bluuebunny/crossref_metadata_2025_split huggingface dataset:
SARS-CoV-2 and other human coronavirus show genome patterns previously associated to reduced viral recognition and altered immune response
Authors: Franzo Giovanni 
Published: May 2021

AbstractA new pandemic caused by the betacoronavirus SARS-CoV-2 originated in China in late 2019. Although often asymptomatic, a relevant percentage of affected people can develop severe pneumonia. Initial evidence suggests that dysregulation of the immune response could contribute to the pathogenesis, as previously demonstrated for SARS-CoV. The presence of genome composition features involved in delaying viral recognition is herein investigated for human coronaviruses (HCoVs), with a special emphasis on SARS-CoV-2. A broad collection of HCoVs polyprotein, envelope, matrix, nucleocapsid and spike coding sequences was downloaded and several statistics representative of genome composition and codon bias were investigated. A model able to evaluate and test the presence of a significant under- or over-representation of dinucleotide pairs while accounting for the underlying codon bias and protein sequence was also implemented. The study revealed the significant under-representation of CpG dinucleotide pair in all HcoV, but especially in SARS-CoV and even more in SARS-CoV-2. The presence of forces acting to minimize CpG content was confirmed by relative synonymous codon usage pattern. Codons containing the CpG pair were severely under-represented, primarily in the polyprotein and spike coding sequences of SARS-CoV-2. Additionally, a significant under-representation of the TpA pair was observed in the N and S region of SARS-CoV and SARS-CoV-2. Increasing experimental evidence has proven that CpG and TpA are targeted by innate antiviral host defences, contributing both to RNA degradation and RIG-1 mediated interferon production. The low content of these dinucleotides could contribute to a delayed interferon production, dysregulated immune response, higher viral replication and poor outcome. Significantly, the RIG-1 signalling pathway was proven to be defective in elderlies, suggesting a likely interaction between limited viral recognition and lower responsiveness in interferon production that could justify the higher disease severity and mortality in older patients.
Ocean fertilization by pyrogenic aerosol iron
Authors: Ito Akinori , Ye Ying , Baldo Clarissa , Shi Zongbo 
Published: May 2021

AbstractAerosols supply bioaccessible iron to marine biota which could affect climate through biogeochemical feedbacks. This paper review progresses in research on pyrogenic aerosol iron. Observations and laboratory experiments indicate that the iron solubility of pyrogenic aerosol can be considerably higher than lithogenic aerosol. Aerosol models highlight a significant contribution of pyrogenic aerosols (~20%) to the atmospheric supply of dissolved iron into the ocean. Some ocean models suggest a higher efficiency of pyrogenic iron in enhancing marine productivity than lithogenic sources. It is, however, challenging to quantitatively estimate its impact on the marine biogeochemical cycles under the changing air quality and climate.
Common DNA methylation dynamics in endometriod adenocarcinoma and glioblastoma suggest universal epigenomic alterations in tumorigenesis
Authors: Karlow Jennifer A. , Miao Benpeng , Xing Xiaoyun , Wang Ting , Zhang Bo 
Published: May 2021

AbstractTrends in altered DNA methylation have been defined across human cancers, revealing global loss of methylation (hypomethylation) and focal gain of methylation (hypermethylation) as frequent cancer hallmarks. Although many cancers share these trends, little is known about the specific differences in DNA methylation changes across cancer types, particularly outside of promoters. Here, we present a comprehensive comparison of DNA methylation changes between two distinct cancers, endometrioid adenocarcinoma (EAC) and glioblastoma multiforme (GBM), to elucidate common rules of methylation dysregulation and changes unique to cancers derived from specific cells. Both cancers exhibit significant changes in methylation over regulatory elements. Notably, hypermethylated enhancers within EAC samples contain several transcription factor binding site clusters with enriched disease ontology terms highlighting uterine function, while hypermethylated enhancers in GBM are found to overlap active enhancer marks in adult brain. These findings suggest that loss of original cellular identity may be a shared step in tumorigenesis.
Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities
Authors: Acinas Silvia G. , Sánchez Pablo , Salazar Guillem , Cornejo-Castillo Francisco M. , Sebastián Marta , Logares Ramiro , Royo-Llonch Marta , Paoli Lucas , Sunagawa Shinichi , Hingamp Pascal , Ogata Hiroyuki , Lima-Mendez Gipsi , Roux Simon , González José M. , Arrieta Jesús M. , Alam Intikhab S. , Kamau Allan , Bowler Chris , Raes Jeroen , Pesant Stéphane , Bork Peer , Agustí Susana , Gojobori Takashi , Vaqué Dolors , Sullivan Matthew B. , Pedrós-Alió Carlos , Massana Ramon , Duarte Carlos M. , Gasol Josep M. 
Published: May 2021

AbstractThe deep sea, the largest ocean’s compartment, drives planetary-scale biogeochemical cycling. Yet, the functional exploration of its microbial communities lags far behind other environments. Here we analyze 58 metagenomes from tropical and subtropical deep oceans to generate the Malaspina Gene Database. Free-living or particle-attached lifestyles drive functional differences in bathypelagic prokaryotic communities, regardless of their biogeography. Ammonia and CO oxidation pathways are enriched in the free-living microbial communities and dissimilatory nitrate reduction to ammonium and H2oxidation pathways in the particle-attached, while the Calvin Benson-Bassham cycle is the most prevalent inorganic carbon fixation pathway in both size fractions. Reconstruction of the Malaspina Deep Metagenome-Assembled Genomes reveals unique non-cyanobacterial diazotrophic bacteria and chemolithoautotrophic prokaryotes. The widespread potential to grow both autotrophically and heterotrophically suggests that mixotrophy is an ecologically relevant trait in the deep ocean. These results expand our understanding of the functional microbial structure and metabolic capabilities of the largest Earth aquatic ecosystem.
Active suppression prevents the return of threat memory in humans
Authors: Wang Ye , Zhu Zijian , Hu Jingchu , Schiller Daniela , Li Jian 
Published: May 2021

AbstractUnbidden distressing memories inflict serious damage on mental health. Extant research highlights the importance of associative learning in modulating aversive memory. We report that conscious active suppression eliminates learned fear responses independent of memory triggers and is related to individual difference in thought control ability; in contrast, thought diversion only reduces cue-specific fear response. These results suggest potential avenues for treatment of persistent maladaptive memories by engaging declarative mnemonic control mechanisms.
Optical interferometry based micropipette aspiration provides real-time sub-nanometer spatial resolution
Authors: Berardi Massimiliano , Bielawski Kevin , Rijnveld Niek , Gruca Grzegorz , Aardema Hilde , van Tol Leni , Wuite Gijs , Akca B. Imran 
Published: May 2021

AbstractMicropipette aspiration (MPA) is an essential tool in mechanobiology; however, its potential is far from fully exploited. The traditional MPA technique has limited temporal and spatial resolution and requires extensive post processing to obtain the mechanical fingerprints of samples. Here, we develop a MPA system that measures pressure and displacement in real time with sub-nanometer resolution thanks to an interferometric readout. This highly sensitive MPA system enables studying the nanoscale behavior of soft biomaterials under tension and their frequency-dependent viscoelastic response.
Telomere damage promotes vascular smooth muscle cell senescence and immune cell recruitment after vessel injury
Authors: Uryga Anna K. , Grootaert Mandy O. J. , Garrido Abel M. , Oc Sebnem , Foote Kirsty , Chappell Joel , Finigan Alison , Rossiello Francesca , d’Adda di Fagagna Fabrizio , Aravani Dimitra , Jorgensen Helle F. , Bennett Martin R. 
Published: May 2021

AbstractAccumulation of vascular smooth muscle cells (VSMCs) is a hallmark of multiple vascular pathologies, including following neointimal formation after injury and atherosclerosis. However, human VSMCs in advanced atherosclerotic lesions show reduced cell proliferation, extensive and persistent DNA damage, and features of premature cell senescence. Here, we report that stress-induced premature senescence (SIPS) and stable expression of a telomeric repeat-binding factor 2 protein mutant (TRF2T188A) induce senescence of human VSMCs, associated with persistent telomeric DNA damage. VSMC senescence is associated with formation of micronuclei, activation of cGAS-STING cytoplasmic sensing, and induction of multiple pro-inflammatory cytokines. VSMC-specific TRF2T188A expression in a multicolor clonal VSMC-tracking mouse model shows no change in VSMC clonal patches after injury, but an increase in neointima formation, outward remodeling, senescence and immune/inflammatory cell infiltration or retention. We suggest that persistent telomere damage in VSMCs inducing cell senescence has a major role in driving persistent inflammation in vascular disease.
Global earthworm distribution and activity windows based on soil hydromechanical constraints
Authors: Ruiz Siul A. , Bickel Samuel , Or Dani 
Published: May 2021

AbstractEarthworm activity modifies soil structure and promotes important hydrological ecosystem functions for agricultural systems. Earthworms use their flexible hydroskeleton to burrow and expand biopores. Hence, their activity is constrained by soil hydromechanical conditions that permit deformation at earthworm’s maximal hydroskeletal pressure (≈200kPa). A mechanistic biophysical model is developed here to link the biomechanical limits of earthworm burrowing with soil moisture and texture to predict soil conditions that permit bioturbation across biomes. We include additional constraints that exclude earthworm activity such as freezing temperatures, low soil pH, and high sand content to develop the first predictive global map of earthworm habitats in good agreement with observed earthworm occurrence patterns. Earthworm activity is strongly constrained by seasonal dynamics that vary across latitudes largely due to soil hydromechanical status. The mechanistic model delineates the potential for earthworm migration via connectivity of hospitable sites and highlights regions sensitive to climate.
Role of avoided crossing and weak value amplification on enhanced Faraday effect in magnetoplasmonic systems
Authors: Nayak Jeeban K. , Guchhait Shyamal , Singh Ankit K. , Ghosh Nirmalya 
Published: May 2021

AbstractEnhancement of magneto-optical effects in hybrid magneto-plasmonic systems has attracted considerable recent attention because of their potential for building non-reciprocal nanophotonic devices. Quantitative understanding of the fundamental origin and contributing mechanisms for the enhancement is crucial for optimizing applications. Here, we unravel different physical origins of the giant enhancement of Faraday rotation and ellipticity in a hybrid magneto-plasmonic system, namely, waveguided magneto-plasmonic crystal for excitation with transverse electric (TE) and transverse magnetic (TM) polarized light. With TE polarization excitation, where the surface plasmons are not directly excited, the natural weak value amplification of Faraday effects appearing due to the spectral domain interference of Fano resonance is the dominant cause of the enhancement. For TM polarization excitation, on the other hand, waveguide-plasmon strong coupling and its universal manifestation of avoided crossing plays an important role, leading to maximum enhancement of the magneto-optical effects in the avoided crossing regime.
Hard magnet topological semimetals in XPt3 compounds with the harmony of Berry curvature
Authors: Markou Anastasios , Gayles Jacob , Derunova Elena , Swekis Peter , Noky Jonathan , Zhang Liguo , Ali Mazhar N. , Sun Yan , Felser Claudia 
Published: May 2021

AbstractTopological magnetic semimetals, like Co3Sn2S2 and Co2MnGa, display exotic transport properties, such as large intrinsic anomalous (AHE) due to uncompensated Berry curvature. The highly symmetric XPt3 compounds exhibit anti-crossing gapped nodal lines, a driving mechanism in the intrinsic Berry curvature Hall effects. Uniquely, these compounds contain two sets of gapped nodal lines that harmoniously dominate the Berry curvature in this complex multi band system. We calculate a maximum AHE of 1965 S cm-1 in the CrPt3 by first principles electronic structure. We have grown high-quality CrPt3 thin films with perpendicular magnetic anisotropy by magnetron sputtering and measured a robust AHE of 1750 S cm−1 for different sputtering growth conditions. Additionally, the cubic films display an easy magnetic axis along [111] direction. The facile and scalable fabrication of these materials is prime candidates for integration into topological devices.
Solving quasiparticle band spectra of real solids using neural-network quantum states
Authors: Yoshioka Nobuyuki , Mizukami Wataru , Nori Franco 
Published: May 2021

AbstractEstablishing a predictive ab initio method for solid systems is one of the fundamental goals in condensed matter physics and computational materials science. The central challenge is how to encode a highly-complex quantum-many-body wave function compactly. Here, we demonstrate that artificial neural networks, known for their overwhelming expressibility in the context of machine learning, are excellent tool for first-principles calculations of extended periodic materials. We show that the ground-state energies in real solids in one-, two-, and three-dimensional systems are simulated precisely, reaching their chemical accuracy. The highlight of our work is that the quasiparticle band spectra, which are both essential and peculiar to solid-state systems, can be efficiently extracted with a computational technique designed to exploit the low-lying energy structure from neural networks. This work opens up a path to elucidate the intriguing and complex many-body phenomena in solid-state systems.
The efficacy and safety of Curcuma longa extract and curcumin supplements on osteoarthritis: a systematic review and meta-analysis
Authors: Zeng Liuting , Yu Ganpeng , Hao Wensa , Yang Kailin , Chen Hua 
Published: May 2021

Abstract
Objective: To assess the efficacy and safety of Curcuma longa extract and curcumin supplements on osteoarthritis (OA).
Methods: The databases such as Pubmed and Cochrane Library were searched to collect the article about Curcuma longa extract and curcumin in the treatment of OA. Then, randomized controlled trials (RCTs) were selected and their data were extracted. Finally, the RevMan5.3 was utilized for risk of bias assessment and meta-analysis, the STATA15.0 were utilized for publication bias assessment, and GRADE tool were used for the evidence quality assessment of primary outcomes.
Results: A total of 15 RCTs involving 1621 participants were included. (1) Compared with placebo, Curcuma longa extract and curcumin (C.) can decrease the visual analog scale (VAS) and The Western Ontario and McMaster Universities (WOMAC) score-pain, the WOMAC score-function and the WOMAC score-stiffness. In terms of adverse events, Curcuma longa extract and curcumin are comparable with those of placebo. (2) Compared with non-steroidal anti-inflammatory drugs (NSAIDs), Curcuma longa extract and curcumin have similar effects on joint pain, function and stiffness. The incidence of adverse events in Curcuma longa extract and curcumin was lower. (3) Compared with the NSAIDs group, C.+NSAIDs can also decrease the VAS and WOMAC score-pain, the WOMAC score-function and the WOMAC score-stiffness. In terms of adverse events, the addition of Curcuma longa extract and curcumin to NSAIDs did not increase adverse events.
Conclusion: Curcuma longa extract and curcumin may be a safer and effective supplement for OA patients. It is recommended to use Curcuma longa extract and curcumin supplement for OA patients for more than 12 weeks.
Practice Mediates Bidirectional Dual-Task Interference When Performing a Novel Sequential Nonword Repetition Task
Authors: Whitfield Jason A. , Holdosh Serena R. 
Published: May 2021

Introduction
The current study examined the extent to which practice amount mediates dual-task interference patterns associated with concurrent performance of a novel speech task and attention-demanding visuomotor task.

Method
A Sequential Nonword Repetition Task was used to examine the effect of practice on interference associated with concurrent performance of a Visuomotor Pursuit Task. Twenty-five young adult participants were assigned to either an Extended Practice Group or a Limited Practice Group and performed a novel Sequential Nonword Repetition Task in isolation and while performing a concurrent visuomotor pursuit rotor task.

Results
Participants in the Limited Practice Group who were afforded a limited amount of practice exhibited dual-task interference (i.e., dual-task performance reductions) for both the speech and visuomotor tasks (i.e., bidirectional dual-task interference). Conversely, participants in the Extended Practice Group who were afforded extended practice exhibited little-to-no observable dual-task interference on the nonword repetition task.

Conclusion
Data from the current investigation suggest that the amount of initial practice mediates the degree of dual-task interference observed when a novel speech production task is performed with an attention-demanding Visuomotor Pursuit Task.

Supplemental Material

https://doi.org/10.23641/asha.14608071
Augmented reality display of neurosurgery craniotomy lesions based on feature contour matching
Authors: Zhang Hao , Sun Qi‐Yuan , Liu Zhen‐Zhong 
Published: May 2021

AbstractTraditional neurosurgical craniotomy primarily uses two‐dimensional cranial medical images to estimate the location of a patient’s intracranial lesions. Such work relies on the experience and skills of the doctor and may result in accidental injury to important intracranial physiological tissues. To help doctors more intuitively determine patient lesion information and improve the accuracy of surgical route formulation and craniotomy safety, an augmented reality method for displaying neurosurgery craniotomy lesions based on feature contour matching is proposed. This method uses threshold segmentation and region growing algorithms to reconstruct a 3‐D Computed tomography image of the patient’s head. The augmented reality engine is used to adjust the reconstruction model’s relevant parameters to meet the doctor’s requirements and determine the augmented reality matching method for feature contour matching. By using the mobile terminal to align the real skull model, the virtual lesion model is displayed. Using the designed user interface, doctors can view the patient’s personal information and can zoom in, zoom out, and rotate the virtual model. Therefore, the patient’s lesions information can be visualized accurately, which provides a visual basis for preoperative preparation.
A survey of learning‐based robot motion planning
Authors: Wang Jiankun , Zhang Tianyi , Ma Nachuan , Li Zhaoting , Ma Han , Meng Fei , Meng Max Q.‐H. 
Published: May 2021

AbstractA fundamental task in robotics is to plan collision‐free motions among a set of obstacles. Recently, learning‐based motion‐planning methods have shown significant advantages in solving different planning problems in high‐dimensional spaces and complex environments. This article serves as a survey of various different learning‐based methods that have been applied to robot motion‐planning problems, including supervised, unsupervised learning, and reinforcement learning. These learning‐based methods either rely on a human‐crafted reward function for specific tasks or learn from successful planning experiences. The classical definition and learning‐related definition of motion‐planning problem are provided in this article. Different learning‐based motion‐planning algorithms are introduced, and the combination of classical motion‐planning and learning techniques is discussed in detail.
Spectral recovery‐guided hyperspectral super‐resolution using transfer learning
Authors: Zhang Shaolei , Fu Guangyuan , Wang Hongqiao , Zhao Yuqing 
Published: May 2021

AbstractSingle hyperspectral image (HSI) super‐resolution (SR) has attracted researcher's attention; however, most existing methods directly model the mapping between low‐ and high‐resolution images from an external training dataset, which requires large memory and computing resources. Moreover, there are few such available training datasets in real cases, which prevent deep‐learning‐based methods from further improving performance. Here, a novel single HSI SR method based on transfer learning is proposed. The proposed method is composed of two stages: spectral down‐sampled image SR reconstruction based on transfer learning and HSI reconstruction via spectral recovery module. Instead of directly applying the learned knowledge from the colour image domain to HSI SR, the spectral down‐sampled image is fed into a spatial SR model to obtain a high‐resolution image, which acts as a bridge between the colour image and HSI. The spectral recovery network is used to restore the HSI from the bridge image. In addition, pre‐training and collaborative fine‐tuning are proposed to promote the performance of SR and spectral recovery. Experiments on two public HSI datasets show that the proposed method achieves promising SR performance with a small paired HSI dataset.
Optimal synthesis of reconfigurable planar arrays for monopulse radar applications: Use of subarrays and distributions with common aperture tail
Authors: Qi Zhengdong , Zhang Xinggan , Bai Yechao , Wang Qiong , Yu Chunhua , Chen Hao , Lu Yangyi , Wu Shaopeng 
Published: May 2021

AbstractAn approach for the synthesis of sum and difference patterns in monopulse antennas is described. The proposed approach provides a significant reduction in the complexity of the beam‐forming network that is fulfilled by reducing the number of array elements and keeping the elements at the edges of the array that share common excitations for both sum and difference modes. An iterative constrained optimisation method is used where the non‐convex lower‐bound constraints on the beam pattern are cast as an equivalent multi‐convex optimisation problem while concurrently minimising a reweighted l1‐norm of the magnitudes of the elements in the beam‐forming weight vector. Thus, better radiation performance of beam pattern (e.g. narrower beamwidth, lower peak sidelobe level), a much narrower spatial aperture and a smaller number of elements can be achieved compared with the case of uniformly spaced arrays. To compensate for array imperfection in practice, robust beam pattern constraints are derived in the optimisation stage using a worst‐case performance optimisation technique. Numerical examples show the effectiveness and advantages of the proposed synthesis approach.