bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bioinformatics analysis reveals the potential role of matrix metalloproteinases in immunity and urolithiasis
Authors: Hong Sen-Yuan , Jiang Hong-Cheng , Xu Wen-Chao , Zeng He-Song , Wang Shao-Gang , Qin Bao-Long 
Published: March 2023

BackgroundThe pathogenesis of urolithiasis remains unclear, making the development of medications for treatment and prevention stagnant. Randall’s plaques (RPs) begin as interstitial calcium phosphate crystal deposits, grow outward and breach the renal papillary surface, acting as attachment for CaOx stones. Since matrix metalloproteinases (MMPs) can degrade all components of extracellular matrix (ECM), they might participate in the breach of RPs. Besides, MMPs can modulate the immune response and inflammation, which were confirmed to be involved in urolithiasis. We aimed to investigate the role of MMPs in the development of RPs and stone formation.MethodsThe public dataset GSE73680 was mined to identify differentially expressed MMPs (DEMMPs) between normal tissues and RPs. WGCNA and three machine learning algorithms were performed to screen the hub DEMMPs. In vitro experiments were conducted for validation. Afterwards, RPs samples were classified into clusters based on the hub DEMMPs expression. Differentially expressed genes (DEGs) between clusters were identified and functional enrichment analysis and GSEA were applied to explore the biological role of DEGs. Moreover, the immune infiltration levels between clusters were evaluated by CIBERSORT and ssGSEA.ResultsFive DEMMPs, including MMP1, MMP3, MMP9, MMP10, and MMP12, were identified between normal tissues and RPs, and all of them were elevated in RPs. Based on WGCNA and three machine learning algorithms, all of five DEMMPs were regarded as hub DEMMPs. In vitro validation found the expression of hub DEMMPs also increased in renal tubular epithelial cells under lithogenic environment. RPs samples were divided into two clusters and cluster A exhibited higher expression of hub DEMMPs compared to cluster B. Functional enrichment analysis and GSEA found DEGs were enriched in immune-related functions and pathways. Moreover, increased infiltration of M1 macrophages and enhanced levels of inflammation were observed in cluster A by immune infiltration analysis.ConclusionWe assumed that MMPs might participate in RPs and stone formation through ECM degradation and macrophages-mediated immune response and inflammation. Our findings offer a novel perspective on the role of MMPs in immunity and urolithiasis for the first time, and provide potential biomarkers to develop targets for treatment and prevention.
Biological soil crust development affects bacterial communities in the Caragana microphylla community in alpine sandy areas
Authors: Zhou Hong , Li Lun , Liu Yunxiang 
Published: March 2023

IntroductionBiological soil crusts (BSCs) constitute a substantial portion of primary production in dryland ecosystems. They successionally mature to deliver a series of ecosystem services. Bacteria, as an important community in BSCs, play critical roles in maintaining the structure and functions of BSCs. However, the process by which bacterial diversity and community are altered with BSC development is not fully understood.MethodsIn this study, amplicons sequencing was used to investigate bacterial diversity and community compositions across five developmental stages of BSCs (bare sand, microbial crusts, algae crusts, lichen crusts, and moss crusts) and their relationship with environmental variables in the Gonghe basin sandy land in Qinghai-Tibet Plateau, northwestern China.ResultsThe results showed that Proteobacteria, Actinobacteria, Cyanobacteria, Acidobacteria, Bacteroidetes, and Firmicutes were predominant in different developmental stages of BSCs, accounting for more than 77% of the total relative abundance. The phyla of Acidobacteria and Bacteroidetes were abundant in this region. With BSC development, bacterial diversity significantly increased, and the taxonomic community composition significantly altered. The relative abundance of copiotrophic bacteria, such as Actinobacteria, Acidobacteria, Bacteroidetes, Verrucomicrobia, Planctomycetes, and Gemmatimonadetes significantly increased, whereas the relative abundance of oligotrophic bacteria, such as Proteobacteria and Firmicutes significantly decreased. The relative abundance of Cyanobacteria in the algae crusts was significantly higher than that in the other developmental stages (p &lt; 0.05).ConclusionVariations in bacterial composition suggested that the potential ecological functions of the bacterial community were altered with BSC development. The functions varied from enhancing soil surface stability by promoting soil particle cementation in the early stages to promoting material circulation of the ecosystem by fixing carbon and nitrogen and decomposing litter in the later stages of BSC development. Bacterial community is a sensitive index of water and nutrient alterations during BSC development. SWC, pH value, TC, TOC, TN, NO3−, TP and soil texture were the primary environmental variables that promoted changes in the bacterial community composition of BSCs.
Feasibility and usability of a digital health technology system to monitor mobility and assess medication adherence in mild-to-moderate Parkinson's disease
Authors: Debelle Héloïse , Packer Emma , Beales Esther , Bailey Harry G. B. , Mc Ardle Ríona , Brown Philip , Hunter Heather , Ciravegna Fabio , Ireson Neil , Evers Jordi , Niessen Martijn , Shi Jian Qing , Yarnall Alison J. , Rochester Lynn , Alcock Lisa , Del Din Silvia 
Published: March 2023

IntroductionParkinson's disease (PD) is a neurodegenerative disorder which requires complex medication regimens to mitigate motor symptoms. The use of digital health technology systems (DHTSs) to collect mobility and medication data provides an opportunity to objectively quantify the effect of medication on motor performance during day-to-day activities. This insight could inform clinical decision-making, personalise care, and aid self-management. This study investigates the feasibility and usability of a multi-component DHTS to remotely assess self-reported medication adherence and monitor mobility in people with Parkinson's (PwP).MethodsThirty participants with PD [Hoehn and Yahr stage I (n = 1) and II (n = 29)] were recruited for this cross-sectional study. Participants were required to wear, and where appropriate, interact with a DHTS (smartwatch, inertial measurement unit, and smartphone) for seven consecutive days to assess medication adherence and monitor digital mobility outcomes and contextual factors. Participants reported their daily motor complications [motor fluctuations and dyskinesias (i.e., involuntary movements)] in a diary. Following the monitoring period, participants completed a questionnaire to gauge the usability of the DHTS. Feasibility was assessed through the percentage of data collected, and usability through analysis of qualitative questionnaire feedback.ResultsAdherence to each device exceeded 70% and ranged from 73 to 97%. Overall, the DHTS was well tolerated with 17/30 participants giving a score &gt; 75% [average score for these participants = 89%, from 0 (worst) to 100 (best)] for its usability. Usability of the DHTS was significantly associated with age (ρ = −0.560, BCa 95% CI [−0.791, −0.207]). This study identified means to improve usability of the DHTS by addressing technical and design issues of the smartwatch. Feasibility, usability and acceptability were identified as key themes from PwP qualitative feedback on the DHTS.ConclusionThis study highlighted the feasibility and usability of our integrated DHTS to remotely assess medication adherence and monitor mobility in people with mild-to-moderate Parkinson's disease. Further work is necessary to determine whether this DHTS can be implemented for clinical decision-making to optimise management of PwP.
Clinical features and prognosis of pediatric idiopathic sudden sensorineural hearing loss: A bi-center retrospective study
Authors: Li Yingqiang , Zhou Xiaowei , Dou Zhiyong , Deng Dongzhou , Bing Dan 
Published: March 2023

ObjectiveLimited research has focused on the clinical features of sudden sensorineural hearing loss (SSNHL) in pediatric patients. This study is aimed to investigate the relationship between clinical features and the baseline hearing severity and outcomes of SSNHL in the pediatric population.MethodWe conducted a bi-center retrospective observational study in 145 SSNHL patients aged no more than 18 years who were recruited between November 2013 and October 2022. Data extracted from medical records, audiograms, complete blood count (CBC) and coagulation tests have been assessed for the relationship with the severity (the thresholds of the initial hearing) and outcomes (recovery rate, hearing gain and the thresholds of the final hearing).ResultsA lower lymphocyte count (P = 0.004) and a higher platelet-to-lymphocyte ratio (PLR) (P = 0.041) were found in the patient group with profound initial hearing than in the less severe group. Vertigo (β = 13.932, 95%CI: 4.082–23.782, P = 0.007) and lymphocyte count (β = −6.686, 95%CI: −10.919 to −2.454, P = 0.003) showed significant associations with the threshold of the initial hearing. In the multivariate logistic model, the probability of recovery was higher for patients with ascending and flat audiograms compared to those with descending audiograms (ascending: OR 8.168, 95% CI 1.450–70.143, P = 0.029; flat: OR 3.966, 95% CI 1.341–12.651, P = 0.015). Patients with tinnitus had a 3.2-fold increase in the probability of recovery (OR 3.222, 95% CI 1.241–8.907, P = 0.019), while the baseline hearing threshold (OR 0.968, 95% CI 0.936–0.998, P = 0.047) and duration to the onset of therapy (OR 0.942, 95% CI 0.890–0.977, P = 0.010) were negatively associated with the odds of recovery.ConclusionsThe present study showed that accompanying tinnitus, the severity of initial hearing loss, the time elapse and the audiogram configuration might be related to the prognosis of pediatric SSNHL. Meanwhile, the presence of vertigo, lower lymphocytes and higher PLR were associated with worse severity.
μ-band desynchronization in the contralateral central and central-parietal areas predicts proprioceptive acuity
Authors: Albanese Giulia Aurora , Marini Francesca , Morasso Pietro , Campus Claudio , Zenzeri Jacopo 
Published: March 2023

IntroductionPosition sense, which belongs to the sensory stream called proprioception, is pivotal for proper movement execution. Its comprehensive understanding is needed to fill existing knowledge gaps in human physiology, motor control, neurorehabilitation, and prosthetics. Although numerous studies have focused on different aspects of proprioception in humans, what has not been fully investigated so far are the neural correlates of proprioceptive acuity at the joints.MethodsHere, we implemented a robot-based position sense test to elucidate the correlation between patterns of neural activity and the degree of accuracy and precision exhibited by the subjects. Eighteen healthy participants performed the test, and their electroencephalographic (EEG) activity was analyzed in its μ band (8–12 Hz), as the frequency band related to voluntary movement and somatosensory stimulation.ResultsWe observed a significant positive correlation between the matching error, representing proprioceptive acuity, and the strength of the activation in contralateral hand motor and sensorimotor areas (left central and central-parietal areas). In absence of visual feedback, these same regions of interest (ROIs) presented a higher activation level compared to the association and visual areas. Remarkably, central and central-parietal activation was still observed when visual feedback was added, although a consistent activation in association and visual areas came up.ConclusionSumming up, this study supports the existence of a specific link between the magnitude of activation of motor and sensorimotor areas related to upper limb proprioceptive processing and the proprioceptive acuity at the joints.
A hybrid P300-SSVEP brain-computer interface speller with a frequency enhanced row and column paradigm
Authors: Bai Xin , Li Minglun , Qi Shouliang , Ng Anna Ching Mei , Ng Tit , Qian Wei 
Published: March 2023

ObjectiveThis study proposes a new hybrid brain-computer interface (BCI) system to improve spelling accuracy and speed by stimulating P300 and steady-state visually evoked potential (SSVEP) in electroencephalography (EEG) signals.MethodsA frequency enhanced row and column (FERC) paradigm is proposed to incorporate the frequency coding into the row and column (RC) paradigm so that the P300 and SSVEP signals can be evoked simultaneously. A flicker (white-black) with a specific frequency from 6.0 to 11.5 Hz with an interval of 0.5 Hz is assigned to one row or column of a 6 × 6 layout, and the row/column flashes are carried out in a pseudorandom sequence. A wavelet and support vector machine (SVM) combination is adopted for P300 detection, an ensemble task-related component analysis (TRCA) method is used for SSVEP detection, and the two detection possibilities are fused using a weight control approach.ResultsThe implemented BCI speller achieved an accuracy of 94.29% and an information transfer rate (ITR) of 28.64 bit/min averaged across 10 subjects during the online tests. An accuracy of 96.86% is obtained during the offline calibration tests, higher than that of only using P300 (75.29%) or SSVEP (89.13%). The SVM in P300 outperformed the previous linear discrimination classifier and its variants (61.90–72.22%), and the ensemble TRCA in SSVEP outperformed the canonical correlation analysis method (73.33%).ConclusionThe proposed hybrid FERC stimulus paradigm can improve the performance of the speller compared with the classical single stimulus paradigm. The implemented speller can achieve comparable accuracy and ITR to its state-of-the-art counterparts with advanced detection algorithms.
Roxadustat (FG-4592) abated lipopolysaccharides-induced depressive-like symptoms via PI3K signaling
Authors: Li Axiang , Liu Zizhen , Ali Tahir , Gao Ruyan , Luo Yanhua , Gong Qichao , Zheng Chenyou , Li Weifen , Guo Hongling , Liu Xinshe , Li Shupeng , Li Tao 
Published: March 2023

BackgroundDespite its role in inflammation and the redox system under hypoxia, the effects and molecular mechanisms of hypoxia-inducible factor (HIF) in neuroinflammation-associated depression are poorly explored. Furthermore, Prolyl hydroxylase domain-containing proteins (PHDs) regulate HIF-1; however, whether and how PHDs regulate depressive-like behaviors under Lipopolysaccharides (LPS)-induced stress conditions remain covered.MethodsTo highlight the roles and underlying mechanisms of PHDs-HIF-1 in depression, we employed behavioral, pharmacological, and biochemical analyses using the LPS-induced depression model.ResultsLipopolysaccharides treatment induced depressive-like behaviors, as we found, increased immobility and decreased sucrose preference in the mice. Concurrently, we examined increased cytokine levels, HIF-1 expression, mRNA levels of PHD1/PHD2, and neuroinflammation upon LPS administration, which Roxadustat reduced. Furthermore, the PI3K inhibitor wortmannin reversed Roxadustat-induced changes. Additionally, Roxadustat treatment attenuated LPS-induced synaptic impairment and improved spine numbers, ameliorated by wortmannin.ConclusionLipopolysaccharides-dysregulates HIF-PHDs signaling may contribute to neuroinflammation-coincides depression via PI3K signaling.
Consumption of sugar sweetened beverages, artificially sweetened beverages and fruit juices and risk of type 2 diabetes, hypertension, cardiovascular disease, and mortality: A meta-analysis
Authors: Li Baoyu , Yan Ni , Jiang Hong , Cui Meng , Wu Min , Wang Lina , Mi Baibing , Li Zhaofang , Shi Jia , Fan Yahui , Azalati Mougni Mohamed , Li Chao , Chen Fangyao , Ma Mao , Wang Duolao , Ma Le 
Published: March 2023

IntroductionSugar-sweetened beverage (SSB) intake is associated with an increased risk of cardiometabolic diseases. However, evidence regarding associations of artificially sweetened beverages (ASBs) and fruit juices with cardiometabolic diseases is mixed. In this study, we aimed to investigate the association between the SSB, ASB and fruit juice consumption with the incidence of cardiometabolic conditions and mortality.MethodsRelevant prospective studies were identified by searching PubMed, Web of Science, Embase, and Cochrane Library until December 2022 without language restrictions. The pooled relative risk (RR) and 95% confidence intervals (CIs) were estimated for the association of SSBs, ASBs, and fruit juices with the risk of type 2 diabetes (T2D), cardiovascular disease (CVD), and mortality by using random-effect models.ResultsA total of 72 articles were included in this meta-analysis study. Significantly positive associations were observed between the consumption of individual beverages and T2D risk (RR: 1.27; 95% CI: 1.17, 1.38 for SSBs; RR: 1.32; 95% CI: 1.11, 1.56 for ASBs; and RR:0.98; 95% CI: 0.93, 1.03 for fruit juices). Moreover, our findings showed that intakes of SSBs and ASBs were significantly associated with risk of hypertension, stroke, and all-cause mortality (RR ranging from 1.08 to 1.54; all p &lt; 0.05). A dose-response meta-analysis showed monotonic associations between SSB intake and hypertension, T2D, coronary heart disease (CHD), stroke and mortality, and the linear association was only significant between ASB consumption and hypertension risk. Higher SSB and ASB consumptions were associated with a greater risk of developing cardiometabolic diseases and mortality. Fruit juice intake was associated with a higher risk of T2D.ConclusionTherefore, our findings suggest that neither ASBs nor fruit juices could be considered as healthier beverages alternative to SSBs for achieving improved health.Systematic Review Registration: [PROSPERO], identifier [No. CRD42022307003].
An inverse causal association between genetically predicted vitamin D and chronic obstructive pulmonary disease risk
Authors: Lu Kening , Tan Jiang-Shan , Li Tian-Qi , Yuan Jiaqin , Wang Han , Wang Wenting 
Published: March 2023

AimObservational studies have reported that levels of vitamin D were associated with the incidence of chronic obstructive pulmonary disease (COPD), but the relationship between them may have been confounded in previous studies. In this study, we aimed to determine the relationship between the levels of 25-hydroxyvitamin D (25OHD) and the risk of COPD by two-sample Mendelian randomization (MR) analysis.MethodsSummary statistics for 25OHD and COPD in this study were obtained from the EBI (n = 496,946) consortium and Finn (n = 187,754) consortium. MR was adopted to explore the effect of the genetically predicted levels of 25OHD on the risk of COPD. Based on three assumptions of MR analysis, inverse variance weighting was used as the main analysis. To make our results more robust and reliable, MR Egger’s intercept test, Cochran’s Q test, funnel plot, and “leave-one-out” sensitivity analysis were used to assess the potential pleiotropy and heterogeneity in this study. Then, colocalization analysis and MR Steiger approaches were used to estimate the possible directions of estimates between them. Finally, we analyzed the causal associations between the four core genes (DHCR7, GC, CYP2R1, and CYP24A1) of vitamin D and the levels of 25OHD or the risk of COPD.ResultsOur results showed that each 1 standard deviation (SD) increase in the genetically predicted 25OHD level was associated with a 57.2% lower relative risk of COPD [odds ratio (OR): 0.428, 95% Cl: 0.279–0.657, p = 1.041 × 10−4], and the above association was also verified by maximum likelihood (OR: 0.427, 95% Cl: 0.277–0.657, p = 1.084 × 10−4), MR–Egger (OR: 0.271, 95% CI: 0.176–0.416, p = 2.466 × 10−4), MR-PRESSO (OR: 0.428, 95% Cl: 0.281–0.652, p = 1.421 × 10−4) and MR-RAPS (OR: 0.457, 95% Cl: 0.293–0.712, p = 5.450 × 10−4). Furthermore, colocalization analyses (rs3829251, PP.H4 = 0.99) and MR Steiger (“TRUE”) also showed a reverse association between them. Besides, the core genes of vitamin D also showed similar results except for CYP24A1.ConclusionOur findings provide evidence for a reverse association between genetically predicted 25OHD levels and COPD risk. Taking measures to supplement 25OHD may help reduce the incidence of COPD.
Factors affecting the role of canonical Wnt inhibitor Dickkopf-1 in cancer progression
Authors: Doucet Dakota , Brubaker Connor , Turner Donald , Gregory Carl A. 
Published: March 2023

BackgroundThe canonical Wnt inhibitor Dickkopf-1 (Dkk-1) has the capacity to modulate homeostasis between canonical and non-canonical Wnt pathways and also signal independently of Wnt. The specific effects of Dkk-1 activity on tumor physiology are therefore unpredictable with examples of Dkk-1 serving as either a driver or suppressor of malignancy. Given that Dkk-1 blockade may serve as a potential treatment for some types of cancer, we questioned whether it is possible to predict the role of Dkk-1 on tumor progression based on the tissue origin of the tumor.MethodsOriginal research articles that described Dkk-1 in terms a tumor suppressor or driver of cancer growth were identified. To determine the association between tumor developmental origin and the role of Dkk-1, a logistic regression was performed. The Cancer Genome Atlas database was interrogated for survival statistics based on tumor Dkk-1 expression.ResultsWe report that Dkk-1 is statistically more likely to serve as a suppressor in tumors arising from the ectoderm (p = 0.0198) or endoderm (p = 0.0334) but more likely to serve as a disease driver in tumors of mesodermal origin (p = 0.0155). Survival analyses indicated that in cases where Dkk-1 expression could be stratified, high Dkk-1 expression is usually associated with poor prognosis. This in part may be due to pro-tumorigenic role Dkk-1 plays on tumor cells but also through its influence on immunomodulatory and angiogenic processes in the tumor stroma.ConclusionDkk-1 has a context-specific dual role as a tumor suppressor or driver. Dkk-1 is significantly more likely to serve as a tumor suppressor in tumors arising from ectoderm and endoderm while the converse is true for mesodermal tumors. Patient survival data indicated high Dkk-1 expression is generally a poor prognostic indicator. These findings provide further support for the importance of Dkk-1 as a therapeutic cancer target in some cases.