bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sea Surface and Snowflakes as Natural Targets Connecting FY‐3G and GPM‐CO Dual‐Frequency Radars
Authors: Liu Bo , Li Haoran , Liu Liping , Shang Jian , Yin Honggang , Kuo Kwo‐Sen 
Published: December 2024

AbstractThe Precipitation Measurement Radar (PMR) onboard FengYun‐3G consists of a Ku‐/Ka‐band radar, which is characterized by similar configurations with the Dual‐frequency Precipitation Radar (DPR) carried by Global Precipitation Measurement mission Core Observatory. However, directly comparing observations from two radars is challenging due to a scarcity of their coincidences. In this study, sea surface echoes in their track intersections were employed to cross‐calibrate PMR. Then, we show that the dual‐frequency ratio (DFR) in snow stably increases with Ku‐band reflectivity in statistics, allowing for an assessment of the consistency between PMR and DPR observations. Surprisingly, our results reveal a underestimation of DFR in DPR inner swath, while observations from PMR are in good agreement with those from DPR outer swath. This study demonstrates the novel use of natural targets for spaceborne dual‐frequency radar calibration, and presents a unique view into the connection between the two spaceborne precipitation radar missions in operation.
Slow‐to‐Fast Transition and Shear Localization in Accelerating Creep of Clayey Soil
Authors: Chang Chengrui , Noda Hiroyuki , Xu Qiang , Huang Dongliang , Yamaguchi Tetsuo 
Published: December 2024

AbstractAccelerating creep before catastrophic failure commonly follows a power‐law velocity‐acceleration relationship, with the exponent typically near 2 but often evolving from 1 to 2 at a certain point, indicating a dynamic transition. The underlying mechanisms, however, remain unclear. Here we investigate this transition by monitoring the slip displacement of clayey soil during fluid‐injection creep experiments. This transition is discontinuous in the first run but becomes continuous in the initially pre‐sheared sample. Using a regularized rate‐and‐state friction model, we explicitly examine the relationship between the exponent and the frictional properties of the soil. This model describes the dynamic transition, with the exponent evolving from 1 to 2 across a broad range of frictional parameters. Furthermore, by incorporating idealized shear localization processes, the model qualitatively reproduces the shear‐history‐dependent transition. Our study demonstrates that a combination of structural evolutions and frictional properties may explain slow and fast slips observed in various shear systems.
The Linked Complexity of Coseismic and Postseismic Faulting Revealed by Seismo‐Geodetic Dynamic Inversion of the 2004 Parkfield Earthquake
Authors: Schliwa Nico , Gabriel Alice‐Agnes , Premus Jan , Gallovič František 
Published: December 2024

AbstractSeveral regularly recurring moderate‐size earthquakes motivated dense instrumentation of the Parkfield section of the San Andreas fault (SAF), providing an invaluable near‐fault observatory. We present a seismo‐geodetic dynamic inversion of the 2004 Parkfield earthquake, which illuminates the interlinked complexity of faulting across time scales. Using fast‐velocity‐weakening rate‐and‐state friction, we jointly model coseismic dynamic rupture and the 90‐day evolution of postseismic slip in a 3D domain. We utilize a parallel tempering Markov chain Monte Carlo approach to solve this non‐linear high‐dimensional inverse problem, constraining spatially varying prestress and fault friction parameters by 30 strong motion and 12 GPS stations. From visiting 2 million models, we discern complex coseismic rupture dynamics that transition from a strongly radiating pulse‐like phase to a mildly radiating crack‐like phase. Both coseismic phases are separated by a shallow strength barrier that nearly arrests rupture and leads to a gap in the afterslip, reflecting the geologic heterogeneity along this segment of the SAF. Coseismic rupture termination involves distinct arrest mechanisms that imprint on afterslip kinematics. A backward propagating afterslip front may drive delayed aftershock activity above the hypocenter. Trade‐off analysis of the 10,500 best‐fitting models uncovers local correlations between prestress levels and the reference friction coefficient, alongside an anticorrelation between prestress and rate‐state parameters . We find that a complex, fault‐local interplay of dynamic parameters determines the nucleation, propagation, and arrest of both, co‐ and postseismic faulting. This study demonstrates the potential of inverse physics‐based modeling to reveal novel insights and detailed characterizations of well‐recorded earthquakes.
Internal Tides From SWOT: A 75‐Day Instantaneous Mode‐1 M2 ${\mathrm{M}}_{2}$ Internal Tide Model
Authors: Zhao Zhongxiang 
Published: December 2024

AbstractSeventy‐five days of sea surface height measurements made by the Surface Water and Ocean Topography (SWOT) mission from 7 September to 21 November 2023 are used to explore SWOT's capability of observing internal tides. Mode‐1 internal tides are mapped by our updated mapping technique. SWOT‐75d represents a 75‐day instantaneous model. Nadir‐30y is constructed using 30 years of nadir altimetry data from 1993 to 2022 and represents a climate normal. The nadir altimetry data in 2023 are used for model evaluation. Despite its large errors, SWOT‐75d reveals the basic features of the global mode‐1 internal tide field, and causes positive variance reduction in regions of strong internal tides. Nadir‐30y performs better overall, but SWOT‐75d performs better in the tropical South Atlantic Ocean, the central North Pacific Ocean, and the Melanesian region. Evaluation using seasonally subsetted altimetry data reveals that internal tides have significant temporal variations. SWOT‐75d performs the best in fall, because the model is constructed using data largely in fall. SWOT‐75d has large phase anomalies, which are spatially smoothed and used to adjust the phases in Nadir‐30y. The phase‐adjusted model can better make internal tide correction for SWOT and its performance is improved by 20%. Our results demonstrate that (a) mode‐1 internal tides can be extracted from 75 days of SWOT data by our mapping technique, and (b) the instantaneous internal tide model can be used to improve internal tide correction for SWOT.
Boreal Winter Hadley Cell Contraction in Response to the Incorporation of a Comprehensive Ocean Surface Albedo in CESM2
Authors: Wei Jian , Yang Ping , Fu Qiang 
Published: December 2024

AbstractThis study investigates the causes of shifts in the subsiding edge of the boreal winter Hadley cell (HC) in response to a comprehensive treatment of ocean surface albedo (OSA) in the fully coupled CESM2. The focus is on an in‐depth understanding of the atmospheric dynamical processes that influence the HC subsiding edge. Two sets of experiments were performed: one utilizing the default OSA, and the other employing the comprehensive OSA that accounts for realistic physical mechanisms. The results show that implementing the comprehensive OSA simulates an El Niño‐like warming pattern in reference to the default experiment, which leads to an HC contraction. Examination of zonal mean momentum dynamics in the upper troposphere reveals that variations in meridional winds, crucial for determining the HC extent, are primarily driven by the differences in the horizontal eddy momentum flux derivative. The findings indicate that the equatorward shift in meridional temperature gradients enhances subtropical zonal winds and baroclinicity along their equatorial flanks, amplifying equatorward‐propagating Rossby waves. This, in turn, alters the eddy momentum flux, reshaping the pattern of the derivatives of horizontal eddy momentum flux, constraining meridional winds, and resulting in the equatorward movement of the HC subsiding edge. A scaling theory further supports the results of the HC contraction, showing that the increased subtropical zonal winds and the equatorward shift of the Intertropical Convergence Zone (ITCZ) elevate the atmospheric angular momentum and eventually limit the expansion of the HC.
Optimizing Polar Air Traffic: Strategies for Mitigating the Effects of Space Weather‐Induced Communication Failures Poleward of 82°N
Authors: Xue Dabin , Liu Zhizhao , Zhang Donghe , Wu Cheng‐Lung , Yang Jian 
Published: December 2024

AbstractAviation communication is significant for the safe, efficient, and orderly operation of air traffic. The aviation industry relies on a sophisticated network to maintain air‐ground communications. However, space weather events can disrupt the ionosphere conditions and damage satellites, leading to High‐Frequency (HF) communication blackouts and satellite communication failures. These disruptions can jeopardize flight safety, especially for flights over polar regions. In response, strategies such as cancellations, rescheduling, or rerouting to lower latitudes may be necessary, despite the low flight efficiency and substantial financial losses. With the background of the anticipated solar maximum in 2025 and a growing number of polar flights, it is indispensable to have a comprehensive understanding of the space weather effects on aviation communication and develop constructive strategies from an Air Traffic Management (ATM) perspective. Hence, we simulate scenarios with different durations of communication failures and assess the corresponding economic losses. Based on the data derived from historical polar flights in 2019, there are daily 18 polar flights with trajectories crossing the north polar region higher than 82°N. Simulation results show that the economic losses associated with these polar flights can range from €0.03 million to €1.32 million, depending on both the duration of communication failures and the adopted air traffic management strategies. We believe that this study can shed light on the effects of space weather‐induced communication failures on polar flight operations and provide guidance for mitigating these effects in the aviation industry.
From benign to pathogenic variants and vice versa: pyrimidine transitions at position -3 of TAG and CAG 3' splice sites
Authors: Vořechovský Igor 
Published: December 2024

Abstract
In the human genome, CAG 3' splice sites (3'ss) are more than twice as frequent as TAG 3'ss. The greater abundance of the former has been attributed to a higher probability of exon skipping upon cytosine-to-thymine transitions at intron position -3 (-3C > T) than thymine-to-cytosine variants (-3T > C). However, molecular mechanisms underlying this bias and its clinical impact are poorly understood. In this study, base-pairing probabilities (BPPs) and RNA secondary structures were compared between CAG 3'ss that produced more skipping of downstream exons than their mutated UAG versions (termed “laggard” CAG 3'ss) and UAG 3'ss that resulted in more skipping than their mutated CAG counterparts (canonical 3'ss). The laggard CAG 3’ss showed significantly higher BPPs across intron-exon boundaries than canonical 3'ss. The difference was centered on positions -5 to -1 relative to the intron-exon junction, the region previously shown to exhibit the strongest high-resolution ultraviolet crosslinking to the small subunit of auxiliary factor of U2 snRNP (U2AF1). RNA secondary structure predictions suggested that laggard CAG 3'ss were more often sequestered in paired conformations and in longer stem structures while canonical 3'ss were more frequently unpaired. Taken together, the excess of base-pairing at 3'ss has a potential to alter the hierarchy in intrinsic splicing efficiency of human YAG 3'ss from canonical CAG > UAG to non-canonical UAG > CAG, to modify the clinical impact of transitions at this position and to change their classification from pathogenic to benign or vice versa.
Ethical challenges in conducting maternal-fetal surgery trials. A systematic review
Authors: Cavolo Alice , Gastmans Chris , Crombag Neeltje 
Published: December 2024

Abstract
Objective
To present the ethical challenges embedded in published maternal-fetal surgery (MFS) trials and their potential solutions.

Method
Systematic review of normative and empirical literature. We selected articles based on predefined inclusion criteria. QUAGOL methodology was used for analysis.

Results
Forty-three articles were included. We identified two main themes. First, clinical ethics issues. One of the main challenges is balancing rights of the fetus with the rights of the pregnant person. There seems to be an agreement that the pregnant person has the right to decide whether to participate regardless of fetal benefit. Second, research ethics issues. The main issues are difficulties in obtaining a sizeable sample, which lead to trials delays and cancellations, and in obtaining appropriate standardization. These difficulties have important ethical ramifications. For example, trial cancellations due the lack of proper sample size generate a waste of resources and pointlessly place participants at risk as conclusive evidence on MFS efficacy was not obtained.

Conclusions
We need to develop creative solutions that can prevent some of these ethical concerns. We need to involve all the relevant stakeholders in the development process. Further, researchers should discuss what practical issues they encountered and how they addressed them in their publications.

Impact statement

Understanding the ethical challenges embedded in MFS trials will help improving future trials and, consequently, clinical outcomes.

To our knowledge, this is the first systematic review unveiling the ethical challenges in maternal-fetal surgery trials. To offer a complete overview of the challenges, we included both normative and empirical literature.

We found that the main ethical challenges are practical difficulties that have important ethical ramification. E.g., difficulties in recruitment might hinder scientific validity, which in turn might lead to suboptimal treatment.
Label-free single-cell RNA multiplexing leveraging genetic variability
Authors: Hoeft Konrad , Bleckwehl Tore , Schumacher David , Kim Hyojin , Meyer Robert , Long Qingqing , Zhang Ling , Möller Christian , Clahsen-van Groningen Marian C. , Babler Anne , Saritas Turgay , Kurth Ingo , Milting Hendrik , Hayat Sikander , Kramann Rafael 
Published: December 2024

AbstractSingle cell RNA sequencing has provided unprecedented insights into the molecular cues and cellular heterogeneity underlying human disease. However, the high costs and complexity of single cell methods remain a major obstacle for generating large-scale human cohorts. Here, we compare current state-of-the-art single cell multiplexing technologies, and provide a widely applicable demultiplexing method, SoupLadle, that enables simple, yet robust high-throughput multiplexing leveraging genetic variability of patients.
Integrative multi-omics analysis uncovers tumor-immune-gut axis influencing immunotherapy outcomes in ovarian cancer
Authors: Rosario Spencer R. , Long Mark D. , Chilakapati Shanmuga , Gomez Eduardo Cortes , Battaglia Sebastiano , Singh Prashant K. , Wang Jianmin , Wang Katy , Attwood Kristopher , Hess Suzanne M. , McGray AJ Robert , Odunsi Kunle , Segal Brahm H. , Paragh Gyorgy , Liu Song , Wargo Jennifer A. , Zsiros Emese 
Published: December 2024

AbstractRecurrent ovarian cancer patients, especially those resistant to platinum, lack effective curative treatments. To address this, we conducted a phase 2 clinical trial (NCT02853318) combining pembrolizumab with bevacizumab, to increase T cell infiltration into the tumor, and oral cyclophosphamide, to reduce the number of regulatory T cells. The trial accrued 40 heavily pretreated recurrent ovarian cancer patients. The primary endpoint, progression free survival, was extended to a median of 10.2 months. The secondary endpoints demonstrated an objective response rate of 47.5%, and disease control in 30% of patients for over a year while maintaining a good quality of life. We performed comprehensive molecular, immune, microbiome, and metabolic profiling on samples of trial patients. Here, we show increased T and B cell clusters and distinct microbial patterns with amino acid and lipid metabolism are linked to exceptional clinical responses. This study suggests the immune milieu and host-microbiome can be leveraged to improve antitumor response in future immunotherapy trials.
Osmotic disruption of chromatin induces Topoisomerase 2 activity at sites of transcriptional stress
Authors: Gittens William H. , Allison Rachal M. , Wright Ellie M. , Brown George G. B. , Neale Matthew J. 
Published: December 2024

AbstractTranscription generates superhelical stress in DNA that poses problems for genome stability, but determining when and where such stress arises within chromosomes is challenging. Here, using G1-arrested S. cerevisiae cells, and employing rapid fixation and ultra-sensitive enrichment, we utilise the physiological activity of endogenous topoisomerase 2 (Top2) as a probe of transcription-induced superhelicity. We demonstrate that Top2 activity is surprisingly uncorrelated with transcriptional activity, suggesting that superhelical stress is obscured from Top2 within chromatin in vivo. We test this idea using osmotic perturbation—a treatment that transiently destabilises chromatin in vivo—revealing that Top2 activity redistributes within sub-minute timescales into broad zones patterned by long genes, convergent gene arrays, and transposon elements—and also by acute transcriptional induction. We propose that latent superhelical stress is normally absorbed by the intrinsic topological buffering capacity of chromatin, helping to avoid spurious topoisomerase activity arising within the essential coding regions of the genome.
Fluorescence imaging of individual ions and molecules in pressurized noble gases for barium tagging in 136Xe
Authors: Byrnes N. K. , Dey E. , Foss F. W. , Jones B. J. P. , Madigan R. , McDonald A. D. , Miller R. L. , Norman L. R. , Navarro K. E. , Nygren D. R. ,   NEXT Collaboration, Adams C. , Almazán H. , Álvarez V. , Aparicio B. , Aranburu A. I. , Arazi L. , Arnquist I. J. , Auria-Luna F. , Ayet S. , Azevedo C. D. R. , Barcelon J. E. , Bailey K. , Ballester F. , del Barrio-Torregrosa M. , Bayo A. , Benlloch-Rodríguez J. M. , Borges F. I. G. M. , Brodolin A. , Cárcel S. , Castillo A. , Cebrián S. , Church E. , Cid L. , Conde C. A. N. , Contreras T. , Cossío F. P. , Díaz G. , Dickel T. , Echevarria C. , Elorza M. , Escada J. , Esteve R. , Felkai R. , Fernandes L. M. P. , Ferrario P. , Ferreira A. L. , Freixa Z. , García-Barrena J. , Gómez-Cadenas J. J. , González R. , Grocott J. W. R. , Guenette R. , Hauptman J. , Henriques C. A. O. , Hernando Morata J. A. , Herrero-Gómez P. , Herrero V. , Hervés Carrete C. , Ho P. , Ifergan Y. , Kellerer F. , Larizgoitia L. , Larumbe A. , Lebrun P. , Lopez F. , López-March N. , Mano R. D. P. , Marques A. P. , Martín-Albo J. , Martínez-Lema G. , Martínez-Vara M. , Mistry K. , Molina-Canteras J. , Monrabal F. , Monteiro C. M. B. , Mora F. J. , Novella P. , Nuñez A. , Oblak E. , Palacio J. , Palmeiro B. , Para A. , Parmaksiz I. , Pazos A. , Pelegrin J. , Pérez Maneiro M. , Querol M. , Redwine A. B. , Renner J. , Rivilla I. , Rogero C. , Rogers L. , Romeo B. , Romo-Luque C. , Santos F. P. , dos Santos J. M. F. , Seemann M. , Shomroni I. , Silva P. A. O. C. , Simón A. , Soleti S. R. , Sorel M. , Soto-Oton J. , Teixeira J. M. R. , Teruel-Pardo S. , Toledo J. F. , Tonnelé C. , Torrent J. , Trettin A. , Usón A. , Valle P. R. G. , Veloso J. F. C. A. , Waiton J. , Yubero-Navarro A. 
Published: December 2024

AbstractThe imaging of individual Ba2+ ions in high pressure xenon gas is one possible way to attain background-free sensitivity to neutrinoless double beta decay and hence establish the Majorana nature of the neutrino. In this paper we demonstrate selective single Ba2+ ion imaging inside a high-pressure xenon gas environment. Ba2+ ions chelated with molecular chemosensors are resolved at the gas-solid interface using a diffraction-limited imaging system with scan area of 1 × 1 cm2 located inside 10 bar of xenon gas. This form of microscopy represents key ingredient in the development of barium tagging for neutrinoless double beta decay searches in 136Xe. This also provides a new tool for studying the photophysics of fluorescent molecules and chemosensors at the solid-gas interface to enable bottom-up design of catalysts and sensors.
Critical genes in genitourinary embryogenesis are related to the development of adult hydrocele
Authors: Roberson Jeffrey L. , Neylan Christopher J , Judy Renae , Walker Venexia , Tsao Philip S. , Damrauer Scott M. , Maguire Lillias H. 
Published: December 2024

AbstractDespite being a common urologic disorder with potentially complicated sequela, the genetic background of adult hydrocele has not previously been described. We performed a multi-population genome-wide association study of 363,460 men in the United Kingdom BioBank and FinnGen cohorts. We identified 6,548 adult men with hydrocele. We analyzed common variants (minor allele frequency > 0.01) associated with hydrocele and set the threshold for genome-wide significance at p < 5 × 10− 8. Meta-analysis of genome-wide association studies identified 7 genome-wide significant loci which mapped to 24 genes. Multiple gene prioritization strategies highlighted PAX8, INHBB, AMHR2, and SHH, all known to be critical to genitourinary embryogenesis and associated with Mendelian genitourinary syndromes and model organism phenotypes. Identified loci affect gene expression in genitourinary structures and are associated with multiple markers of renal function. These common variants in genes critical for genitourinary embryogenesis are associated with adult hydrocele, suggesting these genes may maintain normal scrotal anatomy in adults. This large study of nearly 400,000 men is the first genomic study of idiopathic hydrocele and defines our current understanding of the genetic background of this common condition.
Multi-omics analysis detail a submicroscopic inv(15)(q14q15) generating fusion transcripts and MEIS2 and NUSAP1 haploinsufficiency
Authors: Ek Marlene , Kvarnung Malin , Pettersson Maria , Soller Maria Johansson , Anderlid Britt-Marie , Thonberg Håkan , Eisfeldt Jesper , Lindstrand Anna 
Published: December 2024

AbstractInversions are balanced structural variants that often remain undetected in genetic diagnostics. We present a female proband with a de novo Chromosome 15 paracentric inversion, disrupting MEIS2 and NUSAP1. The inversion was detected by short-read genome sequencing and confirmed with adaptive long-read sequencing. The breakpoint junction analysis revealed a 96 bp (bp) deletion and an 18 bp insertion in the two junctions, suggesting that the rearrangement arose through a replicative error. Transcriptome sequencing of cultured fibroblasts revealed normal MEIS2 levels and 0.61-fold decreased expression of NUSAP1. Furthermore, three fusion transcripts were detected and confirmed by Sanger sequencing. Heterozygous loss of MEIS2 (MIM# 600987) is associated with a cleft palate, heart malformations, and intellectual impairment, which overlap with the clinical symptoms observed in the proband. The observed fusion transcripts are likely non-functional, and MEIS2 haploinsufficiency is the likely disease causative mechanism. Altogether, this study’s findings illustrate the importance of including inversions in rare disease diagnostic testing and highlight the value of long read sequencing for the validation and characterization of such variants.