bluuebunny/crossref_metadata_2025_split huggingface dataset:
Beta-glucan intake with energy and carbohydrate restricted meals: impact on subjective appetite and gastrointestinal appetite hormones in overweight adults
Authors: Baobid N. , Khodova V. , Clak M. , Albalji M. , Edwards C.A , Malkova D. 
Published: July 2024

Energy restriction is commonly used as body weight-loss interventions (1). However, it modifies secretion of gastrointestinal appetite hormones, which might be expected to upregulate appetite and thus impair the ability to comply with prescribed intervention(1). Supplementation with soluble fibre may potentially counteract this matter (2). This study aimed to investigate whether addition of β- glucan to energy and carbohydrate-restricted meals impacts postprandial responses of gastrointestinal appetite hormones and subjective appetite in overweight adults.Twenty-three sedentary individuals living with overweight or obesity (age: 36 ± 8.5 years, BMI: 31.12 ± 4.04 kg/m2) participated in a double-blind randomised crossover study with two experimental arms, each lasting over two days. On day 1, participants consumed Counterweight PRO800 meal replacement shakes/soups for breakfast and dinner at home, each providing ~200 kcal and a carbohydrate-restricted lunch providing 35% of their habitual energy intake. On day 2, participants attended the metabolic investigation room where they consumed the same breakfast and lunch as on day 1. On both days, each meal was taken with either 3g β-glucan (Oat Well) or cellulose (Comprecel) as placebo. On Day 2, fasting and postprandial appetite scores were recorded, and fasting and postprandial blood samples were obtained for the measurements of plasma concentration of acylated ghrelin, PYY, and GLP-1. The study is registered at www.clinicaltrials.gov as NCT05981404.Two-way ANOVA showed that the postprandial concentrations of acylated ghrelin (β-glucan arm, 383 ± 23 pg/ml; placebo arm, 428 ± 23 pg/ml, P=0.02, treatment effect) and composite appetite scores (P=0.003, treatment effect) were significantly lower and PYY concentrations (β-glucan arm, 132 ± 5 pg/ml; Placebo arm, 110 ± 4 pg/ml, P= 0.003, treatment effect) significantly higher in the β- glucan arm than in the Placebo arm. The concentrations of GLP-1 were not different between arms (β-glucan arm, 29 ± 1 pM; placebo arm, 28 ± 0.9 pM, P=0.36, treatment effect).The obtained data suggests that consuming β -glucan with energy and carbohydrate-restricted meals can be expected to attenuate reduction in satiety and diminish increase in hunger. Therefore, supplementation with β-glucan during energy restriction intervention applied to body weight loss might lead to improve compliance and reduce discomfort of negative energy balance.
Tissue-resident memory T cells break tolerance to renal autoantigens and orchestrate immune-mediated nephritis
Authors: Arnold Frederic , Kupferschmid Laurence , Weissenborn Philipp , Heldmann Lukas , Hummel Jonas F. , Zareba Paulina , Sagar  , Rogg Manuel , Schell Christoph , Tanriver Yakup 
Published: July 2024

AbstractImmune-mediated nephritis is a leading cause of acute kidney injury and chronic kidney disease. While the role of B cells and antibodies has been extensively investigated in the past, the advent of immune-checkpoint inhibitors has led to a reappraisal of the role of T cells in renal immunology. However, it remains elusive how T cells with specificity for renal autoantigens are activated and participate in immune-mediated nephritis. Here, we followed the fate and function of pathogen-activated autoreactive CD8 T cells that are specific for a renal autoantigen. We demonstrate that recently activated splenic CD8 T cells developed a hybrid phenotype in the context of renal autoantigen cross-presentation, combining hallmarks of activation and T cell dysfunction. While circulating memory T cells rapidly disappeared, tissue-resident memory T cells emerged and persisted within the kidney, orchestrating immune-mediated nephritis. Notably, T cells infiltrating kidneys of patients with interstitial nephritis also expressed key markers of tissue residency. This study unveils how a tissue-specific immune response can dissociate from its systemic counterpart driving a compartmentalized immune response in the kidneys of mice and man. Consequently, targeting tissue-resident memory T cells emerges as a promising strategy to control immune-mediated kidney disease.
ezSingleCell: an integrated one-stop single-cell and spatial omics analysis platform for bench scientists
Authors: Sethi Raman , Ang Kok Siong , Li Mengwei , Long Yahui , Ling Jingjing , Chen Jinmiao 
Published: July 2024

AbstractezSingleCell is an interactive and easy-to-use application for analysing various single-cell and spatial omics data types without requiring prior programing knowledge. It combines the best-performing publicly available methods for in-depth data analysis, integration, and interactive data visualization. ezSingleCell consists of five modules, each designed to be a comprehensive workflow for one data type or task. In addition, ezSingleCell allows crosstalk between different modules within a unified interface. Acceptable input data can be in a variety of formats while the output consists of publication ready figures and tables. In-depth manuals and video tutorials are available to guide users on the analysis workflows and parameter adjustments to suit their study aims. ezSingleCell’s streamlined interface can analyse a standard scRNA-seq dataset of 3000 cells in less than five minutes. ezSingleCell is available in two forms: an installation-free web application (https://immunesinglecell.org/ezsc/) or a software package with a shinyApp interface (https://github.com/JinmiaoChenLab/ezSingleCell2) for offline analysis.
Recreating the biological steps of viral infection on a cell-free bioelectronic platform to profile viral variants of concern
Authors: Chao Zhongmou , Selivanovitch Ekaterina , Kallitsis Konstantinos , Lu Zixuan , Pachaury Ambika , Owens Róisín , Daniel Susan 
Published: July 2024

AbstractViral mutations frequently outpace technologies used to detect harmful variants. Given the continual emergence of SARS-CoV-2 variants, platforms that can identify the presence of a virus and its propensity for infection are needed. Our electronic biomembrane sensing platform recreates distinct SARS-CoV-2 host cell entry pathways and reports the progression of entry as electrical signals. We focus on two necessary entry processes mediated by the viral Spike protein: virus binding and membrane fusion, which can be distinguished electrically. We find that closely related variants of concern exhibit distinct fusion signatures that correlate with trends in cell-based infectivity assays, allowing us to report quantitative differences in their fusion characteristics and hence their infectivity potentials. We use SARS-CoV-2 as our prototype, but we anticipate that this platform can extend to other enveloped viruses and cell lines to quantifiably assess virus entry.
Environmental damping and vibrational coupling of confined fluids within isolated carbon nanotubes
Authors: Tu Yu-Ming , Kuehne Matthias , Misra Rahul Prasanna , Ritt Cody L. , Oliaei Hananeh , Faucher Samuel , Li Haokun , Xu Xintong , Penn Aubrey , Yang Sungyun , Yang Jing Fan , Sendgikoski Kyle , Chakraverty Joshika , Cumings John , Majumdar Arun , Aluru Narayana R. , Hachtel Jordan A. , Blankschtein Daniel , Strano Michael S. 
Published: July 2024

AbstractBecause of their large surface areas, nanotubes and nanowires demonstrate exquisite mechanical coupling to their surroundings, promising advanced sensors and nanomechanical devices. However, this environmental sensitivity has resulted in several ambiguous observations of vibrational coupling across various experiments. Herein, we demonstrate a temperature-dependent Radial Breathing Mode (RBM) frequency in free-standing, electron-diffraction-assigned Double-Walled Carbon Nanotubes (DWNTs) that shows an unexpected and thermally reversible frequency downshift of 10 to 15%, for systems isolated in vacuum. An analysis based on a harmonic oscillator model assigns the distinctive frequency cusp, produced over 93 scans of 3 distinct DWNTs, along with the hyperbolic trajectory, to a reversible increase in damping from graphitic ribbons on the exterior surface. Strain-dependent coupling from self-tensioned, suspended DWNTs maintains the ratio of spring-to-damping frequencies, producing a stable saturation of RBM in the low-tension limit. In contrast, when the interior of DWNTs is subjected to a water-filling process, the RBM thermal trajectory is altered to that of a Langmuir isobar and elliptical trajectories, allowing measurement of the enthalpy of confined fluid phase change. These mechanisms and quantitative theory provide new insights into the environmental coupling of nanomechanical systems and the implications for devices and nanofluidic conduits.
Multi-modal generative modeling for joint analysis of single-cell T cell receptor and gene expression data
Authors: Drost Felix , An Yang , Bonafonte-Pardàs Irene , Dratva Lisa M. , Lindeboom Rik G. H. , Haniffa Muzlifah , Teichmann Sarah A. , Theis Fabian , Lotfollahi Mohammad , Schubert Benjamin 
Published: July 2024

AbstractRecent advances in single-cell immune profiling have enabled the simultaneous measurement of transcriptome and T cell receptor (TCR) sequences, offering great potential for studying immune responses at the cellular level. However, integrating these diverse modalities across datasets is challenging due to their unique data characteristics and technical variations. Here, to address this, we develop the multimodal generative model mvTCR to fuse modality-specific information across transcriptome and TCR into a shared representation. Our analysis demonstrates the added value of multimodal over unimodal approaches to capture antigen specificity. Notably, we use mvTCR to distinguish T cell subpopulations binding to SARS-CoV-2 antigens from bystander cells. Furthermore, when combined with reference mapping approaches, mvTCR can map newly generated datasets to extensive T cell references, facilitating knowledge transfer. In summary, we envision mvTCR to enable a scalable analysis of multimodal immune profiling data and advance our understanding of immune responses.
How to catch a shear band and explain plasticity of metallic glasses with continuum mechanics
Authors: Glushko Oleksandr , Pippan Reinhard , Şopu Daniel , Mitterer Christian , Eckert Jürgen 
Published: July 2024

AbstractCapturing a shear band in a metallic glass during its propagation experimentally is very challenging. Shear bands are very narrow but extend rapidly over macroscopic distances, therefore, characterization of large areas at high magnification and high speed is required. Here we show how to control the shear bands in a pre-structured thin film metallic glass in order to directly measure local strains during initiation, propagation, or arrest events. Based on the experimental observations, a model describing the shear banding phenomenon purely within the frameworks of continuum mechanics is formulated. We claim that metallic glasses exhibit an elastic limit of about 5% which must be exceeded locally either at a stress concentrator to initiate a shear banding event, or at the tip of a shear band during its propagation. The model can successfully connect micro- and macroscopic plasticity of metallic glasses and suggests an alternative interpretation of controversial experimental observations.
Rockfish: A transformer-based model for accurate 5-methylcytosine prediction from nanopore sequencing
Authors: Stanojević Dominik , Li Zhe , Bakić Sara , Foo Roger , Šikić Mile 
Published: July 2024

AbstractDNA methylation plays an important role in various biological processes, including cell differentiation, ageing, and cancer development. The most important methylation in mammals is 5-methylcytosine mostly occurring in the context of CpG dinucleotides. Sequencing methods such as whole-genome bisulfite sequencing successfully detect 5-methylcytosine DNA modifications. However, they suffer from the serious drawbacks of short read lengths and might introduce an amplification bias. Here we present Rockfish, a deep learning algorithm that significantly improves read-level 5-methylcytosine detection by using Nanopore sequencing. Rockfish is compared with other methods based on Nanopore sequencing on R9.4.1 and R10.4.1 datasets. There is an increase in the single-base accuracy and the F1 measure of up to 5 percentage points on R.9.4.1 datasets, and up to 0.82 percentage points on R10.4.1 datasets. Moreover, Rockfish shows a high correlation with whole-genome bisulfite sequencing, requires lower read depth, and achieves higher confidence in biologically important regions such as CpG-rich promoters while being computationally efficient. Its superior performance in human and mouse samples highlights its versatility for studying 5-methylcytosine methylation across varied organisms and diseases. Finally, its adaptable architecture ensures compatibility with new versions of pores and chemistry as well as modification types.
Magnetic excitations in strained infinite-layer nickelate PrNiO2 films
Authors: Gao Qiang , Fan Shiyu , Wang Qisi , Li Jiarui , Ren Xiaolin , Biało Izabela , Drewanowski Annabella , Rothenbühler Pascal , Choi Jaewon , Sutarto Ronny , Wang Yao , Xiang Tao , Hu Jiangping , Zhou Ke-Jin , Bisogni Valentina , Comin Riccardo , Chang J. , Pelliciari Jonathan , Zhou X. J. , Zhu Zhihai 
Published: July 2024

AbstractStrongly correlated materials respond sensitively to external perturbations such as strain, pressure, and doping. In the recently discovered superconducting infinite-layer nickelates, the superconducting transition temperature can be enhanced via only ~ 1% compressive strain-tuning with the root of such enhancement still being elusive. Using resonant inelastic x-ray scattering (RIXS), we investigate the magnetic excitations in infinite-layer PrNiO2 thin films grown on two different substrates, namely SrTiO3 (STO) and (LaAlO3)0.3(Sr2TaAlO6)0.7 (LSAT) enforcing different strain on the nickelates films. The magnon bandwidth of PrNiO2 shows only marginal response to strain-tuning, in sharp contrast to the enhancement of the superconducting transition temperature Tc in the doped superconducting samples. These results suggest the bandwidth of spin excitations of the parent compounds is similar under strain while Tc in the doped ones is not, and thus provide important empirics for the understanding of superconductivity in infinite-layer nickelates.
A rapid aureochrome opto-switch enables diatom acclimation to dynamic light
Authors: Zhang Huan , Xiong Xiaofeng , Guo Kangning , Zheng Mengyuan , Cao Tianjun , Yang Yuqing , Song Jiaojiao , Cen Jie , Zhang Jiahuan , Jiang Yanyou , Feng Shan , Tian Lijin , Li Xiaobo 
Published: July 2024

AbstractDiatoms often outnumber other eukaryotic algae in the oceans, especially in coastal environments characterized by frequent fluctuations in light intensity. The identities and operational mechanisms of regulatory factors governing diatom acclimation to high light stress remain largely elusive. Here, we identified the AUREO1c protein from the coastal diatom Phaeodactylum tricornutum as a crucial regulator of non-photochemical quenching (NPQ), a photoprotective mechanism that dissipates excess energy as heat. AUREO1c detects light stress using a light-oxygen-voltage (LOV) domain and directly activates the expression of target genes, including LI818 genes that encode NPQ effector proteins, via its bZIP DNA-binding domain. In comparison to a kinase-mediated pathway reported in the freshwater green alga Chlamydomonas reinhardtii, the AUREO1c pathway exhibits a faster response and enables accumulation of LI818 transcript and protein levels to comparable degrees between continuous high-light and fluctuating-light treatments. We propose that the AUREO1c-LI818 pathway contributes to the resilience of diatoms under dynamic light conditions.
Advantages of cone beam computed tomography for evaluation of subchondral insufficiency fractures of the knee compared to MRI
Authors: Delsmann Maximilian M. , Delsmann Julian , Jandl Nico Maximilian , Maas Kai-Jonathan , Beil Frank Timo , Amling Michael , Henes Frank Oliver , Rolvien Tim , Spink Clemens 
Published: July 2024

AbstractTo determine the diagnostic yield of cone beam computed tomography (CBCT) compared with 3 T magnetic resonance imaging (MRI) for the evaluation of subchondral insufficiency fractures of the knee. Consecutive patients with subchondral insufficiency fractures of the knee examined by 3 T MRI and CBCT of the femoral condyles were reviewed. Two experienced raters graded the lesion severity on 3 T MRI and CBCT images: grade 1: no signs of a subchondral bone lesion; grade 2: subchondral trabecular fracture or cystic changes, but without infraction of the subchondral bone plate; grade 3: collapse of the subchondral bone plate. Ratings were repeated after six weeks to determine reliability. In addition, the bone lesion size was measured as elliptical area (mm2) and compared between CBCT and T1-weighted MRI sequences. Among 30 patients included (43.3% women; mean age: 60.9 ± 12.8 years; body mass index (BMI) 29.0 ± 12.8 kg/m2), the medial femoral condyle was affected in 21/30 patients (70%). The grading of subchondral lesions between MRI and CBCT did not match in 12 cases (40%). Based on MRI images, an underestimation (i.e., undergrading) compared with CBCT was observed in nine cases (30%), whereas overgrading occurred in three cases (10%). Compared to CBCT, routine T1-weighted 3 T sequences significantly overestimated osseus defect zones in sagittal (84.7 ± 68.9 mm2 vs. 35.9 ± 38.2 mm2, p < 0.01, Cohen’s d = 1.14) and coronal orientation (53.1 ± 24.0 mm2 vs. 22.0 ± 15.2 mm2, p < 0.01, Cohen’s d = 1.23). The reproducibility of the grading determined by intra- and inter-rater agreement was very high in MRI (intra-class correlation coefficient (ICC) 0.78 and 0.90, respectively) and CBCT (ICC 0.96 and 0.96, respectively). In patients with subchondral insufficiency fractures of the knee, the use of CBCT revealed discrepancies in lesion grading compared with MRI. These findings are clinically relevant, as precise determination of subchondral bone plate integrity may influence the decision about conservative or surgical treatment. CBCT represents our imaging modality of choice for grading the lesion and assessing subchondral bone plate integrity. MRI remains the gold standard modality to detect especially early stages.
Identification of hub genes associated with diabetic cardiomyopathy using integrated bioinformatics analysis
Authors: Cui Hailong , Hu Die , Xu Jing , Zhao Shuiying , Song Yi , Qin Guijun , Liu Yanling 
Published: July 2024

AbstractDiabetic cardiomyopathy (DCM) is a common cardiovascular complication of diabetes, which may threaten the quality of life and shorten life expectancy in the diabetic population. However, the molecular mechanisms underlying the diabetes cardiomyopathy are not fully elucidated. We analyzed two datasets from Gene Expression Omnibus (GEO). Differentially expressed and weighted gene correlation network analysis (WGCNA) was used to screen key genes and molecules. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, and protein–protein interaction (PPI) network analysis were constructed to identify hub genes. The diagnostic value of the hub gene was evaluated using the receiver operating characteristic (ROC). Quantitative real-time PCR (RT-qPCR) was used to validate the hub genes. A total of 13 differentially co-expressed modules were selected by WGCNA and differential expression analysis. KEGG and GO analysis showed these DEGs were mainly enriched in lipid metabolism and myocardial hypertrophy pathway, cytomembrane, and mitochondrion. As a result, six genes were identified as hub genes. Finally, five genes (Pdk4, Lipe, Serpine1, Igf1r, and Bcl2l1) were found significantly changed in both the validation dataset and experimental mice with DCM. In conclusion, the present study identified five genes that may help provide novel targets for diagnosing and treating DCM.
Top coal drawing law for an extra thick coal seam under the single round group drawing method
Authors: Pan Weidong , Zhao Zhining , Li Xinyuan , Xu Yongxin , Zhang Kunming 
Published: July 2024

AbstractTo solve the problems of poor top coal drawing, lagging collapse, and difficulty in parallel operation of mining and drawing in extra-thick coal seams, considering the 8222 working face of the Tashan Mine as the engineering background, we first investigate the basic problems of fully mechanized top coal drawing mining in extra-thick coal seams using the single-round group drawing method (GDM). We then analyze the drawing law of top coal with different thicknesses under the single-round GDM from the aspects of top coal recovery (TCR) and drawing efficiency, coal loss mechanism, and the relation between TCR and gangue content (GC), providing a basis for determining the process parameters of GDM. Results indicate that as the top coal thickness increases, the number of drawing openings considerably influences drawing efficiency and top coal loss. And there is a notable thickness effect of the number of drawing openings on the top coal loss. There is a quantitative relationship among TCR, cumulative GC (CGC) and instantaneous GC (IGC), and CGC and TCR can be predicted based on the IGC. Consequently, theoretical analysis and numerical simulation results indicate that the optimal IGC threshold at the coal drawing openings between 31.2 and 40%. Through optimizing the coal drawing method and strictly controlling the IGC at the coal drawing openings on-site, the measured working face TCR increased from 75.25 to 90.12%, and CGC was controlled at approximately 9%. Meanwhile, the average coordination efficiency of mining and drawing time reaches 68.2%, effectively ensuring the construction of a coal mine with an annual output of 15 million tons.