bluuebunny/crossref_metadata_2025_split huggingface dataset:
The proteomic landscape of soft tissue sarcomas
Authors: Burns Jessica , Wilding Christopher P. , Krasny Lukas , Zhu Xixuan , Chadha Madhumeeta , Tam Yuen Bun , PS Hari , Mahalingam Aswanth H. , Lee Alexander T. J. , Arthur Amani , Guljar Nafia , Perkins Emma , Pankova Valeriya , Jenks Andrew , Djabatey Vanessa , Szecsei Cornelia , McCarthy Frank , Ragulan Chanthirika , Milighetti Martina , Roumeliotis Theodoros I. , Crosier Stephen , Finetti Martina , Choudhary Jyoti S. , Judson Ian , Fisher Cyril , Schuster Eugene F. , Sadanandam Anguraj , Chen Tom W. , Williamson Daniel , Thway Khin , Jones Robin L. , Cheang Maggie C. U. , Huang Paul H. 
Published: June 2023

AbstractSoft tissue sarcomas (STS) are rare and diverse mesenchymal cancers with limited treatment options. Here we undertake comprehensive proteomic profiling of tumour specimens from 321 STS patients representing 11 histological subtypes. Within leiomyosarcomas, we identify three proteomic subtypes with distinct myogenesis and immune features, anatomical site distribution and survival outcomes. Characterisation of undifferentiated pleomorphic sarcomas and dedifferentiated liposarcomas with low infiltrating CD3 + T-lymphocyte levels nominates the complement cascade as a candidate immunotherapeutic target. Comparative analysis of proteomic and transcriptomic profiles highlights the proteomic-specific features for optimal risk stratification in angiosarcomas. Finally, we define functional signatures termed Sarcoma Proteomic Modules which transcend histological subtype classification and show that a vesicle transport protein signature is an independent prognostic factor for distant metastasis. Our study highlights the utility of proteomics for identifying molecular subgroups with implications for risk stratification and therapy selection and provides a rich resource for future sarcoma research.
Learning in a sensory cortical microstimulation task is associated with elevated representational stability
Authors: Pancholi Ravi , Ryan Lauren , Peron Simon 
Published: June 2023

AbstractSensory cortical representations can be highly dynamic, raising the question of how representational stability impacts learning. We train mice to discriminate the number of photostimulation pulses delivered to opsin-expressing pyramidal neurons in layer 2/3 of primary vibrissal somatosensory cortex. We simultaneously track evoked neural activity across learning using volumetric two-photon calcium imaging. In well-trained animals, trial-to-trial fluctuations in the amount of photostimulus-evoked activity predicted animal choice. Population activity levels declined rapidly across training, with the most active neurons showing the largest declines in responsiveness. Mice learned at varied rates, with some failing to learn the task in the time provided. The photoresponsive population showed greater instability both within and across behavioral sessions among animals that failed to learn. Animals that failed to learn also exhibited a faster deterioration in stimulus decoding. Thus, greater stability in the stimulus response is associated with learning in a sensory cortical microstimulation task.
Sequence variants affecting the genome-wide rate of germline microsatellite mutations
Authors: Kristmundsdottir Snaedis , Jonsson Hakon , Hardarson Marteinn T. , Palsson Gunnar , Beyter Doruk , Eggertsson Hannes P. , Gylfason Arnaldur , Sveinbjornsson Gardar , Holley Guillaume , Stefansson Olafur A. , Halldorsson Gisli H. , Olafsson Sigurgeir , Arnadottir Gudny. A. , Olason Pall I. , Eiriksson Ogmundur , Masson Gisli , Thorsteinsdottir Unnur , Rafnar Thorunn , Sulem Patrick , Helgason Agnar , Gudbjartsson Daniel F. , Halldorsson Bjarni V. , Stefansson Kari 
Published: June 2023

AbstractMicrosatellites are polymorphic tracts of short tandem repeats with one to six base-pair (bp) motifs and are some of the most polymorphic variants in the genome. Using 6084 Icelandic parent-offspring trios we estimate 63.7 (95% CI: 61.9–65.4) microsatellite de novo mutations (mDNMs) per offspring per generation, excluding one bp repeats motifs (homopolymers) the estimate is 48.2 mDNMs (95% CI: 46.7–49.6). Paternal mDNMs occur at longer repeats than maternal ones, which are in turn larger with a mean size of 3.4 bp vs 3.1 bp for paternal ones. mDNMs increase by 0.97 (95% CI: 0.90–1.04) and 0.31 (95% CI: 0.25–0.37) per year of father’s and mother’s age at conception, respectively. Here, we find two independent coding variants that associate with the number of mDNMs transmitted to offspring; The minor allele of a missense variant (allele frequency (AF) = 1.9%) in MSH2, a mismatch repair gene, increases transmitted mDNMs from both parents (effect: 13.1 paternal and 7.8 maternal mDNMs). A synonymous variant (AF = 20.3%) in NEIL2, a DNA damage repair gene, increases paternally transmitted mDNMs (effect: 4.4 mDNMs). Thus, the microsatellite mutation rate in humans is in part under genetic control.
Single cell Hi-C identifies plastic chromosome conformations underlying the gastrulation enhancer landscape
Authors: Rappoport Nimrod , Chomsky Elad , Nagano Takashi , Seibert Charlie , Lubling Yaniv , Baran Yael , Lifshitz Aviezer , Leung Wing , Mukamel Zohar , Shamir Ron , Fraser Peter , Tanay Amos 
Published: June 2023

AbstractEmbryonic development involves massive proliferation and differentiation of cell lineages. This must be supported by chromosome replication and epigenetic reprogramming, but how proliferation and cell fate acquisition are balanced in this process is not well understood. Here we use single cell Hi-C to map chromosomal conformations in post-gastrulation mouse embryo cells and study their distributions and correlations with matching embryonic transcriptional atlases. We find that embryonic chromosomes show a remarkably strong cell cycle signature. Despite that, replication timing, chromosome compartment structure, topological associated domains (TADs) and promoter-enhancer contacts are shown to be variable between distinct epigenetic states. About 10% of the nuclei are identified as primitive erythrocytes, showing exceptionally compact and organized compartment structure. The remaining cells are broadly associated with ectoderm and mesoderm identities, showing only mild differentiation of TADs and compartment structures, but more specific localized contacts in hundreds of ectoderm and mesoderm promoter-enhancer pairs. The data suggest that while fully committed embryonic lineages can rapidly acquire specific chromosomal conformations, most embryonic cells are showing plastic signatures driven by complex and intermixed enhancer landscapes.
Lattice oxygen-mediated electron tuning promotes electrochemical hydrogenation of acetonitrile on copper catalysts
Authors: Wei Cong , Fang Yanyan , Liu Bo , Tang Chongyang , Dong Bin , Yin Xuanwei , Bian Zenan , Wang Zhandong , Liu Jun , Qian Yitai , Wang Gongming 
Published: June 2023

AbstractCopper is well-known to be selective to primary amines via electrocatalytic nitriles hydrogenation. However, the correlation between the local fine structure and catalytic selectivity is still illusive. Herein, we find that residual lattice oxygen in oxide-derived Cu nanowires (OD-Cu NWs) plays vital roles in boosting the acetonitrile electroreduction efficiency. Especially at high current densities of more than 1.0 A cm−2, OD-Cu NWs exhibit relatively high Faradic efficiency. Meanwhile, a series of advanced in situ characterizations and theoretical calculations uncover that oxygen residues, in the form of Cu4-O configuration, act as electron acceptors to confine the free electron flow on the Cu surface, consequently improving the kinetics of nitriles hydrogenation catalysis. This work could provide new opportunities to further improve the hydrogenation performance of nitriles and beyond, by employing lattice oxygen-mediated electron tuning engineering.
Inhibition of chitin deacetylases to attenuate plant fungal diseases
Authors: Liu Lin , Xia Yeqiang , Li Yingchen , Zhou Yong , Su Xiaofeng , Yan Xiaojing , Wang Yan , Liu Wende , Cheng Hongmei , Wang Yuanchao , Yang Qing 
Published: June 2023

AbstractPhytopathogenic fungi secrete chitin deacetylase (CDA) to escape the host’s immunological defense during infection. Here, we showed that the deacetylation activity of CDA toward chitin is essential for fungal virulence. Five crystal structures of two representative and phylogenetically distant phytopathogenic fungal CDAs, VdPDA1 from Verticillium dahliae and Pst_13661 from Puccinia striiformis f. sp. tritici, were obtained in ligand-free and inhibitor-bound forms. These structures suggested that both CDAs have an identical substrate-binding pocket and an Asp-His-His triad for coordinating a transition metal ion. Based on the structural identities, four compounds with a benzohydroxamic acid (BHA) moiety were obtained as phytopathogenic fungal CDA inhibitors. BHA exhibited high effectiveness in attenuating fungal diseases in wheat, soybean, and cotton. Our findings revealed that phytopathogenic fungal CDAs share common structural features, and provided BHA as a lead compound for the design of CDA inhibitors aimed at attenuating crop fungal diseases.
The intersection of the retrieval state and internal attention
Authors: Long Nicole M. 
Published: June 2023

AbstractLarge-scale brain states or distributed patterns of brain activity modulate downstream processing and behavior. Sustained attention and memory retrieval states impact subsequent memory, yet how these states relate to one another is unclear. I hypothesize that internal attention is a central process of the retrieval state. The alternative is that the retrieval state specifically reflects a controlled, episodic retrieval mode, engaged only when intentionally accessing events situated within a spatiotemporal context. To test my hypothesis, I developed a mnemonic state classifier independently trained to measure retrieval state evidence and applied this classifier to a spatial attention task. I find that retrieval state evidence increases during delay and response intervals when participants are maintaining spatial information. Critically, retrieval state evidence is positively related to the amount of maintained spatial location information and predicts target detection reaction times. Together, these findings support the hypothesis that internal attention is a central process of the retrieval state.
The mRNA methyltransferase Mettl3 modulates cytokine mRNA stability and limits functional responses in mast cells
Authors: Leoni Cristina , Bataclan Marian , Ito-Kureha Taku , Heissmeyer Vigo , Monticelli Silvia 
Published: June 2023

AbstractMast cells are central players in allergy and asthma, and their dysregulated responses lead to reduced quality of life and life-threatening conditions such as anaphylaxis. The RNA modification N6-methyladenosine (m6A) has a prominent impact on immune cell functions, but its role in mast cells remains unexplored. Here, by optimizing tools to genetically manipulate primary mast cells, we reveal that the m6A mRNA methyltransferase complex modulates mast cell proliferation and survival. Depletion of the catalytic component Mettl3 exacerbates effector functions in response to IgE and antigen complexes, both in vitro and in vivo. Mechanistically, deletion of Mettl3 or Mettl14, another component of the methyltransferase complex, lead to the enhanced expression of inflammatory cytokines. By focusing on one of the most affected mRNAs, namely the one encoding the cytokine IL-13, we find that it is methylated in activated mast cells, and that Mettl3 affects its transcript stability in an enzymatic activity-dependent manner, requiring consensus m6A sites in the Il13 3’-untranslated region. Overall, we reveal that the m6A machinery is essential in mast cells to sustain growth and to restrain inflammatory responses.
Hierarchical conductive metal-organic framework films enabling efficient interfacial mass transfer
Authors: Huang Chuanhui , Shang Xinglong , Zhou Xinyuan , Zhang Zhe , Huang Xing , Lu Yang , Wang Mingchao , Löffler Markus , Liao Zhongquan , Qi Haoyuan , Kaiser Ute , Schwarz Dana , Fery Andreas , Wang Tie , Mannsfeld Stefan C. B. , Hu Guoqing , Feng Xinliang , Dong Renhao 
Published: June 2023

AbstractHeterogeneous reactions associated with porous solid films are ubiquitous and play an important role in both nature and industrial processes. However, due to the no-slip boundary condition in pressure-driven flows, the interfacial mass transfer between the porous solid surface and the environment is largely limited to slow molecular diffusion, which severely hinders the enhancement of heterogeneous reaction kinetics. Herein, we report a hierarchical-structure-accelerated interfacial dynamic strategy to improve interfacial gas transfer on hierarchical conductive metal-organic framework (c-MOF) films. Hierarchicalc-MOF films are synthesized via the in-situ transformation of insulating MOF film precursors usingπ-conjugated ligands and comprise both a nanoporous shell and hollow inner voids. The introduction of hollow structures in thec-MOF films enables an increase of gas permeability, thus enhancing the motion velocity of gas molecules toward thec-MOF film surface, which is more than 8.0-fold higher than that of bulk-type film. Thec-MOF film-based chemiresistive sensor exhibits a faster response towards ammonia than other reported chemiresistive ammonia sensors at room temperature and a response speed 10 times faster than that of the bulk-type film.
Interpretable discovery of semiconductors with machine learning
Authors: Choubisa Hitarth , Todorović Petar , Pina Joao M. , Parmar Darshan H. , Li Ziliang , Voznyy Oleksandr , Tamblyn Isaac , Sargent Edward H. 
Published: June 2023

AbstractMachine learning models of material properties accelerate materials discovery, reproducing density functional theory calculated results at a fraction of the cost1–6. To bridge the gap between theory and experiments, machine learning predictions need to be distilled in the form of interpretable chemical rules that can be used by experimentalists. Here we develop a framework to address this gap by combining evolutionary algorithm-powered search with machine-learning surrogate models. We then couple the search results with supervised learning and statistical testing. This strategy enables the efficient search of a materials space while providing interpretable design rules. We demonstrate its effectiveness by developing rules for the design of direct bandgap materials, stable UV emitters, and IR perovskite emitters. Finally, we conclusively show how DARWIN-generated rules are statistically more robust and applicable to a wide range of applications including the design of UV halide perovskites.
Optimal measurement structures for contextuality applications
Authors: Liu Yuan , Ramanathan Ravishankar , Horodecki Karol , Rosicka Monika , Horodecki Paweł 
Published: June 2023

AbstractThe Kochen-Specker (KS) theorem is a cornerstone result in the foundations of quantum mechanics describing the fundamental difference between quantum theory and classical non-contextual theories. Recently specific substructures termed 01-gadgets were shown to exist within KS proofs that capture the essential contradiction of the theorem. Here, we show these gadgets and their generalizations provide an optimal toolbox for contextuality applications including (i) constructing classical channels exhibiting entanglement-assisted advantage in zero-error communication, (ii) identifying large separations between quantum theory and binary generalized probabilistic theories, and (iii) finding optimal tests for contextuality-based semi-device-independent randomness generation. Furthermore, we introduce and study a generalization to definite prediction sets for more general logical propositions, that we term higher-order gadgets. We pinpoint the role these higher-order gadgets play in KS proofs by identifying these as induced subgraphs within KS graphs and showing how to construct proofs of state-independent contextuality using higher-order gadgets as building blocks. The constructions developed here may help in solving some of the remaining open problems regarding minimal proofs of the Kochen-Specker theorem.
Massively scalable Kerr comb-driven silicon photonic link
Authors: Rizzo Anthony , Novick Asher , Gopal Vignesh , Kim Bok Young , Ji Xingchen , Daudlin Stuart , Okawachi Yoshitomo , Cheng Qixiang , Lipson Michal , Gaeta Alexander L. , Bergman Keren 
Published: June 2023

AbstractThe growth of computing needs for artificial intelligence and machine learning is critically challenging data communications in today’s data-centre systems. Data movement, dominated by energy costs and limited ‘chip-escape’ bandwidth densities, is perhaps the singular factor determining the scalability of future systems. Using light to send information between compute nodes in such systems can dramatically increase the available bandwidth while simultaneously decreasing energy consumption. Through wavelength-division multiplexing with chip-based microresonator Kerr frequency combs, independent information channels can be encoded onto many distinct colours of light in the same optical fibre for massively parallel data transmission with low energy. Although previous high-bandwidth demonstrations have relied on benchtop equipment for filtering and modulating Kerr comb wavelength channels, data-centre interconnects require a compact on-chip form factor for these operations. Here we demonstrate a massively scalable chip-based silicon photonic data link using a Kerr comb source enabled by a new link architecture and experimentally show aggregate single-fibre data transmission of 512 Gb s−1 across 32 independent wavelength channels. The demonstrated architecture is fundamentally scalable to hundreds of wavelength channels, enabling massively parallel terabit-scale optical interconnects for future green hyperscale data centres.
Photonic radar for contactless vital sign detection
Authors: Zhang Ziqian , Liu Yang , Stephens Tegan , Eggleton Benjamin J. 
Published: June 2023

AbstractVital sign detection is used across ubiquitous scenarios in medical and health settings, and contact and wearable sensors have been widely deployed. However, they are unsuitable for patients with burn wounds or infants with insufficient areas for attachment. Contactless detection can be achieved using camera imaging, but it is susceptible to ambient light conditions and has privacy concerns. Here we report a photonic radar for non-contact vital sign detection to overcome these challenges. This photonic radar can achieve millimetre-level range resolution based on synthesized radar signals with a bandwidth of up to 30 GHz. The high resolution of the radar system enables accurate respiratory detection from breathing simulators and a cane toad as a human proxy. Moreover, we demonstrate that the optical signals generated from the proposed system can enable vital sign detection based on light detection and ranging (LiDAR). This demonstration reveals the potential of a sensor-fusion architecture that can combine the complementary features of radar and LiDAR to achieve improved sensing accuracy and system resilience. The work provides a technical basis for contactless and high-resolution vital sign detection to meet the increasing demands of future medical and healthcare applications.
Hierarchical TAF1-dependent co-translational assembly of the basal transcription factor TFIID
Authors: Bernardini Andrea , Mukherjee Pooja , Scheer Elisabeth , Kamenova Ivanka , Antonova Simona , Mendoza Sanchez Paulina Karen , Yayli Gizem , Morlet Bastien , Timmers H.T. Marc , Tora László 
Published: June 2023

AbstractLarge heteromeric multiprotein complexes play pivotal roles at every step of gene expression in eukaryotic cells. Among them, the 20-subunit basal transcription factor TFIID nucleates the RNA polymerase II preinitiation complex at gene promoters. Here, by combining systematic RNA-immunoprecipitation (RIP) experiments, single-molecule imaging, proteomics and structure–function analyses, we show that human TFIID biogenesis occurs co-translationally. We discovered that all protein heterodimerization steps happen during protein synthesis. We identify TAF1—the largest protein in the complex—as a critical factor for TFIID assembly. TAF1 acts as a flexible scaffold that drives the co-translational recruitment of TFIID submodules preassembled in the cytoplasm. Altogether, our data suggest a multistep hierarchical model for TFIID biogenesis that culminates with the co-translational assembly of the complex onto the nascent TAF1 polypeptide. We envision that this assembly strategy could be shared with other large heteromeric protein complexes.
A nationwide collapse of a priority grassland bird related to livestock conversion and intensification
Authors: Silva João Paulo , Marques Ana Teresa , Carrapato Carlos , Machado Rui , Alcazar Rita , Delgado Ana , Godinho Carlos , Elias Gonçalo , Gameiro João 
Published: June 2023

AbstractGrassland birds are among the most threatened and fastest declining terrestrial vertebrate species in Europe, principally due to agricultural intensification and transformation. The little bustard is a priority grassland bird under the European Directive (2009/147/CE) that led to the classification of a network of Special Protected Areas (SPAs) in Portugal. A third national survey carried out in 2022 reveals a worsening of an ongoing population collapse at a national scale. The population declined by 77% and 56% compared to the previous surveys in 2006 and 2016, respectively. We found that the little bustard has greatly disappeared outside SPAs, while the remaining breeding population concentrated within the protected area network is showing a steep decline at a rate of 9% a year. This decline is now twice as fast when compared to the period 2006–2016. Analysis of the variation of the breeding densities between 2006 and 2022 at 49 survey sites revealed that those that initially had higher bustard densities and shifted toward a higher proportion of cattle among the total stocking rate experienced steeper declines. Areas where the density of roads increased also experienced declines over the course of the study period. Agricultural areas converted to or dominated by beef production likely relate to low breeding success and mortality of nesting females in fodder crops. Still, major habitat conversion outside SPAs to permanent crops led to overall habitat destruction, which contributed to the species decline and range contraction. Other threats are likely acting synergistically such as fragmentation, climate change and anthropogenic mortality. The extinction of the little bustard in Portugal is expected in the short term if no conservation actions are put in place.