bluuebunny/crossref_metadata_2025_split huggingface dataset:
Channeling acceleration in crystals and nanostructures and studies of solid plasmas: new opportunities
Authors: Gilljohann Max F. , Mankovska Yuliia , San Miguel Claveria Pablo , Sytov Alexei , Bandiera Laura , Ariniello Robert , Davoine Xavier , Ekerfelt Henrik , Fiuza Frederico , Gremillet Laurent , Knetsch Alexander , Martinez Bertrand , Matheron Aimé , Piekarz Henryk , Storey Doug , Taborek Peter , Tajima Toshiki , Shiltsev Vladimir , Corde Sébastien 
Published: November 2023

Abstract
Plasma wakefield acceleration (PWFA) has shown illustrious
progress and resulted in an impressive demonstration of tens of GeV
particle acceleration in meter-long single structures. To reach even
higher energies in the 1 TeV to 10 TeV range, a promising scheme
is channeling acceleration in solid-density plasmas within crystals
or nanostructures.

The E336 experiment studies the beam-nanotarget interaction
with the highly compressed electron bunches available at the
FACET-II accelerator. These studies furthermore involve an in-depth
research on dynamics of beam-plasma instabilities in ultra-dense
plasma, its development and suppression in structured media like
carbon nanotubes and crystals, and its potential use to transversely
modulate the electron bunch.
Modular 3D printed platform for fluidically connected human brain organoid culture
Authors: Rezaei Babak , Giacomoni Jessica , Nilsson Fredrik , Sozzi Edoardo , Fiorenzano Alessandro , Parmar Malin , Keller Stephan S , Kajtez Janko 
Published: November 2023

Abstract
Brain organoid technology has transformed both basic and applied biomedical research and paved the way for novel insights into developmental processes and disease states of the human brain. While the use of brain organoids has been rapidly growing in the past decade, the accompanying bioengineering and biofabrication solutions have remained scarce. As a result, most brain organoid protocols still rely on commercially available tools and culturing platforms that had previously been established for different purposes, thus entailing suboptimal culturing conditions and excessive use of plasticware. To address these issues, we developed a 3D printing pipeline for the fabrication of tailor-made culturing platforms for fluidically connected but spatially separated brain organoid array culture. This all-in-one platform allows all culturing steps—from cellular aggregation, spheroid growth, hydrogel embedding, and organoid maturation—to be performed in a single well plate without the need for organoid manipulation or transfer. Importantly, the approach relies on accessible materials and widely available 3D printing equipment. Furthermore, the developed design principles are modular and highly customizable. As such, we believe that the presented technology can be easily adapted by other research groups and fuel further development of culturing tools and platforms for brain organoids and other 3D cellular systems.
Spatial and temporal evolution of electromagnetic pulses from solid target irradiated with multi-hundred-terawatt laser pulse inside target chamber
Authors: HE 何 Qiangyou 强友 , DENG 邓 Zhigang 志刚 , ZHANG 张 Zhimeng 智猛 , XIA 夏 Yadong 亚东 , ZHANG 张 Bo 博 , MENG 孟 Lingbiao 令彪 , HE 贺 Shukai 书凯 , HUANG 黄 Hua 华 , YANG 杨 Lei 雷 , LIU 刘 Hongjie 红杰 , FAN 范 Wei 伟 , LIN 林 Chen 晨 , ZHOU 周 Weimin 维民 , LI 李 Tingshuai 廷帅 , YAN 颜 Xueqing 学庆 
Published: November 2023

Abstract
Giant electromagnetic pulses (EMPs) induced by high-power laser irradiating solid targets interfere with various experimental diagnoses and even damage equipment, so unveiling the evolution of EMPs inside the laser chamber is crucial for designing effective EMP shielding. In this work, the transmission characteristics of EMPs as a function of distances from the target chamber center (TCC) are studied using B-dot probes. The mean EMP amplitude generated by picosecond laser-target interaction reaches 561 kV m−1, 357 kV m−1, 395 kV m−1, and 341 kV m−1 at 0.32 m, 0.53 m, 0.76 m, and 1 m from TCC, which decreases dramatically from 0.32 m to 0.53 m. However, it shows a fluctuation from 0.53 m to 1 m. The temporal features of EMPs indicate that time-domain EMP signals near the target chamber wall have a wider full width at half maximum compared to that close to TCC, mainly due to the echo oscillation of electromagnetic waves inside the target chamber based on simulation and experimentation. The conclusions of this study will provide a new approach to mitigate strong electromagnetic pulses by decreasing the echo oscillation of electromagnetic waves inside the target chamber during laser coupling with targets.
Development of a 2D spatial displacement estimation method for turbulence velocimetry of the gas puff imaging system on EAST
Authors: LI 李 Letian 乐天 , LIU 刘 Shaocheng 少承 , YAN 颜 Ning 宁 , LIU 刘 Xiaoju 晓菊 , GAO 高 Xiang 翔 
Published: November 2023

Abstract
A gas puff imaging (GPI) diagnostic has been developed and operated on EAST since 2012, and the time-delay estimation (TDE) method is used to derive the propagation velocity of fluctuations from the two-dimensional GPI data. However, with the TDE method it is difficult to analyze the data with fast transient events, such as edge-localized mode (ELM). Consequently, a method called the spatial displacement estimation (SDE) algorithm is developed to estimate the turbulence velocity with high temporal resolution. Based on the SDE algorithm, we make some improvements, including an adaptive median filter and super-resolution technology. After the development of the algorithm, a straight-line movement and a curved-line movement are used to test the accuracy of the algorithm, and the calculated speed agrees well with preset speed. This SDE algorithm is applied to the EAST GPI data analysis, and the derived propagation velocity of turbulence is consistent with that from the TDE method, but with much higher temporal resolution.
Intelligent processing of electromagnetic data using detrended and identification
Authors: Zhang Xian , Li Diquan , Liu Bei , Hu Yanfang , Mo Yao 
Published: November 2023

Abstract
The application of the electromagnetic method has accelerated due to the demand for the development of mineral resource, however the strong electromagnetic interference seriously lowers the data quality, resolution and detect effect. To suppress the electromagnetic interference, this paper proposes an intelligent processing method based on detrended and identification, and applies for wide field electromagnetic method (WFEM) data. First, we combined the improved intrinsic time scale decomposition and detrended fluctuation analysis algorithm for removing the trend noise. Then, we extracted the time domain characteristics of the WFEM data after removing the trend noise. Next, the arithmetic optimization algorithm was utilized to search for the optimal smoothing factor of the probabilistic neural network (PNN) algorithm, which realized to intelligently identify the noise data and WFEM effective data. Finally, the Fourier transform was performed to extract the spectrum amplitude of the effective frequency points from the reconstructed WFEM data, and the electric field curve was obtained. In these studies and applications, the fuzzy c-mean and PNN algorithm are contrasted. The proposed method indicated that the trend noise can be adaptively extracted and eliminated, the abnormal waveform or noise interference can be intelligently identified, the reconstructed WFEM data can effectively recover the pseudo-random signal waveform, and the shape of electric field curves were more stable. Simulation experiments and measured applications has verified that the proposed method can provide technical support for deep underground exploration.
New horizons in evidence synthesis for older adults
Authors: Cooper Nicola , Germeni Evi , Freeman Suzanne C , Jaiswal Nishant , Nevill Clareece R , Sutton Alex J , Taylor-Rowan Martin , Quinn Terence J 
Published: November 2023

Abstract
Evidence synthesis, embedded within a systematic review of the literature, is a well-established approach for collating and combining all the relevant information on a particular research question. A robust synthesis can establish the evidence base, which underpins best practice guidance. Such endeavours are frequently used by policymakers and practitioners to inform their decision making. Traditionally, an evidence synthesis of interventions consisted of a meta-analysis of quantitative data comparing two treatment alternatives addressing a specific and focussed clinical question. However, as the methods in the field have evolved, especially in response to the increasingly complex healthcare questions, more advanced evidence synthesis techniques have been developed. These can deal with extended data structures considering more than two treatment alternatives (network meta-analysis) and complex multicomponent interventions. The array of questions capable of being answered has also increased with specific approaches being developed for different evidence types including diagnostic, prognostic and qualitative data. Furthermore, driven by a desire for increasingly up-to-date evidence summaries, living systematic reviews have emerged. All of these methods can potentially have a role in informing older adult healthcare decisions. The aim of this review is to increase awareness and uptake of the increasingly comprehensive array of newer synthesis methods available and highlight their utility for answering clinically relevant questions in the context of older adult research, giving examples of where such techniques have already been effectively applied within the field. Their strengths and limitations are discussed, and we suggest user-friendly software options to implement the methods described.
Effects of PRRT2 mutation on brain gray matter networks in paroxysmal kinesigenic dyskinesia
Authors: Li Xiuli , Lei Du , Qin Kun , Li Lei , Zhang Yingying , Zhou Dong , Kemp Graham J , Gong Qiyong 
Published: November 2023

Abstract
Although proline-rich transmembrane protein 2 is the primary causative gene of paroxysmal kinesigenic dyskinesia, its effects on the brain structure of paroxysmal kinesigenic dyskinesia patients are not yet clear. Here, we explored the influence of proline-rich transmembrane protein 2 mutations on similarity-based gray matter morphological networks in individuals with paroxysmal kinesigenic dyskinesia. A total of 51 paroxysmal kinesigenic dyskinesia patients possessing proline-rich transmembrane protein 2 mutations, 55 paroxysmal kinesigenic dyskinesia patients possessing proline-rich transmembrane protein 2 non-mutation, and 80 healthy controls participated in the study. We analyzed the structural connectome characteristics across groups by graph theory approaches. Relative to paroxysmal kinesigenic dyskinesia patients possessing proline-rich transmembrane protein 2 non-mutation and healthy controls, paroxysmal kinesigenic dyskinesia patients possessing proline-rich transmembrane protein 2 mutations exhibited a notable increase in characteristic path length and a reduction in both global and local efficiency. Relative to healthy controls, both patient groups showed reduced nodal metrics in right postcentral gyrus, right angular, and bilateral thalamus; Relative to healthy controls and paroxysmal kinesigenic dyskinesia patients possessing proline-rich transmembrane protein 2 non-mutation, paroxysmal kinesigenic dyskinesia patients possessing proline-rich transmembrane protein 2 mutations showed almost all reduced nodal centralities and structural connections in cortico-basal ganglia-thalamo-cortical circuit including bilateral supplementary motor area, bilateral pallidum, and right caudate nucleus. Finally, we used support vector machine by gray matter network matrices to classify paroxysmal kinesigenic dyskinesia patients possessing proline-rich transmembrane protein 2 mutations and paroxysmal kinesigenic dyskinesia patients possessing proline-rich transmembrane protein 2 non-mutation, achieving an accuracy of 73%. These results show that proline-rich transmembrane protein 2 related gray matter network deficits may contribute to paroxysmal kinesigenic dyskinesia, offering new insights into its pathophysiological mechanisms.
International Institutions as Forms and Fora: Rao Geping and the Law of International Organizations in China
Authors: Chen Yifeng 
Published: November 2023

Abstract
This article examines the emergence and development in China of the discipline of international organizations law by specifically focusing on the scholarship of Professor Rao Geping, a founding figure of the discipline. Rao’s writings are read in light of his personal life and professional career as well as China’s economic and social reforms and its foreign policy. A communitarian, cooperative and legal approach to international organizations emerged as Rao’s choice. International organizations are seen mostly as fora for interstate deliberations and negotiations and are approached mainly from their procedural aspect and channelling function. What has been highlighted is a facilitative, procedural and instrumental conception of international organizations rather than an autonomous, functional or regulatory one. Rao advocates an inclusive approach to international organizations, which tends to include flexible, informal frameworks into the ambit of the study of international organizations. In constructing institutions as forms and fora, Rao’s writings effectively play a double role, translating the liberal, progressive ideas of international organizations into domestic international legal studies and facilitating China’s continuous economic reform and political integration into the international system. Rao’s scholarship presents an instructive example of how a scholar from a semi-periphery country may navigate various tensions and paradoxes behind universal concepts and negotiate their concept of international organizations.
Characterization of Cell Type Abundance and Gene Expression Timeline from Burned Skin Bulk Transcriptomics by Deconvolution
Authors: Fei Xiaoyi , Zhu Min , Li Xueling 
Published: November 2023

Abstract
Currently, no timeline of cell heterogeneity in thermally injured skin has been reported. In this study, we proposed an approach to deconvoluting cell type abundance and expression from skin bulk transcriptomics with cell type signature matrix constructed by combining independent normal skin and peripheral blood scRNA-seq datasets. Using CIBERSORTx group mode deconvolution, we identified perturbed cell type fractions and cell type-specific gene expression in three stages postthermal injury. We found an increase in cell proportions and cell type-specific gene expression perturbation of neutrophils, macrophages, and endothelial cells and a decrease in CD4+ T cells, keratinocytes, melanocyte, and fibroblast cells, and cell type-specific gene expression perturbation postburn injury. Keratinocyte, fibroblast, and macrophage up regulated genes were dynamically enriched in overlapping and distinct Gene Ontology biological processes including acute phase response, leukocyte migration, metabolic, morphogenesis, and development process. Down-regulated genes were enriched in Wnt signaling, mesenchymal cell differentiation, gland and axon development, epidermal morphogenesis, and fatty acid and glucose metabolic process. We noticed an increase in the expression of CCL7, CCL2, CCL20, CCR1, CCR5, CCXL8, CXCL2, CXCL3, MMP1, MMP8, MMP3, IL24, IL6, IL1B, IL18R1, and TGFBR1 and a decrease in expression of CCL27, CCR10, CCR6, CCR8, CXCL9, IL37, IL17, IL7, IL11R, IL17R, TGFBR3, FGFR1-4, and IGFR1 in keratinocytes and/or fibroblasts. The inferred timeline of wound healing and CC and CXC genes in keratinocyte was validated on independent dataset GSE174661 of purified keratinocytes. The timeline of different cell types postburn may facilitate therapeutic timing.
A Bayesian latent class model for integrating multi-source longitudinal data: application to the CHILD cohort study
Authors: Lu Zihang , Subbarao Padmaja , Lou Wendy 
Published: November 2023

AbstractMulti-source longitudinal data have become increasingly common. This type of data refers to longitudinal datasets collected from multiple sources describing the same set of individuals. Representing distinct features of the individuals, each data source may consist of multiple longitudinal markers of distinct types and measurement frequencies. Motivated by the CHILD cohort study, we develop a model for joint clustering multi-source longitudinal data. The proposed model allows each data source to follow source-specific clustering, and they are aggregated to yield a global clustering. The proposed model is demonstrated through real-data analysis and simulation study.
Efficient repair of human genetic defect by CRISPR/Cas9-mediated interlocus gene conversion
Authors: Yang Fei , Wang Yiyun , Wang Qiudao , Pang Jingtao , Liu Guolong , Yang Yang , Qin Shenguang , Zhang Ying , Lai Yongrong , Fu Bin , Zhu Yating , Wang Mengyao , Kurita Ryo , Nakamura Yukio , Liang Dan , Wu Yuxuan 
Published: November 2023

Abstract
DNA double-strand breaks (DSBs) induced by gene-editing tools are primarily repaired through non-homologous end joining (NHEJ) or homology-directed repair (HDR) using synthetic DNA templates. However, error-prone NHEJ may result in unexpected indels at the targeted site. For most genetic disorders, precise HDR correction using exogenous homologous sequence is ideal. But, the therapeutic application of HDR might be especially challenging given the requirement for the codelivery of exogenous DNA templates with toxicity into cells, and the low efficiency of HDR could also limit its clinical application. In this study, we efficiently repair pathogenic mutations in HBB coding regions of hematopoietic stem cells (HSCs) using CRISPR/Cas9-mediated gene conversion (CRISPR/GC) using the paralog gene HBD as the internal template. After transplantation, these edited HSCs successfully repopulate the hematopoietic system and generate erythroid cells with significantly reduced thalassemia propensity. Moreover, a range of pathogenic gene mutations causing β-thalassemia in HBB coding regions were effectively converted to normal wild-type sequences without exogenous DNA templates using CRISPR/GC. This highlights the promising potential of CRISPR/GC, independent of synthetic DNA templates, for genetic disease gene therapy.
Vesiclepedia 2024: an extracellular vesicles and extracellular particles repository
Authors: Chitti Sai V , Gummadi Sriram , Kang Taeyoung , Shahi Sanjay , Marzan Akbar L , Nedeva Christina , Sanwlani Rahul , Bramich Kyle , Stewart Sarah , Petrovska Monika , Sen Biswadeep , Ozkan Alper , Akinfenwa Maria , Fonseka Pamali , Mathivanan Suresh 
Published: November 2023

Abstract
Vesiclepedia (http://www.microvesicles.org) is a free web-based compendium of DNA, RNA, proteins, lipids and metabolites that are detected or associated with extracellular vesicles (EVs) and extracellular particles (EPs). EVs are membranous vesicles that are secreted ubiquitously by cells from all domains of life from archaea to eukaryotes. In addition to EVs, it was reported recently that EPs like exomeres and supermeres are secreted by some mammalian cells. Both EVs and EPs contain proteins, nucleic acids, lipids and metabolites and has been proposed to be implicated in several key biological functions. Vesiclepedia catalogues proteins, DNA, RNA, lipids and metabolites from both published and unpublished studies. Currently, Vesiclepedia contains data obtained from 3533 EV studies, 50 550 RNA entries, 566 911 protein entries, 3839 lipid entries, 192 metabolite and 167 DNA entries. Quantitative data for 62 822 entries from 47 EV studies is available in Vesiclepedia. The datasets available in Vesiclepedia can be downloaded as tab-delimited files or accessible through the FunRich-based Vesiclepedia plugin.
TE-TSS: an integrated data resource of human and mouse transposable element (TE)-derived transcription start site (TSS)
Authors: Gu Xiaobing , Wang Mingdong , Zhang Xiao-Ou 
Published: November 2023

Abstract
Transposable elements (TEs) are abundant in the genome and serve as crucial regulatory elements. Some TEs function as epigenetically regulated promoters, and these TE-derived transcription start sites (TSSs) play a crucial role in regulating genes associated with specific functions, such as cancer and embryogenesis. However, the lack of an accessible database that systematically gathers TE-derived TSS data is a current research gap. To address this, we established TE-TSS, an integrated data resource of human and mouse TE-derived TSSs (http://xozhanglab.com/TETSS). TE-TSS has compiled 2681 RNA sequencing datasets, spanning various tissues, cell lines and developmental stages. From these, we identified 5768 human TE-derived TSSs and 2797 mouse TE-derived TSSs, with 47% and 38% being experimentally validated, respectively. TE-TSS enables comprehensive exploration of TSS usage in diverse samples, providing insights into tissue-specific gene expression patterns and transcriptional regulatory elements. Furthermore, TE-TSS compares TE-derived TSS regions across 15 mammalian species, enhancing our understanding of their evolutionary and functional aspects. The establishment of TE-TSS facilitates further investigations into the roles of TEs in shaping the transcriptomic landscape and offers valuable resources for comprehending their involvement in diverse biological processes.
RMBase v3.0: decode the landscape, mechanisms and functions of RNA modifications
Authors: Xuan Jiajia , Chen Lifan , Chen Zhirong , Pang Junjie , Huang Junhong , Lin Jinran , Zheng Lingling , Li Bin , Qu Lianghu , Yang Jianhua 
Published: November 2023

Abstract
Although over 170 chemical modifications have been identified, their prevalence, mechanism and function remain largely unknown. To enable integrated analysis of diverse RNA modification profiles, we have developed RMBase v3.0 (http://bioinformaticsscience.cn/rmbase/), a comprehensive platform consisting of eight modules. These modules facilitate the exploration of transcriptome-wide landscape, biogenesis, interactome and functions of RNA modifications. By mining thousands of epitranscriptome datasets with novel pipelines, the ‘RNA Modifications’ module reveals the map of 73 RNA modifications of 62 species. the ‘Genes’ module allows to retrieve RNA modification profiles and clusters by gene and transcript. The ‘Mechanisms’ module explores 23 382 enzyme-catalyzed or snoRNA-guided modified sites to elucidate their biogenesis mechanisms. The ‘Co-localization’ module systematically formulates potential correlations between 14 histone modifications and 6 RNA modifications in various cell-lines. The ‘RMP’ module investigates the differential expression profiles of 146 RNA-modifying proteins (RMPs) in 18 types of cancers. The ‘Interactome’ integrates the interactional relationships between 73 RNA modifications with RBP binding events, miRNA targets and SNPs. The ‘Motif’ illuminates the enriched motifs for 11 types of RNA modifications identified from epitranscriptome datasets. The ‘Tools’ introduces a novel web-based ‘modGeneTool’ for annotating modifications. Overall, RMBase v3.0 provides various resources and tools for studying RNA modifications.