bluuebunny/crossref_metadata_2025_split huggingface dataset:
Degree-preserving graph dynamics: a versatile process to construct random networks
Authors: Erdős Péter L , Kharel Shubha R , Mezei Tamás R , Toroczkai Zoltan 
Published: December 2023

Abstract
Real-world networks evolve over time via the addition or removal of vertices and edges. In current network evolution models, vertex degree varies or grows arbitrarily. A recently introduced degree-preserving network growth (DPG) family of models preserves vertex degree, resulting in structures significantly different from and more diverse than previous models ([Nature Physics 2021, DOI:10.1038/s41567-021-01417-7]). Despite its degree preserving property, the DPG model is able to replicate the output of several well-known real-world network growth models. Simulations showed that many real-world networks can also be constructed from small seed graphs via the DPG process. Here, we start the development of a rigorous mathematical theory underlying the DPG family of network growth models. We prove that the degree sequence of the output of some of the well-known, real-world network growth models can be reconstructed via the DPG process, using proper parametrization. We also show that the general problem of deciding whether a simple graph can be obtained via the DPG process from a small seed (DPG feasibility) is, however, NP-complete. It is an intriguing open problem to uncover whether there is a structural reason behind the DPG-constructability of real-world networks. Keywords: network growth models; degree-preserving growth (DPG); matching theory; synthetic networks; power-law degree distribution.
Tooth mobility restriction by multistranded and CAD/CAM retainers—an in vitro study
Authors: Roser Christoph J , Rues Stefan , Erber Ralf , Hodecker Lutz , Lux Christopher J , Bauer Carolien A J 
Published: December 2023

Abstract

Objectives
Orthodontic retainers should restrict physiological tooth mobility as little as possible. While this has been investigated for multistranded retainers, there is a lack of data for novel CAD/CAM retainers. To address this, the present study compared the restriction of physiological tooth mobility in multistranded retainers and different CAD/CAM retainers.

Material/methods
One group of multistranded (n = 8) and five groups of CAD/CAM retainers (nickel-titanium (NiTi), titanium grade 5 (Ti5), polyetheretherketone (PEEK), zirconia (ZrO2), and cobalt-chromium (CoCr); each n = 8) bonded from canine to canine were investigated for their influence on vertical and horizontal tooth mobility using an in vitro model of a lower arch in a universal testing machine. Load–deflection curves were determined and statistically analysed.

Results
All retainers restricted tooth mobility to varying extents. The retainers had less of an influence on vertical tooth mobility, with less of a difference between retainers (14%–38% restriction). In contrast, significant (P ≤ 0.05) differences were observed between retainers in the restriction of horizontal tooth mobility. ZrO2 retainers had the greatest impact, restricting horizontal tooth mobility by 82% (68 ± 20 µm/100N), followed by CoCr (75%, 94 ± 26 µm/100N) and PEEK (73%, 103 ± 28 µm/100N) CAD/CAM retainers, which had comparable effects on horizontal tooth mobility. Ti5 (54%, 175 ± 66 µm/100N) and NiTi (34%, 248 ± 119 µm/100N) CAD/CAM retainers had less of an influence on horizontal tooth mobility, and were comparable to multistranded retainers (44%, 211 ± 77 µm/100N).

Limitations
This is an in vitro study, so clinical studies are needed to draw clinical conclusions.

Conclusions
Multistranded and CAD/CAM retainers have different effects on tooth mobility in vitro. These effects should be further explored in future in vivo studies.
Unraveling the Molecular Basis of Stabilizing Selection by Experimental Evolution
Authors: Schlötterer Christian 
Published: December 2023

Abstract
Stabilizing selection provides a challenge to molecular population genetics. Although stabilizing selection is ubiquitous, its genomic signature is difficult to distinguish from demographic signals. Experimental evolution provides a promising approach to characterize genomic regions exposed to stabilizing selection. A recent experimental evolution study of Aedes aegypti populations evolving either with or without sexual selection found a pattern of genetic differentiation suggestive of relaxed stabilizing selection. I argue that this study could not have detected the signal of relaxed stabilizing selection. I highlight why incorrect statistical methods resulted in a high number of false positive candidate single nucleotide polymorphism (SNPs) and discuss the fallacy of functional validation of candidate SNPs for polygenic traits by RNA-mediated knockdown.
Deciphering the distinct transcriptomic and gene regulatory map in adult macaque basal ganglia cells
Authors: Li Zihao , Sun Yunong , Ding Lingjun , Yang Jing , Huang Jinrong , Cheng Mengnan , Wu Liang , Zhuang Zhenkun , Chen Cheng , Huang Yunqi , Zhu Zhiyong , Jiang Siyuan , Huang Fubaoqian , Wang Chunqing , Liu Shiping , Liu Longqi , Lei Ying 
Published: December 2023

Abstract

Background
The basal ganglia are a complex of interconnected subcortical structures located beneath the mammalian cerebral cortex. The degeneration of dopaminergic neurons in the basal ganglia is the primary pathological feature of Parkinson's disease. Due to a lack of integrated analysis of multiomics datasets across multiple basal ganglia brain regions, very little is known about the regulatory mechanisms of this area.

Findings
We utilized high-throughput transcriptomic and epigenomic analysis to profile over 270,000 single-nucleus cells to create a cellular atlas of the basal ganglia, characterizing the cellular composition of 4 regions of basal ganglia in adult macaque brain, including the striatum, substantia nigra (SN), globus pallidum, and amygdala. We found a distinct epigenetic regulation on gene expression of neuronal and nonneuronal cells across regions in basal ganglia. We identified a cluster of SN-specific astrocytes associated with neurodegenerative diseases and further explored the conserved and primate-specific transcriptomics in SN cell types across human, macaque, and mouse. Finally, we integrated our epigenetic landscape of basal ganglia cells with human disease heritability and identified a regulatory module consisting of candidate cis-regulatory elements that are specific to medium spiny neurons and associated with schizophrenia.

Conclusions
In general, our macaque basal ganglia atlas provides valuable insights into the comprehensive transcriptome and epigenome of the most important and populous cell populations in the macaque basal ganglia. We have identified 49 cell types based on transcriptomic profiles and 47 cell types based on epigenomic profiles, some of which exhibit region specificity, and characterized the molecular relationships underlying these brain regions.
DriverMP enables improved identification of cancer driver genes
Authors: Liu Yangyang , Han Jiyun , Kong Tongxin , Xiao Nannan , Mei Qinglin , Liu Juntao 
Published: December 2023

Abstract

Background
Cancer is widely regarded as a complex disease primarily driven by genetic mutations. A critical concern and significant obstacle lies in discerning driver genes amid an extensive array of passenger genes.

Findings
We present a new method termed DriverMP for effectively prioritizing altered genes on a cancer-type level by considering mutated gene pairs. It is designed to first apply nonsilent somatic mutation data, protein‒protein interaction network data, and differential gene expression data to prioritize mutated gene pairs, and then individual mutated genes are prioritized based on prioritized mutated gene pairs. Application of this method in 10 cancer datasets from The Cancer Genome Atlas demonstrated its great improvements over all the compared state-of-the-art methods in identifying known driver genes. Then, a comprehensive analysis demonstrated the reliability of the novel driver genes that are strongly supported by clinical experiments, disease enrichment, or biological pathway analysis.

Conclusions
The new method, DriverMP, which is able to identify driver genes by effectively integrating the advantages of multiple kinds of cancer data, is available at https://github.com/LiuYangyangSDU/DriverMP. In addition, we have developed a novel driver gene database for 10 cancer types and an online service that can be freely accessed without registration for users. The DriverMP method, the database of novel drivers, and the user-friendly online server are expected to contribute to new diagnostic and therapeutic opportunities for cancers.
Multi-omics landscape to decrypt the distinct flavonoid biosynthesis of Scutellaria baicalensis across multiple tissues
Authors: Guo Dandan , Zhu Zhenyu , Wang Zhe , Feng Fei , Cao Qi , Xia Zhewei , Jia Xinlei , Lv Diya , Han Ting , Chen Xiaofei 
Published: December 2023

Abstract
Scutellaria baicalensis Georgi, also known as huang-qin in traditional Chinese medicine, is a widely used herbal remedy due to its anticancer, antivirus, and hepatoprotective properties. The S. baicalensis genome was sequenced many years ago; by contrast, the proteome as the executer of most biological processes of S. baicalensis in the aerial parts, as well as the secondary structure of the roots (xylem, phloem, and periderm), is far less comprehensively characterized. Here we attempt to depict the molecular landscape of the non-model plant S. baicalensis through a multi-omics approach, with the goal of constructing a highly informative and valuable reference dataset. Furthermore, we provide an in-depth characterization dissection to explain the two distinct flavonoid biosynthesis pathways that exist in the aerial parts and root, at the protein and phosphorylated protein levels. Our study provides detailed spatial proteomic and phosphoproteomic information in the context of secondary structures, with implications for the molecular profiling of secondary metabolite biosynthesis in non-model medicinal plants.
Tracking organelle activities through efficient and stable root genetic transformation system in woody plants
Authors: Gong Jinli , Chen Yishan , Xu Yanna , Gu Miaofeng , Ma Haijie , Hu Xiaoli , Li Xiaolong , Jiao Chen , Sun Xuepeng 
Published: December 2023

Abstract
Due to the protracted transgenic timeline and low efficiency in stable genetic transformation of woody plants, there has been limited exploration of real-time organelle imaging within stable transgenic woody plant cells. Here, we established an efficient in vivo genetic transformation system for woody plants using an Agrobacterium rhizogenes-mediated approach. This system was successfully validated in multiple perennial woody species. Using citrus as a model, we introduced organelle-targeted fluorescent reporters via genetic transformation and investigated their subcellular localization and dynamics using advanced imaging techniques, such as confocal microscopy and live-cell imaging. Moreover, we subjected transgenic MT-GFP-labeled mitochondria in root cells to stress conditions simulating agricultural adversities faced by fruit crops. The stress-induced experiments revealed notable alterations in mitochondrial morphology. Our study contributes novel insights into membrane trafficking processes, protein localization dynamics, and cellular physiology in woody plants, while also providing stable and efficient genetic transformation methods for perennial woody species.
An efficient protoplast-based genome editing protocol for Vitis species
Authors: Tricoli David M , Debernardi Juan M 
Published: December 2023

Abstract
CRISPR-Cas technologies allow for precise modifications in plant genomes and promise to revolutionize agriculture. These technologies depend on the delivery of editing components into plant cells and the regeneration of fully edited plants. In vegetatively propagated plants, such as grape, protoplast culture provides one of the best avenues for producing non-chimeric and transgene-free genome-edited plants. However, poor regeneration of plants from protoplasts has hindered their implementation for genome editing. Here, we report an efficient protocol for regenerating plants from protoplasts from multiple grape varieties. By encapsulating the protoplasts in calcium alginate beads and co-culturing them with feeder cultures, the protoplasts divide to form callus colonies that regenerate into embryos and ultimately plants. This protocol worked successfully in wine and table grape (Vitis vinifera) varieties, as well as grape rootstocks and the grapevine wild relative Vitis arizonica. Moreover, by transfecting protoplasts with CRISPR-plasmid or ribonucleoprotein (RNP) complexes, we regenerated albino plants with edits in VvPHYTOENE DESATURASE gene in three varieties and in V. arizonica. The results reveal the potential of this platform to facilitate genome editing in Vitis species.
The Interrelationship between EFL Learning Motivation and Dictionary Use
Authors: Fajt Balázs , Bánhegyi Mátyás , Márkus Katalin P 
Published: December 2023

Abstract
Using dictionaries has been seen as an important aspect of L2 learning at all levels of L2 proficiency. Yet, in many cases dictionary use seems a considerably neglected part of L2 teaching. There is no doubt, however, that L2 learners should be encouraged to use dictionaries independently and autonomously, as they will be unable to rely on language teachers or other proficient L2 speakers to assist them throughout their whole lives. Using Dörnyei’s (2005) L2 Motivational Self System (L2MSS) framework, this quantitative study (N=925) investigates the interrelationship between L2 learning motivation, willingness to pay for dictionaries, reading dictionaries’ usage guides and willingness to use dictionaries. The accumulated data were analysed through structural equation modelling (SEM). Even though not necessarily generalisable to other contexts, the results show that EFL learning motivation has an impact on willingness to buy dictionaries and willingness to use dictionaries. Our data reveal that in the L2MSS, two components (motivated language learning behaviour and the ideal L2 self) have an impact on attitudes to dictionary use.
Greenness Assessment and Validation of HPLC Method for Simultaneous Determination of Resveratrol and Vitamin E in Dietary Supplements
Authors: Topkoska Marina , Miloshevska Martina , Piponski Marjan , Slaveska Spirevska Irena , Nakov Natalija , Brezovska Katerina , Acevska Jelena 
Published: December 2023

Abstract

Background
There is an increasing interest in the use of a combination of trans-resveratrol and vitamin E in dietary supplements. Determination of the content of both components is essential for confirmation of the quality of the product.

Objective
To establish the applicability and ensure the greenness of the previously developed high-throughput HPLC/UV method for the simultaneous determination of trans-resveratrol and alpha-tocopherol acetate (vitamin E) in dietary supplements.

Method
Separation was performed on RP C8 Select B chromatographic column, using acetonitrile and water in the mobile phase, with gradient elution. Full method validation was performed in accordance with ICH Q2(R1). The greenness of the method was assessed using the analytical eco-scale (AES) methodology and the analytical greenness metric (AGREE).

Results
The method is selective, linear, precise, and accurate over defined concentration ranges (185–369 µg/mL of trans-resveratrol and 37–75 µg/mL of alpha-tocopherol acetate), and it has a suitable sensitivity (limits of detection and quantification are 7.7 and 23.3 µg/mL for resveratrol and 2.6 and 7.8 µg/mL for tocopherol acetate, respectively). The obtained analytical eco-scale score of 77 and the pale green AGREE pictogram with an overall score of 0.61 confirm the method’s greenness.

Conclusions
The sensitivity and selectivity of the method, its short analysis time (7 min), the low negative environmental impact, and the simple sample preparation make the method readily applicable to inline quality control procedures.

Highlights
A method for simultaneously analyzing vitamin E and resveratrol in dietary supplements is presented. The method is rapid, includes a simple sample preparation procedure, and has a low environmental impact.
VMAT with DIBH in hypofractionated radiotherapy for left-sided breast cancer after breast-conserving surgery: results of a non-inferiority clinical study
Authors: Jingu Keiichi , Ito Kengo , Sato Kiyokazu , Umezawa Rei , Yamamoto Takaya , Takahashi Noriyoshi , Suzuki Yu , Kishida Keita , Omata So , Harada Hinako , Seki Yasuhiro , Chiba Nanae , Kadoya Noriyuki 
Published: December 2023

Abstract
The purpose of this study was to show the safety of volumetric modulated arc therapy (VMAT) with deep inspiration breath-hold (DIBH) in hypofractionated radiotherapy for left-sided breast cancer after breast-conserving surgery in a clinical setting. Twenty-five Japanese women, aged 20–59 years, who were enrolled in this prospective non-inferiority study received VMAT under the condition of DIBH with 42.4 Gy/16 fractions for whole-breast irradiation (WBI) ± boost irradiation for the tumor bed to show the non-inferiority of VMAT with DIBH to conventional fractionated WBI with free breathing. The primary endpoint was the rate of occurrence of radiation dermatitis of Grade 3 or higher or pneumonitis of Grade 2 or higher within 6 months after the start of radiotherapy. This study was registered with UMIN00004321. All of the enrolled patients completed the planned radiotherapy without interruption. The evaluation of adverse events showed that three patients (12.0%) had Grade 2 radiation dermatitis. There was no other Grade 2 adverse event and there was no patient with an adverse event of Grade 3 or higher. Those results confirmed our hypothesis that the experimental treatment method is non-inferior compared with our historical results. There was no patient with locoregional recurrence or metastases. In conclusion, VMAT under the condition of DIBH in hypofractionated radiotherapy for left-sided breast cancer after breast-conserving surgery can be performed safely in a clinical setting.
Modelling JWST mid-infrared counts: excellent consistency with models derived for IRAS, ISO, and Spitzer
Authors: Rowan-Robinson Michael 
Published: December 2023

ABSTRACT
Models derived in 2009 to fit mid-infrared (8–24 micron) source counts from the IRAS, ISO, and Spitzer missions, provide an excellent fit to deep counts with JWST, demonstrating that the evolution of dusty star-forming galaxies is well understood. The evolution of dust in galaxies at high redshifts is discussed and a simple prescription is proposed to model this. This allows more realistic models for source-counts at submillimetre wavelength. A reasonable fit to 250, 500, 850, and 1100 micron counts is obtained. This paper therefore draws together the IRAS, ISO, Spitzer, Akari, Herschel, submillimetre ground-based, and JWST surveys into a single picture.
Ursa: A Comprehensive Multiomics Toolbox for High-Throughput Single-Cell Analysis
Authors: Pan Lu , Mou Tian , Huang Yue , Hong Weifeng , Yu Min , Li Xuexin 
Published: December 2023

Abstract
The burgeoning amount of single-cell data has been accompanied by revolutionary changes to computational methods to map, quantify, and analyze the outputs of these cutting-edge technologies. Many are still unable to reap the benefits of these advancements due to the lack of bioinformatics expertise. To address this issue, we present Ursa, an automated single-cell multiomics R package containing 6 automated single-cell omics and spatial transcriptomics workflows. Ursa allows scientists to carry out post-quantification single or multiomics analyses in genomics, transcriptomics, epigenetics, proteomics, and immunomics at the single-cell level. It serves as a 1-stop analytic solution by providing users with outcomes to quality control assessments, multidimensional analyses such as dimension reduction and clustering, and extended analyses such as pseudotime trajectory and gene-set enrichment analyses. Ursa aims bridge the gap between those with bioinformatics expertise and those without by providing an easy-to-use bioinformatics package for scientists in hoping to accelerate their research potential. Ursa is freely available at https://github.com/singlecellomics/ursa.
Cryptotis nigrescens (Eulipotyphla: Soricidae)
Authors: Woodman Neal , Timm Robert M 
Published: December 2023

Abstract
The blackish small-eared shrew, Cryptotis nigrescens (Allen, 1895), is a blarinine soricid that occurs in high-elevation premontane wet forest and cloud forest in the Central American countries of Costa Rica and Panama. The species is taxonomically monotypic, although it exhibits size variation that manifests as a gradual increase in size from northwest to southeast. Habitat loss is currently the greatest threat to the species’ existence, although populations in the few areas where C. nigrescens has been studied appear to be healthy, and the International Union for Conservation of Nature (IUCN) classifies it as a species whose conservation status is “Least Concern” (LC). We include a complete synonymy for the genus Cryptotis Pomel, 1848.
A Bayesian noisy logic model for inference of transcription factor activity from single cell and bulk transcriptomic data
Authors: Arriojas Argenis , Patalano Susan , Macoska Jill , Zarringhalam Kourosh 
Published: December 2023

Abstract
The advent of high-throughput sequencing has made it possible to measure the expression of genes at relatively low cost. However, direct measurement of regulatory mechanisms, such as transcription factor (TF) activity is still not readily feasible in a high-throughput manner. Consequently, there is a need for computational approaches that can reliably estimate regulator activity from observable gene expression data. In this work, we present a noisy Boolean logic Bayesian model for TF activity inference from differential gene expression data and causal graphs. Our approach provides a flexible framework to incorporate biologically motivated TF–gene regulation logic models. Using simulations and controlled over-expression experiments in cell cultures, we demonstrate that our method can accurately identify TF activity. Moreover, we apply our method to bulk and single cell transcriptomics measurements to investigate transcriptional regulation of fibroblast phenotypic plasticity. Finally, to facilitate usage, we provide user-friendly software packages and a web-interface to query TF activity from user input differential gene expression data: https://umbibio.math.umb.edu/nlbayes/.
Sizes of Countable Sets
Authors: Trlifajová Kateřina 
Published: December 2023

Abstract
The paper introduces the notion of size of countable sets, which preserves the Part-Whole Principle. The sizes of the natural and the rational numbers, their subsets, unions, and Cartesian products are algorithmically enumerable as sequences of natural numbers. The method is similar to that of Numerosity Theory, but in comparison it is motivated by Bolzano’s concept of infinite series, it is constructive because it does not use ultrafilters, and set sizes are uniquely determined. The results mostly agree, but some differ, such as the size of rational numbers. However, set sizes are only partially, not linearly, ordered. Quid pro quo.