bluuebunny/crossref_metadata_2025 huggingface dataset:
Methanol extract of Inonotus obliquus improves type 2 diabetes mellitus through modifying intestinal flora
Authors: Ye Xuewei , Wu Kefei , Xu Langyu , Cen Yingxin , Ni Jiahui , Chen Junyao , Zheng Wenxin , Liu Wei
Published: January 2023

Type 2 diabetes mellitus (T2DM) poses a significant risk to human health. Previous research demonstrated that Inonotus obliquus possesses good hypolipidemic, anti-inflammatory, and anti-tumor properties. In this research, we aim to investigate the potential treatment outcomes of Inonotus obliquus for T2DM and discuss its favourable influences on the intestinal flora. The chemical composition of Inonotus obliquus methanol extracts (IO) was analyzed by ultra-high-performance liquid chromatography-Q extractive-mass spectrometry. IO significantly improved the blood glucose level, blood lipid level, and inflammatory factor level in T2DM mice, and effectively alleviated the morphological changes of colon, liver and renal. Acetic acid, propionic acid, and butyric acid levels in the feces of the IO group were restored. 16S rRNA gene sequencing revealed that the intestinal flora composition of mice in the IO group was significantly modulated. Inonotus obliquus showed significant hypoglycemic and hypolipidemic effects with evident anti-inflammatory activity and improved the morphological structure of various organs and cells. Inonotus obliquus increased the levels of short-chain fatty acids in the environment by increasing the population of certain bacteria that produce acid, such as Alistipes and Akkermansia, which are beneficial to improve intestinal flora disorders and maintain intestinal flora homeostasis. Meanwhile, Inonotus obliquus further alleviated T2DM symptoms in db/db mice by down-regulating the high number of microorganisms that are dangerous, such as Proteobacteria and Rikenellaceae_RC9_gut_group and up-regulating the abundance of beneficial bacteria such as Odoribacter and Rikenella. Therefore, this study provides a new perspective for the treatment of T2DM by demonstrating that drug and food homologous active substances could relieve inflammation via regulating intestinal flora.
Analysis of the fine-mesh subgroup method and its feasible improvement
Authors: Li Song , Zhang Qian , Liu Lei , Zhang Yongfa , Hao Jianli , Wang Xiaolong , Jiang Lizhi , Liu Xiaoya
Published: January 2023

The fine-mesh subgroup method (FSM) is proposed to treat the significant resonance self-shielding effect both effectively and accurately. Similar to the ultra-fine group method, the fine-mesh subgroup method adopts a fine group structure on the resonance energy range to avoid the extra resonance interference effect correction. To improve the efficiency, on the one hand, the one-group micro-level optimization is adopted, so the subgroup fixed-source equations will be only calculated on a certain number of pre-determined subgroup levels, and an interpolation process is employed to obtain the actual subgroup flux. On the other hand, the slowing-down calculation is carried out for group condensation for multigroup transport calculation. The main theory and feasible improvements of the fine-mesh subgroup method are analyzed in this paper. Several pin cell and lattice problems are applied to test the performance of the fine-mesh subgroup method, and the particle swarm optimization method is adopted to find the better group structure. The numerical results indicate a good performance both for accuracy and efficiency.
Optimal operation of urban tidal drainage pumping station based on genetic algorithm coupled with head-water level successive approximation
Authors: Yi Gong , Wenhao Zou
Published: January 2023

Aiming at the method of solving the optimization scheme for urban tidal drainage pumping stations during heavy rainfall below the urban drainage design standard, and the problems such as the mismatch between the head and water level of pumping stations at each divided time period during the solution process, a nonlinear mathematical model for optimal operation of urban tidal drainage pumping station was constructed which took the minimal operation cost of drainage pumping station during given operating period as the study target, and the blade angle of each pump unit in each divided time period as decision variables with the constraints of total water quantity of target drainage, matched motor power of each pump unit, water level of in the drainage area, number of switches and the shortest operation time of pump unit. For the problem of head-water level mismatch at each divided time period of pumping station, the genetic algorithm of coupled head-water level successive approximation is proposed, which can make the optimization scheme realize the matching of river network water level and pumping station operating head. Taking Guazhou Pumping Station in Yangzhou City of Jiangsu Province encountering 10% frequency designed rainfall as an example, optimization schemes under typical working conditions which included different starting drainage water levels and peak-valley electricity prices was obtained, as well as the influence of electricity price of divided time period, average head of each divided time period and inflow on the optimization scheme was carried out. The unit optimal operation drainage costs of Guazhou Pumping Station is 45.46 yuan/104 m3 and 51.32 yuan/104 m3 respectively when the starting drainage water level is set as 4.8 m and 4.6 m, which has the corresponding operation benefit of 15.34% and 4.40% less than that of conventional operation, and the water level variation of river network has dropped 6.61% and 7.85% than that of conventional operation. The constructed optimal operation model of urban tidal drainage pumping station and the proposed solution method can effectively improve the matching degree of pumping head and water level variation, and effectively make a compromise of economic operation of drainage pumping station and the safety requirements of water level control of river network in drainage area. The obtained optimization schemes can offer decision-making reference for relevant dispatching and management departments of drainage pumping stations.
Thermo-economic evaluation and optimization of solar-driven power-to-chemical systems with thermal, electricity, and chemical storage
Authors: Huang Shengwei , Zhang Yumeng , Guo Xinyu , Qian Meng , Zhao Yongming , Li Liang , Zhou Xing
Published: January 2023

This paper evaluates the thermo-economics of power-to-chemicals using solar energy, with the chemicals being methane, methanol, and gasoline. In addition to the optimal technology sizing and heat cascade utilization, this paper also considers the optimal molten-salt solar power tower (MSPT) design, as the MSPT significantly affects the levelized product cost. A bi-level optimization is proposed, employing mixed-integer linear programming at the lower level with heat and mass integration for optimizing sizes and operating strategies of technologies, and with heat cascade utilization and a genetic algorithm at the upper level for optimizing the MSPT design. In the upper level, the full-load storage hours, design direct normal irradiance, solar multiple, and sizes of the MSPT are optimized. The electricity sources considered are the MSPT, photovoltaic (PV) with daily electricity storage, and the electrical grid as a complementary technology to satisfy the targeted daily product demand. Cost-competitiveness of solar-driven chemical synthesis is thoroughly assessed via considering sensitivity analysis on 1) regional solar resource endowments and actual local demands; 2) electricity sources, that is, PV vs. MSPT; and 3) the scale effect represented by different chemicals’ yield. The results show that the levelized methane cost ranges from 4.5 to 8.5 €/kg, depending on the location, plant size, and annual power contribution of concentrated solar power. Due to the larger mass production, the levelized cost of methanol and gasoline is lower: 1.5–2.2 €/kg for methanol and 4–6 €/kg for gasoline. The findings highlight the significance of location choice, that is, natural endowment of solar radiation and carbon sources. Using the syngas co-electrolysis pathway and direct solar radiation 100 kWh/m2 higher, the methane production cost is decreased by 2.4 €/kg. Sensitivity analysis performed on plant scale reveals that a compact, small-scale system is far too expensive. The levelized cost of methane could be decreased by 1.2 €/kg when the plant is scaled up from 4,000 to 20,000 kg/day H2. Due to its expensive electricity storage and limited working hours, PV is typically not chosen as a power source. Overall, solar fuels are unlikely to be cost-competitive in the near future when compared to market prices for all three compounds under consideration.
Re-Fracturing vs. CO2 Huff-n-Puff Injection in a Tight Shale Reservoir for Enhancing Gas Production
Authors: Wang Dong , Li Yongming , Wang Bo , Shan Jiquan , Dai Libin
Published: January 2023

Field production data indicate that the shale gas production rate decreases sharply after a few years of the first fracking. Feasible enhanced gas recovery (EGR) approaches are very necessary to be investigated. In this study, we compared re-fracturing with a huff-n-puff gas injection scheme in a shale gas reservoir for EGR. A fully compositional simulation approach coupled with a dual porosity and dual permeability model is used. The gas production performances by using different fracturing fluids (i.e., slickwater and supercritical CO2) are evaluated. The effects of huff-n-puff parameters and matrix permeability on the gas production rate and carbon sequestration are investigated. The results show that using a re-fracturing approach yields a better recovery performance than the huff-n-puff gas injection method. Re-fracturing using supercritical CO2 performs better than using slickwater because the former can create complex three-dimensional fracture networks. Huff-n-puff CO2 injection can enhance the gas recovery effectively in ultra-tight formations. In a relatively high permeable formation, viscous flow instead of adsorption-desorption isotherms becomes the primary mass transfer mechanisms, resulting in a lower gas recovery. Both the re-fracturing treatment and huff-n-puff CO2 injection are profitable from a long-term cash flowback perspective.
Differences in production decline characteristics of horizontal wells in tight gas sandstone reservoirs with different qualities: A case study of the Sulige gas field, Ordos Basin
Authors: Cheng Minhua , Wei Yunsheng , Ji Guang , Ning Bo , Zhao Meng
Published: January 2023

Development of horizontal wells is one of the important means to improve the well production of the tight gas reservoir and realize the effective development of tight gas. Based on abundant static and dynamic data of a large number of horizontal wells that have been put into operation, structure characteristics of a tight reservoir carried out, detailed geologic analysis of the effective reservoir drilled by horizontal wells, and development dynamic analysis, three effective reservoir lateral distribution modes of the block concentrated development mode, medium layer, and thin layer superimposed mode and thin layer isolated model mode are proposed and their adaptability to the horizontal well deployment is evaluated. The drilled reservoir is divided into three types: high-quality reservoir, suboptimal reservoir, and poor reservoir, and the quantitative classification standard is established. On this basis, the decline rule and the difference of horizontal well drilling in different quality reservoirs are discussed, and the quantitative evaluation standard of the horizontal well development effect is established. The initial decline rates of the three types of horizontal wells are 32.9%, 35%, and 40%, and the estimate ultimate recoveries (EURs) of three types of horizontal wells are 89 million cm3, 68 million cm3, and 31 million cm3, respectively. The results of this study provide technical support for the optimal deployment of new horizontal wells in the Sulige gas field and a reference for the development of horizontal wells in the same types of gas reservoirs.
Spatiotemporal changes in temperature projections over Bangladesh using multi-model ensemble data
Authors: Islam H. M. Touhidul , Kamruzzaman Mohammad , Shahid Shamsuddin , Mainuddin Mohammed , Alam Edris , Islam Abu Reza Md. Towfiqul , Biswas Jatish Chnadra , Islam Md. Azharul
Published: January 2023

Temperature rise is a concern for future agriculture in different regions of the globe. This study aimed to reveal the future changes and variabilities in minimum temperature (Tmin) and maximum temperature (Tmax) in the monthly, seasonal, and annual scale over Bangladesh using 40 General Circulation Models (GCMs) of Coupled Model Intercomparison Project Phase 5 (CMIP5) for two radiative concentration pathways (RCPs, RCP4.5 and RCP8.5). The statistical downscaling climate model (SimCLIM) was used for downscaling and to ensemble temperature projections (Tmax and Tmin) for the near (2021–2060) and far (2071–2100) periods compared to the base period (1986–2005). Multi-model ensemble (MME) exhibited increasing Tmax and Tmin for all the timescales for all future periods and RCPs. Sen’s slope (SS) analysis showed the highest increase in Tmax and Tmin in February and relatively less increase in July and August. The mean annual Tmax over Bangladesh would increase by 0.61°C and 1.75°C in the near future and 0.91°C and 3.85°C in the far future, while the mean annual Tmin would rise by 0.65°C and 1.85°C in the near future and 0.96°C and 4.07°C in the far future, for RCP4.5 and RCP8.5, respectively. The northern and northwestern parts of the country would experience the highest rise in Tmax and Tmin, which have traditionally been exposed to temperature extremes. In contrast, the southeastern coastal region would experience the least rise in temperature. A higher increase in Tmin than Tmax was detected for all timescales, signifying a future decrease in the diurnal temperature range (DTR). The highest increase in Tmax and Tmin will be in winter compared to other seasons for both the periods and RCPs. The spatial variability of Tmax and Tmin changes can be useful for the long-term planning of the country.
The ability of three climbing plant species to capture particulate matter and their physiological responses at different environmental sampling sites
Authors: Lyu Xiaoqian , Chang Lu , Lu Zhengyan , Li Junfeng
Published: January 2023

The adsorption of particulate matter (PM) by the leaves of urban plants can effectively reduce the particulate matter concentration in the atmosphere. The use of climbing plants to abate particulate matter is an important means of urban greening in China, which is rich in climbing plant species. In this study, three evergreen climbing plants were selected to assess their ability to adsorb particulate matter and determine their physiological responses to particulate pollution. PM deposition was determined gravimetrically. There were four key results. 1) The adsorption capacity of the three evergreen climbers followed the order of Hedera nepalensis var > Ficus pumila Linn > Euonymus fortunei, and was significantly higher in an overpass environment than in a campus environment for all three species. 2) The seasonal characteristics of particulate adsorption by the three types of climbers in both the overpass and campus environments followed the order of winter > autumn > spring > summer. 3) The net photosynthetic rate of the three climbing plants was significantly affected by particulate matter in a size dependent manner, with fine particulate matter on the plant leaf surface and coarse particulate matter in the leaf waxy layer being important factors affecting plant photosynthesis. 4) Particulate pollution led to changes in the activities of plant protective enzymes in plants, with increases in the superoxide dismutase (SOD) and peroxidase (POD) activity, and the malondialdehyde (MDA) and soluble protein contents. There were different trends in the soluble sugar content among the different plant species. In conclusion, F. pumila had a strong resistance to particulate pollutants, while H. nepalensis was considered suitable for planting in polluted areas where it could improve ambient air quality by adsorbing large amounts of particulate matter.
Is environmental tax legislation effective for pollution abatement in emerging economies? Evidence from China
Authors: Tang Wenliang , Yang Xue
Published: January 2023

This study estimates the effect of environmental tax legislation on air pollution, using the implementation of China’s Environmental Protection Tax Law (EPTL) as a quasi-natural experiment. For cities which have been authorized to raise tax rates by the EPTL, the air quality index (AQI) is 2.36 lower after the reform. The effect is reinforced in cities with stricter tax enforcement, lower fiscal stress, as well as higher initial pollution levels. Heterogeneity analyses show that the reform is more effective in cities with lower levels of marketization and legalization, as well as in developed cities. In addition, the impact of the reform is more significant in cities with higher levels of public participation in environmental governance, higher tax competition levels, and higher share of secondary industry. A series of robustness tests corroborates the results. This paper provides evidence that environmental tax legislation is efficacious in pollution abatement for developing economies.
An analysis of finding the best strategies of water security for water source areas using an integrated IT2FVIKOR with machine learning
Authors: Zamri Nurnadiah , Azman Wan Nur Amira Wan , Pairan Mohamad Ammar , Abas Siti Sabariah , Gao Miaomiao
Published: January 2023

Worldwide, water security is adversely affected by factors such as population growth, rural–urban migration, climate, hydrological conditions, over-abstraction of groundwater, and increased per-capita water use. Water security modeling is one of the key strategies to better manage water safety and develop appropriate policies to improve security. In view of the growing global demand for safe water, intelligent methods and algorithms must be developed. Therefore, this paper proposes an integrated interval type-2 Fuzzy VIseKriterijumska Optimizcija I Kompromisno Resenje (IT2FVIKOR) with unsupervised machine learning (ML). This includes IT2FVIKOR for ranking and selecting a set of alternatives. Unsupervised machine learning includes hierarchical clustering, self-organizing map, and autoencoder for clustering, silhouette analysis and elbow method to find the most optimal cluster count, and finally Adjusted Rank Index (ARI) to find the best comparison within two clusters. This proposed integrated method can be divided into a two-phase fuzzy-machine learning-based framework to select the best water security strategies and categorize the polluted area using the water datasets from the Terengganu River, one of Malaysia’s rivers. Phase 1 focuses on the IT2FVIKOR method to select five different strategies with five different criteria using five decision makers for finding the best water security strategies. Phase 2 continues the unsupervised machine learning where three different clustering algorithms, namely, hierarchical clustering, self-organizing map, and autoencoder, are used to cluster the polluted area in the Terengganu River. Silhouette analysis is applied along with the clustering algorithms to estimate the number of optimal clusters in a dataset. Then, the ARI is applied to find the best comparison within the original data with hierarchical clustering, self-organizing map, and autoencoder. Next, the elbow method is applied to double-confirm the best clusters for each clustering algorithm. Last, lists of polluted areas in each cluster are retrieved. Finally, this 2-phase fuzzy-Machine learning–based framework offers an alternative intelligent model to solve the water security problems and find the most polluted area.
What is really social about social insect cognition?
Authors: Poissonnier Laure-Anne , Tait Catherine , Lihoreau Mathieu
Published: January 2023

It is often assumed that social life imposes specific cognitive demands for animals to communicate, cooperate and compete, ultimately requiring larger brains. The “social brain” hypothesis is supported by data in primates and some other vertebrates, but doubts have been raised over its applicability to other taxa, and in particular insects. Here, we review recent advances in insect cognition research and ask whether we can identify cognitive capacities that are specific to social species. One difficulty involved in testing the social brain hypothesis in insects is that many of the model species used in cognition studies are highly social (eusocial), and comparatively little work has been done in insects that live in less integrated social structures or that are solitary. As more species are studied, it is becoming clear that insects share a rich cognitive repertoire and that these abilities are not directly related to their level of social complexity. Moreover, some of the cognitive mechanisms involved in many social interactions may not differ from those involved in non-social behaviors. We discuss the need for a more comparative and neurobiologically grounded research agenda to better understand the evolution of insect brains and cognition.
A Wooly Way? Fiber technologies and cultures 3,000-years-ago along the Inner Asian Mountain Corridor
Authors: Doumani Dupuy Paula N. , Tabaldiev Kubatbek , Matuzeviciute Giedre Motuzaite
Published: January 2023

Wool-focused economies yielded a pastoralist materiality that visibly shaped the lived experiences of Central Asian populations today. In this paper, we investigate the earlier application of fibers through a key mountain corridor for social interactions during Prehistory. We focus on the site of Chap 1 located in the highlands of the Tien Shan Mountains of Kyrgyzstan where researchers have found a complex agropastoral subsistence culture was established from at least ca. 3,000 BCE. The perishable materials that would have accompanied the early spread of cultural and technological traditions related to fiber-based crafts throughout this area are under-documented due to poor organic preservation. Hence, there has been little consideration of the role that textiles played in highland occupation and how woven fabrics might have facilitated settlement in the extreme climates of Central Asia. We address this ongoing problem through a multi-application survey of Chap’s unpublished textile evidence preserved as impressions in coarseware ceramics of its Final Bronze Age. We consider evidence that sheep wool formed a key cultural adaptation for surviving the extreme winters of Central Asia’s highland regions.
Soil nitrogen and carbon storages and carbon pool management index under sustainable conservation tillage strategy
Authors: Yuan Jianyu , Liang Yunliang , Zhuo Macao , Sadiq Mahran , Liu Li , Wu Jiangqi , Xu Guorong , Liu Shuainan , Li Guang , Yan Lijuan
Published: January 2023

Agricultural practices are significant to increase the soil nitrogen and organic carbon sequestration to adapt and mitigate the climate change in a recent climate change scenario. With this background, we carried out research in the Longzhong Loess Plateau region of China. This research was conducted under a randomized complete block design, with three replicates. Adopt the method of combining outdoor positioning field test with indoor index measurement to explore the soil bulk density (BD), nitrogen components (viz., nitrate nitrogen (NO3−-N), ammonia nitrogen (NH4+-N), total nitrogen (TN), microbial biomass nitrogen (MBN) and nitrogen storage (NS), and carbon components [viz., soil organic carbon (SOC), easily oxidized organic carbon (EOC), microbial biomass carbon (MBC) and carbon storage (CS), carbon pool index (CPI), carbon pool activity (A) and carbon pool activity index (AI) and carbon pool management index (CPMI)] and C/N, ratio under different tillage practices [namely., conventional tillage (CT), no tillage (NT), straw mulch with conventional tillage (CTS) and straw mulch with no tillage (NTS)]. Our results depicted that different conservation tillage systems significantly increased soil BD over conventional tillage. Compared with CT, the NTS, CTS and NT reduced soil NO3−-N, increased the soil NH4+-N, TN, MBN and NS, among them, NS under NTS, CTS and NT treatment was 25.0, 14.8 and 13.1% higher than that under CT treatment, respectively. Additionally, conservation tillage significantly increased SOC, EOC, MBC, CS, CPI, AI, CPMI and C/N, ratio than CT. Inside, CS under NTS, CTS and NT treatment was 19.4, 12.1 and 13.4% higher than that under CT treatment, respectively. Moreover, during the 3-year study period, the CPMI under NTS treatment was the largest (139.26, 140.97, and 166.17). Consequently, we suggest that NTS treatment was more sustainable strategy over other investigated conservation tillage practices and should be recommended as climate mitigation technique under climate change context.
Forest management plans as data source for the assessment of the conservation status of European Union habitat types
Authors: Alterio Edoardo , Campagnaro Thomas , Sallustio Lorenzo , Burrascano Sabina , Casella Laura , Sitzia Tommaso
Published: January 2023

Natura 2000 is a European network of protected sites that should enable natural habitats to be maintained or restored at a favorable conservation status. Progress toward this objective must be periodically reported by states members of the European Union. We investigated how forest management plans might provide data to support the reporting. The study was done in the forests of the Dolomites and Venetian Prealps, Italy. Here, about 200 forest management plans, divided into several forest compartments, have been drawn up and revised every 10–15 years. Stand structure variables were retrieved from past (OR, 1970–1980) and more recent revisions (NR, 2000–2010) of 331 forest compartments ranging between 0.35 and 53.1 ha. In the beech and spruce forest habitat types (coded 9130 and 9410 in Annex I of the Directive 92/43/EEC, respectively), we found an increase from OR to NR in the density of large trees (from 32 to 46/ha and from 31 to 50/ha, respectively for the two habitats), basal area (from 27.3 to 31.5 m2/ha and from 31 to 34.5 m2/ha), mean diameter (from 34.1 to 36.2 cm and from 33.9 to 36 cm) and Gini index (from 0.35 to 0.37 and from 0.33 to 0.36). Pursuant to the Directive 92/43/EEC, the conservation status of these two habitat types should be taken as “favorable” with regards to the criterion related to the habitats’ specific structure and functions that are necessary for its long-term maintenance. We conclude that forest management plans provide a great portion of the information needed for assessing and monitoring the conservation status of forest habitat types in the Natura 2000 framework.
CRISPR medicine for blood disorders: Progress and challenges in delivery
Authors: Mohammadian Gol Tahereh , Ureña-Bailén Guillermo , Hou Yujuan , Sinn Ralph , Antony Justin S. , Handgretinger Rupert , Mezger Markus
Published: January 2023

Blood disorders are a group of diseases including hematological neoplasms, clotting disorders and orphan immune deficiency diseases that affects human health. Current improvements in genome editing based therapeutics demonstrated preclinical and clinical proof to treat different blood disorders. Genome editing components such as Cas nucleases, guide RNAs and base editors are supplied in the form of either a plasmid, an mRNA, or a ribonucleoprotein complex. The most common delivery vehicles for such components include viral vectors (e.g., AAVs and RV), non-viral vectors (e.g., LNPs and polymers) and physical delivery methods (e.g., electroporation and microinjection). Each of the delivery vehicles specified above has its own advantages and disadvantages and the development of a safe transferring method for ex vivo and in vivo application of genome editing components is still a big challenge. Moreover, the delivery of genome editing payload to the target blood cells possess key challenges to provide a possible cure for patients with inherited monogenic blood diseases and hematological neoplastic tumors. Here, we critically review and summarize the progress and challenges related to the delivery of genome editing elements to relevant blood cells in an ex vivo or in vivo setting. In addition, we have attempted to provide a future clinical perspective of genome editing to treat blood disorders with possible clinical grade improvements in delivery methods.
Positive regulation of innate immune response by miRNA-let-7a-5p
Authors: Ueta Mayumi , Nishigaki Hiromi , Komai Seitaro , Mizushima Katsura , Tamagawa-Mineoka Risa , Naito Yuji , Katoh Norito , Sotozono Chie , Kinoshita Shigeru
Published: January 2023

Background: We have hypothesized that different factors are involved in the severity of ACD and AD because some but not all patients with atopic dermatitis (AD) present with allergic conjunctival disease (ACD) including severe types such as atopic keratoconjunctivitis (AKC) with/without giant papillae. We previously reported that plasma miR-628-3p was up-regulated in AD with severe ACD, but not in severe AD without severe ACD or in our healthy controls. In this study, to investigate the pathogenesis of AD with and without severe ACD, we performed comprehensive plasma miRNA analysis and studied the function of some miRNAs which were significantly up-regulated in ACD.

Methods: Transcriptomics analysis of miRNA was performed using the microarray platform from the plasma of nine individuals (AD, severe ACD, controls: n = 3 each). To confirm up-regulation of the 12 miRNAs of the eight miRNA groups we focused on, we performed quantitative miRNA polymerase chain reaction (PCR) assays using 80 plasma samples (AD: 23, severe ACD: 17, controls: 40). To study the function of the eight miRNAs which were significantly up-regulated in ACD, we transfected their mimic to THP-1 cells, a monocyte cell line, and performed comprehensive gene expression analysis of them. The up-regulation of gene expression of interest in transfected THP-1 cells with the hsa-let-7a-5p miRNA mimic was confirmed by quantitative RT-qPCR assay.

Results: Quantitative miRNA PCR assays showed that hsa-let-7a-5p, hsa-let-7days-3p, hsa-let-7e-5p, and hsa-miR-151a-5p were significantly up-regulated in both AD-ACD+ and AD-ACD- as were hsa-miR-130a-3p, hsa-miR-151a-3p, has-miR-27b-3p, and hsa-miR-146a-5p in AD-ACD+ but not in AD-ACD-. The functions of each miRNA were investigated by comprehensive gene expression analysis of THP-1 cells transfected with each miRNA mimic. Of the eight miRNAs, hsa-let-7a-5p, hsa-let-7e-5p, has-miR-27b-3p, and hsa-miR-146a-5p mimic-transfected THP-1 cells showed the up-regulation of CXCL10 (IP-10; interferon gamma-induced protein 10), which might be one of the innate immune-related genes. Quantitative RT-qPCR assays of transfected THP-1 cells with the hsa-let-7a-5p miRNA mimic showed that the 17 genes up-regulated more than 10-fold in the comprehensive gene expression analysis, and TLR3, RIG-I, and MDA5, important innate immune-related genes, were significantly up-regulated. TNFSF13B, AIM2, USP41, STAP1, GBP4, CCL8, and IFI27, reportedly down-regulated by the hsa-miR-628-3p mimic, were also significantly up-regulated in the transfected cells.

Conclusion: Hsa-let-7a-5p, which was significantly up-regulated in AD-ACD+ and AD-ACD-, could positively regulate the important innate immune-related genes such as TLR3, RIG-I, and MDA5. It is possible that in an allergic disease such as atopic keratoconjunctivitis and/or dermatitis, innate immune responses might be positively regulated by hsa-let-7a-5p in the plasma.
Genome-wide identification and characterization of toll-like receptor 5 (TLR5) in fishes
Authors: Zhang Kai , Chen Ming , He Haobin , Kou Hongyan , Lin Li , Liang Rishen
Published: January 2023

Toll-like receptors 5 (TLR5), a member of the toll-like receptors (TLRs) family, is a class of pattern recognition receptors (PRRs) that recognize pathogen-associated molecular patterns (PAMPs). It responds to vertebrate recognition of bacterial flagellin and participates in innate immune responses. However, genome-wide identification and characterization of TLR5 in fishes have not been investigated. Here, three TLR5M isotypes (TLR5Ma, TLR5Mb1, and TLR5Mb2) and a TLR5S are all extracted from fish genomes on the basis of phylogenetic and synteny analyses. We confirmed that the non-teleost fishes have one TLR5M gene, as well as additional TLR5 genes (TLR5M and TLR5S) in teleost fishes. In addition, some special teleost fishes possess two to three TLR5 genes, which have undergone the fourth whole-genome duplication (WGD). According to our results, we inferred that the diversity of TLR5 genes in fishes seems to be the result of combinations of WGD and gene loss. Furthermore, TLR5 isoforms displayed differences at the flagellin interaction sites and viral binding sites, and showed lineage-specific, which indicated that TLR5 duplicates may generate functional divergence. Bacterial experiments also supported the idea that CiTLR5Ma and CiTLR5Mb are subfunctionalized to sense bacterial flagellin. In summary, our present comparative genomic survey will benefit for further functional investigations of TLR5 genes in fish.
Full-length transcriptome sequencing reveals the molecular mechanism of monoterpene and sesquiterpene biosynthesis in Cinnamomum burmannii
Authors: Hou Chen , Zhang Qian , Xie Peiwu , Lian Huiming , Wang Yingli , Liang Dongcheng , Cai Yanling , He Boxiang
Published: January 2023

Essential oil of Cinnamomum burmannii is rich in monoterpenes and sesquiterpenes and is widely used in cosmetics and medicines. Knowledge about the enzymes that catalyze the formation of monoterpenes and sesquiterpenes in C. burmannii is insufficient. Therefore, anatomy observation of C. burmannii at the four developmental stages (7 days, CBS1; 14 days, CBS2; 21 days, CBS3, and 28 days, CBS4) were conducted to elucidate the origins of essential oil production. Twelve full-length transcriptomes of C. burmannii leaves at the four stages were generated using Oxford Nanopore Technologies. GC-MS analysis revealed 15 monoterpene and sesquiterpenes dramatically increased from CBS1 to CBS4. A weighted correlation network analysis (WGCNA) in association and differentially expressed genes across four developmental stages were performed. A total of 44 differentially expressed genes (DEGs) were involved in terpenoid syntheses during leaf development. Among them, the DEGs of the mevalonate acid (MVA) pathway were predominantly expressed at CBS1, while those of the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway showed increased expression from CBS2 to CBS4. Besides, fourteen genes were associated with monoterpene synthesis and nine with sesquiterpene synthesis. Functions of these DEGs were further predicted with regard to gene expression profile and phylogenetic relationship with those characterized in previous studies. In addition, 922 long noncoding RNAs (lncRNAs) were detected, of which twelve were predicted to regulate monoterpene and sesquiterpene biosynthesis. The present study provided new insights the molecular mechanisms of monoterpenoid and sesquiterpenoid syntheses of C. burmannii.
High expression of KNL1 in prostate adenocarcinoma is associated with poor prognosis and immune infiltration
Authors: Zhang Yetao , Ji Qianying , Wang Jun , Dong Yuxiang , Pang Mingyang , Fu Shengqiang , Wei Yong , Zhu Qingyi
Published: January 2023

Prostate adenocarcinoma (PRAD) is a common malignancy with increasing morbidity and mortality. Kinetochore scaffold 1 (KNL1) has been reported to be involved in tumor progression and prognosis in other tumors, but its role in PRAD has not been reported in detail. KNL1 expression analysis, clinicopathological parameters analysis, prognostic correlation analysis, molecular interaction network and functional abdominal muscle analysis and immune infiltration analysis by using multiple online databases and downloaded expression profile. The results suggest that KNL1 is highly expressed in PRAD, which is associated with worse prognosis in PRAD patients. KnL1-related genes are highly enriched in mitotic function, which is considered to be highly related to the development of cancer. Finally, KNL1 expression is associated with a variety of tumor infiltrating immune cells, especially Treg and Th2 cells. In conclusion, our findings provide preliminary evidence that KNL1 may be an independent prognostic predictor of PRAD and is associated with immune infiltration.
Liquid biopsy in pediatric brain tumors
Authors: Tripathy Arushi , John Vishal , Wadden Jack , Kong Seongbae , Sharba Sana , Koschmann Carl
Published: January 2023

Malignant primary brain tumors are the most common cancer in children aged 0–14 years, and are the most common cause of death among pediatric cancer patients. Compared to other cancers, pediatric brain tumors have been difficult to diagnose and study given the high risk of intracranial biopsy penetrating through vital midline structures, where the majority of pediatric brain tumors originate (Ostrom et al., 2015). Furthermore, the vast majority of these tumors recur. With limitations in the ability to monitor using clinical and radiographic methods alone, minimally invasive methods such as liquid biopsy will be crucial to our understanding and treatment. Liquid biopsy of blood, urine, and cerebrospinal fluid (CSF) can be used to sample cfDNA, ctDNA, RNA, extracellular vesicles, and tumor-associated proteins. In the past year, four seminal papers have made significant advances in the use of liquid biopsy in pediatric brain tumor patients (Liu et al., 2021; Cantor et al., 2022; Miller et al., 2022; Pagès et al., 2022). In this review, we integrate the results of these studies and others to discuss how the newest technologies in liquid biopsy are being developed for molecular diagnosis and treatment response in pediatric brain tumors.
Diagnostic application of exome sequencing in Chinese children with suspected inherited kidney diseases
Authors: Gao Min , Yu Fengling , Dong Rui , Zhang Kaihui , Lv Yuqiang , Ma Jian , Wang Dong , Zhang Hongxia , Gai Zhongtao , Liu Yi
Published: January 2023

Background: Inherited kidney diseases (IKDs) are a group of kidney diseases characterized by abnormal kidney structure or function caused by genetic factors, but they are not easily diagnosed in childhood due to either nonspecific symptoms and signs or clinically silent symptoms in the early stages until the progressive stages, even end-stages. Early diagnosis of IKDs is very urgent for timely treatment and improving outcomes of patients. So far, the etiological diagnosis has been accelerated with the advance of clinical genetic technology, particularly the advent of next-generation sequencing (NGS) that is not only a powerful tool for prompt and accurate diagnosis of IKDs but also gives therapy guidance to decrease the risk of unnecessary and harmful interventions.

Methods: The patients presenting with urinalysis abnormalities or structural abnormalities from 149 Chinese families were enrolled in this study. The clinical features of the patients were collected, and the potentially causative gene variants were detected using exome sequencing. The clinical diagnostic utility of the genetic testing was assessed after more detailed clinical data were analyzed.

Result: In total, 55 patients identified having causative variants by exome sequencing were genetically diagnosed, encompassing 16 (29.1%) autosomal dominant IKDs, 16 (29.1%) autosomal recessive IKDs, and 23 (41.8%) X-linked IKDs, with 25 unreported and 45 reported variants. The diagnostic yield was 36.9%. The utility of the exome sequencing was accessed, 12 patients (21.8%) were confirmed to have suspected IKDs, 26 patients (47.3%) discerned the specific sub-types of clinical category, and 17 patients (30.9%) with unknown etiology or lack of typical manifestations were reclassified.

Conclusion: Our study supported that genetic testing plays a crucial role in the early diagnosis for children with IKDs, which affected follow-up treatment and prognostic assessment in clinical practice. Moreover, the variant spectrum associated with IKDs was expanded.
Incorporating genome-wide and transcriptome-wide association studies to identify genetic elements of longissimus dorsi muscle in Huaxi cattle
Authors: Liang Mang , An Bingxing , Deng Tianyu , Du Lili , Li Keanning , Cao Sheng , Du Yueying , Xu Lingyang , Zhang Lupei , Gao Xue , Cao Yang , Zhao Yuming , Li Junya , Gao Huijiang
Published: January 2023

Locating the genetic variation of important livestock and poultry economic traits is essential for genetic improvement in breeding programs. Identifying the candidate genes for the productive ability of Huaxi cattle was one crucial element for practical breeding. Based on the genotype and phenotype data of 1,478 individuals and the RNA-seq data of 120 individuals contained in 1,478 individuals, we implemented genome-wide association studies (GWAS), transcriptome-wide association studies (TWAS), and Fisher’s combined test (FCT) to identify the candidate genes for the carcass trait, the weight of longissimus dorsi muscle (LDM). The results indicated that GWAS, TWAS, and FCT identified seven candidate genes for LDM altogether: PENK was located by GWAS and FCT, PPAT was located by TWAS and FCT, and XKR4, MTMR3, FGFRL1, DHRS4, and LAP3 were only located by one of the methods. After functional analysis of these candidate genes and referring to the reported studies, we found that they were mainly functional in the progress of the development of the body and the growth of muscle cells. Combining advanced breeding techniques such as gene editing with our study will significantly accelerate the genetic improvement for the future breeding of Huaxi cattle.
Smoking, alcohol consumption, diabetes, body mass index, and peptic ulcer risk: A two-sample Mendelian randomization study
Authors: Liu Yi , Xiao Zhihan , Ye Kun , Xu Linlin , Zhang Yanping
Published: January 2023

Background: Observational evidence has shown that smoking, alcohol consumption, type 2 diabetes, and body mass index (BMI) are risk factors for peptic ulcer disease (PUD), including gastric ulcer (GU) and duodenal ulcer (DU). However, the observed associations may be confounding factors. Herein, we use Mendelian randomization (MR) to examine causal associations such as smoking, alcohol, type 2 diabetes, BMI, and risks of PUD.

Methods: We used 8,17,41,325,82, 231, and 616 identified genetic variants as proxies for age of smoking initiation (AgeSmk), smoking cessation (SmkCes, current/former), number of cigarettes smoked per day (CigDay), smoking status (SmkIni, ever/never), alcohol consumption, type 2 diabetes, and BMI to obtain unconfounded effect estimates on the GU and DU levels among 452,264 participants from the Gene ATLAS. The causal relationship was estimated by using inverse-variance weighted (IVW) as the main method. Sensitivity analysis includes Cochran’s Q test, the MR-Egger test, MR pleiotropy residual sum and outlier (MR-PRESSO), and MR-robust adjusted profile score (MR-RAPS). In addition, secondary MR analysis was conducted within summary data using genetic risk scores (GRSs) as instrumental variables (IVs).

Results: In our two-sample MR analyses, genetic predisposition to smoking (SmkInit) and BMI were associated with an increased risk of GU. The beta values were 0.0035 (95% CI, 0.0021, 0.0049, p = 1.56E-06) for smoking (SmkInit) and 0.0021 (95% CI, 0.0009, 0.0033, p = 0.0008) for BMI. Genetic predisposition to smoking (SmkInit) and higher genetically predicted BMI were associated with an increased risk of DU. The beta values of DU were 0.0029 (95% CI, 0.0017, 0.0041, p = 2.43E-06) for smoking (SmkInit) and 0.0018 (95% CI, 0.0007, 0.0029, p = 0.001) for BMI. No other causal association between smoking (AgeSmk, CigDay, and SmkCes), alcohol consumption, type 2 diabetes, and GU or DU was observed. Consistent results were obtained in sensitivity analyses. Furthermore, the GRS approach showed similar results in the several MR methods.

Conclusion: These findings do not support a causal role of AgeSmk, CigDay, SmkCes, alcohol consumption, and type 2 diabetes in the development of GU and DU. However, it is confirmed that SmkInit and BMI have a causal part in the development of GU and DU.
Clinical and immunological characteristics of TGM3 in pan-cancer: A potential prognostic biomarker
Authors: Zhang Wenqing , Wu Chenglong , Zhou Kaili , Cao Yu , Zhou Wange , Zhang Xue , Deng Dan
Published: January 2023

Background: Recent studies have identified that transglutaminases (TGMs) are involved in a widespread epigenetic modification in tumorigenesis. However, it remains unclear how transglutaminase 3 (TGM3) affects in pan-cancer. The present study aimed to explore the clinical and prognostic function of TGM3 in pan-cancer as well as to explore the relationship of TGM3 expression with clinical stage, survival rate, prognosis condition, immune infiltration and mutation indicators.

Methods: The relevant data of tumors were obtained from The Cancer Genome Atlas (TCGA), TARGET, Cancer Cell Line Encyclopedia (CCLE) and Genotype-Tissue Expression (GTEx) databases. According to the Human Protein Atlas (HPA) and TIMER databases, we evaluated the protein expression levels of TGM3 in different organs and tissues as well as their association with immune cell infiltration and immunotherapeutic response in pan-cancers. Expression differences between normal and tumor tissues as well as survival and prognosis situation, clinical data characteristics, tumor mutational burden (TMB), microsatellite instability (MSI), and RNA methylation were also assessed. Oncogenic analyses were also evaluated by GSEA.

Results: Compared to normal tissues, some tumor tissues had a lower expression level of TGM3, while other tumor tissues had a high expression level of TGM3. Further studies showed that high TGM3 expression had a certain risk impact on pan-cancer as high TGM3 expression levels were detrimental to the survival of several cancers, except for pancreatic cancer (PAAD). High expression level of TGM3 was also related to higher clinical stages in most cancers. The expression level of TGM3 was significantly negatively correlated with the expression of immune infiltration-related cells, including B cells, CD8+ T cells, CD4+ T cells, neutrophils, macrophages and dendritic cells (DCs). Furthermore, in most cancer types, TGM3 was inversely correlated with TMB, MSI, and methylation, suggesting that TGM3 expression can be used to assess potential therapeutic response, especially immune-related targeted therapy. GSEA analysis elucidated the biological and molecular function of TGM3 in various cancer types. Taken together, these bioinformatic analyses identified TGM3 as an important biomarker for clinical tumor prognosis and evaluation of treatment efficacy.

Conclusion: We comprehensively analyzed the clinical characteristics, tumor stages, immune infiltration, methylation level, gene mutation, functional enrichment analysis and immunotherapeutic value of TGM3 in pan-cancer, providing implications for the function of TGM3 and its role in clinical treatment.
Circular RNAs in extracellular vesicles: Promising candidate biomarkers for schizophrenia
Authors: Guo Chuang , Lv Haibing , Bai Yulong , Guo Meng , Li Pengfei , Tong Shuping , He Kuanjun
Published: January 2023

As one of common and severe mental illnesses, schizophrenia is difficult to be diagnosed exactly. Both its pathogenesis and the causes of its development are still uncertain because of its etiology complexity. At present, the diagnosis of schizophrenia is mainly based on the patient’s symptoms and signs, lacking reliable biomarkers that can be used for diagnosis. Circular RNAs in extracellular vesicles (EV circRNAs) can be used as promising candidate biomarkers for schizophrenia and other diseases, for they are not only high stability and disease specificity, but also are rich in contents and easy to be detected. The review is to focus on the research progress of the correlation between circRNAs and schizophrenia, and then to explores the possibility of EV circRNAs as new biomarkers for the schizophrenia diagnosis.