bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimizing an efficient ensemble approach for high-quality de novo transcriptome assembly of Thymus daenensis
Authors: Ahmadi Hosein , Sheikh-Assadi Morteza , Fatahi Reza , Zamani Zabihollah , Shokrpour Majid 
Published: July 2023

AbstractNon-erroneous and well-optimized transcriptome assembly is a crucial prerequisite for authentic downstream analyses. Each de novo assembler has its own algorithm-dependent pros and cons to handle the assembly issues and should be specifically tested for each dataset. Here, we examined efficiency of seven state-of-art assemblers on ~ 30 Gb data obtained from mRNA-sequencing of Thymus daenensis. In an ensemble workflow, combining the outputs of different assemblers associated with an additional redundancy-reducing step could generate an optimized outcome in terms of completeness, annotatability, and ORF richness. Based on the normalized scores of 16 benchmarking metrics, EvidentialGene, BinPacker, Trinity, rnaSPAdes, CAP3, IDBA-trans, and Velvet-Oases performed better, respectively. EvidentialGene, as the best assembler, totally produced 316,786 transcripts, of which 235,730 (74%) were predicted to have a unique protein hit (on uniref100), and also half of its transcripts contained an ORF. The total number of unique BLAST hits for EvidentialGene was approximately three times greater than that of the worst assembler (Velvet-Oases). EvidentialGene could even capture 17% and 7% more average BLAST hits than BinPacker and Trinity. Although BinPacker and CAP3 produced longer transcripts, the EvidentialGene showed a higher collinearity between transcript size and ORF length. Compared with the other programs, EvidentialGene yielded a higher number of optimal transcript sets, further full-length transcripts, and lower possible misassemblies. Our finding corroborates that in non-model species, relying on a single assembler may not give an entirely satisfactory result. Therefore, this study proposes an ensemble approach of accompanying EvidentialGene pipelines to acquire a superior assembly for T. daenensis.
The impact of industrial collaborative agglomeration on total factor carbon emission efficiency in China
Authors: Yuan Honglin , Liu Jia , Li Xiaona , Zhong Shen 
Published: July 2023

AbstractImproving total factor carbon emission efficiency (TCE) is the key to achieving carbon emission reduction targets while ensuring economic growth. In this paper, the global Malmquist index based on the SBM model is used to measure TCE of 283 cities in China from 2011 to 2019. On this basis, this paper uses the spatial econometric model and intermediary effect model to empirically analyze the impact of industrial co-agglomeration on TCE and its transmission mechanism. Furthermore, considering the differences in geographical location and resource endowment among regions, this paper analyzes the heterogeneous effect of industrial collaboration agglomeration on TCE in different regions and cities. The results show that: (1) Industrial co-agglomeration can improve TCE, and its main transmission channel is technological innovation. (2) Industrial co-agglomeration has a positive spatial spillover effect. Industrial co-agglomeration in one region can improve the TCE in the surrounding regions. (3) Industrial co-agglomeration of cities with different geographic locations and resource endowments has a heterogeneous effect on TCE. Regarding geographical heterogeneity, the industrial co-agglomeration in the eastern region has the greatest promoting effect on TCE, followed by the central region. However, the impact of industrial co-agglomeration in the western region on TCE is not significant. Regarding resource endowment heterogeneity, the industrial co-agglomeration in non-resource-based cities has a greater promoting effect on TCE than that in resource-based cities.
Long-term activity of social insects responsible for the physical fertility of soils in the tropics
Authors: Bruand Ary , Reatto Adriana , Brossard Michel , Jouquet Pascal , de Souza Martins Éder 
Published: July 2023

AbstractFerralsols correspond to the red and yellow soils that are common in the tropics. They are deeply weathered but physical fertility is high because they exhibit a strong microgranular structure whose origin is still actively debated. In the present study, we looked for evidence of the biological origin of the structure resulting from soil fauna activity. We present results recorded with Brazilian Ferralsols developed under native vegetation. It was found that the Ferralsols studied exhibit morphological features related to the activity of social insects. We showed the presence of potassium 2:1 clays originating from the saprolite in the microaggregates of all the Ferralsols studied. These 2:1 clays were earlier discussed as markers of long-term termite activity. This highlights the threat that weighs on the physical fertility of these soils, and more broadly on the water cycle in the tropical regions concerned, if intensive agriculture reduces the soil fauna biodiversity, as indicated by several studies.
MAT as a promising therapeutic strategy against triple-negative breast cancer via inhibiting PI3K/AKT pathway
Authors: Wei Shijie , Zhang Yubao , Ma Xiaoran , Yao Yan , Zhou Qinqin , Zhang Wenfeng , Zhou Chao , Zhuang Jing 
Published: July 2023

AbstractTriple-negative breast cancer (TNBC), a highly aggressive and heterogeneous subtype of breast cancer, lacks effective treatment options. Sophora flavescens Aiton, a Chinese medicinal plant, is often used in traditional Chinese medicine to treat cancer. Matrine (MAT) is an alkaloid extracted from Sophora flavescens. It has good anticancer effects, and thus can be explored as a new therapeutic agent in TNBC research. We performed bioinformatics analysis to analyze the differentially expressed genes between normal breast tissues and TNBC tissues, and comprehensive network pharmacology analyses. The activity and invasion ability of TNBC cells treated with MAT were analyzed. Apoptosis and cell cycle progression were determined using cytometry. We used Monodansylcadaverine (MDC) staining to determine the condition of autophagosomes. Finally, the expression levels of the key target proteins of the PI3K/AKT pathway were determined using western blotting. The proliferation and invasion ability of MDA-MB-231 and MDA-MB-468 can be effectively inhibited by MAT. The results of flow cytometry indicated that MAT arrested the TNBC cell cycle and induced apoptosis. In addition, we confirmed that MAT inhibited the expression of BCL-2 while up-regulating the expression of cleaved caspase-3. Moreover, enhanced intensity of MDC staining and high LC3-II expression were observed, which confirmed that MAT induced autophagy in TNBC cells. Western blotting showed that MAT inhibited the PI3K/AKT pathway and downregulated the expressions of PI3K, AKT, p-AKT, and PGK1. This study provides feasible methods, which include bioinformatics analysis and in vitro experiments, for the identification of compounds with anti-TNBC properties. MAT inhibited the PI3K/AKT signaling pathway, arrested cell cycle, as well as promoted cell apoptosis and autophagy. These experiments provide evidence for the anti-TNBC effect of MAT and identified potential targets against TNBC.
Exploring the micromorphological characteristics of adult lower cervical vertebrae based on micro-computed tomography
Authors: Li Kun , Yang Yang , Wang Peng , Song Haoyu , Ma Chunying , Zhang Yansong , Dang Xingye , Shi Jun , Zhang Shaojie , Li Zhijun , Wang Xing 
Published: July 2023

AbstractWe will use micro-computed tomography to scan 31 sets of the adult lower cervical vertebrae (155 vertebrae) to observe the morphological characteristics and direction of trabeculae in the lower cervical vertebrae by outlining and reconstructing the regions of interest and to calculate the variation laws of the microstructure in the regions of interest to reveal their structural characteristics and weak areas. As a result, the images showed that the trabeculae in the lower cervical pedicle near the medial and lateral cortices were relatively dense, and their bone plates were lamellar. There were cavities between the superior and inferior articular processes where the ossification centers had not been absorbed after ossified. The lamellar trabeculae in the vertebral plates near the cortical bones were only 1–2 layers, extended and transformed into rod-shaped trabeculae in a radial shape toward the medullary space. The lamellar trabeculae of the vertebral plate extend over the spinous process near the cortical bone. The statistical results of the trabeculae's morphological parameters showed significant differences in bone volume fraction values among the four parts (P < 0.05). There were substantial differences in BS/BV, except for no differences between the pedicle and the vertebral plate (P < 0.05). There was a significant difference in trabecular pattern factor values between the articular process, the spinous process, and the vertebral plate (P < 0.05) and a significant difference between the pedicle, the spinous process, and the vertebral plate (P < 0.05). There were no significant differences in trabecular bone thickness and trabecular space values among the four parts (P < 0.05). The anatomical microstructural perspective confirms that the optimal choice is internal fixation via the pedicle. If using pedicle screws, the nail tract needs to be placed into the spinous process to increase its holding power and resistance to extraction.
Activation of cAMP (EPAC2) signaling pathway promotes hepatocyte attachment
Authors: Helena Grace Aprilia , Watanabe Teruhiko , Kato Yusuke , Shiraki Nobuaki , Kume Shoen 
Published: July 2023

AbstractPrimary Human Hepatocyte (PHH) remains undefeated as the gold standard in hepatic studies. Despite its valuable properties, partial attachment loss due to the extraction process and cryopreservation remained the main hurdle in its application. We hypothesized that we could overcome the loss of PHH cell attachment through thawing protocol adjustment and medium composition. We reported a novel use of a medium designed for iPSC-derived hepatocytes, increasing PHH attachment on the collagen matrix. Delving further into the medium composition, we discovered that removing BSA and exposure to cAMP activators such as IBMX and Forskolin benefit PHH attachment. We found that activating EPAC2, the cAMP downstream effector, by S-220 significantly increased PHH attachment. We also found that EPAC2 activation induced bile canaliculi formation in iPS-derived hepatocytes. Combining these factors in studies involving PHH or iPS-hepatocyte culture provides promising means to improve cell attachment and maintenance of hepatic function.
Magnesium ions mediate ligand binding and conformational transition of the SAM/SAH riboswitch
Authors: Hu Guodong , Zhou Huan-Xiang 
Published: July 2023

AbstractThe SAM/SAH riboswitch binds S-adenosylmethionine (SAM) and S-adenosylhomocysteine (SAH) with similar affinities. Mg2+ is generally known to stabilize RNA structures by neutralizing phosphates, but how it contributes to ligand binding and conformational transition is understudied. Here, extensive molecular dynamics simulations (totaling 120 μs) predicted over 10 inner-shell Mg2+ ions in the SAM/SAH riboswitch. Six of them line the two sides of a groove to widen it and thereby pre-organize the riboswitch for ligand entry. They also form outer-shell coordination with the ligands and stabilize an RNA-ligand hydrogen bond, which effectively diminishes the selectivity between SAM and SAH. One Mg2+ ion unique to the apo form maintains the Shine–Dalgarno sequence in an autonomous mode and thereby facilitates its release for ribosome binding. Mg2+ thus plays vital roles in SAM/SAH riboswitch function.
The thermodynamic and mechanical properties of Earth-abundant metal ternary boride Mo2(Fe,Mn)B2 solid solutions for impact- and wear-resistant alloys
Authors: Prysyazhnyuk Pavlo , Di Tommaso Devis 
Published: July 2023

Substitutional solid solutions of the Mo2FeB2–Mo2MnB2 system exhibit high stability and a sufficient level of mechanical properties to be used as a reinforcement phase in high-manganese alloys (steels), providing both impact- and wear-resistance.
Influence characteristics of water penetration on fibre‐reinforced polymer/rigid polyurethane foam interface of the composite cross‐arm considering natural ageing
Authors: Xie Jun , Zhou Zhe , Liu Ziqian , Tian Haonan , Zhang Sigang , Xie Qing 
Published: July 2023

AbstractFibre‐reinforced polymer (FRP)/rigid polyurethane foam (RPUF) interface is susceptible to moisture intrusion in addition to natural ageing during operation. This study investigated the influence of moisture intrusion on the FRP/RPUF interface under natural ageing using experiments and molecular dynamics (MD) simulations. Water absorption, shear strength, and leakage current tests were used to clarify the changes in the interface performance. The degradation mechanism of moisture intrusion at the interface under natural ageing was revealed by MD simulation and micro‐characterisation. The results show that the natural ageing of interfacial materials will slightly reduce the quality of the interface but will reduce the water resistance of the material and promote the process of water intrusion into the interface. In addition, water mainly invades the interface through RPUF. After water penetration, the interfacial bonding strength and insulation performance significantly decreased. Plasticisation and hydrolysis of interfacial materials are the main reasons for decreased interfacial adhesion. Hydrolysis can cause irreversible damage to the interface, increasing interface defects and water absorption. The vicious cycle of material hydrolysis is the ultimate cause of interfacial debonding. The polar molecules produced by this process and the water absorbed by the interface caused the degradation of the interface insulation performance.
Image segmentation by selecting eigenvectors based on extended information entropy
Authors: Zhang Daming , Zhang Xueyong , Liu Huayong 
Published: July 2023

AbstractFor spectral clustering algorithm, the quality of eigenvectors of graph affinity matrix is very important for the clustering result. So, how to obtain high‐quality eigenvectors is crucial. In this paper, the authors aim to propose some new measurement methods to evaluate each eigenvector of affinity matrix for spectral selection. Based on extended information entropy, three criteria, i.e. Spectral Distinguishability (SD), Spectral Distinguishability Validity (SDV) and pectral Distinguishability ‐Degree (SDD), are defined respectively. The compactness of clusters for each eigenvector is measured by SD; SDV is used to remove the inefficient eigenvectors for clustering; SDD is used to evaluate the contribution of eigenvectors to clustering and is exploited to build a selective spectral ensemble scheme. To indicate the merits of the authors’ algorithm, the authors consider varied artificial data and natural images, including Berkeley image segmentation data set as benchmark data set. The authors’ simulation results confirm the superior performance of the proposed method in developing spectral clustering compared to conventional clustering methods and recent eigenvectors‐selection‐based algorithms.
3D geometry‐based UAV to vehicle multiple‐input multiple‐output channel model incorporating Unmanned aerial vehicle heaving motion
Authors: Ahmed Naeem , Hua Boyu , Ali Farman , Zhu Qiuming , Ni Haoran , Bao Junwei , Mao Kai 
Published: July 2023

AbstractUnmanned aerial vehicles (UAVs) play a vital role in the beyond fifth‐generation (B5G) and sixth‐generation (6G) wireless communication scenarios. This paper proposes a non‐stationary three‐dimensional (3D) geometry‐based multiple‐input multiple‐output channel model for UAV to vehicle (U2V) communications considering UAV heaving motion. The proposed model incorporates the effects of UAV heaving along with the rotation, acceleration, and 3D velocity variation for matching the realistic U2V communication scenarios. The computation methods for time variant channel parameters such as Doppler frequencies, angle of arrival, and angle of departure are given and analysed. The theoretical and statistical properties, including spatial temporal correlation function, TCF, level crossing rate, average fade duration, and Doppler power spectral density are derived and analysed aiming to evaluate the proposed model. Simulation results show that the output statistical characteristics agree with the hypothetical and simulated outcomes, which shows the validity of both the channel model and theoretical derivations.The cover image is based on the Research Article 3D geometry‐based UAV to vehicle multiple‐input multiple‐output channel model incorporating Unmanned aerial vehicle heaving motion by Naeem Ahmed et al., https://doi.org/10.1049/mia2.12393
Dual‐band bandpass filter with high selectivity based on 3D printable groove gap waveguide
Authors: Yao Beini , Huang Nengcai , Zhang Gang , Zhou Xin , Lu Jing , Tam Kam Weng , Zhang Wenfei , Tang Wanchun 
Published: July 2023

AbstractA compact dual‐band bandpass filter (BPF) with high selectivity based on 3D printable groove gap waveguide (GGW) for millimeter application is proposed by the authors. Two stacked dual‐mode GGW resonant cavities including TE102 and TE201 are used to realise a compact structure. The dual‐band bandpass response of the GGW BPF is developed from a split‐type coupling topology which produced two transmission zeros (TZs) between the two passbands. In addition, two TZs are generated outside the two passbands after introducing a source‐load coupling, which achieves a higher frequency selectivity. For verification, a prototype is designed, fabricated and measured. The measured results agree well with the simulated ones, which validates the proposal.
Two‐plane waveguide coupler with arbitrary coupling ratios in the H‐plane and E‐plane directions
Authors: Li Qi , Hirokawa Jiro , Tomura Takashi 
Published: July 2023

AbstractA comprehensive theoretical analysis of two‐plane waveguide coupler with arbitrary coupling ratios in the H‐plane and E‐plane directions is provided and a design of the two‐plane coupler with coupling ratio in the H‐plane direction and coupling ratio in the E‐plane direction is reported. The analysis of the two‐plane waveguide coupler is fully refined and accomplished by the authors. To realise an arbitrary and different coupling ratio in the two directions, it is crucial to specifically constrain the transition phase of the quarter model of the two‐plane coupler for different boundaries as necessitated by mode polarity. A prototype of the proposed two‐plane coupler is manufactured and measured to verify the concept. Its performance is observed from 27.0 to 29.5 GHz (8.85% fractional bandwidth). The measurement results are basically in accord with the simulation results, demonstrating the reliability of the theoretical analysis. Finally, samples of designed conventional H‐plane and E‐plane couplers are provided, cascading of which can realise the same functionality as the proposed two‐plane coupler. Compared with one‐plane couplers, the two‐plane coupler reported realises overall miniaturisation rates in terms of length and volume around 58.4% and 50.1%, respectively. According to the demonstration and verification of the two‐plane couplers having arbitrary coupling ratios, the employment of the two‐plane couplers to replace the conventional one‐plane couplers to realise miniaturisation of 2‐D beam switching matrices will be promoted in future applications.
Evolution and optimization of a brushless doubly‐fed machine with an asymmetrical reluctance and magductance rotor
Authors: Long Dingbang , Wen Honghui , Shuai Zhikang , Ma Zhengzhou 
Published: July 2023

AbstractThe brushless doubly‐fed machine (BDFM) utilizes an asymmetric composite rotor featuring salient pole reluctance and magductance to effectively compensate for the phase shift in space, as well as enhance magnetic field modulation effects, and is therefore used as a modulator. This paper evaluates the modulation capability of the modulator from the perspective of the magnetic field conversion mechanism. The theoretical evolutions of the average magnetic field conversion factors and torque contributions of various airgap field harmonics are accomplished. Additionally, multi‐objective optimization is conducted for better performance, using stratified sensitivity analysis on typical 4/2 pole pair BDFMs featuring symmetrical and asymmetric composite rotors. As a result, further improved modulation of the air gap magnetic field is expected, the cross‐coupling efficiency of the rotor is improved, and a lower output torque ripple is also achieved compared to the conventional symmetrical counterpart. Theoretical investigation of the optimized BDFM, including its effectiveness in enhancing performance metrics such as coupling factor, airgap flux density, and phase shift mechanism, is verified through 2D finite element analysis. Furthermore, a proof‐of‐concept prototype for experimentation was manufactured, which achieved good agreement with the theoretical predictions.
Relativistic dynamical friction in stellar systems
Authors: Chiari Caterina , Di Cintio Pierfrancesco 
Published: July 2023

Aims.We extend the classical formulation of the dynamical friction effect on a test star by Chandrasekhar to the case of relativistic velocities and velocity distributions, also accounting for post-Newtonian corrections to the gravitational force.Methods.The original kinetic framework was revised and used to construct a special-relativistic dynamical friction formula where the relative velocity changes in subsequent encounters are added up with Lorentz transformation, and the velocity distribution of the field stars accounts for relativistic velocities. Furthermore, a simple expression is obtained for systems where the post-Newtonian correction on the gravitational forces become relevant even at non-relativistic particle velocities. Finally, using a linearized Lagrangian we derived another expression for the dynamical friction expression in a more compact form than previously used.Results.Comparing our formulation with the classical one, we observe that a given test particle undergoes a slightly stronger drag when moving through a distribution of field stars with relativistic velocity distribution. Vice versa, a purely classical treatment of a system where post-Newtonian (PN) corrections should be included, overestimates the effect of dynamical friction at low test particle velocity, regardless of the form of velocity distribution. Finally, a first-order PN dynamical friction covariant formulation is weaker its classical counterpart at small velocities, but much higher for large velocities over a broad range of mass ratios.