bluuebunny/crossref_metadata_2025 huggingface dataset:
Soil samples from sporotrichosis transmission belt area: Searching for fungal species and their antagonistic activity against Sporothrix brasiliensis
Authors: Lara da Costa Gisela , Escórcio Ferreira Isabella , Corrêa-Moreira Danielly , Marinho Anna , Benedito de Almeida Adilson , Antônio Pereira Sandro , Moraes Borba Cintia , Marques Evangelista Oliveira Manoel
Published: December 2022

Since 1998, the state of Rio de Janeiro, Brazil, has become a public health problem regarding sporotrichosis, a disease caused by Sporothrix spp. involving contact with infected cats. Efforts to isolate these species from environmental sources are not always successful. In our study, soil from residences situated in cities of Rio de Janeiro where cats with sporotrichosis live was collected and cultured an attempt to isolate Sporothrix spp. but it was not successful. However, other saprophytic fungal species were isolated from soil and identified and among them Purpureocillium lilacinum was the most frequent. From there, we decided to study the in vitro interaction of this species with S. brasiliensis, the principal agent that causes sporotrichosis in this state. The results showed that ten isolates of P. lilacinum inhibited the radial mycelial growth of S. brasiliensis with different percentage of inhibition. The interaction between them revealed the pattern described as overgrowth by antagonist. In conclusion, our data suggest that fungal species with very fast growth and capable of producing metabolites could hinder the growth of Sporothrix spp., it also opens the way for the identification of secondary metabolites with biological activity that could be tested against pathogenic fungi.
The management of Helicobacter pylori infection and prevention and control of gastric cancer in China
Authors: Hu Yi , Zhu Yin , Lu Nong-Hua
Published: December 2022

Helicobacter pylori (H. pylori) infection, a type-1 carcinogen, was closely associated with gastric cancer (GC). Successfully eradicating H. pylori infection could reduce the incidence of GC. China was a country with high incidence of GC and high prevalence of H. pylori infection. Nearly half of worldwide GC new cases and deaths attributed to H. pylori infection occurred in China. H. pylori prevalence varied over time with the improvement of socioeconomic status and sanitary conditions. The knowledge of antibiotic resistance rate in time was important to guide the clinical choice of antibiotics use in the regimens. With the publication of five Chinese consensus reports on the management of H. pylori infection and the effort of public preach of H. pylori-related knowledge, the standardization of H. pylori diagnosis and treatment by clinicians was improved. Bismuth-containing quadruple therapy was widely applied in clinical practice of H. pylori eradication because of high efficacy and safety. High-dose Proton Pump Inhibitor-amoxicillin dual therapy or vonoprazan-amoxicillin dual therapy showed comparable efficacy and lower side effects than bismuth-containing quadruple therapy, which were the alternative choice. The diagnosis rate of early GC was low and distinguishing Chinese GC risk population for the further endoscopy screening was important. Efforts have been done to establish prediction models to stratify GC risk in the Chinese GC risk population. We reviewed the current situation of the management of H. pylori infection and prevention and control of GC in China here.
Fecal microbiota transplantation treatment of autoimmune-mediated type 1 diabetes: A systematic review
Authors: Zhang Shuo , Deng Feiying , Chen Jingxian , Chen Fengwu , Wu Zezhen , Li Liping , Hou Kaijian
Published: December 2022

There is a strong link between fecal microbiota and the development of type 1 diabetes. As an emerging therapeutic modality, fecal microbiota transplantation has been shown to be safe and effective in the treatment of many intestinal and extraintestinal diseases. Various studies have found that fecal microbiota transplantation can treat diseases by correcting patients’ immune disorders. Besides, many studies have found that fecal microbiota transplantation can improve glycemic control and insulin resistance in diabetic patients. Therefore, this paper reviews the mechanism of action of fecal microbiota transplantation on autoimmune-mediated T1DM and the current research progress, feasibility, and issues that need to be addressed in the future development of fecal microbiota transplantation in the treatment of autoimmune-mediated T1DM.
Effects of temporal framing and hazard experience on receptivity to hurricane risk messages: A survey of U.S. Gulf Coast residents
Authors: Retchless David P. , Ross Ashley D.
Published: December 2022

Introduction

As knowledge in the scientific community increases regarding how anthropogenic CO2 loading of the atmosphere will impact future hurricane activity, the need for effective and accurate communication of hurricane risk in coastal communities—specifically to non-scientific stakeholders—also increases.

Methods

To better inform hurricane risk communication, this study employs a survey of U.S. Gulf Coast residents immediately following the active 2017 hurricane season to consider how message framing (as established by communicator word choice) and stakeholders' experience may affect receptivity to hurricane hazard information. Specifically, it tests how respondents' perceptions of hurricane risk varied with prior experience and following exposure to randomly assigned, infographic-based depictions of trends in major hurricane (≥ category 3, Saffir Simpson Scale) frequency. The set of randomly assigned infographics varied in both temporal framing (past-to-present trends based on paleo data versus present-to-future trends based on climate projections) and causal framing (‘climate change' versus ‘ocean and atmospheric change').

Results

Damaging hurricane experience may be associated with a tendency towards increasing hurricane risk perceptions after viewing the infographics. For framing effects, temporal framing of hurricane risk messages matters, with forward-looking framings (future projections) causing increased perceptions of risk and storm frequency; effects of causal framing were not significant. The results also show that Gulf Coast residents tend to be more optimistic about the future frequency of major hurricanes than most scientists and, consistent with confirmation and optimism biases, are somewhat resistant to changing their prior risk beliefs based on infographic exposure.

Discussion

These results suggest that future projections – rather than paelo analogs – may be best for quickly communicating expected increases in hurricane risk. Communicators should consider these factors when translating scientific hurricane risk information to the public.
Construction of a diagnostic signature and immune landscape of pulmonary arterial hypertension
Authors: Duo Mengjie , Liu Zaoqu , Zhang Yuyuan , Li Pengfei , Weng Siyuan , Xu Hui , Wang Yu , Jiang Tianci , Wu Ruhao , Cheng Zhe
Published: December 2022

Background

Molecular biomarkers are widely used for disease diagnosis and exploration of pathogenesis. Pulmonary arterial hypertension (PAH) is a rapidly progressive cardiopulmonary disease with delayed diagnosis. Studies were limited regarding molecular biomarkers correlated with PAH from a broad perspective.

Methods

Two independent microarray cohorts comprising 73 PAH samples and 36 normal samples were enrolled in this study. The weighted gene co-expression network analysis (WGCNA) was performed to identify the key modules associated with PAH. The LASSO algorithm was employed to fit a diagnostic model. The latent biology mechanisms and immune landscape were further revealed via bioinformatics tools.

Results

The WGCNA approach ultimately identified two key modules significantly associated with PAH. For genes within the two models, differential expression analysis between PAH and normal samples further determined nine key genes. With the expression profiles of these nine genes, we initially developed a PAH diagnostic signature (PDS) consisting of LRRN4, PI15, BICC1, PDE1A, TSHZ2, HMCN1, COL14A1, CCDC80, and ABCB1 in GSE117261 and then validated this signature in GSE113439. The ROC analysis demonstrated outstanding AUCs with 0.948 and 0.945 in two cohorts, respectively. Besides, patients with high PDS scores enriched plenty of Th17 cells and neutrophils, while patients with low PDS scores were dramatically related to mast cells and B cells.

Conclusion

Our study established a robust and promising signature PDS for diagnosing PAH, with key genes, novel pathways, and immune landscape offering new perspectives for exploring the molecular mechanisms and potential therapeutic targets of PAH.
Student conceptual level scale: Development and initial validation
Authors: Yang Xi , Dong Jia , Tan DingLiang
Published: December 2022

The conceptual level is an index of personality development. In the field of teaching, the conceptual level is seen as a dynamic learning style. It has important implications for student learning and individual growth, as well as guidance for teaching. However, the lack of a measurement tool with a clear internal structure for the conceptual level of students has slowed the development of the theory and made it difficult to implement the teaching. To address these issues, this study describes the initial development and validation of the Student Conceptual Level Scale (SCLS) with four samples of students (n = 1,321) drawn from eight secondary schools in China. We constructed a second-order three-factor model of the SCLS consisting of three factors—learning awareness level, autonomous input level, and environmental coping level—each with its own independent set of items. This study validated the use of full-scale and subscale scores and examined their relationship with different validity criteria: autonomous learning, mental effort, and academic scores. This updated measure reflects the value and role of the conceptual level in the learning and individual development of students and also provides a more complete frame of reference for the use of the conceptual level in teaching and learning.
Combined treatment by burosumab and a calcimimetic can ameliorate hypophosphatemia due to excessive actions of FGF23 and PTH in adult XLH with tertiary hyperparathyroidism: A case report
Authors: Takashi Yuichi , Toyokawa Kyoko , Oda Naoki , Muta Yoshimi , Yokomizo Hisashi , Fukumoto Seiji , Kawanami Daiji
Published: December 2022

Introduction

X-linked hypophosphatemia (XLH) is the most prevalent type of heritable fibroblast growth factor 23 (FGF23)-related hypophosphatemic rickets. Recently, anti-FGF23 antibody, burosumab, has become clinically available. We herein report a patient with adult XLH and tertiary hyperparathyroidism.

Case presentation

The serum phosphate level and tubular maximum reabsorption of phosphate per glomerular filtration rate (TmP/GFR) remained low, despite burosumab treatment. While the influence of the relationship between FGF23 and parathyroid hormone (PTH) on the phosphaturic effect is unclear, it was considered that a high level of PTH due to tertiary hyperparathyroidism remains to suppress renal phosphate reabsorption. A calcimimetic, evocalcet, increased the serum phosphate level and TmP/GFR.

Discussion and conclusion

Therefore, it is important to evaluate the presence of secondary-tertiary hyperparathyroidism in patients whose serum phosphate level does not increase with burosumab treatment.
Protein O-GlcNAcylation as a nutrient sensor signaling placental dysfunction in hypertensive pregnancy
Authors: dos Passos Junior Rinaldo Rodrigues , de Freitas Raiany Alves , Dela Justina Vanessa , San Martín Sebastián , Lima Victor Vitorino , Giachini Fernanda Regina
Published: December 2022

Introduction

During pregnancy, arterial hypertension may impair placental function, which is critical for a healthy baby's growth. Important proteins during placentation are known to be targets for O-linked β-N-acetylglucosamine modification (O-GlcNAcylation), and abnormal protein O-GlcNAcylation has been linked to pathological conditions such as hypertension. However, it is unclear how protein O-GlcNAcylation affects placental function and fetal growth throughout pregnancy during hypertension.

Methods

To investigate this question, female Wistar and spontaneously hypertensive rats (SHR) were mated with male Wistar rats, and after pregnancy confirmation by vaginal smear, rats were divided into groups of 14, 17, and 20 days of pregnancy (DOPs). On the 14th, 17th, and 20th DOP, rats were euthanized, fetal parameters were measured, and placentas were collected for western blot, immunohistochemical, and morphological analyses.

Results

SHR presented a higher blood pressure than the Wistar rats (p=0.001). Across all DOPs, SHR showed reduced fetal weight and an increase in small-for-gestational-age fetuses. While near-term placentas were heavier in SHR (p=0.006), placental efficiency decreased at 17 (p=0.01) and 20 DOPs (p<0.0001) in this group. Morphological analysis revealed reduced junctional zone area and labyrinth vasculature changes on SHR placentas in all DOPs. O-GlcNAc protein expression was lower in placentas from SHR compared with Wistar at 14, 17, and 20 DOPs. Decreased expression of O-GlcNAc transferase (p=0.01) and O-GlcNAcase (p=0.002) enzymes was found at 14 DOPs in SHR. Immunohistochemistry showed reduced placental O-GlcNAc content in both the junctional zone and labyrinth of the placentas from SHR. Periodic acid-Schiff analysis showed decreased glycogen cell content in the placentas from SHR at 14, 17, and 20 DOPs. Moreover, glucose transporter 1 expression was decreased in placentas from SHR in all DOPs.

Conclusions

These findings suggest that decreased protein O-GlcNAcylation caused by insufficient placental nutritional apport contributes to placental dysfunction during hypertensive pregnancy, impairing fetal growth.
Renal outcomes with sodium-glucose cotransporters 2 inhibitors
Authors: Sun Xiaoya , Wang Guohong
Published: December 2022

Diabetic nephropathy (DN) is one of the most serious complications of diabetes. Therefore, delaying and preventing the progression of DN becomes an important goal in the clinical treatment of type 2 diabetes mellitus. Recent studies confirm that sodium-glucose cotransporters 2 inhibitors (SGLT2is) have been regarded as effective glucose-lowering drugs with renal protective effect. In this review, we summarize in detail the present knowledge of the effects of SGLT2is on renal outcomes by analyzing the experimental data in preclinical study, the effects of SGLT2is on estimated glomerular flitration rates (eGFRs) and urinary albumin-creatinine ratios (UACRs) from clinical trials and observational studies, and renal events (such as renal death or renal failure requiring renal replacement therapy) in some large prospective cardiovaslucar outcomes trials. The underlying mechanisms for renoprotective activity of SGLT2is have been demondtrated in multiple diabetic and nondiabetic animal models including kidney-specific effects and secondary kidney effects related to amelioration in blood glucose and blood pressure. In conclusion, these promising results show that SGLT2is act beneficially in terms of the kidney for diabetic patients.
Identification of a basement membrane-related gene signature for predicting prognosis and estimating the tumor immune microenvironment in breast cancer
Authors: Cai Jiehui , Zhang Xinkang , Xie Wanchun , Li Zhiyang , Liu Wei , Liu An
Published: December 2022

Introduction

Breast cancer (BC) is the most common malignancy in the world and has a high cancer-related mortality rate. Basement membranes (BMs) guide cell polarity, differentiation, migration and survival, and their functions are closely related to tumor diseases. However, few studies have focused on the association of basement membrane-related genes (BMRGs) with BC. This study aimed to explore the prognostic features of BMRGs in BC and provide new directions for the prevention and treatment of BC.

Methods

We collected transcriptomic and clinical data of BC patients from TCGA and GEO datasets and constructed a predictive signature for BMRGs by using univariate, least absolute shrinkage and selection operator (LASSO) and multivariate Cox regression analysis. The reliability of the model was further evaluated and validated by Kaplan-Meier survival curves and receiver operating characteristic curves (ROC). Column line plots and corresponding calibration curves were constructed. Possible biological pathways were investigated by enrichment analysis. Afterward, we assessed the mutation status by tumor mutational burden (TMB) analysis and compared different subtypes using cluster analysis. Finally, we examined drug treatment sensitivity and immunological correlation to lay the groundwork for more in-depth studies in this area.

Results

The prognostic risk model consisted of 7 genes (FBLN5, ITGB2, LAMC3, MMP1, EVA1B, SDC1, UNC5A). After validation, we found that the model was highly reliable and could accurately predict the prognosis of BC patients. Cluster analysis showed that patients with cluster 1 had more sensitive drugs and had better chances of better clinical outcomes. In addition, TMB, immune checkpoint, immune status, and semi-inhibitory concentrations were significantly different between high and low-risk groups, with lower-risk patients having the better anti-cancer ability.

Discussion

The basement membrane-related gene signature that we established can be applied as an independent prognostic factor for BC and can provide a reference for individualized treatment of BC patients.
Drivers of global carbon emission changes: A heterogeneity perspective of decomposition and attribution analysis
Authors: Liu Xiao , Zhang Yancai , Wang Qunwei
Published: December 2022

Due to the differences in economic development, resource endowment, and historical accumulation, different types of countries have significant technical heterogeneity in carbon emissions. Identifying the driving factors of carbon emission changes, under the premise of distinguishing national heterogeneity, can provide a basis for the formulation of the “Differentiated Responsibilities” emission reduction policies. Therefore, this study introduces the idea of Meta-frontier into the traditional production-theoretical decomposition analysis, and constructs a new influencing factor analysis framework. Based on the newly built method, the empirical study of 60 representative countries draws the following three meaningful conclusion: 1) Different types of countries have obvious heterogeneity in technology, efficiency and change trend of energy use. Specifically, countries with higher energy intensity values generally have a quicker decline rate than those with lower energy intensity values. There exists “catch-up” effects for the backward to the advanced countries. 2) Decomposition results show that potential energy intensity (PEI) is the dominant factor reducing carbon emissions, especially for those large economic output with large energy consumption (Group-L) countries (0.604). Economic activity effect (ECA) is the most significant driving force for countries with small economic output and small energy consumption (Group-S), reaching 1.806. Meanwhile, the attribution results showed different characteristics in different groups of countries. The impact of various factors that reflect the heterogeneity of production process on carbon emissions mainly comes from the contribution of Group-L. 3) We suggest that, in the process of carbon reduction, large energy consumption countries should pay more attention to the gap between the development and speed of the world’s cutting-edge technologies.
Land comprehensive carrying capacity and spatio-temporal analysis of the guangdong-Hong Kong-Macau Greater Bay Area
Authors: Wu Zhanglan , Su Yantao , Xiong Mingliang
Published: December 2022

The Guangdong-Hong Kong-Macao Greater Bay Area (GBA) is one of the fastest growing and most dynamic regions in China. Changes in land comprehensive carrying capacity (LCCC) is of vital significance. In China, various studies have assessed LCCC, however, they majorly focused on single cities, with less studies focusing on urban agglomeration, particularly GBA. Based on social, economic, resource and technology aspects, we established an index system for evaluating LCCC by the entropy method. It analyses temporal and spatial evolution characteristics of LCCC from 11 cities in the GBA of China, 2009–2018. There are many social, economic, resource and technology differences among the 4 subsystems. We established that technology is the prominent factor in LCCC. With regards to LCCC, these cities have their respective strengths and weaknesses. On a temporal basis, there were rising trends in LCCC curves, with different degrees of the 11 cities. Spatially, LCCC is relatively high in central cities and it exhibits a declining pattern of the carrying capacity from the city center outwards. Therefore, regional collaborative efforts are vital for increasing LCCC.
Tillage and N-source affect soil fertility, enzymatic activity, and crop yield in a maize–rice rotation system in the Indian Terai zone
Authors: Sahoo Samaresh , Mukhopadhyay Prabir , Mowrer Jake , Maity Pragati Pramanik , Maity Aniruddha , Sinha A.K. , Sow Prodipto , Rakesh S
Published: December 2022

A field experiment (2017–2019) was undertaken to study the short-term effects of tillage [zero tillage (ZT), conventional tillage (CT), and alternate tillage (AT)] and sources of organic and mineral fertilizer N [NS0—control, NS1—recommended doses of fertilizer (160:50:100), NS2—recommended level of fertilizer and crop residue (6 Mg·ha−1), NS3—75% of recommended N as fertilizer (120 kg·ha⁻1) and 25% N (40 kg·ha⁻1) as farm yard manure (FYM), and NS4—75% of recommended N as fertilizer and 25% N as vermicompost] on yield and soil quality under a maize–rice rotation system. Among N sources, NS4 produced the highest maize grain yield (10 Mg·ha⁻1). Residual effects of N sources on mean rice grain yield were evident only in crop residue (NS2)- and vermicompost (NS4)-treated plots. After the harvest of two complete maize–rice crop cycles, higher content of dehydrogenase activity (DHA) and urease activity (UR) were observed in the soil under AT as compared to ZT and CT at 0–10 cm (p < 0.05). Similarly, microbial biomass carbon (MBC) and microbial biomass nitrogen (MBN) also recorded positive changes at 0–10 cm soil depth, especially in NS2 and NS4 treatments. AT resulted in the highest total soil carbon (TOC) (8.10 g·kg−1), followed by CT (6.73 g·kg−1) and ZT (5.98 g·kg−1). Fertilizer N treatments, however, influenced the NO3-N accumulation beyond the root zone, where crop residue-based (NS2) fertilizer N treatment resulted in the highest NO3-N (32.52 kg·ha−1), and the lowest NO3-N (14.48 kg·ha−1) was observed in the FYM-based (NS3) treatment. Therefore, the practice of alternate tillage and integration of vermicompost (40 kg·N·ha−1) and chemical fertilizer (total 120 kg·ha−1) sources should be mostly recommended to farmers in the Terai region of India.
Heterogeneous individual motility biases group composition in a model of aggregating cells
Authors: Forget Mathieu , Adiba Sandrine , Brunnet Leonardo Gregory , De Monte Silvia
Published: December 2022

Aggregative life cycles are characterized by alternating phases of unicellular growth and multicellular development. Their multiple, independent evolutionary emergence suggests that they may have coopted pervasive properties of single-celled ancestors. Primitive multicellular aggregates, where coordination mechanisms were less efficient than in extant aggregative microbes, must have faced high levels of conflict between different co-aggregating populations. Such conflicts within a multicellular body manifest in the differential reproductive output of cells of different types. Here, we study how heterogeneity in cell motility affects the aggregation process and creates a mismatch between the composition of the population and that of self-organized groups of active adhesive particles. We model cells as self-propelled particles and describe aggregation in a plane starting from a dispersed configuration. Inspired by the life cycle of aggregative model organisms such as Dictyostelium discoideum or Myxococcus xanthus, whose cells interact for a fixed duration before the onset of chimeric multicellular development, we study finite-time configurations for identical particles and in binary mixes. We show that co-aggregation results in three different types of frequency-dependent biases, one of which is associated to evolutionarily stable coexistence of particles with different motility. We propose a heuristic explanation of such observations, based on the competition between delayed aggregation of slower particles and detachment of faster particles. Unexpectedly, despite the complexity and non-linearity of the system, biases can be largely predicted from the behavior of the two corresponding homogenous populations. This model points to differential motility as a possibly important factor in driving the evolutionary emergence of facultatively multicellular life-cycles.
Does ESG performance promote total factor productivity? Evidence from China
Authors: Ma Jiangming , Gao Di , Sun Jing
Published: December 2022

Currently, environmental, social, and corporate governance (ESG) has become an all-pervasive term in the industrial sector, owing to its significant impact on corporate decision-making. While most of the studies provide evidence that the ESG significantly improves a firm's performance and value in the long run, few studies quantitatively analyzed the linkage between ESG and total factor productivity (TFP). Using the data of Chinese-listed companies during 2010–2020, we found that there is a positive relationship between ESG performance and TFP. ESG also improves the corporate TFP by reducing the financial constraints and improving the innovation input. Our extended analysis revealed that this beneficial effect tends to be stronger for SOEs (state-owned enterprises) and industries with high pollution levels. This study also brought to light some implications for Chinese firms in relation to their ESG practices and sustainable development.
Identification and validation of a prognostic model based on ferroptosis-associated genes in head and neck squamous cancer
Authors: Wei Ming , Tian Yongquan , Lv Yunxia , Liu Guancheng , Cai Gengming
Published: December 2022

Ferroptosis is that under the action of ferrous iron or ester oxygenase, unsaturated fatty acids highly expressed on the cell membrane are catalyzed to undergo lipid peroxidation, thereby inducing cell death. In this study, we used ferroptosis marker genes to identify 3 stable molecular subtypes (C1, C2, C3) with distinct prognostic, mutational, and immune signatures by consensus clustering; TP53, CDKN2A, etc. Have higher mutation frequencies in the three subtypes. C3 has a better prognosis, while the C1 subtype has a worse prognosis. WGCNA is used to identify molecular subtype-related gene modules.After filting, we obtained a total of 540 genes related to the module feature vector (correlation>0.7).We performed univariate COX regression analysis on these genes, and identified a total of 97 genes (p < 0.05) that had a greater impact on prognosis, including 8 ‘‘Risk” and 89 ‘‘Protective” genes. After using lasso regression, we identified 8 genes (ZNF566, ZNF541, TMEM150C, PPAN, PGLYRP4, ENDOU, RPL23 and MALSU1) as ferroptosis-related genes affecting prognosis. The ferroptosis prognosis-related risk score (FPRS) was calculated for each sample in TCGA-HNSC dataset. The results showed that FPRS was negatively correlated with prognosis.The activated pathways in the PFRS-high group mainly include immune-related pathways and invasion-related pathways. We assessed the extent of immune cell infiltration in patients in our TCGA-HNSC cohort by using the expression levels of gene markers in immune cells. The FPRS-high group had a higher level of immune cell infiltration. We found that the expression of immune checkpoints was significantly up-regulated in the FPRS-low group and the FPRS-high group had a higher probability of immune escape and a lower probability of benefiting from immunotherapy. In this work, we constructed a scoring Ferroptosis-related prognostic model that can well reflect risk and positive factors for prognosis in patients with head and neck squamous cell carcinoma. It can be used to guide individualized adjuvant therapy and chemotherapy for patients with head and neck cancer. Therefore, it has a good survival prediction ability and provides an important reference for clinical treatment.
A novel approach for a joint analysis of isomiR and mRNA expression data reveals features of isomiR targeting in breast cancer
Authors: Nersisyan Stepan , Zhiyanov Anton , Engibaryan Narek , Maltseva Diana , Tonevitsky Alexander
Published: December 2022

A widely used procedure for selecting significant miRNA-mRNA or isomiR-mRNA pairs out of predicted interactions involves calculating the correlation between expression levels of miRNAs/isomiRs and mRNAs in a series of samples. In this manuscript, we aimed to assess the validity of this procedure by comparing isomiR-mRNA correlation profiles in sets of sequence-based predicted target mRNAs and non-target mRNAs (negative controls). Target prediction was carried out using RNA22 and TargetScan algorithms. Spearman’s correlation analysis was conducted using miRNA and mRNA sequencing data of The Cancer Genome Atlas Breast Invasive Carcinoma (TCGA-BRCA) project. Luminal A, luminal B, basal-like breast cancer subtypes, and adjacent normal tissue samples were analyzed separately. Using the sets of putative targets and non-targets, we introduced adjusted isomiR targeting activity (ITA)—the number of negatively correlated potential isomiR targets adjusted by the background (estimated using non-target mRNAs). We found that for most isomiRs a significant negative correlation between isomiR-mRNA expression levels appeared more often in a set of predicted targets compared to the non-targets. This trend was detected for both classical seed region binding types (8mer, 7mer-m8, 7mer-A1, 6mer) predicted by TargetScan and the non-classical ones (G:U wobbles and up to one mismatch or unpaired nucleotide within seed sequence) predicted by RNA22. Adjusted ITA distributions were similar for target sites located in 3′-UTRs and coding mRNA sequences, while 5′-UTRs had much lower scores. Finally, we observed strong cancer subtype-specific patterns of isomiR activity, highlighting the differences between breast cancer molecular subtypes and normal tissues. Surprisingly, our target prediction- and correlation-based estimates of isomiR activities were practically non-correlated with the average isomiR expression levels neither in cancerous nor in normal samples.
Resident macrophages of the lung and liver: The guardians of our tissues
Authors: Kulle Amelia , Thanabalasuriar Ajitha , Cohen Taylor S. , Szydlowska Marta
Published: December 2022

Resident macrophages play a unique role in the maintenance of tissue function. As phagocytes, they are an essential first line defenders against pathogens and much of the initial characterization of these cells was focused on their interaction with viral and bacterial pathogens. However, these cells are increasingly recognized as contributing to more than just host defense. Through cytokine production, receptor engagement and gap junction communication resident macrophages tune tissue inflammatory tone, influence adaptive immune cell phenotype and regulate tissue structure and function. This review highlights resident macrophages in the liver and lung as they hold unique roles in the maintenance of the interface between the circulatory system and the external environment. As such, we detail the developmental origin of these cells, their contribution to host defense and the array of tools these cells use to regulate tissue homeostasis.
Interferon and interferon-stimulated genes in HBV treatment
Authors: Li Qirong , Sun Baozhen , Zhuo Yue , Jiang Ziping , Li Rong , Lin Chao , Jin Ye , Gao Yongjian , Wang Dongxu
Published: December 2022

Human hepatitis B virus (HBV) is a small enveloped DNA virus with a complex life cycle. It is the causative agent of acute and chronic hepatitis. HBV can resist immune system responses and often causes persistent chronic infections. HBV is the leading cause of liver cancer and cirrhosis. Interferons (IFNs) are cytokines with antiviral, immunomodulatory, and antitumor properties. IFNs are glycoproteins with a strong antiviral activity that plays an important role in adaptive and innate immune responses. They are classified into three categories (type I, II, and III) based on the structure of their cell-surface receptors. As an effective drug for controlling chronic viral infections, Type I IFNs are approved to be clinically used for the treatment of HBV infection. The therapeutic effect of interferon will be enhanced when combined with other drugs. IFNs play a biological function by inducing the expression of hundreds of IFN-stimulated genes (ISGs) in the host cells, which are responsible for the inhibiting of HBV replication, transcription, and other important processes. Animal models of HBV, such as chimpanzees, are also important tools for studying IFN treatment and ISG regulation. In the present review, we summarized the recent progress in IFN-HBV treatment and focused on its mechanism through the interaction between HBV and ISGs.
Lung cancer patients with chronic obstructive pulmonary disease benefit from anti-PD-1/PD-L1 therapy
Authors: Lin Mao , Huang Zongyao , Chen Yingfu , Xiao Hongtao , Wang Ting
Published: December 2022

Lung cancer (LC) and chronic obstructive pulmonary disease (COPD) are two of the most fatal respiratory diseases, seriously threatening human health and imposing a heavy burden on families and society. Although COPD is a significant independent risk factor for LC, it is still unclear how COPD affects the prognosis of LC patients, especially when LC patients with COPD receive immunotherapy. With the development of immune checkpoint inhibition (ICI) therapy, an increasing number of inhibitors of programmed cell death-1 (PD-1) and PD-1 ligand (PD-L1) have been applied to the treatment of LC. Recent studies suggest that LC patients with COPD may benefit more from immunotherapy. In this review, we systematically summarized the outcomes of LC patients with COPD after anti-PD-1/PD-L1 treatment and discussed the tumor immune microenvironment (TIME) regulated by COPD in LC immunotherapy, which provides novel insights for the clinical treatment of LC patients with COPD.
Whole-transcriptome analyses of sheep embryonic testicular cells infected with the bluetongue virus
Authors: Lu Danfeng , Li Zhuoyue , Zhu Pei , Yang Zhenxing , Yang Heng , Li Zhanhong , Li Huachun , Li Zhuoran
Published: December 2022

Introduction

bluetongue virus (BTV) infection triggers dramatic and complex changes in the host's transcriptional profile to favor its own survival and reproduction. However, there is no whole-transcriptome study of susceptible animal cells with BTV infection, which impedes the in-depth and systematical understanding of the comprehensive characterization of BTV-host interactome, as well as BTV infection and pathogenic mechanisms.

Methods

to systematically understand these changes, we performed whole-transcriptome sequencing in BTV serotype 1 (BTV-1)-infected and mock-infected sheep embryonic testicular cells, and subsequently conducted bioinformatics differential analyses.

Results

there were 1504 differentially expressed mRNAs, 78 differentially expressed microRNAs, 872 differentially expressed long non-coding RNAs, and 59 differentially expressed circular RNAs identified in total. Annotation from the Gene Ontology, enrichment from the Kyoto Encyclopedia of Genes and Genomes, and construction of competing endogenous RNA networks revealed differentially expressed RNAs primarily related to virus-sensing and signaling transduction pathways, antiviral and immune responses, inflammation, and development and metabolism related pathways. Furthermore, a protein-protein interaction network analysis found that BTV may contribute to abnormal spermatogenesis by reducing steroid biosynthesis. Finally, real-time quantitative PCR and western blotting results showed that the expression trends of differentially expressed RNAs were consistent with the whole-transcriptome sequencing data.

Discussion

this study provides more insights of comprehensive characterization of BTV-host interactome, and BTV infection and pathogenic mechanisms.
Phosphorylation of RIPK1 serine 25 mediates IKK dependent control of extrinsic cell death in T cells
Authors: Blanchett Sam , Dondelinger Yves , Barbarulo Alessandro , Bertrand Mathieu J. M. , Seddon Benedict
Published: December 2022

The Inhibitor of Kappa B Kinase (IKK) complex is a critical regulator of NF-κB activation. More recently, IKK has also been shown to repress RIPK1 dependent extrinsic cell death pathways by directly phosphorylating RIPK1 at serine 25. In T cells, IKK expression is essential for normal development in the thymus, by promoting survival of thymocytes independently of NF-κB activation. RIPK1 undergoes extensive phosphorylation following TNF stimulation in T cells, though which targets are required to repress RIPK1 has not been defined. Here, we show that TNF induced phosphorylation of RIPK1 at S25 is IKK dependent. We test the relevance of this phosphorylation event in T cells using mice with a RIPK1S25D phosphomimetic point mutation to endogenous RIPK1. We find that this mutation protects T cells from TNF induced cell death when IKK activity is inhibited in vitro, and can rescues development of IKK deficient thymocytes in vivo to a degree comparable with kinase dead RIPK1D138N. Together, these data show that phosphorylation of RIPK1S25 by IKK represents a key regulatory event promoting survival of T cells by IKK.
SFRP4+IGFBP5hi NKT cells induced neural-like cell differentiation to contribute to adenomyosis pain
Authors: Chen Yichen , Zhu Jue , Chen Liang , Shen Yuanyuan , Zhang Jing , Wang Qiming
Published: December 2022

Background

Adenomyosis is an estrogen-dependent gynecological disease. The pathogenesis of chronic pain, the main clinical symptom of adenomyosis, remains undefined. As a combination lymphocyte with both T-cell and natural killer (NK)–cell properties, NK T (NKT) cells play a role in immune defense against numerous diseases and modulate cell differentiation.

Method

This study analyzed the tissue-cell samples from adenomyosis with or without pain by single-cell sequencing.

Result

We found a specific population of secreted frizzled-related protein 4 (SFRP4)+NKT cells and a large amount of undifferentiated multipotent stem cells in the adenomyosis pain group. We discovered that a high expression of IGFBP5 in SFRP4+NKT cells could promote the differentiation of multipotent stem cells into neural-like cells via the single-cell trajectory. Through verification by the sample, we found that the degree of the expression of the neuronal marker NEFM was correlated with the duration of pain in adenomyosis patients. The expression of IGFBP5 was positively correlated with the pain scores of adenomyosis patients.

Conclusion

Collectively, these findings suggest that SFRP4+IGFBP5hi NKT cells were capable of converting part of the stem cells into neurogenic cells and inducing adenomyosis pain.
Association of parental HLA-G polymorphisms with soluble HLA-G expressions and their roles on recurrent implantation failure: A systematic review and meta-analysis
Authors: Hu Lian , He Dongmei , Zeng Hong
Published: December 2022

Introduction

HLA-G plays a central role in immune tolerance at the maternal-fetal interface. The HLA-G gene is characterized by low allelic polymorphism and restricted tissue expression compared with classical HLA genes. HLA-G polymorphism is associated with HLA-G expression and linked to pregnancy complications. However, the association of parental HLA-G polymorphisms with soluble HLA-G (sHLA-G) expression and their roles in recurrent implantation failure (RIF) is unclear. The study aims to systematically review the association of HLA-G polymorphisms with RIF, the association of sHLA-G expression with RIF, and the association of HLA-G polymorphisms with sHLA-G expressions in patients attending in-vitro fertilization (IVF) treatment.

Methods

Studies that evaluated the association of HLA-G polymorphisms with RIF, the association between sHLA-G expression with RIF, and the association between HLA-G polymorphisms with sHLA-G expressions in patients attending IVF treatment were included. Meta-analysis was performed by random-effect models. Sensitivity analysis was performed by excluding one study each time. Subgroup analysis was performed based on ethnicity.

Results

HLA-G 14bp ins variant is associated with a lower expression of sHLA-G in seminal or blood plasma of couples attending IVF treatment. The maternal HLA-G*010101 and paternal HLA-G*010102 alleles are associated with RIF risk compared to other alleles. However, single maternal HLA-G 14bp ins/del polymorphism, HLA-G -725 C>G/T polymorphism, or circulating sHLA-G concentration was not significantly associated with RIF in the general population. HLA-G 14bp ins/ins homozygous genotype or ins variant was associated with a higher risk of RIF in the Caucasian population.

Discussion

Specific HLA-G alleles or HLA-G polymorphisms are associated with sHLA-G expression in couples attending IVF treatment. Several HLA-G polymorphisms may be related to RIF, considering different ethnic backgrounds. A combined genetic effect should be considered in future studies to confirm the association of HLA-G polymorphisms and sHLA-G expressions in relation to RIF.
Zooplankton functional traits in a tropical estuarine system: Are lower and upper estuaries functionally different?
Authors: Sanvicente-Añorve Laura , Sánchez-Campos Mitzi , Alatorre-Mendieta Miguel , Lemus-Santana Elia , Guerra-Castro Edlin
Published: December 2022

Functional diversity measures help to understand the underlying mechanisms explaining the relationship between organisms and environment. This work examined the mesozooplankton community of an estuary under the hypothesis that the upper (< 25 psu) and lower (> 25 psu) zones are functionally different in terms of feeding strategies, trophic groups, camouflage, buoyancy, and defense against predators, due to the salinity gradient. We used the ‘community-weighted mean trait values’ (CWM) and a fuzzy correspondence analysis (FCA) in combination with three functional indices (FRic: functional richness, FEve: functional evenness, FDiv: functional divergence) to test our hypothesis. Zooplankton samples were taken in the tropical Sontecomapan estuary, southern Gulf of Mexico, in June 2018 and October 2019. A total of 21 zooplankton groups were recognized, all of them present in the lower estuary. Results showed significant differences (p< 0.05) in the FRic and FDiv values between the two zones, as well in the CWM metric. Results of the FCA showed that the lower estuary was characterized by herbivorous filter feeders that use watery bodies, flattened body forms, mucus houses, or ‘wings’ for buoyancy; highly transparent bodies (associated with gelatinous body structure) for camouflage and predators’ avoidance and, shells or carapaces as antipredator tactics. The upper estuary was characterized by omnivorous cruising predators that use their appendages or swim bladders for buoyancy, with ‘medium’ and ‘low’ levels of transparency, associated with chitinous and skin-protected body structures, which provide alternative ways for camouflage and spines or fast swimming behavior to protect from predators. These findings evidenced that the upper and lower zones of an estuary exhibit differences in the function of the zooplankton community and shed new light on the comprehension of estuaries’ ecological function.
Temporal patterns in coral reef fish assemblages with varying disturbance levels: A tale of two National Parks in Hawai´i
Authors: Fukunaga Atsuko , McKenna Sheila A. , Brown Eric K. , McCutcheon Amanda L. , Burns John H. R.
Published: December 2022

Long-term ecological monitoring of coral reefs can reveal the state of the reef communities and responses of different reef components to various pulse and press disturbance events. Here, we describe long-term monitoring of reef fish assemblages from two U.S. National Parks in Hawai‘i, Kaloko-Honokōhau National Historical Park (KAHO) and Kalaupapa National Historical Park (KALA) over the past decade. These two parks experience different anthropogenic disturbances as KAHO is highly accessible with multiple types of adjacent land use while KALA is relatively inaccessible, surrounded by large expanses of native forest, and known for having the highest documented fish biomass within the main Hawaiian Islands. The fish assemblages in KAHO were numerically dominated by small-bodied damselfish Chromis spp. and herbivorous surgeonfishes Acanthurus nigrofuscus, Ctenochaetus strigosus and Zebrasoma flavescens, while those in KALA were numerically dominated by Chromis vanderbilti, A. nigrofuscus, Thalassoma duperrey and Paracirrhites arcatus. Multivariate control charts detected anomalies in the fish assemblages in some years. In KAHO, gradual shifts in the assemblages were detected in recent years due to changes (both increases and decreases) in relative abundances of numerically dominant species including Chromis agilis, C. vanderbilti, A. nigrofuscus, C. strigosus and Z. flavescens. There was a documented reduction in live coral cover in KAHO due to a bleaching event in 2015, and potential delayed effects of the coral mortality on the fish assemblages were found particularly in the North and South regions of the park. In KALA, increases in the abundances of Acanthurus (A. blochii, A. leucopareius, A. nigrofuscus, A. thompsoni and A. triostegus) and C. strigosus were found in 2014, likely due to a large recruitment event that had not been well reported. As localized thermal stress events were detected in both KAHO and KALA in 2019, continuous monitoring of these two parks is critical to assess how the coral-reef ecosystems under two different human-use scenarios respond to repeated heating events and whether there are immediate as well as delayed effects on reef organisms resulting from losses of live coral tissue and a subsequent decrease in structural complexity provided by the coral.
Microplastic pollution in finless porpoises and their habitats along the Fujian coast of the East China Sea
Authors: Wang Daling , Zhen Yu , Wei Lili , Dai Yufei , Wang Xianyan , Tong Shenhan , Zhao Liyuan
Published: December 2022

Microplastics (MPs) pose serious threats to various marine organisms, including many threatened apex predators such as cetaceans. However, information on microplastic contamination in cetaceans from Asian waters is limited. Based on the analysis of Fourier transform infrared spectroscopy (FTIR), we reported MPs from finless porpoise intestinal samples and from their habitats along the Fujian coast of the East China Sea. MPs proved to be ubiquitous in both intestinal and habitat water samples. Most intestinal MPs were fibers (86.90%), transparent (51.19%), small sizes (<1.0 mm, 77.38%), and composed of polyamide (41.67%) or polyethylene terephthalate (45.24%). Seawater MPs were predominantly fibers (90.25%), transparent (82.45%), < 1.0 mm (83.76%) and composed of polypropylene (67.32%). Concentrations of MPs in coastal waters were greater than those in offshore waters. The concentration and composition of fibrous MPs indicate a likely textile industry origin. A recommendation is made to further assess the risks of MPs consumption in threatened species and develop scientific protection and management strategies.