bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bringing physics into the coarse‐grid selection: Approximate diffusion distance/effective resistance measures for network analysis and algebraic multigrid for graph Laplacians and systems of elliptic partial differential equations
Authors: Lee Barry 
Published: November 2023

AbstractIn a recent paper, the author examined a correlation affinity measure for selecting the coarse degrees of freedom (CDOFs) or coarse nodes (C nodes) in systems of elliptic partial differential equations (PDEs). This measure was applied to a set of relaxed vectors, which exposed the near‐nullspace components of the PDE operator. Selecting the CDOFs using this affinity measure and constructing the interpolation operators using a least‐squares procedure, an algebraic multigrid (AMG) method was developed. However, there are several noted issues with this AMG solver. First, to capture strong anisotropies, a large number of test vectors may be needed; and second, the solver's performance can be sensitive to the initial set of random test vectors. Both issues reflect the sensitive statistical nature of the measure. In this article, we derive several other statistical measures that ameliorate these issues and lead to better AMG performance. These measures are related to a Markov process, which the PDE itself may model. Specifically, the measures are based on the diffusion distance/effective resistance for such process, and hence, these measures incorporate physics into the CDOF selection. Moreover, because the diffusion distance/effective resistance can be used to analyze graph networks, these measures also provide a very economical scheme for analyzing large‐scale networks. In this article, the derivations of these measures are given, and numerical experiments for analyzing networks and for AMG performance on weighted‐graph Laplacians and systems of elliptic boundary‐value problems are presented.
Experimental validation study on snap through and coiling up of deployable composite shells
Authors: Chang Zhongliang , Zhao Peng , Wu Chenchen , Zou Guangping , Zhang Zhijun 
Published: November 2023

AbstractBistable reeled composite shells (BRCS) have been widely used in deployable space structures due to advanced properties of light weight and large volume reduction. A finite element simulation and experimental validation to study the transition of BRCS between their two stable states are performed. In this article, multiscale representative volume element (RVE) modeling is used to compute the equivalent mechanical properties of carbon/epoxy plain woven fabrics that were utilized to construct the deployable composite laminates, followed by experimental verification. The deformation characteristics and strain energy distribution of the deployable composite shell (DCS) during snap through and coiling up are investigated using finite element analysis (FEA) and verified by strain‐gauge and digital image correlation (DIC) tests. The results show that the strain energy distribution in the snap through and coiling up of the carbon/epoxy plain woven BRCS with laminate stacking sequence of [+45/−45] is approximately symmetric. Additionally, an offset phenomena is observed during the coiling up of the BRCS in the finite element modeling. A parametric analysis is complemented to investigate effects of fiber angles on the deformation characteristics and strain energy distribution of the shell structures during snap through and coiling up.Highlights
Shell deformation during snap through and coiling up was investigated.
DIC test was performed to capture the shell deformation.
Strain energy distribution of the deployable composite shell was discussed.
Offset phenomena are observed during the coiling up.
Investigation on using graphite filler for 3D printing of flexible electrically conductive polymer by extrusion‐based additive manufacturing
Authors: Bajpai Arpit , Jain Prashant Kumar 
Published: November 2023

AbstractThe rapid use of additive manufacturing (AM) in electronic industry identifies the need of flexible electrically conductive materials suitable for 3D printing. Challenges like buckling of flexible filament and complexity in addition of conductive fillers makes pellet‐based extrusion the most suitable alternative for part printing. In the present work, graphite powder is combined with ethylene vinyl acetate (EVA) to print flexible electrically conductive parts. EVA graphite composite with filler loading up to 30% has been investigated for its electrical conductivity and part printability. The composite made was found electrically conductive and suitable for part printing. The parts were printed on a CNC milling machine by using a retrofitted material extrusion tool with nozzle of 0.4 mm diameter and temperature range of 130–140°C. Parts were printed on a detchable heating bed placed on the milling machine setup. Samples of EVA with graphite filler by weight of 5%, 10%, 20%, and 30% were printed and were checked for electrical conductivity. When the filler content was increased from 10% to 20%, the electrical resistance of the composite was reduced by 62.6%. The presence and uniform dispersion of graphite flakes in the polymer matrix of EVA were guaranteed by the rheological and morphological characterization of the composite. Applications of 3D printable flexible electrically conductive parts lies in numerous domains including biosensors, wearable health monitoring devices, capacitors, field effective transistors, light emitting diodes, solar cells, and electronic displays.Highlights
CNC milling machine‐assisted 3D printing is used for part printing.
Graphite powder is combined with EVA pellets.
Pellet‐based extrusion is used to print flexible parts.
3D printability of parts with resistivity 32.64 Ω‐cm was achieved.
Efficacy of plyometric exercises on upper extremity function, selective motor control and hand grip strength in children with unilateral cerebral palsy: A randomized controlled study
Authors: Abd‐elmonem Amira M. , Ali Hazem A. , Saad‐eldien Sara S. , El‐nabie Walaa A. Abd 
Published: November 2023

AbstractBackgroundImpairment in unimanual upper limb function is frequent among children with unilateral cerebral palsy (UCP), which affects their ability to perform functional activities.AimTo assess the efficacy of plyometric exercises on the function of upper extremity, selective motor control (SMC) and hand grip strength (HGS) in children with UCP.DesignThis was a double‐masked, randomized, controlled clinical trial.SettingOutpatient Clinics of Faculty of Physical Therapy, Cairo University and Center for Physical Medicine, Rehabilitation and Rheumatology, Al‐Agouza Hospital, Giza, Egypt.PopulationForty children with UCP, ranging in age from 8 to 12 years, were randomly allocated to two groups equal in numbers.MethodChildren were allocated to receive conventional therapy (CONV‐group; n = 20) or plyometric exercises (PLYO‐group; n = 20) for 45 min. In addition, children of both groups received selected physical and occupational therapy programs (each lasted for 30 min) twice a week over 3‐month. The intervention was delivered on non‐consecutive days. Upper extremity function, SMC and HGS were assessed by using quality of upper extremity skills test (QUEST), Test of arm selective control and pneumatic squeeze bulb dynamometer, respectively.ResultsOverall, 35 children (18 in the CONV‐group, 17 in the PLYO‐group) completed data collection and treatment. With‐in group comparison showed significant improvement in the study groups while post‐treatment comparisons revealed a significant difference from mean difference in upper extremity function is 9.55 (8.71:10.39), SMC is 2.12 (1.51:2.72) and HGS is 2.91 (2.13:3.68) (p < 0.05; 95% Confidence interval) in favor of the PLYO‐group.ConclusionsPlyometric exercises have the capability to enhance upper extremity function and strength in children with UCP.
Critical assessment of methods of protein structure prediction (CASP)—Round XV
Authors: Kryshtafovych Andriy , Schwede Torsten , Topf Maya , Fidelis Krzysztof , Moult John 
Published: November 2023

AbstractComputing protein structure from amino acid sequence information has been a long‐standing grand challenge. Critical assessment of structure prediction (CASP) conducts community experiments aimed at advancing solutions to this and related problems. Experiments are conducted every 2 years. The 2020 experiment (CASP14) saw major progress, with the second generation of deep learning methods delivering accuracy comparable with experiment for many single proteins. There is an expectation that these methods will have much wider application in computational structural biology. Here we summarize results from the most recent experiment, CASP15, in 2022, with an emphasis on new deep learning‐driven progress. Other papers in this special issue of proteins provide more detailed analysis. For single protein structures, the AlphaFold2 deep learning method is still superior to other approaches, but there are two points of note. First, although AlphaFold2 was the core of all the most successful methods, there was a wide variety of implementation and combination with other methods. Second, using the standard AlphaFold2 protocol and default parameters only produces the highest quality result for about two thirds of the targets, and more extensive sampling is required for the others. The major advance in this CASP is the enormous increase in the accuracy of computed protein complexes, achieved by the use of deep learning methods, although overall these do not fully match the performance for single proteins. Here too, AlphaFold2 based method perform best, and again more extensive sampling than the defaults is often required. Also of note are the encouraging early results on the use of deep learning to compute ensembles of macromolecular structures. Critically for the usability of computed structures, for both single proteins and protein complexes, deep learning derived estimates of both local and global accuracy are of high quality, however the estimates in interface regions are slightly less reliable. CASP15 also included computation of RNA structures for the first time. Here, the classical approaches produced better agreement with experiment than the new deep learning ones, and accuracy is limited. Also, for the first time, CASP included the computation of protein–ligand complexes, an area of special interest for drug design. Here too, classical methods were still superior to deep learning ones. Many new approaches were discussed at the CASP conference, and it is clear methods will continue to advance.
Molecular insights into the salt stress response of Pearl millet (Pennisetum glaucum): Pathways, differentially expressed genes and transcription factors
Authors: Dhawi Faten 
Published: November 2023

AbstractIntroductionPearl millet (Pennisetum glaucum) plays a crucial role as a cereal crop in arid and semi‐arid regions, where it confronts the formidable challenge of salt stress.Materials and MethodsTo unravel the underlying molecular mechanisms that underpin its salt stress resilience, we subjected 14‐day‐old seedlings to three distinct groups: Control, 75 mM NaCl and 150 mM NaCl. These pots received daily irrigation with their respective treatment solutions for a duration of 7 days. Following this week‐long treatment, we measured plant chlorophyll content, as well as the fresh and dry weights of shoots and roots. It became evident that the saline treatment, particularly in the 150 mM NaCl group, had a more pronounced impact on both weight and chlorophyll content in comparison to the control group, surpassing the effects observed in the 75 mM NaCl group. Subsequently, we conducted RNA sequence analysis on the leaves of Pearl millet from both the control and 150 mM NaCl‐treated groups.ResultsThe results revealed that 27.6% of Pennisetum glaucum genes exhibited differential expression, with 3246 genes being upregulated and 7408 genes downregulated when compared to the control group. Principal component analysis underscored distinct variations in gene expression patterns between the control and salt‐stressed groups. Pathway analysis sheds light on the upregulated differentially expressed genes (DEGs), highlighting their involvement in crucial pathways such as phytyl‐PP biosynthesis, lysine degradation, glutamate biosynthesis, nitrate assimilation and DLO biosynthesis. Conversely, the downregulated DEGs were associated with pathways like coumarins biosynthesis, pinobanksin biosynthesis, UDP‐
d‐glucuronate biosynthesis and cholesterol biosynthesis, among others. Furthermore, our transcription factor analysis unveiled specific families associated with the salt stress response, including bHLH, ERF, NAC, WRKY, bZIP, MYB and HD‐ZIP.ConclusionsThese findings represent a significant advancement in our comprehension of Pearl millet's capacity to withstand salt stress and provide potential targets for the development of salt‐resistant crops, contributing to the advancement of sustainable agriculture in regions affected by salinity.
Zinc Oxide Nanoparticles as Efficient Heterogeneous Catalyst for Synthesis of Bio‐active Heterocyclic Compounds
Authors: Kumar Gourav , Tomar Vijesh , Kumar Parveen , Nemiwal Meena 
Published: November 2023

AbstractAmong the most effective recoverable catalytic systems, metal‐oxide nanoparticles (NPs) are well known for their extensive uses in a broad range of industries, pharmaceuticals, and nano‐biotechnology. In addition, heterogeneous catalysis uses clearly defined materials which are present an extensive range of new possibilities for the research and production of innovative catalysts that help to solve the world's energy and environmental problems. ZnO‐NPs have been used as effective nanocatalysts according to the literature for various kinds of organic reactions. The extensive advantages of ZnO‐NPs over bulk materials suggest that this is a promising field for further research. This review article provides an in‐depth overview of the several ZnO‐NPs that have been reported to catalyse organic transformations including the production of bio‐active compounds like benzofuran, coumarin, imidazole, indole, pyrazole, pyridine pyrimidine, thiazole, diazepine, azoles derivatives. Recent synthetic routes for modifying and functionalizing ZnO‐NPs to increase their catalytic efficacy were also addressed, and illustrated with schematics. The development of novel, highly effective, and reusable modified ZnO‐NPs as catalysts, which would clear the way for the establishment of greener and sustainable technologies, provides the key to the future of catalysis. Researchers attempting to synthesise new functionalized ZnO‐NPs for sustainable development will find this review informative.
Multifunctional DNA‐Based Hydrogel Promotes Diabetic Alveolar Bone Defect Reconstruction
Authors: Peng Ge , Li Wei , Peng Linrui , Li Ruoqing , Wang Zhenghao , Zhou Ye , Gou Liping , Zhu Xinyue , Xie Qingxing , Zhang Xinyi , Shen Sumin , Wu Lei , Hu Liqiang , Wang Chengshi , Zheng Xiaofeng , Tong Nanwei 
Published: November 2023

AbstractDiabetic alveolar bone defect (DABD) causes persistent bacterial infection, prolonged inflammation, and delayed bone healing, making it a considerable clinical challenge. In this study, by integrating silver nanoclusters (AgNCs) and M2 macrophage‐derived extracellular vesicles (M2EVs), a multifunctional DNA‐based hydrogel, called Agevgel, is developed with antibacterial, anti‐inflammatory, immunomodulatory, and osteogenic properties to promote DABD rebuilding. AgNCs are tightly embedded into the DNA scaffolds and exhibit effective anti‐bacterial activity, while immunomodulatory M2EVs are encapsulated within the shape‐variable DNA scaffolds and exhibit potent anti‐inflammatory and osteogenic properties. The results reveal that Agevgel effectively prolongs the local retention time and bioactivity of M2EVs in vivo. In particular, the sustained release of M2EVs can last for at least 7 days when applying Agevgel to DABD. Compared to free M2EVs or Aggel (AgNCs encapsulated within the DNA hydrogel) treatments, the Agevgel treatment accelerates the defect healing rate of alveolar bone and dramatically improves the trabecular architecture. Mechanistically, Agevgel plays a key role in regulating macrophage polarization and promoting the expression of proliferative and osteogenic factors. In summary, Agevgel provides a comprehensive treatment strategy for DABD with a great clinical translational value, highlighting the application of DNA hydrogels as an ideal bioscaffolds for periodontal diseases.
Remodeling of Mitochondrial Metabolism by a Mitochondria‐Targeted RNAi Nanoplatform for Effective Cancer Therapy
Authors: Xu Rui , Huang Linzhuo , Liu Jiayu , Zhang Yuxuan , Xu Ya , Li Rong , Su Shicheng , Xu Xiaoding 
Published: November 2023

AbstractEmerging evidence has demonstrated the significant contribution of mitochondrial metabolism dysfunction to promote cancer development and progression. Aberrant expression of mitochondrial genome (mtDNA)‐encoded proteins widely involves mitochondrial metabolism dysfunction, and targeted regulation of their expression can be an effective strategy for cancer therapy, which however is challenged due to the protection by the mitochondrial double membrane. Herein, a mitochondria‐targeted RNAi nanoparticle (NP) platform for effective regulation of mitochondrial metabolism and breast cancer (BCa) therapy is developed. This nanoplatform is composed of a hydrophilic polyethylene glycol (PEG) shell, a hydrophobic poly(2‐(diisopropylamino)ethyl methacrylate) (PDPA) core, and charged‐mediated complexes of mitochondria‐targeting and membrane‐penetrating peptide amphiphile (MMPA) and small interfering RNA (siRNA) embedded in the core. After tumor accumulation and internalization by tumor cells, these NPs can respond to the endosomal pH to expose the MMPA/siRNA complexes, which can specifically transport siRNA into the mitochondria to down‐regulate mtDNA‐encoded protein expression (e.g., ATP6 and CYB). More importantly, because ATP6 down‐regulation can suppress ATP production and enhance reactive oxygen species (ROS) generation to induce mitochondrial damage and mtDNA leakage into tumor tissues, the NPs can combinatorially inhibit tumor growth via suppressing ATP production and repolarizing tumor‐associated macrophages (TAMs) into tumor‐inhibiting M1‐like macrophages by mtDNA.
Live Mapping of the Brain Extracellular Matrix and Remodeling in Neurological Disorders
Authors: Ge Xiaoqian , Xu Xueqi , Cai Qi , Xiong Hejian , Xie Chen , Hong Yi , Gao Xiaofei , Yao Yao , Bachoo Robert , Qin Zhenpeng 
Published: November 2023

AbstractLive imaging of the brain extracellular matrix (ECM) provides vital insights into changes that occur in neurological disorders. Current techniques such as second or third‐harmonic generation offer limited contrast for live imaging of the brain ECM. Here, a new method, pan‐ECM via chemical labeling of extracellular proteins, is introduced for live brain ECM imaging. pan‐ECM labels all major ECM components in live tissue including the interstitial matrix, basement membrane, and perineuronal nets. pan‐ECM enables in vivo observation of the ECM heterogeneity between the glioma core and margin, as well as the assessment of ECM deterioration under stroke condition, without ECM shrinkage from tissue fixation. These findings indicate that the pan‐ECM approach is a novel way to image the entire brain ECM in live brain tissue with optical resolution. pan‐ECM has the potential to advance the understanding of ECM in brain function and neurological diseases.
Hsa_circ_0001707 regulates endothelial‐mesenchymal transition in esophageal squamous cell carcinoma via miR‐203a‐3p/Snail2 pathway
Authors: Gao Han , Sun Mingjun , Gao Zhikui , Song Jing , Tang Derong , Liu Ran 
Published: November 2023

AbstractEsophageal squamous cell carcinoma (ESCC) is a malignant tumor with high mortality and poor prognosis. Despite intensive research focused on tumor suppression, the 5‐year survival rate of ESCC is lower than 15%. Therefore, investigate fundamental mechanisms involved in ESCC is on‐demand crucial for diagnostics and developing targeted therapeutic drugs. Circular RNAs (circRNAs), as an emerging class of non‐coding RNA, have been elucidated that circRNAs participated in regulating a variety of pathological processes and tumorigenesis. Nevertheless, the functional role of circRNAs in the occurrence and development of ESCC remains unclear. We identify a novel circRNA (hsa_circ_0001707), which was highly expressed in ESCC patients' tissues and cell lines. Furthermore, gain‐ and loss‐of‐function assays were performed and found that overexpression of hsa_circ_0001707 significantly promote tumor proliferation, metastasis, and invasion. By functioning as a competing endogenous RNA (ceRNA), the dual‐luciferase activity assay verified that hsa_circ_0001707 can endogenously bind with miR‐203a‐3p and regulate its downstream gene Snail2. Rescue assay further confirms that hsa_circ_0001707 downregulation could partially attenuate the facilitation effect of miR‐203a‐3p, thereby inhibiting the endothelial‐mesenchymal transition (EMT) process of ESCC. Our results suggested that hsa_circ_0001707 play an oncogenic role in the pathogenesis of ESCC, which might be a potential biomarker for diagnostics and targeting therapy.
Adjacency for scattering amplitudes from the Gröbner fan
Authors: Bossinger L. , Drummond J. M. , Glew R. 
Published: November 2023

Abstract
Scattering amplitudes in planar $$ \mathcal{N} $$
N
= 4 super Yang-Mills theory exhibit singularities which reflect various aspects of the cluster algebras associated to the Grassmannians Gr(4, n) and their tropical counterparts. Here we investigate the potential origins of such structures and examine the extent to which they can be recovered from the Gröbner structure of the underlying Plücker ideals, focussing on the Grassmannians corresponding to finite cluster algebras.Starting from the Plücker ideal, we describe how the polynomial cluster variables are encoded in non-prime initial ideals associated to certain maximal cones of the positive tropical fan. Following [1] we show that extending the Plücker ideal by such variables leads to a Gröbner fan with a single maximal Gröbner cone spanned by the positive tropical rays. The associated initial ideal encodes the compatibility relations among the full set of cluster variables. Thus we find that the Gröbner structure naturally encodes both the symbol alphabet and the cluster adjacency relations exhibited by scattering amplitudes without invoking the cluster algebra at all.As a potential application of these ideas we then examine the kinematic ideal associated to non-dual conformal massless scattering written in terms of spinor helicity variables. For five-particle scattering we find that the ideal can be identified with the Plücker ideal for Gr(3, 6) and the corresponding tropical fan contains a number of non-prime ideals which encode all additional letters of the two-loop pentagon function alphabet present in various calculations of massless five-point finite remainders.