bluuebunny/crossref_metadata_2025_split huggingface dataset:
Advanced optical assessment and modeling of extrusion bioprinting
Authors: Lamberger Zan , Schubert Dirk W. , Buechner Margitta , Cabezas Nathaly Chicaiza , Schrüfer Stefan , Murenu Nicoletta , Schaefer Natascha , Lang Gregor 
Published: June 2024

AbstractIn the context of tissue engineering, biofabrication techniques are employed to process cells in hydrogel-based matrices, known as bioinks, into complex 3D structures. The aim is the production of functional tissue models or even entire organs. The regenerative production of biological tissues adheres to a multitude of criteria that ultimately determine the maturation of a functional tissue. These criteria are of biological nature, such as the biomimetic spatial positioning of different cell types within a physiologically and mechanically suitable matrix, which enables tissue maturation. Furthermore, the processing, a combination of technical procedures and biological materials, has proven highly challenging since cells are sensitive to stress, for example from shear and tensile forces, which may affect their vitality. On the other hand, high resolutions are pursued to create optimal conditions for subsequent tissue maturation. From an analytical perspective, it is prudent to first investigate the printing behavior of bioinks before undertaking complex biological tests. According to our findings, conventional shear rheological tests are insufficient to fully characterize the printing behavior of a bioink. For this reason, we have developed optical methods that, complementarily to the already developed tests, allow for quantification of printing quality and further viscoelastic modeling of bioinks.
Multivariate testing and effect size measures for batch effect evaluation in radiomic features
Authors: Horng Hannah , Scott Christopher , Winham Stacey , Jensen Matthew , Pantalone Lauren , Mankowski Walter , Kerlikowske Karla , Vachon Celine M. , Kontos Despina , Shinohara Russell T. 
Published: June 2024

AbstractWhile precision medicine applications of radiomics analysis are promising, differences in image acquisition can cause “batch effects” that reduce reproducibility and affect downstream predictive analyses. Harmonization methods such as ComBat have been developed to correct these effects, but evaluation methods for quantifying batch effects are inconsistent. In this study, we propose the use of the multivariate statistical test PERMANOVA and the Robust Effect Size Index (RESI) to better quantify and characterize batch effects in radiomics data. We evaluate these methods in both simulated and real radiomics features extracted from full-field digital mammography (FFDM) data. PERMANOVA demonstrated higher power than standard univariate statistical testing, and RESI was able to interpretably quantify the effect size of site at extremely large sample sizes. These methods show promise as more powerful and interpretable methods for the detection and quantification of batch effects in radiomics studies.
Trajectory-based global sensitivity analysis in multiscale models
Authors: Bazyleva Valentina , Garibay Victoria M. , Roy Debraj 
Published: June 2024

AbstractThis research introduces a novel global sensitivity analysis (GSA) framework for agent-based models (ABMs) that explicitly handles their distinctive features, such as multi-level structure and temporal dynamics. The framework uses Grassmannian diffusion maps to reduce output data dimensionality and sparse polynomial chaos expansion (PCE) to compute sensitivity indices for stochastic input parameters. To demonstrate the versatility of the proposed GSA method, we applied it to a non-linear system dynamics model and epidemiological and economic ABMs, depicting different dynamics. Unlike traditional GSA approaches, the proposed method enables a more general estimation of parametric sensitivities spanning from the micro level (individual agents) to the macro level (entire population). The new framework encourages the use of manifold-based techniques in uncertainty quantification, enhances understanding of complex spatio-temporal processes, and equips ABM practitioners with robust tools for detailed model analysis. This empowers them to make more informed decisions when developing, fine-tuning, and verifying models, thereby advancing the field and improving routine practice for GSA in ABMs.
Nasal cathelicidin is expressed in early life and is increased during mild, but not severe respiratory syncytial virus infection
Authors: Sintoris Sofia , Binkowska Justyna M. , Gillan Jonathan L. , Zuurbier Roy P. , Twynam-Perkins Jonathan , Kristensen Maartje , Melrose Lauren , Parga Paula Lusaretta , Rodriguez Alicia Ruiz , Chu Mei Ling , van Boeckel Sara R. , Wildenbeest Joanne G. , Bowdish Dawn M. E. , Currie Andrew J. , Thwaites Ryan S. , Schwarze Jurgen , van Houten Marlies A. , Boardman James P. , Cunningham Steve , Bogaert Debby , Davidson Donald J. 
Published: June 2024

AbstractRespiratory syncytial virus is the major cause of acute lower respiratory tract infections in young children, causing extensive mortality and morbidity globally, with limited therapeutic or preventative options. Cathelicidins are innate immune antimicrobial host defence peptides and have antiviral activity against RSV. However, upper respiratory tract cathelicidin expression and the relationship with host and environment factors in early life, are unknown. Infant cohorts were analysed to characterise early life nasal cathelicidin levels, revealing low expression levels in the first week of life, with increased levels at 9 months which are comparable to 2-year-olds and healthy adults. No impact of prematurity on nasal cathelicidin expression was observed, nor were there effects of sex or birth mode, however, nasal cathelicidin expression was lower in the first week-of-life in winter births. Nasal cathelicidin levels were positively associated with specific inflammatory markers and demonstrated to be associated with microbial community composition. Importantly, levels of nasal cathelicidin expression were elevated in infants with mild RSV infection, but, in contrast, were not upregulated in infants hospitalised with severe RSV infection. These data suggest important relationships between nasal cathelicidin, upper airway microbiota, inflammation, and immunity against RSV infection, with interventional potential.
Insights into structure, codon usage, repeats, and RNA editing of the complete mitochondrial genome of Perilla frutescens (Lamiaceae)
Authors: Wang Ru , Luo Yongjian , Lan Zheng , Qiu Daoshou 
Published: June 2024

Abstract

Perilla frutescens (L.) Britton, a member of the Lamiaceae family, stands out as a versatile plant highly valued for its unique aroma and medicinal properties. Additionally, P. frutescens seeds are rich in Îś-linolenic acid, holding substantial economic importance. While the nuclear and chloroplast genomes of P. frutescens have already been documented, the complete mitochondrial genome sequence remains unreported. To this end, the sequencing, annotation, and assembly of the entire Mitochondrial genome of P. frutescens were hereby conducted using a combination of Illumina and PacBio data. The assembled P. frutescens mitochondrial genome spanned 299,551 bp and exhibited a typical circular structure, involving a GC content of 45.23%. Within the genome, a total of 59 unique genes were identified, encompassing 37 protein-coding genes, 20 tRNA genes, and 2 rRNA genes. Additionally, 18 introns were observed in 8 protein-coding genes. Notably, the codons of the P. frutescens mitochondrial genome displayed a notable A/T bias. The analysis also revealed 293 dispersed repeat sequences, 77 simple sequence repeats (SSRs), and 6 tandem repeat sequences. Moreover, RNA editing sites preferentially produced leucine at amino acid editing sites. Furthermore, 70 sequence fragments (12,680 bp) having been transferred from the chloroplast to the mitochondrial genome were identified, accounting for 4.23% of the entire mitochondrial genome. Phylogenetic analysis indicated that among Lamiaceae plants, P. frutescens is most closely related to Salvia
miltiorrhiza and Platostoma chinense. Meanwhile, inter-species Ka/Ks results suggested that Ka/Ks

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for 28 PCGs, indicating that these genes were evolving under purifying selection. Overall, this study enriches the mitochondrial genome data for P. frutescens and forges a theoretical foundation for future molecular breeding research.
Investigation on the influence of the skin tone on hyperspectral imaging for free flap surgery
Authors: Pachyn Ester , Aumiller Maximilian , Freymüller Christian , Linek Matthäus , Volgger Veronika , Buchner Alexander , Rühm Adrian , Sroka Ronald 
Published: June 2024

AbstractHyperspectral imaging (HSI) is a new emerging modality useful for the noncontact assessment of free flap perfusion. This measurement technique relies on the optical properties within the tissue. Since the optical properties of hemoglobin (Hb) and melanin overlap, the results of the perfusion assessment and other tissue-specific parameters are likely to be distorted by the melanin, especially at higher melanin concentrations. Many spectroscopic devices have been shown to struggle with a melanin related bias, which results in a clinical need to improve non-invasive perfusion assessment, especially for a more pigmented population. This study investigated the influence of skin tones on tissue indices measurements using HSI. In addition, other factors that might affect HSI, such as age, body mass index (BMI), sex or smoking habits, were also considered. Therefore, a prospective feasibility study was conducted, including 101 volunteers from whom tissue indices measurements were performed on 16 different body sites. Skin tone classification was performed using the Fitzpatrick skin type classification questionnaire, and the individual typology angle (ITA) acquired from the RGB images was calculated simultaneously with the measurements. Tissue indices provided by the used HSI-device were correlated to the possible influencing factors. The results show that a dark skin tone and, therefore, higher levels of pigmentation influence the HSI-derived tissue indices. In addition, possible physiological factors influencing the HSI-measurements were found. In conclusion, the HSI-based tissue indices can be used for perfusion assessment for people with lighter skin tone levels but show limitations in people with darker skin tones. Furthermore, it could be used for a more individual perfusion assessment if different physiological influencing factors are respected.
Homeobox and Polycomb target gene methylation in human solid tumors
Authors: Blanchett Reid , Lau Kin H. , Pfeifer Gerd P. 
Published: June 2024

AbstractDNA methylation is an epigenetic mark that plays an important role in defining cancer phenotypes, with global hypomethylation and focal hypermethylation at CpG islands observed in tumors. These methylation marks can also be used to define tumor types and provide an avenue for biomarker identification. The homeobox gene class is one that has potential for this use, as well as other genes that are Polycomb Repressive Complex 2 targets. To begin to unravel this relationship, we performed a pan-cancer DNA methylation analysis using sixteen Illumina HM450k array datasets from TCGA, delving into cancer-specific qualities and commonalities between tumor types with a focus on homeobox genes. Our comparisons of tumor to normal samples suggest that homeobox genes commonly harbor significant hypermethylated differentially methylated regions. We identified two homeobox genes, HOXA3 and HOXD10, that are hypermethylated in all 16 cancer types. Furthermore, we identified several potential homeobox gene biomarkers from our analysis that are uniquely methylated in only one tumor type and that could be used as screening tools in the future. Overall, our study demonstrates unique patterns of DNA methylation in multiple tumor types and expands on the interplay between the homeobox gene class and oncogenesis.
Railway contactless checkout process with identification assisted by gait recognition
Authors: Li Beibei , Zhu Jiansheng , Li Wen 
Published: June 2024

AbstractWith business process optimization, technological advancement, equipment capability enhancement, and other means, the Railway Passenger Service Department in China is consistently working to improve the efficiency and convenience of passenger entry and exit procedures at railway stations. Concerning passengers’ checkout, not only conventional identification approaches based on manual control, identification card, and magnetic thermal paper ticket are supported, but also a recent contactless identification process based on face recognition is applied in some stations. To further improve the contactless identification ability for checkout, an advanced contactless checkout process based on gait-augmented face recognition is innovatively put forward, in which a weakly-supervised body segmentation network named Dwsegnet and an improved GaitSet model are proposed. Through comparison with various models, the effectiveness of both Dwsegnet and the improved GaitSet is validated. Specifically, the contactless identification rate of gait-augmented face recognition is improved by 2.31% when compared to single-modal face recognition, which demonstrates the superiority of the proposed process.
Hyperthyroidism increases the risk of osteoarthritis in individuals aged 60–80 years
Authors: Zhao Jinlong , Liang Haodong , Liang Guihong , Hong Kunhao , Yang Weiyi , Luo Minghui , Zeng Lingfeng , Liu Jun 
Published: June 2024

AbstractTo elucidate the currently unknown relationship between hyperthyroidism and osteoarthritis (OA). During 2007–2012, 7,433 participants (hyperthyroidism patients = 125; OA patients = 675) were included in the National Health and Nutrition Examination Survey database. We used a weighted multivariable-adjusted logistic regression analysis to assess the association between hyperthyroidism and OA. We also assessed the causality of that relationship using publicly available genome-wide association study data and three Mendelian randomization (MR) analysis methods. The heterogeneity test, pleiotropy test, and leave-one-out tests were used for sensitivity analysis. In this cross-sectional study, after adjusting for potential confounding factors, we found that hyperthyroidism significantly (P = 0.018) increased the risk of OA (odds ratio [OR] = 2.23, 95% confidence interval [CI] = 1.2–4.17). Age-stratified analysis revealed that hyperthyroidism was associated with a greater risk of OA in the 60–80-year-old age group (OR = 2.86, 95% CI = 1.46–5.59, P = 0.002), with no significant association in the 18–59-year-old age group (all P > 0.05). The results of the inverse-variance weighting (IVW) analysis showed that hyperthyroidism increased the risk of OA (OR = 1.23, 95% CI = 1.04–1.46; P = 0.017). The weighted median estimator (WME) and MR-Egger method also confirmed this causal association (OR = 1.27 and OR = 1.32, respectively). The sensitivity analysis results confirmed the reliability of this conclusion. In addition, IVW-based reverse-MR analysis revealed that OA did not increase the risk of hyperthyroidism (OR = 1.02, 95% CI = 0.97–1.08; P = 0.449). Hyperthyroidism is associated with an increased risk of OA, but the underlying pathological mechanism still needs to be clarified in future research.
The Nurr1 ligand indole acetic acid hydrazide loaded onto ZnFe2O4 nanoparticles suppresses proinflammatory gene expressions in SimA9 microglial cells
Authors: Qasim Raneen , Thiab Tuqa Abu , Alhindi Tareq , Al-Hunaiti Afnan , Imraish Amer 
Published: June 2024

AbstractThe nuclear receptor-related factor 1 (Nurr1), an orphan nuclear receptor in microglia, has been recognized as a major player in attenuating the transcription of the pro-inflammatory genes to maintain CNS homeostasis. In this study, we investigate Nurr1 trans-repression activity by targeting this receptor with one of the indole derivatives 3-Indole acetic acid hydrazide (IAAH) loaded onto zinc iron oxide (ZnFe2O4) NPs coated with PEG. XRD, SEM, FTIR, UV–Vis spectroscopy, and DLS were used to characterize the synthesized IAAH-NPs. The anti-inflammatory properties of IAAH-NPs on LPS-stimulated SimA9 microglia were assayed by measuring pro-inflammatory cytokine gene expressions and protein levels using RT-PCR and ELISA, respectively. As a result, IAAH-NPs showed an ability to suppress pro-inflammatory genes, including IL-6, IL-1β, and TNF-α in LPS-stimulated SimA9 via targeting Nurr1. The current study suggests that ZnFe2O4 NPs as a delivery system can increase the efficiency of cellular uptake and enhance the IAAH ability to inhibit the pro-inflammatory cytokines. Collectively, we demonstrate that IAAH-NPs is a potential modulator of Nurr1 that combines nanotechnology as a delivery system to suppress neuroinflammation in CNS which opens a window for possible ambitious neuroprotective therapeutic approaches to neuro disorders.
Outcomes and factors associated with prolonged stays among patients admitted to adult intensive care unit in a resource-limited setting: a multicenter chart review
Authors: Bekele Tola Getachew , Melaku Birhanu , Demisse Lemlem Beza , Abza Legese Fekede , Assen Awol Seid 
Published: June 2024

AbstractThe length of stay in an intensive care unit is used as a benchmark for measuring resource consumption and quality of care and predicts a higher risk of readmission. The study aimed to assess the outcome and factors associated with prolonged intensive care unit stays among those admitted to adult intensive care units of selected public hospitals in Addis Ababa from January 1, 2022, to December 31, 2022. A multicenter retrospective chart review was conducted involving 409 adult patients. Binary logistic regression was used to assess factors associated with a prolonged stay and chi-square tests were used to assess associations and differences in outcomes for prolonged stays. The study, involving 409 of 421 individuals, revealed a predominantly male (55.0%) and the median age of study participants was 38, with an interquartile range (27, 55). Approximately 16.9% experienced prolonged stays, resulting in a 43.5% mortality rate. After adjustments for confounders, there were significant associations with prolonged stays for sedative/hypnotics, readmission, and complications. The study revealed that for every six patients admitted to the intensive care unit, one patient stayed longer, with nearly half experiencing mortality, demanding increased attention. The study emphasized the critical need for improvement in addressing associations between sedative/hypnotics, readmissions, complications, and prolonged stays.
Artificial neural network based on strong track and square root UKF for INS/GNSS intelligence integrated system during GPS outage
Authors: Yang Yi , Wang Xueyao , Zhang Nan , Gao Zhaohui , Li Yingliang 
Published: June 2024

AbstractWhen INS/GNSS (inertial navigation system/global navigation satellite system) integrated system is applied, it will be affected by the insufficient number of visible satellites, and even the satellite signal will be lost completely. At this time, the positioning error of INS accumulates with time, and the navigation accuracy decreases rapidly. Therefore, in order to improve the performance of INS/GNSS integration during the satellite signals interruption, a novel learning algorithm for neural network has been presented and used for intelligence integrated system in this article. First of all, determine the input and output of neural network for intelligent integrated system and a nonlinear model for weighs updating during neural network learning has been established. Then, the neural network learning based on strong tracking and square root UKF (unscented Kalman filter) is proposed for iterations of the nonlinear model. In this algorithm, the square root of the state covariance matrix is used to replace the covariance matrix in the classical UKF to avoid the filter divergence caused by the negative definite state covariance matrix. Meanwhile, the strong tracking coefficient is introduced to adjust the filter gain in real-time and improve the tracking capability to mutation state. Finally, an improved calculation method of strong tracking coefficient is presented to reduce the computational complexity in this algorithm. The results of the simulation test and the field-positioning data show that the proposed learning algorithm could improve the calculation stability and robustness of neural network. Therefore, the error accumulation of INS/GNSS integration is effectively compensated, and then the positioning accuracy of INS/GNSS intelligence integrated system has been improved.
Genome-wide identification of starch phosphorylase gene family in Rosa chinensis and expression in response to abiotic stress
Authors: Li Xu , Chen Yang , Zhang Zaiqi , He Qin , Tian Tingting , Jiao Yangmiao , Cao Liang 
Published: June 2024

AbstractChinese rose (Rosa chinensis) is an important ornamental plant, with economic, cultural, and symbolic significance. During the application of outdoor greening, adverse environments such as high temperature and drought are often encountered, which affect its application scope and ornamental quality. The starch phosphorylase (Pho) gene family participate in the synthesis and decomposition of starch, not only related to plant energy metabolism, but also plays an important role in plant stress resistance. The role of Pho in combating salinity and high temperature stress in R. chinensis remains unknown. In this work, 4 Phos from R. chinensis were detected with Pfam number of Pho (PF00343.23) and predicted by homolog-based prediction (HBP). The Phos are characterized by sequence lengths of 821 to 997 bp, and the proteins are predicted to subcellularly located in the plastid and cytoplasm. The regulatory regions of the Phos contain abundant stress and phytohormone-responsive cis-acting elements. Based on transcriptome analysis, the Phos were found to respond to abiotic stress factors such as drought, salinity, high temperature, and plant phytohormone of jasmonic acid and salicylic acid. The response of Phos to abiotic stress factors such as salinity and high temperature was confirmed by qRT-PCR analysis. To evaluate the genetic characteristics of Phos, a total of 69 Phos from 17 species were analyzed and then classified into 3 groups in phylogenetic tree. The collinearity analysis of Phos in R. chinensis and other species was conducted for the first time. This work provides a view of evolution for the Pho gene family and indicates that Phos play an important role in abiotic stress response of R. chinensis.
The influence of Chinese typography on information dissemination in graphic design: based on eye-tracking data
Authors: Chen Weilong , Yang Jiqiang , Wang Yiluo 
Published: June 2024

AbstractThe arrangement of Chinese characters has a significant impact on the visual effect and information dissemination in graphic design. In traditional Chinese layout, vertical arrangement of characters is predominant, but in recent times, there has been a gradual transition towards horizontal arrangement. To compare the influence of different character arrangement forms on visual meaning generation and information dissemination, This study employed an eye-tracking experiment to investigate two common Chinese character layouts in posters—horizontal and vertical, and collected data such as eye-tracking heatmap, pupil diameter and eye-tracking trajectory map. Based on objective eye-tracking data, combined with post-test interviews and questionnaire surveys, it was found that vertical character arrangement in Chinese typography is more effective in attracting visual attention and facilitating the expression and stimulating interest in viewing/reading under the premise of meeting formal requirements, which may provide guidance and inspiration for the practical application of Chinese characters in layout design, advertising design, packaging design, exhibition design, UI design, and other related fields.