bluuebunny/crossref_metadata_2025 huggingface dataset:
Do state-owned participation shareholders improve the environmental governance level of private enterprises? Evidence from Chinese listed firms
Authors: Zou Ling , Ma Jiejing
Published: January 2023

In recent years, whether the mixed-ownership reform system of introducing state-owned participation shareholders into private enterprises helps to improve the environmental governance of private enterprises has been a matter of much attention and discussion. Based on data from 2007 to 2019 for Chinese A-share privately listed companies, this paper examines how the state-owned participation shareholders affect the environmental governance level of private enterprises. The results show that state-owned participating shareholder participation can improve the environmental governance level of private enterprises, and this phenomenon is more significant among industrial enterprises and enterprises in regions with a higher degree of marketization. Furthermore, there is a substitution effect between the state-owned participation shareholders, the executive team’s participation in politics, and the Party organization establishment in improving the environmental governance level of private enterprises, and the state-owned participation shareholders play a relatively larger role. In addition, the supervision effect is better when state-owned participation shareholders are from the local area and have a higher level of participation.
Variation in diet of desert bighorn sheep (Ovis canadensis nelsoni): Tradeoffs associated with parturition
Authors: Blum Marcus E. , Stewart Kelley M. , Cox Mike , Shoemaker Kevin T. , Bennett Joe R. , Sullivan Benjamin W. , Wakeling Brian F. , Bleich Vernon C.
Published: January 2023

Selection of forage and habitats is driven by nutritional needs of individuals. Some species may sacrifice nutritional quality of forage for the mother in favor of safety of offspring (risk-averse strategy), immediately following parturition. We studied diet quality and forage selection by bighorn sheep before and following parturition to determine how nutritional demands associated with rearing offspring influenced forage acquisition. We used desert bighorn sheep, Ovis canadensis nelsoni, to investigate that potential tradeoff. We captured and radio-collared female bighorn sheep from 2016 to 2018. We used vaginal implant transmitters (VIT)s in pregnant females to identify parturition and to capture and radio-collar neonates to monitor survival of young. We collected fecal samples throughout the breeding season and throughout the year to understand diet quality and composition throughout those temporal periods. We determined diet quality and composition for pre-parturient females, females provisioning offspring, females that lost offspring, and non-pregnant individuals using fecal nitrogen and DNA metabarcoding analyses. Additionally, we compared the diet quality and composition of offspring and adult females during the spring, as well as summer and winter months. Our results indicated differences in diet quality between individuals provisioning offspring and those whose offspring had died. Females that were provisioning dependent young had lower quality diets than those that lost their offspring. Diet composition among those groups was also markedly different; females that had lost an offspring had a more diverse diet than did females with dependent young. Diet quality differed among seasons, wherein offspring and adult females had higher quality diets during the spring months, with decreasing quality as the year progressed. Diet diversity was similar across seasons, although spring months tended to be most diverse. Our results support tradeoffs associated with risk-averse strategies made by adult females associated with parturition. Nutritional quality of forage was linked to provisioning status, indicating that females were trading diet quality for safety of offspring, but those females whose offspring had died selected high quality forages. Those results help explain habitat selection observed in mountain ungulates around parturition and provide further insight into the evolutionary processes and adaptive significance exhibited by those specialized artiodactyls.
Sea level rise may pose conservation challenges for the endangered Cape Sable seaside sparrow
Authors: Romañach Stephanie S. , Haider Saira M. , Benscoter Allison M.
Published: January 2023

Biodiversity conservation under a changing climate is a challenging endeavor. Landscapes are shifting as a result of climate change and sea level rise but plant communities in particular may not keep up with the pace of change. Predictive ecological models can help decision makers understand how species are likely to respond to change and then adjust management actions to align with desired future conditions. Florida’s Everglades is a wetland ecosystem that is host to many species, including a large number of endangered and endemic species. Everglades ecosystem restoration has been ongoing for decades, but consideration of sea level rise impacts in restoration planning is more recent. Incorporating potential impacts from sea level rise into restoration planning should benefit species and their coastal habitats, most notably at the southern Florida peninsula. The endangered Cape Sable seaside sparrow (Ammospiza maritima mirabilis) occurs in marl prairie habitat at the southern end of the Everglades. The locations of three of its six subpopulations are proximate to the coast. We used a spatially explicit predictive model, EverSparrow, to estimate probability of sparrow presence considering both hydrologic change from restoration and sea level rise. We found that the probability of sparrow presence decreased with increasing sea level rise. Within approximately 50 years, probability of presence significantly decreased for all three coastal subpopulation areas, with areas above 40% probability increasingly limited. Given the exceptionally low dispersal ability of this species and the geographic restrictions for habitat expansion, our results highlight the importance of freshwater flow into the southern Everglades marl prairie for habitat conservation.
Exploring the prognostic value of HK3 and its association with immune infiltration in glioblastoma multiforme
Authors: Yang Yuling , Fu Xing , Liu Runsha , Yan Lijuan , Yang Yiping
Published: January 2023

Background: Hexokinase 3 (HK3) is one of the key enzymes involved in glucose phosphorylation (the first step in most glucose metabolic pathways). Many studies have demonstrated the vital role of dysregulation of HK3 in several tumors. However, there is a need for in-depth characterization of the role of HK3 in glioblastoma multiforme (GBM).

Methods: All data were sourced from The Cancer Genome Atlas (TCGA) and Chinese Glioma Genome Atlas (CGGA). Kaplan-Meier analysis and univariate regression were applied for survival analysis. Gene set enrichment analysis (GSEA) was used for enrichment analysis. Tumor Immune Single Cell Hub (TISCH) database was applied for single-cell analysis. Tumor Immune Dysfunction and Exclusion (TIDE) analysis was applied to evaluate the immune response.

Results: HK3 expression was upregulated in GBM and correlated with poor prognosis. The high HK3 expression group was primarily enriched in adaptive immune response, chemokine signaling pathway, and cytokine-cytokine receptor interaction. The high HK3 expression group showed significantly greater enrichment of the majority of immune cells and immune-related pathways. HK3 showed significant correlation with most immune cells, especially macrophages (p < .001, R = .81). TISCH analysis showed that HK3 was predominantly expressed in macrophages in most cancers. HK3 showed significant correlation with most immune-related genes, such as PD-1 (p < .001, R = .41), PDL-1 (p < .001, R = .27), and CTLA-4 (p < .001, R = .29). TIDE analysis revealed that the low HK3 expression group has a lower TIDE score and may benefit from immunotherapy. Drug sensitivity analysis showed that patients with high HK3 expression frequently showed drug resistance.

Conclusion: HK3 was associated with poor prognosis and may serve as a biomarker of macrophages in GBM. HK3 was also associated with immune response and drug resistance. Our findings may provide novel insights for GBM immunotherapy.
DNA methylation signature of psychological resilience in young adults: Constructing a methylation risk score using a machine learning method
Authors: Lu Andrew Ke-Ming , Hsieh Shulan , Yang Cheng-Ta , Wang Xin-Yu , Lin Sheng-Hsiang
Published: January 2023

Resilience is a process associated with the ability to recover from stress and adversity. We aimed to explore the resilience-associated DNA methylation signatures and evaluate the abilities of methylation risk scores to discriminate low resilience (LR) individuals. The study recruited 78 young adults and used Connor-Davidson Resilience Scale (CD-RISC) to divide them into low and high resilience groups. We randomly allocated all participants of two groups to the discovery and validation sets. We used the blood DNA of the subjects to conduct a genome-wide methylation scan and identify the significant methylation differences of CpG Sites in the discovery set. Moreover, the classification accuracy of the DNA methylation probes was confirmed in the validation set by real-time quantitative methylation-specific polymerase chain reaction. In the genome-wide methylation profiling between LR and HR individuals, seventeen significantly differentially methylated probes were detected. In the validation set, nine DNA methylation signatures within gene coding regions were selected for verification. Finally, three methylation probes [cg18565204 (AARS), cg17682313 (FBXW7), and cg07167608 (LINC01107)] were included in the final model of the methylation risk score for LR versus HR. These methylation risk score models of low resilience demonstrated satisfactory discrimination by logistic regression and support vector machine, with an AUC of 0.81 and 0.93, accuracy of 72.3% and 87.1%, sensitivity of 75%, and 87.5%, and specificity of 70% and 80%. Our findings suggest that methylation signatures can be utilized to identify individuals with LR and establish risk score models that may contribute to the field of psychology.
Mitochondrial genome characteristics and phylogenetic analysis of the medicinal and edible plant Mesona chinensis Benth
Authors: Tang Danfeng , Huang Suhua , Quan Changqian , Huang Yuan , Miao Jianhua , Wei Fan
Published: January 2023

Mesona chinensis Benth (MCB) (or Platostoma palustre or Platostoma chinense) is an important edible and medicinal plant in China. However, the mitochondrial genome (mitogenome, or mtDNA) of MCB has not been characterized or reported yet. In this study, we first sequenced and characterized the complete mitogenome of MCB. The MCB mitogenome was 494,599 bp in length and encoded 59 genes containing 37 protein-coding genes (PCGs), 19 tRNAs, and 3 rRNAs. Gene transfer analysis revealed that a total of 12 transfer segments with more than 93% identity (total length of 25,427 bp) were detected in the MCB mitogenome. Simple sequence repeats (SSR) analysis showed that 212 simple sequence repeats (SSR) were identified. Repeat sequence analysis revealed 305 repeat sequences (158 forward and 147 palindromic repeats) ranging from 30 bp to 48,383 bp and the 30–39 bp repeats were the majority type. Relative synonymous codon usage (RSCU) analysis uncovered that in total, 9,947 codons were encoding the protein-coding genes (PCGs). Serine (909, 9.1%) and leucine (879, 8.8%) were the two most abundant amino acids, while terminator (32, .3%) was the least abundant amino acid. Ka/Ks analysis indicated that almost all genes were subject to purification selection, except ccmB. Analysis of Lamiaceae mitogenomes constitution revealed that atpB and atpE were unique to the Rotheca serrata and Salvia miltiorrhiza mitogenomes. mttB gene loss was unique to the Boea hygrometrica mitogenome. The core fragments of the Lamiaceae mitogenomes harbored a higher GC content than the specific and variable fragments. In addition, phylogenetic analysis revealed that MCB was closely related to Salvia miltiorrhiza based on the mitogenomes. The current study provided valuable genomic resources for understanding and utilizing this important medicinal plant in the future.
Individual effects of GSTM1 and GSTT1 polymorphisms on cervical or ovarian cancer risk: An updated meta-analysis
Authors: Ye Jing , Mu Yi-Yang , Wang Jiong , He Xiao-Feng
Published: January 2023

Background: Studies have shown that glutathione S-transferase M1 (GSTM1) and. glutathione S-transferase T1 (GSTT1) null genotype may increase the risk of cervical cancer (CC) or ovarian cancer (OC), however, the results of published original studies and meta-analyses are inconsistent.

Objectives: To investigate the association between GSTM1 present/null and GSTT1 present/null polymorphisms, with the risk of cervical cancer or ovarian cancer.

Methods: The odds ratios (ORs) and 95% confidence intervals (CIs) were used to assess the association between GSTM1 present/null and GSTT1 present/null polymorphisms and the risk of cervical cancer or ovarian cancer. To assess the confidence of statistically significant associations, we applied false positive reporting probability (FPRP) and bayesian false discovery probability (BFDP) tests.

Results: Overall analysis showed that GSTM1 null was associated with an increased risk of cervical cancer, and subgroup analysis showed a significant increase in cervical cancer risk in Indian and Chinese populations; GSTT1 was not found null genotype are significantly associated with cervical cancer. Overall analysis showed that GSTM1 and GSTT1 null were not associated with the risk of ovarian cancer, subgroup analysis showed that GSTM1 null was associated with an increased risk of OC in East Asia, and GSTT1 null was associated with an increased risk of OC in South America. However, when we used false positive reporting probability and bayesian false discovery probability to verify the confidence of a significant association, all positive results showed “low confidence” (FPRP > .2, BFDP > .8).

Conclusion: Overall, this study strongly suggests that all positive results should be interpreted with caution and are likely a result of missing plausibility rather than a true association.
A cellular senescence-related genes model allows for prognosis and treatment stratification of hepatocellular carcinoma: A bioinformatics analysis and experimental verification
Authors: Li Jiaming , Tan Rongzhi , Wu Jie , Guo Wenjie , Wang Yupeng , You Guoxing , Zhang Yuting , Yu Zhiyong , Geng Yan , Zan Jie , Su Jianfen
Published: January 2023

Introduction: Hepatocellular carcinoma (HCC) is the most common type of primary liver cancer with low 5-year survival rate. Cellular senescence, characterized by permanent and irreversible cell proliferation arrest, plays an important role in tumorigenesis and development. This study aims to develop a cellular senescence-based stratified model, and a multivariable-based nomogram for guiding clinical therapy for HCC.

Materials and methods: The mRNAs expression data of HCC patients and cellular senescence-related genes were obtained from TCGA and CellAge database, respectively. Through multiple analysis, a four cellular senescence-related genes-based prognostic stratified model was constructed and its predictive performance was validated through various methods. Then, a nomogram based on the model was constructed and HCC patients stratified by the model were analyzed for tumor mutation burden, tumor microenvironment, immune infiltration, drug sensitivity and immune checkpoint. Functional enrichment analysis was performed to explore potential biological pathways. Finally, we verified this model by siRNA transfection, scratch assay and Transwell Assay.

Results: We established an cellular senescence-related genes-based stratified model, and a multivariable-based nomogram, which could accurately predict the prognosis of HCC patients in the ICGC database. The low and high risk score HCC patients stratified by the model showed different tumor mutation burden, tumor microenvironment, immune infiltration, drug sensitivity and immune checkpoint expressions. Functional enrichment analysis suggested several biological pathways related to the process and prognosis of HCC. Scratch assay and transwell assay indicated the promotion effects of the four cellular senescence-related genes (EZH2, G6PD, CBX8, and NDRG1) on the migraiton and invasion of HCC.

Conclusion: We established a cellular senescence-based stratified model, and a multivariable-based nomogram, which could predict the survival of HCC patients and guide clinical treatment.
Identifying and validating molecular subtypes of biliary atresia using multiple high-throughput data integration analysis
Authors: Wang Dingding , Yang Shen , Zhao Yong , Zhang Yanan , Hua Kaiyun , Gu Yichao , Li Shuangshuang , Liao Junmin , Yang Ting , Zhao Jiawei , Huang Jinshi
Published: January 2023

Background

Biliary atresia (BA) is the most common form of severe neonatal obstructive jaundice. The etiology and pathogenesis of BA are multifactorial, and different factors may interact to produce heterogeneous pathological features and clinical outcomes. Despite different pathological features, all patients received the same treatment strategy. This study performed integrative clustering analysis based on multiple high-throughput datasets to identify the molecular subtypes of BA and provide a new treatment strategy for personalized treatment of the different subtypes of BA.

Methods

The RNA sequence dataset GSE122340 in the Gene Expression Omnibus (GEO) database was downloaded; 31 BA and 20 control normal liver tissues were collected at our center for transcriptome sequencing, and clinical and follow-up data of BA patients were available. Molecular subtypes were identified using integrated unsupervised cluster analysis involving gene expression, biliary fibrosis, and immune enrichment scores based on the transcriptome dataset, and the results were validated using independent datasets.

Results

Based on the results of the integrated unsupervised clustering analysis, four molecular subtypes were identified: autoimmune, inflammatory, virus infection-related, and oxidative stress. The autoimmune subtype with a moderate prognosis was dominated by autoimmune responses and morphogenesis, such as the Fc-gamma receptor and Wnt signaling pathway. The biological process of the inflammatory subtype was mainly the inflammatory response, with the best prognosis, youngest age at surgery, and lowest liver stiffness. The virus infection-related subtype had the worst prognosis and was enriched for a variety of biological processes such as viral infection, immunity, anatomical morphogenesis, and epithelial mesenchymal transition. The oxidative stress subtype was characterized by the activation of oxidative stress and various metabolic pathways and had a poor prognosis. The above results were verified independently in the validation sets.

Conclusions

This study identified four molecular subtypes of BA with distinct prognosis and biological processes. According to the pathological characteristics of the different subtypes, individualized perioperative and preoperative treatment may be a new strategy to improve the prognosis of BA.
Chemo-immunoablation of solid tumors: A new concept in tumor ablation
Authors: Meng Liangliang , Wei Yingtian , Xiao Yueyong
Published: January 2023

Chemical ablation was designed to inject chemical agents directly into solid tumors to kill cells and is currently only used clinically for the palliative treatment of tumors. The application and combination of different drugs, from anhydrous ethanol, and glacial acetic acid to epi-amycin, have been clinically tested for a long time. The effectiveness is unsatisfactory due to chemical agents’ poor diffusion and concentration. Immunotherapy is considered a prospective oncologic therapeutic. Still, the clinical applications were limited by the low response rate of patients to immune drugs and the immune-related adverse effects caused by high doses. The advent of intratumoral immunotherapy has well addressed these issues. However, the efficacy of intratumoral immunotherapy alone is uncertain, as suggested by the results of preclinical and clinical studies. In this study, we will focus on the research of immunosuppressive tumor microenvironment with chemoablation and intratumoral immunotherapy, the synergistic effect between chemotherapeutic drugs and immunotherapy. We propose a new concept of intratumoral chemo-immunoablation. The concept opens a new perspective for tumor treatment from direct killing of tumor cells while, enhancing systemic anti-tumor immune response, and significantly reducing adverse effects of drugs.
TERT promoter mutations and methylation for telomerase activation in urothelial carcinomas: New mechanistic insights and clinical significance
Authors: Liu Tiantian , Li Shihong , Xia Chuanyou , Xu Dawei
Published: January 2023

Telomerase, an RNA-dependent DNA polymerase synthesizing telomeric TTAGGG sequences, is primarily silent in normal human urothelial cells (NHUCs), but widely activated in urothelial cell-derived carcinomas or urothelial carcinomas (UCs) including UC of the bladder (UCB) and upper track UC (UTUC). Telomerase activation for telomere maintenance is required for the UC development and progression, and the key underlying mechanism is the transcriptional de-repression of the telomerase reverse transcriptase (TERT), a gene encoding the rate-limiting, telomerase catalytic component. Recent mechanistic explorations have revealed important roles for TERT promoter mutations and aberrant methylation in activation of TERT transcription and telomerase in UCs. Moreover, these TERT-featured genomic and epigenetic alterations have been evaluated for their usefulness in non-invasive UC diagnostics, recurrence monitoring, outcome prediction and response to treatments such as immunotherapy. Importantly, the detection of the mutated TERT promoter and TERT mRNA as urinary biomarkers holds great promise for urine-based UC liquid biopsy. In the present article, we review recent mechanistic insights into altered TERT promoter-mediated telomerase activation in UCs and discuss potential clinical implications. Specifically, we compare differences in senescence and transformation between NHUCs and other types of epithelial cells, address the interaction between TERT promoter mutations and other factors to affect UC progression and outcomes, evaluate the impact of TERT promoter mutations and TERT-mediated activation of human endogenous retrovirus genes on UC immunotherapy including Bacillus Calmette-Guérin therapy and immune checkpoint inhibitors. Finally, we suggest the standardization of a TERT assay and evaluation system for UC clinical practice.
Subunit vaccines for Acinetobacter baumannii
Authors: Yang Ning , Jin Xiao , Zhu Chenghua , Gao Fenglin , Weng Zheqi , Du Xingran , Feng Ganzhu
Published: January 2023

Acinetobacter baumannii is a gram-negative bacterium and a crucial opportunistic pathogen in hospitals. A. baumannii infection has become a challenging problem in clinical practice due to the increasing number of multidrug-resistant strains and their prevalence worldwide. Vaccines are effective tools to prevent and control A. baumannii infection. Many researchers are studying subunit vaccines against A. baumannii. Subunit vaccines have the advantages of high purity, safety, and stability, ease of production, and highly targeted induced immune responses. To date, no A. baumannii subunit vaccine candidate has entered clinical trials. This may be related to the easy degradation of subunit vaccines in vivo and weak immunogenicity. Using adjuvants or delivery vehicles to prepare subunit vaccines can slow down degradation and improve immunogenicity. The common immunization routes include intramuscular injection, subcutaneous injection, intraperitoneal injection and mucosal vaccination. The appropriate immunization method can also enhance the immune effect of subunit vaccines. Therefore, selecting an appropriate adjuvant and immunization method is essential for subunit vaccine research. This review summarizes the past exploration of A. baumannii subunit vaccines, hoping to guide current and future research on these vaccines.
Differential expression profiles and functional prediction of circRNA in mice with traumatic heterotopic ossification
Authors: Wang Zheng , Yi Xinzeyu , Liu Yuhang , Liu Qiaoyun , Li Zonghuan , Yu Aixi
Published: January 2023

Background

Traumatic heterotopic ossification (HO) is an intractable sequela incited by inflammatory insult. To date, the exact molecular mechanisms of traumatic HO formation remain unclear. Recent studies have indicated that circular RNAs (circRNAs) participate in various human skeletal diseases. Although the formation of HO recapitulates many programs during bone development and remodeling, few data are available concerning whether circRNAs could participate in this pathological osteogenesis.

Methods

To investigate the differentially expressed circRNAs (DE-circRNAs) in HO formation, microarray assay was performed to analyze the circRNA expression profile in four pairs of mice HO tissues and normal tissues. Then, qRT-PCR was applied to verify the microarray data. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed the biological functions of the differentially expressed circRNAs target genes. Cytoscape software was used to construct the circRNA–miRNA–mRNA network for circRNAs with different expression levels as well as the target genes.

Results

We demonstrated that 491 circRNAs were significantly differentially expressed in mouse HO tissues by a fold-change ≥ 2 and p-value ≤ 0.05. Among them, the expressions of 168 circRNAs were increased, while 323 were decreased. The expression levels of 10 selected circRNAs were verified successfully by qRT-PCR. GO analysis exhibited that these DE-circRNAs participated in a series of cellular processes. KEGG pathway analysis revealed that multiple upregulated and downregulated pathways were closely related to the DE-circRNAs in HO mice. The circRNA-miRNA-mRNA networks demonstrated that DE-circRNAs may be involved in the pathological osteogenesis of HO through the circRNA-targeted miRNA-mRNA axis.

Conclusion

Our study first demonstrated the expression profiles and predicted the potential functions of DE-circRNAs in mice traumatic HO, which may shed new light on the elucidation of mechanisms as well as provide novel potential peripheral biological diagnostic markers and therapeutic targets for traumatic HO.
An environmentally relevant concentration of antibiotics impairs the immune system of zebrafish (Danio rerio) and increases susceptibility to virus infection
Authors: Pereiro Patricia , Rey-Campos Magalí , Figueras Antonio , Novoa Beatriz
Published: January 2023

In this work, we analysed the transcriptome and metatranscriptome profiles of zebrafish exposed to an environmental concentration of the two antibiotics most frequently detected in European inland surface water, sulfamethoxazole (SMX) and clarithromycin (CLA). We found that those animals exposed to antibiotics (SMX+CLA) for two weeks showed a higher bacterial load in both the intestine and kidney; however, significant differences in the relative abundance of certain bacterial classes were found only in the intestine, which also showed an altered fungal profile. RNA-Seq analysis revealed that the complement/coagulation system is likely the most altered immune mechanism, although not the only one, in the intestine of fish exposed to antibiotics, with numerous genes inhibited compared to the control fish. On the other hand, the effect of SMX+CLA in the kidney was more modest, and an evident impact on the immune system was not observed. However, infection of both groups with spring viremia of carp virus (SVCV) revealed a completely different response to the virus and an inability of the fish exposed to antibiotics to respond with an increase in the transcription of complement-related genes, a process that was highly activated in the kidney of the untreated zebrafish after SVCV challenge. Together with the higher susceptibility to SVCV of zebrafish treated with SMX+CLA, this suggests that complement system impairment is one of the most important mechanisms involved in antibiotic-mediated immunosuppression. We also observed that zebrafish larvae exposed to SMX+CLA for 7 days showed a lower number of macrophages and neutrophils.
Sipunculus nudus genome provides insights into evolution of spiralian phyla and development
Authors: Qi Yi , Chen Liang , Wu Binhua , Tang Xiaoning , Zhu Xiao , Li Ru , Wu Kefeng , Luo Hui
Published: January 2023

Introduction

Sipunculus nudus is the most known species in the genus Sipunculus, distributed in tropical and subtropical coastal waters.

Methods

PacBio sequencing and Illumina sequencing were combined for whole-genome sequencing of S. nudus. LC-MS/MS analysis was performed for the metabolomics of S. nudus.

Results

Herein, we report a 1.75 Gb complete genome assembly with a contig N50 size of 450 kb of the S. nudus based on a strategy combining third-generation long-read sequencing and Illumina sequencing. A total of 80391 protein-coding genes are annotated in this genome. Furthermore, gene family evolution analysis shows that S. nudus belonged to Mollusca or was close to Mollusca, but distinct with Annelida. Transcriptome analysis indicates the involvement of complex developmental events in larve. KEGG pathway analysis of differentially expressed genes showed that these DEGs were mainly enriched in the pathway of amino acid metabolism, lipid metabolism and transport and catabolism. LC-MS/MS analysis shows that S. nudus was rich in a variety of nutritional and functional components, such as carnitine, free amino acids, unsaturated fatty acids, inosine and methionine sulfoxide. Combined transcriptome with LC-MS/MS analysis, the results showed that gene expression and metabolic level involved in the inosine, arginine and proline biosynthesis of S. nudus during different growth stages were significantly changed.

Discussion

Our genome assembly provides an important genome resource and new insight into the relationships of Sipuncula to other spiralian phyla. Meanwhile, transcriptome and LC-MS/MS analysis reveal the systematic gene expression profiles and metabolite components of S. nudus during different growth stages, which provide new insight into the exploration and development of bioactive molecules of S. nudus.
Sedimentation of cohesive sediments at the subtidal flat affected by wind wave in high turbidity estuary
Authors: Shen Qi , Zhu Qin , Liu Shuguang , Lou Sha , Wu Hualin , Zhu Zhenchang , Xu Bin , Yuan Rui
Published: January 2023

Sedimentation is an important mechanism to mitigate the shrinking of tidal flat and to restore its ecological function by means of sand or mud nourishment. To explore the sedimentation of cohesive sediments, a seabed tripod observation system was deployed at the subtidal region of the Hengsha Shoal adjacent to the turbidity maximum zone of the Yangtze Estuary for 11 days. The results showed that the fine sediment with the median grain size around 8 mm occupied the whole water column. The seabed was in relative equilibrium state with the fluctuation of bed level smaller than 16 mm during the moderate wind condition while the seabed experienced a rapid erosion of 38mm and a successive intensive accretion of 68mm during the process of wind wave and swell. The bottom hydrodynamic at 0.3mab during the bed accretion was stronger than that during the bed erosion. The deposition process of cohesive sediments can be better described by the simultaneous deposition paradigm than that by the exclusive deposition paradigm according to the direct data-model comparison of the bed level changes, especially during the impact of fluid mud. Three possible reasons for the better performance of the simultaneous deposition paradigm were proposed. The first possibility is that the fine suspended sediments do maintain a continuous contact with the sediment bed since the direct bed level changes during our observation period has been well reproduced by the simultaneous deposition paradigm. The second possibility is the SSC-induced turbulence damping which facilitates the fine sediment settling in the form of cohesive sediment flocs, indicating the settling of sediments can’t be judged by the critical shear stress for deposition just based on the single particle grain size. The last possibility is the fluid mud-induced overestimated bed shear stress by using turbulent velocity fluctuation above the fluid mud-water interface, which produces excess sediment erosion waiting to be compensated by the simultaneous deposition paradigm. For practical modeling purposes, modeling under the simultaneous deposition paradigm can give satisfactory results for the sedimentation of cohesive sediment especially during the impact of wave or swell.
A spatial and temporal assessment of microplastics in seafloor sediments: A case study for the UK
Authors: Bakir Adil , Doran Denise , Silburn Briony , Russell Josie , Archer-Rand Simeon , Barry Jon , Maes Thomas , Limpenny Caroline , Mason Claire , Barber Jon , Nicolaus E.E. Manuel
Published: January 2023

Seafloor sediments have been defined as sinks for microplastics in the marine environment and could therefore represent suitable matrices for their long-term monitoring. On a regional aspect, the adoption of a common indicator for microplastics in seafloor sediments would allow regional monitoring and assessments through international frameworks such as OSPAR. This study presents the findings of a research and development project monitoring the occurrence and abundance of microplastics in UK seafloor sediments for the period 2013-2021, supporting the development of a national monitoring programme for microplastics in seafloor sediments for the UK (England and Wales). A fast-screening technique based on Nile Red staining of polymers coupled with µ-FTIR was applied and validated using µ-FTIR-FPA. Microplastic particles were detected in all 189 sediment samples from 15 stations selected around the UK for each investigated year (2013 - 2021). Microplastic concentrations (20 – 5000 µm) ranged from 133 – 6,933 particles kg-1 dry weight sediment for 2020-2021. Microplastics mainly consisted of fragments (73%), fibres (19%) and spheres (8%). Plastic fragments ranged from 46 to 3276 µm and plastic fibres from 300 to 1731 µm in length with a mean diameter of 16 µm. Single particle analysis using µ-FTIR indicated a prevalence of Rayon, PP, Rayon/Nylon/Polyester blends, Rubber, PS, PE, PA, PVC, Acrylic, EMAA and PET. Fragments were mainly white in colour (46%) followed by brown (38%), black (1%), blue (1%) and orange (1%). Fibres were mainly white in colour (57%) followed by black (14%), orange (14%) and red (14%). A trend assessment at the UK regional seas levels indicated little visual evidence of any trends in the abundance of microplastics over time in any of the regional seas – with the possible exception of the Northern North Sea with a reduction in abundance over time for the time-period 2013-2021.
Shoreline change due to global climate change and human activity at the Shandong Peninsula from 2007 to 2020
Authors: Gao Wei , Du Jun , Gao Shan , Xu Yuanqin , Li Bing , Wei Xia , Zhang Zhuoli , Liu Jie , Li Ping
Published: January 2023

In this study, how shoreline change responses to global climate change and human activity at the Shandong Peninsula was quantified by analyzing shoreline locations, inshore erosion/accretion rates, and sandy beach profiles for 2007–2020. During the study period, the total shoreline length decreased from 3345.55 km to 3310.18 km, whereas the natural shoreline decreased by 25.41%. As a dominant shore type, the artificial shoreline increased by 827.89 km. Human activities, such as land reclamation and harbor construction, have caused continuous shoreline advance, resulting in a net land increase of 672.40 km2. However, natural shores (e.g., sandy shore) receded at an average annual rate of −1.0 m due to ongoing erosion. The inshore waters of the Shandong Peninsula were largely sedimentary as erosion occurred only at a few hotspots. Therefore, seaward sediment deposition dominated the erosion/accretion trends of the inshore areas of the peninsula. However, global climate change and human activities have exacerbated the erosion caused by sea level rise. Specifically, the climate change caused absolute sea level rise and increasing frequency of extreme weather events, whereas the human activity dominated the transport and supply of sediment in the coastal zone. In the short term, the shoreline of the Shandong Peninsula continues to advance toward the sea due to the growing artificial shoreline. However, this disrupts the balance between sediment supply and marine energies in the coastal zone, and the system then rebalance itself by eroding unprotected natural shores. In the long term, main shoreline evolution trends depend on global climate change and sea level rise which plays a decisive role in shoreline retreat in the Shandong Peninsula.
Insights from the management of offshore energy resources: Toward an ecosystem-services based management approach for deep-ocean industries
Authors: Bravo M. Emilia , Brandt Miriam I. , van der Grient Jesse M. A. , Dahlgren Thomas G. , Esquete Patricia , Gollner Sabine , Jones Daniel O. B. , Levin Lisa A. , McClain Craig R. , Narayanaswamy Bhavani E. , Sutton Tracey , Victorero Lissette , Cordes Erik E.
Published: January 2023

The deep ocean comprises complex ecosystems made up of numerous community and habitat types that provide multiple services that benefit humans. As the industrialization of the deep sea proceeds, a standardized and robust set of methods and metrics need to be developed to monitor the baseline conditions and any anthropogenic and climate change-related impacts on biodiversity, ecosystem function, and ecosystem services. Here, we review what we have learned from studies involving offshore-energy industries, including state-of-the-art technologies and strategies for obtaining reliable metrics of deep-sea biodiversity and ecosystem function. An approach that includes the detection and monitoring of ecosystem services, with open access to baseline data from multiple sectors, can help to improve our global capacity for the management of the deep ocean.
Significance of non-uniform heat source/sink and cattaneo-christov model on hybrid nanofluid flow in a Darcy-forchheimer porous medium between two parallel rotating disks
Authors: Rawat Sawan Kumar , Yaseen Moh , Khan Umair , Kumar Manoj , Eldin Sayed M. , Alotaibi Abeer M. , Galal Ahmed M.
Published: January 2023

The suspension of nanoparticles in fluid influences several properties of the resulting fluid. Many production and manufacturing applications need knowledge of the heat transference mechanism in nanofluids. The current paper concerns the influence of non-uniform heat source/sink on (MoS2-Go/water flow) hybrid nanofluid flow and (Go/water flow) nanofluid flow in a Darcy-Forchheimer porous medium between two parallel and infinite spinning disks in the occurrence of radiation. The Cattaneo-Christov model is utilized to analyze heat and mass transmission. The Cattaneo-Christov model introduces the time lag factors in the process of heat and mass transmission, known as the thermal relaxation parameter and solutal relaxation parameter, respectively. The governing equations are numerically solved employing the “bvp4c function in MATLAB.” The effect of the primary relevant parameters on the velocity, temperature, nanoparticle concentration, and is graphically depicted. Finally, a table is drawn to show the relationships of various critical factors on the Nusselt number, and Sherwood number. Results reveal that an increase in the thermal relaxation parameter reduces the heat transmission rate at both the upper and lower plate. Furthermore, an increase in the nanoparticle’s volume fraction causes enhancement in thermal conduction, which increases the heat transmission rate at the upper disk. The results of this study will be helpful to many transportation processes, architectural design systems, enhanced oil recovery systems, medical fields that utilize nanofluids, and so on.
Improving care for patients with Clostridioides difficile infection: A clinical practice and healthcare systems perspective
Authors: Hocking Lucy , Wilcox Mark , Petrosillo Nicola , Griffin Paul , Steiner Theodore , Attara Gail , Doré Joel , Cabling Mark , Stockwell Stephanie , Romanelli Robert J. , Marjanovic Sonja
Published: January 2023

Introduction

Arriving at a C. difficile infection (CDI) diagnosis, treating patients and dealing with recurrences is not straightforward, but a comprehensive and well-rounded understanding of what is needed to improve patient care is lacking. This manuscript addresses the paucity of multidisciplinary perspectives that consider clinical practice related and healthcare system-related challenges to optimizing care delivery.

Methods

We draw on narrative review, consultations with clinical experts and patient representatives, and a survey of 95 clinical and microbiology experts from the UK, France, Italy, Australia and Canada, adding novel multi-method evidence to the knowledge base.

Results and discussion

We examine the patient pathway and variations in clinical practice and identify, synthesize insights on and discuss associated challenges. Examples of key challenges include the need to conduct multiple tests for a conclusive diagnosis, treatment side-effects, the cost of some antibiotics and barriers to access of fecal microbiota transplantation, difficulties in distinguishing recurrence from new infection, workforce capacity constraints to effective monitoring of patients on treatment and of recurrence, and ascertaining whether a patient has been cured. We also identify key opportunities and priorities for improving patient care that target both clinical practice and the wider healthcare system. While there is some variety across surveyed countries’ healthcare systems, there is also strong agreement on some priorities. Key improvement actions seen as priorities by at least half of survey respondents in at least three of the five surveyed countries include: developing innovative products for both preventing (Canada, Australia, UK, Italy, and France) and treating (Canada, Australia, and Italy) recurrences; facilitating more multidisciplinary patient care (UK, Australia, and France); updating diagnosis and treatment guidelines (Australia, Canada, and UK); and educating and supporting professionals in primary care (Italy, UK, Canada, and Australia) and those in secondary care who are not CDI experts (Italy, Australia, and France) on identifying symptoms and managing patients. Finally, we discuss key evidence gaps for a future research agenda.
Real-time associations among MS symptoms and cognitive dysfunction using ecological momentary assessment
Authors: Chen Michelle H. , Cherian Christine , Elenjickal Karen , Rafizadeh Caroline M. , Ross Mindy K. , Leow Alex , DeLuca John
Published: January 2023

Introduction

Multiple sclerosis (MS) is characterized by a wide range of disabling symptoms, including cognitive dysfunction, fatigue, depression, anxiety, pain, and sleep difficulties. The current study aimed to examine real-time associations between non-cognitive and cognitive symptoms (latter measured both objectively and subjectively in real-time) using smartphone-administered ecological momentary assessment (EMA).

Methods

Forty-five persons with MS completed EMA four times per day for 3 weeks. For each EMA, participants completed mobile versions of the Trail-Making Test part B (mTMT-B) and a finger tapping task, as well as surveys about symptom severity. Multilevel models were conducted to account for within-person and within-day clustering.

Results

A total of 3,174 EMA sessions were collected; compliance rate was 84%. There was significant intra-day variability in mTMT-B performance (p < 0.001) and levels of self-reported fatigue (p < 0.001). When participants reported depressive symptoms that were worse than their usual levels, they also performed worse on the mTMT-B (p < 0.001), independent of upper extremity motor functioning. Other self-reported non-cognitive symptoms were not associated with real-time performance on the mTMT-B [p > 0.009 (Bonferroni-corrected)]. In contrast, when self-reported fatigue (p < 0.001), depression (p < 0.001), anxiety (p < 0.001), and pain (p < 0.001) were worse than the individual’s typical levels, they also reported more severe cognitive dysfunction at the same time. Further, there was a statistical trend that self-reported cognitive dysfunction (not mTMT-B performance) predicted one’s self-reported sense of accomplishment in real-time.

Discussion

The current study was the first to identify divergent factors that influence subjectively and objectively measured cognitive functioning in real time among persons with MS. Notably, it is when symptom severity was worse than the individual’s usual levels (and not absolute levels) that led to cognitive fluctuations, which supports the use of EMA in MS symptom monitoring.
COVID-19 vaccine and booster hesitation around the world: A literature review
Authors: Shah Aashka , Coiado Olivia C.
Published: January 2023

The development of COVID-19 vaccines has helped limit the extent of the pandemic, which over the past 2 years has claimed the lived of millions of people. The Moderna and Pfizer COVID-19 vaccines were the first to be manufactured using mRNA technology. Since then, other manufacturers have built their own vaccines which utilize adenovirus vector, whole inactivated coronavirus, and protein subunit methods. Given the continued mutation of the SARS-CoV-2 virus, a booster of the COVID-19 vaccine offers additional protection for citizens, especially those with comorbid conditions. However, uptake of the vaccine and booster has faced hurdles. This literature review aims to analyze the acceptance of the COVID-19 booster among different populations throughout the world. Keywords searched include “COVID-19 vaccine rates OR COVID-19 booster rates,” “COVID-19 vaccine hesitancy,” “COVID-19 booster hesitancy,” “reasons against COVID-19 vaccine,” “reasons for COVID-19 vaccine,” and “COVID-19 vaccine acceptance” (for each country). Research articles indexed in PubMed, University of Illinois Urbana-Champaign Library, and Google Scholar were included. Despite the proven effectiveness of the COVID-19 booster, vaccine hesitancy is still causing suboptimal compliance to the primary vaccine and booster, thus slowing down control of the pandemic. Reasons for vaccine hesitancy differ by country and acceptance is affected by misinformation, political circumstances, and cultural values. Among the most common reasons found are distrust in the government, a lack of safety information, and fear of side effects. Uptake of the COVID-19 vaccine has also been delayed in low and middle income countries due to resource allocation and as a result, these countries have fallen behind vaccination benchmarks. The future of COVID-19 vaccination is unknown, but vaccine mandates and additional booster doses are a possibility. Determining the ethical impact that these policies could have will allow for the best implementation.