bluuebunny/crossref_metadata_2025 huggingface dataset:
Endometriosis Is Undervalued: A Call to Action
Authors: Ellis Katherine , Munro Deborah , Clarke Jennifer
Published: May 2022

Endometriosis is an inflammatory chronic pain condition caused by uterine tissue growing outside of the uterus that afflicts at least 11% of women (and people assigned female at birth) worldwide. This condition results in a substantial burden to these women, and society at large. Although endometriosis was first identified over 160 years ago, substantial knowledge gaps remain, including confirmation of the disease's etiology. Research funding for endometriosis is limited, with funding from bodies like the National Institutes of Health (NIH) constituting only 0.038% of the 2022 health budget—for a condition that affects 6.5 million women in the US alone and over 190 million worldwide. A major issue is that diagnosis of endometriosis is frequently delayed because surgery is required to histologically confirm the diagnosis. This delay increases symptom intensity, the risk of central and peripheral sensitization and the costs of the disease for the patient and their nation. Current conservative treatments of presumed endometriosis are pain management and birth control. Both of these methods are flawed and can be entirely ineffective for the reduction of patient suffering or improving ability to work, and neither addresses the severe infertility issues or higher risk of certain cancers. Endometriosis research deserves the funding and attention that befits a disease with its substantial prevalence, effects, and economic costs. This funding could improve patient outcomes by introducing less invasive and more timely methods for diagnosis and treatment, including options such as novel biomarkers, nanomedicine, and microbiome alterations.
Changes in the Small Noncoding RNAome During M1 and M2 Macrophage Polarization
Authors: Ma Ding , Zhou Xing , Wang Yu , Dai Liming , Yuan Jie , Peng Jianping , Zhang Xiaoling , Wang Chuandong
Published: May 2022

Macrophages belong to a special phagocytic subgroup of human leukocytes and are one of the important cells of the human immune system. Small noncoding RNAs are a group of small RNA molecules that can be transcribed without the ability to encode proteins but could play a specific function in cells. SncRNAs mainly include microRNAs (miRNAs) and piwi-interacting RNAs (piRNAs), small nucleolar RNAs (snoRNAs), small nuclear RNAs (snRNAs) and repeat RNAs. We used high-throughput sequencing analysis and qPCR to detect the expression changes of the small noncoding RNAome during macrophage polarization. Our results showed that 84 miRNAs and 47 miRNAs with were downregulated during M1 macrophage polarization and that 11 miRNAs were upregulated and 19 miRNAs were downregulated during M2 macrophage polarization. MiR-novel-3-nature and miR-27b-5p could promote expression of TNF-α which was marker gene of M1 macrophages. The piRNA analysis results showed that 69 piRNAs were upregulated and 61 piRNAs were downregulated during M1 macrophage polarization and that 3 piRNAs were upregulated and 10 piRNAs were downregulated during M2 macrophage polarization. DQ551351 and DQ551308 could promote the mRNA expression of TNF-α and DQ551351overexpression promoted the antitumor activity of M1 macrophages. SnoRNA results showed that 62 snoRNAs were upregulated and 59 snoRNAs were downregulated during M1 macrophage polarization, whereas 6 snoRNAs were upregulated and 10 snoRNAs were downregulated during M2 macrophage polarization. Overexpression of snoRNA ENSMUST00000158683.2 could inhibit expression of TNF-α. For snRNA, we found that 12 snRNAs were upregulated and 15 snRNAs were downregulated during M1 macrophage polarization and that 2 snRNAs were upregulated during M2 macrophage polarization. ENSMUSG00000096786 could promote expression of IL-1 and iNOS and ENSMUSG00000096786 overexpression promoted the antitumor activity of M1 macrophages. Analysis of repeat RNAs showed that 7 repeat RNAs were upregulated and 9 repeat RNAs were downregulated during M1 macrophage polarization and that 2 repeat RNAs were downregulated during M2 macrophage polarization. We first reported the expression changes of piRNA, snoRNA, snRNA and repeat RNA during macrophage polarization, and preliminarily confirmed that piRNA, snoRNA and snRNA can regulate the function of macrophages.
Beyond Maternal Tolerance: Education of Uterine Natural Killer Cells by Maternal MHC Drives Fetal Growth
Authors: Depierreux Delphine M. , Kieckbusch Jens , Shreeve Norman , Hawkes Delia A. , Marsh Bryan , Blelloch Robert , Sharkey Andrew , Colucci Francesco
Published: May 2022

Reproductive immunology has moved on from the classical Medawar question of 60 years ago “why doesn’t the mother reject the fetus?”. Looking beyond fetal-maternal tolerance, modern reproductive immunology focuses on how the maternal immune system supports fetal growth. Maternal uterine natural killer (uNK) cells, in partnership with fetal trophoblast cells, regulate physiological vascular changes in the uterus of pregnant women and mice. These vascular changes are necessary to build the placenta and sustain fetal growth. NK cell functions in the uterus and elsewhere, including anti-viral and anti-tumour immunity mediated mostly by blood NK cells, are modulated by NK cell education, a quantifiable process that determines cellular activation thresholds. This process relies largely on interactions between self-MHC class I molecules and inhibitory NK cell receptors. By getting to know self, the maternal immune system sets up uNK cells to participate to tissue homeostasis in the womb. Placentation can be viewed as a form of natural transplantation unique in vertebrates and this raises the question of how uNK cell education or missing-self recognition affect their function and, ultimately fetal growth. Here, using combinations of MHC-sufficient and -deficient mice, we show that uNK cell education is linked to maternal and not fetal MHC, so that MHC-deficient dams produce more growth-restricted fetuses, even when the fetuses themselves express self-MHC. We also show that, while peripheral NK cells reject bone marrow cells according to the established rules of missing-self recognition, uNK cells educated by maternal MHC do not reject fetuses that miss self-MHC and these fetuses grow to their full potential. While these results are not directly applicable to clinical research, they show that NK education by maternal MHC-I is required for optimal fetal growth.
Comprehensive Analysis of Ferroptosis- and Immune-Related Signatures to Improve the Prognosis and Diagnosis of Kidney Renal Clear Cell Carcinoma
Authors: Xing Xiao-Liang , Liu Yan , Liu Jiheng , Zhou Huanfa , Zhang Huirong , Zuo Qi , Bu Ping , Duan Tong , Zhou Yan , Xiao Zhiquan
Published: May 2022

Background

Almost 40% of patients with kidney renal clear cell carcinoma (KIRC) with advanced cancers eventually develop to metastases, and their 5-year survival rates are approximately 10%. Aberrant DNA methylations are significantly associated with the development of KIRC. The aim of our present study was to identify suitable ferroptosis- and immune-related (FI) biomarkers correlated with aberrant methylations to improve the prognosis and diagnosis of KIRC.

Methods

ChAMP and DESeq2 in R (3.6.2) were used to screen the differentially expressed methylation probes and differentially expressed genes, respectively. Univariate and multivariate Cox regression were used to identify the overall survival (OS)–related biomarkers.

Results

We finally identified five FI biomarkers (CCR4, CMTM3, IFITM1, MX2, and NR3C2) that were independently correlated with the OS of KIRC. The area under the curve value of the receiver operating characteristic value of prognosis model was 0.74, 0.68, and 0.72 in the training, validation, and entire cohorts, respectively. The sensitivity and specificity of the diagnosis model were 0.8698 and 0.9722, respectively. In addition, the prognosis model was also significantly correlated with several immune cells and factors.

Conclusion

Our present study suggested that these five FI-DEGs (CCR4, CMTM3, IFITM1, MX2, and NR3C2) could be used as prognosis and diagnosis biomarkers for patients with KIRC, but further cross-validation clinical studies are still needed to confirm them.
Complement Factor I Variants in Complement-Mediated Renal Diseases
Authors: Zhang Yuzhou , Goodfellow Renee X. , Ghiringhelli Borsa Nicolo , Dunlop Hannah C. , Presti Stephen A. , Meyer Nicole C. , Shao Dingwu , Roberts Sarah M. , Jones Michael B. , Pitcher Gabriella R. , Taylor Amanda O. , Nester Carla M. , Smith Richard J. H.
Published: May 2022

C3 glomerulopathy (C3G) and atypical hemolytic uremic syndrome (aHUS) are two rare diseases caused by dysregulated activity of the alternative pathway of complement secondary to the presence of genetic and/or acquired factors. Complement factor I (FI) is a serine protease that downregulates complement activity in the fluid phase and/or on cell surfaces in conjunction with one of its cofactors, factor H (FH), complement receptor 1 (CR1/CD35), C4 binding protein (C4BP) or membrane cofactor protein (MCP/CD46). Because altered FI activity is causally related to the pathogenesis of C3G and aHUS, we sought to test functional activity of select CFI missense variants in these two patient cohorts. We identified 65 patients (16, C3G; 48, aHUS; 1 with both) with at least one rare variant in CFI (defined as a MAF < 0.1%). Eight C3G and eleven aHUS patients also carried rare variants in either another complement gene, ADAMTS13 or THBD. We performed comprehensive complement analyses including biomarker profiling, pathway activity and autoantibody testing, and developed a novel FI functional assay, which we completed on 40 patients. Seventy-eight percent of rare CFI variants (31/40) were associated with FI protein levels below the 25th percentile; in 22 cases, FI levels were below the lower limit of normal (type 1 variants). Of the remaining nine variants, which associated with normal FI levels, two variants reduced FI activity (type 2 variants). No patients carried currently known autoantibodies (including FH autoantibodies and nephritic factors). We noted that while rare variants in CFI predispose to complement-mediated diseases, phenotypes are strongly contingent on the associated genetic background. As a general rule, in isolation, a rare CFI variant most frequently leads to aHUS, with the co-inheritance of a CD46 loss-of-function variant driving the onset of aHUS to the younger age group. In comparison, co-inheritance of a gain-of-function variant in C3 alters the phenotype to C3G. Defects in CFH (variants or fusion genes) are seen with both C3G and aHUS. This variability underscores the complexity and multifactorial nature of these two complement-mediated renal diseases.
Ferroptosis: A Critical Moderator in the Life Cycle of Immune Cells
Authors: Wang Ping , Lu Yuan-Qiang
Published: May 2022

Ferroptosis is a form of programmed cell death that was only recognized in 2012. Until recently, numerous researchers have turned their attention to the mechanism and function of ferroptosis. A large number of studies have shown potential links between cell ferroptosis and infection, inflammation, and tumor. At the same time, immune cells are vital players in these above-mentioned processes. To date, there is no comprehensive literature review to summarize the relationship between ferroptosis and immune cells. Therefore, it is of great significance to explore the functional relationship between the two. This review will attempt to explain the link between ferroptosis and various immune cells, as well as determine the role ferroptosis plays in infection, inflammation, and malignancies. From this, we may find the potential therapeutic targets of these diseases.
PANDORA: A Fast, Anchor-Restrained Modelling Protocol for Peptide: MHC Complexes
Authors: Marzella Dario F. , Parizi Farzaneh M. , Tilborg Derek van , Renaud Nicolas , Sybrandi Daan , Buzatu Rafaella , Rademaker Daniel T. , ‘t Hoen Peter A. C. , Xue Li C.
Published: May 2022

Deeper understanding of T-cell-mediated adaptive immune responses is important for the design of cancer immunotherapies and antiviral vaccines against pandemic outbreaks. T-cells are activated when they recognize foreign peptides that are presented on the cell surface by Major Histocompatibility Complexes (MHC), forming peptide:MHC (pMHC) complexes. 3D structures of pMHC complexes provide fundamental insight into T-cell recognition mechanism and aids immunotherapy design. High MHC and peptide diversities necessitate efficient computational modelling to enable whole proteome structural analysis. We developed PANDORA, a generic modelling pipeline for pMHC class I and II (pMHC-I and pMHC-II), and present its performance on pMHC-I here. Given a query, PANDORA searches for structural templates in its extensive database and then applies anchor restraints to the modelling process. This restrained energy minimization ensures one of the fastest pMHC modelling pipelines so far. On a set of 835 pMHC-I complexes over 78 MHC types, PANDORA generated models with a median RMSD of 0.70 Å and achieved a 93% success rate in top 10 models. PANDORA performs competitively with three pMHC-I modelling state-of-the-art approaches and outperforms AlphaFold2 in terms of accuracy while being superior to it in speed. PANDORA is a modularized and user-configurable python package with easy installation. We envision PANDORA to fuel deep learning algorithms with large-scale high-quality 3D models to tackle long-standing immunology challenges.
Characterization of Co-Stimulatory Ligand CD80/86 and Its Effect as a Molecular Adjuvant on DNA Vaccine Against Vibrio anguillarum in Flounder (Paralichthys olivaceus)
Authors: Liu Wenjing , Xing Jing , Tang Xiaoqian , Sheng Xiuzhen , Chi Heng , Zhan Wenbin
Published: May 2022

The CD80/86 molecule is one of the important co-stimulatory ligands and involves antigen-specific immune responses by ligating with CD28 and then delivering the required second signal to T-cell activation. In this study, a CD80/86 homolog was identified, and its expression characteristics were studied in flounder (Paralichthys olivaceus). The open reading frame (ORF) ofCD80/86is 906 bp, encoding 301 aa, and the extracellular amino acid sequence encoded two IgV- and IgC-like structural domains;fCD80/86is highly expressed in head kidney, peripheral blood leukocytes (PBLs), and spleen, and has relatively high expression in muscle. Antibodies specific for CD80/86 were produced, and CD80/86 was colocalized with MHCII+, CD40+, and CD83+ leukocytes but not with IgM+, CD3+, or CD4+ lymphocytes. The cloned CD80/86 in flounder shares conserved structural features with its mammalian counterparts and is mainly distributed on antigen-presenting cells. Based on these data, CD80/86 as an adjuvant to enhance the immune response of DNA vaccine was investigated. A bicistronic DNA vaccine expressing both CD80/86 and the outer membrane protein (OmpK) ofVibrio anguillarum(p-OmpK-CD80/86) was successfully constructed. After immunization, p-OmpK-CD80/86 could induce the upregulation of the proportion of IgM+ and CD4+ cells in flounder, compared to the p-OmpK- or p-CD80/86-immunized group;CD28genes were significantly induced in the p-CD80/86 and p-OmpK-CD80/86 groups. Compared to the p-OmpK group, the higher expression ofCD83,MHCI,CD4,CD8, andIL-2was detected at the injection site. The relative percent survival (RPS) produced by p-OmpK-CD80/86 is 66.11% following theV. anguillarumchallenge, while the RPS of p-OmpK or p-CD80/86 is 46.30% and 5.56%, respectively. The results revealed that CD80/86 is mainly found in antigen-presenting cells, and could help elicit humoral immune responses in teleost through the CD80/86-CD28 signaling pathway involving CD4+ lymphocytes.
Autophagy-Related Genes Are Involved in the Progression and Prognosis of Asthma and Regulate the Immune Microenvironment
Authors: Yang Fan , Kong Jingwei , Zong Yuhan , Li Zhuqing , Lyu Mingsheng , Li Wanyang , Li Wenle , Zhu Haoyue , Chen Shunqi , Zhao Xiaoshan , Wang Ji
Published: May 2022

Background

Autophagy has been proven to play an important role in the pathogenesis of asthma and the regulation of the airway epithelial immune microenvironment. However, a systematic analysis of the clinical importance of autophagy-related genes (ARGs) regulating the immune microenvironment in patients with asthma remains lacking.

Methods

Clustering based on the k-means unsupervised clustering method was performed to identify autophagy-related subtypes in asthma. ARG-related diagnostic markers in low-autophagy subtypes were screened, the infiltration of immune cells in the airway epithelium was evaluated by the CIBERSORT, and the correlation between diagnostic markers and infiltrating immune cells was analyzed. On the basis of the expression of ARGs and combined with asthma control, a risk prediction model was established and verified by experiments.

Results

A total of 66 differentially expressed ARGs and 2 subtypes were identified between mild to moderate and severe asthma. Significant differences were observed in asthma control and FEV1 reversibility between the two subtypes, and the low-autophagy subtype was closely associated with severe asthma, energy metabolism, and hormone metabolism. The autophagy gene SERPINB10 was identified as a diagnostic marker and was related to the infiltration of immune cells, such as activated mast cells and neutrophils. Combined with asthma control, a risk prediction model was constructed, the expression of five risk genes was supported by animal experiments, was established for ARGs related to the prediction model.

Conclusion

Autophagy plays a crucial role in the diversity and complexity of the asthma immune microenvironment and has clinical value in treatment response and prognosis.
The Next Generation Is Here: A Review of Transcriptomic Approaches in Marine Ecology
Authors: Page Tessa M. , Lawley Jonathan W.
Published: May 2022

As we enter the United Nations Decade of Ocean Science for Sustainable Development, extensive efforts to reverse the decline of ocean health are taking place. Moreover, the need to utilize innovative and integrative approaches to aid in these efforts and address marine ecological questions are urgent. Transcriptomic technologies provide tools to further our understanding of an organism’s biology by allowing researchers to rapidly gain information on the genetic variation of populations and the regulation of cellular processes and pathways through gene presence, absence, and expression. Here, we review the application of transcriptomics in the field of marine ecology over the last decade, following a systematic literature review approach. We found 478 articles that fit our search criteria of using transcriptomic approaches to address ecological hypotheses, with 70% of these studies occurring within the last 5 years. Among the analysed articles, 51.7% involved a type of stressor, 16.6% used transcriptomics to study adaptation, and another 15.9% researched ecological interactions. Most articles investigated species from kingdom Animalia, with a high representation from both molluscs (19.5%) and chordates (13.3%), and only 22% of studies had a fieldwork component. Our review demonstrates how the use of transcriptomic techniques in the field of marine ecology is increasing and how they are being applied. Although there are still challenges researchers experience using such techniques, particularly when annotating genes in non-model species and those with no prior genomic resources, these innovative technologies are extremely valuable in investigating differential gene expression, molecular pathways, and generating genomic resources.
High-Resolution Projections of Global Sea Surface Temperatures Reveal Critical Warming in Humpback Whale Breeding Grounds
Authors: von Hammerstein Hannah , Setter Renee O. , van Aswegen Martin , Currie Jens J. , Stack Stephanie H.
Published: May 2022

Anthropogenic greenhouse gas emissions are triggering changes in global climate and warming the ocean. This will affect many marine organisms, particularly those with high site fidelity and habitat temperature preferences, such as humpback whales on their breeding grounds. To study the impacts of a warming ocean on marine organisms, large-scale projections of climatic variables are crucial. Global models are of 0.25 - 1° (~25-100 km) resolution, and not ideal to predict localized changes. Here, we provide 0.05° resolution (~5 km) sea surface temperature (SST) projections, statistically downscaled using the delta method. We illustrate the shifting isotherms of the critical 21 and 28°C boundaries, which border the climatic envelope that humpback whales prefer for their breeding grounds, over the course of the 21st century on a decadal temporal resolution. Results show by the end of the 21st century, 35% of humpback whale breeding areas will experience SSTs above or within 1°C of current thresholds if present-day social, economic, and technological trends continue (‘middle of the road’ CMIP6 greenhouse gas trajectory SSP2-RCP4.5). This number rises to 67% under the scenario describing rapid economic growth in carbon-intensive industries (‘fossil-fueled development’ CMIP6 greenhouse gas trajectory SSP5-RCP8.5). These projections highlight the importance of reducing global greenhouse gas emissions and minimizing further SST increases to preserve ecological integrity of humpback whale breeding areas. In this context, our results emphasize the need to focus on protection of critical ocean habitat and to provide high-resolution climate data for this purpose.
Into the Plastisphere, Where Only the Generalists Thrive: Early Insights in Plastisphere Microbial Community Succession
Authors: Wallbank Jessica A. , Lear Gavin , Kingsbury Joanne M. , Weaver Louise , Doake Fraser , Smith Dawn A. , Audrézet François , Maday Stefan D. M. , Gambarini Victor , Donaldson Lloyd , Theobald Beatrix , Barbier Maxime , Pantos Olga
Published: May 2022

The ubiquity of plastic debris in marine environments raises the question, what impacts do plastics have on our marine microbiota? To investigate this, we applied bacterial 16S rRNA gene and fungal ITS2 region sequencing to identify changes in microbial biofilm community compositions on marine plastic, over time. We sampled biofilm on virgin linear low-density polyethylene (LLDPE), nylon-6 (PA) and glass after 2, 6 and 12 weeks of constant immersion in Te Whakaraupō-Lyttelton Harbour, Aotearoa-New Zealand. Of the prokaryotes, Proteobacteria and Bacteroidetes were predominant in all samples and Verrucomicrobiota were most abundant in mature biofilms. Microbial communities on the three substrate types were significantly distinct from those in the surrounding seawater, regardless of age, but not between attachment substrates. Bacterial communities occurring two weeks after immersion and fungal communities at six weeks were found to vary more among substrate types than at other times; however, no significant substrate-specific communities were identified overall. Taxa closely related to previously reported plastic-biodegrading species were found in very low abundance across all substrates, including on the glass slides. Our findings suggest that microorganisms do not selectively persist on the LLDPE or PA surfaces to gain significant direct metabolic benefit, instead using these plastics primarily as an attachment surface on which they form generalist biofilm communities.
Changes in Organic Carbon Delivery to the Yangtze River Delta Over the Last 2000 Years
Authors: Zhou Liang , Yang Yang , Shi Yong , Xu Xiaomei , Wang Ya Ping , Jia Jianjun , Gao Jian Hua , Gao Shu
Published: May 2022

Natural processes and anthropogenic activities are vital in dictating the amount and character of organic carbon (OC) input into large river deltas and adjacent shelves. Previous studies have indicated that sediment from the Huanghe River (HR) has significantly affected the formation of the northern Yangtze River subaqueous delta (YRD) over the past several hundred years. However, whether this process has changed sedimentary OC burial in the YRD remains unclear. A sediment core was collected from the YRD in 2018 CE for optically stimulated luminescence and 210Pb dating as well as grain size, total OC, total nitrogen, and stable-isotope analyses to investigate temporal changes in sedimentary OC over the past 2000 years. The results indicate that changes in terrestrial OC inputs to the YRD have been controlled mainly by the East Asian summer monsoon and anthropogenic influences in the past 2000 years. However, the decreased terrestrial OC inputs after 1385 CE, have been significantly affected by increased contribution of HR sediment to the YRD when the HR lower courses shifted to enter the southern Yellow Sea. This study demonstrates that sediment source changes should not be neglected in analyses of mechanisms and variations in OC burial in estuarine and coastal areas.
When Scientists and Industry Technologies Mitigate Habitat Loss: The First Bioconstruction Relocation in the Mediterranean Sea
Authors: Casoli Edoardo , Ventura Daniele , Mancini Gianluca , Belluscio Andrea , Ardizzone Giandomenico
Published: May 2022

The need for habitat recovery in coastal areas, especially those subjected to intensive exploitation, has increased because of significant historical loss and alteration of habitats and, therefore, adverse ecological impacts. The present study defines a stepwise approach to mitigate habitat loss in deep coastal environments, describing the planning, intervention, and monitoring phases following the Trans Adriatic Pipeline (TAP) laying along the Apulian coast (Adriatic Sea, Italy). Preliminary field activities encompassed morpho-bathymetric data (MBES and SSS), SCUBA and ROV observations to accurately map and characterize the mesophotic reefs built by invertebrates found in the area. The pipeline route interfered with 30 outcrops between 50 and 80 m depth, mostly colonized by 15 taxa/morphological groups. A functional/conservative approach was adopted to recognize the taxa/morphological groups on which to focus the removal and following relocation activities based on their abundance, conservation status, and functional traits. Saturation divers teams, ROV pilot technicians, and researchers collaborated to minimize the physical impact and the loss of organisms due to the pipeline installation. They relocated a total of 899 living portions (nuclei) from the 30 interfered reefs on the top of the pipeline. The following monitoring activities, carried out after fourteen months since the intervention, revealed a high mean survival rate (88.1%) and slight variations in the structure of the nuclei assemblages. This study represents a paradigmatic case of involvement and support of the private oil and gas sector to mitigate habitat loss in the Mediterranean Sea, and stresses the need for integrated management involving different stakeholders to mitigate the effects of the exploitation of marine resources through ante operam assessment and active restoration actions.
Comparative Study of Nitrogen Cycling Between a Bay With Riverine Input and a Bay Without Riverine Input, Inferred From Stable Isotopes
Authors: Chen Chunqing , Lao Qibin , Shen Youli , Jin Guangzhe , Chen Fajin , Su Qizhong , Lei Xuetie , Zhou Xin , Lu Xuan , Zhu Qingmei , Liu Guoqiang
Published: May 2022

The eutrophication degree in the coastal bay has been increasing significantly for the past years, due to the increasing nutrient discharge. However, the factors controlling sources and nitrogen (N) cycling in the different types of bays are still poorly understood. In this comparative study, nitrate dual isotopes (δ15N−NO3− and δ18O−NO3−) and ammonium nitrogen isotope (δ15N−NH4+), were used to determine the origin of nitrate in Qinzhou Bay (with riverine input) and Tieshangang Bay (without riverine input) in Beibu Gulf and to study biogeochemical processes associated with nitrogen cycling. The nutrient concentrations generally showed a decreased trend from the upper bay to the outer bay. The isotopic values in Tieshangang Bay were generally higher than that in the Qinzhou Bay, suggesting that there are differences in nitrate sources and transformation processes between the two bays. The dominant sources from manure and sewage (41%) and soil N (30%) from runoff input were responsible for the high nitrate observed in the upper Qinzhou Bay. Though manure and sewage (59%) were also dominant nitrate sources in the upper Tieshangang Bay, a decrease in source from soil N (20%) occurred due to less runoff input. Nutrients were retained in the upper Tieshangang Bay due to weak hydrodynamic conditions, which caused higher NH4+ concentrations in the upper bay. Significant nitrate loss occurred in the outer Qinzhou Bay, which was related to the intense hydrodynamic condition. Moreover, phytoplankton assimilation mainly utilized NH4+ due to sufficient NH4+ in the outer Qinzhou Bay. In contrast, nitrate loss was also found in the outer Tieshangang Bay, which is mainly related to the phytoplankton assimilation due to the weak hydrodynamic condition. In addition, the greater enrichment of δ18O−NO3− than δ15N−NO3− during both bays suggests that atmospheric deposition also contributes to the nitrate pool in the water and the impact of atmospheric deposition on the whole Beibu Gulf is relatively consistent. By this comparative study, we found that different nitrate biogeochemical processes occurred in these two types of bays, which were mainly determined by the difference of human activities and hydrodynamic conditions.
Dynamic Cause of the Sudden Death Event of Small Yellow Croaker (Larimichthys polyactis) in the East China Sea in Winter 2017
Authors: Wei Zilu , Jiao Xiaohui , Zhang Jicai , Du Yunfei , Rong Zengrui , Wu Hui , Wang Ya Ping
Published: May 2022

Small yellow croaker (Larimichthys polyactis), a benthic fish species widely distributed in the Northwest Pacific Ocean, plays an important role in the fishery catch of coastal countries. A large amount of dead small yellow croaker floated on the sea surface near 30.2°N, 125.3°E in the East China Sea on 19 February 2017, and more than 9,000 kilograms were caught by fishermen, which had never been recorded before. This study aims to investigate the dynamic causes of this sudden death event based on available in-situ, satellite and modelling data. The event occurred near the overwintering ground of small yellow croaker, where a majority of these fish assembled in winter. There were persistent ocean fronts at target site with average intensity of 0.05°C/km at sea surface and bottom in February 2017, which was the strongest in the past 5 years from 2015 to 2019. The fronts provided nutrients and food to fish, and the intense gradients prevented fish from crossing, thus forming “water barriers” to restrict the horizontal movement of fish. Due to enhanced convection, the water was well-mixed, enabling the demersal croaker to float to sea surface. The sea temperature was particularly warm in winter 2017, but then experienced a significant drop by more than 4.5°C in 40 days according to satellite and modelling datasets due to the northerly wind and the southeastward movement of cold eddy. The drop of temperature led to ‘cold shock’ of fish, affecting their physiological regulation and survival. Under the combined influence of these factors, a large number of small yellow croaker died and aggregated near the target site. This paper has a great reference value for further study on the living habits of small yellow croaker and their responses to marine dynamic changes.
Surface Form Accuracy Evaluation in Abrasive Lapping of Single-Crystal Silicon Wafers
Authors: Wang Zhengwei , Lei Yang , Wu Xiaofeng
Published: May 2022

Silicon-based materials still dominate the current semiconductor industry for the foreseeable years such that it is needed in continuously developing the related advanced manufacturing technologies. For the abrasive precision lapping of single-crystal silicon wafers, the surface form accuracy is very important which can significantly improve its efficiency and reduce the cost in the following ultra-precision polishing process. In this study, a novel driving system is proposed in the single-side planetary lapping process that could realize the irrational rotation speed ratio of the lapping plate to the workpiece, and it is found from the numerical qualitative and quantitative analysis that the uniformity of the particle trajectories moving on the target surface has been significantly improved using the irrational rotation speed ratio and hence resulting in the higher surface form accuracy than that driven by the rational rotation speed ratio. Moreover, an in-house developed irrational rotation speed ratio driving system has been designed for the experimental study, and it is found that the effect of the rational and irrational rotation speed ratios on surface roughness is not significant, while all the five essential values related to the surface form accuracy are better under the rotation speed ratio of i = 1.0772… than that under the rotation speed ratio of i = 1, which demonstrates that the irrational rotation speed ratio driving system has the advantage of being able to obtain a good surface form accuracy and agrees well with the numerical simulation results.
Related Effects of Methamphetamine on the Intestinal Barrier via Cytokines, and Potential Mechanisms by Which Methamphetamine May Occur on the Brain-Gut Axis
Authors: Li Yuansen , Kong Deshenyue , Bi Ke , Luo Huayou
Published: May 2022

Methamphetamine (METH) is an illegal drug widely abused in many countries. Methamphetamine abuse is a major health and social problem all over the world. However, the effects of METH on the digestive system have rarely been reported. Previous studies and clinical cases have shown that METH use can lead to the impaired intestinal barrier function and severe digestive diseases. METH can cause multiple organ dysfunction, especially in the central nervous system (CNS). The gut microbiota are involved in the development of various CNS-related diseases via the gut-brain axis (GBA). Here, we describe the related effects of METH on the intestinal barrier via cytokines and the underlying mechanisms by which METH may occur in the brain-gut axis.
Stress and Pain. Predictive (Neuro)Pattern Identification for Chronic Back Pain: A Longitudinal Observational Study
Authors: Wippert Pia-Maria , Puerto Valencia Laura , Drießlein David
Published: May 2022

Introduction

Low back pain (LBP) leads to considerable impairment of quality of life worldwide and is often accompanied by psychosomatic symptoms.

Objectives

First, to assess the association between stress and chronic low back pain (CLBP) and its simultaneous appearance with fatigue and depression as a symptom triad. Second, to identify the most predictive stress-related pattern set for CLBP for a 1-year diagnosis.

Methods

In a 1-year observational study with four measurement points, a total of 140 volunteers (aged 18–45 years with intermittent pain) were recruited. The primary outcomes were pain [characteristic pain intensity (CPI), subjective pain disability (DISS)], fatigue, and depressive mood. Stress was assessed as chronic stress, perceived stress, effort reward imbalance, life events, and physiological markers [allostatic load index (ALI), hair cortisol concentration (HCC)]. Multiple linear regression models and selection procedures for model shrinkage and variable selection (least absolute shrinkage and selection operator) were applied. Prediction accuracy was calculated by root mean squared error (RMSE) and receiver-operating characteristic curves.

Results

There were 110 participants completed the baseline assessments (28.2 ± 7.5 years, 38.1% female), including HCC, and a further of 46 participants agreed to ALI laboratory measurements. Different stress types were associated with LBP, CLBP, fatigue, and depressive mood and its joint occurrence as a symptom triad at baseline; mainly social-related stress types were of relevance. Work-related stress, such as “excessive demands at work”[b = 0.51 (95%CI -0.23, 1.25), p = 0.18] played a role for upcoming chronic pain disability. “Social overload” [b = 0.45 (95%CI -0.06, 0.96), p = 0.080] and “over-commitment at work” [b = 0.28 (95%CI -0.39, 0.95), p = 0.42] were associated with an upcoming depressive mood within 1-year. Finally, seven psychometric (CPI: RMSE = 12.63; DISS: RMSE = 9.81) and five biomarkers (CPI: RMSE = 12.21; DISS: RMSE = 8.94) could be derived as the most predictive pattern set for a 1-year prediction of CLBP. The biomarker set showed an apparent area under the curve of 0.88 for CPI and 0.99 for DISS.

Conclusion

Stress disrupts allostasis and favors the development of chronic pain, fatigue, and depression and the emergence of a “hypocortisolemic symptom triad,” whereby the social-related stressors play a significant role. For translational medicine, a predictive pattern set could be derived which enables to diagnose the individuals at higher risk for the upcoming pain disorders and can be used in practice.
Eosinophilic Granulomatosis With Polyangiitis Presenting With Oral Granuloma as the Initial Symptom: A Case Report
Authors: Lin Lirong , Yu Rongjie , Zheng Luquan , Gong Shuyu , Yang Jurong
Published: May 2022

Antineutrophil cytoplasmic antibody associated vasculitis includes granulomatosis with polyangiitis, eosinophilic granulomatosis with polyangiitis (EGPA), and microscopic polyangiitis. While EGPA has no specific symptoms, it usually presents as necrotizing vasculitis, eosinophil infiltration of the tissues and organs, and extravascular granuloma formation. Here, we report a patient who had a rare initial presentation of oral granuloma and had been previously misdiagnosed several times at other hospitals. He was finally diagnosed with EGPA and recovered after methylprednisolone and cyclophosphamide treatment. The disease EGPA can present with a rare initial presentation of oral granuloma, methylprednisolone, and cyclophosphamide can be a suitable choice of treatment.
Predictive and Prognostic Roles of Gut Microbial Variation in Liver Transplant
Authors: Wong Hon Jen , Lim Wen Hui , Ng Cheng Han , Tan Darren Jun Hao , Bonney Glenn K. , Kow Alfred W. C. , Huang Daniel Q. , Siddiqui Mohammad Shadab , Noureddin Mazen , Syn Nicholas , Muthiah Mark D.
Published: May 2022

Patients undergoing liver transplant (LTX) typically confront a challenging postoperative journey. A dysbiotic gut microbiome is associated with the development of complications, including post-LTX allograft rejection, metabolic diseases and de novo or recurrent cancer. A major explanation of this are the bipartite interactions between the gut microbiota and host immunity, which modulates the alloimmune response towards the liver allograft. Furthermore, bacterial translocation from dysbiosis causes pathogenic changes in the concentrations of microbial metabolites like lipopolysaccharides, short-chain fatty acids (SCFAs) and Trimethylamine-N-Oxide, with links to cardiovascular disease development and diabetes mellitus. Gut dysbiosis also disrupts bile acid metabolism, with implications for various post-LTX metabolic diseases. Certain taxonomy of microbiota such as lactobacilli, F.prausnitzii and Bacteroides appear to be associated with these undesired outcomes. As such, an interesting but as yet unproven hypothesis exists as to whether induction of a “beneficial” composition of gut microbiota may improve prognosis in LTX patients. Additionally, there are roles of the microbiome as predictive and prognostic indicators for clinicians in improving patient care. Hence, the gut microbiome represents an exceptionally exciting avenue for developing novel prognostic, predictive and therapeutic applications.
The Gut Microbiota of Healthy and Flavobacterium psychrophilum-Infected Rainbow Trout Fry Is Shaped by Antibiotics and Phage Therapies
Authors: Donati Valentina Laura , Madsen Lone , Middelboe Mathias , Strube Mikael Lenz , Dalsgaard Inger
Published: May 2022

In the aquaculture sector, there is an increased interest in developing environmentally friendly alternatives to antibiotics in the treatment and prevention of bacterial infections. This requires an understanding of the effects of different treatments on the fish microbiota as a measure for improving the fish health status. In this study, we focused on the freshwater pathogen Flavobacterium psychrophilum and investigated the effects of antibiotics (florfenicol) and phage therapies on the gut microbiota of healthy and infected rainbow trout fry (1–2 g). Florfenicol-coated feed was administered for 10 days, starting two days after the infection procedure. A two-component mix of phage targeting F. psychrophilum (FpV4 and FPSV-D22) was continuously delivered by feed with a prophylactic period of 12 days. Samples of the distal intestine were collected over time (day -1 and 1, 8, and 33 days post-infection) and analyzed by community analysis targeting the 16S rRNA gene (V3–V4 region). Results showed the dysbiosis effect caused both by the infection and by florfenicol administration. Shifts in the overall composition were detected by β-diversity analysis, and changes in specific populations were observed during taxonomic mapping. Measures of α-diversity were only affected in infected fish (large variation observed 1 and 8 dpi). These community alterations disappeared again when fish recovered from the infection and the antibiotic treatment was terminated (33 dpi). Interestingly, phage addition altered the microbiota of the fish independently of the presence of their target bacterium. The overall gut bacterial community in fish fed phage-treated feed was different from the controls at each time point as revealed by β-diversity analysis. However, it was not possible to identify specific bacterial populations responsible for these changes except for an increase of lactic acid bacteria 33 dpi. Overall, the results indicate that the administered phages might affect the complex network of phage-bacteria interactions in the fish gut. Nevertheless, we did not observe negative effects on fish health or growth, and further studies should be directed in understanding if these changes are beneficial or not for the fish health with an additional focus on the host immune response.
Development of Phage Cocktails to Treat E. coli Catheter-Associated Urinary Tract Infection and Associated Biofilms
Authors: Sanchez Belkys C. , Heckmann Emmaline R. , Green Sabrina I. , Clark Justin R. , Kaplan Heidi B. , Ramig Robert F. , Muldrew Kenneth L. , Hines-Munson Casey , Skelton Felicia , Trautner Barbara W. , Maresso Anthony W.
Published: May 2022

High rates of antimicrobial resistance and formation of biofilms makes treatment of Escherichia coli catheter-associated urinary tract infections (CAUTI) particularly challenging. CAUTI affect 1 million patients per year in the United States and are associated with morbidity and mortality, particularly as an etiology for sepsis. Phage have been proposed as a potential therapeutic option. Here, we report the development of phage cocktails that lyse contemporary E. coli strains isolated from the urine of patients with spinal cord injury (SCI) and display strong biofilm-forming properties. We characterized E. coli phage against biofilms in two in vitro CAUTI models. Biofilm viability was measured by an MTT assay that determines cell metabolic activity and by quantification of colony forming units. Nine phage decreased cell viability by >80% when added individually to biofilms of two E. coli strains in human urine. A phage cocktail comprising six phage lyses 82% of the strains in our E. coli library and is highly effective against young and old biofilms and against biofilms on silicon catheter materials. Using antibiotics together with our phage cocktail prevented or decreased emergence of E. coli resistant to phage in human urine. We created an anti-biofilm phage cocktail with broad host range against E. coli strains isolated from urine. These phage cocktails may have therapeutic potential against CAUTI.
Comparative Analysis of Metagenomics and Metataxonomics for the Characterization of Vermicompost Microbiomes
Authors: Pérez-Losada Marcos , Narayanan Dhatri Badri , Kolbe Allison R. , Ramos-Tapia Ignacio , Castro-Nallar Eduardo , Crandall Keith A. , Domínguez Jorge
Published: May 2022

The study of microbial communities or microbiotas in animals and environments is important because of their impact in a broad range of industrial applications, diseases and ecological roles. High throughput sequencing (HTS) is the best strategy to characterize microbial composition and function. Microbial profiles can be obtained either by shotgun sequencing of genomes, or through amplicon sequencing of target genes (e.g., 16S rRNA for bacteria and ITS for fungi). Here, we compared both HTS approaches at assessing taxonomic and functional diversity of bacterial and fungal communities during vermicomposting of white grape marc. We applied specific HTS workflows to the same 12 microcosms, with and without earthworms, sampled at two distinct phases of the vermicomposting process occurring at 21 and 63 days. Metataxonomic profiles were inferred in DADA2, with bacterial metabolic pathways predicted via PICRUSt2. Metagenomic taxonomic profiles were inferred in PathoScope, while bacterial functional profiles were inferred in Humann2. Microbial profiles inferred by metagenomics and metataxonomics showed similarities and differences in composition, structure, and metabolic function at different taxonomic levels. Microbial composition and abundance estimated by both HTS approaches agreed reasonably well at the phylum level, but larger discrepancies were observed at lower taxonomic ranks. Shotgun HTS identified ~1.8 times more bacterial genera than 16S rRNA HTS, while ITS HTS identified two times more fungal genera than shotgun HTS. This is mainly a consequence of the difference in resolution and reference richness between amplicon and genome sequencing approaches and databases, respectively. Our study also revealed great differences and even opposite trends in alpha- and beta-diversity between amplicon and shotgun HTS. Interestingly, amplicon PICRUSt2-imputed functional repertoires overlapped ~50% with shotgun Humann2 profiles. Finally, both approaches indicated that although bacteria and fungi are the main drivers of biochemical decomposition, earthworms also play a key role in plant vermicomposting. In summary, our study highlights the strengths and weaknesses of metagenomics and metataxonomics and provides new insights on the vermicomposting of white grape marc. Since both approaches may target different biological aspects of the communities, combining them will provide a better understanding of the microbiotas under study.