bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Parametric Study of Locally Generated Magnetosonic Waves by Ring‐Beam Hot Protons in the Martian Heavy Ion‐Rich Environment
Authors: Wang Jing , Yu Jiang , Chen Zuzheng , Cui Jun , Cao Jinbin , Liu Xu 
Published: August 2024

AbstractMagnetosonic (MS) waves with frequencies above the proton gyrofrequency can be locally generated by ring‐beam protons in the Martian heavy ion‐rich ionosphere. In this study, we conduct a parametric analysis to investigate the effects of heavy ion concentrations, energy (Erb), and angle (αrb) of ring‐beam protons, and wave normal angle on the excitation features of Martian ionospheric MS waves. We find the growth rates and frequency range of MS waves decrease by including O+ and O2+ ions but are insensitive to their relative concentrations. With increasing Erb or αrb, the growth rates of MS waves show a general dropping tendency. Meanwhile, their frequency and wavenumber range are almost unaffected by increasing Erb but shrink to a narrower range mainly distributed in high frequencies by increasing αrb. Unstable MS waves expand to a wider wavenumber range but shrink to a narrower frequency range as they become more oblique.
Internal Tides Reverse Tidal Currents Around Southern Taiwan
Authors: Yu Hao‐Cheng , Zhang Y. Joseph , Jan Sen , Yu Jason C. S. , Chu Chi‐Hao , Terng Chuen‐Teyr , Chiu Chi‐Min 
Published: August 2024

AbstractWe present a highly unusual case in southern Taiwan where internal tides (ITs) completely reverse the barotropic currents. A 3D baroclinic model is first validated and confirms the unexpected tidal current in that area. A series of sensitivity simulations are then used to progressively reveal the exact cause. Contrary to popular belief, a large canyon in that area is not responsible for the flow reversal. Results from using a relaxation technique in the model together with an energy flux analysis indicate that the energy of the large ITs emanated from the Luzon Strait is converted to the barotropic energy near the steep slope, which generates a local circulation and reverses the tidal flow there.
An Investigation on Causes of the Detected Surface Solar Radiation Brightening in Europe Using Satellite Data
Authors: Schilliger Linda , Tetzlaff Anke , Bourgeois Quentin , Correa Lucas Ferreira , Wild Martin 
Published: August 2024

AbstractSurface solar radiation is fundamental for terrestrial life. It provides warmth to make our planet habitable, drives atmospheric circulation, the hydrological cycle and photosynthesis. Europe has experienced an increase in surface solar radiation, termed “brightening,” since the 1980s. This study investigates the causative factors behind this brightening. A novel algorithm from the EUMETSAT satellite application facility on climate monitoring (CM SAF) provides the unique opportunity to simulate surface solar radiation under various atmospheric conditions for clouds (clear‐sky or all‐sky), aerosol optical depth (time‐varying or climatological averages) and water vapor content (with or without its direct influence on surface solar radiation). Through a multiple linear regression approach, the study attributes brightening trends to changes in these atmospheric parameters. Analyzing 61 locations distributed across Europe from 1983 to 2020, aerosols emerge as key driver during 1983–2002, with Southern Europe and high elevations showing subdued effects (0%/decade–1%/decade) versus more pronounced impacts in Northern and Eastern Europe (2%/decade–6%/decade). Cloud effects exhibit spatial variability, inducing a negative effect on surface solar radiation (−3%/decade–−2%/decade) at most investigated locations in the same period. In the period 2001–2020, aerosol effects are much smaller, while cloud effects dominate the observed brightening (2%/decade–5%/decade). This study therefore finds a substantial decrease in the cloud radiative effect over Europe in the first two decades of the 21st century. Water vapor exerts negligible influence in both sub‐periods.
Estimating Grain Stress and Distinguishing Between Mobility and Transportability Improves Bedload Transport Estimates in Coarse‐Bedded Mountain Rivers
Authors: Gilbert Jordan , Wilcox Andrew C. 
Published: August 2024

AbstractEstimating sediment transport in mountain rivers is challenging because of sediment supply limitation, broad grain size distributions, complex flow hydraulics, and large form drag. Consequently, sediment transport equations are lacking for application in rivers where the bed is coarse and largely immobile, but small fractions of finer, transportable sized material contribute disproportionately to bedload transport. We introduce a framework for estimating sediment transport in mountain rivers that addresses two limitations: estimating the shear stress acting on mobile grains, and accounting for the difference between mobility of size fractions, that is, whether or not a specific grain size can move at a given flow, and transportability, which we define as how much of that size present in the bed will be recruited into transport. We use two bedload data sets to develop equations for predicting incipient motion and transport rates of each grain size fraction present in the bed. We tested the new equations against incipient motion and sediment transport data we collected from streams in the Rocky Mountains, USA, and against published regional sediment yield data. Using this method results in transport estimates where the finer fractions, despite being a small fraction of the bed surface, make up a large part of the total yield. Fractions greater than the median bed grain size are mobile only during peak flood flows, consistent with the existing mountain river bedload data sets. The approach is parsimonious, requiring only data that are often readily available or obtainable: a bed grain size distribution, hydraulic geometry measurements, and discharge.
Single-cell transcriptome profiles the heterogeneity of tumor cells and microenvironments for different pathological endometrial cancer and identifies specific sensitive drugs
Authors: Ren Fang , Wang Lingfang , Wang Yuyouye , Wang Jiaxuan , Wang Yuanpei , Song Xiaole , Zhang Gong , Nie Fangfang , Lin Shitong 
Published: August 2024

AbstractEndometrial cancer (EC) is a highly heterogeneous malignancy characterized by varied pathology and prognoses, and the heterogeneity of its cancer cells and the tumor microenvironment (TME) remains poorly understood. We conducted single-cell RNA sequencing (scRNA-seq) on 18 EC samples, encompassing various pathological types to delineate their specific unique transcriptional landscapes. Cancer cells from diverse pathological sources displayed distinct hallmarks labeled as immune-modulating, proliferation-modulating, and metabolism-modulating cancer cells in uterine clear cell carcinomas (UCCC), well-differentiated endometrioid endometrial carcinomas (EEC-I), and uterine serous carcinomas (USC), respectively. Cancer cells from the UCCC exhibited the greatest heterogeneity. We also identified potential effective drugs and confirmed their effectiveness using patient-derived EC organoids for each pathological group. Regarding the TME, we observed that prognostically favorable CD8+ Tcyto and NK cells were prominent in normal endometrium, whereas CD4+ Treg, CD4+ Tex, and CD8+ Tex cells dominated the tumors. CXCL3+ macrophages associated with M2 signature and angiogenesis were exclusively found in tumors. Prognostically relevant epithelium-specific cancer-associated fibroblasts (eCAFs) and SOD2+ inflammatory CAFs (iCAFs) predominated in EEC-I and UCCC groups, respectively. We also validated the oncogenic effects of SOD2+ iCAFs in vitro. Our comprehensive study has yielded deeper insights into the pathogenesis of EC, potentially facilitating personalized treatments for its varied pathological types.
Pushing redox potentials to highly positive values using inert fluorobenzenes and weakly coordinating anions
Authors: Armbruster Christian , Sellin Malte , Seiler Matthis , Würz Tanja , Oesten Friederike , Schmucker Maximilian , Sterbak Tabea , Fischer Julia , Radtke Valentin , Hunger Johannes , Krossing Ingo 
Published: August 2024

AbstractWhile the development of weakly coordinating anions (WCAs) received much attention, the progress on weakly coordinating and inert solvents almost stagnated. Here we study the effect of strategic F-substitution on the solvent properties of fluorobenzenes C6FxH6−x (xFB, x = 1–5). Asymmetric fluorination leads to dielectric constants as high as 22.1 for 3FB that exceeds acetone (20.7). Combined with the WCAs [Al(ORF)4]− or [(FRO)3Al-F-Al(ORF)3]− (RF = C(CF3)3), the xFB solvents push the potentials of Ag+ and NO+ ions to +1.50/+1.52 V vs. Fc+/Fc. The xFB/WCA-system has electrochemical xFB stability windows that exceed 5 V for all xFBs with positive upper limits between +1.82 V (1FB) and +2.67 V (5FB) vs. Fc+/Fc. High-level ab initio calculations with inclusion of solvation energies show that these high potentials result from weak interactions of the ions with solvent and counterion. To access the available positive xFB potential range with stable reagents, the innocent deelectronator salts [anthraceneF]+∙[WCA]− and [phenanthreneF]+∙[WCA]− with potentials of +1.47 and +1.89 V vs. Fc+/Fc are introduced.
A standardized image processing and data quality platform for rodent fMRI
Authors: Desrosiers-Grégoire Gabriel , Devenyi Gabriel A. , Grandjean Joanes , Chakravarty M. Mallar 
Published: August 2024

Abstract
Functional magnetic resonance imaging in rodents holds great potential for advancing our understanding of brain networks. Unlike the human community, there remains no standardized resource in rodents for image processing, analysis and quality control, posing significant reproducibility limitations. Our software platform, Rodent Automated Bold Improvement of EPI Sequences, is a pipeline designed to address these limitations for preprocessing, quality control, and confound correction, along with best practices for reproducibility and transparency. We demonstrate the robustness of the preprocessing workflow by validating performance across multiple acquisition sites and both mouse and rat data. Building upon a thorough investigation into data quality metrics across acquisition sites, we introduce guidelines for the quality control of network analysis and offer recommendations for addressing issues. Taken together, this software platform will allow the emerging community to adopt reproducible practices and foster progress in translational neuroscience.
Electrically tunable layer-hybridized trions in doped WSe2 bilayers
Authors: Perea-Causin Raul , Brem Samuel , Buchner Fabian , Lu Yao , Watanabe Kenji , Taniguchi Takashi , Lupton John M. , Lin Kai-Qiang , Malic Ermin 
Published: August 2024

AbstractDoped van der Waals heterostructures host layer-hybridized trions, i.e. charged excitons with layer-delocalized constituents holding promise for highly controllable optoelectronics. Combining a microscopic theory with photoluminescence (PL) experiments, we demonstrate the electrical tunability of the trion energy landscape in naturally stacked WSe2 bilayers. We show that an out-of-plane electric field modifies the energetic ordering of the lowest lying trion states, which consist of layer-hybridized $$\Lambda$$
Λ
-point electrons and layer-localized K-point holes. At small fields, intralayer-like trions yield distinct PL signatures in opposite doping regimes characterized by weak Stark shifts in both cases. Above a doping-asymmetric critical field, interlayer-like species are energetically favored and produce PL peaks with a pronounced Stark red-shift and a counter-intuitively large intensity arising from efficient phonon-assisted recombination. Our work presents an important step forward in the microscopic understanding of layer-hybridized trions in van der Waals heterostructures and paves the way towards optoelectronic applications based on electrically controllable atomically-thin semiconductors.
Distinct regulation of ATM signaling by DNA single-strand breaks and APE1
Authors: Zhao Haichao , Li Jia , You Zhongsheng , Lindsay Howard D. , Yan Shan 
Published: August 2024

AbstractIn response to DNA double-strand breaks or oxidative stress, ATM-dependent DNA damage response (DDR) is activated to maintain genome integrity. However, it remains elusive whether and how DNA single-strand breaks (SSBs) activate ATM. Here, we provide direct evidence in Xenopus egg extracts that ATM-mediated DDR is activated by a defined SSB structure. Our mechanistic studies reveal that APE1 promotes the SSB-induced ATM DDR through APE1 exonuclease activity and ATM recruitment to SSB sites. APE1 protein can form oligomers to activate the ATM DDR in Xenopus egg extracts in the absence of DNA and can directly stimulate ATM kinase activity in vitro. Our findings reveal distinct mechanisms of the ATM-dependent DDR activation by SSBs in eukaryotic systems and identify APE1 as a direct activator of ATM kinase.
Engineering new-to-nature biochemical conversions by combining fermentative metabolism with respiratory modules
Authors: Schulz-Mirbach Helena , Krüsemann Jan Lukas , Andreadaki Theofania , Nerlich Jana Natalie , Mavrothalassiti Eleni , Boecker Simon , Schneider Philipp , Weresow Moritz , Abdelwahab Omar , Paczia Nicole , Dronsella Beau , Erb Tobias J. , Bar-Even Arren , Klamt Steffen , Lindner Steffen N. 
Published: August 2024

AbstractAnaerobic microbial fermentations provide high product yields and are a cornerstone of industrial bio-based processes. However, the need for redox balancing limits the array of fermentable substrate-product combinations. To overcome this limitation, here we design an aerobic fermentative metabolism that allows the introduction of selected respiratory modules. These can use oxygen to re-balance otherwise unbalanced fermentations, hence achieving controlled respiro-fermentative growth. Following this design, we engineer and characterize an obligate fermentative Escherichia coli strain that aerobically ferments glucose to stoichiometric amounts of lactate. We then re-integrate the quinone-dependent glycerol 3-phosphate dehydrogenase and demonstrate glycerol fermentation to lactate while selectively transferring the surplus of electrons to the respiratory chain. To showcase the potential of this fermentation mode, we direct fermentative flux from glycerol towards isobutanol production. In summary, our design permits using oxygen to selectively re-balance fermentations. This concept is an advance freeing highly efficient microbial fermentation from the limitations imposed by traditional redox balancing.
Adaptive gene loss in the common bean pan-genome during range expansion and domestication
Authors: Cortinovis Gaia , Vincenzi Leonardo , Anderson Robyn , Marturano Giovanni , Marsh Jacob Ian , Bayer Philipp Emanuel , Rocchetti Lorenzo , Frascarelli Giulia , Lanzavecchia Giovanna , Pieri Alice , Benazzo Andrea , Bellucci Elisa , Di Vittori Valerio , Nanni Laura , Ferreira Fernández Juan José , Rossato Marzia , Aguilar Orlando Mario , Morrell Peter Laurent , Rodriguez Monica , Gioia Tania , Neumann Kerstin , Alvarez Diaz Juan Camilo , Gratias Ariane , Klopp Christophe , Bitocchi Elena , Geffroy Valérie , Delledonne Massimo , Edwards David , Papa Roberto 
Published: August 2024

AbstractThe common bean (Phaseolus vulgaris L.) is a crucial legume crop and an ideal evolutionary model to study adaptive diversity in wild and domesticated populations. Here, we present a common bean pan-genome based on five high-quality genomes and whole-genome reads representing 339 genotypes. It reveals ~234 Mb of additional sequences containing 6,905 protein-coding genes missing from the reference, constituting 49% of all presence/absence variants (PAVs). More non-synonymous mutations are found in PAVs than core genes, probably reflecting the lower effective population size of PAVs and fitness advantages due to the purging effect of gene loss. Our results suggest pan-genome shrinkage occurred during wild range expansion. Selection signatures provide evidence that partial or complete gene loss was a key adaptive genetic change in common bean populations with major implications for plant adaptation. The pan-genome is a valuable resource for food legume research and breeding for climate change mitigation and sustainable agriculture.
Determination of DTaP vaccine potency by multiplex immunogenicity testing using electrochemiluminescence
Authors: Friedrichs Bärbel , Rehg Simone , Hanschmann Kay-Martin , Öppling Volker , Bekeredjian-Ding Isabelle 
Published: August 2024

AbstractLot release testing of diphtheria, tetanus and acellular pertussis vaccines traditionally relied on in vivo protection models involving challenge of laboratory animals with toxins. Meanwhile, many labs have switched to serological testing of these vaccines, which is often performed in separate in vivo assays, even if all components were formulated into one vaccine product. Here we describe the results of simultaneous serological potency determination of diphtheria (D), tetanus (T) and acellular pertussis (aP) antigens obtained following immunization of guinea pigs with multicomponent pediatric and booster vaccines from different manufacturers. The 4th World Health Organization (WHO) International Standard (IS) for diphtheria toxoid (No. 07/216) and the 4th WHO IS for tetanus toxoid (No. 08/218) were used as reference preparations. For aP, a pediatric vaccine batch containing the antigens pertussis toxoid, filamentous hemagglutinin, pertactin and fimbriae proteins type 2/3 was established as internal control. Quantification of IgG against D, T and aP antigens in guinea pig sera was performed using a hexaplex electrochemiluminescence immunoassay. We further provide proof-of-concept using experimental vaccine samples lacking or containing reduced amounts of diphtheria toxoid in the presence of full amounts of tetanus and pertussis antigens and alum adjuvant. Importantly, the assay confirmed dose-response relationships for all antigens tested and was able to detect diphtheria out-of-specification batches. The results confirmed the suitability of the protocol for combined serology batch release testing of DTaP combination vaccines as first measure towards implementation of full in vitro testing of DTaP vaccines. This report summarizes the data and the protocol used for validation prior to implementation of this method in routine batch release testing of DTaP vaccines, which led to replacement of in vivo challenge experiments in our laboratory following the 3 R (replace, reduce, refine) principle.
AI-based automation of enrollment criteria and endpoint assessment in clinical trials in liver diseases
Authors: Iyer Janani S. , Juyal Dinkar , Le Quang , Shanis Zahil , Pokkalla Harsha , Pouryahya Maryam , Pedawi Aryan , Stanford-Moore S. Adam , Biddle-Snead Charles , Carrasco-Zevallos Oscar , Lin Mary , Egger Robert , Hoffman Sara , Elliott Hunter , Leidal Kenneth , Myers Robert P. , Chung Chuhan , Billin Andrew N. , Watkins Timothy R. , Patterson Scott D. , Resnick Murray , Wack Katy , Glickman Jon , Burt Alastair D. , Loomba Rohit , Sanyal Arun J. , Glass Ben , Montalto Michael C. , Taylor-Weiner Amaro , Wapinski Ilan , Beck Andrew H. 
Published: August 2024

AbstractClinical trials in metabolic dysfunction-associated steatohepatitis (MASH, formerly known as nonalcoholic steatohepatitis) require histologic scoring for assessment of inclusion criteria and endpoints. However, variability in interpretation has impacted clinical trial outcomes. We developed an artificial intelligence-based measurement (AIM) tool for scoring MASH histology (AIM-MASH). AIM-MASH predictions for MASH Clinical Research Network necroinflammation grades and fibrosis stages were reproducible (κ = 1) and aligned with expert pathologist consensus scores (κ = 0.62–0.74). The AIM-MASH versus consensus agreements were comparable to average pathologists for MASH Clinical Research Network scores (82% versus 81%) and fibrosis (97% versus 96%). Continuous scores produced by AIM-MASH for key histological features of MASH correlated with mean pathologist scores and noninvasive biomarkers and strongly predicted progression-free survival in patients with stage 3 (P < 0.0001) and stage 4 (P = 0.03) fibrosis. In a retrospective analysis of the ATLAS trial (NCT03449446), responders receiving study treatment showed a greater continuous change in fibrosis compared with placebo (P = 0.02). Overall, these results suggest that AIM-MASH may assist pathologists in histologic review of MASH clinical trials, reducing inter-rater variability on trial outcomes and offering a more sensitive and reproducible measure of patient responses.
Bayesian spatial analysis of incomplete vaccination among children aged 12–23 months in Nigeria
Authors: Ahmed Lanre Quadri , Adebowale Ayo S. , Palamuleni Martin E. 
Published: August 2024

AbstractHigh childhood disease prevalence and under-five mortality rates have been consistently reported in Nigeria. Vaccination is a cost-effective preventive strategy against childhood diseases. Therefore, this study aimed to identify the determinants of Incomplete Vaccination (IV) among children aged 12–23 months in Nigeria. This cross-sectional design study utilized the 2018 Nigeria Demographic and Health Survey (NDHS) dataset. A two-stage cluster sampling technique was used to select women of reproductive age who have children (n = 5475) aged 12–23 months. The outcome variable was IV of children against childhood diseases. Data were analyzed using Integrated Nested Laplace Approximation and Bayesian binary regression models (α0.05). Visualization of incomplete vaccination was produced using the ArcGIS software. Children’s mean age was 15.1 ± 3.2 months and the median number of vaccines received was four. Northern regions contributed largely to the IV. The likelihood of IV was lower among women aged 25–34 years (aOR = 0.67, 95% CI = 0.54–0.82, p < 0.05) and 35–49 years (aOR = 0.59, 95%CI = 0.46–0.77, p < 0.05) compared to younger women in the age group 15–24 years. An increasing level of education reduces the risk of odds of IV. Other predictors of IV were delivery at the health facility (aOR = 0.64, 95% CI = 053–0.76, p < 0.05), and media exposure (aOR = 0.63, 95%CI = 0.54–0.79, p < 0.05). Mothers’ characteristics explained most of the variability in the IV, relatively to smaller overall contributions from the community and state-level factors (p < 0.05). The level of IV against childhood diseases was high in Nigeria. However, disparities exist across the regions and other socioeconomic segments of the population. More efforts are required to improve vaccination sensitization programs and campaigns in Nigeria.