bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ab Initio Atomistic Simulations of Ca‐Perovskite Melting
Authors: Hernandez J.‐A. , Mohn C. E. , Guren M. G. , Baron M. A. , Trønnes R. G. 
Published: October 2022

AbstractMelting curves of Ca‐perovskite (pure CaSiO3) were determined by ab initio density functional theory, using two solid‐liquid coexistence methods and two free energy approaches, in the form of thermodynamic integration and two‐phase thermodynamics. The melting curves based on the solid‐liquid coexistence methods and thermodynamic integration rise steeply from 2000 K at 14 GPa to 7000 K at 136 GPa. The melting temperature at 136 GPa is 1400 K higher than previous ab initio predictions. The high thermal stability of Ca‐perovskite is linked to its high‐symmetry isometric structure and consistent with experiments, demonstrating that Ca‐perovskite is the most refractory phase in basaltic compositions in the lower mantle pressure range. The steep dT/dp slope of the melting curve also shows that the Ca‐perovskite liquidus field expands relative to those of bridgmanite and silica with increasing pressure, in agreement with experimental evidence from simple and complex systems.
Increasing Hurricane Intensification Rate Near the US Atlantic Coast
Authors: Balaguru Karthik , Foltz Gregory R. , Leung L. Ruby , Xu Wenwei , Kim Dongmin , Lopez Hosmay , West Robert 
Published: October 2022

AbstractHurricanes often cause severe damage and loss of life, and storms that intensify close to the coast pose a particularly serious threat. While changes in hurricane intensification and environment have been examined at basin scales previously, near‐coastal changes have not been adequately explored. In this study, we address this using a suite of observations and climate model simulations. Over the 40‐year period of 1979–2018, the mean 24‐hr hurricane intensification rate increased by ∼1.2 kt 6‐hr−1 near the US Atlantic coast. However, a significant increase in intensification did not occur near the Gulf coast over the same period. The enhanced hurricane intensification along the Atlantic coast is consistent with an increasingly favorable dynamic and thermodynamic environment there, which is well simulated by climate models over the historical period. Further, multi‐model projections suggest a continued enhancement of the storm environment and hurricane intensification near the Atlantic coast in the future.
Disruption of Arctic Staircases by Shear
Authors: Brown Justin M. , Radko Timour 
Published: October 2022

AbstractThough thermohaline staircases exist in a large fraction of the Arctic halocline, the interactions of such staircases with shear and turbulence are still largely unexplored. We perform a series of three‐dimensional Direct Numerical Simulations with and without shear and demonstrate the capacity of shear to disrupt Arctic staircases. We force an oscillating shear throughout the domain in order to represent the effects of passing internal waves of wavelengths much larger than the simulated domain. Shear is shown to disrupt staircases when the Richardson number falls below 1/4 for small layer heights (0.5 m thick), but larger layers (1 m thick) are more resistant. We determine the presence and strength of the layers using measures of steppiness from the literature, finding that a metric based on the rms temperature gradient proves most accurate. This work demonstrates that double‐diffusive interfaces can be surprisingly robust, sometimes even maintaining their structure in strong, dynamically unstable shears.
Fluid‐Induced Fault Reactivation Due To Brucite + Antigorite Dehydration Triggered the Mw7.1 September 19th Puebla‐Morelos (Mexico) Intermediate‐Depth Earthquake
Authors: Gutiérrez‐Aguilar F. , Hernández‐Uribe D. , Holder R. M. , Condit C. B. 
Published: October 2022

AbstractThe Puebla‐Morelos (Mexico) 2017 earthquake nucleated ∼250 km inland from the trench within the Cocos oceanic plate mantle. Here, we argue that the Puebla‐Morelos (Mexico) 2017 earthquake resulted from changes in effective stress due to the reaction brucite + antigorite = olivine + H2O leading to the reactivation of pre‐existing seafloor faults. Fluid release (∼185 kg of H2O per m3 of subducted hydrated harzburgite) and volume increase (ΔVr solid+fluid = ∼0.8%) likely occur along subducted seafloor‐inherited faults. The amount of H2O released, and magnitude of volume change depends on the degree of faults hydration; only highly hydrated (>40% of hydration) faults will stabilize brucite and experience this reaction at depth. The brucite + antigorite dehydration reaction may be key for intermediate seismicity worldwide.
Modeling the Effects of Drift Shell Splitting in Two Case Studies of Simultaneous Observations of Substorm‐Driven Pi1B and IPDP‐Type EMIC Waves
Authors: Salzano Michelle , Lessard Marc R. , Noh Sungjun , Kim Hyomin , Waters Colin , Engebretson Mark J. , Horne Richard , Clilverd Mark , Kadokura Akira , Tanaka Yoshimasa , Kim Khan‐Hyuk , Matzka Jürgen , Fromm Tanja , Goldstein Jerry , Kim Myeong Joon 
Published: October 2022

AbstractIntervals of pulsations of diminishing periods (IPDPs) are a subtype of electromagnetic ion cyclotron (EMIC) waves that can be triggered by substorm onset. Pi1B waves are ultralow frequency (ULF) broadband bursts that are well correlated with substorm onset. IPDPs are associated with increased fluxes of 40–60 keV substorm‐injected protons which undergo gradient‐curvature drifting and interact with the cold plasmasphere population. While particle trajectories and the generation of IPDPs have been modeled in the past, those models neglect the role that drift shell splitting plays in the process. This research investigates the different pathways that Pi1B and IPDPs take from their shared origin in substorm onset to their distinct observations on the ground, including the effects of drift shell splitting en route. This paper presents two case studies using data from an array of four ground‐based Antarctic magnetometers that cover the evening sector, as well as in situ magnetometer data, proton fluxes, and proton pitch angles from the Van Allen Probes spacecraft. These observations identify a separation in geomagnetic latitude between Pi1Bs and IPDPs, and pinpoint a separation in magnetic local time (MLT). From these observations we model the drift shell splitting which injected particles undergo post‐onset. This study shows that simulations that incorporate drift shell splitting across a full injection front are dominated by injection boundary effects, and that the inclusion of drift shell splitting introduces a slight horizontal component to the time axis of the time–frequency dependence of the IPDPs.
The Role of Zooplankton Grazing and Nutrient Recycling for Global Ocean Biogeochemistry and Phytoplankton Phenology
Authors: Karakuş Onur , Völker Christoph , Iversen Morten , Hagen Wilhelm , Hauck Judith 
Published: October 2022

AbstractZooplankton plays a notable role in ocean biogeochemical cycles. However, it is often simulated as one generic group and top closure term in ocean biogeochemical models. This study presents the description of three zooplankton functional types (zPFTs, micro‐, meso‐ and macrozooplankton) in the ocean biogeochemical model FESOM‐REcoM. In the presented model, microzooplankton is a fast‐growing herbivore group, mesozooplankton is another major consumer of phytoplankton, and macrozooplankton is a slow‐growing group with a low temperature optimum. Meso‐ and macrozooplankton produce fast‐sinking fecal pellets. With three zPFTs, the annual mean zooplankton biomass increases threefold to 210 Tg C. The new food web structure leads to a 25% increase in net primary production and a 10% decrease in export production globally. Consequently, the export ratio decreases from 17% to 12% in the model. The description of three zPFTs reduces model mismatches with observed dissolved inorganic nitrogen and chlorophyll concentrations in the South Pacific and the Arctic Ocean, respectively. Representation of three zPFTs also strongly affects phytoplankton phenology: Fast nutrient recycling by zooplankton sustains higher chlorophyll concentrations in summer and autumn. Additional zooplankton grazing delays the start of the phytoplankton bloom by 3 weeks and controls the magnitude of the bloom peak in the Southern Ocean. As a result, the system switches from a light‐controlled Sverdrup system to a dilution‐controlled Behrenfeld system. Overall, the results suggest that representation of multiple zPFTs is important to capture underlying processes that may shape the response of ecosystems and ecosystem services to on‐going and future environmental change in model projections.
Atmospheric Contributions to Global Ocean Tides for Satellite Gravimetry
Authors: Balidakis Kyriakos , Sulzbach Roman , Shihora Linus , Dahle Christoph , Dill Robert , Dobslaw Henryk 
Published: October 2022

AbstractTo mitigate temporal aliasing effects in monthly mean global gravity fields from the GRACE and GRACE‐FO satellite tandem missions, both tidal and non‐tidal background models describing high‐frequency mass variability in atmosphere and oceans are needed. To quantify tides in the atmosphere, we exploit the higher spatial (31 km) and temporal (1 hr) resolution provided by the latest atmospheric ECMWF reanalysis, ERA5. The oceanic response to atmospheric tides is subsequently modeled with the general ocean circulation model MPIOM (in a recently revised TP10L40 configuration that includes the feedback of self‐attraction and loading to the momentum equations and has an improved bathymetry around Antarctica) as well as the shallow water model TiME (employing a much higher spatial resolution and more elaborate tidal dissipation than MPIOM). Both ocean models consider jointly the effects of atmospheric pressure variations and surface wind stress. We present the characteristics of 16 waves beating at frequencies in the 1–6 cpd band and find that TiME typically outperforms the corresponding results from MPIOM and also FES2014b as measured from comparisons with tide gauge data. Moreover, we note improvements in GRACE‐FO laser ranging interferometer range‐acceleration pre‐fit residuals when employing the ocean tide solutions from TiME, in particular, for the S1 spectral line with most notable improvements around Australia, India, and the northern part of South America.
A qualitative characterization of meso-activity factors to estimate soil exposure for agricultural workers
Authors: Lupolt Sara N. , Agnew Jacqueline , Ramachandran Gurumurthy , Burke Thomas A. , Kennedy Ryan David , Nachman Keeve E. 
Published: October 2022

Abstract
Background
Agricultural workers’ exposure to soil contaminants is not well characterized. Activity pattern data are a useful exposure assessment tool to estimate extent of soil contact, though existing data do not sufficiently capture the range and magnitude of soil contact in the agricultural context.

Objective
We introduce meso-activity, or specific tasks, to improve traditional activity pattern methodology. We propose a conceptual framework to organize the factors that may modify soil exposure and impact soil contact estimates within each meso-activity in agriculture. We build upon models from the US EPA to demonstrate an application of this framework to dose estimation.

Methods
We conducted in-depth interviews with sixteen fruit and vegetable growers in Maryland to characterize factors that influence soil exposure in agriculture. For illustrative purposes, we demonstrate the application of the framework to translate our qualitative data into quantitative estimates of soil contact using US EPA models for ingestion and dermal exposure.

Results
Growers discussed six tasks, or meso-activities, involving interaction with soil and described ten factors that may impact the frequency, duration and intensity of soil contact. We organized these factors into four categories (i.e., Environmental, Activity, Timing and Receptor; EAT-R) and developed a framework to improve agricultural exposure estimation and guide future research. Using information from the interviews, we estimated average daily doses for several agricultural exposure scenarios. We demonstrated how the integration of EAT-R qualitative factors into quantitative tools for exposure assessment produce more rigorous estimates of exposure that better capture the true variability in agricultural work.

Significance
Our study demonstrates how a meso-activity-centered framework can be used to refine estimates of exposure for agricultural workers. This framework will support the improvement of indirect exposure assessment tools (e.g., surveys and questionnaires) and inform more comprehensive and appropriate direct observation approaches to derive quantitative estimations of soil exposure.

Impact statement
We propose a novel classification of activity pattern data that links macro and micro-activities through the quantification and characterization of meso-activities and demonstrate how the application of our qualitative framework improves soil exposure estimation for agricultural workers. These methodological advances may inform a more rigorous approach to the evaluation of pesticide and other chemical and biological exposures incurred by persons engaged in the cultivation of agricultural commodities in soil.
Distinct molecular subtypes of papillary thyroid carcinoma and gene signature with diagnostic capability
Authors: Hong Shubin , Xie Yubin , Cheng Zhen , Li Jie , He Weiman , Guo Zhuming , Zhang Quan , Peng Sui , He Minghui , Yu Shuang , Xu Lixia , Liu Rengyun , Xu Tianyi , Zhang Yunjian , Li Yanbing , Wang Jiguang , Lv Weiming , Yu Jun , Xiao Haipeng 
Published: October 2022

AbstractPapillary thyroid carcinoma (PTC) is heterogeneous and its molecular characteristics remain elusive. We integrated transcriptomic sequencing, genomic analysis and clinicopathologic information from 582 tissue samples of 216 PTC and 75 benign thyroid nodule (BTN) patients. We discovered four subtypes of PTC including Immune-enriched Subtype, BRAF-enriched Subtype, Stromal Subtype and CNV-enriched Subtype. Molecular subtypes were validated in an external cohort of 497 PTC cases from the TCGA. Tumors in the Immune-enriched Subtype showed higher immune infiltration and overexpression of immune checkpoints, whilst BRAF-enriched Subtype showed a higher tendency for extrathyroidal extension and more advanced TNM stage. Key oncogenes including LRRK2, SLC34A2, MUC1, FOXQ1 and KRT19 were overexpressed and enriched in oncogenic MAPK and PI3K/AKT signaling pathways in BRAF-enriched subtype. Further analysis of BRAF-enriched Subtype identified three subclasses with different degrees of malignancies. We also uncovered the molecular link of the initiation and progression from BTN to subtypes of PTC using trajectory analysis. Moreover, a 20-gene expression signature was generated for differential diagnosis of PTC from BTN patients. Together, our work identified previously unreported molecular subtypes of PTC, offering opportunities to stratify patients into optimal treatment plans based on molecular subtyping.
Integrative immune transcriptomic classification improves patient selection for precision immunotherapy in advanced gastro-oesophageal adenocarcinoma
Authors: Cabeza-Segura Manuel , Gambardella Valentina , Gimeno-Valiente Francisco , Carbonell-Asins Juan Antonio , Alarcón-Molero Lorena , González-Vilanova Arturo , Zuñiga-Trejos Sheila , Rentero-Garrido Pilar , Villagrasa Rosana , Gil Mireia , Durá Ana , Richart Paula , Alonso Noelia , Huerta Marisol , Roselló Susana , Roda Desamparados , Tarazona Noelia , Martínez-Ciarpaglini Carolina , Castillo Josefa , Cervantes Andrés , Fleitas Tania 
Published: October 2022

AbstractBackgroundAdvanced gastro-oesophageal cancer (GEA) treatment has been improved by the introduction of immune checkpoint inhibitors (CPIs), yet identifying predictive biomarkers remains a priority, particularly in patients with a combined positive score (CPS) < 5, where the benefit is less clear. Our study assesses certain immune microenvironment features related to sensitivity or resistance to CPIs with the aim of implementing a personalised approach across CPS < 5 GEA.DesignThrough integrative transcriptomic and clinicopathological analyses, we studied in both a retrospective and a prospective cohort, the immune tumour microenvironment features. We analysed the cell types composing the immune infiltrate highlighting their functional activity.ResultsThis integrative study allowed the identification of four different groups across our patients. Among them, we identified a cluster whose tumours expressed the most gene signatures related to immunomodulatory pathways and immunotherapy response. These tumours presented an enriched immune infiltrate showing high immune function activity that could potentially achieve the best benefit from CPIs. Finally, our findings were proven in an external CPI-exposed population, where the use of our transcriptomic results combined with CPS helped better identify those patients who could benefit from immunotherapy than using CPS alone (p = 0.043).ConclusionsThis transcriptomic classification could improve precision immunotherapy for GEA.
Proband-mediated interventions to increase disclosure of genetic risk in families with a BRCA or Lynch syndrome condition: a systematic review
Authors: Young Alison Luk , Imran Aalya , Spoelma Michael J. , Williams Rachel , Tucker Katherine M. , Halliday Jane , Forrest Laura E. , Wakefield Claire E. , Butow Phyllis N. 
Published: October 2022

AbstractInterventions to assist family communication about inherited cancer risk have the potential to improve family cancer outcomes. This review aimed to evaluate the efficacy of proband-mediated interventions employed within genetics clinics to increase disclosure of genetic risk to at-risk relatives. MEDLINE, Embase, CINAHL, PubMed and PsycINFO were searched for publications between 1990–2020. The quality of studies was assessed. From 5605 records reviewed, 9 studies (4 randomised control trials and 5 cohort studies) were included involving families with BRCA1, BRCA2 and Lynch syndrome. Intervention delivery modes included genetic counselling with additional telephone or in-person follow-up, letters, videos, and decision aids. The percentages of at-risk relatives informed by the proband about their risk ranged from 54.0% to 95.5% in the intervention or family-mediated comparison group. Of those who were informed, 24.4–60.0% contacted a genetics clinic and 22.8–76.2% had genetic testing after they were counselled at a genetics clinic. Significant differences between intervention and control group were reported on all three outcomes by one study, and with relatives contacting a genetics clinic by another study. The studies suggest but do not conclusively show, that tailored genetic counselling with additional follow-up can increase both the proportion of informed relatives and relatives who contact the genetics clinic. With the increase in germline testing, interventions are required to consider the family communication process and address post-disclosure variables (e.g., relative’s perceptions, emotional reactions) through engagement with probands and relatives to maximise the public health benefit of identifying inherited cancer risk in families.
Biallelic loss of LDB3 leads to a lethal pediatric dilated cardiomyopathy
Authors: Koopmann Tamara T. , Jamshidi Yalda , Naghibi-Sistani Mohammad , van der Klift Heleen M. , Birjandi Hassan , Al-Hassnan Zuhair , Alwadai Abdullah , Zifarelli Giovanni , Karimiani Ehsan G. , Sedighzadeh Sahar , Bahreini Amir , Nouri Nayereh , Peter Merlene , Watanabe Kyoko , van Duyvenvoorde Hermine A. , Ruivenkamp Claudia A. L. , Teunissen Aalbertine K. K. , Ten Harkel Arend D. J. , van Duinen Sjoerd G. , Haak Monique C. , Prada Carlos E. , Santen Gijs W. E. , Maroofian Reza 
Published: October 2022

AbstractAutosomal dominant variants in LDB3 (also known as ZASP), encoding the PDZ-LIM domain-binding factor, have been linked to a late onset phenotype of cardiomyopathy and myofibrillar myopathy in humans. However, despite knockout mice displaying a much more severe phenotype with premature death, bi-allelic variants in LDB3 have not yet been reported. Here we identify biallelic loss-of-function variants in five unrelated cardiomyopathy families by next-generation sequencing. In the first family, we identified compound heterozygous LOF variants in LDB3 in a fetus with bilateral talipes and mild left cardiac ventricular enlargement. Ultra-structural examination revealed highly irregular Z-disc formation, and RNA analysis demonstrated little/no expression of LDB3 protein with a functional C-terminal LIM domain in muscle tissue from the affected fetus. In a second family, a homozygous LDB3 nonsense variant was identified in a young girl with severe early-onset dilated cardiomyopathy with left ventricular non-compaction; the same homozygous nonsense variant was identified in a third unrelated female infant with dilated cardiomyopathy. We further identified homozygous LDB3 frameshift variants in two unrelated probands diagnosed with cardiomegaly and severely reduced left ventricular ejection fraction. Our findings demonstrate that recessive LDB3 variants can lead to an early-onset severe human phenotype of cardiomyopathy and myopathy, reminiscent of the knockout mouse phenotype, and supporting a loss of function mechanism.
Updated Stroke Gene Panels: Rapid evolution of knowledge on monogenic causes of stroke
Authors: Ilinca Andreea , Puschmann Andreas , Putaala Jukka , de Leeuw Frank Erik , Cole John , Kittner Stephen , Kristoffersson Ulf , Lindgren Arne G. 
Published: October 2022

AbstractThis article updates our previous Stroke Gene Panels (SGP) from 2017. Online Mendelian Inheritance in Man and PubMed were searched. We divided detected genes into two SGP groups, SGP1: genes reported in at least one person with stroke and associated with one or more clinical subgroups: large artery atherosclerotic, large artery non-atherosclerotic (tortuosity, dolichoectasia, aneurysm, non-atherosclerotic dissection or occlusion), cerebral small vessel diseases, cardio-embolic (arrhythmia, heart defect, cardiomyopathy), coagulation dysfunctions (venous thrombosis, arterial thrombosis, bleeding tendency), intracerebral hemorrhage, vascular malformations (cavernoma, arteriovenous malformations) and metabolism disorders; and SGP2: genes related to diseases that may predispose to stroke. We identified 168 SGP1 genes, 70 of these were validated for clinical practice. We also detected 72 SGP2 genes. Nine genes were removed because of conflicting evidence. The number of genes increased from 168 to 240 during 4.5-years, reflecting a dynamic evolution and the need for regular updates for research and clinical use.
Genetic model of the El Laco magnetite-apatite deposits by extrusion of iron-rich melt
Authors: Keller Tobias , Tornos Fernando , Hanchar John M. , Pietruszka Dorota K. , Soldati Arianna , Dingwell Donald B. , Suckale Jenny 
Published: October 2022

AbstractMagnetite-apatite deposits are important sources of iron and other metals. A prominent example are the magnetite lavas at the El Laco volcano, Northern Chile. Their formation processes remain debated. Here, we test the genetic hypothesis that an Fe-rich melt separated from silicate magma and ascended along collapse-related fractures. We complement recent analyses with thermodynamic modelling to corroborate Fe-Si liquid immiscibility evident in melt inclusions at El Laco and present viscometry of Fe- and Si-rich melts to assess the time and length scales of immiscible liquid separation. Using a rock deformation model, we demonstrate that volcano collapse can form failure zones extending towards the edifice flanks along which the ore liquid ascends towards extrusion driven by vapour exsolution despite its high density. Our results support the proposed magmatic genesis for the El Laco deposits. Geochemical and textural similarities indicate magnetite-apatite deposits elsewhere form by similar processes.