bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fully Developed Open Channel Flow Over Clusters of Freshwater Mussels Partially Buried in a Gravel Bed
Authors: Lazzarin T. , Constantinescu G. , Wu H. , Viero D. P. 
Published: August 2024

AbstractThe present study uses results of eddy‐resolving numerical simulations to investigate the open channel flow over large clusters of freshwater mussels (Unio elongatulus) partially buried in a rough, gravel bed. The density of the mussels forming the array varies from 26 to 500 mussels/m2. The flow structure is analyzed at large distances from the leading edge of the mussel bed, where the flow can be considered fully developed. The effects of changing the mussel bed density, the filtering discharge, the burial level and the roughness of the bed surface in which mussels are burrowed, are investigated in terms of flow field, turbulent structures, drag forces, and bed shear stresses. It is found that strong interactions occur between energetic eddies generated by the larger gravels on the exposed bed surface and by the mussel shells. Simulations results show that for a burial depth close to 50% and a ratio between the average gravel size and the mussel protruding height of 0.13, the shell induced turbulence becomes dominant for mussel bed densities around 50 mussels/m2. The influence of the bed roughness becomes less relevant with increasing mussel density, as the generation of energetic eddies is mostly controlled by mussel‐to‐mussel interactions. For fixed bed roughness, burial level and filtering velocity, the mean streamwise drag force and the associated drag coefficient for the exposed part of each mussel decrease with increasing mussel density, even if strong variations are observed for individual mussels. For constant mussel bed density and burial level, the mean streamwise drag force and the mean drag coefficient decrease slightly with increasing bed roughness. Increasing the burial level decreases not only the drag forces but also the drag coefficients because of the more streamlined shape of the top of the mussels. Strong active filtering acts toward decreasing the mean streamwise force and the mean drag coefficient. The spanwise drag forces contribute significantly to the total drag force, especially for high mussel bed densities. Based on smooth bed calculations, bed‐averaged shear stresses are reduced in highly dense clusters.
Interaction of Cosmic Rays With Magnetic Flux Ropes
Authors: Lara Alejandro , Borgazzi A. , Guennam Eduardo , Niembro Tatiana , Arunbabu K. P. 
Published: August 2024

AbstractThe heliosphere is full of galactic cosmic rays (GCR), high‐energy charged particles coming isotropically from the galaxy. The GCR interact with the solar wind blown by the Sun carrying out plasma, magnetic fields and transient structures such as interplanetary coronal mass ejections (ICMEs) and their associated magnetic flux ropes (MFR). The GCR interaction with ICMEs has been extensively studied particularly the GCR flux attenuation (known as Forbush decreases) as a result of interacting with the ICME sheath and magnetic field. In this work, we investigate the opposite effect: the MFR's ability to generate GCR anisotropies which an observer may detect as an increase in the GCR flux. To achieve this, we simulated a flux of protons with energies in the 10–160 GeV range arriving from all directions to a cylindrical MFR (with and without sheath) with plasma, magnetic field, and spatial dimensions found in average ICMEs observed at 1 au. By following the individual trajectories of the injected particles we found that the MFR deviates the charged particles preferentially in one direction parallel to the MFR–axis. We also found that the peak of this anisotropic GCR flux depends on: the angle between the MFR and ambient magnetic fields; the presence or not of the sheath region; the energy of the incident particles and the observer location inside the MFR.
Hypotheses Concerning Global Magnetospheric Convection, Magnetosphere‐Ionosphere Coupling, and Auroral Activity at Uranus
Authors: Turner Drew L. , Cohen Ian J. , Clark George , Kollmann Peter , Regoli Leonardo , Caggiano Joe , McNutt Ralph , Mauk Barry 
Published: August 2024

AbstractWe investigate the unique magnetosphere of Uranus and its interaction with the solar wind. Following the work of Masters (2014), https://doi.org/10.1002/2014ja020077 and others, we developed and validated a simple yet valuable and illustrative model of Uranus' offset, tilted, and rapidly‐spinning magnetic field and magnetopause (nominal and fit to the Voyager‐2 inbound crossing point) in three‐dimensional space. With this model, we investigated details of the seasonal and interplanetary magnetic field (IMF) orientation dependencies of dayside and flank reconnection along the Uranian magnetopause. We found that anti‐parallel (magnetic field shear angle greater than 170°) reconnection occurs nearly continuously along the Uranian dayside and/or flank magnetopause under all seasons of the 84 (Earth) year Uranian orbit and the most likely IMF orientations. Such active and continuous driving of the Uranian magnetosphere should result in constant loading and unloading of the Uranian magnetotail, which may be further complicated and destabilized by sudden changes in the IMF orientation and solar wind conditions plus the reconfigurations from the rotation of Uranus itself. We demonstrate that unlike the other magnetospheric systems that are Dungey‐cycle driven (i.e., Mercury and Earth) or rotationally driven (Jupiter and Saturn), global magnetospheric convection of plasma, magnetic flux, and energy flow may occur via three distinct cycles, two of which are unique to Uranus (and possibly also Neptune). Our simple model is also used to map signatures of dayside and flank reconnection down to the Uranian ionosphere, as a function of planetary latitude and longitude. Such mapping demonstrates that “spot‐like” auroral features should be very common on the Uranian dayside, consistent with observations from Hubble Space Telescope. We further detail how the combination of Uranus' rapid rotation and unique and very active global magnetospheric convection should be consistent with fueling of the surprisingly intense trapped radiation environment observed by Voyager‐2 during its single flyby. Summarizing, Uranus is a very interesting magnetosphere that offers new insights on the nature, complexity, and diversity of planetary magnetospheric systems and the acceleration of particles in space plasmas, which might have important analogs to exoplanetary magnetospheric systems. Our hypotheses can be tested with further work involving more advanced models, new auroral observations, and unprecedented missions to explore the in situ environment from orbit around Uranus, which should include a complement of magnetospheric instruments in the payload.
Correlations of Plasma Properties Between the Upstream Magnetosheath and the Downstream Outflow Region of Magnetopause Reconnection
Authors: Han Yimin , Dai Lei , Ren Yong , Wang Chi , Gonzalez Walter , Zhu Minghui 
Published: August 2024

AbstractThe impact of upstream conditions on magnetopause reconnection has been an intriguing question in solar wind‐magnetosphere coupling. In this study, we conduct a statistical analysis of plasma properties in the reconnection outflow region and the associated upstream solar wind/magnetosheath. We observe that the normalized ion density (N/Nsw) decreases and the flow speed (V/Vsw) increases in the upstream magnetosheath with distance from the subsolar point, consistent with previous models and observations. The magnetic field strength (|B|), ion density (N), and ion bulk speed (|V|) in the upstream magnetosheath exhibit close correlations with those in the reconnection outflow region. This upstream‐downstream correlation likely arises from the process of forming reconnection outflows, where most upstream ions cross the separatrix and mix with ion outflow already accelerated near the X‐line. High‐speed part of reconnection outflow is mostly located on the magnetosphere side of the magnetopause current layer, with outflow velocities peaking close to the upstream magnetosheath Alfvén speed. The spatial extent of high‐speed outflow is greater in conditions of lower solar wind Alfvén Mach number (MA,sw). Additionally, the southward magnetic field in the magnetosheath and |B| of magnetopause current layer are larger in the cases of lower MA,sw. These findings indicate a close connection of plasma properties between the outflow region of magnetopause reconnection and the upstream magnetosheath.
Impact of systemic disease on CNS disease control after stereotactic radiosurgery to breast cancer brain metastases (The SYBRA Study)
Authors: Schick Alex , Hardy Sara , Strawderman Myla , Zheng Dandan , Cummings Michael , Milano Michael T. , Magnuson Allison , Behr Jacqueline , Sammons Sarah , Usuki Kenneth , Mohile Nimish , O’Regan Ruth , Anders Carey K. , Hicks David , Dhakal Ajay 
Published: August 2024

AbstractThe objective of the study is to assess impact of systemic disease (SD) status on overall survival and brain metastasis (BM) control, adopting a novel landmark approach to categorize SD among breast cancer (BC) patients. This single institution retrospective study included BCBM patients who have received stereotactic radiosurgery (SRS) to brain. Separate endpoints [CNS failure-free survival (cFFS), overall survival (OS)] were analyzed from each Landmark (LM): LM1 (3-months), LM2 (6-months). Patients were categorized into early and non-early progression (EP, NEP) groups depending on SD status before LMs. Median survivals from LM were assessed with Kaplan Meier plots, compared with Log-Rank test. EP was associated with worse median cFFS and OS vs NEP in both LM analyses (cFFS- LM1: 3.6 vs. 9.7 months, p = 0.0016; LM2: 2.3 vs. 12.5 months, p < 0.0001; OS- LM1: 3.6 vs. 24.3 months, p < 0.0001; LM2: 5.3 vs. 30.2 months, p < 0.0001). In multivariate analyses, EP was associated with shorter cFFS [LM1: Hazard Ratio (HR) with 95% confidence interval (CI) 3.16, 1.46–6.83, p = 0.0034; LM2: 5.32, 2.33–12.15, p = <0.0001] and shorter OS (LM1: HR with 95% CI 4.28, 1.98–9.12, p = 0.0002; LM2: 7.40, 3.10–17.63, p = <0.0001) vs NEP. Early systemic disease progressions after 1st SRS to brain is associated with worse cFFS and OS in patients with BCBM.
Phenotype prediction using biologically interpretable neural networks on multi-cohort multi-omics data
Authors: van Hilten Arno , van Rooij Jeroen ,   BIOS consortium, Heijmans Bastiaan T. , ’t Hoen Peter A. C. , Meurs Joyce van , Jansen Rick , Franke Lude , Boomsma Dorret I. , Pool René , van Dongen Jenny , Hottenga Jouke J. , van Greevenbroek Marleen M. J. , Stehouwer Coen D. A. , van der Kallen Carla J. H. , Schalkwijk Casper G. , Wijmenga Cisca , Zhernakova Sasha , Tigchelaar Ettje F. , Slagboom P. Eline , Beekman Marian , Deelen Joris , van Heemst Diana , Veldink Jan H. , van den Berg Leonard H. , van Duijn Cornelia M. , Hofman Bert A. , Isaacs Aaron , Uitterlinden André G. , Jhamai P. Mila , Verbiest Michael , Suchiman H. Eka D. , Verkerk Marijn , van der Breggen Ruud , van Rooij Jeroen , Lakenberg Nico , Mei Hailiang , van Iterson Maarten , van Galen Michiel , Bot Jan , van ’t Hof Peter , Deelen Patrick , Nooren Irene , Moed Matthijs , Vermaat Martijn , Luijk René , Jan Bonder Marc , van Dijk Freerk , Arindrarto Wibowo , Kielbasa Szymon M. , Swertz Morris A. , van Zwet Erik. W. , Ikram M. Arfan , Niessen Wiro J. , van Meurs Joyce. B. J. , Roshchupkin Gennady V. 
Published: August 2024

AbstractIntegrating multi-omics data into predictive models has the potential to enhance accuracy, which is essential for precision medicine. In this study, we developed interpretable predictive models for multi-omics data by employing neural networks informed by prior biological knowledge, referred to as visible networks. These neural networks offer insights into the decision-making process and can unveil novel perspectives on the underlying biological mechanisms associated with traits and complex diseases. We tested the performance, interpretability and generalizability for inferring smoking status, subject age and LDL levels using genome-wide RNA expression and CpG methylation data from the blood of the BIOS consortium (four population cohorts, Ntotal = 2940). In a cohort-wise cross-validation setting, the consistency of the diagnostic performance and interpretation was assessed. Performance was consistently high for predicting smoking status with an overall mean AUC of 0.95 (95% CI: 0.90–1.00) and interpretation revealed the involvement of well-replicated genes such as AHRR, GPR15 and LRRN3. LDL-level predictions were only generalized in a single cohort with an R2 of 0.07 (95% CI: 0.05–0.08). Age was inferred with a mean error of 5.16 (95% CI: 3.97–6.35) years with the genes COL11A2, AFAP1, OTUD7A, PTPRN2, ADARB2 and CD34 consistently predictive. For both regression tasks, we found that using multi-omics networks improved performance, stability and generalizability compared to interpretable single omic networks. We believe that visible neural networks have great potential for multi-omics analysis; they combine multi-omic data elegantly, are interpretable, and generalize well to data from different cohorts.
CFTIlandslides, Italian database of historical earthquake-induced landslides
Authors: Zei Caterina , Tarabusi Gabriele , Ciuccarelli Cecilia , Burrato Pierfrancesco , Sgattoni Giulia , Taccone Rita Chiara , Mariotti Dante 
Published: August 2024

AbstractKnowing the location, the extent and the characteristics of any earthquake-induced environmental phenomenon is becoming an increasingly pressing need for civil protection agencies and local administrations. In particular, earthquake-triggered landslides are known for being among the most important sources of secondary hazard, as they may cause significant losses and may delay rescue operations across large areas. The combination of the relatively frequent seismic release with a very high landslide susceptibility makes the Italian territory especially prone to the occurrence of earthquake-induced landslides. The CFTIlandslides dataset features over 1,000 landslides triggered by historical Italian earthquakes (up to 1997). The landslides effects are subdivided into classes based on location accuracy and type of movement. Knowing the distribution of the past earthquake-induced landslides provides the input information for assessing the related hazard. This dataset is addressed to a large audience of potential users, including researchers and scholars, administrators and technicians belonging to local institutions, and civil protection authorities.
Computational studies on the catalytic potential of the double active site for enzyme engineering
Authors: Krishna Naveen Banchallihundi , Roopa Lalitha , Pravin Kumar R. , S Gopenath T 
Published: August 2024

AbstractProteins possessing double active sites have the potential to revolutionise enzyme design strategies. This study extensively explored an enzyme that contains both a natural active site (NAS) and an engineered active site (EAS), focusing on understanding its structural and functional properties. Metadynamics simulations were employed to investigate how substrates interacted with their respective active sites. The results revealed that both the NAS and EAS exhibited similar minimum energy states, indicating comparable binding affinities. However, it became apparent that the EAS had a weaker binding site for the substrate due to its smaller pocket and constrained conformation. Interestingly, the EAS also displayed dynamic behaviour, with the substrate observed to move outside the pocket, suggesting the possibility of substrate translocation. To gain further insights, steered molecular dynamics (SMD) simulations were conducted to study the conformational changes of the substrate and its interactions with catalytic residues. Notably, the substrate adopted distinct conformations, including near-attack conformations, in both the EAS and NAS. Nevertheless, the NAS demonstrated superior binding minima for the substrate compared to the EAS, reinforcing the observation that the engineered active site was less favourable for substrate binding due to its limitations. The QM/MM (Quantum mechanics and molecular mechanics) analyses highlight the energy disparity between NAS and EAS. Specifically, EAS exhibited elevated energy levels due to its engineered active site being located on the surface. This positioning exposes the substrate to solvents and water molecules, adding to the energy challenge. Consequently, the engineered enzyme did not provide a significant advantage in substrate binding over the single active site protein. Further, the investigation of internal channels and tunnels within the protein shed light on the pathways facilitating transport between the two active sites. By unravelling the complex dynamics and functional characteristics of this double-active site protein, this study offers valuable insights into novel strategies of enzyme engineering. These findings establish a solid foundation for future research endeavours aimed at harnessing the potential of double-active site proteins in diverse biotechnological applications.
Enhanced strength of ultrasonically-welded austenitic stainless steels joints by introducing dynamic recrystallization of interlayers
Authors: Chung Yun-Ta , Chu Hue-En , Juan Yu-Hsuan , Yang Yo-Lun , Lin Jhe-Yu 
Published: August 2024

AbstractThis study investigated the role of interfacial deformability in bond integrity and strength, particularly in the production of robust joints between harder austenitic stainless steels (SS) during ultrasonic welding. The specimen without the interlayer experienced limited strength enhancement owing to internal cracking from continuous sliding at interfacial temperatures below 0.6 times the melting point (Tm), which is attributed to the limited deformability of the austenitic SS. In contrast, introducing Fe and Ni interlayers between the substrates resulted in a notable increase in the interfacial strength, surpassing 2500 N in the peak load within a reduced welding duration. The correlation between the interfacial strength and the peak temperature suggests that a substantial decrease in hardness below 0.4 Tm is sufficient for extensive bond formation. Moreover, dynamic recrystallization (DRX) led to grain refinement in the Fe interlayer owing to shorter weld durations, whereas grain growth was observed in the Ni interlayer due to higher peak temperatures. Both the Fe and Ni interlayers significantly improved the bonding integrity by accommodating plasticity through the above phenomena without severe damage to the substrates, leading to increase of interfacial strength by 24% (2050 N to 2500 N) and reduction of weld duration by 40% (1.5 s in Fe interlayer). In addition, the fracture position after the lap shear test shifted from the edge of the weld area to the SS substrate.
The influence of biotic and abiotic factors on the bacterial microbiome of gentoo penguins (Pygoscelis papua) in their natural environment
Authors: Kaczvinsky Chloe , Levy Hila , Preston Stephen , Youngflesh Casey , Clucas Gemma , Lynch Heather J. , Hart Tom , Smith Adrian L. 
Published: August 2024

AbstractThe microbiome is a key factor in the health, well-being, and success of vertebrates, contributing to the adaptive capacity of the host. However, the impact of geographic and biotic factors that may affect the microbiome of wild birds in polar environments is not well defined. To address this, we determined the bacterial 16S rRNA gene sequence profiles in faecal samples from pygoscelid penguin populations in the Scotia Arc, focusing on gentoo penguins. This mesopredatory group breeds in defined colonies across a wide geographic range. Since diet could influence microbiome structure, we extracted dietary profiles from a eukaryotic 18S rRNA gene sequence profile. The bacterial microbiome profiles were considered in the context of a diverse set of environmental and ecological measures. Integrating wide geographic sampling with bacterial 16S and eukaryotic 18S rRNA gene sequencing of over 350 faecal samples identified associations between the microbiome profile and a suite of geographic and ecological factors. Microbiome profiles differed according to host species, colony identity, distance between colonies, and diet. Interestingly there was also a relationship between the proportion of host DNA (in relation to total 18S rRNA gene signal) and the microbiome, which may reflect gut passage time. Colony identity provided the strongest association with differences in microbiome profiles indicating that local factors play a key role in the microbiome structure of these polar seabirds. This may reflect the influence of local transfer of microbes either via faecal-oral routes, during chick feeding or other close contact events. Other factors including diet and host species also associate with variation in microbiome profile, and in at least some locations, the microbiome composition varies considerably between individuals. Given the variation in penguin microbiomes associated with diverse factors there is potential for disruption of microbiome associations at a local scale that could influence host health, productivity, and immunological competence. The microbiome represents a sensitive indicator of changing conditions, and the implications of any changes need to be considered in the wider context of environmental change and other stressors.
InSAR data for detection and modelling of overexploitation-induced subsidence: application in the industrial area of Prato (Italy)
Authors: Medici Camilla , Del Soldato Matteo , Fibbi Gabriele , Bini Lorenzo , Confuorto Pierluigi , Mannori Gaddo , Mucci Alessandra , Pellegrineschi Vania , Bianchini Silvia , Raspini Federico , Casagli Nicola 
Published: August 2024

AbstractSpaceborne-based monitoring for environmental purposes has become a well-established practice. The recent progress of synthetic aperture radar (SAR) sensors, including through the European Space Agency’s (ESA) Sentinel-1 constellation, has enabled the scientific community to identify and monitor several geohazards, including subsidence ground deformations. A case study in the Tuscany Region, Italy, highlights the effectiveness of interferometric synthetic aperture radar (InSAR) in detecting abrupt increases in ground deformation rates in an industrial area of Montemurlo municipality. In this case, InSAR data enabled prompt identification of the phenomenon, supporting the authorities in charge of environmental management to thoroughly investigate the situation. First, an on-site validation was performed via field surveys confirming the presence of cracks and fissures on some edifices. Further analysis, including water pumping rates, settlement gauge and topographic levelling, corroborated the InSAR data's findings regarding vertical deformation. Integration of collected data allowed for spatial identification and assessment of the subsidence bowl and its source depth recognized by the remote sensing data. The Montemurlo case offers a procedural guideline for managing abrupt accelerations, identified by InSAR data in subsidence-prone areas due to fluid overexploitation. In fact, these data proved useful in helping local authorities responsible for hydrogeomorphological risk management. With the exacerbation of deformation issues in subsidence-prone regions due to climate change, early detection and monitoring of such phenomena are increasingly crucial, with InSAR data playing a central role in achieving this goal.