bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of water level changes on the hydrological connectivity and water quality of a lake-type wetland
Authors: Lin Yemiao , Dai Junfeng , Peng Xinyue , Li Zheqing , Wan Zupeng 
Published: February 2025

IntroductionUnderstanding the effects of water level fluctuations on wetland ecosystems is crucial for water resource management and ecological conservation. While there have been some studies on this topic, comprehensive analyses of how water level changes affect the hydrological connectivity and water quality of complex lake-type wetlands remain relatively limited. This work aims to explore the effects of water level changes on the connectivity and water quality of lake-type water bodies in the Huixian Karst Wetland, Guilin.MethodsWater quality data for Mudong Lake from January 2021 to December 2022 were obtained by collecting monthly water samples and conducting laboratory tests for six common water quality parameters. Through a combination of remote sensing image data, drone image data and actual measured data on the Mudong Lake water level, the comprehensive ecological-hydrological connectivity index and comprehensive water quality index were used to evaluate the water level changes in Mudong Lake, water body connectivity, and water quality. The correlations between them were then analysed.ResultsThe results show that as the water level increases, the degree of landscape fragmentation decreases, and the water connectivity index increases by 262%. In addition, as the water level increases, the comprehensive water quality pollution index shows an overall downward trend.DiscussionHowever, the factors affecting lake water quality are complex and changeable. Future research could consider increasing the monitoring frequency during critical periods of rapid hydrological change, such as rainfall-runoff events, to capture more precise and detailed hydrological and water quality data. This study provides an important example of the effects of changes in water level and wetland connectivity on the water quality of a lake ecosystem.
A structural genomics approach to investigate Dystrophin mutations and their impact on the molecular pathways of Duchenne muscular dystrophy
Authors: Elasbali Abdelbaset Mohamed , Anjum Farah , AlKhamees Osama A. , Abu Al-Soud Waleed , Adnan Mohd , Shamsi Anas , Hassan Md. Imtaiyaz 
Published: February 2025

BackgroundDystrophin is a key protein encoded by the DMD gene, serves as a scaffold linking the cytoskeleton to the extracellular matrix that plays a critical role in muscle contraction, relaxation, and structural integrity. Mutations, particularly single-point amino acid substitutions, can lead to dysfunctional Dystrophin, causing muscular dystrophies, with Duchenne muscular dystrophy (DMD) being the most severe form.ObjectiveThis study aimed to evaluate the effects of 184 single-point amino acid substitutions on the structure and function of Dystrophin using computational approaches.MethodsMany computational tools were used to predict the impact of amino acid substitutions on protein stability, solubility, and function. Pathogenic potential was assessed using disease phenotype predictors and CADD scores, while allele frequency data from gnomAD contextualized mutation prevalence. Additionally, aggregation propensity, frustration analysis, and post-translational modification sites were analyzed for functional disruptions.ResultsOf the 184 substitutions analyzed, 50 were identified as deleterious, with 41 predicted to be pathogenic. Seventeen mutations were localized in the Calponin-homology (CH) 1 domain, a critical functional region of Dystrophin. Six substitutions (N26H, N26K, G47W, D98G, G109A, and G109R) were predicted to decrease protein solubility and were located in minimally frustrated regions, potentially compromising Dystrophin functionality and contributing to DMD pathogenesis.ConclusionThis study provides novel insights into the molecular mechanisms of DMD, highlighting specific mutations that disrupt Dystrophin’s solubility and function. These findings could inform future therapeutic strategies targeting Dystrophin mutations to address DMD pathogenesis.
Genome-wide identification of oat TCP gene family and expression patterns under abiotic stress
Authors: Nie Jiaming , Zhao Hongbin , Guo Xiaodong , Zhang Tao , Han Bing , Liu Huiyan 
Published: February 2025

TCP transcription factors are a unique class of transcription factors that play important roles in alleviating abiotic stresses such as drought and salt. In this study, the whole-genome data of three cultivated varieties, namely, “SFS”, “Sang” and “OT3098v2”, were utilized to identify and analyze the members of the TCP gene family in oats, and their responses to two abiotic stresses, drought and salt, were also investigated. Results showed that there are 83, 65, and 30 non-redundant TCP genes in the three oats, with the highest number of TCP genes specific to the “SFS”, reaching 22 genes. The oat TCP genes can be classified into three subfamilies: PCF, CIN, and CYC/TB1. Most AsTCP genes have important motifs, Motif 1 and Motif 2, which are part of the bHLH domain. Additionally, various cis-acting elements related to hormone response, abiotic stress, light response, and growth and development were found in the promoters of AsTCP genes. The main amplification mechanism of the oat TCP gene family is fragment duplication. Two tandem duplications, AsTCP058/AsTCP059 and AsTCP023/AsTCP025, are stably present in the three oats. The highest number of AsTCP collinear relationships exist in the “SFS” with 89 pairs. After drought and salt stress treatments, significant differences in gene expression were observed among different oat cultivars and treatment periods. Genes that showed significant expression changes under both treatments (AsTCP021, AsTCP033, AsTCP044, AsTCP053, and AsTCP058) may play important roles in oat’s response to abiotic stresses. Notably, AsTCP053 gene was significantly upregulated at 24 h of stress treatment and showed a more sensitive response to salt stress. This study provides insights into the functional characterization of the oat TCP gene family and its molecular mechanisms underlying stress tolerance.
Detection of viral antigen and inflammatory mediators in fatal pediatric dengue: a study on lung immunopathogenesis
Authors: Moragas Leandro Junqueira , Arruda Laíza Vianna , Oliveira Lucca de Lima Siqueira , Alves Felipe de Andrade Vieira , Salomão Natália Gedeão , da Silva Jemima Fuentes Ribeiro , Basílio-de-Oliveira Carlos Alberto , Basílio-de-Oliveira Rodrigo Panno , Mohana-Borges Ronaldo , Azevedo Caio Gonçalves , Oliveira Gabriela Xavier de , Carvalho Jorge José de , Rosman Fernando Colonna , Paes Marciano Viana , Rabelo Kíssila 
Published: February 2025

IntroductionThe dengue virus (DENV) is the etiological agent that causes dengue fever illness, an arbovirus with a major endemic potential that has become increasingly prevalent in Brazil and has already been associated with fatal cases in children. DENV has tropism for several organs, including lungs causing pulmonary complications. The aim of this article was to evaluate the inflammatory and histopathological profile of the lung tissue of three fatal cases of children infected with DENV, which represents a group more susceptible to fatality due to its incomplete development.MethodsHistopathological analysis was carried out using Hematoxylin and Eosin staining and special stains. While the characterization of the inflammatory response and cellular expression was done by marking the viral protein, macrophages, lymphocytes and pro-inflammatory cytokines.Results and discussionThe results confirm that vascular dysfunctions such as hemorrhage, vascular congestion and edema associated with a mononuclear infiltrate were observed in all three cases. In addition, the presence of viral replication and increased expression of inflammatory markers were also observed. Such findings contribute to the study and description of dengue, especially its effects on lung tissue.
Responses of a soil-inhabiting collembolan (Entomobrya proxima Folsom) to organic fertilizer addition illustrated by functional traits and gut bacterial community
Authors: Yang Xinyue , Li Gang , Xiu Weiming 
Published: February 2025

IntroductionOrganic fertilizer offers significant advantages for sustainable agricultural development compared to inorganic fertilizers and is increasingly becoming the predominant fertilizer strategy. Functional traits and gut microbiota of soil fauna are recognized as potential indicators of environmental changes. However, there is a dearth of research examining the correlation between functional traits and intestinal microorganisms in response to organic fertilizer.MethodsIn this study, we selected Entomobrya proxima Folsom, a predominant soil collembolan species found in cropland across North China, as our subject of study. We set treatments with no organic fertilizer (CK) and three different concentrations of organic fertilizer at 1% (O1), 6% (O2), and 10% (O3). Stereomicroscopy and high-throughput amplicon sequencing were employed to elucidate the response of soil fauna to organic fertilizer through host functional traits and associated gut microbial communities.ResultsThe results indicated that the impact of organic fertilizer on the functional traits of collembolans was closely linked to the input concentration. Specifically, low input concentrations positively influenced all functional traits of Entomobrya proxima Folsom; conversely, higher input concentrations exerted an overall detrimental effect. For the gut bacterial community, the addition of organic fertilizer resulted in a significant decrease in abundance, adversely affected α-diversity, and significantly altered the structure of the gut bacterial community compared to CK. However, there was no significant effect of fertilizer concentration on these three parameters. The composition of the gut bacterial community varied due to the addition of organic fertilizer, with significant changes observed in the relative abundances of six phyla and three genera. Furthermore, body length and foreleg length may serve as potential indicators for characterizing the proportions of Alcanivorax and Sphingobacterium of gut bacterial community. Additionally, the assembly process of the gut bacterial community was strongly influenced by the amount of organic fertilizer added; this led to a narrowing niche width that is believed to contribute to an increase in species richness.DiscussionIn conclusion, adding organic fertilizer exerted multiple impacts on soil fauna, with effect sizes related to its concentration. These findings provide insights for conserving soil animals while maximizing their ecological functions and offer perspectives on optimizing sustainable agricultural management practices.
Transcriptomic and metabolomic analysis of recalcitrant phosphorus solubilization mechanisms in Trametes gibbosa
Authors: Chen Yulan , Farooq Akasha , Wei XieLuyao , Qin Leitao , Wang Yong , Zhang Lingzi , Xiang Quanju , Zhao Ke , Yu Xiumei , Chen Qiang , Gao Xue , Nyima Tashi , Penttinen Petri , Gu Yunfu 
Published: February 2025

IntroductionPhosphorus (P) is a crucial growth-limiting nutrient in soil, much of which remains challenging for plants to absorb and use. Unlike chemical phosphate fertilizers, phosphate-solubilizing microorganisms (PSMs) offer a means to address available phosphorus deficiency without causing environmental harm. PSMs possess multiple mechanisms for phosphorus solubilization. Although the phosphorus-solubilizing mechanisms of phosphate-solubilizing bacteria (PSB) have been well characterized, the mechanisms utilized by phosphate-solubilizing fungi (PSF) remain largely unexplored.MethodsThis study isolated a PSF strain, Trametes gibbosa T-41, from soil and evaluated its phosphorus solubilizing capacity with organic (calcium phytin; Phytin-P) and inorganic (tricalcium phosphate; Ca-P) phosphorus sources. The phosphorus solubilization, enzyme activity, and organic acid production of T-41 were measured. And the P-solubilizing mechanism conducted by transcriptomic and metabolomic analyses.Results and discussionT-41 exhibited varying phosphorus solubilizing capacity when grown with organic (calcium phytin; Phytin-P) and inorganic (tricalcium phosphate; Ca-P) phosphorus sources (109.80 ± 8.9 mg/L vs. 57.5 ± 7.9 mg/L, p &lt; 0.05). Compared with the Ca-P treatment, T-41 demonstrated a stronger alkaline phosphatase (ALP) production capacity under Phytin-P treatment (34.5 ± 1.2 μmol/L/h vs. 19.8 ± 0.8 μmol/L/h, p &lt; 0.05). Meanwhile, the production of oxalic acid, maleic acid, and succinic acid was higher under Phytin-P treatment (p &lt; 0.05). Transcriptomic and metabolomic analysis revealed that different phosphorus sources altered metabolic pathways such as galactose metabolism, glyoxylate and dicarboxylic acid metabolism, and ascorbate and aldolate metabolism. Key metabolites like myo-inositol, 2-oxoglutarate, and pyruvate were found to impact the performance of T. gibbosa T-41 differently under the two P sources. Notably, synthesis in Ca-P vs. Pytin-P, T-41 upregulated genes involved in myo-inositol synthesis, potentially enhancing its P-solubilizing ability. These results provide new insights into the molecular mechanisms of PSF at the transcriptomic and metabolomic levels, laying a theoretical foundation for the broader application of PSF as bio-phosphorus fertilizers in the future.
Cecum microbiota composition, fermentation characteristics, and immunometabolic biomarkers of Yunshang black goat fed varying dietary energy and protein levels
Authors: Fu Binlong , Zhao Xiaoqi , Khan Muhammad , Jiang Yanting , Li Weijuan , Mushtaq Maida , Danzeng Baiji , Ni Xiaojun , Azeem Zobia , Shao Qingyong , Xue Bai , Ouyang Yina 
Published: February 2025

IntroductionRuminants including goats have diverse microcosms of microbiota involved in diet digestion, absorption, and assimilation. Moreover, it is well known that changes in dietary regimens including nutrient levels result in varied gut microbiota composition, and ultimately, the performance and health of these animals.MethodsThe current study examined the effects of varying dietary energy and protein levels on the cecal fermentation, immune biomarkers, and microbiota characteristics of 80 male Yunshan Black Goats (6 months, ~35.82 ± 2.79 kg), divided into four diets: 1) High Energy-High Protein (HEHP), 2) High Energy-Low Protein (HELP), 3) Low Energy-High Protein (LEHP), and 4) Low Energy-Low Protein (LELP). Twenty goats (five from each treatment group) were randomly slaughtered after a 50-day feeding trial, and cecal digesta and tissue were sampled for microbial analysis.ResultsThe cecal content revealed that the high-energy groups (HEHP, HELP) had lower pH levels than the LEHP group (p &lt; 0.05) and significantly higher valeric and isovaleric acid concentrations in HEHP. Although species richness (Chao1 index) remained consistent, the HEHP group showed higher diversity (Shannon and Simpson indices) than LEHP (p &lt; 0.05). Dominant phyla included Bacteroidetes and Firmicutes; LEHP and LELP had significantly higher Bacteroidetes abundance than HELP, while HELP had higher Firmicutes abundance than LEHP (p &lt; 0.05). Verrucomicrobia abundance was lower in LEHP than in HELP and LELP (p &lt; 0.05). At the genus level, 311 genera were identified, with Clostridium, Prevotella, unidentified_BS11, and others showing significant variation. The HELP group had lower unidentified_BS11 than LEHP and LELP, and higher unidentified_Ruminococcaceae, Clostridium, and Lachnospiraceae than LEHP (p &lt; 0.05). VFA metabolism, absorption, cytokine expression, and tight junction protein mRNA in cecal tissue were also analyzed. Genes like MCT-1 and SLC16A4, linked to VFA absorption, positively correlated with Paludibacter, which was associated with immune markers (TLR-3, TLR-4, IFN-γ) and Occludin expression. In contrast, VFA-related genes and tight junction proteins negatively correlated with unidentified Fibrobacterales, suggesting a microbial role in adaptive immunity.ConclusionThis study demonstrated that dietary energy and protein levels significantly influenced cecal fermentation, immune biomarkers, and microbiota composition in Yunshan Black Goats.
Age-related immune response disparities between adults and children with severe COVID-19: a case–control study in China
Authors: Chen Hongliang , Li Yuan , Yuan Liping , Liu Fen , Sun Qian , Luo Qingkai , Lei Yefei , Hou Yinglan , Li Jiayan , Cai Liang , Tang Shixing 
Published: February 2025

BackgroundElucidation of immune response differences is critical for uncovering underlying mechanisms and developing potential intervention measures among adults and children with COVID-19.MethodsIn this retrospective study, we analyzed serum biochemical markers and cytokine profiles among adults and children with COVID-19 in the First People’s Hospital of Chenzhou in Hunan, China from 1 December 2022 to 13 February 2023. A case–control study was conducted using propensity score matching (PSM) to mitigate possible confounding factors.ResultsThe significant differences observed included lymphocyte exhaustion, an increased neutrophil-to-lymphocyte (NEU/LYM) ratio, high levels of C-reactive protein (CRP), and a cytokine storm, characterized by high levels of Th1 proinflammatory cytokines, including interleukin 1β (IL-1β), IL-6, IL-8, interferon type I (IFN-γ), and tumor necrosis factor (TNF-α) in the lung among severe adult COVID-19 patients. Additionally, systemic immune responses were observed in children with COVID-19.ConclusionSignificant differences in immune responses between adults and children with COVID-19 highlight the different mechanisms and potential intervention measures of COVID-19.
Identification of Parkinson’s disease using MRI and genetic data from the PPMI cohort: an improved machine learning fusion approach
Authors: Yang Yifeng , Hu Liangyun , Chen Yang , Gu Weidong , Lin Guangwu , Xie YuanZhong , Nie Shengdong 
Published: February 2025

ObjectiveThis study aim to leverage advanced machine learning techniques to develop and validate novel MRI imaging features and single nucleotide polymorphism (SNP) gene data fusion methodologies to enhance the early identification and diagnosis of Parkinson’s disease (PD).MethodsWe leveraged a comprehensive dataset from the Parkinson’s Progression Markers Initiative (PPMI), which includes high-resolution neuroimaging data, genetic single-nucleotide polymorphism (SNP) profiles, and detailed clinical information from individuals with early-stage PD and healthy controls. Two multi-modal fusion strategies were used: feature-level fusion, where we employed a hybrid feature selection algorithm combining Fisher discriminant analysis, an ensemble Lasso (EnLasso) method, and partial least squares (PLS) regression to identify and integrate the most informative features from neuroimaging and genetic data; and decision-level fusion, where we developed an adaptive ensemble stacking (AE_Stacking) model to synergistically integrate the predictions from multiple base classifiers trained on individual modalities.ResultsThe AE_Stacking model achieving the highest average balanced accuracy of 95.36% and an area under the receiver operating characteristic curve (AUC) of 0.974, significantly outperforming feature-level fusion and single-modal models (p &lt; 0.05). Furthermore, by analyzing the features selected across multiple iterations of our models, we identified stable brain region features [lh 6r (FD) and rh 46 (GI)] and key genetic markers (rs356181 and rs2736990 SNPs within the SNCA gene region; rs213202 SNP within the VPS52 gene region), highlighting their potential as reliable early diagnostic indicators for the disease.ConclusionThe AE_Stacking model, trained on MRI and genetic data, demonstrates potential in distinguishing individuals with PD. Our findings enhance understanding of the disease and advance us toward the goal of precision medicine for neurodegenerative disorder.
Auditory steady state response can predict declining EF in healthy elderly individuals
Authors: Mao Xiaopeng , Shenton Nelly , Puthusserypady Sadasivan , Lauritzen Martin Johannes , Benedek Krisztina 
Published: February 2025

BackgroundThe aging population imposes significant economic and societal challenges, underscoring the need for early detection of individuals at risk of cognitive decline prior to the onset of clinical symptoms. This study explores the association between gamma-band Auditory Steady-State Responses (ASSRs) and subclinical cognitive decline using longitudinal data from healthy volunteers in the Metropolit Birth Cohort (MBC).MethodsLongitudinal recordings of cognitive test results and ASSRs at 40 Hz stimulation were analyzed. Generalized Linear Models (GLMs) were employed to determine the association between ASSR characteristics and cognitive performance with an emphasis on Executive Function (EF) at ages 61–68. Additionally, Vision Transformers (ViTs) were trained to distinguish between individuals with declining and stable cognitive performance.ResultsSubjects with declining cognitive performance through midlife showed a larger area of entrainment and delayed neural assembly of ASSRs compared to those with stable cognitive performance. These neurophysiological changes were correlated with poorer EF, as measured by the Stockings of Cambridge (SOC) task. The ViTs trained and cross-validated on time-frequency-transformed Electroencephalograms (EEGs) achieved an average cross-subject accuracy of 51.8% in identifying cognitive decline.ConclusionGamma-band ASSR characteristics are linked to early cognitive decline in middle-aged individuals, offering potential as biomarkers. However, the limited predictive accuracy of ML models emphasizes the need for further refinement to enhance their clinical applicability.
Association between hemoglobin glycation index and poor outcome after endovascular thrombectomy in acute ischemic stroke
Authors: Yang Yan , Liu Mei , Huang Shungui , Zhu Chen , Li Guangzong , Wang Bin , Luo Xiaojing , Zhang Lingwen , Song Weizheng 
Published: February 2025

BackgroundThe prognostic significance of hemoglobin glycation index (HGI) on acute ischemic stroke (AIS) patients treated with endovascular thrombectomy (EVT) remained unclear. This study aimed to investigate the association between HGI and the risk of poor outcome after EVT.MethodsWe retrospectively enrolled AIS patients with large vessel occlusion in the anterior circulation treated with EVT from a multicenter study. Poor outcome was defined as a modified Rankin scale score &gt; 2 points at 90 days after EVT. We used multivariable logistic regression models to investigate the association between HGI and poor outcome. We employed the restricted cubic spline curve to visualize the association between HGI and the risk of poor outcome after EVT.ResultsAmong the 403 enrolled patients (median age, 72 years; 63.8% male), a total of 198 (49.1%) patients had poor outcome at 90 days. The restricted cubic spline curve showed that there was a U-shape relationship between HGI and the risk of poor outcome (P for non-linearity &lt; 0.001). After divided patients into three groups based on HGI tertiles, HGI (tertile 1 vs. 2) was significantly associated with poor outcome [odds ratio (OR), 3.84; 95% confidence interval (CI), 2.08–7.22; P &lt; 0.001] and early neurological deterioration (OR, 3.11; 95% CI, 1.55–6.44; P = 0.002) in multivariable analyses. Adding HGI into models improved the discriminative ability for poor outcome (P &lt; 0.001).ConclusionIn conclusion, our study identified a U-shaped relationship between HGI and poor outcome, with low HGI levels significantly associated with poor outcome after EVT.