bluuebunny/crossref_metadata_2025_split huggingface dataset:
DFT based atomic modeling and Analog/RF analysis of ferroelectric HfO2 based improved FET device
Authors: Pathak Yash , Dhar Malhotra Bansi , Chaujar Rishu 
Published: July 2023

Abstract
In this study, we systematically investigated the Analog/RF and linearity parameter of SM DGNCFET (single metal double gate negative capacitance field effect transistor) and DM DGNCFET (double metal double gate negative capacitance Field effect transistor) with the help of Cogenda Visual TCAD simulator, and also demonstrated the enhancement in the electronic and optical properties of Si-doping bulk structure by using the Quantum ATK. The analog parameters are enhanced for SM DGNCFET such better performance of switching ratio 279 times better, DIBL 54% lower, SS decay, and some other improved parameter transconductance, TGF and Radio frequency parameter is also enhanced, transconductance frequency product (TFP) for improving reliability and stability of device. Linearity parameters like that second and third order transconductance (gm2, g
m3), voltage intercept point for 2nd, 3rd. Tran Blaha modified Becke Johnson (TB-mBJ) approxiamation gives the accurate band gap of crystal. In DFT based atomic study, 12.5% of Si doping in bulk structure reveals better results for ferroelectric HfO2 based crystal in the direct band gap of bandstructure is zero, Density of state (DOS) is also improved conductivity for Si doping crystal. Hence, Si doping in crystal structure is also better for conductivity.
Effective thermo-electro-mechanical properties of Menger sponge-like fractal structures: a finite element study
Authors: Gaur Aditya , Chawla Komal , Kiran Raj , Patel Satyanarayan 
Published: July 2023

Abstract
Menger sponges are hierarchical structures with tunable mechanical and electrical properties. In this work, different orders (0th, 1st, 2nd and 3rd) of hierarchical structures were studied for their effective properties by square, circular and hexagonal-shaped cavities. The elastic modulus, Poisson’s ratio, thermal and electrical conductivities were investigated as a functions of the density. The variation of normalized parameters with normalized density for square, cylindrical, and hexagonal-shaped cavities was used to obtain the empirical relations. The normalized specific modulus and Poisson’s ratio were validated using available analytical models for all cavities. The normalized Poisson’s ratio, thermal conductivity and electrical conductivity decreased with a reduction in the effective density. The effect of a different cavity (square, cylindrical and hexagonal) on the Menger sponge’s mechanical and electrical behaviour shows variation after the effective density falls below 0.8. Menger sponge with a square cavity shows the maximum decrement in thermal and electrical conductivity among other cavities with increasing order of structure. Menger sponge with hexagonal cavity consists of least reduced normalized thermal and electrical conductivity with decreasing effective density. An increment in the order of fractals leads to a near-zero value for Poisson’s ratio. These structures can be used for medical, aerospace, and industrial applications according to the properties required in different applications.
Mechanically tuned cholesteric elastomer waveguide slab
Authors: Adapta Oswaldo , Adrian Reyes J 
Published: July 2023

Abstract
In this research, a planar waveguide whose core is a cholesteric liquid crystalline elastomer whose helical axis is perpendicular to its planar boundaries, is studied. The electrodynamics equations are established, together with the constitutive equations. The mechanical stress is tuned through elastic deformations in the parallel direction along the helix axis, in order to control the propagation parameters. The resulting equations system is solved numerically by assuming the guide to be surrounded either by air or vacuum. The propagation parameter and the ratio between the magnetic and electrical modes are obtained as a function of frequency, which provides the band structure of the aforementioned modes. The amplitudes of the profiles of the electromagnetic fields and the Poynting vector distributions are also sought as a function of position. Finally, the mixing of transverse electric and magnetic modes to generate new eigenmodes and their conditions for propagation within the waveguide, are also studied.
Orchestrating information across tissues via a novel multitask GAT framework to improve quantitative gene regulation relation modeling for survival analysis
Authors: Duan Meiyu , Wang Yueying , Zhao Dong , Liu Hongmei , Zhang Gongyou , Li Kewei , Zhang Haotian , Huang Lan , Zhang Ruochi , Zhou Fengfeng 
Published: July 2023

AbstractSurvival analysis is critical to cancer prognosis estimation. High-throughput technologies facilitate the increase in the dimension of genic features, but the number of clinical samples in cohorts is relatively small due to various reasons, including difficulties in participant recruitment and high data-generation costs. Transcriptome is one of the most abundantly available OMIC (referring to the high-throughput data, including genomic, transcriptomic, proteomic and epigenomic) data types. This study introduced a multitask graph attention network (GAT) framework DQSurv for the survival analysis task. We first used a large dataset of healthy tissue samples to pretrain the GAT-based HealthModel for the quantitative measurement of the gene regulatory relations. The multitask survival analysis framework DQSurv used the idea of transfer learning to initiate the GAT model with the pretrained HealthModel and further fine-tuned this model using two tasks i.e. the main task of survival analysis and the auxiliary task of gene expression prediction. This refined GAT was denoted as DiseaseModel. We fused the original transcriptomic features with the difference vector between the latent features encoded by the HealthModel and DiseaseModel for the final task of survival analysis. The proposed DQSurv model stably outperformed the existing models for the survival analysis of 10 benchmark cancer types and an independent dataset. The ablation study also supported the necessity of the main modules. We released the codes and the pretrained HealthModel to facilitate the feature encodings and survival analysis of transcriptome-based future studies, especially on small datasets. The model and the code are available at http://www.healthinformaticslab.org/supp/.
The structure and mechanism of action of a distinct class of dicistrovirus intergenic region IRESs
Authors: Abaeva Irina S , Young Christina , Warsaba Reid , Khan Nadiyah , Tran Lan Vy , Jan Eric , Pestova Tatyana V , Hellen Christopher U T 
Published: July 2023

Abstract
Internal ribosomal entry sites (IRESs) engage with the eukaryotic translation apparatus to promote end-independent initiation. We identified a conserved class of ∼150 nt long intergenic region (IGR) IRESs in dicistrovirus genomes derived from members of the phyla Arthropoda, Bryozoa, Cnidaria, Echinodermata, Entoprocta, Mollusca and Porifera. These IRESs, exemplified by Wenling picorna-like virus 2, resemble the canonical cricket paralysis virus (CrPV) IGR IRES in comprising two nested pseudoknots (PKII/PKIII) and a 3′-terminal pseudoknot (PKI) that mimics a tRNA anticodon stem–loop base-paired to mRNA. However, they are ∼50 nt shorter than CrPV-like IRESs, and PKIII is an H-type pseudoknot that lacks the SLIV and SLV stem–loops that are primarily responsible for the affinity of CrPV-like IRESs for the 40S ribosomal subunit and that restrict initial binding of PKI to its aminoacyl (A) site. Wenling-class IRESs bound strongly to 80S ribosomes but only weakly to 40S subunits. Whereas CrPV-like IRESs must be translocated from the A site to the peptidyl (P) site by elongation factor 2 for elongation to commence, Wenling-class IRESs bound directly to the P site of 80S ribosomes, and decoding begins without a prior translocation step. A chimeric CrPV clone containing a Wenling-class IRES was infectious, confirming that the IRES functioned in cells.
Histone divergence in trypanosomes results in unique alterations to nucleosome structure
Authors: Deák Gauri , Wapenaar Hannah , Sandoval Gorka , Chen Ruofan , Taylor Mark R D , Burdett Hayden , Watson James A , Tuijtel Maarten W , Webb Shaun , Wilson Marcus D 
Published: July 2023

AbstractEukaryotes have a multitude of diverse mechanisms for organising and using their genomes, but the histones that make up chromatin are highly conserved. Unusually, histones from kinetoplastids are highly divergent. The structural and functional consequences of this variation are unknown. Here, we have biochemically and structurally characterised nucleosome core particles (NCPs) from the kinetoplastid parasite Trypanosoma brucei. A structure of the T. brucei NCP reveals that global histone architecture is conserved, but specific sequence alterations lead to distinct DNA and protein interaction interfaces. The T. brucei NCP is unstable and has weakened overall DNA binding. However, dramatic changes at the H2A-H2B interface introduce local reinforcement of DNA contacts. The T. brucei acidic patch has altered topology and is refractory to known binders, indicating that the nature of chromatin interactions in T. brucei may be unique. Overall, our results provide a detailed molecular basis for understanding evolutionary divergence in chromatin structure.
PLASMe: a tool to identify PLASMid contigs from short-read assemblies using transformer
Authors: Tang Xubo , Shang Jiayu , Ji Yongxin , Sun Yanni 
Published: July 2023

AbstractPlasmids are mobile genetic elements that carry important accessory genes. Cataloging plasmids is a fundamental step to elucidate their roles in promoting horizontal gene transfer between bacteria. Next generation sequencing (NGS) is the main source for discovering new plasmids today. However, NGS assembly programs tend to return contigs, making plasmid detection difficult. This problem is particularly grave for metagenomic assemblies, which contain short contigs of heterogeneous origins. Available tools for plasmid contig detection still suffer from some limitations. In particular, alignment-based tools tend to miss diverged plasmids while learning-based tools often have lower precision. In this work, we develop a plasmid detection tool PLASMe that capitalizes on the strength of alignment and learning-based methods. Closely related plasmids can be easily identified using the alignment component in PLASMe while diverged plasmids can be predicted using order-specific Transformer models. By encoding plasmid sequences as a language defined on the protein cluster-based token set, Transformer can learn the importance of proteins and their correlation through positionally token embedding and the attention mechanism. We compared PLASMe and other tools on detecting complete plasmids, plasmid contigs, and contigs assembled from CAMI2 simulated data. PLASMe achieved the highest F1-score. After validating PLASMe on data with known labels, we also tested it on real metagenomic and plasmidome data. The examination of some commonly used marker genes shows that PLASMe exhibits more reliable performance than other tools.
Aromatic amino acid biosynthesis impacts root hair development and symbiotic associations inLotus japonicus
Authors: Montiel Jesús , García-Soto Ivette , James Euan K , Reid Dugald , Cárdenas Luis , Napsucialy-Mendivil Selene , Ferguson Shaun , Dubrovsky Joseph G , Stougaard Jens 
Published: July 2023

AbstractLegume roots can be symbiotically colonized by arbuscular mycorrhizal (AM) fungi and nitrogen-fixing bacteria. In Lotus japonicus, the latter occurs intracellularly by the cognate rhizobial partner Mesorhizobium loti or intercellularly with the Agrobacterium pusense strain IRBG74. Although these symbiotic programs show distinctive cellular and transcriptome signatures, some molecular components are shared. In this study, we demonstrate that 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase 1 (DAHPS1), the first enzyme in the biosynthetic pathway of aromatic amino acids (AAAs), plays a critical role in root hair development and for AM and rhizobial symbioses in Lotus. Two homozygous DAHPS1 mutants (dahps1-1 and dahps1-2) showed drastic alterations in root hair morphology, associated with alterations in cell wall dynamics and a progressive disruption of the actin cytoskeleton. The altered root hair structure was prevented by pharmacological and genetic complementation. dahps1-1 and dahps1-2 showed significant reductions in rhizobial infection (intracellular and intercellular) and nodule organogenesis and a delay in AM colonization. RNAseq analysis of dahps1-2 roots suggested that these phenotypes are associated with downregulation of several cell wall–related genes, and with an attenuated signaling response. Interestingly, the dahps1 mutants showed no detectable pleiotropic effects, suggesting a more selective recruitment of this gene in certain biological processes. This work provides robust evidence linking AAA metabolism to root hair development and successful symbiotic associations.
Comparing genomes of Fructus Amomi-producing species reveals genetic basis of volatile terpenoid divergence
Authors: Yang Peng , Ling Xu-Yi , Zhou Xiao-Fan , Chen Yuan-Xia , Wang Tian-Tian , Lin Xiao-Jing , Zhao Yuan-Yuan , Ye Yu-Shi , Huang Lin-Xuan , Sun Ye-Wen , Qi Yu-Xin , Ma Dong-Ming , Zhan Ruo-Ting , Huang Xue-Shuang , Yang Jin-Fen 
Published: July 2023

Abstract
Wurfbainia longiligularis and Wurfbainia villosa are both rich in volatile terpenoids and are 2 primary plant sources of Fructus Amomi used for curing gastrointestinal diseases. Metabolomic profiling has demonstrated that bornyl diphosphate (BPP)-related terpenoids are more abundant in the W. villosa seeds and have a wider tissue distribution in W. longiligularis. To explore the genetic mechanisms underlying the volatile terpenoid divergence, a high-quality chromosome-level genome of W. longiligularis (2.29 Gb, contig N50 of 80.39 Mb) was assembled. Functional characterization of 17 terpene synthases (WlTPSs) revealed that WlBPPS, along with WlTPS 24/26/28 with bornyl diphosphate synthase (BPPS) activity, contributes to the wider tissue distribution of BPP-related terpenoids in W. longiligularis compared to W. villosa. Furthermore, transgenic Nicotiana tabacum showed that the GCN4-motif element positively regulates seed expression of WvBPPS and thus promotes the enrichment of BPP-related terpenoids in W. villosa seeds. Systematic identification and analysis of candidate TPS in 29 monocot plants from 16 families indicated that substantial expansion of TPS-a and TPS-b subfamily genes in Zingiberaceae may have driven increased diversity and production of volatile terpenoids. Evolutionary analysis and functional identification of BPPS genes showed that BPP-related terpenoids may be distributed only in the Zingiberaceae of monocot plants. This research provides valuable genomic resources for breeding and improving Fructus Amomi with medicinal and edible value and sheds light on the evolution of terpenoid biosynthesis in Zingiberaceae.
Vacuolar sugar transporter EARLY RESPONSE TO DEHYDRATION6-LIKE4 affects fructose signaling and plant growth
Authors: Khan Azkia , Cheng Jintao , Kitashova Anastasia , Fürtauer Lisa , Nägele Thomas , Picco Cristiana , Scholz-Starke Joachim , Keller Isabel , Neuhaus H Ekkehard , Pommerrenig Benjamin 
Published: July 2023

Abstract
Regulation of intracellular sugar homeostasis is maintained by regulation of activities of sugar import and export proteins residing at the tonoplast. We show here that the EARLY RESPONSE TO DEHYDRATION6-LIKE4 (ERDL4) protein, a member of the monosaccharide transporter family, resides in the vacuolar membrane in Arabidopsis (Arabidopsis thaliana). Gene expression and subcellular fractionation studies indicated that ERDL4 participates in fructose allocation across the tonoplast. Overexpression of ERDL4 increased total sugar levels in leaves due to a concomitantly induced stimulation of TONOPLAST SUGAR TRANSPORTER 2 (TST2) expression, coding for the major vacuolar sugar loader. This conclusion is supported by the finding that tst1-2 knockout lines overexpressing ERDL4 lack increased cellular sugar levels. ERDL4 activity contributing to the coordination of cellular sugar homeostasis is also indicated by 2 further observations. First, ERDL4 and TST genes exhibit an opposite regulation during a diurnal rhythm, and second, the ERDL4 gene is markedly expressed during cold acclimation, representing a situation in which TST activity needs to be upregulated. Moreover, ERDL4-overexpressing plants show larger rosettes and roots, a delayed flowering time, and increased total seed yield. Consistently, erdl4 knockout plants show impaired cold acclimation and freezing tolerance along with reduced plant biomass. In summary, we show that modification of cytosolic fructose levels influences plant organ development and stress tolerance.
Faculty-Librarian Collaboration to Enhance Information Literacy Skills in an Online Nursing Course
Authors: Mahmoud Sally , Withorn Tessa 
Published: July 2023

Abstract
This article describes an exemplary collaboration in which a librarian was fully embedded in beginner undergraduate nursing courses in a baccalaureate nursing program. The goal was to increase academic help-seeking behaviors and information literacy skills. Students benefited from the intervention and increasingly demonstrated the use of better sources for their evidence-based practice assignments. Library tutorials were permanently integrated into the courses. A collaborative approach to designing research assignments allowed the librarian and nursing faculty to lay a foundation of information literacy in the nursing program and encourage academic help-seeking behaviors.
Novel Pulsed Ultrahigh-frequency Spinal Cord Stimulation Inhibits Mechanical Hypersensitivity and Brain Neuronal Activity in Rats after Nerve Injury
Authors: Yang Chin-Tsang , Guan Yun , Chen Chih-Cheng , Lin Wei-Tso , Lu Kuo-Hsiang , Lin Chung-Ren , Shyu Bai-Chuang , Wen Yeong-Ray 
Published: July 2023

Background
Spinal cord stimulation (SCS) is an important pain treatment modality. This study hypothesized that a novel pulsed ultrahigh-frequency spinal cord stimulation (pUHF-SCS) could safely and effectively inhibit spared nerve injury–induced neuropathic pain in rats.

Methods
Epidural pUHF-SCS (± 3V, 2-Hz pulses comprising 500-kHz biphasic sinewaves) was implanted at the thoracic vertebrae (T9 to T11). Local field brain potentials after hind paw stimulation were recorded. Analgesia was evaluated by von Frey–evoked allodynia and acetone-induced cold allodynia.

Results
The mechanical withdrawal threshold of the injured paw was 0.91 ± 0.28 g lower than that of the sham surgery (24.9 ± 1.2 g). Applying 5-, 10-, or 20-min pUHF-SCS five times every 2 days significantly increased the paw withdrawal threshold to 13.3 ± 6.5, 18.5 ± 3.6, and 21.0 ± 2.8 g at 5 h post–SCS, respectively (P = 0.0002, < 0.0001, and < 0.0001; n = 6 per group) and to 6.1 ± 2.5, 8.2 ± 2.7, and 14.3 ± 5.9 g on the second day, respectively (P = 0.123, 0.013, and < 0.0001). Acetone-induced paw response numbers decreased from pre–SCS (41 ± 12) to 24 ± 12 and 28 ± 10 (P = 0.006 and 0.027; n = 9) at 1 and 5 h after three rounds of 20-min pUHF-SCS, respectively. The areas under the curve from the C component of the evoked potentials at the left primary somatosensory and anterior cingulate cortices were significantly decreased from pre–SCS (101.3 ± 58.3 and 86.9 ± 25.5, respectively) to 39.7 ± 40.3 and 36.3 ± 20.7 (P = 0.021, and 0.003; n = 5) at 60 min post–SCS, respectively. The intensity thresholds for pUHF-SCS to induce brain and sciatic nerve activations were much higher than the therapeutic intensities and thresholds of conventional low-frequency SCS.

Conclusions
Pulsed ultrahigh-frequency spinal cord stimulation inhibited neuropathic pain–related behavior and paw stimulation evoked brain activation through mechanisms distinct from low-frequency SCS.

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Radiomics-based Machine Learning Methods for Volume Doubling Time Prediction of Pulmonary Ground-glass Nodules With Baseline Chest Computed Tomography
Authors: Huang Wenjun , Zhang Hanxiao , Ge Yanming , Duan Shaofeng , Ma Yanqing , Wang Xiaoling , Zhou Xiuxiu , Zhou Taohu , Tu Wenting , Wang Yun , Liu Shiyuan , Dong Peng , Fan Li 
Published: July 2023

Purpose:
Reliable prediction of volume doubling time (VDT) is essential for the personalized management of pulmonary ground-glass nodules (GGNs). We aimed to determine the optimal VDT prediction method by comparing different machine learning methods only based on the baseline chest computed tomography (CT) images.

Materials and Methods:
Seven classical machine learning methods were evaluated in terms of their stability and performance for VDT prediction. The VDT, calculated by the preoperative and baseline CT, was divided into 2 groups with a cutoff value of 400 days. A total of 90 GGNs from 3 hospitals constituted the training set, and 86 GGNs from the fourth hospital served as the external validation set. The training set was used for feature selection and model training, and the validation set was used to evaluate the predictive performance of the model independently.

Results:
The eXtreme Gradient Boosting showed the highest predictive performance (accuracy: 0.890±0.128 and area under the ROC curve (AUC): 0.896±0.134), followed by the neural network (NNet) (accuracy: 0.865±0.103 and AUC: 0.886±0.097). While regarding stability, the NNet showed the highest robustness against data perturbation (relative SDs [%] of mean AUC: 10.9%). Therefore, the NNet was chosen as the final model, achieving high accuracy of 0.756 in the external validation set.

Conclusion:
The NNet is a promising machine learning method to predict the VDT of GGNs, which would assist in the personalized follow-up and treatment strategies for GGNs reducing unnecessary follow-up and radiation dose.
A Novel Imaging Technique for Analyzing Condylar Movement During Mastication in Patients With Jaw Deformities: Four-Dimensional Computed Tomography
Authors: Kimoto Akira , Yamashita Junya , Ohori Hiroaki , Negi Noriyuki , Sekitani Toshinori , Komori Hiroki , Shioyasono Atsushi , Tateishi Chizu , Hasegawa Takumi , Akashi Masaya 
Published: July 2023

Objective:
This study aimed to reveal characteristic condylar movements in patients with jaw deformities.

Study Design:
Thirty patients with jaw deformities before surgery were enrolled and instructed to chew a cookie during 4-dimensional computed tomography (4DCT). The distance between the most anterior and posterior positions of the bilateral condyles on 4DCT images was measured and compared among patients with different skeletal classes. Correlations between the condylar protrusion and cephalometric values were also determined.

Results:
The distances of condylar protrusion during mastication were significantly greater in the skeletal class II group than in the skeletal class III group (P=0.0002). Significant correlations were found between the distances of condylar protrusion during mastication and the sella-nasion–B point angle (r=−0.442, P=0.015), A point–nasion–B point angle (r=0.516, P=0.004), sella-nasion plane to ramus plane angle (r=0.464, P=0.01), sella-nasion plane to occlusal plane angle (r=0.367, P=0.047), and condylion–gonion length (r=−0.366, P=0.048).

Conclusion:
Motion analysis with 4DCT images revealed that condylar movement in patients with retrognathism was larger than in patients with mandibular prognathism. Skeletal structure was therefore correlated with condylar movement during mastication.