bluuebunny/crossref_metadata_2025 huggingface dataset:
Azimuthal Dependence of GNSS‐R Scattering Cross‐Section in Hurricanes
Authors: Balasubramaniam Rajeswari , Ruf Christopher
Published: June 2020

Global Navigation Satellite System‐Reflectometry (GNSS‐R) measurements of the ocean surface are sensitive to roughness scales ranging from a few cms to several kms. Inside a hurricane the surface roughness changes drastically due to varying sea age and fetch length conditions and complex wave‐wave interactions caused by its cyclonic rotation and translational motion. As a result, the relationship between the surface roughness at different scale sizes becomes azimuthally dependent, as does the relationship between scattering cross‐section and wind speed as represented by a Geophysical Model Function (GMF). In this work, the impact of this azimuthal variation on the scattering cross‐section is assessed. An empirical GMF is constructed using measurements by the NASA CYclone GNSS (CYGNSS) matched to HWRF reanalysis surface winds for 19 hurricanes in 2017 and 2018. The analysis reveals a 2–8% variation in scattering cross‐section due to azimuthal location, and the magnitude of the azimuthal dependence is found to grow with wind speed.
Assessing Temporal Changes in Groundwater Recharge Using Spatial Variations in Groundwater Ages
Authors: McCallum James L. , Dogramaci Shawan , Bai Albert , Cook Peter G. , Engdahl Nicholas B. , Simmons Craig T. , Skrzypek Grzegorz , Grierson Pauline F.
Published: June 2020

Determining variations in groundwater replenishment over a variety of time scales remains a challenge in the management and protection of groundwater resources. Specifically, capacity to use hydraulic data collected in small windows of time to infer long‐term changes can be limited by system responses. Groundwater ages offer an alternative approach as they represent the time since recharge occurred. Here we use spatial variations in groundwater ages and environmental tracer concentrations to infer temporal variations in groundwater recharge and apply the method to a mine site in northwest Australia, where a stream has been modified from ephemeral to perennial, resulting in enhanced recharge to groundwater. Measurements of 14C and CFC‐12 at five transects along an ephemeral stream were interpreted with the new model to identify recharge rates and the proportion of recharge attributable to enhanced versus natural recharge from flood events. Enhanced recharge varied between 0.03 and 0.66 m/year compared to flood‐generated recharge values ranging between 0.07 and 1.3 m/year. Our results show that spatial variations of groundwater ages and environmental tracer concentrations preserve information about past flow regimes. While our study has demonstrated decadal variations in recharge, application of the method on larger scales could infer much greater extent of temporal variability in recharge, with the potential for significant insight into climate effects on groundwater.
Exosomes: roles and therapeutic potential in osteoarthritis
Authors: Ni Zhenhong , Zhou Siru , Li Song , Kuang Liang , Chen Hangang , Luo Xiaoqing , Ouyang Junjie , He Mei , Du Xiaolan , Chen Lin
Published: June 2020

Exosomes participate in many physiological and pathological processes by regulating cell–cell communication, which are involved in numerous diseases, including osteoarthritis (OA). Exosomes are detectable in the human articular cavity and were observed to change with OA progression. Several joint cells, including chondrocytes, synovial fibroblasts, osteoblasts, and tenocytes, can produce and secrete exosomes that influence the biological effects of targeted cells. In addition, exosomes from stem cells can protect the OA joint from damage by promoting cartilage repair, inhibiting synovitis, and mediating subchondral bone remodeling. This review summarizes the roles and therapeutic potential of exosomes in OA and discusses the perspectives and challenges related to exosome-based treatment for OA patients in the future.
Spin injection through energy-band symmetry matching with high spin polarization in atomically controlled ferromagnet/ferromagnet/semiconductor structures
Authors: Yamada Michihiro , Kuroda Fumiaki , Tsukahara Makoto , Yamada Shinya , Fukushima Tetsuya , Sawano Kentarou , Oguchi Tamio , Hamaya Kohei
Published: June 2020

Electrical injection of spin-polarized electrons from ferromagnets into semiconductors has been generally demonstrated through a tunneling process with insulator barrier layers that can dominate the device performance, including the electric power at the electrodes. Here, we show an efficient spin injection technique for a semiconductor using an atomically controlled ferromagnet/ferromagnet/semiconductor heterostructure with low-resistive Schottky-tunnel barriers. On the basis of symmetry matching of the electronic bands between the top highly spin-polarized ferromagnet and the semiconductor, the magnitude of the spin signals in lateral spin-valve devices can be enhanced by up to one order of magnitude compared to those obtained with conventional ferromagnet/semiconductor structures. This approach provides a new solution for the simultaneous achievement of highly efficient spin injection and low electric power at the electrodes in semiconductor devices, leading to novel semiconductor spintronic architectures at room temperature.
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

MLKL 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

Profiling 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

Physical 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

Class 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

Bosonic 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

Quadrupole 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

Cells 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

Previous 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

The 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

Whole-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

Revealing 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

On-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

Integration 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

The 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.
Author Correction: Integrative molecular and clinical modeling of clinical outcomes to PD1 blockade in patients with metastatic melanoma
Authors: Liu David , Schilling Bastian , Liu Derek , Sucker Antje , Livingstone Elisabeth , Jerby-Arnon Livnat , Zimmer Lisa , Gutzmer Ralf , Satzger Imke , Loquai Carmen , Grabbe Stephan , Vokes Natalie , Margolis Claire A. , Conway Jake , He Meng Xiao , Elmarakeby Haitham , Dietlein Felix , Miao Diana , Tracy Adam , Gogas Helen , Goldinger Simone M. , Utikal Jochen , Blank Christian U. , Rauschenberg Ricarda , von Bubnoff Dagmar , Krackhardt Angela , Weide Benjamin , Haferkamp Sebastian , Kiecker Felix , Izar Ben , Garraway Levi , Regev Aviv , Flaherty Keith , Paschen Annette , Van Allen Eliezer M. , Schadendorf Dirk
Published: June 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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

Nerve 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

Laryngeal 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

Rett 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.
Plant traits and vegetation data from climate warming experiments along an 1100 m elevation gradient in Gongga Mountains, China
Authors: Vandvik Vigdis , Halbritter Aud H. , Yang Yan , He Hai , Zhang Li , Brummer Alexander B. , Klanderud Kari , Maitner Brian S. , Michaletz Sean T. , Sun Xiangyang , Telford Richard J. , Wang Genxu , Althuizen Inge H. J. , Henn Jonathan J. , Garcia William Fernando Erazo , Gya Ragnhild , Jaroszynska Francesca , Joyce Blake L. , Lehman Rebecca , Moerland Michelangelo Sergio , Nesheim-Hauge Elisabeth , Nordås Linda Hovde , Peng Ahui , Ponsac Claire , Seltzer Lorah , Steyn Christien , Sullivan Megan K. , Tjendra Jesslyn , Xiao Yao , Zhao Xiaoxiang , Enquist Brian J.
Published: June 2020

Functional trait data enhance climate change research by linking climate change, biodiversity response, and ecosystem functioning, and by enabling comparison between systems sharing few taxa. Across four sites along a 3000–4130 m a.s.l. gradient spanning 5.3 °C in growing season temperature in Mt. Gongga, Sichuan, China, we collected plant functional trait and vegetation data from control plots, open top chambers (OTCs), and reciprocally transplanted vegetation turfs. Over five years, we recorded vascular plant composition in 140 experimental treatment and control plots. We collected trait data associated with plant resource use, growth, and life history strategies (leaf area, leaf thickness, specific leaf area, leaf dry matter content, leaf C, N and P content and C and N isotopes) from local populations and from experimental treatments. The database consists of 6,671 plant records and 36,743 trait measurements (increasing the trait data coverage of the regional flora by 500%) covering 11 traits and 193 plant taxa (ca. 50% of which have no previous published trait data) across 37 families.
Massive online data annotation, crowdsourcing to generate high quality sleep spindle annotations from EEG data
Authors: Lacourse Karine , Yetton Ben , Mednick Sara , Warby Simon C.
Published: June 2020

Spindle event detection is a key component in analyzing human sleep. However, detection of these oscillatory patterns by experts is time consuming and costly. Automated detection algorithms are cost efficient and reproducible but require robust datasets to be trained and validated. Using the MODA (Massive Online Data Annotation) platform, we used crowdsourcing to produce a large open-source dataset of high quality, human-scored sleep spindles (5342 spindles, from 180 subjects). We evaluated the performance of three subtype scorers: “experts, researchers and non-experts”, as well as 7 previously published spindle detection algorithms. Our findings show that only two algorithms had performance scores similar to human experts. Furthermore, the human scorers agreed on the average spindle characteristics (density, duration and amplitude), but there were significant age and sex differences (also observed in the set of detected spindles). This study demonstrates how the MODA platform can be used to generate a highly valid open source standardized dataset for researchers to train, validate and compare automated detectors of biological signals such as the EEG.
Multi-channel EEG recording during motor imagery of different joints from the same limb
Authors: Ma Xuelin , Qiu Shuang , He Huiguang
Published: June 2020

Motor imagery (MI) is one of the important brain-computer interface (BCI) paradigms, which can be used to control peripherals without external stimulus. Imagining the movements of different joints of the same limb allows intuitive control of the outer devices. In this report, we describe an open access multi-subject dataset for MI of different joints from the same limb. This experiment collected data from twenty-five healthy subjects on three tasks: 1) imagining the movement of right hand, 2) imagining the movement of right elbow, and 3) keeping resting with eyes open, which results in a total of 22,500 trials. The dataset provided includes data of three stages: 1) raw recorded data, 2) pre-processed data after operations such as artifact removal, and 3) trial data that can be directly used for feature extraction and classification. Different researchers can reuse the dataset according to their needs. We expect that this dataset will facilitate the analysis of brain activation patterns of the same limb and the study of decoding techniques for MI.
Combating climate change with matching-commitment agreements
Authors: Molina Chai , Akçay Erol , Dieckmann Ulf , Levin Simon A. , Rovenskaya Elena A.
Published: June 2020

Countries generally agree that global greenhouse gas emissions are too high, but prefer other countries reduce emissions rather than reducing their own. The Paris Agreement is intended to solve this collective action problem, but is likely insufficient. One proposed solution is a matching-commitment agreement, through which countries can change each other’s incentives by committing to conditional emissions reductions, before countries decide on their unconditional reductions. Here, we study matching-commitment agreements between two heterogeneous countries. We find that such agreements (1) incentivize both countries to make matching commitments that in turn incentivize efficient emissions reductions, (2) reduce emissions from those expected without an agreement, and (3) increase both countries’ welfare. Matching-commitment agreements are attractive because they do not require a central enforcing authority and only require countries to fulfil their promises; countries are left to choose their conditional and unconditional emissions reductions according to their own interests.
Publisher Correction: Optical clumped isotope thermometry of carbon dioxide
Authors: Prokhorov Ivan , Kluge Tobias , Janssen Christof
Published: June 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
System dynamics modelling of urbanization under energy constraints in China
Authors: Gu Chaolin , Ye Xinyue , Cao Qiwen , Guan Weihua , Peng Chong , Wu Yutong , Zhai Wei
Published: June 2020

The rapid urbanization in China has been associated with a growing hunger for energy consumption and steadily-increasing CO2 emissions. In this paper, an integrated system dynamics model composed of four sub-models is developed to simulate the urbanization and energy consumption in China from 1998 to 2050. Three scenarios are provided: accelerated economic development, emission reduction constraint, and low-carbon oriented. The result reveals that rapid economic growth and sufficient energy supply will foster China’s urbanization in all three scenarios. Under the low carbon transition scenario, China’s urbanization rate is expected to reach 76.41% in 2050, both reducing carbon emissions and promoting eco-friendly development. All three scenarios witness a dramatic growth of residential energy consumption and a steady increase of industrial energy consumption. China still has a long way to achieve the low-carbon transition goal. China should promote renewable resources and energy, pursue a low-carbon lifestyle, and reduce energy intensity over the next few decades.
Daytime mid-latitude F2-layer Q-disturbances: A formation mechanism
Authors: Perrone Loredana , Mikhailov Andrey V. , Nusinov Anatoly A.
Published: June 2020

Negative and positive near noontime prolonged (≥3 hours) F2-layer Q-disturbances with deviations in NmF2 > 35% occurred at Rome have been analyzed using aeronomic parameters inferred from fp180 (plasma frequency at 180 km height) and foF2 observations. Both types of NmF2 perturbations occur under quiet (daily Ap < 15 nT) geomagnetic conditions. Day-to-day atomic oxygen [O] variations at F2-region heights specify the type (positive or negative) of Q-disturbance. The [O] concentration is larger on positive and is less on negative Q-disturbance days compared to reference days. This difference takes place not only on average but for all individual Q-disturbances in question. An additional contribution to Q-disturbances formation is provided by solar EUV day-to-day variations. Negative Q-disturbance days are characterized by lower hmF2 while positive – by larger hmF2 compared to reference days. This is due to larger average Tex and vertical plasma drift W on positive Q-disturbance days, the inverse situation takes place for negative Q-disturbance days. Day-to-day changes in global thermospheric circulation may be considered as a plausible mechanism. The analyzed type of F2-layer Q-disturbances can be explained in the framework of contemporary understanding of the thermosphere-ionosphere interaction based on solar and geomagnetic activity as the main drivers.
Aging and trace elements in human coronal tooth dentine
Authors: Fernández-Escudero Ana C. , Legaz Isabel , Prieto-Bonete Gemma , López-Nicolás Manuel , Maurandi-López Antonio , Pérez-Cárceles María D.
Published: June 2020

Teeth are a fundamental tool in forensic odontology for identification in a legal context of those individuals who cannot be identified visually or by other means. Dentine presents physiological exchanges of in trace elements after a period of mineralization and several factors can affect its concentration. The aim of this study was to investigate the concentration of 25 trace elements in the coronal dentine according to sex and type of tooth to determine their relationship with age. A total of 25 trace elements were analyzed in 150 human coronal dentine. Teeth were classified into three age groups, sex and tooth type. The trace elements were grouped as potentially toxic or essential. Inductively Coupled Plasma-Mass Spectrometry and Atomic Emission Spectroscopy were used. The toxic and essential elements were detected in the following order of concentration: Al > Pb > Sn > Li > As > Cd and Ca > P > Mg > Na > S > K > Sr > Zn > Ba > Fe > B > Ti > Mn > Cr > Ni > Cu > Co > Se > V. Our findings show an increase in the concentration of toxic (Pb, Li and Sn) and essential (B, Ba, K, Sr, S and Mg) elements in coronal dentin related to the age of the teeth, regardless of sex. The concentrations of Pb and K in dentin of molars and premolars are the elements that best relate their variations with age. In view of our results, the analysis of these trace elements in dentin in combination with other types of techniques could be established as an element to consider in age dating studies in different forensic situations.
Transcriptional Regulation of the Angptl8 Gene by Hepatocyte Nuclear Factor-1 in the Murine Liver
Authors: Watanabe Takuya , Ozawa Atsushi , Masuda Shinnosuke , Yoshino Satoshi , Ishida Emi , Kondo Yuri , Matsumoto Shunichi , Katano-Toki Akiko , Horiguchi Kazuhiko , Nakajima Yasuyo , Yamada Eijiro , Tomaru Takuya , Saito Tsugumichi , Ishii Sumiyasu , Shibusawa Nobuyuki , Okada Shuichi , Satoh Tetsurou , Yamada Masanobu
Published: June 2020

Brief refeeding times (~60 min) enhanced hepatic Angptl8 expression in fasted mice. We cloned the mouse Angptl8 promoter region to characterise this rapid refeeding-induced increase in hepatic Angptl8 expression. Deletion of the −309/−60 promoter region significantly attenuated basal promoter activity in hepatocytes. A computational motif search revealed a potential binding motif for hepatocyte nuclear factor 1α/1β (HNF-1α/β) at −84/−68 bp of the promoter. Mutation of the HNF-1 binding site significantly decreased the promoter activity in hepatocytes, and the promoter carrying the mutated HNF-1 site was not transactivated by co-transfection of HNF-1 in a non-hepatic cell line. Silencing Hnf-1 in hepatoma cells and mouse primary hepatocytes reduced Angptl8 protein levels. Electrophoretic mobility-shift assays confirmed direct binding of Hnf-1 to its Angptl8 promoter binding motif. Hnf-1α expression levels increased after short-term refeeding, paralleling the enhanced in vivo expression of the Angptl8 protein. Chromatin immunoprecipitation (ChIP) confirmed the recruitment of endogenous Hnf-1 to the Angptl8 promoter region. Insulin-treated primary hepatocytes showed increased expression of Angptl8 protein, but knockdown of Hnf-1 completely abolished this enhancement. HNF-1 appears to play essential roles in the rapid refeeding-induced increases in Angptl8 expression. HNF-1α may therefore represent a primary medical target for ANGPTL8-related metabolic abnormalities. The study revealed the transcriptional regulation of the mouse hepatic Angptl8 gene by HNF-1.
Antibiotic effect and microbiome persistence vary along the European seabass gut
Authors: Kokou Fotini , Sasson Goor , Mizrahi Itzhak , Cnaani Avner
Published: June 2020

The constant increase in aquaculture production has led to extensive use of antibiotics as a means to prevent and treat diseases, with adverse implications on the environment, animal health and commensal microbes. Gut microbes are important for the host proper functioning, thus evaluating such impacts is highly crucial. Examining the antibiotic impact on gut segments with different physiological roles may provide insight into their effects on these microhabitats. Hence, we evaluated the effect of feed-administrated antibiotics on the composition and metabolic potential of the gut microbiome in the European seabass, an economically important aquaculture species. We used quantitative PCR to measure bacterial copy numbers, and amplicon sequencing of the 16S rRNA gene to describe the composition along the gut, after 7-days administration of two broad-range antibiotic mixtures at two concentrations. While positive correlation was found between antibiotic concentration and bacterial abundance, we showed a differential effect of antibiotics on the composition along the gut, highlighting distinct impacts on these microbial niches. Moreover, we found an increase in abundance of predicted pathways related to antibiotic-resistance. Overall, we show that a high portion of the European seabass gut microbiome persisted, despite the examined antibiotic intake, indicating high stability to perturbations.
Effect of 9-month Pilates program on sagittal spinal curvatures and hamstring extensibility in adolescents: randomised controlled trial
Authors: González-Gálvez Noelia , Marcos-Pardo Pablo Jorge , Trejo-Alfaro Henry , Vaquero-Cristóbal Raquel
Published: June 2020

The percentage of spine misalignment increases during the childhood and adolescence stages. The Pilates method has been associated with an improvement in the sagittal spine disposition, but no studies have been conducted on adolescents. Therefore, the present study aimed to evaluate the effectiveness of a 9-month Pilates exercise program (PEP) on hamstring extensibility and sagittal spinal curvatures on adolescents. This randomised controlled trial included 236 adolescents. The experimental group (EG) received a PEP (9 months, 2 sessions/week, 15 minutes/session). The control group (CG) did not receive any intervention. Hamstring extensibility was measured with the passive and active straight leg raise and toe-touch tests. Sagittal spinal curvatures and pelvic tilt was assessed in relaxed standing, active alignment and toe-touch test positions. The EG had significant changes in hamstring extensibility, lumbar curvature and pelvic tilt in standing sagittal curvature. The CG became significantly worse in thoracic kyphosis in standing. This study provides evidence of nine-months of a PEP increased the hamstring extensibility; averted the increase of the thoracic curvature, and decreased the curvature of the lumbar lordosis and pelvic tilt in standing position; avoided a greater increase of thoracic curvature in active alignment in standing position; and avoided the increase of thoracic curvature in trunk flexion.
Effects of magnetic monopoles charge on the cracking reversal processes in artificial square ices
Authors: de Paiva T. S. , Rodrigues J. H. , Mól L. A. S. , Pereira A. R. , Borme J. , Freitas P. P. , de Araujo C. I. L.
Published: June 2020

In this paper we perform nanofabrication of square artificial spin ices with different lattice parameters, in order to investigate the roles of vertex excitation on the features of the system. In particular, the character of magnetic charge distribution asymmetry on the vertices are observed under magnetic hysteresis loop experiments. We then compare our results with simulation using an emergent Hamiltonian containing objects such as magnetic monopoles and dipoles in the vertices of the array (instead of the usual Hamiltonian based on the dipolar interactions among the magnetic nanoislands). All possible interactions between these objects are considered (monopole-monopole, monopole-dipole and dipole-dipole). Using realistic parameters we observe very good match between experiments and theory, which allow us to better understand the system dynamics in function of monopole charge intensity.
Boosting the sterile insect technique with pyriproxyfen increases tsetse flies Glossina palpalis gambiensis sterilization in controlled conditions
Authors: Laroche L. , Ravel S. , Baldet T. , Lancelot R. , Chandre F. , Rossignol M. , Le Goff V. , Duhayon M. , Fafet J.-F. , Parker A. G. , Bouyer J.
Published: June 2020

Tsetse flies (Diptera: Glossinidae) are the main vectors of animal and human trypanosomoses in Africa. The Sterile Insect Technique (SIT) has proven effective in controlling tsetse flies when applied to isolated populations but necessitates the production of large numbers of sterile males. A new approach, called boosted SIT, combining SIT with the contamination of wild females by sterile males coated with biocides has been proposed for large-scale control of vector populations. The aim of the study was to evaluate this new approach using pyriproxyfen on the riverine species Glossina palpalis gambiensis (Vanderplank, 1949) in the laboratory. The contamination dose and persistence of pyriproxyfen on sterile males, the impact of pyriproxyfen on male survival, and the dynamics of pyriproxyfen transfer from a sterile male to a female during mating, as well as the impact of pyriproxyfen on pupal production and adult emergence, were evaluated in the laboratory. For this purpose, a method of treatment by impregnating sterile males with a powder containing 40% pyriproxyfen has been developed. The results showed that the pyriproxyfen has no impact on the survival of sterile males. Pyriproxyfen persisted on sterile males for up to 10 days at a dose of 100 ng per fly. In addition, the horizontal transfer of pyriproxyfen from a treated sterile male to a female during mating could be measured with an average of 50 ng of pyriproxyfen transferred. After contacts without mating, the average quantity transferred was more than 10 ng. Finally, the pyriproxyfen powder was very effective on G. p. gambiensis leading to 0% emergence of the pupae produced by contaminated females. These promising results must be confirmed in the field. A large-scale assessment of this boosted pyriproxyfen-based SIT approach will be carried out against tsetse flies in Senegal (West Africa).