bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring Multifunctional Markers of Biological Age in Farmed Gilthead Sea Bream (<em>Sparus aurata</em>). A Transcriptomic and Epigenetic Interplay for an Improved Fish Welfare Assessment Approach
Authors: Belenguer Álvaro , Naya-Català Fernando , Calduch-Giner Josep Alvar , Pérez-Sánchez Jaume 
Published: June 2024

DNA-methylation clocks inform not only about chronological but also biological age, which brings a high resolution and precise understanding of age-related pathology and physiology. Attempts based on transcriptomic and epigenetic approaches arise as integrative biomarkers linking the quantification of stress response with a given fitness trait and may help to identify biological age markers, also considered welfare indicators. In gilthead sea bream, targeted gene expression and DNA-methylation analyses in white skeletal muscle proved sirt1 as a reliable marker of age-mediated changes of energy metabolism. To complete the list of welfare auditing biomarkers, wide-analyses of gene expression and DNA-methylation in one- and three-year old fish were combined. After discriminant analysis, 668 differentially expressed transcripts were matched with those containing differentially methylated (DM) regions (14,366), and 172 were overlapping. Through enrichment analyses and selection, two sets of genes were retained: 33 showing an opposite trend for DNA-methylation and expression, and 57 down-regulated and hypo-methylated. The first set displayed apparently a more reproducible and reliable pattern and 10 multifunctional genes with DM CpG in regulatory regions (sirt1, smad1, ramp1, psmd2 – up-regulated; col5a1, calcrl, bmp1, thrb, spred2, atp1a2 – down-regulated) were deemed candidate biological age markers for an improved welfare auditing in gilthead sea bream.
SCLEROCHRONOLOGICAL EVIDENCE OF LIFE HISTORY AND AMBIENT TEMPERATURE FROM MODERN AND EARLY PLEISTOCENE GLYCYMERIS AMERICANA (MOLLUSCA:BIVALVIA) OF THE U.S. EASTERN SEABOARD
Authors: JOHNSON ANDREW L.A. , SCHÖNE BERND R. , LENG MELANIE J. , BHATTACHARYA TRIPTI , MOSS DAVID K. , IVANY LINDA C. , DUFF RICHARD P. 
Published: June 2024

Abstract
Growth-increment and isotopic studies of shells of the marine bivalve Glycymeris americana are a potential source of information bearing on its life history and preferred environment over the late Cenozoic on the U.S. eastern seaboard. We demonstrate that the ages of shells can be determined from growth bands and ontogenetic profiles of oxygen isotope (δ18O) composition, and that shell aragonite is deposited in oxygen isotopic equilibrium with seawater, enabling calculation of ambient temperatures by means of a generic transfer function. Modern specimens from North Carolina rarely reach the large size commonly attained by modern forms from Florida and Early Pleistocene forms from both states, and modern populations from North Carolina probably include fewer old individuals, the most certain disparity being with Early Pleistocene populations from the state. The temporal change in age structure in North Carolina may be an effect of recent scallop trawling but earlier non-anthropogenic environmental change cannot be ruled out as the cause. Maximum and minimum temperatures calculated from the δ18O profiles of Early Pleistocene shells indicate a larger seasonal range than now in both Florida and North Carolina, due to cooler winters. This may reflect greater southward penetration of cool northern waters, with transport along the shelf supplemented by upwelling of water brought south at depth.
Theoretically-informed vs standard cover letter to improve participant response to mailed questionnaire: results of an embedded randomised retention trial
Authors: Everett Colin Charles , Brown Sarah T , Dennett Joanna L , Collier Howard , Davies Claire L , Game Frances , Nelson Andrea 
Published: June 2024

Abstract

Background Participant non-response is a source of bias in all research, especially in randomised controlled trials. Participants followed-up remotely can have high non-response rates. Four trials have been conducted of a cover letter with content informed by behaviour-change theory to overcome hypothesised barriers to responding to a mailed questionnaire. Pooled results to date have suggested further research to be worthwhile. We conducted an embedded randomised study within a trial of such cover letters in the hope that we would improve response rates to our postal quality of life questionnaires.
Methods 148 participants in the CODIFI2 diabetic foot ulcer sampling trial were randomised 1:1 to receive one of two different cover letters at follow-up visits: either a standard cover letter accompanying their postal follow-up questionnaires, or to an “enhanced” (theory-informed) cover letter. Questionnaires were mailed at 39, 52 and (for some participants) 104 weeks post randomisation. Outcome measures were response to mailing at each timepoint. Analysis was restricted to those for whom a questionnaire and letter was issued. Owing to limited recruitment, a reduced analysis plan, comprising solely observed response rates and 95% confidence intervals for difference in response rates was followed. Post hoc, we added our week 52 results to an already-published meta-analysis.
Results 67/74 enhanced cover letter group (Enhanced) and 67/74 standard cover letter group (Standard) participants who had not already died or withdrawn were sent their first mailing at 39 weeks. The 39-week response rates were, 70.1% (47/67) and 58.2% (39/67) for Enhanced and Standard participants, respectively. At week 52 the response rates were 70.3% (45/64) and 55.6% (35/63) for Enhanced and Standard participants, respectively. At week 104, the response rates were 72.7% (24/33) and 57.6% (19/33) for the Enhanced and Standard participants, respectively. Adding our week 52 results to a published meta-analysis increased the pooled estimate of differences in response rates to 0.04 (-0.01 to 0.09) favouring enhanced letters.
Conclusion While this embedded randomised trial observed greater response rates at all times among those randomised to the enhanced letter, the reduced trial sample size meant that these results are imprecise.
Trial registration: ISRCTN74929588, registered 5th March 2019.
Prognostic Value of Hyperlactatemia and Lactate Clearance in Septic Patients With Hematological Malignancies
Authors: Inci Kamil , Aygencel Gülbin , Gökçe Onur , Türkoğlu Melda , Kaynar Lale Aydın , Can Ferda , Yeğin Zeynep Arzu , Özkurt Zübeyde Nur , Yağcı Münci 
Published: June 2024

Abstract

Background:
The coexistence of sepsis and hematological malignancies increases patient vulnerability, revealing the need for precise prognostic markers. This study explores the prognostic significance of lactate levels and clearance in septic patients with hematological malignancies.
Material and Methods:
A retrospective cohort study conducted from January 2016 to December 2019 in a tertiary hematological intensive care unit (ICU) included 167 adults with hematological malignancies and sepsis. The relationship between lactate levels, hyperlactatemia, lactate clearance, and ICU outcomes was investigated. ICU survivors and non-survivors were compared to identify the factors affecting ICU mortality.
Results:
Patients were primarily with lymphoma and acute leukemia (66%) and had frequent hyperlactatemia (64%) on ICU admission. ICU non-survivors demonstrated higher lactate levels and hyperlactatemia frequency at various time points (0, 6, and 12 hours) than survivors. Lactate clearance, however, did not differ significantly between the two groups. Invasive mechanical ventilation [OR (95% confidence interval-CI): 20.4 (2.4–79.8), p < 0.01], requirement of vasopressors [OR (95% CI): 5.6 (1.3–24.5), p < 0.01], Lactate level at the 6th hour [OR (95% CI): 1.51 (1.1–2.07), p = 0.01], and APACHE II score (OR (95% CI): 1.16 (1.01–1.34), p = 0.05) were independent risk factors for ICU mortality. The Area Under the Curve for APACHE II score and lactate level at the 6th hour were 0.774 (95% CI: 0.682–0.866) and 0.703 (95% CI: 0.602–0.804), respectively.
Conclusion:
While elevated lactate levels correlated with mortality rate and Lactate level at the 6th hour is an independent risk factor for mortality, the absence of a significant difference in lactate clearance challenges traditional assumptions. These results question the commonly accepted perspective regarding lactate dynamics in sepsis among individuals with hematological malignancies.
RETRACTED: Optimization of a Protocol for the High-Yield Isolation of Active Muscle Stem Cells from Bovine Skeletal Muscle Tissue
Authors: Lee Seung Tae , Lee Hyun , Jeon Yerin , Kim Keun cheon , Lee Young Jae , Namkung Ha Rin , Nam So Yeon , Kim Min Seong , Park Hee Ho 
Published: June 2024

Abstract

The authors have requested that this preprint be removed from Research Square.
Resistance to Zabrotes subfasciatus (Boheman, 1833) (Coleoptera: Chrysomelidae) in common bean (Phaseolus vulgaris L.) and relationship with Fe and Zn content
Authors: Lamz Alexis , Santiago Roberto R. Ruiz , Jiménez María I. Gómez , Londono Luis Fernando , Bueno Juan Miguel , Olivas-Orozco Guadalupe I. , Corral Francisco J. Molina , Florido-Bacallao Marilyn , Delgado-Oramas Belkis Peteira 
Published: June 2024

Abstract

Zabrotes subfasciatus (Boheman, 1833) is one of the main storage pests affecting common bean (Phaseolus vulgaris L.) in tropical areas. The objective of this work was to evaluate resistance to Z. subfasciatus in common bean genotypes and its relationship with Fe and Zn content. For this purpose, resistance was evaluated of 63 genotypes, by means of: “no-choice experiments”, Fe and Zn mineral content was determined by Energy-Dispersive X-ray Fluorescence and correlation analyses were carried out to know the relationship between these variables. Commercial cultivars from Cuba were susceptible to the arthropod. The wild accessions from which the resistance originated and RAZ lines were resistant, associated with the presence of arcelin variants that confer resistance in the order Arc1 > Arc6 > Arc7 > Arc5 > Arc2. The Arc4 conferred intermediate resistance and Arc3 it didn't confer resistance to this insect. No relationship was detected between resistance to Z. subfasciatus and Fe and Zn content. These results constitute the first report of the absence of relationships between Z. subfasciatus resistance and Fe and Zn mineral content.
Microbial fertilizer and organic manure combined fertilization changes the rhizosphere bacterial community and carotenoids of Citrus reticulata Blanco ‘Orah’
Authors: Huang Qichun , Zhou Wei , Zeng Zhikang , Wang Nina , Huang Yanxiao , Cheng Hao , Huang Quyan , Liu Jimin , Lu Fuping , Liao Huihong , Hu Chengxiao , Chen Dongkui , Wei Shaolong , Li Chaosheng , Qin Zelin 
Published: June 2024

Abstract

Background
Citrus reticulata Blanco ‘Orah’ is one of the most widely grown citrus varieties in southern China. It has been proven that microbial fertilizer and organic manure combined fertilization could improve the yields and appearances of ‘Orah’ fruits. However, details regarding the mechanisms underlying the effects of combined fertilization on the agronomic traits and rhizosphere bacterial community of plants still need to be elucidated.
Results
This study compared the rhizosphere bacterial community and carotenoids of ‘Orah’ with (WYT group) and without (WYCK group) combined fertilization. The WYT group was sprayed with 50 ml Strongreen and 250 g of Yumeiren five times while WYCK group did not sprayed. Combined fertilization increased fruit weight and the Citrus color index (CCI) significantly (P < 0.05). By 16s rRNA sequencing, 7,126 operational taxonomic units (OTU) were obtained. A higher Shannon index was observed in the WYT group compared to that in the WYCK group. Comparison between the two groups showed that Pseudomonas was enriched in the WTY group, and Cyanobacteria was enriched in the WYCK group. At the family level, Phyllobacteriaceae was significantly abundant in the WTY group, whereas Thermosporothrix and Sphingobium were significantly abundant in the WYCK group. A total of 51 carotenoid components were tested using UPLC-MS/MS. In the pulp tissues, 37 carotenoid components were decreased in the WTY group compared to those in the WYCK group. In fruit skin, 24 significantly different components (7 downregulated and 17 upregulated) were identified in WTY compared to those in WYCK. Correlation analysis revealed that the network between OTUs and carotenoids contained seven carotenoid components and four OTUs. Four OTUs, strain TRA3-20 (a eubacterium), Roseiflexus, OPB35, and Fictibacillus contributed to carotenoid accumulation regulation in fruit skin.
Conclusions
By exploring the complex interactions between soil microbiota and fruit traits, our research has illuminated potential pathways through which these microbial communities influence the biosynthesis and accumulation of carotenoids. In conclusion, this study provides valuable information regarding soil bacterial communities related to carotenoid accumulation in ‘Orah’.
Lower limb motion recognition based on surface electromyography decoding using S-transform energy concentration
Authors: Li Baoyu , Xu Guanghau , Pei Jinju , Luo Dan , Li Hui , Du Chenghang , Zhang Sicong 
Published: June 2024

Abstract

Lower limb motion recognition of based surface electromyography (EMG) aims to provide a more natural and effective human-computer interaction for intelligent prostheses. Accurate motion recognition relies on high-quality EMG decoding, and the key to improving the efficiency of EMG pattern recognition is to optimize signal feature extraction. The phase information of the EMG signal cannot be neglected for motion pattern recognition. Therefore, we proposed a decoding scheme for surface EMG signals based on S-transform energy concentration for lower limb motion recognition, including level walk, stair ascent, stair descent, and crossing obstacles. First, six-channel lower limb EMG signals of the 10 subjects during four kinds of movements were experimentally acquired, and the correlation of multi-channel EMG signals was analyzed to find the best combination of the EMG signal for exploring the classification effect based on the support vector machine (SVM) between single-channel signals and multi-channel signals fusion. The results showed that based on the simple time-frequency domain features with better motion recognition are the semi-tendon muscle and the rectus femoris muscle, and based on the S-transform energy concentration with better motion recognition is the medial gastrocnemius muscle and the rectus femoris muscle. Finally, taking the rectus femoris signal as an example, the motion recognition accuracy of 10 subjects under the two schemes was calculated. The mean value of motion recognition accuracy based on simple time-frequency domain features was 80.71%, and the mean value of motion recognition accuracy based on S-transformed energy concentration was 93.70%. It validated that the S-transform energy concentration scheme has a better recognition effect, and the accuracy of multi-channel signal fusion pattern recognition based on S-transform energy concentration is higher than 96%, which is beneficial to promote the practical application of EMG signals in motion recognition. It has the potential to improve the adaptive human-robot interaction control of the prosthesis.
Blockchain-based Access Control Protocol with collaborative authentication
Authors: Ci Limian , Zhang Liyuan , Wu Yonghong , Wiwatanapataphee Benchawan 
Published: June 2024

Abstract

In a complex and globalized business environment, cross-organizational cooperation has become increasingly important for enterprises, due to the growing need for information sharing. However, traditional access control models have limitations in the scenarios of cross-organizational cooperation scenarios without central leadership. To address these challenges, this paper proposes a decentralized access control framework with identity verification based on the blockchain technology and zero-knowledge proof. The access control protocol in the proposed access control framework integrates the role-based access control with the attribute-based access control, enabling our model to achieve more granular access control while requiring low computing resources. We implement the proposed access control protocol using smart contracts and apply it in a supply chain scenario to verify its feasibility. In addition, we analyze and evaluate the proposed protocol in terms of cost, running time, security and flexibility. For the limitation of no administrator rights brought by complete decentralization, we propose to use governance protocols to achieve high flexibility and scalability while maintaining the complete decentralization of the proposed framework.
The Pons as an Optimal Background Reference Region for Spinal 18F-FET PET/MRI Evaluation
Authors: Huang Jing , Wang Jiyuan , Cui Bixiao , Yang Hongwei , Tian Defeng , Ma Jie , Duan Wanru , Chen Zan , Lu Jie 
Published: June 2024

Abstract

Background
This study aims to evaluate the effect of various background reference regions on spinal 18F-FET PET imaging, with a focus on distinguishing between spinal tumors and myelitis. To enhance diagnostic accuracy, we investigated the pons and several other spinal cord area as potential references, given the challenges in interpreting spinal PET results.
Results
A retrospective analysis was conducted on 30 patients, 15 with cervical myelitis and 15 with cervical tumors, who underwent O-(2-[18F]-fluoroethyl)-L-tyrosine (FET) PET/MR imaging. The stability of uptake across four regions, including the pons, C2, C2 ~ C7, and T1 ~ T3, was compared. The standardized uptake value ratio (SUVR) was then evaluated using various background regions, and their effectiveness in differentiating between spinal tumors and myelitis was compared. Additionally, we correlated the SUVR values derived from these regions with the Ki-67 proliferation index in tumor patients. The study found no significant difference in SUVmax (U = 110, p = 0.93) and SUVmean (U = 89, p = 0.35) values at lesion sites between myelitis and tumor patients. The pons had the highest average uptake (p < 0.001) compared to the other three regions. However, its coefficient of variation (CV) was significantly lower than that of the C2 ~ C7 (p < 0.0001) and T1 ~ T3 segments (p < 0.05). The SUVRmax values, calculated using the regions of pons, C2 ~ C7 and T1 ~ T3, were found to significantly differentiate between tumors and myelitis (p < 0.05). However, only the pons-based SUVRmean was able to significantly distinguish between the two groups (p < 0.05). Additionally, the pons-based SUVRmax (r = 0.63, p = 0.013) and SUVRmean (r = 0.67, p = 0.007) demonstrated a significant positive correlation with the Ki-67 index.
Conclusions
This study suggests that the pons may be considered a suitable reference region for spinal 18F-FET PET imaging, which can improve the differentiation between spinal tumors and myelitis. The significant correlation between pons-based SUVR values and the Ki-67 index further highlights the potential of this approach in assessing tumor cell proliferation.
Demystifying Machine Learning Predictions: A Comparative Analysis with Explainable AI for Parkinson's Disease
Authors: S Jayanthi , Sithik K. M. Abubakkar , U U Balashivudu 
Published: June 2024

Abstract

Background
Early diagnosis of Parkinson's disease (PD) is crucial for personalized medicine and improved patient outcomes. Traditional methods often lack transparency, raising concerns about reliability. This study proposes developing interpretable Machine Learning (ML) models that leverage Explainable Artificial Intelligence (XAI) techniques. Vocal biomarkers from PD dataset are used to train these models for early PD prediction. This approach aims to empower healthcare professionals by providing insights into the "why" behind model predictions, fostering trust, and identifying potential voice biomarkers for PD.
Methods
We analyzed vocal features extracted from PD dataset, creating visualizations to uncover distribution patterns and relationships. We experimented with various ML algorithms, including Random Forest, Gradient Boosting, and AdaBoost, as well as established methods like Logistic Regression, Support Vector Machines (SVM), and K-Nearest Neighbors (KNN). We incorporated a Multi-Layer Perceptron (MLP) for non-linear modeling. XAI techniques such as SHAP and LIME were used to understand model predictions and build trust in their application.
Results
Ten-fold cross-validation ensured robust evaluation, with accuracy ranging from 0.95 to 1.0. AdaBoost emerged as the most efficient algorithm (accuracy: 100%, training time: 0.0036 seconds, prediction time: 0.0016), outperforming others. SVM (accuracy: 0.82) and KNN (accuracy: 0.85) showed lower accuracy and limitations in PD classification. MLP had good accuracy (around 0.87) but a lower AUC-ROC score. Notably, Random Forest demonstrated superiority on the test dataset. SHAP and LIME provided insights into model decisions, identifying specific vocal characteristics indicative of PD. Exploratory data analysis revealed significant differences in vocal features between PD patients and healthy controls, with features like jitter and shimmer showing strong positive correlations with PD status.
Conclusion
This study demonstrates the effectiveness of using XAI techniques to understand model reasoning, fostering trust and providing insights into potential voice biomarkers for PD. Employing a diverse range of machine learning algorithms ensures robust and accurate PD prediction. The findings highlight the importance of balancing model accuracy with interpretability, contributing to the development of more transparent and trustworthy diagnostic tools in clinical settings.
The relationship of heart rate variability measures with trait emotional intelligence in the presence of acute mental stress
Authors: GHORI SHAGUFTA , AFTAB MEHA FATIMA , ROY BEDANTA , HABIB NASRIN , SHENG ALEX LIM LIAN 
Published: June 2024

Abstract

Objective:
Emotional intelligence (EI) is essential for effective stress management and may influence cardiac responses. This study seeks to investigate the relationship between EI and heart rate variability (HRV) due to limited physiological data, contributing valuable insights into this unexplored connection and its potential impact on overall well-being.
Results:
In a study of 55 participants, mainly undergraduate students (45.5%) and single (70.9%), females constituted 56.4% of the sample. The highest well-being score was 5.187 (Cronbach’s alpha = 0.76). One-way repeated measures ANOVA showed significant HRV differences across time points. Median HF at stress induction was 0.193 (IQR: 0.160–0.217), significantly decreasing from baseline (Z = -4.926, p < 0.001). LF/HF ratio increased at T2 (M = 0.579, p < 0.001), with SD2/SD1 ratio rising to 2.171. Pairwise comparisons indicated differences between baseline and stress induction (M = -0.018, p < 0.001), and stress induction and post-induction periods (M = 0.174, p = 0.032). SDNN correlated positively at T1 (r = 0.321, p = 0.020) and T3 (r = 0.280, p = 0.045). pNN50% correlated positively at T1 (r = 0.332, p = 0.020), while stress index showed negative correlations at T1 (r = -0.318, p = 0.023) and T3 (r = -0.337, p = 0.012). Sociability negatively correlated with HRV measures (r = -0.407, p = 0.002), indicating autonomic nervous system activity links.