bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide mapping and cryo-EM structural analyses of the overlapping tri-nucleosome composed of hexasome-hexasome-octasome moieties
Authors: Nishimura Masahiro , Fujii Takeru , Tanaka Hiroki , Maehara Kazumitsu , Morishima Ken , Shimizu Masahiro , Kobayashi Yuki , Nozawa Kayo , Takizawa Yoshimasa , Sugiyama Masaaki , Ohkawa Yasuyuki , Kurumizaka Hitoshi 
Published: January 2024

AbstractThe nucleosome is a fundamental unit of chromatin in which about 150 base pairs of DNA are wrapped around a histone octamer. The overlapping di-nucleosome has been proposed as a product of chromatin remodeling around the transcription start site, and previously found as a chromatin unit, in which about 250 base pairs of DNA continuously bind to the histone core composed of a hexamer and an octamer. In the present study, our genome-wide analysis of human cells suggests another higher nucleosome stacking structure, the overlapping tri-nucleosome, which wraps about 300-350 base-pairs of DNA in the region downstream of certain transcription start sites of actively transcribed genes. We determine the cryo-electron microscopy (cryo-EM) structure of the overlapping tri-nucleosome, in which three subnucleosome moieties, hexasome, hexasome, and octasome, are associated by short connecting DNA segments. Small angle X-ray scattering and coarse-grained molecular dynamics simulation analyses reveal that the cryo-EM structure of the overlapping tri-nucleosome may reflect its structure in solution. Our findings suggest that nucleosome stacking structures composed of hexasome and octasome moieties may be formed by nucleosome remodeling factors around transcription start sites for gene regulation.
A new role for erythropoietin in the homeostasis of red blood cells
Authors: Arias Clemente F. , Valente-Leal Nuno , Bertocchini Federica , Marques Sofia , Acosta Francisco J. , Fernandez-Arias Cristina 
Published: January 2024

AbstractThe regulation of red blood cell (RBC) homeostasis is widely assumed to rely on the control of cell production by erythropoietin (EPO) and the destruction of cells at a fixed, species-specific age. In this work, we show that such a regulatory mechanism would be a poor homeostatic solution to satisfy the changing needs of the body. Effective homeostatic control would require RBC lifespan to be variable and tightly regulated. We suggest that EPO may control RBC lifespan by determining CD47 expression in newly formed RBCs and SIRP-α expression in sinusoidal macrophages. EPO could also regulate the initiation and intensity of anti-RBC autoimmune responses that curtail RBC lifespan in some circumstances. These mechanisms would continuously modulate the rate of RBC destruction depending on oxygen availability. The control of RBC lifespan by EPO and autoimmunity emerges as a key mechanism in the homeostasis of RBCs.
Rescue of ApoE4-related lysosomal autophagic failure in Alzheimer’s disease by targeted small molecules
Authors: Balasubramaniam Meenakshisundaram , Narasimhappagari Jagadeesh , Liu Ling , Ganne Akshatha , Ayyadevara Srinivas , Atluri Ramani , Ayyadevara Haarika , Caldwell Guy , Reis Robert J. Shmookler , Barger Steven W. , Griffin W. Sue T. 
Published: January 2024

AbstractHomozygosity for the ε4 allele of APOE increases the odds of developing Alzheimer’s by 12 to 15 times relative to the most common ε3;ε3 genotype, and its association with higher plaque loads comports with evidence that APOEε4 compromises autophagy. The ApoE4 protein specifically binds a cis element (“CLEAR”) in the promoters of several autophagy genes to block their transcription. We used a multifaceted approach to identify a druggable site in ApoE4, and virtual screening of lead-like compounds identified small molecules that specifically bind to this site to impede ApoE4::DNA binding. We validated these molecules both in vitro and in vivo with models expressing ApoE4, including ApoE4 targeted-replacement mice. One compound was able to significantly restore transcription of several autophagy genes and protected against amyloid-like aggregation in a C. elegans AD model. Together, these findings provide proof-of-principle evidence for pharmacological remediation of lysosomal autophagy by ApoE4 via ApoE4-targeted lead molecules that represent a novel tack on neurodegenerative disorders.
Efficient generation and amplification of intense vortex and vector laser pulses via strongly-coupled stimulated Brillouin scattering in plasmas
Authors: Wu Yipeng , Zhang Chaojie , Nie Zan , Sinclair Mitchell , Farrell Audrey , Marsh Kenneth A. , Alves E. Paulo , Tsung Frank , Mori Warren B. , Joshi Chan 
Published: January 2024

AbstractThe past decade has seen tremendous progress in the production and utilization of vortex and vector laser pulses. Although both are considered as structured light beams, the vortex lasers have helical phase fronts and phase singularities, while the vector lasers have spatially variable polarization states and polarization singularities. In contrast to the vortex pulses that carry orbital angular momentum (OAM), the vector laser pulses have a complex spin angular momentum (SAM) and OAM coupling. Despite many potential applications enabled by such pulses, the generation of high-power/-intensity vortex and vector beams remains challenging. Here, we demonstrate using theory and three-dimensional simulations that the strongly-coupled stimulated Brillouin scattering (SC-SBS) process in plasmas can be used as a promising amplification technique with up to 65% energy transfer efficiency from the pump beam to the seed beam for both vortex and vector pulses. We also show that SC-SBS is strongly polarization-dependent in plasmas, enabling an all-optical polarization control of the amplified seed beam. Additionally, the interaction of such structured lasers with plasmas leads to various angular momentum couplings and decouplings that produce intense new light structures with controllable OAM and SAM. This scheme paves the way for novel optical devices such as plasma-based amplifiers and light field manipulators.
WVD‐GAN: A Wigner‐Ville distribution enhancement method based on generative adversarial network
Authors: Quan Daying , Ren Feitao , Wang Xiaofeng , Xing Mengdao , Jin Ning , Zhang Dongping 
Published: January 2024

AbstractTime‐frequency analysis based on Wigner‐Ville distribution (WVD) plays a significant role in analysing non‐stationary signals, but it is susceptible to interference from cross‐terms (CTs) for multi‐component signals. To address this issue, a novel WVD enhancement method based on generative adversarial networks (namely WVD‐GAN) is proposed, to achieve highly‐concentrated time‐frequency (TF) representation. Specifically, a deep feature extraction module is designed with multiple residual connections in the generator of WVD‐GAN to leverage the latent information encoded in the shallow representations. Meanwhile, a simple and effective attention module is introduced to enhance auto‐term features. Moreover, a multi‐scale discriminator is proposed based on dilated convolutions to guide the generator to reconstruct high‐resolution TF images by discriminating CT. Finally, a comparative analysis is provided to demonstrate the effectiveness and robustness of the proposed method on different simulated and real‐life datasets. Extensive experiments demonstrate that the proposed method outperforms several state‐of‐the‐art methods.
AB Aur, a Rosetta stone for studies of planet formation
Authors: Rivière-Marichalar P. , Macías E. , Baruteau C. , Fuente A. , Neri R. , Ribas Á. , Esplugues G. , Navarro-Almaida D. , Osorio M. , Anglada G. 
Published: January 2024

Context. Observational constraints on dust properties in protoplanetary disks are key to better understanding disk evolution, their dynamics, and the pathway to planet formation, but also surface chemistry, the main driver of chemical complexity.
Aims. We continue our exploration of the protoplanetary disk around AB Aur by characterizing its dust properties at different millimeter wavelengths.
Methods. We present new ALMA observations at 2.2 mm and VLA observations at 6.8 mm. Together with previous ALMA and NOEMA observations at 0.87 and 1.1 mm, these new observations are used to compute global spectral index profiles as well as spectral index maps to probe the dust properties throughout the disk. On the interpretation side, we present the results of a simple isothermal slab model to help constrain dust properties along the non-axisymmetric ring of continuum emission outside the millimeter cavity. We also present new results of dust radiative transfer calculations based on a disk-planet hydrodynamical simulation to explain how the azimuthal contrast ratio of the ring emission varies with millimeter wavelength.
Results. The spectral energy distribution and the radial profiles of the spectral index indicate that the radiation from the compact source towards the center is not dominated by dust thermal emission, but most likely by free-free emission originating in the radio jet; it constitutes 93% of the emission at 6.8 mm, and 37% at 0.87 mm. The protoplanetary disk has a typical spectral index of 2.3, computed using the 0.87, 1.1, and 2.2 mm bands. We estimate a dust disk mass of 8 × 10−5 M⊙ which, assuming a mean gas-to-dust ratio of 40, gives a total disk mass of 3.2 × 10−3 M⊙. The azimuthal contrast ratio of the ring outside the millimeter cavity is smaller at 2.2 mm than at 1.1 mm, in agreement with previous findings. The VLA image shows several knots of 5σ emission all along the ring, which, with the help of our dust radiative transfer calculations, are consistent with the ring emission being nearly axisymmetric at that wavelength. The decrease in the azimuthal contrast ratio of the ring emission from 0.87 to 6.8 mm can be explained by a dust-losing decaying vortex at the outer edge of a planet gap.
The GAPS programme at TNG
Authors: Di Maio C. , Petralia A. , Micela G. , Lanza A. F. , Rainer M. , Malavolta L. , Benatti S. , Affer L. , Maldonado J. , Colombo S. , Damasso M. , Maggio A. , Biazzo K. , Bignamini A. , Borsa F. , Boschin W. , Cabona L. , Cecconi M. , Claudi R. , Covino E. , Di Fabrizio L. , Gratton R. , Lorenzi V. , Mancini L. , Messina S. , Molinari E. , Molinaro M. , Nardiello D. , Poretti E. , Sozzetti A. 
Published: January 2024

Context. The intrinsic variability due to the magnetic activity of young active stars is one of the main challenges in detecting and characterising exoplanets. The stellar activity is responsible for jitter effects observed both in photometric and spectroscopic observations that can impact our planetary detection sensitivity.
Aims. We present a method able to model the stellar photosphere and its surface inhomogeneities (starspots) in young, active, and fast-rotating stars based on the cross-correlation function (CCF) technique, and we extract information about the spot configuration of the star.
Methods. We developed Spot CCF, a tool able to model the deformation of the CCF profile due to the presence of multiple spots on the stellar surface. Within the Global Architecture of Planetary Systems (GAPS) Project at the Telescopio Nazionale Galileo, we analysed more than 300 spectra of the young planet-hosting star V1298 Tau provided by the HARPS-N high-resolution spectrograph. By applying the SpotCCF model to the CCFs, we extracted the spot configuration (latitude, longitude, and projected filling factor) of this star, and provide a new radial velocity (RV) time series for this target.
Results. We find that the features identified in the CCF profiles of V1298 Tau are modulated by the stellar rotation, supporting our assumption that they are caused by starspots. The analysis suggests a differential rotation velocity of the star with lower rotation at higher latitudes. Also, we find that SpotCCF provides an improvement in RV extraction, with a significantly lower dispersion with respect to the commonly used pipelines. This allows mitigation of the stellar activity contribution modulated with stellar rotation. A detection sensitivity test, involving the direct injection of a planetary signal into the data, confirms that the SpotCCF model improves the sensitivity and ability to recover planetary signals.
Conclusions. Our method enables us to model the stellar photosphere and extract the spot configuration of young, active, and rapidly rotating stars. It also allows the extraction of optimised RV time series, thereby enhancing our detection capabilities for new exoplanets and advancing our understanding of stellar activity.
Preparation of berberine magnetic nanoparticles and their inhibition of human gastric cancer BGC-823 cells
Authors: Liu Xianglong , Wang Jiao , Chen Bodong , Niu Ben , Li Jin 
Published: January 2024

A new drug delivery system loaded with the drug berberine on carboxymethyl chitosan-coated magnetic nanoparticles (Fe3O4@CMCS-BBR) was prepared and characterized through x-ray diffraction, Fourier transform-infrared spectroscopy, a vibrating sample magnetometer, and transmission electron microscopy. By comparing the size of the uncoated nanoparticles (39.26 nm) and the size of the coated magnetite nanoparticles (73.75 nm), it was found that with the CMCS coating on the magnetite nanoparticles, the dispersion of the nanoparticle improved. The optimum pH testing showed a higher drug encapsulation of 51.23% and drug loading of 17.10% at a pH of 5.5 because of the better interaction of the NH3+ group with the negative functional groups of the CMCS. Furthermore, 85.89% of the drug was released within 72 h. The CCK-8 test results showed that Fe3O4@CMCS-BBR magnetic nanocomposites had good biocompatibility with gastric cancer BGC-823 cells and that Fe3O4@CMCS-BBR effectively inhibited the proliferation of cancer cells. The magnetic experimental results showed that Fe3O4@CMCS-BBR had good responsiveness to external magnetic fields and aggregated in the presence of a magnetic field. The results of targeting experiments showed that fluorescein isothiocyanate emitted a strong yellowish fluorescence in cells, which became stronger over time, and the killing effect on cancer cells became greater. The apoptosis results showed that the apoptosis rate induced by the magnetic nanodrug was 54.90%, indicating that the drug had a promoting effect on the apoptosis of BGC-823 cells.
Inference of reliability model with burr type XII distribution under two sample balanced progressive censored samples
Authors: Lone Showkat Ahmad , Panahi Hanieh , Anwar Sadia , Shahab Sana 
Published: January 2024

Abstract
The balanced joint progressive censoring scheme gives guidelines for researchers in reducing the expense and period of the experiment with modified efficiency. In this paper, the stress-strength reliability model are considered and investigated, in which two independent samples are generated from Burr Type XII distributions under balanced joint progressive censoring scheme. In the classical analysis, the maximum likelihood estimate of the reliability parameter is derived, then the relevant confidence interval is provided based on the Fisher matrix. Under the Bayesian framework, the Lindley’s technique and hybrid Gibbs within Metropolis-Hastings algorithm are applied to acquire the estimates of the parameters, and the corresponding highest posterior density credible interval of the reliability model is also constructed. The reliability inference is realized by numerical simulation, and the validity of the inference method is analyzed based on the splashing data of silicone oil droplets impact (SSODI) under two surfaces wettability conditions.
Postponing entanglement sudden death by quantum interferences
Authors: Nair Anjali N , Arun R 
Published: January 2024

Abstract
We investigate the entanglement dynamics in a 2 ⨂ 3 quantum system consisting of a two-level atom and a three-level V-type atom interacting independently with their environments. Pure and mixed initial states, including one-parameter and two-parameter states of the atoms are analyzed. It is observed that the entanglement in the qubit-qutrit system disappears in a finite time, commonly referred to as ESD (entanglement sudden death). We analytically calculate the ESD time using the negativity as an entanglement measure. Remarkably, the presence of vacuum-induced coherence in the three-level atom (qutrit) delays the occurrence of ESD and effectively protects the entanglement from decoherence.
Quantum advantage beyond entanglement in Bayesian game theory
Authors: Lowe A 
Published: January 2024

Abstract
Quantum discord has been utilised in order to find quantum advantage in an extension of the Clauser, Horne, Shimony, and Holt game. By writing the game explicitly as a Bayesian game, the resulting game is modified such the payoff’s are different. Crucially, restrictions are imposed on the measurements that Alice and Bob can perform. By imposing these restrictions, it is found that there exists quantum advantage beyond entanglement for a given quantum state. This is shown by decomposing the expected payoff into a classical and quantum term. By optimising over the expected payoff, the classical limit is surpassed for the given state in the restricted measurement space. This gives an operational framework in order to witness and determine the quantum discord for specific states, whilst demonstrating the importance of measurement in quantum advantage.
The impact of metal dopants on the properties of nZVI: a theoretical study
Authors: White Jessica Jein , Hinsch Jack Jon , Bennett William W , Wang Yun 
Published: January 2024

Abstract
The substitution of Fe with metal dopants shows potential for enhancing the wastewater remediation performance of nanoscale zero-valent iron (nZVI). However, the specific roles and impacts of these dopants remain unclear. To address this knowledge gap, we employed density functional theory (DFT) to investigate metal-doped nZVI on stepped surfaces. Four widely used metal dopants (Ag, Cu, Ni, and Pd) were investigated by replacing Fe atoms at the edge of the stepped surface. Previous research has indicated that these Fe atoms exhibit chemical reactivity and are vulnerable to water oxidation. Our DFT calculations revealed that the replacement of Fe atoms on the edge of the stepped surface is energetically more favorable than that on the flat Fe(110) surface. Our results shed light on the effects of metal dopants on the surface properties of nZVI. Notably, the replacement of Fe atoms with a metal dopant generally led to weaker molecular and dissociated water adsorption across all systems. The results from this study enhance our understanding of the complex interplay between dopants and the surface properties of nZVI, offering theoretical guidance for the development and optimization of metal-doped nZVI for efficient and sustainable wastewater remediation applications.
Application of autoencoders artificial neural network and principal component analysis for pattern extraction and spatial regionalization of global temperature data
Authors: Ibebuchi Chibuike Chiedozie , Obarein Omon A , Abu Itohan-Osa 
Published: January 2024

Abstract
Spatial regionalization is instrumental in simplifying the spatial complexity of the climate system. To identify regions of significant climate variability, pattern extraction is often required prior to spatial regionalization with a clustering algorithm. In this study, the autoencoder (AE) artificial neural network was applied to extract the inherent patterns of global temperature data (from 1901 to 2021). Subsequently, Fuzzy C-means clustering was applied to the extracted patterns to classify the global temperature regions. Our analysis involved comparing AE-based and principal component analysis (PCA)-based clustering results to assess consistency. We determined the number of clusters by examining the average percentage decrease in Fuzzy Partition Coefficient (FPC) and its 95% confidence interval, seeking a balance between obtaining a high FPC and avoiding over-segmentation. This approach suggested that for a more general model, four clusters is reasonable. The Adjusted Rand Index between the AE-based and PCA-based clusters is 0.75, indicating that the AE-based and PCA-based clusters have considerable overlap. The observed difference between the AE-based clusters and PCA-based clusters is suggested to be associated with AE’s capability to learn and extract complex non-linear patterns, and this attribute, for example, enabled the clustering algorithm to accurately detect the Himalayas region as the ‘third pole’ with similar temperature characteristics as the polar regions. Finally, when the analysis period is divided into two (1901–1960 and 1961–2021), the Adjusted Rand Index between the two clusters is 0.96 which suggests that historical climate change has not significantly affected the defined temperature regions over the two periods. In essence, this study indicates both AE’s potential to enhance our understanding of climate variability and reveals the stability of the historical temperature regions.
Specific network information gain for detecting the critical state of colorectal cancer based on gut microbiome
Authors: Peng Xueqing , Gao Rong , Ren Jing , Lu Jianbo , Ma Xu , Li Peiluan 
Published: January 2024

Abstract
There generally exists a critical state or tipping point from a stable state to another in the development of colorectal cancer (CRC) beyond which a significant qualitative transition occurs. Gut microbiome sequencing data can be collected non-invasively from fecal samples, making it more convenient to obtain. Furthermore, intestinal microbiome sequencing data contain phylogenetic information at various levels, which can be used to reliably identify critical states, thereby providing early warning signals more accurately and effectively. Yet, pinpointing the critical states using gut microbiome data presents a formidable challenge due to the high dimension and strong noise of gut microbiome data. To address this challenge, we introduce a novel approach termed the specific network information gain (SNIG) method to detect CRC’s critical states at various taxonomic levels via gut microbiome data. The numerical simulation indicates that the SNIG method is robust under different noise levels and that it is also superior to the existing methods on detecting the critical states. Moreover, utilizing SNIG on two real CRC datasets enabled us to discern the critical states preceding deterioration and to successfully identify their associated dynamic network biomarkers at different taxonomic levels. Notably, we discovered certain ‘dark species’ and pathways intimately linked to CRC progression. In addition, we accurately detected the tipping points on an individual dataset of type I diabetes.
Parametric cardiovascular magnetic resonance imaging in takotsubo syndrome: a case report
Authors: Sunnasy Ritesh , Mohiaddin Raad Hashem 
Published: January 2024

Abstract

Background
Takotsubo syndrome (TTS) causes angina with ventricular dysfunction that can mimic acute coronary syndrome. Normal coronary angiography leads to cardiovascular magnetic resonance imaging (CMR) in the diagnostic pathway. Historically, TTS was thought to be associated with the absence of late gadolinium enhancement on CMR. This case report highlights the presence of late gadolinium enhancement in a case of TTS while demonstrating the other characteristic findings, including quantitative parametric T1/T2 mapping.

Case summary
A 69-year-old lady was admitted with chest pain and shortness of breath. She was found to have classical TTS with the characteristic wall motion abnormalities on echocardiogram, left ventricular angiogram, and CMR. Her CMR also demonstrated strongly positive myocardial T1/T2 mapping that matched the wall motion abnormalities and the less frequently described positive early and late gadolinium enhancement.

Discussion
This case highlights the diagnostic pathway in TTS and the ability of CMR to make a diagnosis in myocardial infarction with non-obstructed coronary arteries. We describe the characteristic cardiac imaging features of TTS while discussing the positive late gadolinium enhancement patterns that may help confirm the diagnosis.