bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biodiversity changes in abandoned military training areas: relationships to different management approaches in multiple taxa
Authors: Reif Jiří , Chajma Petr , Dvořáková Lenka , Koptík Jiří , Marhoul Pavel , Čížek Oldřich , Kadlec Tomáš 
Published: November 2023

Introduction:Abandoned military training areas are biodiversity strongholds, and this is particularly true for open-habitat and threatened species in Central Europe. Such species benefited from a specific disturbance regime created by military activities that maintained small-grained environmental heterogeneity. However, the disturbance regime no longer occurs after abandonment and the biodiversity is at risk due to forest and shrub encroachment if the areas are left unmanaged. To combat these adverse changes, several management options are used. As these options are not always applied for conservation purposes and substantially differ in their implementation, it is essential to assess their impacts on biodiversity.Methods:We performed repeated standardized surveys (first in 2009–2010, second in 2020–2022) of vascular plants, grasshoppers, butterflies and birds in 42 abandoned military training areas in Czechia, a Central European country. We calculated changes of species richness and abundance between periods for each taxon and related these changes to six different management types (woody plant cutting, mowing for conservation, mowing for agriculture, grazing for conservation, grazing for agriculture, vehicle movement) performed in these areas between periods.Results:Vascular plants and grasshoppers showed generally positive changes, whereas the reverse was true for butterflies, and birds experienced mixed changes. Although beta-diversity increased between periods in plants, grasshoppers and butterflies, this increase was driven by extirpation of common species. Management impacts greatly different between respective types and between taxa. Woody plant cutting showed solely positive impacts (on plants and grasshoppers), while the impacts of both types of grazing were mixed (positive on plants and birds, negative on butterflies, mixed on grasshoppers). Mowing for agriculture supported plants and birds but had negative effects on grasshoppers. Mowing for conservation and vehicle movement were linked solely to negative biodiversity changes (former in plants, latter in butterflies).Discussion:Some components of biodiversity, i.e. plants and grasshoppers, indicate that abandoned military training areas still serve as their strongholds and the management most likely contributes to this favourable state. In contrast, the pattern found for butterflies is worrying since the management performed up to now apparently does not meet their requirements, likely because they are based on smaller-scale habitat mosaic than currently occurs in the areas. Our results may serve as a guide for future prioritization of environmental management, and we urge for development of more nuanced approaches to save the butterflies.
Study on the substitutability of nighttime light data for SDG indicators: a case study of Yunnan Province
Authors: Quan Xuefeng , Song Xiaoyu , Miao Junxia , Huang Chunlin , Gao Feng , Li Jie , Ying Luyao 
Published: November 2023

Introdution: One crucial method to attain Sustainable Development Goals (SDGs) involves timely adjustment of development policies, promoting the realization of SDGs through a time-series assessment of the degree of accomplishment. In practical applications, data acquisition is a significant constraint in evaluating the SDGs, not only in China but across the globe. Hence, expanding data channels and exploring the feasibility of various data sources for sustainable development assessment are effective strategies to tackle the challenge of data acquisition.Methods: In light of this issue, this study selected Nighttime Light Data, a remote sensing data source closely linked to human social activities, as an alternative data source. Using Yunnan Province as an example, 16 localized indicators of social, economic, and environmental types were chosen. These indicators were then subjected to a correlation analysis with the Total Nighttime Light Index (TNLI). The relationships between different types of indicators and TNLI were analyzed at both temporal and spatial scales, thus identifying the indicators for which TNLI could serve as a suitable substitute measure.Results: The study indicates that when the SDG indicators are classified into economic, social and environmental categories, the total value of nighttime light presents a significant correlation and substitutability with economic indicators; significantly correlated with some social indicators, it can reveal the weak links in the development of underdeveloped areas; it is not significantly correlated with environmental indicators, while a trend correlation exists, which can provide some reference values.Discussion: This study has demonstrated the feasibility of using Nighttime Light Data for sustainable development assessment. It provides a novel evaluation method for countries that, despite a lack of resources for conducting sustainable development assessments, have a greater need for such assessments due to their lower economic development. Furthermore, a multitude of assessment methods can be developed based on Nighttime Light Data.
Integrative analysis of non-targeted metabolome and transcriptome reveals the mechanism of volatile formation in pepper fruit
Authors: Liu Yuhua , Zhou Jiahao , Yi Cheng , Chen Fengqingyang , Liu Yan , Liao Yi , Zhang Zhuqing , Liu Wei , Lv Junheng 
Published: November 2023

Introduction: Aroma is a key inherent quality attributes of pepper fruit, yet the underlying mechanisms of aroma compound biosynthesis remain unclear.Methods: In this study, the volatile profile of the QH (cultivated Capsicum chinense) and WH (cultivated Capsicum annuum) pepper varieties were putatively identified during fruit development using gas chromatography-mass spectrometry (GC-MS).Results and discussion: The results identified 203 volatiles in pepper, and most of the esters, terpenes, aldehydes and alcohols were significantly down-regulated with fruit ripening. The comparison of volatile components between varieties revealed that aldehydes and alcohols were highly expressed in the WH fruit, while esters and terpenes with fruity or floral aroma were generally highly accumulated in the QH fruit, providing QH with a fruity odor. Transcriptome analysis demonstrated the close relationship between the synthesis of volatiles and the fatty acid and terpene metabolic pathways, and the high expression of the ADH, AAT and TPS genes was key in determining the accumulation of volatiles in pepper fruit. Furthermore, integrative metabolome and transcriptome analysis revealed that 208 differentially expressed genes were highly correlated with 114 volatiles, and the transcription factors of bHLH, MYB, ARF and IAA were identified as fundamental for the regulation of volatile synthesis in pepper fruit. Our results extend the understanding of the synthesis and accumulation of volatiles in pepper fruit.
Significance of NotchScore and JAG1 in predicting prognosis and immune response of low-grade glioma
Authors: Shi Bo , Ge Fei , Cai Liangliang , Yang Yi , Guo Xiaohui , Wu Rui , Fan Zhehao , Cao Binjie , Wang Ning , Si Yue , Lin Xinyue , Dong Weibing , Sun Haibo 
Published: November 2023

IntroductionLow-grade glioma (LGG) is a prevalent malignant tumor in the intracranial region. Despite the advancements in treatment methods for this malignancy over the past decade, significant challenges still persist in the form of drug resistance and tumor recurrence. The Notch signaling pathway plays essential roles in many physiological processes as well as in cancer development. However, the significance of the pathway and family genes in LGG are poorly understood. MethodsWe conducted gene expression profiling analysis using the TCGA dataset to investigate the gene set associated with the Notch signaling pathway. we have proposed a metric called "NotchScore" that quantifies the strength of the Notch signaling pathway and enables us to assess its significance in predicting prognosis and immune response in LGG. We downregulated JAG1 in low-grade gliomas to assess its influence on the proliferation and migration of these tumors. Ultimately, we determined the impact of the transcription factor VDR on the transcription of PDL1 through chip-seq data analysis.ResultsOur findings indicate that tumors with a higher NotchScore, exhibit poorer prognosis, potentially due to their ability to evade the anti-tumor effects of immune cells by expressing immune checkpoints. Among the genes involved in the Notch signaling pathway, JAG1 has emerged as the most representative in terms of capturing the characteristics of both NotchScore and Notch pathways. The experimental results demonstrate that silencing JAG1 yielded a significant decrease in tumor cell proliferation in LGG cell lines. Our study revealed mechanisms by which tumors evade the immune system through the modulation of PDL1 transcription levels via the PI3K-Akt signaling pathway. Additionally, JAG1 potentially influences PDL1 in LGG by regulating the PI3K-Akt signaling pathway and the expression of the transcription factor VDR.DiscussionThese findings contribute to our understanding of immune evasion by tumors in LGG. The insights gained from this research may have implications for the development of therapeutic interventions for LGG.
Regional neuroinflammation induced by peripheral infection contributes to fatigue-like symptoms: a [18F]DPA-714 positron emission tomography study in rats
Authors: Li Danxi , Hu Di , Ochi Yuta , Arakaki Wakiko , Mawatari Aya , Shigeta Mika , Wu Yuping , Hayashinaka Emi , Neyama Hiroyuki , Tahara Tsuyoshi , Wada Yasuhiro , Li Feng , Doi Hisashi , Watanabe Yasuyoshi , Cui Yilong 
Published: November 2023

IntroductionA series of symptoms, including fever, widespread pain, fatigue, and even ageusia, have frequently been reported in the context of various infections, such as COVID-19. Although the pathogenic mechanisms underlying an infection causing fever and pain have been well established, the mechanisms of fatigue induced by infection in specific brain regions remain unclear.MethodsTo elucidate whether and how the peripheral infection cause fatigue via regional neuroinflammation, we performed a brain-wide investigation of neuroinflammation in a peripheral pseudoinfection rat model using [18F]DPA-714 positron emission tomography (PET) imaging analysis, in which the polyriboinosinic: polyribocytidylic acid (poly I:C) was intraperitoneally injected.ResultsTransient fever lasting for several hours and subsequent suppression of spontaneous activity lasting a few days were induced by poly I:C treatment. Significant increase in plasma interleukin (IL)-1β, IL-6 and tumour necrosis factor (TNF)-α were observed at 2 and 4 h following poly I:C treatment. PET imaging analysis revealed that the brain uptake of [18F]DPA-714 was significantly increased in several brain regions one day after poly I:C treatment, such as the dorsal raphe (DR), parvicellular part of red nucleus (RPC), A5 and A7 noradrenergic nucleus, compared with the control group. The accumulation of [18F]DPA-714 in the DR, RPC and A5 was positively correlated with subsequent fatigue-like behavior, and that in the A7 tended to positively correlate with fever.DiscussionThese findings suggest that peripheral infection may trigger regional neuroinflammation, which may cause specific symptoms such as fatigue. A similar mechanism might be involved in COVID-19.
Machine learning to characterize bone biomarkers profile in rheumatoid arthritis
Authors: Adami Giovanni , Fassio Angelo , Rossini Maurizio , Benini Camilla , Bixio Riccardo , Rotta Denise , Viapiana Ombretta , Gatti Davide 
Published: November 2023

BackgroundBone metabolism is disrupted in rheumatoid arthritis (RA); however, the bone metabolic signature of RA is poorly known. The objective of the study is to further characterize the bone metabolic profile of RA and compare it to psoriatic arthritis (PsA), systemic sclerosis (SSc) and healthy controls.MethodsWe did a cross-sectional case-control study on consecutively enrolled patients and age-matched controls. We collected clinical characteristics, serum biomarkers related to bone metabolism and Bone Mineral Density (BMD). A multiple correlation analysis using Spearman's rank correlation coefficient was conducted within the RA patient group to investigate associations between biomarker levels and clinical variables. Machine learning (ML) models and Principal Component Analysis (PCA) was performed to evaluate the ability of bone biomarker profiles to differentiate RA patients from controls.ResultsWe found significantly lower BMD in RA patients compared to PsA, and Systemic Sclerosis SSc groups. RA patients exhibited higher Dkk1, sclerostin and lower P1nP and B-ALP levels compared to controls. No significant differences in CTX levels were noted. Correlation analysis revealed associations between bone biomarkers and clinical variables. PCA and ML highlighted distinct biomarker patterns in RA which can effectively discriminated bone biomarkers profile in RA from controls.ConclusionOur study helped uncover the distinct bone profile in RA, including changes in bone density and unique biomarker patterns. These findings enhance our comprehension of the intricate links between inflammation, bone dynamics, and RA activity, offering potential insights for diagnostic and therapeutic advancements in managing bone involvement in this challenging condition.
Axitinib targets cardiac fibrosis in pressure overload-induced heart failure through VEGFA-KDR pathway
Authors: Jiao Tiantian , Wang Yuanqi , Lin Xueqi , Song Wei , Wang Liang , Rahman Tapu Md Sakibur , Xu Linghao , Nie Lindong , Zhang Qi , Li Jiming 
Published: November 2023

BackgroundThere are no specific clinical medications that target cardiac fibrosis in heart failure (HF). Recent studies have shown that tyrosine kinase inhibitors (TKIs) may benefit fibrosis in various organs. However, there is limited research on their application in cardiac fibrosis. Axitinib, an FDA-approved tyrosine kinase inhibitor, was used to evaluate its effects on cardiac fibrosis and function in pressure overload-induced heart failure.MethodsTo build a pharmacological network, the pharmacological targets of axitinib were first retrieved from databases and coupled with key heart failure gene molecules for analysis and prediction. To validate the results outlined above, 8-week-old male C57BL/6 J mice were orally administrated of axitinib (30 mg/kg) daily for 8 weeks after Transverse Aortic Constriction (TAC) surgery. Mouse cardiomyocytes and cardiac fibroblasts were used as cell lines to test the function and mechanism of axitinib.ResultsWe found that the pharmacological targets of axitinib could form a pharmacological network with key genes involved in heart failure. The VEGFA-KDR pathway was found to be closely related to the differential gene expression of human heart-derived primary cardiomyocyte cell lines treated with axitinib, based on analysis of the publicly available dataset. The outcomes of animal experiments demonstrated that axitinib therapy greatly reduced cardiac fibrosis and improved TAC-induced cardiac dysfunction. Further research has shown that the expression of transforming growth factor-β(TGF-β) and other fibrosis genes was significantly reduced in vivo and in vitro.ConclusionOur study provides evidence for the repurposing of axitinib to combat cardiac fibrosis, and offers new insights into the treatment of patients with HF.
Computer vision detects inflammatory arthritis in standardized smartphone photographs in an Indian patient cohort
Authors: Phatak Sanat , Chakraborty Somashree , Goel Pranay 
Published: November 2023

IntroductionComputer vision extracts meaning from pixelated images and holds promise in automating various clinical tasks. Convolutional neural networks (CNNs), a deep learning network used therein, have shown promise in analyzing X-ray images and joint photographs. We studied the performance of a CNN on standardized smartphone photographs in detecting inflammation in three hand joints and compared it to a rheumatologist’s diagnosis.MethodsWe enrolled 100 consecutive patients with inflammatory arthritis with an onset period of less than 2 years, excluding those with deformities. Each patient was examined by a rheumatologist, and the presence of synovitis in each joint was recorded. Hand photographs were taken in a standardized manner, anonymized, and cropped to include joints of interest. A ResNet-101 backbone modified for two class outputs (inflamed or not) was used for training. We also tested a hue-augmented dataset. We reported accuracy, sensitivity, and specificity for three joints: wrist, index finger proximal interphalangeal (IFPIP), and middle finger proximal interphalangeal (MFPIP), taking the rheumatologist’s opinion as the gold standard.ResultsThe cohort consisted of 100 individuals, of which 22 of them were men, with a mean age of 49.7 (SD 12.9) years. The majority of the cohort (n = 68, 68%) had rheumatoid arthritis. The wrist (125/200, 62.5%), MFPIP (94/200, 47%), and IFPIP (83/200, 41.5%) were the three most commonly inflamed joints. The CNN achieved the highest accuracy, sensitivity, and specificity in detecting synovitis in the MFPIP (83, 77, and 88%, respectively), followed by the IFPIP (74, 74, and 75%, respectively) and the wrist (62, 90, and 21%, respectively).DiscussionWe have demonstrated that computer vision was able to detect inflammation in three joints of the hand with reasonable accuracy on standardized photographs despite a small dataset. Feature engineering was not required, and the CNN worked despite a diversity in clinical diagnosis. Larger datasets are likely to improve accuracy and help explain the basis of classification. These data suggest a potential use of computer vision in screening and follow-up of inflammatory arthritis.
Pediatric intensive care unit treatment alters the diversity and composition of the gut microbiota and antimicrobial resistance gene expression in critically ill children
Authors: Xu Jiayue , Kong Xiangmei , Li Jiru , Mao Haoyun , Zhu Yueniu , Zhu Xiaodong , Xu Yaya 
Published: November 2023

IntroductionCommon critical illnesses are a growing economic burden on healthcare worldwide. However, therapies targeting the gut microbiota for critical illnesses have not been developed on a large scale. This study aimed to investigate the changes in the characteristics of the gut microbiota in critically ill children after short-term pediatric intensive care unit (PICU) treatments.MethodsAnal swab samples were prospectively collected from March 2021 to March 2022 from children admitted to the PICU of Xinhua Hospital who received broad-spectrum antibiotics on days 1 (the D1 group) and 7 (the D7 group) of the PICU treatment. The structural and functional characteristics of the gut microbiota of critically ill children were explored using metagenomic next-generation sequencing (mNGS) technology, and a comparative analysis of samples from D1 and D7 was conducted.ResultsAfter 7 days of PICU admission, a significant decrease was noted in the richness of the gut microbiota in critically ill children, while the bacterial diversity and the community structure between groups remained stable to some extent. The relative abundance of Bacilli and Lactobacillales was significantly higher, and that of Campylobacter hominis was significantly lower in the D7 group than in the D1 group. The random forest model revealed that Prevotella coporis and Enterobacter cloacae were bacterial biomarkers between groups. LEfSe revealed that two Gene Ontology entries, GO:0071555 (cell wall organization) and GO:005508 (transmembrane transport), changed significantly after the short-term treatment in the PICU. In addition, 30 KEGG pathways were mainly related to the activity of enzymes and proteins during the processes of metabolism, DNA catabolism and repair, and substance transport. Finally, 31 antimicrobial resistance genes had significantly different levels between the D7 and D1 groups. The top 10 up-regulated genes were Erm(A), ErmX, LptD, eptB, SAT-4, tetO, adeJ, adeF, APH(3′)-IIIa, and tetM.ConclusionThe composition, gene function, and resistance genes of gut microbiota of critically ill children can change significantly after short PICU treatments. Our findings provide a substantial basis for a better understanding of the structure and function of gut microbiota and their role in critical illnesses.
The analysis of Lactobacillus spp. distribution in the vaginal microbiota of Polish women with abnormal Pap smear result
Authors: Frąszczak Karolina , Barczyński Bartłomiej , Siwiec Radosław , Kondracka Adrianna , Malm Anna , Kotarski Jan , Witt Elzbieta , Korona-Głowniak Izabela 
Published: November 2023

IntroductionA healthy vaginal microbiota is represented mainly by Lactobacillus spp. and plays a vital role in maintaining the functional balance in the vaginal environment. Scientists have drawn attention to possible correlations between the vaginal microbiome and gynecological neoplasms. Several recent studies have shown a potential link between the vaginal microbiome and the risk of developing cervical cancer from human papillomavirus (HPV) infection. This study aimed to compare the prevalence and abundance of various lactic acid bacteria species (LABs) in vaginal swabs from healthy controls and patients with abnormal Pap smear results.MethodsThe study included 100 women (79 patients with abnormal cervical Pap smear results and 21 controls) from whom vaginal swabs were collected. Real-time quantitative PCR was used to determine seven lactic acid bacteria (LAB) species and their quantities.ResultsMost patients were colonized by two Lactobacillus species, primarily Lactobacillus gasseri (93%) and L. crispatus (83%). Patient age and place of residence were associated with the diversity of LAB in the vaginal microbiota. The abundance of L. delbrueckii in the vaginal microbiota increased, whereas the abundance of L. gasseri abundance decreased, with patient age. Lactobacillus acidophilus and Limosilactobacillus fermentum were significantly more often detected in patients living in rural versus urban areas. Statistical analysis did not show any significant differences in LAB between groups of patients with various changes on smear tests.DiscussionThe degree of dysplastic changes in the endothelium or the presence of a group of atypical cervical stratified epithelial cells was not associated with significant changes in the studied vaginal bacteria.