bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiple mitogenomes indicate Things Fall Apart with Out of Africa or Asia hypotheses for the phylogeographic evolution of Honey Bees (Apis mellifera)
Authors: Carr Steven M. 
Published: June 2023

AbstractPrevious morpho-molecular studies of evolutionary relationships within the economically important genus of honey bees (Apis), including the Western Honey Bee (A. mellifera L.), have suggested Out of Africa or Asia origins and subsequent spread to Europe. I test these hypotheses by a meta-analysis of complete mitochondrial DNA coding regions (11.0 kbp) from 22 nominal subspecies represented by 78 individual sequences in A. mellifera. Parsimony, distance, and likelihood analyses identify six nested clades: Things Fall Apart with Out of Africa or Asia hypotheses. Molecular clock-calibrated phylogeographic analysis shows instead a basal origin of A. m. mellifera in Europe ~ 780 Kya, and expansion to Southeast Europe and Asia Minor ~ 720 Kya. Eurasian bees spread southward via a Levantine/Nilotic/Arabian corridor into Africa ~ 540 Kya. An African clade re-established in Iberia ~ 100 Kya spread thereafter to westerly Mediterranean islands and back into North Africa. Nominal subspecies within the Asia Minor and Mediterranean clades are less differentiated than are individuals within other subspecies. Names matter: paraphyletic anomalies are artefacts of mis-referral in GenBank of sequences to the wrong subspecies, or use of faulty sequences, which are clarified by inclusion of multiple sequences from available subspecies.
Oily fish and raw vegetable consumption can decrease the risk of AQP4-positive neuromyelitis optica spectrum disorders: a Mendelian-randomization study
Authors: Wang Shengnan , Pan Lin , Wu Rui , Shao Yanqing , Xue Mengru , Zhu Hao , Min Wanwan , Zheng Xiangyu , Liang Yekun , Zhu Mingqin 
Published: June 2023

AbstractNeuromyelitis optica spectrum disorders (NMOSD) are severe inflammatory disorders of the central nervous system targeting aquaporin‐4 (AQP4). The risk factors for NMOSD remain to be determined, though they may be related to diet and nutrition. This study aimed to explore the possibility of a causal relationship between specific food intake and AQP4-positive NMOSD risk. The study followed a two-sample Mendelian randomization (MR) design. Genetic instruments and self-reported information on the intake of 29 types of food were obtained from a genome-wide association study (GWAS) on 445,779 UK Biobank participants. A total of 132 individuals with AQP4-positive NMOSD and 784 controls from this GWAS were included in our study. The associations were evaluated using inverse-variance-weighted meta-analysis, weighted-median analysis, and MR-Egger regression. A high consumption of oily fish and raw vegetables was associated with a decreased risk of AQP4-positive NMOSD (odds ratio [OR] = 1.78 × 10−16, 95% confidence interval [CI] = 2.60 × 10−25–1.22 × 10−7, p = 0.001; OR = 5.28 × 10−6, 95% CI = 4.67 × 10−11–0.598, p = 0.041, respectively). The results were consistent in the sensitivity analyses, and no evidence of directional pleiotropy was observed. Our study provides useful implications for the development of AQP4-positive NMOSD prevention strategies. Further research is needed to determine the exact causal relationship and mechanisms underlying the association between specific food intake and AQP4-positive NMOSD.
Gravity-driven controls on fluid and carbonate precipitation distributions in fractures
Authors: Xu Zhenyu , Cao Hongfan , Yoon Seonkyoo , Kang Peter K. , Jun Young-Shin , Kneafsey Timothy , Sheets Julia M. , Cole David , Pyrak-Nolte Laura J. 
Published: June 2023

AbstractMany challenges related to carbon-dioxide ($$\hbox {CO}_2$$

CO
2

) sequestration in subsurface rock are linked to the injection of fluids through induced or existing fracture networks and how these fluids are altered through geochemical interactions. Here, we demonstrate that fluid mixing and carbonate mineral distributions in fractures are controlled by gravity-driven chemical dynamics. Using optical imaging and numerical simulations, we show that a density contrast between two miscible fluids causes the formation of a low-density fluid runlet that increases in areal extent as the fracture inclination decreases from 90$$^\circ$$

∘

(vertical fracture plane) to 30$$^\circ$$

∘

. The runlet is sustained over time and the stability of the runlet is controlled by the gravity-driven formation of 3D vortices that arise in a laminar flow regime. When homogeneous precipitation was induced, calcium carbonate covered the entire surface for horizontal fractures (0$$^\circ$$

∘

). However, for fracture inclinations greater than 10$$^\circ$$

∘

, the runlet formation limited the areal extent of the precipitation to less than 15% of the fracture surface. These insights suggest that the ability to sequester $$\hbox {CO}_2$$

CO
2

through mineralization along fractures will depend on the fracture orientation relative to gravity, with horizontal fractures more likely to seal uniformly.
Fibroblasts are not just fibroblasts: clear differences between dermal and pulmonary fibroblasts’ response to fibrotic growth factors
Authors: Madsen Sofie Falkenløve , Sand Jannie Marie Bülow , Juhl Pernille , Karsdal Morten , Thudium Christian S. , Siebuhr Anne Sofie , Bay-Jensen Anne-Christine 
Published: June 2023

AbstractSystemic Sclerosis (SSc) hallmark is skin fibrosis, but up to 80% of the patients have fibrotic involvement in the pulmonary system. Antifibrotic drugs which have failed in a general SSc population have now been approved in patients with SSc-associated interstitial lung disease (ILD). This indicates that the fibrotic progression and regulation of fibroblasts likely depend on local factors specific to the tissue type. This study investigated the difference between dermal and pulmonary fibroblasts in a fibrotic setting, mimicking the extracellular matrix. Primary healthy fibroblasts were grown in a crowded environment and stimulated with TGF-β1 and PDGF-AB. The viability, morphology, migration capacity, extracellular matrix formation, and gene expression were assessed: TGF-β1 only increased the viability in the dermal fibroblasts. PDGF-AB increased the migration capacity of dermal fibroblasts while the pulmonary fibroblasts fully migrated. The morphology of the fibroblasts was different without stimulation. TGF-β1 increased the formation of type III collagen in pulmonary fibroblasts, while PDGF-AB increased it in dermal fibroblasts. The gene expression trend of type VI collagen was the opposite after PDGF-AB stimulation. The fibroblasts exhibit different response profiles to TGF-β1 and PDGF-AB; this suggests that drivers of fibrosis are tissue-dependent, which needs to be considered in drug development.
Fragment size and diversity of mulches affect their decomposition, nutrient dynamics, and mycorrhizal root colonisation
Authors: Gaitanis Dimitrios , Lukac Martin , Tibbett Mark 
Published: June 2023

AbstractPlant-based mulch has been proposed as a sustainable way of maintaining soil fertility. However, the role of mulch diversity, quality, and size in decomposition dynamics, and their effect on crop yield, has not been fully explored. We investigated how mulch quality, proxied by the constituent plant species diversity, and residue size drive mulch decomposition, nutrient release, crop nutrition, and yield. A rhizotron experiment was set up with barley as a model crop, with the addition of mulch of two particle sizes (1.5 and 30 cm) and four different plant residue mixes of differing biodiversity (17, 12, 6, and 1 species) in a fully factorial design. Soil nutrient dynamics were measured at advanced decomposition stages, together with residue quality, arbuscular mycorrhizal fungal (AMF) root colonisation, and crop yield. Residue mass loss was significantly affected by its chemical composition. Initial NDF content was more restricted factor in C and N mineralisation than C:N or lignin. Long residues retained significantly higher C and N content, than short residues. Crop yield was not affected by residue type or size. Residue size significantly affected barley growth rate, influencing seed protein content. Soil available K was significantly increased by residues with a higher initial C:N ratio. Short residues resulted in higher soil Zn. Residues of higher diversity resulted inhigher AMF root colonisationof the barley plants. Generally, long residue mulches maintain higher fertilisation capacity at advanced stage of decomposition than short ones, without a deleterious effect on crop yield. Further investigation should evaluate the effect of continuous application of long residue mulches on soil fertility and microbial symbiosis.
A traffic light control method based on multi-agent deep reinforcement learning algorithm
Authors: Liu Dongjiang , Li Leixiao 
Published: June 2023

AbstractIntelligent traffic light control (ITLC) algorithms are very efficient for relieving traffic congestion. Recently, many decentralized multi-agent traffic light control algorithms are proposed. These researches mainly focus on improving reinforcement learning method and coordination method. But, as all the agents need to communicate while coordinating with each other, the communication details should be improved as well. To guarantee communication effectiveness, two aspect should be considered. Firstly, a traffic condition description method need to be designed. By using this method, traffic condition can be described simply and clearly. Secondly, synchronization should be considered. As different intersections have different cycle lengths and message sending event happens at the end of each traffic signal cycle, every agent will receive messages of other agents at different time. So it is hard for an agent to decide which message is the latest one and the most valuable. Apart from communication details, reinforcement learning algorithm used for traffic signal timing should also be improved. In the traditional reinforcement learning based ITLC algorithms, either queue length of congested cars or waiting time of these cars is considered while calculating reward value. But, both of them are very important. So a new reward calculation method is needed. To solve all these problems, in this paper, a new ITLC algorithm is proposed. To improve communication efficiency, this algorithm adopts a new message sending and processing method. Besides, to measure traffic congestion in a more reasonable way, a new reward calculation method is proposed and used. This method takes both waiting time and queue length into consideration.
Stacked SiGe nanosheets p-FET for Sub-3 nm logic applications
Authors: Chu Chun-Lin , Hsu Shu-Han , Chang Wei-Yuan , Luo Guang-Li , Chen Szu-Hung 
Published: June 2023

AbstractThe fabrication of vertically stacked SiGe nanosheet (NS) field-effect transistors (FETs) was demonstrated in this study. The key process technologies involved in this device fabrication are low pressure chemical vapor deposition SiGe/Si multilayer epitaxy, selective etching of Si layers over SiGe layers using tetramethyl-ammonium-hydroxide wet solution, and atomic layer deposition of Y2O3 gate dielectric. For the fabricated stacked SiGe NS p-GAAFETs with a gate length of 90 nm, ION/IOFF ratio of around 5.0 × 105 and subthreshold swing of 75 mV/dec were confirmed via electrical measurements. Moreover, owing to its high quality of Y2O3 gate dielectric, the device showed a very small drain-induced barrier-lowering phenomenon. These designs can improve the gate controllability of channel and device characteristics.
Chemical resolution of spiroindanones and synthesis of chiroptical polymers with circularly polarized luminescence
Authors: Du Jiping , Li Hui , Wu Tanping , Wang Menglei , Cheng Rui , Wu Di , Yang Yudong , Lan Jingbo 
Published: June 2023

Chemical resolution of 1,1′-spirobisindane-3,3′-dione is accomplished for the first time using chiral diols as recyclable resolution reagents. The derived chiroptical polymers exhibit TADF emission and CPL characteristics withglum values of up to 2.4 × 10−3.
Surface–particle interactions control the escape time of a particle from a nanopore-gated nanocavity system: a coarse grained simulation
Authors: Zando Robert , Chinappi Mauro , Giordani Cristiano , Cecconi Fabio , Zhang Zhen 
Published: June 2023

We developed a coarse-grained model to investigate the dwell time of a spherical Brownian analyte inside a nanopore-gated nanocavity, and discovered the conditions where the transition from bulk 3D to surface 2D diffusion happen for the analyte.
Regional autonomous security cooperative spectrum sensing method based on trust value
Authors: Chen Chengxiao , Qi Xiaogang , Cai Ying , Zhang Jiaxin 
Published: June 2023

AbstractIn order to solve the problems of spectrum resource shortage, low spectrum utilization and shadow effect, a regional autonomous security cooperative spectrum sensing (CSS) method based on trust value is proposed to address the vulnerability of CSS technology in cognitive radio to malicious node attacks. Considering the difference in node position, the vulnerability of CSS to malicious node attacks, the large amount of centralized sensing data processing, and the large energy consumption of distributed sensing, based on the trust value update mechanism of ‘slow growth and fast recovery’, the perception area is divided and managed, and the final perception result is determined by majority voting based on the centralized sensing. The convergence value of the time difference of the perceptual process trust value is used to detect the anomaly of the node, and the cumulative difference in trust values between the nodes can detect and locate the malicious node. Experimental simulation results show that the proposed model is superior to traditional algorithms in spectral perception accuracy and malicious node detection.
An inverse scattering reconstruction method for perfect electric conductor‐dielectric hybrid target based on physics‐inspired network
Authors: Zhang Qian‐qian , Yin Cheng‐you , Li An‐qi , Liu Han 
Published: June 2023

AbstractTo improve the imaging accuracy in solving inverse scattering problems with mixed boundary conditions, the authors propose an inverse scattering imaging method based on a physics‐inspired neural network. First, the contrast source inversion and the T‐matrix method are unified to establish a combined parameter model, in which the characteristics of perfect electric conductor and dielectric scatterers are represented by the T‐matrix coefficients t and the dielectric contrast respectively. Considering the influence of singularity of conductor contrast, the PEC region and the DIE contrast are reconstructed separately. Then, an alternative parameter updating neural network method, called APU‐Net, is proposed to update the contrast of dielectric scatterers and the T‐matrix of perfect electric conductor scatterers alternately. The experimental results demonstrate the strong performance of APU‐Net for inverse scattering imaging of PEC‐DIE hybrid targets as well as its improved generalisation ability over existing methods.
High-energy-resolution angle-resolved inverse-photoelectron spectroscopy apparatus for damage-free measurements of conduction band structures of functional materials
Authors: Kashimoto Yuki , Ideta Satoshi , Sato Haruki , Orio Hibiki , Kawamura Keita , Yoshida Hiroyuki 
Published: June 2023

The energy band structure of the conduction band (energy–momentum relation of electrons) is crucial to understanding the electron transport of crystalline materials. In this paper, we describe an angle-resolved low-energy inverse photoelectron spectroscopy (AR-LEIPS) apparatus that examines the conduction band structures of materials sensitive to the electron beam, such as organic semiconductors and organic–inorganic hybrid perovskites. The principle of this apparatus is based on AR inverse photoelectron spectroscopy. To minimize radiation damage and improve energy resolution, we employed our previous approach used in LEIPS [H. Yoshida, Chem. Phys. Lett. 539–540, 180 (2012)]. We obtained an overall energy resolution of 0.23 eV with a momentum resolution of 0.9 nm−1 at the electron kinetic energy of 2 eV or higher.
Studying excited-state-specific perturbation theory on the Thiel set
Authors: Clune Rachel , Shea Jacqueline A. R. , Hardikar Tarini S. , Tuckman Harrison , Neuscamman Eric 
Published: June 2023

We explore the performance of a recently introduced N5-scaling excited-state-specific second order perturbation theory (ESMP2) on the singlet excitations of the Thiel benchmarking set. We find that, without regularization, ESMP2 is quite sensitive to π system size, performing well in molecules with small π systems but poorly in those with larger π systems. With regularization, ESMP2 is far less sensitive to π system size and shows a higher overall accuracy on the Thiel set than CC2, equation of motion-coupled cluster with singles and doubles, CC3, and a wide variety of time-dependent density functional approaches. Unsurprisingly, even regularized ESMP2 is less accurate than multi-reference perturbation theory on this test set, which can, in part, be explained by the set’s inclusion of some doubly excited states but none of the strong charge transfer states that often pose challenges for state-averaging. Beyond energetics, we find that the ESMP2 doubles norm offers a relatively low-cost way to test for doubly excited character without the need to define an active space.
Stance in Flemish Sign Language
Authors: Andries Fien , Brône Geert , Vermeerbergen Myriam 
Published: June 2023

Abstract
In this contribution, we offer a first exploration of stance expressions in Flemish Sign Language (VGT). Biber and Finegan (1989) define stance as the expression of feelings, attitudes,
judgments, commitments, and assessments. The few studies focusing on stance in signed languages have shown that stance can be
expressed by various structures and mechanisms such as lexical signs, manual gestures (e.g., Palm Up gestures) and
embodiment/mental space blends. We will examine if these findings apply to Flemish Sign Language, and we will identify other means
of expressing stance in VGT.
In this exploratory study, we focus on the following questions: (1) which articulators and semiotic resources can
be used in Flemish Sign Language to express stance?; and (2) How are visible bodily actions through different articulators
integrated temporally in stance expressions?
Our study is based on the analysis of about five hours of data from the Corpus Flemish Sign Language. We
present examples from our dataset to illustrate that stance can be expressed through a range of structures and mechanisms (such as
lexical signs, manual gestures, enactment, and non-manual features), expressed either sequentially or simultaneously by a
multitude of articulators. Moreover, we zoom in on the phenomenon of stance-stacking and analyse how multiple stance expressions
can be combined in VGT.
Gesture at the crossroads
Authors: Shaw Emily 
Published: June 2023

Abstract
Task-based exchanges are known to have multiple co-occurring interactive structures that prompt interlocutors to integrate various semiotic fields (Goodwin 2000). In addition to underlying norms of cooperative interaction, task-based exchanges include joint accomplishment of some activity. In this study, a group of co-workers (two hearing and one deaf) engaged in a team-building exercise where they jointly constructed a container fit for protecting an egg. They communicated, in part, via a sign language interpreter. Clark’s (2016) methods of communication were applied to the interpreter-mediated interaction (IMI) to determine whether certain semiotic modes were more (or less) accessible to the respective linguistic groups. Micro-analysis of three activity phases revealed moments when the participants responded to and integrated semiotic fields displayed in front of them. While not all content was accessible, like the complex depictive structures produced by the deaf person, some instances of mutual understanding without interpretation were achieved via integration of meaningful components of visibly accessible semiotic fields. Results challenge traditional views of IMIs where interpreters are positioned as channelling communicative content exclusively through them.
Turning points as a tool in narrative research
Authors: Wieslander Malin , Löfgren Håkan 
Published: June 2023

AbstractThis article focuses on how the concept of “turning points” can be used in narrative research when studying people’s (professional) identities and identity formation. By examining various understandings of turning points, we aim to show how they can be identified and used as analytical tools in different ways when conducting narrative analyses of (professional) identity formation. A case study from a research project on police identity is used to illustrate the application of various perspectives on turning points. The article offers guidance for researchers on choosing a context and focus for analysing turning points, as well as on the theoretical perspectives that come with these choices, and thereby suggests directions for analytical attention. The article shows how different perspectives on turning points have consequences for the understanding of professional identities.
Variable projection methods for separable nonlinear inverse problems with general-form Tikhonov regularization
Authors: Español Malena I , Pasha Mirjeta 
Published: June 2023

Abstract
The variable projection (VarPro) method is an efficient method to solve separable nonlinear least squares problems. In this paper, we propose a modified VarPro method for solving separable nonlinear least squares problems with general-form Tikhonov regularization. In particular, we apply the Gauss–Newton method to the corresponding reduced problem and investigate its convergence when different approximations of the Jacobian matrix are used. For special cases when computing the generalized singular value decomposition is feasible or a joint spectral decomposition of both forward and regularization operators exists, we provide efficient ways to compute the Jacobians and the solution of the linear subproblems. For large-scale problems, where matrix decompositions are not an option, we compute a reduced Jacobian and apply projection-based iterative methods and generalized Krylov subspace methods to solve the linear subproblems. In all cases, the regularization parameter can be computed automatically at each iteration using generalized cross validation. Several numerical examples highlight the proposed approach’s performance in the quality of the reconstructed image and the reconstructed forward operator, including large-scale two-dimensional imaging problems arising from semi-blind deblurring.
Deterministic nanoscale quantum spin-defect implantation and diffraction strain imaging
Authors: Delegan Nazar , Whiteley Samuel J , Zhou Tao , Bayliss Sam L , Titze Michael , Bielejec Edward , Holt Martin V , Awschalom David D , Heremans F Joseph 
Published: June 2023

Abstract
Local crystallographic features negatively affect quantum spin defects by changing the local electrostatic environment, often resulting in degraded or varied qubit optical and coherence properties. Few tools exist that enable the deterministic synthesis and study of such intricate systems on the nano-scale, making defect-to-defect strain environment quantification difficult. In this paper, we highlight state-of-the-art capabilities from the U.S. Department of Energy’s Nanoscale Science Research Centers that directly address these shortcomings. Specifically, we demonstrate how complementary capabilities of nano-implantation and nano-diffraction can be used to demonstrate the quantum relevant, spatially deterministic creation of neutral divacancy centers in 4H silicon carbide, while investigating and characterizing these systems on the

≤
25

nm

scale with strain sensitivities on the order of

1
×

10

−
6

,

relevant to defect formation dynamics. This work lays the foundation for ongoing studies into the dynamics and deterministic formation of low strain homogeneous quantum relevant spin defects in the solid state.