bluuebunny/crossref_metadata_2025_split huggingface dataset:
A method to implement inter-track interactions in Monte Carlo simulations with TOPAS-nBio and their influence on simulated radical yields following water radiolysis
Authors: Derksen Larissa , Flatten Veronika , Engenhart-Cabillic Rita , Zink Klemens , Baumann Kilian-Simon 
Published: June 2023

Abstract

Objective. In FLASH radiotherapy (dose rates ≥40 Gy s−1), a reduced normal tissue toxicity has been observed, while maintaining the same tumor control compared to conventional radiotherapy (dose rates ≤0.03 Gy s−1). This protecting effect could not be fully explained yet. One assumption is that interactions between the chemicals of different primary ionizing particles, so-called inter-track interactions, trigger this outcome. In this work, we included inter-track interactions in Monte Carlo track structure simulations and investigated the yield of chemicals (G-value) produced by ionizing particles. Approach. For the simulations, we used the Monte Carlo toolkit TOPAS, in which inter-track interactions cannot be implemented without further effort. Thus, we developed a method enabling the simultaneous simulation of N original histories in one event allowing chemical species to interact with each other. To investigate the effect of inter-track interactions we analyzed the G-value of different chemicals using various radiation sources. We used electrons with an energy of 60 eV in different spatial arrangements as well as a 10 MeV and 100 MeV proton source. For electrons we set N between 1 and 60, for protons between 1 and 100. Main results. In all simulations, the total G-value decreases with increasing N. In detail, the G-value for •OH , H3O and eaq decreases with increasing N, whereas the G-value of OH− , H2O2 and H2 increases slightly. The reason is that with increasing N, the concentration of chemical radicals increases allowing for more chemical reactions between the radicals resulting in a change of the dynamics of the chemical stage. Significance. Inter-track interactions resulting in a variation of the yield of chemical species, may be a factor explaining the FLASH effect. To verify this hypothesis, further simulations are necessary in order to evaluate the impact of varying G-values on the yield of DNA damages.
A unified hybrid transformer for joint MRI sequences super-resolution and missing data imputation
Authors: Wang Yulin , Hu Haifeng , Yu Shangqian , Yang Yuxin , Guo Yihao , Song Xiaopeng , Chen Feng , Liu Qian 
Published: June 2023

Abstract

Objective. High-resolution multi-modal magnetic resonance imaging (MRI) is crucial in clinical practice for accurate diagnosis and treatment. However, challenges such as budget constraints, potential contrast agent deposition, and image corruption often limit the acquisition of multiple sequences from a single patient. Therefore, the development of novel methods to reconstruct under-sampled images and synthesize missing sequences is crucial for clinical and research applications. Approach. In this paper, we propose a unified hybrid framework called SIFormer, which utilizes any available low-resolution MRI contrast configurations to complete super-resolution (SR) of poor-quality MR images and impute missing sequences simultaneously in one forward process. SIFormer consists of a hybrid generator and a convolution-based discriminator. The generator incorporates two key blocks. First, the dual branch attention block combines the long-range dependency building capability of the transformer with the high-frequency local information capture capability of the convolutional neural network in a channel-wise split manner. Second, we introduce a learnable gating adaptation multi-layer perception in the feed-forward block to optimize information transmission efficiently. Main results. Comparative evaluations against six state-of-the-art methods demonstrate that SIFormer achieves enhanced quantitative performance and produces more visually pleasing results for image SR and synthesis tasks across multiple datasets. Significance. Extensive experiments conducted on multi-center multi-contrast MRI datasets, including both healthy individuals and brain tumor patients, highlight the potential of our proposed method to serve as a valuable supplement to MRI sequence acquisition in clinical and research settings.
Influence NiO on the structure, elastic properties and buildup factor of BaO-CdO-borosilicate glasses
Authors: Sayyed M I , Abdo M A , Ali H Elhosiny , Ahmed H. A. , Sadeq M S 
Published: June 2023

Abstract
In this work, the structure, elasticity parameters, and buildup factor of borosilicate glasses doped with BaO, CdO and NiO have been studied. Infrared (IR) spectroscopy was utilized to study the internal structure of the present system. IR spectra are broad, especially since the superposition between the borate and silicate occurs in the same spectral region. A deconvolution process was carried out to extract these spectra into their individual bands. The values of tetrahedrally-coordinated boron atoms ratio (

N

4

) barely increased from 37.9% for 1 mol% of NiO to 39.5% for 4 mol% of NiO. This increase indicates the transformation of three coordinated boron atoms (

BO

3

) to four coordinated boron atoms (

BO

4

) units with further NiO additions. The

N

4

values were used along with the dissociation energies density and packing density parameters to calculate the elastic moduli; Young, shear, bulk, and Poisson ratio. The obtained values of Young’s modulus increase with further NiO additions. This increased behavior of Young’s modulus demonstrates the augmented ability of the current glasses to withstand variations in their length under lengthwise tensile tension or compression with further NiO additions. The rest of the elasticity moduli showed increased behaviors as well. These increased behaviors support the results obtained from structural properties analyses. An increment of BO4 units with decreasing the nonbridging oxygens ions (NBO) in the internal structure of present glasses produces an increase in the elastic parameters of these glasses. At photons energy of 0.2 MeV, the energy exposure buildup factor (EBF) values are low for glasses with a high concentration of CdO (low concentration of NiO), but the value of EBF is larger for glasses with a low concentration of CdO (high concentration of NiO).
Critical states of a superconducting slab subjected to tension and bending
Authors: Ma Puhuan , Li Yingxu , Salmi Tiina 
Published: June 2023

Abstract
This work is an extension of a previous critical-state model proposed by the same author [Li and Gao, SuST (2015)]. We want to show the evolution of critical states for a rather long time, and the physics behind the evolution is also desired. It is another purpose to make clear the role of mechanical deformation played in the evolution process of critical state. We thus develop the model with two new features: (a) mechanical loads are applied to both ends of the slab, instead of no external force applied in the previous model; (b) the critical current density is now a function of position, rather than a constant over the slab volume as in the previous model. The new results by the model consist of: (a) the evolution with time for a given strain value is generally the same as the strain-free case; (b) stretching accelerates the development of the critical state, and bending has no significant effect on the critical state; (c) the detailed critical-state profiles may provide how to regulate the electromagnetic field by strain in a superconducting device with slab geometry for practical purpose.
A proposition: feasibility of classical plate theory on bending monolayer graphene
Authors: Yan J W , Jiang S C , He L H , Gong M L 
Published: June 2023

Abstract
In this paper, we carry out a comparison study between classical plate theory and ‘bottom to top’ atomistic-continuum multiscale model regarding the prediction of bending of monolayer graphene to state the general feasibility of classical plate theory. We replace the commonly used interlayer spacing value by the newly launched intrinsic material thickness value as the monolayer graphene thickness. Based on this correction, we amend the flexural rigidity and find that classical plate theory gives a much better prediction of the force-bending deflection curve for various graphene obtained by the atomistic-continuum multiscale approach. The onset of weak nonlinearity observed by the atomistic-continuum approach is at a midpoint deflection of ∼0.01 nm, approximately 0.14 w/h ratio, which secondarily confirm the feasibility of our newly proposed intrinsic material thickness value. The effect of boundary constraint, graphene size and loading mode on the bending of graphene is discussed to explain the cause of deviation between the two methods, and finally we confirm the feasibility of classical plate theory on bending monolayer graphene.
Dirac gauge theory for topological spinors in 3+1 dimensional networks
Authors: Bianconi Ginestra 
Published: June 2023

Abstract
Gauge theories on graphs and networks are attracting increasing attention not only as approaches to quantum gravity but also as models for performing quantum computation. Here we propose a Dirac gauge theory for topological spinors in

3
+
1

dimensional networks associated to an arbitrary metric. Topological spinors are the direct sum of 0-cochains and 1-cochains defined on a network and describe a matter field defined on both nodes and links of a network. Recently in Bianconi (2021 J. Phys. Complex.
2 035022) it has been shown that topological spinors obey the topological Dirac equation driven by the discrete Dirac operator. In this work we extend these results by formulating the Dirac equation on weighted and directed

3
+
1

dimensional networks which allow for the treatment of a local theory. The commutators and anti-commutators of the Dirac operators are non vanishing an they define the curvature tensor and magnetic field of our theory respectively. This interpretation is confirmed by the non-relativistic limit of the proposed Dirac equation. In the non-relativistic limit of the proposed Dirac equation the sector of the spinor defined on links follows the Schrödinger equation with the correct giromagnetic moment, while the sector of the spinor defined on nodes follows the Klein–Gordon equation and is not negligible. The action associated to the proposed field theory comprises of a Dirac action and a metric action. We describe the gauge invariance of the action under both Abelian and non-Abelian transformations and we propose the equation of motion of the field theory of both Dirac and metric fields. This theory can be interpreted as a limiting case of a more general gauge theory valid on any arbitrary network in the limit of almost flat spaces.
Microplastic contained in gill, stomach and intestine of milkfish (Chanos chanos) and chub mackerel (Scomber japonicus) at Rau Market, Serang City, Banten
Authors: Hasanah A N , Aryani D , Khalifa M A , Rahmawati A , Munandar E , Radityani F A 
Published: June 2023

Abstract
Microplastics are plastic particles <5mm from various sources. Fish contaminated by microplastics is a threat to food safety which microplastics contain toxicants. It is harmful to human health when consumed. Milkfish and Chub mackerel as consumption fish that can be easily found in some aquaculture ponds and marine water. The Previous study shows that microplastic content founded in the gill, stomach, and intestines. This study aims to determine microplastic content, microplastic abundance, and the correlation of organ weight with microplastic abundance in Milkfish and Chub mackerel. The methods used were descriptive qualitative. Milkfish and Chub mackerel samples were obtained from Rau Market, Serang City. The stages of the research carried with sampling, measuring, dissecting, dissolving, separating microplastic particles, filtering particles, and direct visual identification using a microscope. The results of the study found microplastics in the gills, intestines, and stomachs of milkfish and chub mackerel. In milkfish, most microplastic was found in the stomach (126 pieces), followed by the gill (111 pieces), and the intestine (65 pieces). While in chub mackerel, microplastics were mostly found in the gills (232 pieces, followed by the stomach (137 pieces), and the intestine (122 pieces). The types of microplastics found were fragments, films, and fibers. The number of microplastic types of fragments, films, and fibers with the colors of microplastics varied i.e. red, white, black, green, and yellow. There was no correlation between organ weight and microplastic abundance.
Substitution of Water Hyacinth Flour (Eichhornia crassipes) in Feed on The Growth Performance of Bileh Fish (Rasbora sp.)
Authors: Islama D , Diansyah S , Diana F , Mariana R , Muktaridha O 
Published: June 2023

AbstractThe objective of the present study was to determine the optimal dose substitution of water hyacinth flour (Eichhornia crassipes) in feed on the growth performance of Bileh (Rasborasp.) fingerlings. The Completely Randomized Design (CRD) used in this study consisted of four treatments and three replications. Four doses ofEichhornia crassipeswere tested: P0 = Feed without substitution of fermented water hyacinth flour as control, P1 = The substitution of fermented water hyacinth flour 5% in feed, P2 = The substitution of fermented water hyacinth flour 10 % in feed, P3 = The substitution of fermented water hyacinth flour 15% in feed. Bileh used as test fish have a length range of 2-2,5 cm. Feed was given three times withat satiationmethod. Bileh is stored for 30 days. The results showed that the absolute weight growth, absolute length growth, specific growth rate, and feed efficiency were higher in substituting 15% water hyacinth flour in Feed (P3). However, the substitution of water hyacinth flour in Feed had no significant effect on the survival rate and daily growth rate of bileh (P>0.05). The best dose of substitution of water hyacinth flour to increase the growth of Bileh fish and is more economical is 15% in Feed.
Large conventional and inverse electrocaloric effects in PbMg0.5W0.5O3 multilayer capacitors above and below the Néel temperature
Authors: Hirose Sakyo , Usui Tomoyasu , Hiroto Takanobu , Nair Bhasi , Moya Xavier , Mathur Neil D 
Published: June 2023

Abstract
Bulk PbMg0.5W0.5O3 (PMW) is an antiferroelectric in which an electric field of 12 V μm−1 is sufficient to initiate a nominally reversible transition to a dipole-aligned (ferroelectric) phase if operating just below the Néel temperature T
N, near room temperature (Li et al 2021 Adv. Funct. Mater.
31 2101176). Here we describe multilayer capacitors (MLCs) of PMW that permit 27 V µm−1 to be applied without breakdown. Below T
N, nominally reversible driving of the partial (full) antiferroelectric–ferroelectric (AF–FE) transition over a wide (narrow) range of temperatures yields large inverse electrocaloric (EC) effects that peak at ΔTj
∼ –2.6 K when applying 25 V μm−1 at 293 K (ΔTj
denotes directly measured temperature jumps). Above T
N, nominally reversible driving of the partial (full) paraelectric–ferroelectric (PE–FE) transition yields large conventional EC effects that peak at ΔTj
∼ +5.2 K when applying 25 V μm−1 at 302 K. This good EC performance near room temperature implies that MLCs of PMW could be exploited in prototype EC coolers.
Anomalous delocalization of resonant states in graphene & the vacancy magnetic moment
Authors: Leccese Mirko , Martinazzo Rocco 
Published: June 2023

Abstract
Carbon atom vacancies in graphene give rise to a local magnetic moment of

σ
+
π

origin, whose magnitude is yet uncertain and debated. Partial quenching of π magnetism has been ubiquitously reported in periodic first principles calculations, with magnetic moments scattered in the range 1.0–2.0 µ
B, slowly converging to the lower or the upper end, depending on how the diluted limit is approached. By contrast, (ensemble) density functional theory calculations on cluster models neatly converge to the value of

2

μ

B

when increasing the system size. This stunning discrepancy has sparked a debate about the role of defect–defect interactions and self-doping, and about the importance of the self-interaction-error in the density-functional-theory description of the vacancy-induced states. Here, we settle this puzzle by showing that the problem has a fundamental, mono-electronic origin which is related to the special (periodic) arrangement of defects that results when using the slab-supercell approach. Specifically, we report the existence of resonant states that are anomalously delocalized over the lattice and that make the π midgap band unphysically dispersive, hence prone to self-doping and quenching of the π magnetism. Hybrid functionals fix the problem by widening the gap between the spin-resolved π midgap bands, without reducing their artificial widths. As a consequence, while reconciling the magnetic moment with expectations, they predict a spin-splitting which is one order of magnitude larger than found in experiments.
Comparing invariants of toric ideals of bipartite graphs
Authors: Bhaskara Kieran , Van Tuyl Adam 
Published: June 2023

Let

G
G

be a finite simple graph and let

I
G

I_G

denote its associated toric ideal in the polynomial ring

R
R

. For each integer

n
≥
2

n\geq 2

, we completely determine all the possible values for the tuple

(
reg
⁡
(
R

/

I
G

)
,
deg
⁡
(

h

R

/

I
G

(
t
)
)
,
pdim
⁡
(
R

/

I
G

)
,
depth
⁡
(
R

/

I
G

)
,
dim
⁡
(
R

/

I
G

)
)

(\operatorname {reg}(R/I_G), \deg (h_{R/I_G}(t)), \operatorname {pdim}(R/I_G), \operatorname {depth}(R/I_G), \dim (R/I_G))

when

G
G

is a connected bipartite graph on

n
n

vertices.
Role of BraRGL1 in regulation of Brassica rapa bolting and flowering
Authors: Wang Yudan , Song Shiwei , Hao Yanwei , Chen Changming , Ou Xi , He Bin , Zhang Jiewen , Jiang Zhehao , Li Chengming , Zhang Shuaiwei , Su Wei , Chen Riyuan 
Published: June 2023

Abstract
Gibberellin (GA) plays a major role in controlling Brassica rapa stalk development. As an essential negative regulator of GA signal transduction, DELLA proteins may exert significant effects on stalk development. However, the regulatory mechanisms underlying this regulation remain unclear. In this study, we report highly efficient and inheritable mutagenesis using the CRISPR/Cas9 gene editing system in BraPDS (phytoene desaturase) and BraRGL1 (key DELLA protein) genes. We observed a loss-of-function mutation in BraRGL1 due to two amino acids in GRAS domain. The flower bud differentiation and bolting time of BraRGL1 mutants were significantly advanced. The expression of GA-regulatory protein (BraGASA6), flowering related genes (BraSOC1, BraLFY), expansion protein (BraEXPA11) and xyloglucan endotransferase (BraXTH3) genes was also significantly upregulated in these mutants. BraRGL1-overexpressing plants displayed the contrasting phenotypes. BraRGL1 mutants were more sensitive to GA signaling. BraRGL1 interacted with BraSOC1, and the interaction intensity decreased after GA3 treatment. In addition, BraRGL1 inhibited the transcription-activation ability of BraSOC1 for BraXTH3 and BraLFY genes, but the presence of GA3 enhanced the activation ability of BraSOC1, suggesting that the BraRGL1-BraSOC1 module regulates bolting and flowering of B. rapa through GA signal transduction. Thus, we hypothesized that BraRGL1 is degraded, and BraSOC1 is released in the presence of GA3, which promotes the expression of BraXTH3 and BraLFY, thereby inducing stalk development in B. rapa. Further, the BraRGL1-M mutant promoted the flower bud differentiation without affecting the stalk quality. Thus, BraRGL1 can serve as a valuable target for the molecular breeding of early maturing varieties.
Interlacing in Atomic Resolution Scanning Transmission Electron Microscopy
Authors: Peters Jonathan J P , Mullarkey Tiarnan , Gott James A , Nelson Elizabeth , Jones Lewys 
Published: June 2023

Abstract
Fast frame rates are desirable in scanning transmission electron microscopy for a number of reasons: controlling electron beam dose, capturing in situ events, or reducing the appearance of scan distortions. While several strategies exist for increasing frame rates, many impact image quality or require investment in advanced scan hardware. Here, we present an interlaced imaging approach to achieve minimal loss of image quality with faster frame rates that can be implemented on many existing scan controllers. We further demonstrate that our interlacing approach provides the best possible strain precision for a given electron dose compared with other contemporary approaches.
Characterization of candidate factors associated with the metastasis and progression of high-grade serous ovarian cancer
Authors: Liu Huiping , Zhou Ling , Cheng Hongyan , Wang Shang , Luan Wenqing , Cai E , Ye Xue , Zhu Honglan , Cui Heng , Li Yi , Chang Xiaohong 
Published: June 2023

Abstract

Background:
High-grade serous ovarian cancer (HGSOC) is the biggest cause of gynecological cancer-related mortality because of its extremely metastatic nature. This study aimed to explore and evaluate the characteristics of candidate factors associated with the metastasis and progression of HGSOC.

Methods:
Transcriptomic data of HGSOC patients' samples collected from primary tumors and matched omental metastatic tumors were obtained from three independent studies in the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were selected to evaluate the effects on the prognosis and progression of ovarian cancer using data from The Cancer Genome Atlas (TCGA) database. Hub genes' immune landscapes were estimated by the Tumor Immune Estimation Resource (TIMER) database. Finally, using 25 HGSOC patients' cancer tissues and 10 normal fallopian tube tissues, immunohistochemistry (IHC) was performed to quantify the expression levels of hub genes associated with International Federation of Gynecology and Obstetrics (FIGO) stages.

Results:
Fourteen DEGs, ADIPOQ, ALPK2, BARX1, CD37, CNR2, COL5A3, FABP4, FAP, GPR68, ITGBL1, MOXD1, PODNL1, SFRP2, and TRAF3IP3, were upregulated in metastatic tumors in every database while CADPS, GATA4, STAR, and TSPAN8 were downregulated. ALPK2, FAP, SFRP2, GATA4, STAR, and TSPAN8 were selected as hub genes significantly associated with survival and recurrence. All hub genes were correlated with tumor microenvironment infiltration, especially cancer-associated fibroblasts and natural killer (NK) cells. Furthermore, the expression of FAP and SFRP2 was positively correlated with the International Federation of Gynecology and Obstetrics (FIGO) stage, and their increased protein expression levels in metastatic samples compared with primary tumor samples and normal tissues were confirmed by IHC (P = 0.0002 and P = 0.0001, respectively).

Conclusions:
This study describes screening for DEGs in HGSOC primary tumors and matched metastasis tumors using integrated bioinformatics analyses. We identified six hub genes that were correlated with the progression of HGSOC, particularly FAP and SFRP2, which might provide effective targets to predict prognosis and provide novel insights into individual therapeutic strategies for HGSOC.