bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of Municipal Water Uses in the Contiguous United States
Authors: Chinnasamy Cibi Vishnu , Arabi Mazdak , Sharvelle Sybil , Warziniack Travis , Furth Canon D. , Dozier Andre 
Published: June 2021

AbstractThis study investigates municipal water use patterns across the Contiguous United States (CONUS). The objectives of this study are to explore temporal trends in water use, improve characterization of indoor and outdoor uses, and improve characterization of commercial, industrial, and institutional (CII) water use in cities across the CONUS. A comprehensive survey was conducted to compile monthly water use data from 126 municipalities for the period 2005–2017 with specific information about residential and CII water use categories. Changes in liters per capita per day and the CII to Residential water use ratio were related to climatic, urban‐geologic and socio‐economic variables. Results indicate an overall decreasing trend in municipal water uses with higher reductions achieved in residential sector. Both residential and CII water use exhibit high seasonality over an average year. The CII to Residential ratio increases with city population and is highest in cities in the Northeast Census region. Cities in South and West Census regions have high municipal water uses and highest reductions in annual per capita‐day water use. Cities in arid climate regions have the highest water uses, compared to other cities, due to landscape irrigation. April precipitation, annual vapor pressure deficit, number of employees in the manufacturing (or, other services except public administration) sector, total percentage of houses built before 1950 and total percentage of single‐family houses explain much of the variation in CII to Residential water use ratio across the CONUS. This study guides improved characterization of municipal water uses and water demand management strategies.
Shock‐Induced Incongruent Melting of Olivine in Kamargaon L6 Chondrite
Authors: Tiwari Kishan , Ghosh Sujoy , Miyahara Masaaki , Ray Dwijesh 
Published: June 2021

AbstractIn this study, we report for the first‐time shock‐induced incongruent melting of olivine in an ordinary chondrite. Several olivine grains (Fo74), entrained in the shock‐melt vein of the Kamargaon L6 chondrite, were dissociated into magnesiowüstite (XFe = 0.71) and orthoenstatite (XFe = 0.22). We propose that the breakdown of olivine took place as a result of incongruent melting to produce magnesiowüstite and Mg‐rich liquid. We suggest that bridgmanite may have crystallized as the second phase from the olivine melt which back‐transformed to a low‐pressure phase of orthoenstatite from subsequent high‐temperature and low‐pressure events. In this case, olivine grains may have experienced pressure and temperature of ∼25 GPa and ∼2500°C, respectively. Our results suggest that the incongruent melting of olivine may possibly operate as one of the alternative mechanisms of dissociation reaction driving the phase transformation of olivine in the natural systems.
Biomass Burning is an Important Source of Organic Aerosols in Interior Alaska
Authors: Haque Md. Mozammel , Kawamura Kimitaka , Deshmukh Dhananjay K. , Kunwar Bhagawati , Kim Yongwon 
Published: June 2021

AbstractBiomass burning (BB) affects air quality, the global cycling of carbon, climate, and human health. Intensive BB activities occur throughout the year due to wildfires and domestic wood burning in Fairbanks. We collected total suspended particle samples from the air in Fairbanks from June 2008 to June 2009. Here, we report seasonal variations in the molecular composition of organic aerosols and its BB contributions in Fairbanks. Levoglucosan is the dominant BB tracer (annual mean 67 ± 77 ng m−3), showing a winter maximum (145 ± 47 ng m−3) and spring minimum (12 ± 12 ng m−3). Levoglucosan showed significant correlations (p < 0.001) with organic carbon (OC), water‐soluble organic carbon (WSOC), and PM2.5, indicating a significant contribution of BB to hazes in Fairbanks. However, no correlation exists between levoglucosan and non‐sea salt potassium (nss‐K+), which has been proposed as a BB tracer. We hypothesize that nss‐K+ is removed by deposition on the inner surfaces of woodstove chimneys. Levoglucosan contributes 3.6% to OC and 6.3% to WSOC in winter, indicating that BB significantly affects carbonaceous aerosols in central Alaska. Moreover, positive matrix factorization analysis demonstrates that BB is an important source (47.5%) of Fairbanks year‐round aerosols. We conclude that domestic wood burning is an important source of atmospheric particles that impact the air quality of Fairbanks, especially in winter. We presumed that Fairbanks BB products might be transported to the remote Arctic, potentially affecting the chemical composition of Arctic aerosols. These findings will be useful to better understand the seasonal influence of BB on the Arctic and subarctic aerosols.
The clinical use of blood-test factors for Alzheimer’s disease: improving the prediction of cerebral amyloid deposition by the QPLEXTM Alz plus assay kit
Authors: Kim Haeng Jun , Park Jong-Chan , Jung Keum Sim , Kim Jiyeong , Jang Ji Sung , Kwon Sunghoon , Byun Min Soo , Yi Dahyun , Byeon Gihwan , Jung Gijung , Kim Yu Kyeong , Lee Dong Young , Han Sun-Ho , Mook-Jung Inhee 
Published: June 2021

AbstractAlzheimer’s disease (AD) is the leading cause of dementia, and many studies have focused on finding effective blood biomarkers for the accurate diagnosis of this disease. Predicting cerebral amyloid deposition is considered the key for AD diagnosis because a cerebral amyloid deposition is the hallmark of AD pathogenesis. Previously, blood biomarkers were discovered to predict cerebral amyloid deposition, and further efforts have been made to increase their sensitivity and specificity. In this study, we analyzed blood-test factors (BTFs) that can be commonly measured in medical health check-ups from 149 participants with cognitively normal, 87 patients with mild cognitive impairment, and 64 patients with clinically diagnosed AD dementia with brain amyloid imaging data available. We demonstrated that four factors among regular health check-up blood tests, cortisol, triglyceride/high-density lipoprotein cholesterol ratio, alanine aminotransferase, and free triiodothyronine, showed either a significant difference by or correlation with cerebral amyloid deposition. Furthermore, we made a prediction model for Pittsburgh compound B-positron emission tomography positivity, using BTFs and the previously discovered blood biomarkers, the QPLEXTMAlz plus assay kit biomarker panel, and the area under the curve was significantly increased up to 0.845% with 69.4% sensitivity and 90.6% specificity. These results show that BTFs could be used as co-biomarkers and that a highly advanced prediction model for amyloid plaque deposition could be achieved by the combinational use of diverse biomarkers.
Divergence of a genomic island leads to the evolution of melanization in a halophyte root fungus
Authors: Yuan Zhilin , Druzhinina Irina S , Gibbons John G , Zhong Zhenhui , Van de Peer Yves , Rodriguez Russell J , Liu Zhongjian , Wang Xinyu , Wei Huanshen , Wu Qi , Wang Jieyu , Shi Guohui , Cai Feng , Peng Long , Martin Francis M 
Published: June 2021

Abstract
Understanding how organisms adapt to extreme living conditions is central to evolutionary biology. Dark septate endophytes (DSEs) constitute an important component of the root mycobiome and they are often able to alleviate host abiotic stresses. Here, we investigated the molecular mechanisms underlying the beneficial association between the DSE Laburnicola rhizohalophila and its host, the native halophyte Suaeda salsa, using population genomics. Based on genome-wide Fst (pairwise fixation index) and Vst analyses, which compared the variance in allele frequencies of single-nucleotide polymorphisms (SNPs) and copy number variants (CNVs), respectively, we found a high level of genetic differentiation between two populations. CNV patterns revealed population-specific expansions and contractions. Interestingly, we identified a ~20 kbp genomic island of high divergence with a strong sign of positive selection. This region contains a melanin-biosynthetic polyketide synthase gene cluster linked to six additional genes likely involved in biosynthesis, membrane trafficking, regulation, and localization of melanin. Differences in growth yield and melanin biosynthesis between the two populations grown under 2% NaCl stress suggested that this genomic island contributes to the observed differences in melanin accumulation. Our findings provide a better understanding of the genetic and evolutionary mechanisms underlying the adaptation to saline conditions of the L. rhizohalophila–S. salsa symbiosis.
R2DT is a framework for predicting and visualising RNA secondary structure using templates
Authors: Sweeney Blake A. , Hoksza David , Nawrocki Eric P. , Ribas Carlos Eduardo , Madeira Fábio , Cannone Jamie J. , Gutell Robin , Maddala Aparna , Meade Caeden D. , Williams Loren Dean , Petrov Anton S. , Chan Patricia P. , Lowe Todd M. , Finn Robert D. , Petrov Anton I. 
Published: June 2021

AbstractNon-coding RNAs (ncRNA) are essential for all life, and their functions often depend on their secondary (2D) and tertiary structure. Despite the abundance of software for the visualisation of ncRNAs, few automatically generate consistent and recognisable 2D layouts, which makes it challenging for users to construct, compare and analyse structures. Here, we present R2DT, a method for predicting and visualising a wide range of RNA structures in standardised layouts. R2DT is based on a library of 3,647 templates representing the majority of known structured RNAs. R2DT has been applied to ncRNA sequences from the RNAcentral database and produced >13 million diagrams, creating the world’s largest RNA 2D structure dataset. The software is amenable to community expansion, and is freely available at https://github.com/rnacentral/R2DT and a web server is found at https://rnacentral.org/r2dt.
Structural insight on assembly-line catalysis in terpene biosynthesis
Authors: Faylo Jacque L. , van Eeuwen Trevor , Kim Hee Jong , Gorbea Colón Jose J. , Garcia Benjamin A. , Murakami Kenji , Christianson David W. 
Published: June 2021

AbstractFusicoccadiene synthase from Phomopsis amygdali (PaFS) is a unique bifunctional terpenoid synthase that catalyzes the first two steps in the biosynthesis of the diterpene glycoside Fusicoccin A, a mediator of 14-3-3 protein interactions. The prenyltransferase domain of PaFS generates geranylgeranyl diphosphate, which the cyclase domain then utilizes to generate fusicoccadiene, the tricyclic hydrocarbon skeleton of Fusicoccin A. Here, we use cryo-electron microscopy to show that the structure of full-length PaFS consists of a central octameric core of prenyltransferase domains, with the eight cyclase domains radiating outward via flexible linker segments in variable splayed-out positions. Cryo-electron microscopy and chemical crosslinking experiments additionally show that compact conformations can be achieved in which cyclase domains are more closely associated with the prenyltransferase core. This structural analysis provides a framework for understanding substrate channeling, since most of the geranylgeranyl diphosphate generated by the prenyltransferase domains remains on the enzyme for cyclization to form fusicoccadiene.
Formation of three-dimensional bicontinuous structures via molten salt dealloying studied in real-time by in situ synchrotron X-ray nano-tomography
Authors: Liu Xiaoyang , Ronne Arthur , Yu Lin-Chieh , Liu Yang , Ge Mingyuan , Lin Cheng-Hung , Layne Bobby , Halstenberg Phillip , Maltsev Dmitry S. , Ivanov Alexander S. , Antonelli Stephen , Dai Sheng , Lee Wah-Keat , Mahurin Shannon M. , Frenkel Anatoly I. , Wishart James F. , Xiao Xianghui , Chen-Wiegart Yu-chen Karen 
Published: June 2021

AbstractThree-dimensional bicontinuous porous materials formed by dealloying contribute significantly to various applications including catalysis, sensor development and energy storage. This work studies a method of molten salt dealloying via real-time in situ synchrotron three-dimensional X-ray nano-tomography. Quantification of morphological parameters determined that long-range diffusion is the rate-determining step for the dealloying process. The subsequent coarsening rate was primarily surface diffusion controlled, with Rayleigh instability leading to ligament pinch-off and creating isolated bubbles in ligaments, while bulk diffusion leads to a slight densification. Chemical environments characterized by X-ray absorption near edge structure spectroscopic imaging show that molten salt dealloying prevents surface oxidation of the metal. In this work, gaining a fundamental mechanistic understanding of the molten salt dealloying process in forming porous structures provides a nontoxic, tunable dealloying technique and has important implications for molten salt corrosion processes, which is one of the major challenges in molten salt reactors and concentrated solar power plants.
Manganese doping for enhanced magnetic brightening and circular polarization control of dark excitons in paramagnetic layered hybrid metal-halide perovskites
Authors: Neumann Timo , Feldmann Sascha , Moser Philipp , Delhomme Alex , Zerhoch Jonathan , van de Goor Tim , Wang Shuli , Dyksik Mateusz , Winkler Thomas , Finley Jonathan J. , Plochocka Paulina , Brandt Martin S. , Faugeras Clément , Stier Andreas V. , Deschler Felix 
Published: June 2021

AbstractMaterials combining semiconductor functionalities with spin control are desired for the advancement of quantum technologies. Here, we study the magneto-optical properties of novel paramagnetic Ruddlesden-Popper hybrid perovskites Mn:(PEA)2PbI4(PEA = phenethylammonium) and report magnetically brightened excitonic luminescence with strong circular polarization from the interaction with isolated Mn2+ions. Using a combination of superconducting quantum interference device (SQUID) magnetometry, magneto-absorption and transient optical spectroscopy, we find that a dark exciton population is brightened by state mixing with the bright excitons in the presence of a magnetic field. Unexpectedly, the circular polarization of the dark exciton luminescence follows the Brillouin-shaped magnetization with a saturation polarization of 13% at 4 K and 6 T. From high-field transient magneto-luminescence we attribute our observations to spin-dependent exciton dynamics at early times after excitation, with first indications for a Mn-mediated spin-flip process. Our findings demonstrate manganese doping as a powerful approach to control excitonic spin physics in Ruddlesden-Popper perovskites, which will stimulate research on this highly tuneable material platform with promise for tailored interactions between magnetic moments and excitonic states.
Multication perovskite 2D/3D interfaces form via progressive dimensional reduction
Authors: Proppe Andrew H. , Johnston Andrew , Teale Sam , Mahata Arup , Quintero-Bermudez Rafael , Jung Eui Hyuk , Grater Luke , Cui Teng , Filleter Tobin , Kim Chang-Yong , Kelley Shana O. , De Angelis Filippo , Sargent Edward H. 
Published: June 2021

AbstractMany of the best-performing perovskite photovoltaic devices make use of 2D/3D interfaces, which improve efficiency and stability – but it remains unclear how the conversion of 3D-to-2D perovskite occurs and how these interfaces are assembled. Here, we use in situ Grazing-Incidence Wide-Angle X-Ray Scattering to resolve 2D/3D interface formation during spin-coating. We observe progressive dimensional reduction from 3D to n = 3 → 2 → 1 when we expose (MAPbBr3)0.05(FAPbI3)0.95 perovskites to vinylbenzylammonium ligand cations. Density functional theory simulations suggest ligands incorporate sequentially into the 3D lattice, driven by phenyl ring stacking, progressively bisecting the 3D perovskite into lower-dimensional fragments to form stable interfaces. Slowing the 2D/3D transformation with higher concentrations of antisolvent yields thinner 2D layers formed conformally onto 3D grains, improving carrier extraction and device efficiency (20% 3D-only, 22% 2D/3D). Controlling this progressive dimensional reduction has potential to further improve the performance of 2D/3D perovskite photovoltaics.
Exposing the hidden influence of selection rules on phonon–phonon scattering by pressure and temperature tuning
Authors: Ravichandran Navaneetha K. , Broido David 
Published: June 2021

AbstractSelection rules act to restrict the intrinsic anharmonic interactions between phonons in all crystals. Yet their influence on phonon propagation is hidden in most materials and so, hard to interrogate experimentally. Using ab initio calculations, we show that the otherwise invisible impact of selection rules on three-phonon scattering can be exposed through anomalous signatures in the pressure (P) and temperature (T) dependence of the thermal conductivities, κ, of certain compounds. Boron phosphide reveals such underlying behavior through an exceptionally sharp initial rise in κ with increasing P, which may be the steepest of any material, and also a peak and decrease in κ at high P. These features are in stark contrast to the measured behavior for many solids, and they occur at experimentally accessible conditions. These findings give a deep understanding of phonon lifetimes and heat conduction in solids, and motivate experimental efforts to observe the predicted behavior.
Clinical and molecular characteristics of COVID-19 patients with persistent SARS-CoV-2 infection
Authors: Yang Bin , Fan Junpeng , Huang Jia , Guo Ensong , Fu Yu , Liu Si , Xiao Rourou , Liu Chen , Lu Funian , Qin Tianyu , He Chao , Wang Zizhuo , Qin Xu , Hu Dianxing , You Lixin , Li Xi , Wang Tian , Wu Peng , Chen Gang , Zhou Jianfeng , Li Kezhen , Sun Chaoyang 
Published: June 2021

AbstractThe characteristics of COVID-19 patients with persistent SARS-CoV-2 infection are not yet well described. Here, we compare the clinical and molecular features of patients with long duration of viral shedding (LDs) with those from patients with short duration patients (SDs), and healthy donors (HDs). We find that several cytokines and chemokines, such as interleukin (IL)-2, tumor necrosis factor (TNF) and lymphotoxin α (LT-α) are present at lower levels in LDs than SDs. Single-cell RNA sequencing shows that natural killer (NK) cells and CD14+ monocytes are reduced, while regulatory T cells are increased in LDs; moreover, T and NK cells in LDs are less activated than in SDs. Importantly, most cells in LDs show reduced expression of ribosomal protein (RP) genes and related pathways, with this inversed correlation between RP levels and infection duration further validated in 103 independent patients. Our results thus indicate that immunosuppression and low RP expression may be related to the persistence of the viral infection in COVID-19 patients.
Dislocation interactions in olivine control postseismic creep of the upper mantle
Authors: Wallis David , Hansen Lars N. , Wilkinson Angus J. , Lebensohn Ricardo A. 
Published: June 2021

AbstractChanges in stress applied to mantle rocks, such as those imposed by earthquakes, commonly induce a period of transient creep, which is often modelled based on stress transfer among slip systems due to grain interactions. However, recent experiments have demonstrated that the accumulation of stresses among dislocations is the dominant cause of strain hardening in olivine at temperatures ≤600 °C, raising the question of whether the same process contributes to transient creep at higher temperatures. Here, we demonstrate that olivine samples deformed at 25 °C or 1150–1250 °C both preserve stress heterogeneities of ~1 GPa that are imparted by dislocations and have correlation lengths of ~1 μm. The similar stress distributions formed at these different temperatures indicate that accumulation of stresses among dislocations also provides a contribution to transient creep at high temperatures. The results motivate a new generation of models that capture these intragranular processes and may refine predictions of evolving mantle viscosity over the earthquake cycle.
Site-specific ubiquitylation acts as a regulator of linker histone H1
Authors: Höllmüller Eva , Geigges Simon , Niedermeier Marie L. , Kammer Kai-Michael , Kienle Simon M. , Rösner Daniel , Scheffner Martin , Marx Andreas , Stengel Florian 
Published: June 2021

AbstractDecoding the role of histone posttranslational modifications (PTMs) is key to understand the fundamental process of epigenetic regulation. This is well studied for PTMs of core histones but not for linker histone H1 in general and its ubiquitylation in particular due to a lack of proper tools. Here, we report on the chemical synthesis of site-specifically mono-ubiquitylated H1.2 and identify its ubiquitin-dependent interactome on a proteome-wide scale. We show that site-specific ubiquitylation of H1 at position K64 modulates interactions with deubiquitylating enzymes and the deacetylase SIRT1. Moreover, it affects H1-dependent chromatosome assembly and phase separation resulting in a more open chromatosome conformation generally associated with a transcriptionally active chromatin state. In summary, we propose that site-specific ubiquitylation plays a general regulatory role for linker histone H1.
Probing the biogenesis pathway and dynamics of thylakoid membranes
Authors: Huokko Tuomas , Ni Tao , Dykes Gregory F. , Simpson Deborah M. , Brownridge Philip , Conradi Fabian D. , Beynon Robert J. , Nixon Peter J. , Mullineaux Conrad W. , Zhang Peijun , Liu Lu-Ning 
Published: June 2021

AbstractHow thylakoid membranes are generated to form a metabolically active membrane network and how thylakoid membranes orchestrate the insertion and localization of protein complexes for efficient electron flux remain elusive. Here, we develop a method to modulate thylakoid biogenesis in the rod-shaped cyanobacterium Synechococcus elongatus PCC 7942 by modulating light intensity during cell growth, and probe the spatial-temporal stepwise biogenesis process of thylakoid membranes in cells. Our results reveal that the plasma membrane and regularly arranged concentric thylakoid layers have no physical connections. The newly synthesized thylakoid membrane fragments emerge between the plasma membrane and pre-existing thylakoids. Photosystem I monomers appear in the thylakoid membranes earlier than other mature photosystem assemblies, followed by generation of Photosystem I trimers and Photosystem II complexes. Redistribution of photosynthetic complexes during thylakoid biogenesis ensures establishment of the spatial organization of the functional thylakoid network. This study provides insights into the dynamic biogenesis process and maturation of the functional photosynthetic machinery.