bluuebunny/crossref_metadata_2025_split huggingface dataset:
Formation of Standing Whistler Wave in Earth's Magnetosheath
Authors: Wang Yang , Zhong Jun , Lee Lou‐Chuang , He Jiansen , Zhang Hui , Rong Zhaojin , Wei Yong 
Published: October 2024

AbstractThe dispersion of shock is universal in various media, and in plasmas, standing whistler waves represent the dispersion of collisionless shocks. These standing whistler waves are usually observed upstream of low Mach number planetary bow shocks and interplanetary shocks. However, our understanding of the plasma behavior and electric field properties within these waves remains limited. Using conjoint THEMIS and Magnetospheric Multiscale (MMS) observations, we report the first observation of standing whistler wave upstream of a fast shock in Earth's magnetosheath resulting from the interaction between a solar wind tangential discontinuity and the bow shock. High‐resolution MMS measurements provide unprecedented insights into these waves, characterizing their circular polarization, near‐parallel propagation to the shock normal, and fixed phase relative to the shock ramp. The observed field and particle characteristics are discussed in detail.
Evaluation of Autoconversion Representation in E3SMv2 Using an Ensemble of Large‐Eddy Simulations of Low‐Level Warm Clouds
Authors: Ovchinnikov Mikhail , Ma Po‐Lun , Kaul Colleen M. , Pressel Kyle G. , Huang Meng , Shpund Jacob , Tang Shuaiqi 
Published: October 2024

AbstractIn numerical atmospheric models that treat cloud and rain droplet populations as separate condensate categories, precipitation initiation in warm clouds is often represented by an autoconversion rate , which is the rate of formation of new rain droplets through the collisions of cloud droplets. Being a function of the cloud droplet size distribution (DSD), the local is commonly parameterized as a function of DSD moments: cloud droplet number and mass concentrations. When applied in a large‐scale model, the grid‐mean must also include a correction, or enhancement factor, to account for the horizontal variability of the cloud properties across the model grid. In this study, we evaluate the Au representation in the Energy Exascale Earth System Model version 2 (E3SMv2) climate model using large‐eddy simulations (LES), which explicitly resolve cloud droplet spectra, and therefore the local , as well as its spatial variability. The analysis of an ensemble of warm low‐level cloud cases shows that the E3SMv2 formulation represents the reasonably well compared to the horizontally averaged explicitly computed rate from LES. The agreement, however, comes from a combination of an underestimated E3SM‐tuned local rate and an overestimated subgrid cloud variability enhancement factor. The latter bias is traced to neglecting the horizontal variability of and its co‐variability with in parameterizing the grid‐mean .
Aperture Field Anisotropy Control on Immiscible Displacement Patterns in Rough Fractures
Authors: Xing Kun , Shi Xiaoqing , Yang Zhibing , Kang Xueyuan , Qiang Siyuan , Wu Jichun 
Published: October 2024

AbstractTwo‐phase flow displacement in rock fractures is crucial for various subsurface mass transfer processes and engineering applications. In fractures, the displacement of a less viscous fluid by a more viscous one (i.e., viscosity ratio M > 1) involves viscous forces help stabilizing the displacement front in presence of capillary pressure fluctuations. Although previous studies have reported displacement patterns in isotropic fractures, the impact of anisotropic fractures on displacement patterns has not been systematically examined. In this study, we conducted flow‐rate‐controlled drainage experiments to examine how anisotropic aperture fields affect displacement patterns. We observed the transition of displacement patterns from capillary fingering (CF) to crossover zone (CZ) to compact displacement pattern (CD) based on variations in transverse pore‐filling event (TPFE) frequency, which characterizes the competition between capillary and viscous forces. Increasing aperture correlation length in the transverse direction leads to increased TPFE frequency at a low flow rate, destabilizing displacement front. While the increasing aperture correlation length in longitudinal direction suppressed TPFE frequency, stabilizing displacement front. Therefore, the critical capillary number (CaCF‐CZ), which indicates the onset of the CF‐CZ transition, decreases as the aperture field varies from transversely to longitudinally correlated. At high flow rates, TPFEs almost disappeared, indicating that anisotropy did not affect CZ‐CD transition (CaCZ‐CD). Furthermore, we modified theoretical models of CaCF‐CZ and CaCZ‐CD by incorporating the aperture anisotropy factor, achieving a good fit with the experimental data. This study demonstrates the critical role of aperture field anisotropy in controlling two‐phase displacement patterns and provides a theoretical framework for predicting multiphase flow behavior in natural fractures.
Impaired activation of succinate-induced type 2 immunity and secretory cell production in the small intestines of Ptk6−/− male mice
Authors: Vlajic Katarina , Bie Wenjun , Gilic Milica B. , Tyner Angela L. 
Published: October 2024

AbstractProtein tyrosine kinase 6 (PTK6) is an intracellular tyrosine kinase that is distantly related to the SRC family of tyrosine kinases. It is expressed in epithelial linings and regulates regeneration and repair of the intestinal epithelium. Analysis of publicly available datasets showed Ptk6 is upregulated in tuft cells upon activation of type 2 immunity. We found that disruption of Ptk6 influences gene expression involved in intestinal immune responses. Administration of succinate, which mimics infection and activates tuft cells, revealed PTK6-dependent activation of innate immune responses in male but not female mice. In contrast to all wild type and Ptk6−/− female mice, Ptk6−/− male mice do not activate innate immunity or upregulate differentiation of the tuft and goblet secretory cell lineages following succinate treatment. Mechanistically, we found that PTK6 regulates Il25 and Irag2, genes that are required for tuft cell effector functions and activation of type 2 innate immunity, in organoids derived from intestines of male but not female mice. In patients with Crohn’s disease, PTK6 is upregulated in tuft cells in noninflamed regions of intestine. These data highlight roles for PTK6 in contributing to sex differences in intestinal innate immunity and provide new insights into the regulation of IL-25.
Defining ethical criteria to guide the expanded use of Noninvasive Prenatal Screening (NIPS): Lessons about severity from preimplantation genetic testing
Authors: Gallois Hortense , Ravitsky Vardit , Roy Marie-Christine , Laberge Anne-Marie 
Published: October 2024

Abstract
We hypothesized that ethical criteria that guide the use of preimplantation genetic testing (PGT) could be used to inform policies about expanded use of non-invasive prenatal screening (NIPS). We used a systematic review of reasons approach to assess ethical criteria used to justify using (or not using) PGT for genetic conditions. Out of 1135 identified documents, we retained and analyzed 216 relevant documents. Results show a clear distinction in acceptability of PGT for medical vs. non-medical conditions. Criteria to decide on use of PGT for medical conditions are largely based on their severity, but there is no clear definition of “severity”. Instead, characteristics of the condition that relate to severity are used as sub-criteria to assess severity. We found that characteristics that are used as sub-criteria for assessing severity include monogenic etiology, high penetrance, absence of treatment, early age of onset, shortened lifespan, and reduced quality of life. Consensus about the use of PGT is highest for conditions that meet most of these criteria. There is no consensus around the acceptability of using PGT to detect non-medical conditions. We propose that the same severity criteria could be used by policymakers to assess the acceptability of using other genetic tests in screening and practice, including for the use of NIPS for additional conditions as indications broaden.
Genomic landscape of adult testicular germ cell tumours in the 100,000 Genomes Project
Authors: Ní Leathlobhair Máire , Frangou Anna , Kinnersley Ben , Cornish Alex J. , Chubb Daniel , Lakatos Eszter , Arumugam Prabhu , Gruber Andreas J. , Law Philip , Tapinos Avraam , Jakobsdottir G. Maria , Peneva Iliana , Sahli Atef , Smyth Evie M. , Ball Richard Y. , Sylva Rushan , Benes Ksenija , Stark Dan , Young Robin J. , Lee Alexander T. J. , Wolverson Vincent , Houlston Richard S. , Sosinsky Alona , Protheroe Andrew , Murray Matthew J. , Wedge David C. , Verrill Clare ,   Testicular Cancer Genomics England Clinical Interpretation Partnership Consortium,   Genomics England Research Consortium
Published: October 2024

AbstractTesticular germ cell tumours (TGCT), which comprise seminoma and non-seminoma subtypes, are the most common cancers in young men. In this study, we present a comprehensive whole genome sequencing analysis of adult TGCTs. Leveraging samples from participants recruited via the UK National Health Service and data from the Genomics England 100,000 Genomes Project, our results provide an extended description of genomic elements underlying TGCT pathogenesis. This catalogue offers a comprehensive, high-resolution map of copy number alterations, structural variation, and key global genome features, including mutational signatures and analysis of extrachromosomal DNA amplification. This study establishes correlations between genomic alterations and histological diversification, revealing divergent evolutionary trajectories among TGCT subtypes. By reconstructing the chronological order of driver events, we identify a subgroup of adult TGCTs undergoing relatively late whole genome duplication. Additionally, we present evidence that human leukocyte antigen loss is a more prevalent mechanism of immune disruption in seminomas. Collectively, our findings provide valuable insights into the developmental and immune modulatory processes implicated in TGCT pathogenesis and progression.
DINGO: increasing the power of locus discovery in maternal and fetal genome-wide association studies of perinatal traits
Authors: Hwang Liang-Dar , Cuellar-Partida Gabriel , Yengo Loic , Zeng Jian , Toivonen Jarkko , Arvas Mikko , Beaumont Robin N. , Freathy Rachel M. , Moen Gunn-Helen , Warrington Nicole M. , Evans David M. 
Published: October 2024

AbstractPerinatal traits are influenced by fetal and maternal genomes. We investigate the performance of three strategies to detect loci in maternal and fetal genome-wide association studies (GWASs) of the same quantitative trait: (i) the traditional strategy of analysing maternal and fetal GWASs separately; (ii) a two-degree-of-freedom test which combines information from maternal and fetal GWASs; and (iii) a one-degree-of-freedom test where signals from maternal and fetal GWASs are meta-analysed together conditional on estimated sample overlap. We demonstrate that the optimal strategy depends on the extent of sample overlap, correlation between phenotypes, whether loci exhibit fetal and/or maternal effects, and whether these effects are directionally concordant. We apply our methods to summary statistics from a recent GWAS meta-analysis of birth weight. Both the two-degree-of-freedom and meta-analytic approaches increase the number of genetic loci for birth weight relative to separately analysing the scans. Our best strategy identifies an additional 62 loci compared to the most recently published meta-analysis of birth weight. We conclude that whilst the two-degree-of-freedom test may be useful for the analysis of certain perinatal phenotypes, for most phenotypes, a simple meta-analytic strategy is likely to perform best, particularly in situations where maternal and fetal GWASs only partially overlap.
Deletion upstream of MAB21L2 highlights the importance of evolutionarily conserved non-coding sequences for eye development
Authors: Ceroni Fabiola , Cicekdal Munevver B. , Holt Richard , Sorokina Elena , Chassaing Nicolas , Clokie Samuel , Naert Thomas , Talbot Lidiya V. , Muheisen Sanaa , Bax Dorine A. , Kesim Yesim , Kivuva Emma C. , Vincent-Delorme Catherine , Lienkamp Soeren S. , Plaisancié Julie , De Baere Elfride , Calvas Patrick , Vleminckx Kris , Semina Elena V. , Ragge Nicola K. 
Published: October 2024

AbstractAnophthalmia, microphthalmia and coloboma (AMC) comprise a spectrum of developmental eye disorders, accounting for approximately 20% of childhood visual impairment. While non-coding regulatory sequences are increasingly recognised as contributing to disease burden, characterising their impact on gene function and phenotype remains challenging. Furthermore, little is known of the nature and extent of their contribution to AMC phenotypes. We report two families with variants in or near MAB21L2, a gene where genetic variants are known to cause AMC in humans and animal models. The first proband, presenting with microphthalmia and coloboma, has a likely pathogenic missense variant (c.338 G > C; p.[Trp113Ser]), segregating within the family. The second individual, presenting with microphthalmia, carries an ~ 113.5 kb homozygous deletion 19.38 kb upstream of MAB21L2. Modelling of the deletion results in transient small lens and coloboma as well as midbrain anomalies in zebrafish, and microphthalmia and coloboma in Xenopus tropicalis. Using conservation analysis, we identify 15 non-coding conserved elements (CEs) within the deleted region, while ChIP-seq data from mouse embryonic stem cells demonstrates that two of these (CE13 and 14) bind Otx2, a protein with an established role in eye development. Targeted disruption of CE14 in Xenopus tropicalis recapitulates an ocular coloboma phenotype, supporting its role in eye development. Together, our data provides insights into regulatory mechanisms underlying eye development and highlights the importance of non-coding sequences as a source of genetic diagnoses in AMC.
DGCNN approach links metagenome-derived taxon and functional information providing insight into global soil organic carbon
Authors: Gardiner Laura-Jayne , Marshall Matthew , Reusch Katharina , Dearden Chris , Birmingham Mark , Carrieri Anna Paola , Pyzer-Knapp Edward O. , Krishna Ritesh , Neal Andrew L. 
Published: October 2024

AbstractMetagenomics can provide insight into the microbial taxa present in a sample and, through gene identification, the functional potential of the community. However, taxonomic and functional information are typically considered separately in downstream analyses. We develop interpretable machine learning (ML) approaches for modelling metagenomic data, combining the biological representation of species with their associated genetically encoded functions within models. We apply our methods to investigate soil organic carbon (SOC) stocks. First, we combine a diverse global set of soil microbiome samples with environmental data, improving the predictive performance of classic ML and providing new insights into the role of soil microbiomes in global carbon cycling. Our network analysis of predictive taxa identified by classical ML models provides context for their ecological significance, extending the focus beyond just the most predictive taxa to ‘hidden’ features within the model that might be considered less predictive using standard methods for explainability. We next develop unique graph representations for individual microbiomes, linking microbial taxa to their associated functions directly, enabling predictions of SOC via deep graph convolutional neural networks (DGCNNs). Interpretation of the DGCNNs distinguished between the importance of functions of key individual species, providing genome sequence differences, e.g., gene loss/acquisition, that associate with SOC. These approaches identify several members of the Verrucomicrobiaceae family and a range of genetically encoded functions, e.g., related to carbohydrate metabolism, as important for SOC stocks and effective global SOC predictors. These relatively understudied but widespread organisms could play an important role in SOC dynamics globally.
Extending radiowave frequency detection range with dressed states of solid-state spin ensembles
Authors: Hermann Jens C. , Rizzato Roberto , Bruckmaier Fleming , Allert Robin D. , Blank Aharon , Bucher Dominik B. 
Published: October 2024

AbstractQuantum sensors using solid-state spin defects excel in the detection of radiofrequency (RF) fields, serving various applications in communication, ranging, and sensing. For this purpose, pulsed dynamical decoupling (PDD) protocols are typically applied, which enhance sensitivity to RF signals. However, these methods are limited to frequencies of a few megahertz, which poses a challenge for sensing higher frequencies. We introduce an alternative approach based on a continuous dynamical decoupling (CDD) scheme involving dressed states of nitrogen vacancy (NV) ensemble spins driven within a microwave resonator. We compare the CDD methods to established PDD protocols and demonstrate the detection of RF signals up to ~85 MHz, about ten times the current limit imposed by the PDD approach under identical conditions. Implementing the CDD method in a heterodyne/synchronized protocol combines the high-frequency detection with high spectral resolution. This advancement extends to various domains requiring detection in the high frequency (HF) and very high frequency (VHF) ranges of the RF spectrum, including spin sensor-based magnetic resonance spectroscopy at high magnetic fields.
Robust projective measurements through measuring code-inspired observables
Authors: Ouyang Yingkai 
Published: October 2024

AbstractQuantum measurements are ubiquitous in quantum information processing tasks, but errors can render their outputs unreliable. Here, we present a scheme that implements a robust projective measurement through measuring code-inspired observables. Namely, given a projective POVM, a classical code, and a constraint on the number of measurement outcomes each observable can have, we construct commuting observables whose measurement is equivalent to the projective measurement in the noiseless setting. Moreover, we can correct t errors on the classical outcomes of the observables’ measurement if the classical code corrects t errors. Since our scheme does not require the encoding of quantum data onto a quantum error correction code, it can help construct robust measurements for near-term quantum algorithms that do not use quantum error correction. Moreover, our scheme works for any projective POVM, and hence can allow robust syndrome extraction procedures in non-stabilizer quantum error correction codes.
Tunable magnonic crystal in a hybrid superconductor–ferrimagnet nanostructure
Authors: Kharlan Julia , Szulc Krzysztof , Kłos Jarosław W. , Centała Grzegorz 
Published: October 2024

AbstractOne of the most intriguing properties of magnonic systems is their reconfigurability, where an external magnetic field alters the static magnetic configuration to influence magnetization dynamics. In this paper, we present an alternative approach to tunable magnonic systems. We studied theoretically and numerically a magnonic crystal induced within a uniform magnetic layer by a periodic magnetic field pattern created by the sequence of superconducting strips. We showed that the spin-wave spectrum can be tuned by the inhomogeneous stray field of the superconductor in response to a small uniform external magnetic field. Additionally, we demonstrated that modifying the width of superconducting strips and separation between them leads to the changes in the internal field which are unprecedented in conventional magnonic structures. The paper presents the results of semi-analytical calculations for realistic structures, which are verified by finite-element method computations.
Knowledge graph driven medicine recommendation system using graph neural networks on longitudinal medical records
Authors: Mishra Rajat , Shridevi S. 
Published: October 2024

AbstractMedicine recommendation systems are designed to aid healthcare professionals by analysing a patient’s admission data to recommend safe and effective medications. These systems are categorised into two types: instance-based and longitudinal-based. Instance-based models only consider the current admission, while longitudinal models consider the patient’s medical history. Electronic Health Records are used to incorporate medical history into longitudinal models. This project proposes a novel Knowledge Graph-Driven Medicine Recommendation System using Graph Neural Networks, KGDNet, that utilises longitudinal EHR data along with ontologies and Drug-Drug Interaction knowledge to construct admission-wise clinical and medicine Knowledge Graphs for every patient. Recurrent Neural Networks are employed to model a patient’s historical data, and Graph Neural Networks are used to learn embeddings from the Knowledge Graphs. A Transformer-based Attention mechanism is then used to generate medication recommendations for the patient, considering their current clinical state, medication history, and joint medical records. The model is evaluated on the MIMIC-IV EHR data and outperforms existing methods in terms of precision, recall, F1 score, Jaccard score, and Drug-Drug Interaction control. An ablation study on our models various inputs and components to provide evidence for the importance of each component in providing the best performance. Case study is also performed to demonstrate the real-world effectiveness of KGDNet.