bluuebunny/crossref_metadata_2025_split huggingface dataset:
Potential immunosuppressive clonal hematopoietic mutations in tumor infiltrating immune cells in breast invasive carcinoma
Authors: Anandakrishnan Ramu , Zyvoloski Ian J , Zyvoloski Lucas R , Opoku Nana K , Dai Andrew , Antony Veneeth 
Published: November 2022

Abstract
A hallmark of cancer is a tumor cell’s ability to evade immune destruction. Somatic mutations in tumor cells that prevent immune destruction have been extensively studied. However, somatic mutations in tumor infiltrating immune (TII) cells, to our knowledge, have not been previously studied. Understandably so since normal hematopoiesis prevents the accumulation of somatic mutations in immune cells. However, clonal hematopoiesis, does result in the accumulation of somatic mutations in immune cells. These mutations cannot “drive” tumor growth, however, they may “facilitate” it by inhibiting an effective anti-tumor immune response. To identify potential immunosuppressive clonal hematopoietic (CH) mutations in TII cells, we analyzed exome and RNA sequencing data from matched tumor and normal blood samples, and single-cell RNA sequencing data, from breast cancer patients. We selected mutations that were somatic, present in TII cells, clonally expanded, potentially pathogenic, expressed in TII cells, unlikely to be a passenger mutation, and in immune response associated genes. We identified eight potential immunosuppressive CH mutations in TII cells. This work is a first step towards determining if immunosuppressive CH mutations in TII cells can affect the progression of solid tumors. Subsequent experimental confirmation could represent a new paradigm in the etiology of cancer.
A method to mitigating toxicity high concentrations of 1, 2, 4 Triazole (a nitrification inhibitor) in plant with use of the root symbiotic fungi
Authors: Padash Akbar , Azarmi Rasoul , Toularoud Ali Ashraf Soltani , Cruz Cristina , Esmaielpour Behrooz 
Published: November 2022

Abstract
Soil contamination with nitrification inhibitors has received a lot of attention in the last few decades due to their potential toxic effects on the plant and soil, but no action has been taken to control and eliminate contamination with nitrification inhibitors. This work tested the hypothesis that symbiotic interactions between fungi and plant roots can reduce the negative effects of the nitrification inhibitor 1, 2, 4-Triazole (TZ) in plants by reducing its uptake. A greenhouse experiment was conducted, using a complete randomized design, to test the effect of symbiotic fungi (Serendipita indica, Glomus etunicatum and mosseae) on the phytotoxicity of TZ applied at four concentrations (Control, 5, 50 and 100 mg / kg soil). Lactuca sativa, cultivar Siyahoo, was selected for this experiment due to its economic value all over the world. HPLC results the concentration of TZ nitrification inhibitor in lettuce leaves was very important. It was found that plants colonized with symbiotic fungi had lower levels of TZ compared to non-colonized plants. Plants treated with S. indica had 65 and 75 percent lower TZ levels (at 50 and 100 mg / kg, respectively) compared with non-colonized plants. TZ at concentrations of 50 and 100 mg / kg also caused a sharp decrease in root colonization, chlorophyll, fresh weight and dry weight of leaves and root growth.
Title：IRAK-M has effects in regulation of lung epithelial inflammation through JNK and p38 MAPK pathways
Authors: Li Jia , Zheng Zhoude , Liu Yi , Zhang Hongbing , Zhang Youming , Gao Jinming 
Published: November 2022

Abstract
Background: Epithelial barrier is important for asthma development by shaping immune responses. Airway expressing-IL-1 receptor-associated kinase (IRAK)-M of Toll-like receptor pathway is involved in immunoregulation of airway inflammation through influencing activities of macrophages and dendritic cells or T cell differentiation. IRAK-M is highly inducible in lung epithelial cells. Whether IRAK-M has effect on cellular immunity in airway epithelial cells in response to external stimulation remains unclear.
Methods: We modeled cellular inflammation induced by IL-1β, TNF-α, IL-33, and house dust mite (HDM) in A549 cells. Cytokine production and pathway activation were used to reflect the effects of IRAK-M siRNA knockdown on epithelial immunity. The findings in A549 were validated in BEAS-2B cells. Genotyping an asthma-susceptible IRAK-M SNP rs1624395 and measurement of serum CXCL-10 levels were performed in asthma patients.
Results: IRAK-M expression was significantly induced in A549 and BEAS-2B cells after stimulation. IRAK-M knockdown increased the production of cytokines and chemokines, including IL-6, IL-8, CXCL10, and CXCL11, at both mRNA and protein levels. Lung epithelial cells showed excessive activation of JNK and p38 MAPK pathways by IRAK-M silencing after stimulation. While antagonizing JNK or p38 MAPK inhibited increased secretion of CXCL10 mediated by IRAK-M silencing in cells. Asthma patients carrying G/G genotypes had significantly higher levels of serum CXCL-10 than those carrying homozygote A/A.
Conclusion: Our findings suggested that the immunoregulatory effect of IRAK-M on lung epithelial inflammation, with a particular impact on CXCL10 production via JNK and p38 MAPK pathways. IRAK-M modulation might indicate a new insight into asthma pathogenesis from disease origin.
Atypical Monkeypox Presentation in a Previously Vaccinated Msm Hiv-Positive Adult
Authors: Crosato Verena , Antoni Melania Degli , Izzo Ilaria , Cerini Carlo , Pennati Francesca , Gulletta Maurizio , Odolini Silvia , Tomasoni Lina Rachele , Matteelli Alberto , Castelli Francesco 
Published: November 2022

Abstract
The outbreak of monkeypox virus (MPXV) in non-endemic countries is an international public health emergency and the diversity in manifestations poses challenges for early diagnosis and isolation. We describe an atypical case of monkeypox (MPX) in a 46-year-old homosexual male with compensated HIV infection. He reported one day duration fever, a lesion on his chin that, over a period of 18 days, had gradually enlarged and ulcerated. Biopsy examination performed at an external centre revealed pyoderma gangrenous, unconfirmed at a subsequent biopsy. When he reported to our hospital outpatients’ clinic the chin lesion had a diameter of 5x5 cm, necrotic margins and ulcerated base and signs of superinfection. was admitted for further investigations. Three swabs collected from pharynx, skin, and chin lesion resulted positive for MPXV. He had a favourable clinical course and was discharged soon after. Pending the achievement of optimal vaccination coverage in at-risk groups, early identification and isolation of infectious patients represent the cornerstones of the containment strategy. Atypical cases of MPX manifestations are not uncommon, particularly in patients with HIV infection. A high level of suspicion should be maintained to identify infectious cases at an early stage and avoid further spread of the infection.
Hydrogen storage and sensing ability of group 8B transition metal−doped B 12 N 12 nanocages: A DFT investigation
Authors: Rakrai Wandee , Tabtimsai Chanukorn , Kaewtong Chatthai , Chuekachang Sopis , Keawwangchai Somchai , Keawwangchai Tasawan , Wanno Banchob 
Published: November 2022

Abstract
Density functional theory calculations have been performed to investigate nH2 (n = 1 − 4) molecules adsorbed on the pristine and group 8B transition metal (TM = Fe, Co, Ni, Ru, Rh, Pd, Os, Ir, and Pt) doping on B or N site of boron nitride nanocage (B12N12). The structural stability, adsorption ability, and electronic property of before and after different numbers of H2 molecule adsorption on the pristine and the TM − doped B12N12 nanocages have been investigated. The calculated results point out that all TM atoms display strong binding with B12N12 nanocage in which the Os atom displays the strongest interaction with B12N12. In addition, the pristine B12N12 has a weak interaction with the H2 molecules. For hydrogen molecules adsorbed on TM − doped B12N12 nanocages, the hydrogen molecules can be strongly adsorption on the TM − doped B12N12 with appreciable adsorption energy, in which the OsB11N12 displays the strongest interaction with the hydrogen molecules. Accordingly, the hydrogen adsorption abilities of B12N12 can be significantly improved through TM doping. Electronic properties of the pristine B12N12 are significantly changed after TM − doping, especially the energy gap of the B12N12 is dramatically decreased. Moreover, electronic properties of the TM − doped B12N12 nanocages are noticeably changed after adsorptions compared with the pristine B12N12. Therefore, the TM − doped B12N12 can be used for hydrogen storage and sensing applications of B12N12 nanomaterials.
GABBR1 as a predictor of prognosis and Its correlation with immune infiltration and dysfunction in clear cell renal cell carcinoma
Authors: Wu Wensong , Chang Fan , Zhang Jianghui , Tang Shuai , Chen Fangmin 
Published: November 2022

Abstract
Background
Although neurotransmitter receptors have a role in cancer formation, it is uncertain how they impact renal clear cell carcinoma (ccRCC) development and the surrounding immune system. This work intended to explore the role of Gamma-Aminobutyric Acid Type B Receptor Subunit 1 (GABBR1) in renal clear cell carcinoma formation, methylation, immunological milieu, and immune dysfunction.
Method
The Cancer Genome Atlas (TCGA) database supplied the patients' clinical data and gene expression pattern, as well as the UALCAN and MethSurv databases provided the methylation data. The single sample gene enrichment approach was utilized to determine immune cell infiltration, and the TIDE database was used to quantify the therapeutic value of immunological checkpoints. R (version 3.6.3) was used to conduct each and every statistical analysis.
Result
The data indicated that increased GABBR1 expression was related with lower overall survival (OS) and disease-specific survival (DSS) (p < 0.001). Multiple methylation sites on the gene also connected to lower survival rates. However, GABBR1 hypermethylation is a marker of poorer clinicopathological characteristics. Immune infiltration algorithm findings reveal that GABBR1 is related with a host type of immune cell infiltration in ccRCC, comprising DC cells, T cells, B cells, and NK cells. GABBR1 shows a favorable association with numerous immunosuppressants, including PD-1, CTLA4, CD200, and LAG3, and it has the capacity to foresee the efficacy of immune checkpoint treatment.
Conclusion
GABBR1 is projected to emerge as a new marker for the identification, prognosis, and therapy of renal clear cell carcinoma.
The Portuguese Forest and the Common Agricultural Policy
Authors: Viegas Miguel , Batista Paulo , Cordovil Francisco 
Published: November 2022

Abstract
Objectives.
The article aims to assess the impact of support from the European Union on the prevalence of fires in Portugal. The study has a territorial dimension that identifies the support distribution pattern and the location of forest spaces.
Methods.
The study uses several databases on the territory and on the funds of the European Union distributed by the municipalities of the Portuguese mainland. It uses a spatial econometrics model from endogenous variables constructed from a principal component analysis.
Results.
The results infer that support is concentrated in the most prosperous agricultural regions. The poorest regions where the forest surface is proportionally larger receive little support. There is no correlation between European Union support for forests and the prevalence of fires.
Conclusions.
To reduce the risk and prevalence of fire, it is necessary to promote an active management of forest areas. To this end, it is necessary to review the way in which support from the Common Agricultural Policy is distributed so that vulnerable territories can receive more support, empowering populations and promoting rural development.
Single cell RNA sequence combined with bulk RNA sequence to construct and validate a novel prognostic signature based on cell developmental trajectory- related genes to predict prognosis and immunotherapeutic response in Hepatocellular Carcinoma
Authors: Gao Biao , Wang Yafei , Li Chonghui , Lu Shichun 
Published: November 2022

Abstract
Background: Immunotherapy is the first-line treatment for advanced liver cancer. However, there is a dearth of validated molecular indicators to predict immunotherapy response.
Methods:Through a combined analysis of bulk RNA sequence data from 365 HCC cases and single cell sequence data from 2 HCC cases, we created a predictive signature based on cell developmental trajectory-related genes. Some comprehensive examinations, such as Microsatellite Instability (MSI), Tumor Mutation Burden (TMB), somatic mutations, and Tumor Immune Dysfunction and Exclusion (TIDE), were carried out to study the connection of immunotherapy response to prognostic signature. External datasets and immunotherapy datas were downloaded and analysed to validate the robustness and superiority of the signature.
Results:365 HCC patients were divided into high-risk group or low-risk group based on scores assessed by the prognosis signature. T stage and Tumor Grade were found to be positively correlated with risk scores. And prognosis in low-risk group was much better when compared with high-risk group. We also confirmed this prognostic signature using external independent data. Interestingly, the high-risk patients had a higher proportion of intratumoral immune cell infiltration, a higher MSI score, a higher TMB score, and a lower TIDE score. These findings suggest that high-risk patients may be more responsive and suitable for immunotherapy. IMvigor210 immunotherapy data confirmed higher response rates in the high-risk group of patients.
Conclusion : Our prognostic signature based on cell developmental trajectory-related genes showed superior performance in predicting the prognosis and immunotherapy response in HCC patients, and has the potential to be an effective tool for clinicians to screen a population suitable for immunotherapy in the future.
Transcriptomic Analysis Identifies Diagnostic Genes in Polycystic Ovary Syndrome and Periodontitis
Authors: Liu Xiaodan , Wang Haojie , Li Ming , Zhang Jingran , Gao Zhanyi , Wan Meng , Zhang Zhihui , Cai Yu , Luan Qingxian , Wang Xiao 
Published: November 2022

AbstractBackground:Over the last decade, there has been an increasing number of clinical and laboratory evidence supporting associations between Polycystic ovary syndrome (PCOS) and periodontitis, but few studies have been conducted on the underlying mechanisms of the two diseases through the transcriptomic approach. In this study, gene co-expression networks between PCOS and periodontitis were analyzed by bioinformatics tools.Methods:PCOS and periodontitis expression data were downloaded from the GEO database, and the differentially expressed genes (DEGs) were identified. After obtaining Intersected genes, GO and KEGG pathway enrichment analysis and random forest (RF) algorithm were used to screen hub genes in PCOS and periodontitis. The functions of the hub genes were analyzed by GSEA, and the correlations between hub genes and immune infiltration in two diseases were examined. Furthermore, a TF-ceRNA regulatory network of hub genes was constructed.Results:There were 1,661 DEGs in PCOS and 701 DEGs in periodontitis compared to the controls. After overlapping, 66 intersected genes were shown to be involved in PCOS and periodontitis, and were mainly enriched in immune and inflammation-related biological processes and pathways. 40 common genes were selected from the PPI network constructed by STRING. The RF algorithm demonstrated that ACSL5, NLRP12, CCRL2, and CEACAM3 were hub genes in PCOS and periodontitis, and the GSEA result revealed their close relationship with the antigen processing and presentation, and chemokine signaling pathway. Moreover, the data showed that those 4 hub genes may serve as diagnostic genes for PCOS and periodontitis.Conclusion:This study identified ACSL5, NLRP12, CCRL2, and CEACAM3 as the diagnostic genes at the intersection of PCOS and periodontitis, and establish a ceRNA network, which could provide a molecular basis for future experimental studies on the association between PCOS and periodontitis.
Towards Improving Agility in Public Administration
Authors: Looks Hanna , Fangmann Jannik , Thomaschewski Jörg , Escalona María José , Eva-Maria Schön 
Published: November 2022

Abstract
In times of crises, such as the refugee crisis or the corona pandemic, the workload in public administrations increases because of the demands of citizens or short-term legal changes. In addition, there is an increasing need for digitalization or to be able to react flexibly to changes. Agile process models and agile practices are appropriate to overcome these challenges. The objective of this paper is to investigate how public administrations can measure their degree of agility to identify potential for improving it. The authors conducted a descriptive single-case study which included multiple units of analysis in a public administration in Germany. The case study was supported by their questionnaire for measuring the degree of agility. One outcome of this study is a conceptual framework that can be used to drive agile transformation in public administrations by continuously measuring agility. Therefore, a questionnaire for measuring agility at team level in public administrations has been developed. The application of the questionnaire in three teams provide insights into dysfunctionality in the interdisciplinary teams as well as optimization potential in terms of affinity to change. The adoption of agility in public administration is a challenge, given that resistance to change is still prevalent. A transformational change is a constant journey and therefore the measurement of progress plays an important role in the continuous improvement of an organization. The applied approach delivers high potential for improvement in terms of agility and provides interesting insights for both practitioners and academics.
Comprehensive investigation on physicochemical properties, flavor profile, and anti-gastric ulcer potentialities of fermented oyster products
Authors: Liu Li , Liu Xue , Yang Xinyi , Xu Xinxing , Zeng Mingyong 
Published: November 2022

Abstract
Molecular sensory science and alcoholic gastric ulcer model were employed to explore the quality and gastroprotection of different fermented oyster products. The fermented oyster hydrolysates (OYF) were rich in amino acids and fatty acids. Lysine, leucine, and valine increased after fermentation, while UFAs exhibited a downward trend. The structure of different fermented oyster products was evaluated by FT-IR and UV, which were mainly manifested in the changes of protein and lipid. “Grass,” “acidic,” “milky,” “fishy,” and “metallic” were identified as the key sensory attributes. Forty-five volatiles were identified by gas chromatography-mass spectrometry. 4-Hexen-1-ol, hexanoic acid, 2-pentenyl-furan, and acetic acid contributed for the aroma profile after fermentation. Moreover, OYF could alleviate oxidative stress, reduce the expression of pro-inflammatory cytokines (TNF-α, IL-β, and NF-κB protein) and increase defense factors. The research demonstrates the relation of quality and bioactivities in OYF and provides a reference for the intensive processing of oyster industry.
Manganese-catalysed Selective Upgrading of Primary Alcohols with Ethanol under Solvent-free Conditions
Authors: Shao Zhihui , Li Xinyan , Zhang Xiaoyu , Zhao Mingqin 
Published: November 2022

Abstract

The transition metal-catalysed Guerbet reaction allows the utilisation of feedstock alcohols and provides a direct and benign approach for the construction of C–C bonds. Herein, we describe the first non-noble metal manganese catalytic system that enables the efficient synthesis of higher-order alcohols via the cross-coupling of biomass-derived ethanol with primary alcohols. The process proceeded with high selectivity in the presence of a well-defined manganese pincer complex under solvent-free conditions. Catalyst loadings as low as 0.03 mol% can be used, leading to a record turnover number of 2336. A wide range of benzylic alcohols (> 20 examples) and aliphatic alcohols can be converted to longer linear alcohols in high yields and with excellent functional group tolerance.
Taxonomic and Functional Community Composition of Ground Beetles (Coleoptera: Carabidae) Changes with Prescribed Fire Severity
Authors: Mason Stephen C. , Shirey Vaughn , Waite Evan S. , Gallagher Michael R. , Skowronkski Nicholas 
Published: November 2022

Abstract
Prescribed fire is a conservation management tool that is frequently used to foster biodiversity by attempting to mimic historic wildfire regimes, reduce invasive species, and maintain habitat integrity. Simultaneously, insects that provide essential ecosystem services such as decomposition, nutrient cycling, and pest control, are globally declining. Within the pyroentomology literature there are mixed reports of positive and negative effects that prescribed fires have on insect communities. This is likely due to generalizing prescribed fires and not accounting for fire heterogeneity created by the fire characteristics such as fire severity. To better understand if prescribed fire severity can affect insect communities, we used multispectral reflectance data collected by Sentinel-2 to methodically quantify prescribed fire severity and compared ground beetle (Coleoptera: Carabidae) taxonomic and functional community composition responses between an unburned site and two sites burned with contrasting fire impacts. We found 23 ground beetle species and used 30 morphological, physiological, phenological, and ecological functional traits for each species. We found that our moderate fire severity site had different taxonomic and functional community compositions from both our unburned and high severity site. Surprisingly, we did not find a strong difference in taxonomic or functional ground beetle composition between our unburned and high severity site. Thus, we provide support that prescribed fire severity does affect ground beetle community composition and encourage future pyroentomology studies to account for fire severity which will help guide conservation managers to make more accurate decisions and predictions about prescribed fire effects on biodiversity in our native landscapes.
Systemic inflammation leads to changes in the intracellular localization of Klk6 in oligodendrocytes in spinal cord white matter
Authors: Furube Eriko , Ohgidani Masahiro , Yoshida Shigetaka 
Published: November 2022

Abstract
Axonal injury and demyelination occur in demyelinating diseases, such as multiple sclerosis, and the detachment of myelin from axons precedes its degradation. Paranodes are the areas at which each layer of the myelin sheath adheres tightly to axons. The destruction of nodal and paranodal structures during inflammation is an important pathophysiology of various neurological disorders. However, the underlying pathological changes in these structures remain unclear. Kallikrein 6 (Klk6), a serine protease produced by oligodendrocytes, is involved in demyelinating diseases. In the present study, we intraperitoneally injected mice with LPS for several days and examined changes in the localization of Klk6. Transient changes in the intracellular localization of Klk6 to paranodes in the spinal cord were observed during LPS-induced systemic inflammation. However, these changes were not detected in the upper part of brain white matter. LPS-induced changes were suppressed by minocycline, suggesting the involvement of microglia. Moreover, nodal lengths were elongated in LPS-treated wild-type mice, but not in LPS-treated Klk6-KO mice. These results demonstrate the potential involvement of Klk6 in the process of demyelination.