bluuebunny/crossref_metadata_2025_split huggingface dataset:
A New Theory for Energetic Electron Generation Behind Dipolarization Front
Authors: Fu H. S. , Zhao M. J. , Yu Y. , Wang Z. 
Published: March 2020

AbstractA long‐standing problem concerning dipolarization front (DF) is why energetic electrons only appear in half the DF events? By analyzing MMS measurements, here we answer this question. We find a DF structure, behind which energetic‐electron fluxes are modulated by magnetosonic waves: At wave troughs (B‐minimum) electron fluxes are high; at wave crests (B‐maximum) electron fluxes are low. This phenomenon challenges the classical theory of betatron mechanism, so we need to propose a new theory to explain it. In our theory, there exists a magnetic bottle with time‐varying belly but steady neck behind the DF. When the belly expands, a magnetic bottle is formed, and electrons are trapped; when the belly contracts, the magnetic bottle disappears, and electrons are expelled. Quantitatively, we validate the existence of this bottle and estimate its size as 2–3 RE. Our theory can explain both the presence and absence of energetic electrons behind DFs.
Thank You to Our 2019 Reviewers
Authors: Lugaz Noé , Knipp Delores J. , Gannon Jennifer L. , Hapgood Michael , Liu Huixin , O'Brien T. Paul , Welling Daniel T. 
Published: March 2020

AbstractPeer reviewing is the foundation of modern scholarship, with external specialists being asked to fairly check and evaluate submitted work. This difficult and often time‐consuming activity is performed voluntarily, with the understanding that one's own scholarship shall benefit down the line from a careful analysis of its assumption, results, accuracy, and yes, language, as we are now evaluating someone else's work. At Space Weather, we pride ourselves on a fair but quick review process yielding high‐quality articles with a time from submission to first decision of under one month. This would not be possible without the hard work of all our reviewers. Once a year, we take the occasion to name these women and men in order to thank them for their service to the journal and the community.
Blackjack mutations improve the on-target activities of increased fidelity variants of SpCas9 with 5′G-extended sgRNAs
Authors: Kulcsár Péter István , Tálas András , Tóth Eszter , Nyeste Antal , Ligeti Zoltán , Welker Zsombor , Welker Ervin 
Published: March 2020

AbstractIncreased fidelity mutants of the SpCas9 nuclease constitute the most promising approach to mitigating its off-target effects. However, these variants are effective only in a restricted target space, and many of them are reported to work less efficiently when applied in clinically relevant, pre-assembled, ribonucleoprotein forms. The low tolerance to 5′-extended, 21G-sgRNAs contributes, to a great extent, to their decreased performance. Here, we report the generation of Blackjack SpCas9 variant that shows increased fidelity yet remain effective with 21G-sgRNAs. Introducing Blackjack mutations into previously reported increased fidelity variants make them effective with 21G-sgRNAs and increases their fidelity. Two “Blackjack” nucleases, eSpCas9-plus and SpCas9-HF1-plus are superior variants of eSpCas9 and SpCas9-HF1, respectively, possessing matching on-target activity and fidelity but retaining activity with 21G-sgRNAs. They facilitate the use of existing pooled sgRNA libraries with higher specificity and show similar activities whether delivered as plasmids or as pre-assembled ribonucleoproteins.
Analysis of DNA methylation associates the cystine–glutamate antiporter SLC7A11 with risk of Parkinson’s disease
Authors: Vallerga Costanza L. , Zhang Futao , Fowdar Javed , McRae Allan F. , Qi Ting , Nabais Marta F. , Zhang Qian , Kassam Irfahan , Henders Anjali K. , Wallace Leanne , Montgomery Grant , Chuang Yu-Hsuan , Horvath Steve , Ritz Beate , Halliday Glenda , Hickie Ian , Kwok John B. , Pearson John , Pitcher Toni , Kennedy Martin , Bentley Steven R. , Silburn Peter A. , Yang Jian , Wray Naomi R. , Lewis Simon J. G. , Anderson Tim , Dalrymple-Alford John , Mellick George D. , Visscher Peter M. , Gratten Jacob 
Published: March 2020

AbstractAn improved understanding of etiological mechanisms in Parkinson’s disease (PD) is urgently needed because the number of affected individuals is projected to increase rapidly as populations age. We present results from a blood-based methylome-wide association study of PD involving meta-analysis of 229 K CpG probes in 1,132 cases and 999 controls from two independent cohorts. We identify two previously unreported epigenome-wide significant associations with PD, including cg06690548 on chromosome 4. We demonstrate that cg06690548 hypermethylation in PD is associated with down-regulation of the SLC7A11 gene and show this is consistent with an environmental exposure, as opposed to medications or genetic factors with effects on DNA methylation or gene expression. These findings are notable because SLC7A11 codes for a cysteine-glutamate anti-porter regulating levels of the antioxidant glutathione, and it is a known target of the environmental neurotoxin β-methylamino-L-alanine (BMAA). Our study identifies the SLC7A11 gene as a plausible biological target in PD.
Simulating the mechanisms of serrated flow in interstitial alloys with atomic resolution over diffusive timescales
Authors: Zhao Yue , Dezerald Lucile , Pozuelo Marta , Zhou Xinran , Marian Jaime 
Published: March 2020

AbstractThe Portevin-Le Chatelier (PLC) effect is a phenomenon by which plastic slip in metallic materials becomes unstable, resulting in jerky flow and the onset of inhomogeneous deformation. The PLC effect is thought to be fundamentally caused by the dynamic interplay between dislocations and solute atoms. However, this interplay is almost always inaccessible experimentally due to the extremely fine length and time scales over which it occurs. In this paper, simulations of jerky flow in W-O interstitial solid solutions reveal three dynamic regimes emerging from the simulated strain rate-temperature space: one resembling standard solid solution strengthening, another one mimicking solute cloud formation, and a third one where dislocation/solute coevolution leads to jerky flow as a precursor of dynamic strain aging. The simulations are carried out in a stochastic framework that naturally captures rare events in a rigorous manner, providing atomistic resolution over diffusive time scales using no adjustable parameters.
Interplay between DNA damage repair and apoptosis shapes cancer evolution through aneuploidy and microsatellite instability
Authors: Auslander Noam , Wolf Yuri I. , Koonin Eugene V. 
Published: March 2020

AbstractDriver mutations and chromosomal aneuploidy are major determinants of tumorigenesis that exhibit complex relationships. Here, we identify associations between driver mutations and chromosomal aberrations that define two tumor clusters, with distinct regimes of tumor evolution underpinned by unique sets of mutations in different components of DNA damage response. Gastrointestinal and endometrial tumors comprise a separate cluster for which chromosomal-arm aneuploidy and driver mutations are mutually exclusive. The landscape of driver mutations in these tumors is dominated by mutations in DNA repair genes that are further linked to microsatellite instability. The rest of the cancer types show a positive association between driver mutations and aneuploidy, and a characteristic set of mutations that involves primarily genes for components of the apoptotic machinery. The distinct sets of mutated genes derived here show substantial prognostic power and suggest specific vulnerabilities of different cancers that might have therapeutic potential.
Development and identification of three functional markers associated with starch content in lotus (Nelumbo nucifera)
Authors: Cheng Teng , Zheng Xingwen , Xie Keqiang , Liu Jiangdong , Zheng Xingfei , Jin Surong , Diao Ying , Hu Zhongli , Wang Jianxiong 
Published: March 2020

AbstractIt have been significantly demonstrated that Hexokinase (HXK), Granule-bound starch synthase (GBSS) and ADP-glucose pyrophosphorylase (AGPase) are three critical enzymes in the starch biosynthetic pathway and are related to starch (amylose, amylopectin and total starch) content in lotus. It is important to develop functional markers in marker-assisted selection of lotus breeding. So far there have been few reports about lotus functional markers. In this study, based on insertion-deletions (INDELs) and single-nucleotide polymorphisms (SNPs), we developed three functional markers, FMHXK-E1, FMGBSS-I8 and FMAGPL-I1. FMHXK-E1 was developed based on polymorphisms of two haplotypes of NnHXK. 26 lotus cultivars that the 320-bp fragment presented in NnHXK had a lower content of amylose and a higher content of amylopectin. FMGBSS-I8 was developed based on polymorphisms of two haplotypes of NnGBSS. The group containing 32 lotus cultivars with the 210-bp fragment had less amylose content and more amylopectin content. FMAGPL-I1 was developed based on polymorphisms of two haplotypes of NnAGPL (ADP-glucose pyrophosphorylase large subunit gene). The group containing 40 lotus cultivars with the 362-bp fragment had less amylopectin, total starch content and more amylose content. According to the study, FMHXK-E1, FMGBSS-I8 and FMAGPL-I1 are closely related to lotus starch content. It could be provided research basis for molecular assisted selection of lotus starch content improve breeding efficiency.
Socio-ecological factors determine crop performance in agricultural systems
Authors: Nkurunziza Libère , Watson Christine A. , Öborn Ingrid , Smith Henrik G. , Bergkvist Göran , Bengtsson Jan 
Published: March 2020

AbstractAgricultural production systems are affected by complex interactions between social and ecological factors, which are often hard to integrate in a common analytical framework. We evaluated differences in crop production among farms by integrating components of several related research disciplines in a single socio-ecological analysis. Specifically, we evaluated spring barley (Hordeum vulgare, L.) performance on 34 farms (organic and conventional) in two agro-ecological zones to unravel the importance of ecological, crop and management factors in the performance of a standard crop. We used Projections to Latent Structures (PLS), a simple but robust analytical tool widely utilized in research disciplines dealing with complex systems (e.g. social sciences and chemometrics), but infrequently in agricultural sciences. We show that barley performance on organic farms was affected by previous management, landscape structure, and soil quality, in contrast to conventional farms where external inputs were the main factors affecting biomass and grain yield. This indicates that more complex management strategies are required in organic than in conventional farming systems. We conclude that the PLS method combining socio-ecological and biophysical factors provides improved understanding of the various interacting factors determining crop performance and can help identify where improvements in the agricultural system are most likely to be effective.
Acoustic levitation with optimized reflective metamaterials
Authors: Polychronopoulos Spyros , Memoli Gianluca 
Published: March 2020

AbstractThe simplest and most commonly used acoustic levitator is comprised of a transmitter and an opposing reflecting surface. This type of device, however, is only able to levitate objects along one direction, at distances multiple of half of a wavelength. In this work, we show how a customised reflective acoustic metamaterial enables the levitation of multiple particles, not necessarily on a line and with arbitrary mutual distances, starting with a generic input wave. We establish a heuristic optimisation technique for the design of the metamaterial, where the local height of the surface is used to introduce delay patterns to the reflected signals. Our method stands for any type and number of sources, spatial resolution of the metamaterial and system’s variables (i.e. source position, phase and amplitude, metamaterial’s geometry, relative position of the levitation points, etc.). Finally, we explore how the strength of multiple levitation points changes with their relative distance, demonstrating sub-wavelength field control over levitating polystyrene beads into various configurations.
Microstates-based resting frontal alpha asymmetry approach for understanding affect and approach/withdrawal behavior
Authors: Kaur Ardaman , Chinnadurai Vijayakumar , Chaujar Rishu 
Published: March 2020

AbstractThe role of resting frontal alpha-asymmetry in explaining neural-mechanisms of affect and approach/withdrawal behavior is still debatable. The present study explores the ability of the quasi-stable resting EEG asymmetry information and the associated neurovascular synchronization/desynchronization in bringing more insight into the understanding of neural-mechanisms of affect and approach/withdrawal behavior. For this purpose, a novel frontal alpha-asymmetry based on microstates, that assess quasi-stable EEG scalp topography information, is proposed and compared against standard frontal-asymmetry. Both proposed and standard frontal alpha-asymmetries were estimated from thirty-nine healthy volunteers resting-EEG simultaneously acquired with resting-fMRI. Further, neurovascular mechanisms of these asymmetry measures were estimated through EEG-informed fMRI. Subsequently, the Hemodynamic Lateralization Index (HLI) of the neural-underpinnings of both asymmetry measures was assessed. Finally, the robust correlation of both asymmetry-measures and their HLI’s with PANAS, BIS/BAS was carried out. The standard resting frontal-asymmetry and its HLI yielded no significant correlation with any psychological-measures. However, the microstate resting frontal-asymmetry correlated significantly with negative affect and its neural underpinning’s HLI significantly correlated with Positive/Negative affect and BIS/BAS measures. Finally, alpha-BOLD desynchronization was observed in neural-underpinning whose HLI correlated significantly with negative affect and BIS. Hence, the proposed resting microstate-frontal asymmetry better assesses the neural-mechanisms of affect, approach/withdrawal behavior.
Anemia and the risk of Parkinson’s disease in Korean older adults: A nationwide population-based study
Authors: Cho In Young , Shin Dong Wook , Roh Younjin , Jang Wooyoung , Cho Jin Whan , Lee Eun Ae , Ko Hyeonyoung , Han Kyungdo , Yoo Jun Hyun 
Published: March 2020

AbstractEvidence of the association between anemia and risk of PD (Parkinson’s disease) have been accumulating. This study aimed to examine the relationship between anemia and risk of PD in Korean older adults. Korean adults aged 50 years or older who participated in the Korean National Screening Program (n = 12,342,278) between 2009 and 2013 were followed until 2015. Cox proportional hazards regression models were used to calculate the hazard ratio (HR) of PD, and participants were followed for a mean period of 5.0 years. At the end of follow-up, 3,844 adults were diagnosed with PD. After adjusting for potential confounders, participants with anemia had decreased risk of PD compared to adults without anemia (adjusted HR (aHR) 0.894, 95% CI: 0.809–0.989). Furthermore, aHR of PD was 0.698 (95% CI: 0.546–0.891) in moderate to severe anemia and 0.938 (95% CI: 0.843–1.044) in mild anemia. The protective effect of anemia was also more profound in men (aHR 0.888, 95% CI: 0.774–1.02) than in women (aHR 0.905, 95% CI: 0.782–1.048). In conclusion, anemia was associated with lower risk of PD, particularly for patients with moderate to severe anemia. Our study suggests that further studies may be needed to clarify the relationship between anemia and PD.
Prognostic value of miR-21 in gliomas: comprehensive study based on meta-analysis and TCGA dataset validation
Authors: Jiang Guli , Mu Jing , Liu Xing , Peng Xiangni , Zhong Feiya , Yuan Wenliang , Deng Fang , Peng Xiaoning , Peng Sihua , Zeng Xiaomin 
Published: March 2020

AbstractRecent studies have highlighted the value of microRNA-21 (miR-21) as a prognostic biomarker in gliomas. However, the role of miR-21 in predicting prognosis remains controversial. We performed a comprehensive study based upon a meta-analysis and The Cancer Genome Atlas (TCGA) glioma dataset validation to clarify the prognostic significance of miR-21 in glioma patients. In this study, we searched Embase, PubMed, Web of science, CNKI, SinoMed, and Wanfang databases for records up to May 2018. Relevant data were extracted to assess the correlation between miR-21 expression and survival in glioma patients. Pooled hazard ratios (HRs) with 95% confidence intervals (CIs) were used to describe association strength. We further used multivariate Cox regression analysis to assess miR-21 expression in the TCGA glioma dataset to validate the relationship between miR-21 expression and survival. Nine studies were included in the meta-analysis. Among them, eight studies provided data on overall survival (OS) with a pooled HR of 1.91 (95% CI: 1.34, 2.73), indicating that higher expression of miR-21 was significantly associated with worse OS in glioma patients; for the other study, which provided data on progression-free survival (PFS), no statistically significant HR was reported for PFS in the glioma patients (HR = 1.23, 95% CI: 0.41, 3.72). A multivariate Cox regression analysis of the miR-21 expression in the TCGA glioma dataset revealed that overexpression of miR-21 was a potential independent prognostic biomarker of poorer OS (HR = 1.27, 95% CI: 1.01, 1.59) and poorer PFS (HR = 1.46, 95% CI: 1.17, 1.82). Our findings suggest that higher expression of miR-21 is correlated with poorer glioma prognosis.
Morphological Evidence for the Sensitivity of the Ear Canal of Odontocetes as shown by Immunohistochemistry and Transmission Electron Microscopy
Authors: De Vreese Steffen , André Michel , Cozzi Bruno , Centelleghe Cinzia , van der Schaar Mike , Mazzariol Sandro 
Published: March 2020

AbstractThe function of the external ear canal in cetaceans is still under debate and its morphology is largely unknown. Immunohistochemical (IHC) analyses using antibodies specific for nervous tissue (anti-S100, anti-NSE, anti-NF, and anti-PGP 9.5), together with transmission electron microscopy (TEM) and various histological techniques, were carried out to investigate the peripheral nervous system of the ear canals of several species of toothed whales and terrestrial Cetartiodactyla. This study highlights the innervation of the ear canal with the presence of lamellar corpuscles over its entire course, and their absence in all studied terrestrial mammals. Each corpuscle consisted of a central axon, surrounded by lamellae of Schwann receptor cells, surrounded by a thin cellular layer, as shown by IHC and TEM. These findings indicate that the corpuscles are mechanoreceptors that resemble the inner core of Pacinian corpuscles without capsule or outer core, and were labelled as simple lamellar corpuscles. They form part of a sensory system that may represent a unique phylogenetic feature of cetaceans, and an evolutionary adaptation to life in the marine environment. Although the exact function of the ear canal is not fully clear, we provide essential knowledge and a preliminary hypothetical deviation on its function as a unique sensory organ.
The lateral prefrontal cortex of primates encodes stimulus colors and their behavioral relevance during a match-to-sample task
Authors: Schwedhelm Philipp , Baldauf Daniel , Treue Stefan 
Published: March 2020

AbstractThe lateral prefrontal cortex of primates (lPFC) plays a central role in complex cognitive behavior, in decision-making as well as in guiding top-down attention. However, how and where in lPFC such behaviorally relevant signals are computed is poorly understood. We analyzed neural recordings from chronic microelectrode arrays implanted in lPFC region 8Av/45 of two rhesus macaques. The animals performed a feature match-to-sample task requiring them to match both motion and color information in a test stimulus. This task allowed to separate the encoding of stimulus motion and color from their current behavioral relevance on a trial-by-trial basis. We found that upcoming motor behavior can be robustly predicted from lPFC activity. In addition, we show that 8Av/45 encodes the color of a visual stimulus, regardless of its behavioral relevance. Most notably, whether a color matches the searched-for color can be decoded independent of a trial’s motor outcome and while subjects detect unique feature conjunctions of color and motion. Thus, macaque area 8Av/45 computes, among other task-relevant information, the behavioral relevance of visual color features. Such a signal is most critical for both the selection of responses as well as the deployment of top-down modulatory signals, like feature-based attention.
No effect of targeted memory reactivation during sleep on retention of vocabulary in adolescents
Authors: Wilhelm Ines , Schreiner Thomas , Beck Jonas , Rasch Björn 
Published: March 2020

AbstractRe-exposure of newly acquired vocabulary during sleep improves later memory recall in healthy adults. The success of targeted memory reactivation (TMR) during sleep presumably depends on the presence of slow oscillations (i.e., EEG activity at a frequency of about 0.75 Hz). As slow oscillating activity is at its maximum during adolescence, we hypothesized that TMR is even more beneficial at this developmental stage. In the present study, adolescents aged 11 to 13 learnt Dutch vocabulary in the evening and were tested on recall performance the next morning. Half of the words were presented via loudspeakers during post-learning periods of NREM (Non Rapid Eye Movement) sleep in order to stimulate memory reactivation. Unexpectedly, TMR during sleep did not improve memory on the behavioral level in adolescents. On the oscillatory level, successful reactivation during sleep resulted in the characteristic increase in theta power over frontal brain regions, as reported in adults. However, we observed no increase in spindle power during successful reactivation. Possible factors that may explain the lacking effect of TMR in adolescents in this study such as differences in learning abilities and pre-sleep performance levels are discussed.
SVD-clustering, a general image-analyzing method explained and demonstrated on model and Raman micro-spectroscopic maps
Authors: Szalontai B. , Debreczeny M. , Fintor K. , Bagyinka Cs. 
Published: March 2020

AbstractAn image analyzing method (SVD-clustering) is presented. Amplitude vectors of SVD factorization (V1…Vi) were introduced into the imaging of the distribution of the corresponding Ui basis-spectra. Since each Vi vector contains each point of the map, plotting them along the X, Y, Z dimensions of the map reconstructs the spatial distribution of the corresponding Ui basis-spectrum. This gives valuable information about the first, second, etc. higher-order deviations present in the map. We extended SVD with a clustering method, using the significant Vi vectors from the VT matrix as coordinates of image points in a ne-dimensional space (ne is the effective rank of the data matrix). This way every image point had a corresponding coordinate in the ne-dimensional space and formed a point set. Clustering was applied to this point set. SVD-clustering is universal; it is applicable to any measurement where data are recorded as a function of an external parameter (time, space, temperature, concentration, species, etc.). Consequently, our method is not restricted to spectral imaging, it can find application in many different 2D and 3D image analyses. Using SVD-clustering, we have shown on models the theoretical possibilities and limitations of the method, especially in the context of creating, meaning/interpreting of cluster spectra. Then for real-world samples, two examples are presented, where we were able to reveal minute alterations in the samples (changing cation ratios in minerals, differently structured cellulose domains in plant root) with spatial resolution.