bluuebunny/crossref_metadata_2025_split huggingface dataset:
Surface deformation simulation for InSAR detection using a machine learning approach on the hantangang river volcanic field: A case study on the orisan mountain
Authors: Fadhillah Muhammad Fulki , Hakim Wahyu Luqmanul , Park Sungjae , Kim Daewoo , Park Yu-Chul , Kim Chang-Hwan , Lee Chang-Wook 
Published: August 2022

Recent developments in remote sensing research have resulted in a large amount of variability in the data provided by researchers. Synthetic aperture radar (SAR) is a tool used to measure surface deformation and assess changes in the Earth’s surface. Here, we consider the usefulness of Interferometric Synthetic Aperture Radar (InSAR) in assessing past volcanic activity as a key to learning the characteristics of the deformation around a volcano. The Hantangang River volcanic field (HRVF) is a geoheritage site in the Korean Peninsula that has interesting geological characteristics. This volcanic field has formed along 110 km of the paleochannel of the Hantangang River. Since the eruptions occurred from 0.15 to 0.51 Ma, the source is limited, which has raised interest in the assessment of volcanic landforms. The recent integration of machine learning and InSAR processing has shown promising results for many purposes, such as classifying, modeling, and detecting surface deformation. To examine the future impact based on information from the past, we utilized a synthetic interferogram with the Okada model and transferred it to a machine learning algorithm. The synthetic interferogram was formed based on Sentinel-1 C-band satellite data to simulate the deformation phases. The orbital errors, the topographical data errors, and the atmospheric effect were also simulated and added to the synthetic interferogram to enrich the learning input. A convolutional neural network (CNN) trained with the unwrapped simulated interferogram data and its performance was evaluated. Our proposed method exhibits the capability to detect volcanic activity’s deformation patterns with synthetic interferogram data. The results show that an overall accuracy of more than 80% was achieved using the CNN algorithms on the validation dataset. This study is the first to use machine learning approaches for detecting prehistorical volcanic deformation and demonstrates potential techniques for developing an approach based on satellite imagery. In addition, this study has introduced the possibility of developing a rapid detection of surface deformation using InSAR data based on a machine learning approach.
Microplastics in soil induce a new microbial habitat, with consequences for bulk soil microbiomes
Authors: Kublik Susanne , Gschwendtner Silvia , Magritsch Tobias , Radl Viviane , Rillig Matthias C. , Schloter Michael 
Published: August 2022

Microplastic (MP) pollution poses a threat to agricultural soils and may induce a significant loss of the soil quality and services provided by these ecosystems. Studies in marine environments suggest that this impact is mediated by shifts in the microbiome. However, studies on the mode of action of MP materials on the soil microbiome are rare, particularly when comparing the effects of different MP materials. In this study, we characterized the microbiota colonizing two different MP materials, granules made of polypropylene (PP) and expanded polystyrene (ePS), introduced into arable soil and incubated for 8 weeks using a molecular barcoding approach. We further assessed the consequences on the microbiome of bulk soil. The complexity of the bacterial communities colonizing MP materials was significantly higher on ePS compared to PP. Many of the detected genera colonizing the MP materials belonged to taxa, that are known to degrade polymeric substances, including TM7a, Phenylobacterium, Nocardia, Arthrobacter and Streptomyces. Interestingly, in bulk soil samples amended with MP materials, microbial diversity was higher after 8 weeks compared to the control soil, which was incubated without MP materials. The composition of bacterial communities colonizing the MP materials and bulk soil differed. Mainly Acidobacteria were mostly found in bulk soil, whereas they were rare colonizers of the MP materials. Differences in diversity and community composition between the MP affected bulk soil samples were not found. Overall, our data indicate that MP materials form a new niche for microbes in soil, with a specific community composition depending on the materials used, strongly influencing the bulk soil microbiota in the short term. Long-term consequences for the soil microbiome and associated functions including different soils need to be further elaborated in the future for a proper risk assessment of the mode of action of MP materials in terrestrial ecosystems.
Detection of a Cryptic 25 bp Deletion and a 269 Kb Microduplication by Nanopore Sequencing in a Seemingly Balanced Translocation Involving the LMLN and LOC105378102 Genes
Authors: Wang Yanan , Zhao Zhenhua , Fu Xinyu , Li Shufang , Zhang Qiuyan , Kong Xiangdong 
Published: August 2022

Preimplantation genetic testing plays a critical role in enabling a balanced translocation carrier to obtain the normal embryo. Identifying the precise breakpoints for the carriers with phenotypic abnormity, allows us to reveal disrupted genes. In this study, a seemingly balanced translocation 46, XX, t (3; 6) (q29; q26) was first detected using conventional karyotype analysis. To locate the precise breakpoints, whole genomes of DNA were sequenced based on the nanopore GridION platform, and bioinformatic analyses were further confirmed by polymerase-chain-reaction (PCR) and copy number variation (CNV). Nanopore sequencing results were consistent with the karyotype analysis. Meanwhile, two breakpoints were successfully validated using polymerase-chain-reaction and Sanger Sequencing. LOC105378102 and LMLN genes were disrupted at the breakpoint junctions. Notably, observations found that seemingly balanced translocation was unbalanced due to a cryptic 269 kilobases (Kb) microduplication and a 25 bp deletion at the breakpoints of chromosome (chr) 6 and chr 3, respectively. Furthermore, 269 Kb microduplication was also confirmed by copy number variation analyses. In summary, nanopore sequencing was a rapid and direct method for identifying the precise breakpoints of a balanced translocation despite low coverage (3.8×). In addition, cryptic deletion and duplication were able to be detected at the single-nucleotide level.
Pancancer analysis of a potential gene mutation model in the prediction of immunotherapy outcomes
Authors: Yu Lishan , Gong Caifeng 
Published: August 2022

Background: Immune checkpoint blockade (ICB) represents a promising treatment for cancer, but predictive biomarkers are needed. We aimed to develop a cost-effective signature to predict immunotherapy benefits across cancers.Methods: We proposed a study framework to construct the signature. Specifically, we built a multivariate Cox proportional hazards regression model with LASSO using 80% of an ICB-treated cohort (n = 1661) from MSKCC. The desired signature named SIGP was the risk score of the model and was validated in the remaining 20% of patients and an external ICB-treated cohort (n = 249) from DFCI.Results: SIGP was based on 18 candidate genes (NOTCH3, CREBBP, RNF43, PTPRD, FAM46C, SETD2, PTPRT, TERT, TET1, ROS1, NTRK3, PAK7, BRAF, LATS1, IL7R, VHL, TP53, and STK11), and we classified patients into SIGP high (SIGP-H), SIGP low (SIGP-L) and SIGP wild type (SIGP-WT) groups according to the SIGP score. A multicohort validation demonstrated that patients in SIGP-L had significantly longer overall survival (OS) in the context of ICB therapy than those in SIGP-WT and SIGP-H (44.00 months versus 13.00 months and 14.00 months, p &lt; 0.001 in the test set). The survival of patients grouped by SIGP in non-ICB-treated cohorts was different, and SIGP-WT performed better than the other groups. In addition, SIGP-L + TMB-L (approximately 15% of patients) had similar survivals to TMB-H, and patients with both SIGP-L and TMB-H had better survival. Further analysis on tumor-infiltrating lymphocytes demonstrated that the SIGP-L group had significantly increased abundances of CD8+ T cells.Conclusion: Our proposed model of the SIGP signature based on 18-gene mutations has good predictive value for the clinical benefit of ICB in pancancer patients. Additional patients without TMB-H were identified by SIGP as potential candidates for ICB, and the combination of both signatures showed better performance than the single signature.
Ferroptosis-related lncRNAs signature to predict the survival and immune evasion for lung squamous cell carcinoma
Authors: Zhang Rusi , Zhang Xuewen , Yang Han , Lin Yongbin , Wen Yingsheng , Zhao Dechang , Chen Lianjuan , Lin Peng , Zhang Lanjun 
Published: August 2022

Introduction: the investigation on the interactions between ferroptosis and lncRNAs for lung squamous cell carcinoma (LUSC) has been scare, and its impact on tumor immune microenvironment remained unknown. We aim to not only identify a ferroptosis-related lncRNAs signature for LUSC prognosis, but also evaluate its correlation to tumor immune evasion.Methods: RNA sequencing data and survival information were obtained from The Cancer Genome Atlas database. A ferroptosis-related lncRNAs signature (FerRLSig) was developed and validated by univariate Cox regression, Least Absolute Shrinkage and Selection Operator regression and multivariate Cox regression. The tumor immune microenvironment and immune evasion were subsequently evaluated based on the FerRLSig stratification.Results: the FerRLSig consisted of 10 ferroptosis-related lncRNAs and significantly associated with overall survival with satisfactory area under curve (HR = 2.240, 95% CI: 1.845–2.720, p &lt; 0.001, 5-years AUC: 0.756). Based on the FerRLSig stratification, the high-risk group demonstrated not only significantly higher immune infiltration, but also more profound T cell dysfunction and immune evasion, which might ultimately lead to the resistance to current immune checkpoint inhibitors.Conclusion: a robust prognostic FerRLSig for LUSC has been developed and validated, demonstrating a close association not only with tumor immune cell infiltration, but also with T cell dysfunction and immune evasion. Further investigation is warranted to better improve the survival of LUSC patients based on the FerRLSig stratification.
Global research trends on precision cancer medicine-related rashes (2008-2021): A bibliographic study
Authors: Zhao Fangmin , Yu Rui , Chen Shuyi , Zhao Shuya , Sun Lin , Xu Zeting , Zhang Yao , Dai Shuying , Zhang Gaochenxi , Shu Qijin 
Published: August 2022

BackgroundPrecision cancer medicine-related rashes are a kind of skin and mucous lesions caused by precision therapy. More and more evidences indicated that such events should not be ignored in the course of anti-tumor therapy. Since cancer treatment entered the “Precision Era”, there has been a rapid increase in this field. However, there was few bibliometric studies to provide an overall review of this field. This study aims to evaluate the literature output and trends in researches on precision cancer medicine-related rashes from a global perspective.MethodsCollected publications on precision cancer medicine-related rashes from the Web of Science Core Collection database, which were limited to articles and reviews in English. Microsoft Excel, VOS viewer and CiteSpace V were used for quantitative and visual analysis.ResultsA total of 1,229 papers were identified. From 2008 to 2021, annual publications increased year by year. The United States published the most papers in this field (44.9%) and ranking first in citation frequency (19,854 times) and H-index (69). The University of Texas system ranks first with 98 papers published. Lacouture M.E and Robert C were the principal investigators. Cancers has the largest number of articles published, with 70 articles. In recent years, there have been research hotspots related to immunotherapy, including ipilimumab, immunotherapy, tumor microenvironment, association, checkpoint inhibitor, and cutaneous adverse event.ConclusionPrecision cancer medicine-related rashes are a hot research topic in oncology. The number of relevant publications will increase dramatically. “Checkpoint inhibitors”, “skin adverse events”, “associations” and “tumor microenvironment” may become research hotspots in the future.
Natural history of type 1 diabetes on an immunodysregulatory background with genetic alteration in B-cell activating factor receptor: A case report
Authors: Di Lorenzo Biagio , Pacillo Lucia , Milardi Giulia , Jofra Tatiana , Di Cesare Silvia , Gerosa Jolanda , Marzinotto Ilaria , Zapparoli Ettore , Rivalta Beatrice , Cifaldi Cristina , Barzaghi Federica , Giancotta Carmela , Zangari Paola , Rapini Novella , Deodati Annalisa , Amodio Giada , Passerini Laura , Carrera Paola , Gregori Silvia , Palma Paolo , Finocchi Andrea , Lampasona Vito , Cicalese Maria Pia , Schiaffini Riccardo , Di Matteo Gigliola , Merelli Ivan , Barcella Matteo , Aiuti Alessandro , Piemonti Lorenzo , Cancrini Caterina , Fousteri Georgia 
Published: August 2022

The immunological events leading to type 1 diabetes (T1D) are complex and heterogeneous, underscoring the necessity to study rare cases to improve our understanding. Here, we report the case of a 16-year-old patient who showed glycosuria during a regular checkup. Upon further evaluation, stage 2 T1D, autoimmune thrombocytopenic purpura (AITP), and common variable immunodeficiency (CVID) were diagnosed. The patient underwent low carb diet, losing &gt; 8 kg, and was placed on Ig replacement therapy. Anti-CD20 monoclonal antibody (Rituximab, RTX) was administered 2 years after diagnosis to treat peripheral polyneuropathy, whereas an atypical mycobacteriosis manifested 4 years after diagnosis and was managed with prolonged antibiotic treatment. In the fifth year of monitoring, the patient progressed to insulin dependency despite ZnT8A autoantibody resolution and IA-2A and GADA autoantibody decline. The patient had low T1D genetic risk score (GRS = 0.22817) and absence of human leukocyte antigen (HLA) DR3/DR4-DQ8. Genetic analysis identified the monoallelic mutation H159Y in TNFRSF13C, a gene encoding B-cell activating factor receptor (BAFFR). Significant reduced blood B-cell numbers and BAFFR levels were observed in line with a dysregulation in BAFF–BAFFR signaling. The elevated frequency of PD-1+ dysfunctional Tfh cells composed predominantly by Th1 phenotype was observed at disease onset and during follow-up. This case report describes a patient progressing to T1D on a BAFFR-mediated immunodysregulatory background, suggesting a role of BAFF–BAFFR signaling in islet-specific tolerance and T1D progression.
Immune responses in COVID-19 and tuberculosis coinfection: A scoping review
Authors: Flores-Lovon Kevin , Ortiz-Saavedra Brando , Cueva-Chicaña Luis A. , Aperrigue-Lira Shalom , Montes-Madariaga Elizbet S. , Soriano-Moreno David R. , Bell Brett , Macedo Rodney 
Published: August 2022

Background and aimPatients with COVID-19 and tuberculosis coinfection are at an increased risk of severe disease and death. We therefore sought to evaluate the current evidence which assessed the immune response in COVID-19 and tuberculosis coinfectionMethodsWe searched Pubmed/MEDLINE, EMBASE, Scopus, and Web of Science to identify articles published between 2020 and 2021. We included observational studies evaluating the immune response in patients with tuberculosis and COVID-19 compared to patients with COVID-19 alone.ResultsFour cross-sectional studies (372 participants) were identified. In patients with asymptomatic COVID-19 and latent tuberculosis (LTBI), increased cytokines, chemokines, growth factors and humoral responses were found. In addition, patients with symptomatic COVID-19 and LTBI had higher leukocytes counts and less inflammation. Regarding patients with COVID-19 and active tuberculosis (aTB), they exhibited decreased total lymphocyte counts, CD4 T cells specific against SARS-CoV-2 and responsiveness to SARS-CoV-2 antigens compared to patients with only COVID-19.ConclusionAlthough the evidence is limited, an apparent positive immunomodulation is observed in patients with COVID-19 and LTBI. On the other hand, patients with COVID-19 and aTB present a dysregulated immune response. Longitudinal studies are needed to confirm these findings and expand knowledge.
Acute changes in free and extracellular vesicle-associated circulating miRNAs and myokine profile in professional sky-runners during the Gran Sasso d’Italia vertical run
Authors: Faraldi M. , Sansoni V. , Perego S. , Gomarasca M. , Gerosa L. , Ponzetti M. , Rucci N. , Banfi G. , Lombardi G. 
Published: August 2022

The modification of gene expression profile, a first step in adaptation to exercise, leads to changes in the level of molecules associated with skeletal muscle activity and energy metabolism—such as myokines—as well as those involved in their transcriptional regulation, like microRNA. This study aimed to investigate the influence of strenuous exercise on circulating microRNAs and their possible association with myokine response. Pre-competition and post-competition plasma samples were collected from 14 male athletes participating in a vertical run (+1,000 m gain, 3,600 m length). Circulating total (t-miRNA) and extracellular vesicle-associated (EV-miRNA) miRNAs were extracted from the pooled plasma. Nanoparticle tracking analysis was performed to investigate pre- and post-competition EV concentration and size distribution. A panel of 179 miRNAs was assayed by qPCR and analyzed by Exiqon GenEx v6 normalized on the global mean. t-miRNA and EV-miRNAs whose level was ≥5-fold up- or down-regulated were validated for each single subject. Target prediction on MirWalk v3.0, Gene-Ontology, and pathway enrichment analysis on Panther v17.0 were performed to define the potential biological role of the identified miRNAs. A panel of 14 myokines was assayed in each sample by a multiplex immunoassay. In whole plasma, five miRNAs were upregulated and two were downregulated; in the EV fraction, five miRNAs were upregulated and three were downregulated. Nanoparticle tracking analysis revealed a similar EV size distribution in pre- and post-competition samples and a decreased concentration in post-competition samples related to pre-competition samples. Gene-Ontology and pathway enrichment analysis revealed that the identified t-miRNAs and EV-miRNAs were potentially involved in metabolism regulation in response to exercise. Correlation between fold-change of the post-competition relative to pre-competition plasma level of both t-miRNAs and EV-miRNAs and myokines further confirmed these results. This study provides an example of a systemic response to acute endurance exercise, in which circulating miRNAs play a pivotal role.
The influence of mindfulness-based interventions on the academic performance of students measured by their GPA. A systematic review and meta-analysis
Authors: Ostermann Thomas , Pawelkiwitz Martin , Cramer Holger 
Published: August 2022

Objective: Mindfulness-based interventions are increasingly used in health, economic and educational systems. There are numerous studies demonstrating the effectiveness of mindfulness-based interventions in the educational sectors (primary, secondary, and tertiary). This systematic review and meta-analysis assessed the current state of research on the effectiveness of mindfulness-based interventions on the academic performance of students as measured by their grade point average (GPA).Methods: Literature search was conducted in Psychology and Behavioral Sciences Collection, PsycARTICLES, PubMed, and Google Scholar through March 2022. The inclusion criteria were: (1) the use of GPA as a measure of students’ academic performance, (2) a sample that was subjected to a mindfulness-based intervention without medical indication, (3) the student status of the subjects. Meta-analysis was conducted using a random effects model with the generic inverse variance method.Results: The search included a total of 759 studies, of which six randomized controlled trials met the inclusion criteria. In these trials, significant group differences for GPA were found with effect sizes ranging from d = 0.16–1.62 yielding a significant overall effect of d = 0.42 (95% CI: 0.15–0.69) and a low magnitude of heterogeneity of I2 = 37%.Discussion: In conclusion, the first results of this emerging research field seem promising. However, the exact mechanisms of action are still unclear.
Bilateral Dysfunction of Otolith Pathway in Patients With Unilateral Idiopathic BPPV Detected by ACS-VEMPs
Authors: Niu Xiaorong , Han Peng , Duan Maoli , Chen Zichen , Hu Juan , Chen Yanfei , Xu Min , Ren Pengyu , Zhang Qing 
Published: August 2022

ObjectiveTo observe the functional status of the otolith pathway in patients with unilateral idiopathic benign paroxysmal positional vertigo (BPPV) by combining air-conducted sound elicited cervical vestibular-evoked myogenic potential (ACS-cVEMP) and ocular vestibular-evoked myogenic potential (ACS-oVEMP).MethodsOne hundred and eighty patients with BPPV were recruited for conventional cVEMP and oVEMP tests. The abnormal rates of VEMPs were compared between BPPV patients and control participants.ResultsThe abnormal rates of cVEMP and oVEMP in BPPV patients were 46.7% (84/180) and 57.2% (103/180) in affected ears, respectively, and 45.0% (81/180) and 56.7% (102/180) in unaffected ears, respectively; both were significantly higher than the abnormal rates of cVEMP and oVEMP in normal control ears. Compared with normal subjects, the cVEMP response rate was lower in affected and unaffected ears in BPPV patients. The abnormal rates of cVEMP and oVEMP were 48.1% (76/158) and 57.6% (91/158) in patients with posterior semicircular canal BPPV, and 36.4% (8/22) and 54.5% (12/22) in lateral semicircular canal BPPV. There was no significant difference in VEMP abnormalities between posterior semicircular canal BPPV and lateral semicircular canal BPPV.ConclusionThe prevalence of abnormal cVEMPs and oVEMPs in both affected and unaffected ears of patients with BPPV was significantly higher than that observed in the control group. The pathological mechanism of unilateral idiopathic BPPV may be associated with bilateral degeneration of otolith pathways.