bluuebunny/crossref_metadata_2025 huggingface dataset:
“Forest fire emissions: A contribution to global climate change”
Authors: Singh Swati
Published: November 2022

Forest fires are emitting substantial amounts of greenhouse gases and particulate matter into the atmosphere than assumed in state climate targets. It can play an important role in combustible environments, such as shrublands, grasslands, and forests, and contribute to climate change. Thus, forest fire, and climate change is intertwined concepts. As vegetation burns, release the carbon stored within them. This is the main reason why large-scale forest fires release atmospheric carbon dioxide (CO2) and hence, are responsible for increasing the rate of climate change to a great extent. It is extremely significant to measure the contribution of global forest fire and emissions trends of greenhouse gases. In this context, continental-scale carbon emissions assessments were primarily attempted using ground-based datasets for forest ecosystem fires. Considerable research has been published employing remote sensing data from coast to coast. While ground-based data are valuable, they have some restrictions that can be overcome by remote sensing. Ground-based fire data are primarily limited to the total burned area, with their completeness changing yearly with the location. Remote sensing can provide additional spatio-temporal fire information to improve fire emission estimates. In this paper, the factors driving forest fire, with a brief discussion on the triangular relationship between fire, land degradation, and climate change, the role of Remote Sensing and Geographic Information Systems (GIS), machine learning (ML), and a critical overview of state-of-the-art global climate change are presented.
The forgotten half? Women in the forest management and development discourse in Africa: A review
Authors: Duguma Lalisa A. , Nzyoka Judith , Obwocha Everlyne , Minang Peter , Wainaina Priscilla , Muthee Kennedy
Published: November 2022

Numerous theoretical and empirical studies examining women's engagement in sustainable forest management (SFM) have shown that women bring distinctive interests and values to forest management. However, their effective engagement is still low due to bottlenecks such as rules of entry, ownership, labor division, social norms, perceptions, rules of practice, personal endowments, institutional outcomes, and other organizational cultures. Key among those are the gendered perceptions that marginalize them from the onset. As a result, women's potential to promote SFM in Africa has not been exploited effectively, yet. This raises concerns for gender and social equity as the current practice socially excludes groups that hold specific ecological knowledge, skills, and interests that influence SFM practices. By critically reviewing systematically selected 104 studies conducted on gender issues and forest management in Africa, this paper explores how women's role in forest management and the broader development discourse is constrained. It also characterizes the prevailing engagement models and shows how they influence inclusive processes of deploying SFM practices. Women's engagement in SFM is dominated by public/civic engagement and significantly lags in effectively engaging them as stakeholders, experts, or households. Of the 104 studies reviewed, 54% (n = 57) characterized women's engagement as largely through public meetings compared to 5% (n = 5) as stakeholders and 4% (n = 4) as experts. Thirty-four percent (n = 36) did not clearly categorize the engagement type. Women's engagement in SFM is merely to fill the gender ‘representation' requirements and any effective roles such as decision making, ownership, and benefits are not under the control of women at large. As a result, women's potential to promote forest management and avert ongoing forest loss is not exploited. There is a need to transition from mere representation to a meaningful engagement of women in the sector for inclusive forest management to flourish. In general, capturing, recognizing, and effectively utilizing women's voices and potential in forest management and development discourse requires institutions that deliberately embrace inclusivity and promote equity in general and across gender.
Hortaea werneckii isolates exhibit different pathogenic potential in the invertebrate infection model Galleria mellonella
Authors: Anthonies Stephanie , Vargas-Muñiz José M.
Published: November 2022

Hortaea werneckii is a black yeast with a remarkable tolerance to salt. Most studies have been dedicated to understanding how H. werneckii adapts to hypersaline environments. H. werneckii has an unconventional cell cycle in which it alternates between fission and budding, which is modulated by cell density. Additionally, H. werneckii can cause superficial mycosis of the palm and sole of humans. Here, we determine the impact of salt concentration on the EXF-2000 strain’s cell division pattern and morphology by performing timelapse microscopy at different salt concentrations. At low density and no salt, EXF-2000 primarily grows as pseudohyphae dividing mainly by septation. When grown in the presence of salt at a similar concentration to saltwater or hypersaline environments, we observe it grows first by undergoing fission followed by budding at the poles. Then, we examined a collection of 16 isolates in the presence of 0.6M NaCl, including isolates from marine and hypersaline environments and isolates from patients. These isolates exhibit a wide diversity in colony shape and cellular morphology. The isolates grew as yeast, pseudohyphae, and true hyphae, indicating that isolates can exhibit various cell morphologies under similar environmental conditions. We used the insect larvae Galleria mellonella to determine the pathogenic potential of our isolates. We observe that only a subset of isolates can cause death in our model, and there was no correlation between H. werneckii morphology and capacity to cause disease. Taken together, H. werneckii genomic and phenotypic diversity can serve as a model to better understand how phenotypes and pathogenic potential evolve in environmental fungi.
Insights on variant analysis in silico tools for pathogenicity prediction
Authors: Garcia Felipe Antonio de Oliveira , Andrade Edilene Santos de , Palmero Edenir Inez
Published: November 2022

Molecular biology is currently a fast-advancing science. Sequencing techniques are getting cheaper, but the interpretation of genetic variants requires expertise and computational power, therefore is still a challenge. Next-generation sequencing releases thousands of variants and to classify them, researchers propose protocols with several parameters. Here we present a review of several in silico pathogenicity prediction tools involved in the variant prioritization/classification process used by some international protocols for variant analysis and studies evaluating their efficiency.
Novel targets in renal fibrosis based on bioinformatic analysis
Authors: Yuan Yuan , Xiong Xi , Li Lili , Luo Pengcheng
Published: November 2022

Background: Renal fibrosis is a widely used pathological indicator of progressive chronic kidney disease (CKD), and renal fibrosis mediates most progressive renal diseases as a final pathway. Nevertheless, the key genes related to the host response are still unclear. In this study, the potential gene network, signaling pathways, and key genes under unilateral ureteral obstruction (UUO) model in mouse kidneys were investigated by integrating two transcriptional data profiles.

Methods: The mice were exposed to UUO surgery in two independent experiments. After 7 days, two datasets were sequenced from mice kidney tissues, respectively, and the transcriptome data were analyzed to identify the differentially expressed genes (DEGs). Then, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were executed. A Protein-Protein Interaction (PPI) network was constructed based on an online database STRING. Additionally, hub genes were identified and shown, and their expression levels were investigated in a public dataset and confirmed by quantitative real time-PCR (qRT-PCR) in vivo.

Results: A total of 537 DEGs were shared by the two datasets. GO and the KEGG analysis showed that DEGs were typically enriched in seven pathways. Specifically, five hub genes (Bmp1, CD74, Fcer1g, Icam1, H2-Eb1) were identified by performing the 12 scoring methods in cytoHubba, and the receiver operating characteristic (ROC) curve indicated that the hub genes could be served as biomarkers.

Conclusion: A gene network reflecting the transcriptome signature in CKD was established. The five hub genes identified in this study are potentially useful for the treatment and/or diagnosis CKD as biomarkers.
A high-efficiency differential expression method for cancer heterogeneity using large-scale single-cell RNA-sequencing data
Authors: Yuan Xin , Ma Shuangge , Fa Botao , Wei Ting , Ma Yanran , Wang Yifan , Lv Wenwen , Zhang Yue , Zheng Junke , Chen Guoqiang , Sun Jing , Yu Zhangsheng
Published: November 2022

Colorectal cancer is a highly heterogeneous disease. Tumor heterogeneity limits the efficacy of cancer treatment. Single-cell RNA-sequencing technology (scRNA-seq) is a powerful tool for studying cancer heterogeneity at cellular resolution. The sparsity, heterogeneous diversity, and fast-growing scale of scRNA-seq data pose challenges to the flexibility, accuracy, and computing efficiency of the differential expression (DE) methods. We proposed HEART (high-efficiency and robust test), a statistical combination test that can detect DE genes with various sources of differences beyond mean expression changes. To validate the performance of HEART, we compared HEART and the other six popular DE methods on various simulation datasets with different settings by two simulation data generation mechanisms. HEART had high accuracy (F1 score >0.75) and brilliant computational efficiency (less than 2 min) on multiple simulation datasets in various experimental settings. HEART performed well on DE genes detection for the PBMC68K dataset quantified by UMI counts and the human brain single-cell dataset quantified by read counts (F1 score = 0.79, 0.65). By applying HEART to the single-cell dataset of a colorectal cancer patient, we found several potential blood-based biomarkers (CTTN, S100A4, S100A6, UBA52, FAU, and VIM) associated with colorectal cancer metastasis and validated them on additional spatial transcriptomic data of other colorectal cancer patients.
Screening prognostic genes related to leucovorin, fluorouracil, and irinotecan treatment sensitivity by performing co-expression network analysis for colon cancer
Authors: Wu Pingping , Pan Xuan , Lu Kecen , Gu Ning
Published: November 2022

Background: Colon cancer is one of the most common malignant tumors in the world. FOLFIRI (leucovorin, fluorouracil, and irinotecan) is a common combination in chemotherapy regimens. However, insensitivity to FOLFIRI is an important factor in the effectiveness of the treatment for advanced colon cancer. Our study aimed to explore precise molecular targets associated with chemotherapy responses in colon cancer.

Methods: Gene expression profiles of 21 patients with advanced colorectal cancer who received chemotherapy based on FOLFIRI were obtained from the Gene Expression Omnibus (GEO) database. The gene co-expression network was constructed by the weighted gene co-expression network analysis (WGCNA) and functional gene modules were screened out. Clinical phenotypic correlation analysis was used to identify key gene modules. Gene Ontology and pathway enrichment analysis were used to screen enriched genes in key modules. Protein–protein interaction (PPI) analysis was used to screen out key node genes. Based on the Gene Expression Profiling Interactive Analysis (GEPIA) database, the correlation between the expression levels of these genes and the overall survival (OS) and disease-free survival (DFS) of colon cancer patients was investigated, and the hub genes were screened out. Immunohistochemistry of candidate hub genes was identified using the Human Protein Atlas database. Finally, clinical information and RNA sequencing data of colon cancer were obtained from The Cancer Genome Atlas project database (TCGA), the GEPIA, and the Human Atlas databases for validation.

Results: The WGCNA revealed that three hub genes were closely related to chemotherapy insensitivity of colon cancer: AEBP1, BGN, and TAGLN. The protein expression levels of AEBP1, BGN, and TAGLN in tumor tissues were higher than those in normal tissues. In addition, the gene expression levels of AEBP1, BGN, and TAGLN were negatively correlated with OS and DFS in colon cancer patients. Therefore, AEBP1, BGN, and TAGLN have been identified as potential biomarkers related to the response to FOLFIRI treatment of colon cancer.

Conclusion: We found that AEBP1, BGN, and TAGLN, as potential predictive biomarkers, may play an important role in the response to FOLFIRI treatment of colon cancer and as a precise molecular target associated with chemotherapy response in colon cancer.
miR-17-92 cluster in osteoarthritis: Regulatory roles and clinical utility
Authors: Pan Xuefeng , Cen Xiao , Xiong Xiner , Zhao Zhihe , Huang Xinqi
Published: November 2022

Osteoarthritis (OA) is the most prevalent articular disease, especially in aged population. Caused by multi-factors (e.g., trauma, inflammation, and overloading), OA leads to pain and disability in affected joints, which decreases patients’ quality of life and increases social burden. In pathophysiology, OA is mainly characterized by cartilage hypertrophy or defect, subchondral bone sclerosis, and synovitis. The homeostasis of cell–cell communication is disturbed as well in such pro-inflammatory microenvironment, which provides clues for the diagnosis and treatment of OA. MicoRNAs (miRNAs) are endogenous non-coding RNAs that regulate various processes via post-transcriptional mechanisms. The miR-17-92 cluster is an miRNA polycistron encoded by the host gene called MIR17HG. Mature miRNAs generated from MIR17HG participate in biological activities such as oncogenesis, neurogenesis, and modulation of the immune system. Accumulating evidence also indicates that the expression level of miRNAs in the miR-17-92 cluster is tightly related to the pathological processes of OA, such as chondrocyte apoptosis, extracellular matrix degradation, bone remodeling, and synovitis. In this review, we aim to summarize the roles of the miR-17-92 cluster in the underlying molecular mechanism during the development and progression of OA and shed light on the new avenue of the diagnosis and treatment of OA.
Educational attainment and endometrial cancer: A Mendelian randomization study
Authors: Wang Qixia , Wang Runchen , Chen Chao , Feng Yi , Ye Zhiming , Zhan Miaorong , Wen Hao , Guo Kaimin
Published: November 2022

Background: Low educational attainment has been reported as a risk factor for many diseases. However, conclusion on the association between educational attainment and endometrial cancer (EC) are inconsistent in previous observational studies. This study aims to explore the potential causal association between educational attainment and EC.

Methods: A Mendelian Randomization analysis was performed using publicly summary-level data sets of genome-wide association studies (GWAS). A total of 306 single-nucleotide polymorphisms (SNPs) were extracted as instrumental variables for the exposure of educational attainment from the Social Science Genetic Association Consortium GWAS summary data of 1,131,881 participants of European ancestry. SNPs of EC were obtained from the Endometrial Cancer Association Consortium, the Epidemiology of Endometrial Cancer Consortium and the UK Biobank involving 121,885 people. We conducted inverse variance weighted (IVW) to estimate the causal effect as our primary outcome. And we perform several sensitivity analyses, including MR-Egger regression, weighted median method, MR-PRESSO (Mendelian Randomization Pleiotropy Residual Sum and Outlier) global test, and leave-one-out sensitivity analysis, to evaluate the effect of pleiotropism on the causal estimates.

Results: Genetic predisposition towards 4.2 years of additional educational attainment was associated with 38% lower risk of EC. (odds ratio 0.72, 95% confidence interval 0.62 to 0.83; p = 1.65*10−5). The consistent results of sensitivity analyses indicated our causal estimates were reliable. Genetic predisposition towards longer educational attainment was associated with lower risk of obesity, high waist-to-hip ratio (WHR), and diabetes.

Conclusion: This study indicated that low educational attainment was a causal risk factor for EC, especially for EC with endometrioid histology. Low educational attainment might lead to EC through the mediator of obesity, high WHR, and diabetes.
Occurrence and role of lung megakaryocytes in infection and inflammation
Authors: Gelon Lucie , Fromont Léa , Lefrançais Emma
Published: November 2022

Megakaryocytes (MKs) are large cells giving rise to platelets. It is well established that in adults, MKs develop from hematopoietic stem cells and reside in the bone marrow. MKs are also rare but normal constituents of the venous blood returning to the lungs, and MKs are found in the lung vasculature (MKcirc), suggesting that these cells are migrants from the bone marrow and get trapped in lung capillaries where the final steps of platelet production can occur. An unprecedented increase in the number of lung and circulating MKs was described in coronavirus disease 2019 (COVID-19) patients, suggesting that lung thrombopoiesis may be increased during lung infection and/or thromboinflammation. In addition to the population of platelet-producing intravascular MKs in the lung, a population of lung-resident megakaryocytes (MKL) has been identified and presents a specific immune signature compared to its bone marrow counterparts. Recent single-cell analysis and intravital imaging have helped us gain a better understanding of these populations in mouse and human. This review aims at summarizing the recent data on increased occurrence of lung MKs and discusses their origin, specificities, and potential role in homeostasis and inflammatory and infectious lung diseases. Here, we address remaining questions, controversies, and methodologic challenges for further studies of both MKcirc and MKL.
The impact of aging on intestinal mucosal immune function and clinical applications
Authors: Zheng Han , Zhang Chi , Wang Qianqian , Feng Shuyan , Fang Yi , Zhang Shuo
Published: November 2022

Immune cells and immune molecules in the intestinal mucosa participate in innate and adaptive immunity to maintain local and systematic homeostasis. With aging, intestinal mucosal immune dysfunction will promote the emergence of age-associated diseases. Although there have been a number of studies on the impact of aging on systemic immunity, relatively fewer studies have been conducted on the impact of aging on the intestinal mucosal immune system. In this review, we will briefly introduce the impact of aging on the intestinal mucosal barrier, the impact of aging on intestinal immune cells as well as immune molecules, and the process of interaction between intestinal mucosal immunity and gut microbiota during aging. After that we will discuss potential strategies to slow down intestinal aging in the elderly.
Development of a copper metabolism-related gene signature in lung adenocarcinoma
Authors: Chang Wuguang , Li Hongmu , Zhong Leqi , Zhu Tengfei , Chang Zenghao , Ou Wei , Wang Siyu
Published: November 2022

Purpose

The dysregulation of copper metabolism is closely related to the occurrence and progression of cancer. This study aims to investigate the prognostic value of copper metabolism-related genes (CMRGs) in lung adenocarcinoma (LUAD) and its characterization in the tumor microenvironment (TME).

Methods

The differentially expressed CMRGs were identified in The Cancer Genome Atlas (TCGA) of LUAD. The least absolute shrinkage and selection operator regression (LASSO) and multivariate Cox regression analysis were used to establish the copper metabolism-related gene signature (CMRGs), which was also validated in Gene Expression Omnibus (GEO) database (GSE72094). The expression of key genes was verified by quantitative real-time PCR (qRT-PCR). Then, the CMRGS was used to develop a nomogram to predict the 1-year, 3-year, and 5-year overall survival (OS). In addition, differences in tumor mutation burden (TMB), biological characteristics and immune cell infiltration between high-risk and low-risk groups were systematically analyzed. Immunophenoscore (IPS) and an anti-PD-L1 immunotherapy cohort (IMvigor210) were used to verify whether CMRGS can predict the response to immunotherapy in LUAD.

Results

34 differentially expressed CMRGs were identified in the TCGA dataset, 11 of which were associated with OS. The CMRGS composed of 3 key genes (LOXL2, SLC31A2 and SOD3) had showed good clinical value and stratification ability in the prognostic assessment of LUAD patients. The results of qRT-PCR confirmed the expression of key CMRGs in LUAD and normal tissues. Then, all LUAD patients were divided into low-risk and high-risk groups based on median risk score. Those in the low-risk group had a significantly longer OS than those in the high-risk group (P<0.0001). The area under curve (AUC) values of the nomogram at 1, 3, and 5 years were 0.734, 0.735, and 0.720, respectively. Calibration curves comparing predicted and actual OS were close to ideal model, indicating a good consistency between prediction and actual observation. Functional enrichment analysis showed that the low-risk group was enriched in a large number of immune pathways. The results of immune infiltration analysis also confirmed that there were a variety of immune cell infiltration in the low-risk group. In addition, multiple immune checkpoints were highly expressed in the low-risk group and may benefit better from immunotherapy.

Conclusion

CMRGS is a promising biomarker to assess the prognosis of LUAD patients and may be serve as a guidance on immunotherapy.
Immune landscape and immunotherapy for penile cancer
Authors: Tang Yaxiong , Hu Xu , Wu Kan , Li Xiang
Published: November 2022

Penile cancer is a rare malignancy and usually refers to penile squamous cell carcinoma (PSCC), which accounts for more than 95% of all penile malignancies. Although organ-sparing surgery is an effective treatment for early-stage PSCC, surgical intervention alone is often not curative for advanced PSCC with metastases to the inguinal and/or pelvic lymph nodes; thus, systemic therapy is required (usually platinum-based chemotherapy and surgery combined). However, chemotherapy for PSCC has proven to be of limited efficacy and is often accompanied by high toxicity, and patients with advanced PSCC usually have poor prognosis. The limited treatment options and poor prognosis indicate the unmet need for advanced PSCC. Immune-based therapies have been approved for a variety of genitourinary and squamous cell carcinomas but are rarely reported in PSCC. To date, several studies have reported high expression of PDL1 in PSCC, supporting the potential application of immune checkpoint inhibitors in PSCC. In addition, human papillomavirus (HPV) infection is highly prevalent in PSCC and plays a key role in the carcinogenesis of HPV-positive PSCC, suggesting that therapeutic HPV vaccine may also be a potential treatment modality. Moreover, adoptive T cell therapy (ATC) has also shown efficacy in treating advanced penile cancer in some early clinical trials. The development of new therapeutics relies on understanding the underlying biological mechanisms and processes of tumor initiation, progression and metastasis. Therefore, based on the interest, we reviewed the tumor immune microenvironment and the emerging immunotherapy for penile cancer.
Three-dimensional analyses of vascular network morphology in a murine lymph node by X-ray phase-contrast tomography with a 2D Talbot array
Authors: Schwarzenberg Florian L. , Schütz Paul , Hammel Jörg U. , Riedel Mirko , Bartl Jasmin , Bordbari Sharareh , Frank Svea-Celina , Walkenfort Bernd , Busse Madleen , Herzen Julia , Lohr Christian , Wülfing Clemens , Henne Stephan
Published: November 2022

With growing molecular evidence for correlations between spatial arrangement of blood vasculature and fundamental immunological functions, carried out in distinct compartments of the subdivided lymph node, there is an urgent need for three-dimensional models that can link these aspects. We reconstructed such models at a 1.84 µm resolution by the means of X-ray phase-contrast imaging with a 2D Talbot array in a short time without any staining. In addition reconstructions are verified in immunohistochemistry staining as well as in ultrastructural analyses. While conventional illustrations of mammalian lymph nodes depict the hilus as a definite point of blood and lymphatic vessel entry and exit, our method revealed that multiple branches enter and emerge from an area that extends up to one third of the organ’s surface. This could be a prerequisite for the drastic and location-dependent remodeling of vascularization, which is necessary for lymph node expansion during inflammation. Contrary to corrosion cast studies we identified B-cell follicles exhibiting a two times denser capillary network than the deep cortical units of the T-cell zone. In addition to our observation of high endothelial venules spatially surrounding the follicles, this suggests a direct connection between morphology and B-cell homing. Our findings will deepen the understanding of functional lymph node composition and lymphocyte migration on a fundamental basis.
Single-cell RNA-sequencing in asthma research
Authors: Tang Weifeng , Li Mihui , Teng Fangzhou , Cui Jie , Dong Jingcheng , Wang Wenqian
Published: November 2022

Asthma is a complex and heterogeneous disease with multicellular involvement, and knowledge gaps remain in our understanding of the pathogenesis of asthma. Efforts are still being made to investigate the immune pathogenesis of asthma in order to identify possible targets for prevention. Single cell RNA sequencing (scRNA-seq) technology is a useful tool for exploring heterogeneous diseases, identifying rare cell types and distinct cell subsets, enabling elucidation of key processes of cell differentiation, and understanding regulatory gene networks that predict immune function. In this article, we provide an overview of the importance of scRNA-seq for asthma research, followed by an in-depth discussion of the results in recent years, in order to provide new ideas for the pathogenesis, drug development and treatment of asthma.
Altered dental plaque microbiota correlated with salivary inflammation in female methamphetamine users
Authors: Deng Zhuohang , Guo Kaili , Cao Fengdi , Fan Tiantian , Liu Bin , Shi Mingyue , Liu Yue , Ma Zhe
Published: November 2022

Poor oral health is the most immediate and overlooked hazard of methamphetamine abuse in humans. Previous studies have reported methamphetamine-associated alterations in saliva microbiota, but the cause of methamphetamine-induced alterations in the oral microenvironment remains unclear. The present study aimed to investigate the alterations in dental plaque microbiota in methamphetamine users, and to explore their relationship with local immune inflammation in the oral cavity. This may provide new ideas on the development of methamphetamine-related oral microenvironment changes. Questionnaires and samples were obtained from 30 female methamphetamine users and 15 sex- and age-matched healthy controls. Microbial profiles of supragingival dental plaque were analyzed using 16S rRNA gene sequencing. Inflammatory factors in saliva were measured using enzyme-linked immunosorbent assay. Methamphetamine users had worse oral self-evaluation. Compared with healthy controls, methamphetamine users showed no differences in oral dental plaque microbial diversity but exhibited differences in the relative abundance of several microbial taxa. At the phylum level, a higher abundance of Proteobacteria and a lower abundance of Firmicutes were detected in methamphetamine users. Moreover, function prediction using the MetaCyc database showed that 33 pathways were significantly upregulated in methamphetamine users; Only the glycolytic (Pyrococcus) pathway was enriched in the C group. Importantly, salivary inflammatory factors showed complex significant associations with bacterial genera in methamphetamine users. Specifically, the genus Neisseria was positively correlated with IL-17 levels in saliva, and both were high in methamphetamine users. In contrast, the genus Streptococcus, with a lower abundance, was positively correlated with lower IL-10 levels. Overall, This study is the first to provide evidence for a link between altered dental plaque microbiota and salivary inflammation in methamphetamine users. Further elucidation of the interactions between methamphetamine use and oral microenvironment would be beneficial for appropriate interventions to improve oral health.
Temporal variations, distribution, ecological risks, and sources of antibiotics in the marine ecosystem of Dapeng Cove, Shenzhen, South China
Authors: Su Haochang , Li Wenjun , Hu Xiaojuan , Xu Wujie , Xu Yu , Wen Guoliang , Cao Yucheng
Published: November 2022

Introduction

Antibiotics are widely used in medical and health services, as well as livestock farming. High concentrations of antibiotics are eventually discarded into rivers due to incomplete metabolism and removal. Bays connect rivers to the sea, and have important ecological functions. Although the occurrence, concentrations, and distribution of antibiotics in bays have been widely studied, the temporal variations in the concentration, contamination indicators and sources of antibiotics, as well as related ecological risk factors, remain unclear.

Methods

Within this context, we investigate the sources, concentrations, temporal variations, and ecological risks associated with antibiotics in water and sediment samples from Dapeng Cove, Shenzhen, South China, in three rainy seasons.

Results

Eight and ten different antibiotics were detected in the water and sediment samples, respectively. Of these, the detection rates of erythromycin-H2O (ETM) and clarithromycin were highest in both sample types (100%), while trimethoprim (TMP) and ETM were the most abundant antibiotics in the water and sediment samples, respectively. The total concentration (TC) of antibiotics was highest in water and sediment samples from a local domestic sewage site, at 301.96 ng/L and 18.67 ng/g, respectively. Several environmental factors and the concentrations of the predominant antibiotics TMP and ETM were positively correlated. Multiple linear regression analysis revealed TMP and ETM to be the predominant antibiotics influencing the TC of the target antibiotics, with partial regression coefficients of 1.28 and 1.136, respectively (p < 0.01). Notably, ETM had risk quotients of 0.43–7.91, indicating medium to high risk, while samples from the inner bay and domestic sewage outlet had high ecological risk levels. Redundancy analysis showed that the domestic sewage and inner bay samples were clustered closely but separately from the other samples.

Discussion

The results of our study indicate that domestic sewage is the dominant source of antibiotics in the bay.
Destination of New Guinea Coastal Undercurrent in the western tropical Pacific: Variability and linkages
Authors: Azminuddin Fuad , Jang Chan Joo , Jeon Dongchull
Published: November 2022

The New Guinea Coastal Undercurrent (NGCUC) is considered a bottleneck in the western tropical Pacific (WTP), carrying upper-to-intermediate waters from the south to the northwestern Pacific, thereby playing a fundamen tal role in the interhemispheric water mass exchange. However, how the NGCUC links to the circulation in the WTP was insufficiently studied. This work explores the destination of NGCUC waters, its spatiotemporal changes, and possible physical processes linked with the downstream NGCUC using ocean reanalysis for 22 years (1994 – 2015). Lagrangian particle tracking discloses eight major destinations of the NGCUC: The Equatorial Undercurrent (EUC, 35.26%), the North Equatorial Countercurrent (NECC, 12.3%), the North (13.33%) and South (8.85%) Subsurface Countercurrents, the Equatorial Deep Jet (11.49%), the Mindanao Undercurrent (13.24%), and the Indonesian (3.47%) and Halmahera (0.86%) Throughflows. The NGCUC waters are distributed mainly to the east (81.65%) and their dissemination varies markedly with depth. These destinations exhibit significant variations on seasonal and interannual time scales. The NGCUC strengthens (weakens) during summer (winter) and more NGCUC waters are distributed westward and northeastward (eastward). Interannually, the distribution of the NGCUC water is influenced by El Niño-Southern Oscillation, in which most of its eastward-distributed waters shift northward (equatorward) in El Niño (La Niña) phase joining the strengthened NECC (EUC). Changes in the NGCUC water destination can transform the water mass properties in the WTP. The findings of this study also emphasize the fundamental role of eddies in trapping and redistributing the NGCUC waters and linking the currents in the WTP.
Ocean kinetic energy and photosynthetic biomass are important drivers of planktonic foraminifera diversity in the Atlantic Ocean
Authors: Rufino Marta M. , Salgueiro Emilia , Voelker Antje A. H. L. , Polito Paulo S. , Cermeño Pedro A. , Abrantes Fatima
Published: November 2022

To assess the anthropogenic effect on biodiversity, it is essential to understand the global diversity distribution of the major groups at the base of the food chain, ideally before global warming initiation (1850 Common Era CE). Since organisms in the plankton are highly interconnected and carbonate synthesizing species have a good preservation state in the Atlantic Ocean, the diversity distribution pattern of planktonic foraminifera from 1741 core-top surface sediment samples (expanded ForCenS database) provides a case study to comprehend centennial to decadal time-averaged diversity patterns at pre-1970 CE times, the tempo of the substantial increase in tropospheric warming. In this work, it is hypothesized and tested for the first time, that the large-scale diversity patterns of foraminifera communities are determined by sea surface temperature (SST, representing energy), Chl-a (a surrogate for photosynthetic biomass), and ocean kinetic energy (as EKE). Alpha diversity was estimated using species richness (S), Shannon Wiener index (H), and Simpson evenness (E), and mapped using geostatistical approaches. The three indices are significantly related to SST, Chl-a, and EKE (71-88% of the deviance in the generalized additive mixed model, including a spatial component). Beta diversity was studied through species turnover using gradient forest analysis (59% of the variation). The primary community thresholds of foraminifera species turnover were associated with 5-10 °C and 22-28 °C SST, 0.05-0.15 mg m-3 Chl-a, and 1.2-2.0 cm2 s-2 log10 EKE energy, respectively. Six of the most important foraminifera species identified for the environmental thresholds of beta diversity are also fundamental in transfer functions, further reinforcing the approaches used. The geographic location of the transition between the four main biogeographic zones was redefined based on the results of beta diversity analysis and incorporating the new datasets, identifying the major marine latitudinal gradients, the most important upwelling areas (Benguela Current, Canary Current), the Equatorial divergence, and the subtropical fronts (Gulf Stream-North Atlantic Drift path in the north, and the South Atlantic current in the south). In conclusion, we provide statistical proof that energy (SST), food supply (Chl-a), and currents (EKE) are the main environmental drivers shaping planktonic foraminifera diversity in the Atlantic ocean and define the associated thresholds for species change on those variables.
Short- and long-term follow-up and additional benefits in a sickle cell disease patient experienced severe crizanlizumab infusion-related vaso-occlusive crisis: A case report
Authors: Alshurafa Awni , Yassin Mohamed A.
Published: November 2022

Sickle cell disease is an autosomal recessive disorder characterized by the presence of sickle hemoglobin that leads to chronic hemolysis and vaso-occlusive crisis. After decades of limited therapy options, crizanlizumab is a humanized monoclonal antibody approved by the Food and Drug Administration (FDA) in 2019 for sickle cell-related pain crises for patients 16 years of age and above. Although rare, infusion-related reactions, including painful crises, occurred in 3% as per the package insert. However, the data on how to deal with such reactions and about further treatment outcomes are limited as most patients stopped crizanlizumab after the reaction. Herein, we report the good outcome of 13 doses of crizanlizumab in a 19-year-old female patient with sickle cell disease on hydroxyurea, despite experiencing a severe infusion-related painful crisis during the second infusion. Additional benefits of crizanlizumab, in this case, were preventing new episodes of acute chest syndrome, quitting chronic narcotics use, and a remarkable improvement in quality of life and overall performance.
The efficacy and safety of Sacubitril/Valsartan on pulmonary hypertension in hemodialysis patients
Authors: Zhao Cong , Guo Yanhong , Wang Yulin , Wang Liuwei , Yu Lu , Liang Yan , Zhai Zihan , Tang Lin
Published: November 2022

Background

Pulmonary hypertension (PH) is a common complication of end-stage renal disease which is associated with adverse outcomes including all-cause mortality and cardiovascular events. Recent studies have demonstrated that Sacubitril/Valsartan (Sac/Val) as an enkephalinase inhibitor and angiotensin II receptor blocker could reduce pulmonary artery systolic pressure (PASP) and improve the prognosis of patients with heart failure. However, whether Sac/Val is effective in hemodialysis (HD) patients with PH is essentially unknown. In this retrospective study, we aimed to evaluate the efficacy and safety of Sac/Val in the treatment of PH in HD patients.

Methods

A total of 122 HD patients with PH were divided into Sac/Val group (n = 71) and ARBs group (n = 51) based on the treatment regimen. The PASP, other cardiac parameters measured by echocardiography, and cardiac biomarkers including N-terminal fragment of BNP (NT-proBNP) and cardiac troponin I (cTnI) were observed at baseline and 3 months after treatment.

Results

There were no significant differences in the baseline characteristics between the two groups. PASP decreased significantly from 45(38, 54) to 28(21, 40) mmHg in Sac/Val group (p < 0.001). PASP reduced from 41(37, 51) to 34(27, 44) mmHg in ARBs group (p < 0.001), and the decrease was more pronounced in the Sac/Val group (p < 0.001). In addition, improvements in the right atrial diameter (RAD), left ventricular diameter (LVD), left ventricular posterior wall thickness (LVPWT), left atrial diameter (LAD), pulmonary artery diameter (PAD), left ventricular end-diastolic volume (LVEDV), left ventricular end-systolic volume (LVESV), left ventricular ejection fraction (LVEF), and fractional shortening (FS) were found in Sac/Val group (ps < 0.05). After 3 months, LVD, LAD, LVEDV, LVESV, LVEF, SV, and PASP were significantly improved in Sac/Val group compared with ARBs group (ps <0.05). Significant reduction in NT-proBNP [35,000 (15,000, 70,000) pg/ml vs. 7,042 (3,126, 29,060) pg/ml, p < 0.001] and cTnI [0.056(0.031, 0.085) ng/ml vs. 0.036 (0.012, 0.056) ng/ml, p < 0.001) were observed in Sac/Val group. No significant differences were observed in adverse events between the two groups (ps > 0.05).

Conclusion

Sac/Val seems to be an efficacious regimen in PH with favorable safety and has huge prospects for treating PH in HD patients.
Seasonal patterns of rhizosphere microorganisms suggest carbohydrate-degrading and nitrogen-fixing microbes contribute to the attribute of full-year shooting in woody bamboo Cephalostachyum pingbianense
Authors: Li Lushuang , Xia Tize , Yang Hanqi
Published: November 2022

Compared with the ordinary single-season shooting among woody bamboos in Poaceae, the attribute of full-year shooting in Cephalostachyum pingbianense represents a unique shooting type or mechanism. Nevertheless, except for the overall physiological mechanism, the effect of ecological factors, especially soil microorganisms, on this full-year shooting characteristic remains unclear. In this study, 16S rRNA and ITS rRNA genes were sequenced using the Illumina platform. Our aims were to detect the seasonal changes in rhizospheric microbial communities of C. pingbianense and to discover the correlations of soil microbes with soil properties and bamboo shoot productivity. The results showed that seasonal change had no significant effect on bacterial alpha diversity, but significantly affected bacterial and fungal community structures as well as fungal richness. Among all soil properties examined, soil temperature, soil moisture and organic matter were the predominant factors affecting bacterial community diversity and structure. Soil temperature and soil moisture also significantly influenced fungal community structure, while available phosphorus had the greatest effect on fungal diversity. In each season, bacterial genera Acidothermus, Roseiarcus, and Bradyrhizobium, along with fungal genera Saitozyma, Mortierella, Trichoderma, etc., were dominant in bacterial and fungal communities, respectively. Bacterial community functions in four seasons were dominated by chemoheterotrophy, cellulolysis, and nitrogen fixation. Saprotrophic fungi occupied a high proportion in soil samples of all seasons. In addition, correlation analysis revealed that the bamboo shoot productivity was positively correlated with multiple microbial taxa involved in carbon and nitrogen cycles. It is proposed that highly abundant microbes involved in carbohydrate degradation and nitrogen fixation in the rhizosphere soil may contribute to the attribute of producing bamboo shoots all year round in C. pingbianense. This study is among the few cases revealing the connection between bamboo shooting characteristics and soil microorganisms, and provides new physiological and ecological insights into the forest management of woody bamboos.
Whole genome sequencing and prediction of antimicrobial susceptibilities in non-tuberculous mycobacteria
Authors: Solanki Priya , Lipman Marc , McHugh Timothy D. , Satta Giovanni
Published: November 2022

Non-tuberculous mycobacteria (NTM) are opportunistic pathogens commonly causing chronic, pulmonary disease which is notoriously hard to treat. Current treatment for NTM infections involves at least three active drugs (including one macrolide: clarithromycin or azithromycin) over 12 months or longer. At present there are limited phenotypic in vitro drug susceptibility testing options for NTM which are standardised globally. As seen with tuberculosis, whole genome sequencing has the potential to transform drug susceptibility testing in NTM, by utilising a genotypic approach. The Comprehensive Resistance Prediction for Tuberculosis is a database used to predict Mycobacterium tuberculosis resistance: at present there are no similar databases available to accurately predict NTM resistance. Recent studies have shown concordance between phenotypic and genotypic NTM resistance results. To benefit from the advantages of whole genome sequencing, further advances in resistance prediction need to take place, as well as there being better information on novel drug mutations and an understanding of the impact of whole genome sequencing on NTM treatment outcomes.
The structure and assembly of rhizobacterial communities are influenced by poplar genotype
Authors: Zhu Qi Liang , Yan Kun , Wang Nian Zhao , Ma Shu Qi , Lu De Shan , Su Xiao Hua , Yuan Zheng Sai , Dong Yu Feng , Wang Yan Ping , Ding Chang Jun
Published: November 2022

The interaction between plants and microbes dominates plant growth and fitness in specific environments. The study of the relationship between plant genotypes and rhizobacterial community structure would provide a deep insight into the recruitment strategies of plants toward soil bacteria. In this study, three genotypes of 18-year-old mature poplar (H1, H2, and H3) derived from four different parents were selected from a germplasm nursery of Populus deltoides. Rhizosphere soil carbon, nitrogen, and phosphorus properties as well as the 16S rDNA sequences of rhizobacterial communities were analyzed to determine the relationship between poplar genotypes and rhizobacterial communities assembly. The results showed there were significant differences in the diversity (Chao1, ACE index, and Shannon index) of rhizobacterial communities between H1 and H2, as well as between H2 and H3, but no difference between H1 and H3. Principal component analysis also revealed a similar structure of rhizobacterial communities between H1 and H3, whereas the rhizobacterial communities of H2 demonstrated significant differences from H1 and H3. Linear discriminant effect size analysis indicated that there were 11 and 14 different biomarkers in the H1 and H3 genotype, respectively, but 42 in the H2 genotype. Co-occurrence network analysis indicated that the rhizobacterial communities of H2 had a distinct network structure compared to those of the other two genotypes, whereas H1 and H3 had a similar pattern of co-occurrence network. Threshold indicator taxa analysis revealed that 63 genera responded significantly to NO3–-N content and 58 genera to NH4+-N/NO3–-N ratio. Moreover, the stochastic assembly process was found to be decreased with increasing NO3–-N content and fluctuated with increasing NH4+-N/NO3–-N ratio. All results indicated that the structure of poplar rhizobacterial communities were influenced by host genotypes, and available nitrogen might play a dominant role in the assembly of rhizobacterial communities. This study would promote the future selection and utilization of rhizobacteria in poplar breeding.
Review of the relationship and underlying mechanisms between the Qinghai–Tibet plateau and host intestinal flora
Authors: Lv Jin , Qi Ping , Bai Liu-Hui , Yan Xiang-Dong , Zhang Lei
Published: November 2022

The intestinal microbial community is the largest ecosystem in the human body, in which the intestinal flora plays a dominant role and has a wide range of biological functions. However, it is vulnerable to a variety of factors, and exposure to extreme environments at high altitudes, as seen on the Qinghai–Tibet plateau, may cause changes in the structure and function of the host intestinal flora. Conversely, the intestinal flora can help the host adapt to the plateau environment through a variety of ways. Herein, we review the relationship and underlying mechanism between the host intestinal flora and the plateau environment by discussing the characteristics of the plateau environment, its influence on the intestinal flora, and the important role of the intestinal flora in host adaptation to the plateau environment. This review aimed to provide a reference for maintaining the health of the plateau population.