bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrative proteogenomic characterization of hepatocellular carcinoma across etiologies and stages
Authors: Ng Charlotte K. Y. , Dazert Eva , Boldanova Tuyana , Coto-Llerena Mairene , Nuciforo Sandro , Ercan Caner , Suslov Aleksei , Meier Marie-Anne , Bock Thomas , Schmidt Alexander , Ketterer Sylvia , Wang Xueya , Wieland Stefan , Matter Matthias S. , Colombi Marco , Piscuoglio Salvatore , Terracciano Luigi M. , Hall Michael N. , Heim Markus H. 
Published: May 2022

AbstractProteogenomic analyses of hepatocellular carcinomas (HCC) have focused on early-stage, HBV-associated HCCs. Here we present an integrated proteogenomic analysis of HCCs across clinical stages and etiologies. Pathways related to cell cycle, transcriptional and translational control, signaling transduction, and metabolism are dysregulated and differentially regulated on the genomic, transcriptomic, proteomic and phosphoproteomic levels. We describe candidate copy number-driven driver genes involved in epithelial-to-mesenchymal transition, the Wnt-β-catenin, AKT/mTOR and Notch pathways, cell cycle and DNA damage regulation. The targetable aurora kinase A and CDKs are upregulated.CTNNB1andTP53mutations are associated with altered protein phosphorylation related to actin filament organization and lipid metabolism, respectively. Integrative proteogenomic clusters show that HCC constitutes heterogeneous subgroups with distinct regulation of biological processes, metabolic reprogramming and kinase activation. Our study provides a comprehensive overview of the proteomic and phophoproteomic landscapes of HCCs, revealing the major pathways altered in the (phospho)proteome.
Doubly stereoconvergent construction of vicinal all-carbon quaternary and tertiary stereocenters by Cu/Mg-catalyzed propargylic substitution
Authors: Pu Xiang , Dang Qiu-Di , Yang Lei , Zhang Xia , Niu Dawen 
Published: May 2022

AbstractThe construction of vicinal, congested stereocenters with high selectivities is of general utility in chemistry. To build two such stereocenters in one step from readily available starting materials is very desirable, but remains challenging. We report here a doubly stereoconvergent, Cu/Mg-catalyzed asymmetric propargylic substitution reaction to convert simple starting materials to products with vicinal tertiary and all-carbon quaternary stereocenters in high yields and excellent diastereo- and enantioselectivities. Both the nucleophiles and the electrophiles employed in this transformation are racemic. This reaction uses earth abundant metal catalysts, operates under ambient conditions, and demonstrates broad substrate scope. The products of this reaction are functional group rich and synthetically versatile. Key to the success of this development is the devise of a Cu/Mg dual catalytic system and the identification of a bulky tridentate pyridinebisimidazoline (PyBim) ligand.
Superconducting spintronic tunnel diode
Authors: Strambini E. , Spies M. , Ligato N. , Ilić S. , Rouco M. , González-Orellana Carmen , Ilyn Maxim , Rogero Celia , Bergeret F. S. , Moodera J. S. , Virtanen P. , Heikkilä T. T. , Giazotto F. 
Published: May 2022

AbstractDiodes are key elements for electronics, optics, and detection. Their evolution towards low dissipation electronics has seen the hybridization with superconductors and the realization of supercurrent diodes with zero resistance in only one direction. Here, we present the quasi-particle counterpart, a superconducting tunnel diode with zero conductance in only one direction. The direction-selective propagation of the charge has been obtained through the broken electron-hole symmetry induced by the spin selection of the ferromagnetic tunnel barrier: a EuS thin film separating a superconducting Al and a normal metal Cu layer. The Cu/EuS/Al tunnel junction achieves a large rectification (up to ∼40%) already for a small voltage bias (∼200 μV) thanks to the small energy scale of the system: the Al superconducting gap. With the help of an analytical theoretical model we can link the maximum rectification to the spin polarization (P) of the barrier and describe the quasi-ideal Shockley-diode behavior of the junction. This cryogenic spintronic rectifier is promising for the application in highly-sensitive radiation detection for which two different configurations are evaluated. In addition, the superconducting diode may pave the way for future low-dissipation and fast superconducting electronics.
Transition from predictable to variable motor cortex and striatal ensemble patterning during behavioral exploration
Authors: Kondapavulur Sravani , Lemke Stefan M. , Darevsky David , Guo Ling , Khanna Preeya , Ganguly Karunesh 
Published: May 2022

AbstractAnimals can capitalize on invariance in the environment by learning and automating highly consistent actions; however, they must also remain flexible and adapt to environmental changes. It remains unclear how primary motor cortex (M1) can drive precise movements, yet also support behavioral exploration when faced with consistent errors. Using a reach-to-grasp task in rats, along with simultaneous electrophysiological monitoring in M1 and dorsolateral striatum (DLS), we find that behavioral exploration to overcome consistent task errors is closely associated with tandem increases in M1 and DLS neural variability; subsequently, consistent ensemble patterning returns with convergence to a new successful strategy. We also show that compared to reliably patterned intracranial microstimulation in M1, variable stimulation patterns result in significantly greater movement variability. Our results thus indicate that motor and striatal areas can flexibly transition between two modes, reliable neural pattern generation for automatic and precise movements versus variable neural patterning for behavioral exploration.
Bilayer-folded lamellar mesophase induced by random polymer sequence
Authors: Shin Minjoong , Kim Hayeon , Park Geonhyeong , Park Jongmin , Ahn Hyungju , Yoon Dong Ki , Lee Eunji , Seo Myungeun 
Published: May 2022

AbstractRandomness is perceived in two different extremes, in macroscopic homogeneity and local heterogeneity, but apparently far away from order. Here we show that a periodic order spontaneously arises from a binary random copolymer when self-assembly occurs in an ensemble containing > 1015 possible chain sequences. A Bernoullian distribution of hydrophilic and hydrophobic side chains grafted onto a linear backbone was constructed by random copolymerization. When the polymer chains associate in water, a sequence matching problem occurs because of the drastic heterogeneity in sequence: this is believed to generate local curvature mismatches which deviate from the ensemble-averaged interfacial curvature. Periodic folding of the self-assembled bilayer stabilizes the curvature instability as recurring hinges. Reminiscent of chain-folded lamellae found in polymer crystallization, this new liquid crystalline mesophase, characterized as bilayer-folded lamellae, manifests itself as an anisotropically alignable birefringent hydrogel with structural hierarchy across multiple length scales.
Identification of DAXX as a restriction factor of SARS-CoV-2 through a CRISPR/Cas9 screen
Authors: Mac Kain Alice , Maarifi Ghizlane , Aicher Sophie-Marie , Arhel Nathalie , Baidaliuk Artem , Munier Sandie , Donati Flora , Vallet Thomas , Tran Quang Dinh , Hardy Alexandra , Chazal Maxime , Porrot Françoise , OhAinle Molly , Carlson-Stevermer Jared , Oki Jennifer , Holden Kevin , Zimmer Gert , Simon-Lorière Etienne , Bruel Timothée , Schwartz Olivier , van der Werf Sylvie , Jouvenet Nolwenn , Nisole Sébastien , Vignuzzi Marco , Roesch Ferdinand 
Published: May 2022

AbstractInterferon restricts SARS-CoV-2 replication in cell culture, but only a handful of Interferon Stimulated Genes with antiviral activity against SARS-CoV-2 have been identified. Here, we describe a functional CRISPR/Cas9 screen aiming at identifying SARS-CoV-2 restriction factors. We identify DAXX, a scaffold protein residing in PML nuclear bodies known to limit the replication of DNA viruses and retroviruses, as a potent inhibitor of SARS-CoV-2 and SARS-CoV replication in human cells. Basal expression of DAXX is sufficient to limit the replication of SARS-CoV-2, and DAXX over-expression further restricts infection. DAXX restricts an early, post-entry step of the SARS-CoV-2 life cycle. DAXX-mediated restriction of SARS-CoV-2 is independent of the SUMOylation pathway but dependent on its D/E domain, also necessary for its protein-folding activity. SARS-CoV-2 infection triggers the re-localization of DAXX to cytoplasmic sites and promotes its degradation. Mechanistically, this process is mediated by the viral papain-like protease (PLpro) and the proteasome. Together, these results demonstrate that DAXX restricts SARS-CoV-2, which in turn has evolved a mechanism to counteract its action.
Catalytically efficient Ni-NiOx-Y2O3 interface for medium temperature water-gas shift reaction
Authors: Xu Kai , Ma Chao , Yan Han , Gu Hao , Wang Wei-Wei , Li Shan-Qing , Meng Qing-Lu , Shao Wei-Peng , Ding Guo-Heng , Wang Feng Ryan , Jia Chun-Jiang 
Published: May 2022

AbstractThe metal-support interfaces between metals and oxide supports have long been studied in catalytic applications, thanks to their significance in structural stability and efficient catalytic activity. The metal-rare earth oxide interface is particularly interesting because these early transition cations have high electrophilicity, and therefore good binding strength with Lewis basic molecules, such as H2O. Based on this feature, here we design a highly efficient composite Ni-Y2O3 catalyst, which forms abundant active Ni-NiOx-Y2O3 interfaces under the water-gas shift (WGS) reaction condition, achieving 140.6 μmolCO gcat−1 s−1 rate at 300 °C, which is the highest activity for Ni-based catalysts. A combination of theory and ex/in situ experimental study suggests that Y2O3 helps H2O dissociation at the Ni-NiOx-Y2O3 interfaces, promoting this rate limiting step in the WGS reaction. Construction of such new interfacial structure for molecules activation holds great promise in many catalytic systems.
Modulating Pt-O-Pt atomic clusters with isolated cobalt atoms for enhanced hydrogen evolution catalysis
Authors: Zhao Yufei , Kumar Priyank V. , Tan Xin , Lu Xinxin , Zhu Xiaofeng , Jiang Junjie , Pan Jian , Xi Shibo , Yang Hui Ying , Ma Zhipeng , Wan Tao , Chu Dewei , Jiang Wenjie , Smith Sean C. , Amal Rose , Han Zhaojun , Lu Xunyu 
Published: May 2022

AbstractPlatinum is the most efficient catalyst for hydrogen evolution reaction in acidic conditions, but its widespread use has been impeded by scarcity and high cost. Herein, Pt atomic clusters (Pt ACs) containing Pt-O-Pt units were prepared using Co/N co-doped carbon (CoNC) as support. Pt ACs are anchored to single Co atoms on CoNC by forming strong interactions. Pt-ACs/CoNC exhibits only 24 mV overpotential at 10 mA cm−2 and a high mass activity of 28.6 A mg−1 at 50 mV, which is more than 6 times higher than commercial Pt/C with any Pt loadings. Spectroscopic measurements and computational modeling reveal the enhanced hydrogen generation activity attributes to the charge redistribution between Pt and O atoms in Pt-O-Pt units, making Pt atoms the main active sites and O linkers the assistants, thus optimizing the proton adsorption and hydrogen desorption. This work opens an avenue to fabricate noble-metal-based ACs stabilized by single-atom catalysts with desired properties for electrocatalysis.
Diversity of bacterial small RNAs drives competitive strategies for a mutual chaperone
Authors: Roca Jorjethe , Santiago-Frangos Andrew , Woodson Sarah A. 
Published: May 2022

AbstractHundreds of bacterial small RNAs (sRNAs) require the Hfq chaperone to regulate mRNA expression. Hfq is limiting, thus competition among sRNAs for binding to Hfq shapes the proteomes of individual cells. To understand how sRNAs compete for a common partner, we present a single-molecule fluorescence platform to simultaneously visualize binding and release of multiple sRNAs with Hfq. We show that RNA residents rarely dissociate on their own. Instead, clashes between residents and challengers on the same face of Hfq cause rapid exchange, whereas RNAs that recognize different surfaces may cohabit Hfq for several minutes before one RNA departs. The prevalence of these pathways depends on the structure of each RNA and how it interacts with Hfq. We propose that sRNA diversity creates many pairwise interactions with Hfq that allow for distinct biological outcomes: active exchange favors fast regulation whereas co-residence of dissimilar RNAs favors target co-recognition or target exclusion.
Drivers of ecological assembly in the hindgut of Atlantic Cod fed a macroalgal supplemented diet
Authors: Keating C. , Bolton-Warberg M. , Hinchcliffe J. , Davies R. , Whelan S. , Wan A. H. L. , Fitzgerald R. D. , Davies S. J. , Smith C. J. , Ijaz U. Z. 
Published: May 2022

AbstractIt is difficult to disentangle the many variables (e.g. internal or external cues and random events) that shape the microbiota in the gastrointestinal tract of any living species. Ecological assembly processes applied to microbial communities can elucidate these drivers. In our study, farmed Atlantic cod (Gadus morhua) were fed a diet of 10% macroalgae supplement (Ulva rigida [ULVA] or Ascophyllum nodosum [ASCO] or a non-supplemented control diet [CTRL]) over 12 weeks. We determined the influence of ecological assembly processes using a suite of null-modelling tools. We observed dissimilarity in the abundance of common OTUs over time, which was driven by deterministic assembly. The CTRL samples showed selection as a critical assembly process. While dispersal limitation was a driver of the gut microbiome for fish fed the macroalgae supplemented diet at Week 12 (i.e., ASCO and ULVA). Fish from the ASCO grouping diverged into ASCO_N (normal) and ASCO_LG (lower growth), where ASCO_LG individuals found the diet unpalatable. The recruitment of new taxa overtime was altered in the ASCO_LG fish, with the gut microbiome showing phylogenetic underdispersion (nepotistic species recruitment). Finally, the gut microbiome (CTRL and ULVA) showed increasing robustness to taxonomic disturbance over time and lower functional redundancy. This study advances our understanding of the ecological assembly and succession in the hindgut of juvenile Atlantic cod across dietary treatments. Understanding the processes driving ecological assembly in the gut microbiome, in fish research specifically, could allow us to manipulate the microbiome for improved health or resilience to disease for improved aquaculture welfare and production.
Lipid exposure activates gene expression changes associated with estrogen receptor negative breast cancer
Authors: Yadav Shivangi , Virk Ranya , Chung Carolina H. , Eduardo Mariana Bustamante , VanDerway David , Chen Duojiao , Burdett Kirsten , Gao Hongyu , Zeng Zexian , Ranjan Manish , Cottone Gannon , Xuei Xiaoling , Chandrasekaran Sriram , Backman Vadim , Chatterton Robert , Khan Seema Ahsan , Clare Susan E. 
Published: May 2022

AbstractImproved understanding of local breast biology that favors the development of estrogen receptor negative (ER−) breast cancer (BC) would foster better prevention strategies. We have previously shown that overexpression of specific lipid metabolism genes is associated with the development of ER− BC. We now report results of exposure of MCF-10A and MCF-12A cells, and mammary organoids to representative medium- and long-chain polyunsaturated fatty acids. This exposure caused a dynamic and profound change in gene expression, accompanied by changes in chromatin packing density, chromatin accessibility, and histone posttranslational modifications (PTMs). We identified 38 metabolic reactions that showed significantly increased activity, including reactions related to one-carbon metabolism. Among these reactions are those that produce S-adenosyl-L-methionine for histone PTMs. Utilizing both an in-vitro model and samples from women at high risk for ER− BC, we show that lipid exposure engenders gene expression, signaling pathway activation, and histone marks associated with the development of ER− BC.
Genetic associations with learning over 100 days of practice
Authors: Youn Cherry , Grotzinger Andrew D. , Lill Christina M. , Bertram Lars , Schmiedek Florian , Lövdén Martin , Lindenberger Ulman , Nivard Michel , Harden K. Paige , Tucker-Drob Elliot M. 
Published: May 2022

AbstractCognitive performance is both heritable and sensitive to environmental inputs and sustained practice over time. However, it is currently unclear how genetic effects on cognitive performance change over the course of learning. We examine how polygenic scores (PGS) created from genome-wide association studies of educational attainment and cognitive performance are related to improvements in performance across nine cognitive tests (measuring perceptual speed, working memory, and episodic memory) administered to 131 adults (N = 51, ages = 20–31, andN = 80, ages = 65–80 years) repeatedly across 100 days. We observe that PGS associations with performance on a given task can change over the course of learning, with the specific pattern of change in associations differing across tasks. PGS correlations with pre-test to post-test scores may mask variability in how soon learning occurs over the course of practice. The associations between PGS and learning do not appear to simply reconstitute patterns of association between baseline performance and subsequent learning. Associations involving PGSs, however, were small with large confidence intervals. Intensive longitudinal research such as that described here may be of substantial value for clarifying the genetics of learning when implemented as far larger scale.
MALDI mass spectrometry imaging workflow for the aquatic model organisms Danio rerio and Daphnia magna
Authors: Schirmer Elisabeth , Ritschar Sven , Ochs Matthias , Laforsch Christian , Schuster Stefan , Römpp Andreas 
Published: May 2022

AbstractLipids play various essential roles in the physiology of animals. They are also highly dependent on cellular metabolism or status. It is therefore crucial to understand to which extent animals can stabilize their lipid composition in the presence of external stressors, such as chemicals that are released into the environment. We developed a MALDI MS imaging workflow for two important aquatic model organisms, the zebrafish (Danio rerio) and water flea (Daphnia magna). Owing to the heterogeneous structure of these organisms, developing a suitable sample preparation workflow is a highly non-trivial but crucial part of this work and needs to be established first. Relevant parameters and practical considerations in order to preserve tissue structure and composition in tissue sections are discussed for each application. All measurements were based on high mass accuracy enabling reliable identification of imaged compounds. In zebrafish we demonstrate that a detailed mapping between histology and simultaneously determined lipid composition is possible at various scales, from extended structures such as the brain or gills down to subcellular structures such as a single axon in the central nervous system. For D. magna we present for the first time a MALDI MSI workflow, that demonstrably maintains tissue integrity during cryosectioning of non-preserved samples, and allows the mapping of lipids in the entire body and the brood chamber inside the carapace. In conclusion, the lipid signatures that we were able to detect with our method provide an ideal basis to analyze changes caused by pollutants in two key aquatic model organisms.
North Asian population relationships in a global context
Authors: Kidd Kenneth K. , Evsanaa Baigalmaa , Togtokh Ariunaa , Brissenden Jane E. , Roscoe Janet M. , Dogan Mustafa , Neophytou Pavlos I. , Gurkan Cemal , Bulbul Ozlem , Cherni Lotfi , Speed William C. , Murtha Michael , Kidd Judith R. , Pakstis Andrew J. 
Published: May 2022

AbstractPopulation genetic studies of North Asian ethnic groups have focused on genetic variation of sex chromosomes and mitochondria. Studies of the extensive variation available from autosomal variation have appeared infrequently. We focus on relationships among population samples using new North Asia microhaplotype data. We combined genotypes from our laboratory on 58 microhaplotypes, distributed across 18 autosomes, on 3945 individuals from 75 populations with corresponding data extracted for 26 populations from the Thousand Genomes consortium and for 22 populations from the GenomeAsia 100 K project. A total of 7107 individuals in 122 total populations are analyzed using STRUCTURE, Principal Component Analysis, and phylogenetic tree analyses. North Asia populations sampled in Mongolia include: Buryats, Mongolians, Altai Kazakhs, and Tsaatans. Available Siberians include samples of Yakut, Khanty, and Komi Zyriane. Analyses of all 122 populations confirm many known relationships and show that most populations from North Asia form a cluster distinct from all other groups. Refinement of analyses on smaller subsets of populations reinforces the distinctiveness of North Asia and shows that the North Asia cluster identifies a region that is ancestral to Native Americans.