bluuebunny/crossref_metadata_2025 huggingface dataset:
Insights into SusCD-mediated glycan import by a prominent gut symbiont
Authors: Gray Declan A. , White Joshua B. R. , Oluwole Abraham O. , Rath Parthasarathi , Glenwright Amy J. , Mazur Adam , Zahn Michael , Baslé Arnaud , Morland Carl , Evans Sasha L. , Cartmell Alan , Robinson Carol V. , Hiller Sebastian , Ranson Neil A. , Bolam David N. , van den Berg Bert
Published: January 2021

In Bacteroidetes, one of the dominant phyla of the mammalian gut, active uptake of large nutrients across the outer membrane is mediated by SusCD protein complexes via a “pedal bin” transport mechanism. However, many features of SusCD function in glycan uptake remain unclear, including ligand binding, the role of the SusD lid and the size limit for substrate transport. Here we characterise the β2,6 fructo-oligosaccharide (FOS) importing SusCD from Bacteroides thetaiotaomicron (Bt1762-Bt1763) to shed light on SusCD function. Co-crystal structures reveal residues involved in glycan recognition and suggest that the large binding cavity can accommodate several substrate molecules, each up to ~2.5 kDa in size, a finding supported by native mass spectrometry and isothermal titration calorimetry. Mutational studies in vivo provide functional insights into the key structural features of the SusCD apparatus and cryo-EM of the intact dimeric SusCD complex reveals several distinct states of the transporter, directly visualising the dynamics of the pedal bin transport mechanism.
Global computational alignment of tumor and cell line transcriptional profiles
Authors: Warren Allison , Chen Yejia , Jones Andrew , Shibue Tsukasa , Hahn William C. , Boehm Jesse S. , Vazquez Francisca , Tsherniak Aviad , McFarland James M.
Published: January 2021

Cell lines are key tools for preclinical cancer research, but it remains unclear how well they represent patient tumor samples. Direct comparisons of tumor and cell line transcriptional profiles are complicated by several factors, including the variable presence of normal cells in tumor samples. We thus develop an unsupervised alignment method (Celligner) and apply it to integrate several large-scale cell line and tumor RNA-Seq datasets. Although our method aligns the majority of cell lines with tumor samples of the same cancer type, it also reveals large differences in tumor similarity across cell lines. Using this approach, we identify several hundred cell lines from diverse lineages that present a more mesenchymal and undifferentiated transcriptional state and that exhibit distinct chemical and genetic dependencies. Celligner could be used to guide the selection of cell lines that more closely resemble patient tumors and improve the clinical translation of insights gained from cell lines.
MOF-in-COF molecular sieving membrane for selective hydrogen separation
Authors: Fan Hongwei , Peng Manhua , Strauss Ina , Mundstock Alexander , Meng Hong , Caro Jürgen
Published: January 2021

Covalent organic frameworks (COFs) are promising materials for advanced molecular-separation membranes, but their wide nanometer-sized pores prevent selective gas separation through molecular sieving. Herein, we propose a MOF-in-COF concept for the confined growth of metal-organic framework (MOFs) inside a supported COF layer to prepare MOF-in-COF membranes. These membranes feature a unique MOF-in-COF micro/nanopore network, presumably due to the formation of MOFs as a pearl string-like chain of unit cells in the 1D channel of 2D COFs. The MOF-in-COF membranes exhibit an excellent hydrogen permeance (>3000 GPU) together with a significant enhancement of separation selectivity of hydrogen over other gases. The superior separation performance for H2/CO2 and H2/CH4 surpasses the Robeson upper bounds, benefiting from the synergy combining precise size sieving and fast molecular transport through the MOF-in-COF channels. The synthesis of different combinations of MOFs and COFs in robust MOF-in-COF membranes demonstrates the versatility of our design strategy.
Interfacial jamming reinforced Pickering emulgel for arbitrary architected nanocomposite with connected nanomaterial matrix
Authors: Zhang Yuanyuan , Zhu Guangming , Dong Biqin , Wang Feng , Tang Jiaoning , Stadler Florian J. , Yang Guanghui , Hong Shuxian , Xing Feng
Published: January 2021

Three-dimensional (3D) nanocomposite (NC) printing has emerged as a major approach to translate nanomaterial physical properties to 3D geometries. However, 3D printing of conventional NCs with polymer matrix lacks control over nanomaterial connection that facilitates maximizing nanomaterial advantages. Thus, a printable NC that features nanomaterials matrix necessitates development, nevertheless, faces a challenge in preparation because of the trade-off between viscosity and interfacial stability. Here, we develop viscoelastic Pickering emulgels as NC inks through jamming nanomaterials on interfaces and in continuous phase. Emulgel composed of multiphases allow a vast range of composition options and superior printability. The excellent attributes initiate NC with spatial control over geometrics and functions through 3D printing of graphene oxide/phase-change materials emulgel, for instance. This versatile approach provides the means for architecting NCs with nanomaterial continuous phase whose performance does not constrain the vast array of available nanomaterials and allows for arbitrary hybridization and patterns.
Structural multi-colour invisible inks with submicron 4D printing of shape memory polymers
Authors: Zhang Wang , Wang Hao , Wang Hongtao , Chan John You En , Liu Hailong , Zhang Biao , Zhang Yuan-Fang , Agarwal Komal , Yang Xiaolong , Ranganath Anupama Sargur , Low Hong Yee , Ge Qi , Yang Joel K. W.
Published: January 2021

Four-dimensional (4D) printing of shape memory polymer (SMP) imparts time responsive properties to 3D structures. Here, we explore 4D printing of a SMP in the submicron length scale, extending its applications to nanophononics. We report a new SMP photoresist based on Vero Clear achieving print features at a resolution of ~300 nm half pitch using two-photon polymerization lithography (TPL). Prints consisting of grids with size-tunable multi-colours enabled the study of shape memory effects to achieve large visual shifts through nanoscale structure deformation. As the nanostructures are flattened, the colours and printed information become invisible. Remarkably, the shape memory effect recovers the original surface morphology of the nanostructures along with its structural colour within seconds of heating above its glass transition temperature. The high-resolution printing and excellent reversibility in both microtopography and optical properties promises a platform for temperature-sensitive labels, information hiding for anti-counterfeiting, and tunable photonic devices.
Early-life-trauma triggers interferon-β resistance and neurodegeneration in a multiple sclerosis model via downregulated β1-adrenergic signaling
Authors: Khaw Yee Ming , Majid Danish , Oh Sungjong , Kang Eunjoo , Inoue Makoto
Published: January 2021

Environmental triggers have important functions in multiple sclerosis (MS) susceptibility, phenotype, and trajectory. Exposure to early life trauma (ELT) has been associated with higher relapse rates in MS patients; however, the underlying mechanisms are not well-defined. Here we show ELT induces mechanistic and phenotypical alterations during experimental autoimmune encephalitis (EAE). ELT sustains downregulation of immune cell adrenergic receptors, which can be attributed to chronic norepinephrine circulation. ELT-subjected mice exhibit interferon-β resistance and neurodegeneration driven by lymphotoxin and CXCR2 involvement. These phenotypic changes are observed in control EAE mice treated with β1 adrenergic receptor antagonist. Conversely, β1 adrenergic receptor agonist treatment to ELT mice abrogates phenotype changes via restoration of immune cell β1 adrenergic receptor function. Our results indicate that ELT alters EAE phenotype via downregulation of β1 adrenergic signaling in immune cells. These results have implications for the effect of environmental factors in provoking disease heterogeneity and might enable prediction of long-term outcomes in MS.
Experimental validation of a modeling framework for upconversion enhancement in 1D-photonic crystals
Authors: Hofmann Clarissa L. M. , Fischer Stefan , Eriksen Emil H. , Bläsi Benedikt , Reitz Christian , Yazicioglu Deniz , Howard Ian A. , Richards Bryce S. , Goldschmidt Jan Christoph
Published: January 2021

Photonic structures can be designed to tailor luminescence properties of materials, which becomes particularly interesting for non-linear phenomena, such as photon upconversion. However, there is no adequate theoretical framework to optimize photonic structure designs for upconversion enhancement. Here, we present a comprehensive theoretical model describing photonic effects on upconversion and confirm the model’s predictions by experimental realization of 1D-photonic upconverter devices with large statistics and parameter scans. The measured upconversion photoluminescence enhancement reaches 82 ± 24% of the simulated enhancement, in the mean of 2480 separate measurements, scanning the irradiance and the excitation wavelength on 40 different sample designs. Additionally, the trends expected from the modeled interaction of photonic energy density enhancement, local density of optical states and internal upconversion dynamics, are clearly validated in all experimentally performed parameter scans. Our simulation tool now opens the possibility of precisely designing photonic structure designs for various upconverting materials and applications.
TARM1 contributes to development of arthritis by activating dendritic cells through recognition of collagens
Authors: Yabe Rikio , Chung Soo-Hyun , Murayama Masanori A. , Kubo Sachiko , Shimizu Kenji , Akahori Yukiko , Maruhashi Takumi , Seno Akimasa , Kaifu Tomonori , Saijo Shinobu , Iwakura Yoichiro
Published: January 2021

TARM1 is a member of the leukocyte immunoglobulin-like receptor family and stimulates macrophages and neutrophils in vitro by associating with FcRγ. However, the function of this molecule in the regulation of the immune system is unclear. Here, we show thatTarm1expression is elevated in the joints of rheumatoid arthritis mouse models, and the development of collagen-induced arthritis (CIA) is suppressed inTarm1–/–mice. T cell priming against type 2 collagen is suppressed inTarm1–/–mice and antigen-presenting ability of GM-CSF-induced dendritic cells (GM-DCs) fromTarm1–/–mouse bone marrow cells is impaired. We show that type 2 collagen is a functional ligand for TARM1 on GM-DCs and promotes DC maturation. Furthermore, soluble TARM1-Fc and TARM1-Flag inhibit DC maturation and administration of TARM1-Fc blocks the progression of CIA in mice. These results indicate that TARM1 is an important stimulating factor of dendritic cell maturation and could be a good target for the treatment of autoimmune diseases.
Non-invasive assessment of telomere maintenance mechanisms in brain tumors
Authors: Viswanath Pavithra , Batsios Georgios , Mukherjee Joydeep , Gillespie Anne Marie , Larson Peder E. Z. , Luchman H. Artee , Phillips Joanna J. , Costello Joseph F. , Pieper Russell O. , Ronen Sabrina M.
Published: January 2021

Telomere maintenance is a universal hallmark of cancer. Most tumors including low-grade oligodendrogliomas use telomerase reverse transcriptase (TERT) expression for telomere maintenance while astrocytomas use the alternative lengthening of telomeres (ALT) pathway. Although TERT and ALT are hallmarks of tumor proliferation and attractive therapeutic targets, translational methods of imaging TERT and ALT are lacking. Here we show that TERT and ALT are associated with unique 1H-magnetic resonance spectroscopy (MRS)-detectable metabolic signatures in genetically-engineered and patient-derived glioma models and patient biopsies. Importantly, we have leveraged this information to mechanistically validate hyperpolarized [1-13C]-alanine flux to pyruvate as an imaging biomarker of ALT status and hyperpolarized [1-13C]-alanine flux to lactate as an imaging biomarker of TERT status in low-grade gliomas. Collectively, we have identified metabolic biomarkers of TERT and ALT status that provide a way of integrating critical oncogenic information into non-invasive imaging modalities that can improve tumor diagnosis and treatment response monitoring.
Anomalous collapses of Nares Strait ice arches leads to enhanced export of Arctic sea ice
Authors: Moore G. W. K. , Howell S. E. L. , Brady M. , Xu X. , McNeil K.
Published: January 2021

The ice arches that usually develop at the northern and southern ends of Nares Strait play an important role in modulating the export of Arctic Ocean multi-year sea ice. The Arctic Ocean is evolving towards an ice pack that is younger, thinner, and more mobile and the fate of its multi-year ice is becoming of increasing interest. Here, we use sea ice motion retrievals from Sentinel-1 imagery to report on the recent behavior of these ice arches and the associated ice fluxes. We show that the duration of arch formation has decreased over the past 20 years, while the ice area and volume fluxes along Nares Strait have both increased. These results suggest that a transition is underway towards a state where the formation of these arches will become atypical with a concomitant increase in the export of multi-year ice accelerating the transition towards a younger and thinner Arctic ice pack.
Filamentous recombinant human Tau activates primary astrocytes via an integrin receptor complex
Authors: Wang Peng , Ye Yihong
Published: January 2021

Microtubule-associated protein Tau can form protein aggregates transmissible within the brain, correlating with the progression of tauopathies in humans. The transmission of aggregates requires neuron-released Tau to interact with surface receptors on target cells. However, the underlying molecular mechanisms in astrocytes and downstream effects are unclear. Here, using a spatially resolved proteomic mapping strategy, we show that integrin αV/β1 receptor binds recombinant human Tau, mediating the entry of Tau fibrils in astrocytes. The binding of distinct Tau species to the astrocytic αV/β1 receptor differentially activate integrin signaling. Furthermore, Tau-mediated activation of integrin signaling results in NFκB activation, causing upregulation of pro-inflammatory cytokines and chemokines, induction of a sub-group of neurotoxic astrocytic markers, and release of neurotoxic factors. Our findings suggest that filamentous recombinant human Tau-mediated activation of integrin signaling induces astrocyte conversion towards a neurotoxic state, providing a mechanistic insight into tauopathies.
The aging transcriptome and cellular landscape of the human lung in relation to SARS-CoV-2
Authors: Chow Ryan D. , Majety Medha , Chen Sidi
Published: January 2021

Age is a major risk factor for severe coronavirus disease-2019 (COVID-19). Here, we interrogate the transcriptional features and cellular landscape of the aging human lung. By intersecting these age-associated changes with experimental data on SARS-CoV-2, we identify several factors that may contribute to the heightened severity of COVID-19 in older populations. The aging lung is transcriptionally characterized by increased cell adhesion and stress responses, with reduced mitochondria and cellular replication. Deconvolution analysis reveals that the proportions of alveolar type 2 cells, proliferating basal cells, goblet cells, and proliferating natural killer/T cells decrease with age, whereas alveolar fibroblasts, pericytes, airway smooth muscle cells, endothelial cells and IGSF21+ dendritic cells increase with age. Several age-associated genes directly interact with the SARS-CoV-2 proteome. Age-associated genes are also dysregulated by SARS-CoV-2 infection in vitro and in patients with severe COVID-19. These analyses illuminate avenues for further studies on the relationship between age and COVID-19.
QKI is a critical pre-mRNA alternative splicing regulator of cardiac myofibrillogenesis and contractile function
Authors: Chen Xinyun , Liu Ying , Xu Chen , Ba Lina , Liu Zhuo , Li Xiuya , Huang Jie , Simpson Ed , Gao Hongyu , Cao Dayan , Sheng Wei , Qi Hanping , Ji Hongrui , Sanderson Maria , Cai Chen-Leng , Li Xiaohui , Yang Lei , Na Jie , Yamamura Kenichi , Liu Yunlong , Huang Guoying , Shou Weinian , Sun Ning
Published: January 2021

The RNA-binding protein QKI belongs to the hnRNP K-homology domain protein family, a well-known regulator of pre-mRNA alternative splicing and is associated with several neurodevelopmental disorders.Qkiis found highly expressed in developing and adult hearts. By employing the human embryonic stem cell (hESC) to cardiomyocyte differentiation system and generating QKI-deficient hESCs (hESCs-QKIdel) using CRISPR/Cas9 gene editing technology, we analyze the physiological role of QKI in cardiomyocyte differentiation, maturation, and contractile function. hESCs-QKIdellargely maintain normal pluripotency and normal differentiation potential for the generation of early cardiogenic progenitors, but they fail to transition into functional cardiomyocytes. In this work, by using a series of transcriptomic, cell and biochemical analyses, and the Qki-deficient mouse model, we demonstrate that QKI is indispensable to cardiac sarcomerogenesis and cardiac function through its regulation of alternative splicing in genes involved in Z-disc formation and contractile physiology, suggesting thatQKIis associated with the pathogenesis of certain forms of cardiomyopathies.
Minutes-timescale 3D isotropic imaging of entire organs at subcellular resolution by content-aware compressed-sensing light-sheet microscopy
Authors: Fang Chunyu , Yu Tingting , Chu Tingting , Feng Wenyang , Zhao Fang , Wang Xuechun , Huang Yujie , Li Yusha , Wan Peng , Mei Wei , Zhu Dan , Fei Peng
Published: January 2021

Rapid 3D imaging of entire organs and organisms at cellular resolution is a recurring challenge in life science. Here we report on a computational light-sheet microscopy able to achieve minute-timescale high-resolution mapping of entire macro-scale organs. Through combining a dual-side confocally-scanned Bessel light-sheet illumination which provides thinner-and-wider optical sectioning of deep tissues, with a content-aware compressed sensing (CACS) computation pipeline which further improves the contrast and resolution based on a single acquisition, our approach yields 3D images with high, isotropic spatial resolution and rapid acquisition over two-order-of-magnitude faster than conventional 3D microscopy implementations. We demonstrate the imaging of whole brain (~400 mm3), entire gastrocnemius and tibialis muscles (~200 mm3) of mouse at ultra-high throughput of 5~10 min per sample and post-improved subcellular resolution of ~ 1.5 μm (0.5-μm iso-voxel size). Various system-level cellular analyses, such as mapping cell populations at different brain sub-regions, tracing long-distance projection neurons over the entire brain, and calculating neuromuscular junction occupancy across whole muscle, are also readily accomplished by our method.
The patterns of deleterious mutations during the domestication of soybean
Authors: Kim Myung-Shin , Lozano Roberto , Kim Ji Hong , Bae Dong Nyuk , Kim Sang-Tae , Park Jung-Ho , Choi Man Soo , Kim Jaehyun , Ok Hyun-Choong , Park Soo-Kwon , Gore Michael A. , Moon Jung-Kyung , Jeong Soon-Chun
Published: January 2021

Globally, soybean is a major protein and oil crop. Enhancing our understanding of the soybean domestication and improvement process helps boost genomics-assisted breeding efforts. Here we present a genome-wide variation map of 10.6 million single-nucleotide polymorphisms and 1.4 million indels for 781 soybean individuals which includes 418 domesticated (Glycine max), 345 wild (Glycine soja), and 18 natural hybrid (G. max/G. soja) accessions. We describe the enhanced detection of 183 domestication-selective sweeps and the patterns of putative deleterious mutations during domestication and improvement. This predominantly selfing species shows 7.1% reduction of overall deleterious mutations in domesticated soybean relative to wild soybean and a further 1.4% reduction from landrace to improved accessions. The detected domestication-selective sweeps also show reduced levels of deleterious alleles. Importantly, genotype imputation with this resource increases the mapping resolution of genome-wide association studies for seed protein and oil traits in a soybean diversity panel.
Error correction enables use of Oxford Nanopore technology for reference-free transcriptome analysis
Authors: Sahlin Kristoffer , Medvedev Paul
Published: January 2021

Oxford Nanopore (ONT) is a leading long-read technology which has been revolutionizing transcriptome analysis through its capacity to sequence the majority of transcripts from end-to-end. This has greatly increased our ability to study the diversity of transcription mechanisms such as transcription initiation, termination, and alternative splicing. However, ONT still suffers from high error rates which have thus far limited its scope to reference-based analyses. When a reference is not available or is not a viable option due to reference-bias, error correction is a crucial step towards the reconstruction of the sequenced transcripts and downstream sequence analysis of transcripts. In this paper, we present a novel computational method to error correct ONT cDNA sequencing data, called isONcorrect. IsONcorrect is able to jointly use all isoforms from a gene during error correction, thereby allowing it to correct reads at low sequencing depths. We are able to obtain a median accuracy of 98.9–99.6%, demonstrating the feasibility of applying cost-effective cDNA full transcript length sequencing for reference-free transcriptome analysis.
Self-strengthening biphasic nanoparticle assemblies with intrinsic catch bonds
Authors: Dansuk Kerim C. , Keten Sinan
Published: January 2021

Protein–ligand complexes with catch bonds exhibit prolonged lifetimes when subject to tensile force, which is a desirable yet elusive attribute for man-made nanoparticle interfaces and assemblies. Most designs proposed so far rely on macromolecular linkers with complicated folds rather than particles exhibiting simple dynamic shapes. Here, we establish a scissor-type X-shaped particle design for achieving intrinsic catch bonding ability with tunable force-enhanced lifetimes under thermal excitations. Molecular dynamics simulations are carried out to illustrate equilibrium self-assembly and force-enhanced bond lifetime of dimers and fibers facilitated by secondary interactions that form under tensile force. The non-monotonic force dependence of the fiber breaking kinetics is well-estimated by an analytical model. Our design concepts for shape-changing particles illuminates a path towards novel nanoparticle or colloidal assemblies that have the passive ability to tune the strength of their interfaces with applied force, setting the stage for self-assembling materials with novel mechanical functions and rheological properties.
Long first exons and epigenetic marks distinguish conserved pachytene piRNA clusters from other mammalian genes
Authors: Yu Tianxiong , Fan Kaili , Özata Deniz M. , Zhang Gen , Fu Yu , Theurkauf William E. , Zamore Phillip D. , Weng Zhiping
Published: January 2021

In the male germ cells of placental mammals, 26–30-nt-long PIWI-interacting RNAs (piRNAs) emerge when spermatocytes enter the pachytene phase of meiosis. In mice, pachytene piRNAs derive from ~100 discrete autosomal loci that produce canonical RNA polymerase II transcripts. These piRNA clusters bear 5′ caps and 3′ poly(A) tails, and often contain introns that are removed before nuclear export and processing into piRNAs. What marks pachytene piRNA clusters to produce piRNAs, and what confines their expression to the germline? We report that an unusually long first exon (≥ 10 kb) or a long, unspliced transcript correlates with germline-specific transcription and piRNA production. Our integrative analysis of transcriptome, piRNA, and epigenome datasets across multiple species reveals that a long first exon is an evolutionarily conserved feature of pachytene piRNA clusters. Furthermore, a highly methylated promoter, often containing a low or intermediate level of CG dinucleotides, correlates with germline expression and somatic silencing of pachytene piRNA clusters. Pachytene piRNA precursor transcripts bind THOC1 and THOC2, THO complex subunits known to promote transcriptional elongation and mRNA nuclear export. Together, these features may explain why the major sources of pachytene piRNA clusters specifically generate these unique small RNAs in the male germline of placental mammals.
Metaxins are core components of mitochondrial transport adaptor complexes
Authors: Zhao Yinsuo , Song Eli , Wang Wenjuan , Hsieh Chung-Han , Wang Xinnan , Feng Wei , Wang Xiangming , Shen Kang
Published: January 2021

Trafficking of mitochondria into dendrites and axons plays an important role in the physiology and pathophysiology of neurons. Mitochondrial outer membrane protein Miro and adaptor proteins TRAKs/Milton link mitochondria to molecular motors. Here we show that metaxins MTX-1 and MTX-2 contribute to mitochondrial transport into both dendrites and axons of C. elegans neurons. MTX1/2 bind to MIRO-1 and kinesin light chain KLC-1, forming a complex to mediate kinesin-1-based movement of mitochondria, in which MTX-1/2 are essential and MIRO-1 plays an accessory role. We find that MTX-2, MIRO-1, and TRAK-1 form another distinct adaptor complex to mediate dynein-based transport. Additionally, we show that failure of mitochondrial trafficking in dendrites causes age-dependent dendrite degeneration. We propose that MTX-2 and MIRO-1 form the adaptor core for both motors, while MTX-1 and TRAK-1 specify each complex for kinesin-1 and dynein, respectively. MTX-1 and MTX-2 are also required for mitochondrial transport in human neurons, indicative of their evolutionarily conserved function.
Interface-induced sign reversal of the anomalous Hall effect in magnetic topological insulator heterostructures
Authors: Wang Fei , Wang Xuepeng , Zhao Yi-Fan , Xiao Di , Zhou Ling-Jie , Liu Wei , Zhang Zhidong , Zhao Weiwei , Chan Moses H. W. , Samarth Nitin , Liu Chaoxing , Zhang Haijun , Chang Cui-Zu
Published: January 2021

The Berry phase picture provides important insights into the electronic properties of condensed matter systems. The intrinsic anomalous Hall (AH) effect can be understood as the consequence of non-zero Berry curvature in momentum space. Here, we fabricate TI/magnetic TI heterostructures and find that the sign of the AH effect in the magnetic TI layer can be changed from being positive to negative with increasing the thickness of the top TI layer. Our first-principles calculations show that the built-in electric fields at the TI/magnetic TI interface influence the band structure of the magnetic TI layer, and thus lead to a reconstruction of the Berry curvature in the heterostructure samples. Based on the interface-induced AH effect with a negative sign in TI/V-doped TI bilayer structures, we create an artificial “topological Hall effect”-like feature in the Hall trace of the V-doped TI/TI/Cr-doped TI sandwich heterostructures. Our study provides a new route to create the Berry curvature change in magnetic topological materials that may lead to potential technological applications.
ZBP1 promotes LPS-induced cell death and IL-1β release via RHIM-mediated interactions with RIPK1
Authors: Muendlein Hayley I. , Connolly Wilson M. , Magri Zoie , Smirnova Irina , Ilyukha Vladimir , Gautam Avishekh , Degterev Alexei , Poltorak Alexander
Published: January 2021

Inflammation and cell death are closely linked arms of the host immune response to infection, which when carefully balanced ensure host survival. One example of this balance is the tightly regulated transition from TNFR1-associated pro-inflammatory complex I to pro-death complex II. By contrast, here we show that a TRIF-dependent complex containing FADD, RIPK1 and caspase-8 (that we have termed the TRIFosome) mediates cell death in response to Yersinia pseudotuberculosis and LPS. Furthermore, we show that constitutive binding between ZBP1 and RIPK1 is essential for the initiation of TRIFosome interactions, caspase-8-mediated cell death and inflammasome activation, thus positioning ZBP1 as an effector of cell death in the context of bacterial blockade of pro-inflammatory signaling. Additionally, our findings offer an alternative to the TNFR1-dependent model of complex II assembly, by demonstrating pro-death complex formation reliant on TRIF signaling.
The vortex-driven dynamics of droplets within droplets
Authors: Tiribocchi A. , Montessori A. , Lauricella M. , Bonaccorso F. , Succi S. , Aime S. , Milani M. , Weitz D. A.
Published: January 2021

Understanding the fluid-structure interaction is crucial for an optimal design and manufacturing of soft mesoscale materials. Multi-core emulsions are a class of soft fluids assembled from cluster configurations of deformable oil-water double droplets (cores), often employed as building-blocks for the realisation of devices of interest in bio-technology, such as drug-delivery, tissue engineering and regenerative medicine. Here, we study the physics of multi-core emulsions flowing in microfluidic channels and report numerical evidence of a surprisingly rich variety of driven non-equilibrium states (NES), whose formation is caused by a dipolar fluid vortex triggered by the sheared structure of the flow carrier within the microchannel. The observed dynamic regimes range from long-lived NES at low core-area fraction, characterised by a planetary-like motion of the internal drops, to short-lived ones at high core-area fraction, in which a pre-chaotic motion results from multi-body collisions of inner drops, as combined with self-consistent hydrodynamic interactions. The onset of pre-chaotic behavior is marked by transitions of the cores from one vortex to another, a process that we interpret as manifestations of the system to maximize its entropy by filling voids, as they arise dynamically within the capsule.
Programmable phase-change metasurfaces on waveguides for multimode photonic convolutional neural network
Authors: Wu Changming , Yu Heshan , Lee Seokhyeong , Peng Ruoming , Takeuchi Ichiro , Li Mo
Published: January 2021

Neuromorphic photonics has recently emerged as a promising hardware accelerator, with significant potential speed and energy advantages over digital electronics for machine learning algorithms, such as neural networks of various types. Integrated photonic networks are particularly powerful in performing analog computing of matrix-vector multiplication (MVM) as they afford unparalleled speed and bandwidth density for data transmission. Incorporating nonvolatile phase-change materials in integrated photonic devices enables indispensable programming and in-memory computing capabilities for on-chip optical computing. Here, we demonstrate a multimode photonic computing core consisting of an array of programable mode converters based on on-waveguide metasurfaces made of phase-change materials. The programmable converters utilize the refractive index change of the phase-change material Ge2Sb2Te5 during phase transition to control the waveguide spatial modes with a very high precision of up to 64 levels in modal contrast. This contrast is used to represent the matrix elements, with 6-bit resolution and both positive and negative values, to perform MVM computation in neural network algorithms. We demonstrate a prototypical optical convolutional neural network that can perform image processing and recognition tasks with high accuracy. With a broad operation bandwidth and a compact device footprint, the demonstrated multimode photonic core is promising toward large-scale photonic neural networks with ultrahigh computation throughputs.
Universal and tunable liquid–liquid separation by nanoparticle-embedded gating membranes based on a self-defined interfacial parameter
Authors: Li Xiangyu , Liu Jingjing , Qu Ruixiang , Zhang Weifeng , Liu Yanan , Zhai Huajun , Wei Yen , Hu Hanshi , Feng Lin
Published: January 2021

Superwetting porous membranes with tunable liquid repellency are highly desirable in broad domains including scientific research, chemical industry, and environmental protection. Such membranes should allow for controllable droplet bouncing or spreading, which is difficult to achieve for low surface energy organic liquids (OLs). Here we develop an interfacial physical parameter to regulate the OL wettability of nanoparticle-embedded membranes by structuring synergistic layers with reconfigurable surface energy components. Under the tunable solid-liquid interaction in the aggregation-induced process, the membranes demonstrate positive/negative liquid gating regularity for polar protic liquids, polar aprotic liquids, and nonpolar liquids. Such a membrane can be employed as self-adaptive gating for various immiscible liquid mixtures with superior separation efficiency and permeation flux, even afford successive achievement of high-performance in situ extraction-back extraction coupling. This study should provide distinctive insights into intrinsic wetting behaviors and have pioneered a rational strategy to design high-performance separation materials for diverse applications.
Visualizing atomic structure and magnetism of 2D magnetic insulators via tunneling through graphene
Authors: Qiu Zhizhan , Holwill Matthew , Olsen Thomas , Lyu Pin , Li Jing , Fang Hanyan , Yang Huimin , Kashchenko Mikhail , Novoselov Kostya S. , Lu Jiong
Published: January 2021

The discovery of two-dimensional (2D) magnetism combined with van der Waals (vdW) heterostructure engineering offers unprecedented opportunities for creating artificial magnetic structures with non-trivial magnetic textures. Further progress hinges on deep understanding of electronic and magnetic properties of 2D magnets at the atomic scale. Although local electronic properties can be probed by scanning tunneling microscopy/spectroscopy (STM/STS), its application to investigate 2D magnetic insulators remains elusive due to absence of a conducting path and their extreme air sensitivity. Here we demonstrate that few-layer CrI3 (FL-CrI3) covered by graphene can be characterized electronically and magnetically via STM by exploiting the transparency of graphene to tunneling electrons. STS reveals electronic structures of FL-CrI3 including flat bands responsible for its magnetic state. AFM-to-FM transition of FL-CrI3 can be visualized through the magnetic field dependent moiré contrast in the dI/dV maps due to a change of the electronic hybridization between graphene and spin-polarised CrI3 bands with different interlayer magnetic coupling. Our findings provide a general route to probe atomic-scale electronic and magnetic properties of 2D magnetic insulators for future spintronics and quantum technology applications.
Missing Shapiro steps in topologically trivial Josephson junction on InAs quantum well
Authors: Dartiailh Matthieu C. , Cuozzo Joseph J. , Elfeky Bassel H. , Mayer William , Yuan Joseph , Wickramasinghe Kaushini S. , Rossi Enrico , Shabani Javad
Published: January 2021

Josephson junctions hosting Majorana fermions have been predicted to exhibit a 4π periodic current phase relation. One experimental consequence of this periodicity is the disappearance of odd steps in Shapiro steps experiments. Experimentally, missing odd Shapiro steps have been observed in a number of materials systems with strong spin-orbit coupling and have been interpreted in the context of topological superconductivity. Here we report on missing odd steps in topologically trivial Josephson junctions fabricated on InAs quantum wells. We ascribe our observations to the high transparency of our junctions allowing Landau-Zener transitions. The probability of these processes is shown to be independent of the drive frequency. We analyze our results using a bi-modal transparency distribution which demonstrates that only few modes carrying 4π periodic current are sufficient to describe the disappearance of odd steps. Our findings highlight the elaborate circumstances that have to be considered in the investigation of the 4π Josephson junctions in relationship to topological superconductivity.
Standardization of ELISA protocols for serosurveys of the SARS-CoV-2 pandemic using clinical and at-home blood sampling
Authors: Klumpp-Thomas Carleen , Kalish Heather , Drew Matthew , Hunsberger Sally , Snead Kelly , Fay Michael P. , Mehalko Jennifer , Shunmugavel Anandakumar , Wall Vanessa , Frank Peter , Denson John-Paul , Hong Min , Gulten Gulcin , Messing Simon , Hicks Jennifer , Michael Sam , Gillette William , Hall Matthew D. , Memoli Matthew J. , Esposito Dominic , Sadtler Kaitlyn
Published: January 2021

The extent of SARS-CoV-2 infection throughout the United States population is currently unknown. High quality serology is key to avoiding medically costly diagnostic errors, as well as to assuring properly informed public health decisions. Here, we present an optimized ELISA-based serology protocol, from antigen production to data analyses, that helps define thresholds for IgG and IgM seropositivity with high specificities. Validation of this protocol is performed using traditionally collected serum as well as dried blood on mail-in blood sampling kits. Archival (pre-2019) samples are used as negative controls, and convalescent, PCR-diagnosed COVID-19 patient samples serve as positive controls. Using this protocol, minimal cross-reactivity is observed for the spike proteins of MERS, SARS1, OC43 and HKU1 viruses, and no cross reactivity is observed with anti-influenza A H1N1 HAI. Our protocol may thus help provide standardized, population-based data on the extent of SARS-CoV-2 seropositivity, immunity and infection.
Bis-silylation of internal alkynes enabled by Ni(0) catalysis
Authors: Zhang Yun , Wang Xi-Chao , Ju Cheng-Wei , Zhao Dongbing
Published: January 2021

1,2-Bis-silyl alkenes have exciting synthetic potential for programmable sequential synthesis via manipulation of the two vicinal silyl groups. Transition metal-catalyzed bis-silylation of alkynes with disilanes is the most straightforward strategy to access such useful building blocks. However, this process has some limitations: (1) symmetric disilanes are frequently employed in most of the reactions to assemble two identical silyl groups, which makes chemoselective differentiation for stepwise downstream transformations difficult; (2) the main catalysts are low-valent platinum group transition metal complexes, which are expensive; and (3) internal alkynes remain challenging substrates with low inherent reactivity. Thus, the development of abundant metal-catalyzed bis-silylation of internal alkynes with unsymmetrical disilanes is of significance. Herein, we solve most of the aforementioned limitations in bis-silylation of unsaturated bonds by developing a strongly coordinating disilane reagent and a Ni(0) catalytic system. Importantly, we sufficiently realize the stepwise recognition of the two silyl groups, making this synthetic protocol of wide potential utility.
Deletion of Trim28 in committed adipocytes promotes obesity but preserves glucose tolerance
Authors: Bond Simon T. , King Emily J. , Henstridge Darren C. , Tran Adrian , Moody Sarah C. , Yang Christine , Liu Yingying , Mellett Natalie A. , Nath Artika P. , Inouye Michael , Tarling Elizabeth J. , de Aguiar Vallim Thomas Q. , Meikle Peter J. , Calkin Anna C. , Drew Brian G.
Published: January 2021

The effective storage of lipids in white adipose tissue (WAT) critically impacts whole body energy homeostasis. Many genes have been implicated in WAT lipid metabolism, including tripartite motif containing 28 (Trim28), a gene proposed to primarily influence adiposity via epigenetic mechanisms in embryonic development. However, in the current study we demonstrate that mice with deletion of Trim28 specifically in committed adipocytes, also develop obesity similar to global Trim28 deletion models, highlighting a post-developmental role for Trim28. These effects were exacerbated in female mice, contributing to the growing notion that Trim28 is a sex-specific regulator of obesity. Mechanistically, this phenotype involves alterations in lipolysis and triglyceride metabolism, explained in part by loss of Klf14 expression, a gene previously demonstrated to modulate adipocyte size and body composition in a sex-specific manner. Thus, these findings provide evidence that Trim28 is a bona fide, sex specific regulator of post-developmental adiposity and WAT function.
Coherence resonance in influencer networks
Authors: Tönjes Ralf , Fiore Carlos E. , Pereira Tiago
Published: January 2021

Complex networks are abundant in nature and many share an important structural property: they contain a few nodes that are abnormally highly connected (hubs). Some of these hubs are called influencers because they couple strongly to the network and play fundamental dynamical and structural roles. Strikingly, despite the abundance of networks with influencers, little is known about their response to stochastic forcing. Here, for oscillatory dynamics on influencer networks, we show that subjecting influencers to an optimal intensity of noise can result in enhanced network synchronization. This new network dynamical effect, which we call coherence resonance in influencer networks, emerges from a synergy between network structure and stochasticity and is highly nonlinear, vanishing when the noise is too weak or too strong. Our results reveal that the influencer backbone can sharply increase the dynamical response in complex systems of coupled oscillators.
Author Correction: Tree mode of death and mortality risk factors across Amazon forests
Authors: Esquivel-Muelbert Adriane , Phillips Oliver L. , Brienen Roel J. W. , Fauset Sophie , Sullivan Martin J. P. , Baker Timothy R. , Chao Kuo-Jung , Feldpausch Ted R. , Gloor Emanuel , Higuchi Niro , Houwing-Duistermaat Jeanne , Lloyd Jon , Liu Haiyan , Malhi Yadvinder , Marimon Beatriz , Marimon Junior Ben Hur , Monteagudo-Mendoza Abel , Poorter Lourens , Silveira Marcos , Torre Emilio Vilanova , Dávila Esteban Alvarez , del Aguila Pasquel Jhon , Almeida Everton , Loayza Patricia Alvarez , Andrade Ana , Aragão Luiz E. O. C. , Araujo-Murakami Alejandro , Arets Eric , Arroyo Luzmila , Aymard C. Gerardo A. , Baisie Michel , Baraloto Christopher , Camargo Plínio Barbosa , Barroso Jorcely , Blanc Lilian , Bonal Damien , Bongers Frans , Boot René , Brown Foster , Burban Benoit , Camargo José Luís , Castro Wendeson , Moscoso Victor Chama , Chave Jerome , Comiskey James , Valverde Fernando Cornejo , da Costa Antonio Lola , Cardozo Nallaret Davila , Di Fiore Anthony , Dourdain Aurélie , Erwin Terry , Llampazo Gerardo Flores , Vieira Ima Célia Guimarães , Herrera Rafael , Honorio Coronado Eurídice , Huamantupa-Chuquimaco Isau , Jimenez-Rojas Eliana , Killeen Timothy , Laurance Susan , Laurance William , Levesley Aurora , Lewis Simon L. , Ladvocat Karina Liana Lisboa Melgaço , Lopez-Gonzalez Gabriela , Lovejoy Thomas , Meir Patrick , Mendoza Casimiro , Morandi Paulo , Neill David , Nogueira Lima Adriano José , Vargas Percy Nuñez , de Oliveira Edmar Almeida , Camacho Nadir Pallqui , Pardo Guido , Peacock Julie , Peña-Claros Marielos , Peñuela-Mora Maria Cristina , Pickavance Georgia , Pipoly John , Pitman Nigel , Prieto Adriana , Pugh Thomas A. M. , Quesada Carlos , Ramirez-Angulo Hirma , de Almeida Reis Simone Matias , Rejou-Machain Maxime , Correa Zorayda Restrepo , Bayona Lily Rodriguez , Rudas Agustín , Salomão Rafael , Serrano Julio , Espejo Javier Silva , Silva Natalino , Singh James , Stahl Clement , Stropp Juliana , Swamy Varun , Talbot Joey , ter Steege Hans , Terborgh John , Thomas Raquel , Toledo Marisol , Torres-Lezama Armando , Gamarra Luis Valenzuela , van der Heijden Geertje , van der Meer Peter , van der Hout Peter , Martinez Rodolfo Vasquez , Vieira Simone Aparecida , Cayo Jeanneth Villalobos , Vos Vincent , Zagt Roderick , Zuidema Pieter , Galbraith David
Published: January 2021

A Correction to this paper has been published: https://doi.org/10.1038/s41467-020-20537-x
Publisher Correction: An epigenetic gene silencing pathway selectively acting on transgenic DNA in the green alga Chlamydomonasis
Authors: Neupert Juliane , Gallaher Sean D. , Lu Yinghong , Strenkert Daniela , Segal Na’ama , Barahimipour Rouhollah , Fitz-Gibbon Sorel T. , Schroda Michael , Merchant Sabeeha S. , Bock Ralph
Published: January 2021

A Correction to this paper has been published: https://doi.org/10.1038/s41467-020-20623-0
Author Correction: An investigation of causal relationships between prediabetes and vascular complications
Authors: Mutie Pascal M. , Pomares-Millan Hugo , Atabaki-Pasdar Naeimeh , Jordan Nina , Adams Rachel , Daly Nicole L. , Tajes Juan Fernandes , Giordano Giuseppe N. , Franks Paul W.
Published: January 2021

A Correction to this paper has been published: https://doi.org/10.1038/s41467-020-20663-6
Publisher Correction: Increasing the reproducibility of fluid biomarker studies in neurodegenerative studies
Authors: Mattsson-Carlgren Niklas , Palmqvist Sebastian , Blennow Kaj , Hansson Oskar
Published: January 2021

A Correction to this paper has been published: https://doi.org/10.1038/s41467-020-20693-0.
Accelerating phase-field-based microstructure evolution predictions via surrogate models trained by machine learning methods
Authors: Montes de Oca Zapiain David , Stewart James A. , Dingreville Rémi
Published: January 2021

The phase-field method is a powerful and versatile computational approach for modeling the evolution of microstructures and associated properties for a wide variety of physical, chemical, and biological systems. However, existing high-fidelity phase-field models are inherently computationally expensive, requiring high-performance computing resources and sophisticated numerical integration schemes to achieve a useful degree of accuracy. In this paper, we present a computationally inexpensive, accurate, data-driven surrogate model that directly learns the microstructural evolution of targeted systems by combining phase-field and history-dependent machine-learning techniques. We integrate a statistically representative, low-dimensional description of the microstructure, obtained directly from phase-field simulations, with either a time-series multivariate adaptive regression splines autoregressive algorithm or a long short-term memory neural network. The neural-network-trained surrogate model shows the best performance and accurately predicts the nonlinear microstructure evolution of a two-phase mixture during spinodal decomposition in seconds, without the need for “on-the-fly” solutions of the phase-field equations of motion. We also show that the predictions from our machine-learned surrogate model can be fed directly as an input into a classical high-fidelity phase-field model in order to accelerate the high-fidelity phase-field simulations by leaping in time. Such machine-learned phase-field framework opens a promising path forward to use accelerated phase-field simulations for discovering, understanding, and predicting processing–microstructure–performance relationships.
Theoretical prediction of high melting temperature for a Mo–Ru–Ta–W HCP multiprincipal element alloy
Authors: Hong Qi-Jun , Schroers Jan , Hofmann Douglas , Curtarolo Stefano , Asta Mark , van de Walle Axel
Published: January 2021

While rhenium is an ideal material for rapid thermal cycling applications under high temperatures, such as rocket engine nozzles, its high cost limits its widespread use and prompts an exploration of viable cost-effective substitutes. In prior work, we identified a promising pool of candidate substitute alloys consisting of Mo, Ru, Ta, and W. In this work we demonstrate, based on density functional theory melting temperature calculations, that one of the candidates, Mo0.292Ru0.555Ta0.031W0.122, exhibits a high melting temperature (around 2626 K), thus supporting its use in high-temperature applications.