bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification and characterization of intact glycopeptides in human urine
Authors: Garcia-Marques Fernando , Fuller Keely , Bermudez Abel , Shamsher Nikhiya , Zhao Hongjuan , Brooks James D. , Flory Mark R. , Pitteri Sharon J. 
Published: February 2024

AbstractGlycoproteins in urine have the potential to provide a rich class of informative molecules for studying human health and disease. Despite this promise, the urine glycoproteome has been largely uncharacterized. Here, we present the analysis of glycoproteins in human urine using LC–MS/MS-based intact glycopeptide analysis, providing both the identification of protein glycosites and characterization of the glycan composition at specific glycosites. Gene enrichment analysis reveals differences in biological processes, cellular components, and molecular functions in the urine glycoproteome versus the urine proteome, as well as differences based on the major glycan class observed on proteins. Meta-heterogeneity of glycosylation is examined on proteins to determine the variation in glycosylation across multiple sites of a given protein with specific examples of individual sites differing from the glycosylation trends in the overall protein. Taken together, this dataset represents a potentially valuable resource as a baseline characterization of glycoproteins in human urine for future urine glycoproteomics studies.
Rhythmic motor behavior explains individual differences in grammar skills in adults
Authors: Kim Hyun-Woong , Kovar Jessica , Bajwa Jesper Singh , Mian Yasir , Ahmad Ayesha , Mancilla Moreno Marisol , Price Theodore J. , Lee Yune Sang 
Published: February 2024

AbstractA growing body of literature has reported the relationship between music and language, particularly between individual differences in perceptual rhythm skill and grammar competency in children. Here, we investigated whether motoric aspects of rhythm processing—as measured by rhythmic finger tapping tasks—also explain the rhythm-grammar connection in 150 healthy young adults. We found that all expressive rhythm skills (spontaneous, synchronized, and continued tapping) along with rhythm discrimination skill significantly predicted receptive grammar skills on either auditory sentence comprehension or grammaticality well-formedness judgment (e.g., singular/plural, past/present), even after controlling for verbal working memory and music experience. Among these, synchronized tapping and rhythm discrimination explained unique variance of sentence comprehension and grammaticality judgment, respectively, indicating differential associations between different rhythm and grammar skills. Together, we demonstrate that even simple and repetitive motor behavior can account for seemingly high-order grammar skills in the adult population, suggesting that the sensorimotor system continue to support syntactic operations.
Flexible metallic core–shell nanostructured electrodes for neural interfacing
Authors: Rodilla Beatriz L. , Arché-Núñez Ana , Ruiz-Gómez Sandra , Domínguez-Bajo Ana , Fernández-González Claudia , Guillén-Colomer Clara , González-Mayorga Ankor , Rodríguez-Díez Noelia , Camarero Julio , Miranda Rodolfo , López-Dolado Elisa , Ocón Pilar , Serrano María C. , Pérez Lucas , González M. Teresa 
Published: February 2024

AbstractElectrodes with nanostructured surface have emerged as promising low-impedance neural interfaces that can avoid the charge‐injection restrictions typically associated to microelectrodes. In this work, we propose a novel approximation, based on a two-step template assisted electrodeposition technique, to obtain flexible nanostructured electrodes coated with core–shell Ni–Au vertical nanowires. These nanowires benefit from biocompatibility of the Au shell exposed to the environment and the mechanical properties of Ni that allow for nanowires longer and more homogeneous in length than their only-Au counterparts. The nanostructured electrodes show impedance values, measured by electrochemical impedance spectroscopy (EIS), at least 9 times lower than those of flat reference electrodes. This ratio is in good accordance with the increased effective surface area determined both from SEM images and cyclic voltammetry measurements, evidencing that only Au is exposed to the medium. The observed EIS profile evolution of Ni–Au electrodes over 7 days were very close to those of Au electrodes and differently from Ni ones. Finally, the morphology, viability and neuronal differentiation of rat embryonic cortical cells cultured on Ni–Au NW electrodes were found to be similar to those on control (glass) substrates and Au NW electrodes, accompanied by a lower glial cell differentiation. This positive in-vitro neural cell behavior encourages further investigation to explore the tissue responses that the implantation of these nanostructured electrodes might elicit in healthy (damaged) neural tissues in vivo, with special emphasis on eventual tissue encapsulation.
Excreta flow mapping along the sanitation service chain, a case of Kombolcha town, Ethiopia
Authors: Endris Seid , Kebede Andinet , Assefa Eshetu , Ali Almayehu , Desale Tewodrose 
Published: February 2024

AbstractPoor management of fecal sludge (FSM) presents significant risks to public health and the environment. This study employed qualitative and quantitative data collection methods, along with the Shit Flow Diagram (SFD) data analyzing tool to investigate FSM patterns in Kombolcha town, Ethiopia. The findings indicate that 75.7% of housing unites in the town are shared toilets, with multiple households sharing a single facility. The primary toilet technologies used include cistern flush toilets (2.1%), pour/manual flush toilets (19.8%), ventilated improved pit latrines (11.1%), pit latrines with slabs (56.4%), and pit latrines without slabs (10.6%). However, 98.5% of these toilet types had either unlined or only partially lined containments. Furthermore, only 37% of households practice safe pit or sludge tank emptying. As a result, only 17% of fecal sludge goes through the sanitation value chain and is effectively treated, while 39% remains onsite and unemptied, and the remaining 44% is disposed of in a manner that poses risks to the environment and public health. The study highlights the significant public health and environmental risks associated with the high reliance on shared toilets, the prevalence of inadequately lined toilet types, and the low adoption of proper fecal sludge management practices. Addressing these challenges requires the implementation of sanitation bylaws and building code regulations that prioritize hygienic standards and promote improved toilet technologies.
Revealing the associated microflora hosted by the globally significant parasite Trichostrongylus colubriformis
Authors: Paz Erwin A. , Chua Eng Guan , Palmer Dieter G. , Greeff Johan C. , Liu Shimin , Cheuquemán Carolina , Hassan Shamshad Ul , Martin Graeme B. , Tay Chin Yen 
Published: February 2024

AbstractTrichostrongylus colubriformis is a parasitic helminth that primarily infects small ruminants, causing substantial economic losses in the livestock industry. Exploring the microbiome of this helminth might provide insights into the potential influence of its microbial community on the parasite’s survival. We characterised the intestinal microbiome of T. colubriformis that had been collected from the duodenum of sheep, and compared the helminth microbiome with the duodenal microbiome of its host, aiming to identify contributions from the helminth’s environment. At the same time, we explored the isolation of fastidious organisms from the harvested helminth. Primary alpha and beta diversity analyses of bacterial species revealed statistically significant differences between the parasite and the host, in terms of species richness and ecological composition. 16S rRNA differential abundance analysis showed that Mycoplasmoides and Stenotrophomonas were significantly present in T. colubriformis but not in the duodenal microbiome of the sheep. Furthermore, two bacteria, Aeromonas caviae and Aeromonas hydrophila, were isolated from T. colubriformis. Examinations of the genome highlight differences in genome size and profiles of antimicrobial resistance genes. Our results suggest that T. colubriformis carries a specific bacterial community that could be supporting the helminth’s long-term survival in the host’s digestive system.
Shared attention in virtual immersive reality enhances electrophysiological correlates of implicit sensory learning
Authors: Sarasso Pietro , Ronga Irene , Piovesan Francesca , Barbieri Paolo , Del Fante Elena , De Luca Daniela , Bechis Ludovico , Osello Anna , Sacco Katiuscia 
Published: February 2024

AbstractShared attention effects on learning and memory demonstrate that experiences are amplified when we are not alone. Virtual reality poses new challenges to the study of co-presence. Above all, is coattending together with someone else’s avatar in an immersive VR setting comparable with shared experiences at a neural processing level? In the present study we investigate shared attention effects in VR for the first time. We recorded mismatch negativities (MMN) during an auditory roving paradigm, a well-known index of implicit perceptual learning. EEG responses to deviant and standard sounds were registered while subjects were alone (Solo condition) or together (Other condition) with a virtual avatar (Virtual scenario) or physically present confederate (Physical scenario). We found an overall main effect of co-presence on MMN revealed by a point-by-point 2 × 2 ANOVA, thereby replicating previous studies on physical co-presence. Additionally, we found no significant interaction between the scenario (Physical vs. Virtual) and co-presence (Solo vs. Other). Our results indicate that virtual immersive co-presence mimics physical co-presence.
Deep learning assisted XRF spectra classification
Authors: Andric Velibor , Kvascev Goran , Cvetanovic Milos , Stojanovic Sasa , Bacanin Nebojsa , Gajic-Kvascev Maja 
Published: February 2024

AbstractEDXRF spectrometry is a well-established and often-used analytical technique in examining materials from which cultural heritage objects are made. The analytical results are traditionally subjected to additional multivariate analysis for archaeometry studies to reduce the initial data’s dimensionality based on informative features. Nowadays, artificial intelligence (AI) techniques are used more for this purpose. Different soft computing techniques are used to improve speed and accuracy. Choosing the most suitable AI method can increase the sustainability of the analytical process and postprocessing activities. An autoencoder neural network has been designed and used as a dimension reduction tool of initial $$40 \times 2048$$

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data collected in the raw EDXRF spectra, containing information about the selected points’ elemental composition on the canvas paintings’ surface. The autoencoder network design enables the best possible reconstruction of the original EDXRF spectrum and the most informative feature extraction, which has been used for dimension reduction. Such configuration allows for efficient classification algorithms and their performances. The autoencoder neural network approach is more sustainable, especially in processing time consumption and experts’ manual work.
Characterization of graded 6-Hydroxydopamine unilateral lesion in medial forebrain bundle of mice
Authors: Cui Juntao , Zhao Di , Xu Manman , Li Zheheng , Qian Junliang , Song Ning , Wang Jun , Xie Junxia 
Published: February 2024

AbstractParkinson’s disease (PD) is the second most common age-related neurodegenerative disease, with a progressive loss of dopaminergic cells and fibers. The purpose of this study was to use different doses of 6-hydroxydopamine (6-OHDA) injection into the medial forebrain bundle (MFB) of mice to mimic the different stages of the disease and to characterize in detail their motor and non-motor behavior, as well as neuropathological features in the nigrostriatal pathway. MFB were injected with 0.5 μg, 1 μg, 2 μg of 6-OHDA using a brain stereotaxic technique. 6-OHDA induced mitochondrial damage dose-dependently, as well as substantia nigra pars compacta (SNpc) tyrosine hydroxylase-positive (TH+) cell loss and striatal TH fiber loss. Activation of astrocytes and microglia in the SNpc and striatum were consistently observed at 7 weeks, suggesting a long-term glial response in the nigrostriatal system. Even with a partial or complete denervation of the nigrostriatal pathway, 6-OHDA did not cause anxiety, although depression-like behavior appeared. Certain gait disturbances were observed in 0.5 μg 6-OHDA lesioned mice, and more extensive in 1 μg group. Despite the loss of more neurons from 2 μg 6-OHDA, there was no further impairment in behaviors compared to 1 μg 6-OHDA. Our data have implications that 1 μg 6-OHDA was necessary and sufficient to induce motor and non-motor symptoms in mice, thus a valuable mouse tool to explore disease progression and new treatment in PD.
Potential Alzheimer’s early biomarkers in a transgenic rat model and benefits of diazoxide/dibenzoylmethane co-treatment on spatial memory and AD-pathology
Authors: Wallace Charles H. , Oliveros Giovanni , Xie Lei , Serrano Peter , Rockwell Patricia , Figueiredo-Pereira Maria 
Published: February 2024

AbstractAlzheimer’s disease (AD) is the major form of dementia prevalent in older adults and with a high incidence in females. Identification of early biomarkers is essential for preventive intervention to delay its progression. Furthermore, due to its multifactorial nature, a multi-target approach could be therapeutically beneficial. Our studies included 4- (pre-pathology) and 11-month (mild-pathology) TgF344-AD rats, a transgenic Alzheimer’s model that exhibits age-dependent AD progression. We identified two potential early biomarker genes for AD, early growth response 2 (EGR2) and histone 1H2AA (HIST1H2AA), in the hippocampus of 4-month females. Out of 17,168 genes analyzed by RNA sequencing, expression of these two genes was significantly altered in 4-month TgF344-AD rats compared to wild-type littermates. We also evaluated co-treatment with diazoxide (DZ), a potassium channel activator, and dibenzoylmethane (DIB), which inhibits eIF2α-P activity, on TgF344-AD and wild-type rats. DZ/DIB-treatment mitigated spatial memory deficits and buildup of hippocampal Aβ plaques and tau PHF in 11-month TgF344-AD rats but had no effect on wild-type littermates. To our knowledge, this preclinical study is the first to report EGR2 and HIST1H2AA as potential AD biomarkers in females, and the benefits of DZ/DIB-treatment in AD. Evaluations across multiple AD-related models is warranted to corroborate our findings.
Nanoscale morphology, optical dynamics and gas sensor of porous silicon
Authors: Ghaderi Atefeh , Sabbaghzadeh Jamshid , Dejam Laya , Behzadi Pour Ghobad , Moghimi Emad , Matos Robert S. , da Fonseca Filho Henrique Duarte , Țălu Ștefan , Salehi shayegan Amirhossein , Aval Leila Fekri , Astani Doudaran Mahdi , Sari Amirhossein , Solaymani Shahram 
Published: February 2024

AbstractWe investigated the multifaceted gas sensing properties of porous silicon thin films electrodeposited onto (100) oriented P-type silicon wafers substrates. Our investigation delves into morphological, optical properties, and sensing capabilities, aiming to optimize their use as efficient gas sensors. Morphological analysis revealed the development of unique surfaces with distinct characteristics compared to untreated sample, yielding substantially rougher yet flat surfaces, corroborated by Minkowski Functionals analysis. Fractal mathematics exploration emphasized that despite increased roughness, HF/ethanol-treated surfaces exhibit flatter attributes compared to untreated Si sample. Optical approaches established a correlation between increased porosity and elevated localized states and defects, influencing the Urbach energy value. This contributed to a reduction in steepness values, attributed to heightened dislocations and structural disturbances, while the transconductance parameter decreases. Simultaneously, porosity enhances the strength of electron‒phonon interaction. The porous silicon thin films were further tested as effective gas sensors for CO2 and O2 vapors at room temperature, displaying notable changes in electrical resistance with varying concentrations. These findings bring a comprehensive exploration of some important characteristics of porous silicon surfaces and established their potential for advanced industrial applications.
Genetic and environmental contributions to gaze lateralization across social and non-social stimuli in human infants
Authors: Viktorsson Charlotte , Portugal Ana Maria , Falck-Ytter Terje 
Published: February 2024

AbstractA tendency to look at the left side of faces from the observer’s point of view has been found in older children and adults, but it is not known when this face-specific left gaze bias develops and what factors may influence individual differences in gaze lateralization. Therefore, the aims of this study were to estimate gaze lateralization during face observation and to more broadly estimate lateralization tendencies across a wider set of social and non-social stimuli, in early infancy. In addition, we aimed to estimate the influence of genetic and environmental factors on lateralization of gaze. We studied gaze lateralization in 592 5-month-old twins (282 females, 330 monozygotic twins) by recording their gaze while viewing faces and two other types of stimuli that consisted of either collections of dots (non-social stimuli) or faces interspersed with objects (mixed stimuli). A right gaze bias was found when viewing faces, and this measure was moderately heritable (A = 0.38, 95% CI 0.24; 0.50). A left gaze bias was observed in the non-social condition, while a right gaze bias was found in the mixed condition, suggesting that there is no general left gaze bias at this age. Genetic influence on individual differences in gaze lateralization was only found for the tendency to look at the right versus left side of faces, suggesting genetic specificity of lateralized gaze when viewing faces.
Investigation on explainable machine learning models to predict chronic kidney diseases
Authors: Ghosh Samit Kumar , Khandoker Ahsan H. 
Published: February 2024

AbstractChronic kidney disease (CKD) is a major worldwide health problem, affecting a large proportion of the world’s population and leading to higher morbidity and death rates. The early stages of CKD sometimes present without visible symptoms, causing patients to be unaware. Early detection and treatments are critical in reducing complications and improving the overall quality of life for people afflicted. In this work, we investigate the use of an explainable artificial intelligence (XAI)-based strategy, leveraging clinical characteristics, to predict CKD. This study collected clinical data from 491 patients, comprising 56 with CKD and 435 without CKD, encompassing clinical, laboratory, and demographic variables. To develop the predictive model, five machine learning (ML) methods, namely logistic regression (LR), random forest (RF), decision tree (DT), Naïve Bayes (NB), and extreme gradient boosting (XGBoost), were employed. The optimal model was selected based on accuracy and area under the curve (AUC). Additionally, the SHAP (SHapley Additive exPlanations) and LIME (Local Interpretable Model-agnostic Explanations) algorithms were utilized to demonstrate the influence of the features on the optimal model. Among the five models developed, the XGBoost model achieved the best performance with an AUC of 0.9689 and an accuracy of 93.29%. The analysis of feature importance revealed that creatinine, glycosylated hemoglobin type A1C (HgbA1C), and age were the three most influential features in the XGBoost model. The SHAP force analysis further illustrated the model’s visualization of individualized CKD predictions. For further insights into individual predictions, we also utilized the LIME algorithm. This study presents an interpretable ML-based approach for the early prediction of CKD. The SHAP and LIME methods enhance the interpretability of ML models and help clinicians better understand the rationale behind the predicted outcomes more effectively.
Probiotic performance of B. subtilis MS. 45 improves aquaculture of rainbow trout Oncorhynchus mykiss during acute hypoxia stress
Authors: Neissi Alireza , Majidi Zahed Hamed , Roshan Reza 
Published: February 2024

AbstractThe aim of this study was to produce mutant strains of Bacillus subtilis with high probiotic performance for use in the aquaculture of rainbow trout Oncorhynchus mykiss. The main strain of B. subtilis (MS) was irradiated with gamma rays (5.3 KGy). Subsequently, the B. subtilis mutant strain no. 45 (MS. 45) was selected for bacterial growth performance, resistance to acidic conditions, resistance to bile salts and antibacterial activity against Aeromonas hydrophila and Pseudomonas fluorescens. After 60 days, the rainbow trout (70.25 ± 3.89 g) fed with MS. 45 and MS were exposed to hypoxia stress (dissolved oxygen = 2 ppm). Subsequently, immune indices (lysozyme, bacterial activity and complement activity), hematological indices [hematocrit, hemoglobin, WBC, RBC, mean corpuscular volume (MCV)] and antioxidant factors (T-AOC, SOD and MDA)) were analyzed after and before hypoxia exposure. The expression of immunological genes (IFN-γ, TNF-α, IL-1β, IL-8) in the intestine and the expression of hypoxia-related genes (HIF-1α, HIF-2α, FIH1) in the liver were compared between the different groups under hypoxia and normoxia conditions. Growth, immunological and antioxidant indices improved in group MS. 45 compared to the other groups. Stress indices and associated immunologic and hypoxia expressions under hypoxia and normoxia conditions improved in MS. 45 compared to the other groups. This resulted in improved growth, immunity and stress responses in fish fed with the microbial supplement of MS. 45 (P < 0.05) under hypoxia and normoxia conditions, (P < 0.05), resulting in a significant improvement in trout aquaculture.
Evaluating the relationship between ocular blood flow and systemic organ blood flow in hemorrhagic shock using a rabbit model
Authors: Watanabe Kento , Shiba Tomoaki , Takahara Akira , Homma Hiroshi , Komatsu Tetsuya , Tanino Yusuke , Nagasawa Yoshinobu , Aimoto Megumi , Hori Yuichi 
Published: February 2024

AbstractThis study aimed to investigate the feasibility of utilizing noninvasive ocular blood flow measurements as potential indicators of systemic circulation in rabbits experiencing hemorrhagic shock. Using Laser speckle flowgraphy, ocular blood flow indices, relative flow volume (RFV), and mean blur rate in the choroidal area (MBR-CH) were assessed in New Zealand White rabbits (n = 10) subjected to controlled blood removal and return. Hemodynamic parameters and biochemical markers were monitored alongside ocular circulation during blood removal and return phases. Additionally, correlations between ocular parameters and systemic indices were examined. The results indicated that RFV and MBR-CH exhibited significant correlations with renal and intestinal blood flows, with stronger correlations observed during blood removal. Additionally, ocular blood flow changes closely mirrored systemic dynamics, suggesting their potential as real-time indicators of shock progression and recovery. These findings indicate that ocular blood flow measurements may serve as real-time indicators of the systemic circulation status during hemorrhagic shock, offering potential insights into shock management and guiding tailored interventions. Thus, noninvasive ocular blood flow evaluation holds promise as an innovative tool for assessing systemic circulation dynamics during hemorrhagic shock.