bluuebunny/crossref_metadata_2025_split huggingface dataset:
Splicing-associated chromatin signatures: a combinatorial and position-dependent role for histone marks in splicing definition
Authors: Agirre E. , Oldfield A. J. , Bellora N. , Segelle A. , Luco R. F. 
Published: January 2021

AbstractAlternative splicing relies on the combinatorial recruitment of splicing regulators to specific RNA binding sites. Chromatin has been shown to impact this recruitment. However, a limited number of histone marks have been studied at a global level. In this work, a machine learning approach, applied to extensive epigenomics datasets in human H1 embryonic stem cells and IMR90 foetal fibroblasts, has identified eleven chromatin modifications that differentially mark alternatively spliced exons depending on the level of exon inclusion. These marks act in a combinatorial and position-dependent way, creating characteristic splicing-associated chromatin signatures (SACS). In support of a functional role for SACS in coordinating splicing regulation, changes in the alternative splicing of SACS-marked exons between ten different cell lines correlate with changes in SACS enrichment levels and recruitment of the splicing regulators predicted by RNA motif search analysis. We propose the dynamic nature of chromatin modifications as a mechanism to rapidly fine-tune alternative splicing when necessary.
Quantum frequency doubling in the topological insulator Bi2Se3
Authors: He Pan , Isobe Hiroki , Zhu Dapeng , Hsu Chuang-Han , Fu Liang , Yang Hyunsoo 
Published: January 2021

AbstractThe nonlinear Hall effect due to Berry curvature dipole (BCD) induces frequency doubling, which was recently observed in time-reversal-invariant materials. Here we report novel electric frequency doubling in the absence of BCD on a surface of the topological insulator Bi2Se3 under zero magnetic field. We observe that the frequency-doubling voltage transverse to the applied ac current shows a threefold rotational symmetry, whereas it forbids BCD. One of the mechanisms compatible with the symmetry is skew scattering, arising from the inherent chirality of the topological surface state. We introduce the Berry curvature triple, a high-order moment of the Berry curvature, to explain skew scattering under the threefold rotational symmetry. Our work paves the way to obtain a giant second-order nonlinear electric effect in high mobility quantum materials, as the skew scattering surpasses other mechanisms in the clean limit.
The nuclear envelope protein Net39 is essential for muscle nuclear integrity and chromatin organization
Authors: Ramirez-Martinez Andres , Zhang Yichi , Chen Kenian , Kim Jiwoong , Cenik Bercin K. , McAnally John R. , Cai Chunyu , Shelton John M. , Huang Jian , Brennan Ana , Evers Bret M. , Mammen Pradeep P. A. , Xu Lin , Bassel-Duby Rhonda , Liu Ning , Olson Eric N. 
Published: January 2021

AbstractLamins and transmembrane proteins within the nuclear envelope regulate nuclear structure and chromatin organization. Nuclear envelope transmembrane protein 39 (Net39) is a muscle nuclear envelope protein whose functions in vivo have not been explored. We show that mice lacking Net39 succumb to severe myopathy and juvenile lethality, with concomitant disruption in nuclear integrity, chromatin accessibility, gene expression, and metabolism. These abnormalities resemble those of Emery–Dreifuss muscular dystrophy (EDMD), caused by mutations in A-type lamins (LMNA) and other genes, like Emerin (EMD). We observe that Net39 is downregulated in EDMD patients, implicating Net39 in the pathogenesis of this disorder. Our findings highlight the role of Net39 at the nuclear envelope in maintaining muscle chromatin organization, gene expression and function, and its potential contribution to the molecular etiology of EDMD.
New generation geostationary satellite observations support seasonality in greenness of the Amazon evergreen forests
Authors: Hashimoto Hirofumi , Wang Weile , Dungan Jennifer L. , Li Shuang , Michaelis Andrew R. , Takenaka Hideaki , Higuchi Atsushi , Myneni Ranga B. , Nemani Ramakrishna R. 
Published: January 2021

AbstractAssessing the seasonal patterns of the Amazon rainforests has been difficult because of the paucity of ground observations and persistent cloud cover over these forests obscuring optical remote sensing observations. Here, we use data from a new generation of geostationary satellites that carry the Advanced Baseline Imager (ABI) to study the Amazon canopy. ABI is similar to the widely used polar orbiting sensor, the Moderate Resolution Imaging Spectroradiometer (MODIS), but provides observations every 10–15 min. Our analysis of NDVI data collected over the Amazon during 2018–19 shows that ABI provides 21–35 times more cloud-free observations in a month than MODIS. The analyses show statistically significant changes in seasonality over 85% of Amazon forest pixels, an area about three times greater than previously reported using MODIS data. Though additional work is needed in converting the observed changes in seasonality into meaningful changes in canopy dynamics, our results highlight the potential of the new generation geostationary satellites to help us better understand tropical ecosystems, which has been a challenge with only polar orbiting satellites.
In-situ generation of large numbers of genetic combinations for metabolic reprogramming via CRISPR-guided base editing
Authors: Wang Yu , Cheng Haijiao , Liu Yang , Liu Ye , Wen Xiao , Zhang Kun , Ni Xiaomeng , Gao Ning , Fan Liwen , Zhang Zhihui , Liu Jiao , Chen Jiuzhou , Wang Lixian , Guo Yanmei , Zheng Ping , Wang Meng , Sun Jibin , Ma Yanhe 
Published: January 2021

AbstractReprogramming complex cellular metabolism requires simultaneous regulation of multigene expression. Ex-situ cloning-based methods are commonly used, but the target gene number and combinatorial library size are severely limited by cloning and transformation efficiencies. In-situ methods such as multiplex automated genome engineering (MAGE) depends on high-efficiency transformation and incorporation of heterologous DNA donors, which are limited to few microorganisms. Here, we describe a Base Editor-Targeted and Template-free Expression Regulation (BETTER) method for simultaneously diversifying multigene expression. BETTER repurposes CRISPR-guided base editors and in-situ generates large numbers of genetic combinations of diverse ribosome binding sites, 5’ untranslated regions, or promoters, without library construction, transformation, and incorporation of DNA donors. We apply BETTER to simultaneously regulate expression of up to ten genes in industrial and model microorganismsCorynebacterium glutamicumandBacillus subtilis. Variants with improved xylose catabolism, glycerol catabolism, or lycopene biosynthesis are respectively obtained. This technology will be useful for large-scale fine-tuning of multigene expression in both genetically tractable and intractable microorganisms.
Determination of the Dzyaloshinskii-Moriya interaction using pattern recognition and machine learning
Authors: Kawaguchi Masashi , Tanabe Kenji , Yamada Keisuke , Sawa Takuya , Hasegawa Shun , Hayashi Masamitsu , Nakatani Yoshinobu 
Published: January 2021

AbstractMachine learning is applied to a large number of modern devices that are essential in building an energy-efficient smart society. Audio and face recognition are among the most well-known technologies that make use of such artificial intelligence. In materials research, machine learning is adapted to predict materials with certain functionalities, an approach often referred to as materials informatics. Here, we show that machine learning can be used to extract material parameters from a single image obtained in experiments. The Dzyaloshinskii–Moriya (DM) interaction and the magnetic anisotropy distribution of thin-film heterostructures, parameters that are critical in developing next-generation storage class magnetic memory technologies, are estimated from a magnetic domain image. Micromagnetic simulation is used to generate thousands of random images for training and model validation. A convolutional neural network system is employed as the learning tool. The DM exchange constant of typical Co-based thin-film heterostructures is studied using the trained system: the estimated values are in good agreement with experiments. Moreover, we show that the system can independently determine the magnetic anisotropy distribution, demonstrating the potential of pattern recognition. This approach can considerably simplify experimental processes and broaden the scope of materials research.
Predicting adsorption ability of adsorbents at arbitrary sites for pollutants using deep transfer learning
Authors: Wang Zhilong , Zhang Haikuo , Ren Jiahao , Lin Xirong , Han Tianli , Liu Jinyun , Li Jinjin 
Published: January 2021

AbstractAccurately evaluating the adsorption ability of adsorbents for heavy metal ions (HMIs) and organic pollutants in water is critical for the design and preparation of emerging highly efficient adsorbents. However, predicting adsorption capabilities of adsorbents at arbitrary sites is challenging, with currently unavailable measuring technology for active sites and the corresponding activities. Here, we present an efficient artificial intelligence (AI) approach to predict the adsorption ability of adsorbents at arbitrary sites, as a case study of three HMIs (Pb(II), Hg(II), and Cd(II)) adsorbed on the surface of a representative two-dimensional graphitic-C3N4. We apply the deep neural network and transfer learning to predict the adsorption capabilities of three HMIs at arbitrary sites, with the predicted results of Cd(II) > Hg(II) > Pb(II) and the root-mean-squared errors less than 0.1 eV. The proposed AI method has the same prediction accuracy as the ab initio DFT calculation, but is millions of times faster than the DFT to predict adsorption abilities at arbitrary sites and only requires one-tenth of datasets compared to training from scratch. We further verify the adsorption capacity of g-C3N4 towards HMIs experimentally and obtain results consistent with the AI prediction. It indicates that the presented approach is capable of evaluating the adsorption ability of adsorbents efficiently, and can be further extended to other interdisciplines and industries for the adsorption of harmful elements in aqueous solution.
Risks of poor asthma outcome in 14,405 children and young people in London
Authors: Levy Mark L. 
Published: January 2021

AbstractThis is a 12-month retrospective data analysis (2018/19) of asthma risk factors in 350 North West London general practices. Fourteen thousand four hundred and five of the 482,029 (40% female) children and young people (CYP) had diagnosed asthma. Exacerbations are as follows: (i) 749 (5%) CYP had 797 hospital admissions; 32 (<1%) had 2–6; (ii) 910 (6%) had 1168 recorded asthma attacks; 170 (1%) had 2–12; (iii) 1485 (10%) had 2123 oral corticosteroid courses; 408 (3%) had 2–11. Excess short-acting bronchodilators were prescribed in over half of the CYP. Of the 10,077 (70%) CYP prescribed inhaled corticosteroid preventers, 7279 (72%) were issued with <4 ICS inhaler prescriptions during the year; these CYP accounted for 11% of the admission spells. In all, 30% of CYP had poor symptom control. At least 10% of the CYP having had recent attacks are at risk and dashboards such as those available in North West London could easily facilitate recognition of risk and optimisation of care.
Measurement-free preparation of grid states
Authors: Hastrup Jacob , Park Kimin , Brask Jonatan Bohr , Filip Radim , Andersen Ulrik Lund 
Published: January 2021

AbstractQuantum computing potentially offers exponential speed-ups over classical computing for certain tasks. A central, outstanding challenge to making quantum computing practical is to achieve fault tolerance, meaning that computations of any length or size can be realized in the presence of noise. The Gottesman-Kitaev-Preskill code is a promising approach toward fault-tolerant quantum computing, encoding logical qubits into grid states of harmonic oscillators. However, for the code to be fault tolerant, the quality of the grid states has to be extremely high. Approximate grid states have recently been realized experimentally, but their quality is still insufficient for fault tolerance. Current implementable protocols for generating grid states rely on measurements of ancillary qubits combined with either postselection or feed forward. Implementing such measurements take up significant time during which the states decohere, thus limiting their quality. Here, we propose a measurement-free preparation protocol, which deterministically prepares arbitrary logical grid states with a rectangular or hexagonal lattice. The protocol can be readily implemented in trapped-ion or superconducting-circuit platforms to generate high-quality grid states using only a few interactions, even with the noise levels found in current systems.
High-accuracy Ising machine using Kerr-nonlinear parametric oscillators with local four-body interactions
Authors: Kanao Taro , Goto Hayato 
Published: January 2021

AbstractA two-dimensional array of Kerr-nonlinear parametric oscillators (KPOs) with local four-body interactions is a promising candidate for realizing an Ising machine with all-to-all spin couplings, based on adiabatic quantum computation in the Lechner–Hauke–Zoller (LHZ) scheme. However, its performance has been evaluated only for a symmetric network of three KPOs, and thus it has been unclear whether such an Ising machine works in general cases with asymmetric networks. By numerically simulating an asymmetric network of more KPOs in the LHZ scheme, we find that the asymmetry in the four-body interactions causes inhomogeneity in photon numbers and hence degrades the performance. We then propose a method for reducing the inhomogeneity, where the discrepancies of the photon numbers are corrected by tuning the detunings of KPOs depending on their positions, without monitoring their states during adiabatic time evolution. Our simulation results show that the performance can be dramatically improved by this method. The proposed method, which is based on the understanding of the asymmetry, is expected to be useful for general networks of KPOs in the LHZ scheme and thus for their large-scale implementation.
Durable natural killer cell responses after heterologous two-dose Ebola vaccination
Authors: Wagstaffe Helen R. , Susannini Giada , Thiébaut Rodolphe , Richert Laura , Lévy Yves , Bockstal Viki , Stoop Jeroen N. , Luhn Kerstin , Douoguih Macaya , Riley Eleanor M. , Lacabaratz Christine , Goodier Martin R. 
Published: January 2021

AbstractNatural killer (NK) cells are implicated among immune effectors after vaccination against viral pathogens, including Ebola virus. The two-dose heterologous Ebola virus vaccine regimen, adenovirus type 26.ZEBOV followed by modified vaccinia Ankara-BN-Filo (EBOVAC2 consortium, EU Innovative Medicines Initiative), induces NK cell activation and anti-Ebola glycoprotein (GP) antibody-dependent NK cell activation post-dose 1, which is further elevated post-dose 2. Here, in a multicentre, phase 2 clinical trial (EBL2001), we demonstrate durable ex vivo NK cell activation 180 days after dose 2, with responses enriched in CD56bright NK cells. In vitro antibody-dependent responses to immobilised Ebola GP increased after dose 1, and remained elevated compared to pre-vaccination levels in serum collected 180 days later. Peak NK cell responses were observed post-dose 2 and NK cell IFN-γ responses remained significantly elevated at 180 days post-dose 2. Individual variation in NK cell responses were influenced by both anti-Ebola GP antibody concentrations and intrinsic interindividual differences in NK cell functional capacity. In summary, this study demonstrates durable NK cell responses after Ad26.ZEBOV, MVA-BN-Filo Ebola virus vaccination and could inform the immunological evaluation of future iterations of the vaccine regimen and vaccination schedules.
A parasitic coevolution since the Miocene revealed by phase-contrast synchrotron X-ray microtomography and the study of natural history collections
Authors: Perreau Michel , Haelewaters Danny , Tafforeau Paul 
Published: January 2021

AbstractThe discovery of a new fossil species of the Caribbeo-Mexican genusProptomaphaginus(Coleoptera, Leiodidae, Cholevinae) from Dominican amber, associated with a new fossil parasitic fungus in the genusColumnomyces(Ascomycota, Laboulbeniales), triggered an investigation of extant species ofProptomaphaginusand revealed the long-enduring parasitic association between these two genera. This effort resulted in the description of the fossil species †Proptomaphaginus allenisp. nov., and one fossil and two extant species ofColumnomyces, selectively associated with species ofProptomaphaginus: †Columnomyces electrisp. nov. associated with the fossil †Proptomaphaginus alleniin Dominican amber,Columnomyces hispaniolensissp. nov. with the extantProptomaphaginus hispaniolensis(endemic of Hispaniola), andColumnomyces peckiisp. nov. with the extantProptomaphaginus puertoricensis(endemic of Puerto Rico). Based on biogeography, our current understanding is that the Caribbean species ofProptomaphaginusand their parasitic species ofColumnomyceshave coevolved since the Miocene. This is the first occurrence of such a coevolution between a genus of parasitic fungus and a genus of Coleoptera. The phylogenetic relations amongProptomaphaginusspecies are also addressed based on a parsimony analysis. Fossil specimens were observed by propagation phase-contrast synchrotron X-ray microtomography (PPC-SRμCT) and extant specimens were obtained through the study of preserved dried, pinned insects, attesting for the importance of (i) technological advancement and (ii) natural history collections in the study of microparasitic relationships.
Dispersal and competitive release affect the management of native and invasive tephritid fruit flies in large and smallholder farms in Ethiopia
Authors: Biasazin Tibebe Dejene , Wondimu Tadiwos W. , Herrera Sebastian Larsson , Larsson Mattias , Mafra-Neto Agenor , Gessese Yitbarek W. , Dekker Teun 
Published: January 2021

AbstractAfrican horticulture is seriously affected by fruit flies, both native and invasive. Novel sustainable control methods need testing against the backdrop of smallholder-dominated farming of Africa. We evaluated the potential of male-specific attractants (parapheromones) laced with insecticide to suppress the alien invasiveBactrocera dorsalisand nativeCeratitis capitata. In large-scale guava, methyl-eugenol (ME)-bait stations combined with toxic protein baits suppressedB. dorsaliswithin 8 months but resulted in a resurgence of the displacedCeratitis capitata. In smallholder farms, intervention using SPLAT-ME laced with spinosad was surprisingly unsuccessful. Subsequent mark-release-recapture experiments showed high dispersal rates of flies, covering many times a typical farm size, leading to a continuous influx of flies from surrounding areas. Several other factors important for intervention were evaluated. SPLAT-MAT-ME dollops remained attractive for over two weeks, although gradually becoming less attractive than fresh baits. Further, competitive displacement was observed:C. capitataselectively emerged from fruits in whichB. dorsalisinfestation was low. Finally, we evaluated whether ME could be combined withC. capitatamale attractants [trimedlure (TML) and terpinyl acetate (TA)] without affecting attraction. Combining male lures did not affect catches directly, although at very high populations ofB. dorsalisattracted to ME interfered withC. capitatatrap entry. Although ME-based methods can effectively suppressB. dorsalis, they were not effective at single smallholder scale due to the high dispersive propensity of tephritids. Further, competitive release implies the need for a combination of lures and methods. These observations are important for developing control schemes tailored for African smallholder settings.
Absorption of α-tocopheryl acetate is limited in mink kits (Mustela vison) during weaning
Authors: Lashkari Saman , Clausen Tove N. , Foldager Leslie , Jensen Søren K. 
Published: January 2021

AbstractBioavailability of α-tocopherol varies with source, dose and duration of supplementation. The effect of source and dose of α-tocopherol on response of α-tocopherol stereoisomers in plasma and tissues of mink kits during the weaning period was studied. Twelve mink kits were euthanised in CO2 at the beginning of the experiment, and 156 mink kits (12 replicates per treatment group) were randomly assigned to thirteen treatment groups: no added α-tocopherol in the feed (0 dose) or four different doses (50, 75, 100 and 150 mg/kg of diet) of RRR-α-tocopherol (ALC), RRR-α-tocopheryl acetate (ACT) or all-rac-α-tocopheryl acetate (SYN). Six mink kits per treatment group were euthanised 3 weeks after initiation of the experiment, and the remaining six were euthanised 6 weeks after initiation of the experiment. The RRR-α-tocopherol content in plasma, liver, heart and lungs was affected by interaction between source and dose (P < 0.01 for all). The highest RRR-α-tocopherol content in plasma (13.6 µg/ml; LS-means for source across dose and week), liver (13.6 µg/mg), heart (7.6 µg/mg) and lungs (9.8 µg/mg) was observed in mink kits fed ALC. The RRR-α-tocopherol content in plasma and tissues depended on source and dose interaction and increased linearly with supplementation. In conclusion, the interaction between source and dose reveals a limitation in hydrolysis of ester bond in α-tocopheryl acetate in mink kits around weaning as the likely causative explanation for the higher response of ALC at the highest doses. Thus, considerable attention has to be paid to the source of α-tocopherol during weaning of mink kits fed a high dose of α-tocopherol.
Quantifying individual influence in leading-following behavior of Bechstein’s bats
Authors: Mavrodiev Pavlin , Fleischmann Daniela , Kerth Gerald , Schweitzer Frank 
Published: January 2021

AbstractLeading-following behavior as a way of transferring information about the location of resources is wide-spread in many animal societies. It represents active information transfer that allows a given social species to reach collective decisions in the presence of limited information. Although leading-following behavior has received much scientific interest in the form of field studies, there is a need for systematic methods to quantify and study the individual contributions in this information transfer, which would eventually lead us to hypotheses about the individual mechanisms underlying this behaviour. In this paper we propose a general methodology that allows us to (a) infer individual leading-following behaviour from discrete observational data and (b) quantify individual influence based on methods from social network analysis. To demonstrate our methodology, we analyze longitudinal data of the roosting behavior of two different colonies of Bechstein’s bats in different years. Regarding (a) we show how the inference of leading-following events can be calibrated from data making it a general approach when only discrete observations are available. This allows us to address (b) by constructing social networks in which nodes represent individual bats and directed and weighted links—the leading-following events. We then show how social network theory can be used to define and quantify individual influence in a way that reflects the dynamics of the specific social network. We find that individuals can be consistently ranked regarding their influence in the information transfer. Moreover, we identify a small set of individuals that play a central role in leading other bats to roosts. In the case of Bechstein’s bats this finding can direct future studies on the individual-level mechanisms that result in such collective pattern. More generally, we posit that our data-driven methodology can be used to quantify leading-following behavior and individual impact in other animal systems, solely based on discrete observational data.