bluuebunny/crossref_metadata_2025 huggingface dataset:
Petrography, geochemistry and geochronology of igneous rocks from the Jiangnan Orogen, South China: constraints on the Early Paleozoic tectonic evolution of the South China Block
Authors: Tang Yuanyuan , Shi Yu , Weng Boyin , Zhou Yuxi , Lan Yuanchun
Published: June 2023

The Early Paleozoic tectonic evolution of the South China Block (SCB) remains controversial related to intracontinental orogenic and oceanic subduction processes. We present whole-rock major and trace elemental data, LA-ICP-MS zircon U-Pb age and Lu-Hf isotopic data for the Early Paleozoic igneous rocks including granodiorites from the Yuechengling pluton and volcanic breccias from the Damingshan pluton from the western segment of the Jiangnan Orogen in the SCB. LA-ICP-MS zircon U-Pb dating yielded emplacement ages for the Yuechengling S-type granitoids of 438–436 Ma and the deposited age for the Damingshan volcaniclastic rocks to be later than 451 Ma. The Yuechengling granitoids have consistent SiO2, TiO2, Fe2O3T, MgO, and P2O5 contents, higher Al2O3 contents, and Na2O + K2O values, but lower Mg# values, compared with those of the Damingshan volcaniclastic rocks. All the studied samples exhibit enrichment in LREEs and moderate negative Eu anomalies (δEu = 0.63–0.75), with negative Ba, Sr, Nb, Ta, P, and Ti anomalies, and positive Rb, Th, U, Pb, and K anomalies. The granitoids have variable CaO/Na2O ratios of 0.22–1.11, negative εHf(t) values of −11.98 to −0.90, and corresponding TDM2 ages distributed from 2.37 to 1.55 Ga. The petrographic and geochemical characteristics of the Yuechengling granitoids indicate that their parental magma was derived from a crustal meta-greywacke and meta-pelite components in the Paleoproterozoic basement, and have undergone some degree of fractional crystallization. The volcaniclastic rocks have mostly negative εHf(t) values with partially positive (−27.54 to 8.73), and zircons with negative εHf(t) values (−27.54 to −0.14) show TDM2 ages of 3.79 to 1.63 Ga. Combined with petrographic and geochemical data, we suggest that the Damingshan volcaniclastic rocks were derived from Neoarchean-Neoproterozoic crustal materials and the felsic parental magma has undergone some degree of magma mixing with mantle material, and deposited soon after a Late Ordovician volcanic eruption (later than 451 Ma). Integrated with previous studies, our new data support the intracontinental orogenic model to account for the Early Paleozoic tectonic evolution. Thus, we suggest that the Early Paleozoic tectonic setting of the SCB was intracontinental orogeny rather than oceanic subduction-collision.
Assessing the working practices and the inclusive programs to students with disabilities in the Egyptian museums: challenges and possibilities for facilitating learning and promoting inclusion
Authors: Zakaria Nevine Nizar
Published: June 2023

Following the implementation of 2018’s laws on the rights of persons with disabilities (PWDs) in Egypt, students with disabilities (SWDs) have both legal and moral rights to meaningful learning opportunities and inclusive education. Despite that, SWDs still have very limited education resources which limit their career aspirations and quality of life. In this respect, education whether as part of formal education or lifelong learning is central to the museum’s mission. Museums, as part of non-formal education, are being acknowledged for their educative powers and investments in the development of quality formal, non-formal, and informal learning experiences. Further, phrases such as “inclusivity,” “accessibility,” and “diversity” were notably included in the newly approved museum definition by ICOM (2022) emphasizing museums’ obligations to embrace societal issues and shape a cultural attitude concerning disability rights, diversity, and equality together with overcoming exclusionary educational practices. The study seeks to investigate the existing resources and inclusive practices in Egyptian museums to achieve non-formal education for SWDs. Qualitative research approaches have been employed to answer a specific question: How can Egyptian museums work within their governing systems to support the learning of SWDs beyond their formal education system? The study aims to assess the potential of Egyptian museums in facilitating learning for SWDs. Further, it examines the capability of Egyptian museums in contributing to informal and non-formal learning for SWDs and striving for inclusive education inspired by the social model of disability that fosters inclusive educational programs and adopts a human rights-based approach. The results revealed that Egyptian museums contributed to the learning of SWDs, yet small-scale programs and individual efforts, but they are already engaged in active inclusive practices that address the learning of SWDs. The study suggests that they need to be acknowledged and supported by the government as state instruments and direct actors in advancing inclusive education and implementing appropriate pedagogies in favor of SWDs.
Vitamin D supplementation alleviates insulin resistance in prediabetic rats by modifying IRS-1 and PPARγ/NF-κB expressions
Authors: Krisnamurti Desak Gede Budi , Louisa Melva , Poerwaningsih Erni H. , Tarigan Tri Juli Edi , Soetikno Vivian , Wibowo Heri , Nugroho Christian Marco Hadi
Published: May 2023

Background

Prediabetes is a condition of intermediate hyperglycemia that may progress to type 2 diabetes. Vitamin D deficiency has been frequently linked to insulin resistance and diabetes. The study aimed to investigate the role of D supplementation and its possible mechanism of action on insulin resistance in prediabetic rats.

Method

The study was conducted on 24 male Wistar rats that were randomly divided into 6 rats as healthy controls and 18 prediabetic rats. Prediabetic rats were induced with a high-fat and high-glucose diet (HFD-G) combined with a low dose of streptozotocin. Rats with the prediabetic condition were then randomized into three groups of 12-week treatment: one group that received no treatment, one that received vitamin D3 at 100 IU/kg BW, and one group that received vitamin D3 at 1000 IU/kg BW. The high-fat and high-glucose diets were continuously given throughout the twelve weeks of treatment. At the end of the supplementation period, glucose control parameters, inflammatory markers, and the expressions of IRS1, PPARγ, NF-κB, and IRS1 were measured.

Results

Vitamin D3 dose-dependently improves glucose control parameters, as shown by the reduction of fasting blood glucose (FBG), oral glucose tolerance test (OGTT), glycated albumin, insulin levels, and markers of insulin resistance (HOMA-IR). Upon histological analysis, vitamin D supplementation resulted in a reduction of the islet of Langerhans degeneration. Vitamin D also enhanced the ratio of IL-6/IL-10, reduced IRS1 phosphorylation at Ser307, increased expression of PPAR gamma, and reduced phosphorylation of NF-KB p65 at Ser536.

Conclusion

Vitamin D supplementation reduces insulin resistance in prediabetic rats. The reduction might be due to the effects of vitamin D on IRS, PPARγ, and NF-κB expression.
Characteristics and factors influencing hypothalamic pituitary dysfunction in patients with craniopharyngioma
Authors: Guo Ying , Pei Lili , Li Yuzheng , Li Chunde , Gui Songbai , Ni Ming , Liu Pinan , Zhang Yazhuo , Zhong Liyong
Published: June 2023

Background

Craniopharyngioma is a benign tumor originating from the sellar region. Damages in this area caused by the tumor itself, surgery, or radiotherapy may result in severe hypothalamic-pituitary dysfunction (HPD) and eventually lead to a significant impairment in the long-term quality of life of patients. This study aimed to investigate the characteristics of HPD in patients with adamantinomatous craniopharyngioma (ACP) or papillary craniopharyngioma (PCP) and to identify the factors affecting HPD after surgery.

Methods

In this single-center retrospective study, a total of 742 patients with craniopharyngioma were included. The neuroendocrine function of these patients before and after surgery was investigated. The differences in hypothalamic-pituitary function between the ACP and PCP groups were compared. The factors influencing the aggravation of HPD after surgery were identified.

Results

The median follow-up after surgery was 15 months. Before surgery, the proportion of patients with diabetes insipidus (DI) and hyperprolactinemia in the PCP group was significantly higher than that in the ACP group (P<0.01), and the proportion of patients with adrenocortical hypofunction in the PCP group was significantly lower than that in the ACP group (P=0.03). Most cases of ACP originated in the sellar region, while most cases of PCP originated in the suprasellar region (P<0.01). More patients experienced adenohypophyseal hypofunction, DI, and hypothalamic obesity at postoperative follow-up than at onset in both the ACP and PCP groups (both P<0.01), with a higher increase observed in the ACP group (P<0.01). Older age at CP onset, tumor recurrence or progression, and ACP type were risk factors for postoperative aggravation of HPD in CP patients.

Conclusion

Surgical treatment significantly aggravated HPD in both the ACP and PCP groups, but the specific characteristics and risk factors leading to aggravation were different between the two groups.
An electricity load forecasting model based on multilayer dilated LSTM network and attention mechanism
Authors: Wang Ye , Jiang Wenshuai , Wang Chong , Song Qiong , Zhang Tingting , Dong Qi , Li Xueling
Published: June 2023

From national development to daily life, electric energy is integral to people’s lives. Although the development of electricity should be expected, expansion without restriction will only result in energy waste. The forecasting of electricity load plays an important role in the adjustment of power enterprises’ strategies and the stability of power operation. Recently, the electricity-related data acquisition system has been perfected, and the available load information has gradually reached the minute level. This means that the related load series lengthens and the time and spatial information of load become increasingly complex. In this paper, a load forecasting model based on multilayer dilated long and short-term memory neural network is established. The model uses a multilayer dilated structure to extract load information from long series and to extract information from different dimensions. Moreover, the attention mechanism is used to make the model pay closer attention to the key information in the series as an intermediate variable. Such structures can greatly alleviate the loss in the extraction of long time series information and make use of more valid historical information for future load forecasting. The proposed model is validated using two real datasets. According to load forecasting curves, error curve, and related indices, the proposed method is more accurate and stable in electricity load forecasting than the comparison methods.
Research on the deep peak-shaving cost allocation mechanism considering the responsibility of the load side
Authors: Yang Zhao , Yibo Wang , Chuang Liu , Guowei Cai , Weichun Ge , Yueyang Xu , Ziwei Xiang
Published: June 2023

With the goal of carbon reduction, China has carried out a series of institutional reforms and innovations in renewable energy consumption. However, the existing allocation rules for peak-shaving costs concentrate on the power side only. In the context of high energy penetration rates, peak-shaving cost significantly increases, and the economic pressure on the power side sharply increases. As the beneficiaries of peak shaving, the load side, while enjoying clean energy, also needs to bear the responsibility of peak shaving and share part of the peak-shaving cost. In this regard, this paper proposes a peak-shaving cost allocation mechanism considering load-side participation. First, it uses the marginal contribution theory to establish the peak-shaving value evaluation model of the power and load. Then, based on the waveform similarity theory, it sets two indicators “Fluctuation Trend Similarity” and “Waveform Amplitude Difference” to evaluate each load’s renewable energy consumption responsibility. Finally, the peak-shaving cost allocation rules on the power source side and the load side are obtained. An example shows that the proposed allocation mechanism can initially realize the uniform distribution of power and load in peak-shaving cost. Furthermore, the method can promote the fairness of the peak-shaving market and guide users to reasonably participate in the peak-shaving market.
The effect of urbanization on agricultural eco-efficiency and mediation analysis
Authors: Zhao Xiaojing , Yang Jiamin , Chen Huijie , Zhang Xiaoyu , Xi Yanling
Published: June 2023

Improving agricultural eco-efficiency (AEE) is a promising way to achieve the sustainability of agricultural development. Although AEE evaluation and driving forces were widely explored, few studies have systematically examined how urbanization, the core driving force, affected AEE. To supplement the existing literature, the GB-US-SBM model was used to assess AEE in China during 2004–2020. Furtherly, it used the mediation effect model to investigate how urbanization influenced the AEE in different agriculture development regions by reducing agricultural labor and changing rural residents’ income. The results showed that: 1) During 2004–2020, China’s AEE revealed a stable improvement, with the mean score increasing from 0.138 to 0.744. Regarding spatial distribution, AEE exhibited a gradient decrease: optimized development region > moderate development region > protected development region. 2) Urbanization had a significantly positive effect on AEE, with the magnitude of the effect greatest in the protected development region, followed by the moderate development region and the optimized development region. 3) The mediator variables, agricultural labor and rural residents’ income, positively mediated the relationship between urbanization and AEE, and the former had a larger mediating effect. Notably, rural residents’ income did not mediate the effect of urbanization on AEE in the protected development region. According to the findings, to improve sustainable agriculture development and urbanization development in China, some policy suggestions were put forward from the aspects of transforming agricultural development mode, accelerating the urbanization process, enhancing vocational education for the middle-aged and young rural labor force, and expanding channels for increasing rural residents’ income.
Spatiotemporal patterns and driving mechanism of tourism ecological security in Guangxi, China
Authors: Liang Yiqiao , Liu Hongying , Chiaka Jeffrey Chiwuikem , Jiang Chengtao , Wei Nannan , Liang Yihang
Published: May 2023

Tourism ecological security (TES) is an important index reflecting the sustainable development of the regional economy. The construction of the China and ASEAN Free Trade Area has increased the total tourist consumption of Guangxi province by 36.48%. Unfortunately, overconsumption of resources, air pollution, disturbance of indigenous life, and other environmental degradation problems emerged due to the significant increase in tourists. Measuring the resilience of the tourism ecosystem is an urgent need to promote the high-quality development of tourism in Guangxi. To explore the dynamic changes in TES and its driving mechanism, the DPSIR (driver–pressure–state–impact–response) model for the tourism ecosystem was developed. The dynamic changes in TES and its driving mechanism from 2010 to 2019 were analyzed using fuzzy matter-element analysis, Markov chains, Geodetector, and other methods. The results show that: (1) the TES value increased steadily by 72.73%; the improvement speed was Northeast > Southwest > Southeast > Northwest; (2) TES was negatively correlated with location, 14 cities developed independently; (3) the TES has a smaller probability to shift the lower level; (4) urbanization, water consumption, green area, tourism revenue, and the number of students in colleges had significant effects on TES. Four policies were proposed to improve TES: (1) developing forest tourism; (2) implementing greening projects in abandoned mining areas; (3) increasing tourism technical personnel; and (4) reducing clearance time for inbound tourists.
The effect of soil microplastics on Oryza sativa L. root growth traits under alien plant invasion
Authors: Li Guanlin , Zhao Xiaoxun , Iqbal Babar , Zhao Xin , Liu Jingjing , Javed Qaiser , Du Daolin
Published: June 2023

Invasive alien plants pose severe threats to agroecosystems. Microplastic (MP) contamination in farmland soil is also concerning, as it causes crop stress and reduces productivity. However, the effects of the interactions between invasive alien plants and MP in the soil impact crops remain unclear. Herein, belowground plant characteristics associated with stress responses were examined in a pot experiment using root scan analyzes of rice plants exposed to Solidago canadensis L. invasion, polyethylene MP contamination, and a combined treatment. The observed changes in root growth traits under Canada goldenrod (Solidago canadensis L.) invasion were the least adverse, whereas S. canadensis invasion combined with soil MP contamination had the most adverse effects on root growth. Solidago canadensis L. invasion increased all belowground indices except root height and mean root diameter, which was upregulated in the soil MP contamination treatment. The combined treatment (S. canadensis invasion and soil MP contamination) reduced the belowground root growth traits more than the other treatments. The root growth traits may have been affected by changes in the antioxidant enzyme activity of the roots caused by the treatments. The combined effects of S. canadensis invasion and MP toxicity on rice root growth traits raise concerns regarding potential yields, financial damage, and consequences related to a potential move into the food web.
Dynamic change, driving mechanism and spatiotemporal prediction of the normalized vegetation index: a case study from Yunnan Province, China
Authors: Han Yang , Lin Yilin , Zhou Peng , Duan Jinjiang , Cao Zhaoxiang
Published: June 2023

Vegetation indexes have been widely used to qualitatively and quantitatively evaluate vegetation cover and its growth vigor. To further extend the study of vegetation indexes, this paper proposes to study the spatial and temporal distribution characteristics and specific driving mechanisms of vegetation indexes based on the example of Yunnan Province, China, and also adds the study of spatial and temporal prediction methods of vegetation indexes. This paper used data on this region’s normalized vegetation index (NDVI), three meteorological factors, and eight social factors from 1998 to 2019. The dynamic change in and driving mechanism of the NDVI were studied using mean value analysis, univariate linear trend regression analysis, and partial correlation analysis. In addition, the Fourier function model and the CA–Markov model were also used to predict the NDVI of Yunnan Province from 2020 to 2030 in time and space. The results show that: (1) The NDVI value in Yunnan Province is high, showing a significant growth trend. The increased vegetation coverage area has increased in the past 22 years without substantial vegetation degradation. (2) The positive promotion of meteorological factors is greater than the negative inhibition. The partial correlation of relative humidity among meteorological factors is the highest, which is the main driving factor. (3) The NDVI value is significantly positively correlated with population and economy and negatively correlated with pasture land and agricultural area. (4) The NDVI values are predicted well in time (R = 0.64) and space (Kappa = 0.8086 and 0.806), satisfying the accuracy requirements. This paper aims to enrich the theoretical and technical system of ecological environment research by studying the dynamic change, driving mechanism, and spatiotemporal prediction of the normalized vegetation index. Its results can provide the necessary theoretical basis for the simulation and prediction of vegetation indexes.
Ecophysiological traits change little along a successional gradient in a tropical dry deciduous woodland from Margarita Island, Venezuela
Authors: Ávila-Lovera Eleinis , Urich Rosa , Coronel Ilsa , Tezara Wilmer
Published: June 2023

Tropical dry forests (TDFs) are the most threatened terrestrial ecosystems and studying how functional traits of plant species change as secondary succession advances is important for understanding how and how fast can TDFs recover from disturbance. In this work we asked the question: how do functional traits change during secondary succession in a tropical dry woodland? We studied functional traits, especially ecophysiological traits, such as gas exchange, plant-water relations, leaf carbon isotope composition (δ13C), specific leaf area (SLA) and nitrogen concentration, in shrubs and trees in three successional stages (6 and 20 years after abandonment, and the dry deciduous woodland, 6 years, 20 years, and DW, respectively) along a successional gradient in a TDF in both wet and dry seasons to understand how TDFs recover after disturbance by opencast sand mining. During the wet season, similar mass-based photosynthetic rates (Amass), water potential, relative water content, instantaneous and intrinsic water-use efficiency (WUE and IWUE) and SLA were found in the 6 years and DW stages. During seasonal drought, similar reductions in these variables were observed for all three successional stages. However, δ13C of the 6 years species was higher than in 20 years and DW species, indicating a higher long-term integrated WUE in the former due to a strong reduction in stomatal conductance (gs) in the dry season. Species from the DW seem to couple metabolic changes to their characteristically low gs, such that nitrogen concentration per unit mass explained 86% of the variation in Amass. Given the functional similarity among species from the different successional stages, native species from the DW stage could have good physiological performance in the 6 and 20 years sites, and therefore could be used to restore these degraded areas.
Performance of SNP barcodes to determine genetic diversity and population structure of Plasmodium falciparum in Africa
Authors: Argyropoulos Dionne C. , Tan Mun Hua , Adobor Courage , Mensah Benedicta , Labbé Frédéric , Tiedje Kathryn E. , Koram Kwadwo A. , Ghansah Anita , Day Karen P.
Published: June 2023

Panels of informative biallelic single nucleotide polymorphisms (SNPs) have been proposed to be an economical method to fast-track the population genetic analysis of Plasmodium falciparum in malaria-endemic areas. Whilst used successfully in low-transmission areas where infections are monoclonal and highly related, we present the first study to evaluate the performance of these 24- and 96-SNP molecular barcodes in African countries, characterised by moderate-to-high transmission, where multiclonal infections are prevalent. For SNP barcodes it is generally recommended that the SNPs chosen i) are biallelic, ii) have a minor allele frequency greater than 0.10, and iii) are independently segregating, to minimise bias in the analysis of genetic diversity and population structure. Further, to be standardised and used in many population genetic studies, these barcodes should maintain characteristics i) to iii) across various iv) geographies and v) time points. Using haplotypes generated from the MalariaGEN P. falciparum Community Project version six database, we investigated the ability of these two barcodes to fulfil these criteria in moderate-to-high transmission African populations in 25 sites across 10 countries. Predominantly clinical infections were analysed, with 52.3% found to be multiclonal, generating high proportions of mixed-allele calls (MACs) per isolate thereby impeding haplotype construction. Of the 24- and 96-SNPs, loci were removed if they were not biallelic and had low minor allele frequencies in all study populations, resulting in 20- and 75-SNP barcodes respectively for downstream population genetics analysis. Both SNP barcodes had low expected heterozygosity estimates in these African settings and consequently biased analyses of similarity. Both minor and major allele frequencies were temporally unstable. These SNP barcodes were also shown to identify weak genetic differentiation across large geographic distances based on Mantel Test and DAPC. These results demonstrate that these SNP barcodes are vulnerable to ascertainment bias and as such cannot be used as a standardised approach for malaria surveillance in moderate-to-high transmission areas in Africa, where the greatest genomic diversity of P. falciparum exists at local, regional and country levels.
CLARITY: a Shiny app for interactive visualisation of the bovine physical-genetic map
Authors: Melzer Nina , Qanbari Saber , Ding Xi , Wittenburg Dörte
Published: June 2023

The arrangement of markers on the genome can be defined in either physical or linkage terms. While a physical map represents the inter-marker distances in base pairs, a genetic (or linkage) map pictures the recombination rate between pairs of markers. High-resolution genetic maps are key elements for genomic research, such as fine-mapping of quantitative trait loci, but they are also needed for creating and updating chromosome-level assemblies of whole-genome sequences. Based on published results on a large pedigree of German Holstein cattle and newly obtained results with German/Austrian Fleckvieh cattle, we aim at providing a platform that allows users to interactively explore the bovine genetic and physical map. We developed the R Shiny app CLARITY available online at https://nmelzer.shinyapps.io/clarity and as R package at https://github.com/nmelzer/CLARITY that provides access to the genetic maps built on the Illumina Bovine SNP50 genotyping array with markers ordered according to the physical coordinates of the most recent bovine genome assembly ARS-UCD1.2. The user is able to interconnect the physical and genetic map for a whole chromosome or a specific chromosomal region and can inspect a landscape of recombination hotspots. Moreover, the user can investigate which of the frequently used genetic-map functions locally fits best. We further provide auxiliary information about markers being putatively misplaced in the ARS-UCD1.2 release. The corresponding output tables and figures can be downloaded in various formats. By ongoing data integration from different breeds, the app also facilitates comparison of different genome features, providing a valuable tool for education and research purposes.
OCRFinder: a noise-tolerance machine learning method for accurately estimating open chromatin regions
Authors: Ren Jiayi , Liu Yuqian , Zhu Xiaoyan , Wang Xuwen , Li Yifei , Liu Yuxin , Hu Wenqing , Zhang Xuanping , Wang Jiayin
Published: June 2023

Open chromatin regions are the genomic regions associated with basic cellular physiological activities, while chromatin accessibility is reported to affect gene expressions and functions. A basic computational problem is to efficiently estimate open chromatin regions, which could facilitate both genomic and epigenetic studies. Currently, ATAC-seq and cfDNA-seq (plasma cell-free DNA sequencing) are two popular strategies to detect OCRs. As cfDNA-seq can obtain more biomarkers in one round of sequencing, it is considered more effective and convenient. However, in processing cfDNA-seq data, due to the dynamically variable chromatin accessibility, it is quite difficult to obtain the training data with pure OCRs or non-OCRs, and leads to a noise problem for either feature-based approaches or learning-based approaches. In this paper, we propose a learning-based OCR estimation approach with a noise-tolerance design. The proposed approach, named OCRFinder, incorporates the ideas of ensemble learning framework and semi-supervised strategy to avoid potential overfitting of noisy labels, which are the false positives on OCRs and non-OCRs. Compared to different noise control strategies and state-of-the-art approaches, OCRFinder achieved higher accuracies and sensitivities in the experiments. In addition, OCRFinder also has an excellent performance in ATAC-seq or DNase-seq comparison experiments.
Methylene blue reduces the serum levels of interleukin-6 and inhibits STAT3 activation in the brain and the skin of lipopolysaccharide-administered mice
Authors: Li Yujia , Ying Weihai
Published: May 2023

It is valuable to search for novel and economical agents for inhibiting STAT3 activation and blocking increases in IL-6 levels, due to the important roles of STAT3 and IL-6 in inflammation. Since Methylene Blue (MB) has shown therapeutical potential for multiple diseases, it has become increasingly important to investigate the mechanisms underlying the effects of MB on inflammation. Using a mouse model of lipopolysaccharide (LPS)-induced inflammation, we investigated the mechanisms underlying the effects of MB on inflammation, obtaining the following findings: First, MB administration attenuated the LPS-induced increases in the serum levels of IL-6; second, MB administration attenuated LPS-induced STAT3 activation of the brain; and third, MB administration attenuated LPS-induced STAT3 activation of the skin. Collectively, our study has suggested that MB administration can decrease the levels of IL-6 and STAT3 activation - two important factors in inflammation. Since MB is a clinically used and relatively economical drug, our findings have suggested therapeutic potential of MB for multiple inflammation-associated diseases due to its effects on STAT3 activation and IL-6 levels.
MAPK8 and CAPN1 as potential biomarkers of intervertebral disc degeneration overlapping immune infiltration, autophagy, and ceRNA
Authors: Zhang Yuxin , Zhang Jiahui , Sun Zhongyi , Wang Hui , Ning Ruonan , Xu Longyu , Zhao Yichen , Yang Kai , Xi Xiaobing , Tian Jiwei
Published: May 2023

Background

Intervertebral disc degeneration (IDD) is one of the most common health problems in the elderly and a major causative factor in low back pain (LBP). An increasing number of studies have shown that IDD is closely associated with autophagy and immune dysregulation. Therefore, the aim of this study was to identify autophagy-related biomarkers and gene regulatory networks in IDD and potential therapeutic targets.

Methods

We obtained the gene expression profiles of IDD by downloading the datasets GSE176205 and GSE167931 from the Gene Expression Omnibus (GEO) public database. Subsequently, differentially expressed genes (DEGs) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, gene ontology (GO), and gene set enrichment analysis (GSEA) were performed to explore the biological functions of DEGs. Differentially expressed autophagy-related genes (DE-ARGs) were then crossed with the autophagy gene database. The hub genes were screened using the DE-ARGs protein–protein interaction (PPI) network. The correlation between the hub genes and immune infiltration and the construction of the gene regulatory network of the hub genes were confirmed. Finally, quantitative PCR (qPCR) was used to validate the correlation of hub genes in a rat IDD model.

Results

We obtained 636 DEGs enriched in the autophagy pathway. Our analysis revealed 30 DE-ARGs, of which six hub genes (MAPK8, CTSB, PRKCD, SNCA, CAPN1, and EGFR) were identified using the MCODE plugin. Immune cell infiltration analysis revealed that there was an increased proportion of CD8+ T cells and M0 macrophages in IDD, whereas CD4+ memory T cells, neutrophils, resting dendritic cells, follicular helper T cells, and monocytes were much less abundant. Subsequently, the competitive endogenous RNA (ceRNA) network was constructed using 15 long non-coding RNAs (lncRNAs) and 21 microRNAs (miRNAs). In quantitative PCR (qPCR) validation, two hub genes, MAPK8 and CAPN1, were shown to be consistent with the bioinformatic analysis results.

Conclusion

Our study identified MAPK8 and CAPN1 as key biomarkers of IDD. These key hub genes may be potential therapeutic targets for IDD.
Dietary Lactobacillus plantarum Relieves Nile Tilapia (Oreochromis niloticus) Juvenile From Oxidative Stress, Immunosuppression, and Inflammation Induced by Deltamethrin and Aeromonas hydrophila
Authors: Gewaily Mahmoud S. , Shukry Mustafa , Abdel-Kader Marwa F. , Alkafafy Mohamed , Farrag Foad A. , Moustafa Eman M. , Doan Hien Van , Abd-Elghany Mohamed F. , Abdelhamid Ahmed F. , Eltanahy Azhar , Dawood Mahmoud A. O.
Published: June 2023

Aeromonas hydrophila infection is one of the major diseases that cause inflammation and immunodepression in aquatic animals. Likewise, waterborne toxins are known for their negative impact on the immunity and antioxidant responses of aquatic organisms. In this study, Lactobacillus plantarum (LP20) was incorporated in Nile tilapia, Oreochromis niloticus, diets (50 mg/kg) to investigate its role in the antioxidant capacity, immunity, and anti-inflammation induced by deltamethrin (DLM) toxicity (96-h LC50 was 14.9 μg/L) and A. hydrophila (LD50, 2 × 108 CFU/ml). One hundred and twenty healthy fish with an initial weight of 28.21 ± 1.34 g were allotted in 12 glass aquaria (60 L) and divided randomly into four groups (triplicates, 10 fish per aquarium). The control fish neither received LP20 nor were exposed to DLM. The second group of fish was fed the control diet and subjected to DLM (DLM group). The third group of fish was provided with LP20 without DLM toxicity (LP20 group), and the fourth group of fish was fed LP20 and subjected to DLM (DLM + LP20 group). After 30 days, fish were intraperitoneally injected with A. hydrophila. Ten days post infection, the survival rate was lower in fish exposed to DLM than those exposed to LP20. Further, fish fed on LP20 had elevated serum total protein (sTP), albumin (ALB), globulin (GLB), phagocytic index (PI), phagocytic (PA), and lysozyme activities (LZM), but they had lower urea, uric acid bilirubin, creatinine, glucose, aspartate aminotransferase (AST), alkaline phosphatase (ALP), and alanine aminotransferase (ALT) activities after 24 h, 48 h, and 1 week post A. hydrophila challenge. However, fish exposed to DLM had lower sTP, ALB, GLB and higher urea, uric acid, bilirubin, creatinine, glucose, ALT, AST, and ALP after 24 h, 48 h, and 1 week post A. hydrophila challenge. Markedly, after the A. hydrophila challenge, fish exposed to DLM + LP20 displayed upregulated levels of superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GPx) genes. The transcription of interferon gamma (IFN-γ), interleukin 12 (IL-12), and tumor necrosis factor alpha (TNF-α) was upregulated in DLM and DLM + LP20 groups. Fish exposed to DLM downregulated interleukin 8 (IL-8) gene expression after A. hydrophila challenge. Further, fish displayed upregulation of heat shock protein 70 (HSP70) gene expression after DLM toxicity. Besides, fish exposed to DLM toxicity and A. hydrophila infection had severe inflammatory features in the liver, spleen, gills, and intestine, while dietary LP20 relieved the inflammatory features. In summary, dietary LP20 relieves Nile tilapia from oxidative stress, immunosuppression, and inflammation induced by DLM and A. hydrophila infection.
Biogeochemical structure of the Laptev Sea in 2015-2020 associated with the River Lena plume
Authors: Xie Lina , Yakushev Evgeniy , Semiletov Igor , Grinko Andrey , Gangnus Ivan , Berezina Anfisa , Osadchiev Alexander , Zhdanov Igor , Polukhin Alexander , Moiseeva Julia , Purgina Darya , Pipko Irina , Pugach Svetlana , Dudarev Oleg , Ge Zhenming
Published: May 2023

The discharge of rivers and the subsequent dispersion of their plumes play a pivotal role in the biogeochemical cycling of the Arctic Ocean. Based on the data collected during annual transects conducted in the autumn period (September-October) from 2015-2020, this study explores the effect of River Lena plume dispersion on the seasonal and interannual changes in the hydrophysical and biogeochemical structure of the southeastern Laptev Sea. The temperature-salinity relationship (T-S), Redfield ratio and multiparameter cluster analysis were used to investigate variations in the water mass structure along the transect. The results revealed that the plume’s interannual and seasonal spreading patterns play a crucial role in regulating the local physical, biogeochemical, and biological processes in the southern Laptev Sea. During September-October, the hydrochemical water mass structure along the transects shifted from highly stratified to unstratified as the plume’s mixing intensity increased. Anomalous hydrochemical distributions were observed due to coastal upwelling, which was primarily characterized by high total alkalinity and nitrate levels, and low organic phosphorus, nitrite, and ammonia levels in the seawater. Wind and cold weather conditions drive deep vertical mixing of seawater, causing the resuspension of bottom sediment and the subsequent enrichment of bottom water by nutrients. Multi-parameter cluster analysis is used to describe the details of water mass structures in the highly dynamic southern Laptev Sea, with water mass structures typically undergoing significant changes within two weeks between September and October. The migration and transformation of water masses throughout the seasons are influenced by the volume of river discharge, fall-winter cooling, and atmospheric circulation patterns. Furthermore, the general atmospheric circulation is confirmed to be the primary cause of the interannual variation in the spread of the Lena River plume over the southeast Laptev Sea.
Research progress in calculating net community production of marine ecosystem by remote sensing
Authors: Wang Yingqi , Wang Kui , Bai Yan , Wu Di , Zheng Hao
Published: June 2023

Net community production (NCP) is defined as the difference between gross primary production (GPP) and total community respiration (R). NCP indicates the balance between the production and consumption of community organic carbon, therefore making it a key parameter for evaluating the efficiency of carbon sequestration using the biological pump (BP). It is difficult to quantify NCP directly via satellite, because there are complex processes in community production and respiration. We reviewed previous research on satellite-based NCP and classified the methods into two primary categories: empirical methods and semi-analytical methods. The former category was established based on numerical relationships between NCP and satellite-based proxies, while the latter was developed by utilizing mechanistic analysis to establish quantitative expressions linking NCP to such proxies. Although satellite-based calculations of NCP have been attempted, they still suffer from significant uncertainties. Future research should focus on the precise calculation of satellite-based NCP by investigating the underlying processes and mechanisms that regulate NCP, developing regional models, and increasing the resolution of satellite sensors, as well as applying satellite lidar and coordinated multi-sensor observation technology.
Inter-examiner and intra-examiner reliability of optical coherence tomography angiography in vascular density measurement of retinal and choriocapillaris plexuses in healthy children aged 6–15 years
Authors: Diao Kai , Huang Xiaomin , Yao Mingyu , Li Jiawei , Fan Feifei , Pan Hongxian , Yu Jinjin , Yang Yizhou , Lu Weiwei , Lian Hengli , Wang Qinmei , Huang Jinhai , Chen Ruru
Published: June 2023

Objective

This study aimed to test the inter-examiner and intra-examiner reliability of macular vascular density (VD) measurement of retinal and choriocapillaris plexuses in healthy children using optical coherence tomography angiography (OCTA).

Materials and methods

Ninety-two school children were prospectively recruited. Macular OCTA images (6 × 6 mm2) were obtained thrice by two examiners using the RTVue-XR Avanti OCT system. The coefficient of variation (COV), intraclass correlation coefficient (ICC), and Bland–Altman plots were used to evaluate the repeatability and reproducibility.

Results

Ninety participants aged 6–15 years were enrolled; two participants were excluded because of low-quality images. In the retina, the reproducibility and repeatability of VD became poorer from superficial to deep retinal capillary plexus (superficial: COV = 4.61–11.11%; intermediate: COV = 7.73–14.15%; deep: COV = 14.60–32.28%). For both reproducibility and repeatability, the ICC ranged from moderate to high (superficial plexus: ICC = 0.570–0.976; intermediate plexus: ICC = 0.720–0.968; deep plexus: ICC = 0.628–0.954). In the choroid, the inter-examiner reproducibility and intra-examiner repeatability of the VD measurement of choriocapillaris were excellent in the macula, fovea, parafovea, and perifovea (COV = 1.00–6.10%; ICC = 0.856–0.950). The parameters of the foveal avascular zone (FAZ) also showed significant reproducibility and repeatability (COV = 0.01–0.21%; ICC = 0.743–0.994).

Conclusion

The VD measurements of the choriocapillaris and FAZ parameters using OCTA showed excellent inter-examiner and intra-examiner reliability in school children. The reproducibility and repeatability of the VD of three retinal capillary plexuses depended on the depth of the retinal capillary plexus.
Physiological changes during torpor favor association with Endozoicomonas endosymbionts in the urochordate Botrylloides leachii
Authors: Hyams Yosef , Rubin-Blum Maxim , Rosner Amalia , Brodsky Leonid , Rinkevich Yuval , Rinkevich Baruch
Published: May 2023

Environmental perturbations evoke down-regulation of metabolism in some multicellular organisms, leading to dormancy, or torpor. Colonies of the urochordate Botrylloides leachii enter torpor in response to changes in seawater temperature and may survive for months as small vasculature remnants that lack feeding and reproductive organs but possess torpor-specific microbiota. Upon returning to milder conditions, the colonies rapidly restore their original morphology, cytology and functionality while harboring re-occurring microbiota, a phenomenon that has not been described in detail to date. Here we investigated the stability of B. leachii microbiome and its functionality in active and dormant colonies, using microscopy, qPCR, in situ hybridization, genomics and transcriptomics. A novel lineage of Endozoicomonas, proposed here as Candidatus Endozoicomonas endoleachii, was dominant in torpor animals (53–79% read abundance), and potentially occupied specific hemocytes found only in torpid animals. Functional analysis of the metagenome-assembled genome and genome-targeted transcriptomics revealed that Endozoicomonas can use various cellular substrates, like amino acids and sugars, potentially producing biotin and thiamine, but also expressing various features involved in autocatalytic symbiosis. Our study suggests that the microbiome can be linked to the metabolic and physiological states of the host, B. leachii, introducing a model organism for the study of symbioses during drastic physiological changes, such as torpor.
Disentangling hindgut metabolism in the American cockroach through single-cell genomics and metatranscriptomics
Authors: Dukes Helen E. , Tinker Kara A. , Ottesen Elizabeth A.
Published: May 2023

Omnivorous cockroaches host a complex hindgut microbiota comprised of insect-specific lineages related to those found in mammalian omnivores. Many of these organisms have few cultured representatives, thereby limiting our ability to infer the functional capabilities of these microbes. Here we present a unique reference set of 96 high-quality single cell-amplified genomes (SAGs) from bacterial and archaeal cockroach gut symbionts. We additionally generated cockroach hindgut metagenomic and metatranscriptomic sequence libraries and mapped them to our SAGs. By combining these datasets, we are able to perform an in-depth phylogenetic and functional analysis to evaluate the abundance and activities of the taxa in vivo. Recovered lineages include key genera within Bacteroidota, including polysaccharide-degrading taxa from the genera Bacteroides, Dysgonomonas, and Parabacteroides, as well as a group of unclassified insect-associated Bacteroidales. We also recovered a phylogenetically diverse set of Firmicutes exhibiting a wide range of metabolic capabilities, including—but not limited to—polysaccharide and polypeptide degradation. Other functional groups exhibiting high relative activity in the metatranscriptomic dataset include multiple putative sulfate reducers belonging to families in the Desulfobacterota phylum and two groups of methanogenic archaea. Together, this work provides a valuable reference set with new insights into the functional specializations of insect gut symbionts and frames future studies of cockroach hindgut metabolism.
Genome-wide identification and oxacillinase OXA distribution characteristics of Acinetobacter spp. based on a global database
Authors: Li Jia , Li Yang , Cao Xiaoli , Zheng Jie , Zhang Yan , Xie Hui , Li Chuchu , Liu Chang , Shen Han
Published: June 2023

Objective

To use genomic analysis to identify Acinetobacter spp. and to explore the distribution characteristics of ß-lactamase oxallicinases (blaOXA) among Acinetobacter species globally.

Methods

Genomes of global Acinetobacter spp. were downloaded from GenBank using Aspera batch. After quality check using CheckM and QUAST software, the genomes were annotated using Prokka software to investigate the distribution of blaOXAs across Acinetobacter spp.; a phylogenetic tree was constructed to explore the evolutionary relationship among the blaOXA genes in Acinetobacter spp. Average-nucleotide identification (ANI) was performed to re-type the Acinetobacter spp. BLASTN comparison analysis was implemented to determine the sequence type (ST) of Acinetobacter baumannii strain.

Results

A total of 7,853 genomes were downloaded, of which only 6,639 were left for further analysis after quality check. Among them, 282 blaOXA variants were identified from the genomes of 5,893 Acinetobacter spp.; blaOXA-23 (n = 3,168, 53.8%) and blaOXA-66 (2,630, 44.6%) were the most frequent blaOXAs, accounting for 52.6% (3,489/6639), and the co-carriage of blaOXA-23 and blaOXA-66 was seen in 2223 (37.7%) strains. The 282 blaOXA variants were divided into 27 clusters according to the phylogenetic tree. The biggest clade was blaOXA-51-family carbapenem-hydrolyzing enzymes composed of 108 blaOXA variants. Overall, 4,923 A. baumannii were identified out of the 6,639 Acinetobacter spp. strains and 291 distinct STs were identified among the 4,904 blaOXA-carrying A. baumannii. The most prevalent ST was ST2 (n = 3,023, 61.6%) followed by ST1 (n = 228, 4.6%).

Conclusion

OXA-like carbapenemases were the main blaOXA-type β-lactamase spread widely across Acinetobacter spp. Both blaOXA-23 and blaOXA-66 were the predominant blaOXAs, among all A. baumannii strains, with ST2 (belonging to CC2) being the main clone disseminated globally.