bluuebunny/crossref_metadata_2025 huggingface dataset:
TOC prediction and grading evaluation based on variable coefficient △logR method and its application for unconventional exploration targets in Songliao Basin
Authors: Yu Zhanqing , Ma Shizhong , Liu Chao
Published: March 2023

The prediction of total organic carbon (TOC) content and grading evaluation of shale formation are very much significant and essential for reservoir description of rolling exploration and development in the new shale exploration area (Shuangcheng) in Songliao basin, China. In order to improve exploration efficiency and obtain continuous TOC content curve of wells, the variable coefficient △logR technique was developed for TOC estimating which is based on the two of acoustic time difference and deep lateral resistivity logging curve and the variable scale coefficient (K) between them as well as another scale coefficient (A) between TOC and △logR. A prediction model of TOC was established for the well which TOC is measured by evaluation of side wall cores, then apply it to other wells to verify the reliability of the model. The application result of eleven exploration Wells in Shuangcheng area show that the TOC of shale is linearly correlated with △logR, and the maximum prediction accuracy k value varies with wells, so it is necessary to determine the undetermined coefficient k according to a single well, but the A value having no big change from one well to another in similar sedimentary facies and thermal evolution degree of shale. The average relative error of TOC between prediction model and core measurement is 10.6% which verifies the accuracy of this method. On this basis of TOC prediction, we establish shale grading evaluation criteria for the study area. In the establishment process, not only the relationship between TOC and S1, but also vitrinite reflectance (Ro) are considered. The shale in Shuangcheng area can be divided into three types (Class I: TOC > 3.5% and Ro > 0.9%; Class II: TOC 2%–3.5% and Ro > 0.9; Class III: TOC < 2% or Ro < 0.9%), and achieved shale classification on the well profile with TOC and Ro which are easy to predict and reliable. According to the relationship between the thickness of shale of disparate classes and the total thickness of shale in different zones, the thickness of shale of disparate classes in each well is predicted.
Supporting Ph.D. students' skills development: A three-stage doctoral program
Authors: Chaló Paulo , Huet Isabel , Nikoletou Dimitra , Pereira Anabela
Published: March 2023

Introduction

Sustainable development is increasingly recognized as a crucial component of education at all levels, including specialized academic work. As a result, the importance of Ph.D. training in producing highly skilled academics and professionals who can contribute to sustainable development has been acknowledged, leading to increased investments in doctoral training across Europe. However, the diversity in Ph.D. training across countries and universities suggests a lack of studies based on best practices for developing effective doctoral training programs.

Methods

This study aimed to contribute to this discussion by combining the perspectives of 31 Ph.D. supervisors and directors from Portugal and England regarding the best practices for Ph.D. training. Participants from different disciplines were interviewed using semi-structured face-to-face interviews, and the data were analyzed using inductive thematic analysis.

Results

The study found that, despite coming from different countries, the participants' perceptions regarding the challenges and strategies for improving doctoral education were similar. Based on these findings, the study proposes a three-stage program for structuring doctoral training, consisting of initial intensive training, assessment of individual needs, and tailored training.

Discussion

The proposed program has the potential to be valuable in the development or restructuring of Ph.D. programs to address the primary needs of Ph.D. students, optimize institutional resources, and promote on-time completion by facilitating the timely development of necessary competencies for Ph.D. research. Furthermore, this approach could enhance the quality of Ph.D. education, broaden the spectrum and quality of graduates' competencies, and contribute to achieving sustainable development goals.
Study on hot air heating characteristics of greenhouse in cold region
Authors: Zhang Chenghu , Zou Dezhi , Huang Xinpeng , Wu Yaling
Published: March 2023

Agriculture is the main industry in northeast China. As an important part of facility agriculture, agricultural greenhouses are playing a more and more important role. Due to geographical location, Northeast China is cold in winter, and the solar radiation energy is less, therefore, the large-span greenhouses commonly used in northeast China are prone to uneven temperature and insufficient heating. In this paper, in order to solve the phenomenon of uneven air flow field, humidity field and temperature field in greenhouse, based on AIRPAK simulation, four kinds of hot air heating return air modes, such as upper air supply and lower air return mode, lower air supply and upper air return mode, two-side air supply mode and left air supply and right air return mode, we explored the influence of temperature field, humidity field and air flow field in greenhouse. The results showed that the heat load of the greenhouse in winter is 161.51 kW, using two-side air supply mode is the best way. The air supply wind speed is 1.6 m/s, and the return wind speed is 3.1 m/s. The environment of the greenhouse can be maintained at about 15°C day and night, and the relative humidity is relatively uniform. In the crop growing area, the wind speed is between 0 m/s and 0.25 m/s. According to this research, suitable crops can be selected for reasonable planting and distribution in the greenhouse to maximize productivity.
Big data help to define climate change challenges for the typical Mediterranean species Cistus ladanifer L.
Authors: Almeida Alice Maria , Ribeiro Maria Margarida , Ferreira Miguel R. , Roque Natália , Quintela-Sabarís Celestino , Fernandez Paulo
Published: March 2023

Climate change’s huge impact on Mediterranean species’ habitat suitability and spatial and temporal distribution in the coming decades is expected. The present work aimed to reconstruct rockrose (Cistus ladanifer L.) historical and future spatial distribution, a typically Mediterranean species with abundant occurrence in North Africa, Iberian Peninsula, and Southern France. The R ensemble modeling approach was made using the biomod2 package to assess changes in the spatial distribution of the species in the Last Interglacial (LIG), the Last Glacial Maximum (LGM), and the Middle Holocene (MH), in the present, and in the future (for the years 2050 and 2070), considering two Representative Concentration Pathways (RCP 4.5 and RCP 8.5). The current species potential distribution was modeled using 2,833 occurrences, six bioclimatic variables, and four algorithms, Generalized Linear Model (GLM), MaxEnt, Multivariate Adaptive Regression Splines (MARS), and Artificial Neural Networks (ANN). Two global climate models (GCMs), CCSM4 and MRI-CGCM3, were used to forecast past and future suitability. The potential area of occurrence of the species is equal to 15.8 and 14.1% of the study area for current and LIG conditions, while it decreased to 3.8% in the LGM. The species’ presence diaminished more than half in the RCP 4.5 (to 6.8% in 2050 and 7% in 2070), and a too low figure (2.2%) in the worst-case scenario (RCP 8.5) for 2070. The results suggested that the current climatic conditions are the most suitable for the species’ occurrence and that future changes in environmental conditions may lead to the loss of suitable habitats, especially in the worst-case scenario. The information unfolded by this study will help to understand future predictable desertification in the Mediterranean region and to help policymakers to implement possible measures for biodiversity maintenance and desertification avoidance.
Integrated mangrove aquaculture: The sustainable choice for mangroves and aquaculture?
Authors: McSherry Madeline , Davis Robert P. , Andradi-Brown Dominic A. , Ahmadia Gabby N. , Van Kempen Malou , Wingard Brian Susanna
Published: March 2023

Aquaculture production is projected to surpass wild-capture fisheries as the primary source of aquatic animal protein in the near future. Farmed shrimp—which are amongst the most valuable aquaculture commodities—are raised predominantly in Southeast Asia and Latin America in a variety of production systems, spanning from extensive to intensive farming. Shrimp aquaculture has been widely criticized for causing mangrove forest degradation and loss, leading to calls for more sustainable aquaculture approaches that protect mangroves. Here we examine an approach promoted as more sustainable—integrated mangrove aquaculture (IMA): a type of farming where mangroves are planted in or alongside shrimp ponds. We argue that mangroves within IMA shrimp systems provide biodiversity and ecosystem functions and services that are, at best, compromised, especially when compared to intact mangrove forests. Given the rapid adoption of IMA approaches, including advocacy for uptake from many governments and non-governmental organizations, there is an urgent need to ensure that these and other aquaculture systems do not result in any conversion of intact mangrove ecosystems into aquaculture ponds, and to identify any benefits (or lack thereof) provided by IMA systems. The increasing adoption of IMA may offer false promises for managing trade-offs between increasing aquaculture productivity and mangrove forest conservation.
Maternal genetic polymorphisms in the major mitotic checkpoint genes MAD1L1 and MAD2L1 associated with the risk of survival in abnormal chromosomal fetuses
Authors: Chan Ying , Liu Yize , Kong Yamin , Xu Weiming , Zeng Xiaohong , Li Haichun , Guo Yan , Tang Xinhua , Zhang Jinman , Zhu Baosheng
Published: March 2023

Background: The genetic etiology of fetal chromosome abnormalities remains unknown, which brings about an enormous burden for patients, families, and society. The spindle assembly checkpoint (SAC) controls the normal procedure of chromosome disjunction and may take part in the process.

Objective: The aim of this study was to explore the association between polymorphisms of MAD1L1 rs1801368 and MAD2L1 rs1283639804, involved in SAC and fetal chromosome abnormalities.

Methods: The case–control study collected 563 cases and 813 health controls to test the genotypes of MAD1L1 rs1801368 and MAD2L1 rs1283639804 polymorphisms by polymerase chain reaction–restrictive fragment length polymorphism methods (PCR-RFLP).

Results:MAD1L1 rs1801368 polymorphism was associated with fetal chromosome abnormalities alone or combined to lower homocysteine (HCY) levels (alone: dominant: OR: 1.75, 95%CI: 1.19–2.57, and p = 0.005; CT vs. CC: OR = 0.73, 95%CI: 0.57–0.94, and p = 0.016; lower HCY: C vs. T: OR = 0.74, 95%CI: 0.57–0.95, and p = 0.02; dominant: OR = 1.75, 95%CI: 0.79–1.92, and p = 0.005). No significant differences were found in other genetic models or subgroups (p > 0.05, respectively). MAD2L1 rs1283639804 polymorphism revealed a sole genotype in the studied population. HCY is significantly associated with fetal chromosome abnormalities in younger groups (OR: 1.78, 95%CI: 1.28–2.47, and p = 0.001).

Conclusion: The results implied that the polymorphism of MAD1L1 rs1801368 may become the susceptibility factor to fetal chromosome abnormalities alone or combined to lower HCY levels but not to MAD2L1 rs1283639804 polymorphism. In addition, HCY significantly affects fetal chromosomal abnormalities in younger women.
Case report: Rubella virus-induced cutaneous granulomas in a girl with atypical SCID caused by DCLRE1C gene mutations
Authors: Deng Sihan , Rao Shijia , Wang Alun R. , Shi Wei
Published: March 2023

Here, we report a case of rubella virus-induced granulomatous dermatitis in a young girl with immunodeficiency caused by DCLRE1C gene mutations. The patient was a 6-year-old girl who presented with multiple erythematous plaques on the face and limbs. Biopsies of the lesions revealed tuberculoid necrotizing granulomas. No pathogens could be identified on extensive special stains, tissue cultures, or PCR-based microbiology assays. Metagenomic next-generation sequencing analysis revealed the rubella virus. Underlying atypical severe combined immunodeficiency was recognized based on the patient’s history of repetitive infections since birth, low T-cell, B-cell, and NK cell counts, and abnormal immunoglobulins and complements. Whole-exome sequencing revealed the genetic abnormality of the atypical severe combined immunodeficiency (SCID), and compound heterozygous mutations of the DCLRE1C gene were detected. This report highlights the diagnostic values of metagenomic next-generation sequencing in identifying rare pathogens causing cutaneous granulomas in patients with atypical SCID.
Analysis of eight types of RNA modification regulators and their correlation with the prognosis in hepatocellular carcinoma
Authors: Qin Wan , Jin Chen , Zou Jun
Published: March 2023

RNA modification plays important role in the occurrence and development of hepatocellular carcinoma. The best characterized RNA modification is m6A, while other kinds of RNA modifications have not been fully investigated in hepatocellular carcinoma (HCC). In the current study, we investigated the roles of one hundred RNA modification regulators belonging to eight different types of cancer-related RNA modifications in HCC. Expression analysis revealed that nearly 90% RNA regulators exhibited significantly higher expression in tumors than normal tissues. By consensus clustering, we identified two clusters with distinct biological characteristics, immune microenvironment, and prognostic pattern. An RNA modification score (RMScore) was constructed and stratified patients into high- and low-risk group, which showed significantly different prognosis. Moreover, a nomogram including clinicopathologic features and the RMScore could well predict the survival in HCC patients. This study indicated the important role of eight types of RNA modification in HCC and develop a RMScore, which will be a new method to forecast the prognosis of HCC patients.
Pan-cancer analysis identifies PD-L2 as a tumor promotor in the tumor microenvironment
Authors: Lv Jingfang , Jiang Zheng , Yuan Junhu , Zhuang Meng , Guan Xu , Liu Hengchang , Yin Yefeng , Ma Yiming , Liu Zheng , Wang Hongying , Wang Xishan
Published: March 2023

Background

Programmed cell death protein 1 (PD-1) receptor has two ligands,programmed death-ligand 1 (PD-L1) and PD-L2. When compared with PD-L1, PD-L2 has not received much attention, and its role remains unclear.

Methods

The expression profiles of pdcd1lg2 (PD-L2-encoding gene) mRNA and PD-L2 protein were analyzed using TCGA, ICGC, and HPA databases. Kaplan-Meier and Cox regression analyses were used to assess the prognostic significance of PD-L2. We used GSEA, Spearman’s correlation analysis and PPI network to explore the biological functions of PD-L2. PD-L2-associated immune cell infiltration was evaluated using the ESTIMATE algorithm and TIMER 2.0. The expressions of PD-L2 in tumor-associated macrophages (TAMs) in human colon cancer samples, and in mice in an immunocompetent syngeneic setting were verified using scRNA-seq datasets, multiplex immunofluorescence staining, and flow cytometry. After fluorescence-activated cell sorting, flow cytometry and qRT-PCR and transwell and colony formation assays were used to evaluate the phenotype and functions of PD-L2+TAMs. Immune checkpoint inhibitors (ICIs) therapy prediction analysis was performed using TIDE and TISMO. Last, a series of targeted small-molecule drugs with promising therapeutic effects were predicted using the GSCA platform.

Results

PD-L2 was expressed in all the common human cancer types and deteriorated outcomes in multiple cancers. PPI network and Spearman’s correlation analysis revealed that PD-L2 was closely associated with many immune molecules. Moreover, both GSEA results of KEGG pathways and GSEA results for Reactome analysis indicated that PD-L2 expression played an important role in cancer immune response. Further analysis showed that PD-L2 expression was strongly associated with the infiltration of immune cells in tumor tissue in almost all cancer types, among which macrophages were the most positively associated with PD-L2 in colon cancer. According to the results mentioned above, we verified the expression of PD-L2 in TAMs in colon cancer and found that PD-L2+TAMs population was not static. Additionally, PD-L2+TAMs exhibited protumor M2 phenotype and increased the migration, invasion, and proliferative capacity of colon cancer cells. Furthermore, PD-L2 had a substantial predictive value for ICIs therapy cohorts.

Conclusion

PD-L2 in the TME, especially expressed on TAMs, could be applied as a potential therapeutic target.
Perivascular adipose tissue promotes vascular dysfunction in murine lupus
Authors: Shi Hong , Goo Brandee , Kim David , Kress Taylor C. , Ogbi Mourad , Mintz James , Wu Hanping , Belin de Chantemèle Eric J. , Stepp David , Long Xiaochun , Guha Avirup , Lee Richard , Carbone Laura , Annex Brian H. , Hui David Y. , Kim Ha Won , Weintraub Neal L.
Published: March 2023

Introduction

Patients with systemic lupus erythematosus (SLE) are at elevated risk for Q10 cardiovascular disease (CVD) due to accelerated atherosclerosis. Compared to heathy control subjects, lupus patients have higher volumes and densities of thoracic aortic perivascular adipose tissue (PVAT), which independently associates with vascular calcification, a marker of subclinical atherosclerosis. However, the biological and functional role of PVAT in SLE has not been directly investigated.

Methods

Using mouse models of lupus, we studied the phenotype and function of PVAT, and the mechanisms linking PVAT and vascular dysfunction in lupus disease.

Results and discussion

Lupus mice were hypermetabolic and exhibited partial lipodystrophy, with sparing of thoracic aortic PVAT. Using wire myography, we found that mice with active lupus exhibited impaired endothelium-dependent relaxation of thoracic aorta, which was further exacerbated in the presence of thoracic aortic PVAT. Interestingly, PVAT from lupus mice exhibited phenotypic switching, as evidenced by “whitening” and hypertrophy of perivascular adipocytes along with immune cell infiltration, in association with adventitial hyperplasia. In addition, expression of UCP1, a brown/beige adipose marker, was dramatically decreased, while CD45-positive leukocyte infiltration was increased, in PVAT from lupus mice. Furthermore, PVAT from lupus mice exhibited a marked decrease in adipogenic gene expression, concomitant with increased pro-inflammatory adipocytokine and leukocyte marker expression. Taken together, these results suggest that dysfunctional, inflamed PVAT may contribute to vascular disease in lupus.
Analysis of potential immune-related genes involved in the pathogenesis of ischemia-reperfusion injury following liver transplantation
Authors: Guo Jiayu , Han Shangting , Chen Qi , Wang Tianyu , Yu Bo , Zhou Jiangqiao , Qiu Tao
Published: March 2023

Background

Hepatic ischemia-reperfusion (I/R) injury is an unavoidable pathological process that occurs after liver transplantation. However, the immune-related molecular mechanism still remains unclear. This study aims to further explore the biological mechanisms of immune-related genes in hepatic I/R injury.

Methods

Gene microarray data was downloaded from the Gene Expression Omnibus (GEO) expression profile database and the differentially expressed genes (DEGs) were taken for intersection. After identifying common DEGs, functional annotation, protein-protein interaction (PPI) network, and modular construction were performed. The immune-related hub genes were obtained, which their upstream transcription factors and non-RNAs were predicted. Validation of the hub genes expression and immune infiltration were performed in a mouse model of hepatic I/R injury.

Results

A total of 71 common DEGs were obtained from three datasets (GSE12720, GSE14951, GSE15480). The GO and KEGG enrichment analysis results indicated that immune and inflammatory response played an important role in hepatic I/R injury. Finally, 9 immune-related hub genes were identified by intersecting cytoHubba with immune-related genes, including SOCS3, JUND, CCL4, NFKBIA, CXCL8, ICAM1, IRF1, TNFAIP3, and JUN.

Conclusion

Our study revealed the importance of the immune and inflammatory response in I/R injury following liver transplantation and provided new insights into the therapeutic of hepatic I/R injury.
Galectin-9 promotes natural killer cells activity via interaction with CD44
Authors: Rahmati Amirhossein , Bigam Steven , Elahi Shokrollah
Published: March 2023

Natural killer (NK) cells are a potent innate source of cytokines and cytoplasmic granules. Their effector functions are tightly synchronized by the balance between the stimulatory and inhibitory receptors. Here, we quantified the proportion of NK cells and the surface presence of Galectin-9 (Gal-9) from the bone marrow, blood, liver, spleen, and lungs of adult and neonatal mice. We also examined the effector functions of Gal-9+NK cells compared with their Gal-9- counterparts. Our results revealed that Gal-9+NK cells are more abundant in tissues, in particular, in the liver than in the blood and bone marrow. We found Gal-9 presence was associated with enhanced cytotoxic effector molecules granzyme B (GzmB) and perforin expression. Likewise, Gal-9 expressing NK cells displayed greater IFN-γ and TNF-α expression than their negative counterparts under hemostatic circumstances. Notably, the expansion of Gal-9+NK cells in the spleen of mice infected with E. coli implies that Gal-9+NK cells may provide a protective role against infection. Similarly, we found the expansion of Gal-9+NK cells in the spleen and tumor tissues of melanoma B16-F10 mice. Mechanistically, our results revealed the interaction of Gal-9 with CD44 as noted by their co-expression/co-localization. Subsequently, this interaction resulted in enhanced expression of Phospho-LCK, ERK, Akt, MAPK, and mTOR in NK cells. Moreover, we found Gal-9+NK cells exhibited an activated phenotype as evidenced by increased CD69, CD25, and Sca-1 but reduced KLRG1 expression. Likewise, we found Gal-9 preferentially interacts with CD44high in human NK cells. Despite this interaction, we noted a dichotomy in terms of effector functions in NK cells from COVID-19 patients. We observed that the presence of Gal-9 on NK cells resulted in a greater IFN-γ expression without any changes in cytolytic molecule expression in these patients. These observations suggest differences in Gal-9+NK cell effector functions between mice and humans that should be considered in different physiological and pathological conditions. Therefore, our results highlight the important role of Gal-9 via CD44 in NK cell activation, which suggests Gal-9 is a potential new avenue for the development of therapeutic approaches to modulate NK cell effector functions.
Do peripheral neuropathies differ among immune checkpoint inhibitors? Reports from the European post-marketing surveillance database in the past 10 years
Authors: Ruggiero Rosanna , Balzano Nunzia , Di Napoli Raffaella , Fraenza Federica , Pentella Ciro , Riccardi Consiglia , Donniacuo Maria , Tesorone Marina , Danesi Romano , Del Re Marzia , Rossi Francesco , Capuano Annalisa
Published: March 2023

Although the immunotherapy advent has revolutionized cancer treatment, it, unfortunately, does not spare cancer patients from possible immune-related adverse events (irAEs), which can also involve the peripheral nervous system. Immune checkpoint inhibitors (ICIs), blocking cytotoxic T-lymphocyteassociated protein 4 (CTLA-4), programmed cell death protein 1 (PD-1), or programmed cell death ligand 1 (PD-L1), can induce an immune imbalance and cause different peripheral neuropathies (PNs). Considering the wide range of PNs and their high impact on the safety and quality of life for cancer patients and the availability of large post-marketing surveillance databases, we chose to analyze the characteristics of ICI-related PNs reported as suspected drug reactions from 2010 to 2020 in the European real-world context. We analyzed data collected in the European pharmacovigilance database, Eudravigilance, and conducted a systematic and disproportionality analysis. In our study, we found 735 reports describing 766 PNs occurred in patients treated with ICIs. These PNs included Guillain-Barré syndrome, Miller-Fisher syndrome, neuritis, and chronic inflammatory demyelinating polyradiculoneuropathy. These ADRs were often serious, resulting in patient disability or hospitalization. Moreover, our disproportionality analysis revealed an increased reporting frequency of PNs with tezolizumab compared to other ICIs. Guillain-Barré syndrome is a notable potential PN related to ICIs, as it is associated with a significant impact on patient safety and has had unfavorable outcomes, including a fatal one. Continued monitoring of the safety profile of ICIs in real-life settings is necessary, especially considering the increased frequency of PNs associated with atezolizumab compared with other ICIs.
Energy multi-scale method to analyze the scale effect of soil particles
Authors: Chen Jian , Tong Huawei , Yuan Jie , Fang Yingguang , Huang Xiaofeng
Published: March 2023

As a common geological material, soil is a key aspect of construction engineering. Soil has typical multi-scale characteristics, but current multi-scale methods analyze these characteristics only in regard to geometric space. More exploration of the coupling influence mechanism of the basic properties of particles on the microstructure and macroscopic properties of soil is needed. This study analyzed the influence of geometric scale and mineral composition on the surface energy of particles at the microscopic level for development of the energy multi-scale method. Experiments were performed to determine the influence of mineral composition and particle size on the plasticity index (Ip) of the soil, and experimental results are discussed and interpreted quantitatively using the energy multi-scale method. The conclusions derived from this work are as follows: 1) the mineral composition and particle size of the soil can cause interface and surface effects; 2) the comprehensive ratio of micro-force to weight (CRFW) of the particles can be determined using the energy multi-scale method and quantitatively reflects the influence of particle size and mineral composition on the microscopic properties of the soil; and 3) the energy multi-scale method explains the mechanism of the plasticity index of soil and has allowed identification of a new division of soil plasticity. When the CRFW was used as the control index, the plasticity index of the three materials was practically the same, even if the mineral composition and particle sizes of the three materials were different.
Interstitial lung disease associated with inflammatory myositis: Autoantibodies, clinical phenotypes, and progressive fibrosis
Authors: Ceribelli Angela , Tonutti Antonio , Isailovic Natasa , De Santis Maria , Selmi Carlo
Published: March 2023

Progressive pulmonary fibrosis is generally diagnosed when interstitial lung disease progression occurs in the absence of any other cause, and a subset of patients with myositis and associated interstitial lung disease may develop progressive pulmonary fibrosis. Numerous autoantibodies (e.g., against tRNA-synthetase, MDA5, Ro52) increase the risk of this clinical feature in myositis and we speculate that serum biomarkers, sought using the most sensitive laboratory techniques available (i.e., immunoprecipitation) may predict pulmonary involvement and allow the early identification of progressive pulmonary fibrosis. We herein provide a narrative review of the literature and also present original data on pulmonary fibrosis in a cohort of patients with myositis and serum anti-Ro52 with interstitial lung disease. Our results fit into the previous evidence and support the association between anti-Ro52 and signs of pulmonary fibrosis in patients with inflammatory myositis. We believe that the combination of available and real-life data has significant clinical relevance as a paradigm of serum autoantibodies that prove useful in determining precision medicine in rare connective tissue diseases.
Case report: COVID-19-associated mucormycosis co-infection with Lomentospora prolificans: The first case and review on multiple fungal co-infections during COVID-19 pandemic
Authors: Erami Mahzad , Mirhendi Hossein , Momen-Heravi Mansooreh , Sharif Alireza , Hashemi Hezaveh Seyed Jamal , Matini Amir Hassan , Ahsaniarani Amir Hossein , Aboutalebian Shima
Published: March 2023

Along with the pandemic COVID-19 spreads, new clinical challenges have emerged in the health care settings, among which there is a high risk of secondary invasive fungal infections with significant mortality. Here, we report a case of invasive fungal rhino orbital sinusitis due to the simultaneous co-infection by Rhizopus oryzae and Lomentospora prolificans, both identified by sequencing, in a 70-year-old Afghanistanian female with COVID-19. The patient was subjected to surgical debridement as well as taking liposomal amphotericin B, voriconazole, and on discharge, her condition was good. As far as we know, this is the first case of co-infection of COVID-19-associated mucormycosis (CAM) and Lomentospora prolificans infection. Multiple fungal co-infections in COVID-19 patients are reviewed.
Beyond vision:Cataract and health status in old age, a narrative review
Authors: Mencucci Rita , Stefanini Simone , Favuzza Eleonora , Cennamo Michela , De Vitto Chiara , Mossello Enrico
Published: March 2023

Cataract is a leading cause of visual impairment in old age. Lens opacification is notoriously associated with several geriatric conditions, including frailty, fall risk, depression and cognitive impairment. The association is largely attributable to visual impairment, while other mechanisms, associated with extraocular comorbidity and lifestyle, might partly explain this correlation. Available literature suggests that cataract surgery may be effective in decreasing fall risk, improving depressive symptoms and limiting the risk of cognitive impairment and dementia incidence, although intervention studies on these outcomes are still limited. In this review we also emphasize the need to move from the concept of visual acuity to functional vision, especially in the context of the geriatric patient. Research is needed regarding the effect on the cited outcomes of different cataract treatment strategies, such as systematic bilateral versus monolateral surgery and use of different intraocular lenses.
Application of biomaterials in the eradication of Helicobacter pylori: A bibliometric analysis and overview
Authors: Shu Chunxi , Xu Zhou , He Cong , Xu Xinbo , Zhou Yanan , Cai Baihui , Zhu Yin
Published: March 2023

Helicobacter pylori is a prominent cause of gastritis, peptic ulcer, and gastric cancer. It is naturally colonized on the surface of the mucus layer and mucosal epithelial cells of the gastric sinus, surrounded not only by mucus layer with high viscosity that prevents the contact of drug molecules with bacteria but also by multitudinous gastric acid and pepsin, inactivating the antibacterial drug. With high-performance biocompatibility and biological specificity, biomaterials emerge as promising prospects closely associated with H. pylori eradication recently. Aiming to thoroughly summarize the progressing research in this field, we have screened 101 publications from the web of science database and then a bibliometric investigation was performed on the research trends of the application of biomaterials in eradicating H. pylori over the last decade utilizing VOSviewer and CiteSpace to establish the relationship between the publications, countries, institutions, authors, and most relevant topics. Keyword analysis illustrates biomaterials including nanoparticles (NPs), metallic materials, liposomes, and polymers are employed most frequently. Depending on their constituent materials and characterized structures, biomaterials exhibit diverse prospects in eradicating H. pylori regarding extending drug delivery time, avoiding drug inactivation, target response, and addressing drug resistance. Furthermore, we overviewed the challenges and forthcoming research perspective of high-performance biomaterials in H. pylori eradication based on recent studies.
Influence of mental health medication on microbiota in the elderly population in the Valencian region
Authors: Pesantes Nicole , Barberá Ana , Pérez-Rocher Benjamí , Artacho Alejandro , Vargas Sergio Luís , Moya Andrés , Ruiz-Ruiz Susana
Published: March 2023

Spain has an aging population; 19.93% of the Spanish population is over 65. Aging is accompanied by several health issues, including mental health disorders and changes in the gut microbiota. The gut-brain axis is a bidirectional network linking the central nervous system with gastrointestinal tract functions, and therefore, the gut microbiota can influence an individual’s mental health. Furthermore, aging-related physiological changes affect the gut microbiota, with differences in taxa and their associated metabolic functions between younger and older people. Here, we took a case–control approach to study the interplay between gut microbiota and mental health of elderly people. Fecal and saliva samples from 101 healthy volunteers over 65 were collected, of which 28 (EE|MH group) reported using antidepressants or medication for anxiety or insomnia at the time of sampling. The rest of the volunteers (EE|NOMH group) were the control group. 16S rRNA gene sequencing and metagenomic sequencing were applied to determine the differences between intestinal and oral microbiota. Significant differences in genera were found, specifically eight in the gut microbiota, and five in the oral microbiota. Functional analysis of fecal samples showed differences in five orthologous genes related to tryptophan metabolism, the precursor of serotonin and melatonin, and in six categories related to serine metabolism, a precursor of tryptophan. Moreover, we found 29 metabolic pathways with significant inter-group differences, including pathways regulating longevity, the dopaminergic synapse, the serotoninergic synapse, and two amino acids.
Knowledge domain and emerging trends in HIV pre-exposure prophylaxis: A visualization analysis via CiteSpace
Authors: Chen Xi , Lai Yu
Published: March 2023

Background

As an effective strategy that reduces transmission among people at high risk of human immunodeficiency virus (HIV), pre-exposure prophylaxis (PrEP) has revolutionized HIV prevention. Our study aims to provide a reference for the development of relevant research and the formulation of prevention and control policies for HIV.

Methods

Through CiteSpace software, this study aims to present a comprehensive overview of the HIV PrEP knowledge structure, hotspots, and frontiers. We searched the Web of Science Core Collection for studies published between 2012 and 2022 related to HIV PrEP, and 3,243 papers remained after selection.

Results

The number of HIV PrEP publications has increased over the past few years. A close integration and exchange of HIV PrEP research findings has taken place between countries and authors. Major ongoing research trends include long-term injection PrEP, the impact of chlamydia on HIV PrEP, and individual awareness of and attitudes toward HIV PrEP. Thus, more attention should be paid to innovations and breakthroughs in drugs, the factors that affect HIV transmission and susceptibility, and the future promotion of public acceptance of HIV PrEP.

Conclusion

This study offers a systematic, objective, and comprehensive analysis of the related articles. It will assist scholars in understanding the dynamic evolution of HIV PrEP research and identifying future research areas to better advance the development of the field.
Analysis of the external signals driving the transcriptional regulation of the main genes involved in denitrification in Haloferax mediterranei
Authors: Miralles-Robledillo Jose María , Martínez-Espinosa Rosa María , Pire Carmen
Published: March 2023

Haloferax mediterranei is the model microorganism for the study of the nitrogen cycle in haloarchaea. This archaeon not only assimilate N-species such as nitrate, nitrite, or ammonia, but also it can perform denitrification under low oxygen conditions, using nitrate or nitrite as alternative electron acceptors. However, the information currently available on the regulation of this alternative respiration in this kind of microorganism is scarce. Therefore, in this research, the study of haloarchaeal denitrification using H. mediterranei has been addressed by analyzing the promoter regions of the four main genes of denitrification (narGH, nirK, nor, and nosZ) through bioinformatics, reporter gene assays under oxic and anoxic conditions and by site-directed mutagenesis of the promoter regions. The results have shown that these four promoter regions share a common semi-palindromic motif that plays a role in the control of the expression levels of nor and nosZ (and probably nirK) genes. Regarding the regulation of the genes under study, it has been concluded that nirK, nor, and nosZ genes share some expression patterns, and therefore their transcription could be under the control of the same regulator whereas nar operon expression displays differences, such as the activation by dimethyl sulfoxide with respect to the expression in the absence of an electron acceptor, which is almost null under anoxic conditions. Finally, the study with different electron acceptors demonstrated that this haloarchaea does not need complete anoxia to perform denitrification. Oxygen concentrations around 100 μM trigger the activation of the four promoters. However, a low oxygen concentration per se is not a strong signal to activate the promoters of the main genes involved in this pathway; high activation also requires the presence of nitrate or nitrite as final electron acceptors.
A food poisoning caused by ST7 Staphylococcal aureus harboring sea gene in Hainan province, China
Authors: Guo Yahui , Yu Xiaojie , Wang Jixiao , Hua De , You Yuanhai , Wu Qingbo , Ji Qinglong , Zhang Jianzhong , Li Liefei , Hu Yuan , Wu Zhonghui , Wei Xiaoyue , Jin Lianqun , Meng Fanliang , Yang Yuhua , Hu Xiaofeng , Long Lijin , Hu Songnian , Qi Heyuan , Ma Juncai , Bei Wenwen , Yan Xiaomei , Wang Haibin , He Zilong
Published: March 2023

ST7 Staphylococcus aureus is highly prevalent in humans, pigs, as well as food in China; however, staphylococcal food poisoning (SFP) caused by this ST type has rarely been reported. On May 13, 2017, an SFP outbreak caused by ST7 S. aureus strains occurred in two campuses of a kindergarten in Hainan Province, China. We investigated the genomic characteristics and phylogenetic analysis of ST7 SFP strains combined with the 91 ST7 food-borne strains from 12 provinces in China by performing whole-genome sequencing (WGS). There was clear phylogenetic clustering of seven SFP isolates. Six antibiotic genes including blaZ, ANT (4′)-Ib, tetK, lnuA, norA, and lmrS were present in all SFP strains and also showed a higher prevalence rate in 91 food-borne strains. A multiple resistance plasmid pDC53285 was present in SFP strain DC53285. Among 27 enterotoxin genes, only sea and selx were found in all SFP strains. A ФSa3int prophage containing type A immune evasion cluster (sea, scn, sak, and chp) was identified in SFP strain. In conclusion, we concluded that this SFP event was caused by the contamination of cakes with ST7 S. aureus. This study indicated the potential risk of new emergencing ST7 clone for SFP.
Assessment of the safety and probiotic characteristics of Lactobacillus salivarius CGMCC20700 based on whole-genome sequencing and phenotypic analysis
Authors: Jiang Yu-Hang , Yang Rui-Si , Lin Yi-Cen , Xin Wei-Gang , Zhou Huan-Yu , Wang Feng , Zhang Qi-Lin , Lin Lian-Bing
Published: March 2023

Lactic acid bacteria are generally regarded as alternatives to antibiotics in livestock and poultry farming, especially Lactobacillus strains, which are safe and have probiotic potential. Although Lactobacillus salivarius has long been proposed to be a probiotic, the understanding of the roles of this species is still in its infancy. Here, a strain of L. salivarius CGMCC20700 isolated from the intestinal mucosa of Yunnan black-bone chicken broilers was investigated in the context of its safety and probiotic characteristics by whole-genome sequencing in parallel with phenotypic analysis. Whole-genome sequencing results showed that L. salivarius CGMCC20700 has a single scaffold of 1,737,577 bp with an average guanine-to-cytosine (GC) ratio of 33.51% and 1,757 protein-coding genes. The annotation of Clusters of Orthologous Groups (COG) classified the predicted proteins from the assembled genome as possessing cellular, metabolic, and information-related functions. Sequences related to risk assessment, such as antibiotic resistance and virulence genes, were identified, and the strain was further confirmed as safe according to the results of antibiotic resistance, hemolytic, and acute oral toxicology tests. Two gene clusters of antibacterial compounds and broad-spectrum antimicrobial activity were identified using genome mining tools and antibacterial spectrum tests. Stress resistance genes, active stressor removal genes, and adhesion related genes that were identified and examined with various phenotypic assays (such as stress tolerance tests in acids and bile salts and auto aggregation and hydrophobicity assays). The strain showed a high survival rate in the presence of bile salts and under acidic conditions and exhibited significant auto aggregation capacity and hydrophobicity. Overall, L. salivarius CGMCC20700 demonstrated excellent safety and probiotic potential at both the genomic and physiological levels and can be considered an appropriate candidate probiotic for livestock and poultry farming.
A review of probiotics in the treatment of autism spectrum disorders: Perspectives from the gut–brain axis
Authors: Feng Pengya , Zhao Shuai , Zhang Yangyang , Li Enyao
Published: March 2023

Autism spectrum disorders (ASD) are a class of neurodevelopmental conditions with a large societal impact. Despite existing evidence suggesting a link between ASD pathogenesis and gut–brain axis dysregulation, there is no systematic review of the treatment of probiotics on ASD and its associated gastrointestinal abnormalities based on the gut–brain axis. Therefore, we performed an analysis for ASD based on preclinical and clinical research to give a comprehensive synthesis of published evidence of a potential mechanism for ASD. On the one hand, this review aims to elucidate the link between gastrointestinal abnormalities and ASD. Accordingly, we discuss gut microbiota dysbiosis regarding gut–brain axis dysfunction. On the other hand, this review suggests that probiotic administration to regulate the gut–brain axis might improve gastrointestinal symptoms, restore ASD-related behavioral symptoms, restore gut microbiota composition, reduce inflammation, and restore intestinal barrier function in human and animal models. This review suggests that targeting the microbiota through agents such as probiotics may represent an approach for treating subsets of individuals with ASD.
Lactiplantibacillus plantarum N-1 improves autism-like behavior and gut microbiota in mouse
Authors: Qiu Zhongqing , Luo Dongmei , Yin Heng , Chen Yajun , Zhou Zhiwei , Zhang Jing , Zhang Linzhu , Xia Jinrong , Xie Jiang , Sun Qun , Xu Wenming
Published: March 2023

Introduction

The gut-brain axis has been widely recognized in autism spectrum disorder (ASD), and probiotics are considered to potentially benefit the rescuing of autism-like behaviors. As a probiotic strain, Lactiplantibacillus plantarumN-1(LPN-1) was utilized to investigate its effects on gut microbiota and autism-like behaviors in ASD mice constructed by maternal immune activation (MIA).

Methods

Adult offspring of MIA mice were given LPN-1 at the dosage of 2  ×  109  CFU/g for 4  weeks before subject to the behavior and gut microbiota evaluation.

Results

The behavioral tests showed that LPN-1 intervention was able to rescue autism-like behaviors in mice, including anxiety and depression. In which the LPN-1 treatment group increased the time spent interacting with strangers in the three-chamber test, their activity time and distance in the central area increased in the open field test, and their immobility time decreased when hanging their tails. Moreover, the supplementation of LPN-1 reversed the intestinal flora structure of ASD mice by enhancing the relative abundance of the pivotal microorganisms of Allobaculum and Oscillospira, while reducing those harmful ones like Sutterella at the genus level.

Discussion

These results suggested that LPN-1 supplementation may improve autism-like behaviors, possibly via regulating the gut microbiota.
Arbuscular mycorrhizal fungi alleviates salt stress in Xanthoceras sorbifolium through improved osmotic tolerance, antioxidant activity, and photosynthesis
Authors: Zong Jianwei , Zhang Zhilong , Huang Peilu , Yang Yuhua
Published: March 2023

Mycorrhizal inoculation was widely reported to alleviate the damage resulting from NaCl by various physiological ways. However, the symbiotic benefit under distant NaCl concentrations and the relationship among different responsive physiological processes were elusive. In this study, saline resistant plant Xanthoceras sorbifolium was selected as the experimental material and five concentrations of NaCl in the presence or absence of Arbuscular Mycorrhiza Fungi (AMF) were conducted, in order to understand the differences and similarities on the photosynthesis, antioxidant activity, and osmotic adjustment between arbuscular mycorrhizal (AM) plants and non-arbuscular mycorrhizal (NM) plants. Under low salt stress, X. sorbifolium can adapt to salinity by accumulating osmotic adjustment substances, such as soluble protein and proline, increasing superoxide dismutase (SOD), catalase (CAT) activity, and glutathione (GSH). However, under high concentrations of NaCl [240 and 320 mM (mmol·L−1)], the resistant ability of the plants significantly decreased, as evidenced by the significant downregulation of photosynthetic capacity and biomass compared with the control plants in both AM and NM groups. This demonstrates that the regulatory capacity of X. sorbifolium was limiting, and it played a crucial role mainly under the conditions of 0–160 mM NaCl. After inoculation of AMF, the concentration of Na+ in roots was apparently lower than that of NM plants, while Gs (Stomatal conductance) and Ci (Intercellular CO2 concentration) increased, leading to increases in Pn (Net photosynthetic rate) as well. Moreover, under high salt stress, proline, soluble protein, GSH, and reduced ascorbic acid (ASA) in AM plants are higher in comparison with NM plants, revealing that mycorrhizal symbiotic benefits are more crucial against severe salinity toxicity. Meanwhile, X. sorbifolium itself has relatively high tolerance to salinity, and AMF inoculation can significantly increase the resistant ability against NaCl, whose function was more important under high concentrations.