bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long-read powered viral metagenomics in the oligotrophic Sargasso Sea
Authors: Warwick-Dugdale Joanna , Tian Funing , Michelsen Michelle L. , Cronin Dylan R. , Moore Karen , Farbos Audrey , Chittick Lauren , Bell Ashley , Zayed Ahmed A. , Buchholz Holger H. , Bolanos Luis M. , Parsons Rachel J. , Allen Michael J. , Sullivan Matthew B. , Temperton Ben 
Published: May 2024

AbstractDominant microorganisms of the Sargasso Sea are key drivers of the global carbon cycle. However, associated viruses that shape microbial community structure and function are not well characterised. Here, we combined short and long read sequencing to survey Sargasso Sea phage communities in virus- and cellular fractions at viral maximum (80 m) and mesopelagic (200 m) depths. We identified 2,301 Sargasso Sea phage populations from 186 genera. Over half of the phage populations identified here lacked representation in global ocean viral metagenomes, whilst 177 of the 186 identified genera lacked representation in genomic databases of phage isolates. Viral fraction and cell-associated viral communities were decoupled, indicating viral turnover occurred across periods longer than the sampling period of three days. Inclusion of long-read data was critical for capturing the breadth of viral diversity. Phage isolates that infect the dominant bacterial taxa Prochlorococcus and Pelagibacter, usually regarded as cosmopolitan and abundant, were poorly represented.
Tracking nuclear motion in single-molecule magnets using femtosecond X-ray absorption spectroscopy
Authors: Barlow Kyle , Phelps Ryan , Eng Julien , Katayama Tetsuo , Sutcliffe Erica , Coletta Marco , Brechin Euan K. , Penfold Thomas J. , Johansson J. Olof 
Published: May 2024

AbstractThe development of new data storage solutions is crucial for emerging digital technologies. Recently, all-optical magnetic switching has been achieved in dielectrics, proving to be faster than traditional methods. Despite this, single-molecule magnets (SMMs), which are an important class of magnetic materials due to their nanometre size, remain underexplored for ultrafast photomagnetic switching. Herein, we report femtosecond time-resolved K-edge X-ray absorption spectroscopy (TR-XAS) on a Mn(III)-based trinuclear SMM. Exploiting the elemental specificity of XAS, we directly track nuclear dynamics around the metal ions and show that the ultrafast dynamics upon excitation of a crystal-field transition are dominated by a magnetically active Jahn-Teller mode. Our results, supported by simulations, reveal minute bond length changes from 0.01 to 0.05 Å demonstrating the sensitivity of the method. These geometrical changes are discussed in terms of magneto-structural relationships and consequently our results illustrate the importance of TR-XAS for the emerging area of ultrafast molecular magnetism.
Transfer learning enables identification of multiple types of RNA modifications using nanopore direct RNA sequencing
Authors: Wu You , Shao Wenna , Yan Mengxiao , Wang Yuqin , Xu Pengfei , Huang Guoqiang , Li Xiaofei , Gregory Brian D. , Yang Jun , Wang Hongxia , Yu Xiang 
Published: May 2024

AbstractNanopore direct RNA sequencing (DRS) has emerged as a powerful tool for RNA modification identification. However, concurrently detecting multiple types of modifications in a single DRS sample remains a challenge. Here, we develop TandemMod, a transferable deep learning framework capable of detecting multiple types of RNA modifications in single DRS data. To train high-performance TandemMod models, we generate in vitro epitranscriptome datasets from cDNA libraries, containing thousands of transcripts labeled with various types of RNA modifications. We validate the performance of TandemMod on both in vitro transcripts and in vivo human cell lines, confirming its high accuracy for profiling m6A and m5C modification sites. Furthermore, we perform transfer learning for identifying other modifications such as m7G, Ψ, and inosine, significantly reducing training data size and running time without compromising performance. Finally, we apply TandemMod to identify 3 types of RNA modifications in rice grown in different environments, demonstrating its applicability across species and conditions. In summary, we provide a resource with ground-truth labels that can serve as benchmark datasets for nanopore-based modification identification methods, and TandemMod for identifying diverse RNA modifications using a single DRS sample.
Three-dimensional liquid metal-based neuro-interfaces for human hippocampal organoids
Authors: Wu Yan , Cheng Jinhao , Qi Jie , Hang Chen , Dong Ruihua , Low Boon Chuan , Yu Hanry , Jiang Xingyu 
Published: May 2024

AbstractHuman hippocampal organoids (hHOs) derived from human induced pluripotent stem cells (hiPSCs) have emerged as promising models for investigating neurodegenerative disorders, such as schizophrenia and Alzheimer’s disease. However, obtaining the electrical information of these free-floating organoids in a noninvasive manner remains a challenge using commercial multi-electrode arrays (MEAs). The three-dimensional (3D) MEAs developed recently acquired only a few neural signals due to limited channel numbers. Here, we report a hippocampal cyborg organoid (cyb-organoid) platform coupling a liquid metal-polymer conductor (MPC)-based mesh neuro-interface with hHOs. The mesh MPC (mMPC) integrates 128-channel multielectrode arrays distributed on a small surface area (~2*2 mm). Stretchability (up to 500%) and flexibility of the mMPC enable its attachment to hHOs. Furthermore, we show that under Wnt3a and SHH activator induction, hHOs produce HOPX+ and PAX6+ progenitors and ZBTB20+PROX1+ dentate gyrus (DG) granule neurons. The transcriptomic signatures of hHOs reveal high similarity to the developing human hippocampus. We successfully detect neural activities from hHOs via the mMPC from this cyb-organoid. Compared with traditional planar devices, our non-invasive coupling offers an adaptor for recording neural signals from 3D models.
Children exhibit superior memory for attended but outdated information compared to adults
Authors: Fu Yingtao , Guo Tingyu , Zheng Jiewei , He Jie , Shen Mowei , Chen Hui 
Published: May 2024

AbstractResearch on the development of cognitive selectivity predominantly focuses on attentional selection. The present study explores another facet of cognitive selectivity—memory selection—by examining the ability to filter attended yet outdated information in young children and adults. Across five experiments involving 130 children and 130 adults, participants are instructed to use specific information to complete a task, and then unexpectedly asked to report this information in a surprise test. The results consistently demonstrate a developmental reversal-like phenomenon, with children outperforming adults in reporting this kind of attended yet outdated information. Furthermore, we provide evidence against the idea that the results are due to different processing strategies or attentional deployments between adults and children. These results suggest that the ability of memory selection is not fully developed in young children, resulting in their inefficient filtering of attended yet outdated information that is not required for memory retention.
Regulation of cerebral blood flow boosts precise brain targeting of vinpocetine-derived ionizable-lipidoid nanoparticles
Authors: Bian Xufei , Yang Ling , Jiang Dingxi , Grippin Adam J. , Ma Yifan , Wu Shuang , Wu Linchong , Wang Xiaoyou , Tang Zhongjie , Tang Kaicheng , Pan Weidong , Dong Shiyan , Kim Betty Y. S. , Jiang Wen , Yang Zhaogang , Li Chong 
Published: May 2024

AbstractDespite advances in active drug targeting for blood-brain barrier penetration, two key challenges persist: first, attachment of a targeting ligand to the drug or drug carrier does not enhance its brain biodistribution; and second, many brain diseases are intricately linked to microcirculation disorders that significantly impede drug accumulation within brain lesions even after they cross the barrier. Inspired by the neuroprotective properties of vinpocetine, which regulates cerebral blood flow, we propose a molecular library design centered on this class of cyclic tertiary amine compounds and develop a self-enhanced brain-targeted nucleic acid delivery system. Our findings reveal that: (i) vinpocetine-derived ionizable-lipidoid nanoparticles efficiently breach the blood-brain barrier; (ii) they have high gene-loading capacity, facilitating endosomal escape and intracellular transport; (iii) their administration is safe with minimal immunogenicity even with prolonged use; and (iv) they have potent pharmacologic brain-protective activity and may synergize with treatments for brain disorders as demonstrated in male APP/PS1 mice.
Structural basis of human NOX5 activation
Authors: Cui Chenxi , Jiang Meiqin , Jain Nikhil , Das Sourav , Lo Yu-Hua , Kermani Ali A. , Pipatpolkai Tanadet , Sun Ji 
Published: May 2024

AbstractNADPH oxidase 5 (NOX5) catalyzes the production of superoxide free radicals and regulates physiological processes from sperm motility to cardiac rhythm. Overexpression of NOX5 leads to cancers, diabetes, and cardiovascular diseases. NOX5 is activated by intracellular calcium signaling, but the underlying molecular mechanism of which — in particular, how calcium triggers electron transfer from NADPH to FAD — is still unclear. Here we capture motions of full-length human NOX5 upon calcium binding using single-particle cryogenic electron microscopy (cryo-EM). By combining biochemistry, mutagenesis analyses, and molecular dynamics (MD) simulations, we decode the molecular basis of NOX5 activation and electron transfer. We find that calcium binding to the EF-hand domain increases NADPH dynamics, permitting electron transfer between NADPH and FAD and superoxide production. Our structural findings also uncover a zinc-binding motif that is important for NOX5 stability and enzymatic activity, revealing modulation mechanisms of reactive oxygen species (ROS) production.
Chemical manipulation of an activation/inhibition switch in the nuclear receptor PXR
Authors: Garcia-Maldonado Efren , Huber Andrew D. , Chai Sergio C. , Nithianantham Stanley , Li Yongtao , Wu Jing , Poudel Shyaron , Miller Darcie J. , Seetharaman Jayaraman , Chen Taosheng 
Published: May 2024

AbstractNuclear receptors are ligand-activated transcription factors that can often be useful drug targets. Unfortunately, ligand promiscuity leads to two-thirds of receptors remaining clinically untargeted. PXR is a nuclear receptor that can be activated by diverse compounds to elevate metabolism, negatively impacting drug efficacy and safety. This presents a barrier to drug development because compounds designed to target other proteins must avoid PXR activation while retaining potency for the desired target. This problem could be avoided by using PXR antagonists, but these compounds are rare, and their molecular mechanisms remain unknown. Here, we report structurally related PXR-selective agonists and antagonists and their corresponding co-crystal structures to describe mechanisms of antagonism and selectivity. Structural and computational approaches show that antagonists induce PXR conformational changes incompatible with transcriptional coactivator recruitment. These results guide the design of compounds with predictable agonist/antagonist activities and bolster efforts to generate antagonists to prevent PXR activation interfering with other drugs.
Enabling nucleophilic reactivity in molecular calcium fluoride complexes
Authors: Struijs Job J. C. , Ellwanger Mathias A. , Crumpton Agamemnon E. , Gouverneur Véronique , Aldridge Simon 
Published: May 2024

AbstractCalcium fluoride is the ultimate source of all fluorochemicals. Current synthetic approaches rely on the use of HF, generated from naturally occurring fluorspar and sulfuric acid. Methods for constructing E–F bonds directly from CaF2 have long been frustrated by its high lattice energy, low solubility and impaired fluoride ion nucleophilicity. Little fundamental understanding of the reactivity of Ca–F moieties is available to guide methodology development; well-defined molecular species containing Ca–F bonds are extremely rare, and existing examples are strongly aggregated and evidence no nucleophilic fluoride delivery. Here, by contrast, we show that by targeting anionic systems of the type [Ln(X)2CaF]−, monomeric calcium fluoride complexes containing single Ca–F bonds can be synthesized, including via routes involving fluoride abstraction from existing C–F bonds. Comparative structural and spectroscopic studies of mono- and dinuclear systems allow us to define structure–activity relationships for E–F bond formation from molecular calcium fluorides.
A lithium–aluminium heterobimetallic dimetallocene
Authors: Bischoff Inga-Alexandra , Danés Sergi , Thoni Philipp , Morgenstern Bernd , Andrada Diego M. , Müller Carsten , Lambert Jessica , Gießelmann Elias C. J. , Zimmer Michael , Schäfer André 
Published: May 2024

AbstractHomobimetallic dimetallocenes exhibiting two identical metal atoms sandwiched between two η5 bonded cyclopentadienyl rings is a narrow class of compounds, with representative examples being dizincocene and diberyllocene. Here we report the synthesis and structural characterization of a heterobimetallic dimetallocene, accessible through heterocoupling of lithium and aluminylene fragments with pentaisopropylcyclopentadienyl ligands. The Al–Li bond features a high ionic character and profits from attractive dispersion interactions between the isopropyl groups of the cyclopentadienyl ligands. A key synthetic step is the isolation of a cyclopentadienylaluminylene monomer, which also enables the structural characterization of this species. In addition to their structural authentication by single-crystal X-ray diffraction analysis, both compounds were characterized by multinuclear NMR spectroscopy in solution and in the solid state. Furthermore, reactivity studies of the lithium–aluminium heterobimetallic dimetallocene with an N-heterocyclic carbene and different heteroallenes were performed and show that the Al–Li bond is easily cleaved.
Parsimonious estimation of hourly surface ozone concentration across China during 2015–2020
Authors: Zhang Wenxiu , Liu Di , Tian Hanqin , Pan Naiqin , Yang Ruqi , Tang Wenhan , Yang Jia , Lu Fei , Dayananda Buddhi , Mei Han , Wang Siyuan , Shi Hao 
Published: May 2024

AbstractSurface ozone is an important air pollutant detrimental to human health and vegetation productivity, particularly in China. However, high resolution surface ozone concentration data is still lacking, largely hindering accurate assessment of associated environmental impacts. Here, we collected hourly ground ozone observations (over 6 million records), remote sensing products, meteorological data, and social-economic information, and applied recurrent neural networks to map hourly surface ozone data (HrSOD) at a 0.1° × 0.1° resolution across China during 2015–2020. The coefficient of determination (R2) values in sample-based, site-based, and by-year cross-validations were 0.72, 0.65 and 0.71, respectively, with the root mean square error (RMSE) values being 11.71 ppb (mean = 30.89 ppb), 12.81 ppb (mean = 30.96 ppb) and 11.14 ppb (mean = 31.26 ppb). Moreover, it exhibits high spatiotemporal consistency with ground-level observations at different time scales (diurnal, seasonal, annual), and at various spatial levels (individual sites and regional scales). Meanwhile, the HrSOD provides critical information for fine-resolution assessment of surface ozone impacts on environmental and human benefits.
Confined bioprinting and culture in inflatable bioreactor for the sterile bioproduction of tissues and organs
Authors: Dufour Alexandre , Essayan Lucie , Thomann Céline , Petiot Emma , Gay Isabelle , Barbaroux Magali , Marquette Christophe 
Published: May 2024

AbstractThe future of organ and tissue biofabrication strongly relies on 3D bioprinting technologies. However, maintaining sterility remains a critical issue regardless of the technology used. This challenge becomes even more pronounced when the volume of bioprinted objects approaches organ dimensions. Here, we introduce a novel device called the Flexible Unique Generator Unit (FUGU), which is a unique combination of flexible silicone membranes and solid components made of stainless steel. Alternatively, the solid components can also be made of 3D printed medical-grade polycarbonate. The FUGU is designed to support micro-extrusion needle insertion and removal, internal volume adjustment, and fluid management. The FUGU was assessed in various environments, ranging from custom-built basic cartesian to sophisticated 6-axis robotic arm bioprinters, demonstrating its compatibility, flexibility, and universality across different bioprinting platforms. Sterility assays conducted under various infection scenarios highlight the FUGU’s ability to physically protect the internal volume against contaminations, thereby ensuring the integrity of the bioprinted constructs. The FUGU also enabled bioprinting and cultivation of a 14.5 cm3 human colorectal cancer tissue model within a completely confined and sterile environment, while allowing for the exchange of gases with the external environment. This FUGU system represents a significant advancement in 3D bioprinting and biofabrication, paving the path toward the sterile production of implantable tissues and organs.
Hematological and renal toxicity in mice after three cycles of high activity [177Lu]Lu-PSMA-617 with or without human α1-microglobulin
Authors: Kristiansson Amanda , Vilhelmsson Timmermand Oskar , Altai Mohamed , Strand Sven-Erik , Åkerström Bo , Örbom Anders 
Published: May 2024

AbstractRadioligand therapy with [177Lu]Lu-PSMA-617 can be used to prolong life and reduce tumor burden in terminally ill castration resistant prostate cancer patients. Still, accumulation in healthy tissue limits the activity that can be administered. Therefore, fractionated therapy is used to lower toxicity. However, there might be a need to reduce toxicity even further with e.g. radioprotectors. The aim of this study was to (i). establish a preclinical mouse model with fractionated high activity therapy of three consecutive doses of 200 MBq [177Lu]Lu-PSMA-617 in which we aimed to (ii). achieve measurable hematotoxicity and nephrotoxicity and to (iii). analyze the potential protective effect of co-injecting recombinant α1-microglobulin (rA1M), a human antioxidant previously shown to have radioprotective effects. In both groups, three cycles resulted in increased albuminuria for each cycle, with large individual variation. Another marker of kidney injury, serum blood urea nitrogen (BUN), was only significantly increased compared to control animals after the third cycle. The number of white and red blood cells decreased significantly and did not reach the levels of control animals during the experiment. rA1M did reduce absorbed dose to kidney but did not show significant protection here, but future studies are warranted due to the recent clinical studies showing a significant renoprotective effect in patients.
Unveiling the influence of global innovation networks on corporate innovation: evidence from the international semiconductor industry
Authors: Wu Yingna , Ding Liang , Li Na , Yu Xin 
Published: May 2024

AbstractIn this study, we investigate the influence of global innovation networks (GINs) on the innovation output of semiconductor firms. Utilizing negative binomial regression and network analysis, we assess how network positions, specifically degree, betweenness, and closeness centrality, affect firms’ innovation performance, revealing significant positive impacts. Moreover, our results identify a positive U-shaped relationship between structural holes in GINs and innovation performance, suggesting that while moderate network engagement aids innovation, too much can be detrimental. This research provides key insights into optimizing GIN participation for better innovation results in the competitive semiconductor sector.
Deciphering genetic diversity in conserved cattle bulls to achieve sustainable development goals
Authors: Kumar Amod , Aggarwal Rajeev Anand Kumar , Tantia M. S. 
Published: May 2024

AbstractThe primary objective of Sustainable Development Goal target 2.5 established by the United Nations is to ensure the preservation of genetic diversity in domesticated animals. The ICAR-National Bureau of Animal Genetic Resources in India has been actively engaged in the conservation of cattle and buffalo bull semen for long-term storage. This present study aimed to assess the genetic diversity present in the conserved cattle bull semen, which would aid in determining the most suitable strategy for future conservation management. A total of 192 bull semen belonging to 19 cattle breeds were selected to evaluate genetic diversity using 17 pairs of FAO recommended microsatellite primers. Total 267 alleles were detected across all the samples which indicates substantial amount of allelic variation is being maintained in conserved bulls. Further, all cattle bulls semen conserved showed higher observed heterozygosity than expected heterozygosity which indicates excess genetic diversity in all the populations. The FST, FITand FISvalue across the loci and population is 0.146 ± 0.009, 0.054 ± 0.038, and − 0.105 ± 0.035, respectively, which suggests lack of inbreeding in conserved cattle bull semen. This study has established genetic diversity in conserved cattle semen samples to achieve sustainable development goals. In addition, it provides compelling evidence that the current approach for conserving cattle bull semen is heading in the correct direction.
Assessing the distribution of cancer stem cells in tumorspheres
Authors: Fotinós Jerónimo , Marks María Paula , Barberis Lucas , Vellón Luciano 
Published: May 2024

AbstractCancer Stem Cells presumably drive tumor growth and resistance to conventional cancer treatments. From a previous computational model, we inferred that these cells are not uniformly distributed in the bulk of a tumorsphere. To confirm this result, we cultivated tumorspheres enriched in stem cells, and performed immunofluorescent detection of the stemness marker SOX2 using confocal microscopy. In this article, we present an image processing method that reconstructs the amount and location of the Cancer Stem Cells in the spheroids. Its advantage is the use of a statistical criterion to classify the cells in Stem and Differentiated, instead of setting an arbitrary threshold. Moreover, the analysis of the experimental images presented in this work agrees with the results from our computational models, thus enforcing the notion that the distribution of Cancer Stem Cells in a tumorsphere is non-homogeneous. Additionally, the method presented here provides a useful tool for analyzing any image in which different kinds of cells are stained with different markers.