bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dark Sage: Next-generation semi-analytic galaxy evolution with multidimensional structure and minimal free parameters
Authors: Stevens Adam R. H. , Sinha Manodeep , Rohl Alexander , Sammons Mawson W. , Hadzhiyska Boryana , Hernández-Aguayo César , Hernquist Lars 
Published: February 2024

Abstract
After more than five years of development, we present a new version of Dark Sage, a semi-analytic model (SAM) of galaxy formation that breaks the mould for models of its kind. Included among the major changes is an overhauled treatment of stellar feedback that is derived from energy conservation, operates on local scales, affects gas gradually over time rather than instantaneously, and predicts a mass loading factor for every galaxy. Building on the model’s resolved angular momentum structure of galaxies, we now consider the heating of stellar discs, delivering predictions for disc structure both radially and vertically. We add a further dimension to stellar discs by tracking the distribution of stellar ages in each annulus. Each annulus–age bin has its own velocity dispersion and metallicity evolved in the model. This allows Dark Sage to make structural predictions for galaxies that previously only hydrodynamic simulations could. We present the model as run on the merger trees of the highest-resolution gravity-only simulation of the MillenniumTNG suite. Despite its additional complexity relative to other SAMs, Dark Sage only has three free parameters, the least of any SAM, which we calibrate exclusively against the cosmic star formation history and the

$z = 0$

stellar and H i mass functions using a particle-swarm optimisation method. The Dark Sage codebase, written in C and python, is publicly available at https://github.com/arhstevens/DarkSage.
COMPARATIVE FEATURES OF BINP AMS AND MICADAS FACILITIES WORKING AT AMS GOLDEN VALLEY, RUSSIA
Authors: Petrozhitskiy A V , Parkhomchuk E V , Ignatov M M , Kuleshov D V , Kutnyakova L A , Konstantinov E S , Parkhomchuk V V 
Published: February 2024

ABSTRACTThe AMS Golden Valley radiocarbon analysis laboratory is equipped with two accelerator mass spectrometers: AMS facility from Budker Institute of Nuclear Physics (BINP AMS) and MIni CArbon DAting System (MICADAS-28) from Ionplus AG and two graphitization systems: Automated Graphitization Equipment (AGE-3) from Ionplus AG and Absorption-catalytic setup developed in Boreskov Institute of Catalysis (ACS BIC). The laboratory provides routine 14C analyses of various samples: collagen, cellulose, humic acids, carbonates from sediments, etc. The main focus of the laboratory is to determine the age of archaeological artifacts by radiocarbon dating. This work presents a comprehensive description of the BINP AMS facility, with its operation compared with that of MICADAS in the same laboratory. In 2022, the AMS Golden Valley laboratory participated for the first time in the Glasgow International Radiocarbon Inter-comparison (GIRI). The samples were graphitized on the AGE-3 and subsequently measured in both AMS facilities. A comparison of the results of the two series of experiments, namely AGE-3 + MICADAS-28 and AGE-3 + BINP AMS, is given.
Feedbacks Between Estuarine Metabolism and Anthropogenic CO2 Accelerate Local Rates of Ocean Acidification and Hasten Threshold Exceedances
Authors: Pacella Stephen R. , Brown Cheryl A. , Labiosa Rochelle G. , Hales Burke , Mochon Collura T. Chris , Evans Wiley , Waldbusser George G. 
Published: February 2024

AbstractAttribution of the ocean acidification (OA) signal in estuarine carbonate system observations is necessary for quantifying the impacts of global anthropogenic CO2 emissions on water quality, and informing managers of the efficacy of potential mitigation options. We present an analysis of observational data to characterize dynamics and drivers of seasonal carbonate system variability in two seagrass habitats of Puget Sound, WA, USA, and estimate how carbon accumulations due to anthropogenic CO2 emissions (Canth) interact with these drivers of carbonate chemistry to determine seasonally resolved rates of acidification in these habitats. Three independent simulations of Canth accumulation from 1765 to 2100 were run using two previously published methods and one novel method for Canth estimation. Our results revealed persistent seasonal differences in the magnitude of carbonate system responses to anthropogenic CO2 emissions caused by seasonal metabolic changes to the buffering capacity of estuarine waters. The seasonal variability of pHT and pCO2 is increased (while that of Ωaragonite is decreased) and acidification rates are accelerated when compared with open‐ocean estimates, highlighting how feedbacks between local metabolism and Canth can control the susceptibility of estuarine habitats to OA impacts. The changes in seasonal variability can shorten the timeline to exceedance of established physiological thresholds for endemic organisms and existing Washington State water quality criteria for pH. We highlight how Canth estimation uncertainties manifest in shallow coastal waters and limit our ability to predict impacts to coastal organisms and ecosystems from anthropogenic CO2 emissions.
Simulating the Unsteady Stable Boundary Layer With a Stochastic Stability Equation
Authors: Boyko Vyacheslav , Vercauteren Nikki 
Published: February 2024

AbstractTurbulence in very stable boundary layers is typically unsteady and intermittent. The study implements a stochastic modeling approach to represent unsteady mixing possibly associated with intermittency of turbulence and with unresolved fluid motions such as dirty waves or drainage flows. The stochastic parameterization is introduced by randomizing the mixing lengthscale used in a Reynolds average Navier‐Stokes (RANS) model with turbulent kinetic energy closure, resulting in a stochastic unsteady RANS model. The randomization alters the turbulent momentum diffusion and accounts for sporadic events of possibly unknown origin that cause unsteady mixing. The paper shows how the proposed stochastic parameterization can be integrated into a RANS model used in weather‐forecasting and its impact is analyzed using neutrally and stably stratified idealized numerical case studies. The simulations show that the framework can successfully model intermittent mixing in stably stratified conditions, and does not alter the representation of neutrally stratified conditions. It could thus present a way forward for dealing with the complexities of unsteady flows in numerical weather prediction or climate models.
The Infrared Auroral Footprint Tracks of Io, Europa and Ganymede at Jupiter Observed by Juno‐JIRAM
Authors: Moirano A. , Mura A. , Hue V. , Bonfond B. , Head L. A. , Connerney J. E. P. , Adriani A. , Altieri F. , Castagnoli C. , Cicchetti A. , Dinelli B. M. , Grassi D. , Migliorini A. , Moriconi M. L. , Noschese R. , Piccioni G. , Plainaki C. , Scarica P. , Sindoni G. , Sordini R. , Tosi F. , Turrini D. , Zambon F. 
Published: February 2024

AbstractThe electromagnetic coupling between the Galilean satellites at Jupiter and the planetary ionosphere generates an auroral footprint, which is detected with high spatial resolution in the infrared L band by the Jovian InfraRed Auroral Mapper (JIRAM) onboard the Juno spacecraft. We report the JIRAM data acquired since 27 August 2016 until 23 May 2022, which are used to compute the average position of the footprint tracks of Io, Europa and Ganymede. The result of the present analysis help to test the reliability of magnetic field models, to calibrate ground‐based observations and to highlight the variability in the footprint positions, which can be used to probe the plasma environment at the orbit of the satellites. The determination of the plasma properties around the moons is particularly relevant to complement the Juno flybys of the moons during its extended mission, and to support the future Juice and Europa Clipper missions. Lastly, we report no clear evidence of the auroral footprint of Callisto, which is likely due to a combination of its low expected brightness and its position very close to the main Jovian aurora.
NOTCH localizes to mitochondria through the TBC1D15-FIS1 interaction and is stabilized via blockade of E3 ligase and CDK8 recruitment to reprogram tumor-initiating cells
Authors: Choi Hye Yeon , Zhu Yicheng , Zhao Xuyao , Mehta Simran , Hernandez Juan Carlos , Lee Jae-Jin , Kou Yi , Machida Risa , Giacca Mauro , Del Sal Giannino , Ray Ratna , Eoh Hyungjin , Tahara Stanley M. , Chen Lin , Tsukamoto Hidekazu , Machida Keigo 
Published: February 2024

AbstractThe P53-destabilizing TBC1D15-NOTCH protein interaction promotes self-renewal of tumor-initiating stem-like cells (TICs); however, the mechanisms governing the regulation of this pathway have not been fully elucidated. Here, we show that TBC1D15 stabilizes NOTCH and c-JUN through blockade of E3 ligase and CDK8 recruitment to phosphodegron sequences. Chromatin immunoprecipitation (ChIP-seq) analysis was performed to determine whether TBC1D15-dependent NOTCH1 binding occurs in TICs or non-TICs. The TIC population was isolated to evaluate TBC1D15-dependent NOTCH1 stabilization mechanisms. The tumor incidence in hepatocyte-specific triple knockout (Alb::CreERT2;Tbc1d15Flox/Flox;Notch1Flox/Flox;Notch2Flox/Flox;HCV-NS5A) Transgenic (Tg) mice and wild-type mice was compared after being fed an alcohol-containing Western diet (WD) for 12 months. The NOTCH1-TBC1D15-FIS1 interaction resulted in recruitment of mitochondria to the perinuclear region. TBC1D15 bound to full-length NUMB and to NUMB isoform 5, which lacks three Ser phosphorylation sites, and relocalized NUMB5 to mitochondria. TBC1D15 binding to NOTCH1 blocked CDK8- and CDK19-mediated phosphorylation of the NOTCH1 PEST phosphodegron to block FBW7 recruitment to Thr-2512 of NOTCH1. ChIP-seq analysis revealed that TBC1D15 and NOTCH1 regulated the expression of genes involved in mitochondrial metabolism-related pathways required for the maintenance of TICs. TBC1D15 inhibited CDK8-mediated phosphorylation to stabilize NOTCH1 and protect it from degradation The NUMB-binding oncoprotein TBC1D15 rescued NOTCH1 from NUMB-mediated ubiquitin-dependent degradation and recruited NOTCH1 to the mitochondrial outer membrane for the generation and expansion of liver TICs. A NOTCH-TBC1D15 inhibitor was found to inhibit NOTCH-dependent pathways and exhibited potent therapeutic effects in PDX mouse models. This unique targeting of the NOTCH-TBC1D15 interaction not only normalized the perinuclear localization of mitochondria but also promoted potent cytotoxic effects against TICs to eradicate patient-derived xenografts through NOTCH-dependent pathways.
Fear memory regulation by the cAMP signaling pathway as an index of reexperiencing symptoms in posttraumatic stress disorder
Authors: Hori Hiroaki , Fukushima Hotaka , Nagayoshi Taikai , Ishikawa Rie , Zhuo Min , Yoshida Fuyuko , Kunugi Hiroshi , Okamoto Kenichi , Kim Yoshiharu , Kida Satoshi 
Published: February 2024

AbstractPosttraumatic stress disorder (PTSD) is a psychiatric disorder associated with traumatic memory, yet its etiology remains unclear. Reexperiencing symptoms are specific to PTSD compared to other anxiety-related disorders. Importantly, reexperiencing can be mimicked by retrieval-related events of fear memory in animal models of traumatic memory. Recent studies revealed candidate PTSD-associated genes that were related to the cyclic adenosine monophosphate (cAMP) signaling pathway. Here, we demonstrate the tight linkage between facilitated cAMP signaling and PTSD by analyzing loss- and gain-of-cAMP signaling effects on fear memory in mice and the transcriptomes of fear memory-activated mice and female PTSD patients with reexperiencing symptoms. Pharmacological and optogenetic upregulation or downregulation of cAMP signaling transduction enhanced or impaired, respectively, the retrieval and subsequent maintenance of fear memory in mice. In line with these observations, integrative mouse and human transcriptome analysis revealed the reduced mRNA expression of phosphodiesterase 4B (PDE4B), an enzyme that degrades cAMP, in the peripheral blood of PTSD patients showing more severe reexperiencing symptoms and the mouse hippocampus after fear memory retrieval. Importantly, more severe reexperiencing symptoms and lower PDE4B mRNA levels were correlated with decreased DNA methylation of a locus within PDE4B, suggesting the involvement of methylation in the mechanism of PTSD. These findings raise the possibility that the facilitation of cAMP signaling mediating the downregulation of PDE4B expression enhances traumatic memory, thereby playing a key role in the reexperiencing symptoms of PTSD patients as a functional index of these symptoms.
Experiences of pediatric cancer patients (age 12–18 years) with extensive germline sequencing for cancer predisposition: a qualitative study
Authors: Bon Sebastian B. B. , Wouters Roel H. P. , Bakhuizen Jette J. , Jongmans Marjolijn C. J. , van den Heuvel-Eibrink Marry M. , Grootenhuis Martha A. 
Published: February 2024

AbstractThis study explored the experiences and needs of adolescents, ranging from 12 to 18 years old, who have recently been diagnosed with cancer and participated in a nationwide germline genetic sequencing study within the context of pediatric oncology. The 21 adolescents in this qualitative interview study viewed genetic sequencing as an integral part of their cancer journey. They often characterized germline sequencing as “good-to-know” without specifying immediate utility. While the adolescents comprehended the significance of germline genetic sequencing, they were less focused on its potential long-term implications. Adolescents expressed a strong desire to be actively engaged in decisions related to genetics. They advocated for a participatory role in genetic decision-making from a young age onwards. They recommended that re-consent should be sought before re-analysis of their genetic data is performed and believe that patients should have the opportunity to provide (re-)consent once they reach adulthood. Moreover, the adolescents emphasized the importance of developing counseling materials that are not only concise but also visually attractive. In conclusion, this study underscores the positive perception that adolescents diagnosed with cancer hold regarding germline genetic sequencing. They articulate a strong interest in being actively involved in genetic decision-making. To address these articulated needs and preferences, we recommend the development of visually engaging counseling materials. These materials should effectively convey both the immediate and long-term implications of genetic sequencing, enabling adolescents with cancer to make informed decisions about genetic sequencing.
Location selection for offshore wind power station using interval-valued intuitionistic fuzzy distance measure-RANCOM-WISP method
Authors: Rani Pratibha , Mishra Arunodaya Raj , Cavallaro Fausto , Alrasheedi Adel Fahad 
Published: February 2024

AbstractThe development opportunities and high-performance capacity of offshore wind energy project depends on the selection of the suitable offshore wind power station (OWPS) location. The present study aims to introduce a decision-making model for assessing the locations for OWPS from multiple criteria and uncertainty perspectives. In this regard, the concept of interval-valued intuitionistic fuzzy set (IVIFS) is utilized to express uncertain information. To quantify the degree of difference between IVIFSs, an improved distance measure is proposed and further utilized for deriving the objective weights of criteria. Numerical examples are discussed to illustrate the usefulness of introduced IVIF-distance measure. The RANking COMparison (RANCOM) based on interval-valued intuitionistic fuzzy information is presented to determine the subjective weights of criteria. With the combination of objective and subjective weights of criteria, an integrated weighting tool is presented to find the numeric weights of criteria under IVIFS environment. Further, a hybrid interval-valued intuitionistic fuzzy Weighted integrated Sum Product (WISP) approach is developed to prioritize the OWPS locations from multiple criteria and uncertainty perspectives. This approach combines the benefits of two normalization tools and four utility measures, which approves the effect of beneficial and non-beneficial criteria by means of weighted sum and weighted product measures. Further, the developed approach is applied to the OWPS location selection problem of Gujarat, India. Sensitivity and comparative analyses are presented to confirm the robustness and stability of the present WISP approach. This study provides an innovative decision analysis framework, which makes a significant contribution to the OWPS locations assessment problem under uncertain environment.
Association of tissue oxygen saturation levels with skeletal muscle injury in the critically ill
Authors: Sugiya Ryuji , Arizono Shinichi , Higashimoto Yuji , Kimoto Yuta , Shiraishi Masashi , Mizusawa Hiroki , Tawara Yuichi , Shigeoka Hironori , Bakker Jan , Shinozaki Koichiro 
Published: February 2024

AbstractThis study aimed to investigate the association between the level of tissue oxygen saturation (StO2) and quadriceps/skeletal muscle dysfunction, measured using the Medical Research Council (MRC) scale and ultrasonography, in critically ill patients. Thirty-four patients hospitalized at the Critical Care Medicine Center of Kindai University Hospital, between January 2022 and March 2023, were enrolled in this study. The StO2 of the quadriceps muscle was measured via near-infrared spectroscopy. Muscle atrophy was measured by the thickness, cross-sectional area (CSA), and echo intensity of the rectus femoris (RF). These values were evaluated every alternate day until 13 days after admission or until discharge, whichever occurred first. Muscle weakness was assessed using the sum score of the MRC scale (MRC-SS), with the patient sitting at bedside. The mean age of the patients was 67.3 ± 15.3 years, and 20 (59%) were men. Seven patients (21%) were admitted for trauma, and 27 (79%) were admitted for medical emergencies or others. The mean score for the MRC-SS was 51.0 ± 7.9 points. RF thickness and CSA significantly decreased after day 7 (p < 0.05). There were no significant changes in StO2 levels during hospitalization. However, there were positive correlations between the nadir StO2 during hospitalization and MRC-SS, and changes in RF thickness and CSA at discharge (r = 0.41, p = 0.03; r = 0.37, p = 0.03; and r = 0.35, p = 0.05, respectively). StO2 in the quadriceps muscle may be useful for predicting muscle atrophy and dysfunction in patients with critical illnesses.
The value of five scoring systems in predicting the prognosis of patients with sepsis-associated acute respiratory failure
Authors: Fan Shiqin , Ma Jing 
Published: February 2024

AbstractOur study aimed to identify the optimal scoring system for predicting the prognosis of patients with sepsis-associated acute respiratory failure (SA-ARF). All data were taken from the fourth version of the Markets in Intensive Care Medicine (MIMIC-IV) database. Independent risk factors for death in hospitals were confirmed by regression analysis. The predictive value of the five scoring systems was evaluated by receiving operating characteristic (ROC) curves. Kaplan‒Meier curves showed the impact of acute physiology score III (APSIII) on survival and prognosis in patients with SA-ARF. Decision curve analysis (DCA) identified a scoring system with the highest net clinical benefit. ROC curve analysis showed that APS III (AUC: 0.755, 95% Cl 0.714–0.768) and Logical Organ Dysfunction System (LODS) (AUC: 0.731, 95% Cl 0.717–0.7745) were better than Simplified Acute Physiology Score II (SAPS II) (AUC: 0.727, 95% CI 0.713–0.741), Oxford Acute Severity of Illness Score (OASIS) (AUC: 0.706, 95% CI 0.691–0.720) and Sequential Organ Failure Assessment (SOFA) (AUC: 0.606, 95% CI 0.590–0.621) in assessing in-hospital mortality. Kaplan‒Meier survival analysis patients in the high-APS III score group had a considerably poorer median survival time. The DCA curve showed that APS III may provide better clinical benefits for patients. We demonstrated that the APS III score is an excellent predictor of in-hospital mortality.
The human PTGR1 gene expression is controlled by TE-derived Z-DNA forming sequence cooperating with miR-6867-5p
Authors: Lee Du Hyeong , Bae Woo Hyeon , Ha Hongseok , Kim Woo Ryung , Park Eun Gyung , Lee Yun Ju , Kim Jung-min , Shin Hae Jin , Kim Heui-Soo 
Published: February 2024

AbstractZ-DNA, a well-known non-canonical form of DNA involved in gene regulation, is often found in gene promoters. Transposable elements (TEs), which make up 45% of the human genome, can move from one location to another within the genome. TEs play various biological roles in host organisms, and like Z-DNA, can influence transcriptional regulation near promoter regions. MicroRNAs (miRNAs) are a class of small non-coding RNA molecules that play a critical role in the regulation of gene expression. Although TEs can generate Z-DNA and miRNAs can bind to Z-DNA, how these factors affect gene transcription has yet to be elucidated. Here, we identified potential Z-DNA forming sequence (ZFS), including TE-derived ZFS, in the promoter of prostaglandin reductase 1 (PTGR1) by data analysis. The transcriptional activity of these ZFS in PTGR1 was confirmed using dual-luciferase reporter assays. In addition, we discovered a novel ZFS-binding miRNA (miR-6867-5p) that suppressed PTGR1 expression by targeting to ZFS. In conclusion, these findings suggest that ZFS, including TE-derived ZFS, can regulate PTGR1 gene expression and that miR-6867-5p can suppress PTGR1 by interacting with ZFS.
Survival analysis of early intention of antenatal care among women in Bangladesh
Authors: Hossain Md. Ismail , Rahman Tanjima , Sadia Tahsin Shams , Saleheen Ahmed Abdus Saleh , Sarkar Shuvongkar , Khan Maruf , Ohi Tahsina Fariha , Haq Iqramul 
Published: February 2024

AbstractThis study focuses on the importance of early and regular Antenatal Care (ANC) visits in reducing maternal and child mortality rates in Bangladesh, a country where such health indicators are a concern. The research utilized data from the Bangladesh Demographic and Health Survey (BDHS) conducted in 2017–18 and employed the Cox proportional hazard model to identify factors influencing women’s intention of ANC services. The results revealed that 40.4% of women engaged in at least one ANC activity during the first trimester, which, although higher than in other countries, falls below the global average. Notably, women between the aged of 25 and 29 years took 15% less time for their first ANC visit compared to their younger counterparts, suggesting higher awareness and preparedness in this age group. Education, both for women and their partners, had a significant influence on the intention to visit ANC early. Women in the poor wealth quantile exhibited lower odds of seeking timely ANC, whereas those with a planned pregnancy were more likely to do so. Moreover, access to mass media decreased the timing of ANC visits by 26% compared to women who were not exposed. Moreover, living in rural areas was linked to a 17% delay in the timing of the first ANC visit compared to urban areas. These findings underscore the importance of addressing these determinants to improve the timeliness and accessibility of ANC services, thereby enhancing maternal and child health outcomes in Bangladesh.