bluuebunny/crossref_metadata_2025_split huggingface dataset:
Migration of primordial germ cells and their relationship of PGCs with sex development in transgenic germline-specific fluorescent freshwater angelfish (Pterophyllum scalare)
Authors: Chu Wai-Kwan , Huang Shih-Chin , Chang Ching-Fong , Wu Jen-Leih , Gong Hong-Yi 
Published: January 2025

AbstractPrimordial germ cells (PGCs), the progenitors of gametes, are essential for teleost reproduction. While their formation is conserved across teleosts, the activation, migration routes, and localization periods vary among species. In this study, we developed a novel transgenic line, Tg(ddx4:TcCFP13-nanos3), based on the Nile tilapia genome, to label PGCs with clear fluorescent signals in the freshwater angelfish (Pterophyllum scalare). Our findings reveal a complex, multistage PGCs migration process in angelfish, with a significantly extended localization period (168 hpf) compared to zebrafish (24 hpf). Notably, individual differences in PGCs abundance were observed during early somite development. Analysis of PGCs counts and subsequent sexual maturation demonstrate a potential correlation between PGCs abundance and sex determination: 90% of PGCs-reduced individuals developed as males, while 83% of PGCs-rich individuals developed as females. This study provides a foundation for understanding PGCs migration and sex development in freshwater angelfish, offering valuable insights into reproductive biology and ornamental fish species. Furthermore, this in vivo PGCs tracking system for Cichlids provides a versatile tool for advancing research and applications in germ cell biology.
Hepatovirus infections in juvenile seals from the North Sea
Authors: Mirolo Monica , Kühl Bianca , Roji Melvin Daniel , Rubio-García Ana , Lima Valéria Andrade , Puff Christina , Martina Byron , Beineke Andreas , Wohlsein Peter , Baumgärtner Wolfgang , Ludlow Martin , Osterhaus Albert 
Published: January 2025

AbstractThe discovery of several novel hepatovirus species in marine and terrestrial mammals has expanded the recognised members of the genus Hepatovirus and has provided better understanding on the evolutionary origins of human hepatovirus A (HAV). Using high throughput sequencing we detected a seal hepatovirus (SealHAV_NL/PV/21), in liver tissue of a deceased harbor seal (Phoca vitulina) originating from the Dutch North Sea coast. RT-PCR screening of liver samples of 88 harbor seals and 12 grey seals (Halichoerus grypus) from the same region identified seal hepatovirus in nine juvenile harbor seals in which minor sequence variation was observed in the VP1 gene. Whole-genome sequence analysis showed that SealHAV_NL/PV/21 displayed 95.6% nucleotide indentity to New England seal hepatovirus but had a 5′-UTR which contained additional 51 bp. Phylogenetic analysis showed that seal hepatoviruses clustered in a monophyletic group separate from other hepatovirus species that have been identified in terrestrial mammals. Assessment of seal hepatovirus RNA loads in organs of all infected animals showed that the liver had the highest number of RNA copies with up to 107 RNA copies per mg of tissue. Seal hepatovirus RNA was readily detected by in situ hybridization in hepatocytes in the liver but was not associated with pathological lesions. Serological screening of 90 contemporary seal sera using a HAV-based ELISA showed the presence of hepatovirus antibodies in 14 harbor seals and one juvenile grey seal. These findings collectively show that seal hepatovirus is enzootic among seals of the North Sea, causing quiescent infections in young animals.
Intravitreal Enzyme Replacement Therapy Slows Retinopathy in Late Infantile Ceroid Lipofuscinosis Type 2
Authors: Priglinger Claudia S. , Courage Carolina , Lotz-Havla Amelie S. , Gerhardt Maximilian , Ehrt Oliver , Kurz Matthias , Pudritz Harald , Rudolph Günther , Jackson Christopher B. , Maier Esther M. 
Published: January 2025

AbstractCeroid lipofuscinosis type 2 (CLN2) is caused by biallelic pathogenic variants in the TPP1 gene, encoding lysosomal tripeptidyl peptidase 1 (TPP1). The classical late-infantile phenotype has an age of onset between 2 and 4 years and is characterized by psychomotor regression, myoclonus, ataxia, blindness, and shortened life expectancy. Vision loss occurs due to retinal degeneration, usually when severe neurological symptoms are already evident.Intracerebroventricular enzyme replacement therapy (ICV-ERT) using recombinant human TPP1 (rhTPP-1) was shown to slow the neurological decline; however, it does not prevent loss of vision. Intravitreal rhTPP-1 (IVT-ERT) was described to halt retinal degeneration in a canine CLN2 model and a compassionate-use study in humans.We report on the clinical and ophthalmological outcome in an early-treated patient homozygous for a pathogenic variant in TPP1 known to be associated with severe CLN2 retinopathy.He was started on ICV-ERT at the age of 40 months and 4 weekly IVT-ERT in one eye at the age of 60 months. The other eye served as untreated control.Baseline best corrected visual acuity (BCVA) was 0.5 with mild bull's eye maculopathy evident in both eyes. After 24 months of IVT-ERT, BCVA in the treated eye was 0.2 with bull's eye maculopathy sparing outer retinal layers, whereas the untreated eye had progressed to endstage retinopathy and BCVA <0.02. No intraocular side effects occurred.Our results provide further evidence that IVT-ERT appears to be safe and markedly delays retinal degeneration preserving visual function and increasing the patient's quality of life, especially if started early.
Accuracy of approximate methods for the calculation of fluorescence-type linear spectra with a complex system–bath coupling
Authors: Nöthling J. A. , Mančal Tomáš , Krüger T. P. J. 
Published: January 2025

Much can be learned about molecular aggregates by modeling their fluorescence-type spectra. In this study, we systematically describe the accuracy of various methods for simulating fluorescence-type linear spectra in a dimer system with a complex system–environment interaction, which serves as a model for various molecular aggregates, including most photosynthetic light-harvesting complexes (LHCs). We consider the approximate full cumulant expansion (FCE), complex time-dependent Redfield (ctR), time-independent Redfield, and modified Redfield methods and calculate their accuracy as a function of the site energy gap and coupling, excitonic energy gap, and dipole factor (i.e., type of spectrum). We find that the FCE method is the most accurate method for couplings smaller than 300 cm−1 at 300 K, but this method fails for very strong couplings or low temperatures due to inaccurate modeling of the equilibrium initial state. The ctR method performs well for the calculation of fluorescence and linear anisotropy spectra but poorer for circularly polarized fluorescence spectra or for all spectra when the coupling is strong (∼100cm−1). The Redfield and modified Redfield methods generally perform much more poorly than the ctR and FCE methods—especially for small excitonic energy gaps and strong couplings. We show that accurate modeling of the Stokes shift is crucial and present a version of the ctR method that treats both the Stokes shift and initial state correctly for the parameter ranges in plant LHCs. Apart from the application to LHCs, our results will be useful for the spectral characterization and design of organic molecular aggregates.
Restoring rotational symmetry of multicomponent wavefunctions with nuclear orbitals
Authors: Moncada Félix , Reyes Andrés , Pettersson Lars G. M. 
Published: January 2025

In this work, we present a non-orthogonal configuration interaction (NOCI) approach to address the rotational corrections in multicomponent quantum chemistry calculations where hydrogen nuclei and electrons are described with orbitals under Hartree–Fock (HF) and density functional theory (DFT) frameworks. The rotational corrections are required in systems such as diatomic (HX) and nonlinear triatomic molecules (HXY), where localized broken-symmetry nuclear orbitals have a lower energy than delocalized orbitals with the correct symmetry. By restoring rotational symmetry with the proposed NOCI approach, we demonstrate significant improvements in proton binding energy predictions at the HF level, with average rotational corrections of 0.46 eV for HX and 0.23 eV for HXY molecules. For computing rotational excitation energies, our results indicate that HF kinetic energy corrections are consistently accurate, while discrepancies arise in total energy predictions, primarily from an incomplete treatment of dynamical correlation effects. Rotational energy corrections in multicomponent DFT calculations, using the epc17-2 proton–electron correlation functional, lead to an overestimation of proton binding energies. This is as a result of double-counting of proton–electron correlation effects in the off-diagonal NOCI terms. As a correction, we propose a scaling scheme that effectively adjusts the proton–electron correlation contributions, bringing our results into close agreement with reference CCSD(T) data. The scaled rotational corrections, on average, increase the epc17-2 proton binding energy predictions by 0.055 eV for HX and 0.025 eV for HXY and yield average deviations of 1.0 cm−1 for rotational transitions.
Biodegradable Tenebrio molitor antifreeze protein modified kinetic hydrate inhibitor: Insights into molecular interactions and structural flexibility
Authors: Zhang Nan , Huang Hui-Yi , Li Yan-Nan , Zhang Li-Rong , Liu Jun-Jie 
Published: January 2025

The formation of natural gas hydrates presents significant economic and safety challenges to the petroleum and gas industry, necessitating the development of effective prevention strategies. This study investigates an environmentally sustainable Tenebrio molitor antifreeze protein (TmAFP) modified to be a potential kinetic hydrate inhibitor. The aim of this study was to enhance the inhibitory activity of TmAFP by systematically substituting threonine (Thr) residues with glycine (Gly), alanine (Ala), or serine (Ser) at positions 29, 39, and 53. The Ala mutant demonstrated superior inhibition of hydrate formation, attributed to its optimized spatial conformation and enhanced hydrophobic interactions, followed by the Gly and Ser mutants. The wild-type TmAFP showed limited efficacy. The radial distribution function (RDF) analysis indicated that the mutations facilitated a better accommodation of adjacent residues within the hydrate crystal structure by adjusting the distance between Thri and Thri+2 to closely match the second peak in the RDF of methane molecules at 6.4 Å. The potential of mean force (PMF) calculations revealed that the Ala and Ser mutants exhibited enhanced interactions with hydrate cages, with PMF values of −0.73 and −0.71 kJ/mol, respectively, compared to the Gly mutant, which had a PMF value of 1.46 kJ/mol. By identifying the optimal mutation combination (T29 39 53A) to significantly increase the potency of TmAFP, this study provides a fundamental basis for the further development of hydrate inhibition strategies.
Representing Ireland and the Irish in the 17th- and 18th-century English press
Authors: Claridge Claudia 
Published: January 2025

Abstract
The treatment of Ireland in the London press from 1640 to 1800 is investigated with the help of the
ZEN and Lampeter corpora, following up on De
Nie’s (2004) hypothesis that views of the Irish could have functioned as a foil for creating a British
identity. Mentions of the Irish and Irish affairs matters are not only very infrequent, but also are of a nature to
deny agency to the Irish. Within this picture of discursive neglect, apparently based on true English disinterest,
three aspects stand out, which partly contribute to (unsystematic) othering: (i) Irish Catholicism, styled as hostile
to Britain, (ii) a set of mocking stereotypes, and (iii) Ireland seen as subservient to the economic interests of
England.
Revolutionary news
Authors: Dooley Brendan , Boerio Davide 
Published: January 2025

Abstract
News travelled quickly during the troubled 1640s in Europe and had almost palpable effects. But how
did news travel, and who got it first? Weekly handwritten newsletters transmitted from sites of crisis to the Tuscan
Grand Ducal court and elsewhere, are a still under-used source. This chapter analyses the similarities and differences
between weekly handwritten news reporting about two places, London and
Naples, both of which experienced regime-changing commotions in the 1640s, among others similarly afflicted at the
time. More concretely, we will be comparing and contrasting these two cases of popular unrest resulting in the
creation of new forms of government, and the linguistic ramifications of this in the realms of diction, word usage,
sentiment and sense of belonging.
Revising the Algemene Nederlandse Spraakkunst
Authors: Dhondt Arne , Colleman Timothy , Caluwe Johan De 
Published: January 2025

Abstract
The third, fully revised version of the Algemene Nederlandse Spraakkunst (ANS), the main reference grammar of Dutch, aims to describe grammatical variation in the national standard varieties of Dutch. This paper investigates whether this pluricentric perspective is compatible with the geographical distribution patterns of Dutch grammatical variants. We provide an overview of the distribution patterns described in the second edition of the ANS and we check this description against frequency data from newspaper corpora for four selected variants which represent different distribution patterns. Although the observed distribution patterns do not always coincide with national borders, we argue that the pluricentric model does not (necessarily) conflict with linguistic reality and that it is the appropriate choice to meet the needs of Dutch language users.
Parametric level-sets enhanced to improve reconstruction (PaLEnTIR)
Authors: Ozsar Ege , Kilmer Misha , de Sturler Eric , Saibaba Arvind K , Miller Eric 
Published: January 2025

Abstract
We introduce parametric level-set enhanced to improve reconstruction (PaLEnTIR), a significantly enhanced parametric level-set (PaLS) method addressing the restoration and reconstruction of piecewise constant objects. Our key contribution involves a unique PaLS formulation utilizing a single level-set function to restore scenes containing multi-contrast piecewise constant objects without requiring knowledge of the number of objects or their contrasts. Unlike standard PaLS methods employing radial basis functions (RBFs), our model integrates anisotropic basis functions (ABFs), thereby expanding its capacity to represent a wider class of shapes. Furthermore, PaLEnTIR streamlines the model by reducing redundancy and indeterminacy in the parameterization, resulting in improved numerical performance. We compare PaLEnTIR’s performance to state-of-the art alternatives via a diverse collection of experiments encompassing denoising, deconvolution, sparse and limited angle of view x-ray computed tomography (2D and 3D), and nonlinear diffuse optical tomography tasks using both real and simulated data sets.
Computational prediction of novel two-dimensional tungsten nitride superconductors
Authors: Hernández-Tecorralco J , Ríos-Ramírez J J , Olea-Amezcua M A 
Published: January 2025

Abstract
Transition metal nitrides are well-known 3D superconductor materials. However, there is a lack of knowledge related to their two-dimensional (2D) counterparts, which have several potential technological applications. In this work, we predict, using an evolutionary algorithm coupled with a first-principles approach, a set of novel 2D superconductive structures based on tungsten nitride. Through a systematic process including energetic and dynamical analysis, three thermodynamically stable compositions along with metastable compounds were studied in the following stoichiometries: W4N2, W2N2, and W2N3. Their superconductive temperature (

T

c

) values, estimated by means of the Eliashberg superconductive theory and the McMillan equation, range from 2.3 to 21.6 K, where the highest

T

c

value corresponds to a W2N3 metastable hexagonal system. A systematic analysis of the structural, electronic, vibrational and electron–phonon (e–ph) properties, allowed us to recognize the variables that modulate the

T

c

in theses systems. The superconductive behavior is strongly affected by changes in the nitrogen density of states at Fermi level, the e–ph coupling constant and the lattice symmetry. The present results aim to encourage further theoretical and experimental efforts over non fully explored superconductors in two dimensions.
Lightweight multi-scale encoder– decoder network with locally enhanced attention mechanism for concrete crack segmentation
Authors: Dong Shuai , Cao Jin , Wang Yunlong , Ma Jia , Kuang Zhiwei , Zhang Zhenhao 
Published: January 2025

Abstract
Concrete surface crack detection and maintenance are crucial for ensuring structural safety. Deep learning-based techniques for detecting concrete cracks have become popular due to the quick advancement of artificial intelligence. However, the actual uses of these methods are limited due to issues like large model sizes and significant dependence on powerful computing hardware. To address these issues, this paper presents a lightweight multi-scale encoder–decoder network (LMED-Net) for crack detection of concrete structures. LMED-Net employs MobileNetV2 as the encoder for the initial feature extraction. A multi-scale feature extraction (MFE) module is developed and serially attached after the encoder for refining feature extraction. Finally, to strengthen the network’s perception of pixels surrounding the cracks, a novel enhanced attention mechanism (EAM) is deployed in the decoder. By improving the network’s attention to information within the crack regions, this mechanism keeps contextual information from being lost. Comparative experimental results show that the proposed network achieves an F1 score (F1) of 60.32% and a mean intersection over union (mIoU) of 71.04% on the crack forest dataset. On the DeepCrack dataset, the F1 and mIoU increase to 79.09% and 81.85% respectively. Notably, LMED-Net performs exceptionally well in crack segmentation since its model size and parameters count are much smaller than those of other image segmentation methods. Furthermore, ablation studies further validate the effectiveness of the proposed MFE module and EAM.
A precision method for measuring large-diameter, high-gradient surface profiles using a chromatic confocal sensor and mirror assembly
Authors: Yang Zhipeng , Wang Wei , Huang Daixin , Jiao Sicheng , Xu Min 
Published: January 2025

Abstract
High-gradient surfaces with large diameters are extensively utilized in various fields such as high-performance optical systems and aerospace engineering. Accurate measurement technologies are crucial to ensure that the machining precision of these surfaces meets application requirements. However, the need for sensor rotation axes and coupling devices imposes many limitations on current technologies and equipments when measuring these types of surfaces. To address this issue, this paper proposes an optical measurement method using a chromatic confocal sensor (CCS) and a mirror assembly that eliminates the need for rotation axes and coupling devices. This method deflects the optical path of the CCS by translating mirrors with different inclinations and achieves measurement of the entire surface using a four-axis system. This method lowers both the cost and complexity of the system, reduces potential error sources, and streamlines the measurement process. An experimental measurement of a hemispherical shell was conducted, resulting in a maximum deviation of 0.858 μm for the profiles reconstructed by the proposed system, compared to those obtained from the LUPHOScan260. The verification result demonstrates the feasibility and effectiveness of this method.
Hybrid contrastive representations and SBO-based samples generation for rotating machinery anomaly detection based on driven-end current signal
Authors: Lin Weiqi , Zhang Shaohui , Li Tao , Jiang Fei , Wu Zhaoqian , Zhong Zhi 
Published: January 2025

Abstract
While deep learning methods based on cross-entropy function have made great advancements in maintaining equipment reliability, their learning paradigm appears less suitable for anomaly detection tasks, which focus on extracting specific target features and ignore the discriminability between classes. Besides, incomplete dataset still hinders the robustness of intelligent detection models, especially when the training dataset only contains normal samples. Therefore, a hybrid contrastive representation and soft Brownian offset (SBO)-based samples generation (HCRS) method based on driven-end current signals is proposed to distinguish normal and abnormal samples in incomplete data scenarios where only normal signals are available. In the proposed HCRS detection framework, an autoencoder is initially trained using only normal current samples. It is then combined with the SBO method to generate abnormal samples, relieving the issues of incomplete dataset. Subsequently, a supervised contrastive learning-based deep feature extractor is trained using both the generated abnormal samples and the collected normal samples. This process aims to learn high-level fine-grained representations with discriminability. Finally, these learned representations are utilized to train a data-driven classifier, enabling effective anomaly detection in rotating machinery. In addition, experiments on two datasets suggest that the proposed HCRS can effectively achieve higher accuracy anomaly detection with only normal current signals and outperform existing detection approaches.
Spin-momentum locking as a source of spin-splitting anisotropy in inverted HgTe quantum wells
Authors: Kubisa Maciej , Ryczko Krzysztof 
Published: January 2025

Abstract
We show theoretically that Rashba spin–orbit coupling in gated heterostructures results in strong anisotropy of electron spin splitting. A simple analytical expression for the splitting energy is derived and shown to be in excellent agreement with multiband numerical calculations. Moreover, our theory successfully explains recent experimental results for inverted HgTe quantum wells.
Consequences of non-Markovian healing processes on epidemic models with recurrent infections on networks
Authors: Carlos M Silva José , Silva Diogo H , Rodrigues Francisco A , Ferreira Silvio C 
Published: January 2025

Abstract
Infectious diseases are marked by recovering time distributions which can be far from the exponential one associated with Markovian/Poisson processes, broadly applied in epidemic models. In the present work, we tackled this problem by investigating a susceptible-infected-recovered-susceptible model on networks with η independent infectious compartments (SI

η

RS), each one with a Markovian dynamics, that leads to a Gamma-distributed recovering time. We analytically develop a theory for the epidemic lifespan on star graphs with a center and K leaves, which mimic hubs on networks, showing that the epidemic lifespan scales with a non-universal power-law. Compared with standard susceptible-infected-recovered-susceptible dynamics, the epidemic lifespan on star graphs is severely reduced as the number of stages increases. In particular, the case

η
→
∞

leads to a finite lifespan. Numerical simulations support the approximated analytical calculations. We investigated the SI

η

RS dynamics on random power-law networks. When the epidemic processes are ruled by a maximum k-core activation, either the epidemic threshold or the epidemic localization pattern are unaltered. When hub mutual activation is at work, the localization is reduced but not sufficiently to alter the threshold scaling with the network size. Therefore, the activation mechanisms remain the same as in the case of Markovian healing.