bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transnational agricultural land acquisitions threaten biodiversity in the Global South
Authors: Davis Kyle Frankel , Müller Marc F , Rulli Maria Cristina , Tatlhego Mokganedi , Ali Saleem , Baggio Jacopo A , Dell’Angelo Jampel , Jung Suhyun , Kehoe Laura , Niles Meredith T , Eckert Sandra 
Published: February 2023

Abstract
Agricultural large-scale land acquisitions have been linked with enhanced deforestation and land use change. Yet the extent to which transnational agricultural large-scale land acquisitions (TALSLAs) contribute to—or merely correlate with—deforestation, and the expected biodiversity impacts of the intended land use changes across ecosystems, remains unclear. We examine 178 georeferenced TALSLA locations in 40 countries to address this gap. While forest cover within TALSLAs decreased by 17% between 2000 and 2018 and became more fragmented, the spatio-temporal patterns of deforestation varied substantially across regions. While deforestation rates within initially forested TALSLAs were 1.5 (Asia) to 2 times (Africa) higher than immediately surrounding areas, we detected no such difference in Europe and Latin America. Our findings suggest that, whereas TALSLAs may have accelerated forest loss in Asia, a different mechanism might emerge in Africa where TALSLAs target areas already experiencing elevated deforestation. Regarding biodiversity (here focused on vertebrate species), we find that nearly all (91%) studied deals will likely experience substantial losses in relative species richness (−14.1% on average within each deal)—with mixed outcomes for relative abundance—due to the intended land use transitions. We also find that 39% of TALSLAs fall at least partially within biodiversity hotspots, placing these areas at heightened risk of biodiversity loss. Taken together, these findings suggest distinct regional differences in the nature of the association between TALSLAs and forest loss and provide new evidence of TALSLAs as an emerging threat to biodiversity in the Global South.
An exact formula for the variance of linear statistics in the one-dimensional jellium model
Authors: Flack Ana , Majumdar Satya N , Schehr Grégory 
Published: February 2023

Abstract
We consider the jellium model of N particles on a line confined in an external harmonic potential and with a pairwise one-dimensional Coulomb repulsion of strength α > 0. Using a Coulomb gas method, we study the statistics of

s
=
(
1

/

N
)

∑

i
=
1

N

f
(

x
i

)

where f(x), in principle, is an arbitrary smooth function. While the mean of s is easy to compute, the variance is nontrivial due to the long-range Coulomb interactions. In this paper we demonstrate that the fluctuations around this mean are Gaussian with a variance

Var

(
s
)
≈
b

/

N
3

for large N. In this paper, we provide an exact compact formula for the constant

b
=
1

/

(
4
α
)

∫

−
2
α

2
α

[

f

′

(
x
)

]
2

d
x

. In addition, we also calculate the full large deviation function characterizing the tails of the full distribution

for several different examples of f(x). Our analytical predictions are confirmed by numerical simulations.
Rail Structure Interaction Analysis for Providing CWR on Un-Ballasted Multi-Span Open Web Steel Girder Bridge
Authors: Prakash D Jeetendra , Sravana P , Rao P Srinivasa 
Published: February 2023

Abstract
Rail structure interaction (RSI) requires thorough study to understand the force transfer mechanism between the track and bridge components due to train vertical live loads, braking/traction loads and thermal loads accordingly. RSI analysis gives us an outline of the axial stress in rail, support reactions transferred to the bridge components and the relative displacement caused between the track and bridge. This paper investigates rail structure interaction analysis of unballasted multi-span steel through girder railway bridge carrying dedicated freight corridor (DFC) of 32.5t axle load. For this purpose, RSI analysis is performed as per the guidelines given in UIC774-3R [7] Code of Practice (International Union of Railways) for two different multi-span bridge with a span configuration of 7x63m and 6x48m respectively and the axial stress in rail, relative displacement between rail and bridge and support reactions transferred to the bridge components are calculated based on the span and stiffnesses of the bridges. From the analysis results, it shall be concluded whether to explore the possibility of providing a provision of continuous welded rail (CWR) on the bridge or to adopt switch expansion joints (SEJ) or other expansion devices accordingly.
Free Vibration Analysis of Symmetric and Asymmetric RCC Structures
Authors: Seeram Madhuri , Kumar Pramod 
Published: February 2023

Abstract
Symmetric and asymmetric structures behave differently under external loads even though they are of an equal number of stories or equal in dimensions. It is necessary to estimate the dynamic properties of the asymmetric structures carefully to avoid failure. Modal analysis for symmetric and asymmetric multi-storied reinforced concrete (RC) buildings is very essential to assess the dynamic characteristics of the structure. The plan asymmetric buildings with the shift of core from a central position to different positions and vertical asymmetry with the mass variation in vertical direction and setback stories are considered for the present study. Flexural beam elements are modelled to represent the columns. Two translations i.e., longitudinal, and transverse displacements of the building and rotation about the vertical axis of the structure are taken as global degrees of freedom at each node. The distance between the mass center and stiffness centre on each floor is taken as eccentricity. A finite element model is developed using MATLAB code to estimate the natural frequencies. Different RCC structures of 5 to 20-storied buildings are modelled by developing global stiffness and mass matrices based on the member connectivity. Eigen-value technique is used to estimate the natural frequencies. From the study it is observed that the natural period in asymmetric structures is found more than the symmetric building. The structure with setback also showed larger natural period.
Floquet topological phases on a honeycomb lattice using elliptically polarized light
Authors: Seshadri Ranjani 
Published: February 2023

Abstract
We study the effect of driving a two-dimensional honeycomb system out of equilibrium using an elliptically polarized light as a time-dependent perturbation. In particular, we try to understand the topological phase diagram of this driven system when the external drive is a vector potential given by

A
(
t
)
=
(

A

0
x

cos
(
Ω
t
)
,

A

0
y

cos
(
Ω
t
+

ϕ

0

)
)

. These topological phases are characterized by the Floquet Chern number which, in each of these phases, is related to the number of robust edge modes on a nanoribbon. We show that varying the ratio A
0x
/A
0y
of the external drive is a possible way to take the system from a trivial to a topological phase and vice versa.
Enhanced the sensitivity of one-dimensional photonic crystals infiltrated with cancer cells
Authors: Segovia-Chaves Francis , Carlos Trujillo Juan , Trabelsi Youssef 
Published: February 2023

Abstract
In this work, we use a one-dimensional photonic crystal as a biosensor composed of alternating GaAs and air layers. Within the cavity where they are infiltrated, the Normal, Jurkat, HeLa, PC-12, MDA-MB-231, and MCF-7 cells are bounded by layers of nanocomposite and graphene to increase biosensor sensitivity. The transmission spectrum was calculated using the transfer matrix method. We observed that, when the structural periodicity is broken, defect modes that characterize each cell are created. These defect modes move at a wavelength as the dielectric constant increases. Additionally, the separation between defect modes and bandwidth determines sensitivity, Q factor, and FOM, in which average values of 406.84 nm/RIU, 1765.53, and 535.44 were obtained, respectively, for normal light incidence. Regarding Transverse-Electric (TE) and Transverse-Magnetic (TM) polarization, the defect modes shift toward shorter wavelengths as the angle of incidence increases. For TE polarization, transmittance decreased and the distance between the modes increased. At a 50° angle, sensitivity, Q factor, and FOM increased up to 497.55 nm/RIU, 3182.02, and 1401.25, respectively. Conversely, at a 50° angle in TM polarization, sensitivity remained constant at a value of 407 nm/RIU, along with increased transmittance and decreased performance. Finally, sensitivity and performance were optimized by modifying the cavity thickness value at an incidence angle of 30° for TE polarization, and at an incidence angle of 10° for TM polarization. In both cases, the increased cavity thickness shifted the defect modes toward longer wavelengths while increasing sensitivity up to 495.75 nm/RIU for TE and 451.33 nm/RIU for TM.
Helical streamers guided by surface electromagnetic standing waves
Authors: ZOU Dandan , TU Chensheng , CUI Chunmei 
Published: February 2023

Abstract
The streamer that is driven by the specific pulse DC discharge parameters can stably form a three-dimensional helical plasma channel in a long dielectric tube in the low-temperature plasma experiment, in cases when there were neither external background magnetic field or other factors that destroyed the poloidal symmetry of the tube. The formation mechanism and chirality of helical streamers are discussed according to the surface electromagnetic standing wave theory. The shape of the helical streamers and the characteristics of helical branches are quantitatively analyzed to further expand the application of plasma and streamer theory in the helix problem and chiral catalytic synthesis.
The Dirac impenetrable barrier in the limit point of the Klein energy zone
Authors: De Vincenzo Salvatore 
Published: February 2023

Abstract
We reanalyze the problem of a 1D Dirac single particle colliding with the electrostatic potential step of height V
0 with a positive incoming energy that tends to the limit point of the so-called Klein energy zone, i.e. E → V
0 − mc
2, for a given V
0. In such a case, the particle is actually colliding with an impenetrable barrier. In fact, V
0 → E + mc
2, for a given relativistic energy E( < V
0), is the maximum value that the height of the step can reach and that ensures the perfect impenetrability of the barrier. Nevertheless, we note that, unlike the nonrelativistic case, the entire eigensolution does not completely vanish, either at the barrier or in the region under the step, but its upper component does satisfy the Dirichlet boundary condition at the barrier. More importantly, by calculating the mean value of the force exerted by the impenetrable wall on the particle in this eigenstate and taking its nonrelativistic limit, we recover the required result. We use two different approaches to obtain the latter two results. In one of these approaches, the corresponding force on the particle is a type of boundary quantum force. Throughout the article, various issues related to the Klein energy zone, the transmitted solutions to this problem, and impenetrable barriers related to boundary conditions are also discussed. In particular, if the negative-energy transmitted solution is used, the lower component of the scattering solution satisfies the Dirichlet boundary condition at the barrier, but the mean value of the external force when V
0 → E + mc
2 does not seem to be compatible with the existence of the impenetrable barrier.
Biskyrmion-based artificial neuron
Authors: Ribeiro de Assis Ismael , Mertig Ingrid , Göbel Börge 
Published: February 2023

Abstract
Magnetic skyrmions are nanoscale magnetic whirls that are highly stable and can be moved by currents. They have led to the prediction of a skyrmion-based artificial neuron device with leak-integrate-fire functionality. However, so far, these devices lack a refractory process, estimated to be crucial for neuronal dynamics. Here we demonstrate that a biskyrmion-based artificial neuron overcomes this insufficiency. When driven by spin-orbit torques, a single biskyrmion splits into two subskyrmions that move towards a designated location and can be detected electrically, ultimately resembling the excitation process of a neuron that fires. The attractive interaction of the two skyrmions leads to a unique trajectory: Once they reach the detector area, they automatically return to the center to reform the biskyrmion but on a different path. During this reset period, the neuron cannot fire again. Our suggested device resembles a biological neuron with the leak, integrate, fire and refractory characteristics increasing the bio-fidelity of current skyrmion-based devices.
Facilitators and barriers to implementing an acute geriatric community hospital in the Netherlands: a qualitative study
Authors: Ribbink Marthe E , de Vries-Mols Wieteke C B M , MacNeil Vroomen Janet L , Franssen Remco , Resodikromo Melissa N , Buurman Bianca M ,   the AGCH study group, Struan F A , van den Broek R H A , Frenkel W J , Henstra M J , Kaland K J , Koelé M , van Maanen M A , Melkert C J M , Parlevliet J L , van Poelgeest E P , Potgieter E , Oudejans I , Smorenberg A , van Rijn P M A , van der Velde N , van der Woude S , Willems H C , Wyatt D 
Published: February 2023

Abstract

Background
there is a trend across Europe to enable more care at the community level. The Acute Geriatric Community Hospital (AGCH) in the Netherlands in an acute geriatric unit situated in a skilled nursing facility (SNF). It provides hospital-level care for older adults with acute medical conditions. The aim of this study is to identify barriers and facilitators associated with implementing the AGCH in a SNF.

Methods
semi-structured interviews (n = 42) were carried out with clinical and administrative personnel at the AGCH and university hospital and stakeholders from the partnering care organisations and health insurance company. Data were analysed using thematic analysis.

Results
facilitators to implementing the AGCH concept were enthusiasm for the AGCH concept, organising preparatory sessions, starting with low-complex patients, good team leadership and ongoing education of the AGCH team. Other facilitators included strong collaboration between stakeholders, commitment to shared investment costs and involvement of regulators.
Barriers to implementation were providing hospital care in an SNF, financing AGCH care, difficulties selecting patients at the emergency department, lack of protocols and guidelines, electronic health records unsuited for hospital care, department layout on two different floors and complex shared business operations. Furthermore, transfer of acute care to the community care meant that some care was not reimbursed.

Conclusions
the AGCH concept was valued by all stakeholders. The main facilitators included the perceived value of the AGCH concept and enthusiasm of stakeholders. Structural financing is an obstacle to the expansion and continuation of this care model.
Genetically downregulated Interleukin-6 signalling is associated with a lower risk of frailty
Authors: Mourtzi Niki , Georgakis Marios K , Ntanasi Eva , Hatzimanolis Alexandros , Ramirez Alfredo , Heilmann-Heimbach Stephanie , Grenier-Boley Benjamin , Lambert Jean-Charles , Yannakoulia Mary , Kosmidis Mary , Dardiotis Efthimios , Hadjigeorgiou Giorgos , Sakka Paraskevi , Scarmeas Nikolaos 
Published: February 2023

AbstractBackgroundnumerous studies point towards a critical role of Interleukin 6 (IL-6) pathway in frailty pathogenesis yet the causal relationship between the two remains elusive.Methodswe selected genetic variants near the IL-6 receptor locus (IL-6R) associated with reduced C-reactive protein (CRP) levels, a downstream effector of IL-6 pathway, and we used them as genetic proxies of IL-6 signalling downregulation. We then performed a two-sample Mendelian randomisation (MR) to investigate the association with frailty status, as defined by the Frailty Index (FI) in 11,171 individuals from the Hellenic Longitudinal Investigation of Ageing and Diet (HELIAD) study. MR analysis was repeated after excluding depression or cognition-related FI items as well as following age or sex stratification. Association with frailty was also examined using an alternative instrument, weighted on s-IL-6R levels. Replication was attempted in UK Biobank dataset.Resultsgenetic predisposition to IL-6 signalling downregulation, weighted on CRP levels, was associated with lower risk of frailty, inserted either as categorical (odds ratio [95% confidence interval] = 0.15 [−3.39, −0.40], P = 0.013) or continuous variable (beta [se] = −0.09 [0.003], P = 0.0009). Sensitivity analyses revealed similar estimates across different MR methods with no evidence for horizontal pleiotropy or heterogeneity. Results remained robust after exclusion of depression or cognition-related FI items and following sex or age stratification. Genetically increased s-IL-6R levels were negatively correlated with frailty and this finding remained significant in a meta-analysis of UK Biobank and HELIAD cohorts.Conclusionour results support a potential causal effect of IL-6 signalling on frailty and further suggest that downregulation of IL-6 levels may reduce frailty risk.
Epistatic interactions among multiple copies of FLC genes with naturally occurring insertions correlate with flowering time variation in radish
Authors: Mitsui Yuki , Yokoyama Hinano , Nakaegawa Wataru , Tanaka Keisuke , Komatsu Kenji , Koizuka Nobuya , Okuzaki Ayako , Matsumoto Takashi , Takahara Manabu , Tabei Yutaka 
Published: February 2023

Abstract
Brassicaceae crops, which underwent whole-genome triplication during their evolution, have multiple copies of flowering-related genes. Interactions among multiple gene copies may be involved in flowering time regulation; however, this mechanism is poorly understood. In this study, we performed comprehensive, high-throughput RNA sequencing analysis to identify candidate genes involved in the extremely late-bolting (LB) trait in radish. Then, we examined the regulatory roles and interactions of radish FLOWERING LOCUS C (RsFLC) paralogs, the main flowering repressor candidates. Seven flowering integrator genes, five vernalization genes, nine photoperiodic/circadian clock genes and eight genes from other flowering pathways were differentially expressed in the early-bolting (EB) cultivar ‘Aokubinagafuto’ and LB radish cultivar ‘Tokinashi’ under different vernalization conditions. In the LB cultivar, RsFLC1 and RsFLC2 expression levels were maintained after 40 days of cold exposure. Bolting time was significantly correlated with the expression rates of RsFLC1 and RsFLC2. Using the EB × LB F2 population, we performed association analyses of genotypes with or without 1910- and 1627-bp insertions in the first introns of RsFLC1 and RsFLC2, respectively. The insertion alleles prevented the repression of their respective FLC genes under cold conditions. Interestingly, genotypes homozygous for RsFLC2 insertion alleles maintained high RsFLC1 and RsFLC3 expression levels under cold conditions, and two-way analysis of variance revealed that RsFLC1 and RsFLC3 expression was influenced by the RsFLC2 genotype. Our results indicate that insertions in the first introns of RsFLC1 and RsFLC2 contribute to the late-flowering trait in radish via different mechanisms. The RsFLC2 insertion allele conferred a strong delay in bolting by inhibiting the repression of all three RsFLC genes, suggesting that radish flowering time is determined by epistatic interactions among multiple FLC gene copies.
An immune-suppressing protein in human endogenous retroviruses
Authors: Zhang Huan , Ni Shengliang , Frith Martin C 
Published: February 2023

Abstract

Motivation
Retroviruses are important contributors to disease and evolution in vertebrates. Sometimes, retrovirus DNA is heritably inserted in a vertebrate genome: an endogenous retrovirus (ERV). Vertebrate genomes have many such virus-derived fragments, usually with mutations disabling their original functions.

Results
Some primate ERVs appear to encode an overlooked protein. This protein is homologous to protein MC132 from Molluscum contagiosum virus, which is a human poxvirus, not a retrovirus. MC132 suppresses the immune system by targeting NF-κB, and it had no known homologs until now. The ERV homologs of MC132 in the human genome are mostly disrupted by mutations, but there is an intact copy on chromosome 4. We found homologs of MC132 in ERVs of apes, monkeys and bushbaby, but not tarsiers, lemurs or non-primates. This suggests that some primate retroviruses had, or have, an extra immune-suppressing protein, which underwent horizontal genetic transfer between unrelated viruses.

Contact
mcfrith@edu.k.u-tokyo.ac.jp
scBGEDA: deep single-cell clustering analysis via a dual denoising autoencoder with bipartite graph ensemble clustering
Authors: Wang Yunhe , Yu Zhuohan , Li Shaochuan , Bian Chuang , Liang Yanchun , Wong Ka-Chun , Li Xiangtao 
Published: February 2023

Abstract

Motivation
Single-cell RNA sequencing (scRNA-seq) is an increasingly popular technique for transcriptomic analysis of gene expression at the single-cell level. Cell-type clustering is the first crucial task in the analysis of scRNA-seq data that facilitates accurate identification of cell types and the study of the characteristics of their transcripts. Recently, several computational models based on a deep autoencoder and the ensemble clustering have been developed to analyze scRNA-seq data. However, current deep autoencoders are not sufficient to learn the latent representations of scRNA-seq data, and obtaining consensus partitions from these feature representations remains under-explored.

Results
To address this challenge, we propose a single-cell deep clustering model via a dual denoising autoencoder with bipartite graph ensemble clustering called scBGEDA, to identify specific cell populations in single-cell transcriptome profiles. First, a single-cell dual denoising autoencoder network is proposed to project the data into a compressed low-dimensional space and that can learn feature representation via explicit modeling of synergistic optimization of the zero-inflated negative binomial reconstruction loss and denoising reconstruction loss. Then, a bipartite graph ensemble clustering algorithm is designed to exploit the relationships between cells and the learned latent embedded space by means of a graph-based consensus function. Multiple comparison experiments were conducted on 20 scRNA-seq datasets from different sequencing platforms using a variety of clustering metrics. The experimental results indicated that scBGEDA outperforms other state-of-the-art methods on these datasets, and also demonstrated its scalability to large-scale scRNA-seq datasets. Moreover, scBGEDA was able to identify cell-type specific marker genes and provide functional genomic analysis by quantifying the influence of genes on cell clusters, bringing new insights into identifying cell types and characterizing the scRNA-seq data from different perspectives.

Availability and implementation
The source code of scBGEDA is available at https://github.com/wangyh082/scBGEDA. The software and the supporting data can be downloaded from https://figshare.com/articles/software/scBGEDA/19657911.

Supplementary information
Supplementary data are available at Bioinformatics online.