bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effective Emission Heights of Various OH Lines From X‐Shooter and SABER Observations of a Passing Quasi‐2‐Day Wave
Authors: Noll S. , Schmidt C. , Kausch W. , Bittner M. , Kimeswenger S. 
Published: December 2022

AbstractChemiluminescent radiation of the vibrationally and rotationally excited hydroxyl (OH) radical, which dominates the nighttime near‐infrared emission of the Earth's atmosphere in wide wavelength regions, is an important tracer of the chemical and dynamical state of the mesopause region between 80 and 100 km. As radiative lifetimes and rate coefficients for collision‐related transitions depend on the OH energy level, line‐dependent emission profiles are expected. However, except for some height differences for whole bands mostly revealed by satellite‐based measurements, there is a lack of data for individual lines. We succeeded in deriving effective emission heights for 298 OH lines thanks to the joint observation of a strong quasi‐2‐day wave (Q2DW) in eight nights in 2017 with the medium‐resolution spectrograph X‐shooter at the Very Large Telescope at Cerro Paranal in Chile and the limb‐sounding SABER radiometer on the TIMED satellite. Our fitting procedure revealed the most convincing results for a single wave with a period of about 44 hr and a vertical wavelength of about 32 km. The line‐dependent as well as altitude‐resolved phases of the Q2DW then resulted in effective heights which differ by up to 8 km and tend to increase with increasing vibrational and rotation excitation. The measured dependence of emission heights and wave amplitudes (which were strongest after midnight) on the line parameters implies the presence of a cold thermalized and a hot non‐thermalized population for each vibrational level.
Global Distribution of Key Features of Streamer Corona Discharges in Thunderclouds
Authors: Soler S. , Gordillo‐Vázquez F. J. , Pérez‐Invernón F. J. , Luque A. , Li D. , Neubert T. , Chanrion O. , Reglero V. , Navarro‐González J. , Østgaard N. 
Published: December 2022

AbstractWe present nighttime worldwide distributions of key features of Blue LUminous Events (BLUEs) detected by the Modular Multispectral Imaging Array of the Atmosphere‐Space Interaction Monitor. Around 10% of all detected BLUEs exhibit an impulsive single pulse shape. The rest of BLUEs are unclear (impulsive or not) single, multiple or with ambiguous pulse shapes. BLUEs exhibit two distinct populations with peak power density <25 µWm−2 (common) and ≥25 µWm−2 (rare) with different rise times and durations. The altitude (and depth below cloud tops) zonal distribution of impulsive single pulse BLUEs indicate that they are commonly present between cloud tops and a depth of ≤4 km in the tropics and ≤1 km in mid and higher latitudes. Impulsive single pulse BLUEs in the tropics are the longest (up to ∼4 km height) and have the largest number of streamers (up to ∼3 × 109). Additionally, the analysis of BLUEs has turned out to be particularly complex due to the abundance of radiation belt particles (at high latitudes and in the South Atlantic Anomaly [SAA]) and cosmic rays all over the planet. True BLUEs can not be fully distinguished from radiation belt particles and cosmic rays unless other ground‐based measurements associated with the optically detected BLUEs are available. Thus, the search algorithm of BLUEs presented in Soler et al. (2021), https://doi.org/10.1029/2021gl094657 is now completed with a new additional step that, if used, can considerably smooth the SAA shadow but can also underestimate the number of BLUEs worldwide.
Impact of Eocene‐Oligocene Antarctic Glaciation on the Paleoceanography of the Weddell Sea
Authors: Hojnacki Victoria , Lepp Allison , Horowitz Castaldo Josie , States Abbey , Li Xiaona , Passchier Sandra 
Published: December 2022

AbstractThe Eocene‐Oligocene Transition (EOT) at ∼34 Ma marked a climatic shift from greenhouse to icehouse conditions, toward long‐lasting lower global temperatures and a continental ice sheet in the Antarctic. We report on sedimentological and inorganic geochemical results across the EOT at Ocean Drilling Program (ODP) Site 696 in the Weddell Sea, within the Antarctic limb of the Atlantic circulation. The geochemical composition of detrital, authigenic and biogenic marine sediment components, and sortable silt proxies demonstrate the impact of ice growth on high latitude water masses. Sortable silt grain size and Zr/Rb ratios attest to a period of vigorous circulation at ∼36.2–35.8 Ma, coincident with a known warm interval in the Southern Ocean. Across the EOT, detrital provenance suggests that regional ice growth in the western Weddell Sea was stepwise, first expanding in the Antarctic Peninsula, followed by parts of West Antarctica. In conjunction with regional ice growth, high uranium enrichment factors (U EF) in sediments spanning the EOT interval indicate anoxic conditions in the sediment with evidence of carbonate dissolution. Following glacial expansion and sea‐ice formation at ∼33.6 Ma, a return to oxic conditions and carbonate preservation is observed with excess barium and phosphorous indicative of an increase in productivity, and potentially carbon export. Our results highlight the important connections between ice growth and the changing properties of high‐latitude water masses at the EOT with impacts on the global ocean circulation.
Improved Geological Slip Rate Estimations in the Complex Alhama de Murcia Fault Zone (SE Iberia) and Its Implications for Fault Behavior
Authors: Gómez‐Novell O. , Ortuño M. , García‐Mayordomo J. , Insua‐Arévalo J. M. , Rockwell T. K. , Baize S. , Martínez‐Díaz J. J. , Pallàs R. , Masana E. 
Published: December 2022

AbstractFault slip rate is one of the most crucial parameters to characterize earthquake occurrence in fault‐based seismic hazard assessments (SHA). Accordingly, paleoseismic studies have increasingly focused on constraining this parameter in active faults worldwide. We present a comprehensive paleoseismic study in the Alhama de Murcia Fault (AMF), one of the most active faults in SE Spain and source of destructing earthquakes such as the 2011 Mw 5.2 Lorca event. Contrasting with previous studies, we integrate paleoseismic data from four fault strands in the AMF and, based on trench slip analysis and numerical dates, we derive slip rate estimates of each strand over the whole transect and assess their time variability. The AMF has a minimum net slip rate between 1.35+0.16/−0.10 and 1.64+0.16/−0.11 mm/yr for the past 18 ± 1 to 15.2 ± 1.1 ka. These results prove the importance of accounting for the complete sections of a geological structure as they are almost twice the previous estimates for a single fault branch. Slip rate variability is identified in the AMF, with cyclic acceleration‐quiescence patterns that could be related to stress field changes driven by fault interaction or synchronicity with neighboring faults (e.g., Carrascoy). We hope that the data presented here motivates their inclusion into forthcoming fault‐based SHAs. In this regard, limitations related to the lack of paleoseismic data for one fault strand, along with poor characterization of the strike component of slip and insufficient age control of the units for another strand are highlighted and need to be accounted for by modelers.
Hydrology and Seasonality Shape the Coupling of Dissolved Hg and Methyl‐Hg With DOC in Boreal Rivers in Northern Québec
Authors: Fink‐Mercier Caroline , del Giorgio Paul A. , Amyot Marc , Lapierre Jean‐François 
Published: December 2022

AbstractCo‐loading of mercury (Hg) with dissolved organic carbon (DOC) is a key driver of the observed spatial and temporal Hg patterns among aquatic ecosystems. Their strong biogeochemical coupling has spurred the use of DOC as a predictor of Hg concentrations and exports in boreal regions where sampling logistics for Hg are costly and complex. Yet relationships between Hg and methylmercury (MeHg) with DOC have recently been shown to be highly variable in terms of slope and strength, suggesting that mechanisms other than co‐transport along the land‐water continuum may drive the relationship between Hg and DOC across landscapes. In this study, we explore the relationship between Hg and MeHg with DOC across 18 boreal rivers collectively draining over 350,000 km2 of the eastern James Bay territory (Québec), comprising watersheds with a wide range of vegetation, water residence time and riverine DOC concentrations and optical properties. Our results show that although a large portion of the variation in Hg and MeHg is explained by concentrations of DOC, Hg‐DOC and MeHg‐DOC relationships and ratios vary greatly both spatially and temporally. We show that ratios and strength of the coupling can be predicted from system hydrology, with declines in Hg:DOC and increase in MeHg:DOC ratios and stronger coupling during the seasonal progression to warmer temperatures, higher water evaporation, and longer residence time. Our study highlights the role of seasonal hydrology and biogeochemical processing in governing Hg, MeHg and DOC patterns in boreal rivers.
Abdominal Near Infrared Spectroscopy can be reliably used to measure splanchnic oxygenation changes in preterm infants
Authors: Thomas R. A. , Ballard M-R , Aladangady N. , Banerjee J. 
Published: December 2022

Abstract
Objective
Near-infrared spectroscopy (NIRS) allows assessment of regional tissue oxygen delivery and extraction. There are doubts regarding reliability of gut NIRS measurements. This study assesses reliability of NIRS for monitoring gut oxygenation.

Study design
Splanchnic tissue haemoglobin index (sTHI), tissue oxygenation index (sTOI) and fractional tissue oxygen extraction (sFTOE) changes during blood transfusion were measured using NIRS and compared to stable control infants. Infants were grouped into 3 chronological age groups: 1–7, 8–28 and ≥29 days of life.

Results
sTHI, sTOI significantly increased, and sFTOE reduced following blood transfusion in all age group infants (n = 59), with no changes seen in control infants (n = 12). Baseline characteristics including gestational age and feed volumes did not differ between groups.

Conclusion
Gut perfusion measured by NIRS improved in infants who received blood transfusion, a change not seen in the control group, thus suggesting NIRS is a reliable method to measure splanchnic tissue oxygenation.
Remineralization of molar incisor hypomineralization (MIH) with a hydroxyapatite toothpaste: an in-situ study
Authors: Amaechi Bennett Tochukwu , Farah Rayane , Liu Jungyi Alexis , Phillips Thais Santiago , Perozo Betty Isabel , Kataoka Yuko , Meyer Frederic , Enax Joachim 
Published: December 2022

AbstractAimThis randomized, double-blind, crossover, in-situ study, compared the efficacy of toothpastes based on microcrystalline hydroxyapatite (HAP; fluoride-free) or fluoride, in remineralizing molar incisor hypomineralization (MIH).MethodsTwo lesion-bearing enamel blocks were produced from each of thirty extracted permanent molars diagnosed with MIH. Sixty produced blocks were randomly assigned to two groups (30/group): 20% HAP or 1450 ppm fluoride toothpaste. Each group was subdivided into, etched (n = 20), with lesion surface treated with 32% phosphoric acid-etchant for 5 s, and unetched (n = 10). Blocks were cemented into intra-oral appliances (2 blocks/appliance) worn full-time by 15 subjects. Subjects used the toothpastes in a two-phase crossover manner, lasting 14 days per phase, after one-week washout period. Baseline and post-treatment mineral density (MD) was quantified using microcomputed tomography.ResultsOverall, both groups showed statistically significant (pairedt-test;p < 0.001) net-gain when MD was compared pre-treatment and post-treatment. HAP: pre-treatment (1.716 ± 0.315) and post-treatment (1.901 ± 0.354), Fluoride: pre-treatment (1.962 ± 0.363) and post-treatment (2.072 ± 0.353). Independentt-test demonstrated a practically significantly (≥10%) higher percentage remineralization with HAP toothpaste (26.02 ± 20.68) compared with fluoride toothpaste (14.64 ± 9.60). Higher percentage remineralization was observed in etched than unetched samples.ConclusionThe tested toothpaste based on hydroxyapatite can remineralize MIH lesions. Pre-treating the tooth surface with acid-etchant enhanced remineralization.
Impact of chronic graft-versus-host-disease on intensive care outcome in allogeneic hematopoietic stem cell recipients
Authors: Lueck Catherina , Tzalavras Asterios , Wohlfarth Philipp , Meedt Elisabeth , Kiehl Michael , Turki Amin T. , Hoeper Marius M. , Eder Matthias , Cserna Julia , Buchtele Nina , Wolff Daniel , Schellongowski Peter , Beutel Gernot , Liebregts Tobias 
Published: December 2022

AbstractChronic graft-vs-host-disease (cGvHD) is the most relevant long-term complication after allogeneic stem cell transplantation (HSCT) with major impact on non-relapse mortality, but data on intensive care unit (ICU) outcome are missing. In this retrospective, multicenter study we analyzed 174 adult HSCT recipients with cGvHD requiring intensive care treatment. Skin, pulmonary, liver, and intestinal involvement were present in 76.7%, 47.1%, 38.1% and 24.1%, respectively, and a total of 63.2% had severe cGvHD. Main reasons for ICU admission were respiratory failure (69.7%) and sepsis (34.3%). Hospital- and 3-year OS rates were 51.7% and 28.6%, respectively. Global severity of cGvHD did not impact short- and long-term survival. However, patients with severe liver cGvHD or the overlap subtype had a reduced hospital survival, while severe pulmonary cGvHD was associated with worse long-term survival. In multivariate analysis need for invasive ventilation (HR 1.08 (95% CI 1.02–1.14)) or hemodialysis (HR 1.73 (95% CI 1.14–2.62)) and <1 year since HSCT (HR 1.56 (95% CI 1.03–2.39)) were independently associated with a poorer survival. While the global severity of cGvHD does not per se affect patients’ survival after intensive care treatment, pre-existing severe hepatic, intestinal or pulmonary cGvHD is associated with worse outcomes.
Performance evaluation of six popular short-read simulators
Authors: Milhaven Mark , Pfeifer Susanne P. 
Published: December 2022

AbstractHigh-throughput sequencing data enables the comprehensive study of genomes and the variation therein. Essential for the interpretation of this genomic data is a thorough understanding of the computational methods used for processing and analysis. Whereas “gold-standard” empirical datasets exist for this purpose in humans, synthetic (i.e., simulated) sequencing data can offer important insights into the capabilities and limitations of computational pipelines for any arbitrary species and/or study design—yet, the ability of read simulator software to emulate genomic characteristics of empirical datasets remains poorly understood. We here compare the performance of six popular short-read simulators—ART, DWGSIM, InSilicoSeq, Mason, NEAT, and wgsim—and discuss important considerations for selecting suitable models for benchmarking.
Structure of nucleosome-bound human PBAF complex
Authors: Wang Li , Yu Jiali , Yu Zishuo , Wang Qianmin , Li Wanjun , Ren Yulei , Chen Zhenguo , He Shuang , Xu Yanhui 
Published: December 2022

AbstractBAF and PBAF are mammalian SWI/SNF family chromatin remodeling complexes that possess multiple histone/DNA-binding subunits and create nucleosome-depleted/free regions for transcription activation. Despite previous structural studies and recent advance of SWI/SNF family complexes, it remains incompletely understood how PBAF-nucleosome complex is organized. Here we determined structure of 13-subunit human PBAF in complex with acetylated nucleosome in ADP-BeF3-bound state. Four PBAF-specific subunits work together with nine BAF/PBAF-shared subunits to generate PBAF-specific modular organization, distinct from that of BAF at various regions. PBAF-nucleosome structure reveals six histone-binding domains and four DNA-binding domains/modules, the majority of which directly bind histone/DNA. This multivalent nucleosome-binding pattern, not observed in previous studies, suggests that PBAF may integrate comprehensive chromatin information to target genomic loci for function. Our study reveals molecular organization of subunits and histone/DNA-binding domains/modules in PBAF-nucleosome complex and provides structural insights into PBAF-mediated nucleosome association complimentary to the recently reported PBAF-nucleosome structure.
CRL2ZER1/ZYG11B recognizes small N-terminal residues for degradation
Authors: Li Yao , Zhao Yueling , Yan Xiaojie , Ye Chen , Weirich Sara , Zhang Bing , Wang Xiaolu , Song Lili , Jiang Chenhao , Jeltsch Albert , Dong Cheng , Mi Wenyi 
Published: December 2022

AbstractN-degron pathway plays an important role in the protein quality control and maintenance of cellular protein homeostasis. ZER1 and ZYG11B, the substrate receptors of the Cullin 2-RING E3 ubiquitin ligase (CRL2), recognize N-terminal (Nt) glycine degrons and participate in the Nt-myristoylation quality control through the Gly/N-degron pathway. Here we show that ZER1 and ZYG11B can also recognize small Nt-residues other than glycine. Specifically, ZER1 binds better to Nt-Ser, -Ala, -Thr and -Cys than to -Gly, while ZYG11B prefers Nt-Gly but also has the capacity to recognize Nt-Ser, -Ala and -Cys in vitro. We found that Nt-Ser, -Ala and -Cys undergo Nt-acetylation catalyzed by Nt-acetyltransferase (NAT), thereby shielding them from recognition by ZER1/ZYG11B in cells. Instead, ZER1/ZYG11B readily targets a selection of small Nt-residues lacking Nt-acetylation for degradation in NAT-deficient cells, implicating its role in the Nt-acetylation quality control. Furthermore, we present the crystal structures of ZER1 and ZYG11B bound to various small Nt-residues and uncover the molecular mechanism of non-acetylated substrate recognition by ZER1 and ZYG11B.
A widely distributed family of eukaryotic and bacterial deubiquitinases related to herpesviral large tegument proteins
Authors: Erven Ilka , Abraham Elena , Hermanns Thomas , Baumann Ulrich , Hofmann Kay 
Published: December 2022

AbstractDistinct families of eukaryotic deubiquitinases (DUBs) are regulators of ubiquitin signaling. Here, we report on the presence of an additional DUB class broadly distributed in eukaryotes and several bacteria. The only described members of this family are the large tegument proteins of herpesviruses, which are attached to the outside of the viral capsid. By using a bioinformatics screen, we have identified distant homologs of this VTD (Viral tegument-like DUB) family in vertebrate transposons, fungi, insects, nematodes, cnidaria, protists and bacteria. While some VTD activities resemble viral tegument DUBs in that they favor K48-linked ubiquitin chains, other members are highly specific for K6- or K63-linked ubiquitin chains. The crystal structures of K48- and K6-specific members reveal considerable differences in ubiquitin recognition. The VTD family likely evolved from non-DUB proteases and spread through transposons, many of which became ‘domesticated’, giving rise to the Drosophila male sterile (3)76Ca gene and several nematode genes with male-specific expression.
The establishment of COPD organoids to study host-pathogen interaction reveals enhanced viral fitness of SARS-CoV-2 in bronchi
Authors: Chan Louisa L. Y. , Anderson Danielle E. , Cheng Hong Sheng , Ivan Fransiskus Xaverius , Chen Si , Kang Adrian E. Z. , Foo Randy , Gamage Akshamal M. , Tiew Pei Yee , Koh Mariko Siyue , Lee Ken Cheah Hooi , Nichol Kristy , Pathinayake Prabuddha S. , Chan Yik Lung , Yeo Tsin Wen , Oliver Brian G. , Wark Peter A. B. , Liu Linbo , Tan Nguan Soon , Wang Lin-Fa , Chotirmall Sanjay H. 
Published: December 2022

AbstractChronic obstructive pulmonary disease (COPD) is characterised by airflow limitation and infective exacerbations, however, in-vitro model systems for the study of host-pathogen interaction at the individual level are lacking. Here, we describe the establishment of nasopharyngeal and bronchial organoids from healthy individuals and COPD that recapitulate disease at the individual level. In contrast to healthy organoids, goblet cell hyperplasia and reduced ciliary beat frequency were observed in COPD organoids, hallmark features of the disease. Single-cell transcriptomics uncovered evidence for altered cellular differentiation trajectories in COPD organoids. SARS-CoV-2 infection of COPD organoids revealed more productive replication in bronchi, the key site of infection in severe COVID-19. Viral and bacterial exposure of organoids induced greater pro-inflammatory responses in COPD organoids. In summary, we present an organoid model that recapitulates the in vivo physiological lung microenvironment at the individual level and is amenable to the study of host-pathogen interaction and emerging infectious disease.
Prethermalization in one-dimensional quantum many-body systems with confinement
Authors: Birnkammer Stefan , Bastianello Alvise , Knap Michael 
Published: December 2022

AbstractUnconventional nonequilibrium phases with restricted correlation spreading and slow entanglement growth have been proposed to emerge in systems with confined excitations, calling their thermalization dynamics into question. Here, we show that in confined systems the thermalization dynamics after a quantum quench instead exhibits multiple stages with well separated time scales. As an example, we consider the confined Ising spin chain, in which domain walls in the ordered phase form bound states reminiscent of mesons. The system first relaxes towards a prethermal state, described by a Gibbs ensemble with conserved meson number. The prethermal state arises from rare events in which mesons are created in close vicinity, leading to an avalanche of scattering events. Only at much later times a true thermal equilibrium is achieved in which the meson number conservation is violated by a mechanism akin to the Schwinger effect. The discussed prethermalization dynamics is directly relevant to generic one-dimensional, many-body systems with confined excitations.
Venus’ light slab hinders its development of planetary-scale subduction
Authors: Chen Junxing , Jiang Hehe , Tang Ming , Hao Jihua , Tian Meng , Chu Xu 
Published: December 2022

AbstractTerrestrial planet Venus has a similar size, mass, and bulk composition to Earth. Previous studies proposed that local plume-induced subduction existed on both early Earth and Venus, and this prototype subduction might initiate plate tectonics on Earth but not on Venus. In this study, we simulate the buoyancy of submerged slabs in a hypothesized 2-D thermo-metamorphic model. We analyze the thermal state of the slab, which is then used for calculating density in response to thermal and phase changes. The buoyancy of slab mantle lithosphere is primarily controlled by the temperatures and the buoyancy of slab crust is dominated by metamorphic phase changes. Difference in the eclogitization process contributes most to the slab buoyancy difference between Earth and Venus, which makes the subducted Venus’ slab consistently less dense than Earth’s. The greater chemical buoyancy on Venus, acting as a resistance to subduction, may have impeded the transition into self-sustained subduction and led to a different tectonic regime on Venus. This hypothesis may be further tested as more petrological data of Venus become available, which will further help to assess the impact of petro-tectonics on the planet’s habitability.