bluuebunny/crossref_metadata_2025_split huggingface dataset:
Seasonal Arctic Sea Ice Prediction Using a Newly Developed Fully Coupled Regional Model With the Assimilation of Satellite Sea Ice Observations
Authors: Yang Chao‐Yuan , Liu Jiping , Xu Shiming 
Published: April 2020

AbstractTo increase our capability to predict Arctic sea ice and climate, we have developed a coupled atmosphere‐sea ice‐ocean model configured for the pan‐Arctic with sufficient flexibility. The Los Alamos Sea Ice Model is coupled with the Weather Research and Forecasting Model and the Regional Ocean Modeling System in the Coupled Ocean‐Atmosphere‐Wave‐Sediment Transport modeling system. It is well known that dynamic models used to predict Arctic sea ice at short‐term periods strongly depend on model initial conditions. Parallel Data Assimilation Framework is implemented into the new modeling system to assimilate sea ice observations and generate skillful model initialization, which aid in the prediction procedures. The Special Sensor Microwave Imager/Sounder sea ice concentration, the CyroSat‐2, and Soil Moisture and Ocean Salinity sea ice thickness are assimilated with the localized error subspace transform ensemble Kalman filter. We conduct Arctic sea ice prediction for the melting seasons of 2017 and 2018. Predictions with improved initial sea ice conditions show reasonable sea ice evolution and small biases in the minimum sea ice extent, although the ice refreezing is delayed. Our prediction experiments suggest that the use of appropriate uncertainty for the observed sea ice thickness can lead to improved spatial distribution of the initial ice thickness and thus the predicted sea ice distribution. Our new modeling system initialized by the output of the National Centers for Environmental Prediction Climate Forecast System seasonal forecasts with data assimilation can significantly increase the sea ice prediction skills in sea ice extent for the entire Arctic as well as in the Northern Sea Route compared with the predictions by the National Centers for Environmental Prediction Climate Forecast System.
Repeated horizontal gene transfers triggered parallel evolution of magnetotaxis in two evolutionary divergent lineages of magnetotactic bacteria
Authors: Monteil Caroline L , Grouzdev Denis S , Perrière Guy , Alonso Béatrice , Rouy Zoé , Cruveiller Stéphane , Ginet Nicolas , Pignol David , Lefevre Christopher T 
Published: April 2020

Abstract
Under the same selection pressures, two genetically divergent populations may evolve in parallel toward the same adaptive solutions. Here, we hypothesized that magnetotaxis (i.e., magnetically guided chemotaxis) represents a key adaptation to micro-oxic habitats in aquatic sediments and that its parallel evolution homogenized the phenotypes of two evolutionary divergent clusters of freshwater spirilla. All magnetotactic bacteria affiliated to the Magnetospirillum genus (Alphaproteobacteria class) biomineralize the same magnetic particle chains and share highly similar physiological and ultrastructural features. We looked for the processes that could have contributed at shaping such an evolutionary pattern by reconciling species and gene trees using newly sequenced genomes of Magnetospirillum related bacteria. We showed that repeated horizontal gene transfers and homologous recombination of entire operons contributed to the parallel evolution of magnetotaxis. We propose that such processes could represent a more parsimonious and rapid solution for adaptation compared with independent and repeated de novo mutations, especially in the case of traits as complex as magnetotaxis involving tens of interacting proteins. Besides strengthening the idea about the importance of such a function in micro-oxic habitats, these results reinforce previous observations in experimental evolution suggesting that gene flow could alleviate clonal interference and speed up adaptation under some circumstances.
A high-content RNAi screen reveals multiple roles for long noncoding RNAs in cell division
Authors: Stojic Lovorka , Lun Aaron T. L. , Mascalchi Patrice , Ernst Christina , Redmond Aisling M. , Mangei Jasmin , Barr Alexis R. , Bousgouni Vicky , Bakal Chris , Marioni John C. , Odom Duncan T. , Gergely Fanni 
Published: April 2020

AbstractGenome stability relies on proper coordination of mitosis and cytokinesis, where dynamic microtubules capture and faithfully segregate chromosomes into daughter cells. With a high-content RNAi imaging screen targeting more than 2,000 human lncRNAs, we identify numerous lncRNAs involved in key steps of cell division such as chromosome segregation, mitotic duration and cytokinesis. Here, we provide evidence that the chromatin-associated lncRNA, linc00899, leads to robust mitotic delay upon its depletion in multiple cell types. We perform transcriptome analysis of linc00899-depleted cells and identify the neuronal microtubule-binding protein, TPPP/p25, as a target of linc00899. We further show that linc00899 binds TPPP/p25 and suppresses its transcription. In cells depleted of linc00899, upregulation of TPPP/p25 alters microtubule dynamics and delays mitosis. Overall, our comprehensive screen uncovers several lncRNAs involved in genome stability and reveals a lncRNA that controls microtubule behaviour with functional implications beyond cell division.
Spatially resolved analyses link genomic and immune diversity and reveal unfavorable neutrophil activation in melanoma
Authors: Mitra Akash , Andrews Miles C. , Roh Whijae , De Macedo Marianna Petaccia , Hudgens Courtney W. , Carapeto Fernando , Singh Shailbala , Reuben Alexandre , Wang Feng , Mao Xizeng , Song Xingzhi , Wani Khalida , Tippen Samantha , Ng Kwok-Shing , Schalck Aislyn , Sakellariou-Thompson Donald A. , Chen Eveline , Reddy Sangeetha M. , Spencer Christine N. , Wiesnoski Diana , Little Latasha D. , Gumbs Curtis , Cooper Zachary A. , Burton Elizabeth M. , Hwu Patrick , Davies Michael A. , Zhang Jianhua , Bernatchez Chantale , Navin Nicholas , Sharma Padmanee , Allison James P. , Wargo Jennifer A. , Yee Cassian , Tetzlaff Michael T. , Hwu Wen-Jen , Lazar Alexander J. , Futreal P. Andrew 
Published: April 2020

AbstractComplex tumor microenvironmental (TME) features influence the outcome of cancer immunotherapy (IO). Here we perform immunogenomic analyses on 67 intratumor sub-regions of a PD-1 inhibitor-resistant melanoma tumor and 2 additional metastases arising over 8 years, to characterize TME interactions. We identify spatially distinct evolution of copy number alterations influencing local immune composition. Sub-regions with chromosome 7 gain display a relative lack of leukocyte infiltrate but evidence of neutrophil activation, recapitulated in The Cancer Genome Atlas (TCGA) samples, and associated with lack of response to IO across three clinical cohorts. Whether neutrophil activation represents cause or consequence of local tumor necrosis requires further study. Analyses of T-cell clonotypes reveal the presence of recurrent priming events manifesting in a dominant T-cell clonotype over many years. Our findings highlight the links between marked levels of genomic and immune heterogeneity within the physical space of a tumor, with implications for biomarker evaluation and immunotherapy response.
A gravity-based three-dimensional compass in the mouse brain
Authors: Angelaki Dora E. , Ng Julia , Abrego Amada M. , Cham Henry X. , Asprodini Eftihia K. , Dickman J. David , Laurens Jean 
Published: April 2020

AbstractGravity sensing provides a robust verticality signal for three-dimensional navigation. Head direction cells in the mammalian limbic system implement an allocentric neuronal compass. Here we show that head-direction cells in the rodent thalamus, retrosplenial cortex and cingulum fiber bundle are tuned to conjunctive combinations of azimuth and tilt, i.e. pitch or roll. Pitch and roll orientation tuning is anchored to gravity and independent of visual landmarks. When the head tilts, azimuth tuning is affixed to the head-horizontal plane, but also uses gravity to remain anchored to the allocentric bearings in the earth-horizontal plane. Collectively, these results demonstrate that a three-dimensional, gravity-based, neural compass is likely a ubiquitous property of mammalian species, including ground-dwelling animals.
XPO5 promotes primary miRNA processing independently of RanGTP
Authors: Wang Jingjing , Lee Jerome E. , Riemondy Kent , Yu Yang , Marquez Steven M. , Lai Eric C. , Yi Rui 
Published: April 2020

AbstractXPO5 mediates nuclear export of miRNA precursors in a RanGTP-dependent manner. However, XPO5-associated RNA species have not been determined globally and it is unclear whether XPO5 has any additional functions other than nuclear export. Here we show XPO5 pervasively binds to double-stranded RNA regions found in some clustered primary miRNA precursors and many cellular RNAs. Surprisingly, the binding of XPO5 to pri-miRNAs such as mir-17~92 and mir-15b~16-2 and highly structured RNAs such as vault RNAs is RanGTP-independent. Importantly, XPO5 enhances the processing efficiency of pri-mir-19a and mir-15b~16-2 by the DROSHA/DGCR8 microprocessor. Genetic deletion of XPO5 compromises the biogenesis of most miRNAs and leads to severe defects during mouse embryonic development and skin morphogenesis. This study reveals an unexpected function of XPO5 for recognizing and facilitating the nuclear cleavage of clustered pri-miRNAs, identifies numerous cellular RNAs bound by XPO5, and demonstrates physiological functions of XPO5 in mouse development.
Regulation of reactive oxygen species during plant immunity through phosphorylation and ubiquitination of RBOHD
Authors: Lee DongHyuk , Lal Neeraj K. , Lin Zuh-Jyh Daniel , Ma Shisong , Liu Jun , Castro Bardo , Toruño Tania , Dinesh-Kumar Savithramma P. , Coaker Gitta 
Published: April 2020

AbstractProduction of reactive oxygen species (ROS) is critical for successful activation of immune responses against pathogen infection. The plant NADPH oxidase RBOHD is a primary player in ROS production during innate immunity. However, how RBOHD is negatively regulated remains elusive. Here we show that RBOHD is regulated by C-terminal phosphorylation and ubiquitination. Genetic and biochemical analyses reveal that the PBL13 receptor-like cytoplasmic kinase phosphorylates RBOHD’s C-terminus and two phosphorylated residues (S862 and T912) affect RBOHD activity and stability, respectively. Using protein array technology, we identified an E3 ubiquitin ligase PIRE (PBL13 interacting RING domain E3 ligase) that interacts with both PBL13 and RBOHD. Mimicking phosphorylation of RBOHD (T912D) results in enhanced ubiquitination and decreased protein abundance. PIRE and PBL13 mutants display higher RBOHD protein accumulation, increased ROS production, and are more resistant to bacterial infection. Thus, our study reveals an intricate post-translational network that negatively regulates the abundance of a conserved NADPH oxidase.
Transcriptional repression of GIF1 by the KIX-PPD-MYC repressor complex controls seed size in Arabidopsis
Authors: Liu Zupei , Li Na , Zhang Yueying , Li Yunhai 
Published: April 2020

AbstractSeed size is a key agronomic trait that greatly determines plant yield. Elucidating the molecular mechanism underlying seed size regulation is also an important question in developmental biology. Here, we show that the KIX-PPD-MYC-GIF1 pathway plays a crucial role in seed size control in Arabidopsis thaliana. Disruption of KIX8/9 and PPD1/2 causes large seeds due to increased cell proliferation and cell elongation in the integuments. KIX8/9 and PPD1/2 interact with transcription factors MYC3/4 to form the KIX-PPD-MYC complex in Arabidopsis. The KIX-PPD-MYC complex associates with the typical G-box sequence in the promoter of GRF-INTERACTING FACTOR 1 (GIF1), which promotes seed growth, and represses its expression. Genetic analyses support that KIX8/9, PPD1/2, MYC3/4, and GIF1 function in a common pathway to control seed size. Thus, our results reveal a genetic and molecular mechanism by which the transcription factors MYC3/4 recruit KIX8/9 and PPD1/2 to the promoter of GIF1 and repress its expression, thereby determining seed size in Arabidopsis.
Atomic imaging of mechanically induced topological transition of ferroelectric vortices
Authors: Chen Pan , Zhong Xiangli , Zorn Jacob A. , Li Mingqiang , Sun Yuanwei , Abid Adeel Y. , Ren Chuanlai , Li Yuehui , Li Xiaomei , Ma Xiumei , Wang Jinbin , Liu Kaihui , Xu Zhi , Tan Congbing , Chen Longqing , Gao Peng , Bai Xuedong 
Published: April 2020

AbstractFerroelectric vortices formed through complex lattice–charge interactions have great potential in applications for future nanoelectronics such as memories. For practical applications, it is crucial to manipulate these topological states under external stimuli. Here, we apply mechanical loads to locally manipulate the vortices in a PbTiO3/SrTiO3 superlattice via atomically resolved in-situ scanning transmission electron microscopy. The vortices undergo a transition to the a-domain with in-plane polarization under external compressive stress and spontaneously recover after removal of the stress. We reveal the detailed transition process at the atomic scale and reproduce this numerically using phase-field simulations. These findings provide new pathways to control the exotic topological ferroelectric structures for future nanoelectronics and also valuable insights into understanding of lattice-charge interactions at nanoscale.
Genome-wide analysis highlights contribution of immune system pathways to the genetic architecture of asthma
Authors: Han Yi , Jia Qiong , Jahani Pedram Shafiei , Hurrell Benjamin P. , Pan Calvin , Huang Pin , Gukasyan Janet , Woodward Nicholas C. , Eskin Eleazar , Gilliland Frank D. , Akbari Omid , Hartiala Jaana A. , Allayee Hooman 
Published: April 2020

AbstractAsthma is a chronic and genetically complex respiratory disease that affects over 300 million people worldwide. Here, we report a genome-wide analysis for asthma using data from the UK Biobank and the Trans-National Asthma Genetic Consortium. We identify 66 previously unknown asthma loci and demonstrate that the susceptibility alleles in these regions are, either individually or as a function of cumulative genetic burden, associated with risk to a greater extent in men than women. Bioinformatics analyses prioritize candidate causal genes at 52 loci, including CD52, and demonstrate that asthma-associated variants are enriched in regions of open chromatin in immune cells. Lastly, we show that a murine anti-CD52 antibody mimics the immune cell-depleting effects of a clinically used human anti-CD52 antibody and reduces allergen-induced airway hyperreactivity in mice. These results further elucidate the genetic architecture of asthma and provide important insight into the immunological and sex-specific relevance of asthma-associated risk variants.
Origin of micro-scale heterogeneity in polymerisation of photo-activated resin composites
Authors: Sirovica Slobodan , Solheim Johanne H. , Skoda Maximilian W. A. , Hirschmugl Carol J. , Mattson Eric C. , Aboualizadeh Ebrahim , Guo Yilan , Chen Xiaohui , Kohler Achim , Romanyk Dan L. , Rosendahl Scott M. , Morsch Suzanne , Martin Richard A. , Addison Owen 
Published: April 2020

AbstractPhoto-activated resin composites are widely used in industry and medicine. Despite extensive chemical characterisation, the micro-scale pattern of resin matrix reactive group conversion between filler particles is not fully understood. Using an advanced synchrotron-based wide-field IR imaging system and state-of-the-art Mie scattering corrections, we observe how the presence of monodispersed silica filler particles in a methacrylate based resin reduces local conversion and chemical bond strain in the polymer phase. Here we show that heterogeneity originates from a lower converted and reduced bond strain boundary layer encapsulating each particle, whilst at larger inter-particulate distances light attenuation and monomer mobility predominantly influence conversion. Increased conversion corresponds to greater bond strain, however, strain generation appears sensitive to differences in conversion rate and implies subtle distinctions in the final polymer structure. We expect these findings to inform current predictive models of mechanical behaviour in polymer-composite materials, particularly at the resin-filler interface.
The optical conductivity of few-layer black phosphorus by infrared spectroscopy
Authors: Zhang Guowei , Huang Shenyang , Wang Fanjie , Xing Qiaoxia , Song Chaoyu , Wang Chong , Lei Yuchen , Huang Mingyuan , Yan Hugen 
Published: April 2020

AbstractThe strength of light-matter interaction is of central importance in photonics and optoelectronics. For many widely studied two-dimensional semiconductors, such as MoS2, the optical absorption due to exciton resonances increases with thickness. However, here we will show, few-layer black phosphorus exhibits an opposite trend. We determine the optical conductivity of few-layer black phosphorus with thickness down to bilayer by infrared spectroscopy. On the contrary to our expectations, the frequency-integrated exciton absorption is found to be enhanced in thinner samples. Moreover, the continuum absorption near the band edge is almost a constant, independent of the thickness. We will show such scenario is related to the quanta of the universal optical conductivity of graphene (σ0 = e2/4ħ), with a prefactor originating from the band anisotropy.
Increased burden of ultra-rare structural variants localizing to boundaries of topologically associated domains in schizophrenia
Authors: Halvorsen Matthew , Huh Ruth , Oskolkov Nikolay , Wen Jia , Netotea Sergiu , Giusti-Rodriguez Paola , Karlsson Robert , Bryois Julien , Nystedt Björn , Ameur Adam , Kähler Anna K. , Ancalade NaEshia , Farrell Martilias , Crowley James J. , Li Yun , Magnusson Patrik K. E. , Gyllensten Ulf , Hultman Christina M. , Sullivan Patrick F. , Szatkiewicz Jin P. 
Published: April 2020

AbstractDespite considerable progress in schizophrenia genetics, most findings have been for large rare structural variants and common variants in well-imputed regions with few genes implicated from exome sequencing. Whole genome sequencing (WGS) can potentially provide a more complete enumeration of etiological genetic variation apart from the exome and regions of high linkage disequilibrium. We analyze high-coverage WGS data from 1162 Swedish schizophrenia cases and 936 ancestry-matched population controls. Our main objective is to evaluate the contribution to schizophrenia etiology from a variety of genetic variants accessible to WGS but not by previous technologies. Our results suggest that ultra-rare structural variants that affect the boundaries of topologically associated domains (TADs) increase risk for schizophrenia. Alterations in TAD boundaries may lead to dysregulation of gene expression. Future mechanistic studies will be needed to determine the precise functional effects of these variants on biology.
Effect of decades of corrosion on the microstructure of altered glasses and their radiation stability
Authors: Mir Anamul Haq , Jan Amreen , Delaye Jean-Marc , Donnelly Stephen , Hinks Jonathan , Gin Stephane 
Published: April 2020

AbstractUnderstanding the microstructural evolution of glasses during their interaction with water and radiation is of fundamental importance in addressing the corrosion of nuclear waste forms under geological disposal conditions. Here we report the results of more than 21 years of corrosion of two borosilicate glasses showing the formation of mesoporous C–S–H gels in Ca-bearing glasses and a mainly microporous microstructure in Al-bearing glasses. These porous corroded glasses were then irradiated with heavy ions to simulate the effects of recoil nucleus damage and monitored in real time using transmission electron microscopy with in situ ion irradiation. The ballistic collisions remarkably healed the porous corroded glasses to a pore-free homogeneous microstructure. Besides providing new insights and predictions about how doped glasses and actual waste forms may evolve under corrosion and irradiation, the results highlight the non-universal nature of the existing corrosion models and the important role that the glass composition and radiation damage play in the evolution of the microstructure during corrosion.
Altered pathways in methylome and transcriptome longitudinal analysis of normal weight and bariatric surgery women
Authors: Nicoletti C. F. , Pinhel M. A. S. , Noronha N. Y. , de Oliveira B. A. , Salgado Junior W. , Jácome A. , Diaz-Lagares A. , Casanueva F. , Crujeiras A. B. , Nonino C. B. 
Published: April 2020

AbstractDNA methylation could provide a link between environmental, genetic factors and weight control and can modify gene expression pattern. This study aimed to identify genes, which are differentially expressed and methylated depending on adiposity state by evaluating normal weight women and obese women before and after bariatric surgery (BS). We enrolled 24 normal weight (BMI: 22.5 ± 1.6 kg/m2) and 24 obese women (BMI: 43.3 ± 5.7 kg/m2) submitted to BS. Genome-wide methylation analysis was conducted using Infinium Human Methylation 450 BeadChip (threshold for significant CpG sites based on delta methylation level with a minimum value of 5%, a false discovery rate correction (FDR) of q < 0.05 was applied). Expression levels were measured using HumanHT-12v4 Expression BeadChip (cutoff of p ≤ 0.05 and fold change ≥2.0 was used to detect differentially expressed probes). The integrative analysis of both array data identified four genes (i.e. TPP2, PSMG6, ARL6IP1 and FAM49B) with higher methylation and lower expression level in pre-surgery women compared to normal weight women: and two genes (i.e. ZFP36L1 and USP32) that were differentially methylated after BS. These methylation changes were in promoter region and gene body. All genes are related to MAPK cascade, NIK/NF-kappaB signaling, cellular response to insulin stimulus, proteolysis and others. Integrating analysis of DNA methylation and gene expression evidenced that there is a set of genes relevant to obesity that changed after BS. A gene ontology analysis showed that these genes were enriched in biological functions related to adipogenesis, orexigenic, oxidative stress and insulin metabolism pathways. Also, our results suggest that although methylation plays a role in gene silencing, the majority of effects were not correlated.
Azimuthal multiplexing 3D diffractive optics
Authors: Wang Haiyan , Piestun Rafael 
Published: April 2020

AbstractDiffractive optics have increasingly caught the attention of the scientific community. Classical diffractive optics are 2D diffractive optical elements (DOEs) and computer-generated holograms (CGHs), which modulate optical waves on a solitary transverse plane. However, potential capabilities are missed by the inherent two-dimensional nature of these devices. Previous work has demonstrated that extending the modulation from planar (2D) to volumetric (3D) enables new functionalities, such as generating space-variant functions, multiplexing in the spatial or spectral domain, or enhancing information capacity. Unfortunately, despite significant progress fueled by recent interest in metasurface diffraction, 3D diffractive optics still remains relatively unexplored. Here, we introduce the concept of azimuthal multiplexing. We propose, design, and demonstrate 3D diffractive optics showing this multiplexing effect. According to this new phenomenon, multiple pages of information are encoded and can be read out across independent channels by rotating one or more diffractive layers with respect to the others. We implement the concept with multilayer diffractive optical elements. An iterative projection optimization algorithm helps solve the inverse design problem. The experimental realization using photolithographically fabricated multilevel phase layers demonstrates the predicted performance. We discuss the limitations and potential of azimuthal multiplexing 3D diffractive optics.