bluuebunny/crossref_metadata_2025 huggingface dataset:
Microenvironment commits breast tumor ECs to dedifferentiation by micro-RNA-200-b-3p regulation and extracellular matrix remodeling
Authors: Wilkus-Adamczyk Kinga , Brodaczewska Klaudia , Majewska Aleksandra , Kieda Claudine
Published: May 2023

Introduction: Hypoxia shapes the tumor microenvironment, modulates distinct cell population activities, and activates pathological angiogenesis in cancer, where endothelial cells (ECs) are the most important players. This study aimed to evidence the influences of the tumor microenvironment on the global gene expression pattern characteristic for ECs and the distinct responses displayed by tumor-derived ECs in comparison to the healthy endothelium during endothelial to mesenchymal transition (EndMT) and its regulation by miR-200-b-3p.

Methodology: Immortalized lines of ECs from the same patient with breast cancer, healthy breast tissue (HBH.MEC), and primary tumor (HBCa.MEC) were used. The experiments were performed in normoxia and hypoxia for 48 h. By using the wound healing test, we investigated the migration abilities of ECs. Global gene expression analysis with NGS was carried out to detect new pathways altered in pathological ECs and find the most changed miRNAs. The validation of NGS data from RNA and miRNA was estimated by qPCRs. Mimic miR-200b-3p was used in HBH.MEC, and the targets VEGF, Bcl2, ROCK2, and SP1 were checked.

Results: Hypoxia influences EC migration properties in wound healing assays. In hypoxia, healthy ECs migrate slower than they do in normoxia, as opposed to HBCa.MEC, where no decreased migration ability is induced by hypoxia due to EndMT features. NGS data identified this process to be altered in cancer ECs through extracellular matrix (ECM) organization. The deregulated genes, validated by qPCR, included SPP1, ITGB6, COL4A4, ADAMST2, LAMA1, GAS6, PECAM1, ELN, FBLN2, COL6A3, and COL9A3. NGS also identified collagens, laminins, fibronectins, and integrins, as being deregulated in tumor-derived ECs. Moreover, the analysis of the 10 most intensively modified miRNAs, when breast tumor–derived ECs were compared to healthy ECs, shed light on miR-200b-3p, which is strongly upregulated in HBCa.MECs when compared to HBH.MECs.

Discussion and conclusion: The pathological ECs differed significantly, both phenotypically and functionally, from the normal corresponding tissue, thus influencing their microenvironment cross-talk. The gene expression profile confirms the EndMT phenotype of tumor-derived ECs and migratory properties acquisition. Moreover, it indicates the role of miR-200b-3p, that is, regulating EndMT in pathological ECs and silencing several angiogenic growth factors and their receptors by directly targeting their mRNA transcripts.
Lipid metabolism and tumor immunotherapy
Authors: Wang Yue , Guo Zongjin , Isah Adamu Danbala , Chen Shuangwei , Ren Yongfei , Cai Huazhong
Published: May 2023

In recent years, the relationship between lipid metabolism and tumour immunotherapy has been thoroughly investigated. An increasing number of studies have shown that abnormal gene expression and ectopic levels of metabolites related to fatty acid synthesis or fatty acid oxidation affect tumour metastasis, recurrence, and drug resistance. Tumour immunotherapy that aims to promote an antitumour immune response has greatly improved the outcomes for tumour patients. However, lipid metabolism reprogramming in tumour cells or tumour microenvironment-infiltrating immune cells can influence the antitumour response of immune cells and induce tumor cell immune evasion. The recent increase in the prevalence of obesity-related cancers has drawn attention to the fact that obesity increases fatty acid oxidation in cancer cells and suppresses the activation of immune cells, thereby weakening antitumour immunity. This article reviews the changes in lipid metabolism in cells in the tumour microenvironment and describes the relationship between lipid metabolism reprogramming in multiple cell types and tumour immunotherapy.
Complete genome analysis of Tequatrovirus ufvareg1, a Tequatrovirus species inhibiting Escherichia coli O157:H7
Authors: Lopez Maryoris Elisa Soto , Gontijo Marco Tulio Pardini , Cardoso Rodrigo Rezende , Batalha Laís Silva , Eller Monique Renon , Bazzolli Denise Mara Soares , Vidigal Pedro Marcus Pereira , Mendonça Regina Célia Santos
Published: May 2023

Introduction

Bacteriophages infecting human pathogens have been considered potential biocontrol agents, and studying their genetic content is essential to their safe use in the food industry. Tequatrovirus ufvareg1 is a bacteriophage named UFV-AREG1, isolated from cowshed wastewater and previously tested for its ability to inhibit Escherichia coli O157:H7.

Methods

T. ufvareg1 was previously isolated using E. coli O157:H7 (ATCC 43895) as a bacterial host. The same strain was used for bacteriophage propagation and the one-step growth curve. The genome of the T. ufvareg1 was sequenced using 305 Illumina HiSeq, and the genome comparison was calculated by VIRIDIC and VIPTree.

Results

Here, we characterize its genome and compare it to other Tequatrovirus. T. ufvareg1 virions have an icosahedral head (114 x 86 nm) and a contracted tail (117 x 23 nm), with a latent period of 25 min, and an average burst size was 18 phage particles per infected E. coli cell. The genome of the bacteriophage T. ufvareg1 contains 268 coding DNA sequences (CDS) and ten tRNA genes distributed in both negative and positive strains. T. ufvareg1 genome also contains 40 promoters on its regulatory regions and two rho-independent terminators. T. ufvareg1 shares an average intergenomic similarity (VIRIDC) of 88.77% and an average genomic similarity score (VipTree) of 88.91% with eight four reference genomes for Tequatrovirus available in the NCBI RefSeq database. The pan-genomic analysis confirmed the high conservation of Tequatrovirus genomes. Among all CDS annotated in the T. ufvareg1 genome, there are 123 core genes, 38 softcore genes, 94 shell genes, and 13 cloud genes. None of 268 CDS was classified as being exclusive of T. ufvareg1.

Conclusion

The results in this paper, combined with other previously published findings, indicate that T. ufvareg1 bacteriophage is a potential candidate for food protection against E. coli O157:H7 in foods.
High-sensitivity HBV DNA test for the diagnosis of occult HBV infection: commonly used but not reliable
Authors: Wang Chengwei , Xue Rongrong , Wang Xinru , Xiao Li , Xian Jianchun
Published: May 2023

Occult hepatitis B virus (HBV) infection (OBI) is a condition in which replication-competent viral DNA is detected in the liver (with detectable or undetectable HBV DNA in serum) of individual testing negative for HBV surface antigen (HBsAg). It is a risk factor for transfusion or transplant transmission, reactivation after immunosuppression or chemotherapy, and progression of chronic liver disease and hepatocarcinogenesis. The long-term stable presence of covalently closed circular DNA (cccDNA), which is fully replicative in the nucleus of infected hepatocytes is the molecular basis for the formation of OBI. HBV genome in liver tissue, HBV DNA and anti-HBc test in serum are the gold standard, common method and alternative markers for OBI diagnosis, respectively. Due to the stability of covalently closed circular DNA (cccDNA) and the long half-life of hepatocytes, the existence of OBI is extensive and prolonged. The low and/or intermittent replication of HBV in OBI patients, the limitations of the sensitivity of serological tests, and the non-standardized and invasive nature of liver histology render the “commonly used” serological tests are unreliable and the “gold standard” liver histology is impractical, thus the findings from studies on the formation, diagnosis and transplantation or transfusion transmission of HBV in OBI strongly suggest that the “alternative” marker, the anti-HBc test, may be the most reliable and practical approach for OBI diagnosis.
The climate-biodiversity-health nexus: a framework for integrated community sustainability planning in the Anthropocene
Authors: Newell Robert
Published: May 2023

Integrated approaches to planning and policy are important for making progress toward sustainability. A variety of frameworks have been developed for facilitating such approaches to planning and policy, such as the water-energy-food (WEF) nexus. However, the WEF nexus has been criticized for a lack of clarity in how to apply the framework, whereas a goals-oriented framework potentially could be more easily applied and operationalized. This paper proposes such a framework, referred to here as the climate-biodiversity-health (CBH) nexus. The paper details the features of the CBH nexus framework, the interactions among its domains, and its potential applications. The CBH nexus consists of three domains (i.e., climate action, biodiversity conservation, and community health) and six subdomains (i.e., climate change mitigation, climate change adaptation, habitat protection and regeneration, wildlife health and welfare, physical health, and mental health). The framework can be applied in practice to develop checklists/toolkits for guiding new development and as a basis for creating community indicator systems. It can also be applied in research to identify gaps in planning and policy documents and as a lens for participatory modeling exercises. Continued experimentation with, and improvement of, the CBH framework will reveal its most useful applications, thereby opening new opportunities for communities to effectively develop and implement integrated sustainability plans and policies.
Interpreting high-temperature magnetic susceptibility data of natural systems
Authors: Muxworthy Adrian R. , Turney Jack N. , Qi Liang , Baker Evelyn B. , Perkins Joseph R. , Abdulkarim Maryam A.
Published: May 2023

High-temperature susceptibility (HT-χ) data are routinely measured in Earth, planetary, and environmental sciences to rapidly identify the magnetic mineralogy of natural systems. The interpretation of such data can be complicated. Whilst some minerals are relatively unaltered by heating and are easy to identify through their Curie or Néel temperature, other common magnetic phases, e.g., iron sulphides, are very unstable to heating. This makes HT-χinterpretation challenging, especially in multi-mineralogical samples. Here, we report a review of the HT-χdata measured primarily at Imperial College London of common magnetic minerals found in natural samples. We show examples of “near pure” natural samples, in addition to examples of interpretation of multi-phase HT-χdata. We hope that this paper will act be the first reference paper for HT-χdata interpretation.
Post-COVID-19 syndrome and diabetes mellitus: a propensity-matched analysis of the International HOPE-II COVID-19 Registry
Authors: Abumayyaleh Mohammad , Núñez Gil Iván J. , Viana-LLamas María C. , Raposeiras Roubin Sergio , Romero Rodolfo , Alfonso-Rodríguez Emilio , Uribarri Aitor , Feltes Gisela , Becerra-Muñoz Víctor Manuel , Santoro Francesco , Pepe Martino , Castro Mejía Alex Fernando , Signes-Costa Jaime , Gonzalez Adelina , Marín Francisco , López-País Javier , Manzone Edoardo , Vazquez Cancela Olalla , Paeres Carolina Espejo , Masjuan Alvaro López , Velicki Lazar , Weiß Christel , Chipayo David , Fernandez-Ortiz Antonio , El-Battrawy Ibrahim , Akin Ibrahim ,   HOPE COVID-19 investigators
Published: May 2023

Background

Diabetes mellitus (DM) is one of the most frequent comorbidities in patients suffering from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with a higher rate of severe course of coronavirus disease (COVID-19). However, data about post-COVID-19 syndrome (PCS) in patients with DM are limited.

Methods

This multicenter, propensity score-matched study compared long-term follow-up data about cardiovascular, neuropsychiatric, respiratory, gastrointestinal, and other symptoms in 8,719 patients with DM to those without DM. The 1:1 propensity score matching (PSM) according to age and sex resulted in 1,548 matched pairs.

Results

Diabetics and nondiabetics had a mean age of 72.6 ± 12.7 years old. At follow-up, cardiovascular symptoms such as dyspnea and increased resting heart rate occurred less in patients with DM (13.2% vs. 16.4%;p= 0.01) than those without DM (2.8% vs. 5.6%;p= 0.05), respectively. The incidence of newly diagnosed arterial hypertension was slightly lower in DM patients as compared to non-DM patients (0.5% vs. 1.6%;p= 0.18). Abnormal spirometry was observed more in patients with DM than those without DM (18.8% vs. 13;p= 0.24). Paranoia was diagnosed more frequently in patients with DM than in non-DM patients at follow-up time (4% vs. 1.2%;p= 0.009). The incidence of newly diagnosed renal insufficiency was higher in patients suffering from DM as compared to patients without DM (4.8% vs. 2.6%;p= 0.09). The rate of readmission was comparable in patients with and without DM (19.7% vs. 18.3%;p= 0.61). The reinfection rate with COVID-19 was comparable in both groups (2.9% in diabetics vs. 2.3% in nondiabetics;p= 0.55). Long-term mortality was higher in DM patients than in non-DM patients (33.9% vs. 29.1%;p= 0.005).

Conclusions

The mortality rate was higher in patients with DM type II as compared to those without DM. Readmission and reinfection rates with COVID-19 were comparable in both groups. The incidence of cardiovascular symptoms was higher in patients without DM.
Multilevel converter to access maximum power from distributed energy source based smart grids
Authors: Alkhaledi Khaled , Cheema Khalid Mehmood , Elbarbary Z. M. Salem , Park Woo-Hyung , El-Sherbeeny Ahmed M.
Published: May 2023

The distributed power generation is increasing rapidly, and its integration into the power system is a critical issue for the existing power network. Therefore, a three-level converter is developed to access and control the medium voltage DC generated from a photovoltaic system in a smart grid. A conventional three-level neutral point clamped circuit is incorporated into the conventional inverter. The conventional inverter is a pulse width modulation-based inverter that achieves zero switching currents and supplies power to the load. This technique suppresses the switching power loss up to a large extent. Additionally, switches conduct half of the input voltage; therefore, the output voltage is significantly similar to the voltage of the output filter. Moreover, in the proposed converter, the stress of voltage on diodes is minimal, which increases the input range of voltage in smart grids. The overall efficiency of converter is around 97.9% and voltage gain is around 42. In addition to these, a detailed design description and analysis are carried out in this paper. In the end, a prototype is developed for experimental analysis to validate the operating principle and characteristics of the proposed converter.
Data-driven comparison of urban sustainability towards sustainable urban development under sustainable development goals (SDGs): a review based on bibliometric analysis
Authors: Wang Di , Dong Liang , Di Siyan
Published: May 2023

As urbanization has increased rapidly, the issue of sustainability has become more prominent, and urban sustainability should be the key to achieving the sustainable agenda raised by the UN. This study combines bibliometrics and text mining to analyze the research progress of urban sustainability. A total of 1,031 keywords from 240 documents screened by the PRISMA method are coded to draw heat maps in accordance with the sustainable triple bottom line principle and its cross-scope (Environment, Society, Economics, Environment & Society, Environment & Economics, Society & Economics, Environment, and Society & Economics) with its emphasis on 17 SDGs. The innovation of this study is manifested as the use of heat maps. The results indicate that the existing relevant research still focuses on environmental protection. Besides the general “sustainability” topics, “land use,” “decision-making,” “green city,” and “eco-city” have been more discussed than others. For the SDGs, the SDG 6, 7, 9, 11, 12, and 15 represent clean water, affordable and clean energy, industry, innovation and infrastructure, sustainable cities and communities, and responsible consumption and production and life on land, respectively. Only a small part of the research has begun to focus on the sustainable development of the community. More comprehensive and complete insights should be gained into sustainable development. This study suggests that the research on urban sustainability will be further deepened, and it should be significantly integrated with SGDs and place a focus on the coupling of urban sustainability and economic growth.
LINC00426 is a potential immune phenotype-related biomarker and an overall survival predictor in PAM50 luminal B breast cancer
Authors: Fonseca-Montaño Marco Antonio , Cisneros-Villanueva Mireya , Coales Isabelle , Hidalgo-Miranda Alfredo
Published: May 2023

Background: Breast cancer (BRCA) represents the most frequent diagnosed malignancy in women worldwide. Despite treatment advances, BRCAs eventually develop resistance to targeted therapies, resulting in poor prognosis. The identification of new biomarkers, like immune-related long non-coding RNAs (lncRNAs), could contribute to the clinical management of BRCA patients. In this report, we evaluated the LINC00426 expression in PAM50 BRCA subtypes from two clinical independent cohorts (BRCA-TCGA and GEO-GSE96058 datasets).

Methods and results: Using Cox regression models and Kaplan-Meier survival analyses, we identified that LINC00426 expression was a consistent overall survival (OS) predictor in luminal B (LB) BRCA patients. Subsequently, differential gene expression and gene set enrichment analyses identified that LINC00426 expression was associated with different immune-related and cancer-related pathways and processes in LB BRCA. Additionally, the LINC00426 expression was correlated with the infiltration level of diverse immune cell populations, alongside immune checkpoint and cytolytic activity-related gene expression.

Conclusion: This evidence suggests that LINC00426 is a potential biomarker of immune phenotype and an OS predictor in PAM50 LB BRCA.
Atazanavir-induced unconjugated hyperbilirubinemia prevents vascular hyporeactivity during experimental human endotoxemia
Authors: Dorresteijn Mirrin J. , Dekker Douwe , Zwaag Jelle , Heemskerk Suzanne , Roelofs Hennie M.J. , Smits Paul , van der Hoeven Johannes G. , Wagener Frank A.D.T.G. , Pickkers Peter
Published: May 2023

Objective

Inflammation-induced free radical release is important in the pathogenesis of several diseases, including atherosclerosis and sepsis. Heme oxygenase (HO) breaks down heme into carbon monoxide, iron, and biliverdin. Biliverdin IXα is directly converted to bilirubin by biliverdin reductase. Unconjugated bilirubin is a powerful antioxidant, and elevated levels have beneficial effects in preclinical models and human cardiovascular disease. However, its impact during acute inflammation in humans is unknown. In the present study, we investigated the impact of atazanavir-induced (unconjugated) hyperbilirubinemia on antioxidant capacity, inflammation, and vascular dysfunction in human experimental endotoxemia.

Approach and results

Following double-blinded four-day treatment with atazanavir 2dd300 mg (or placebo), twenty healthy male volunteers received 2 ng/kg Escherichia coli lipopolysaccharide intravenously. Blood was drawn to determine the bilirubin levels, antioxidant capacity, and cytokine response. It was demonstrated that following atazanavir treatment, total bilirubin concentrations increased to maximum values of 4.67 (95%CI 3.91-5.59) compared to 0.82 (95%CI 0.64-1.07) mg/dL in the control group (p<0.01). Furthermore, the anti-oxidant capacity, as measured by the ferric-reducing ability of plasma (FRAP), was significantly increased with 36% in hyperbilirubinemia subjects (p<0.0001), and FRAP concentrations correlated strongly to bilirubin concentrations (R2 = 0.77, p<0.001). Hyperbilirubinemia attenuated the release of interleukin-10 from 377 (95%CI 233-609) to 219 (95%CI 152-318) pg/mL (p=0.01), whereas the release of pro-inflammatory cytokines remained unaltered. In vitro, in the absence of hyperbilirubinemia, atazanavir did not influence lipopolysaccharide-induced cytokine release in a whole blood assay. Vascular function was assessed using forearm venous occlusion plethysmography after intra-arterial infusion of acetylcholine and nitroglycerin. Hyperbilirubinemia completely prevented the LPS-associated blunted vascular response to acetylcholine and nitroglycerin.

Conclusions

Atazanavir-induced hyperbilirubinemia increases antioxidant capacity, attenuates interleukin-10 release, and prevents vascular hyporesponsiveness during human systemic inflammation elicited by experimental endotoxemia.

Clinical trial registration

http://clinicaltrials.gov, identifier NCT00916448.
Efficient complement-mediated clearance of immunosuppressed T cells by macrophages
Authors: Gankema Angela A. F. , Furumaya Charita , Fernández-Hermira Sara , Hoogenboezem Mark , Matlung Hanke L. , van Bruggen Robin , Kuijpers Taco W.
Published: May 2023

Cancer is one of the leading causes of death worldwide. Treatment outcome is largely dictated by the tumor type, disease stage, and treatment success rates, but also by the variation among patients in endogenous anti-tumor responses. Studies indicate that the presence of neutrophils in the tumor microenvironment is associated with a worse patient outcome due to their ability to suppress local anti-tumor T cell activity. Our previous studies investigated the mechanisms by which neutrophils suppress and damage T cells to become smaller in size (small T cells), debilitating their effector activities. Several studies indicate a role for tumor-associated macrophages in scavenging damaged or dead cells. We hypothesized that the observed lack of small T cells in the TME by confocal microscopy is due to immediate uptake by macrophages. In this study, we confirmed that indeed only the smaller, damaged T cells are taken up by macrophages, once serum-opsonized. Damaged T cells opsonized with complement factor C3 fragments were phagocytosed by macrophages, resulting in almost instantaneous and highly efficient uptake of these small T cells. Inhibition of the complement receptors CR1, CR3 and CR4 expressed by macrophages completely blocked phagocytosis. By contrast, actively proliferating T cells (large T cells) were neither impaired in neutrophil-MDSC activity nor opsonized for phagocytosis by macrophages. Rapid removal of damaged T cells suggests a role of complement and macrophages within the tumor microenvironment to clear suppressed T cells in cancer patients.
Comparison of methods generating antibody-epitope conjugates for targeting cancer with virus-specific T cells
Authors: van der Wulp Willemijn , Gram Anna M. , Bleijlevens Boris , Hagedoorn Renate S. , Araman Can , Kim Robbert Q. , Drijfhout Jan Wouter , Parren Paul W. H. I. , Hibbert Richard G. , Hoeben Rob C. , van Kasteren Sander I. , Schuurman Janine , Ressing Maaike E. , Heemskerk Mirjam H. M.
Published: May 2023

Therapeutic antibody-epitope conjugates (AECs) are promising new modalities to deliver immunogenic epitopes and redirect virus-specific T-cell activity to cancer cells. Nevertheless, many aspects of these antibody conjugates require optimization to increase their efficacy. Here we evaluated different strategies to conjugate an EBV epitope (YVL/A2) preceded by a protease cleavage site to the antibodies cetuximab and trastuzumab. Three approaches were taken: chemical conjugation (i.e. a thiol-maleimide reaction) to reduced cysteine side chains, heavy chain C-terminal enzymatic conjugation using sortase A, and genetic fusions, to the heavy chain (HC) C-terminus. All three conjugates were capable of T-cell activation and target-cell killing via proteolytic release of the EBV epitope and expression of the antibody target was a requirement for T-cell activation. Moreover, AECs generated with a second immunogenic epitope derived from CMV (NLV/A2) were able to deliver and redirect CMV specific T-cells, in which the amino sequence of the attached peptide appeared to influence the efficiency of epitope delivery. Therefore, screening of multiple protease cleavage sites and epitopes attached to the antibody is necessary. Taken together, our data demonstrated that multiple AECs could sensitize cancer cells to virus-specific T cells.
Aerosol vaccination of chicken pullets with irradiated avian pathogenic Escherichia coli induces a local immunostimulatory effect
Authors: Bagheri Sina , Mitra Taniya , Paudel Surya , Abdelhamid Mohamed Kamal , Könnyü Simon , Wijewardana Viskam , Kangethe Richard Thiga , Cattoli Giovanni , Lyrakis Manolis , Hess Claudia , Hess Michael , Liebhart Dieter
Published: May 2023

The present study investigated the expression of cytokines and cellular changes in chickens following vaccination with irradiated avian pathogenic Escherichia coli (APEC) and/or challenge. Four groups of 11-week-old pullets, each consisting of 16 birds were kept separately in isolators before they were sham inoculated (N), challenged only (C), vaccinated (V) or vaccinated and challenged (V+C). Vaccination was performed using irradiated APEC applied via aerosol. For challenge, the homologous strain was administered intratracheally. Birds were sacrificed on 3, 7, 14 and 21 days post challenge (dpc) to examine lesions, organ to body weight ratios and bacterial colonization. Lung and spleen were sampled for investigating gene expression of cytokines mediating inflammation by RT-qPCR and changes in the phenotype of subsets of mononuclear cells by flow cytometry. After re-stimulation of immune cells by co-cultivation with the pathogen, APEC-specific IFN-γ producing cells were determined. Challenged only birds showed more severe pathological and histopathological lesions, a higher probability of bacterial re-isolation and higher organ to body weight ratios compared to vaccinated and challenged birds. In the lung, an upregulation of IL-1β and IL-6 following vaccination and/or challenge at 3 dpc was observed, whereas in the spleen IL-1β was elevated. Changes were observed in macrophages and TCR-γδ+ cells within 7 dpc in spleen and lung of challenged birds. Furthermore, an increase of CD4+ cells in spleen and a rise of Bu-1+ cells in lung were present in vaccinated and challenged birds at 3 dpc. APEC re-stimulated lung and spleen mononuclear cells from only challenged pullets showed a significant increase of IFN-γ+CD8α+ and IFN-γ+TCR-γδ+ cells. Vaccinated and challenged chickens responded with a significant increase of IFN-γ+CD8α+ T cells in the lung and IFN-γ+TCR-γδ+ cells in the spleen. Re-stimulation of lung mononuclear cells from vaccinated birds resulted in a significant increase of both IFN-γ+CD8α+ and IFN-γ+TCR-γδ+ cells. In conclusion, vaccination with irradiated APEC caused enhanced pro-inflammatory response as well as the production of APEC-specific IFN-γ-producing γδ and CD8α T cells, which underlines the immunostimulatory effect of the vaccine in the lung. Hence, our study provides insights into the underlying immune mechanisms that account for the defense against APEC.
Distribution of genetic diversity of neotropical Biomphalaria (Preston 1910) (Basommatophora: Planorbidae) intermediate hosts for schistosomiasis in Southeast Brazil
Authors: Palasio Raquel Gardini Sanches , Chiaravalloti-Neto Francisco , Tuan Roseli
Published: May 2023

Introduction

Biomphalaria glabrata, B. tenagophila, and B. straminea occurrence are crucial for estimating the risk of infectious human schistosomiasis in the neotropics. How different geographic sample strategies influence snail genetic diversity estimations were here investigated for three Schistosoma mansoni hosts.

Methods

Mitochondrial gene sequences were employed for Cytochrome C Oxidase I (COI), ribosomal RNA (rRNA) 16S, and a dataset with concatenated gene sequences (COI+16S), resulting in an improved scientific hypothesis regarding the geographical distribution of snail species. This study compared the sequences of snails from the Middle Paranapanema (MP) hydrographic basin in a geographically restricted area (inner group) to snails widely distributed across a broad geographical range in São Paulo (outer group), Brazil from 1999 to 2017. DNA sequence polymorphisms and haplotype diversity were estimated using DNAsp software. Haplotype network trees were constructed using a network program. The geographical distribution of the haplotypes was mapped using QGIS. Haplotype variation and distribution were tested for population structure using analysis of molecular variance (AMOVA).

Results and discussion

The genetic diversity of B. glabrata, sampled from disconnected but geographically close freshwater collections, was partitioned into two sequence groups. The haplotype network showed that the diversity of B. straminea was more spatially partitioned than in B. tenagophila, which exhibited two population groups. The haplotype distribution pattern for B. tenagophila showed many unique and exclusive haplotypes for all three loci. AMOVA showed that genetic diversity could be high in species inhabiting small geographical areas, and a large river is not a local geographical barrier for snail migration. This study found that the survey dimensions and snail samplings influenced the genetic diversity results obtained by mitochondrial DNA molecular markers.
Distributions, sources, and air-sea fluxes of nitrous oxide in Bohai Bay, China
Authors: Wang Zhi , Gu Ting , Wen Yujian , Cui XuDong , Jia Dai , Sun Jun
Published: May 2023

Introduction

Polluted bays are one of the critical areas for the production and emissions of marine nitrous oxide (N2O), which has a strong effect on global warming and plays a critical role in stratospheric ozone depletion.

Methods

In 2020, the distributions of N2O concentrations and emissions in the water column of Bohai Bay (BHB) were surveyed during two cruises.

Results and discussion

The average N2O concentrations were higher in summer compared to autumn, with the oversaturation of N2O in both seasons. A declining gradient of N2O was found from the Hai River and Yellow River estuarine areas to the offshore sea, particularly in summer, implying riverine input was an important source of N2O. The vertical distribution of N2O was uniform in each season owing to the vertical mixing of water columns in the offshore sea, with N2O hotspots at the bottom of the two estuaries in summer and at the surface of the Hai River estuary in autumn. Moreover, the dominant sources of dissolved N2O were analyzed. N2O in the water column was predominately produced by nitrification and coupled nitrification-denitrification on suspended particulate matter. The mixing of water masses, particularly polluted water masses from coastal input, provides high N2O to the entire area of BHB, particularly in summer. Notably, nutrient and organic matter input from the coast could also indirectly drive N2O production by stimulating microbe activities of nitrification and denitrification under the water currents. In addition, statistical analysis revealed that ammonium, dissolved oxygen, and temperature were the dominant controlling factors of N2O in BHB. The annual flux of N2O in BHB was evaluated to be 6.5 Gg, accounting for 0.15% of the global oceanic N2O emission with 0.0044% of the global ocean area. Hence, as a typical polluted bay, BHB acted as a strong N2O source to the atmosphere on a per-unit-area basis.
Assessing ocean ensemble drift predictions by comparison with observed oil slicks
Authors: de Aguiar Victor , Röhrs Johannes , Johansson Anna Malin , Eltoft Torbjørn
Published: May 2023

Geophysical models are cornerstone pieces in marine forecasting of floating objects and pollution, such as marine surface oil slicks. Trajectory forecasts of oil spills inherit the uncertainties from the underlying geophysical forcing. In this work we compare the forecast capabilities of an ocean ensemble prediction system (EPS) to those from a higher resolution deterministic model on the representation of oil slick drift. As reference, we use produced water (PW) slicks detected and delineated from 41 C–band Sentinel-1A/B satellite synthetic aperture radar images between April and December, 2021. We found that the EPS provided at least equivalent member-wise results relative to simulations forced with the deterministic model. Ensemble verification through rank histograms and spread-error relationship showed that including the ocean fields is necessary to address model uncertainties. Whether considering the ocean field or not, the modeled slicks were counterclockwise rotated between 20° and 30° relative to the ones observed in the satellite images, and these were deflected about 45° to the right of the observed wind direction.
MCSTNet: a memory-contextual spatiotemporal transfer network for prediction of SST sequences and fronts with remote sensing data
Authors: Ma Ying , Liu Wen , Chen Ge , Zhong Guoqiang , Tian Fenglin
Published: May 2023

Ocean fronts are a response to the variabilities of marine hydrographic elements and are an important mesoscale ocean phenomenon, playing a significant role in fish farming and fishing, sea-air exchange, marine environmental protection, etc. The horizontal gradients of sea surface temperature (SST) are frequently applied to reveal ocean fronts. Up to now, existing spatiotemporal prediction approaches have suffered from low prediction precision and poor prediction quality for non-stationary data, particularly for long-term prediction. It is a challenging task for medium- and long-term fine-grained prediction for SST sequences and fronts in oceanographic research. In this study, SST sequences and fronts are predicted for future variation trends based on continuous mean daily remote sensing satellite of SST data. To enhance the precision of the predicted SST sequences and fronts, this paper proposes a novel memory-contextual spatiotemporal transfer network (MCSTNet) for SST sequence and front predictions. MCSTNet involves three components: the encoder-decoder structure, a time transfer module, and a memory-contextual module. The encoder-decoder structure is used to extract the rich contextual and semantic information in SST sequences and frontal structures from the SST data. The time transfer module is applied to transfer temporal information and fuse low-level, fine-grained temporal information with high-level semantic information to improve medium- and long-term prediction precision. And the memory-contextual module is employed to fuse low-level, spatiotemporal information with high-level semantic information to enhance short-term prediction precision. In the training process, mean squared error (MSE) loss and contextual loss are combined to jointly guide the training of MCSTNet. Extensive experiments demonstrate that MCSTNet predicts more authentic and reasonable SST sequences and fronts than the state-of-the-art (SOTA) models on the SST data.
Comparison genetic diversity and population structure of four Pseudaspius leptocephalus populations in Heilongjiang River Basin based on mitochondrial COI gene
Authors: Wei Haijun , Geng Longwu , Shang Xinchi , Li Lei , Ma Bo , Zhang Yuyong , Li Wang , Xu Wei
Published: May 2023

The Pseudaspius leptocephalus is a unique fish in the Heilongjiang River Basin and has important economic and ecological value. In the present study, the complete mitochondrial genome of P. leptocephalus were determined, and COI partial sequences of 85 individuals from Erguna river (EH), Mohe (MH), Fuyuan (FY), Hulan (HL) were used to evaluated the genetic diversity of four populations of P. leptocephalus in Heilongjiang River Basin. The mitogenome is 16,607 bp in length and contained one D-loop, 2 rRNA, 13 PCG, and 22 tRNA. 4 variable sites and 5 haplotypes were detected in 705 bp COI, and 705 bp COI exhibited a lower content of C + G (45.95%) than A + T (54.05%). The nucleotide diversity (π) and haplotype diversity (h) indices ranged from 0.00027 (HL) to 0.00065 (EH and FY) and from 0.192 (HL) to 0.462 (EH), respectively. The genetic distance within the population and between populations ranged from 0.0006554 to 0.0002728 and from 0.0003541 to 0.0006974, respectively. Pairwise values of FST and Nm showed that there was moderate genetic differentiation between EH population and other populations and individuals between EH population and other populations can mate randomly (0.15 > FST > 0.05, Nm > 4). Significant negative values of neutrality tests (P < 0.05) indicated that MH and FY populations may had experienced population expansion, but mismatch distribution analysis suggested that all populations have remained basically stable. These results provide strong basis for the protection and utilization of P. leptocephalus germplasm resources, and provide valuable information for the population structure and genetic diversity of P. leptocephalus.
Evaporation induced convection enhances mixing in the upper ocean
Authors: Falor Devang , Gayen Bishakhdatta , Sengupta Debasis , Ivey Gregory N.
Published: May 2023

The upper ocean surface layer is directly affected by the air-sea fluxes. The diurnal variations in these fluxes also cause the upper ocean mixed layer turbulence and mixing to diurnally vary. The underlying thermohaline structure also varies accordingly throughout the day. Here we use large-eddy simulation to quantify the role of surface evaporation in modulating the diurnal mixed layer turbulence and mixing in the presence of wind forcing. During daytime, the upper ocean boundary layer becomes thermally stratified, and a salinity inversion layer is formed in the upper 10m, leading to double diffusive salt-fingering instability. During nighttime, the mixed layer undergoes convective deepening due to surface buoyancy loss redfrom both surface cooling and evaporation. We find that salinity makes a major contribution to the convective instability during both transitions between day and night. Overall surface evaporation increases the mixed layer depth and irreversible mixing through convection, both during nighttime and daytime, and leads to better prediction of the dynamical variables as sea surface salinity (SSS) and sea surface temperature (SST). Our findings can help improve the ocean parameterizations to improve the forecasts on a diurnal timescale.
Antimicrobial activity of Desplac® oral gel in the subgingival multispecies biofilm formation
Authors: Bueno-Silva Bruno , Kiausinus Karyne Rossit , Gonçalves Francisco Jeferson dos Santos , Moreira Marcus Vinícius Cintra , Oliveira Eder Gonzaga de , Brugnera Junior Aldo , Feres Magda , Figueiredo Luciene Cristina
Published: May 2023

Natural products are well-known due to their antimicrobial properties. This study aimed to evaluate the antimicrobial effect of Desplac® product (composed of Aloe Vera, Propolis Extract, Green Tea, Cranberry, and Calendula) on the subgingival biofilm. Two different protocols were used to treat the 33-species biofilms: (A) 2×/day (12/12  h) for 1  min with Desplac® or Noplak Toothpaste (Chlorhexidine + Cetylpyridinium Chloride) or Oral B ProGengiva (stannous Fluoride) or a placebo gel; (B) a 12-h use of the Desplac® product or 0.12% chlorhexidine gel or a placebo gel. After 7 days of biofilm formation, the metabolic activity (MA) and biofilm profile were determined by 2,3,5-triphenyltetrazolium chloride and Checker-board DNA–DNA hybridization, respectively. Statistical analysis used the Kruskal-Wallis test followed by Dunn’s post-hoc. In protocol A, all treatments presented reduced MA compared to the placebo (p ≤ 0.05). The Desplac®-treated biofilm showed a similar microbial profile to other antimicrobials, although with higher bacterial total counts. In protocol B, MA of Desplac®-treated biofilms was lower than the placebo’s MA but higher than chlorhexidine-treated biofilms (p ≤ 0.05). Pathogen levels in Desplac®-treated biofilms were lower than in placebo-treated biofilms and elevated compared to the chlorhexidine-treated biofilms (p ≤ 0.05). Desplac® inhibited the biofilm development and disrupted the mature subgingival biofilm, highlighting its effect on Tannerella forsythia counts.
Enzymatic synthesis of new antimicrobial peptides for food purposes
Authors: Adaro Mauricio , Ibáñez Ángel Gabriel Salinas , Origone Anabella Lucia , Vallés Diego , Guzmán Fanny , Vega Alba , Barberis Sonia
Published: May 2023

Growing consumer awareness of the potential negative health effects of synthetic antibiotics has prompted the search for more natural preservatives that can improve the safety and quality of food. In this study we report the enzymatic synthesis of N-α-[Carbobenzyloxy]-Ile-Gln (Z-IQ) which is the precursor of Ile-Gln (IQ), a new antibacterial dipeptide, using an aqueous–organic biphasic system formed by 50% (v/v) ethyl acetate in 0.1 M Tris – HCl buffer pH 8. A partially purified proteolytic extract from the fruits of Solanum granuloso leprosum, named granulosain, proved to be a robust biocatalyst for the synthesis of Z-IQ, eliciting 71 ± 0.10% maximal peptide yield in the above described conditions. After cleaving and purifying IQ dipeptide, antimicrobial activity was assayed against Staphylococcus aureus ATCC 25923, Staphylococcus hominis A17771, and Staphylococcus aureus C00195, and MIC values between 118 ± 0.01 μg/mL and 133.7 ± 0.05 μg/mL were obtained. In addition, IQ showed MIC of 82.4 ± 0.01 μg/mL and 85.0 ± 0.00 μg/mL against Escherichia coli ATCC 25922 and Escherichia coli A17683, respectively. IQ did not show inhibitory activity against single-drug resistance (SDR) strains, such as Klebsiella oxytoca A19438 (SDR) and Pseudomonas aeruginosa C00213 (SDR), and against multidrug-resistant Enterococcus faecalis I00125 (MDR). IQ also caused growth inhibition of Helicobacter pylori NCTC 11638 and three wild-type H. pylori strains, which are sensitive to AML, MTZ, LEV and CLA (H. pylori 659), resistant to LEV (H. pylori 661 SDR), and resistant to MTZ (H. pylori 662 SDR). Finally, this study contributes with a new dipeptide (IQ) that can be used as an antimicrobial agent for food preservation or as a safe ingredient of functional foods.
The aeromicrobiome: the selective and dynamic outer-layer of the Earth’s microbiome
Authors: Amato Pierre , Mathonat Frederic , Nuñez Lopez Leslie , Péguilhan Raphaëlle , Bourhane Zeina , Rossi Florent , Vyskocil Jonathan , Joly Muriel , Ervens Barbara
Published: May 2023

The atmosphere is an integral component of the Earth’s microbiome. Abundance, viability, and diversity of microorganisms circulating in the air are determined by various factors including environmental physical variables and intrinsic and biological properties of microbes, all ranging over large scales. The aeromicrobiome is thus poorly understood and difficult to predict due to the high heterogeneity of the airborne microorganisms and their properties, spatially and temporally. The atmosphere acts as a highly selective dispersion means on large scales for microbial cells, exposing them to a multitude of physical and chemical atmospheric processes. We provide here a brief critical review of the current knowledge and propose future research directions aiming at improving our comprehension of the atmosphere as a biome.
Predicting the distribution of serotonergic axons: a supercomputing simulation of reflected fractional Brownian motion in a 3D-mouse brain model
Authors: Janušonis Skirmantas , Haiman Justin H. , Metzler Ralf , Vojta Thomas
Published: May 2023

The self-organization of the brain matrix of serotonergic axons (fibers) remains an unsolved problem in neuroscience. The regional densities of this matrix have major implications for neuroplasticity, tissue regeneration, and the understanding of mental disorders, but the trajectories of its fibers are strongly stochastic and require novel conceptual and analytical approaches. In a major extension to our previous studies, we used a supercomputing simulation to model around one thousand serotonergic fibers as paths of superdiffusive fractional Brownian motion (FBM), a continuous-time stochastic process. The fibers produced long walks in a complex, three-dimensional shape based on the mouse brain and reflected at the outer (pial) and inner (ventricular) boundaries. The resultant regional densities were compared to the actual fiber densities in the corresponding neuroanatomically-defined regions. The relative densities showed strong qualitative similarities in the forebrain and midbrain, demonstrating the predictive potential of stochastic modeling in this system. The current simulation does not respect tissue heterogeneities but can be further improved with novel models of multifractional FBM. The study demonstrates that serotonergic fiber densities can be strongly influenced by the geometry of the brain, with implications for brain development, plasticity, and evolution.
Depression as a cardiovascular disorder: central-autonomic network, brain-heart axis, and vagal perspectives of low mood
Authors: Valenza Gaetano
Published: May 2023

If depressive symptoms are not caused by the physiological effects of a substance or other medical or neurological conditions, they are generally classified as mental disorders that target the central nervous system. However, recent evidence suggests that peripheral neural dynamics on cardiovascular control play a causal role in regulating and processing emotions. In this perspective, we explore the dynamics of the Central-Autonomic Network (CAN) and related brain-heart interplay (BHI), highlighting their psychophysiological correlates and clinical symptoms of depression. Thus, we suggest that depression may arise from dysregulated cardiac vagal and sympathovagal dynamics that lead to CAN and BHI dysfunctions. Therefore, treatments for depression should target the nervous system as a whole, with particular emphasis on regulating vagal and BHI dynamics.