bluuebunny/crossref_metadata_2025 huggingface dataset:
RCP8.5-projected changes in German Bight storm surge characteristics from regionalized ensemble simulations for the end of the twenty-first century
Authors: Mayer Bernhard , Mathis Moritz , Mikolajewicz Uwe , Pohlmann Thomas
Published: November 2022

This study investigates climate-induced changes in height, frequency and duration of storm surges in the German Bight. The regionally coupled climate model system MPIOM-REMO with a focus on the North Sea has been utilized to dynamically downscale 30 members of the global climate model system MPI-ESM1.1-LR for the historical period 1950–2005 and a continuation until 2099 with the RCP8.5 scenario. Results of all members have been collected into the historical (1970–1999) and the rcp85 (2070–2099) data pools amounting to 900 years of the corresponding climate state. The global mean sea level rise was not considered. Nevertheless, the mean ensemble German Bight SSH trend amounts to about 13 ± 1 cm/century (PI control: 3 cm/century) due to adaptation of the ocean circulation to the changing climatic conditions. Storm surges were defined as SSH above mean high tidal water plus 1.5, 2.5, 3.5 m for “regular”, heavy, extreme storm surges, and then clustered to events. Our simulated storm surge events show a clear location-dependent increase in frequency (6–11%), median duration (4–24%), and average duration (9–20%) in the German Bight. Only along the central German Bight coast (Cuxhaven), longer lasting events gain more relevance. Heavy storm surge events show also a strong increase in frequency (7–34%) and average duration (10–22%). Maximum sea levels during storm events increase strongest and most significant along the northern German Bight and Danish coasts with more than 30 cm/century for the 60-year return period at Hörnum and 10–15 cm/century for shorter return periods. Levels of return periods shorter than a few years significantly increase everywhere along the southern German Bight coasts (around 5 cm/century for the 2-year return period). Highest SSH maxima do not change, and consequently, extreme storm surge events show hardly any response to climate change. Furthermore, our results indicate a shift of seasonality from the last to the first quarter of a year. As the main driver for the encountered alteration of German Bight storm surge characteristics, we identified a change in wind conditions with a pronounced increase of frequency of strong westerly winds.
Gut microbiome sheds light on the development and treatment of abdominal aortic aneurysm
Authors: Ling Xuebin , Jie Wei , Qin Xue , Zhang Shuya , Shi Kaijia , Li Tianfa , Guo Junli
Published: November 2022

Abdominal aortic aneurysm (AAA) is an inflammatory vascular disease with high disability and mortality. Its susceptible risk factors include old age, being male, smoking, hypertension, and aortic atherosclerosis. With the improvement of screening techniques, AAA incidence and number of deaths caused by aneurysm rupture increase annually, attracting much clinical attention. Due to the lack of non-invasive treatment, early detection and development of novel treatment of AAA is an urgent clinical concern. The pathophysiology and progression of AAA are characterized by inflammatory destruction. The gut microbiota is an “invisible organ” that directly or indirectly affects the vascular wall inflammatory cell infiltration manifested with enhanced arterial wall gut microbiota and metabolites, which plays an important role in the formation and progression of AAA. As such, the gut microbiome may become an important risk factor for AAA. This review summarizes the direct and indirect effects of the gut microbiome on the pathogenesis of AAA and highlights the gut microbiome-mediated inflammatory responses and discoveries of relevant therapeutic targets that may help manage the development and rupture of AAA.
Lava fountain jet noise during the 2018 eruption of fissure 8 of Kīlauea volcano
Authors: Gestrich Julia E. , Fee David , Matoza Robin S. , Lyons John J. , Dietterich Hannah R. , Cigala Valeria , Kueppers Ulrich , Patrick Matthew R. , Parcheta Carolyn E.
Published: November 2022

Real-time monitoring is crucial to assess hazards and mitigate risks of sustained volcanic eruptions that last hours to months or more. Sustained eruptions have been shown to produce a low frequency (infrasonic) form of jet noise. We analyze the lava fountaining at fissure 8 during the 2018 Lower East Rift Zone eruption of Kīlauea volcano, Hawaii, and connect changes in fountain properties with recorded infrasound signals from an array about 500 m from the fountain using jet noise scaling laws and visual imagery. Video footage from the eruption reveals a change in lava fountain dynamics from a tall, distinct fountain at the beginning of June to a low fountain with a turbulent, out-pouring lava pond surrounded by a tephra cone by mid-June. During mid-June, the sound pressure level reaches a maximum, and peak frequency drops. We develop a model that uses jet noise scaling relationships to estimate changes in volcanic jet diameter and jet velocity from infrasound sound pressure levels and peak frequencies. The results of this model indicate a decrease in velocity in mid-June which coincides with the decrease in fountain height. Furthermore, the model results suggest an increase in jet diameter, which can be explained by the larger width of the fountain that resembles a turbulent lava pond compared to the distinct fountain at the beginning of June. The agreement between the infrasound-derived and visually observed changes in fountain dynamics suggests that jet noise scaling relationships can be used to monitor lava fountain dynamics using infrasound recordings.
Nonalcoholic fatty liver disease is specifically related to the risk of hepatocellular cancer but not extrahepatic malignancies
Authors: Albhaisi Somaya , McClish Donna , Kang Le , Gal Tamas , Sanyal Arun J.
Published: November 2022

Objective

We performed a matched cohort study among individuals with and without nonalcoholic fatty liver disease (NAFLD) to determine: 1) the incidence of cancers (extrahepatic and liver) and their spectrum and 2) if NAFLD increases the risk of extrahepatic cancers.

Methods

The NAFLD and non-NAFLD (control) cohorts were identified from electronic medical records via International Classification of Diseases (ICD) codes from a single center and followed from 2010 to 2019. Cohorts were matched 1:2 for age, sex, race, body mass index (BMI), and type 2 diabetes.

Results

A total of 1,412 subjects were included in the analyses. There were 477 individuals with NAFLD and 935 controls (median age, 52 years; women, 54%; white vs. black: 59% vs. 38%; median BMI, 30.4 kg/m2; type 2 diabetes, 34%). The cancer incidence (per 100,000 person-years) was 535 vs. 1,513 (NAFLD vs. control). Liver cancer incidence (per 100,000 person-years) was 89 in the NAFLD group vs. 0 in the control group, whereas the incidence of malignancy was higher across other types of cancer in the control group vs. in the NAFLD group.

Conclusions

The overall extrahepatic cancer risk in NAFLD is not increased above and beyond the risk from background risk factors such as age, race, sex, BMI, and type 2 diabetes.
Resource-based theory perspective in the textile industry: The impact of the digital supply chain on operational performance
Authors: Men Feng , Yaqub Rana Muhammad Shahid , Yan Rui , Irfan Muhammad , Fatima Misal e
Published: November 2022

In a developing nation such as Pakistan, the textile sector is crucial for employment creation and poverty reduction. As a result of digitization, standard industrial operating processes have altered. The study, which is built on resource-based theory, seeks to determine how the digital supply chain (comprised of blockchain, the internet of things, and big data analytics) influences operational performance. In addition, the relationship between the innovative climate and the operational success of the digital supply chain has been analyzed. Data was collected from 270 respondents, i.e., 65 top level managers and 205 middle level managers. The results indicate that the digitization of the supply chain, which includes the application of big data analytics, the internet of things, and blockchain, greatly enhances operational performance. The innovation climate has not been proven to affect operational performance or digitalization. At the end theoretical and practical implication are highlighted.
Application of the high-density resistivity method in detecting a mined-out area of a quarry in Xiangtan City, Hunan Province
Authors: Jia Xie , Yang Liu , Yulong Lu , Lianzhi Zhang
Published: November 2022

Goaf ground collapse has great constraints on people’s lives, property safety, and social development within the influence scope because of its concealment and suddenly happening characteristics. The high-density resistivity method is used to explore the goaf of a quarry in Xiangtan City, Hunan Province. The surface subsidence of the goaf is analyzed using the apparent resistivity inversion section diagram and the comprehensive analysis results. The filling water or sediment in the goaf is reflected as a low-resistivity abnormal body, with a resistivity change that is significantly different from the resistivity change of the surrounding bedrock and the contour fluctuation. The morphological characteristics and geological conditions of the underground abnormal body in the goaf are deduced. Based on the geophysical prospecting method, geological disasters such as goaf ground collapse can be explored. From the combined analysis and processing of inversion data, the geological structure and stratum information of goaf can be inferred, which provides a theoretical basis for further disaster prevention.
Waiting for love but not forever: Modeling the evolution of waiting time to selfing in hermaphrodites
Authors: Blüml Chantal , Ramm Steven A. , van Benthem Koen J. , Wittmann Meike J.
Published: November 2022

Although mixed mating systems involving both selfing and outcrossing are fairly common in hermaphrodites, the mechanisms maintaining mixed mating are still unknown in many cases. In some species, individuals that have not yet found a mating partner delay self-fertilization for some time. This “waiting time” to selfing (WT) can exhibit heritable variation between individuals and is subject to two opposing selection pressures: waiting longer increases the density-dependent probability to encounter a mate within that time and thereby the chance to avoid inbreeding depression (ID) in offspring, but also increases the risk of dying before reproduction. It has long been hypothesized that fluctuations in population density and thus mate availability can lead to stable intermediate WTs, but to our knowledge there are so far no quantitative models that also take into account the joint evolutionary dynamics of ID. We use an individual-based model and a mathematical approximation to explore how delayed selfing evolves in response to density and density fluctuations. We find that at high density, when individuals meet often, WT evolution is dominated by genetic drift; at intermediate densities, strong ID causes WT to increase; and at low densities, ID is purged and WT approaches zero. Positive feedback loops drive the system to either complete selfing or complete outcrossing. Fluctuating density can slow down convergence to these alternative stable states. However, mixed mating, in the sense of either a stable polymorphism in WT, or stable intermediate waiting times, was never observed. Thus, additional factors need to be explored to explain the persistence of delayed selfing.
Evidence for morphological and genetic structuring of Plebeia flavocincta (Apidae: Meliponini) populations in Northeast Brazil
Authors: Maia Ulysses Madureira , Santos Júnior José Eustáquio dos , Molina Michele , Galaschi-Teixeira Juliana Stephanie , Carvalho Airton Torres , Miranda Leonardo de Sousa , Imperatriz-Fonseca Vera Lucia , Oliveira Guilherme , Giannini Tereza Cristina
Published: November 2022

Tropical dry forests are increasingly threatened by human activities. In Northeast Brazil, the Caatinga, an area of tropical dry forests surrounded by wetlands, is considered globally unique among these habitats. In this region, the stingless beePlebeia flavocinctais found in a variety of environmental, ecological, and demographic conditions. We aimed to characterizeP.flavocinctapopulations within its natural range through wing geometric morphometrics and mitochondrial DNA (mtDNA) analyses. The characterization of population variability can clarify whether the species is morphologically and genetically diverse and whether populations are morphologically and genetically structured. We analyzed 673 samples by wing morphometry and 75 by cytochrome-b assays. Our results revealedP.flavocinctais genetically and morphologically diverse and populations are morphologically and genetically structured. Despite the differentiation between the two most morphologically distant populations, we verified a large overlap of morphological variation between all populations. The genetic analysis showed that the haplotypes were geographically structured into six clusters, four of which were located in coastal areas, and the remaining two in the drier inland region. The characterization ofP.flavocinctapopulations is an important step toward decision-making in programs for the protection, management, and sustainable use of this stingless bee in local breeding efforts.
Positive regulators of T cell proliferation as biomarkers for predicting prognosis and characterizing the immune landscape in lung adenocarcinoma
Authors: Li Yang , Peng Gang , Qin Chaoying , Wang Xiangyu , Li Yue , Li Yueran
Published: November 2022

Lung adenocarcinoma (LUAD) is the one of the most prevalent and fatal form of malignant tumors worldwide. Recently, immunotherapy is widely used in the treatment of patients with LUAD and has proved to be clinically effective in improve the prognosis of patients. But there still has been a tremendous thrust to further improve the efficacy of immunotherapy in individual patients with LUAD. The suppression of T cells and their effector functions in the tumor microenvironment (TME) of LUAD is one of the primary reasons for the low efficacy of immunotherapy in some patients with LUAD. Therefore, identifying positive regulators of T cell proliferation (TPRs) may offer novel avenues for LUAD immunotherapy. In this study, we comprehensively evaluated the infiltration patterns of TPRs in 1,066 patients with LUAD using unsupervised consensus clustering and identified correlations with genomic and clinicopathological characteristics. Three infiltrating TPR clusters were defined, and a TPR-related risk signature composed of nine TPRs was constructed using least absolute shrinkage and selection operator-Cox regression algorithms to classify the individual TPR infiltration patterns. Cluster 1 exhibited high levels of T cell infiltration and activation of immune-related signaling pathways, whereas cluster 2 was characterized by robust T cell immune infiltration and enrichment of pathways associated with carcinogenic gene sets and tumor immunity. Cluster 3 was characterized as an immune-desert phenotype. Moreover, the TPR signature was confirmed as an independent prognostic biomarker for drug sensitivity in patients with LUAD. In conclusion, the TPR signature may serve as a novel tool for effectively characterizing immune characteristics and evaluating the prognosis of patients with LUAD.
Research advances in roles of microRNAs in nasal polyp
Authors: Zhipu Niu , Zitao Huo , Jichao Sha , Cuida Meng
Published: November 2022

MicroRNAs (miRNAs), a subset of endogenous RNAs highly conservative with short chains, play key regulatory role in the biological relevant events of the cells. Exosomes are extracellular vesicles like the plasma membrane components being able to deliver information molecules such as miRNA between cells and to regulate the fate of the target cells. The progression of chronic rhinosinusitis with nasal polyps (CRSwNP) is closely associated with significant alterations of miRNA levels in both cells and exosomes. RNA-binding proteins (RBPs) have been acknowledged to play important roles in intracellular miRNA transport to exosomes, and specific membrane proteins such as caveolin-1 critically involved in HNRNPA1 -mediated transport of miRNA to exosomes. Aberrant alteration in endogenous miRNA levels significantly contributes to the process of airway remodeling in the nasal tissue and to the occurrence and progression of inflammatory responses in CRSwNP. Exogenous miRNAs delivered via exosomes has also been shown to play an important role in activating macrophages or in regulating vascular permeability in the CRSwNP.This paper highlights the mechanism of RBP-mediated delivery of miRNAs to exosomes and the important contribution of endogenous miRNAs to the development of CRSwNP in response to inflammation and airway remodeling. Finally, we discuss the future research directions for regulation of the miRNAs to CRSwNP.Delivery of exogenous miRNAs by exosomes alters the endogenous miRNAs content in nasal mucosal epithelial cells or in associated inflammatory cells in the CRSwNP, and altered endogenous miRNAs affects the inflammatory response and airway remodeling, which then regulates the occurrence and progression of CRSwNP.RBPs and associated membrane proteins such as caveolin-1 may play a crucial role in the entry of exogenous miRNA into exosomes.
Transcriptional mapping of the macaque retina and RPE-choroid reveals conserved inter-tissue transcription drivers and signaling pathways
Authors: Mungale Ameera , McGaughey David M. , Zhang Congxiao , Yousaf Sairah , Liu James , Brooks Brian P. , Maminishkis Arvydas , Fufa Temesgen D. , Hufnagel Robert B.
Published: November 2022

The macula and fovea comprise a highly sensitive visual detection tissue that is susceptible to common disease processes like age-related macular degeneration (AMD). Our understanding of the molecular determinants of high acuity vision remains unclear, as few model organisms possess a human-like fovea. We explore transcription factor networks and receptor-ligand interactions to elucidate tissue interactions in the macula and peripheral retina and concomitant changes in the underlying retinal pigment epithelium (RPE)/choroid. Poly-A selected, 100 bp paired-end RNA-sequencing (RNA-seq) was performed across the macular/foveal, perimacular, and temporal peripheral regions of the neural retina and RPE/choroid tissues of four adult Rhesus macaque eyes to characterize region- and tissue-specific gene expression. RNA-seq reads were mapped to both the macaque and human genomes for maximum alignment and analyzed for differential expression and Gene Ontology (GO) enrichment. Comparison of the neural retina and RPE/choroid tissues indicated distinct, contiguously changing gene expression profiles from fovea through perimacula to periphery. Top GO enrichment of differentially expressed genes in the RPE/choroid included cell junction organization and epithelial cell development. Expression of transcriptional regulators and various disease-associated genes show distinct location-specific preference and retina-RPE/choroid tissue-tissue interactions. Regional gene expression changes in the macaque retina and RPE/choroid is greater than that found in previously published transcriptome analysis of the human retina and RPE/choroid. Further, conservation of human macula-specific transcription factor profiles and gene expression in macaque tissues suggest a conservation of programs required for retina and RPE/choroid function and disease susceptibility.
A machine learning framework for scRNA-seq UMI threshold optimization and accurate classification of cell types
Authors: Bishara Isaac , Chen Jinfeng , Griffiths Jason I. , Bild Andrea H. , Nath Aritro
Published: November 2022

Recent advances in single cell RNA sequencing (scRNA-seq) technologies have been invaluable in the study of the diversity of cancer cells and the tumor microenvironment. While scRNA-seq platforms allow processing of a high number of cells, uneven read quality and technical artifacts hinder the ability to identify and classify biologically relevant cells into correct subtypes. This obstructs the analysis of cancer and normal cell diversity, while rare and low expression cell populations may be lost by setting arbitrary high cutoffs for UMIs when filtering out low quality cells. To address these issues, we have developed a novel machine-learning framework that: 1. Trains cell lineage and subtype classifier using a gold standard dataset validated using marker genes 2. Systematically assess the lowest UMI threshold that can be used in a given dataset to accurately classify cells 3. Assign accurate cell lineage and subtype labels to the lower read depth cells recovered by setting the optimal threshold. We demonstrate the application of this framework in a well-curated scRNA-seq dataset of breast cancer patients and two external datasets. We show that the minimum UMI threshold for the breast cancer dataset could be lowered from the original 1500 to 450, thereby increasing the total number of recovered cells by 49%, while achieving a classification accuracy of >0.9. Our framework provides a roadmap for future scRNA-seq studies to determine optimal UMI threshold and accurately classify cells for downstream analyses.
Mice with lung airway ciliopathy develop persistent Mycobacterium abscessus lung infection and have a proinflammatory lung phenotype associated with decreased T regulatory cells
Authors: Nava Audrey , Hahn Andrew C. , Wu Terry H. , Byrd Thomas F.
Published: November 2022

Introduction

Human pulmonary infection with non-tuberculous mycobacteria (NTM) such as Mycobacterium abscessus (Mabs) occurs in seemingly immunocompetent patients with underlying structural lung disease such as bronchiectasis in which normal ciliary function is perturbed. In addition to alterations in mucociliary clearance, the local immunologic milieu may be altered in patients with structural lung disease, but the nature of these changes and how they relate to NTM persistence remain unclear.

Methods

We used a mouse strain containing a conditional floxed allele of the gene IFT88, which encodes for the protein Polaris. Deletion of this gene in adult mice reportedly leads to loss of cilia on lung airway epithelium and to the development of bronchiectasis. In a series of experiments, IFT88 control mice and IFT88 KO mice received different preparations of Mabs lung inocula with lung CFU assessed out to approximately 8 weeks post-infection. In addition, cytokine levels in bronchoalveolar lavage (BAL) fluid, lung T cell subset analysis, and lung histopathology and morphometry were performed at various time points.

Results

Mabs embedded in agarose beads persisted in the lungs of IFT88 KO mice out to approximately 8 weeks (54 days), while Mabs agarose beads in the lungs of IFT88 control mice was cleared from the lungs of all mice at this time point. T cells subset analysis showed a decrease in the percentage of CD4+FoxP3+ T cells in the total lymphocyte population in the lungs of IFT88 KO mice relative to IFT88 control mice. Proinflammatory cytokines were elevated in the BAL fluid from infected IFT88 KO mice compared to infected IFT88 control mice, and histopathology showed an increased inflammatory response and greater numbers of granulomas in the lungs of infected IFT88 KO mice compared to the lungs of infected IFT88 control mice. Scanning lung morphometry did not show a significant difference comparing lung airway area and lung airway perimeter between IFT88 KO mice and IFT88 control mice.

Discussion

Persistent lung infection in our model was established using Mabs embedded in agarose beads. The utility of using IFT88 mice is that a significant difference in Mabs lung CFU is observed comparing IFT88 KO mice to IFT88 control mice thus allowing for studies assessing the mechanism(s) of Mabs lung persistence. Our finding of minimal differences in lung airway area and lung airway diameter comparing IFT88 KO mice to IFT88 control mice suggests that the development of a proinflammatory lung phenotype in IFT88 KO mice contributes to Mabs lung persistence independent of bronchiectasis. The contribution of cilia to immune regulation is increasingly recognized, and our results suggest that ciliopathy associated with structural lung disease may play a role in NTM pulmonary infection via alteration of the local immunologic lung milieu.
Caspase-8 activation in neutrophils facilitates autoimmune kidney vasculitis through regulating CD4+ effector memory T cells
Authors: Hu Jian , Huang Zhen , Yu Min , Zhang Pei , Xia Zhengkun , Gao Chunlin
Published: November 2022

Anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitides (AAVs) are closely associated with neutrophil recruitment and activation, but the impact of the neutrophil apoptosis process in autoimmune disease has been rarely explained. Here, by integrating and analyzing single-cell transcriptome datasets, we found that the caspase-8-associated pathway in neutrophils was highly activated in the kidney rather than in the blood. To verify the function of caspase-8 in neutrophils on AAVs progression, we constructed neutrophil-specific caspase-8 knockout mice combined with an AAVs model induced by human ANCA from AAVs patients, a rapid and powerful model developed in this study. Our results show that caspase-8 activation of neutrophils up-regulates the expression of several inflammatory and immunoregulatory factors, especially IL23A, regulating the activation and differentiation of tissue-resident CD4+ effector memory T cells. This study reveals that the activation of caspase-8 in neutrophils can worsen glomerulonephritis of AAVs by regulating inflammation and immunity.
The crosstalk between parenchymal cells and macrophages: A keeper of tissue homeostasis
Authors: Chen Yusi , Tang Li
Published: November 2022

Non-parenchymal cells (NPCs) and parenchymal cells (PCs) collectively perform tissue-specific functions. PCs play significant roles and continuously adjust the intrinsic functions and metabolism of organs. Tissue-resident macrophages (TRMs) are crucial members of native NPCs in tissues and are essential for immune defense, tissue repair and development, and homeostasis maintenance. As a plastic-phenotypic and prevalent cluster of NPCs, TRMs dynamically assist PCs in functioning by producing cytokines, inflammatory and anti-inflammatory signals, growth factors, and proteolytic enzymes. Furthermore, the PCs of tissues modulate the functional activity and polarization of TRMs. Dysregulation of the PC‐TRM crosstalk axis profoundly impacts many essential physiological functions, including synaptogenesis, gastrointestinal motility and secretion, cardiac pulsation, gas exchange, blood filtration, and metabolic homeostasis. This review focuses on the PC‐TRM crosstalk in mammalian vital tissues, along with their interactions with tissue homeostasis maintenance and disorders. Thus, this review highlights the fundamental biological significance of the regulatory network of PC‐TRM in tissue homeostasis.
Comprehensive analysis of anoikis-related long non-coding RNA immune infiltration in patients with bladder cancer and immunotherapy
Authors: Zhang Yao-Yu , Li Xiao-Wei , Li Xiao-Dong , Zhou Ting-Ting , Chen Chao , Liu Ji-Wen , Wang Li , Jiang Xin , Wang Liang , Liu Ming , Zhao You-Guang , Li Sha-dan
Published: November 2022

Background

Anoikis is a form of programmed cell death or programmed cell death(PCD) for short. Studies suggest that anoikis involves in the decisive steps of tumor progression and cancer cell metastasis and spread, but what part it plays in bladder cancer remains unclear. We sought to screen for anoikis-correlated long non-coding RNA (lncRNA) so that we can build a risk model to understand its ability to predict bladder cancer prognosis and the immune landscape.

Methods

We screened seven anoikis-related lncRNAs (arlncRNAs) from The Cancer Genome Atlas (TCGA) and designed a risk model. It was validated through ROC curves and clinicopathological correlation analysis, and demonstrated to be an independent factor of prognosis prediction by uni- and multi-COX regression. In the meantime, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, immune infiltration, and half-maximal inhibitory concentration prediction (IC50) were implemented with the model. Moreover, we divided bladder cancer patients into three subtypes by consensus clustering analysis to further study the differences in prognosis, immune infiltration level, immune checkpoints, and drug susceptibility.

Result

We designed a risk model of seven arlncRNAs, and proved its accuracy using ROC curves. COX regression indicated that the model might be an independent prediction factor of bladder cancer prognosis. KEGG enrichment analysis showed it was enriched in tumors and immune-related pathways among the people at high risk. Immune correlation analysis and drug susceptibility results indicated that it had higher immune infiltration and might have a better immunotherapy efficacy for high-risk groups. Of the three subtypes classified by consensus clustering analysis, cluster 3 revealed a positive prognosis, and cluster 2 showed the highest level of immune infiltration and was sensitive to most chemistries. This is helpful for us to discover more precise immunotherapy for bladder cancer patients.

Conclusion

In a nutshell, we found seven arlncRNAs and built a risk model that can identify different bladder cancer subtypes and predict the prognosis of bladder cancer patients. Immune-related and drug sensitivity researches demonstrate it can provide individual therapeutic schedule with greater precision for bladder cancer patients.
Rap1b-loss increases neutrophil lactate dehydrogenase activity to enhance neutrophil migration and acute inflammation in vivo
Authors: Chowdhury Chanchal Sur , Wareham Elizabeth , Xu Juying , Kumar Sachin , Kofron Matthew , Lakshmikanthan Sribalaji , Chrzanowska Magdalena , Filippi Marie-Dominique
Published: November 2022

Introduction

Neutrophils are critical for host immune defense; yet, aberrant neutrophil tissue infiltration triggers tissue damage. Neutrophils are heterogeneous functionally, and adopt ‘normal’ or ‘pathogenic’ effector function responses. Understanding neutrophil heterogeneity could provide specificity in targeting inflammation. We previously identified a signaling pathway that suppresses neutrophilmediated inflammation via integrin-mediated Rap1b signaling pathway.

Methods

Here, we used Rap1-deficient neutrophils and proteomics to identify pathways that specifically control pathogenic neutrophil effector function.

Results

We show neutrophil acidity is normally prevented by Rap1b during normal immune response with loss of Rap1b resulting in increased neutrophil acidity via enhanced Ldha activity and abnormal neutrophil behavior. Acidity drives the formation of abnormal invasive-like protrusions in neutrophils, causing a shift to transcellular migration through endothelial cells. Acidity increases neutrophil extracellular matrix degradation activity and increases vascular leakage in vivo. Pathogenic inflammatory condition of ischemia/reperfusion injury is associated with increased neutrophil transcellular migration and vascular leakage. Reducing acidity with lactate dehydrogenase inhibition in vivo limits tissue infiltration of pathogenic neutrophils but less so of normal neutrophils, and reduces vascular leakage.

Discussion

Acidic milieu renders neutrophils more dependent on Ldha activity such that their effector functions are more readily inhibited by small molecule inhibitor of Ldha activity, which offers a therapeutic window for antilactate dehydrogenase treatment in specific targeting of pathogenic neutrophilsin vivo.
Ecological security assessment of Qinzhou coastal zone based on Driving forces-Pressure-State-Impact-Response (DPSIR) model
Authors: Zhou Jiaodi , Wang Xilong , Lu Dongliang , Dan Solomon Felix , Kang Zhenjun , Xu Yuping , Weng Peiyao , Wei Zhaofu
Published: November 2022

A coastal zone represents the intersection of ocean and land, and is characterized by high primary productivity, biodiversity, and rich resources but with strong sensitivity and vulnerability of the natural environment. In this study, 29 indicators reflecting the status of ecological security were selected to construct an ecological security evaluation index system using the Driving force Pressure State Impact Response (DPSIR) model. The comprehensive index method was used to evaluate the ecological security of Qinzhou coastal zone from 2011 to 2020 and to explore the driving factors of its evolution. The results showed that (1) In the past 10 years, the ecological security of Qinzhou coastal zone fluctuated and developed, and the security level changed from early warning – safer – more dangerous – early warning to safer; and the security level was the lowest (0.361) in 2014. The main reason was the impact of ecological marine disasters, such as three red tides with the eutrophication index of seawater as high as 4.170. (2) Since 2015, the ecological security of the coastal zone has shown an upward trend, which was mainly due to the implementation of the newly revised environmental protection law in the same year, the comprehensive promotion of “The 13th Five-Year Plan for environmental protection”, and a series of measures related to the construction of ecological civilization and environmental protection, which provided a strong guarantee for the ecological security of the coastal zone. This study proposes measures to promote the better development of the ecological environment of Qinzhou coastal zone.
Nutrient composition (Si:N) as driver of plankton communities during artificial upwelling
Authors: Goldenberg Silvan Urs , Taucher Jan , Fernández-Méndez Mar , Ludwig Andrea , Arístegui Javier , Baumann Moritz , Ortiz Joaquin , Stuhr Annegret , Riebesell Ulf
Published: November 2022

Artificial upwelling brings nutrient-rich deep water to the sun-lit surface to boost fisheries or carbon sequestration. Deep water sources under consideration range widely in inorganic silicon (Si) relative to nitrogen (N). Yet, little is known about how such differences in nutrient composition may influence the effectiveness of the fertilization. Si is essential primarily for diatoms that may increase food web and export efficiency via their large size and ballasting mineral shells, respectively. With a month-long mesocosm study in the subtropical North Atlantic, we tested the biological response to artificial upwelling with varying Si:N ratios (0.07-1.33). Community biomass increased 10-fold across all mesocosms, indicating that basic bloom dynamics were upheld despite the wide range in nutrient composition. Key properties of these blooms, however, were influenced by Si. Photosynthetic capacity and nutrient-use efficiency doubled from Si-poor to Si-rich upwelling, leading to C:N ratios as high as 17, well beyond Redfield. Si-rich upwelling also resulted in 6-fold higher diatom abundance and mineralized Si and a corresponding shift from smaller towards larger phytoplankton. The pronounced change in both plankton quantity (biomass) and quality (C:N ratio, size and mineral ballast) for trophic transfer and export underlines the pivotal role of Si in shaping the response of oligotrophic regions to upwelled nutrients. Our findings indicate a benefit of active Si management during artificial upwelling with the potential to optimize fisheries production and CO2 removal.
Variation in mesopelagic fish community composition and structure between Mediterranean and Atlantic waters around the Iberian Peninsula
Authors: Olivar M. Pilar , Castellón Arturo , Sabatés Ana , Sarmiento-Lezcano Airam , Emelianov Mikhail , Bernal Ainhoa , Yang Yang , Proud Roland , Brierley Andrew S.
Published: November 2022

Mesopelagic fish populations are characterised by high species richness and abundance, and have been identified as important contributors to the active carbon fluxes in the open ocean. We report variability in communities of mesopelagic fish between five zones around the Iberian Peninsula, i.e. Balears and Alboran in the Mediterranean, and Cadiz, Lisboa and Galicia in the Atlantic. Day and night samples were collected from 7 layers of the water column with a midwater trawl fitted with a multisampler. Temperature and salinity regimes were very different on the Mediterranean and Atlantic sides of the peninsula, with much higher values through the entire water column in the Mediterranean, characterized by a strong pycnocline. The highest productivity was observed off Lisboa, where Chlorophyll a concentrations were two orders of magnitude higher than in any other zone. Samples from the western Mediterranean held 22 fish species, while 67 were found in the Atlantic. The lowest diversity and the highest dominance were observed in Balears, and the highest diversity in Cadiz zone. In all zones, but particularly in those in the Mediterranean, mesopelagic populations were dominated by a high number of small fish with low individual biomasses. The species Benthosema glaciale, Cyclothone pygmaea and Ceratoscopelus maderensis were common in the Mediterranean populations, whereas in the Atlantic, Cyclothone microdon/livida, Valenciennellus tripunctulatus, Ceratoscopelus warmingii and Benthosema suborbitale were the most common species. Temperature and salinity (both at surface and in the mesopelagic zone) were the main environmental factors explaining variability in assemblage composition. A persistent (day-night) deep scattering layer was observed using the vessel-based echosounder in all zones, and was comprised primarily of the gonostomatid Cyclothone spp. Night-time echosounder observations of scattering layers near the surface were observed in Balears, Alboran, Cadiz and Lisboa, where night surface net collections indicated that Myctophidae, Stomiidae and Phosichthyidae migration extended to the upper 100 m. Sternoptychids and the gonostomatid Sigmops elongatus seldom reached the upper 100 m in their night vertical migrations. Night stratified hauls of 30 m resolution carried out in the epipelagic zone showed that abundances maxima of migratory fish coincided with the location of the Chlorophyll a maxima.
Proteomic and metabolomic analysis on cadmium-induced mitochondrial toxicity in liver tissues of juvenile olive flounder Paralichthys olivaceus
Authors: Lu Zhen , Xiao Zeyu , Wu Sihan , Song Jun , Peng Xiao
Published: November 2022

Introduction

Cadmium (Cd) is one of the most dominant heavy metals in the Bohai Sea. Our previous study proved that Cd could induce gill mitochondrial toxicity in marine animals. Herein, we aimed to elucidate the toxicity mechanism of Cd on liver mitochondria, as liver is the main metabolic and detoxification organ and generally rich in mitochondria.

Methods

The mitochondrial responses induced by Cd (5 and 50 μg/L) were characterized by observing mitochondrial morphology, measuring mitochondrial membrane potential (MMP), and proteomic and metabolomic analysis in juvenile olive flounder Paralichthys olivaceus livers.

Results

After water-bonre exposure for 14 days, two Cd treatments decreased MMPs significantly and caused ultrastructural-damaged mitochondria in flounder livers. NMR-based metabolomics revealed that Cd exposure mainly altered the abundances of metabolites (ATP, AMP, phosphocholine, lactate and succinate) related to energy metabolism in flounder livers. iTRAQ-based mitochondrial proteomics indicated that 27 differentially expressed proteins (DEPs) were screened out from liver mitochondria after Cd treatments. These proteins were mainly associated with energy metabolism (oxidative phosphorylation (OXPHOS) and tricarboxylic acid (TCA) cycle) and apoptosis.

Discussion

These results indicated that Cd disrupted mitochondrial morphology, energy homeostasis and apoptosis in liver mitochondria in flounder P. olivaceus. This work revealed a comprehensive view on Cd-induced mitochondrial responses in the liver tissues of flounder using an integrated proteomic and metabolomic approach.
Further refinements of a continuous radon monitor for surface ocean water measurements
Authors: Li Chunqian , Zhao Shibin , Zhang Chenglun , Li Meng , Guo Jinjia , Dimova Natasha T. , Yang Tong , Liu Wen , Chen Guangquan , Yu Huaming , Xu Bochao
Published: November 2022

Radon is an excellent natural tracer for studying various geophysical processes. In the past centuries, radon isotopes measurement approaches for marine research have been fully developed but still suffer limitations. Here we present the setup and validation of an improved continuous online measurement system (PIC-ORn) to measure dissolved radon in the surface ocean and other water bodies. We demonstrated that the PIC measurement efficiency is ~2 times higher than a RAD7 and is less affected by relative humidity and produces reliable results. Laboratorial measurements indicated that the new PIC-ORn system responded timely to the change of radon activities in water. The new system was successfully deployed during a cruise to the northwest Pacific Ocean in June 2021. Despite low radon-in-water activities, the results obtained by the new PIC-ORn system matched the traditional measurement systems within the estimated uncertainties. The PIC-ORn detector takes advantage of higher efficiency, lower cost, and power consumption, and is less affected by air moisture. The new system does not rely on drying units, further reducing on-site supervision, which would benefit the researches in submarine groundwater advection and diffusion and ocean-atmosphere gas exchange.
Temporal and spatial characteristics of submesoscale motions in the Bohai Sea
Authors: Si Xueying , Wang Tao , Wang Yanping
Published: November 2022

Submesoscale motions are ubiquitous in the ocean, playing a significant role in energy transfer, mass transport, and biogeochemical processes. However, little attention has been drawn to the submesoscale dynamics in shallow coastal waters. In the present study, submesoscale motions in the Bohai Sea, a typical shallow sea with mean depth of about 18 m, are studied using a validated high-resolution (~ 500 m) model based on Regional Oceanic Modeling System (ROMS). The results show that submesoscale structures in the Bohai Sea are mainly located in the shallow coastal regions, the Bohai Strait, the areas around islands and headlands, and mostly tend to be parallel to the isobaths. The periodic variations of submesoscale motions are closely related to the tidal, spring-neap, and seasonal cycles in the Bohai Sea. The spring-neap variations of submesoscale motions are mainly attributed to the curl of vertical mixing, which is stronger during spring tides than neap tides. Compared with winter, the stronger background horizontal and vertical density variance in summer are conducive to frontogenesis, resulting in more active submesoscale motions. The results in this study are expected to contribute to enriching our knowledge about submesoscale dynamics in shallow coastal seas.
Long-term variations in water discharge and sediment load of the Pearl River Estuary: Implications for sustainable development of the Greater Bay Area
Authors: Liu Zezheng , Fagherazzi Sergio , Liu Xinhui , Shao Dongdong , Miao Chiyuan , Cai Yanzi , Hou Congyu , Liu Yeling , Li Xia , Cui Baoshan
Published: November 2022

The water discharge and sediment load have been increasingly altered by climate change and human activities in recent decades. For the Pearl River, however, long-term variations in the sediment regime, especially in the last decade, remain poorly known. Here we updated knowledge of the temporal trends in the sediment regime of the Pearl River at annual, seasonal and monthly time scales from the 1950s to 2020. Results show that the annual sediment load and suspended sediment concentration (SSC) exhibited drastically decreased, regardless of water discharge. Compared with previous studies, we also found that sediment load and SSC reached a conspicuous peak in the 1980s, and showed a significant decline starting in the 2000s and 1990s, respectively. In the last decade, however, water discharge and sediment load showed slightly increasing trends. At the seasonal scale, the wet-season water discharge displays a decreasing trend, while the dry-season water discharge is increasing. At the monthly scale, the flood seasons in the North and East Rivers typically occur one month earlier than that in the West River due to the different precipitation regimes. Precipitation was responsible for the long-term change of discharge, while human activities (e.g. dam construction and land use change) exerted different effects on the variations in sediment load among different periods. Changes in the sediment regime have exerted substantial influences on downstream channel morphology and saltwater intrusion in the Greater Bay Area. Our study proposes a watershed-based solution, and provides scientific guidelines for the sustainable development of the Greater Bay Area.
Climate-induced variation in a temperature suitability index of chub mackerel in the spawning season and its effect on the abundance
Authors: Wang Liangming , Ma Shuyang , Liu Yang , Li Jianchao , Sun Dianrong , Tian Yongjun
Published: November 2022

Chub mackerel (Scomber japonicus) is widely distributed in the northwestern Pacific Ocean and is utilized by China, Korea, and Japan in different seasons and areas. Generally, chub mackerel is divided into Tsushima Warm Current (TWC) and Pacific stocks based on its different distribution, migration, and life-history traits. The two stocks showed obvious interannual to decadal variability in abundance with evident different variation patterns. Chub mackerel has extensive spawning areas in the northwestern Pacific Ocean, with the main spawning period from March to June, and the suitable spawning SST (sea surface temperature) ranging from 15°C to 22°C. To explore the temperature effects on different variations of the two stocks, we estimated the average temperature suitability index (TSI) for chub mackerel in main spawning areas during the spawning period from March to June based on the relationship between the probability of spawning and the specific SST. Results showed that the TSIs in the shelf waters of China seas and the waters of the Tsushima Strait displayed simultaneous abrupt changes in the late 1990s for the TWC stock, whereas the TSI in the Pacific coast of Japan had a regime shift in the late 1970s for the Pacific stock. The spatio-temporal variation in spawning temperature suitability may have had an important impact on the recovery of the Pacific stock after the 2000s. We also found that there is a non-stationary relationship between chub mackerel abundance and TSI, which is driven by climate variabilities such as the Siberian High and the Aleutian Low. Moreover, TWC stock showed non-stationary relationship with TSI, and the threshold years was identified in the 1990s, and the non-stationary relationship between TSI and Pacific stock, with thresholds occurring in the late 1970s. Our research provides a reasonable explanation for the variations in the two stocks and their responses to TSI variability and offers an improved understanding of the climate-induced non-stationary relationships between chub mackerel abundance and physical drivers.