bluuebunny/crossref_metadata_2025_split huggingface dataset:
Learning from virtual experiments to assist users of Small Angle Neutron Scattering in model selection
Authors: Robledo José Ignacio , Frielinghaus Henrich , Willendrup Peter , Lieutenant Klaus 
Published: July 2024

AbstractIn this work, we combine the advantages of virtual Small Angle Neutron Scattering (SANS) experiments carried out by Monte Carlo simulations with the recent advances in computer vision to generate a tool that can assist SANS users in small angle scattering model selection. We generate a dataset of almost 260.000 SANS virtual experiments of the SANS beamline KWS-1 at FRM-II, Germany, intended for Machine Learning purposes. Then, we train a recommendation system based on an ensemble of Convolutional Neural Networks to predict the SANS model from the two-dimensional scattering pattern measured at the position-sensitive detector of the beamline. The results show that the CNNs can learn the model prediction task, and that this recommendation system has a high accuracy in the classification task on 46 different SANS models. We also test the network with real data and explore the outcome. Finally, we discuss the reach of counting with the set of virtual experimental data presented here, and of such a recommendation system in the SANS user data analysis procedure.
Phenotypic characterisation of bovine alveolar macrophages reveals two major subsets with differential expression of CD163
Authors: Randall Emily M. , Sopp Paul , Raper Anna , Dry Inga , Burdon Tom , Hope Jayne C. , Waddell Lindsey A. 
Published: July 2024

AbstractBovine alveolar macrophages (AMs) defend the lungs against pathogens such as Mycobacterium bovis (M. bovis), the causative agent of bovine tuberculosis. However, little is known about the surface molecules expressed by bovine AMs and whether there is heterogeneity within the population. The purpose of this study was to characterise the bovine AM cell surface phenotype using flow cytometry. Bronchoalveolar lavage samples from four different calves were stained with a combination of antibodies against immune cell molecules prior to flow cytometric analysis. To assess the degree of expression, we considered the distribution and relative intensities of stained and unstained cells. We demonstrated that bovine AMs have high expression of CD172a, ADGRE1, CD206, and CD14, moderate expression of CD80, MHC II, CD1b, and CD40, low expression of CX3CR1 and CD86, and little or no expression of CD16 and CD26. Two distinct subsets of bovine AMs were identified based on CD163 expression. Subsequent analysis showed that the CD163+ subset had greater expression of other typical macrophage molecules compared to the CD163- subset, suggesting that these cells may perform different roles during infection. The characterisation of the uninfected bovine AM phenotype will provide a foundation for the examination of M. bovis-infected AMs.
Condensate and superfluid fraction of homogeneous Bose gases in a self-consistent Popov approximation
Authors: Vianello Cesare , Salasnich Luca 
Published: July 2024

AbstractWe study the condensate and superfluid fraction of a homogeneous gas of weakly interacting bosons in three spatial dimensions by adopting a self-consistent Popov approximation, comparing this approach with other theoretical schemes. Differently from the superfluid fraction, we find that at finite temperature the condensate fraction is a non-monotonic function of the interaction strength, presenting a global maximum at a characteristic value of the gas parameter, which grows as the temperature increases. This non-monotonic behavior has not yet been observed, but could be tested with the available experimental setups of ultracold bosonic atoms confined in a box potential. We clearly identify the region of parameter space that is of experimental interest to look for this behavior and provide explicit expressions for the relevant observables. Finite size effects are also discussed within a semiclassical approximation.
Paternal depressive symptoms and factors associated among expectant fathers in a northeastern province of Thailand
Authors: Loekdee Chattarika , Jungjamroonrat Pajaree , Kongsila Tanin , Lundberg Pranee C. , Phoosuwan Nitikorn 
Published: July 2024

AbstractGlobally, depression is a major mental health problem among expectant fathers. Therefore, factors associated with paternal depressive symptoms (PDS) need investigation. This hospital-based cross-sectional study was aimed to investigate the prevalence of and factors associated with PDS among expectant fathers in a northeastern province of Thailand. In the north-eastern province, Sakon Nakhon, 440 expectant fathers from eight hospitals participated in the study by completing a questionnaire related to socio-demographic characteristics, the Edinburgh Postnatal Depression Scale (EPDS), psychosocial factors and social support. An EPDS score of at least eleven out of 30 was interpreted as having PDS. Multivariable linear regression analysis was applied with a statistical significance at 0.05, and the coefficient β was presented. In total, 81 expectant fathers (18.4%, 95% confidence interval 14.6–22.3) had PDS, and the mean (standard deviation) of the EPDS score was 6.65 (4.25). Insufficient money (β = − 0.099, p = 0.016), marital adjustment (β = − 0.098, p = 0.027), self-esteem (β = − 0.150, p < 0.001), wife’s stress (β = 0.079, p = 0.049), and expectant father’s stress (β = 0.400, p < 0.001) were factors independently associated with PDS. In conclusion, screening expectant fathers during the pregnancy period of their wives is essential, and factors associated with PDS should not be neglected by healthcare providers. Also, there is need of an intervention program to prevent the symptoms, especially for expectant fathers having insufficient money or having stress.
Serum levels of leptin, ghrelin putative peptide YY-3 in patients with fetal alcohol spectrum disorders
Authors: Podgórski Rafał , Galiniak Sabina , Mazur Artur , Domin Agnieszka , Podgórska Dominika 
Published: July 2024

AbstractFetal alcohol spectrum disorders (FASD) are a severe developmental condition resulting from exposure to alcohol during pregnancy. The aim of this study was to examine the concentrations of hormones involved in appetite regulation—ghrelin, leptin, and putative peptide YY-3 (PYY)—in the serum of individuals with FASD. Additionally, we investigated the relationship between these hormone levels and clinical indicators. We conducted an enzyme-linked immunosorbent assay on samples collected from 62 FASD patients and 23 individuals without the condition. Our results revealed a significant decrease in leptin levels among FASD patients compared to the control group (5.124 vs. 6.838 ng/mL, p = 0.002). We revealed no statistically significant differences in the levels of other hormones studied (ghrelin and PYY). Comparisons of hormone levels were also conducted in three subgroups: FAS, neurobehavioral disorders associated with prenatal alcohol exposure and FASD risk, as well as by sex. Assignment to FASD subgroups indicated changes only for leptin. Sex had no effect on the levels of hormones. Moreover, the levels of leptin showed a negative correlation with cortisol levels and a positive correlation with BMI and proopiomelanocortin. Alterations in appetite regulation can contribute to the improper development of children with FASD, which might be another factor that should be taken into consideration in the proper treatment of patients.
Membrane topography and the overestimation of protein clustering in single molecule localisation microscopy – identification and correction
Authors: Adler Jeremy , Bernhem Kristoffer , Parmryd Ingela 
Published: July 2024

AbstractAccording to single-molecule localisation microscopy almost all plasma membrane proteins are clustered. We demonstrate that clusters can arise from variations in membrane topography where the local density of a randomly distributed membrane molecule to a degree matches the variations in the local amount of membrane. Further, we demonstrate that this false clustering can be differentiated from genuine clustering by using a membrane marker to report on local variations in the amount of membrane. In dual colour live cell single molecule localisation microscopy using the membrane probe DiI alongside either the transferrin receptor or the GPI-anchored protein CD59, we found that pair correlation analysis reported both proteins and DiI as being clustered, as did its derivative pair correlation-photoactivation localisation microscopy and nearest neighbour analyses. After converting the localisations into images and using the DiI image to factor out topography variations, no CD59 clusters were visible, suggesting that the clustering reported by the other methods is an artefact. However, the TfR clusters persisted after topography variations were factored out. We demonstrate that membrane topography variations can make membrane molecules appear clustered and present a straightforward remedy suitable as the first step in the cluster analysis pipeline.
PEX3 promotes regenerative repair after myocardial injury in mice through facilitating plasma membrane localization of ITGB3
Authors: Sun Jia-Teng , Wang Zi-Mu , Zhou Liu-Hua , Yang Tong-Tong , Zhao Di , Bao Yu-Lin , Wang Si-Bo , Gu Ling-Feng , Chen Jia-Wen , Shan Tian-Kai , Wei Tian-Wen , Wang Hao , Wang Qi-Ming , Kong Xiang-Qing , Xie Li-Ping , Gu Ai-Hua , Zhao Yang , Chen Feng , Ji Yong , Cui Yi-Qiang , Wang Lian-Sheng 
Published: July 2024

AbstractThe peroxisome is a versatile organelle that performs diverse metabolic functions. PEX3, a critical regulator of the peroxisome, participates in various biological processes associated with the peroxisome. Whether PEX3 is involved in peroxisome-related redox homeostasis and myocardial regenerative repair remains elusive. We investigate that cardiomyocyte-specific PEX3 knockout (Pex3-KO) results in an imbalance of redox homeostasis and disrupts the endogenous proliferation/development at different times and spatial locations. Using Pex3-KO mice and myocardium-targeted intervention approaches, the effects of PEX3 on myocardial regenerative repair during both physiological and pathological stages are explored. Mechanistically, lipid metabolomics reveals that PEX3 promotes myocardial regenerative repair by affecting plasmalogen metabolism. Further, we find that PEX3-regulated plasmalogen activates the AKT/GSK3β signaling pathway via the plasma membrane localization of ITGB3. Our study indicates that PEX3 may represent a novel therapeutic target for myocardial regenerative repair following injury.
Acoustic spin-controlled orbital rotations in double spiral acoustic beams
Authors: Chen Di-Chao , Liu Xie , Wu Da-Jian , Zhu Xing-Feng , Wei Qi , Cheng Ying , Liu Xiao-Jun 
Published: July 2024

AbstractSimilar to optical spin-orbit interactions (SOIs), acoustic SOIs are anticipated to offer fresh perspectives and capabilities for acoustic manipulation beyond conventional scalar degrees of freedom. However, the acoustic extrinsic SOIs caused by particular properties of the medium were seldom explored. Here, the acoustic extrinsic SOI is observed in a double spiral acoustic beam (DSAB), as evidenced by the rotation of the spatial intensity pattern along the propagation axis. The interaction of the acoustic plane wave with the well-designed artificial flat structure generates two non-paraxial focused acoustic vortices (NFAVs) with different spin angular momentums. The coaxial coupling between them leads to acoustic spin-controlled orbital rotation (SOR). Theoretical formulations, supported by numerical simulations and experimental results, are provided to demonstrate the validity of acoustic SOR. Our work provides new perspectives and capabilities for understanding sound processing, and may open an avenue for the development of spin-orbit acoustics.
A reduction in self-reported confidence accompanies the recall of memories distorted by prototypes
Authors: Kerrén Casper , Zhao Yiming , Griffiths Benjamin J. 
Published: July 2024

AbstractWhen we recall a past event, we reconstruct the event based on a combination of episodic details and semantic knowledge (e.g., prototypes). Though prototypes can impair the veracity of recall, it remains unclear whether we are metacognitively aware of the distortions they introduce. To address this, we conducted six experiments in which participants learned object-colour/object-location pairs and subsequently recalled the colour/location when cued with the object. Leveraging unsupervised machine learning algorithms, we extracted participant-specific prototypes and embedded responses in two-dimensional space to quantify prototype-based distortions in individual memory traces. Our findings reveal robust and conceptually replicable evidence to suggest that prototype-based distortion is accompanied by a reduction in self-reported confidence - an implicit measure of metacognitive awareness. Critically, we find evidence to suggest that it is prototype-based distortion of a memory trace that undermines confidence, rather than a lack of confidence biasing reconstruction towards the use of prototypes. Collectively, these findings suggest that we possess metacognitive awareness of distortions embedded in our memories.
The value of convergence research for developing trustworthy AI for weather, climate, and ocean hazards
Authors: McGovern Amy , Demuth Julie , Bostrom Ann , Wirz Christopher D. , Tissot Philippe E. , Cains Mariana G. , Musgrave Kate D. 
Published: July 2024

AbstractArtificial Intelligence applications are rapidly expanding across weather, climate, and natural hazards. AI can be used to assist with forecasting weather and climate risks, including forecasting both the chance that a hazard will occur and the negative impacts from it, which means AI can help protect lives, property, and livelihoods on a global scale in our changing climate. To ensure that we are achieving this goal, the AI must be developed to be trustworthy, which is a complex and multifaceted undertaking. We present our work from the NSF AI Institute for Research on Trustworthy AI in Weather, Climate, and Coastal Oceanography (AI2ES), where we are taking a convergence research approach. Our work deeply integrates across AI, environmental, and risk communication sciences. This involves collaboration with professional end-users to investigate how they assess the trustworthiness and usefulness of AI methods for forecasting natural hazards. In turn, we use this knowledge to develop AI that is more trustworthy. We discuss how and why end-users may trust or distrust AI methods for multiple natural hazards, including winter weather, tropical cyclones, severe storms, and coastal oceanography.
A proximity proteomics pipeline with improved reproducibility and throughput
Authors: Zhong Xiaofang , Li Qiongyu , Polacco Benjamin J , Patil Trupti , Marley Aaron , Foussard Helene , Khare Prachi , Vartak Rasika , Xu Jiewei , DiBerto Jeffrey F , Roth Bryan L , Eckhardt Manon , von Zastrow Mark , Krogan Nevan J , Hüttenhain Ruth 
Published: July 2024

AbstractProximity labeling (PL) via biotinylation coupled with mass spectrometry (MS) captures spatial proteomes in cells. Large-scale processing requires a workflow minimizing hands-on time and enhancing quantitative reproducibility. We introduced a scalable PL pipeline integrating automated enrichment of biotinylated proteins in a 96-well plate format. Combining this with optimized quantitative MS based on data-independent acquisition (DIA), we increased sample throughput and improved protein identification and quantification reproducibility. We applied this pipeline to delineate subcellular proteomes across various compartments. Using the 5HT2A serotonin receptor as a model, we studied temporal changes of proximal interaction networks induced by receptor activation. In addition, we modified the pipeline for reduced sample input to accommodate CRISPR-based gene knockout, assessing dynamics of the 5HT2A network in response to perturbation of selected interactors. This PL approach is universally applicable to PL proteomics using biotinylation-based PL enzymes, enhancing throughput and reproducibility of standard protocols.
Bone metabolism – an underappreciated player
Authors: Choi In Ah , Umemoto Akio , Mizuno Masataka , Park-Min Kyung-Hyun 
Published: July 2024

AbstractBone is constantly being remodeled, and this process is orchestrated by a dynamic crosstalk of bone cells, including osteoclasts, osteoblasts, and osteocytes. Recent evidence suggests that cellular metabolism plays a crucial role in the differentiation and function of bone cells and facilitates the adaptation of bone cells to changes in the bone microenvironment. Moreover, bone affects whole-body energy metabolism. However, it is not yet completely understood how different cells in bone coordinate metabolic processes under physiological conditions, and how altered metabolic processes in bone cells contribute to pathological conditions where the balance among bone cells is disrupted. Therefore, gaining a better understanding of the distinct metabolic requirements of bone cells can provide crucial insights into the dysfunction of bone cells in pathological conditions and can be used to identify new therapeutic approaches to treat bone diseases. Here, we discuss recent advances in understanding metabolic reprogramming in bone cells.
Serum and CSF metabolomics analysis shows Mediterranean Ketogenic Diet mitigates risk factors of Alzheimer’s disease
Authors: Schweickart Annalise , Batra Richa , Neth Bryan J. , Martino Cameron , Shenhav Liat , Zhang Anru R. , Shi Pixu , Karu Naama , Huynh Kevin , Meikle Peter J. , Schimmel Leyla , Dilmore Amanda Hazel , Blennow Kaj , Zetterberg Henrik , Blach Colette , Dorrestein Pieter C. , Knight Rob ,   Alzheimer’s Gut Microbiome Project Consortium, Craft Suzanne , Kaddurah-Daouk Rima , Krumsiek Jan 
Published: July 2024

AbstractAlzheimer’s disease (AD) is influenced by a variety of modifiable risk factors, including a person’s dietary habits. While the ketogenic diet (KD) holds promise in reducing metabolic risks and potentially affecting AD progression, only a few studies have explored KD’s metabolic impact, especially on blood and cerebrospinal fluid (CSF). Our study involved participants at risk for AD, either cognitively normal or with mild cognitive impairment. The participants consumed both a modified Mediterranean Ketogenic Diet (MMKD) and the American Heart Association diet (AHAD) for 6 weeks each, separated by a 6-week washout period. We employed nuclear magnetic resonance (NMR)-based metabolomics to profile serum and CSF and metagenomics profiling on fecal samples. While the AHAD induced no notable metabolic changes, MMKD led to significant alterations in both serum and CSF. These changes included improved modifiable risk factors, like increased HDL-C and reduced BMI, reversed serum metabolic disturbances linked to AD such as a microbiome-mediated increase in valine levels, and a reduction in systemic inflammation. Additionally, the MMKD was linked to increased amino acid levels in the CSF, a breakdown of branched-chain amino acids (BCAAs), and decreased valine levels. Importantly, we observed a strong correlation between metabolic changes in the CSF and serum, suggesting a systemic regulation of metabolism. Our findings highlight that MMKD can improve AD-related risk factors, reverse some metabolic disturbances associated with AD, and align metabolic changes across the blood-CSF barrier.
Technical Nuances in the Perioperative Management of Chronic Subdural Hematoma by Twin Burr Hole Craniostomy: Tips, Tricks, and Tactics
Authors: Sethi Jatin K. , Harsh Viraat , Kumar Prashant , Sahay Chandra B. , Kumar Anil 
Published: July 2024

AbstractChronic subdural hematoma (CSDH) remains to be the most common neurosurgical entity usually encountered in the elderly population. With an increasing life expectancy and associated comorbidities, the incidence of CSDH is ever increasing. There is a lack of uniformity among neurosurgeons regarding management of CSDH, but surgical evacuation using twin burr hole craniostomy remains to be the most preferred modality. Other options available are twist drill craniostomy and craniotomy. A conservative approach may be preferred in a thin subdural hematoma with no or minimal neurological deficit or in high operative risk patients. Complications such as pneumocephalus, recollection, or rebleeding may be seen following surgical evacuation of CSDH. Herein we aimed to address the technical nuances associated with twin burr hole evacuation of CSDH to reduce the complications and the overall associated morbidity and mortality.
Toolkitting: an unrecognized form of expertise for overcoming fragmentation in inter- and transdisciplinarity
Authors: Laursen Bethany , Vienni-Baptista Bianca , Bammer Gabriele , Di Giulio Antonietta , Paulsen Theres , Robson-Williams Melissa , Studer Sibylle 
Published: July 2024

AbstractA growing number of inter- and transdisciplinary (ITD) toolkits provide methods, processes, concepts, heuristics, frameworks, and other resources for designing and implementing ITD research. A brief overview of the currently fragmented toolkits landscape is provided, fleshed out through descriptions of four toolkits. Fragmentation means that researchers are unaware of, and do not have access to, the full array of tools that could benefit their investigations. Overcoming fragmentation requires attention to toolkitting, which is the relatively overlooked bundle of practices involved in the creation, use, maintenance, funding, and study of toolkits. In particular, the processes and expertise involved in the creation, maintenance, and study of toolkits are described. Toolkitting as metawork can make resources more accessible, useful, and rigorous, enhancing ITD research. Future toolkitting can be strengthened with attention to key questions that can guide the activities of, respectively, toolkit creators and curators, scholars, and funders. Examining the toolkits landscape through the lens of toolkitting suggests that the development of a comprehensive, ongoing inventory is a first step in overcoming toolkit fragmentation. An inventory could also be the foundation for an even bolder initiative—a federated knowledge bank—that connects and develops the range of existing and future toolkits. The inventory and federated knowledge bank also provide a shared project to bring together the expertise of ITD toolkit creators, curators, users, funders, and scholars to achieve a step-change in enhancing ITD research.
The origin of magnetic ordering and reduced mobility in KTaO3-based 2DEGs: Interfacial interdiffusion
Authors: Fan Zixin , Sui Qiangtao , Ran Feng , Ling Haoming , Li Dingyi , Wang Zihao , Chen Pan , Liang Yan , Zhang Jiandi 
Published: July 2024

Recently, KTaO3 (KTO)-based 5d two-dimensional electron gases (2DEGs), characterized by robust spin–orbit coupling, have emerged as promising candidates for future spintronic devices. However, the carrier mobility of KTO-based 2DEGs is typically lower than that of SrTiO3-based 2DEGs, which limits their further development. It is imperative to explore the underlying causes of diminished carrier mobility and devise strategies to augment it. In addition, the genesis of magnetism within KTO-based 2DEGs remains ambiguous. In this study, the 2DEG within the amorphous-EuTiO3/KTO (a-ETO/KTO) heterostructure demonstrates a high electron mobility of 289.1 cm2 V−1 s−1, which exhibits a significant decrease as the film growth temperatures increase. This decrease can be primarily ascribed to electron scattering by impurities, which is induced by the amplified interfacial element interdiffusion at a higher film growth temperature. In addition, the magnetism of 2DEGs for samples grown at different temperatures shows an increasing trend with growth temperatures, which is predominantly derived from the interdiffusion of Eu atoms. This study provides an in-depth analysis of the origin of magnetic ordering and reduced mobility in KTO-based 2DEGs, which will promote the further development of 2DEGs for future applications in electronic devices.