bluuebunny/crossref_metadata_2025_split huggingface dataset:
Histones with an unconventional DNA-binding mode in vitro are major chromatin constituents in the bacterium Bdellovibrio bacteriovorus
Authors: Hocher Antoine , Laursen Shawn P. , Radford Paul , Tyson Jess , Lambert Carey , Stevens Kathryn M. , Montoya Alex , Shliaha Pavel V. , Picardeau Mathieu , Sockett R. Elizabeth , Luger Karolin , Warnecke Tobias 
Published: October 2023

AbstractHistone proteins bind DNA and organize the genomes of eukaryotes and most archaea, whereas bacteria rely on different nucleoid-associated proteins. Homology searches have detected putative histone-fold domains in a few bacteria, but whether these function like archaeal/eukaryotic histones is unknown. Here we report that histones are major chromatin components in the bacteria Bdellovibrio bacteriovorus and Leptospira interrogans. Patterns of sequence evolution suggest important roles for histones in additional bacterial clades. Crystal structures (<2.0 Å) of the B. bacteriovorus histone (Bd0055) dimer and the histone–DNA complex confirm conserved histone-fold topology but indicate a distinct DNA-binding mode. Unlike known histones in eukaryotes, archaea and viruses, Bd0055 binds DNA end-on, forming a sheath of dimers encasing straight DNA rather than wrapping DNA around their outer surface. Our results demonstrate that histones are present across the tree of life and highlight potential evolutionary innovation in how they associate with DNA.
Characterization of microbial communities in seven wetlands with different anthropogenic burden using Next Generation Sequencing in Bogotá, Colombia
Authors: Ballesteros Nathalia , Páez Luisa , Luna Nicolas , Reina Ariana , Urrea Vanessa , Sánchez Catalina , Ramírez Angie , Ramirez Juan David , Muñoz Marina 
Published: October 2023

AbstractWetlands represent key ecosystems due to their remarkable biodiversity, ecological functions and multiple ecosystem services provided. In Colombia, there are 31,702 wetlands, 13 of which are in Bogotá, capital of the country. Despite the fundamental socioecological support of these aquatic ecosystems, a tremendous loss and degradation of these ecosystems has been observed due to anthropogenic perturbations. Therefore, the aim of this study was to describe the status of seven Bogotá wetlands with variable anthropogenic interventions by measuring organoleptic, physicochemical, and microbiological parameters, using commercial kits, highly sensitive equipment, and next-generation sequencing of the 16S- and 18S-rRNA genes. Our findings describe the status of seven wetlands with different anthropogenic burden in Bogotá-Colombia where physicochemical and microbiology signals of contamination were observed. Additionally, some profiles in the composition of the microbial communities, together with certain physicochemical characteristics, may represent an insight into the environmental dynamics, where Beta Proteobacteria such as Malikia represent a potential keystone in aquatic ecosystems impacted by wastewater effluent discharges; the presence of nitrates and phosphates explain the abundance of bacteria capable of oxidizing these compounds, such as Polynucleobacter. Moreover, the presence of specific prokaryotic and eukaryotic organisms, such as Clostridium, Cryptococcus, Candida, and Naegleria, reported in one or more of the wetlands assessed here, could represent a possible pathogenic risk for human and animal health. This study performed a complete evaluation of seven Bogotá wetlands with different anthropogenic impacts for the first time, and our findings emphasize the importance of maintaining continuous monitoring of these water bodies given their remarkable ecological importance and potential spill-over of several pathogens to humans and animals.
An eye tracking investigation of attention mechanism in driving behavior under emotional issues and cognitive load
Authors: Wang Quan , Zhu Feiyu , Dang Ruochen , Wei Xiaojie , Han Gongen , Huang Jinhua , Hu Bingliang 
Published: October 2023

AbstractEmotions have specific effects on behavior. At present, studies are increasingly interested in how emotions affect driving behavior. We designed the experiment by combing driving tasks and eye tracking. DSM-V assessment scale was applied to evaluate the depression and manic for participants. In order to explore the dual impacts of emotional issues and cognitive load on attention mechanism, we defined the safety-related region as the area of interest (AOI) and quantified the concentration of eye tracking data. Participants with depression issues had lower AOI sample percentage and shorter AOI fixation duration under no external cognitive load. During our experiment, the depression group had the lowest accuracy in arithmetic quiz. Additionally, we used full connected network to detect the depression group from the control group, reached 83.33%. Our experiment supported that depression have negative influences on driving behavior. Participants with depression issues reduced attention to the safety-related region under no external cognitive load, they were more prone to have difficulties in multitasking when faced with high cognitive load. Besides, participants tended to reallocate more attention resources to the central area under high cognitive load, a phenomenon we called "visual centralization" in driving behavior.
Longitudinal change of gut microbiota in hypertensive disorders in pregnancy: a nested case–control and Mendelian randomization study
Authors: Wu Xinrui , Li Qi , Cai Jiawang , Huang Houxiang , Ma Shujuan , Tan Hongzhuan 
Published: October 2023

AbstractMounting evidence has shown that gut microbiota (GM) is related to hypertensive disorders in pregnancy (HDP), however, most studies only focused on one time point in pregnancy. In this study, we conducted a nested case–control study utilizing a follow-up cohort, resulting in the collection of 47 HDP patients and 30 healthy controls. The GM profiles were explored using 16S rRNA sequencing at three time points during pregnancy. The diversity analysis of GM showed no significant difference between HDP patients and controls, however, we found 21 differential GM during pregnancy. Trend analysis showed that there are statistical differences in the relative abundance of Thermomonas, Xanthomonas, and Phenylobacteriumat during pregnancy in the gestational hypertension group, and of Xanthomonas, Polycyclovorans, and Phenylobacterium in the control group. The correlation study found that six genera of GM are related to blood pressure. Furthermore, the MR analysis identified the causal relationship between Methanobrevibacter and pre-eclampsia (PE). This study first explored the longitudinal change of GM in HDP patients during pregnancy, found the differential GM, and detected the causal association. Our findings may promote the prevention and treatment of HDP from the perspective of GM and provide valuable insights into the pathogenesis of HDP.
The role of bodily self-consciousness in episodic memory of naturalistic events: an immersive virtual reality study
Authors: Penaud Sylvain , Yeh Delphine , Gaston-Bellegarde Alexandre , Piolino Pascale 
Published: October 2023

AbstractRecent studies suggest that the human body plays a critical role in episodic memory. Still, the precise relationship between bodily self-consciousness (BSC) and memory formation of specific events, especially in real-life contexts, remains a topic of ongoing research. The present study investigated the relationship between BSC and episodic memory (EM) using immersive virtual reality (VR) technology. Participants were immersed in an urban environment with naturalistic events, while their visuomotor feedback was manipulated in three within-subjects conditions: Synchronous, Asynchronous, and No-body. Our results show that asynchronous visuomotor feedback and not seeing one’s body, compared to synchronous feedback, decrease the sense of self-identification, self-location and agency, and sense of presence. Moreover, navigating in the Asynchronous condition had a detrimental impact on incidental event memory, perceptual details, contextual association, subjective sense of remembering, and memory consolidation. In contrast, participants in the No-Body condition were only impaired in egocentric spatial memory and the sense of remembering at ten-day delay. We discuss these findings in relation to the role of bodily self-representation in space during event memory encoding. This study sheds light on the complex interplay between BSC, sense of presence, and episodic memory processes, and strengthens the potential of embodiment and VR technology in studying and enhancing human cognition.
Cerebrospinal fluid solute transport associated with sensorimotor brain activity in rodents
Authors: Kim Evgenii , Van Reet Jared , Yoo Seung-Schik 
Published: October 2023

AbstractCerebrospinal fluid (CSF) is crucial for maintaining neuronal homeostasis, providing nutrition, and removing metabolic waste from the brain. However, the relationship between neuronal activity and CSF solute transport remains poorly understood. To investigate the effect of regional neuronal activity on CSF solute transport, Sprague–Dawley rats (all male, n = 30) under anesthesia received an intracisternal injection of a fluorescent tracer (Texas Red ovalbumin) and were subjected to unilateral electrical stimulation of a forelimb. Two groups (n = 10 each) underwent two different types of stimulation protocols for 90 min, one including intermittent 7.5-s resting periods and the other without rest. The control group was not stimulated. Compared to the control, the stimulation without resting periods led to increased transport across most of the cortical areas, including the ventricles. The group that received intermittent stimulation showed an elevated level of solute uptake in limited areas, i.e., near/within the ventricles and on the ventral brain surface. Interhemispheric differences in CSF solute transport were also found in the cortical regions that overlap with the forelimb sensorimotor area. These findings suggest that neuronal activity may trigger local and brain-wide increases in CSF solute transport, contributing to waste clearance.
On t-intuitionistic fuzzy graphs: a comprehensive analysis and application in poverty reduction
Authors: Razzaque Asima , Masmali Ibtisam , Latif Laila , Shuaib Umer , Razaq Abdul , Alhamzi Ghaliah , Noor Saima 
Published: October 2023

AbstractThis paper explains the idea of t-intuitionistic fuzzy graphs as a powerful way to analyze and display relationships that are difficult to understand. The article also illustrates the ability of t-intuitionistic fuzzy graphs to establish complex relationships with multiple factors or dimensions of a physical situation under consideration. Moreover, the fundamental set operations of t-intuitionistic fuzzy graphs are proposed. The notions of homomorphism and isomorphism of t-intuitionistic fuzzy graphs are also introduced. Furthermore, the paper highlights a practical application of the proposed technique in the context of poverty reduction within a specific society. By employing t-intuitionistic fuzzy graphs, the research demonstrates the potential to address the multifaceted nature of poverty, considering various contributing factors and their interdependencies. This application showcases the versatility and effectiveness of t-intuitionistic fuzzy graphs as a tool for decision-making and policy planning in complex societal issues.
Weight-cycling over 6 years is associated with pain, physical function and depression in the Osteoarthritis Initiative cohort
Authors: Vincent Heather K. , Johnson Alisa J. , Sibille Kim T. , Vincent Kevin R. , Cruz-Almeida Yenisel 
Published: October 2023

AbstractBody weight significantly impacts health and quality of life, and is a leading risk factor for the development of knee osteoarthritis (OA). Weight cycling may have more negative health consequences compared to steady high or low weight. Using the Osteoarthritis Initiative dataset, we investigated the effects of weight cycling on physical function, quality of life, and depression over 72-months compared to stable or unidirectional body weight trajectories. Participants (n = 731) had knee OA and were classified as: (1) stable-low (BMI < 25), (2) stable-overweight (BMI = 25–29.9), and (3) stable-obese (BMI ≥ 30); (4) steady-weight-loss; (5) steady-weight-gain (weight loss/gain ≥ 2.2 kg every 2-years); (6) gain–loss–gain weight cycling, and (7) loss–gain–loss weight cycling (weight loss/gain with return to baseline), based on bi-annual assessments. We compared Knee Injury and Osteoarthritis Outcome Knee-Related Quality of Life, Function in Sports and Recreation, Physical Activity in the Elderly, Short Form SF-12, repeated chair rise, 20-m gait speed, and Center for Epidemiological Studies Depression using repeated-measures ANOVA. The steady weight loss group demonstrated the worst pain, physical function, and depressive symptoms over time (p’s < 0.05). More research is needed to confirm these findings, and elucidate the mechanisms by which steady weight loss is associated with functional decline in knee OA.
Sensitivity to the sonority sequencing principle in rats (Rattus norvegicus)
Authors: Santolin Chiara , Crespo-Bojorque Paola , Sebastian-Galles Nuria , Toro Juan Manuel 
Published: October 2023

AbstractAlbeit diverse, human languages exhibit universal structures. A salient example is the syllable, an important structure of language acquisition. The structure of syllables is determined by the Sonority Sequencing Principle (SSP), a linguistic constraint according to which phoneme intensity must increase at onset, reaching a peak at nucleus (vowel), and decline at offset. Such structure generates an intensity pattern with an arch shape. In humans, sensitivity to restrictions imposed by the SSP on syllables appears at birth, raising questions about its emergence. We investigated the biological mechanisms at the foundations of the SSP, testing a nonhuman, non-vocal-learner species with the same language materials used with humans. Rats discriminated well-structured syllables (e.g., pras) from ill-structured ones (e.g., lbug) after being familiarized with syllabic structures conforming to the SSP. In contrast, we did not observe evidence that rats familiarized with syllables that violate such constraint discriminated at test. This research provides the first evidence of sensitivity to the SSP in a nonhuman species, which likely stems from evolutionary-ancient cross-species biological predispositions for natural acoustic patterns. Humans’ early sensitivity to the SSP possibly emerges from general auditory processing that favors sounds depicting an arch-shaped envelope, common amongst animal vocalizations. Ancient sensory mechanisms, responsible for processing vocalizations in the wild, would constitute an entry-gate for human language acquisition.
Effect of electrode materials on resistive switching behaviour of NbOx-based memristive devices
Authors: Leonetti Giuseppe , Fretto Matteo , Pirri Fabrizio Candido , De Leo Natascia , Valov Ilia , Milano Gianluca 
Published: October 2023

AbstractMemristive devices that rely on redox-based resistive switching mechanism have attracted great attention for the development of next-generation memory and computing architectures. However, a detailed understanding of the relationship between involved materials, interfaces, and device functionalities still represents a challenge. In this work, we analyse the effect of electrode metals on resistive switching functionalities of NbOx-based memristive cells. For this purpose, the effect of Au, Pt, Ir, TiN, and Nb top electrodes was investigated in devices based on amorphous NbOxgrown by anodic oxidation on a Nb substrate exploited also as counter electrode. It is shown that the choice of the metal electrode regulates electronic transport properties of metal–insulator interfaces, strongly influences the electroforming process, and the following resistive switching characteristics. Results show that the electronic blocking character of Schottky interfaces provided by Au and Pt metal electrodes results in better resistive switching performances. It is shown that Pt represents the best choice for the realization of memristive cells when the NbOxthickness is reduced, making possible the realization of memristive cells characterised by low variability in operating voltages, resistance states and with low device-to-device variability. These results can provide new insights towards a rational design of redox-based memristive cells.
Machine learning-based predictive modelling for the enhancement of wine quality
Authors: Jain Khushboo , Kaushik Keshav , Gupta Sachin Kumar , Mahajan Shubham , Kadry Seifedine 
Published: October 2023

AbstractThe certification of wine quality is essential to the wine industry. The main goal of this work is to develop a machine learning model to forecast wine quality using the dataset. We utilised samples from the red wine dataset (RWD) with eleven distinct physiochemical properties. With the initial RWD, five machine learning (ML) models were trained and put to the test. The most accurate algorithms are Random Forest (RF) and Extreme Gradient Boosting (XGBoost). Using these two ML approaches, the top three features from a total of eleven features are chosen, and ML analysis is performed on the remaining features. Several graphs are employed to demonstrate the feature importance based on the XGBoost model and RF. Wine quality was predicted using relevant characteristics, often referred to as fundamental elements, that were shown to be essential during the feature selection procedure. When trained and tested without feature selection, with feature selection (RF), and with key attributes, the XGBoost classifier displayed 100% accuracy. In the presence of essential variables, the RF classifier performed better. Finally, to assess the precision of their predictions, the authors trained an RF classifier, validated it, and changed its hyperparameters. To address collinearity and decrease the quantity of predictors without sacrificing model accuracy, we have also used cluster analysis.
The better to eat you with: morphological disparity and enamel ultrastructure in odontocetes
Authors: Viglino Mariana , Ezcurra Martín D. , Fordyce R. Ewan , Loch Carolina 
Published: October 2023

AbstractVariations in the shape and size of teeth have been associated with changes in enamel ultrastructure across odontocetes. Characterizing these features in extinct taxa can elucidate their functional morphology and feeding strategy, while also shedding light into macroevolutionary patterns during the evolutionary history of cetaceans. This study aimed to (1) describe the enamel and dentine ultrastructure of the Early Miocene odontocetesNotocetus vanbenedeniandPhoberodon arctirostrisfrom Patagonia (Argentina) and (2) quantify tooth and enamel ultrastructure morphological disparity among odontocetes. Enamel was predominantly prismatic, thin in the anterior tooth ofN. vanbenedeniandP. arctirostris; whilst thick on the posterior tooth ofN. vanbenedeni. Together with skull morphology, data suggests a raptorial feeding strategy forP. arctirostrisand a combination suction feeding method forN. vanbenedeni. Statistical analyses supported these inferences, indicating that enamel characters are useful for paleoecological research. Morphological disparity analyses showed that extant odontocetes occupy a larger morphospace and have more disparate morphologies, whilst extinct odontocetes were more similar among each other than with the extant group. There was no clear phylogenetic-based grouping, suggesting that tooth and enamel ultrastructure disparity were mainly driven by ecological pressures. These results highlight enamel ultrastructure as a source for broader-scale paleoecological studies in cetaceans.
The amniotic fluid proteome changes across gestation in humans and rhesus macaques
Authors: Shorey-Kendrick Lyndsey E. , Crosland B. Adam , Spindel Eliot R. , McEvoy Cindy T. , Wilmarth Phillip A. , Reddy Ashok P. , Zientek Keith D. , Roberts Victoria H. J. , D’Mello Rahul J. , Ryan Kimberly S. , Olyaei Amy F. , Hagen Olivia L. , Drake Matthew G. , McCarty Owen J.T. , Scottoline Brian P. , Lo Jamie O. 
Published: October 2023

AbstractAmniotic fluid is a complex biological medium that offers protection to the fetus and plays a key role in normal fetal nutrition, organogenesis, and potentially fetal programming. Amniotic fluid is also critically involved in longitudinally shaping the in utero milieu during pregnancy. Yet, the molecular mechanism(s) of action by which amniotic fluid regulates fetal development is ill-defined partly due to an incomplete understanding of the evolving composition of the amniotic fluid proteome. Prior research consisting of cross-sectional studies suggests that the amniotic fluid proteome changes as pregnancy advances, yet longitudinal alterations have not been confirmed because repeated sampling is prohibitive in humans. We therefore performed serial amniocenteses at early, mid, and late gestational time-points within the same pregnancies in a rhesus macaque model. Longitudinally-collected rhesus amniotic fluid samples were paired with gestational-age matched cross-sectional human samples. Utilizing LC–MS/MS isobaric labeling quantitative proteomics, we demonstrate considerable cross-species similarity between the amniotic fluid proteomes and large scale gestational-age associated changes in protein content throughout pregnancy. This is the first study to compare human and rhesus amniotic fluid proteomic profiles across gestation and establishes a reference amniotic fluid proteome. The non-human primate model holds promise as a translational platform for amniotic fluid studies.
Flow–solid coupling analysis of underground reinforced concrete forked pipe enclosing rock and structure
Authors: Xiao Ming , Yuan Qingteng , Zhao Binxin , Deng Liang 
Published: October 2023

AbstractThe stability of the surrounding rock for the construction excavation and the reinforcement of the lining structure during operation in the water-rich area is a difficult problem for the design of high-head underground turnout pipes. Firstly, according to the mechanism of excavation load release and surrounding rock damage evolution, the seepage effect of excavation in the construction of the forked caves is coupled to the surrounding rock stress damage, and an iterative method of numerical simulation of the coupled mutual feedback effect of excavation surrounding rock stress and seepage is proposed. Then, based on the cracking characteristics of the high internal water pressure reinforced concrete turnpike lining, a numerical analysis method of the coupling interaction between lining cracking and internal water seepage is proposed by coupling internal water seepage to stress damage in the lining by cracking the forked pipe structure. Applying the aforementioned method to a forked pipe project, the results show that: during the construction period, there is a significant increase in the damage zone, stress, and displacement of the rock around the cavern after considering the coupled iterations; during the operation period, with the increase in internal water pressure, the lining structure accelerates cracking due to the external infiltration of internal water; after the internal water is applied, the surrounding rock bears the main internal water pressure and the reinforcement bears only part of the circumferential force. The method provides theoretical support for the analysis and calculation of the reinforcement of similar underground high-pressure tunnels for rock support and lining structures and has certain theoretical and engineering significance.