bluuebunny/crossref_metadata_2025_split huggingface dataset:
Orbital forcing of ice sheets during snowball Earth
Authors: Mitchell Ross N. , Gernon Thomas M. , Cox Grant M. , Nordsvan Adam R. , Kirscher Uwe , Xuan Chuang , Liu Yebo , Liu Xu , He Xiaofang 
Published: July 2021

AbstractThe snowball Earth hypothesis—that a runaway ice-albedo feedback can cause global glaciation—seeks to explain low-latitude glacial deposits, as well as geological anomalies including the re-emergence of banded iron formation and “cap” carbonates. One of the most significant challenges to snowball Earth has been sedimentological cyclicity that has been taken to imply more climate dynamics than expected when the ocean is completely covered in ice. However, recent climate models suggest that as atmospheric CO2 accumulates, the snowball climate system becomes sensitive to orbital forcing. Here we show the presence of nearly all Milankovitch (orbital) cycles preserved in stratified banded iron formation deposited during the Sturtian snowball Earth. These results provide evidence for orbitally forced cyclicity of global ice sheets that resulted in periodic oxidation of ferrous iron. Orbital glacial advance and retreat cycles provide a simple mechanism to reconcile both the sedimentary dynamics and the enigmatic survival of multicellular life during snowball Earth.
Generation of even and odd high harmonics in resonant metasurfaces using single and multiple ultra-intense laser pulses
Authors: Shcherbakov Maxim R. , Zhang Haizhong , Tripepi Michael , Sartorello Giovanni , Talisa Noah , AlShafey Abdallah , Fan Zhiyuan , Twardowski Justin , Krivitsky Leonid A. , Kuznetsov Arseniy I. , Chowdhury Enam , Shvets Gennady 
Published: July 2021

AbstractHigh harmonic generation (HHG) opens a window on the fundamental science of strong-field light-mater interaction and serves as a key building block for attosecond optics and metrology. Resonantly enhanced HHG from hot spots in nanostructures is an attractive route to overcoming the well-known limitations of gases and bulk solids. Here, we demonstrate a nanoscale platform for highly efficient HHG driven by intense mid-infrared laser pulses: an ultra-thin resonant gallium phosphide (GaP) metasurface. The wide bandgap and the lack of inversion symmetry of the GaP crystal enable the generation of even and odd harmonics covering a wide range of photon energies between 1.3 and 3 eV with minimal reabsorption. The resonantly enhanced conversion efficiency facilitates single-shot measurements that avoid material damage and pave the way to study the controllable transition between perturbative and non-perturbative regimes of light-matter interactions at the nanoscale.
Asymmetric reconstruction of mammalian reovirus reveals interactions among RNA, transcriptional factor µ2 and capsid proteins
Authors: Pan Muchen , Alvarez-Cabrera Ana L. , Kang Joon S. , Wang Lihua , Fan Chunhai , Zhou Z. Hong 
Published: July 2021

AbstractMammalian reovirus (MRV) is the prototypical member of genus Orthoreovirus of family Reoviridae. However, lacking high-resolution structures of its RNA polymerase cofactor μ2 and infectious particle, limits understanding of molecular interactions among proteins and RNA, and their contributions to virion assembly and RNA transcription. Here, we report the 3.3 Å-resolution asymmetric reconstruction of transcribing MRV and in situ atomic models of its capsid proteins, the asymmetrically attached RNA-dependent RNA polymerase (RdRp) λ3, and RdRp-bound nucleoside triphosphatase μ2 with a unique RNA-binding domain. We reveal molecular interactions among virion proteins and genomic and messenger RNA. Polymerase complexes in three Spinoreovirinae subfamily members are organized with different pseudo-D3d symmetries to engage their highly diversified genomes. The above interactions and those between symmetry-mismatched receptor-binding σ1 trimers and RNA-capping λ2 pentamers balance competing needs of capsid assembly, external protein removal, and allosteric triggering of endogenous RNA transcription, before, during and after infection, respectively.
Engineering atomic-scale magnetic fields by dysprosium single atom magnets
Authors: Singha A. , Willke P. , Bilgeri T. , Zhang X. , Brune H. , Donati F. , Heinrich A. J. , Choi T. 
Published: July 2021

AbstractAtomic scale engineering of magnetic fields is a key ingredient for miniaturizing quantum devices and precision control of quantum systems. This requires a unique combination of magnetic stability and spin-manipulation capabilities. Surface-supported single atom magnets offer such possibilities, where long temporal and thermal stability of the magnetic states can be achieved by maximizing the magnet/ic anisotropy energy (MAE) and by minimizing quantum tunnelling of the magnetization. Here, we show that dysprosium (Dy) atoms on magnesium oxide (MgO) have a giant MAE of 250 meV, currently the highest among all surface spins. Using a variety of scanning tunnelling microscopy (STM) techniques including single atom electron spin resonance (ESR), we confirm no spontaneous spin-switching in Dy over days at ≈ 1 K under low and even vanishing magnetic field. We utilize these robust Dy single atom magnets to engineer magnetic nanostructures, demonstrating unique control of magnetic fields with atomic scale tunability.
Flat band carrier confinement in magic-angle twisted bilayer graphene
Authors: Tilak Nikhil , Lai Xinyuan , Wu Shuang , Zhang Zhenyuan , Xu Mingyu , Ribeiro Raquel de Almeida , Canfield Paul C. , Andrei Eva Y. 
Published: July 2021

AbstractMagic-angle twisted bilayer graphene has emerged as a powerful platform for studying strongly correlated electron physics, owing to its almost dispersionless low-energy bands and the ability to tune the band filling by electrostatic gating. Techniques to control the twist angle between graphene layers have led to rapid experimental progress but improving sample quality is essential for separating the delicate correlated electron physics from disorder effects. Owing to the 2D nature of the system and the relatively low carrier density, the samples are highly susceptible to small doping inhomogeneity which can drastically modify the local potential landscape. This potential disorder is distinct from the twist angle variation which has been studied elsewhere. Here, by using low temperature scanning tunneling spectroscopy and planar tunneling junction measurements, we demonstrate that flat bands in twisted bilayer graphene can amplify small doping inhomogeneity that surprisingly leads to carrier confinement, which in graphene could previously only be realized in the presence of a strong magnetic field.
GIGYF1 loss of function is associated with clonal mosaicism and adverse metabolic health
Authors: Zhao Yajie , Stankovic Stasa , Koprulu Mine , Wheeler Eleanor , Day Felix R. , Lango Allen Hana , Kerrison Nicola D. , Pietzner Maik , Loh Po-Ru , Wareham Nicholas J. , Langenberg Claudia , Ong Ken K. , Perry John R. B. 
Published: July 2021

AbstractMosaic loss of chromosome Y (LOY) in leukocytes is the most common form of clonal mosaicism, caused by dysregulation in cell-cycle and DNA damage response pathways. Previous genetic studies have focussed on identifying common variants associated with LOY, which we now extend to rarer, protein-coding variation using exome sequences from 82,277 male UK Biobank participants. We find that loss of function of two genes—CHEK2 and GIGYF1—reach exome-wide significance. Rare alleles in GIGYF1 have not previously been implicated in any complex trait, but here loss-of-function carriers exhibit six-fold higher susceptibility to LOY (OR = 5.99 [3.04–11.81], p = 1.3 × 10−10). These same alleles are also associated with adverse metabolic health, including higher susceptibility to Type 2 Diabetes (OR = 6.10 [3.51–10.61], p = 1.8 × 10−12), 4 kg higher fat mass (p = 1.3 × 10−4), 2.32 nmol/L lower serum IGF1 levels (p = 1.5 × 10−4) and 4.5 kg lower handgrip strength (p = 4.7 × 10−7) consistent with proposed GIGYF1 enhancement of insulin and IGF-1 receptor signalling. These associations are mirrored by a common variant nearby associated with the expression of GIGYF1. Our observations highlight a potential direct connection between clonal mosaicism and metabolic health.
NUDT15 polymorphism influences the metabolism and therapeutic effects of acyclovir and ganciclovir
Authors: Nishii Rina , Mizuno Takanori , Rehling Daniel , Smith Colton , Clark Brandi L. , Zhao Xujie , Brown Scott A. , Smart Brandon , Moriyama Takaya , Yamada Yuji , Ichinohe Tatsuo , Onizuka Makoto , Atsuta Yoshiko , Yang Lei , Yang Wenjian , Thomas Paul G. , Stenmark Pål , Kato Motohiro , Yang Jun J. 
Published: July 2021

AbstractNucleobase and nucleoside analogs (NNA) are widely used as anti-viral and anti-cancer agents, and NNA phosphorylation is essential for the activity of this class of drugs. Recently, diphosphatase NUDT15 was linked to thiopurine metabolism with NUDT15 polymorphism associated with drug toxicity in patients. Profiling NNA drugs, we identify acyclovir (ACV) and ganciclovir (GCV) as two new NNAs metabolized by NUDT15. NUDT15 hydrolyzes ACV and GCV triphosphate metabolites, reducing their effects against cytomegalovirus (CMV) in vitro. Loss of NUDT15 potentiates cytotoxicity of ACV and GCV in host cells. In hematopoietic stem cell transplant patients, the risk of CMV viremia following ACV prophylaxis is associated with NUDT15 genotype (P = 0.015). Donor NUDT15 deficiency is linked to graft failure in patients receiving CMV-seropositive stem cells (P = 0.047). In conclusion, NUDT15 is an important metabolizing enzyme for ACV and GCV, and NUDT15 variation contributes to inter-patient variability in their therapeutic effects.
TOMM40 ‘523’ poly-T repeat length is a determinant of longitudinal cognitive decline in Parkinson’s disease
Authors: Bakeberg Megan C. , Gorecki Anastazja M. , Pfaff Abigail L. , Hoes Madison E. , Kõks Sulev , Akkari P. Anthony , Mastaglia Frank L. , Anderton Ryan S. 
Published: July 2021

AbstractThe translocase of outer mitochondrial membrane 40 (TOMM40) ‘523’ polymorphism has previously been associated with age of Alzheimer’s disease onset and cognitive functioning in non-pathological ageing, but has not been explored as a candidate risk marker for cognitive decline in Parkinson’s disease (PD). Therefore, this longitudinal study investigated the role of the ‘523’ variant in cognitive decline in a patient cohort from the Parkinson’s Progression Markers Initiative. As such, a group of 368 people with PD were assessed annually for cognitive performance using multiple neuropsychological protocols, and were genotyped for the TOMM40 ‘523’ variant using whole-genome sequencing data. Covariate-adjusted generalised linear mixed models were utilised to examine the relationship between TOMM40 ‘523’ allele lengths and cognitive scores, while taking into account the APOE ε genotype. Cognitive scores declined over the 5-year study period and were lower in males than in females. When accounting for APOE ε4, the TOMM40 ‘523’ variant was not robustly associated with overall cognitive performance. However, in APOE ε3/ε3 carriers, who accounted for ~60% of the whole cohort, carriage of shorter ‘523’ alleles was associated with more severe cognitive decline in both sexes, while carriage of the longer alleles in females were associated with better preservation of global cognition and a number of cognitive sub-domains, and with a delay in progression to dementia. The findings indicate that when taken in conjunction with the APOE genotype, TOMM40 ‘523’ allele length is a significant independent determinant and marker for the trajectory of cognitive decline and risk of dementia in PD.
Historical contingency impacts on community assembly and ecosystem function in chemosynthetic marine ecosystems
Authors: Kalenitchenko Dimitri , Peru Erwan , Galand Pierre E. 
Published: July 2021

AbstractPredicting ecosystem functioning requires an understanding of the mechanisms that drive microbial community assembly. Many studies have explored microbial diversity extensively and environmental factors are thought to be the principal drivers of community composition. Community assembly is, however, also influenced by past conditions that might affect present-day assemblages. Historical events, called legacy effects or historical contingencies, remain poorly studied in the sea and their impact on the functioning of the communities is not known. We tested the influence, if any, of historical contingencies on contemporary community assembly and functions in a marine ecosystem. To do so, we verified if different inoculum communities colonizing the same substrate led to communities with different compositions. We inoculated wood with sea water microbes from different marine environments that differ in ecological and evolutionary history. Using 16S rRNA and metagenomic sequencing, it was demonstrated that historical contingencies change the composition and potential metabolisms of contemporary communities. The effect of historical events was transient, dominated by environmental selection as, over time, species sorting was a more important driver of community assembly. Our study shows not only that historical contingencies affect marine ecosystems but takes the analysis a step further by characterizing this effect as strong but transient.
Human sample﻿ authentication in biomedical research: comparison of two platforms
Authors: Manjunath Harshitha Shobha , James Nicola , Mathew Rebecca , Al Hashmi Muna , Silcock Lee , Biunno Ida , De Blasio Pasquale , Manickam Chidambaram , Tomei Sara 
Published: July 2021

AbstractSamples used in biomedical research are often collected over years, in some cases from subjects that may have died and thus cannot be retrieved in any way. The value of these samples is priceless. Sample misidentification or mix-up are unfortunately common problems in biomedical research and can eventually result in the publication of incorrect data. Here we have compared the Fluidigm SNPtrace and the Agena iPLEX Sample ID panels for the authentication of human genomic DNA samples. We have tested 14 pure samples and simulated their cross-contamination at different percentages (2%, 5%, 10%, 25% and 50%). For both panels, we report call rate, allele intensity/probability score, performance in distinguishing pure samples and contaminated samples at different percentages, and sex typing. We show that both panels are reliable and efficient methods for sample authentication and we highlight their advantages and disadvantages. We believe that the data provided here is useful for sample authentication especially in biorepositories and core facility settings.
Recent decadal enhancement of Meiyu–Baiu heavy rainfall over East Asia
Authors: Takahashi Hiroshi G. , Fujinami Hatsuki 
Published: July 2021

AbstractEast of Eurasia, moist air is transported poleward, forming the Meiyu–Baiu front over East Asia in late June and early July. Recently, unusually heavy rainfall may have increased, causing catastrophic flooding in East Asia. Here, unique 23-year precipitation satellite radar data confirm recent enhancement in Meiyu–Baiu heavy rainfall from eastern China to southwestern Japan, which is also evident from independent conventional observations. Decadal changes in rainfall have been physically consistent with enhanced transport of water vapour due to the intensified Pacific subtropical high associated with weakened tropical cyclone activity over the Northwest Pacific. Furthermore, the upper-tropospheric trough, associated with wave train along the subtropical jet, influenced Meiyu–Baiu precipitation over East Asia. Long-term and continuous satellite radar observations reveal that the frequency of heavy precipitation along the Meiyu–Baiu front has increased in the last 22 years. In particular, heavy precipitation (10 mm/h) increased by 24% between 1998–2008 and 2009–2019, and the abruptly-changed level likely induced recent meteorological disasters across East Asia. This trend may also explain the severity of the 2020 Meiyu–Baiu season. Over the last decade, this front has likely transitioned to a new climate state, which requires adaptation of disaster prevention approaches.
Influence of occlusal reduction on pain after endodontic treatment: a systematic review and meta-analysis
Authors: Chagas Carvalho Alves Nayane , Raiane Mamede Veloso Sirley , de Andrade Silva Silmara , de Almeida Andressa Cartaxo , Tavares Velozo Telles Christianne , Romeiro Kaline , de Melo Monteiro Gabriela Queiroz , de Albuquerque Diana Santana 
Published: July 2021

AbstractThe purpose of this systematic review was to analyze the influence of occlusal reduction on the postoperative pain levels after endodontic treatment (instrumentation and obturation of the root canal system). This review followed the PRISMA statement and was registered at PROSPERO (CRD42018107918). Two independent reviewers searched the Lilacs, Cochrane Library, PubMed (Medline), Web of Science, Scopus, Scielo, and ScienceDirect for articles published until April 2021. The research question was, "Does occlusal reduction decrease postoperative pain in endodontically treated teeth?". Only randomized clinical trials were included. The RevMan 5 program was used for meta-analysis, calculating the relative risk (RR) and 95% confidence interval (CI) of the dichotomous outcome (presence or absence of pain). The search strategies retrieved 4114 studies. Twelve studies were included for qualitative analysis and nine for quantitative analysis. The meta-analysis results did not reveal a significant difference in the reduction of postoperative pain levels for endodontic instrumentation at 6, 12, 24, 48 h and for endodontic obturation at 6 or 12 h after occlusal reduction. According to the GRADE tool, the analyzed outcome was classified as having a moderate level of certainty. It is concluded that occlusal reduction does not interfere with postoperative pain levels after endodontic treatment.
The first insight into the genetic structure of the population of modern Serbia
Authors: Drljaca Tamara , Zukic Branka , Kovacevic Vladimir , Gemovic Branislava , Klaassen-Ljubicic Kristel , Perovic Vladimir , Lazarevic Mladen , Pavlovic Sonja , Veljkovic Nevena 
Published: July 2021

AbstractThe complete understanding of the genomic contribution to complex traits, diseases, and response to treatments, as well as genomic medicine application to the well-being of all humans will be achieved through the global variome that encompasses fine-scale genetic diversity. Despite significant efforts in recent years, uneven representation still characterizes genomic resources and among the underrepresented European populations are the Western Balkans including the Serbian population. Our research addresses this gap and presents the first ever targeted sequencing dataset of variants in clinically relevant genes. By measuring population differentiation and applying the Principal Component and Admixture analysis we demonstrated that the Serbian population differs little from other European populations, yet we identified several novel and more frequent variants that appear as its unique genetic determinants. We explored thoroughly the functional impact of frequent variants and its correlation with the health burden of the population of Serbia based on a sample of 144 individuals. Our variants catalogue improves the understanding of genetics of modern Serbia, contributes to research on ancestry, and aids in improvements of well-being and health equity. In addition, this resource may also be applicable in neighboring regions and valuable in worldwide functional analyses of genetic variants in individuals of European descent.
Perception on aggregation induced multicolor emission and emission centers in carbon nanodots using successive dilution, anion exchange chromatography, and multi-way statistics
Authors: Kompany-Zareh Mohsen , Bagheri Saeed 
Published: July 2021

AbstractExploration in the way of understanding the optical behavior and structure of carbon nanodots has been increased due to their vast application. Their emission dependency on excitation wavelengths is the more prevalent and controversial subject. In this report we considered the optical structure of hydrothermally synthesized carbon nanodots using citric acid and 2,3-diaminopyridine as precursors. The presence of different emission centers experimented through anion exchange chromatography which resulted in fractions with more unique optical structures. The quantum confinement effect and energy exchange between different types of carbon nanodots, due to aggregation in higher concentration levels, was studied applying a stepwise dilution experiment. Analysis of the experimental data was done through the parallel factor analysis and the trajectory pattern recognition which resolved more about optical interactions and the presence of different emission centers in different particles. Results from infrared spectroscopy confirmed the dominating density of carboxyl functional groups on the nanodots with negative surface charges and higher influence of amine groups on dots with positive surface charges.
A structure–function based approach to floc hierarchy and evidence for the non-fractal nature of natural sediment flocs
Authors: Spencer Kate L. , Wheatland Jonathan A. T. , Bushby Andrew J. , Carr Simon J. , Droppo Ian G. , Manning Andrew J. 
Published: July 2021

AbstractNatural sediment flocs are fragile, highly irregular, loosely bound aggregates comprising minerogenic and organic material. They contribute a major component of suspended sediment load and are critical for the fate and flux of sediment, carbon and pollutants in aquatic environments. Understanding their behaviour is essential to the sustainable management of waterways, fisheries and marine industries. For several decades, modelling approaches have utilised fractal mathematics and observations of two dimensional (2D) floc size distributions to infer levels of aggregation and predict their behaviour. Whilst this is a computationally simple solution, it is highly unlikely to reflect the complexity of natural sediment flocs and current models predicting fine sediment hydrodynamics are not efficient. Here, we show how new observations of fragile floc structures in three dimensions (3D) demonstrate unequivocally that natural flocs are non-fractal. We propose that floc hierarchy is based on observations of 3D structure and function rather than 2D size distribution. In contrast to fractal theory, our data indicate that flocs possess characteristics of emergent systems including non-linearity and scale-dependent feedbacks. These concepts and new data to quantify floc structures offer the opportunity to explore new emergence-based floc frameworks which better represent natural floc behaviour and could advance our predictive capacity.