bluuebunny/crossref_metadata_2025 huggingface dataset:
Heme Interferes With Complement Factor I-Dependent Regulation by Enhancing Alternative Pathway Activation
Authors: Gerogianni Alexandra , Dimitrov Jordan D. , Zarantonello Alessandra , Poillerat Victoria , Chonat Satheesh , Sandholm Kerstin , McAdam Karin E. , Ekdahl Kristina N. , Mollnes Tom E. , Mohlin Camilla , Roumenina Lubka T. , Nilsson Per H.
Published: July 2022

Hemolysis, as a result of disease or exposure to biomaterials, is characterized by excess amounts of cell-free heme intravascularly and consumption of the protective heme-scavenger proteins in plasma. The liberation of heme has been linked to the activation of inflammatory systems, including the complement system, through alternative pathway activation. Here, we investigated the impact of heme on the regulatory function of the complement system. Heme dose-dependently inhibited factor I-mediated degradation of soluble and surface-bound C3b, when incubated in plasma or buffer with complement regulatory proteins. Inhibition occurred with factor H and soluble complement receptor 1 as co-factors, and the mechanism was linked to the direct heme-interaction with factor I. The heme-scavenger protein hemopexin was the main contaminant in purified factor I preparations. This led us to identify that hemopexin formed a complex with factor I in normal human plasma. These complexes were significantly reduced during acute vasoocclusive pain crisis in patients with sickle cell disease, but the complexes were normalized at their baseline outpatient clinic visit. Hemopexin exposed a protective function of factor I activity in vitro, but only when it was present before the addition of heme. In conclusion, we present a mechanistic explanation of how heme promotes uncontrolled complement alternative pathway amplification by interfering with the regulatory capacity of factor I. Reduced levels of hemopexin and hemopexin-factor I complexes during an acute hemolytic crisis is a risk factor for heme-mediated factor I inhibition.
Receptor–ligand pair typing and prognostic risk model for papillary thyroid carcinoma based on single-cell sequencing
Authors: Cao Zhe Xu , Weng Xin , Huang Jiang Sheng , Long Xia
Published: July 2022

The papillary thyroid carcinoma (PTC) microenvironment consists of various cancer and surrounding cells, and the communication between them is mainly performed through ligand–receptor (LR) interactions. Single-cell RNA sequencing (scRNA-seq) has been performed to investigate the role of intercellular communication networks in tumor progression. In addition, scRNA-seq can accurately identify the characteristics of immune cell subsets, which is of great significance for predicting the efficacy of immunotherapy. In this study, the cell–cell communication network was analyzed through LR pairs, and a new PTC molecular phenotype was developed based on LR pairs. Furthermore, a risk model was established to predict patient response to PD-1 blockade immunotherapy. The scRNA-seq dataset was obtained from GSE184362, and the bulk tumor RNA-seq dataset was obtained from The Cancer Genome Atlas. CellPhoneDB was used for cellular communication analysis. LR pair correlations were calculated and used to identify molecular subtypes, and the least absolute shrinkage and selection operator (Lasso) Cox regression was used to develop a risk model based on LR pairs. The IMvigor210 and GSE78220 cohorts were used as external validations for the LR.score to predict responses to PD-L1 blockade therapy. A total of 149 LR pairs with significant expression and prognostic correlation were included, and three PTC molecular subtypes were obtained from those with significant prognostic differences. Then, five LR pairs were selected to construct the risk scoring model, a reliable and independent prognostic factor in the training set, test set, and whole dataset. Furthermore, two external validation sets confirmed the predictive efficacy of the LR.score for response to PD-1 blockade therapy.
B-1b Cells Have Unique Functional Traits Compared to B-1a Cells at Homeostasis and in Aged Hyperlipidemic Mice With Atherosclerosis
Authors: Srikakulapu Prasad , Pattarabanjird Tanyaporn , Upadhye Aditi , Bontha Sai Vineela , Osinski Victoria , Marshall Melissa A. , Garmey James , Deroissart Justine , Prohaska Thomas A. , Witztum Joseph L. , Binder Christoph J. , Holodick Nichol E. , Rothstein Thomas L. , McNamara Coleen A.
Published: July 2022

Immunoglobulin M (IgM) to oxidation specific epitopes (OSE) are inversely associated with atherosclerosis in mice and humans. The B-1b subtype of B-1 cells secrete IgM to OSE, and unlike B-1a cells, are capable of long-lasting IgM memory. What attributes make B-1b cells different than B-1a cells is unknown. Our objectives were to determine how B-1b cells produce more IgM compared to B-1a cells at homeostatic condition and to see the differences in the B-1a and B-1b cell distribution and IgM CDR-H3 sequences in mice with advanced atherosclerosis. Here,in-vivostudies demonstrated greater migration to spleen, splenic production of IgM and plasma IgM levels inApoE-/-Rag1-/-mice intraperitoneally injected with equal numbers of B-1b compared to B-1a cells. Bulk RNA seq analysis and flow cytometry of B-1a and B-1b cells identified CCR6 as a chemokine receptor more highly expressed on B-1b cells compared to B-1a. Knockout of CCR6 resulted in reduced B-1b cell migration to the spleen. Moreover, B-1b cell numbers were significantly higher in spleen of aged atheroscleroticApoE-/-mice compared to youngApoE-/-mice. Single cell sequencing results of IgHM in B-1a and B-1b cells from peritoneal cavity and spleen of atherosclerotic agedApoE-/-mice revealed significantly more N additions at the V-D and D-J junctions, greater diversity in V region usage and CDR-H3 sequences in B-1b compared to B-1a cells. In summary, B-1b cells demonstrated enhanced CCR6-mediated splenic migration, IgM production, and IgM repertoire diversification compared to B-1a cells. These findings suggest that potential strategies to selectively augment B-1b cell numbers and splenic trafficking could lead to increased and more diverse IgM targeting OSE to limit atherosclerosis.
Age-related increase of mitochondrial content in human memory CD4+ T cells contributes to ROS-mediated increased expression of proinflammatory cytokines
Authors: Chen Yuling , Ye Yuanchun , Krauß Pierre-Louis , Löwe Pelle , Pfeiffenberger Moritz , Damerau Alexandra , Ehlers Lisa , Buttgereit Thomas , Hoff Paula , Buttgereit Frank , Gaber Timo
Published: July 2022

Cellular metabolism modulates effector functions in human CD4+ T (Th) cells by providing energy and building blocks. Conversely, cellular metabolic responses are modulated by various influences, e.g., age. Thus, we hypothesized that metabolic reprogramming in human Th cells during aging modulates effector functions and contributes to “inflammaging”, an aging-related, chronic, sterile, low-grade inflammatory state characterized by specific proinflammatory cytokines. Analyzing the metabolic response of human naive and memory Th cells from young and aged individuals, we observed that memory Th cells exhibit higher glycolytic and mitochondrial fluxes than naive Th cells. In contrast, the metabolism of the latter was not affected by donor age. Memory Th cells from aged donors showed a higher respiratory capacity, mitochondrial content, and intracellular ROS production than those from young donors without altering glucose uptake and cellular ATP levels, which finally resulted in higher secreted amounts of proinflammatory cytokines, e.g., IFN-γ, IP-10 from memory Th cells taken from aged donors after TCR-stimulation which were sensitive to ROS inhibition. These findings suggest that metabolic reprogramming in human memory Th cells during aging results in an increased expression of proinflammatory cytokines through enhanced ROS production, which may contribute to the pathogenesis of inflammaging.
The lymphocyte-to-monocyte ratio predicts intracranial atherosclerotic stenosis plaque instability
Authors: Wu Xiao-Bing , Huang Li-Xin , Huang Zhong-Run , Lu Li-Ming , Luo Bin , Cai Wang-Qing , Liu An-Min , Wang Sheng-Wen
Published: July 2022

Background and purpose

Gadolinium enhancement on high-resolution vessel wall imaging (HR-VWI) is an imaging marker of intracranial atherosclerotic stenosis (ICAS) plaque instability. This study aimed to evaluate the relationships between hematological inflammatory indicators and the enhancement of ICAS plaques and to search for hematological indicators that can predict ICAS plaque instability.

Methods

Consecutive adult patients diagnosed with ICAS from April 2018 to December 2021 were recruited retrospectively, and every patient underwent HR-VWI. Plaque enhancement was measured qualitatively and quantitatively. The plaque-to-pituitary stalk contrast ratio (CR) indicated the degree of plaque enhancement. Clinical and laboratory data, including the lymphocyte-to-monocyte ratio (LMR), neutrophil-to-lymphocyte ratio (NLR), and systemic immune inflammation index (SII), were recorded. The hematological inflammatory indicators were compared between ICAS patients with and without plaque enhancement and between patients with and without symptomatic plaque. The hematological inflammatory indicators and the CR were compared using linear regression. Furthermore, receiver operating characteristic curve analysis was performed to assess the discriminative abilities of the inflammatory indicators to predict plaque instability.

Results

Fifty-nine patients were included. The NLR, SII and LMR were significantly correlated with plaque enhancement. The LMR was independently associated with plaque enhancement, and a linear negative correlation was observed between the LMR and CR (R = 0.716, P < 0.001). The NLR, LMR, plaque enhancement and CR were significantly associated with symptomatic ICAS, and the LMR and plaque enhancement were independent risk factors for symptomatic ICAS. The optimal cutoff value of the admission LMR to distinguish symptomatic plaque from asymptomatic plaque was 4.0 (80.0% sensitivity and 70.6% specificity).

Conclusion

The LMR was independently associated with ICAS plaque enhancement and showed a linear negative correlation with CR. The LMR and plaque enhancement were independent risk factors for symptomatic ICAS. An LMR ≤ 4.0 may predict ICAS plaque instability.
Characterization of the immune cell infiltration landscape in myxofibrosarcoma to aid immunotherapy
Authors: Zhao Zi-Yue , Chen Zhuo-Yuan , Yu Bin , Xiao Bo , Liu Li-Yan , Xia Yu , Li Ao-Yu , Wang Ping-Xiao , Xiang Cheng , Liu Chao , Yang Hui-Qin , Li Hui , Xiao Tao
Published: July 2022

Myxofibrosarcoma (MFS) is a highly malignant subtype of soft tissue sarcoma, accounting for 5% of cases. Immunotherapy guided by immune cell infiltration (ICI) is reportedly a promising treatment strategy. Here, MFS samples (n = 104) from two independent databases were classified as ICI clusters A/B/C and gene clusters A/B/C. Then, a close relationship between ICI and gene clusters was established. We found that the features of these clusters were consistent with the characteristics of immune-inflamed tumors (cluster C), immune-desert tumors (cluster B), and immune-excluded tumors (cluster A). Moreover, cluster C was sensitive to immunotherapy. Finally, an independent ICI score was established to predict the therapeutic effect, which has prospects for application in guiding immunotherapy during clinical practice.
Regulation of metabolic and transcriptional responses by the thyroid hormone in cellular models of murine macrophages
Authors: López-Mateo Irene , Rodríguez-Muñoz Diego , de La Rosa Juan Vladimir , Castrillo Antonio , Alemany Susana , Aranda Ana
Published: July 2022

Oncogene-immortalized bone marrow-derived macrophages are considered to be a good model for the study of immune cell functions, but the factors required for their survival and proliferation are still unknown. Although the effect of the thyroid hormones on global metabolic and transcriptional responses in macrophages has not yet been examined, there is increasing evidence that they could modulate macrophage functions. We show here that the thyroid hormone T3 is an absolute requirement for the growth of immortal macrophages. The hormone regulates the activity of the main signaling pathways required for proliferation and anabolic processes, including the phosphorylation of ERK and p38 MAPKs, AKT, ribosomal S6 protein, AMPK and Sirtuin-1. T3 also alters the levels of metabolites controlling transcriptional and post-transcriptional actions in macrophages, and causes widespread transcriptomic changes, up-regulating genes needed for protein synthesis and cell proliferation, while down-regulating genes involved in immune responses and endocytosis, among others. This is not observed in primary bone marrow-derived macrophages, where only p38 and AMPK activation is regulated by T3 and in which the metabolic and transcriptomic effects of the hormone are much weaker. However, the response to IFN-γ is reduced by T3 similarly in immortalized macrophages and in the primary cells, confirming previous results showing that the thyroid hormones can antagonize JAK/STAT-mediated signaling. These results provide new perspectives on the relevant pathways involved in proliferation and survival of macrophage cell culture models and on the crosstalk between the thyroid hormones and the immune system.
Boosting the VZV-Specific Memory B and T Cell Response to Prevent Herpes Zoster After Kidney Transplantation
Authors: Kho Marcia M. L. , Weimar Willem , Malahe S. Reshwan K. , Zuijderwijk Joke M. , de Kuiper Ronella , Boer-Verschragen Marieken J. , Eijk Annemiek A. van der , Hesselink Dennis A. , Reinders Marlies E. J. , van Besouw Nicole M.
Published: July 2022

Background

Solid organ transplant recipients are at high risk to develop (complicated) herpes zoster (HZ). Booster vaccination could prevent HZ. However, end-stage renal disease (ESRD) patients show poor immunological responses to vaccinations. We studied the effect of a live attenuated VZV booster vaccine on VZV-specific B and T cell memory responses in ESRD patients and healthy controls. NL28557.000.09, www.toetsingonline.nl

Methods

VZV-seropositive patients, aged ≥50 years, awaiting kidney transplantation, were vaccinated with Zostavax®. Gender and age-matched VZV-seropositive potential living kidney donors were included as controls. VZV-specific IgG titers were measured before, at 1, 3 and 12 months post-vaccination. VZV-specific B and T cell responses before, at 3 months and 1 year after vaccination were analysed by flow-cytometry and Elispot, respectively. Occurrence of HZ was assessed at 5 years post-vaccination.

Results

26 patients and 27 donors were included. Median VZV-specific IgG titers were significantly higher at all time-points post-vaccination in patients (mo 1: 3104 IU/ml [1967-3825], p<0.0001; mo 3: 2659 [1615-3156], p=0.0002; mo 12: 1988 [1104-2989], p=0.01 vs. pre: 1397 [613-2248]) and in donors (mo 1: 2981 [2126-3827], p<0.0001; mo 3: 2442 [2014-3311], p<0.0001; mo 12: 1788 [1368-2460], p=0.0005 vs. pre: 1034 [901-1744]. The patients’ IgG titers were comparable to the donors’ at all time-points. The ratio VZV-specific B cells of total IgG producing memory B cells had increased 3 months post-vaccination in patients (0.85 [0.65-1.34] vs. pre: 0.56 [0.35-0.81], p=0.003) and donors (0.85 [0.63-1.06] vs. pre: 0.53 [0.36-0.79], p<0.0001) and remained stable thereafter in donors. One year post-vaccination, the percentage of CD4+ central memory cells had increased in both patients (0.29 [0.08-0.38] vs. 0.12 [0.05-0.29], p=0.005) and donors (0.12 [0.03-0.37] vs. 0.09 [0.01-0.20], p=0.002) and CD4+ effector memory cells had increased in donors (0.07 [0.02-0.14] vs. 0.04 [0.01-0.12], p=0.007). Only 1 patient experienced HZ, which was non-complicated.

Conclusion

VZV booster vaccination increases VZV-specific IgG titers and percentage VZV-specific memory T-cells for at least 1 year both in ESRD patients and healthy controls. VZV-specific memory B cells significantly increased in patients up to 3 months after vaccination. Prophylactic VZV booster vaccination prior to transplantation could reduce HZ incidence and severity after transplantation.
The intellectual base and research fronts of IL-37: A bibliometric review of the literature from WoSCC
Authors: Qin Ya-fei , Ren Shao-hua , Shao Bo , Qin Hong , Wang Hong-da , Li Guang-ming , Zhu Yang-lin , Sun Cheng-lu , Li Chuan , Zhang Jing-yi , Wang Hao
Published: July 2022

Background

IL-37 is a recently identified cytokine with potent immunosuppressive functions. The research fronts of IL-37 are worth investigating, and there is no bibliometric analysis in this field. The purpose of this study is to construct the intellectual base and predict research hotspots of IL-37 research both quantitatively and qualitatively according to bibliometric analysis.

Methods

The articles were downloaded from the Web of Science Core Collection (WoSCC) database from the inception of the database to 1 April 2022. CiteSpace 5.8.R3 (64-bit, Drexel University, Philadelphia, PA, USA) and Online Analysis Platform of Literature Metrology (https://bibliometric.com/) were used to perform bibliometric and knowledge-map analyses.

Results

A total of 534 papers were included in 200 academic journals by 2,783 authors in 279 institutions from 50 countries/regions. The journal Cytokine published the most papers on IL-37, while Nature Immunology was the most co-cited journal. The publications belonged mainly to two categories of Immunology and Cell Biology. USA and China were the most productive countries. Meanwhile, the University of Colorado Denver in USA produced the highest number of publications followed by Radboud University Nijmegen in the Netherlands and Monash University in Australia. Charles A. Dinarello published the most papers, while Marcel F. Nold had the most co-citations. Top 10 co-citations on reviews, mechanisms, and diseases were regarded as the knowledge base. The keyword co-occurrence and co-citations of references revealed that the mechanisms and immune-related disorders were the main aspects of IL-37 research. Notably, the involvement of IL-37 in various disorders and the additional immunomodulatory mechanisms were two emerging hotspots in IL-37 research.

Conclusions

The research on IL-37 was thoroughly reviewed using bibliometrics and knowledge-map analyses. The present study is a benefit for academics to master the dynamic evolution of IL-37 and point out the direction for future research.
Intramuscular Inoculation of AS02-Adjuvanted Respiratory Syncytial Virus (RSV) F Subunit Vaccine Shows Better Efficiency and Safety Than Subcutaneous Inoculation in BALB/c Mice
Authors: Bian Lijun , Zheng Yu , Guo Xiaohong , Li Dongdong , Zhou Jingying , Jing Linyao , Chen Yan , Lu Jingcai , Zhang Ke , Jiang Chunlai , Zhang Yong , Kong Wei
Published: July 2022

We previously explored a panel of adjuvants formulated with pre-fusion RSV-F protein and found that AS02 may be a promising candidate adjuvant for developing RSV-F subunit vaccines with improved immunogenicity and desired immune response type. In this study, we performed a head-to-head comparison of the effect of intramuscular injection to that of subcutaneous injection on the immune response and protective efficacy of recombinant RSV-F subunit vaccine with or without adjuvants (Alhydrogel, squalene-based emulsion adjuvants MF59, AS03, and AS02) in BALB/c mice. After inoculations, antigen-specific antibodies, neutralizing antibodies, antibody subtypes, cytokines, and the persistence of immune response were evaluated. Moreover, challenge tests were also performed to illustrate the possible effect of inoculation routes and adjuvant on virus clearance and histochemistry changes in the lungs of mice. The results indicated that intramuscular inoculation is a more effective and antigen dose-sparing route to enhance the immune response, although subcutaneous inoculation induced faster and stronger IgG antibodies after the initial immunization. Furthermore, adjuvant, but not immunization route, is a more critical factor to affect the humoral/cellular immune response and the immune bias. In addition, adjuvant inoculated via the intramuscular route is safer than that via the subcutaneous route, especially for AS02. This study highlights the importance of the adjuvant and immunization routes in the design and clinical transformation of adjuvanted vaccines. Further investigation is needed to illustrate the mechanism underlying the above difference in both efficiency and safety.
Therapeutic application of quercetin in aging-related diseases: SIRT1 as a potential mechanism
Authors: Cui Zhifu , Zhao Xingtao , Amevor Felix Kwame , Du Xiaxia , Wang Yan , Li Diyan , Shu Gang , Tian Yaofu , Zhao Xiaoling
Published: July 2022

Quercetin, a naturally non-toxic flavonoid within the safe dose range with antioxidant, anti-apoptotic and anti-inflammatory properties, plays an important role in the treatment of aging-related diseases. Sirtuin 1 (SIRT1), a member of NAD+-dependent deacetylase enzyme family, is extensively explored as a potential therapeutic target for attenuating aging-induced disorders. SIRT1 possess beneficial effects against aging-related diseases such as Alzheimer’s disease (AD), Parkinson’s disease (PD), Huntington’s disease (HD), Depression, Osteoporosis, Myocardial ischemia (M/I) and reperfusion (MI/R), Atherosclerosis (AS), and Diabetes. Previous studies have reported that aging increases tissue susceptibility, whereas, SIRT1 regulates cellular senescence and multiple aging-related cellular processes, including SIRT1/Keap1/Nrf2/HO-1 and SIRTI/PI3K/Akt/GSK-3β mediated oxidative stress, SIRT1/NF-κB and SIRT1/NLRP3 regulated inflammatory response, SIRT1/PGC1α/eIF2α/ATF4/CHOP and SIRT1/PKD1/CREB controlled phosphorylation, SIRT1-PINK1-Parkin mediated mitochondrial damage, SIRT1/FoxO mediated autophagy, and SIRT1/FoxG1/CREB/BDNF/Trkβ-catenin mediated neuroprotective effects. In this review, we summarized the role of SIRT1 in the improvement of the attenuation effect of quercetin on aging-related diseases and the relationship between relevant signaling pathways regulated by SIRT1. Moreover, the functional regulation of quercetin in aging-related markers such as oxidative stress, inflammatory response, mitochondrial function, autophagy and apoptosis through SIRT1 was discussed. Finally, the prospects of an extracellular vesicles (EVs) as quercetin loading and delivery, and SIRT1-mediated EVs as signal carriers for treating aging-related diseases, as well as discussed the ferroptosis alleviation effects of quercetin to protect against aging-related disease via activating SIRT1. Generally, SIRT1 may serve as a promising therapeutic target in the treatment of aging-related diseases via inhibiting oxidative stress, reducing inflammatory responses, and restoring mitochondrial dysfunction.
Epigenetic regulation and T-cell responses in endometriosis – something other than autoimmunity
Authors: Szukiewicz Dariusz
Published: July 2022

Endometriosis is defined as the presence of endometrial-like glands and stroma located outside the uterine cavity. This common, estrogen dependent, inflammatory condition affects up to 15% of reproductive-aged women and is a well-recognized cause of chronic pelvic pain and infertility. Despite the still unknown etiology of endometriosis, much evidence suggests the participation of epigenetic mechanisms in the disease etiopathogenesis. The main rationale is based on the fact that heritable phenotype changes that do not involve alterations in the DNA sequence are common triggers for hormonal, immunological, and inflammatory disorders, which play a key role in the formation of endometriotic foci. Epigenetic mechanisms regulating T-cell responses, including DNA methylation and posttranslational histone modifications, deserve attention because tissue-resident T lymphocytes work in concert with organ structural cells to generate appropriate immune responses and are functionally shaped by organ-specific environmental conditions. Thus, a failure to precisely regulate immune cell transcription may result in compromised immunological integrity of the organ with an increased risk of inflammatory disorders. The coexistence of endometriosis and autoimmunity is a well-known occurrence. Recent research results indicate regulatory T-cell (Treg) alterations in endometriosis, and an increased number of highly active Tregs and macrophages have been found in peritoneal fluid from women with endometriosis. Elimination of the regulatory function of T cells and an imbalance between T helper cells of the Th1 and Th2 types have been reported in the endometria of women with endometriosis-associated infertility. This review aims to present the state of the art in recognition epigenetic reprogramming of T cells as the key factor in the pathophysiology of endometriosis in the context of T-cell-related autoimmunity. The new potential therapeutic approaches based on epigenetic modulation and/or adoptive transfer of T cells will also be outlined.
Immunometabolism characteristics and a potential prognostic risk model associated with TP53 mutations in breast cancer
Authors: Jiang Mengping , Wu Xiangyan , Bao Shengnan , Wang Xi , Qu Fei , Liu Qian , Huang Xiang , Li Wei , Tang Jinhai , Yin Yongmei
Published: July 2022

TP53, a gene with high-frequency mutations, plays an important role in breast cancer (BC) development through metabolic regulation, but the relationship between TP53 mutation and metabolism in BC remains to be explored. Our study included 1,066 BC samples from The Cancer Genome Atlas (TCGA) database, 415 BC cases from the Gene Expression Omnibus (GEO) database, and two immunotherapy cohorts. We identified 92 metabolic genes associated with TP53 mutations by differential expression analysis between TP53 mutant and wild-type groups. Univariate Cox analysis was performed to evaluate the prognostic effects of 24 TP53 mutation-related metabolic genes. By unsupervised clustering and other bioinformatics methods, the survival differences and immunometabolism characteristics of the distinct clusters were illustrated. In a training set from TCGA cohort, we employed the least absolute shrinkage and selection operator (LASSO) regression method to construct a metabolic gene prognostic model associated with TP53 mutations, and the GEO cohort served as an external validation set. Based on bioinformatics, the connections between risk score and survival prognosis, tumor microenvironment (TME), immunotherapy response, metabolic activity, clinical characteristics, and gene characteristics were further analyzed. It is imperative to note that our model is a powerful and robust prognosis factor in comparison to other traditional clinical features and also has high accuracy and clinical usefulness validated by receiver operating characteristic (ROC) and decision curve analysis (DCA). Our findings deepen our understanding of the immune and metabolic characteristics underlying the TP53 mutant metabolic gene profile in BC, laying a foundation for the exploration of potential therapies targeting metabolic pathways. In addition, our model has promising predictive value in the prognosis of BC.
Dietary Supplementation of Bacillus sp. PM8313 with β-glucan Modulates the Intestinal Microbiota of Red Sea Bream (Pagrus major) to Increase Growth, Immunity, and Disease Resistance
Authors: Jang Won Je , Jeon Mi-Hyeon , Lee Su-Jeong , Park So Young , Lee Young-Sun , Noh Da-In , Hur Sang Woo , Lee Seunghan , Lee Bong-Joo , Lee Jong Min , Kim Kang-Woong , Lee Eun-Woo , Hasan Md Tawheed
Published: July 2022

A 56-day feeding trial was conducted to determine the effect of dietary supplementation with Bacillus sp. isolated from the intestines of red sea bream on the growth performance, immunity, and gut microbiome composition of red sea bream. Three diets (a control diet and two treatments) were formulated without Bacillus sp. PM8313 or β-glucan (control, CD), 1 × 108 CFU g−1 PM8313 (BSD), and 1 × 108 CFU g−1 PM8313 + 0.1% β-glucan (BGSD). At the end of the experiment, the weight, specific growth rate, feed conversion ratio, and protein efficiency ratio of the fish in the BSD and BGSD diet groups were significantly improved than those of the control group (P < 0.05). Additionally, amylase and trypsin activities were significantly higher (P < 0.05) in both groups compared to the control. Superoxide dismutase and lysozyme activity, which are serum non-specific immune responses, only increased in the BGSD group. The two treatment groups exhibited a marked difference in the intestinal microbiota composition compared to the control group. Furthermore, the treatment groups exhibited an upregulation of IL-6 and NF-κb, coupled with high survival rates when challenged with Edwardsiella tarda. Therefore, dietary supplementation with PM8313 improved the growth performance, digestive enzyme activity, non-specific immunity, and pathogen resistance of red sea bream, in addition to affecting the composition of its intestinal microflora.
Differences in the progression rate of SCTLD in Pseudodiploria strigosa are related to colony size and morphology
Authors: Camacho-Vite Carolina , Estrada-Saldívar Nuria , Pérez-Cervantes Esmeralda , Alvarez-Filip Lorenzo
Published: July 2022

Stony Coral Tissue Loss Disease (SCTLD) impacts are unprecedented concerning the level of devastation they have imposed on Caribbean coral assemblages. Although SCTLD affects nearly 30 different coral species, it has been particularly lethal for Pseudodiploria strigosa. Mortality rates for this species are estimated to be between 60 and 100% in the Caribbean; however, tissue-loss rates have been shown to differ among colonies, which suggests that colony health, environmental conditions, and concurrent transmission events are crucial to the development of the disease at reef scale. To gain insight into the colony-level dynamics of SCTLD, we used a simplified photogrammetry and 3D modeling approach to quantify and compare SCTLD-related tissue-loss rates among 20 colonies of P. strigosa on a shallow back-reef in the Mexican Caribbean. Over a six-month period, SCTLD resulted in the full mortality of 70% of the colonies that were tagged shortly after infection. Although disease progression followed a multifocal-type infection in most cases, tissue-loss rates significantly differed among colonies. Some colonies died within the first 20 days of observation, while others died towards the end of the study period. We found a significant positive effect of colony size on rates of tissue loss disease, as well as evidence suggesting that elongated and vertically compressed colonies have a greater probability of experiencing higher tissue-loss rates than colonies with more spherical shapes. The observed relationship between colony morphology and tissue-loss rates is likely a result of elongated colonies having more flat surface area at the top of the colonies which facilitates accumulation of sediments, which have been shown to be a source of SCTLD transmission.
Community and Marine Conservation in South Africa: Are We Still Missing the Mark?
Authors: Peer Nasreen , Muhl Ella-Kari , Janna Jamila , Brown Michael , Zukulu Sinegugu , Mbatha Philile
Published: July 2022

Marine Protected Areas (MPAs) in South Africa have a long history with currently 5% of the mainland’s ocean territory protected. The MPAs are celebrated and appreciated for their representative coverage of several habitat types and their ecological benefits. However, the story of correlational coastal community exclusion is not one that is often told in the ‘success’ story of South African MPAs. In this review we describe the history of marine conservation in South Africa and examine how the legislation and motivation has evolved since Apartheid. While legislation provides direction in terms of community inclusion, this is rarely the reality as we explore with five case studies. We go on to discuss how top-down governance continues to exclude communities and suggest key lessons drawn from our case-studies that could lead to a more community-involved approach to the ongoing protection and management of our marine habitats for greater conservation success.
Characterizing Nearshore Fish Assemblages From Intact and Altered Mangrove Shorelines in Biscayne Bay, Florida, United States
Authors: Lennon Ellery , Sealey Kathleen Sullivan
Published: July 2022

Biscayne Bay is an urban bay in Southeast Florida, but the southern region of the Bay is dominated by mangroves. Mangrove wetlands provide important habitat for fish, but some regions are altered by drainage canals in southern Biscayne Bay. This study utilized a large public dataset to determine if fish formed distinct species assemblages throughout Biscayne Bay by examining fish surveyed at 12 different sites over 5 years. Six sites were in front of intact mangrove shorelines, while the other six sites were adjacent to mangrove sites altered by drainage canals or residential marinas. Cluster analyses revealed that fish did form distinct species assemblage clusters which were correlated with salinity and depth. Mangrove shoreline type (intact vs. canal-altered) and geographic location did not appear to affect species composition or diversity in fish assemblages across Southern Biscayne Bay.
Risk of aquaculture-derived microplastics in aquaculture areas: An overlooked issue or a non-issue?
Authors: Lin Lin , Chen Ciara Chun , Zhu Xiaoshan , Pan Ke , Xu Xiangrong
Published: July 2022

Plastic equipment such as fishing nets and foam buoys has been widely used in aquaculture. This kind of equipment would gradually decompose while being subject to the long-term effects of physical, chemical, and biological degradation processes, leading to the release of large amounts of microplastics (MPs) into the local marine environment and the generation of aquaculture-derived MPs (AD-MPs). The rapid growth of aquaculture has resulted in an explosion of AD-MPs with various environmental consequences. The accumulation of MPs in aquatic products was found closely related to the abundance of environmental MPs, suggesting the importance of determining whether AD-MPs increase the risk of MP ingestion by aquatic products and thus endanger aquatic food safety. In this short communication, the ecological and health risks of AD-MPs were discussed and perspectives were proposed for future studies.
Effects of Dietary Lipid Sources on the Growth, Gonad Development, Fatty Acid Composition and Spawning Performance of Broodstock, and Early Larvae Quality of Sea Urchin (Strongylocentrotus intermedius)
Authors: Zuo Rantao , Ning Yanchang , Di Weixiao , Heqiu Yuqing , Song Jian , Ding Jun , Chang Yaqing
Published: July 2022

This study was carried out to investigate the effects of five formulated feeds with different lipid sources (colza oil (CO), fish oil (FO), linseed oil (LO), soybean oil (SO), or palm oil (PO)) and kelp (Laminaria japonica) on the growth, reproductive performance of broodstock, and early larvae quality of sea urchin (Strongylocentrotus intermedius). The experimental diets were randomly allocated to a total of 48 (eight urchins per experimental group) individually cultured S. intermedius(initial weight 90.51 ± 0.82g) and the feeding period lasted for 12 weeks. The results showed that the weight gain rate of female sea urchins fed kelp was significantly higher than those fed formulated feeds while the gonadosomatic index of spawned female sea urchins fed kelp was significantly lower than those fed formulated feeds.S. intermedius broodstock fed FO showed the largest egg diameter and fecundity, which could be due to the abundant n-3 LC-PUFA deposited in the gonads of this group. Sea urchins fed SO showed the lowest fecundity and hatching rate, and the highest inflammation level. Sea urchins fed CO showed the highest content of oleic acid in the gonads and eggs, but the lowest fertilization rate. The highest hatching rate was observed in the kelp treatment, which was comparable to that in the LO and PO but was significantly higher than that in CO, FO, and SO. Before mouth opening, all prismatic larvae showed no significant differences in survival during the first 2 days post hatchery (DPH). At the 3 DPH, the survival of S. intermedius larvae was highest in the FO group, followed by those in the PO group, with the lowest survival observed in the kelp group. Thus, FO was accepted as the most ideal lipid source based on growth, reproductive performance, and early larval quality. These results could contribute to adopting an efficient feeding strategy to promote the reproductive performance and offspring quality by choosing the optimal lipid source for S. intermedius broodstock.
Automating the Curation Process of Historical Literature on Marine Biodiversity Using Text Mining: The DECO Workflow
Authors: Paragkamian Savvas , Sarafidou Georgia , Mavraki Dimitra , Pavloudi Christina , Beja Joana , Eliezer Menashè , Lipizer Marina , Boicenco Laura , Vandepitte Leen , Perez-Perez Ruben , Zafeiropoulos Haris , Arvanitidis Christos , Pafilis Evangelos , Gerovasileiou Vasilis
Published: July 2022

Historical biodiversity documents comprise an important link to the long-term data life cycle and provide useful insights on several aspects of biodiversity research and management. However, because of their historical context, they present specific challenges, primarily time- and effort-consuming in data curation. The data rescue process requires a multidisciplinary effort involving four tasks: (a) Document digitisation (b) Transcription, which involves text recognition and correction, and (c) Information Extraction, which is performed using text mining tools and involves the entity identification, their normalisation and their co-mentions in text. Finally, the extracted data go through (d) Publication to a data repository in a standardised format. Each of these tasks requires a dedicated multistep methodology with standards and procedures. During the past 8 years, Information Extraction (IE) tools have undergone remarkable advances, which created a landscape of various tools with distinct capabilities specific to biodiversity data. These tools recognise entities in text such as taxon names, localities, phenotypic traits and thus automate, accelerate and facilitate the curation process. Furthermore, they assist the normalisation and mapping of entities to specific identifiers. This work focuses on the IE step (c) from the marine historical biodiversity data perspective. It orchestrates IE tools and provides the curators with a unified view of the methodology; as a result the documentation of the strengths, limitations and dependencies of several tools was drafted. Additionally, the classification of tools into Graphical User Interface (web and standalone) applications and Command Line Interface ones enables the data curators to select the most suitable tool for their needs, according to their specific features. In addition, the high volume of already digitised marine documents that await curation is amassed and a demonstration of the methodology, with a new scalable, extendable and containerised tool, “DECO” (bioDivErsity data Curation programming wOrkflow) is presented. DECO’s usage will provide a solid basis for future curation initiatives and an augmented degree of reliability towards high value data products that allow for the connection between the past and the present, in marine biodiversity research.
Sedimentary Record of Polycyclic Aromatic Hydrocarbons in the Gulf of Trieste (Northern Adriatic Sea) - Distribution, Origin and Temporal Trends
Authors: Bajt Oliver
Published: July 2022

A mid-term study (2003-2013) of polycyclic aromatic hydrocarbons in Gulf of Trieste sediments was conducted at seven sampling sites. The PAH spatial and temporal distribution and origin were determined. The sediments were sampled with a gravity core sampler. After extraction of PAH, their concentrations were determined by gas chromatography. The results of the study show PAH spatial and temporal variability. The highest mean concentration was measured in the marina of Portoroz (1168 ng/g dw), and the lowest at an offshore site (320 ng/g dw). The results show higher concentrations of PAH in coastal areas and a decreasing trend towards the central part of the Gulf of Trieste. The interannual differences in the concentrations of PAH showed a significant downward trend in the marina of Portorož, in the port of Koper and in the offshore site off Piran. No trend was observed at all other sites. Various evaluation indices showed that PAH are predominantly of pyrolytic origin, with a lower proportion of petrogenic origin, especially in the Bay of Koper. The ecological risk assessment found that concentrations of PAH are well below levels associated with adverse biological effects. According to the presented results, this area can be considered as only moderately contaminated with PAH. However, the applied measures to reduce pollution should be continued and intensified.
The Impact of Economic Development of the Guangdong-Hongkong-Macao Greater Bay Area on Air Pollution: Investigation Based on Remote Sensing Data of Nighttime Lights and Air Pollution
Authors: Ji Xiaole , Li Shaoxing , Jiang Na , Wang Fei , Fan Liya , Niu Xiao
Published: July 2022

Whether the Guangdong-Hongkong-Macao Greater Bay Area (GBA) can achieve the goal of environmental protection at the same time as its rapid economic development is an important issue that deserves attention. In this paper, we obtained remote sensing data on air pollution including CO, NO2, SO2, PM10, PM2.5, and nighttime light data. We combined the remote sensing data with county-level economic statistics to study economic development and air pollution in the Guangdong-Hongkong-Macao GBA. Our research showed that the economic development in the Guangdong-Hongkong-Macao GBA significantly increased the emissions of NO2, PM10, and PM2.5 and did not have significant effects on CO and SO2. We constructed an emission intensity indicator of pollutants per unit of luminance. We found that the unit emission intensity of four categories of pollutants, PM10, PM2.5, SO2, and CO, showed a significant decreasing trend in line with economic development. The emission intensity of NO2 showed a trend of first decreasing and then increasing. The conclusion of this research illustrates that the emission intensity of pollutants per unit of luminosity in the Guangdong-Hongkong-Macao GBA is continuously reducing. The emission of pollutants will gradually change from slow growth to zero growth. However, the emission of NO2 pollution should be an area of focus in achieving the dual goals of economic development and environmental protection.
Effects of decabromodiphenyl ether (BDE-209) on a mangrove plant, Kandelia obovata and the uptake, translocation and accumulation of BDE-209
Authors: Wang Ying , Du Yi-Tong , Tam Nora Fung-Yee
Published: July 2022

Due to close proximity to urban development, mangroves exposed to the contamination of polybrominated diphenyl ethers (PBDEs). Decabromodiphenyl ether (BDE-209) is one of the most predominant PBDE congener. The present study aimed to investigate the toxic effects of BDE-209 on the antioxidative and non-antioxidative responses of Kandelia obovata, a very common mangrove species, under different concentrations of BDE-209, 0.1, 1, 5 and 10 mg l-1. BDE-209 did not exhibit any negative effects on the growth of K. obovata seedlings. The stimulatory effects of BDE-209 on the enzymes including superoxide dismutase, peroxidase and catalase only occurred in weeks 1 and 4 and diminished in week 8. The concentrations of total polyphenols (TP) and extractable condensed tannins (ECT) were not affected by BDE-209. The production of O2·- was induced only at the very high level of BDE-209 (10 mg l-1). H2O2 was induced only in weeks 1 and 4 under BDE-209 treatment. BDE-209 was taken up by the roots of K. obovata, translocated to above-ground tissues, and accumulated in plant tissues with the concentrations declined in the order of root > propagule > stem > leaf. Although BDE-209 has higher molecular weight and higher log Kow than other PBDE congeners, the K. obovata seedlings could absorb, translocate and accumulate BDE-209. These findings suggested that mangrove plants could take up, accumulate PBDEs, and BDE-209 are less toxic than other congeners but more difficult to be removed by mangrove systems.
Evaluating the predictive power of machine learning model for shear transformation in metallic glasses using metrics for an imbalanced dataset
Authors: Lee Jaemin , Ryu Seunghwa
Published: July 2022

Plastic deformation of metallic glasses, which show no long-range structural order, proceeds by shear transformation of a local group of atoms referred to as the shear transformation zone (STZ). Unlike crystalline solids, it is difficult to identify STZs and predict the onset of plasticity from a random atomic configuration under a given loading. Recently, significant efforts have been made to predict the shear transformation with initial atomic properties using machine learning. However, despite the class imbalance, where the atoms participating in shear transformation is much rarer compared to the others, few studies have explored the issue of the proper predictive metric choice, with most studies considering widely used metrics such as Recall or AUC in the machine learning community. Therefore, here we train a graph neural network that predicts the initially activated STZ and evaluate its predictive power using various metrics considered to be proper for handling imbalanced datasets. We find that the AUC value is significantly overestimated due to the class imbalance and too many atoms are misclassified as initial STZ, so other metrics such as the precision, f1, MCC, and AP indicate very low predictive power close to zero. Additionally, we reveal that the predictive performance changes significantly over the threshold value of non-affine displacement, above which an atom is classified as the initially activated STZ, due to the change in the degree of class imbalance. Our study implies that it is crucial to use an identical threshold for this type of classification (i.e., the class ratio) for a fair assessment of ML models adapted in different studies and to holistically evaluate the predictive performance based on various metrics.
Microstructure and Mechanical Properties of High-Carbon-Containing Fe-Ni-Mn-Al-Cr High-Entropy Alloy: Effect of Thermomechanical Treatment
Authors: Mohanty S. , Kothari A. , Raghavan R. , Sahu V. K. , Gurao N. P. , Sahu K. K. , Dhindaw B. K. , Zeng L. , Xia M. , Gollapudi S.
Published: July 2022

The effect of heat treatment on the mechanical properties of two high-carbon-containing (1.5 and 3 at%) single-phase face-centered cubic (fcc) Fe40.4Ni11.3Mn34.8Al7.5Cr6 high-entropy alloys is reported in this study. In the cold-rolled (CR) condition, the 1.5 and 3 at% C-containing alloys, referred to as CR1 and CR2, respectively, demonstrated yield strength values of 1,423 and 1,197 MPa, respectively. The corresponding values of elongation to failure was noted to be 4.05 and 4.46%, respectively. Upon heat treatment at 1,050°C, the CR1 and CR2 samples, referred to as HT1 and HT2 in the heat-treated (HT) condition, demonstrated yield strength values of 358 and 327 MPa, respectively. The elongation to failure of HT1 and HT2 was found to be 37.2 and 26.4%, respectively. The change in mechanical properties brought about by heat treatment was understood by studying the phase composition, microstructure, and crystallographic texture of the material in the CR and HT conditions. Despite the high-temperature heat treatment, the Fe40.4Ni11.3Mn34.8Al7.5Cr6 alloy retained a single-phase structure, indicating good phase stability. However, heat treatment caused a change in the grain structure. The CR materials exhibited an elongated grain structure, whereas the HT materials had an equiaxed microstructure. The CR and HT samples were found to exhibit a weak crystallographic texture although heat treatment had caused the {111} poles to orient themselves parallel to the rolling plane, whereas the CR material had a distribution of {200} poles at 45° to the rolling plane.