bluuebunny/crossref_metadata_2025 huggingface dataset:
Evaluating Noah‐MP Simulated Runoff and Snowpack in Heavily Burned Pacific‐Northwest Snow‐Dominated Catchments
Authors: Abolafia‐Rosenzweig Ronnie , He Cenlin , Chen Fei , Zhang Yongxin , Dugger Aubrey , Livneh Ben , Gochis David
Published: April 2024

Terrestrial hydrology is altered by fires, particularly in snow‐dominated catchments. However, fire impacts on catchment hydrology are often neglected from land surface model (LSM) simulations. Western U.S. wildfire activity has been increasing in recent decades and is projected to continue increasing over at least the next three decades, and thus it is important to evaluate if neglecting fire impacts in operational land surface models (LSMs) is a significant error source that has a noticeable signal among other sources of uncertainty. We evaluate a widely used state‐of‐the‐art LSM (Noah‐MP) in runoff and snowpack simulations at two representative fire‐affected snow‐dominated catchments in the Pacific Northwest: Andrew's Creek in Washington and Johnson Creek in Idaho. These two catchments are selected across all western U.S. fire‐affected catchments because they are snow‐dominated and experienced more than 50% burning in a single fire event with minimal burning outside of this event, which allows analyses of distinct pre‐ and post‐fire periods. There are statistically significant shifts in model skills from pre‐to post‐fire years in simulating runoff and snowpack. At both study catchments, simulations miss enhancements in early‐spring runoff and annual runoff efficiency during post‐fire years, resulting in persistent underestimates of annual runoff anomalies throughout the 12‐year post‐fire analysis periods. Enhanced post‐fire snow accumulation and melt contributes to observed but unmodeled increases of spring runoff and annual runoff efficiency at these catchments. Informing simulations with satellite observed land cover classifications, leaf area index, and green fraction do not consistently improve the model ability to simulate hydrologic responses to fire disturbances.
Modeling Form Roughness Induced by Tidal Sand Waves
Authors: Portos‐Amill Laura , Roos Pieter C. , Damveld Johan H. , Hulscher Suzanne J. M. H.
Published: April 2024

Tide‐dominated sandy shelf seas, such as the Dutch North Sea, are covered by sand waves. Yet, basin‐scale hydrodynamic models do not include any sand wave information because their grid sizes are too coarse to resolve sand waves individually. We explore the possibility of parametrizing the effects of sand waves on the larger‐scale tidal flow by means of a form roughness. Specifically, our aim is to see to what extent the flow over a sand wave field can be reproduced by that over a flat seabed with an increased effective roughness (accounting for both grain and form roughness). To do so, we use two process‐based hydrodynamic models: a second order perturbation approach, and Delft3D. Both models demonstrate that the presence of sand waves causes amplitude decrease and phase shift of the tidal flow. We explore the dependencies of form roughness on different sand wave characteristics (wavelength, height and asymmetry). Shorter and higher sand waves cause a higher form roughness, while our analysis does not reveal any dependency on sand wave asymmetry. Notably, the consideration of a tidal flow, characterized by several tidal constituents, each represented by an amplitude and a phase, results in a more complex form roughness analysis than in a fluvial setting, where the flow is unidirectional and steady. We thus obtain an amplitude‐based form roughness and a phase‐based form roughness, each yielding a different value, yet displaying the same qualitative dependencies.
Characterization of Relativistic Electron Precipitation Events Observed by the CALET Experiment Using Self‐Organizing‐Maps
Authors: Vidal‐Luengo Sergio E. , Blum Lauren W. , Bruno Alessandro , Ficklin Anthony W. , de Nolfo Georgia , Guzik T. Gregory , Bortnik Jacob , Kataoka Ryuho , Torii Shoji
Published: April 2024

Relativistic electron precipitation (REP) is a relatively high‐latitude phenomenon where high‐energy electrons trapped in the outer radiation belt are lost into the Earth’s atmosphere. REP events observed at low Earth orbit show varying temporal profiles and global distributions. While the precipitation origin has been attributed to specific wave modes or scattering sources, the sorting of REP events by type or driver remains an unsolved challenge. In this study, we analyze the temporal profile of relativistic electron precipitation events observed by the CALorimetric Electron Telescope (CALET) experiment on board the International Space Station. We use an unsupervised machine learning technique called Self‐Organizing‐Maps (SOM) to automatically detect and then classify relativistic electron events observed by the two scintillator layers at the top of the apparatus, sensitive to electrons with energies >1.5 MeV and >3.4 MeV, respectively. We calculate the power spectral density (PSD) of the count rates observed by both sensors and use them as an input for the SOM. The SOM technique groups the PSDs by their similarity, resulting in a classification of relativistic electron events by the periodicity of the observed precipitation. We investigate the L‐shell and magnetic local time distribution of the resulting classification, and energy spectral index associated with the observations. Clear precipitation patterns are observed and compared to past precipitation categorization attempts as well as known distributions of various scattering mechanisms. The classification reveals features through the sorting of the variability of the rapid precipitation, allowing the identification of different precipitation populations with varying properties.
Advancing insights into in vivo meningeal lymphatic vessels with stereoscopic wide-field photoacoustic microscopy
Authors: Yang Fei , Wang Zhiyang , Shi Wenbin , Wang Miao , Ma Rui , Zhang Wuyu , Li Xipeng , Wang Erqi , Xie Wenjie , Zhang Zhan , Shen Qi , Zhou Feifan , Yang Sihua
Published: April 2024

Meningeal lymphatic vessels (mLVs) play a pivotal role in regulating metabolic waste from cerebrospinal fluid (CSF). However, the current limitations in field of view and resolution of existing imaging techniques impede understanding the stereoscopic morphology and dynamic behavior of mLVs in vivo. Here, we utilized dual-contrast functional photoacoustic microscopy to achieve wide-field intravital imaging of the lymphatic system, including mLVs and glymphatic pathways. The stereoscopic photoacoustic microscopy based on opto-acoustic confocal features has a depth imaging capability of 3.75 mm, facilitating differentiation between mLVs on the meninges and glymphatic pathways within the brain parenchyma. Subsequently, using this imaging technique, we were able to visualize the dynamic drainage of mLVs and identify a peak drainage period occurring around 20–40 min after injection, along with determining the flow direction from CSF to lymph nodes. Inspiringly, in the Alzheimer’s disease (AD) mouse model, we observed that AD mice exhibit a ~ 70% reduction in drainage volume of mLVs compared to wild-type mice. With the development of AD, there is be continued decline in mLVs drainage volume. This finding clearly demonstrates that the AD mouse model has impaired CSF drainage. Our study opens up a horizon for understanding the brain’s drainage mechanism and dissecting mLVs-associated neurological disorders.
Bile acid metabolism and signaling in health and disease: molecular mechanisms and therapeutic targets
Authors: Fleishman Joshua S. , Kumar Sunil
Published: April 2024

Bile acids, once considered mere dietary surfactants, now emerge as critical modulators of macronutrient (lipid, carbohydrate, protein) metabolism and the systemic pro-inflammatory/anti-inflammatory balance. Bile acid metabolism and signaling pathways play a crucial role in protecting against, or if aberrant, inducing cardiometabolic, inflammatory, and neoplastic conditions, strongly influencing health and disease. No curative treatment exists for any bile acid influenced disease, while the most promising and well-developed bile acid therapeutic was recently rejected by the FDA. Here, we provide a bottom-up approach on bile acids, mechanistically explaining their biochemistry, physiology, and pharmacology at canonical and non-canonical receptors. Using this mechanistic model of bile acids, we explain how abnormal bile acid physiology drives disease pathogenesis, emphasizing how ceramide synthesis may serve as a unifying pathogenic feature for cardiometabolic diseases. We provide an in-depth summary on pre-existing bile acid receptor modulators, explain their shortcomings, and propose solutions for how they may be remedied. Lastly, we rationalize novel targets for further translational drug discovery and provide future perspectives. Rather than dismissing bile acid therapeutics due to recent setbacks, we believe that there is immense clinical potential and a high likelihood for the future success of bile acid therapeutics.
MiR-134-5p inhibits the malignant phenotypes of osteosarcoma via ITGB1/MMP2/PI3K/Akt pathway
Authors: Yan Lei , Zhou Ruhao , Feng Yi , Li Ruoqi , Zhang Long , Pan Yongchun , Qiao Xiaochen , Li Pengcui , Wei Xiaochun , Xu Chaojian , Li Yuan , Niu Xiaochen , Sun Xiaojuan , Lv Zhi , Tian Zhi
Published: April 2024

Micro RNAs (miRs) have been implicated in various tumorigenic processes. Osteosarcoma (OS) is a primary bone malignancy seen in adolescents. However, the mechanism of miRs in OS has not been fully demonstrated yet. Here, miR-134-5p was found to inhibit OS progression and was also expressed at significantly lower levels in OS tissues and cells relative to normal controls. miR-134-5p was found to reduce vasculogenic mimicry, proliferation, invasion, and migration of OS cells, with miR-134-5p knockdown having the opposite effects. Mechanistically, miR-134-5p inhibited expression of the ITGB1/MMP2/PI3K/Akt axis, thus reducing the malignant features of OS cells. In summary, miR-134-5p reduced OS tumorigenesis by modulation of the ITGB1/MMP2/PI3K/Akt axis, suggesting the potential for using miR-134-5p as a target for treating OS.
Group 3 medulloblastoma transcriptional networks collapse under domain specific EP300/CBP inhibition
Authors: Shendy Noha A. M. , Bikowitz Melissa , Sigua Logan H. , Zhang Yang , Mercier Audrey , Khashana Yousef , Nance Stephanie , Liu Qi , Delahunty Ian M. , Robinson Sarah , Goel Vanshita , Rees Matthew G. , Ronan Melissa A. , Wang Tingjian , Kocak Mustafa , Roth Jennifer A. , Wang Yingzhe , Freeman Burgess B. , Orr Brent A. , Abraham Brian J. , Roussel Martine F. , Schonbrunn Ernst , Qi Jun , Durbin Adam D.
Published: April 2024

Chemical discovery efforts commonly target individual protein domains. Many proteins, including the EP300/CBP histone acetyltransferases (HATs), contain several targetable domains. EP300/CBP are critical gene-regulatory targets in cancer, with existing high potency inhibitors of either the catalytic HAT domain or protein-binding bromodomain (BRD). A domain-specific inhibitory approach to multidomain-containing proteins may identify exceptional-responding tumor types, thereby expanding a therapeutic index. Here, we discover that targeting EP300/CBP using the domain-specific inhibitors, A485 (HAT) or CCS1477 (BRD) have different effects in select tumor types. Group 3 medulloblastoma (G3MB) cells are especially sensitive to BRD, compared with HAT inhibition. Structurally, these effects are mediated by the difluorophenyl group in the catalytic core of CCS1477. Mechanistically, bromodomain inhibition causes rapid disruption of genetic dependency networks that are required for G3MB growth. These studies provide a domain-specific structural foundation for drug discovery efforts targeting EP300/CBP and identify a selective role for the EP300/CBP bromodomain in maintaining genetic dependency networks in G3MB.
The gut commensal Blautia maintains colonic mucus function under low-fiber consumption through secretion of short-chain fatty acids
Authors: Holmberg Sandra M. , Feeney Rachel H. , Prasoodanan P.K. Vishnu , Puértolas-Balint Fabiola , Singh Dhirendra K. , Wongkuna Supapit , Zandbergen Lotte , Hauner Hans , Brandl Beate , Nieminen Anni I. , Skurk Thomas , Schroeder Bjoern O.
Published: April 2024

Beneficial gut bacteria are indispensable for developing colonic mucus and fully establishing its protective function against intestinal microorganisms. Low-fiber diet consumption alters the gut bacterial configuration and disturbs this microbe-mucus interaction, but the specific bacteria and microbial metabolites responsible for maintaining mucus function remain poorly understood. By using human-to-mouse microbiota transplantation and ex vivo analysis of colonic mucus function, we here show as a proof-of-concept that individuals who increase their daily dietary fiber intake can improve the capacity of their gut microbiota to prevent diet-mediated mucus defects. Mucus growth, a critical feature of intact colonic mucus, correlated with the abundance of the gut commensal Blautia, and supplementation of Blautia coccoides to mice confirmed its mucus-stimulating capacity. Mechanistically, B. coccoides stimulated mucus growth through the production of the short-chain fatty acids propionate and acetate via activation of the short-chain fatty acid receptor Ffar2, which could serve as a new target to restore mucus growth during mucus-associated lifestyle diseases.
Functional connectivity development along the sensorimotor-association axis enhances the cortical hierarchy
Authors: Luo Audrey C. , Sydnor Valerie J. , Pines Adam , Larsen Bart , Alexander-Bloch Aaron F. , Cieslak Matthew , Covitz Sydney , Chen Andrew A. , Esper Nathalia Bianchini , Feczko Eric , Franco Alexandre R. , Gur Raquel E. , Gur Ruben C. , Houghton Audrey , Hu Fengling , Keller Arielle S. , Kiar Gregory , Mehta Kahini , Salum Giovanni A. , Tapera Tinashe , Xu Ting , Zhao Chenying , Salo Taylor , Fair Damien A. , Shinohara Russell T. , Milham Michael P. , Satterthwaite Theodore D.
Published: April 2024

Human cortical maturation has been posited to be organized along the sensorimotor-association axis, a hierarchical axis of brain organization that spans from unimodal sensorimotor cortices to transmodal association cortices. Here, we investigate the hypothesis that the development of functional connectivity during childhood through adolescence conforms to the cortical hierarchy defined by the sensorimotor-association axis. We tested this pre-registered hypothesis in four large-scale, independent datasets (total n = 3355; ages 5–23 years): the Philadelphia Neurodevelopmental Cohort (n = 1207), Nathan Kline Institute-Rockland Sample (n = 397), Human Connectome Project: Development (n = 625), and Healthy Brain Network (n = 1126). Across datasets, the development of functional connectivity systematically varied along the sensorimotor-association axis. Connectivity in sensorimotor regions increased, whereas connectivity in association cortices declined, refining and reinforcing the cortical hierarchy. These consistent and generalizable results establish that the sensorimotor-association axis of cortical organization encodes the dominant pattern of functional connectivity development.
WindSeer: real-time volumetric wind prediction over complex terrain aboard a small uncrewed aerial vehicle
Authors: Achermann Florian , Stastny Thomas , Danciu Bogdan , Kolobov Andrey , Chung Jen Jen , Siegwart Roland , Lawrance Nicholas
Published: April 2024

Real-time high-resolution wind predictions are beneficial for various applications including safe crewed and uncrewed aviation. Current weather models require too much compute and lack the necessary predictive capabilities as they are valid only at the scale of multiple kilometers and hours – much lower spatial and temporal resolutions than these applications require. Our work demonstrates the ability to predict low-altitude time-averaged wind fields in real time on limited-compute devices, from only sparse measurement data. We train a deep neural network-based model, WindSeer, using only synthetic data from computational fluid dynamics simulations and show that it can successfully predict real wind fields over terrain with known topography from just a few noisy and spatially clustered wind measurements. WindSeer can generate accurate predictions at different resolutions and domain sizes on previously unseen topography without retraining. We demonstrate that the model successfully predicts historical wind data collected by weather stations and wind measured by drones during flight.
Vegetation dieback in the Mississippi River Delta triggered by acute drought and chronic relative sea-level rise
Authors: Elsey-Quirk Tracy , Lynn Austin , Jacobs Michael Derek , Diaz Rodrigo , Cronin James T. , Wang Lixia , Huang Haosheng , Justic Dubravko
Published: April 2024

Vegetation dieback and recovery may be dependent on the interplay between infrequent acute disturbances and underlying chronic stresses. Coastal wetlands are vulnerable to the chronic stress of sea-level rise, which may affect their susceptibility to acute disturbance events. Here, we show that a large-scale vegetation dieback in the Mississippi River Delta was precipitated by salt-water incursion during an extreme drought in the summer of 2012 and was most severe in areas exposed to greater flooding. Using 16 years of data (2007–2022) from a coastwide network of monitoring stations, we show that the impacts of the dieback lasted five years and that recovery was only partial in areas exposed to greater inundation. Dieback marshes experienced an increase in percent time flooded from 43% in 2007 to 75% in 2022 and a decline in vegetation cover and species richness over the same period. Thus, while drought-induced high salinities and soil saturation triggered a significant dieback event, the chronic increase in inundation is causing a longer-term decline in cover, more widespread losses, and reduced capacity to recover from acute stressors. Overall, our findings point to the importance of mitigating the underlying stresses to foster resilience to both acute and persistent causes of vegetation loss.
Cortex-wide transcranial localization microscopy with fluorescently labeled red blood cells
Authors: Zhou Quanyu , Glück Chaim , Tang Lin , Glandorf Lukas , Droux Jeanne , El Amki Mohamad , Wegener Susanne , Weber Bruno , Razansky Daniel , Chen Zhenyue
Published: April 2024

Large-scale imaging of brain activity with high spatio-temporal resolution is crucial for advancing our understanding of brain function. The existing neuroimaging techniques are largely limited by restricted field of view, slow imaging speed, or otherwise do not have the adequate spatial resolution to capture brain activities on a capillary and cellular level. To address these limitations, we introduce fluorescence localization microscopy aided with sparsely-labeled red blood cells for cortex-wide morphological and functional cerebral angiography with 4.9 µm spatial resolution and 1 s temporal resolution. When combined with fluorescence calcium imaging, the proposed method enables extended recordings of stimulus-evoked neuro-vascular changes in the murine brain while providing simultaneous multiparametric readings of intracellular neuronal activity, blood flow velocity/direction/volume, and vessel diameter. Owing to its simplicity and versatility, the proposed approach will become an invaluable tool for deciphering the regulation of cortical microcirculation and neurovascular coupling in health and disease.
Group IV topological quantum alloy and the role of short-range order: the case of Ge-rich Ge1–xPbx
Authors: Liang Yunfan , Chen Shunda , Jin Xiaochen , West Damien , Yu Shui-Qing , Li Tianshu , Zhang Shengbai
Published: April 2024

Despite the explosion of interest in topological materials over the last decades, their applications remain limited due to challenges in growth and incorporation with today’s microelectronics. As a potential bridge to close this gap, we investigate the group-IV alloy Ge1–xPbx, in the Ge-rich condition using density functional theory and show that relatively low concentrations of Pb (~9.4%) can lead to a topological phase transition. Furthermore, the calculation of the Z2 invariant for both the random alloy and the alloy with short-range order (SRO) indicate that the topological phase of the material can be directly modified by the degree of SRO. These findings are understood in terms of local structural relaxation, which decreases the bandgap in the random alloy. However, in the SRO case, the mutual avoidance of Pb leads to minimal structural relaxation, alleviating strain. Our findings not only highlight the emerging importance of SRO in alloy properties but also indicate the possibility of constructing topological interfaces between materials of identical composition (and nominally identical structure). Moreover, they uncover a viable avenue toward the monolithic integration of quantum materials with today’s semiconductor industry.
Full-length transcriptome analysis of a bloom-forming dinoflagellate Prorocentrum shikokuense (Dinophyceae)
Authors: Pan Xiaohui , Liu Hang , Feng Leili , Zong Yanan , Cao Zihao , Guo Li , Yang Guanpin
Published: April 2024

Prorocentrum shikokuense (formerly P. donghaiense) is a pivotal dinoflagellate species associating with the HABs in the East China Sea. The complexity of its large nuclear genome hindered us from understanding its genomic characteristics. Full-length transcriptome sequencing offers a practical solution to decipher the physiological mechanisms of a species without the reference genome. In this study, we employed single-molecule real-time (SMRT) sequencing technology to sequence the full-length transcriptome of Prorocentrum shikokuense. We successfully generated 41.73 Gb of clean SMRT sequencing reads and isolated 105,249 non-redundant full-length non-chimeric reads. Our trial has led to the identification of 11,917 long non-coding RNA transcripts, 514 alternative splicing events, 437 putative transcription factor genes from 17 TF gene families, and 34,723 simple sequence repeats. Additionally, a total of 78,265 open reading frames were identified, of them 15,501 were the protein coding sequences. This dataset is valuable for annotating P. shikokuense genome, and will contribute significantly to the in-depth studies on the molecular mechanisms underlining the dinoflagellate bloom formation.
A real-world pharmacovigilance study of amivantamab-related cardiovascular adverse events based on the FDA adverse event reporting system (FAERS) database
Authors: Sun Rui , Ning Zhen , Qin Henan , Zhang Wenhe , Teng Yibin , Jin Chenxing , Liu Jiwei , Wang Aman
Published: April 2024

Amivantamab is the first dual-specificity antibody targeting EGFR and MET, which is approved for the treatment of locally advanced or metastatic non-small cell lung cancer (NSCLC) with EGFR exon 20 insertion mutations. Cardiovascular toxicities related to amivantamab have not been reported in the CHRYSALIS study. However, the occurrence of cardiovascular events in the real world is unknown. To comprehensively investigate the clinical characteristics, onset times, and outcomes of cardiovascular toxicities associated with amivantamab. The Food and Drug Administration Adverse Event Reporting System (FAERS) database from 1st quarter of 2019 to the 2nd quarter of 2023 was retrospectively queried to extract reports of cardiovascular adverse events (AEs) associated with amivantamab. To perform disproportionality analysis, the reporting odds ratios (RORs) and information components (ICs) were calculated with statistical shrinkage trans-formation formulas and a lower limit of the 95% confidence interval (CI) for ROR (ROR025) > 1 or IC (IC025) > 0 with at least 3 reports was considered statistically significant. A total of 20,270,918 eligible records were identified, among which 98 records were related to cardiovascular events associated with amivantamab. 4 categories of cardiovascular events exhibited positive signals: venous thrombotic diseases, abnormal blood pressure, arrhythmia, and pericardial effusion. Venous thrombotic diseases and abnormal blood pressure were the two most common signals. The median time to onset (TTO) for cardiovascular AEs was 33 days. The cumulative incidence within 90 days was 100% for cardiac failure, 75% for stroke, 63.16% for arrhythmia, 50% for sudden death, and 44.18% for venous thrombotic diseases. Death accounted for 16.3% of all cardiovascular AEs associated with amivantamab. The mortality rates for Major Adverse Cardiovascular Events (MACE) were up to 60%. This pharmacovigilance study systematically explored the cardiovascular adverse events of amivantamab and provided new safety signals based on past safety information. Early and intensified monitoring is crucial, and attention should be directed towards high-risk signals.
Fabrication of pure Bi2WO6 and Bi2WO6/MWCNTs nanocomposite as potential antibacterial and anticancer agents
Authors: Rhoomi Zeena R. , Ahmed Duha S. , Jabir Majid S. , Qadeer Abdul , Ismael Alaa B. , Swelum Ayman A.
Published: April 2024

An essential research area for scientists is the development of high-performing, inexpensive, non-toxic antibacterial materials that prevent the transfer of bacteria. In this study, pure Bi2WO6 and Bi2WO6/MWCNTs nanocomposite were prepared by hydrothermal method. A series of characterization results by using XRD FTIR, Raman, FESEM, TEM, and EDS analyses, reveal the formation of orthorhombic nanoflakes Bi2WO6 by the addition of NaOH and pH adjustment to 7. Compared to pure Bi2WO6, the Bi2WO6/MWCNTs nanocomposite exhibited that CNTs are efficiently embedded into the structure of Bi2WO6 which results in charge transfer between metal ion electrons and the conduction or valence band of Bi2WO6 and MWCNTs and result in shifting to longer wavelength as shown in UV–visible and PL. The results confirmed that MWCNTs are stuck to the surface of the microflowers, and some of them embedded inside the Bi2WO6 nanoflakes without affecting the structure of Bi2WO6 nanoflakes as demonstrated by TEM. In addition, Pure Bi2WO6 and the Bi2WO6/MWCNTs nanocomposite were tested against P. mirabilis and S. mutans., confirming the effect of addition MWCNTs materials had better antibacterial activity in opposition to both bacterial strains than pure Bi2WO6. Besides, pure Bi2WO6 and the Bi2WO6/MWCNTs nanocomposite tested for cytotoxicity against lung MTT test on Hep-G2 liver cancer cells, and flow-cytometry. Results indicated that pure Bi2WO6 and the Bi2WO6/MWCNTs nanocomposite have significant anti-cancer efficacy against Hep-G2 cells in vitro. In addition, the findings demonstrated that Bi2WO6 and Bi2WO6/MWCNTs triggered cell death via increasing ROS. Based on these findings, it appears that pure Bi2WO6 and the Bi2WO6/MWCNTs nanocomposite have the potential to be developed as nanotherapeutics for the treatment of bacterial infections, and liver cancer.
Real space iterative reconstruction for vector tomography (RESIRE-V)
Authors: Pham Minh , Lu Xingyuan , Rana Arjun , Osher Stanley , Miao Jianwei
Published: April 2024

Tomography has had an important impact on the physical, biological, and medical sciences. To date, most tomographic applications have been focused on 3D scalar reconstructions. However, in some crucial applications, vector tomography is required to reconstruct 3D vector fields such as the electric and magnetic fields. Over the years, several vector tomography methods have been developed. Here, we present the mathematical foundation and algorithmic implementation of REal Space Iterative REconstruction for Vector tomography, termed RESIRE-V. RESIRE-V uses multiple tilt series of projections and iterates between the projections and a 3D reconstruction. Each iteration consists of a forward step using the Radon transform and a backward step using its transpose, then updates the object via gradient descent. Incorporating with a 3D support constraint, the algorithm iteratively minimizes an error metric, defined as the difference between the measured and calculated projections. The algorithm can also be used to refine the tilt angles and further improve the 3D reconstruction. To validate RESIRE-V, we first apply it to a simulated data set of the 3D magnetization vector field, consisting of two orthogonal tilt series, each with a missing wedge. Our quantitative analysis shows that the three components of the reconstructed magnetization vector field agree well with the ground-truth counterparts. We then use RESIRE-V to reconstruct the 3D magnetization vector field of a ferromagnetic meta-lattice consisting of three tilt series. Our 3D vector reconstruction reveals the existence of topological magnetic defects with positive and negative charges. We expect that RESIRE-V can be incorporated into different imaging modalities as a general vector tomography method. To make the algorithm accessible to a broad user community, we have made our RESIRE-V MATLAB source codes and the data freely available athttps://github.com/minhpham0309/RESIRE-V.
Increasing obsidian diversity during the Chalcolithic Period at Yeghegis-1 Rockshelter (Armenia) reveals shifts in land use and social networks
Authors: Frahm Ellery , Saribekyan Mariam , Mkrtchyan Satenik , Furquim Laura , Avagyan Ara , Sahakyan Lilit , Azatyan Karen , Roberts Patrick , Fernandes Ricardo , Yepiskoposyan Levon , Amano Noel , Antonosyan Mariya
Published: April 2024

The newly excavated rockshelter of Yeghegis-1 in Armenia reflects an occupation of five centuries, as attested by radiocarbon dates from ∼ 4100 to 4000 cal BCE in the lowest layer to ∼ 3600–3500 cal BCE at the top. It is a partially collapsed cave in which pastoralists, we hypothesize, wintered with their herds. The stone tool assemblage is predominantly obsidian (92.1%), despite the shelter being > 60 km on foot from the nearest sources. We use obsidian sourcing to investigate two purported trends in the Southern Caucasus during the Chalcolithic Period: (1) occupation of more varied high-altitude environments and (2) more expansive social networks. Our data show both trends were dynamic phenomena. There was a greater balance in use of the nearest pasturelands over time, perhaps linked to risk management and/or resource sustainability. During later occupations, artifacts from distant sources reveal more extensive connections. This increase in connectivity likely played a central role in the shifts in societal complexity that gave rise to widely shared material culture throughout the Armenian Highlands around the start of the Early Bronze Age. In such a model, greater social connectivity becomes a key mechanism for, rather than a product of, the spread of cultural and/or technological innovations.
Insights into the genetic architecture of cerebellar lobules derived from the UK Biobank
Authors: Carrión-Castillo Amaia , Boeckx Cedric
Published: April 2024

In this work we endeavor to further understand the genetic architecture of the cerebellum by examining the genetic underpinnings of the different cerebellar lob(ul)es, identifying their genetic relation to cortical and subcortical regions, as well as to psychiatric disorders, as well as traces of their evolutionary trajectories. We confirm the moderate heritability of cerebellar volumes, and reveal genetic clustering and variability across their different substructures, which warranted a detailed analysis using this higher structural resolution. We replicated known genetic correlations with several subcortical volumes, and report new cortico-cerebellar genetic correlations, including negative genetic correlations between anterior cerebellar lobules and cingulate, and positive ones between lateral Crus I and lobule VI with cortical measures in the fusiform region. Heritability partitioning for evolutionary annotations highlighted that the vermis of Crus II has depleted heritability in genomic regions of “archaic introgression deserts”, but no enrichment/depletion of heritability in any other cerebellar regions. Taken together, these findings reveal novel insights into the genetic underpinnings of the different cerebellar lobules.
Investigations on Xenopus laevis body composition and feeding behavior in a laboratory setting
Authors: Böswald Linda F. , Matzek Dana , von La Roche Dominik , Stahr Bianca , Bawidamann Pascal , Popper Bastian
Published: April 2024

The African clawed frog, Xenopus laevis, has been used as a laboratory animal for decades in many research areas. However, there is a lack of knowledge about the nutritional physiology of this amphibian species and the feeding regimen is not standardized. The aim of the present study was to get more insights into the nutrient metabolism and feeding behavior of the frogs. In Trial 1, adult female X. laevis were fed either a Xenopus diet or a fish feed. After 4 weeks, they were euthanized, weighed, measured for morphometrics and dissected for organ weights and whole-body nutrient analysis. There were no significant differences between the diet groups regarding the allometric data and nutrient contents. The ovary was the major determinant of body weight. Body fat content increased with body weight as indicator of energy reserves. In Trial 2, 40 adult female frogs were monitored with a specifically developed digital tracking system to generate heat-maps of their activity before and up to 25 min after a meal. Three diets (floating, sinking, floating & sinking) were used. The main feed intake activity was fanning the feed into the mouth, peaking until 20 min after the meal. The different swimming characteristics of the diets thereby influenced the activity of the animals. Our dataset helps to adjust the feeding needs to the physical composition and also to meet the natural behavioral patterns of feed intake as a prerequisite of animal wellbeing and animal welfare in a laboratory setting.
Breakthrough electroneutron multi-response miniature dosimetry/spectrometry in medical accelerator
Authors: Sohrabi Mehdi , Malekitakbolagh Maryam , Nedaei Hasan Ali
Published: April 2024

Breakthrough multi-response miniature dosimetry/spectrometry of electroneutrons (EN) was made on surface and in-depths of whole-body polyethylene phantom under 10 cm × 10 cm electron beam of 20 MV Varian Clinac 2100C electron medical accelerator commonly applied for prostate treatment. While dosimetry/spectrometry of photoneutrons (PN) has been well characterized for decades, those of ENs lagged behind due to very low EN reaction cross section and lack of sensitive neutron dosimeters/spectrometers meeting neutron dosimetry requirements. Recently, Sohrabi “miniature neutron dosimeter/spectrometer” and “Stripe polycarbonate dosimeter” have broken this barrier and determined seven EN ambient dose equivalent (ENDE) (µSv.Gy–1) responses from electron beam and from albedo ENs including beam thermal (21 ± 2.63), albedo thermal (43 ± 3.70), total thermal (64 ± 6.33), total epithermal (32 ± 3.90), total fast (112.00), total thermal + epithermal (l96 ± 10), and total thermal + epithermal + fast (208 ± 10.23) ENs. Having seven ENDE responses of this study and seven PNDE responses of previous study with the same accelerator obtained at identical conditions by the same principle author provided the opportunity to compare the two sets of responses. The PNDE (µSv.Gy–1) responses have comparatively higher values and 22.60 times at isocenter which provide for the first time breakthrough ENDE responses not yet reported in any studies before worldwide.
Immunotherapy and drug sensitivity predictive roles of a novel prognostic model in hepatocellular carcinoma
Authors: Gao Xiaoge , Ren Xin , Wang Feitong , Ren Xinxin , liu Mengchen , Cui Guozhen , Liu Xiangye
Published: April 2024

Hepatocellular carcinoma (HCC) is one of the most significant causes of cancer-related deaths in the worldwide. Currently, predicting the survival of patients with HCC and developing treatment drugs still remain a significant challenge. In this study, we employed prognosis-related genes to develop and externally validate a predictive risk model. Furthermore, the correlation between signaling pathways, immune cell infiltration, immunotherapy response, drug sensitivity, and risk score was investigated using different algorithm platforms in HCC. Our results showed that 11 differentially expressed genes including UBE2C, PTTG1, TOP2A, SPP1, FCN3, SLC22A1, ADH4, CYP2C8, SLC10A1, F9, and FBP1 were identified as being related to prognosis, which were integrated to construct a prediction model. Our model could accurately predict patients’ overall survival using both internal and external datasets. Moreover, a strong correlation was revealed between the signaling pathway, immune cell infiltration, immunotherapy response, and risk score. Importantly, a novel potential drug candidate for HCC treatment was discovered based on the risk score and also validated through ex vivo experiments. Our finds offer a novel perspective on prognosis prediction and drug exploration for cancer patients.
Regional food self-sufficiency potential in the European Alpine space
Authors: Pecher Caroline , Marsoner Thomas , Tasser Erich
Published: April 2024

The sustainability of the food system needs to be improved, including shortening supply chains and promoting the consumption of regional food. Here, we explore the current potential for regional food self-sufficiency in the European Alpine space by calculating the current regional food/feed energy balance, deriving the regional per capita land footprint based on current food/feed consumption rates, and modelling the current potential for regional food/feed self-sufficiency. We show that 59% of the 560 Pcal of energy currently available in the study area comes from domestic production, and almost 60% of the energy is used for livestock consumption, with high regional variability. The resulting land footprints range from 2301 to 2975 m2 cap−1 y−1. Taking into account changes in cropping patterns, partial intensification, but no expansion of agricultural land, the European Alpine space could produce 89% of its current food demand domestically, with high regional variability due to population density, availability of agricultural land, crop yields, climatic conditions and dietary habits. These findings highlight the potential and limitations of regional mountain food systems and call for new strategies to improve sustainability. Reducing the current high consumption of animal products would reduce the land footprint and increase the potential for food self-sufficiency.
Analyzing the effect of public private partnership mode on sewage treatment in China
Authors: Wen Xin , Meng Fange , Li Shiheng
Published: April 2024

The public–private partnership (PPP) mode is one of the main ways to promote environmental governance through marketization in the sewage treatment industry. This mode is crucial for environmental protection and livelihood improvement. In order to investigate the impact of PPP mode on sewage treatment, the influence of financial development and the government–business relationship on the effectiveness of sewage treatment under PPP mode, and the role of government in this context, an empirical model is established. To achieve this, data from 284 prefecture-level and above cities in China from 2009 to 2017 has been selected as research samples. The total amount of regional sewage treatment PPP projects is used as the proxy variable for participation in the PPP mode. The findings reveal that the PPP mode of sewage treatment effectively reduces the intensity and amount of sewage discharge. Moreover, the results indicate that a higher level of financial development and a more perfect financial system are associated with better sewage treatment effects under the PPP mode. Similarly, a more harmonious government–business relationship and a higher health index of this relationship correspond to improved sewage treatment effects under the PPP mode. The government should actively enhance government transparency, formulate appropriate corporate taxes and fees, clarify the responsibilities and obligations of the government and enterprises, and optimize the business environment in order to optimize the sewage treatment effect of the PPP mode.
Estimating SARS-CoV-2 infection probabilities with serological data and a Bayesian mixture model
Authors: Glemain Benjamin , de Lamballerie Xavier , Zins Marie , Severi Gianluca , Touvier Mathilde , Deleuze Jean-François ,   SAPRIS-SERO study group, Carrat Fabrice , Ancel Pierre-Yves , Charles Marie-Aline , Severi Gianluca , Touvier Mathilde , Zins Marie , Kab Sofiane , Renuy Adeline , Le-Got Stephane , Ribet Celine , Pellicer Mireille , Wiernik Emmanuel , Goldberg Marcel , Artaud Fanny , Gerbouin-Rérolle Pascale , Enguix Mélody , Laplanche Camille , Gomes-Rima Roselyn , Hoang Lyan , Correia Emmanuelle , Barry Alpha Amadou , Senina Nadège , Allegre Julien , Szabo de Edelenyi Fabien , Druesne-Pecollo Nathalie , Esseddik Younes , Hercberg Serge , Deschasaux Mélanie , Charles Marie-Aline , Benhammou Valérie , Ritmi Anass , Marchand Laetitia , Zaros Cecile , Lordmi Elodie , Candea Adriana , de Visme Sophie , Simeon Thierry , Thierry Xavier , Geay Bertrand , Dufourg Marie-Noelle , Milcent Karen , Rahib Delphine , Lydie Nathalie , Lusivika-Nzinga Clovis , Pannetier Gregory , Lapidus Nathanael , Goderel Isabelle , Dorival Céline , Nicol Jérôme , Robineau Olivier , Lai Cindy , Belhadji Liza , Esperou Hélène , Couffin-Cadiergues Sandrine , Gagliolo Jean-Marie , Blanché Hélène , Sébaoun Jean-Marc , Beaudoin Jean-Christophe , Gressin Laetitia , Morel Valérie , Ouili Ouissam , Deleuze Jean-François , Ninove Laetitia , Priet Stéphane , Villarroel Paola Mariela Saba , Fourié Toscane , Ali Souand Mohamed , Amroun Abdenour , Seston Morgan , Ayhan Nazli , Pastorino Boris , de Lamballerie Xavier , Lapidus Nathanaël , Carrat Fabrice
Published: April 2024

The individual results of SARS-CoV-2 serological tests measured after the first pandemic wave of 2020 cannot be directly interpreted as a probability of having been infected. Plus, these results are usually returned as a binary or ternary variable, relying on predefined cut-offs. We propose a Bayesian mixture model to estimate individual infection probabilities, based on 81,797 continuous anti-spike IgG tests from Euroimmun collected in France after the first wave. This approach used serological results as a continuous variable, and was therefore not based on diagnostic cut-offs. Cumulative incidence, which is necessary to compute infection probabilities, was estimated according to age and administrative region. In France, we found that a “negative” or a “positive” test, as classified by the manufacturer, could correspond to a probability of infection as high as 61.8% or as low as 67.7%, respectively. “Indeterminate” tests encompassed probabilities of infection ranging from 10.8 to 96.6%. Our model estimated tailored individual probabilities of SARS-CoV-2 infection based on age, region, and serological result. It can be applied in other contexts, if estimates of cumulative incidence are available.
An efficient lightweight network for image denoising using progressive residual and convolutional attention feature fusion
Authors: Tiantian Wang , Hu Zhihua , Guan Yurong
Published: April 2024

While deep learning has become the go-to method for image denoising due to its impressive noise removal capabilities, excessive network depth often plagues existing approaches, leading to significant computational burdens. To address this critical bottleneck, we propose a novel lightweight progressive residual and attention mechanism fusion network that effectively alleviates these limitations. This architecture tackles both Gaussian and real-world image noise with exceptional efficacy. Initiated through dense blocks (DB) tasked with discerning the noise distribution, this approach substantially reduces network parameters while comprehensively extracting local image features. The network then adopts a progressive strategy, whereby shallow convolutional features are incrementally integrated with deeper features, establishing a residual fusion framework adept at extracting encompassing global features relevant to noise characteristics. The process concludes by integrating the output feature maps from each DB and the robust edge features from the convolutional attention feature fusion module (CAFFM). These combined elements are then directed to the reconstruction layer, ultimately producing the final denoised image. Empirical analyses conducted in environments characterized by Gaussian white noise and natural noise, spanning noise levels 15–50, indicate a marked enhancement in performance. This assertion is quantitatively corroborated by increased average values in metrics such as Peak Signal-to-Noise Ratio (PSNR), Structural Similarity Index (SSIM), and Feature Similarity Index for Color images (FSIMc), outperforming the outcomes of more than 20 existing methods across six varied datasets. Collectively, the network delineated in this research exhibits exceptional adeptness in image denoising. Simultaneously, it adeptly preserves essential image features such as edges and textures, thereby signifying a notable progression in the domain of image processing. The proposed model finds applicability in a range of image-centric domains, encompassing image processing, computer vision, video analysis, and pattern recognition.
A blind image super-resolution network guided by kernel estimation and structural prior knowledge
Authors: Zhang Jiajun , Zhou Yuanbo , Bi Jiang , Xue Yuyang , Deng Wei , He Wenlin , Zhao Tao , Sun Kai , Tong Tong , Gao Qinquan , Zhang Qing
Published: April 2024

The goal of blind image super-resolution (BISR) is to recover the corresponding high-resolution image from a given low-resolution image with unknown degradation. Prior related research has primarily focused effectively on utilizing the kernel as prior knowledge to recover the high-frequency components of image. However, they overlooked the function of structural prior information within the same image, which resulted in unsatisfactory recovery performance for textures with strong self-similarity. To address this issue, we propose a two stage blind super-resolution network that is based on kernel estimation strategy and is capable of integrating structural texture as prior knowledge. In the first stage, we utilize a dynamic kernel estimator to achieve degradation presentation embedding. Then, we propose a triple path attention groups consists of triple path attention blocks and a global feature fusion block to extract structural prior information to assist the recovery of details within images. The quantitative and qualitative results on standard benchmarks with various degradation settings, including Gaussian8 and DIV2KRK, validate that our proposed method outperforms the state-of-the-art methods in terms of fidelity and recovery of clear details. The relevant code is made available on thislinkas open source.
Hydrous mantle plume promoted the generation of continental flood basalts in the Tarim large igneous province
Authors: Bi Yao , Chen Huan , Hanski Eero , Kuritani Takeshi , Wu Hong-Xiang , Zhang Feng-Qi , Liu Jia , Gu Xiao-Yan , Xia Qun-Ke
Published: April 2024

Recent research on the water content of large igneous provinces (LIPs) has revealed that water has a significant impact on the formation of LIPs. However, most studies focus on the water content of mafic–ultramafic rocks, while relatively little attention has been paid to the water content of continental flood basalts (CFB), which form the major part of LIPs and are characterized by huge volumes (> 1 × 105 km3) and short eruption times. Here, we determined water contents of clinopyroxene crystals from the Akesu diabase, which is co-genetic with flood basalts of the Tarim LIP in China. Based on these measurements, we obtained a water content of higher than 1.23 ± 0.49 wt.% for the parental magma to the Tarim CFB and a minimum water content of 1230 ± 490 ppm for the mantle source, thus indicating the presence of a hydrous mantle plume. Combined with previous studies, our results suggest that water plays a key role in the formation of the Tarim LIP. Additionally, the whole-rock compositions of the Akesu diabase indicate a contribution of pyroxenite in the mantle source. This is consistent with a model, in which water was brought into the Tarim mantle plume by a subducted oceanic plate that entered the deep mantle.