bluuebunny/crossref_metadata_2025 huggingface dataset:
Predicting the reaction efficiency of ginkgo biloba residues pyrolysis by using artificial intelligent algorithms under the background of Carbon Neutrality
Authors: Liu Li , Yu Zhenwei , Chen Zheqi , Wang Kai , Xiao Qian , Chen Jingjing
Published: September 2022

Since the beginning of 2016, China’s annual emissions of herbal residues (HR) have exceeded 30 million tons. As a kind of solid waste, HR still contains a large amount of organic matter, which requires further industrial extraction procedure. Most of the existing studies are concerned with the feasibility of utilizing traditional Chinese medicine residues, meanwhile there are very few studies regarding the kinetics of pyrolysis in the process of resource utilization of traditional Chinese medicine residues. In this study, we comprehensively studied the kinetics characteristics of raw materials with various heating rates (10, 20, 30, and 40°C/min) using a synchronous thermogravimetric analysis, and we adopted Coats-Redfern model to study the thermal kinetics and thermal analysis of GBR. A novel method combining Genetic algorithm and Adaboost algorithm (GA-Adaboost) is proposed to predict the thermogravimetric curve of the raw plant material with respect to the heating rate and temperature. The experimental result shows that the activation energy of the raw material was determined by the Kissinger-Akahira-Sunose (KAS) (E=148.71kJ/mol), and the correlation coefficient was greater than 0.99. The optimal reaction mechanism determined by the Coats - Redfern method was random nucleation and subsequent growth. The GA-Adaboost model achieved good performance (with a fitting degree of 99.88% on training data, 99.80% on verification data, and MSE of3.4173) while predicting the pyrolysis process of ginkgo biloba residue. This study will provide theoretical basis and technical support for the efficient resource utilization of pharmaceutical residues and reduce environmental pressure.
Distributed optimization method for multi-area integrated energy systems considering demand response
Authors: Bai Xuetao , Liu Liu , Ju Jiehua , Zhong Xiaoyi , Zhou Yuting , Lin Jian , Huang Yuan , Wu Nianyuan , Xie Shan , Zhao Yingru
Published: September 2022

Modern urban integrated energy systems are usually large in scale and consist of several subsystems located in different areas with various types of users. The design and operation optimization of multi-area integrated energy systems (IES) faces challenges in integrating user engagement, operational independence of subsystems, and the combination of long-term objectives and operation optimization. To solve these problems, the present study proposes a supply-demand coordinated optimization method for multi-area IES to balance the long-term overall objectives with the independence of participants such as users and subsystems. Increasing overall benefits and ensuring fairness can be achieved by using the proposed methods. In the case study, considering long-term objectives, the carbon emissions of the system operation are reduced by 9.43% compared to the case without the long-term objectives. Meanwhile, the results show an approximately 25% reduction in the total cost and a 65% reduction in carbon emission, compared to the baseline. Moreover, the cost of different users decreases by 13%–17% from the baseline at the optimal agreed price. This optimization method provides a holistic framework for the design and operation, supply-demand coordination, and pricing of transactions for multi-area IES involving long-term planning and construction with multiple interests.
Renewable energy, non-renewable energy, economic growth and CO2 emissions in the newly emerging market economies: The moderating role of human capital
Authors: Gnangoin Thierry Yobouet , Kassi Diby Francois , Edjoukou Akadje Jean-Roland , Kongrong OuYang , Yuqing Dai
Published: September 2022

The International Energy Agency revealed in its report in 2021 that the world energy-CO2 emission reached its highest peak during that year. This statistic shows the need to set new environmental protection policies and improve the current ones. Hence, our study aims to highlight the leading role of human capital in the fight against climate change. To do so, by using the Feasible Generalized Least Squares and the Two-Stage Least Squares estimators, we analyze the moderating impact of human capital on the link between renewable energy, nonrenewable energy, economic growth, and CO2 emissions in the case of the 20 newly emerging market economies for the period 1990–2021. We find negative effects of renewable energy consumption, industrialization and trade openness on CO2 emissions. We also find positive effects of nonrenewable energy consumption, economic growth, and human capital on CO2 emissions. In addition, our findings reveal that renewable energy consumption and human capital are complementary levers for reducing CO2 emissions, whereas human capital mitigates the detrimental effect of nonrenewable energy consumption on environmental quality. Besides, the results underline that human capital has an inverted U-shaped effect on CO2 emissions. Regarding policy implications, policymakers should emphasize the complementarity between human capital and renewable energy consumption by facilitating the accumulation of human capital towards productive investments and the use of renewable energy technologies in these countries. They should also raise people’s environmental awareness by implementing educational reforms, effective environmental awareness campaigns, and government regulatory pressures that help people understand global warming issues and adopt environmentally friendly practices in their daily activities. Finally, policymakers should promote the use of renewable energy rather than non-renewable energy sources in the production of goods and services by obliging countries to integrate green policies into their industrialization and trade openness strategies.
Factors influencing the implementation of agroecological practices: Lessons drawn from the Aba-Garima watershed, Ethiopia
Authors: Mekuria Wolde , Dessalegn Mengistu , Amare Dagninet , Belay Beyene , Getnet Banchiamlak , Girma Gonche , Tegegne Desalegn
Published: September 2022

The challenges to agroecological transitions are not the same for all farmers and implementation of agroecological practices in different locations could yield different results. With this consideration, this study was conducted in Aba-Garima watershed in northwestern Ethiopia to characterize the structure and activities of farming households and assess factors influencing the implementation and sustainability of agroecological practices. Data were collected from 218 households, 16 key informants, and 12 focus group discussions. The Multivariate Probit model and descriptive statistics were employed to analyze factors influencing farmers’ choices of different agroecological practices and describe the characteristics of farming households. The qualitative data analysis was processed through topic coding and building categories, themes, and patterns of relationships. Farmers realize the importance of both farm and landscape level agroecological practices to enhance income earning capacity, achieve food security and protect the environment. However, most of the agroecological practices are very difficult to start using for various constraining factors including limited access to water, and shortages of money, land and labor. The results suggest that depending on different socio-economic characteristics of farming households, agroecological practices that appear common practices can be very difficult to use for some farmers, while it would be possible for other farmers. The constraining factors are also differently associated with different practices, involving diverse perspectives of different socio-economic groups. The paper discussed the existing agroecological practices, the perspectives of different socio-economic groups on these practices and the factors influencing the implementation as well as the conditions that can facilitate the wider adoption of agroecological practices in the study area.
Would information acquisition increase enterprises’ willingness to participate in the carbon market? An empirical investigation of equipment manufacturing enterprises in Henan Province, China
Authors: Ma Xin , Xv Fan , Ge Rubing , Chen Tengfei , Cui Caocao , Lv Qi
Published: September 2022

The carbon market is the most important policy tool for achieving carbon peak and carbon neutralization. Enterprises are significant players in the carbon market, and this study aimed to identify if their willingness to participate is connected to the carbon market’s stability and, at the same time, whether it is also relevant for policy design and implementation. Using the technology acceptance model (TAM) and 226 questionnaire data from equipment manufacturing enterprises in Henan Province, China, this study contributes to the empirical analysis of the impact mechanism of information acquisition on the enterprises’ willingness to participate in the carbon market, with a particular focus on evaluating the three main transmission paths: the mediating role of perceived ease of use, the mediating role of perceived usefulness, and the chain mediating role of perceived ease of use and perceived usefulness; moreover, the results of the robustness tests also confirmed the soundness and validity of the research model. The study underlined that when appropriately designing the incentive mechanism for enterprises to participate in the carbon market, it may effectively enhance their willingness to participate in the carbon market by improving their perception of the ease of use and usefulness of the carbon market.
Leader gene identification for digestive system cancers based on human subcellular location and cancer-related characteristics in protein–protein interaction networks
Authors: Chen Hongwei , Rong Zherou , Ge Luanfeng , Yu Hongzheng , Li Chao , Xu Manyi , Zhang Zihan , Lv Junjie , He Yuehan , Li Wan , Chen Lina
Published: September 2022

Stomach, liver, and colon cancers are the most common digestive system cancers leading to mortality. Cancer leader genes were identified in the current study as the genes that contribute to tumor initiation and could shed light on the molecular mechanisms in tumorigenesis. An integrated procedure was proposed to identify cancer leader genes based on subcellular location information and cancer-related characteristics considering the effects of nodes on their neighbors in human protein–protein interaction networks. A total of 69, 43, and 64 leader genes were identified for stomach, liver, and colon cancers, respectively. Furthermore, literature reviews and experimental data including protein expression levels and independent datasets from other databases all verified their association with corresponding cancer types. These final leader genes were expected to be used as diagnostic biomarkers and targets for new treatment strategies. The procedure for identifying cancer leader genes could be expanded to open up a window into the mechanisms, early diagnosis, and treatment of other cancer types.
Genome-wide identification and expression analysis of WRKY family genes under soft rot in Chinese cabbage
Authors: Yan Jinghui , Yu Xinle , Ma Wei , Sun Xiaoxue , Ge Yunjia , Yue Xiaonan , Han Jing , Zhao Jianjun , Lu Yin , Liu Mengyang
Published: September 2022

Complex transcriptional networks regulate plant defense against pathogen attack, and plant transcription factors act as key regulators of the plant immune responses. The differences between transcription factor expression and regulation in Chinese cabbage soft rot (Pectobacterium carotovorum; Pc) have not been revealed. In this study, a total of 148 putative Chinese cabbage WRKY genes (BrWRKYs) were identified from the Chinese cabbage genome (v3.0). These genes were divided into seven subgroups (groups I, IIa–e, and III) based on phylogenomic analysis, with distinct motif compositions in each subgroup. Time-series RNA-seq was carried out to elucidate the dynamic expression patterns of the BrWRKYs on the resistant mutant (sr) and the susceptible wild-type (inbred WT) challenged by Pc. Transcriptional analysis showed that 48 WRKY transcription genes at 0–24 hpi were significantly upregulated in sr under soft rot stress. At the 12-h post-inoculation critical time point, we identified three specifically upregulated genes and two downregulated genes in the resistant mutant, which may provide potential applications for genetic improvement against soft rot. The findings improved our understanding of the WRKY-mediated soft rot stress response regulation in Chinese cabbage. The study thus lays a foundation for the genetic improvement of soft rot resistance.
Challenges in quantifying genome erosion for conservation
Authors: Bosse Mirte , van Loon Sam
Published: September 2022

Massive defaunation and high extinction rates have become characteristic of the Anthropocene. Genetic effects of population decline can lead populations into an extinction vortex, where declining populations show lower genetic fitness, in turn leading to lower populations still. The lower genetic fitness in a declining population due to a shrinking gene pool is known as genetic erosion. Three different types of genetic erosion are highlighted in this review: overall homozygosity, genetic load and runs of homozygosity (ROH), which are indicative of inbreeding. The ability to quantify genetic erosion could be a very helpful tool for conservationists, as it can provide them with an objective, quantifiable measure to use in the assessment of species at risk of extinction. The link between conservation status and genetic erosion should become more apparent. Currently, no clear correlation can be observed between the current conservation status and genetic erosion. However, the high quantities of genetic erosion in wild populations, especially in those species dealing with habitat fragmentation and habitat decline, may be early signs of deteriorating populations. Whole genome sequencing data is the way forward to quantify genetic erosion. Extra screening steps for genetic load and hybridization can be included, since they could potentially have great impact on population fitness. This way, the information yielded from genetic sequence data can provide conservationists with an objective genetic method in the assessment of species at risk of extinction. However, the great complexity of genome erosion quantification asks for consensus and bridging science and its applications, which remains challenging.
Genomic surveillance unfolds the SARS-CoV-2 transmission and divergence dynamics in Bangladesh
Authors: Shishir Tushar Ahmed , Jannat Taslimun , Naser Iftekhar Bin
Published: September 2022

The highly pathogenic virus SARS-CoV-2 has shattered the healthcare system of the world causing the COVID-19 pandemic since first detected in Wuhan, China. Therefore, scrutinizing the genome structure and tracing the transmission of the virus has gained enormous interest in designing appropriate intervention strategies to control the pandemic. In this report, we examined 4,622 sequences from Bangladesh and found that they belonged to thirty-five major PANGO lineages, while Delta alone accounted for 39%, and 78% were from just four primary lineages. Our research has also shown Dhaka to be the hub of viral transmission and observed the virus spreading back and forth across the country at different times by building a transmission network. The analysis resulted in 7,659 unique mutations, with an average of 24.61 missense mutations per sequence. Moreover, our analysis of genetic diversity and mutation patterns revealed that eight genes were under negative selection pressure to purify deleterious mutations, while three genes were under positive selection pressure. Together with an ongoing genomic surveillance program, these data will contribute to a better understanding of SARS-CoV-2, as well as its evolution pattern and pandemic characteristics in Bangladesh.
Integrative pan-cancer analysis and clinical characterization of the N7-methylguanosine (m7G) RNA modification regulators in human cancers
Authors: He Chun-Ming , Zhang Xin-Di , Zhu Song-Xin , Zheng Jia-Jie , Wang Yu-Ming , Wang Qing , Yin Hang , Fu Yu-Jie , Xue Song , Tang Jian , Zhao Xiao-Jing
Published: September 2022

Background: RNA modification is one of the epigenetic mechanisms that regulates post-transcriptional gene expression, and abnormal RNA modifications have been reported to play important roles in tumorigenesis. N7-methylguanosine (m7G) is an essential modification at the 5′ cap of human mRNA. However, a systematic and pan-cancer analysis of the clinical relevance of m7G related regulatory genes is still lacking.

Methods: We used univariate Cox model and Kaplan-Meier analysis to generate the forest plot of OS, PFI, DSS and identified the correlation between the altered expression of m7G regulators and patient survival in 33 cancer types from the TCGA and GTEx databases. Then, the “estimate” R-package, ssGSEA and CIBERSORT were used to depict the pan-cancer immune landscape. Through Spearman’s correlation test, we analyzed the correlation between m7G regulators and the tumor microenvironment (TME), immune subtype, and drug sensitivity of the tumors, which was further validated in NSCLC. We also assessed the changes in the expression of m7G related regulatory genes in NSCLC with regards to the genetic and transcriptional aspects and evaluated the correlation of METTL1 and WDR4 expression with TMB, MSI and immunotherapy in pan-cancer.

Results: High expression of most of the m7G regulators was significantly associated with worse prognosis. Correlation analyses revealed that the expression of majority of the m7G regulators was correlated with tumor immune infiltration and tumor stem cell scores. Drug sensitivity analysis showed that the expression of CYFP1,2 was closely related to drug sensitivity for various anticancer agents (p < 0.001). Analysis of the pan-cancer immune subtype revealed significant differences in the expression of m7G regulators between different immune subtypes (p < 0.001). Additionally, the types and proportions of mutations in METTL1 and WDR4 and their relevance to immunotherapy were further described.

Conclusion: Our study is the first to evaluate the correlation between the altered expression of m7G regulators and patient survival, the degree of immune infiltration, TME and drug sensitivity in pan-cancer datasets.
Acid external and internal environment exchange the Oreochromis niloticus tissue immune gene expression compared to the mouse macrophage polarization model
Authors: Pan Po-Kai , Wu Tsung-Meng , Tsai Hsin-Yuan , Cho I-Cheng , Tseng Hsin-Wei , Lin Tai-Du , Nan Fan-Hua , Wu Yu-Sheng
Published: September 2022

The water environment plays an important role in animal physiology. In this study, we sought to evaluate the effect of the acid environment on theOreochromis niloticus(Nile tilapia) internal microenvironment immune response compare to the mouse macrophage model (J77A.1). The acid environment treated mouse macrophage J774A.1 model have shown that acidic treatment is able to polarize macrophages into M2-like macrophagesviaan increase inYm1, Tgm2, Arg1, Fizz1, andIL-10expression. Metabolic analysis of mouse macrophages (J774A.1) at pH 2 vs. pH 7 and pH 4 vs. pH 7 have been shown to promote the expression of intracellular acetylcholine, choline, prochlorperazine, L-leucine, and bisphenol A,2-amino-3-methylimidazo[4,5-f] quinolone metabolites in the M2-like macrophage. Immune gene expression of theO. niloticusspleen and liver treated at pH 2, 4, and 7 was shown to reduceTNF-α,IL-1 β,IL-8, andIL-12expression compared to pH 7 treatment. Immune gene was induced inO. niloticusfollowing culture at pH 5, 6, and 7 fresh water environment. Taken together, we found that the acid internal environment polarizes tissues into an M2 macrophage developmental microenvironment. However, if the external environment is acid, tissues are exposed to an M1 macrophage developmental microenvironment.
Low baseline IFN-γ response could predict hospitalization in COVID-19 patients
Authors: Cremoni Marion , Allouche Jonathan , Graça Daisy , Zorzi Kevin , Fernandez Céline , Teisseyre Maxime , Benzaken Sylvia , Ruetsch-Chelli Caroline , Esnault Vincent L. M. , Dellamonica Jean , Carles Michel , Barrière Jérôme , Ticchioni Michel , Brglez Vesna , Seitz-Polski Barbara
Published: September 2022

The SARS-CoV-2 infection has spread rapidly around the world causing millions of deaths. Several treatments can reduce mortality and hospitalization. However, their efficacy depends on the choice of the molecule and the precise timing of its administration to ensure viral clearance and avoid a deleterious inflammatory response. Here, we investigated IFN-γ, assessed by a functional immunoassay, as a predictive biomarker for the risk of hospitalization at an early stage of infection or within one month prior to infection. Individuals with IFN-γ levels below 15 IU/mL were 6.57-times more likely to be hospitalized than those with higher values (p<0.001). As confirmed by multivariable analysis, low IFN-γ levels, age >65 years, and no vaccination were independently associated with hospitalization. In addition, we found a significant inverse correlation between low IFN-γ response and high level of IL-6 in plasma (Spearman’s rho=-0.38, p=0.003). Early analysis of the IFN-γ response in a contact or recently infected subject with SARS-CoV-2 could predict hospitalization and thus help the clinician to choose the appropriate treatment avoiding severe forms of infection and hospitalization.
Immunological characterization and function analysis of L-type lectin from spotted knifejaw, Oplegnathus punctatus
Authors: Liu Jinxiang , Liu Xiaobing , Wang Zhigang , Zhang Quanqi
Published: September 2022

Lily-type lectin (LTL) plays significant roles in innate immune response against pathogen infection. LTL in animals and plants has received widespread attention. In the present study, an LTL (OppLTL) was identified from spotted knifejaw Oplegnathus punctatus. The OppLTL encoded a typical Ca2+-dependent carbohydrate-binding protein containing a CRD domain. The qRT-PCR showed that it was mainly expressed in the gill and was significantly upregulated after Vibrio anguillarum challenge. The agglutination analysis showed that the recombinant OppLTL could bind and agglutinate Gram-negative and Gram-positive bacteria in a Ca2+-dependent manner. However, the binding activity was different. Meanwhile, the recombinant OppLTL could hemagglutinate mammalian and teleost erythrocytes. Subcellular localization revealed that OppLTL was mainly detected in the cytoplasm of HEK293T cells. The dual-luciferase analysis revealed that OppLTL could inhibit the activity of the NF-κB signal pathway in HEK293T cells after OppLTL overexpression. These findings collectively demonstrated that OppLTL could be involved in host innate immune response and defense against bacterial infection in spotted knifejaw.
Integration of single-cell RNA sequencing and bulk RNA sequencing to reveal an immunogenic cell death-related 5-gene panel as a prognostic model for osteosarcoma
Authors: Yang Jiaqi , Zhang Jian , Na Song , Wang Zhizhou , Li Hanshuo , Su Yuxin , Ji Li , Tang Xin , Yang Jun , Xu Lu
Published: September 2022

Background

Despite the comparatively low prevalence of osteosarcoma (OS) compared to other cancer types, metastatic OS has a poor overall survival rate of fewer than 30%. Accumulating data has shown the crucial functions of immunogenic cell death (ICD) in various cancers; nevertheless, the relationship between ICD and OS was not previously well understood. This research aims to determine the function of ICD in OS and construct an ICD-based prognostic panel.

Methods

Single cell RNA sequencing data from GSE162454 dataset distinguished malignant cells from normal cells in OS. The discrepancy in ICD scores and corresponding gene expression was intensively explored between malignant cells and normal cells. Using the RNA sequencing data of the TARGET-OS, GSE16091, GSE21257, and GSE39058 datasets, the molecular subtype of OS was determined by clustering seventeen ICD-related genes obtained from the literature. Differentially expressed genes (DEGs) between different molecular subtypes were identified to develop a novel ICD-associated prognostic panel.

Results

The malignant cells had a remarkable decrease in the ICD scores and corresponding gene expression compared with normal cells. A total of 212 OS patients were successfully stratified into two subtypes: C1 and C2. C1-like OS patients were characterized by better prognostic outcomes, overexpression of ICD genes, activation of the ICD pathway, high inflitration abundance of immunocytes, and low expression levels of immune checkpoint genes (ICGs); however, the reverse is true in C2-like OS patients. Utilizing the limma programme in R, the DEGs between two subtypes were determined, and a 5-gene risk panel consisting of BAMBI, TMCC2, NOX4, DKK1, and CBS was developed through LASSO-Cox regression analysis. The internal- and external-verification cohorts were employed to verify the efficacy and precision of the risk panel. The AUC values of ROC curves indicated excellent prognostic prediction values of our risk panel.

Conclusions

Overall, ICD represented a protective factor against OS, and our 5-gene risk panel serving as a biomarker could effectively evaluate the prognostic risk in patients with OS.
Cuproptosis-related gene FDX1 expression correlates with the prognosis and tumor immune microenvironment in clear cell renal cell carcinoma
Authors: Wang Tao , Liu Yufeng , Li Qing , Luo Yang , Liu Dawei , Li Bin
Published: September 2022

Background

Cuproptosis, a newly discovered form of cell death, is regulated by protein lipoylation and is related to mitochondrial metabolism. However, further research is needed to determine how the cuproptosis-related gene ferredoxin 1 (FDX1) affects the tumor immune response and its prognostic significance in clear cell renal cell carcinoma (ccRCC).

Methods

The Cancer Genome Atlas was used to screen for FDX1 gene expression in ccRCC and healthy tissue samples. The results were validated using the Gene Expression Omnibus and the Human Protein Atlas. Multivariable analysis and Kaplan-Meier survival curves were used to examine the relationship between FDX1 gene expression, clinicopathological parameters, and overall survival (OS). The protein network containing FDX1 gene interaction was constructed using the online Search Tool for the Retrieval of Interacting Genes/Proteins. The relationship between FDX1 gene expression and immune cell infiltration in ccRCC was examined using Gene Ontology, gene set enrichment analysis (GSEA), and a single-sample GSEA. Using the Gene Expression Profiling Interactive Analysis and Tumor Immune Estimation Resource databases, we investigated the relationship between FDX1 gene expression, the degree of immune cell infiltration, and the corresponding gene marker sets.

Results

ccRCC samples had significantly (p < 0.05) lower FDX1 gene expression levels than normal tissue samples. Lower FDX1 gene expression levels were strongly associated with higher cancer grades and more advanced tumor–node–metastasis stages. The findings of multivariate and univariate analyses illustrated that the OS in ccRCC patients with low FDX1 expression is shorter than in patients with high FDX1 expression (p < 0.05). Ferredoxin reductase and CYP11A1 are key proteins interacting with the FDX1 gene, and ccRCC with an FDX1 enzyme defect was associated with a low number of invading immune cells and their corresponding marker.

Conclusion

In ccRCC, decreased FDX1 expression was linked to disease progression, an unfavorable prognosis, and dysregulated immune cell infiltration.
Both AMP-activated and cAMP-dependent protein kinase regulate the expression of heat shock protein 70-2 gene in Neopyropia yezoensis
Authors: Sun Zhenjie , Gu Wenhui , Feng Zezhong , Fan Yaqin , Niu Jianfeng , Wang Guangce
Published: September 2022

The upregulation of heat shock protein 70 (hsp70) gene under high temperature stress is a common phenomenon. Although heat shock protein-mediated stress responses play an important role in intertidal Neopyropia yezoensis, the detailed regulatory mechanism of the hsp70 gene expression is still unclear. Here, a full-length sequence of the hsp70-2 gene was cloned and its’ expression regulation was analyzed. There was an activating transcription factors element (ATFE) of cAMP-dependent protein kinase (PKA) was found at the gene promoter region and a highly conserved deduced amino acid sequence with calmodulin-binding activity was detected. Reagents implicated in the induction of the hsp70 gene were then selected to treat the algal samples at 24°C, and the photosynthetic parameters, transcription and translation of this gene were determined. Results showed that quercetin inhibited the transcription of the hsp70-2 gene, significantly decreased the synthesis of the HSP70-2 protein, and lowered the photosynthetic activity of N. yezoensis under high temperature stress conditions. Although the addition of trifluoperazine (TFP), an inhibitor of calmodulin (CAM), downregulated the photosynthetic parameters, the transcription of the hsp70-2 gene was not influenced at high temperature treatment, implying that CAM was not involved in the transcription of the hsp70-2 gene but involved in the heat stress reponding pathways. 5′-aminoimidasole-4-carboxamide-1-β-d-ribofuranoside (AICAR) promoted the synthesis of hsp70-2 transcripts significantly and HSP70-2 protein slightly, which indicated that AMPK regulated the induction of the hsp70-2 gene in N. yezoensis. Forskolin also promoted the upregulation of the hsp70-2 gene. Thus, both AMPK and cAMP-dependent protein kinase (PKA) could phosphorylate HSF and activate the expression of the hsp70-2 gene in N. yezoensis. However, there was no strict correlation between transcripts of the hsp70-2 gene and HSP70-2 protein contents. It was proposed that the posttranscriptional mechanisms were involved in regulating the synthesis of the HSP70-2 protein. Which allowed it to adapt to the extremely variable intertidal environments with an instant responding manner, since the accumulated transcripts could be translated rapidly when needed.
Risk Factors for Acquired Stenotrophomonas maltophilia Pneumonia in Intensive Care Unit: A Systematic Review and Meta-Analysis
Authors: Wang Neng , Tang Congchen , Wang Lichun
Published: September 2022

Background and Aims:Stenotrophomonas maltophilia is increasingly found in critically ill patients, but it is considered a pathogen of limited pathogenicity and therefore it is not often targeted. We systematically evaluated risk factors for S. maltophilia pneumonia in ICU patients for better clinical management.

Methods: Prospective and retrospective studies of S. maltophilia infection in the ICU from database establishment to August 8, 2021, were searched through PubMed, web of science, Cochrane Library Embase and CNKI. The literature was independently screened and extracted by two authors according to inclusion and exclusion criteria, evaluated for quality by the NOS scale, and meta-analyzed by stata 14.0 software.

Results: A total of eight studies with a sample size of 2,320 cases were included. Meta-analysis showed that APACHE-II score > 20 (OR = 10.98, 95% CI: 5.67 ~ 21.26), COPD (OR = 3.97, 95% CI: 2.39 ~ 6.61), malignant tumor (OR = 2.15, 95% CI: 1.03 ~ 4.50), mechanical ventilation (OR = 8.75, 95% CI: 2.59 ~ 29.58), tracheotomy (OR = 6.12, 95% CI: 2.06 ~ 18.18), endotracheal intubation (OR = 4.25, 95% CI: 2.30 ~ 7.84), β- Lactamase inhibitors (OR = 9.98, 95% CI: 1.51 ~ 65.96), aminoglycosides (OR = 4.01, 95% CI: 2.06 ~ 7.80), carbapenems (OR = 2.82, 95% CI: 1.49 ~ 5.31), and quinolones (OR = 2.17, 95% CI: 1.21 ~ 3.89) were risk factors for ICU-acquired S. maltophilia pneumonia.

Conclusion: Many risk factors are associated with S. maltophilia pneumonia in ICU patients. Clinical workers should pay more attention to assessing the risk of infection in ICU patients and enhance the prevention and management of high-risk groups, which will help reduce their risk of S. maltophilia infection.
Anticoagulant for treatment and prophylaxis of venous thromboembolism patients with renal dysfunction: A systematic review and network meta-analysis
Authors: Fan Guohui , Wang Dingyi , Zhang Meng , Luo Xufei , Zhai Zhenguo , Wu Sinan
Published: September 2022

Objective

The aim of this study was to compare the efficacy and safety for particular regimen and dosage in venous thromboembolism (VTE) patients with renal insufficiency.

Methods

English language searches of PubMed, Embase, and Web of Science (inception to May 2021). RCTs evaluating anticoagulants for VTE treatment at acute phase, extension phase, and VTE prophylaxis in patients with renal insufficiency and reporting efficacy (death, recurrence, or occurrence of VTE) and safety (bleeding) outcomes were selected. The methodological quality of each study included was assessed at the outcome level using the risk-of-bias assessment tool developed by the Cochrane Bias Methods Group.

Results

Twenty-one trials that involved 76,574 participants and 8,972 (11.7%) patients with renal insufficiency were enrolled, including 10 trials on VTE treatment in acute phase (3–12 months), four trials on VTE treatment in extension phase (6–36 months), and seven trials for VTE prophylaxis. For acute VTE treatment, compared with dabigatran etexilate, apixaban (RR 5.90, 95%CI 1.00–34.60) and rivaroxaban (RR 6.18, 95%CI 1.17–32.75) were significantly associated with increased risk of death or recurrence. For extension treatment of VTE, aspirin had the highest probability of the most effective and safest treatment, followed by apixaban. For VTE prophylaxis, compared with enoxaparin, desirudin was associated with lower risk of VTE occurrence (RR 0.56, 95% CI 0.34–0.91), but had higher risk of bleeding than dabigatran etexilate.

Conclusion

The network meta-analysis informs the optimal choice of anticoagulants and their particular dosage for treatment and prophylaxis of VTE patients comorbid renal insufficiency.

Systematic review registration

www.crd.york.ac.uk/prospero/, identifier: CRD42021254086.
Global genetic diversity and evolutionary patterns among Potato leafroll virus populations
Authors: Farooq Tahir , Hussain Muhammad Dilshad , Shakeel Muhammad Taimoor , Riaz Hasan , Waheed Ummara , Siddique Maria , Shahzadi Irum , Aslam Muhammad Naveed , Tang Yafei , She Xiaoman , He Zifu
Published: September 2022

Potato leafroll virus (PLRV) is a widespread and one of the most damaging viral pathogens causing significant quantitative and qualitative losses in potato worldwide. The current knowledge of the geographical distribution, standing genetic diversity and the evolutionary patterns existing among global PLRV populations is limited. Here, we employed several bioinformatics tools and comprehensively analyzed the diversity, genomic variability, and the dynamics of key evolutionary factors governing the global spread of this viral pathogen. To date, a total of 84 full-genomic sequences of PLRV isolates have been reported from 22 countries with most genomes documented from Kenya. Among all PLRV-encoded major proteins, RTD and P0 displayed the highest level of nucleotide variability. The highest percentage of mutations were associated with RTD (38.81%) and P1 (31.66%) in the coding sequences. We detected a total of 10 significantly supported recombination events while the most frequently detected ones were associated with PLRV genome sequences reported from Kenya. Notably, the distribution patterns of recombination breakpoints across different genomic regions of PLRV isolates remained variable. Further analysis revealed that with exception of a few positively selected codons, a major part of the PLRV genome is evolving under strong purifying selection. Protein disorder prediction analysis revealed that CP-RTD had the highest percentage (48%) of disordered amino acids and the majority (27%) of disordered residues were positioned at the C-terminus. These findings will extend our current knowledge of the PLRV geographical prevalence, genetic diversity, and evolutionary factors that are presumably shaping the global spread and successful adaptation of PLRV as a destructive potato pathogen to geographically isolated regions of the world.
In vivo Phage Display: A promising selection strategy for the improvement of antibody targeting and drug delivery properties
Authors: André Ana S. , Moutinho Isa , Dias Joana N. R. , Aires-da-Silva Frederico
Published: September 2022

The discovery of hybridoma technology, described by Kohler and Milstein in 1975, and the resulting ability to generate monoclonal antibodies (mAbs) initiated a new era in antibody research and clinical development. However, limitations of the hybridoma technology as a routine antibody generation method in conjunction with high immunogenicity responses have led to the development of alternative approaches for the streamlined identification of most effective antibodies. Within this context, display selection technologies such as phage display, ribosome display, yeast display, bacterial display, and mammalian cell surface display have been widely promoted over the past three decades as ideal alternatives to traditional hybridoma methods. The display of antibodies on phages is probably the most widespread and powerful of these methods and, since its invention in late 1980s, significant technological advancements in the design, construction, and selection of antibody libraries have been made, and several fully human antibodies generated by phage display are currently approved or in various clinical development stages. With evolving novel disease targets and the emerging of a new generation of therapeutic antibodies, such as bispecific antibodies, antibody drug conjugates (ADCs), and chimeric antigen receptor T (CAR-T) cell therapies, it is clear that phage display is expected to continue to play a central role in antibody development. Nevertheless, for non-standard and more demanding cases aiming to generate best-in-class therapeutic antibodies against challenging targets and unmet medical needs, in vivo phage display selections by which phage libraries are directly injected into animals or humans for isolating and identifying the phages bound to specific tissues offer an advantage over conventional in vitro phage display screening procedures. Thus, in the present review, we will first summarize a general overview of the antibody therapeutic market, the different types of antibody fragments, and novel engineered variants that have already been explored. Then, we will discuss the state-of-the-art of in vivo phage display methodologies as a promising emerging selection strategy for improvement antibody targeting and drug delivery properties.
Does filter pore size introduce bias in DNA sequence-based plankton community studies?
Authors: Ma Guolin , Logares Ramiro , Xue Yuanyuan , Yang Jun
Published: September 2022

The cell size of microbial eukaryotic plankton normally ranges from 0.2 to 200 μm. During the past decade, high-throughput sequencing of DNA has been revolutionizing their study on an unprecedented scale. Nonetheless, it is currently unclear whether we can accurately, effectively, and quantitatively depict the microbial eukaryotic plankton community using size-fractionated filtration combined with environmental DNA (eDNA) molecular methods. Here we assessed the microbial eukaryotic plankton communities with two filtering strategies from two subtropical reservoirs, that is one-step filtration (0.2–200 μm) and size-fractionated filtration (0.2–3 and 3–200 μm). The difference of 18S rRNA gene copy abundance between the two filtering treatments was less than 50% of the 0.2–200 μm microbial eukaryotic community for 95% of the total samples. Although the microbial eukaryotic plankton communities within the 0.2–200 μm and the 0.2–3 and 3–200 μm size fractions had approximately identical 18S rRNA gene copies, there were significant differences in their community composition. Furthermore, our results demonstrate that the systemic bias introduced by size-fractionation filtration has more influence on unique OTUs than shared OTUs, and the significant differences in abundance between the two eukaryotic plankton communities largely occurred in low-abundance OTUs in specific seasons. This work provides new insights into the use of size-fractionation in molecular studies of microbial eukaryotes populating the plankton.
Characterization of rumen, fecal, and milk microbiota in lactating dairy cows
Authors: Williamson Jenna R. , Callaway Todd R. , Lourenco Jeferson M. , Ryman Valerie E.
Published: September 2022

Targeting the gastrointestinal microbiome for improvement of feed efficiency and reduction of production costs is a potential promising strategy. However little progress has been made in manipulation of the gut microbiomes in dairy cattle to improve milk yield and milk quality. Even less understood is the milk microbiome. Understanding the milk microbiome may provide insight into how the microbiota correlate with milk yield and milk quality. The objective of this study was to characterize similarities between rumen, fecal, and milk microbiota simultaneously, and to investigate associations between microbiota, milk somatic cell count (SCC), and milk yield. A total of 51 mid-lactation, multiparous Holstein dairy cattle were chosen for sampling of ruminal, fecal, and milk contents that were processed for microbial DNA extraction and sequencing. Cows were categorized based on low, medium, and high SCC; as well as low, medium, and high milk yield. Beta diversity indicated that ruminal, fecal, and milk populations were distinct (p < 0.001). Additionally, the Shannon index demonstrated that ruminal microbial populations were more diverse (p < 0.05) than were fecal and milk populations, and milk microbiota was the least diverse of all sample types (p < 0.001). While diversity indices were not linked (p > 0.1) with milk yield, milk microbial populations from cows with low SCC demonstrated a more evenly distributed microbiome in comparison to cows with high SCC values (p = 0.053). These data demonstrate the complexity of host microbiomes both in the gut and mammary gland. Further, we conclude that there is a significant relationship between mammary health (i.e., SCC) and the milk microbiome. Whether this microbiome could be utilized in efforts to protect the mammary gland remains unclear, but should be explored in future studies.
Assessing the effect of forcefield parameter sets on the accuracy of relative binding free energy calculations
Authors: Sun Shan , Huggins David J.
Published: September 2022

Software for accurate prediction of protein-ligand binding affinity can be a key enabling tool for small molecule drug discovery. Free energy perturbation (FEP) is a computational technique that can be used to compute binding affinity differences between molecules in a congeneric series. It has shown promise in reliably generating accurate predictions and is now widely used in the pharmaceutical industry. However, the high computational cost and use of commercial software, together with the technical challenges to setup, run, and analyze the simulations, limits the usage of FEP. Here, we use an automated FEP workflow which uses the open-source OpenMM package. To enable effective application of FEP, we compared the performance of different water models, partial charge assignments, and AMBER protein forcefields in eight benchmark test cases previously assembled for FEP validation studies.
Clinical parameters predict the effect of bilateral subthalamic stimulation on dynamic balance parameters during gait in Parkinson's disease
Authors: Kelemen Andrea , Halász László , Muthuraman Muthuraman , Erőss Loránd , Barsi Péter , Zádori Dénes , Laczó Bence , Kis Dávid , Klivényi Péter , Fekete Gábor , Bognár László , Bereczki Dániel , Tamás Gertrúd
Published: September 2022

We investigated the effect of deep brain stimulation on dynamic balance during gait in Parkinson's disease with motion sensor measurements and predicted their values from disease-related factors. We recruited twenty patients with Parkinson's disease treated with bilateral subthalamic stimulation for at least 12 months and 24 healthy controls. Six monitors with three-dimensional gyroscopes and accelerometers were placed on the chest, the lumbar region, the two wrists, and the shins. Patients performed the instrumented Timed Up and Go test in stimulation OFF, stimulation ON, and right- and left-sided stimulation ON conditions. Gait parameters and dynamic balance parameters such as double support, peak turn velocity, and the trunk's range of motion and velocity in three dimensions were analyzed. Age, disease duration, the time elapsed after implantation, the Hoehn-Yahr stage before and after the operation, the levodopa, and stimulation responsiveness were reported. We individually calculated the distance values of stimulation locations from the subthalamic motor center in three dimensions. Sway values of static balance were collected. We compared the gait parameters in the OFF and stimulation ON states and controls. With cluster analysis and a machine-learning-based multiple regression method, we explored the predictive clinical factors for each dynamic balance parameter (with age as a confounder). The arm movements improved the most among gait parameters due to stimulation and the horizontal and sagittal trunk movements. Double support did not change after switching on the stimulation on the group level and did not differ from control values. Individual changes in double support and horizontal range of trunk motion due to stimulation could be predicted from the most disease-related factors and the severity of the disease; the latter also from the stimulation-related changes in the static balance parameters. Physiotherapy should focus on double support and horizontal trunk movements when treating patients with subthalamic deep brain stimulation.
Safety and efficacy of tyrosine kinase inhibitors for the treatment of multiple sclerosis: A systematic review and meta-analysis from randomized controlled trials
Authors: Yan Zeya , Gu Feng , Wang Zilan , Meng Jiahao , Tao Xinyu , Dai Qiling , Wang Wei , Liu Meirong , Wang Zhong
Published: September 2022

Background

Multiple sclerosis (MS), an autoimmune disease, is characterized by inflammatory demyelinating lesions in the white matter of the central nervous system. Drugs targeting tyrosine kinase, a critical component of immune cell receptor signaling, have been developed to treat MS. However, the exact efficacy and safety of tyrosine kinase inhibitors (TKIs) are still controversial, and comprehensive analysis with a high level of evidence is needed.

Methods

Medline, Embase, Cochrane Library, and Clinicaltrials.gov for randomized controlled trials (RCTs) evaluating TKIs versus placebo for MS were searched up to April 1st, 2022. The risk ratio (RR) and mean difference (MD) or standard mean difference (SMD) were analyzed using dichotomous outcomes and continuous outcomes, respectively, with a random effect model.

Results

A total of 1,043 patients derived from four clinical trials were included to investigate the efficacy and safety of TKI therapy for MS. According to our analysis, TKIs decreased the cumulative number of gadolinium-enhancing lesions on T1-weighted MRI with the application of high dose (SMD = −0.61, 95% CI: −0.93 to −0.30, P = 0.0001). Meanwhile, TKIs prevented the expanded disability status scale (EDSS) from rising (MD = −0.10, 95% CI: −0.19 to −0.00, P = 0.046). In terms of MS relapse, TKIs have not revealed an obvious statistical difference compared with placebo (RR = 0.96, 95% CI: 0.55–1.65, P = 0.8755). However, more adverse events seem to occur in the TKIs group, both for adverse events (RR = 1.12, 95% CI: 1.05–1.19, P = 0.0009) and serious adverse events (RR = 1.91, 95% CI: 1.30–2.81, P = 0.001).

Conclusion

Tyrosine kinase inhibitors have shown promise in treating MS. Generally, TKIs that attain the effective dose demonstrate definite efficacy and have tolerable side effects. More clinical trials and validation are needed, and we anticipate that TKIs will be a viable alternative for MS patients.