bluuebunny/crossref_metadata_2025 huggingface dataset:
Structures of monomeric and dimeric PRC2:EZH1 reveal flexible modules involved in chromatin compaction
Authors: Grau Daniel , Zhang Yixiao , Lee Chul-Hwan , Valencia-Sánchez Marco , Zhang Jenny , Wang Miao , Holder Marlene , Svetlov Vladimir , Tan Dongyan , Nudler Evgeny , Reinberg Danny , Walz Thomas , Armache Karim-Jean
Published: January 2021

Polycomb repressive complex 2 (PRC2) is a histone methyltransferase critical for maintaining gene silencing during eukaryotic development. In mammals, PRC2 activity is regulated in part by the selective incorporation of one of two paralogs of the catalytic subunit, EZH1 or EZH2. Each of these enzymes has specialized biological functions that may be partially explained by differences in the multivalent interactions they mediate with chromatin. Here, we present two cryo-EM structures of PRC2:EZH1, one as a monomer and a second one as a dimer bound to a nucleosome. When bound to nucleosome substrate, the PRC2:EZH1 dimer undergoes a dramatic conformational change. We demonstrate that mutation of a divergent EZH1/2 loop abrogates the nucleosome-binding and methyltransferase activities of PRC2:EZH1. Finally, we show that PRC2:EZH1 dimers are more effective than monomers at promoting chromatin compaction, and the divergent EZH1/2 loop is essential for this function, thereby tying together the methyltransferase, nucleosome-binding, and chromatin-compaction activities of PRC2:EZH1. We speculate that the conformational flexibility and the ability to dimerize enable PRC2 to act on the varied chromatin substrates it encounters in the cell.
Nontrivial band geometry in an optically active system
Authors: Ren Jiahuan , Liao Qing , Li Feng , Li Yiming , Bleu Olivier , Malpuech Guillaume , Yao Jiannian , Fu Hongbing , Solnyshkov Dmitry
Published: January 2021

Optical activity, also called circular birefringence, is known for two hundred years, but its applications for topological photonics remain unexplored. Unlike the Faraday effect, the optical activity provokes rotation of the linear polarization of light without magnetic effects, thus preserving the time-reversal symmetry. In this work, we report a direct measurement of the Berry curvature and quantum metric of the photonic modes of a planar cavity, containing a birefringent organic microcrystal (perylene) and exhibiting emergent optical activity. This experiment, performed at room temperature and at visible wavelength, establishes the potential of organic materials for implementing non-magnetic and low-cost topological photonic devices.
Comprehensive genomic resources related to domestication and crop improvement traits in Lima bean
Authors: Garcia Tatiana , Duitama Jorge , Zullo Stephanie Smolenski , Gil Juanita , Ariani Andrea , Dohle Sarah , Palkovic Antonia , Skeen Paola , Bermudez-Santana Clara Isabel , Debouck Daniel G. , Martínez-Castillo Jaime , Gepts Paul , Chacón-Sánchez Maria Isabel
Published: January 2021

Lima bean (Phaseolus lunatus L.), one of the five domesticated Phaseolus bean crops, shows a wide range of ecological adaptations along its distribution range from Mexico to Argentina. These adaptations make it a promising crop for improving food security under predicted scenarios of climate change in Latin America and elsewhere. In this work, we combine long and short read sequencing technologies with a dense genetic map from a biparental population to obtain the chromosome-level genome assembly for Lima bean. Annotation of 28,326 gene models show high diversity among 1917 genes with conserved domains related to disease resistance. Structural comparison across 22,180 orthologs with common bean reveals high genome synteny and five large intrachromosomal rearrangements. Population genomic analyses show that wild Lima bean is organized into six clusters with mostly non-overlapping distributions and that Mesomerican landraces can be further subdivided into three subclusters. RNA-seq data reveal 4275 differentially expressed genes, which can be related to pod dehiscence and seed development. We expect the resources presented here to serve as a solid basis to achieve a comprehensive view of the degree of convergent evolution of Phaseolus species under domestication and provide tools and information for breeding for climate change resiliency.
One-step synthesis of single-site vanadium substitution in 1T-WS2 monolayers for enhanced hydrogen evolution catalysis
Authors: Han Ali , Zhou Xiaofeng , Wang Xijun , Liu Sheng , Xiong Qihua , Zhang Qinghua , Gu Lin , Zhuang Zechao , Zhang Wenjing , Li Fanxing , Wang Dingsheng , Li Lain-Jong , Li Yadong
Published: January 2021

Metallic tungsten disulfide (WS2) monolayers have been demonstrated as promising electrocatalysts for hydrogen evolution reaction (HER) induced by the high intrinsic conductivity, however, the key challenges to maximize the catalytic activity are achieving the metallic WS2 with high concentration and increasing the density of the active sites. In this work, single-atom-V catalysts (V SACs) substitutions in 1T-WS2 monolayers (91% phase purity) are fabricated to significantly enhance the HER performance via a one-step chemical vapor deposition strategy. Atomic-resolution scanning transmission electron microscopy (STEM) imaging together with Raman spectroscopy confirm the atomic dispersion of V species on the 1T-WS2 monolayers instead of energetically favorable 2H-WS2 monolayers. The growth mechanism of V SACs@1T-WS2 monolayers is experimentally and theoretically demonstrated. Density functional theory (DFT) calculations demonstrate that the activated V-atom sites play vital important role in enhancing the HER activity. In this work, it opens a novel path to directly synthesize atomically dispersed single-metal catalysts on metastable materials as efficient and robust electrocatalysts.
Expansion within the CYP71D subfamily drives the heterocyclization of tanshinones synthesis in Salvia miltiorrhiza
Authors: Ma Ying , Cui Guanghong , Chen Tong , Ma Xiaohui , Wang Ruishan , Jin Baolong , Yang Jian , Kang Liping , Tang Jinfu , Lai Changjiangsheng , Wang Yanan , Zhao Yujun , Shen Ye , Zeng Wen , Peters Reuben J. , Qi Xiaoquan , Guo Juan , Huang Luqi
Published: January 2021

Tanshinones are the bioactivenor-diterpenoid constituents of the Chinese medicinal herb Danshen (Salvia miltiorrhiza). These groups of chemicals have the characteristic furan D-ring, which differentiates them from the phenolic abietane-type diterpenoids frequently found in the Lamiaceae family. However, how the 14,16-epoxy is formed has not been elucidated. Here, we report an improved genome assembly of Danshen using a highly homozygous genotype. We identify a cytochrome P450 (CYP71D) tandem gene array through gene expansion analysis. We show that CYP71D373 and CYP71D375 catalyze hydroxylation at carbon-16 (C16) and 14,16-ether (hetero)cyclization to form the D-ring, whereas CYP71D411 catalyzes upstream hydroxylation at C20. In addition, we discover a large biosynthetic gene cluster associated with tanshinone production. Collinearity analysis indicates a more specific origin of tanshinones inSalviagenus. It illustrates the evolutionary origin of abietane-type diterpenoids and those with a furan D-ring in Lamiaceae.
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

Alternative 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

The 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

Lamins 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

Assessing 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

Reprogramming 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

Machine 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

Accurately 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

This 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

Quantum 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

A 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

Natural 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

The 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

African 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

Bioavailability 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

Leading-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.
A novel approach for discovering stochastic models behind data applied to El Niño–Southern Oscillation
Authors: Olson Roman , An Soon-Il , Kim Soong-Ki , Fan Yanan
Published: January 2021

Stochastic differential equations (SDEs) are ubiquitous across disciplines, and uncovering SDEs driving observed time series data is a key scientific challenge. Most previous work on this topic has relied on restrictive assumptions, undermining the generality of these approaches. We present a novel technique to uncover driving probabilistic models that is based on kernel density estimation. The approach relies on few assumptions, does not restrict underlying functional forms, and can be used even on non-Markov systems. When applied to El Niño–Southern Oscillation (ENSO), the fitted empirical model simulations can almost perfectly capture key time series properties of ENSO. This confirms that ENSO could be represented as a two-variable stochastic dynamical system. Our experiments provide insights into ENSO dynamics and suggest that state-dependent noise does not play a major role in ENSO skewness. Our method is general and can be used across disciplines for inverse and forward modeling, to shed light on structure of system dynamics and noise, to evaluate system predictability, and to generate synthetic datasets with realistic properties.
Reconstructing population dynamics of a threatened marine mammal using multiple data sets
Authors: Hostetler Jeffrey A. , Martin Julien , Kosempa Michael , Edwards Holly H. , Rood Kari A. , Barton Sheri L. , Runge Michael C.
Published: January 2021

Models of marine mammal population dynamics have been used extensively to predict abundance. A less common application of these models is to reconstruct historical population dynamics, filling in gaps in observation data by integrating information from multiple sources. We developed an integrated population model for the Florida manatee (Trichechus manatus latirostris) to reconstruct its population dynamics in the southwest region of the state over the past 20 years. Our model improved precision of key parameter estimates and permitted inference on poorly known parameters. Population growth was slow (averaging 1.02; 95% credible interval 1.01–1.03) but not steady, and an unusual mortality event in 2013 led to an estimated net loss of 332 (217–466) manatees. Our analyses showed that precise estimates of abundance could be derived from estimates of vital rates and a few input estimates of abundance, which may mean costly surveys to estimate abundance don’t need to be conducted as frequently. Our study also shows that retrospective analyses can be useful to: (1) model the transient dynamics of age distribution; (2) assess and communicate the conservation status of wild populations; and (3) improve our understanding of environmental effects on population dynamics and thus enhance our ability to forecast.
Intra-bundle contractions enable extensile properties of active actin networks
Authors: Bleicher P. , Nast-Kolb T. , Sciortino A. , de la Trobe Y. A. , Pokrant T. , Faix J. , Bausch A. R.
Published: January 2021

The cellular cortex is a dynamic and contractile actomyosin network modulated by actin-binding proteins. We reconstituted a minimal cortex adhered to a model cell membrane mimicking two processes mediated by the motor protein myosin: contractility and high turnover of actin monomers. Myosin reorganized these networks by extensile intra‑bundle contractions leading to an altered growth mechanism. Hereby, stress within tethered bundles induced nicking of filaments followed by repair via incorporation of free monomers. This mechanism was able to break the symmetry of the previously disordered network resulting in the generation of extensile clusters, reminiscent of structures found within cells.
Chimeric synthetic reference standards enable cross-validation of positive and negative controls in SARS-CoV-2 molecular tests
Authors: Madala Bindu Swapna , Reis Andre L. M. , Deveson Ira W. , Rawlinson William , Mercer Tim R.
Published: January 2021

DNA synthesis in vitro has enabled the rapid production of reference standards. These are used as controls, and allow measurement and improvement of the accuracy and quality of diagnostic tests. Current reference standards typically represent target genetic material, and act only as positive controls to assess test sensitivity. However, negative controls are also required to evaluate test specificity. Using a pair of chimeric A/B RNA standards, this allowed incorporation of positive and negative controls into diagnostic testing for the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). The chimeric standards constituted target regions for RT-PCR primer/probe sets that are joined in tandem across two separate synthetic molecules. Accordingly, a target region that is present in standard A provides a positive control, whilst being absent in standard B, thereby providing a negative control. This design enables cross-validation of positive and negative controls between the paired standards in the same reaction, with identical conditions. This enables control and test failures to be distinguished, increasing confidence in the accuracy of results. The chimeric A/B standards were assessed using the US Centres for Disease Control real-time RT-PCR protocol, and showed results congruent with other commercial controls in detecting SARS-CoV-2 in patient samples. This chimeric reference standard design approach offers extensive flexibility, allowing representation of diverse genetic features and distantly related sequences, even from different organisms.
Saccadic reaction time in mirror image sectors across horizontal meridian in eye movement perimetry
Authors: Mazumdar Deepmala , Meethal Najiya S. Kadavath , George Ronnie , Pel Johan J. M.
Published: January 2021

In eye movement perimetry (EMP), the saccadic reaction time (SRT) to ‘seen’ visual stimuli are delayed in glaucoma. Evaluating SRT behaviour in hemi-field sectors could refine its clinical implication. The development phase included 60 controls retrospectively and for the test cohort in evaluation phase, another 30 healthy subjects and 30 glaucoma patients were recruited prospectively. The SRTs were used to calculate the normative limits within 5 predefined hemi-field sectors. Scores were assigned to probabilities for SRT at the level of 5%, 2.5% 1% and 0.5%. Per sector pair, a probability score limit (PSL) was calculated at each of the four levels and were compared with the scores obtained from the test cohort. The classification accuracy ‘normal versus abnormal’ was assessed for PSL in EMP and compared with glaucoma hemi-field test in standard automated perimetry. We found no statistically significant differences in SRTs between the mirror sectors in healthy subjects. The PSL at 2.5% had moderate classification accuracy with a specificity of 77% and sensitivity 70%. This could be suggestive of an SRT delay in the overall visual field in glaucoma.
Transmission dynamics and control measures of COVID-19 outbreak in China: a modelling study
Authors: Zhang Xu-Sheng , Vynnycky Emilia , Charlett Andre , De Angelis Daniela , Chen Zhengji , Liu Wei
Published: January 2021

COVID-19 is reported to have been brought under control in China. To understand the COVID-19 outbreak in China and provide potential lessons for other parts of the world, in this study we apply a mathematical model with multiple datasets to estimate the transmissibility of the SARS-CoV-2 virus and the severity of the illness associated with the infection, and how both were affected by unprecedented control measures. Our analyses show that before 19th January 2020, 3.5% (95% CI 1.7–8.3%) of  infected people were detected; this percentage increased to 36.6% (95% CI 26.1–55.4%) thereafter. The basic reproduction number (R0) was 2.33 (95% CI 1.96–3.69) before 8th February 2020; then the effective reproduction number dropped to 0.04(95% CI 0.01–0.10). This estimation also indicates that control measures taken since 23rd January 2020 affected the transmissibility about 2 weeks after they were introduced. The confirmed case fatality rate is estimated at 9.6% (95% CI 8.1–11.4%) before 15 February 2020, and then it reduced to 0.7% (95% CI 0.4–1.0%). This shows that SARS-CoV-2 virus is highly transmissible but may be less severe than SARS-CoV-1 and MERS-CoV. We found that at the early stage, the majority ofR0comes from undetected infectious people. This implies that successful control in China was achieved through reducing the contact rates among people in the general population and increasing the rate of detection and quarantine of the infectious cases.
Study of mouse behavior in different gravity environments
Authors: Shimomura Michihiko , Yumoto Akane , Ota-Murakami Naoko , Kudo Takashi , Shirakawa Masaki , Takahashi Satoru , Morita Hironobu , Shiba Dai
Published: January 2021

Many experiments have analyzed the effect of the space environment on various organisms. However, except for the group-rearing of mice in space, there has been little information on the behavior of organisms in response to gravity changes. In this study, we developed a simple Active Inactive Separation (AIS) method to extract activity and inactivity in videos obtained from the habitat cage unit of a space experiment. This method yields an activity ratio as a ratio of ‘activity’ within the whole. Adaptation to different gravitational conditions from 1gto hypergravity (HG) and from microgravity (MG) to artificial 1g(AG) was analyzed based on the amount of activity to calculate the activity ratio and the active interval. The result for the activity ratios for the ground control experiment using AIS were close to previous studies, so the effectiveness of this method was indicated. In the case of changes in gravity from 1gto HG, the ratio was low at the start of centrifugation, recovered sharply in the first week, and entered a stable period in another week. The trend in the AG and HG was the same; adapting to different gravity environments takes time.
Dexamethasone increased the survival rate in Plasmodium berghei-infected mice
Authors: Moreira Danilo Reymão , Uberti Ana Carolina Musa Gonçalves , Gomes Antonio Rafael Quadros , Ferreira Michelli Erica Souza , da Silva Barbosa Aline , Varela Everton Luiz Pompeu , Dolabela Maria Fani , Percário Sandro
Published: January 2021

The present study aimed to evaluate the effects of dexamethasone on the redox status, parasitemia evolution, and survival rate of Plasmodium berghei-infected mice. Two-hundred and twenty-five mice were infected with Plasmodium berghei and subjected to stimulation or inhibition of NO synthesis. The stimulation of NO synthesis was performed through the administration of L-arginine, while its inhibition was made by the administration of dexamethasone. Inducible NO synthase (iNOS) inhibition by dexamethasone promoted an increase in the survival rate of P. berghei-infected mice, and the data suggested the participation of oxidative stress in the brain as a result of plasmodial infection, as well as the inhibition of brain NO synthesis, which promoted the survival rate of almost 90% of the animals until the 15th day of infection, with possible direct interference of ischemia and reperfusion syndrome, as seen by increased levels of uric acid. Inhibition of brain iNOS by dexamethasone caused a decrease in parasitemia and increased the survival rate of infected animals, suggesting that NO synthesis may stimulate a series of compensatory redox effects that, if overstimulated, may be responsible for the onset of severe forms of malaria.
Experimental warming increases ecosystem respiration by increasing above-ground respiration in alpine meadows of Western Himalaya
Authors: Tiwari Pankaj , Bhattacharya Pamela , Rawat Gopal Singh , Rai Ishwari Datt , Talukdar Gautam
Published: January 2021

Alpine ecosystems in the Himalaya, despite low primary productivity, store considerable amount of organic carbon. However, these ecosystems are highly vulnerable to climate warming which may stimulate ecosystem carbon efflux leading to carbon-loss and positive feedback. We used open-top chambers to understand warming responses of ecosystem respiration (ER) and soil respiration (SR) in two types of alpine meadows viz., herbaceous meadow (HM) and sedge meadow (SM), in the Western Himalaya. Experimental warming increased ER by 33% and 28% at HM and SM, respectively. No significant effect on SR was observed under warming, suggesting that the increase in ER was primarily due to an increase in above-ground respiration. This was supported by the warming-induced increase in above-ground biomass and decrease in SR/ER ratio. Soil temperature was the dominant controlling factor of respiration rates and temperature sensitivity of both ER and SR increased under warming, indicating an increase in contribution from plant respiration. The findings of the study suggest that climate warming by 1.5–2 °C would promote ER via increase in above-ground respiration during the growing season. Moreover, net C uptake in the alpine meadows may increase due to enhanced plant growth and relatively resistant SR under warming.
Biomechanical properties of a novel nonfusion artificial vertebral body for anterior lumbar vertebra resection and internal fixation
Authors: Liu Jiantao , He Xijing , Niu Binbin , Yang Yin , Gao Yanzheng , Xiu Jintao , Wang Hongbo , Wang Yanbiao
Published: January 2021

The aim of the study was to evaluate the biomechanical properties of a novel nonfused artificial vertebral body in treating lumbar diseases and to compare with those of the fusion artificial vertebral body. An intact finite element model of the L1–L5 lumbar spine was constructed and validated. Then, the finite element models of the fusion group and nonfusion group were constructed by replacing the L3 vertebral body and adjacent intervertebral discs with prostheses. For all finite element models, an axial preload of 500 N and another 10 N m imposed on the superior surface of L1. The range of motion and stress peaks in the adjacent discs, endplates, and facet joints were compared among the three groups. The ranges of motion of the L1–2 and L4–5 discs in flexion, extension, left lateral bending, right lateral bending, left rotation and right rotation were greater in the fusion group than those in the intact group and nonfusion group. The fusion group induced the greatest stress peaks in the adjacent discs and adjacent facet joints compared to the intact group and nonfusion group. The nonfused artificial vertebral body could better retain mobility of the surgical site after implantation (3.6°–8.7°), avoid increased mobility and stress of the adjacent discs and facet joints.
Effects of sagging breasts and other risk factors associated with mastalgia: a case–control study
Authors: Çomçalı Bülent , Kocaoz Servet , Özdemir Buket Altun , Parlak Ömer , Korukluoğlu Birol
Published: January 2021

The aim of this study is to compare patients with and without mastalgia and to analyze the factors affecting mastalgia and its severity. The patient’s age, height, weight, educational status, marital status, and occupation were recorded in all subjects. In addition, the women were asked about the presence of any risk factors for mastalgia, such as tea and coffee consumption, smoking, alcohol consumption, and weight gain. The sternal notch to nipple distance (SNND) was measured to determine whether there was breast sagging. Mastalgia was significantly more common in women with BMIs of > 30 kg/m2 (OR: 2.94, CI 1.65–5.24), those who were primary school graduates or illiterate (OR: 2.96, CI 1.6–5.46), and those with SNND values of 22–25 cm (OR: 2.94, CI 1.79–4.82). In these women, drinking more than 6 cups of tea a day (OR: 2.15, CI 1.32–3.5), smoking at least 10 cigarettes a day (OR: 2.94, CI 1.78–4.83), and drinking alcohol at least once a week (OR: 2.1, CI 1.12–3.91) were found to be important factors that increased the risk of mastalgia. As a result, it has been found that severe mastalgia complaints cause by obesity, sagging breasts, never giving birth, unemployment anxiety, regular smoking, alcohol use, and excessive tea consumption.