bluuebunny/crossref_metadata_2025_split huggingface dataset:
One-Dimensional Experimental Investigation of Polyethylene Microplastic Transport in a Homogeneous Saturated Medium
Authors: Okutan Hande Mahide , Sağir Çağdaş , Fontaine Claude , Nauleau Benoît , Kurtulus Bedri , Le Coustumer Philippe , Razack Moumtaz 
Published: July 2022

Plastics are widely used in every part of life. Microplastics (MPs) are classified as emerging contaminants in nature. Yet, microplastic transportation parameters in groundwater are not characterized well. In this study, microplastic transport in saturated homogeneous media was investigated. For this purpose, one-dimensional column tests were performed using the fluorescent and microplastic tracers to figure out the hydrodynamic conditions for the microplastic transport. Large silica, small silica, sand, and coarse gravel were the tested media. The hydrodynamic transport parameters were calculated by inverse solution methodology using the experimental and the analytical solution results. Only the coarse gravel medium with a minimum 1 mm and maximum 20 mm (5 mm of median) pore sizes and kinematic porosity 40.2% were found to be suitable for the transport of the used polyethylene (PE) whose particle size was between 200 and 500 µm. It is not possible to transport PE particles of selected size from fine-grained media. Transportation occurred in coarse-grained media such as coarse gravel. The calculated dispersivity values for the coarse gravel were 2.58 and 3.02 cm by using fluorescent and PE tracers, respectively. The experiments showed that the used PE particles cannot be transported if the mean flow velocity is lower than 2.02 cm/min in the coarse gravel medium. The microplastic accumulation might be an issue for an actual aquifer rather than the transportation of it considering the actual groundwater flow velocity is generally much lower.
Analysis of Recurrent Times-to-Clinical Malaria Episodes and Plasmodium falciparum Parasitemia: A Joint Modeling Approach Applied to a Cohort Data
Authors: Stanley Christopher C. , Mukaka Mavuto , Kazembe Lawrence N. , Buchwald Andrea G. , Mathanga Don P. , Laufer Miriam K. , Chirwa Tobias F. 
Published: July 2022

BackgroundRecurrent clinical malaria episodes due to Plasmodium falciparum parasite infection are common in endemic regions. With each infection, acquired immunity develops, making subsequent disease episodes less likely. To capture the effect of acquired immunity to malaria, it may be necessary to model recurrent clinical disease episodes jointly with P. falciparum parasitemia data. A joint model of longitudinal parasitemia and time-to-first clinical malaria episode (single-event joint model) may be inaccurate because acquired immunity is lost when subsequent episodes are excluded. This study's informativeness assessed whether joint modeling of recurrent clinical malaria episodes and parasitemia is more accurate than a single-event joint model where the subsequent episodes are ignored.MethodsThe single event joint model comprised Cox Proportional Hazards (PH) sub-model for time-to-first clinical malaria episode and Negative Binomial (NB) mixed-effects sub-model for the longitudinal parasitemia. The recurrent events joint model extends the survival sub-model to a Gamma shared frailty model to include all recurrent clinical episodes. The models were applied to cohort data from Malawi. Simulations were also conducted to assess the performance of the model under different conditions.ResultsThe recurrent events joint model, which yielded higher hazard ratios of clinical malaria, was more precise and in most cases produced smaller standard errors than the single-event joint model; hazard ratio (HR) = 1.42, [95% confidence interval [CI]: 1.22, 2.03] vs. HR = 1.29, [95% CI:1.60, 2.45] among participants who reported not to use LLINs every night compared to those who used the nets every night; HR = 0.96, [ 95% CI: 0.94, 0.98] vs. HR = 0.81, [95% CI: 0.75, 0.88] for each 1-year increase in participants' age; and HR = 1.36, [95% CI: 1.05, 1.75] vs. HR = 1.10, [95% CI: 0.83, 4.11] for observations during the rainy season compared to the dry season.ConclusionThe recurrent events joint model in this study provides a way of estimating the risk of recurrent clinical malaria in a cohort where the effect of immunity on malaria disease acquired due to P. falciparum parasitemia with aging is captured. The simulation study has shown that if correctly specified, the recurrent events joint model can give risk estimates with low bias.
NEAT1/MALAT1/XIST/PKD--Hsa-Mir-101-3p--DLGAP5 Axis as a Novel Diagnostic and Prognostic Biomarker Associated With Immune Cell Infiltration in Bladder Cancer
Authors: Rao Xiaosheng , Cao Haiyan , Yu Qingfeng , Ou Xiuyu , Deng Ruiqi , Huang Jinkun 
Published: July 2022

Background: The clinical value of the biomarkers of bladder cancer (BC) is limited due to their low sensitivity or specificity. As a biomarker, DLG associated protein 5 (DLGAP5) is a potential cell cycle regulator in cancer cell carcinogenesis. However, its functional part in BC remains unclear. Therefore, this study aims to identify DLGAP5 expression in BC and its potential diagnostic and prognostic values. Eventually, it predicts the possible RNA regulatory pathways of BC.Methods: Data on DLGAP5 expression levels in BC and normal bladder tissues were obtained from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) databases. The receiver operating characteristic (ROC), Kaplan–Meier survival curves, and the univariate and multivariate Cox regression analysis determined the diagnostic and prognostic values of DLGAP5 in BC patients. Finally, the StarBase predicted the target RNAs and constructed networks using Cytoscape.Results: DLGAP5 expression was significantly upregulated in BC tissue, verified by the TCGA (p &lt; 0.001), GSE3167, GSE7476, and GSE65635 datasets (p &lt; 0.01). BC patients with increased DLGAP5 had poor overall survival (OS) (p = 0.01), disease specific survival (DSS) (p = 0.006) and progress free interval (DFI) (p = 0.007). The area under the ROC curve (AUC) was 0.913. The multivariate Cox analysis identified that lymphovascular invasion (p = 0.007) and DLGAP5 (p = 0.002) were independent prognostic factors.Conclusion: Increased DLGAP5 expression was closely associated with a poor prognosis in BC patients. In this case, DLGAP5 might be a diagnostic and prognostic biomarker for BC. DLGAP5 expression might be regulated by NEAT1/MALAT1/XIST/PKD--Hsa-mir-101-3p pathways.
Chloroplast Genomes of Genus Tilia: Comparative Genomics and Molecular Evolution
Authors: Yan Linjun , Wang Huanli , Huang Xi , Li Yingchao , Yue Yuanhao , Wang Zhongwei , Tang Shijie 
Published: July 2022

Tilia is a complex genus in the family Malvaceae that has high ecological and economical values. Owing to the lack of sufficient distinguishable morphological and molecular characteristics, interspecific relationships in this genus are not clear. Chloroplast (cp) genomes are small, meanwhile most angiosperms usually undergo matrilineal inheritance. Consequently, they can be used in molecular systematics and phylogenetic analyses. Here, we sequenced and assembled cp genomes from T. endochrysea, T. tomentosa, T. miqueliana, T. americana and T. cordata, and compared them with those of seven previously reported Tilia species. Similar gene contents, gene orders and GC contents existed among the 12 cp genomes, which ranged from 162,564 to 162,855 bp and encoded 113 unique genes. Abundant simple sequence repeats (119–127) and dispersed repeats (97–135) were detected in Tilia cp genomes. In total, 11 hypervariable regions were identified that could be suitable for species identification and phylogenetic studies. A phylogenetic analysis of Malvaceae based on 5 hypervariable genes (matK + ndhF + rpoB + rpoC2+ycf1) revealed that all eight subfamilies were monophyletic groups. Additionally, the genus Tilia was divided into three groups on the basis of all 521 molecular variation loci. The current study provides valuable insights into the genomic evolution of the genus Tilia.
Dynamics in Circulating Proinflammatory Biomarkers for Prognostic Assessment of Patients With Advanced HCC – A Substudy From the SORAMIC Trial
Authors: Schütte Kerstin , Kupčinskas Juozas , Morkunas Egidijus , Öcal Osman , Schinner Regina , Seidensticker Max , De Toni Enrico N. , Ben Khaled Najib , Pech Maciej , Palmer Daniel , Berg Thomas , Sengel Christian , Basu Bristi , Valle Juan W. , Benckert Julia , Gasbarrini Antonio , Sangro Bruno , Malfertheiner Peter , Ricke Jens 
Published: July 2022

IntroductionPrediction of response to treatment in patients with advanced hepatocellular carcinoma (HCC) may assist in the selection of personalized management.ObjectiveThis exploratory analysis of the palliative arm of the SORAMIC trial (ClinicalTrials.gov NCT01126645) evaluated the prognostic potential of basal and dynamic changes in systemic levels of interleukin 6 (IL-6), interleukin 8 (IL-8), systemic vascular endothelial growth factor (VEGF), and lipopolysaccharide (LPS).MethodsWe evaluated the correlations between overall survival (OS) and concentrations of IL-6, IL-8, VEGF, and LPS at follow-up approximately 7-9 weeks after treatment initialization (FU) compared to baseline (BL) in 90 patients treated either with 90Yttrium (90Y) microspheres combined with sorafenib (n = 44) or with sorafenib (n = 46) alone.ResultsChanges in IL-6 concentration during treatment showed correlations with the outcome. An increase in IL-6 concentration of less than 16.8 pg/mL over baseline readings was associated with better survival [median OS 16.3 months compared with 8.9 months (p = 0.0354)]. Correlations with survival were not observed for VEGF or LPS concentrations at baseline, at FU, or changes between these time points.ConclusionsChanges in IL 6 serum levels at 7-9 weeks after treatment initialization but not in IL 8, VEGF, or LPS add important information on the outcome of advanced HCC patients treated palliatively within the SORAMIC trial.
Restricted T-Cell Repertoire in the Epicardial Adipose Tissue of Non-ST Segment Elevation Myocardial Infarction Patients
Authors: Pedicino Daniela , Severino Anna , Di Sante Gabriele , De Rosa Maria Cristina , Pirolli Davide , Vinci Ramona , Pazzano Vincenzo , Giglio Ada F. , Trotta Francesco , Russo Giulio , Ruggio Aureliano , Pisano Eugenia , d’Aiello Alessia , Canonico Francesco , Ciampi Pellegrino , Cianflone Domenico , Cianfanelli Lorenzo , Grimaldi Maria Chiara , Filomia Simone , Luciani Nicola , Glieca Franco , Bruno Piergiorgio , Massetti Massimo , Ria Francesco , Crea Filippo , Liuzzo Giovanna 
Published: July 2022

AimsHuman epicardial adipose tissue, a dynamic source of multiple bioactive factors, holds a close functional and anatomic relationship with the epicardial coronary arteries and communicates with the coronary artery wall through paracrine and vasocrine secretions. We explored the hypothesis that T-cell recruitment into epicardial adipose tissue (EAT) in patients with non-ST segment elevation myocardial infarction (NSTEMI) could be part of a specific antigen-driven response implicated in acute coronary syndrome onset and progression.Methods and ResultsWe enrolled 32 NSTEMI patients and 34 chronic coronary syndrome (CCS) patients undergoing coronary artery bypass grafting (CABG) and 12 mitral valve disease (MVD) patients undergoing surgery. We performed EAT proteome profiling on pooled specimens from three NSTEMI and three CCS patients. We performed T-cell receptor (TCR) spectratyping and CDR3 sequencing in EAT and peripheral blood mononuclear cells of 29 NSTEMI, 31 CCS, and 12 MVD patients. We then used computational modeling studies to predict interactions of the TCR beta chain variable region (TRBV) and explore sequence alignments. The EAT proteome profiling displayed a higher content of pro-inflammatory molecules (CD31, CHI3L1, CRP, EMPRINN, ENG, IL-17, IL-33, MMP-9, MPO, NGAL, RBP-4, RETN, VDB) in NSTEMI as compared to CCS (P &lt; 0.0001). CDR3-beta spectratyping showed a TRBV21 enrichment in EAT of NSTEMI (12/29 patients; 41%) as compared with CCS (1/31 patients; 3%) and MVD (none) (ANOVA for trend P &lt; 0.001). Of note, 11/12 (92%) NSTEMI patients with TRBV21 perturbation were at their first manifestation of ACS. Four patients with the first event shared a distinctive TRBV21-CDR3 sequence of 178 bp length and 2/4 were carriers of the human leukocyte antigen (HLA)-A*03:01 allele. A 3D analysis predicted the most likely epitope able to bind HLA-A3*01 and interact with the TRBV21-CDR3 sequence of 178 bp length, while the alignment results were consistent with microbial DNA sequences.ConclusionsOur study revealed a unique immune signature of the epicardial adipose tissue, which led to a 3D modeling of the TCRBV/peptide/HLA-A3 complex, in acute coronary syndrome patients at their first event, paving the way for epitope-driven therapeutic strategies.
Single-Cell RNA Sequencing Reveals the Pathogenic Relevance of Intracranial Atherosclerosis in Blood Blister-Like Aneurysms
Authors: Wen Dingke , Wang Xing , Chen Ruiqi , Li Hao , Zheng Jun , Fu Wei , Zhang Tianjie , Yang Mu , You Chao , Ma Lu 
Published: July 2022

BackgroundIntracranial non-branching site blood blister-like aneurysms (BBA) are extremely rare and vicious. Their etiology remains elusive, and no molecular study has been carried out to reveal its pathogenic relevance to intracranial atherosclerosis. To investigate its transcriptomic landscape and underlying potential pathogenesis, we performed single-cell RNA sequencing with extensive pathological validation.MethodsIn total, 12,245 cells were recovered for single-cell RNA sequencing analysis from 1 BBA and 2 saccular intracranial aneurysms (IAs). Unbiased clustering using Seurat-based pipeline was used for cellular landscape profiling. Cellchat was used to understand intracellular communications. Furthermore, 10 BBAs and 30 IAs were retrospectively collected for pathological validations like scanning electron microscopy, H&amp;E stain, Masson stain, Verhoeff Van Gielson stain, and immunofluorescence.ResultsSingle-cell transcriptome profiled 14 total subclusters in 6 major groups, namely, 6 monocyte/macrophage clusters, 2 T&amp;NK clusters, 3 vascular smooth muscle cell (VSMC) clusters, 1 dendritic cell, 1 B cell, and 1 endothelial cell cluster. The only mural cell identified in BBAs was VSMC-2 cluster, while mural cells in IAs comprise most clusters of VSMCs and endothelial cells. Upregulated genes in BBA-derived VSMCs are related to arterial mineralization and atherosclerosis, such as PTX3, SPP1, LOX, etc., whereas vasodilation and physiological regulatory genes such as MGP, ACTA2, and MYL9 were conversely enriched in conventional IA-derived VSMCs. Immune cells in the BBA were predominantly macrophages, with a low fraction of T&amp;NK cells, while conventional IAs had a higher percentage of T&amp;NK. Gene enrichment analysis suggested that macrophages in BBA were highly enriched in lipid metabolism as well as atherosclerosis. Ligand–receptor interaction suggested that secretory phosphoprotein 1 (also known as osteopontin) played a major role in mediating the intracellular communication between VSMC and macrophages, especially in BBA. Pathological experiments corroborate with the bioinformatic findings and further characterized BBAs as a thin-walled thrombotic aneurysm with severe atherosclerotic lesions, where ApoE+ macrophages and OPN+ mural cells are intimately involved in the inflammation process.ConclusionsThe preexisting intracranial atherosclerosis might predispose the parent artery to the pathogenic occurrence of BBAs. These data shed light on the pathophysiology of intracranial aneurysms and might assist in the further resolution of the complexity in aneurysm pathogenesis.
Pedunculopontine Nucleus Dysconnectivity Correlates With Gait Impairment in Parkinson’s Disease: An Exploratory Study
Authors: Joza Stephen , Camicioli Richard , Martin W. R. Wayne , Wieler Marguerite , Gee Myrlene , Ba Fang 
Published: July 2022

BackgroundGait impairment is a debilitating and progressive feature of Parkinson’s disease (PD). Increasing evidence suggests that gait control is partly mediated by cholinergic signaling from the pedunculopontine nucleus (PPN).ObjectiveWe investigated whether PPN structural connectivity correlated with quantitative gait measures in PD.MethodsTwenty PD patients and 15 controls underwent diffusion tensor imaging to quantify structural connectivity of the PPN. Whole brain analysis using tract-based spatial statistics and probabilistic tractography were performed using the PPN as a seed region of interest for cortical and subcortical target structures. Gait metrics were recorded in subjects’ medication ON and OFF states, and were used to determine if specific features of gait dysfunction in PD were related to PPN structural connectivity.ResultsTract-based spatial statistics revealed reduced structural connectivity involving the corpus callosum and right superior corona radiata, but did not correlate with gait measures. Abnormalities in PPN structural connectivity in PD were lateralized to the right hemisphere, with pathways involving the right caudate nucleus, amygdala, pre-supplementary motor area, and primary somatosensory cortex. Altered connectivity of the right PPN-caudate nucleus was associated with worsened cadence, stride time, and velocity while in the ON state; altered connectivity of the right PPN-amygdala was associated with reduced stride length in the OFF state.ConclusionOur exploratory analysis detects a potential correlation between gait dysfunction in PD and a characteristic pattern of connectivity deficits in the PPN network involving the right caudate nucleus and amygdala, which may be investigated in future larger studies.
Structural Brain Network Abnormalities in Parkinson’s Disease With Freezing of Gait
Authors: Jin Chaoyang , Yang Lei , Qi Shouliang , Teng Yueyang , Li Chen , Yao Yudong , Ruan Xiuhang , Wei Xinhua 
Published: July 2022

ObjectiveDiffusion tensor imaging (DTI) studies have investigated white matter (WM) integrity abnormalities in Parkinson’s disease (PD). However, little is known about the topological changes in the brain network. This study aims to reveal these changes by comparing PD without freezing of gait (FOG) (PD FOG–), PD with FOG (PD FOG+), and healthy control (HC).Methods21 PD FOG+, 34 PD FOG-, and 23 HC were recruited, and DTI images were acquired. The graph theoretical analysis and network-based statistical method were used to calculate the topological parameters and assess connections.ResultsPD FOG+ showed a decreased normalized clustering coefficient, small-worldness, clustering coefficient, and increased local network efficiency compared with HCs. PD FOG+ showed decreased centrality, degree centrality, and nodal efficiency in the striatum, frontal gyrus, and supplementary motor area (SMA). PD FOG+ showed decreased connections in the frontal gyrus, cingulate gyrus, and caudate nucleus (CAU). The between centrality of the left SMA and left CAU was negatively correlated with FOG questionnaire scores.ConclusionThis study demonstrates that PD FOG+ exhibits disruption of global and local topological organization in structural brain networks, and the disrupted topological organization can be potential biomarkers in PD FOG+. These new findings may provide increasing insight into the pathophysiological mechanism of PD FOG+.
Global Trend in the Research and Development of Acupuncture Treatment on Parkinson's Disease From 2000 to 2021: A Bibliometric Analysis
Authors: Li Xiaoping , Wei Wan , Wang Yuan , Wang Qiang , Liu Zhibin 
Published: July 2022

BackgroundAcupuncture has been widely used in the treatment of patients with Parkinson's disease (PD) in the world. Despite we have an in-depth understanding of acupuncture in this field over the past years, there is no available literature on bibliometric analysis on the development of acupuncture on PD. This study was designed to explore the global trend in the research of acupuncture on PD in the recent 20 years by the software CiteSpace (5.8.R3) and VOSviewer (1.6.14).MethodsPublications regarding acupuncture therapy for PD from 2000 to 2021 were retrieved from the Web of Science Core Collection database. CiteSpace and VOSviewer were used to analyze the number of publications, the contribution of countries, institutions, journals, authors, references, and keywords.ResultsA total of 217 studies were extracted from the database. The outputs of the publications in this field showed an upward trend during the past two decades. The country and institutions with the most publications in this field are China, South Korea, and the USA. They were the main contributors to the research. Kyung Hee University and Capital Medical University were the two most productive organizations. Hi-Joon Park had made the greatest contributions to the field. Evidence-based Complementary and Alternative Medicine was the most popular journals in this field. “Electroacupuncture” and “Bee venom acupuncture” were emerging research hotspots.ConclusionThe research on acupuncture on PD is potential. Authors from different countries/regions and organizations need to remove the language and academic barriers to enhance global cooperation and communications. Scholars in this field need to publish their research findings in high-quality journals to gain more attention worldwide. This study indicated that the mechanism leading to the non-motor symptoms of PD, the establishment of appropriate models that fully reflects the non-motor features of human PD, and the efficacy and safety of promising therapies for patients with PD will remain research frontiers in the future.
Clinical Effect of Electroacupuncture on Acute Sleep Deprivation and Event-Related Potential Affecting the Inhibition Control of the Brain: Study Protocol for a Randomized Controlled Trial
Authors: Li Haiping , Wang Mengyu , Wu Yiming , Chen Xinwang , Xue Cong , Liu Peidong , Zhang Run , Liao Ziyun 
Published: July 2022

BackgroundAcute sleep deprivation (ASD) can effect mood, attention, memory, alertness and metabolism. Especially, it is often accompanied by cognitive impairment of the brain. Acupuncture is safe and effective for improving cognitive function, but its underlying mechanism is not fully understood. In this study, an event-related potential (ERP) technique will be employed to measure the behavioral, cognitive, and physiological changes produced by electroacupuncture intervention after ASD.MethodsWe will recruit 60 healthy subjects. The participants will be randomly divided into a treatment group, a control group, a sham electroacupuncture group and a blank group, at a 1:1:1:1 ratio. The primary outcome will be determined by the change from baseline to 36 h in the MoCA score. The secondary results include the amplitude and latency of ERP N2 and P3, Go-hit rates, Go-RTs, No-Go-FA rates, the WCST, the Digit Span Subtest of the WAIS, the ESS score and FS-14. The 15 healthy subjects will not receive acupuncture treatment and ASD, but will receive EEG records and cognition functions test at the beginning and end of the experiment. Electroacupuncture intervention will be performed for 30 min once every 12 h, a total of three times. ERP measurements and other tests will be performed after baseline and ASD, and the statistician and outcome evaluator will be blinded to treatment allocation.DiscussionThis study is expected to investigate the effectiveness of electroacupuncture in improving cognition for ASD.Trial RegistrationChiCTR2200055999.