bluuebunny/crossref_metadata_2025_split huggingface dataset:
Precisely spun super rotors
Authors: Antonov Ivan O. , Stollenwerk Patrick R. , Venkataramanababu Sruthi , de Lima Batista Ana P. , de Oliveira-Filho Antonio G. S. , Odom Brian C. 
Published: April 2021

AbstractImproved optical control of molecular quantum states promises new applications including chemistry in the quantum regime, precision tests of fundamental physics, and quantum information processing. While much work has sought to prepare ground state molecules, excited states are also of interest. Here, we demonstrate a broadband optical approach to pump trapped SiO+ molecules into pure super rotor ensembles maintained for many minutes. Super rotor ensembles pumped up to rotational state N = 67, corresponding to the peak of a 9400 K distribution, had a narrow N spread comparable to that of a few-kelvin sample, and were used for spectroscopy of the previously unobserved C2Π state. Significant centrifugal distortion of super rotors pumped up to N = 230 allowed probing electronic structure of SiO+ stretched far from its equilibrium bond length.
Oxidized sulfur-rich arc magmas formed porphyry Cu deposits by 1.88 Ga
Authors: Meng Xuyang , Kleinsasser Jackie M. , Richards Jeremy P. , Tapster Simon R. , Jugo Pedro J. , Simon Adam C. , Kontak Daniel J. , Robb Laurence , Bybee Grant M. , Marsh Jeffrey H. , Stern Richard A. 
Published: April 2021

AbstractMost known porphyry Cu deposits formed in the Phanerozoic and are exclusively associated with moderately oxidized, sulfur-rich, hydrous arc-related magmas derived from partial melting of the asthenospheric mantle metasomatized by slab-derived fluids. Yet, whether similar metallogenic processes also operated in the Precambrian remains obscure. Here we address the issue by investigating the origin, fO2, and S contents of calc-alkaline plutonic rocks associated with the Haib porphyry Cu deposit in the Paleoproterozoic Richtersveld Magmatic Arc (southern Namibia), an interpreted mature island-arc setting. We show that the ca. 1886–1881 Ma ore-forming magmas, originated from a mantle-dominated source with minor crustal contributions, were relatively oxidized (1‒2 log units above the fayalite-magnetite-quartz redox buffer) and sulfur-rich. These results indicate that moderately oxidized, sulfur-rich arc magma associated with porphyry Cu mineralization already existed in the late Paleoproterozoic, probably as a result of recycling of sulfate-rich seawater or sediments from the subducted oceanic lithosphere at that time.
Single cell transcriptional and chromatin accessibility profiling redefine cellular heterogeneity in the adult human kidney
Authors: Muto Yoshiharu , Wilson Parker C. , Ledru Nicolas , Wu Haojia , Dimke Henrik , Waikar Sushrut S. , Humphreys Benjamin D. 
Published: April 2021

AbstractThe integration of single cell transcriptome and chromatin accessibility datasets enables a deeper understanding of cell heterogeneity. We performed single nucleus ATAC (snATAC-seq) and RNA (snRNA-seq) sequencing to generate paired, cell-type-specific chromatin accessibility and transcriptional profiles of the adult human kidney. We demonstrate that snATAC-seq is comparable to snRNA-seq in the assignment of cell identity and can further refine our understanding of functional heterogeneity in the nephron. The majority of differentially accessible chromatin regions are localized to promoters and a significant proportion are closely associated with differentially expressed genes. Cell-type-specific enrichment of transcription factor binding motifs implicates the activation of NF-κB that promotes VCAM1 expression and drives transition between a subpopulation of proximal tubule epithelial cells. Our multi-omics approach improves the ability to detect unique cell states within the kidney and redefines cellular heterogeneity in the proximal tubule and thick ascending limb.
Resolving atomic SAPO-34/18 intergrowth architectures for methanol conversion by identifying light atoms and bonds
Authors: Shen Boyuan , Chen Xiao , Fan Xiaoyu , Xiong Hao , Wang Huiqiu , Qian Weizhong , Wang Yao , Wei Fei 
Published: April 2021

AbstractThe micro-structures of catalyst materials basically affect their macro-architectures and catalytic performances. Atomically resolving the micro-structures of zeolite catalysts, which have been widely used in the methanol conversion, will bring us a deeper insight into their structure-property correlations. However, it is still challenging for the atomic imaging of silicoaluminophosphate zeolites by electron microscopy due to the limits of their electron beam sensitivity. Here, we achieve the real-space imaging of the atomic lattices in SAPO-34 and SAPO-18 zeolites, including the Al–O–P atoms and bonds, by the integrated differential phase contrast scanning transmission electron microscopy (iDPC-STEM). The spatial distribution of SAPO-34 and SAPO-18 domains in SAPO-34/18 intergrowths can be clearly resolved. By changing the Si contents and templates in feed, we obtain two SAPO-34/18 catalysts, hierarchical and sandwich catalysts, with highly-mixed and separated SAPO-34 and SAPO-18 lattices respectively. The reduced diffusion distances of inside products greatly improve the catalytic performances of two catalysts in methanol conversion. Based on the observed distributions of lattices and elements in these catalysts, we can have a preliminary understanding on the correlation between the synthesis conditions and structures of SAPO-34/18 intergrowth catalysts to further modify their performances based on unique architectures.
Organic matter mineralization in modern and ancient ferruginous sediments
Authors: Friese André , Bauer Kohen , Glombitza Clemens , Ordoñez Luis , Ariztegui Daniel , Heuer Verena B. , Vuillemin Aurèle , Henny Cynthia , Nomosatryo Sulung , Simister Rachel , Wagner Dirk , Bijaksana Satria , Vogel Hendrik , Melles Martin , Russell James M. , Crowe Sean A. , Kallmeyer Jens 
Published: April 2021

AbstractDeposition of ferruginous sediment was widespread during the Archaean and Proterozoic Eons, playing an important role in global biogeochemical cycling. Knowledge of organic matter mineralization in such sediment, however, remains mostly conceptual, as modern ferruginous analogs are largely unstudied. Here we show that in sediment of ferruginous Lake Towuti, Indonesia, methanogenesis dominates organic matter mineralization despite highly abundant reactive ferric iron phases like goethite that persist throughout the sediment. Ferric iron can thus be buried over geologic timescales even in the presence of labile organic carbon. Coexistence of ferric iron with millimolar concentrations of methane further demonstrates lack of iron-dependent methane oxidation. With negligible methane oxidation, methane diffuses from the sediment into overlying waters where it can be oxidized with oxygen or escape to the atmosphere. In low-oxygen ferruginous Archaean and Proterozoic oceans, therefore, sedimentary methane production was likely favored with strong potential to influence Earth’s early climate.
Broadband generation of perfect Poincaré beams via dielectric spin-multiplexed metasurface
Authors: Liu Mingze , Huo Pengcheng , Zhu Wenqi , Zhang Cheng , Zhang Si , Song Maowen , Zhang Song , Zhou Qianwei , Chen Lu , Lezec Henri J. , Agrawal Amit , Lu Yanqing , Xu Ting 
Published: April 2021

AbstractThe term Poincaré beam, which describes the space-variant polarization of a light beam carrying spin angular momentum (SAM) and orbital angular momentum (OAM), plays an important role in various optical applications. Since the radius of a Poincaré beam conventionally depends on the topological charge number, it is difficult to generate a stable and high-quality Poincaré beam by two optical vortices with different topological charge numbers, as the Poincaré beam formed in this way collapses upon propagation. Here, based on an all-dielectric metasurface platform, we experimentally demonstrate broadband generation of a generalized perfect Poincaré beam (PPB), whose radius is independent of the topological charge number. By utilizing a phase-only modulation approach, a single-layer spin-multiplexed metasurface is shown to achieve all the states of PPBs on the hybrid-order Poincaré Sphere for visible light. Furthermore, as a proof-of-concept demonstration, a metasurface encoding multidimensional SAM and OAM states in the parallel channels of elliptical and circular PPBs is implemented for optical information encryption. We envision that this work will provide a compact and efficient platform for generation of PPBs for visible light, and may promote their applications in optical communications, information encryption, optical data storage and quantum information sciences.
Tissue-specific cell-free DNA degradation quantifies circulating tumor DNA burden
Authors: Zhu Guanhua , Guo Yu A. , Ho Danliang , Poon Polly , Poh Zhong Wee , Wong Pui Mun , Gan Anna , Chang Mei Mei , Kleftogiannis Dimitrios , Lau Yi Ting , Tay Brenda , Lim Wan Jun , Chua Clarinda , Tan Tira J. , Koo Si-Lin , Chong Dawn Q. , Yap Yoon Sim , Tan Iain , Ng Sarah , Skanderup Anders J. 
Published: April 2021

AbstractProfiling of circulating tumor DNA (ctDNA) may offer a non-invasive approach to monitor disease progression. Here, we develop a quantitative method, exploiting local tissue-specific cell-free DNA (cfDNA) degradation patterns, that accurately estimates ctDNA burden independent of genomic aberrations. Nucleosome-dependent cfDNA degradation at promoters and first exon-intron junctions is strongly associated with differential transcriptional activity in tumors and blood. A quantitative model, based on just 6 regulatory regions, could accurately predict ctDNA levels in colorectal cancer patients. Strikingly, a model restricted to blood-specific regulatory regions could predict ctDNA levels across both colorectal and breast cancer patients. Using compact targeted sequencing (<25 kb) of predictive regions, we demonstrate how the approach could enable quantitative low-cost tracking of ctDNA dynamics and disease progression.
Moss enables high sensitivity single-nucleotide variant calling from multiple bulk DNA tumor samples
Authors: Zhang Chuanyi , El-Kebir Mohammed , Ochoa Idoia 
Published: April 2021

AbstractIntra-tumor heterogeneity renders the identification of somatic single-nucleotide variants (SNVs) a challenging problem. In particular, low-frequency SNVs are hard to distinguish from sequencing artifacts. While the increasing availability of multi-sample tumor DNA sequencing data holds the potential for more accurate variant calling, there is a lack of high-sensitivity multi-sample SNV callers that utilize these data. Here we report Moss, a method to identify low-frequency SNVs that recur in multiple sequencing samples from the same tumor. Moss provides any existing single-sample SNV caller the ability to support multiple samples with little additional time overhead. We demonstrate that Moss improves recall while maintaining high precision in a simulated dataset. On multi-sample hepatocellular carcinoma, acute myeloid leukemia and colorectal cancer datasets, Moss identifies new low-frequency variants that meet manual review criteria and are consistent with the tumor’s mutational signature profile. In addition, Moss detects the presence of variants in more samples of the same tumor than reported by the single-sample caller. Moss’ improved sensitivity in SNV calling will enable more detailed downstream analyses in cancer genomics.
Exciton-acoustic phonon coupling revealed by resonant excitation of single perovskite nanocrystals
Authors: Lv Yan , Yin Chunyang , Zhang Chunfeng , Wang Xiaoyong , Yu Zhi-Gang , Xiao Min 
Published: April 2021

AbstractSingle perovskite nanocrystals have attracted great research attention very recently due to their potential quantum-information applications, which critically depend on the development of powerful optical techniques to resolve delicate exciton photophysics. Here we have realized resonant and near-resonant excitations of single perovskite CsPbI3 nanocrystals, with the scattered laser light contributing to only ~10% of the total collected signals. This allows us to estimate an ultranarrow photoluminescence excitation linewidth of ~11.32 µeV for the emission state of a single CsPbI3 nanocrystal, corresponding to an exciton dephasing time of ~116.29 ps. Meanwhile, size-quantized acoustic phonons can be resolved from a single CsPbI3 nanocrystal, whose coupling with the exciton is proposed to arise from the piezoelectric potential. The ability to collect resonance fluorescence from single CsPbI3 nanocrystals, with the subsequent revelation of exciton-acoustic phonon coupling, has marked a critical step towards their steady advancement into superior quantum-light sources.
Computationally-guided exchange of substrate selectivity motifs in a modular polyketide synthase acyltransferase
Authors: Kalkreuter Edward , Bingham Kyle S. , Keeler Aaron M. , Lowell Andrew N. , Schmidt Jennifer J. , Sherman David H. , Williams Gavin J. 
Published: April 2021

AbstractPolyketides, one of the largest classes of natural products, are often clinically relevant. The ability to engineer polyketide biosynthesis to produce analogs is critically important. Acyltransferases (ATs) of modular polyketide synthases (PKSs) catalyze the installation of malonyl-CoA extenders into polyketide scaffolds. ATs have been targeted extensively to site-selectively introduce various extenders into polyketides. Yet, a complete inventory of AT residues responsible for substrate selection has not been established, limiting the scope of AT engineering. Here, molecular dynamics simulations are used to prioritize ~50 mutations within the active site of EryAT6 from erythromycin biosynthesis, leading to identification of two previously unexplored structural motifs. Exchanging both motifs with those from ATs with alternative extender specificities provides chimeric PKS modules with expanded and inverted substrate specificity. Our enhanced understanding of AT substrate selectivity and application of this motif-swapping strategy are expected to advance our ability to engineer PKSs towards designer polyketides.
Cell-type-specific profiling of loaded miRNAs from Caenorhabditis elegans reveals spatial and temporal flexibility in Argonaute loading
Authors: Brosnan Christopher A. , Palmer Alexander J. , Zuryn Steven 
Published: April 2021

AbstractMulticellularity has coincided with the evolution of microRNAs (miRNAs), small regulatory RNAs that are integrated into cellular differentiation and homeostatic gene-regulatory networks. However, the regulatory mechanisms underpinning miRNA activity have remained largely obscured because of the precise, and thus difficult to access, cellular contexts under which they operate. To resolve these, we have generated a genome-wide map of active miRNAs in Caenorhabditis elegans by revealing cell-type-specific patterns of miRNAs loaded into Argonaute (AGO) silencing complexes. Epitope-labelled AGO proteins were selectively expressed and immunoprecipitated from three distinct tissue types and associated miRNAs sequenced. In addition to providing information on biological function, we define adaptable miRNA:AGO interactions with single-cell-type and AGO-specific resolution. We demonstrate spatial and temporal dynamicism, flexibility of miRNA loading, and suggest miRNA regulatory mechanisms via AGO selectivity in different tissues and during ageing. Additionally, we resolve widespread changes in AGO-regulated gene expression by analysing translatomes specifically in neurons.
EFA6B regulates a stop signal for collective invasion in breast cancer
Authors: Fayad Racha , Rojas Monserrat Vázquez , Partisani Mariagrazia , Finetti Pascal , Dib Shiraz , Abelanet Sophie , Virolle Virginie , Farina Anne , Cabaud Olivier , Lopez Marc , Birnbaum Daniel , Bertucci François , Franco Michel , Luton Frédéric 
Published: April 2021

AbstractCancer is initiated by somatic mutations in oncogenes or tumor suppressor genes. However, additional alterations provide selective advantages to the tumor cells to resist treatment and develop metastases. Their identification is of paramount importance. Reduced expression of EFA6B (Exchange Factor for ARF6, B) is associated with breast cancer of poor prognosis. Here, we report that loss of EFA6B triggers a transcriptional reprogramming of the cell-to-ECM interaction machinery and unleashes CDC42-dependent collective invasion in collagen. In xenograft experiments, MCF10 DCIS.com cells, a DCIS-to-IDC transition model, invades faster when knocked-out for EFA6B. In addition, invasive and metastatic tumors isolated from patients have lower expression of EFA6B and display gene ontology signatures identical to those of EFA6B knock-out cells. Thus, we reveal an EFA6B-regulated molecular mechanism that controls the invasive potential of mammary cells; this finding opens up avenues for the treatment of invasive breast cancer.
High-performance large-area quasi-2D perovskite light-emitting diodes
Authors: Sun Changjiu , Jiang Yuanzhi , Cui Minghuan , Qiao Lu , Wei Junli , Huang Yanmin , Zhang Li , He Tingwei , Li Saisai , Hsu Hsien-Yi , Qin Chaochao , Long Run , Yuan Mingjian 
Published: April 2021

AbstractSerious performance decline arose for perovskite light-emitting diodes (PeLEDs) once the active area was enlarged. Here we investigate the failure mechanism of the widespread active film fabrication method; and ascribe severe phase-segregation to be the reason. We thereby introduce L-Norvaline to construct a COO−-coordinated intermediate phase with low formation enthalpy. The new intermediate phase changes the crystallization pathway, thereby suppressing the phase-segregation. Accordingly, high-quality large-area quasi-2D films with desirable properties are obtained. Based on this, we further rationally adjusted films’ recombination kinetics. We reported a series of highly-efficient green quasi-2D PeLEDs with active areas of 9.0 cm2. The peak EQE of 16.4% is achieved in <n > = 3, represent the most efficient large-area PeLEDs yet. Meanwhile, high brightness device with luminance up to 9.1 × 104 cd m−2 has achieved in <n> = 10 film.
Associations between frontal lobe structure, parent-reported obstructive sleep disordered breathing and childhood behavior in the ABCD dataset
Authors: Isaiah Amal , Ernst Thomas , Cloak Christine C. , Clark Duncan B. , Chang Linda 
Published: April 2021

AbstractParents frequently report behavioral problems among children who snore. Our understanding of the relationship between symptoms of obstructive sleep disordered breathing (oSDB) and childhood behavioral problems associated with brain structural alterations is limited. Here, we examine the associations between oSDB symptoms, behavioral measures such as inattention, and brain morphometry in the Adolescent Brain Cognitive Development (ABCD) study comprising 10,140 preadolescents. We observe that parent-reported symptoms of oSDB are associated with composite and domain-specific problem behaviors measured by parent responses to the Child Behavior Checklist. Alterations of brain structure demonstrating the strongest negative associations with oSDB symptoms are within the frontal lobe. The relationships between oSDB symptoms and behavioral measures are mediated by significantly smaller volumes of multiple frontal lobe regions. These results provide population-level evidence for an association between regional structural alterations in cortical gray matter and problem behaviors reported in children with oSDB.
Male fertility thermal limits predict vulnerability to climate warming
Authors: van Heerwaarden Belinda , Sgrò Carla M. 
Published: April 2021

AbstractForecasting which species/ecosystems are most vulnerable to climate warming is essential to guide conservation strategies to minimize extinction. Tropical/mid-latitude species are predicted to be most at risk as they live close to their upper critical thermal limits (CTLs). However, these assessments assume that upper CTL estimates, such as CTmax, are accurate predictors of vulnerability and ignore the potential for evolution to ameliorate temperature increases. Here, we use experimental evolution to assess extinction risk and adaptation in tropical and widespreadDrosophilaspecies. We find tropical species succumb to extinction before widespread species. Male fertility thermal limits, which are much lower than CTmax, are better predictors of species’ current distributions and extinction in the laboratory. We find little evidence of adaptive responses to warming in any species. These results suggest that species are living closer to their upper thermal limits than currently presumed and evolution/plasticity are unlikely to rescue populations from extinction.
Steller’s sea cow genome suggests this species began going extinct before the arrival of Paleolithic humans
Authors: Sharko Fedor S. , Boulygina Eugenia S. , Tsygankova Svetlana V. , Slobodova Natalia V. , Alekseev Dmitry A. , Krasivskaya Anna A. , Rastorguev Sergey M. , Tikhonov Alexei N. , Nedoluzhko Artem V. 
Published: April 2021

AbstractAnthropogenic activity is the top factor directly related to the extinction of several animal species. The last Steller’s sea cow (Hydrodamalis gigas) population on the Commander Islands (Russia) was wiped out in the second half of the 18thcentury due to sailors and fur traders hunting it for the meat and fat. However, new data suggests that the extinction process of this species began much earlier. Here, we present a nuclear de novo assembled genome ofH. gigaswith a 25.4× depth coverage. Our results demonstrate that the heterozygosity of the last population of this animal is low and comparable to the last woolly mammoth population that inhabited Wrangel Island 4000 years ago. Besides, as a matter of consideration, our findings also demonstrate that the extinction of this marine mammal starts along the North Pacific coastal line much earlier than the first Paleolithic humans arrived in the Bering sea region.
Sex-based differences in the activation of peripheral blood monocytes in early Parkinson disease
Authors: Carlisle Samantha M. , Qin Hongwei , Hendrickson R. Curtis , Muwanguzi Jordana E. , Lefkowitz Elliot J. , Kennedy Richard E. , Yan Zhaoqi , Yacoubian Talene A. , Benveniste Etty N. , West Andrew B. , Harms Ashley S. , Standaert David G. 
Published: April 2021

AbstractIncreasing evidence supports the role of brain and systemic inflammation in the etiology of Parkinson disease (PD). We used gene expression profiling to examine the activation state of peripheral blood monocytes in 18 patients with early, untreated PD and 16 healthy control (HC) subjects. Monocytes were isolated by negative selection, and gene expression studied by RNA-seq and gene set enrichment analysis. A computational model that incorporated case/control status, sex, and the interaction between case/control status and sex was utilized. We found that there was a striking effect of sex on monocyte gene expression. There was inflammatory activation of monocytes in females with PD, with enrichment of gene sets associated with interferon gamma stimulation. In males, the activation patterns were more heterogeneous. These data point to the importance of systemic monocyte activation in PD, and the importance of studies which examine the differential effects of sex on pathophysiology of the disease.