bluuebunny/crossref_metadata_2025_split huggingface dataset:
Universal scaling in real dimension
Authors: Bighin Giacomo , Enss Tilman , Defenu Nicolò 
Published: May 2024

AbstractThe concept of universality has shaped our understanding of many-body physics, but is mostly limited to homogenous systems. Here, we present a study of universality on a non-homogeneous graph, the long-range diluted graph (LRDG). Its scaling theory is controlled by a single parameter, the spectral dimension ds, which plays the role of the relevant parameter on complex geometries. The graph under consideration allows us to tune the value of the spectral dimension continuously also to noninteger values and to find the universal exponents as continuous functions of the dimension. By means of extensive numerical simulations, we probe the scaling exponents of a simple instance of $$O({{{{{{{\mathcal{N}}}}}}}})$$
O

(

N

)

symmetric models on the LRDG showing quantitative agreement with the theoretical prediction of universal scaling in real dimensions.
Mycobacterium tuberculosis suppresses host antimicrobial peptides by dehydrogenating L-alanine
Authors: Peng Cheng , Cheng Yuanna , Ma Mingtong , Chen Qiu , Duan Yongjia , Liu Shanshan , Cheng Hongyu , Yang Hua , Huang Jingping , Bu Wenyi , Shi Chenyue , Wu Xiangyang , Chen Jianxia , Zheng Ruijuan , Liu Zhonghua , Ji Zhe , Wang Jie , Huang Xiaochen , Wang Peng , Sha Wei , Ge Baoxue , Wang Lin 
Published: May 2024

AbstractAntimicrobial peptides (AMPs), ancient scavengers of bacteria, are very poorly induced in macrophages infected by Mycobacterium tuberculosis (M. tuberculosis), but the underlying mechanism remains unknown. Here, we report that L-alanine interacts with PRSS1 and unfreezes the inhibitory effect of PRSS1 on the activation of NF-κB pathway to induce the expression of AMPs, but mycobacterial alanine dehydrogenase (Ald) Rv2780 hydrolyzes L-alanine and reduces the level of L-alanine in macrophages, thereby suppressing the expression of AMPs to facilitate survival of mycobacteria. Mechanistically, PRSS1 associates with TAK1 and disruptes the formation of TAK1/TAB1 complex to inhibit TAK1-mediated activation of NF-κB pathway, but interaction of L-alanine with PRSS1, disables PRSS1-mediated impairment on TAK1/TAB1 complex formation, thereby triggering the activation of NF-κB pathway to induce expression of AMPs. Moreover, deletion of antimicrobial peptide gene β-defensin 4 (Defb4) impairs the virulence by Rv2780 during infection in mice. Both L-alanine and the Rv2780 inhibitor, GWP-042, exhibits excellent inhibitory activity against M. tuberculosis infection in vivo. Our findings identify a previously unrecognized mechanism that M. tuberculosis uses its own alanine dehydrogenase to suppress host immunity, and provide insights relevant to the development of effective immunomodulators that target M. tuberculosis.
Polyoxometalate-based plasmonic electron sponge membrane for nanofluidic osmotic energy conversion
Authors: Zhu Chengcheng , Xu Li , Liu Yazi , Liu Jiang , Wang Jin , Sun Hanjun , Lan Ya-Qian , Wang Chen 
Published: May 2024

AbstractNanofluidic membranes have demonstrated great potential in harvesting osmotic energy. However, the output power densities are usually hampered by insufficient membrane permselectivity. Herein, we design a polyoxometalates (POMs)-based nanofluidic plasmonic electron sponge membrane (PESM) for highly efficient osmotic energy conversion. Under light irradiation, hot electrons are generated on Au NPs surface and then transferred and stored in POMs electron sponges, while hot holes are consumed by water. The stored hot electrons in POMs increase the charge density and hydrophilicity of PESM, resulting in significantly improved permselectivity for high-performance osmotic energy conversion. In addition, the unique ionic current rectification (ICR) property of the prepared nanofluidic PESM inhibits ion concentration polarization effectively, which could further improve its permselectivity. Under light with 500-fold NaCl gradient, the maximum output power density of the prepared PESM reaches 70.4 W m−2, which is further enhanced even to 102.1 W m−2 by changing the ligand to P5W30. This work highlights the crucial roles of plasmonic electron sponge for tailoring the surface charge, modulating ion transport dynamics, and improving the performance of nanofluidic osmotic energy conversion.
The 8-17 DNAzyme can operate in a single active structure regardless of metal ion cofactor
Authors: Wieruszewska Julia , Pawłowicz Aleksandra , Połomska Ewa , Pasternak Karol , Gdaniec Zofia , Andrałojć Witold 
Published: May 2024

AbstractDNAzymes – synthetic enzymes made of DNA — have long attracted attention as RNA-targeting therapeutic agents. Yet, as of now, no DNAzyme-based drug has been approved, partially due to our lacking understanding of their molecular mode of action. In this work we report the solution structure of 8–17 DNAzyme bound to a Zn2+ ion solved through NMR spectroscopy. Surprisingly, it turned out to be very similar to the previously solved Pb2+-bound form (catalytic domain RMSD = 1.28 Å), despite a long-standing literature consensus that Pb2+ recruits a different DNAzyme fold than other metal ion cofactors. Our follow-up NMR investigations in the presence of other ions — Mg2+, Na+, and Pb2+ – suggest that at DNAzyme concentrations used in NMR all these ions induce a similar tertiary fold. Based on these findings, we propose a model for 8–17 DNAzyme interactions with metal ions postulating the existence of only a single catalytically-active structure, yet populated to a different extent depending on the metal ion cofactor. Our results provide structural information on the 8-17 DNAzyme in presence of non-Pb2+ cofactors, including the biologically relevant Mg2+ ion.
An improved epigenetic counter to track mitotic age in normal and precancerous tissues
Authors: Zhu Tianyu , Tong Huige , Du Zhaozhen , Beck Stephan , Teschendorff Andrew E. 
Published: May 2024

AbstractThe cumulative number of stem cell divisions in a tissue, known as mitotic age, is thought to be a major determinant of cancer-risk. Somatic mutational and DNA methylation (DNAm) clocks are promising tools to molecularly track mitotic age, yet their relationship is underexplored and their potential for cancer risk prediction in normal tissues remains to be demonstrated. Here we build and validate an improved pan-tissue DNAm counter of total mitotic age called stemTOC. We demonstrate that stemTOC’s mitotic age proxy increases with the tumor cell-of-origin fraction in each of 15 cancer-types, in precancerous lesions, and in normal tissues exposed to major cancer risk factors. Extensive benchmarking against 6 other mitotic counters shows that stemTOC compares favorably, specially in the preinvasive and normal-tissue contexts. By cross-correlating stemTOC to two clock-like somatic mutational signatures, we confirm the mitotic-like nature of only one of these. Our data points towards DNAm as a promising molecular substrate for detecting mitotic-age increases in normal tissues and precancerous lesions, and hence for developing cancer-risk prediction strategies.
Evaluating the utility of multi-gene, multi-disease population-based panel testing accounting for uncertainty in penetrance estimates
Authors: Liang Jane W. , Christensen Kurt D. , Green Robert C. , Kraft Peter 
Published: May 2024

AbstractPanel germline testing allows for the efficient detection of deleterious variants for multiple conditions, but the benefits and harms of identifying these variants are not always well understood. We present a multi-gene, multi-disease aggregate utility formula that allows the user to consider adding or removing each gene in a panel based on variant frequency, estimated penetrances, and subjective disutilities for testing positive but not developing the disease and testing negative but developing the disease. We provide credible intervals for utility that reflect uncertainty in penetrance estimates. Rare, highly penetrant deleterious variants tend to contribute positive net utilities for a wide variety of user-specified disutilities, even when accounting for parameter estimation uncertainty. However, the clinical utility of deleterious variants with moderate, uncertain penetrance depends more on assumed disutilities. The decision to include a gene on a panel depends on variant frequency, penetrance, and subjective utilities and should account for uncertainties around these factors.
Lysosomal and synaptic dysfunction markers in longitudinal cerebrospinal fluid of de novo Parkinson’s disease
Authors: Bartl Michael , Nilsson Johanna , Dakna Mohammed , Weber Sandrina , Schade Sebastian , Xylaki Mary , Fernandes Gomes Bárbara , Ernst Marielle , Muntean Maria-Lucia , Sixel-Döring Friederike , Trenkwalder Claudia , Zetterberg Henrik , Brinkmalm Ann , Mollenhauer Brit 
Published: May 2024

AbstractLysosomal and synaptic dysfunctions are hallmarks in neurodegeneration and potentially relevant as biomarkers, but data on early Parkinson’s disease (PD) is lacking. We performed targeted mass spectrometry with an established protein panel, assessing autophagy and synaptic function in cerebrospinal fluid (CSF) of drug-naïve de novo PD, and sex-/age-matched healthy controls (HC) cross-sectionally (88 PD, 46 HC) and longitudinally (104 PD, 58 HC) over 10 years. Multiple markers of autophagy, synaptic plasticity, and secretory pathways were reduced in PD. We added samples from prodromal subjects (9 cross-sectional, 12 longitudinal) with isolated REM sleep behavior disorder, revealing secretogranin-2 already decreased compared to controls. Machine learning identified neuronal pentraxin receptor and neurosecretory protein VGF as most relevant for discriminating between groups. CSF levels of LAMP2, neuronal pentraxins, and syntaxins in PD correlated with clinical progression, showing predictive potential for motor- and non-motor symptoms as a valid basis for future drug trials.
Large anomalous Hall effect in spin fluctuating devil’s staircase
Authors: Abe Naoki , Hano Yuya , Ishizuka Hiroaki , Kozuka Yusuke , Tadano Terumasa , Tsujimoto Yoshihiro , Yamaura Kazunari , Ishiwata Shintaro , Fujioka Jun 
Published: May 2024

AbstractElectrons in metals can show a giant anomalous Hall effect (AHE) when interacting with characteristic spin texture. The AHE has been discussed in terms of scalar-spin-chirality (SSC) in long-range-ordered noncollinear spin textures typified by Skyrmion. The SSC becomes effective even in the paramagnetic state with thermal fluctuations, but the resultant AHE has been limited to be very small. Here, we report the observation of large AHE caused by the spin fluctuation near the devil’s staircase transition in a collinear antiferromagnetic metal SrCo6O11. The AHE is prominent near and above the transition temperature at moderate magnetic fields, where the anomalous Hall angle becomes the highest level among known oxide collinear ferromagnets/antiferromagnets (>2%). Furthermore, the anomalous Hall conductivity is quadratically scaled to the conductivity. These results imply that the thermally induced solitonic spin defects inherent to the devil’s staircase transition promote SSC-induced skew scattering.
A multi-omics approach for biomarker discovery in neuroblastoma: a network-based framework
Authors: Hussein Rahma , Abou-Shanab Ahmed M. , Badr Eman 
Published: May 2024

AbstractNeuroblastoma (NB) is one of the leading causes of cancer-associated death in children. MYCN amplification is a prominent genetic marker for NB, and its targeting to halt NB progression is difficult to achieve. Therefore, an in-depth understanding of the molecular interactome of NB is needed to improve treatment outcomes. Analysis of NB multi-omics unravels valuable insight into the interplay between MYCN transcriptional and miRNA post-transcriptional modulation. Moreover, it aids in the identification of various miRNAs that participate in NB development and progression. This study proposes an integrated computational framework with three levels of high-throughput NB data (mRNA-seq, miRNA-seq, and methylation array). Similarity Network Fusion (SNF) and ranked SNF methods were utilized to identify essential genes and miRNAs. The specified genes included both miRNA-target genes and transcription factors (TFs). The interactions between TFs and miRNAs and between miRNAs and their target genes were retrieved where a regulatory network was developed. Finally, an interaction network-based analysis was performed to identify candidate biomarkers. The candidate biomarkers were further analyzed for their potential use in prognosis and diagnosis. The candidate biomarkers included three TFs and seven miRNAs. Four biomarkers have been previously studied and tested in NB, while the remaining identified biomarkers have known roles in other types of cancer. Although the specific molecular role is yet to be addressed, most identified biomarkers possess evidence of involvement in NB tumorigenesis. Analyzing cellular interactome to identify potential biomarkers is a promising approach that can contribute to optimizing efficient therapeutic regimens to target NB vulnerabilities.
Comprehensive molecular interaction map of TGFβ induced epithelial to mesenchymal transition in breast cancer
Authors: Gottumukkala Sai Bhavani , Ganesan Trivadi Sundaram , Palanisamy Anbumathi 
Published: May 2024

AbstractBreast cancer is one of the prevailing cancers globally, with a high mortality rate. Metastatic breast cancer (MBC) is an advanced stage of cancer, characterised by a highly nonlinear, heterogeneous process involving numerous singling pathways and regulatory interactions. Epithelial–mesenchymal transition (EMT) emerges as a key mechanism exploited by cancer cells. Transforming Growth Factor-β (TGFβ)-dependent signalling is attributed to promote EMT in advanced stages of breast cancer. A comprehensive regulatory map of TGFβ induced EMT was developed through an extensive literature survey. The network assembled comprises of 312 distinct species (proteins, genes, RNAs, complexes), and 426 reactions (state transitions, nuclear translocations, complex associations, and dissociations). The map was developed by following Systems Biology Graphical Notation (SBGN) using Cell Designer and made publicly available using MINERVA (http://35.174.227.105:8080/minerva/?id=Metastatic_Breast_Cancer_1). While the complete molecular mechanism of MBC is still not known, the map captures the elaborate signalling interplay of TGFβ induced EMT-promoting MBC. Subsequently, the disease map assembled was translated into a Boolean model utilising CaSQ and analysed using Cell Collective. Simulations of these have captured the known experimental outcomes of TGFβ induced EMT in MBC. Hub regulators of the assembled map were identified, and their transcriptome-based analysis confirmed their role in cancer metastasis. Elaborate analysis of this map may help in gaining additional insights into the development and progression of metastatic breast cancer.
Enhanced photocatalytic performance of a rGO-Ca2Fe2O5 nanocomposite for photodegradation of emergent pollutants
Authors: Vavilapalli Durga Sankar , Qin Leiqiang , Palisaitis Justinas , Rosen Johanna 
Published: May 2024

AbstractIn this study, a simple thermal reduction process is used to synthesize a rGO-Ca2Fe2O5 (rGO-CFO) nanocomposite, with the morphological and optical characteristics of the CFO nanomaterial being modified by the rGO incorporation. The interface between rGO nanosheets and CFO nanoparticles facilitates efficient charge separation and resulting transfer of photogenerated charge carriers across the rGO nanosheets, demonstrated from photoluminescence and Mott-Schottky tests. Compared to CFO (2.1 eV), rGO-CFO has a reduced band gap energy of 1.9 eV. As synthesized nanocomposites were initially optimized and utilized for photodegradation of organic effluent Methylene blue (MB). An addition of 5 wt% rGO to the CFO demonstrated an improved photodegradation efficiency (97%) compared to bare CFO (72%). An active species trapping experiment was used to assess the MB photodegradation mechanism. The results demonstrate that hydroxyl radicals and holes are the major active species involved in photodegradation. The optimized composition (5rGO-CFO) was further tested for degradation of Bisphenol-A and Tetracycline (antibiotic). Altogether, these investigations show that the rGO-CFO is a highly efficient photocatalyst that can be used to remediate emerging contaminants in sunlight.
CheXmask: a large-scale dataset of anatomical segmentation masks for multi-center chest x-ray images
Authors: Gaggion Nicolás , Mosquera Candelaria , Mansilla Lucas , Saidman Julia Mariel , Aineseder Martina , Milone Diego H. , Ferrante Enzo 
Published: May 2024

AbstractThe development of successful artificial intelligence models for chest X-ray analysis relies on large, diverse datasets with high-quality annotations. While several databases of chest X-ray images have been released, most include disease diagnosis labels but lack detailed pixel-level anatomical segmentation labels. To address this gap, we introduce an extensive chest X-ray multi-center segmentation dataset with uniform and fine-grain anatomical annotations for images coming from five well-known publicly available databases: ChestX-ray8, CheXpert, MIMIC-CXR-JPG, Padchest, and VinDr-CXR, resulting in 657,566 segmentation masks. Our methodology utilizes the HybridGNet model to ensure consistent and high-quality segmentations across all datasets. Rigorous validation, including expert physician evaluation and automatic quality control, was conducted to validate the resulting masks. Additionally, we provide individualized quality indices per mask and an overall quality estimation per dataset. This dataset serves as a valuable resource for the broader scientific community, streamlining the development and assessment of innovative methodologies in chest X-ray analysis.
Evaluation of DNA yield from various tissue and sampling sources for use in single nucleotide polymorphism panels
Authors: Pearce David L. , Edson Jessie E. , Jennelle Chris S. , Walter W. David 
Published: May 2024

AbstractGenetics studies are used by wildlife managers and researchers to gain inference into a population of a species of interest. To gain these insights, microsatellites have been the primary method; however, there currently is a shift from microsatellites to single nucleotide polymorphisms (SNPs). With the different DNA requirements between microsatellites and SNPs, an investigation into which samples can provide adequate DNA yield is warranted. Using samples that were collected from previous genetic projects from regions in the USA from 2014 to 2021, we investigated the DNA yield of eight sample categories to gain insights into which provided adequate DNA to be used in ddRADseq or already developed high- or medium-density SNP panels. We found seven sample categories that met the DNA requirements for use in all three panels, and one sample category that did not meet any of the three panels requirements; however, DNA integrity was highly variable and not all sample categories that met panel DNA requirements could be considered high quality DNA. Additionally, we used linear random-effects models to determine which covariates would have the greatest influence on DNA yield. We determined that all covariates (tissue type, storage method, preservative, DNA quality, time until DNA extraction and time after DNA extraction) could influence DNA yield.
Knowledge, attitudes, and practices towards urinary system stones among the Chengdu population
Authors: Lv Dong , Tang Liangyou , Chen Yongbo , Wang Rui , Liu Ling , Jian Nenghong , Zhang Ting , Shen Taimin 
Published: May 2024

AbstractThis cross-sectional study aimed to explore the knowledge, attitudes, and practices (KAP) regarding urinary system stones among the general public in Chengdu, China. Conducted between January and June 2023, this research targeted individuals undergoing physical examinations at the Health Management Center of Sichuan Provincial People's Hospital. Structured questionnaires were administered to collect demographic information and assess KAP related to urinary system stones. Following meticulous scrutiny, 1014 valid questionnaires were retained for analysis. The computed scores for knowledge, attitude, and practice were 9.36 ± 4.23 (possible score range 0–17), 37.75 ± 7.20 (possible score range 11–55), and 30.77 ± 4.00 (possible score range 10–50), respectively. These outcomes suggested insufficient knowledge and moderately positive attitudes and practices among the participants. Structural Equation Modeling (SEM) analysis revealed a direct impact of knowledge on attitude (β = 0.967, P < 0.001), with attitude subsequently exerting a direct influence on practice (β = 0.167, P < 0.001). This indicated an indirect impact of knowledge on practice. Additionally, there was a direct effect of knowledge on practice (β = 0.167, P < 0.001). In conclusion, the general populace in Chengdu exhibited insufficient knowledge and moderate attitudes and practices concerning urinary stones. These findings underscore the imperative for targeted educational interventions aimed at enhancing public awareness and fostering positive attitudes and practices toward urinary stone prevention and management.
Social interactions and olfactory cues are required for contagious itch in mice
Authors: Shayan Maryam , Haddadi Nazgol-Sadat , Shokrian Zeini Maryam , Shokrian Zeini Mohadese , Tashak Golroudbari Hasti , Afrooghe Arya , Ahmadi Elham , Rashki Asma , Dehpour Ahmad-Reza 
Published: May 2024

AbstractThe phenomenon of contagious itch, observed in both humans and rodents, remains a topic of ongoing debate concerning its modulators and underlying pathways. This study delves into the relationship between contagious itch and familiar olfactory cues, a non-visual factor contributing to this intriguing behavior. Our findings showed that contagious itch in observer mice occurs during physical interaction with the cagemate itch-demonstrator but not with a stranger demonstrator or in a non-physical encounter condition. Notably, itch-experienced observer mice displayed an increased contagious itch behavior, highlighting the relevance of itch-associated memory in this phenomenon. Furthermore, anosmic observer mice, whether itch-naïve or itch-experienced, displayed no contagious itch behavior. These results demonstrate that the familiar olfactory cues, specifically cagemate body odors, are required for contagious itch behaviors in mice. In line with these behavioral findings, our study reveals increased activity in brain regions associated with olfaction, emotion, and memory during contagious itch, including the olfactory bulb, the amygdala, the hypothalamus, and the hippocampus, with this activity diminished in anosmic mice. In conclusion, our study unveils the critical role of familiar olfactory cues in driving contagious itch in mice, shedding light on the interplay between social factors, sensory perception, and memory in this phenomenon.