bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enhancement of dual autofocusing ability for ring Pearcey edge dislocation beams
Authors: Dong Shun , Jia Heping , Yang Rongcao , Kong Xianyi 
Published: December 2024

Abstract
When the ring with the maximum intensity deviates from the central point, the dual autofocusing performance of the ring Pearcey edge dislocation (RPED) beams in free space is gradually destroyed. To address the degradation in the dual autofocusing ability, we investigate the propagation dynamics of the RPED beams in a system with fractional diffraction effect or parabolic potential. The simulation results show that there exists a critical value for the Lévy index, that results in the RPED beams exhibiting an obvious dual autofocusing phenomenon with equal focusing intensities. When the Lévy index is near the critical value, the RPED beams have dual autofocusing characteristics, and the focusing intensity and focal distance can be controlled by changing the Lévy index. The introducing of the parabolic potential leads to the periodic evolution of the RPED beams, and the dual autofocusing property of the RPED beams with smaller radius can be restored within one evolution cycle by changing the potential depth. Moreover, the positions of the edge dislocation affect the focusing intensity, but have no effect on the number of foci. Our research provides some inspiration for the control of dual autofocusing beams, and has potential applications in optical manipulation and optical trapping.
Attosecond recollision dynamics in nonsequential double ionization of argon by orthogonally polarized two-color laser fields
Authors: Li Na , Qiao Xiaoxiao , Gao Feng , Lu Xiaolong , Liu Jun , Wang Zifeng , Xin Peipei 
Published: December 2024

Abstract
Electronic correlation, as a fundamental physical effect, is one of the most fascinating research topics in laser-matter interaction. Using the three dimensional classical ensemble model (CEM), we investigate the attosecond recollision dynamics in non-sequential double ionization (NSDI) of argon under orthogonally polarized two-color (OPTC) fields consisting of 800-nm and 400-nm laser pulses. We find that the probability distribution of recollision time and energy asymmetric sharing between two electrons, as well as the Coulomb repulsion of electron pairs all have an impact on the correlated behaviors of two electrons. Meanwhile, the emission directions of electrons pairs can be effectively controlled by manipulating the relative phase of the two-color field. By performing a classical trajectory analysis of two electrons, we reveal that not only the first return but also multiple returns of tunneling electrons can make a significant contribution to the recollision dynamics in NSDI.
Classification of static plane symmetric spacetime according to their self similar vector fields
Authors: Akhtar Sumaira Saleem , Shakeel Mehnaz , Zahir Hina , Khan Jamshed , Ahmad Imtiaz 
Published: December 2024

Abstract
This article discusses the use of self-similar symmetry to analyze static plane symmetric spacetime. A computer algorithm is employed to convert the symmetry equations, resulting in a tree structure known as a Riff tree, which is utilized for analyzing the aforementioned symmetry within the specified spacetime. The tree comprises several pivots and branches, with the pivots being subject to specific differential conditions on the metric functions. Furthermore, explicit formulas for the metrics and their corresponding self-similar vector fields (SSVFs) are derived by solving the set of equations using these constraints. Additionally, this work investigates the bounds for certain energy conditions as well as the kinematic variables.
Testing No slip model with pulsar timing arrays: NANOGrav and IPTA
Authors: Davari Mohammadreza , Allahyari Alireza , Khosravi Shahram 
Published: December 2024

Abstract
We perform an observational study of modified gravity considering a potential inflationary interpretation of pulsar timing arrays (PTA). We use a motivated model known as no slip in which the gravitational wave propagation is modified. Specifically, by using two different parametrizations for the model, we find the approximate transfer functions for tensor perturbations. In this way, we obtain the spectral energy density of gravitational waves and use NANOGrav and IPTA second data release to constrain parameters of the model. In parametrization I, ξ is degenerate with log
10
A and γ and in parametrization II, cM
is also degenerate with both log
10
A and γ.
For cM
, we only get an upper bound on the parameter. Thus, it is difficult to constrain them with percent level accuracy with the current PTA data.
diffSph: a Python tool to compute diffuse signals from dwarf spheroidal galaxies
Authors: Vollmann Martin , Welzmüller Finn , Gajović Lovorka 
Published: December 2024

Abstract
So far no diffuse emissions in dwarf spheroidal satellites of the Milky Way have ever been observed.
Given that dwarf galaxies are predominantly composed of Dark Matter, the discovery of these signals could offer valuable insights into understanding the nature of Dark Matter.
We present “diffSph”, a Python tool which in its present version provides fast predictions of such diffuse signals in radio frequencies.
It also features a very comprehensive module for the computation of “J” and “D” factors that are relevant for indirect Dark Matter detection using gamma rays.
Routines are coupled to parton-shower algorithms and Dark Matter halo mass functions from state-of-the-art kinematic fits.
This code is also useful for testing generic hypotheses (not necessarily associated with any Dark Matter candidate) about the cosmic-ray electron/positron sources in the dwarf galaxies.
The diffSph tool has already been employed in searches for diffuse signals from dwarf spheroidal galaxies using the LOw Frequency ARray (LOFAR).
Massive neutrinos and cosmic composition
Authors: Loverde Marilena , Weiner Zachary J. 
Published: December 2024

Abstract
Cosmological data probe massive neutrinos via their effects on the geometry of the
Universe and the growth of structure, both of which are degenerate with the late-time expansion
history. We clarify the nature of these degeneracies and the individual roles of both probes in
neutrino mass inference. Geometry is strongly sensitive to neutrino masses: within ΛCDM,
the primary cosmic microwave background anisotropies alone impose that the matter fraction
Ω
m
must increase fivefold with increasing neutrino mass. Moreover, large-scale structure
observables, like weak lensing of the CMB, are dimensionless and thus depend not on the matter
density (as often quoted) but in fact the matter fraction. We explore the consequential impact of
this distinction on the interplay between probes of structure, low-redshift distances, and CMB
anisotropies. We derive constraints on the neutrino's masses independently from their suppression
of structure and impact on geometry, showing that the latter is at least as important as the
former. While the Dark Energy Spectroscopic Instrument's recent baryon acoustic oscillation data
place stringent bounds largely deriving from their geometric incompatibility with massive
neutrinos, all recent type Ia supernova datasets drive marginal preferences for nonzero neutrino
masses because they prefer substantially larger matter fractions. Recent CMB lensing data,
however, neither exclude neutrinos' suppression of structure nor constrain it strongly enough to
discriminate between mass hierarchies. Current data thus evince not a need for modified dynamics
of neutrino perturbations or structure growth but rather an inconsistent compatibility with
massive neutrinos' impact on the expansion history. We identify two of DESI's measurements that
strongly influence its constraints, and we also discuss neutrino mass measurements in models that
alter the sound horizon.
Stability of volatile organic compounds in thermal desorption tubes and in solution
Authors: Kiland Kristian J , Martins Lucas , Borden Scott A , Lam Stephen , Myers Renelle 
Published: December 2024

Abstract
Exhaled breath volatile organic compounds (VOCs) are often collected and stored in sorbent tubes before thermal desorption-gas chromatography-mass spectrometry (TD-GC-MS) analysis. Information about the stability of VOCs during storage is needed to account for potential artifacts and monitor for losses. Additionally, information about the stability of VOC standards in solution is required to assess their performance as quality control and internal standards. We evaluated the stability of a standard mixture of 42 VOCs in dual-sorbent tubes containing Tenax® TA and Carbotrap 1TD over 60 d at commonly used storage conditions: room temperature (∼21 °C), 4 °C, and −80 °C. The same 42 VOCs were also evaluated for their stability in methanol over 60 d while stored at −20 °C. All samples were analyzed using TD-GC-MS. During storage, most VOCs were stable on sorbent after 60 d: 36/42 (86%), 39/42 (93%), and 41/42 (98%) had not statistically changed for room temperature, 4 °C and −80 °C, respectively, based on Spearman rank correlation coefficients and linear regression analysis. The isotopically labeled VOCs tested here are well-suited to serve as internal standards for pre-analysis or storage. Degradation of VOCs in solution was apparent after 60 d: 27/42 (64%) of VOCs had statistically decreased. The total VOC mixture had dropped to 90% of its original intensity after ∼22 d and a subset of VOCs typically used as internal standards dropped to 90% in ∼16 d. Analysts using similar mixtures should make a fresh solution at least every two weeks to ensure analytical accuracy. This study provides important insights into storage practices for both sorbent tubes and standard solutions, guiding analysts toward improved reliability and accuracy in exhaled breath analysis.
Room-temperature in-plane ferromagnetism in Co-substituted Fe5GeTe2 investigated by magnetic x-ray spectroscopy and microscopy
Authors: Heppell Emily , Fujita Ryuji , Gurung Gautam , Lin Jheng-Cyuan , May Andrew F , Foerster Michael , Waqas Khaliq M , Angel Niño Miguel , Valvidares Manuel , Herrero-Martín Javier , Gargiani Pierluigi , Watanabe Kenji , Taniguchi Takashi , Backes Dirk , van der Laan Gerrit , Hesjedal Thorsten 
Published: December 2024

Abstract
The exploration of two-dimensional (2D) van der Waals ferromagnets has revealed intriguing magnetic properties with significant potential for spintronics applications. In this study, we examine the magnetic properties of Co-doped Fe5GeTe2 using x-ray photoemission electron microscopy (XPEEM) and x-ray magnetic circular dichroism (XMCD), complemented by density functional theory calculations. Our XPEEM measurements reveal that the Curie temperature (

T
C

) of a bilayer of (Co
x
Fe

1
−
x

)

5
−
δ

GeTe2 (with x = 0.28) reaches ∼300 K—a notable enhancement over most 2D ferromagnets in the ultrathin limit. Interestingly, the

T
C

shows only a small dependence on film thickness (bulk

T

C

≈
340

K), in line with the observed in-plane (IP) magnetic anisotropy and robust IP exchange coupling. XMCD measurements indicate that the spin moments for both Fe and Co are significantly reduced compared to the theoretical values. These insights highlight the potential of Co-doped Fe5GeTe2 for stable, high-temperature ferromagnetic applications in 2D materials.
Quantum optics with giant atoms in a structured photonic bath
Authors: Leonforte Luca , Sun Xuejian , Valenti Davide , Spagnolo Bernardo , Illuminati Fabrizio , Carollo Angelo , Ciccarello Francesco 
Published: December 2024

Abstract
We present a general framework to tackle quantum optics problems with giant atoms, i.e. quantum emitters each coupled non-locally to a structured photonic bath (typically a lattice) of any dimension. The theory encompasses the calculation and general properties of Green’s functions, atom-photon bound states, collective master equations and decoherence-free Hamiltonians (DFHs), and is underpinned by a formalism where a giant atom is formally viewed as a normal atom lying at a fictitious location. As a major application, we provide for the first time a general criterion to predict/engineer DFHs of giant atoms, which can be applied both in and out of the photonic continuum and regardless of the structure or dimensionality of the photonic bath. This is used to show novel DFHs in 2D baths such as a square lattice, photonic graphene and an extended photonic Lieb lattice.
NABP-BERT: NANOBODY®-antigen binding prediction based on bidirectional encoder representations from transformers (BERT) architecture
Authors: Ahmed Fatma S , Aly Saleh , Liu Xiangrong 
Published: December 2024

Abstract
Antibody-mediated immunity is crucial in the vertebrate immune system. Nanobodies, also known as VHH or single-domain antibodies (sdAbs), are emerging as promising alternatives to full-length antibodies due to their compact size, precise target selectivity, and stability. However, the limited availability of nanobodies (Nbs) for numerous antigens (Ags) presents a significant obstacle to their widespread application. Understanding the interactions between Nbs and Ags is essential for enhancing their binding affinities and specificities. Experimental identification of these interactions is often costly and time-intensive. To address this issue, we introduce NABP-BERT, a deep-learning model based on the BERT architecture, designed to predict NANOBODY®-Ag binding solely from sequence information. Furthermore, we have developed a general pretrained model with transfer capabilities suitable for protein-related tasks, including protein-protein interaction tasks. NABP-BERT focuses on the surrounding amino acid contexts and outperforms existing methods, achieving an AUROC of 0.986 and an AUPR of 0.985.
GPSD: a hybrid learning framework for the prediction of phosphatase-specific dephosphorylation sites
Authors: Han Cheng , Fu Shanshan , Chen Miaomiao , Gou Yujie , Liu Dan , Zhang Chi , Huang Xinhe , Xiao Leming , Zhao Miaoying , Zhang Jiayi , Xiao Qiang , Peng Di , Xue Yu 
Published: December 2024

Abstract
Protein phosphorylation is dynamically and reversibly regulated by protein kinases and protein phosphatases, and plays an essential role in orchestrating a wide range of biological processes. Although a number of tools have been developed for predicting kinase-specific phosphorylation sites (p-sites), computational prediction of phosphatase-specific dephosphorylation sites remains to be a great challenge. In this study, we manually curated 4393 experimentally identified site-specific phosphatase–substrate relationships for 3463 dephosphorylation sites occurring on phosphoserine, phosphothreonine, and/or phosphotyrosine residues, from the literature and public databases. Then, we developed a hybrid learning framework, the group-based prediction system for the prediction of phosphatase-specific dephosphorylation sites (GPSD). For model training, we integrated 10 types of sequence features and utilized three types of machine learning methods, including penalized logistic regression, deep neural networks, and transformer neural networks. First, a pretrained model was constructed using 561 416 nonredundant p-sites and then fine-tuned to generate computational models for predicting general dephosphorylation sites. In addition, 103 individual phosphatase-specific predictors were constructed via transfer learning and meta-learning. For site prediction, one or multiple protein sequences in FASTA format could be inputted, and the prediction results will be shown together with additional annotations, such as protein–protein interactions, structural information, and disorder propensity. The online service of GPSD is freely available at https://gpsd.biocuckoo.cn/. We believe that GPSD can serve as a valuable tool for further analysis of dephosphorylation.
AthRiboNC: an Arabidopsis database for ncRNAs with coding potential revealed from ribosome profiling
Authors: Shen Yi , Liu Liya , Liu Enyan , Li Sida , Orlov Yuriy , Ivanisenko Vladimir , Chen Ming 
Published: December 2024

Abstract
Non-coding RNAs (ncRNAs) are traditionally considered incapable of encoding proteins, but new evidence suggests that small open reading frames (sORFs) within ncRNAs can actually encode biologically functional small peptides. Despite growing recognition of their importance, a systematic exploration of plant ncRNAs with coding potential has remained largely uncharted territory, especially in the context of their translational activities. By collecting and analyzing Ribo-Seq data from 226 Arabidopsis thaliana samples, we have integrated extensive information on Arabidopsis ncRNAs with coding potential and developed the AthRiboNC database, a novel and dedicated database that consolidates extensive information on ncRNAs with coding potential in Arabidopsis. AthRiboNC covers detailed information on 2743 long non-coding RNAs, 255 microRNAs, and 1871 circular RNA in Arabidopsis, along with 40 162 ORFs identified from these ncRNAs. The database also constructs co-expression networks for ncRNAs with coding potential, revealing correlations and potential biological function interpretations. With a commitment to accessibility and ease-of-use, AthRiboNC features a clear and intuitive interface. We hope that AthRiboNC will serve as a valuable resource for exploring the coding potential of plant ncRNAs.
Database URL: https://bis.zju.edu.cn/athribonc
Diversity and networking of uni-cyanobacterial cultures and associated heterotrophic bacteria from the benthic microbial mat of a desert hydrothermal spring
Authors: Lassoued Khaoula , Mahjoubi Mouna , Asimakis Elias , Bel Mokhtar Naima , Stathopoulou Panagiota , Ben Hamouda Refka , Bousselmi Olfa , Marasco Ramona , Masmoudi Ahmed Slaheddine , Daffonchio Daniele , Tsiamis George , Cherif Ameur 
Published: December 2024

Abstract
Thermal springs harbour microorganisms, often dominated by cyanobacteria, which form biofilms and microbial mats. These phototrophic organisms release organic exudates into their immediate surroundings, attracting heterotrophic bacteria that contribute to the diversity and functioning of these ecosystems. In this study, the microbial mats from a hydrothermal pool in the Ksar Ghilane oasis in the Grand Erg Oriental of the Desert Tunisia were collected to obtain cyanobacterial cultures formed by single cyanobacterial species. High-throughput analysis showed that while the microbial mat hosted diverse cyanobacteria, laboratory cultures selectively enriched cyanobacteria from the Leptolyngbya, Nodosilinea, and Arthronema. Per each of these genera, multiple non-axenic uni-cyanobacterial cultures were established, totalling 41 cultures. Cyanobacteria taxa mediated the assembly of distinct heterotrophic bacterial communities, with members of the Proteobacteria and Actinobacteria phyla dominating. The bacterial communities of uni-cyanobacterial cultures were densely interconnected, with heterotrophic bacteria preferentially co-occurring with each other. Our study highlighted the complex structures of non-axenic uni-cyanobacterial cultures, where taxonomically distinct cyanobacteria consistently associate with specific groups of heterotrophic bacteria. The observed associations were likely driven by common selection pressures in the laboratory, such as cultivation conditions and specific hosts, and may not necessarily reflect the microbial dynamic occurring in the spring microbial mats.
Improvement of Transmural Inflammation With Adalimumab Versus Immunomodulator Maintenance Therapy in Pediatric Crohn’s Disease: Single-Center Prospective Evaluation Using the Pediatric Inflammatory Crohn’s Magnetic Resonance Enterography Index
Authors: Scarallo Luca , McKay Hayley E , Schneider Rilla , Ricciuto Amanda , Walters Thomas D , Greer Mary-Louise C , Griffiths Anne M , Church Peter C 
Published: December 2024

Abstract

Background and Aims
Transmural healing, including as assessed by magnetic resonance enterography (MRE) has been associated with long-term favorable outcomes in Crohn’s Disease (CD), but data concerning MRE improvement and normalization with therapy are sparse. We performed a prospective longitudinal study utilizing the recently developed pediatric MRE-based multi-item measure of inflammation (PICMI) to examine the efficacy of adalimumab (ADA) and immunomodulator (IM) in attaining improvement of transmural inflammation of the small intestine.

Methods
Pediatric patients with CD involving small bowel and initiating ADA or IM were prospectively enrolled and followed with repeat MRE at 1 year. A single radiologist provided global assessment (RGA) and scored PICMI items (wall thickness, wall diffusion restriction, mural ulcers, comb sign, mesenteric edema) blinded to clinical information and to the timing of MRE. The primary outcome was mild improvement in PICMI at one year without a change in therapy.

Results
Sixty-two eligible patients were enrolled, 26 receiving ADA and 36 IM. On intent to treat basis, a decline in PICMI score of &gt;20 points without change of therapy was observed more frequently in ADA versus IM-treated patients (54% vs 31%, P = .01). By RGA, 71% improved with ADA vs 42% with IM (P = .03). MRE normalization was rare with both treatments (9% vs 6%, P = .62). A change in PICMI of &gt;20 points was confirmed as the best cut off for MRE improvement as assessed by RGA also for the small bowel.

Conclusions
ADA therapy was associated with objective improvement in MRE findings of inflammation more frequently than IM. The low rate of MRE normalization suggests that this is not yet a realistic target with existing therapies.
Cephalic ganglia transcriptomics of the American cockroach Periplaneta americana (Blattodea: Blattidae)
Authors: Levy Ilana , Arvidson Ryan 
Published: December 2024

Abstract
The American cockroach Periplaneta americana (L.) (Blattodea, Blattidae) has been a model organism for biochemical and physiological study for almost a century, however, its use does not benefit from the genetic tools found in key model species such as Drosophila melanogaster. To facilitate the use of the cockroach as a model system in neuroscience and to serve as a foundation for functional and translational experimentation, a transcriptome of the cephalic ganglia was assembled and annotated, and differential expression profiles between these ganglia were assessed. The transcriptome assembly yielded &gt;400 k transcripts, with &gt;40 k putative coding sequences. Gene ontology and protein domain searches indicate the cerebral and gnathal ganglia (GNG) have distinct genetic expression profiles. The developmental Toll signaling pathway appears to be active in the adult central nervous system (CNS), which may suggest a separate role for this pathway besides innate immune activation or embryonic development. The catabolic glycolytic and citric acid cycle enzymes are well represented in both ganglia, but key enzymes are more highly expressed in the GNG. Both ganglia express gluconeogenic and trehaloneogenic enzymes, suggesting a larger role of the CNS in regulating hemolymph sugar homeostasis than previously appreciated. The annotation and quantification of the cephalic ganglia transcriptome reveal both canonical and novel pathways in signaling and metabolism in an adult insect and lay a foundation for future functional and genetic analysis.