bluuebunny/crossref_metadata_2025 huggingface dataset:
The Implementation of Fuzzy PSO-PID Adaptive Controller in Pitch Regulation for Wind Turbines Suppressing Multi-Factor Disturbances
Authors: Shao Yixiang , Liu Jian , Huang Junjie , Hu Liping , Guo Liang , Fang Yuan
Published: March 2022

The stability of wind turbine output is affected by multi-factor disturbances, which makes traditional proportion-integral-differential (PID) control strategy hardly achieve a satisfactory effect. Hence, a pitch control strategy based on fuzzy adaptive particle-swarm-optimization (PSO)-PID is proposed in this paper. Firstly, the models of wind turbine, pitch regulator, and permanent magnet synchronous generator (PMSG) are built. Then, the influence of various disturbances, such as blade deformation, installation errors, and external wind speed, on the wind wheel speed is analyzed. Furtherly, a wind turbine pitch control strategy is devised in detail, in which the PID parameters are initially optimized by PSO and adaptively adjusted by fuzzy controller. Simulations under gust wind and turbulent wind conditions are carried out, and the results show that compared with fuzzy PID and PID, the fuzzy adaptive PSO-PID could reduce errors of wind wheel speed and wind turbine output power effectively.
A Novel Energy Absorption-Based Protection Scheme for Surge Transients in Large-Scale Wind Farm System
Authors: Chen Chen , Gao Jiuguo , Chu Penghao
Published: March 2022

Onshore wind farms are usually connected to the power grid by 35 kV transmission lines. Due to the high altitude of the wind turbines and their associated long transmission corridors, lightning activities are more frequent for onshore wind farms compared to the power plant in plain areas. In addition, the insulation levels of 10–35 kV distribution lines are generally low. All these facts make proper lightning strike protection a technical challenge for onshore wind farms. Taking a typical onshore wind farm as the testing object, the structure of the 35 kV distribution line connected to this wind farm is modeled by EMTP software in this paper. The leakage current and absorbed energy of the arrester at the head tower when lightning currents of different amplitudes inject into the overhead line are studied. By calculating the energy accumulated in the arrester within 100 µs, the causes of the lightning trip and damage to the arrester of the distribution line, i.e., the energy accumulation mechanism, are clarified. Eventually, the lightning protection updating scheme for this distribution line is proposed: a combination of refitting the porcelain cross arm at the head and end of the tower and filling the grounding body of the tower with a drag-reduction agent, which shows that the lightning resistance level of the distribution can be improved by 50 times in maximum.
Experimental Study on Operational Stability of Centrifugal Pumps of Varying Impeller Types Based on External Characteristic, Pressure Pulsation and Vibration Characteristic Tests
Authors: Jia XiaoQi , Chu Qingyang , Zhang Li , Zhu ZuChao
Published: March 2022

This study performed external characteristics, dynamic pressure, and vibration tests on the closed impeller model, semi-open type impeller model, and open impeller model in order to study the influence of the impeller structure on the operational stability of the pump. According to the research findings, the external characteristics of the three impellers enjoyed favorable stability with flat curves under low flow rates. As the flow increases, the stability of the external characteristics weakens, and the poorest stability can be observed in the open impeller, while the enclosed impeller has the best stability under a large flow rate. In addition, intense pressure fluctuations arise near the casing tongue due to the dynamic and static interference between the blade and the casing tongue, causing a large amplitude of pressure pulsation near the casing tongue and the pump outlet. It can be seen that the stability of pressure pulsation of the closed impeller in the casing tongue area was the best, whereas the stability of pressure pulsation of the open impeller was the poorest. The minimum casing vibration can be found in the closed impeller, followed by the semi-open impeller, and the open impeller, with the maximum vibration. In addition, the optimum stability of rotor vibration can be observed in the closed impeller, semi-open impeller, and open impeller with similar stability of rotor vibration.
RETRACTED: The Effects of Financial Development and Pandemics Prevalence on Forests: Evidence From Asia-Pacific Region
Authors: Wang Jiajie , Khan Yousaf Ali , Khodaei Mehdi , Khezr Somayeh , Karimi Muhammad Sharif , Salem Sultan
Published: March 2022

Achieving sustainable development and the necessity to pay attention to the quality of the environment is one of the challenges of the new century. Experimental studies on deforestation determinants have focused mainly on analyzing an environmental Kuznets curve for deforestation (EKCd). The present study introduces three contributions to experimental studies using data from 15 Asia-Pacific countries over a 16-year period, from 2005 to 2020. In this regard, the effects of six financial development indexes and a new pandemic uncertainty index on forest regions have been investigated. Furthermore, the effects of the variables have been estimated through a spatial econometric model. This estimation can be used to investigate the variables of neighboring countries on the inland forest cover of countries. Diagnostic tests confirmed the spatial Durbin model. The results indicate the existence of an environmental Kuznets curve hypothesis. The trade openness variable has decreased the inland forest cover; however, the trade openness in neighboring countries has increased the inland forest cover in the countries. Besides, similar results were obtained for urbanization. Furthermore, natural resource rent is a beneficial factor dominating the improvement of forest areas. As confirmed by the results, the financial institution depth has a significant adverse effect on the forest cover of countries. The results for other reductions in financial development are meaningless. Despite the theoretically positive and negative dimensions of pandemics, the estimation results highlight its positive effects in forest regions.
Diptera and Drosophila Karyotype Databases: A Useful Dataset to Guide Evolutionary and Genomic Studies
Authors: Morelli Magnolia W. , Blackmon Heath , Hjelmen Carl E.
Published: March 2022

Karyotypes and chromosome data have been widely used in many subfields of biology over the last century. Unfortunately, this data is largely scattered among hundreds of articles, books, and theses, many of which are only available behind paywalls. This creates a barrier to new researchers wishing to use this data, especially those from smaller institutions or in countries lacking institutional access to much of the scientific literature. We solved this problem by building two datasets for true flies (Order: Diptera and one specific toDrosophila), These datasets are available via a public interactive database that allows users to explore, visualize and download all data. The Diptera karyotype databases currently contain a total of 3,474 karyotype records from 538 publications. Synthesizing this data, we show several groups are of particular interest for future investigations by whole genome sequencing.
Systematic Review of Digital Interventions for Adolescent and Young Adult Women's Body Image
Authors: Mahon Ciara , Seekis Veya
Published: March 2022

Background

A growing number of digital interventions have been developed to address a range of mental health issues including body image. Identifying effective interventions for body image is important given the prevalence of body image concerns and their associated negative outcomes among young women. This review aimed to critically evaluate current evidence on the use of digital interventions for adolescent and young adult women's body image.

Methods

A literature search was performed in November 2021 across three databases, PsychINFO, Web of Science and Pubmed to identify studies published with keywords and synonyms of “body image” and “digital interventions” that have been conducted with girls/women aged 10–25 years. Studies were included if they assessed a universal body image intervention delivered through a digital platform (e.g., web-based, mobile phone) and if they reported body image outcomes using validated measures. Two authors independently screened studies extracted data and assessed the quality of studies.

Results

Eight of 15 interventions were effective in improving at least one body image outcome from pre-post intervention; however, effect sizes were mostly small-medium, and few effects were maintained at follow-up. Studies were heterogeneous in terms of delivery format, duration, sample characteristics, quality, and outcomes.

Discussion

Findings suggest that digitally delivered interventions can effectively improve some body image outcomes in young women. Characteristics of effective studies are discussed and suggestions for future work on intervention development in this field are provided.

Systematic Review Registration

https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42021281435, identifier CRD42021281435.
Osteoarticular Involvement-Associated Biomarkers and Pathways in Psoriasis: The Shared Pathway With Ankylosing Spondylitis
Authors: Zhang Yu-Ping , Wang Xing , Jie Li-Gang , Qu Yuan , Zhu Xiao-Tong , Wu Jing , Yu Qing-Hong
Published: March 2022

Psoriatic arthritis (PsA) is a unique immune-mediated disease with cutaneous and osteoarticular involvement. However, only a few studies have explored the susceptibility of osteoarticular involvement in psoriasis (Ps) at the genetic level. This study investigated the biomarkers associated with osteoarticular participation and potential shared molecular mechanisms for PsA and ankylosing spondylitis (AS).

Methods

The RNA-seq data of Ps, PsA, and AS in the Gene Expression Omnibus (GEO) database were obtained. First, we used the limma package and the weighted gene co-expression network analysis (WGCNA) to identify the potential genes related to PsA and AS. Then, the shared genes in PsA and AS were performed using the GO, KEGG, and GSEA analyses. We also used machine learning to screen hub genes. The results were validated using external datasets and native cohorts. Finally, we used the CIBERSORT algorithm to estimate the correlation between hub genes and the abundance of immune cells in tissues.

Results

An overlap was observed between the PsA and AS-related modules as 9 genes. For differentially expressed genes in AS and PsA, only one overlapping gene was found (COX7B). Gene enrichment analysis showed that the above 9 genes might be related to the mRNA surveillance pathway. The GSEA analyses showed that COX7B was involved in adaptive immune response, cell activation, etc. The PUM1 and ZFP91, identified from the support vector machine, had preferable values as diagnostic markers for osteoarticular involvement in Ps and AS (AUC > 0.7). Finally, CIBERSORT results showed PUM1 and ZFP91 involvement in changes of the immune microenvironment.

Conclusion

For the first time, this study showed that the osteoarticular involvement in psoriasis and AS could be mediated by the mRNA surveillance pathway-mediated abnormal immunologic process. The biological processes may represent the cross talk between PsA and AS. Therefore, PUM1 and ZFP91 could be used as potential biomarkers or therapeutic targets for AS and Ps patients.
Serum IgE Levels Are Associated With the Prognosis of Minimal Change Disease
Authors: Li Heng , Wang Lefeng , Li Xiayu , Chen Wenqing , Zhang Ying , Chen Jianghua
Published: March 2022

Background

Previous reports showed that some patients with minimal change disease (MCD) had high serum immunoglobulin E (IgE) levels. This study aimed to explore the proportion of MCD patients with high serum IgE levels and evaluate the correlation between serum IgE levels and MCD remission and relapse.

Methods

This study enrolled 222 new-onset patients with renal biopsy-confirmed MCD from October 2012 to October 2019 at the First Affiliated Hospital of Zhejiang University in Hangzhou, China. Patients’ demographics and clinical parameters were analyzed.

Results

The results indicated that 70.3% of 222 MCD patients had high serum IgE levels (IgE > 100.0 IU/mL). Moreover, 134 patients were treated with glucocorticoids alone and divided into the low- and high-IgE groups, according to the median serum IgE level (523.5 IU/mL). The mean time to complete remission of the low- and high-IgE groups was 29.0 ± 2.2 and 45.7 ± 4.2 days, respectively (log-rank test; P = 0.002). The mean time to total remission was 19.1 ± 1.4 and 31.6 ± 3.2 days of the low- and high-IgE groups, respectively (log-rank test; P < 0.001). The mean time to first relapse in the low- and high-IgE groups was 701.2 ± 65.0 and 425.0 ± 52.6 days, respectively (log-rank test; P = 0.002). Serum IgE ≥ 523.5 IU/mL was an independent correlation factor affecting the patients’ remission and relapse.

Conclusion

Serum IgE level was an independent correlation factor for MCD remission and relapse. MCD patients with high serum IgE levels were prone to delayed remissions and early relapses.
Transcriptome Sequencing Reveals the Antiviral Innate Immunity by IFN-γ in Chinese Sturgeon Macrophages
Authors: Ding Guangyi , Zheng Chuwen , Wang Bei , Zhang Lifeng , Deng Dan , Li Qian , Guo Huizhi , Zhang Shuhuan , Xu Qiaoqing
Published: March 2022

To further study the biological function of interferon-gamma (IFN-γ) in the Chinese sturgeon (Acipenser sinensis), we conducted a transcriptome analysis of primary macrophages induced by IFN-γ using Illumina sequencing technology. We obtained 88,879 unigenes, with a total length of 93,919,393 bp, and an average length of 1,057bp. We identified 8,490 differentially expressed genes (DEGs) between the untreated and IFN-γ-treated macrophages, with 4,599 upregulated and 3,891 downregulated. Gene ontology (GO) analysis showed that 4,044 DEGs were enriched in the biological, cellular components, and molecular function categories. Kyoto Encyclopedia of Genes and Genomes (KEGG) identified 278 immunity-related pathways enriched for the DEGs. According to the GO enrichment results, eight key immunity-related genes were screened for verification using qPCR. Results indicate that IFN-γ can activate macrophage Interferon Regulatory Factors (IRFs) and type I interferon (IFN-I), activate RIG-I-like and Toll-like receptor-related pathways, and improve the antiviral ability of macrophages in Chinese sturgeon.
Diversity in Habitat Use by White Sturgeon Revealed Using Fin Ray Geochemistry
Authors: Sellheim Kirsten , Willmes Malte , Lewis Levi S. , Sweeney Jamie , Merz Joseph , Hobbs James A.
Published: March 2022

Understanding life-history diversity in a population is imperative to developing effective fisheries management and conservation practices, particularly in degraded environments with high environmental variability. Here, we examined variation in habitat use and migration patterns of White Sturgeon (Acipenser transmontanus), a long-lived migratory fish that is native to the San Francisco Estuary, CA, United States. Annual increment profiles were combined with respective geochemical (87Sr/86Sr) profiles in sturgeon fin rays to reconstruct annual salinity chronologies for 112 individuals from 5 to 30 years old. Results indicated a complex and diverse amphidromous life history across individuals, characterized largely by estuarine residence, a general ontogenetic trend toward higher-salinity brackish habitats, and high variability in habitat use across all age groups. Hierarchical clustering based on fin ray geochemistry during the first 10 years of life, prior to sexual maturation, indicated at least four distinct migratory phenotypes which differed largely in the timing and duration of juvenile to subadult movements between fresh- and brackish-water habitats. This study provides information regarding habitat use and migration in sub-adult fish that was previously lacking. Different migratory phenotypes vary in exposure to stressors across time and space and populations. Understanding White Sturgeon habitat distributions through space and time at different life stages can help identify areas where habitat restoration would be most effective and develop management actions to reduce stressors associated with specific areas where White Sturgeon are present.
Association Between Living Risk and Healthy Life Years Lost Due to Multimorbidity: Observations From the China Health and Retirement Longitudinal Study
Authors: Miao Xinlei , Chen Jun , Meng Wen , Wu Qiong , Wu Zhiyuan , Ren Lin , Cai Yue , Guo Xiuhua , Zhang Xiang , Meng Qun
Published: March 2022

Background

Multimorbidity has an effect on life expectancy, while its effect on healthy life years is unclear. This study aims to investigate the associations between healthy life years lost due to multimorbidity and living risk.

Methods

The participants of The China Health and Retirement Longitudinal Study (CHARLS) were assessed at four visits between 2011 (baseline) and 2018. At baseline, 13,949 individuals were administered surveys. A combined score based on seven health-related factors was calculated, and the participants were classified into 3 groups based on living risk. We used the adjusted Cox regression methods to examine the associations between living risk groups and multimorbidity. We estimated the healthy life years lost due to multimorbidity using the Sullivan method.

Results

A total of 9,091 adults aged 45 years or older (mean age of 59.55 ± 9.50 years with one disease, 52.60% women) were analyzed in the CHARLS. The probability of no multimorbidity over 7 years decreased from 0.9947 to 0.9697 in the low-risk group, whereas the probability of multimorbidity in low living risk was lower than that of high living risk, ranging from HR 1.253 (95% CI.992–1.581; P = 0.058) to 1.431 (1.05–1.949; P = 0.023) in sex, and ranging from HR 1.340 (95% CI 1.106–1.623; P = 0.003) to 2.002 (1.058–3.787; P = 0.033) in area. At 45 years, the healthy life years lost in men was <0.27 years compared to women in the low-risk group. Hypertension increased the risk of multimorbidity with an HR of 1.5 (95% CI 1.21–1.91; P < 0.001) in men. In urban areas, participants with diabetes had 3.2 times (95% CI 1.75–5.94, P < 0.001) higher risk of multimorbidity than participants without diabetes.

Conclusions

These findings indicate that a low-risk lifestyle could decrease the loss of healthy life years under multimorbidity. The probability of multimorbidity in women and in urban areas was high. Hypertension was correlated with the hazard risk of multimorbidity.
Hematological Abnormalities in COVID-19 Disease: Association With Type I Interferon Pathway Activation and Disease Outcomes
Authors: Georgakopoulou Vasiliki E. , Lembessis Panagiotis , Skarlis Charalampos , Gkoufa Aikaterini , Sipsas Nikolaos V. , Mavragani Clio P.
Published: March 2022

Increased expression of interferon (IFN)-stimulated genes (ISGs) in peripheral blood, has been previously reported in viral infections, as well as in autoimmune disorders, in association with reduced leukocyte and platelet counts. Though cytopenias are common in patients with COVID-19 disease and predict severe outcomes, the underlying mechanisms have not been fully elucidated. In the current study, we aimed to determine the prevalence of hematological abnormalities in the setting of active COVID-19 infection and to explore whether they associate with disease outcomes and activation of type I IFN pathway. One-hundred-twenty-three consecutive SARS-CoV2 infected patients were included in the study. Clinical and laboratory parameters were recorded for all study participants. In 114 patients, total RNA was extracted from whole peripheral blood and subjected to real time PCR. The relative expression of three interferon stimulated genes (ISGs; IFIT1, MX-1, and IFI44) was determined and a type I IFN score reflecting peripheral type I IFN activity was calculated. The rates of anemia, leukopenia, and thrombocytopenia were 28.5, 14.6, and 24.4%, respectively. Among leukocytopenias, eosinopenia, and lymphopenia were the most prominent abnormalities being found in 56.9 and 43.1%, respectively. Of interest, patients with either eosinopenia and/or thrombocytopenia but no other hematological abnormalities displayed significantly increased peripheral type I IFN scores compared to their counterparts with normal/high eosinophil and platelet counts. While eosinopenia along with lymphopenia were found to be associated with increased risk for intubation and severe/critical disease, such an association was not detected between other hematological abnormalities or increased type I IFN scores. In conclusion, hematological abnormalities are commonly detected among patients with COVID-19 infection in association with severe disease outcomes and activation of the type I IFN pathway.
Improvement of Mesenchymal Stromal Cell Proliferation and Differentiation via Decellularized Extracellular Matrix on Substrates With a Range of Surface Chemistries
Authors: Yang Michael C. , O'Connor Andrea J. , Kalionis Bill , Heath Daniel E.
Published: March 2022

Decellularized extracellular matrix (dECM) deposited by mesenchymal stromal cells (MSCs) has emerged as a promising substrate for improved expansion of MSCs. To date, essentially all studies that have produced dECM for MSC expansion have done so on tissue culture plastic or glass. However, substrate surface chemistry has a profound impact on the adsorption of proteins that mediate cell-material interactions, and different surface chemistries can cause changes in cell behavior, ECM deposition, and the in vivo response to a material. This study tested the hypothesis that substrate surface chemistry impacts the deposition of ECM and its subsequent bioactivity. This hypothesis was tested by producing glass surfaces with various surface chemistries (amine, carboxylic acid, propyl, and octyl groups) using silane chemistry. ECM was deposited by an immortalized MSC line, decellularized, and characterized through SDS-PAGE and immunofluorescence microscopy. No significant difference was observed in dECM composition or microarchitecture on the different surfaces. The decellularized surfaces were seeded with primary MSCs and their proliferation and differentiation were assessed. The presence of dECM improved the proliferation of primary MSCs by ~100% in comparison to surface chemistry controls. Additionally, the adipogenesis increased by 50–90% on all dECM surfaces in comparison to surface chemistry controls, and the osteogenesis increased by ~50% on the octyl-modified surfaces when dECM was present. However, no statistically significant differences were observed within the set of dECM surfaces or control surfaces. These results support the null hypothesis, meaning surface chemistry (over the range tested in this work) is not a key regulator of the composition or bioactivity of MSC-derived dECM. These results are significant because they provide an important insight into regenerative engineering technologies. Specifically, the utilization of dECM in stem cell manufacturing and tissue engineering applications would require the dECM to be produced on a wide variety of substrates. This work indicates that it can be produced on materials with a range of surface chemistries without undesired changes in the bioactivity of the dECM.
Weeds in the Alfalfa Field Decrease Rhizosphere Microbial Diversity and Association Networks in the North China Plain
Authors: Yang Chao , Tang Wei , Sun Junqi , Guo Haipeng , Sun Shusheng , Miao Fuhong , Yang Guofeng , Zhao Yiran , Wang Zengyu , Sun Juan
Published: March 2022

The competition between weeds and crops for soil nutrients is affected by soil microorganisms, which drive diverse ecological processes and are critical in maintaining the stability of agroecosystems. However, the effects of plant species identity, particularly between forage and weed, on soil microbial diversity, composition, and association are not well understood. Here, we investigate the soil physicochemical properties and bacterial/fungal communities in an agroecosystem with native alfalfa [Medicago stativa (Ms)] and five common weed species (Digitaria sanguinalis, Echinochloa crusgalli, Acalypha australis, Portulaca oleracea, and Chenopodium album) in the North China Plain. The five weeds had a lower plant carbon content than Ms. while the opposite was true for plant nitrogen and phosphorus concentrations. The Shannon diversity of bacterial and fungal communities of the five weeds were significantly lower than in Ms. Soil pH and PO43−-P were identified as the most important factors in shaping the relative abundances of bacteria (Sphingomonadaceae) and fungi (Pleosporaceae), respectively. Importantly, the weeds greatly inhibited the growth of pathogenic fungi (Nectriaceae and Pleosporaceae). Bacterial co-occurrence networks depended on specific species, indicating that Ms. harbored co-occurrence networks that were more complex than those in the bacterial communities of other weed groups. Our study examines how soil nutrients and the soil microbial community structure of five weed species changed in an Ms. field. This analysis of the microbial ecological network enhances our understanding of the influence of weeds on the soil microbiome in agroecosystems.
Effect of Alteration in Precipitation Amount on Soil Microbial Community in a Semi-Arid Grassland
Authors: Li Junyong , Benti Girmaye , Wang Dong , Yang Zhongling , Xiao Rui
Published: March 2022

Climate models predict significant changes in precipitation magnitude in semi-arid grasslands, so it is vital to improve our understanding of how changing precipitation affects microbial communities in grassland ecosystems. Using a long-term field manipulation experiment, we evaluated the responses of microbial communities to a decrease (DP) and an increase (IP) in precipitation on a semi-arid grassland in northern China. The results showed that bacterial species richness decreased significantly with DP but remained stable under IP. Relative abundance of oligotrophic, slow-growing bacterial phyla (e.g., Chloroflexi and Acidobacteria) increased with DP but decreased with IP, whereas the relative abundance of copiotrophic, fast-growing bacterial phyla (e.g., Proteobacteria and Bacteroidetes) decreased with DP but increased with IP. In contrast, diversity, species composition, and relative abundance of different fungal phyla change little with DP or IP. These results indicate a greater sensitivity of bacteria to precipitation changes than fungi, and the sensitivity of bacteria to DP was higher than IP. Our findings are important for understanding soil microbial dynamics under future climate change scenarios.
Cryptic Methane-Cycling by Methanogens During Multi-Year Incubation of Estuarine Sediment
Authors: Kevorkian Richard T. , Sipes Katie , Winstead Rachel , Paul Raegan , Lloyd Karen G.
Published: March 2022

As marine sediments are buried, microbial communities transition from sulfate-reduction to methane-production after sulfate is depleted. When this biogenic methane diffuses into the overlying sulfate-rich sediments, it forms a sulfate-methane transition zone (SMTZ) because sulfate reducers deplete hydrogen concentrations and make hydrogenotrophic methanogenesis exergonic in the reverse direction, a process called the anaerobic oxidation of methane (AOM). Microbial participation in these processes is often inferred from geochemistry, genes, and gene expression changes with sediment depth, using sedimentation rates to convert depth to time. Less is known about how natural sediments transition through these geochemical states transition in real-time. We examined 16S rRNA gene amplicon libraries and metatranscriptomes in microcosms of anoxic sediment from the White Oak River estuary, NC, with three destructively sampled replicates with methane added (586-day incubations) and three re-sampled un-amended replicates (895-day incubations). Sulfate dropped to a low value (∼0.3 mM) on similar days for both experiments (312 and 320 days, respectively), followed by a peak in hydrogen, intermittent increases in methane-cycling archaea starting on days 375 and 362 (mostly Methanolinea spp. and Methanosaeta spp., and Methanococcoides sp. ANME-3), and a methane peak 1 month later. However, methane δ13C values only show net methanogenesis 6 months after methane-cycling archaea increase and 4 months after the methane peak, when sulfate is consistently below 0.1 mM and hydrogen increases to a stable 0.61 ± 0.13 nM (days 553–586, n = 9). Sulfate-reducing bacteria (mostly Desulfatiglans spp. and Desulfosarcina sp. SEEP-SRB1) increase in relative abundance only during this period of net methane production, suggesting syntrophy with methanogens in the absence of sulfate. The transition from sulfate reduction to methane production in marine sediments occurs through a prolonged period of methane-cycling by methanogens at low sulfate concentrations, and steady growth of sulfate reducers along with methanogens after sulfate is depleted.
MxB Disrupts Hepatitis C Virus NS5A–CypA Complex: Insights From a Combined Theoretical and Experimental Approach
Authors: Li Quanjie , An Ni , Yin Xiao , Zhang Ruixin , Shao Huihan , Yi Dongrong , Cen Shan
Published: March 2022

The human myxovirus resistance B (MxB) protein is an interferon-induced restriction factor that fights a wide range of viruses. We previously demonstrated that MxB binds to hepatitis C virus (HCV)-encoded non-structural protein 5A (NS5A) and inhibits HCV infection by impairing the formation of cyclophilin A (CypA)–NS5A complex. However, the molecular details about how the presence of MxB diminishes the binding of NS5A to CypA remain uncovered. In this study, through molecular dynamic simulations and biochemical assays, we characterized that MxB binds to NS5A domain I through its N-terminal and GTPase domains. Specifically, amino acids (aa.) 189–191 and aa. 330–334 within MxB, together with NS5A residues aa. 71–73, are crucial for MxB–NS5A interaction. Furthermore, we predicted the CypA:NS5A and CypA:NS5A:MxB complexes and calculated the per-residue energy decomposition for identified key residues of the CypA–NS5A interface. A 28% decrease in CypA–NS5A binding affinity was observed in the presence of MxB, suggesting a weakened CypA–NS5A association upon binding of MxB to NS5A, which may contribute to the MxB-mediated inhibitory effect on the formation of CypA–NS5A complex. This work provides information for the antiviral mechanism of MxB and may facilitate the discovery of new strategies to combat CypA-dependent viruses.
Exploring the Intestinal Microbiota and Metabolome Profiles Associated With Feed Efficiency in Pacific Abalone (Haliotis discus hannai)
Authors: Yu Wenchao , Lu Yisha , Shen Yawei , Liu Junyu , Gong Shihai , Yu Feng , Huang Zekun , Zou Weiguang , Zhou Mingcan , Luo Xuan , You Weiwei , Ke Caihuan
Published: March 2022

Feed efficiency (FE) is critical to the economic and environmental benefits of aquaculture. Both the intestines and intestinal microbiota play a key role in energy acquisition and influence FE. In the current research, intestinal microbiota, metabolome, and key digestive enzyme activities were compared between abalones with high [Residual feed intake (RFI) = −0.029] and low FE (RFI = 0.022). The FE of group A were significantly higher than these of group B. There were significant differences in intestinal microbiota structures between high- and low-FE groups, while higher microbiota diversity was observed in the high-FE group. Differences in FE were also strongly correlated to variations in intestinal digestive enzyme activity that may be caused by Pseudoalteromonas and Cobetia. In addition, Saprospira, Rhodanobacteraceae, Llumatobacteraceae, and Gaiellales may potentially be utilized as biomarkers to distinguish high- from low-FE abalones. Significantly different microorganisms (uncultured beta proteobacterium, BD1_7_clade, and Lautropia) were found to be highly correlated to significantly different metabolites [DL-methionine sulfoxide Arg-Gln, L-pyroglutamic acid, dopamine, tyramine, phosphatidyl cholines (PC) (16:0/16:0), and indoleacetic acid] in the high- and low-FE groups, and intestinal trypsin activity also significantly differed between the two groups. We propose that interactions occur among intestinal microbiota, intestinal metabolites, and enzyme activity, which improve abalone FE by enhancing amino acid metabolism, immune response, and signal transduction pathways. The present study not only elucidates mechanisms of variations in abalone FE, but it also provides important basic knowledge for improving abalone FE by modulating intestinal microbiota.
The Symbiotic Continuum Within Ticks: Opportunities for Disease Control
Authors: Hussain Sabir , Perveen Nighat , Hussain Abrar , Song Baolin , Aziz Muhammad Umair , Zeb Jehan , Li Jun , George David , Cabezas-Cruz Alejandro , Sparagano Olivier
Published: March 2022

Among blood-sucking arthropods, ticks are recognized as being of prime global importance because of their role as vectors of pathogens affecting human and animal health. Ticks carry a variety of pathogenic, commensal, and symbiotic microorganisms. For the latter, studies are available concerning the detection of endosymbionts, but their role in the physiology and ecology of ticks remains largely unexplored. This review paper focuses on tick endosymbionts of the genera Coxiella, Rickettsia, Francisella, Midichloria, and Wolbachia, and their impact on ticks and tick-pathogen interactions that drive disease risk. Tick endosymbionts can affect tick physiology by influencing nutritional adaptation, fitness, and immunity. Further, symbionts may influence disease ecology, as they interact with tick-borne pathogens and can facilitate or compete with pathogen development within the vector tissues. Rickettsial symbionts are frequently found in ticks of the genera of Ixodes, Amblyomma, and Dermacentor with relatively lower occurrence in Rhipicephalus, Haemaphysalis, and Hyalomma ticks, while Coxiella-like endosymbionts (CLEs) were reported infecting almost all tick species tested. Francisella-like endosymbionts (FLEs) have been identified in tick genera such as Dermacentor, Amblyomma, Ornithodoros, Ixodes, and Hyalomma, whereas Wolbachia sp. has been detected in Ixodes, Amblyomma, Hyalomma, and Rhipicephalus tick genera. Notably, CLEs and FLEs are obligate endosymbionts essential for tick survival and development through the life cycle. American dog ticks showed greater motility when infected with Rickettsia, indirectly influencing infection risk, providing evidence of a relationship between tick endosymbionts and tick-vectored pathogens. The widespread occurrence of endosymbionts across the tick phylogeny and evidence of their functional roles in ticks and interference with tick-borne pathogens suggests a significant contribution to tick evolution and/or vector competence. We currently understand relatively little on how these endosymbionts influence tick parasitism, vector capacity, pathogen transmission and colonization, and ultimately on how they influence tick-borne disease dynamics. Filling this knowledge gap represents a major challenge for future research.
IL-4/IL-13 Axis in Allergic Rhinitis: Elevated Serum Cytokines Levels and Inverse Association With Tight Junction Molecules Expression
Authors: Nur Husna Siti Muhamad , Md Shukri Norasnieda , Tuan Sharif Sharifah Emilia , Tan Hern Tze Tina , Mohd Ashari Noor Suryani , Wong Kah Keng
Published: March 2022

The IL-4/IL-13 axis is involved in the pathogenesis of allergic rhinitis (AR). In this study, we investigated the serum cytokines levels of IL-4, IL-5, IL-6, and IL-13 in AR patients, and the transcript expression levels of their receptors (i.e. IL4R, IL5RA, IL6R, and IL13RA1) in nasal epithelial cells of AR patients versus non-allergic controls. Nasal epithelial cells and blood samples of non-allergic controls (n = 30) and AR patients (n = 30) were collected to examine mRNA expression and serum cytokines levels, respectively. Bioinformatics analyses of IL-4/IL-13 receptor heterodimer association with tight junction (TJ) and JAK/STAT signaling genes were conducted in a gene expression profiling (GEP) dataset (GSE44037) of AR patients (n = 12) and healthy controls (n = 6). Serum IL-4, IL-5, IL-6 or IL-13 levels, and IL13RA1 transcript expression were significantly higher in AR patients compared with non-allergic controls. IL-4 and IL-13 serum levels were positively correlated with IL13RA1 expression in AR patients but not in non-allergic controls. In the GEP dataset (GSE44037), six TJ (CLDN4, CLDN7, CLDN12, CLDN15, TJP1, and TJP2) genes’ expressions were negatively correlated, respectively, with IL-4Rα/IL-13Rα1 heterodimeric receptor expression in AR patients and not in control samples. These six TJ genes contributed to the significant enrichment of tight junction Gene Ontology (GO ID: 0070160). Lastly, STATs DNA binding motif analysis showed that each of these TJ genes contains STATs binding consensus sequence within intronic and intergenic regions. Our results suggest that increased IL-4/IL-13 serum cytokines levels may contribute to decreased TJs expression via IL-4Rα/IL-13Rα1 heterodimeric receptor in nasal epithelium of AR patients.
High-Coverage Serum Metabolomics Reveals Metabolic Pathway Dysregulation in Diabetic Retinopathy: A Propensity Score-Matched Study
Authors: Guo Chengnan , Jiang Depeng , Xu Yixi , Peng Fang , Zhao Shuzhen , Li Huihui , Jin Dongzhen , Xu Xin , Xia Zhezheng , Che Mingzhu , Lai Mengyuan , Huang Ruogu , Wang Hui , Zheng Chao , Mao Guangyun
Published: March 2022

Background: Diabetic retinopathy (DR) is a major diabetes-related disease linked to metabolism. However, the cognition of metabolic pathway alterations in DR remains scarce. We aimed to corroborate alterations of metabolic pathways identified in prior studies and investigate novel metabolic dysregulations that may lead to new prevention and treatment strategies for DR.

Methods: In this case-control study, we tested 613 serum metabolites in 69 pairs of type 2 diabetic patients (T2DM) with DR and propensity score-matched T2DM without DR via ultra-performance liquid chromatography-tandem mass spectrometry system. Metabolic pathway dysregulation in DR was thoroughly investigated by metabolic pathway analysis, chemical similarity enrichment analysis (ChemRICH), and integrated pathway analysis. The associations of ChemRICH-screened key metabolites with DR were further estimated with restricted cubic spline analyses.

Results: A total of 89 differentially expressed metabolites were identified by paired univariate analysis and partial least squares discriminant analysis. We corroborated biosynthesis of unsaturated fatty acids, glycine, serine and threonine metabolism, glutamate and cysteine-related pathways, and nucleotide-related pathways were significantly perturbed in DR, which were identified in prior studies. We also found some novel metabolic alterations associated with DR, including the disturbance of thiamine metabolism and tryptophan metabolism, decreased trehalose, and increased choline and indole derivatives in DR.

Conclusions: The results suggest that the metabolism disorder in DR can be better understood through integrating multiple biological knowledge databases. The progression of DR is associated with the disturbance of thiamine metabolism and tryptophan metabolism, decreased trehalose, and increased choline and indole derivatives.
A Deep Learning-Based Workflow for Dendritic Spine Segmentation
Authors: Vidaurre-Gallart Isabel , Fernaud-Espinosa Isabel , Cosmin-Toader Nicusor , Talavera-Martínez Lidia , Martin-Abadal Miguel , Benavides-Piccione Ruth , Gonzalez-Cid Yolanda , Pastor Luis , DeFelipe Javier , García-Lorenzo Marcos
Published: March 2022

The morphological analysis of dendritic spines is an important challenge for the neuroscientific community. Most state-of-the-art techniques rely on user-supervised algorithms to segment the spine surface, especially those designed for light microscopy images. Therefore, processing large dendritic branches is costly and time-consuming. Although deep learning (DL) models have become one of the most commonly used tools in image segmentation, they have not yet been successfully applied to this problem. In this article, we study the feasibility of using DL models to automatize spine segmentation from confocal microscopy images. Supervised learning is the most frequently used method for training DL models. This approach requires large data sets of high-quality segmented images (ground truth). As mentioned above, the segmentation of microscopy images is time-consuming and, therefore, in most cases, neuroanatomists only reconstruct relevant branches of the stack. Additionally, some parts of the dendritic shaft and spines are not segmented due to dyeing problems. In the context of this research, we tested the most successful architectures in the DL biomedical segmentation field. To build the ground truth, we used a large and high-quality data set, according to standards in the field. Nevertheless, this data set is not sufficient to train convolutional neural networks for accurate reconstructions. Therefore, we implemented an automatic preprocessing step and several training strategies to deal with the problems mentioned above. As shown by our results, our system produces a high-quality segmentation in most cases. Finally, we integrated several postprocessing user-supervised algorithms in a graphical user interface application to correct any possible artifacts.
Inverse Kinematics Solution of 6-DOF Manipulator Based on Multi-Objective Full-Parameter Optimization PSO Algorithm
Authors: Luo Sha , Chu Dianming , Li Qingdang , He Yan
Published: March 2022

A multi-objective full-parameter optimization particle swarm optimization (MOFOPSO) algorithm is proposed in this paper to overcome the drawbacks of poor accuracy, low efficiency, and instability of the existing algorithms in the inverse kinematics(IK) solution of the manipulator. In designing the multi-objective function, the proposed algorithm considers the factors such as position, posture, and joint. To improve PSO, the proposed algorithm comprehensively analyzes all factors affecting the global and local searching abilities. Based on this, the initial population is designed following the localized uniform distribution method. Meanwhile, the inertia weight, asynchronous learning factor, and time factor are respectively designed by introducing the iteration factor. Finally, this paper tests the performance of MOFOPSO with three typical functions to obtain a better inverse kinematics solution of the 6-DOF manipulator. Also, six other algorithms are taken for performance comparison. The experimental results indicate that the proposed method not only ensures the stability of the manipulator but also achieves high accuracy and efficiency in solving the inverse kinematics of the 6-DOF manipulator.
Numerical Optimization and Map-Based Manipulation With a Quadrupole Electromagnetic Actuated System
Authors: Ma Weicheng , Huan Zhijie , Xu Min
Published: March 2022

Electromagnetic actuation is a new technique for non-invasive manipulation, which provides wireless and controllable power source for magnetic micro-/nano-particles. This technique shows great potential in the field of precise mechanics, environment protection, and biomedical engineering. In this paper, a new quadrupole electromagnetic actuated system was constructed, which was composed of four electromagnetic coils, each coil being actuated by an independent DC power supplier. The magnetic field distribution in the workspace was obtained through finite element modeling and numerical simulation via COMSOL software, as well as the effect of the current flow through the coil in the field distribution. Moreover, parameters of the electromagnetic system were optimized through parametric modeling analysis. A magnetic field map was constructed for rapidly solving the desired driving current from the required magnetic flux density. Experiments were conducted to manipulate a micro-particle along the desired circular path. The proposed work provides theoretical references and numerical fundamentals for the control of magnetic particle in future.
PRMT5 Interacting Partners and Substrates in Oligodendrocyte Lineage Cells
Authors: Dansu David K. , Liang Jialiang , Selcen Ipek , Zheng Haiyan , Moore Dirk F. , Casaccia Patrizia
Published: March 2022

The protein arginine methyl transferase PRMT5 is an enzyme expressed in oligodendrocyte lineage cells and responsible for the symmetric methylation of arginine residues on histone tails. Previous work from our laboratory identified PRMT5 as critical for myelination, due to its transcriptional regulation of genes involved in survival and early stages of differentiation. However, besides its nuclear localization, PRMT5 is found at high levels in the cytoplasm of several cell types, including oligodendrocyte progenitor cells (OPCs) and yet, its interacting partners in this lineage, remain elusive. By using mass spectrometry on protein eluates from extracts generated from primary oligodendrocyte lineage cells and immunoprecipitated with PRMT5 antibodies, we identified 1196 proteins as PRMT5 interacting partners. These proteins were related to molecular functions such as RNA binding, ribosomal structure, cadherin and actin binding, nucleotide and protein binding, and GTP and GTPase activity. We then investigated PRMT5 substrates using iTRAQ-based proteomics on cytosolic and nuclear protein extracts from CRISPR-PRMT5 knockdown immortalized oligodendrocyte progenitors compared to CRISPR-EGFP controls. This analysis identified a similar number of peptides in the two subcellular fractions and a total number of 57 proteins with statistically decreased symmetric methylation of arginine residues in the CRISPR-PRMT5 knockdown compared to control. Several PRMT5 substrates were in common with cancer cell lines and related to RNA processing, splicing and transcription. In addition, we detected ten oligodendrocyte lineage specific substrates, corresponding to proteins with high expression levels in neural tissue. They included: PRC2C, a proline-rich protein involved in methyl-RNA binding, HNRPD an RNA binding protein involved in regulation of RNA stability, nuclear proteins involved in transcription and other proteins related to migration and actin cytoskeleton. Together, these results highlight a cell-specific role of PRMT5 in OPC in regulating several other cellular processes, besides RNA splicing and metabolism.