bluuebunny/crossref_metadata_2025_split huggingface dataset:
A missense mutation in the MLKL brace region promotes lethal neonatal inflammation and hematopoietic dysfunction
Authors: Hildebrand Joanne M. , Kauppi Maria , Majewski Ian J. , Liu Zikou , Cox Allison J. , Miyake Sanae , Petrie Emma J. , Silk Michael A. , Li Zhixiu , Tanzer Maria C. , Brumatti Gabriela , Young Samuel N. , Hall Cathrine , Garnish Sarah E. , Corbin Jason , Stutz Michael D. , Di Rago Ladina , Gangatirkar Pradnya , Josefsson Emma C. , Rigbye Kristin , Anderton Holly , Rickard James A. , Tripaydonis Anne , Sheridan Julie , Scerri Thomas S. , Jackson Victoria E. , Czabotar Peter E. , Zhang Jian-Guo , Varghese Leila , Allison Cody C. , Pellegrini Marc , Tannahill Gillian M. , Hatchell Esme C. , Willson Tracy A. , Stockwell Dina , de Graaf Carolyn A. , Collinge Janelle , Hilton Adrienne , Silke Natasha , Spall Sukhdeep K. , Chau Diep , Athanasopoulos Vicki , Metcalf Donald , Laxer Ronald M. , Bassuk Alexander G. , Darbro Benjamin W. , Fiatarone Singh Maria A. , Vlahovich Nicole , Hughes David , Kozlovskaia Maria , Ascher David B. , Warnatz Klaus , Venhoff Nils , Thiel Jens , Biben Christine , Blum Stefan , Reveille John , Hildebrand Michael S. , Vinuesa Carola G. , McCombe Pamela , Brown Matthew A. , Kile Benjamin T. , McLean Catriona , Bahlo Melanie , Masters Seth L. , Nakano Hiroyasu , Ferguson Polly J. , Murphy James M. , Alexander Warren S. , Silke John 
Published: June 2020

AbstractMLKL is the essential effector of necroptosis, a form of programmed lytic cell death. We have isolated a mouse strain with a single missense mutation,MlklD139V, that alters the two-helix ‘brace’ that connects the killer four-helix bundle and regulatory pseudokinase domains. This confers constitutive, RIPK3 independent killing activity to MLKL. Homozygous mutant mice develop lethal postnatal inflammation of the salivary glands and mediastinum. The normal embryonic development ofMlklD139Vhomozygotes until birth, and the absence of any overt phenotype in heterozygotes provides important in vivo precedent for the capacity of cells to clear activated MLKL. These observations offer an important insight into the potential disease-modulating roles of three common humanMLKLpolymorphisms that encode amino acid substitutions within or adjacent to the brace region. Compound heterozygosity of these variants is found at up to 12-fold the expected frequency in patients that suffer from a pediatric autoinflammatory disease, chronic recurrent multifocal osteomyelitis (CRMO).
Profiling immunoglobulin repertoires across multiple human tissues using RNA sequencing
Authors: Mandric Igor , Rotman Jeremy , Yang Harry Taegyun , Strauli Nicolas , Montoya Dennis J. , Van Der Wey William , Ronas Jiem R. , Statz Benjamin , Yao Douglas , Petrova Velislava , Zelikovsky Alex , Spreafico Roberto , Shifman Sagiv , Zaitlen Noah , Rossetti Maura , Ansel K. Mark , Eskin Eleazar , Mangul Serghei 
Published: June 2020

AbstractProfiling immunoglobulin (Ig) receptor repertoires with specialized assays can be cost-ineffective and time-consuming. Here we report ImReP, a computational method for rapid and accurate profiling of the Ig repertoire, including the complementary-determining region 3 (CDR3), using regular RNA sequencing data such as those from 8,555 samples across 53 tissues types from 544 individuals in the Genotype-Tissue Expression (GTEx v6) project. Using ImReP and GTEx v6 data, we generate a collection of 3.6 million Ig sequences, termed the atlas of immunoglobulin repertoires (TAIR), across a broad range of tissue types that often do not have reported Ig repertoires information. Moreover, the flow of Ig clonotypes and inter-tissue repertoire similarities across immune-related tissues are also evaluated. In summary, TAIR is one of the largest collections of CDR3 sequences and tissue types, and should serve as an important resource for studying immunological diseases.
Protonic solid-state electrochemical synapse for physical neural networks
Authors: Yao Xiahui , Klyukin Konstantin , Lu Wenjie , Onen Murat , Ryu Seungchan , Kim Dongha , Emond Nicolas , Waluyo Iradwikanari , Hunt Adrian , del Alamo Jesús A. , Li Ju , Yildiz Bilge 
Published: June 2020

AbstractPhysical neural networks made of analog resistive switching processors are promising platforms for analog computing. State-of-the-art resistive switches rely on either conductive filament formation or phase change. These processes suffer from poor reproducibility or high energy consumption, respectively. Herein, we demonstrate the behavior of an alternative synapse design that relies on a deterministic charge-controlled mechanism, modulated electrochemically in solid-state. The device operates by shuffling the smallest cation, the proton, in a three-terminal configuration. It has a channel of active material, WO3. A solid proton reservoir layer, PdHx, also serves as the gate terminal. A proton conducting solid electrolyte separates the channel and the reservoir. By protonation/deprotonation, we modulate the electronic conductivity of the channel over seven orders of magnitude, obtaining a continuum of resistance states. Proton intercalation increases the electronic conductivity of WO3 by increasing both the carrier density and mobility. This switching mechanism offers low energy dissipation, good reversibility, and high symmetry in programming.
Repurposing type I–F CRISPR–Cas system as a transcriptional activation tool in human cells
Authors: Chen Yuxi , Liu Jiaqi , Zhi Shengyao , Zheng Qi , Ma Wenbin , Huang Junjiu , Liu Yizhi , Liu Dan , Liang Puping , Songyang Zhou 
Published: June 2020

AbstractClass 2 CRISPR–Cas proteins have been widely developed as genome editing and transcriptional regulating tools. Class 1 type I CRISPR–Cas constitutes ~60% of all the CRISPR–Cas systems. However, only type I–B and I–E systems have been used to control mammalian gene expression and for genome editing. Here we demonstrate the feasibility of using type I–F system to regulate human gene expression. By fusing transcription activation domain to Pseudomonas aeruginosa type I–F Cas proteins, we activate gene transcription in human cells. In most cases, type I–F system is more efficient than other CRISPR-based systems. Transcription activation is enhanced by elongating the crRNA. In addition, we achieve multiplexed gene activation with a crRNA array. Furthermore, type I–F system activates target genes specifically without off-target transcription activation. These data demonstrate the robustness and programmability of type I–F CRISPR–Cas in human cells.
Sub-picosecond thermalization dynamics in condensation of strongly coupled lattice plasmons
Authors: Väkeväinen Aaro I. , Moilanen Antti J. , Nečada Marek , Hakala Tommi K. , Daskalakis Konstantinos S. , Törmä Päivi 
Published: June 2020

AbstractBosonic condensates offer exciting prospects for studies of non-equilibrium quantum dynamics. Understanding the dynamics is particularly challenging in the sub-picosecond timescales typical for room temperature luminous driven-dissipative condensates. Here we combine a lattice of plasmonic nanoparticles with dye molecule solution at the strong coupling regime, and pump the molecules optically. The emitted light reveals three distinct regimes: one-dimensional lasing, incomplete stimulated thermalization, and two-dimensional multimode condensation. The condensate is achieved by matching the thermalization rate with the lattice size and occurs only for pump pulse durations below a critical value. Our results give access to control and monitoring of thermalization processes and condensate formation at sub-picosecond timescale.
Quadrupole topological photonic crystals
Authors: He Li , Addison Zachariah , Mele Eugene J. , Zhen Bo 
Published: June 2020

AbstractQuadrupole topological phases, exhibiting protected boundary states that are themselves topological insulators of lower dimensions, have recently been of great interest. Extensions of these ideas from current tight binding models to continuum theories for realistic materials require the identification of quantized invariants describing the bulk quadrupole order. Here we identify the analog of quadrupole order in Maxwell’s equations for a gyromagnetic photonic crystal (PhC) through a double-band-inversion process. The quadrupole moment is quantized by the simultaneous presence of crystalline symmetry and broken time-reversal symmetry, which is confirmed using three independent methods: analysis of symmetry eigenvalues, numerical calculations of the nested Wannier bands and the expectation value of the quadrupole operator. Furthermore, we reveal the boundary manifestations of quadrupole phases as quantized edge polarizations and fractional corner charges. The latter are the consequence of a filling anomaly of energy bands as first predicted in electronic systems.
Talin dissociates from RIAM and associates to vinculin sequentially in response to the actomyosin force
Authors: Vigouroux Clémence , Henriot Véronique , Le Clainche Christophe 
Published: June 2020

AbstractCells reinforce adhesion strength and cytoskeleton anchoring in response to the actomyosin force. The mechanical stretching of talin, which exposes cryptic vinculin-binding sites, triggers this process. The binding of RIAM to talin could regulate this mechanism. However, the mechanosensitivity of the talin-RIAM complex has never been tested. It is also not known whether RIAM controls the mechanosensitivity of the talin-vinculin complex. To address these issues, we designed an in vitro microscopy assay with purified proteins in which the actomyosin force controls RIAM and vinculin-binding to talin. We demonstrate that actomyosin triggers RIAM dissociation from several talin domains. Actomyosin also provokes the sequential exchange of RIAM for vinculin on talin. The effect of RIAM on this force-dependent binding of vinculin to talin varies from one talin domain to another. This mechanism could allow talin to biochemically code a wide range of forces by selecting different combinations of partners.
High flavivirus structural plasticity demonstrated by a non-spherical morphological variant
Authors: Morrone Seamus R. , Chew Valerie S. Y. , Lim Xin-Ni , Ng Thiam-Seng , Kostyuchenko Victor A. , Zhang Shuijun , Wirawan Melissa , Chew Pau-Ling , Lee Jaime , Tan Joanne L. , Wang Jiaqi , Tan Ter Yong , Shi Jian , Screaton Gavin , Morais Marc C. , Lok Shee-Mei 
Published: June 2020

AbstractPrevious flavivirus (dengue and Zika viruses) studies showed largely spherical particles either with smooth or bumpy surfaces. Here, we demonstrate flavivirus particles have high structural plasticity by the induction of a non-spherical morphology at elevated temperatures: the club-shaped particle (clubSP), which contains a cylindrical tail and a disc-like head. Complex formation of DENV and ZIKV with Fab C10 stabilize the viruses allowing cryoEM structural determination to ~10 Å resolution. The caterpillar-shaped (catSP) Fab C10:ZIKV complex shows Fabs locking the E protein raft structure containing three E dimers. However, compared to the original spherical structure, the rafts have rotated relative to each other. The helical tail structure of Fab C10:DENV3 clubSP showed although the Fab locked an E protein dimer, the dimers have shifted laterally. Morphological diversity, including clubSP and the previously identified bumpy and smooth-surfaced spherical particles, may help flavivirus survival and immune evasion.
Setting benchmarks for modelling gas–surface interactions using coherent control of rotational orientation states
Authors: Alkoby Yosef , Chadwick Helen , Godsi Oded , Labiad Hamza , Bergin Matthew , Cantin Joshua T. , Litvin Ilya , Maniv Tsofar , Alexandrowicz Gil 
Published: June 2020

AbstractThe coherent evolution of a molecular quantum state during a molecule-surface collision is a detailed descriptor of the interaction potential which was so far inaccessible to measurements. Here we use a magnetically controlled molecular beam technique to study the collision of rotationally oriented ground state hydrogen molecules with a lithium fluoride surface. The coherent control nature of the technique allows us to measure the changes in the complex amplitudes of the rotational projection quantum states, and express them using a scattering matrix formalism. The quantum state-to-state transition probabilities we extract reveal a strong dependency of the molecule-surface interaction on the rotational orientation of the molecules, and a remarkably high probability of the collision flipping the rotational orientation. The scattering matrix we obtain from the experimental data delivers an ultra-sensitive benchmark for theory to reproduce, guiding the development of accurate theoretical models for the interaction of H2 with a solid surface.
Mass spectrometry reveals the chemistry of formaldehyde cross-linking in structured proteins
Authors: Tayri-Wilk Tamar , Slavin Moriya , Zamel Joanna , Blass Ayelet , Cohen Shon , Motzik Alex , Sun Xue , Shalev Deborah E. , Ram Oren , Kalisman Nir 
Published: June 2020

AbstractWhole-cell cross-linking coupled to mass spectrometry is one of the few tools that can probe protein–protein interactions in intact cells. A very attractive reagent for this purpose is formaldehyde, a small molecule which is known to rapidly penetrate into all cellular compartments and to preserve the protein structure. In light of these benefits, it is surprising that identification of formaldehyde cross-links by mass spectrometry has so far been unsuccessful. Here we report mass spectrometry data that reveal formaldehyde cross-links to be the dimerization product of two formaldehyde-induced amino acid modifications. By integrating the revised mechanism into a customized search algorithm, we identify hundreds of cross-links from in situ formaldehyde fixation of human cells. Interestingly, many of the cross-links could not be mapped onto known atomic structures, and thus provide new structural insights. These findings enhance the use of formaldehyde cross-linking and mass spectrometry for structural studies.
Capturing transient antibody conformations with DNA origami epitopes
Authors: Zhang Ping , Liu Xiaoguo , Liu Pi , Wang Fei , Ariyama Hirotaka , Ando Toshio , Lin Jianping , Wang Lihua , Hu Jun , Li Bin , Fan Chunhai 
Published: June 2020

AbstractRevealing antibody-antigen interactions at the single-molecule level will deepen our understanding of immunology. However, structural determination under crystal or cryogenic conditions does not provide temporal resolution for resolving transient, physiologically or pathologically relevant functional antibody-antigen complexes. Here, we develop a triangular DNA origami framework with site-specifically anchored and spatially organized artificial epitopes to capture transient conformations of immunoglobulin Gs (IgGs) at room temperature. The DNA origami epitopes (DOEs) allows programmed spatial distribution of epitope spikes, which enables direct imaging of functional complexes with atomic force microscopy (AFM). We establish the critical dependence of the IgG avidity on the lateral distance of epitopes within 3–20 nm at the single-molecule level. High-speed AFM imaging of transient conformations further provides structural and dynamic evidence for the IgG avidity from monovalent to bivalent in a single event, which sheds light on various applications including virus neutralization, diagnostic detection and cancer immunotherapy.
Combining predictive coding and neural oscillations enables online syllable recognition in natural speech
Authors: Hovsepyan Sevada , Olasagasti Itsaso , Giraud Anne-Lise 
Published: June 2020

AbstractOn-line comprehension of natural speech requires segmenting the acoustic stream into discrete linguistic elements. This process is argued to rely on theta-gamma oscillation coupling, which can parse syllables and encode them in decipherable neural activity. Speech comprehension also strongly depends on contextual cues that help predicting speech structure and content. To explore the effects of theta-gamma coupling on bottom-up/top-down dynamics during on-line syllable identification, we designed a computational model (Precoss—predictive coding and oscillations for speech) that can recognise syllable sequences in continuous speech. The model uses predictions from internal spectro-temporal representations of syllables and theta oscillations to signal syllable onsets and duration. Syllable recognition is best when theta-gamma coupling is used to temporally align spectro-temporal predictions with the acoustic input. This neurocomputational modelling work demonstrates that the notions of predictive coding and neural oscillations can be brought together to account for on-line dynamic sensory processing.
Structural basis of host protein hijacking in human T-cell leukemia virus integration
Authors: Bhatt Veer , Shi Ke , Salamango Daniel J. , Moeller Nicholas H. , Pandey Krishan K. , Bera Sibes , Bohl Heather O. , Kurniawan Fredy , Orellana Kayo , Zhang Wei , Grandgenett Duane P. , Harris Reuben S. , Sundborger-Lunna Anna C. , Aihara Hideki 
Published: June 2020

AbstractIntegration of the reverse-transcribed viral DNA into host chromosomes is a critical step in the life-cycle of retroviruses, including an oncogenic delta(δ)-retrovirus human T-cell leukemia virus type-1 (HTLV-1). Retroviral integrase forms a higher order nucleoprotein assembly (intasome) to catalyze the integration reaction, in which the roles of host factors remain poorly understood. Here, we use cryo-electron microscopy to visualize the HTLV-1 intasome at 3.7-Å resolution. The structure together with functional analyses reveal that the B56γ (B’γ) subunit of an essential host enzyme, protein phosphatase 2 A (PP2A), is repurposed as an integral component of the intasome to mediate HTLV-1 integration. Our studies reveal a key host-virus interaction underlying the replication of an important human pathogen and highlight divergent integration strategies of retroviruses.
Efficient evaluation of quantum observables using entangled measurements
Authors: Hamamura Ikko , Imamichi Takashi 
Published: June 2020

AbstractThe advent of cloud quantum computing has led to the rapid development of quantum algorithms. In particular, it is necessary to study variational quantum-classical hybrid algorithms, which are executable on noisy intermediate-scale quantum (NISQ) computers. Evaluations of observables appear frequently in the variational quantum-classical hybrid algorithms for NISQ computers. By speeding up the evaluation of observables, it is possible to realize a faster algorithm and save resources of quantum computers. Grouping of observables with separable measurements has been conventionally used, and the grouping with entangled measurements has also been proposed recently by several teams. In this paper, we show that entangled measurements enhance the efficiency of evaluation of observables, both theoretically and experimentally, by taking into account the covariance effect, which may affect the quality of evaluation of observables. We also propose using a part of entangled measurements for grouping to keep the depth of extra gates constant. Our proposed method is expected to be used in conjunction with other related studies. We hope that entangled measurements would become crucial resources, not only for joint measurements but also for quantum information processing.
A clinically and genomically annotated nerve sheath tumor biospecimen repository
Authors: Pollard Kai , Banerjee Jineta , Doan Xengie , Wang Jiawan , Guo Xindi , Allaway Robert , Langmead Shannon , Slobogean Bronwyn , Meyer Christian F. , Loeb David M. , Morris Carol D. , Belzberg Allan J. , Blakeley Jaishri O. , Rodriguez Fausto J. , Guinney Justin , Gosline Sara J. C. , Pratilas Christine A. 
Published: June 2020

AbstractNerve sheath tumors occur as a heterogeneous group of neoplasms in patients with neurofibromatosis type 1 (NF1). The malignant form represents the most common cause of death in people with NF1, and even when benign, these tumors can result in significant disfigurement, neurologic dysfunction, and a range of profound symptoms. Lack of human tissue across the peripheral nerve tumors common in NF1 has been a major limitation in the development of new therapies. To address this unmet need, we have created an annotated collection of patient tumor samples, patient-derived cell lines, and patient-derived xenografts, and carried out high-throughput genomic and transcriptomic characterization to serve as a resource for further biologic and preclinical therapeutic studies. In this work, we release genomic and transcriptomic datasets comprised of 55 tumor samples derived from 23 individuals, complete with clinical annotation. All data are publicly available through the NF Data Portal and at http://synapse.org/jhubiobank.
BAGLS, a multihospital Benchmark for Automatic Glottis Segmentation
Authors: Gómez Pablo , Kist Andreas M. , Schlegel Patrick , Berry David A. , Chhetri Dinesh K. , Dürr Stephan , Echternach Matthias , Johnson Aaron M. , Kniesburges Stefan , Kunduk Melda , Maryn Youri , Schützenberger Anne , Verguts Monique , Döllinger Michael 
Published: June 2020

AbstractLaryngeal videoendoscopy is one of the main tools in clinical examinations for voice disorders and voice research. Using high-speed videoendoscopy, it is possible to fully capture the vocal fold oscillations, however, processing the recordings typically involves a time-consuming segmentation of the glottal area by trained experts. Even though automatic methods have been proposed and the task is particularly suited for deep learning methods, there are no public datasets and benchmarks available to compare methods and to allow training of generalizing deep learning models. In an international collaboration of researchers from seven institutions from the EU and USA, we have created BAGLS, a large, multihospital dataset of 59,250 high-speed videoendoscopy frames with individually annotated segmentation masks. The frames are based on 640 recordings of healthy and disordered subjects that were recorded with varying technical equipment by numerous clinicians. The BAGLS dataset will allow an objective comparison of glottis segmentation methods and will enable interested researchers to train their own models and compare their methods.
Transcriptome data of temporal and cingulate cortex in the Rett syndrome brain
Authors: Aldinger Kimberly A. , Timms Andrew E. , MacDonald James W. , McNamara Hanna K. , Herstein Jennifer S. , Bammler Theo K. , Evgrafov Oleg V. , Knowles James A. , Levitt Pat 
Published: June 2020

AbstractRett syndrome is an X-linked neurodevelopmental disorder caused by mutation in the methyl-CpG-binding protein 2 gene (MECP2) in the majority of cases. We describe an RNA sequencing dataset of postmortem brain tissue samples from four females clinically diagnosed with Rett syndrome and four age-matched female donors. The dataset contains 16 transcriptomes, including two brain regions, temporal and cingulate cortex, for each individual. We compared our dataset with published transcriptomic analyses of postmortem brain tissue from Rett syndrome and found consistent gene expression alterations among regions of the cerebral cortex. Our data provide a valuable resource to explore the biology of the human brain in Rett syndrome.