4 has been demonstrated to be a biomarker for LGG that correlate with immune infiltration. However, the fundamental mechanism by which PLEKHA4 contributes to LGG is still poorly understood.

Methods

Multiple bioinformatic tools, including Tumor Immune Estimation Resource (TIMER), Gene Expression Profiling Interactive Analysis (GEPIA2), Shiny Methylation Analysis Resource Tool (SMART), etc., were incorporated to analyze the PLEKHA4. ESTIMATE, ssGSEA, CIBERSORT, TIDE and CellMiner algorithms were employed to determine the association of PLEKHA4 with TME, immunotherapy response and drug sensitivities. Immunohistochemistry (IHC)-based tissue microarrays and M2 macrophage infiltration assay were conducted to verify their associations.

Results

PLEKHA4 expression was found to be dramatically upregulated and strongly associated with unfavorable overall survival (OS) and disease-specific survival (DSS) in LGG patients, as well as their poor clinicopathological characteristics. Cox regression analysis identified that PLEKHA4 was an independent prognostic factor. Methylation analysis revealed that DNA methylation correlates with PLEKHA4 expression and indicates a better outcome in LGG. Moreover, PLEKHA4 was remarkably correlated with immune responses and TME remodeling, as evidenced by its positive correlation with particular immune marker subsets and the putative infiltration of immune cells. Surprisingly, the proportion of M2 macrophages in TME was strikingly higher than others, inferring that PLEKHA4 may regulate the infiltration and polarization of M2 macrophages. Evidence provided by IHC-based tissue microarrays and M2 macrophage infiltration assay further validated our findings. Moreover, PLEKHA4 expression was found to be significantly correlated with chemokines, interleukins, and their receptors, further supporting the critical role of PLEKHA4 in reshaping the TME. Additionally, we found that PLEKHA4 expression was closely associated with drug sensitivities and immunotherapy responses, indicating that PLEKHA4 expression also had potential clinical significance in guiding immunotherapy and chemotherapy in LGG.

Conclusion

PLEKHA4 plays a pivotal role in reshaping the TME of LGG patients, and may serve as a potential predictor for LGG prognosis and therapy.
Identification of molecular pattern and prognostic risk model based on ligand-receptor pairs in liver cancer
Authors: Hu Pengbo , Xu Liang , Liu Yongqing , Zhang Xiuyuan , Li Zhou , Li Yiming , Qiu Hong
Published: September 2023

Introduction

The tumor microenvironment of hepatocellular carcinoma is composed of multiple cells, and the interactive communication between cells drives tumor progression and characterizes the tumor. Communication between cells is mainly achieved through signal transduction between receptor ligands, and the rise of single-cell technology has made it possible to analyze the communication network between cells.

Methods

We applied a train of bioinformatic techniques and in vitro experiments. We analyzed the composition of the microenvironment of liver cancer by combining single-cell sequencing data and transcriptome sequencing data from liver cancer to construct molecular typing and risk models for LRs. Then, we analyzed association of it with prognosis, mutation, KEGG, tumor microenvironment (TME), immune infiltration, tumor mutational burden (TMB) and drug sensitivity in liver cancer. qPCR and was used to identify SLC1A5 expression in LIHC cell lines and CCK8, transwell and cell colony formation were performed to validate the function of SLC1A5. Meanwhile, we also performed polarization of macrophages.

Results

In this experiment, we found that liver cancer tissues are rich in immune and mesenchymal cells, and there is extensive signaling between individual cells, so we constructed molecular typing and risk models for LRs. Combining clinical data revealed significant differences in clinical characteristics, prognosis and mutated genes between the molecular typing of receptor-ligand pairs, as well as in sensitivity to drugs; similarly, there were significant prognostic differences between the risk models. There were also notable differences in activated signaling pathways, infiltrating immune cells and immune subtypes. Subsequently, we used siRNA to knock down SLC1A5 in hepatocellular carcinoma cells and found that cell proliferation, migration and invasion were diminished.

Conclusions

In conclusion, our LRs model may become a marker to guide clinical treatment and prognosis.
Differential expression patterns of purinergic ectoenzymes and the antioxidative role of IL-6 in hospitalized COVID-19 patient recovery
Authors: Mazzocco Yanina Luciana , Bergero Gastón , Del Rosso Sebastian , Eberhardt Natalia , Sola Claudia , Saka Héctor Alex , Villada Sofía María , Bocco José Luis , Aoki Maria Pilar
Published: September 2023

Introduction

We have acquired significant knowledge regarding the pathogenesis of severe acute respiratory syndrome caused by coronavirus 2 (SARS-CoV-2). However, the underlying mechanisms responsible for disease recovery still need to be fully understood.

Methods

To gain insights into critical immune markers involved in COVID-19 etiopathogenesis, we studied the evolution of the immune profile of peripheral blood samples from patients who had recovered from COVID-19 and compared them to subjects with severe acute respiratory illness but negative for SARS-CoV-2 detection (controls). In addition, linear and clustered correlations between different parameters were determined.

Results

The data obtained revealed a significant reduction in the frequency of inflammatory monocytes (CD14+CD16+) at hospital discharge vs. admission. Remarkably, nitric oxide (NO) production by the monocyte compartment was significantly reduced at discharge. Furthermore, interleukin (IL)-6 plasma levels were negatively correlated with the frequency of NO+CD14+CD16+ monocytes at hospital admission. However, at the time of hospital release, circulating IL-6 directly correlated with the NO production rate by monocytes. In line with these observations, we found that concomitant with NO diminution, the level of nitrotyrosine (NT) on CD8 T-cells significantly diminished at the time of hospital release. Considering that purinergic signaling constitutes another regulatory system, we analyzed the kinetics of CD39 and CD73 ectoenzyme expression in CD8 T-cells. We found that the frequency of CD39+CD8+ T-cells significantly diminished while the percentage of CD73+ cells increased at hospital discharge. In vitro, IL-6 stimulation of PBMCs from COVID-19 patients diminished the NT levels on CD8 T-cells. A clear differential expression pattern of CD39 and CD73 was observed in the NT+ vs. NT-CD8+ T-cell populations.

Discussion

The results suggest that early after infection, IL-6 controls the production of NO, which regulates the levels of NT on CD8 T-cells modifying their effector functions. Intriguingly, in this cytotoxic cell population, the expression of purinergic ectoenzymes is tightly associated with the presence of nitrated surface molecules. Overall, the data obtained contribute to a better understanding of pathogenic mechanisms associated with COVID-19 outcomes.
Lineage origin and transcriptional control of autoantigen-specific T-regulatory type 1 cells
Authors: Angelats Edgar , Santamaria Pere
Published: September 2023

T Regulatory type-1 (TR1) cells represent an immunosuppressive T cell subset, discovered over 25 years ago, that produces high levels of interleukin-10 (IL-10) but, unlike its FoxP3+ T regulatory (Treg) cell counterpart, does not express FoxP3 or CD25. Experimental evidence generated over the last few years has exposed a promising role for TR1 cells as targets of therapeutic intervention in immune-mediated diseases. The discovery of cell surface markers capable of distinguishing these cells from related T cell types and the application of next generation sequencing techniques to defining their transcriptional make-up have enabled a more accurate description of this T cell population. However, the developmental biology of TR1 cells has long remained elusive, in particular the identity of the cell type(s) giving rise to bona fide TR1 cells in vivo. Here, we review the fundamental phenotypic, transcriptional and functional properties of this T cell subset, and summarize recent lines of evidence shedding light into its ontogeny.
Modulation of HIV-1 capsid multimerization by sennoside A and sennoside B via interaction with the NTD/CTD interface in capsid hexamer
Authors: Zhang Da-Wei , Xu Xiao-Shuang , Zhou Rui , Fu Zhiguo
Published: September 2023

Small molecules that bind to the pocket targeted by a peptide, termed capsid assembly inhibitor (CAI), have shown antiviral effects with unique mechanisms of action. We report the discovery of two natural compounds, sennoside A (SA) and sennoside B (SB), derived from medicinal plants that bind to this pocket in the C-terminal domain of capsid (CA CTD). Both SA and SB were identified via a drug-screening campaign that utilized a time-resolved fluorescence resonance energy transfer assay. They inhibited the HIV-1 CA CTD/CAI interaction at sub-micromolar concentrations of 0.18 μM and 0.08 μM, respectively. Mutation of key residues (including Tyr 169, Leu 211, Asn 183, and Glu 187) in the CA CTD decreased their binding affinity to the CA monomer, from 1.35-fold to 4.17-fold. Furthermore, both compounds induced CA assembly in vitro and bound directly to the CA hexamer, suggesting that they interact with CA beyond the CA CTD. Molecular docking showed that both compounds were bound to the N-terminal domain (NTD)/CTD interface between adjacent protomers within the CA hexamer. SA established a hydrogen-bonding network with residues N57, V59, Q63, K70, and N74 of CA1-NTD and Q179 of CA2-CTD. SB formed hydrogen bonds with the N53, N70, and N74 residues of CA1-NTD, and the A177and Q179 residues of CA2-CTD. Both compounds, acting as glue, can bring αH4 in the NTD and αH9 in the CTD of the NTD/CTD interface close to each other. Collectively, our research indicates that SA and SB, which enhance CA assembly, could serve as novel chemical tools to identify agents that modulate HIV-1 CA assembly. These natural compounds may potentially lead to the development of new antiviral therapies with unique mechanisms of action.
Neuron populations across layer 2-6 in the mouse visual cortex exhibit different coding abilities in the awake mice
Authors: Kong Chui , Wang Yangzhen , Xiao Guihua
Published: September 2023

Introduction

The visual cortex is a key region in the mouse brain, responsible for processing visual information. Comprised of six distinct layers, each with unique neuronal types and connections, the visual cortex exhibits diverse decoding properties across its layers. This study aimed to investigate the relationship between visual stimulus decoding properties and the cortical layers of the visual cortex while considering how this relationship varies across different decoders and brain regions.

Methods

This study reached the above conclusions by analyzing two publicly available datasets obtained through two-photon microscopy of visual cortex neuronal responses. Various types of decoders were tested for visual cortex decoding.

Results

Our findings indicate that the decoding accuracy of neuronal populations with consistent sizes varies among visual cortical layers for visual stimuli such as drift gratings and natural images. In particular, layer 4 neurons in VISp exhibited significantly higher decoding accuracy for visual stimulus identity compared to other layers. However, in VISm, the decoding accuracy of neuronal populations with the same size in layer 2/3 was higher than that in layer 4, despite the overall accuracy being lower than that in VISp and VISl. Furthermore, SVM surpassed other decoders in terms of accuracy, with the variation in decoding performance across layers being consistent among decoders. Additionally, we found that the difference in decoding accuracy across different imaging depths was not associated with the mean orientation selectivity index (OSI) and the mean direction selectivity index (DSI) neurons, but showed a significant positive correlation with the mean reliability and mean signal-to-noise ratio (SNR) of each layer's neuron population.

Discussion

These findings lend new insights into the decoding properties of the visual cortex, highlighting the role of different cortical layers and decoders in determining decoding accuracy. The correlations identified between decoding accuracy and factors such as reliability and SNR pave the way for more nuanced understandings of visual cortex functioning.
Case report: Unilateral GPi DBS in secondary myoclonus-dystonia syndrome after acute disseminated encephalomyelitis
Authors: Calvano Alexander , Beccaria Laura , Timmermann Lars , Bopp Miriam H. A. , Gjorgjevski Marko , Nimsky Christopher , Pedrosa David J.
Published: September 2023

Introduction

Deep brain stimulation (DBS) is an established and effective therapy for movement disorders. Here, we present a case of secondary myoclonus-dystonia syndrome following acute disseminated encephalomyelitis (ADEM) in childhood, which was alleviated by DBS. Using a patient-specific connectome analysis, we sought to characterise the fibres and circuits affected by stimulation.

Case report

We report a case of a 20-year-old man with progressive dystonia, myoclonic jerks, and impaired concentration following childhood ADEM. Motor assessments utilising the Unified Myoclonus Rating Scale (UMRS) and the Burke-Fahn-Marsden Dystonia Rating Scale (BFMDRS) revealed a greater improvement in dystonia compared to myoclonus following adjustments of DBS parameters. These adjustments were based on visualisation of electrode position and volume of tissue activated (VTA) 3 years after surgery. A patient-specific connectome analysis using the VTA as a region of interest revealed fibre tracts connecting to the cerebello-thalamo-cortical network and the superior frontal gyrus in addition to basal ganglia circuits as particularly effective.

Conclusion

Globus pallidus internus (GPi) DBS shows promise as a treatment for secondary myoclonus-dystonia syndromes. Personalised structural considerations, tailored to individual symptoms and clinical characteristics, can provide significant benefits. Patient-specific connectome analysis, specifically, offers insights into the structures involved and may enable a favourable treatment response.
Waiting impulsivity in progressive supranuclear palsy-Richardson’s syndrome
Authors: Ahn Jong Hyeon , Kwon Junmo , Won Ji Hye , Byeon Kyoungseob , Youn Jinyoung , Park Hyunjin , Cho Jin Whan
Published: September 2023

Background

Waiting impulsivity in progressive supranuclear palsy-Richardson’s syndrome (PSP-RS) is difficult to assess, and its regulation is known to involve nucleus accumbens (NAc) subregions. We investigated waiting impulsivity using the “jumping the gun” (JTG) sign, which is defined as premature initiation of clapping before the start signal in the three-clap test and compared clinical features of PSP-RS patients with and without the sign and analyzed neural connectivity and microstructural changes in NAc subregions.

Materials and methods

A positive JTG sign was defined as the participant starting to clap before the start sign in the three-clap test. We classified participants into the JTG positive (JTG +) and JTG negative (JTG-) groups and compared their clinical features, microstructural changes, and connectivity between NAc subregions using diffusion tension imaging. The NAc was parcellated into core and shell subregions using data-driven connectivity-based methods.

Results

Seventy-seven patients with PSP-RS were recruited, and the JTG + group had worse frontal lobe battery (FAB) scores, more frequent falls, and more occurrence of the applause sign than the JTG- group. A logistic regression analysis revealed that FAB scores were associated with a positive JTG sign. The mean fiber density between the right NAc core and right medial orbitofrontal gyrus was higher in the JTG + group than the JTG- group.

Discussion

We show that the JTG sign is a surrogate marker of waiting impulsivity in PSP-RS patients. Our findings enrich the current literature by deepening our understanding of waiting impulsivity in PSP patients and introducing a novel method for its evaluation.
Multi-feature fusion learning for Alzheimer's disease prediction using EEG signals in resting state
Authors: Chen Yonglin , Wang Huabin , Zhang Dailei , Zhang Liping , Tao Liang
Published: September 2023

Introduction

Diagnosing Alzheimer's disease (AD) lesions via visual examination of Electroencephalography (EEG) signals poses a considerable challenge. This has prompted the exploration of deep learning techniques, such as Convolutional Neural Networks (CNNs) and Visual Transformers (ViTs), for AD prediction. However, the classification performance of CNN-based methods has often been deemed inadequate. This is primarily attributed to CNNs struggling with extracting meaningful lesion signals from the complex and noisy EEG data.

Methods

In contrast, ViTs have demonstrated proficiency in capturing global signal patterns. In light of these observations, we propose a novel approach to enhance AD risk assessment. Our proposition involves a hybrid architecture, merging the strengths of CNNs and ViTs to compensate for their respective feature extraction limitations. Our proposed Dual-Branch Feature Fusion Network (DBN) leverages both CNN and ViT components to acquire texture features and global semantic information from EEG signals. These elements are pivotal in capturing dynamic electrical signal changes in the cerebral cortex. Additionally, we introduce Spatial Attention (SA) and Channel Attention (CA) blocks within the network architecture. These attention mechanisms bolster the model's capacity to discern abnormal EEG signal patterns from the amalgamated features. To make well-informed predictions, we employ a two-factor decision-making mechanism. Specifically, we conduct correlation analysis on predicted EEG signals from the same subject to establish consistency.

Results

This is then combined with results from the Clinical Neuropsychological Scale (MMSE) assessment to comprehensively evaluate the subject's susceptibility to AD. Our experimental validation on the publicly available OpenNeuro database underscores the efficacy of our approach. Notably, our proposed method attains an impressive 80.23% classification accuracy in distinguishing between AD, Frontotemporal dementia (FTD), and Normal Control (NC) subjects.

Discussion

This outcome outperforms prevailing state-of-the-art methodologies in EEG-based AD prediction. Furthermore, our methodology enables the visualization of salient regions within pathological images, providing invaluable insights for interpreting and analyzing AD predictions.
Contrast-enhanced ultrasonography findings of LAMNs with peritoneal and splenic metastases: a case report and literature review
Authors: Chen Mei , Zhang Shengmin , Xu Youfeng , Jia Xiupeng , Shi Yijiu
Published: September 2023

Low-grade appendiceal mucinous neoplasms (LAMNs) are rare appendiceal tumors that are primarily diagnosed using computed tomography(CT) enhancement and magnetic resonance imaging (MRI). Herein, we report the sonographic features, especially for contrast-enhanced ultrasound (CEUS), of a 70-year-old female with an unusual LAMN metastasizing to the peritoneum and spleen. The patient had a right pelvic mass 2 days prior to presentation. Two-dimensional (2D) ultrasound revealed a mixed cystic-solid mass in the right lower abdomen and spleen parenchyma; CEUS showed heterogeneous enhancement in both areas, suspected to be a mucinous mass. CT enhancement and MRI findings revealed concurrent findings. Histopathologically, LAMN lesions were confirmed in the appendix, spleen, and peritoneum of the specimens obtained during exploratory laparoscopy. No recurrences were reported at three years postoperatively. LAMN lesions may metastasize to abdominal organs, and imaging examinations are essential for diagnosis. This study presents major ultrasonography and CEUS findings for the diagnosis of LAMNs.
Metabolic reprogramming induced by DCA enhances cisplatin sensitivity through increasing mitochondrial oxidative stress in cholangiocarcinoma
Authors: Qin Hanjiao , Zheng Ge , Li Qiao , Shen Luyan
Published: September 2023

Background: Cholangiocarcinoma has obvious primary multidrug resistance and is generally resistant to cisplatin and other chemotherapy drugs and high glycolytic levels may be associated with chemotherapy resistance of cholangiocarcinoma cells. Dichloroacetate (DCA) is a specific inhibitor of PDK, which can promote mitochondrial aerobic oxidation process by activating PDH. In the past few years, there have been an increasing number of studies supporting the action of DCA against cancer, which also provided evidence for targeting metabolism to enhance the efficacy of cholangiocarcinoma chemotherapy.

Methods: Glucose uptake and lactic acid secretion were used to detect cell metabolism level. Cell apoptosis and cell cycle were detected to confirm cell fate induced by cisplatin combined with DCA. Mito-TEMPO was used to inhibit mtROS to explore the relationship between oxidative stress and cell cycle arrest induced by DCA under cisplatin stress. Finally, PCR array and autophagy inhibitor CQ were used to explore the potential protective mechanism under cell stress.

Results: DCA changed the metabolic model from glycolysis to aerobic oxidation in cholangiocarcinoma cells under cisplatin stress. This metabolic reprogramming increased mitochondrial reactive oxygen species (mtROS) levels, which promoted cell cycle arrest, increased the expression of antioxidant genes and activated autophagy. Inhibition of autophagy further increased the synergistic effect of DCA and cisplatin.

Conclusion: DCA increased cisplatin sensitivity in cholangiocarcinoma cells via increasing the mitochondria oxidative stress and cell growth inhibition. Synergistic effects of DCA and CQ were observed in cholangiocarcinoma cells, which further increased the cisplatin sensitivity via both metabolic reprogramming and inhibition of the stress response autophagy.
Effectiveness and safety of pelareorep plus chemotherapy versus chemotherapy alone for advanced solid tumors: a meta-analysis
Authors: Xie Renxian , Huang Hongxin , Chen Tong , Huang Xuehan , Chen Chuangzhen
Published: September 2023

Background: Pelareorep is an oncolytic virus that causes oncolytic effects in many solid tumors, and it has shown therapeutic benefits. However, few studies have compared pelareorep combined with chemotherapy to traditional chemotherapy alone in advanced solid tumors. Consequently, we intended to evaluate the effectiveness and safety of pelareorep plus chemotherapy in this paper.

Methods: We searched four databases including PubMed, Embase, Cochrane Library and Web of Science comprehensively for studies comparing pelareorep combined with chemotherapy to chemotherapy alone in the treatment of advanced solid tumors. The outcomes measures were 1-year overall survival (OS), 2-year OS, 4-month progression-free survival (PFS), 1-year PFS, objective response rate (ORR), any-grade adverse events (any-grade AEs), and severe AEs (grade ≥ 3).

Results: There were five studies involving 492 patients included in the study. Combination therapy did not significantly improve clinical outcomes in terms of 1-year OS [RR = 1.02, 95%CI = (0.82–1.25)], 2-year OS [RR = 1.00, 95%CI = (0.67–1.49)], 4-month PFS [RR = 1.00, 95%CI = (0.67–1.49)], 1-year PFS [RR = 0.79, 95%CI = (0.44–1.42)], and ORR [OR = 0.79, 95%CI = (0.49–1.27)] compared to chemotherapy alone, and the subgroup analysis of 2-year OS, 1-year PFS, and ORR based on countries and tumor sites showed similar results. In all grades, the incidence of AEs was greater with combination therapy, including fever [RR = 3.10, 95%CI = (1.48–6.52)], nausea [RR = 1.19, 95%CI = (1.02–1.38)], diarrhea [RR = 1.87, 95%CI = (1.39–2.52)], chills [RR = 4.14, 95%CI = (2.30–7.43)], headache [RR = 1.46, 95%CI = (1.02–2.09)], vomiting [RR = 1.38, 95%CI = (1.06–1.80)] and flu-like symptoms [RR = 4.18, 95%CI = (2.19–7.98)]. However, severe adverse events did not differ significantly between the two arms.

Conclusion: Pelareorep addition to traditional chemotherapy did not lead to significant improvements in OS, PFS, or ORR in advanced solid tumor patients, but it did partially increase AEs in all grades, with no discernible differences in serious AEs. Therefore, the combination treatment is not recommended in patients with advanced solid tumors.

Systematic Review Registration:https://www.crd.york.ac.uk/PROSPERO/display_record.php?RecordID=400841, identifier CRD42023400841
Effect of sample temperature on laser-induced plasma of silicone rubber
Authors: An Zhiguo , He Yongqi , Chen Qijuan , Du Gang , Wang Xilin
Published: September 2023

Silicone rubber in power transmission and transformation equipment is subjected to considerable temperature changes under different application environment conditions and in different operational states. In tropical areas and the Turpan region of China, surface temperatures of silicone rubber insulators may reach or exceed 70°C. During in situ testing of silicone rubber, the spectral signal may fluctuate or even be distorted when the temperature changes, and consequently, the accuracy of the analysis may be affected. Therefore, we performed a LIBS-based investigation into the dependence of the spectral signal of rubber silicone on the sample temperature. Using high-temperature vulcanized silicone rubber as the experimental material, we determined the trends in spectral line intensity for different elements, plasma temperature, and electron density with temperature when the sample temperature was increased from 25°C to 310°C. The results indicated that the intensities of the Al I 394.40 nm, Al I 396.15 nm, and Si I 390.55 nm lines in the LIBS spectra underwent a gradual decrease as the temperature was increased, whereas the intensity of the Al I 309.27 nm spectral line was essentially stable. However, the spectral line intensity, plasma temperature, and electron density all exhibited a spike at approximately 260°C, which occurred because of the decomposition of aluminum hydroxide. The results of the present study should prove to be of significance in further increasing the accuracy of LIBS analysis as applied to silicone rubber surface monitoring in high-temperature environments.
A MADS-box gene-induced early flowering pear (Pyrus communis L.) for accelerated pear breeding
Authors: Tomes Sumathi , Gunaseelan Kularajathevan , Dragulescu Monica , Wang Yen-Yi , Guo Lindy , Schaffer Robert J. , Varkonyi-Gasic Erika
Published: September 2023

There have been a considerable number of studies that have successfully sped up the flowering cycle in woody perennial horticultural species. One particularly successful study in apple (Malus domestica) accelerated flowering using a silver birch (Betula pendula) APETALA1/FRUITFULL MADS-box gene BpMADS4, which yielded a good balance of vegetative growth to support subsequent flower and fruit development. In this study, BpMADS4 was constitutively expressed in European pear (Pyrus communis) to establish whether this could be used as a tool in a rapid pear breeding program. Transformed pear lines flowered within 6–18 months after grafting onto a quince (Cydonia oblonga) rootstock. Unlike the spindly habit of early flowering apples, the early flowering pear lines displayed a normal tree-like habit. Like apple, the flower appearance was normal, and the flowers were fertile, producing fruit and seed upon pollination. Seed from these transformed lines were germinated and 50% of the progeny flowered within 3 months of sowing, demonstrating a use for these in a fast breeding program.
Comparative transcriptome analysis of genes involved in paradormant bud release response in ‘Summer Black’ grape
Authors: Fan Shaogang , Luo Feixiong , Wang Meijun , Xu Yanshuai , Chen Wenting , Yang Guoshun
Published: September 2023

Grapevines possess a hierarchy of buds, and the fruitful winter bud forms the foundation of the two-crop-a-year cultivation system, yielding biannual harvests. Throughout its developmental stages, the winter bud sequentially undergoes paradormancy, endodormancy, and ecodormancy to ensure survival in challenging environmental conditions. Releasing the endodormancy of winter bud results in the first crop yield, while breaking the paradormancy of winter bud allows for the second crop harvest. Hydrogen cyanamide serves as an agent to break endodormancy, which counteracting the inhibitory effects of ABA, while H2O2 and ethylene function as signaling molecules in the process of endodormancy release. In the context of breaking paradormancy, common agronomic practices include short pruning and hydrogen cyanamide treatment. However, the mechanism of hydrogen cyanamide contributes to this process remains unknown. This study confirms that hydrogen cyanamide treatment significantly improved both the speed and uniformity of bud sprouting, while short pruning proved to be an effective method for releasing paradormancy until August. This observation highlights the role of apical dominance as a primary inhibitory factor in suppressing the sprouting of paradormant winter bud. Comparative transcriptome analysis revealed that the sixth node winter bud convert to apical tissue following short pruning and established a polar auxin transport canal through the upregulated expression of VvPIN3 and VvTIR1. Moreover, short pruning induced the generation of reactive oxygen species, and wounding, ethylene, and H2O2 collectively acted as stimulating signals and amplified effects through the MAPK cascade. In contrast, hydrogen cyanamide treatment directly disrupted mitochondrial function, resulting in ROS production and an extended efficacy of the growth hormone signaling pathway induction.