bluuebunny/crossref_metadata_2025 huggingface dataset:
Recent advances in neuropeptide-related omics and gene editing: Spotlight on NPY and somatostatin and their roles in growth and food intake of fish
Authors: Yu Xiaozheng , Yan Haijun , Li Wensheng
Published: October 2022

Feeding and growth are two closely related and important physiological processes in living organisms. Studies in mammals have provided us with a series of characterizations of neuropeptides and their receptors as well as their roles in appetite control and growth. The central nervous system, especially the hypothalamus, plays an important role in the regulation of appetite. Based on their role in the regulation of feeding, neuropeptides can be classified as orexigenic peptide and anorexigenic peptide. To date, the regulation mechanism of neuropeptide on feeding and growth has been explored mainly from mammalian models, however, as a lower and diverse vertebrate, little is known in fish regarding the knowledge of regulatory roles of neuropeptides and their receptors. In recent years, the development of omics and gene editing technology has accelerated the speed and depth of research on neuropeptides and their receptors. These powerful techniques and tools allow a more precise and comprehensive perspective to explore the functional mechanisms of neuropeptides. This paper reviews the recent advance of omics and gene editing technologies in neuropeptides and receptors and their progresses in the regulation of feeding and growth of fish. The purpose of this review is to contribute to a comparative understanding of the functional mechanisms of neuropeptides in non-mammalians, especially fish.
Identifying the effects of the stability of farmland transfer management rights on the use of organic fertilizer with different farmland scales and crop types
Authors: Zhou Laiyou , Lu Hua , Wu Boying
Published: October 2022

Encouraging farmers to protect the quality of arable land is a focus of the current Chinese government. Enhancing the stability of arable land property rights is considered by the academic community to be an effective way to do so. Based on the survey data of 723 households in the hilly area of Jiangxi Province and using the probit model and robustness test methods, this paper examines the effect of stable farmland transfer management rights on farmers’ use of organic fertilizer and the differences in this effect with different management scales and crop types. The results show that stable management farmland transfer rights significantly encourage farmers to use organic fertilizer. Specifically, signing a written formal contract, increasing the contract registration rate, and extending contracts’ duration can increase farmers’ probability of using organic fertilizer, but whether there is a dispute in a farmland transfer has no significant impact on farmers using organic fertilizer. This study also finds that the impacts of stable arable land transfer management rights vary based on different characteristics of farmers using organic fertilizer. Stable arable land transfer management rights can encourage large-scale farmers and farmers planting grain crops to use organic fertilizer. To increase the stability of these rights, the local government should encourage farmers to sign formal written contracts, standardize their registration, and extend their duration.
The wet scavenging of air pollutants through artificial precipitation enhancement: A case study in the Yangtze River Delta
Authors: Wu Yixuan , Wang Yuying , Zhou Yuquan , Liu Xiaoli , Tang Yahui , Wang Yuxiang , Zhang Rui , Li Zhanqing
Published: October 2022

In this study, the impact of artificial precipitation enhancement operation on the wet scavenging of air pollutants is investigated based on an aircraft precipitation enhancement operation in the Yangtze River Delta region of China on 1 November 2020. Multiple measurement data are used, including the regional meteorological and environmental data and the comprehensive field observation data at the Nanjing University of Information Science and Technology (NUIST) campus site. The results show that the affected areas of this operation cover part of Anhui and Jiangsu provinces. The precipitation ratio between the target and contrast areas is always greater than 1, indicating the effectiveness of the seeding operation of silver iodide for precipitation enhancement. The regional analysis of air pollutants suggests that the enhanced precipitation can prevent the increase of air pollutants, especially for the particulate matter. The impact of enhanced precipitation on regional trace gases is complex because they are easily affected by the primary emissions. More data analysis at NUIST indicates that two cloud layers appear before the precipitation and merge into one thick cloud layer during the precipitation likely due to the impact of catalysis operation on the upper cloud. After the precipitation, the number concentration of aerosols with a diameter lower than 300 nm reduces significantly, the mass concentration of particulate matter with an aerodynamic diameter less than 2.5 μm decreases by about 39%, and the mass concentrations of nitrogen dioxide, sulfur dioxide, and carbon monoxide also decrease in different degrees. These results indicate that it is effective to reduce air pollutants by artificial precipitation enhancement. More studies are needed in the future.
Multi-environment factors dominate plant community structure and diversity in an ombrotrophic bog: The water level is the main regulating mechanism
Authors: Li Yue , Wang Xue , He Chunguang , Jiang Haibo , Sheng Lianxi
Published: October 2022

Understanding the relationship between vegetation and the environment is critical to manage bog ecosystems. However, information on how environmental factors influence the species composition and diversity in the ombrotrophic bog of Northeast China is lacking. Here, we investigated species compositions and environmental characteristics (water level, water conductivity, soil moisture content, bulk density, pH, organic carbon, total nitrogen, total phosphorous) from five sample sites along the water level gradients (the water level is below the surface, near the surface, and above the surface). Plant communities presented a patchy distribution pattern along the environmental gradients and could be divided into five types of communities. Moreover, the distribution of plant communities was mainly determined by water level, water conductivity, soil moisture content, pH, and organic carbon, which significantly explained 32.2%, 30.9%, 29.7%, 29.1%, and 22.5% of the variation in floristic composition. Among these factors, water level was the dominant factor influencing the distribution of plant communities. The partial least squares path model analysis showed that water level could influence plant diversity through different pathways, which could directly affect plant diversity and indirectly affect by changing water chemistry and soil properties. Additionally, soil pH contributed most to the indirect effects of water level on plant diversity. Thus, this study highlighted the high dependence of plant communities on water level and environmental factors driven by water level in ombrotrophic bogs, which provided some valuable implications for regional vegetation restoration and plant community stability.
Assessing the effectiveness of innovative city pilots in improving urban carbon emission performance: A spatial difference-in-difference approach
Authors: Yu Chenyang , Long Hongyu , Tu Chenglin , Tan Yuanfang , Zang Chuanxiang , Zhou Yu
Published: October 2022

Existing studies have focused on the impact of innovation on carbon emission performance but ignore the importance of government support for innovation. To overcome this challenge, this paper adopts a spatial difference-in-difference (DID) model to assess the impact of government support for innovation on urban carbon emission performance based on a quasi-natural experiment of innovative city pilots (ICP) in China. Using the high-resolution carbon emission data of 1 km × 1 km for 238 cities from 2008 to 2019 in China, this paper employees an extended stochastic frontier analysis (SFA) model to measure urban carbon emission performance. Our findings indicate that ICP implementation leads to a 1.3% improvement in local carbon emission performance. Meanwhile, there is a significant spatial spillover effect of ICP implementation, with a 3.3% improvement in the carbon performance of the surrounding areas. The results of the mechanism analysis suggest that government innovation support affects carbon emission performance by promoting total factor productivity improvement, green innovation, and industrial upgrading. Further analysis shows that ICP has the strongest impact on carbon performance in the eastern region, and the impact is stronger for large cities and resource-dependent cities. Finally, the paper carries out a series of robustness tests to ensure the reliability of the analytical results, including parallel trend tests, placebo tests and re-estimation of different methods. Based on the findings, this paper proposes feasible policy recommendations in terms of continuous promotion of government innovation support, regional cooperation and differentiated innovation support formulation.
Spatio-temporal pattern and allocation efficiency of public service land in rural settlements
Authors: Zheng Qiuyue , Jiang Guanghui , Tian Yaya , Meng Liang , Yang Lei
Published: October 2022

The construction of infrastructure and public services is the core of countryside planning. As the carrier of rural public services, the evolutionary pattern and efficiency of rural public service land (RPSL) can directly reflect the development of rural public services. However, existing studies have mainly characterized public service space through the number of public service facilities rather than the area of land occupied. Furthermore, research on public service land in rural settlements is lacking. Taking 273 villages in the Pinggu District of Beijing as an example, this article integrated multi-dimensional data, including geospatial data, big data, and socio-economic data, to analyze the spatio-temporal evolution characteristics of RPSL from 2004 to 2019. The bi-dimensional allocation efficiency index addressing qualitative and quantitative development was introduced to measure the allocation efficiency of RPSL. The results show that the area of RPSL in Pinggu District has increased by 57.28 ha, and the internal land use structure of RPSL has become balanced. The evolution pattern of RPSL was characterized by both agglomeration and dispersion, as well as by a significant tendency to expand along main roads. The uneven distribution of public service facilities and the significant differences in accessibility reflected the non-equalization of public services. The allocation efficiency of RPSL in 79.23% of the villages was at a low level, which is mainly due to the mismatch between the rural public service land area and the population, the non-differentiated allocation of public service facilities, the uneven public service quality, and the low accessibility of RPSL. In the future, policymakers should plan rural public service land rationally from the perspective of the actual situation, such as setting flexible indicators, building a living circle of rural settlements, and so on. This research will not only enrich the research perspective of rural public services but also provide a reference for the study on the utilization and optimization of rural settlements.
Host community composition, community assembly pattern, and disease transmission mode jointly determine the direction and strength of the diversity-disease relationship
Authors: Chen Lifan , Kong Ping , Hou Liying , Zhou Yanli , Zhou Liang
Published: October 2022

Rapid global biodiversity loss and increasing emerging infectious diseases underscore the significance of identifying the diversity-disease relationship. Although experimental evidence supports the existence of dilution effects in several natural ecosystems, we still know very little about the conditions under which a dilution effect will occur. Using a multi-host Susceptible-Infected-Recovered model, we found when disease transmission was density-dependent, the diversity-disease relationship could exhibit an increasing, decreasing, or non-monotonic trend, which mainly depended on the patterns of community assembly. However, the combined effects of the host competence-abundance relationship and species extinction order may reverse or weaken this trend. In contrast, when disease transmission was frequency-dependent, the diversity-disease relationship only showed a decreasing trend, the host competence-abundance relationship and species extinction order did not alter this decreasing trend, but it could reduce the detectability of the dilution effect and affect disease prevalence. Overall, a combination of disease transmission mode, community assembly pattern, and host community composition determines the direction or strength of the diversity-disease relationship. Our work helps explain why previous studies came to different conclusions about the diversity-disease relationship and provides a deeper understanding of the pathogen transmission dynamics in actual communities.
Expression, oncological and immunological characterizations of BZW1/2 in pancreatic adenocarcinoma
Authors: Ge Jiachen , Mu Senmao , Xiao Erwei , Tian Guangjin , Tao Lianyuan , Li Deyu
Published: October 2022

Background: Despite the progress in early diagnosis and treatment, prognosis of pancreatic adenocarcinoma (PAAD) is still poor. Basic leucine zipper and W2 domain-containing protein 1 (BZW1) and protein 2 (BZW2) are attached to the basic leucine zipper (bZIP) superfamily. Recently, BZW1 was identified as an important role in glycolysis of PAAD. However, the comprehensive reports about BZW1/2 in PAAD are not sufficient.

Methods: RNA-seq data in the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases were retrospectively analyzed. We explored the expression of BZW1/2 in PAAD tissues and the associations between BZW1/2 and prognosis. In addition, the potential roles of BZW1/2 in tumor microenvironment (TME) of PAAD were analyzed. Finally, clinicopathological data of 49 patients with PAAD in our institution were collected. Immunohistochemistry was used to determine the expression of BZW1/2 in PAAD samples.

Results: BZW1 and BZW2 were upregulated in PAAD tissues compared to normal tissues (p < 0.05). The expression of BZW1/2 were not significantly correlated with gender, grade and stage of PAAD (p > 0.05). High expression of BZW2 was an independent predictor for poor prognosis of PAAD (HR 1.834, 95%CI 1.303–2.581, p = 0.001). And a nomogram to predict overall survival (OS) of PAAD was established with a C-index of 0.685. BZW1 and BZW2 expression were positively associated with T cell mediated immune response to tumor cell and Th2 cells in xCell database. Tumor Immune Single-Cell Hub (TISCH) analyses indicated that BZW1 and BZW2 were mainly expressed in B cells and malignant cells. External cohort furtherly validated that high expression of BZW1 and BZW2 were predictors for poor prognosis of PAAD.

Conclusion: We found that BZW1 and BZW2 are highly expressed in malignant cells and B cells in the TME of PAAD. BZW2 is an independent predictor for OS of PAAD. BZW1 and BZW2 expression are positively associated with T cell mediated immune response to tumor cell and Th2 cells in PAAD.
Immune-related gene risk score predicting the effect of immunotherapy and prognosis in bladder cancer patients
Authors: Zou Yuantao , Yuan Gangjun , Tan Xingliang , Luo Sihao , Yang Cong , Tang Yi , Wang Yanjun , Yao Kai
Published: October 2022

Background: Immune checkpoint inhibitor therapy has changed the treatment model of metastatic bladder cancer. However, only approximately 20% of patients benefit from this therapy, and robust biomarkers to predict the effect of immunotherapy are still lacking. In this study, we aimed to investigate whether immune-related genes could be indicators for the prognosis of bladder cancer patients and the effect of immunotherapy.

Methods: Based on bladder cancer dataset from the Cancer Genome Atlas (TCGA) and GSE48075, 22 immune microenvironment-related cells were identified by CIBERSORT. After performing a series of bioinformatic and machine learning approaches, we identified distinct tumor microenvironment clusters and three bladder cancer specific immune-related genes (EGFR, OAS1 and MST1R). Then, we constructed immune-related gene risk score (IRGRS) by using the Cox regression method and validated it with the IMvigor210 dataset.

Results: IRGRS-high patients had a worse overall survival than IRGRS-low patients, which was consistent with the result in the IMvigor210 dataset. Comprehensive analysis shows that patients with high IRGRS scores are mainly enriched in basal/squamous type (Ba/Sq), and tumor metabolism-related pathways are more Active, with higher TP53 and RB1 gene mutation rates, lower CD4+/CD8+ T cell infiltration, higher M0 macrophage infiltration, and lower immunotherapy efficacy. In contrast, Patients with low IRGRS scores are mainly enriched in the luminal papillary type (LumP), which is associated with the activation of IL-17 and TNF signaling pathways, higher mutation rates of FGFR3 and CDKN1A genes, higher CD4+/CD8+ T cell infiltration content, and The level of M0 macrophage infiltration was relatively low, and the immunotherapy was more probably effective.

Conclusion: Our study constructed an IRGRS for bladder cancer and clarified the immune and molecular characteristics of IRGRS-defined subgroups of bladder cancer to investigate the association between IRGRS and its potential implications for prognosis and immunotherapy.
Genome-wide identification, characterization and expression of HSP 20 gene family in dove
Authors: Hou Zhe , Li Ang , Huang Changbing
Published: October 2022

Davidia involucrata is a significant living fossil with high abiotic stress tolerance. Although heat shock protein 20 (HSP20) has already been linked to heat stress, nothing is known about HSP20 family protein activities in D. involucrata. The functional dynamics of the D. involucrata HSP20 (DiHSP20) gene family were identified and characterized using a thorough genome-wide investigation. From the genome of D. involucrata, a total of 42 HSP20 genes were identified, which are distributed across 16 chromosomes. The DiHSP20 proteins were grouped into seven separate subfamilies by our phylogenetic analysis, which was validated by the conserved motif composition and gene structure studies. Segmental duplication events were shown to play a crucial role in the expansion of the DiHSP20 gene family. Synteny analysis revealed that 19 DiHSP20 genes of D. involucrata shared a syntenic connection with Arabidopsis genes, 39 with C. acuminata genes, and just 6 with O. sativa genes. Additionally, heat stress differently enhanced the expression levels of D. involucrata HSP20 genes. After 1 hour of heat treatment, the expression levels of most DiHSP20 genes, particularly DiHSP20-7, DiHSP20-29, DiHSP20-30, DiHSP20-32, and DiHSP20-34, were dramatically increased, suggestted that they might be employed as heat tolerance candidate genes. Overall, these findings add to our knowledge of the HSP20 family genes and provide helpful information for breeding heat stress resistance in D. involucrata.
Genetic regulation of newborn telomere length is mediated and modified by DNA methylation
Authors: Wang Congrong , Alfano Rossella , Reimann Brigitte , Hogervorst Janneke , Bustamante Mariona , De Vivo Immaculata , Plusquin Michelle , Nawrot Tim S. , Martens Dries S.
Published: October 2022

Telomere length at birth determines later life telomere length and potentially predicts ageing-related diseases. However, the genetic and epigenetic settings of telomere length in newborns have not been analyzed. In addition, no study yet has reported how the interplay between genetic variants and genome-wide cytosine methylation explains the variation in early-life telomere length. In this study based on 281 mother-newborn pairs from the ENVIRONAGE birth cohort, telomere length and whole-genome DNA methylation were assessed in cord blood and 26 candidate single nucleotide polymorphism related to ageing or telomere length were genotyped. We identified three genetic variants associated with cord blood telomere length and 57 cis methylation quantitative trait loci (cis-mQTLs) of which 22 mQTLs confirmed previous findings and 35 were newly identified. Five SNPs were found to have significant indirect effects on cord blood telomere length via the mediating CpGs. The association between rs911874 (SOD2) and newborn telomere length was modified by nearby DNA methylation indicated by a significant statistical interaction. Our results suggest that DNA methylation in cis might have a mediation or modification effect on the genetic difference in newborn telomere length. This novel approach warrants future follow-up studies that are needed to further confirm and extend these findings.
Bibliometric and visualization analysis of macrophages associated with osteoarthritis from 1991 to 2021
Authors: Yang Zhen , Lin Jianjing , Li Hui , He Zihao , Wang Kai , Lei Liandi , Li Hao , Xing Dan , Lin Jianhao
Published: October 2022

Background

Macrophages significantly contributes to symptomology and structural progression of osteoarthritis (OA) and raise increasing attention in the relative research field. Recent studies have shown that tremendous progress has been made in the research of macrophages associated with osteoarthritis. However, a comprehensive bibliometric analysis is lacking in this research field. This study aimed to introduce the research status as well as hotspots and explore the field of macrophages research in OA from a bibliometric perspective.

Methods

This study collected 1481 records of macrophages associated with osteoarthritis from 1991 to 2021 in the web of science core collection (WoSCC) database. CiteSpace, VOSviewer, and R package “bibliometrix” software were used to analyze regions, institutions, journals, authors, and keywords to predict the latest trends in macrophages associated with osteoarthritis research.

Results

The number of publications related to macrophages associated with osteoarthritis is increasing annually. China and the USA, contributing more than 44% of publications, were the main drivers for research in this field. League of European Research Universities was the most active institution and contributed the most publications. Arthritis and Rheumatism is the most popular journal in this field with the largest publications, while Osteoarthritis and Cartilage is the most co-cited journal. Koch AE was the most prolific writer, while Bondeson J was the most commonly co-cited author. “Rheumatology”, “Orthopedics”, and “Immunology” were the most widely well-represented research areas of OA associated macrophages. “Rheumatoid arthritis research”, “clinical symptoms”, “regeneration research”, “mechanism research”, “pathological features”, and “surgery research” are the primary keywords clusters in this field.

Conclusion

This is the first bibliometric study comprehensively mapped out the knowledge structure and development trends in the research field of macrophages associated with osteoarthritis in recent 30 years. The results comprehensively summarize and identify the research frontiers which will provide a reference for scholars studying macrophages associated with osteoarthritis.
GATA2 haploinsufficient patients lack innate lymphoid cells that arise after hematopoietic cell transplantation
Authors: van Lier Y. F. , Krabbendam L. , Haverkate N. J. E. , Zeerleder S. S. , Rutten C. E. , Blom B. , Spits H. , Hazenberg M. D.
Published: October 2022

Innate lymphoid cells (ILC) are important barrier tissue immune regulators. They play a pivotal role in early non-specific protection against infiltrating pathogens, regulation of epithelial integrity, suppression of pro-inflammatory immune responses and shaping the intestinal microbiota. GATA2 haploinsufficiency causes an immune disorder that is characterized by bone marrow failure and (near) absence of monocytes, dendritic cells, B cells and natural killer (NK) cells. T cells develop normally, albeit at lower numbers. Here, we describe the absence of ILCs and their progenitors in blood and bone marrow of two patients with GATA2 haploinsufficiency and show that all subsets of ILCs appear after allogeneic hematopoietic stem cell transplantation, irrespective of the preparative conditioning regimen. Our data indicate that GATA2 is involved in the development of hematopoietic precursor cells (HPC) towards the ILC lineage.
A real-world retrospective study of safety, efficacy, compliance and cost of combination treatment with rush immunotherapy plus one dose of pretreatment anti-IgE in Chinese children with respiratory allergies
Authors: Zhang Pingping , Bian Sainan , Wang Xibin , Chen Zhuanggui , Yang Lifen , Xiao Feng , Guan Kai
Published: October 2022

Background

The efficacy of allergen immunotherapy (AIT) in treating pediatric allergy has been clearly demonstrated, however, many patients hesitate to initiate AIT due to weekly hospital visits during the 3-4 months up-dosing phase. Meanwhile, rush immunotherapy (RIT) shortens the duration of the up-dosing phase to 7 days. However, considering that patients receiving RIT are exposed to the allergens during a much shorter period of time and thus may be at a greater risk of systemic reactions, RIT is currently underused, especially in children. This study investigated the utility of combination treatment with RIT plus 1 dose of pretreatment anti-IgE in children with respiratory allergies.

Methods

In this retrospective study, we reviewed records of children with allergic rhinitis (AR) and/or allergic asthma (AA) sensitized to dust mite allergens receiving RIT+1 dose of pretreatment anti-IgE (the RIT group) or conventional immunotherapy (the CIT group) at our hospital from January 2020 to March 2021. Data such as visual analogue scale (VAS) scores, comprehensive symptom and medication score (CSMS), allergy blood test results, adverse reactions, compliance and cost were collected and analyzed.

Results

40 patients in the RIT group and 81 patients in the CIT group were included in this study. Both treatments were well tolerated and patients in the 2 treatment groups had comparable local and systemic reactions. Compared to CIT, RIT + anti-IgE combination led to significantly faster symptomatic improvement as demonstrated by significantly decreased VAS and CSMS starting as early as 1 month after AIT initiation (P<0.05). Nobody dropped out in the RIT group during the 1 year follow-up, while 11 out of 81 patients in the CIT group dropped out (loss rate 13.5%). Thus, the RIT group had a significantly higher compliance rate than the CIT group (P<0.05). Finally, the 2 treatment regimens had comparable cost per patient per injection (P> 0.05).

Conclusions

RIT + 1 dose of pretreatment anti-IgE combination has practical advantages over CIT, including comparable safety, better compliance, and probably a faster onset of clinical efficacy at no additional cost, so it can be an useful regimen for the treatment of Chinese children with respiratory allergies.
Generalist in allogeneic hematopoietic stem cell transplantation for MDS or AML: Epigenetic therapy
Authors: Yang Guancui , Wang Xiang , Huang Shiqin , Huang Ruihao , Wei Jin , Wang Xiaoqi , Zhang Xi
Published: October 2022

Allogeneic hematopoietic stem cell transplantation (allo-HSCT) remains the only curative treatment for patients with myeloid malignancies such as myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). However, relapse and graft-versus-host disease (GvHD) still affect the survival of patients who receive allo-HSCT, and more appropriate therapeutic strategies should be applied at all stages of transplantation to prevent these adverse events. The use of epigenetics agents, such as hypomethylating agents (HMAs), has been explored to decrease the risk of relapse by epigenetic modulation, which is especially effective among AML patients with poor mutations in epigenetic regulators. Furthermore, epigenetic agents have also been regarded as prophylactic methods for GvHD management without abrogating graft versus leukemia (GvL) effects. Therefore, the combination of epigenetic therapy and HSCT may optimize the transplantation process and prevent treatment failure. Existing studies have investigated the feasibility and effectiveness of using HMAs in the pretransplant, transplant and posttransplant stages among MDS and AML patients. This review examines the application of HMAs as a bridge treatment to reduce the tumor burden and the determine appropriate dose during allo-HSCT. Within this review, we also examine the efficacy and safety of HMAs alone or HMA-based strategies in posttransplant settings for MDS and AML. Finally, we provide an overview of other epigenetic candidates, which have been discussed in the nontransplant setting.
In search of immune cellular sources of abnormal cytokines in the blood in autism spectrum disorder: A systematic review of case-control studies
Authors: Nour-Eldine Wared , Ltaief Samia M. , Abdul Manaph Nimshitha P. , Al-Shammari Abeer R.
Published: October 2022

Abnormal cytokine levels in circulating blood have been repeatedly reported in autism; however, the underlying cause remains unclear. This systematic review aimed to investigate cytokine levels in peripheral blood compartments and identify their potential immune cellular sources in subjects with autism through comparison with controls. We conducted an electronic database search (PubMed, Scopus, ProQuest Central, Ovid, SAGE Journals, and Wiley Online Library) from inception (no time limits) to July 9, 2020, and identified 75 relevant articles. Our qualitative data synthesis focused on results consistently described in at least three independent studies, and we reported the results according to the PRISMA protocol. We found that compared with controls, in subjects with autism, cytokines IL-6, IL-17, TNF-α, and IL-1β increased in the plasma and serum. We also identified monocytes, neutrophils, and CD4+ T cells as potential sources of these elevated cytokines in autism. Cytokines IFN-γ, TGF-β, RANTES, and IL-8 were increased in the plasma/serum of subjects with autism, and IFN-γwas likely produced by CD4+ T cells and natural killer (NK) cells, although conflicting evidence is present for IFN-γand TGF-β. Other cytokines—IL-13, IL-10, IL-5, and IL-4—were found to be unaltered in the plasma/serum and post-stimulated blood immune cells in autistic individuals as compared with controls. The frequencies of T cells, monocytes, B cells, and NK cells were unchanged in subjects with autism as opposed to controls, suggesting that abnormal cytokines were unlikely due to altered cell numbers but might be due to altered functioning of these cells in autism. Our results support existing studies of abnormal cytokines in autism and provide comprehensive evidence of potential cellular sources of these altered cytokines in the context of autism.

Systematic Review Registration

https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42020205224, identifier [CRD42020205224].
Uncovering the core principles of the gut-lung axis to enhance innate immunity in the chicken
Authors: Saint-Martin Vincent , Quéré Pascale , Trapp Sascha , Guabiraba Rodrigo
Published: October 2022

Research in mammals has evidenced that proper colonization of the gut by a complex commensal microbial community, the gut microbiota (GM), is critical for animal health and wellbeing. It greatly contributes to the control of infectious processes through competition in the microbial environment while supporting proper immune system development and modulating defence mechanisms at distant organ sites such as the lung: a concept named ‘gut-lung axis’. While recent studies point to a role of the GM in boosting immunity and pathogen resilience also in poultry, the mechanisms underlying this role are largely unknown. In spite of this knowledge gap, GM modulation approaches are today considered as one of the most promising strategies to improve animal health and welfare in commercial poultry production, while coping with the societal demand for responsible, sustainable and profitable farming systems. The majority of pathogens causing economically important infectious diseases in poultry are targeting the respiratory and/or gastrointestinal tract. Therefore, a better understanding of the role of the GM in the development and function of the mucosal immune system is crucial for implementing measures to promote animal robustness in commercial poultry production. The importance of early gut colonization in the chicken has been overlooked or neglected in industrial poultry production systems, where chicks are hampered from acquiring a complex GM from the hen. Here we discuss the concept of strengthening mucosal immunity in the chicken through GM modulation approaches favouring immune system development and functioning along the gut-lung axis, which could be put into practice through improved farming systems, early-life GM transfer, feeding strategies and pre-/probiotics. We also provide original data from experiments with germ-free and conventional chickens demonstrating that the gut-lung axis appears to be functional in chickens. These key principles of mucosal immunity are likely to be relevant for a variety of avian diseases and are thus of far-reaching importance for the poultry sector worldwide.
Waves of layered immunity over innate lymphoid cells
Authors: Kogame Toshiaki , Egawa Gyohei , Nomura Takashi , Kabashima Kenji
Published: October 2022

Innate lymphoid cells (ILCs) harbor tissue-resident properties in border zones, such as the mucosal membranes and the skin. ILCs exert a wide range of biological functions, including inflammatory response, maintenance of tissue homeostasis, and metabolism. Since its discovery, tremendous effort has been made to clarify the nature of ILCs, and scientific progress revealed that progenitor cells of ILC can produce ILC subsets that are functionally reminiscent of T-cell subsets such as Th1, Th2, and Th17. Thus, now it comes to the notion that ILC progenitors are considered an innate version of naïve T cells. Another important discovery was that ILC progenitors in the different tissues undergo different modes of differentiation pathways. Furthermore, during the embryonic phase, progenitor cells in different developmental chronologies give rise to the unique spectra of immune cells and cause a wave to replenish the immune cells in tissues. This observation leads to the concept of layered immunity, which explains the ontology of some cell populations, such as B-1a cells, γδ T cells, and tissue-resident macrophages. Thus, recent reports in ILC biology posed a possibility that the concept of layered immunity might disentangle the complexity of ILC heterogeneity. In this review, we compare ILC ontogeny in the bone marrow with those of embryonic tissues, such as the fetal liver and embryonic thymus, to disentangle ILC heterogeneity in light of layered immunity.
Upregulation of microRNA-125b-5p alleviates acute liver failure by regulating the Keap1/Nrf2/HO-1 pathway
Authors: Tao Ya-Chao , Wang Yong-Hong , Wang Meng-Lan , Jiang Wei , Wu Dong-Bo , Chen En-Qiang , Tang Hong
Published: October 2022

Background

Acute liver failure (ALF) and acute-on-chronic liver failure (ACLF) are the two most common subtypes of liver failure. They are both life-threatening clinical problems with high short-term mortality. Although liver transplantation is an effective therapeutic, its application is limited due to the shortage of donor organs. Given that both ACLF and ALF are driven by excessive inflammation in the initial stage, molecules targeting inflammation may benefit the two conditions. MicroRNAs (miRNAs) are a group of small endogenous noncoding interfering RNA molecules. Regulation of miRNAs related to inflammation may serve as promising interventions for the treatment of liver failure.

Aims

To explore the role and mechanism of miR-125b-5p in the development of liver failure.

Methods

Six human liver tissues were categorized into HBV-non-ACLF and HBV-ACLF groups. Differentially expressed miRNAs (DE-miRNAs) were screened and identified through high-throughput sequencing analysis. Among these DE-miRNAs, miR-125b-5p was selected for further study of its role and mechanism in lipopolysaccharide (LPS)/D-galactosamine (D-GalN) -challenged Huh7 cells and mice in vitro and in vivo.

Results

A total of 75 DE-miRNAs were obtained. Of these DE-miRNAs, miR-125b-5p was the focus of further investigation based on our previous findings and preliminary results. We preliminarily observed that the levels of miR-125b-5p were lower in the HBV-ACLF group than in the HBV-non-ACLF group. Meanwhile, LPS/D-GalN-challenged mice and Huh7 cells both showed decreased miR-125b-5p levels when compared to their untreated control group, suggesting that miR-125b-5p may have a protective role against liver injury, regardless of ACLF or ALF. Subsequent results revealed that miR-125b-5p not only inhibited Huh7 cell apoptosis in vitro but also relieved mouse ALF in vivo with evidence of improved liver histology, decreased alanine aminotransferase (ALT) and aspartate aminotransferase (AST) levels, and reduced tumor necrosis factor-α (TNF-α) and IL-1β levels. Based on the results of a biological prediction website, microRNA.org, Kelch-like ECH-associated protein 1 (Keap1) was predicted to be one of the target genes of miR-125b-5p, which was verified by a dual-luciferase reporter gene assay. Western blot results in vitro and in vivo showed that miR-125b-5p could decrease the expression of Keap1 and cleaved caspase-3 while upregulating the expression of nuclear factor (erythroid-derived 2)-like 2 (Nrf2) and heme oxygenase-1(HO-1).

Conclusion

Upregulation of miR-125b-5p can alleviate acute liver failure by regulating the Keap1/Nrf2/HO-1 pathway, and regulation of miR-125b-5p may serve as an alternative intervention for liver failure.
Development and validation of multivariable prediction models of serological response to SARS-CoV-2 vaccination in kidney transplant recipients
Authors: Osmanodja Bilgin , Stegbauer Johannes , Kantauskaite Marta , Rump Lars Christian , Heinzel Andreas , Reindl-Schwaighofer Roman , Oberbauer Rainer , Benotmane Ilies , Caillard Sophie , Masset Christophe , Kerleau Clarisse , Blancho Gilles , Budde Klemens , Grunow Fritz , Mikhailov Michael , Schrezenmeier Eva , Ronicke Simon
Published: October 2022

Repeated vaccination against SARS-CoV-2 increases serological response in kidney transplant recipients (KTR) with high interindividual variability. No decision support tool exists to predict SARS-CoV-2 vaccination response to third or fourth vaccination in KTR. We developed, internally and externally validated five different multivariable prediction models of serological response after the third and fourth vaccine dose against SARS-CoV-2 in previously seronegative, COVID-19-naïve KTR. Using 20 candidate predictor variables, we applied statistical and machine learning approaches including logistic regression (LR), least absolute shrinkage and selection operator (LASSO)-regularized LR, random forest, and gradient boosted regression trees. For development and internal validation, data from 590 vaccinations were used. External validation was performed in four independent, international validation cohorts comprising 191, 184, 254, and 323 vaccinations, respectively. LASSO-regularized LR performed on the whole development dataset yielded a 20- and 10-variable model, respectively. External validation showed AUC-ROC of 0.840, 0.741, 0.816, and 0.783 for the sparser 10-variable model, yielding an overall performance 0.812. A 10-variable LASSO-regularized LR model predicts vaccination response in KTR with good overall accuracy. Implemented as an online tool, it can guide decisions whether to modulate immunosuppressive therapy before additional active vaccination, or to perform passive immunization to improve protection against COVID-19 in previously seronegative, COVID-19-naïve KTR.
Crab contributions as an ecosystem engineer to sediment turnover in the Yellow River Delta
Authors: Xie Tian , Wang Andong , Li Shanze , Cui Baoshan , Bai Junhong , Shao Dongdong
Published: October 2022

Burrowing crabs are widely distributed and have large populations in estuarine wetlands. Crab excavation can have potentially significant bioturbation effects on the vertical structure of sediments, and the processes of nutrients deposition and mineralization. However, the effects of crab micro activities on the geochemical cycling processes of the whole estuarine ecosystems are not clear, specifically the contributions of burrowing crabs to sediment and nutrients turnover in coastal ecosystems. Due to the lack of knowledge on crab burrowing behavior and borrow morphology, it is difficult to accurately estimate the excavation and turnover volumes of crabs. Therefore, this study examined the bioturbation activity of the crab Helice tientsinensis in western Pacific estuary ecosystems by analyzing their burrow morphology and local sediment properties. The common burrow shapes of Helice tientsinensis were J- and Y-shaped burrows. Burrow morphological characteristics such as total burrow depth, curve burrow length, burrow volume, and opening diameter significantly differed among tidal zones. Crab carapace size, water depth, soil hardness, and bulk density were the main factors driving burrow morphology. Sediment excavation by crabs was ~50 times greater than the deposition of sediment into crab burrows. The net transported amounts of sediment (31.66–33.18 g·d-1·m-2) and nutrients (total nitrogen: 0.075–0.090 g·d-1·m-2, total carbon: 3.96–4.55 g·d-1·m-2, and organic matter: 0.44–0.77 g·d-1·m-2) were mainly from the belowground sediment to the surface. These results highlighted the important role of crabs in sediment and nutrients cycling within coastal estuary ecosystems.
More than a whistle: Automated detection of marine sound sources with a convolutional neural network
Authors: White Ellen L. , White Paul R. , Bull Jonathan M. , Risch Denise , Beck Suzanne , Edwards Ewan W. J.
Published: October 2022

The effective analysis of Passive Acoustic Monitoring (PAM) data has the potential to determine spatial and temporal variations in ecosystem health and species presence if automated detection and classification algorithms are capable of discrimination between marine species and the presence of anthropogenic and environmental noise. Extracting more than a single sound source or call type will enrich our understanding of the interaction between biological, anthropogenic and geophonic soundscape components in the marine environment. Advances in extracting ecologically valuable cues from the marine environment, embedded within the soundscape, are limited by the time required for manual analyses and the accuracy of existing algorithms when applied to large PAM datasets. In this work, a deep learning model is trained for multi-class marine sound source detection using cloud computing to explore its utility for extracting sound sources for use in marine mammal conservation and ecosystem monitoring. A training set is developed comprising existing datasets amalgamated across geographic, temporal and spatial scales, collected across a range of acoustic platforms. Transfer learning is used to fine-tune an open-source state-of-the-art ‘small-scale’ convolutional neural network (CNN) to detect odontocete tonal and broadband call types and vessel noise (from 0 to 48 kHz). The developed CNN architecture uses a custom image input to exploit the differences in temporal and frequency characteristics between each sound source. Each sound source is identified with high accuracy across various test conditions, including variable signal-to-noise-ratio. We evaluate the effect of ambient noise on detector performance, outlining the importance of understanding the variability of the regional soundscape for which it will be deployed. Our work provides a computationally low-cost, efficient framework for mining big marine acoustic data, for information on temporal scales relevant to the management of marine protected areas and the conservation of vulnerable species.
Understanding the effects of salinity and Vibrio harveyi on the gut microbiota profiles of Litopenaeus vannamei
Authors: Deris Zulaikha Mat , Iehata Shumpei , Gan Han Ming , Ikhwanuddin Mhd , Najiah Musa , Asaduzzaman Md , Wang Min , Liang Yantao , Danish-Daniel Muhd , Sung Yeong Yik , Wong Li Lian
Published: October 2022

Increasing evidence have revealed a positive correlation between gut microbiota and shrimp health, in which a healthy shrimp gut consists of a complex and stable microbial community. Given that both abiotic and biotic factors constantly regulate shrimp gut microbiota, any changes affecting the levels of these factors could cause modification to the gut microbiota assemblage. The goal of this study was to explore the effects of salinity levels and pathogenic Vibrio harveyi infection on the diversity, structure, composition, interspecies interaction, and functional pathways of Litopenaeus vannamei gut microbiota. Juvenile shrimp were cultured at 5 ppt, 20 ppt, and 30 ppt for two months prior to Vibrio harveyi infection. After pathogenic V. harveyi challenge test, genomic DNA was isolated from the shrimp gut, and subjected to the 16S rRNA metagenomic sequencing analysis. We observed that gut microbiota diversity of shrimp cultured at 5 ppt and 30 ppt were lower than those cultured at 20 ppt after exposure to V. harveyi infection, suggesting that shrimp cultured at the two former salinity levels were more susceptible to V. harveyi infection. Network analysis also showed that shrimp cultured at 20 ppt exhibit a more stable bacterial network with complex interspecies interaction, even after induced by V. harveyi. Moreover, the presence of a high number of beneficial bacteria such as Pseudoruegeria, Rhodovulum, Ruegeria, Shimia and Lactobacillus in shrimp cultured at 20 ppt might have played a role in inhibiting the growth of V. harveyi and other potentially pathogenic bacteria. Besides, bacterial functional pathway prediction has also shown that metabolic pathways such as phenylalanine metabolism, glycine, serine and threonine metabolism, starch and sucrose metabolism, glyoxylate and dicarboxylate metabolism, carbon metabolism and biofilm formation process were significantly higher in shrimp cultured at 20 ppt. Collectively, our results suggested that 20 ppt is an optimal salinity that suppresses the growth of V. harveyi and potential pathogenic bacteria in the shrimp gut, which could possibly minimize the risk of pathogenic infection for sustainable production of healthy shrimp.