bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single cohesin molecules generate force by two distinct mechanisms
Authors: Pobegalov Georgii , Chu Lee-Ya , Peters Jan-Michael , Molodtsov Maxim I. 
Published: July 2023

AbstractSpatial organization of DNA is facilitated by cohesin protein complexes that move on DNA and extrude DNA loops. How cohesin works mechanistically as a molecular machine is poorly understood. Here, we measure mechanical forces generated by conformational changes in single cohesin molecules. We show that bending of SMC coiled coils is driven by random thermal fluctuations leading to a ~32 nm head-hinge displacement that resists forces up to 1 pN; ATPase head engagement occurs in a single step of ~10 nm and is driven by an ATP dependent head-head movement, resisting forces up to 15 pN. Our molecular dynamic simulations show that the energy of head engagement can be stored in a mechanically strained conformation of NIPBL and released during disengagement. These findings reveal how single cohesin molecules generate force by two distinct mechanisms. We present a model, which proposes how this ability may power different aspects of cohesin-DNA interaction.
Whole genome sequencing identifies genetic variants associated with neurogenic inflammation in rosacea
Authors: Deng Zhili , Chen Mengting , Zhao Zhixiang , Xiao Wenqin , Liu Tangxiele , Peng Qinqin , Wu Zheng , Xu San , Shi Wei , Jian Dan , Wang Ben , Liu Fangfen , Tang Yan , Huang Yingxue , Zhang Yiya , Wang Qian , Sun Lunquan , Xie Hongfu , Zhang Guohong , Li Ji 
Published: July 2023

AbstractRosacea is a chronic inflammatory skin disorder with high incidence rate. Although genetic predisposition to rosacea is suggested by existing evidence, the genetic basis remains largely unknown. Here we present the integrated results of whole genome sequencing (WGS) in 3 large rosacea families and whole exome sequencing (WES) in 49 additional validation families. We identify single rare deleterious variants of LRRC4, SH3PXD2A and SLC26A8 in large families, respectively. The relevance of SH3PXD2A, SLC26A8 and LRR family genes in rosacea predisposition is underscored by presence of additional variants in independent families. Gene ontology analysis suggests that these genes encode proteins taking part in neural synaptic processes and cell adhesion. In vitro functional analysis shows that mutations in LRRC4, SH3PXD2A and SLC26A8 induce the production of vasoactive neuropeptides in human neural cells. In a mouse model recapitulating a recurrent Lrrc4 mutation from human patients, we find rosacea-like skin inflammation, underpinned by excessive vasoactive intestinal peptide (VIP) release by peripheral neurons. These findings strongly support familial inheritance and neurogenic inflammation in rosacea development and provide mechanistic insight into the etiopathogenesis of the condition.
Seismic performance evaluation of plastered cellular lightweight concrete (CLC) block masonry walls
Authors: Khan Khalid , Shahzada Khan , Gul Akhtar , Khan Inayat Ullah , Eldin Sayed M. , Iqbal Mudassir 
Published: July 2023

AbstractThe current research presents a novel and sustainable load-bearing system utilizing cellular lightweight concrete block masonry walls. These blocks, known for their eco-friendly properties and increasing popularity in the construction industry, have been studied extensively for their physical and mechanical characteristics. However, this study aims to expand upon previous research by examining the seismic performance of these walls in a seismically active region, where cellular lightweight concrete block usage is emerging. The study includes the construction and testing of multiple masonry prisms, wallets, and full-scale walls using a quasi-static reverse cyclic loading protocol. The behavior of the walls is analyzed and compared in terms of various parameters such as force–deformation curve, energy dissipation, stiffness degradation, deformation ductility factor, response modification factor, and seismic performance levels, as well as rocking, in-plane sliding, and out-of-plane movement. The results indicate that the use of confining elements significantly improves the lateral load capacity, elastic stiffness, and displacement ductility factor of the confined masonry wall in comparison to an unreinforced masonry wall by 102%, 66.67%, and 5.3%, respectively. Overall, the study concludes that the inclusion of confining elements enhances the seismic performance of the confined masonry wall under lateral loading.
Size of living space as a moderator for central and peripheral refractions in children
Authors: Choi Kai Yip , Leung Tsz Wing , Chan Henry Ho-Lung 
Published: July 2023

AbstractUndesirable living environment may impose risk on myopia development. Furthermore, peripheral refractive error was suggested to contribute to juvenile eye growth modulation. This study aimed to investigate the interaction between peripheral refractive error and living environment in relation to central refractive status in Hong Kong schoolchildren. Central and peripheral refractive errors, axial length (AL), and corneal radius of curvature (CR) were measured in 573 schoolchildren (age 9.5 ± 0.9 years). The AL/CR ratio was used to represent the central refractive status, accounting for non-cycloplegic refraction. The relative peripheral refractive errors (RPRE) up to ± 20° eccentricities were converted into power vectors: spherical-equivalent error (SER) and J0 astigmatic components and fitted with quadratic equations. The second-order coefficients of SER (aSER) and J0 astigmatism (aJ0) and home size reported by parental questionnaires were analyzed to indicate their relationships with AL/CR. Our results showed that children with higher AL/CR lived in smaller homes (p = 0.01) and had a more hyperopic (p < 0.001) but less astigmatic RPRE (p = 0.01). We further analyzed the relationship between AL/CR with RPRE for children living in small (< 300 ft2), moderate (300–600 ft2), and large home sizes (> 600 ft2). Regardless of the home size, a higher AL/CR remained moderately correlated with a more hyperopic aSER (all p < 0.001). However, a higher AL/CR was associated with a more positive aJ0 only in children living in large homes, and the relationships were not significant for small and moderate home sizes. Linear regression models further indicated that home size was a significant moderator contributing to the relationship between AL/CR and aJ0. In conclusion, our results were consistent with previous studies, showing that children with axial myopia usually lived in smaller homes and had more hyperopic defocus and more positive J0 astigmatism. However, the relationship between peripheral astigmatism and axial refraction was modulated by the home size of Hong Kong schoolchildren. While peripheral astigmatism is hypothesized as a visual cue for axial refractive development in children, extrinsic environmental factors, such as home size, might interfere with the relationship and dominate refractive development.
Sex-dependent effects of mechanical delousing on the skin microbiome of broodstock Atlantic salmon (Salmo salar L.)
Authors: Casadei Elisa , Mani Amir , Cisco Mariela , Vågnes Øyvind , Salinas Irene , Patel Sonal 
Published: July 2023

AbstractDelousing strategies, including mechanical delousing, are typically used to treat Atlantic salmon (Salmo salar) sea lice infestations. In this study, we evaluate the impact of mechanical delousing (Hydrolicer) on the skin bacterial microbiome of broodstock female and male Atlantic salmon. 16S rDNA sequencing of salmon skin microbial communities was performed immediately before delousing, right after delousing and 2 and 13 days post-delousing (dpd). The skin bacterial community of female salmon was more diverse than that of males at the start of the experiment. Overall, hydrolycer caused losses in alpha diversity in females and increases in alpha diversity in males. Hydrolicer also caused rapid shifts in the skin microbial community composition immediately after delicing in a sex-specific manner. There was a decrease in abundance of Proteobacteria and Bacteriodetes in both female and male salmon, whereas Firmicutes and Tenericutes abundances increased. Interestingly, the female community recovered faster, while the male community remained dysbiotic 13 dpd due to expansions in Bacteroidetes (Pseudomonadaceae) and Firmicutes. Our data suggest that female broodstock are more resilient to Hydrolicer treatment due to their more diverse skin microbiota community, and that sex influences the skin microbial community and therefore host health outcomes during common farming manipulations.
Two local minima for structures of [4Fe–4S] clusters obtained with density functional theory methods
Authors: Jafari Sonia , Ryde Ulf , Irani Mehdi 
Published: July 2023

Abstract[4Fe–4S] clusters are essential cofactors in many proteins involved in biological redox-active processes. Density functional theory (DFT) methods are widely used to study these clusters. Previous investigations have indicated that there exist two local minima for these clusters in proteins. We perform a detailed study of these minima in five proteins and two oxidation states, using combined quantum mechanical and molecular mechanical (QM/MM) methods. We show that one local minimum (L state) has longer Fe–Fe distances than the other (S state), and that the L state is more stable for all cases studied. We also show that some DFT methods may only obtain the L state, while others may obtain both states. Our work provides new insights into the structural diversity and stability of [4Fe–4S] clusters in proteins, and highlights the importance of reliable DFT methods and geometry optimization. We recommend r2SCAN for optimizing [4Fe-4S] clusters in proteins, which gives the most accurate structures for the five proteins studied.
LGR4 and LGR5 form distinct homodimers that only LGR4 complexes with RNF43/ZNRF3 to provide high affinity binding of R-spondin ligands
Authors: Toh Yukimatsu , Wu Ling , Park Soohyun , Wang Allison , Tu Jianghua , Yu Wangsheng , Zuo Mingxin , Carmon Kendra S. , Liu Qingyun J. 
Published: July 2023

AbstractLGR4 and LGR5 are two homologous receptors that potentiate Wnt/β-catenin signaling in response to R-spondin (RSPO) ligands. The RSPO and LGR4 complex binds to and inhibits activities of two related E3 ubiquitin ligases, RNF43 and ZNRF3, and thus protects Wnt receptors from the E3 ligase-mediated degradation. The RSPO and LGR5 complex, however, does not interact with the E3 ligases, and the structural basis of this difference remained unknown. Here we examined the affinities of monovalent and bivalent RSPO ligands in binding to LGR4, RNF43/ZNRF3, and LGR5 in whole cells and found unique features among the receptors and E3 ligases. Monovalent RSPO2 furin domain had much lower affinity in binding to LGR4 or RNF43/ZNRF3 than the bivalent form. In contrast, monovalent and bivalent forms had nearly identical affinity in binding to LGR5. Co-expression of ZNRF3 with LGR4 led to much higher binding affinity of the monovalent form whereas co-expression of ZNRF3 with LGR5 had no effect on the affinity. These results suggest that LGR4 and RNF43/ZNRF3 form a 2:2 dimer that accommodates bivalent binding of RSPO whereas LGR5 forms a homodimer that does not. Structural models are proposed to illustrate how RSPOs bind to LGR4, RNF43/ZNRF3, and LGR5 in whole cells.
Airfoil-shaped filament feed spacer for improved filtration performance in water treatment
Authors: Qamar Adnan , Kerdi Sarah , Vrouwenvelder Johannes S. , Ghaffour Noreddine 
Published: July 2023

AbstractOptimal spacer design enhances the filtration performance in spiral-wound modules by controlling the local hydrodynamics inside the filtration channel. A novel airfoil feed spacer design fabricated using 3D-printing technology is proposed in this study. The design is a ladder-shaped configuration with primary airfoil-shaped filaments facing the incoming feed flow. The airfoil filaments are reinforced by cylindrical pillars supporting the membrane surface. Laterally, all the airfoil filaments are connected by thin cylindrical filaments. The performances of the novel airfoil spacers are evaluated at Angle of Attack (AOA) of 10° (A-10 spacer) and 30° (A-30 spacer) and compared with commercial (COM) spacer. At fixed operating conditions, simulations indicate steady-state hydrodynamics inside the channel for A-10 spacer, while an unsteady state is found for A-30 spacer. Numerical wall shear stress for airfoil spacers is uniformly distributed and has a higher magnitude than the COM spacer. A-30 spacer design is the most efficient in ultrafiltration process with enhanced permeate flux (228%) and reduced specific energy consumption (23%) and biofouling development (74%) as characterized by Optical Coherence Tomography. Results systematically demonstrate the influential role of airfoil-shaped filaments for feed spacer design. Modifying AOA allows localized hydrodynamics to be effectively controlled according to the filtration type and operating conditions.
Immunoassay-based quantification of full-length peptidylglycine alpha-amidating monooxygenase in human plasma
Authors: Ilina Yulia , Kaufmann Paul , Melander Olle , Press Michaela , Thuene Katrin , Bergmann Andreas 
Published: July 2023

AbstractA one-step sandwich chemiluminescence immunometric assay (LIA) was developed for the quantification of bifunctional peptidylglycine-α-amidating monooxygenase (PAM) in human plasma (PAM-LIA). PAM is responsible for the activation of more than half of known peptide hormones through C-terminal α-amidation. The assay employed antibodies targeting specific catalytic PAM-subunits, peptidylglycine alpha-hydroxylating monooxygenase (PHM) and peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL), to ensure detection of full-length PAM. The PAM-LIA assay was calibrated with a human recombinant PAM enzyme and achieved a detection limit of 189 pg/mL and a quantification limit of 250 pg/mL. The assay demonstrated good inter-assay (6.7%) and intra-assay (2.2%) variabilities. It exhibited linearity when accessed by gradual dilution or random mixing of plasma samples. The accuracy of the PAM-LIA was determined to be 94.7% through spiking recovery experiments, and the signal recovery after substance interference was 94–96%. The analyte showed 96% stability after six freeze–thaw cycles. The assay showed strong correlation with matched EDTA and serum samples, as well as matched EDTA and Li-Heparin samples. Additionally, a high correlation was observed between α-amidating activity and PAM-LIA. Finally, the PAM-LIA assay was successfully applied to a sub-cohort of a Swedish population-based study, comprising 4850 individuals, confirming its suitability for routine high throughput screening.
Sensitivity of endogenous autofluorescence in HeLa cells to the application of external magnetic fields
Authors: Uzhytchak Mariia , Smolková Barbora , Frtús Adam , Stupakov Alexandr , Lunova Mariia , Scollo Federica , Hof Martin , Jurkiewicz Piotr , Sullivan Gareth John , Dejneka Alexandr , Lunov Oleg 
Published: July 2023

AbstractDramatically increased levels of electromagnetic radiation in the environment have raised concerns over the potential health hazards of electromagnetic fields. Various biological effects of magnetic fields have been proposed. Despite decades of intensive research, the molecular mechanisms procuring cellular responses remain largely unknown. The current literature is conflicting with regards to evidence that magnetic fields affect functionality directly at the cellular level. Therefore, a search for potential direct cellular effects of magnetic fields represents a cornerstone that may propose an explanation for potential health hazards associated with magnetic fields. It has been proposed that autofluorescence of HeLa cells is magnetic field sensitive, relying on single-cell imaging kinetic measurements. Here, we investigate the magnetic field sensitivity of an endogenous autofluorescence in HeLa cells. Under the experimental conditions used, magnetic field sensitivity of an endogenous autofluorescence was not observed in HeLa cells. We present a number of arguments indicating why this is the case in the analysis of magnetic field effects based on the imaging of cellular autofluorescence decay. Our work indicates that new methods are required to elucidate the effects of magnetic fields at the cellular level.
Distributed finite‐time control with event triggered mechanism for multi‐agent systems under fixed and switching topologies
Authors: Lv Hui , Li Shibo , Chen Yadong , Hu Guolin , Zheng Wenjing 
Published: July 2023

AbstractThis paper addresses the problem of distributed finite‐time (FT) event‐triggered consensus of multi‐agent systems (MASs) under fixed and switching topologies. To conserve the limited communication resources, a new distributed event‐triggered control protocol is proposed, in which the agents exchange information via discontinuous communication among the follower agents. Then, to solve the FT consensus problem, norm‐normalized sign functions are employed, and sufficient Lyapunov conditions are provided. On this basis, the MASs proves capable of reaching consensus within finite time under fixed and switching topologies. Finally, the effectiveness of the developed algorithm is verified via numerical simulation.
A hierarchical multi‐area capacity planning model considering configuration ratios of renewable energy and energy storage systems with multi‐area coordination
Authors: Li Qingtao , Wang Jianxue , Chen Jie , Ding Tao , Gu Chenjia 
Published: July 2023

AbstractThe continuous growth of renewable energy sources (RESs) has increased the demand for flexibility in managing uncertainties of RES generation. Energy storage systems (ESSs) are recognized as one of the promising methods to address this challenge. For multi‐area power system planning problems, capacity allocations of RESs can vary considerably among areas accounting for the geographic diversities in RES generation and load patterns. This paper presents a hierarchical coordinated planning model considering the interaction of local‐area (LA) planning entities and the system‐wide (SW) planner. A novel multi‐objective LA planning model is proposed to compute optimal capacity configuration ratios of RESs and ESSs based on regional resource characteristics. The SW planner acts as a coordinator and further optimizes specific capacities of generation assets. Optimal configuration ratios produced by LA planning entities are important indices reflecting LA planning preferences and serve as a link between the two planning layers. Numerical results on a modified NREL‐118 test system show that the proposed planning model can reduce carbon emission by an average of 10.5% and improve the RES utilization rate by an average of 1.8% compared with planning models without considering configuration ratios and ESS installations.
The role of plasma β in global coronal models: Bringing balance back to the force
Authors: Brchnelova M. , Kuźma B. , Zhang F. , Lani A. , Poedts S. 
Published: July 2023

Context. COolfluid COrona uNstrUcTured (COCONUT) is a global coronal magnetohydrodynamic (MHD) model that was recently developed and will soon be integrated into the ESA Virtual Space Weather Modelling Centre (VSWMC). In order to achieve robustness and fast convergence to a steady state for numerical simulations with COCONUT, several assumptions and simplifications were made during its development, such as prescribing filtered photospheric magnetic maps to represent the magnetic field conditions in the lower corona. This filtering leads to smoothing and lower magnetic field values at the inner boundary (i.e. the solar surface), resulting in an unrealistically high plasma β (greater than 1 in a large portion of the domain).
Aims. We aim to examine the effects of prescribing such filtered magnetograms in global coronal simulations and formulate a method for achieving more realistic plasma β values and improving the resolution of electromagnetic features without losing computational performance.
Methods. We made use of the newly developed COCONUT solver to demonstrate the effects of the highly pre-processed magnetic maps set at the inner boundary and the resulting high plasma β on the features in the computational domain. Then, in our new approach, we shifted the inner boundary to 2 R⊙ from the original 1.01 R⊙ and preserved the prescribed highly filtered magnetic map. With the shifted boundary, the boundary density and pressure were also naturally adjusted to better represent the considered physical location. This effectively reduces the prescribed plasma β and leads to a more realistic setup. The method was applied on a magnetic dipole, a minimum (2008) and a maximum (2012) solar activity case, to demonstrate its effects.
Results. The results obtained with the proposed approach show significant improvements in the resolved density and radial velocity profiles, and far more realistic values of the plasma β at the boundary and inside the computational domain. This is also demonstrated via synthetic white light imaging (WLI) and with the validation against tomography data. The computational performance comparison shows similar convergence to a limit residual on the same grid when compared to the original setup. Considering that the grid can be further coarsened with this new setup, as its capacity to resolve features or structures is superior, the operational performance can be additionally increased if needed.
Conclusions. The newly developed method is thus deemed as a good potential replacement of the original setup for operational purposes, providing higher physical detail of the resolved profiles while preserving a good convergence and robustness of the solver.
Extremely low-frequency electromagnetic field exposure alters DNA methylation levels in the endometrium of pigs during the peri-implantation period
Authors: Wydorski Pawel Jozef , Kozlowska Wiktoria , Drzewiecka Ewa Monika , Zmijewska Agata , Franczak Anita 
Published: July 2023

Context Extremely low-frequency electromagnetic field (ELF-EMF) emission is increasing due to substantial technological progress. The results of previous research provided evidence that ELF-EMF may exert changes in molecular mechanisms that control female reproduction. Aims We hypothesised that short-term ELF-EMF treatment alters the DNA methylation level of genes in the endometrium. Hence, the research aimed to determine the methylation level of selected genes whose expression was altered in response to ELF-EMF radiation in the endometrium of pigs during the peri-implantation period (days 15–16 of pregnancy). Methods Porcine endometrial slices (100 ± 5 mg) were collected during the peri-implantation period and exposed to ELF-EMF at a frequency of 50 Hz for 2 h in vitro. The control endometrium was not exposed to ELF-EMF. The level of DNA methylation in the promoter regions of EGR2, HSD17B2, ID2, IL1RAP, MRAP2, NOS3, PTGER4, SERPINE1, VDR and ZFP57 was tested using qMS-PCR. Key results In the endometrium exposed to ELF-EMF, the level of methylation of HSD17B2, MRAP2, SERPINE1, VDR and ZFP57 was not altered; the level of methylation of EGR2, ID2 and PTGER4 increased, and the level of methylation of IL1RAP and NOS3 decreased. Conclusions ELF-EMF may alter the level of DNA methylation in the endometrium during the peri-implantation period. Implications Changes in the DNA methylation induced by ELF-EMF may affect the transcriptomic profile of the endometrium and disturb physiological processes accompanying implantation and embryo development.