bluuebunny/crossref_metadata_2025_split huggingface dataset:
Iterative SuFEx approach for sequence-regulated oligosulfates and its extension to periodic copolymers
Authors: Kim Min Pyeong , Kayal Swatilekha , Hwang Chiwon , Bae Jonghoon , Kim Hyunseok , Hwang Dong Gyu , Jeon Min Ho , Seo Jeong Kon , Ahn Dowon , Lee Wonjoo , Seo Sangwon , Chun Joong-Hyun , Yu Youngchang , Hong Sung You 
Published: April 2024

AbstractThe synthesis of sequence-regulated oligosulfates has not yet been established due to the difficulties in precise reactivity control. In this work, we report an example of a multi-directional divergent iterative method to furnish oligosulfates based on a chain homologation approach, in which the fluorosulfate unit is regenerated. The oligosulfate sequences are determined by high resolution mass spectrometry of the hydrolyzed fragments, and polysulfate periodic copolymers are synthesized by using oligomeric bisfluorosulfates in a bi-directional fashion. The synthetic utility of this iterative ligation is demonstrated by preparing crosslinked network polymers as synthetic adhesive materials.
A patient-specific lung cancer assembloid model with heterogeneous tumor microenvironments
Authors: Zhang Yanmei , Hu Qifan , Pei Yuquan , Luo Hao , Wang Zixuan , Xu Xinxin , Zhang Qing , Dai Jianli , Wang Qianqian , Fan Zilian , Fang Yongcong , Ye Min , Li Binhan , Chen Mailin , Xue Qi , Zheng Qingfeng , Zhang Shulin , Huang Miao , Zhang Ting , Gu Jin , Xiong Zhuo 
Published: April 2024

AbstractCancer models play critical roles in basic cancer research and precision medicine. However, current in vitro cancer models are limited by their inability to mimic the three-dimensional architecture and heterogeneous tumor microenvironments (TME) of in vivo tumors. Here, we develop an innovative patient-specific lung cancer assembloid (LCA) model by using droplet microfluidic technology based on a microinjection strategy. This method enables precise manipulation of clinical microsamples and rapid generation of LCAs with good intra-batch consistency in size and cell composition by evenly encapsulating patient tumor-derived TME cells and lung cancer organoids inside microgels. LCAs recapitulate the inter- and intratumoral heterogeneity, TME cellular diversity, and genomic and transcriptomic landscape of their parental tumors. LCA model could reconstruct the functional heterogeneity of cancer-associated fibroblasts and reflect the influence of TME on drug responses compared to cancer organoids. Notably, LCAs accurately replicate the clinical outcomes of patients, suggesting the potential of the LCA model to predict personalized treatments. Collectively, our studies provide a valuable method for precisely fabricating cancer assembloids and a promising LCA model for cancer research and personalized medicine.
TAD boundary deletion causes PITX2-related cardiac electrical and structural defects
Authors: Baudic Manon , Murata Hiroshige , Bosada Fernanda M. , Melo Uirá Souto , Aizawa Takanori , Lindenbaum Pierre , van der Maarel Lieve E. , Guedon Amaury , Baron Estelle , Fremy Enora , Foucal Adrien , Ishikawa Taisuke , Ushinohama Hiroya , Jurgens Sean J. , Choi Seung Hoan , Kyndt Florence , Le Scouarnec Solena , Wakker Vincent , Thollet Aurélie , Rajalu Annabelle , Takaki Tadashi , Ohno Seiko , Shimizu Wataru , Horie Minoru , Kimura Takeshi , Ellinor Patrick T. , Petit Florence , Dulac Yves , Bru Paul , Boland Anne , Deleuze Jean-François , Redon Richard , Le Marec Hervé , Le Tourneau Thierry , Gourraud Jean-Baptiste , Yoshida Yoshinori , Makita Naomasa , Vieyres Claude , Makiyama Takeru , Mundlos Stephan , Christoffels Vincent M. , Probst Vincent , Schott Jean-Jacques , Barc Julien 
Published: April 2024

AbstractWhile 3D chromatin organization in topologically associating domains (TADs) and loops mediating regulatory element-promoter interactions is crucial for tissue-specific gene regulation, the extent of their involvement in human Mendelian disease is largely unknown. Here, we identify 7 families presenting a new cardiac entity associated with a heterozygous deletion of 2 CTCF binding sites on 4q25, inducing TAD fusion and chromatin conformation remodeling. The CTCF binding sites are located in a gene desert at 1 Mb from the Paired-like homeodomain transcription factor 2 gene (PITX2). By introducing the ortholog of the human deletion in the mouse genome, we recapitulate the patient phenotype and characterize an opposite dysregulation of PITX2 expression in the sinoatrial node (ectopic activation) and ventricle (reduction), respectively. Chromatin conformation assay performed in human induced pluripotent stem cell-derived cardiomyocytes harboring the minimal deletion identified in family#1 reveals a conformation remodeling and fusion of TADs. We conclude that TAD remodeling mediated by deletion of CTCF binding sites causes a new autosomal dominant Mendelian cardiac disorder.
A comprehensive dataset of protein-protein interactions and ligand binding pockets for advancing drug discovery
Authors: Moine-Franel Alexandra , Mareuil Fabien , Nilges Michael , Ciambur Constantin Bogdan , Sperandio Olivier 
Published: April 2024

AbstractThis dataset represents a collection of pocket-centric structural data related to protein-protein interactions (PPIs) and PPI-related ligand binding sites. The dataset includes high-quality structural information on more than 23,000 pockets, 3,700 proteins on more than 500 organisms, and nearly 3500 ligands that can aid researchers in the fields of bioinformatics, structural biology, and drug discovery. It encompasses a diverse set of PPI complexes with more than 1,700 unique protein families including some with associated ligands, enabling detailed investigations into molecular interactions at the atomic level. This article introduces an indispensable resource designed to unlock the full potential of PPIs while pioneering a novel metric for pocket similarity for hypothesizing protein partners repurposing.
Chromosome-level genome assembly of marine diatom Skeletonema tropicum
Authors: Liu Shuya , Chen Nansheng 
Published: April 2024

AbstractSkeletonema tropicum is a marine diatom of the genus Skeletonema that also includes many well-known species including S. marinoi. S. tropicum is a high temperature preferring species thriving in tropical ocean regions or temperate ocean regions during summer-autumn. However, mechanisms of ecological adaptation of S. tropicum remain poorly understood due partially to the lack of a high-quality whole genome assembly. Here, we report the first high-quality chromosome-scale genome assembly for S. tropicum, using cutting-edge technologies including PacBio single molecular sequencing and high-throughput chromatin conformation capture. The assembled genome has a size of 78.78 Mb with a scaffold N50 of 3.17 Mb, anchored to 23 pseudo-chromosomes. In total, 20,613 protein-coding genes were predicted, of which 17,757 (86.14%) genes were functionally annotated. Collinearity analysis of the genomes of S. tropicum and S. marinoi revealed that these two genomes were highly homologous. This chromosome-level genome assembly of S. tropicum provides a valuable genomic platform for comparative analysis of mechanisms of ecological adaption.
The complete chloroplast genome of Mussaenda pubescens and phylogenetic analysis
Authors: Zhou Caibi , Tao Fang , Long Rupiao , Yang Xiaoting , Wu Xingli , Xiang Lan , Zhou Xiaolu , Girdthai Teerayoot 
Published: April 2024

AbstractThe chloroplast (cp) genome sequence of Mussaenda pubescens, a promising resource that is used as a traditional medicine and drink, is important for understanding the phylogenetic relationships among the Mussaenda family and genetic improvement and reservation. This research represented the first comprehensive description of the morphological characteristics of M. pubescens, as well as an analysis of the complete cp genome and phylogenetic relationship. The results indicated a close relationship between M. pubescens and M. hirsutula based on the morphological characteristics of the flower and leaves. The cp was sequenced using the Illumina NovaSeq 6000 platform. The results indicated the cp genome of M. pubescens spanned a total length of 155,122 bp, including a pair of inverted repeats (IRA and IRB) with a length of 25,871 bp for each region, as well as a large single-copy (LSC) region and a small single-copy (SSC) region with lengths of 85,370 bp and 18,010 bp, respectively. The results of phylogenetic analyses demonstrated that species within the same genus displayed a tendency to group closely together. It was suggested that Antirhea, Cinchona, Mitragyna, Neolamarckia, and Uncaria might have experienced an early divergence. Furthermore, M. hirsutula showed a close genetic connection to M. pubescens, with the two species having partially overlapping distributions in China. This study presents crucial findings regarding the identification, evolution, and phylogenetic research on Mussaenda plants, specifically targeting M. pubescens.
Advanced mapping of inorganic treatments on porous carbonate stones by combined synchrotron radiation high lateral μXRPD and μXRF
Authors: Massinelli G. , Marinoni N. , Colombo C. , Gatta G. D. , Realini M. , Burghammer M. , Possenti E. 
Published: April 2024

AbstractUnderstanding the effects of consolidating inorganic mineral treatments on carbonate stones of cultural heritage, and on the nature and distribution of newly formed products within the matrix, poses a significant challenge in Heritage Science and Conservation Science. Existing analytical methods often fail to deliver spatial and compositional insights into the newly formed crystalline phases with the appropriate high lateral resolution. In this study, we explore the capabilities and limitations of synchrotron radiation (SR) micro-X-ray powder diffraction (μXRPD) mapping combined with micro-X-ray fluorescence (μXRF) to give insight into compounds formed following the application of ammonium oxalate (AmOx) and diammonium phosphate-based (DAP) solutions on porous carbonate stone. Ultimately, the integration of μXRPD mapping and μXRF analysis proved itself a powerful asset in providing precise qualitative and quantitative data on the newly formed phases, in the case of both calcium oxalates (CaOxs) and calcium phosphates (CaPs), and their complex stratigraphic distribution, thus opening a new route for applications to a more comprehensive study of inorganic treatments applied to carbonate substrates.
Testcross performance and combining ability of early-medium maturing quality protein maize inbred lines in Eastern and Southern Africa
Authors: Mebratu Addisalem , Wegary Dagne , Teklewold Adefris , Tarekegne Amsal 
Published: April 2024

AbstractLimited commercial quality protein maize (QPM) varieties with low grain yield potential are currently grown in Eastern and Southern Africa (ESA). This study was conducted to (i) assess the performance of single-cross QPM hybrids that were developed from elite inbred lines using line-by-tester mating design and (ii) estimate the general (GCA) and specific (SCA) combining ability of the QPM inbred lines for grain yield, agronomic and protein quality traits. One hundred and six testcrosses and four checks were evaluated across six environments in ESA during 2015 and 2016. Significant variations (P ≤ 0.01) were observed among environments, genotypes and genotype by environment interaction (GEI) for most traits evaluated. Hybrids H80 and H104 were the highest-yielding, most desirable, and stable QPM hybrids. Combining ability analysis showed both additive and non-additive gene effects to be important in the inheritance of grain yield. Additive effects were more important for agronomic and protein quality traits. Inbred lines L19 and L20 depicted desirable GCA effects for grain yield. Various other inbred lines with favorable GCA effects for agronomic traits, endosperm modification, and protein quality traits were identified. These inbred lines could be utilized for breeding desirable QPM cultivars. The QPM hybrids identified in this study could be commercialized after on-farm verification to replace the low-yielding QPM hybrids grown in ESA.
Coupled responses of thermomechanical waves in functionally graded viscoelastic nanobeams via thermoelastic heat conduction model including Atangana–Baleanu fractional derivative
Authors: Abouelregal Ahmed E. , Marin Marin , Foul Abdelaziz , Askar S. S. 
Published: April 2024

AbstractAccurately characterizing the thermomechanical parameters of nanoscale systems is essential for understanding their performance and building innovative nanoscale technologies due to their distinct behaviours. Fractional thermal transport models are commonly utilized to correctly depict the heat transfer that occurs in these nanoscale systems. The current study presents a novel mathematical thermoelastic model that incorporates a new fractional differential constitutive equation for heat conduction. This heat equation is useful for understanding the effects of thermal memory. An application of a fractional-time Atangana–Baleanu (AB) derivative with a local and non-singular kernel was utilized in the process of developing the mathematical model that was suggested. To deal with effects that depend on size, nonlocal constitutive relations are introduced. Furthermore, in order to take into consideration, the viscoelastic behaviour of the material at the nanoscale, the fractional Kelvin–Voigt model is utilized. The proposed model is highly effective in properly depicting the unusual thermal conductivity phenomena often found in nanoscale devices. The study also considered the mechanical deformation, temperature variations, and viscoelastic characteristics of the functionally graded (FG) nanostructured beams. The consideration was made that the material characteristics exhibit heterogeneity and continuous variation across the thickness of the beam as the nanobeam transitions from a ceramic composition in the lower region to a metallic composition in the upper region. The complicated thermomechanical features of simply supported viscoelastic nanobeams that were exposed to harmonic heat flow were determined by the application of the model that was constructed. Heterogeneity, nonlocality, and fractional operators are some of the important variables that contribute to its success, and this article provides a full study and illustration of the significance of these characteristics. The results that were obtained have the potential to play a significant role in pushing forward the design and development of tools, materials, and nanostructures that have viscoelastic mechanical characteristics and graded functions.
Synthesis, biofilm formation inhibitory, and inflammation inhibitory activities of new coumarin derivatives
Authors: Ahmed Ghada E. , Elshahid Zeinab A. , El-Sawy Eslam Reda , Abdel-Aziz Mohamed S. , Abdel-Aziem Anhar 
Published: April 2024

AbstractCoumarins are heterocycles of great interest in the development of valuable active structures in chemistry and biological domains. The ability of coumarins to inhibit biofilm formation of Gram positive bacterium (Staphylococcus aureus), Gram negative bacterium (Escherichia coli) as well as the methicillin-resistant S. aureus (MRSA) has been previously described. In the present work, new hybrid coumarin-heterocycles have been synthesized via the reaction of coumarin-6-sulfonyl chloride and 6-aminocoumarin with different small heterocycle moieties. The biological efficacy of the new compounds was evaluated towards their ability to inhibit biofilm formation and their anti-inflammatory properties. The antimicrobial activities of the newly synthesized compounds were tested against Gram positive bacterium (S. aureus ATCC 6538), Gram negative bacterium (E. coli ATCC 25922), yeast (Candida albicans ATCC 10231) and the fungus (Aspergillus niger NRRL-A326). Compounds 4d, 4e, 4f, 6a and 9 showed significant MIC and MBC values against S. aureus, E. coli, C. albicans, and methicillin-resistant S. aureus (MRSA) with especial incidence on compound 9 which surpasses all the other compounds giving MIC and MBC values of (4.88 and 9.76 µg/mL for S. aureus), (78.13 and 312.5 µg/mL for E. coli), (9.77 and 78.13 µg/mL for C. albicans), and (39.06 and 76.7 µg/mL for MRSA), respectively. With reference to the antibiofilm activity, compound 9 exhibited potent antibiofilm activity with IC50 of 60, 133.32, and 19.67 µg/mL against S. aureus, E. coli, and MRSA, (respectively) considering the reference drug (neomycin). Out of all studied compounds, the anti-inflammatory results indicated that compound 4d effectively inhibited nitric oxide production in lipopolysaccharide-(LPS-) stimulated RAW264.7 macrophage cells, giving NO% inhibition of 70% compared to Sulindac (55.2%)
Hypergraph regularized nonnegative triple decomposition for multiway data analysis
Authors: Liao Qingshui , Liu Qilong , Razak Fatimah Abdul 
Published: April 2024

AbstractTucker decomposition is widely used for image representation, data reconstruction, and machine learning tasks, but the calculation cost for updating the Tucker core is high. Bilevel form of triple decomposition (TriD) overcomes this issue by decomposing the Tucker core into three low-dimensional third-order factor tensors and plays an important role in the dimension reduction of data representation. TriD, on the other hand, is incapable of precisely encoding similarity relationships for tensor data with a complex manifold structure. To address this shortcoming, we take advantage of hypergraph learning and propose a novel hypergraph regularized nonnegative triple decomposition for multiway data analysis that employs the hypergraph to model the complex relationships among the raw data. Furthermore, we develop a multiplicative update algorithm to solve our optimization problem and theoretically prove its convergence. Finally, we perform extensive numerical tests on six real-world datasets, and the results show that our proposed algorithm outperforms some state-of-the-art methods.
Salvage prostate intensity modulated radiation therapy after cryotherapy failure
Authors: Perennec Tanguy , Rogé Maximilien , Hetet Jean-François , Colls Philippe , Guimas Valentine , Rio Emmanuel , Vaugier Loïg , Supiot Stéphane 
Published: April 2024

AbstractCryotherapy is an ablative therapy that can be used to treat localized prostate cancer. In case of recurrence, treatment options are not well-defined, and their outcomes are unknown. We therefore collected all patients treated with radiotherapy after cryotherapy for prostate cancer recurrence in Nantes (France) between 2012 and 2019. We identified ten patients. After a median follow-up of 5 years, two patients presented late grade 3 toxicities; one patient presented a grade 3 rectal hemorrhage, and one had a grade 3 hematuria. Two patients relapsed at 61 and 62 months, and three patients died of other causes. Radiotherapy to treat local prostate cancer recurrence after cryotherapy seems feasible and effective in local control. These results do not allow us to recommend this technique in current practice but are encouraging for the conduct of prospective trials.
Effects and prediction of cognitive load on encoding model of brain response to auditory and linguistic stimuli in educational multimedia
Authors: Asaadi Amir Hosein , Amiri S. Hamid , Bosaghzadeh Alireza , Ebrahimpour Reza 
Published: April 2024

AbstractMultimedia is extensively used for educational purposes. However, certain types of multimedia lack proper design, which could impose a cognitive load on the user. Therefore, it is essential to predict cognitive load and understand how it impairs brain functioning. Participants watched a version of educational multimedia that applied Mayer’s principles, followed by a version that did not. Meanwhile, their electroencephalography (EEG) was recorded. Subsequently, they participated in a post-test and completed a self-reported cognitive load questionnaire. The audio envelope and word frequency were extracted from the multimedia, and the temporal response functions (TRFs) were obtained using a linear encoding model. We observed that the behavioral data are different between the two groups and the TRFs of the two multimedia versions were different. We saw changes in the amplitude and latencies of both early and late components. In addition, correlations were found between behavioral data and the amplitude and latencies of TRF components. Cognitive load decreased participants’ attention to the multimedia, and semantic processing of words also occurred with a delay and smaller amplitude. Hence, encoding models provide insights into the temporal and spatial mapping of the cognitive load activity, which could help us detect and reduce cognitive load in potential environments such as educational multimedia or simulators for different purposes.
DeepReg: a deep learning hybrid model for predicting transcription factors in eukaryotic and prokaryotic genomes
Authors: Ledesma-Dominguez Leonardo , Carbajal-Degante Erik , Moreno-Hagelsieb Gabriel , Pérez-Rueda Ernesto 
Published: April 2024

AbstractDeep learning models (DLMs) have gained importance in predicting, detecting, translating, and classifying a diversity of inputs. In bioinformatics, DLMs have been used to predict protein structures, transcription factor-binding sites, and promoters. In this work, we propose a hybrid model to identify transcription factors (TFs) among prokaryotic and eukaryotic protein sequences, named Deep Regulation (DeepReg) model. Two architectures were used in the DL model: a convolutional neural network (CNN), and a bidirectional long-short-term memory (BiLSTM). DeepReg reached a precision of 0.99, a recall of 0.97, and an F1-score of 0.98. The quality of our predictions, the bias-variance trade-off approach, and the characterization of new TF predictions were evaluated and compared against those produced by DeepTFactor, as well as against experimental data from three model organisms. Predictions based on our DLM tended to exhibit less variance and bias than those from DeepTFactor, thus increasing reliability and decreasing overfitting.
From sensor fusion to knowledge distillation in collaborative LIBS and hyperspectral imaging for mineral identification
Authors: Lopes Tomás , Capela Diana , Guimarães Diana , Ferreira Miguel F. S. , Jorge Pedro A. S. , Silva Nuno A. 
Published: April 2024

AbstractMultimodal spectral imaging offers a unique approach to the enhancement of the analytical capabilities of standalone spectroscopy techniques by combining information gathered from distinct sources. In this manuscript, we explore such opportunities by focusing on two well-known spectral imaging techniques, namely laser-induced breakdown spectroscopy, and hyperspectral imaging, and explore the opportunities of collaborative sensing for a case study involving mineral identification. In specific, the work builds upon two distinct approaches: a traditional sensor fusion, where we strive to increase the information gathered by including information from the two modalities; and a knowledge distillation approach, where the Laser Induced Breakdown spectroscopy is used as an autonomous supervisor for hyperspectral imaging. Our results show the potential of both approaches in enhancing the performance over a single modality sensing system, highlighting, in particular, the advantages of the knowledge distillation framework in maximizing the potential benefits of using multiple techniques to build more interpretable models and paving for industrial applications.