bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing the effects of burn severity on post-fire tree structures using the fused drone and mobile laser scanning point clouds
Authors: Qi Yangqian , Coops Nicholas C. , Daniels Lori D. , Butson Christopher R. 
Published: August 2022

Wildfires burn heterogeneously across the landscape and create complex forest structures. Quantifying the structural changes in post-fire forests is critical to evaluating wildfire impacts and providing insights into burn severities. To advance the understanding of burn severities at a fine scale, forest structural attributes at the individual tree level need to be examined. The advent of drone laser scanning (DLS) and mobile laser scanning (MLS) has enabled the acquisition of high-density point clouds to resolve fine structures of individual trees. Yet, few studies have used DLS and MLS data jointly to examine their combined capability to describe post-fire forest structures. To assess the impacts of the 2017 Elephant Hill wildfire in British Columbia, Canada, we scanned trees that experienced a range of burn severities 2 years post-fire using both DLS and MLS. After fusing the DLS and MLS data, we reconstructed quantitative structure models to compute 14 post-fire biometric, volumetric, and crown attributes. At the individual tree level, our data suggest that smaller pre-fire trees tend to experience higher levels of crown scorch than larger pre-fire trees. Among trees with similar pre-fire sizes, those within mature stands (age class: &gt; 50 years) had lower levels of crown scorch than those within young stands (age class: 15—50 years). Among pre-fire small- and medium-diameter trees, those experiencing high crown scorch had smaller post-fire crowns with unevenly distributed branches compared to unburned trees. In contrast, pre-fire large-diameter trees were more resistant to crown scorch. At the plot level, low-severity fires had minor effects, moderate-severity fires mostly decreased tree height, and high-severity fires significantly reduced diameter at breast height, height, and biomass. Our exploratory factor analyses further revealed that stands dominated by trees with large crown sizes and relatively wide spacing could burn less severely than stands characterized by regenerating trees with high crown fuel density and continuity. Overall, our results demonstrate that fused DLS-MLS point clouds can be effective in quantifying post-fire tree structures, which facilitates foresters to develop site-specific management plans. The findings imply that the management of crown fuel abundance and configuration could be vital to controlling burn severities.
Detecting slow-moving landslides using InSAR phase-gradient stacking and deep-learning network
Authors: Fu Lv , Zhang Qi , Wang Teng , Li Weile , Xu Qiang , Ge Daqing 
Published: August 2022

Landslides are a major geohazard that endangers human lives and properties. Recently, efforts have been made to use Synthetic Aperture Radar Interferometry (InSAR) for landslide monitoring. However, it is still difficult to effectively and automatically identify slow-moving landslides distributed over a large area due to phase unwrapping errors, decorrelation, troposphere turbulence and computational requirements. In this study, we develop a new approach combining phase-gradient stacking and a deep-learning network based on YOLOv3 to automatically detect slow-moving landslides from large-scale interferograms. Using Sentinel-1 SAR images acquired from 2014 to 2020, we developed a burst-based, phase-gradient stacking algorithm to sum up phase gradients in short-temporal-baseline interferograms along the azimuth and range directions. The stacked phase gradients clearly reveal the characteristics of localized surface deformation that is mainly caused by slow-moving landslides and avoids the errors due to phase unwrapping in partially decorrelated areas and atmospheric effects. Then, we trained the improved Attention-YOLOv3 network with stacked phase-gradient maps of manually labeled landslides to achieve quick and automatic detection. We applied our method in an ∼180,000 km2 area of southwestern China and identified 3,366 slow-moving landslides. By comparing the results with optical imagery and previously published landslides in this region, the proposed method can achieve automatic detection over a large area precisely and efficiently. From the derived landslide density map, we determined that most landslides are distributed along the three large rivers and their branches. In addition to some counties with known high-density landslides, approximately 10 more counties with high landslide density were exposed, which should attract more attention to their risks for geohazards. This application demonstrates the potential value of our newly developed method for slow-moving landslide detection over a nation-wide area, which can be employed before applying more time-consuming time-series InSAR analysis.
Exposure to fenvalerate and tebuconazole exhibits combined acute toxicity in zebrafish and behavioral abnormalities in larvae
Authors: Yao Chunlian , Huang Lan , Li Changsheng , Nie Dongxing , Chen Yajie , Guo Xuanjun , Cao Niannian , Li Xuefeng , Pang Sen 
Published: August 2022

In aquatic ecosystems, pesticide residues meanly present as mixtures of varying complexity, which may lead to compound pollution of organisms. Therefore, it is of great practical importance to evaluate the combined toxic effects of pesticides. In this study, the mixture acute toxicities of fenvalerate with tebuconazole on zebrafish larvae and adults were investigated. The effects of mixture toxicity on swimming behavior of larvae were also analyzed. The mixture acute toxicity of the systems showed antagonistic effects on adult zebrafish when the mixing ratios of fenvalerate and tebuconazole were equal, but the other two ratios of the mixes both showed synergistic effects. The strongest synergistic effect was observed when fenvalerate was mixed with tebuconazole in the ratio of 8:2. The swimming behavior of zebrafish larvae was significantly inhibited after exposure to single or mixed systems for 2 days. However, significant up-regulation of behavioral indicators in zebrafish larvae was observed at the beginning of exposure in the mixture exposure groups. The results showed that fenvalerate and tebuconazole had the risk of synergistic toxic effect on zebrafish. It is recommended that the simultaneous use of both pesticides in agricultural activities near water bodies should be scientifically controlled to avoid adverse effects on aquatic organisms.
Molecular mediators of the association between child obesity and mental health
Authors: Handakas Evangelos , Xu Yiwen , Segal Alexa Blair , Huerta Maria Carmen , Bowman Kirsty , Howe Laura D. , Sassi Franco , Robinson Oliver 
Published: August 2022

Biological mechanisms underlying the association between obesity and depression remain unclear. We investigated the role of metabolites and DNA methylation as mediators of the relationship between childhood obesity and subsequent poor mental health in the English Avon Longitudinal Study of Parents and Children. Obesity was defined according to United Kingdom Growth charts at age 7 years and mental health through the Short Mood and Feelings Questionnaire (SMFQ) completed at age 11 years. Metabolites and DNA methylation were measured by nuclear magnetic resonance spectroscopy and Illumina array in blood at the age of 7 years. The associations between obesity and SMFQ score, as continuous count data or using cut-offs to define depressive symptoms (SMFQ &gt;7) or depression (SMFQ &gt;11), were tested using adjusted Poisson and logistic regression. Candidate metabolite mediators were identified through metabolome-wide association scans for obesity and SMFQ score, correcting for false-discovery rate. Candidate DNA methylation mediators were identified through testing the association of putative BMI-associated CpG sites with SMFQ scores, correcting for look-up false-discovery rate. Mediation by candidate molecular markers was tested. Two-sample Mendelian randomization (MR) analyses were additionally applied to test causal associations of metabolites with depression in independent adult samples. 4,018 and 768 children were included for metabolomics and epigenetics analyses, respectively. Obesity at 7 years was associated with a 14% increase in SMFQ score (95% CI: 1.04, 1.25) and greater odds of depression (OR: 1.46 (95% CI: 0.78, 2.38) at 11 years. Natural indirect effects (mediating pathways) between obesity and depression for tyrosine, leucine and conjugated linoleic acid were 1.06 (95% CI: 1.00, 1.13, proportion mediated (PM): 15%), 1.04 (95% CI: 0.99, 1.10, PM: 9.6%) and 1.06 (95% CI: 1.00, 1.12, PM: 13.9%) respectively. In MR analysis, one unit increase in tyrosine was associated with 0.13 higher log odds of depression (p = 0.1). Methylation at cg17128312, located in the FBXW9 gene, had a natural indirect effect of 1.05 (95% CI: 1.01,1.13, PM: 27%) as a mediator of obesity and SMFQ score. Potential biologically plausible mechanisms involving these identified molecular features include neurotransmitter regulation, inflammation, and gut microbiome modulation. These results require replication in further observational and mechanistic studies.
Identifying hub genes and miRNAs in Crohn’s disease by bioinformatics analysis
Authors: Sun Yuxin , Cai Daxing , Hu Weitao , Fang Taiyong 
Published: August 2022

Introduction:Crohn’s disease (CD) is a disease that manifests mainly as chronic inflammation of the gastrointestinal tract, which is still not well understood in terms of its pathogenesis. The aim of this study was to use bioinformatics analysis to identify differentially expressed genes (DEGs) and miRNAs with diagnostic and therapeutic potential in CD.Materials and methods:Three CD datasets (GSE179285, GSE102133, GSE75214) were downloaded from the Gene Expression Omnibus (GEO) database. DEGs between normal and CD tissues were identified using the GEO2R online tool. The Gene Ontology (GO) term and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of the DEGs were conducted using the clusterProfiler function in the R package. Protein-protein interaction network (PPI) analysis and visualization were performed with STRING and Cytoscape. Ten hub genes were identified using cytoHubba’s MCC algorithm and validated with datasets GSE6731 and GSE52746. Finally, the miRNA gene regulatory network was constructed by Cytoscape and NetworkAnalyst to predict potential microRNAs (miRNAs) associated with DEGs.Results:A total of 97 DEGs were identified, consisting of 88 downregulated genes and 9 upregulated genes. The enriched functions and pathways of the DEGs include immune system process, response to stress, response to cytokine and extracellular region. KEGG pathway analysis indicates that the genes were significantly enriched in Cytokine-cytokine receptor interaction, IL-17 signaling pathway, Rheumatoid arthritis and TNF signaling pathway. In combination with the results of the protein-protein interaction (PPI) network and CytoHubba, 10 hub genes including IL1B, CXCL8, CXCL10, CXCL1, CXCL2, CXCL5, ICAM1, IL1RN, TIMP1 and MMP3 were selected. Based on the DEG-miRNAs network construction, 5 miRNAs including hsa-mir-21-5p, hsa-mir-93-5p, hsa-mir-98-5p, hsa-mir-1-3p and hsa-mir-335-5p were identified as potential critical miRNAs.Conclusion:In conclusion, a total of 97 DEGs, 10 hub genes and 5 miRNAs that may be involved in the progression or occurrence of CD were identified in this study, which could be regarded as biomarkers of CD.
Effect of low-dose dexmedetomidine on sleep quality in postoperative patients with mechanical ventilation in the intensive care unit: A pilot randomized trial
Authors: Sun Yue-Ming , Zhu Sai-Nan , Zhang Cheng , Li Shuang-Ling , Wang Dong-Xin 
Published: August 2022

BackgroundSleep disturbances are prevalent in patients requiring invasive mechanical ventilation in the intensive care unit (ICU) and are associated with worse outcomes. Sedative-dose dexmedetomidine may improve sleep quality in this patient population but is associated with adverse events. Herein, we tested the effect of low-dose dexmedetomidine infusion on nighttime sleep quality in postoperative ICU patients with invasive ventilation.MethodsIn this pilot randomized trial, 80 adult patients who were admitted to the ICU after non-cardiac surgery and required invasive mechanical ventilation were randomized to receive either low-dose dexmedetomidine (0.1 to 0.2 μg/kg/h, n = 40) or placebo (n = 40) for up to 72 h. The primary endpoint was overall subjective sleep quality measured using the Richards–Campbell Sleep Questionnaire (score ranges from 0 to 100, with a higher score indicating better quality) in the night of surgery. Secondary outcomes included sleep structure parameters monitored with polysomnography from 9:00 PM on the day of surgery to the next 6:00 AM.ResultsAll 80 patients were included in the intention-to-treat analysis. The overall subjective sleep quality was median 52 (interquartile 20, 66) with placebo vs. 61 (27, 79) with dexmedetomidine, and the difference was not statistically significant (median difference 8; 95% CI: −2, 22; P = 0.120). Among 68 patients included in sleep structure analysis, those in the dexmedetomidine group tended to have longer total sleep time [median difference 54 min (95% CI: −4, 120); P = 0.061], higher sleep efficiency [median difference 10.0% (95% CI: −0.8%, 22.3%); P = 0.060], lower percentage of stage N1 sleep [median difference −3.9% (95% CI: −11.8%, 0.5%); P = 0.090], higher percentage of stage N3 sleep [median difference 0.0% (95% CI: 0.0%, 0.4%); P = 0.057], and lower arousal index [median difference −0.9 (95% CI −2.2, 0.1); P = 0.091] but not statistically significant. There were no differences between the two groups regarding the incidence of adverse events.ConclusionAmong patients admitted to the ICU after surgery with intubation and mechanical ventilation, low-dose dexmedetomidine infusion did not significantly improve the sleep quality pattern, although there were trends of improvement. Our findings support the conduct of a large randomized trial to investigate the effect of low-dose dexmedetomidine in this patient population.Clinical trial registrationClinicalTrial.gov, identifier: NCT03335527.
Third dose of anti-SARS-CoV-2 inactivated vaccine for patients with RA: Focusing on immunogenicity and effects of RA drugs
Authors: Zhao Ting , Wang Bo , Shen Jiayan , Wei Yuanyuan , Zhu Youyang , Tian Xiaofang , Wen Guangfen , Xu Bonan , Fu Chenyang , Xie Zhaohu , Xi Yujiang , Li Zhenmin , Peng Jiangyun , Wu Yang , Tang Xiaohu , Wan Chunping , Pan Lei , Zhu Wenxin , Li Zhaofu , Qin Dongdong 
Published: August 2022

ObjectivesTo evaluate the immunogenicity of the third dose of inactivated SARS-CoV-2 vaccine in rheumatoid arthritis (RA) patients and explore the effect of RA drugs on vaccine immunogenicity.MethodsWe recruited RA patients (n = 222) and healthy controls (HC, n = 177) who had been injected with a third dose of inactivated SARS-CoV-2 vaccine, and their neutralizing antibody (NAb) titer levels were assessed.ResultsRA patients and HC were age- and gender-matched, and the mean interval between 3rd vaccination and sampling was comparable. The NAb titers were significantly lower in RA patients after the third immunization compared with HC. The positive rate of NAb in HC group was 90.4%, while that in RA patients was 80.18%, and the difference was significant. Furthermore, comparison of NAb titers between RA treatment subgroups and HC showed that the patients in the conventional synthetic (cs) disease-modifying anti-rheumatic drugs (DMARDs) group exhibited no significant change in NAb titers, while in those receiving the treatment of biological DMARDs (bDMARDs), Janus Kinase (JAK) inhibitors, and prednisone, the NAb titers were significantly lower. Spearman correlation analysis revealed that NAb responses to SARS-CoV-2 in HC did differ significantly according to the interval between 3rd vaccination and sampling, but this finding was not observed in RA patients. In addition, NAb titers were not significantly correlated with RA-related laboratory indicators, including RF-IgA, RF-IgG, RF-IgM, anti-CCP antibody; C-RP; ESR; NEUT% and LYMPH%.ConclusionSerum antibody responses to the third dose of vaccine in RA patients were weaker than HC. Our study will help to evaluate the efficacy and safety of booster vaccination in RA patients and provide further guidance for adjusting vaccination strategies.
Acceptance of clinical artificial intelligence among physicians and medical students: A systematic review with cross-sectional survey
Authors: Chen Mingyang , Zhang Bo , Cai Ziting , Seery Samuel , Gonzalez Maria J. , Ali Nasra M. , Ren Ran , Qiao Youlin , Xue Peng , Jiang Yu 
Published: August 2022

BackgroundArtificial intelligence (AI) needs to be accepted and understood by physicians and medical students, but few have systematically assessed their attitudes. We investigated clinical AI acceptance among physicians and medical students around the world to provide implementation guidance.Materials and methodsWe conducted a two-stage study, involving a foundational systematic review of physician and medical student acceptance of clinical AI. This enabled us to design a suitable web-based questionnaire which was then distributed among practitioners and trainees around the world.ResultsSixty studies were included in this systematic review, and 758 respondents from 39 countries completed the online questionnaire. Five (62.50%) of eight studies reported 65% or higher awareness regarding the application of clinical AI. Although, only 10–30% had actually used AI and 26 (74.28%) of 35 studies suggested there was a lack of AI knowledge. Our questionnaire uncovered 38% awareness rate and 20% utility rate of clinical AI, although 53% lacked basic knowledge of clinical AI. Forty-five studies mentioned attitudes toward clinical AI, and over 60% from 38 (84.44%) studies were positive about AI, although they were also concerned about the potential for unpredictable, incorrect results. Seventy-seven percent were optimistic about the prospect of clinical AI. The support rate for the statement that AI could replace physicians ranged from 6 to 78% across 40 studies which mentioned this topic. Five studies recommended that efforts should be made to increase collaboration. Our questionnaire showed 68% disagreed that AI would become a surrogate physician, but believed it should assist in clinical decision-making. Participants with different identities, experience and from different countries hold similar but subtly different attitudes.ConclusionMost physicians and medical students appear aware of the increasing application of clinical AI, but lack practical experience and related knowledge. Overall, participants have positive but reserved attitudes about AI. In spite of the mixed opinions around clinical AI becoming a surrogate physician, there was a consensus that collaborations between the two should be strengthened. Further education should be conducted to alleviate anxieties associated with change and adopting new technologies.
Impact of queuosine modification of endogenous E. coli tRNAs on sense codon reassignment
Authors: Tittle Jillyn M. , Schwark David G. , Biddle Wil , Schmitt Margaret A. , Fisk John D. 
Published: August 2022

The extent to which alteration of endogenous tRNA modifications may be exploited to improve genetic code expansion efforts has not been broadly investigated. Modifications of tRNAs are strongly conserved evolutionarily, but the vast majority of E. coli tRNA modifications are not essential. We identified queuosine (Q), a non-essential, hypermodified guanosine nucleoside found in position 34 of the anticodons of four E. coli tRNAs as a modification that could potentially be utilized to improve sense codon reassignment. One suggested purpose of queuosine modification is to reduce the preference of tRNAs with guanosine (G) at position 34 of the anticodon for decoding cytosine (C) ending codons over uridine (U) ending codons. We hypothesized that introduced orthogonal translation machinery with adenine (A) at position 34 would reassign U-ending codons more effectively in queuosine-deficient E. coli. We evaluated the ability of introduced orthogonal tRNAs with AUN anticodons to reassign three of the four U-ending codons normally decoded by Q34 endogenous tRNAs: histidine CAU, asparagine AAU, and aspartic acid GAU in the presence and absence of queuosine modification. We found that sense codon reassignment efficiencies in queuosine-deficient strains are slightly improved at Asn AAU, equivalent at His CAU, and less efficient at Asp GAU codons. Utilization of orthogonal pair-directed sense codon reassignment to evaluate competition events that do not occur in the standard genetic code suggests that tRNAs with inosine (I, 6-deaminated A) at position 34 compete much more favorably against G34 tRNAs than Q34 tRNAs. Continued evaluation of sense codon reassignment following targeted alterations to endogenous tRNA modifications has the potential to shed new light on the web of interactions that combine to preserve the fidelity of the genetic code as well as identify opportunities for exploitation in systems with expanded genetic codes.
Skill-learning by observation-training with patients after traumatic brain injury
Authors: Avraham Einat , Sacher Yaron , Maaravi-Hesseg Rinatia , Karni Avi , Doron Ravid 
Published: August 2022

Traumatic brain injury (TBI) is a major cause of death and disability in Western society, and often results in functional and neuropsychological abnormalities. Memory impairment is one of the most significant cognitive implications after TBI. In the current study we investigated procedural memory acquisition by observational training in TBI patients. It was previously found that while practicing a new motor skill, patients engage in all three phases of skill learning–fast acquisition, between-session consolidation, and long-term retention, though their pattern of learning is atypical compared to healthy participants. A different set of studies showed that training by observing a motor task, generally prompted effective acquisition and consolidation of procedural knowledge in healthy participants. The aim of our study was to (i) evaluate the potential benefit of action observation in TBI patients. (ii) Examine the possibility of general improvement in performance between the first (24 h post-training) and second (2 weeks post-training) stage of the study. (iii) Investigate the link between patients’ ability to benefit from observational learning (viaperformance gains–speed and accuracy) and common measures of injury (such as severity of injury, functional and cognitive measures).Materials and methodsPatients hospitalized after moderate to severe TBI, were trained by observation for the finger opposition sequence (FOS) motor task. They were then tested for the observation-trained sequence (A) and a similar control sequence (B), at two different time-points (24 h post-training and 2 weeks later).Results revealed(i) a significant difference in performance between the trained (A) and untrained (B) sequences, in favor of the trained sequence. (ii) An increase in performance for both sequences A and B toward the second (retention) session. (iii) The advantage for sequence A was stable and preserved also in the second session. (iv) Participants with lower moderate Functional Independence Measure (FIM) scores gained more from observational-procedural learning, compared with patients with higher functional abilities.ConclusionOverall, these findings support the notion that TBI patients may achieve procedural memory consolidation and retention through observational learning. Moreover, different functional traits may predict the outcomes of observational training in different patients. These findings may have significant practical implications in the future, regarding skill acquisition methods in TBI patients.