bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single-cell guided prenatal derivation of primary fetal epithelial organoids from human amniotic and tracheal fluids
Authors: Gerli Mattia Francesco Maria , Calà Giuseppe , Beesley Max Arran , Sina Beatrice , Tullie Lucinda , Sun Kylin Yunyan , Panariello Francesco , Michielin Federica , Davidson Joseph R. , Russo Francesca Maria , Jones Brendan C. , Lee Dani Do Hyang , Savvidis Savvas , Xenakis Theodoros , Simcock Ian C. , Straatman-Iwanowska Anna A. , Hirst Robert A. , David Anna L. , O’Callaghan Christopher , Olivo Alessandro , Eaton Simon , Loukogeorgakis Stavros P. , Cacchiarelli Davide , Deprest Jan , Li Vivian S. W. , Giobbe Giovanni Giuseppe , De Coppi Paolo 
Published: March 2024

Abstract
Isolation of tissue-specific fetal stem cells and derivation of primary organoids is limited to samples obtained from termination of pregnancies, hampering prenatal investigation of fetal development and congenital diseases. Therefore, new patient-specific in vitro models are needed. To this aim, isolation and expansion of fetal stem cells during pregnancy, without the need for tissue samples or reprogramming, would be advantageous. Amniotic fluid (AF) is a source of cells from multiple developing organs. Using single-cell analysis, we characterized the cellular identities present in human AF. We identified and isolated viable epithelial stem/progenitor cells of fetal gastrointestinal, renal and pulmonary origin. Upon culture, these cells formed clonal epithelial organoids, manifesting small intestine, kidney tubule and lung identity. AF organoids exhibit transcriptomic, protein expression and functional features of their tissue of origin. With relevance for prenatal disease modeling, we derived lung organoids from AF and tracheal fluid cells of congenital diaphragmatic hernia fetuses, recapitulating some features of the disease. AF organoids are derived in a timeline compatible with prenatal intervention, potentially allowing investigation of therapeutic tools and regenerative medicine strategies personalized to the fetus at clinically relevant developmental stages.
Fine-grained urban blue-green-gray landscape dataset for 36 Chinese cities based on deep learning network
Authors: Xu Zhiyu , Zhao Shuqing 
Published: March 2024

AbstractDetailed and accurate urban landscape mapping, especially for urban blue-green-gray (UBGG) continuum, is the fundamental first step to understanding human–nature coupled urban systems. Nevertheless, the intricate spatial heterogeneity of urban landscapes within cities and across urban agglomerations presents challenges for large-scale and fine-grained mapping. In this study, we generated a 3 m high-resolution UBGG landscape dataset (UBGG-3m) for 36 Chinese metropolises using a transferable multi-scale high-resolution convolutional neural network and 336 Planet images. To train the network for generalization, we also created a large-volume UBGG landscape sample dataset (UBGGset) covering 2,272 km2 of urban landscape samples at 3 m resolution. The classification results for five cities across diverse geographic regions substantiate the superior accuracy of UBGG-3m in both visual interpretation and quantitative evaluation (with an overall accuracy of 91.2% and FWIoU of 83.9%). Comparative analyses with existing datasets underscore the UBGG-3m’s great capability to depict urban landscape heterogeneity, providing a wealth of new data and valuable insights into the complex and dynamic urban environments in Chinese metropolises.
Identification of a CpG-based signature coupled with gene expression as prognostic indicators for melanoma: a preliminary study
Authors: Lin Zhen , Yang Liu 
Published: March 2024

AbstractDNA methylation is an important part of the genomic biology, which recently allowed the identification of key biomarkers for a variety of cancers, including cutaneous melanoma. Despite the current knowledge in cutaneous melanoma, there is a clear need for new efficient biomarkers in clinical application of detection. We use The Cancer Genome Atlas data as a training set and a multi-stage screening strategy to identify prognostic characteristics of melanoma based on DNA methylation. Three DNA methylation CpG sites were identified to be related to the overall survival in the skin cutaneous melanoma cohort. This signature was validated in two independent datasets from Gene Expression Omnibus. The stratified analysis by clinical stage, age, gender, and grade retained the statistical significance. The methylation signature was significantly correlated with immune cells and anti-tumor immune response. Moreover, gene expression corresponding to the candidate CpG locus was also significantly correlated with the survival rate of the patient. About 49% of the prognostic effects of methylation are mediated by affecting the expression of the corresponding genes. The prognostic characteristics of DNA methylation combined with clinical information provide a better prediction value tool for melanoma patients than the clinical information alone. However, more experiments are required to validate these findings. Overall, this signature presents a prospect of novel and wide-ranging applications for appropriate clinical adjuvant trails.
Structure and chronology of a star dune at Erg Chebbi, Morocco, reveals why star dunes are rarely recognised in the rock record
Authors: Bristow C. S. , Duller G. A. T. 
Published: March 2024

AbstractStar dunes are the tallest dunes on Earth and are amongst the larger and more spectacular aeolian landforms. Although they are widespread in modern sandy deserts, star dunes are rarely recognised in the rock record probably due to a lack of suitable sedimentary models. This paper presents a new sedimentary model for the structure of a star dune at Erg Chebbi in Morocco (Sahara Desert) on the basis of ground-penetrating radar (GPR) surveys. Individual sedimentary structures in star dunes are similar to those in linear or barchanoid dunes, likely leading to misidentification in the rock record. However, the suite of features described in this paper will permit identification of star dunes in future studies of the rock record. Optically stimulated luminescence (OSL) dating shows that accumulation of the Erg Chebbi star dune post-dates the end of the African Humid Period (AHP). At the base of the dune, there is an ~ 8000-year hiatus in the record. Since then, the dune has grown rapidly to create a 100 m high dune within the past 1000 years and is migrating towards the west. Changes in the cross-strata support the idea that star dune construction was accompanied by a change in the wind directions.
NRF2 activation ameliorates blood–brain barrier injury after cerebral ischemic stroke by regulating ferroptosis and inflammation
Authors: Fan Wei , Chen Hongping , Li Meng , Fan Xuehui , Jiang Fangchao , Xu Chen , Wang Yingju , Wei Wan , Song Jihe , Zhong Di , Li Guozhong 
Published: March 2024

AbstractArterial occlusion-induced ischemic stroke (IS) is a highly frequent stroke subtype. Nuclear factor erythroid 2-related factor 2 (NRF2) is a transcription factor that modulates antioxidant genes. Its role in IS is still unelucidated. The current study focused on constructing a transient middle cerebral artery occlusion (tMCAO) model for investigating the NRF2-related mechanism underlying cerebral ischemia/reperfusion (I/R) injury. Each male C57BL/6 mouse was injected with/with no specific NRF2 activator post-tMCAO. Changes in blood–brain barrier (BBB)-associated molecule levels were analyzed using western-blotting, PCR, immunohistochemistry, and immunofluorescence analysis. NRF2 levels within cerebral I/R model decreased at 24-h post-ischemia. NRF2 activation improved brain edema, infarct volume, and neurological deficits after MCAO/R. Similarly, sulforaphane (SFN) prevented the down-regulated tight junction proteins occludin and zonula occludens 1 (ZO-1) and reduced the up-regulated aquaporin 4 (AQP4) and matrix metalloproteinase 9 (MMP9) after tMCAO. Collectively, NRF2 exerted a critical effect on preserving BBB integrity modulating ferroptosis and inflammation. Because NRF2 is related to BBB injury regulation following cerebral I/R, this provides a potential therapeutic target and throws light on the underlying mechanism for clinically treating IS.
Investigating the efficacy of novel organoclay as a rheological additive for enhancing the performance of oil-based drilling fluids
Authors: Mahmoud Ali , Gajbhiye Rahul , Elkatatny Salaheldin 
Published: March 2024

AbstractOil-based drilling fluids (OBDFs) are extensively used in the drilling industry due to their superior performance in challenging drilling conditions. These fluids control wellbore stability, lubricate the drill bit, and transport drill cuttings to the surface. One important component of oil-based drilling fluids is the viscosifier, which provides rheological properties to enhance drilling operations. This study evaluates the effectiveness of Claytone-IMG 400, a novel rheological agent, in enhancing the performance of OBDFs under high-pressure and high-temperature (HPHT) conditions. A comparative analysis was conducted with a pre-existing organoclay (OC) to assess the improvements achieved by Claytone-IMG 400. The OCs were analyzed using X-ray diffraction (XRD), X-ray fluorescence (XRF), scanning electron microscopy (SEM), and particle size distribution (PSD) to identify their mineral and chemical compositions, morphologies, and particle sizes. The drilling fluid density, electrical stability, sagging tendency, rheological properties, viscoelastic properties, and filtration properties were studied to formulate a stable and high-performance drilling fluid. The results confirmed that the novel OC does not affect the drilling fluid density but enhances the emulsion stability with a 9% increment compared with the drilling fluid formulated with MC-TONE. The sagging experiments showed that Claytone-IMG 400 prevented the sagging issues in both static and dynamic conditions. Also, Claytone-IMG 400 improved the plastic viscosity (PV), yield point (YP), and apparent viscosity (AV). The PV, YP, and AV were improved by 30%, 38%, and 33% increments respectively compared with the drilling fluid formulated with MC-TONE. The YP/PV ratio increased with a 6% increment from 1.12 to 1.19. Moreover, the gel strength (GS) was significantly increased, and the filtration properties were enhanced. The filtration volume was reduced by 10% from 5.0 to 4.5 cm3, and the filter cake thickness had a 37.5% reduction from 2.60 to 1.89 mm. The novelty of this study is highlighted by the introduction and evaluation of Claytone-IMG 400 as a new rheological additive for safe, efficient, and cost-effective drilling operations. The results indicate that Claytone-IMG 400 significantly improves the stability and performance of OBDFs, thereby reducing wellbore instability and drilling-related problems.
Gasless transvaginal natural orifice transluminal endoscopic surgery for hysterectomy and salpingectomy on a robot platform with flexible devices in a porcine model
Authors: Mei Youwen , Wang Yanjun , Zhang Qiang , Xiong Liling , Xu Li , Hou Qiannan , Chen Jiaojiao , He Li , Lin Yonghong 
Published: March 2024

AbstractIn this report, we described a new technique of gasless V-NOTES for hysterectomy and salpingectomy on a robotic platform with flexible devices in a porcine model. As a result, the gynecological procedures were successfully completed. The total operative time was 110 min, while the docking time was 10 min. The estimated blood loss was estimated to be 10 mL with no intraoperative complications. It revealed that gasless V-NOTES for hysterectomy and salpingectomy on a robotic platform with flexible devices appeared to be feasible and safe in the porcine model and has the potential for clinical use in human beings.
Molecular characterization of SARS-CoV-2 Omicron clade and clinical presentation in children
Authors: Scutari Rossana , Fox Valeria , Fini Vanessa , Granaglia Annarita , Vittucci Anna Chiara , Smarrazzo Andrea , Lancella Laura , Calo’ Carducci Francesca , Romani Lorenza , Cursi Laura , Bernaschi Paola , Russo Cristina , Campana Andrea , Bernardi Stefania , Villani Alberto , Perno Carlo Federico , Alteri Claudia 
Published: March 2024

AbstractSince its emergence, SARS-CoV-2 Omicron clade has shown a marked degree of variability and different clinical presentation compared with previous clades. Here we demonstrate that at least four Omicron lineages circulated in children since December 2021, and studied until November 2022: BA.1 (33.6%), BA.2 (40.6%), BA.5 (23.7%) and BQ.1 (2.1%). At least 70% of infections concerned children under 1 year, most of them being infected with BA.2 lineages (n = 201, 75.6%). Looking at SARS-CoV-2 genetic variability, 69 SNPs were found to be significantly associated in pairs, (phi <  − 0.3 or > 0.3 and p-value < 0.001). 16 SNPs were involved in 4 distinct clusters (bootstrap > 0.75). One of these clusters (A23040G, A27259C, T23617G, T23620G) was also positively associated with moderate/severe COVID-19 presentation (AOR [95% CI] 2.49 [1.26–4.89] p-value: 0.008) together with comorbidities (AOR [95% CI] 2.67 [1.36–5.24] p-value: 0.004). Overall, these results highlight the extensive SARS-CoV-2 Omicron circulation in children, mostly aged < 1 year, and provide insights on viral diversification even considering low-abundant SNPs, finally suggesting the potential contribution of viral diversification in affecting disease severity.
The impact of medial temporal and parietal atrophy on cognitive function in dementia
Authors: Susianti Noor Alia , Prodjohardjono Astuti , Vidyanti Amelia Nur , Setyaningsih Indarwati , Gofir Abdul , Setyaningrum Cempaka Thursina Srie , Effendy Christantie , Setyawan Nurhuda Hendra , Setyopranoto Ismail 
Published: March 2024

AbstractAlthough medial temporal atrophy (MTA) and parietal atrophy (Koedam score) have been used to diagnose Alzheimer’s disease (AD), early detection of other dementia types remains elusive. The study aims to investigate the association between these brain imaging markers and cognitive function in dementia. This cross-sectional study collected data from the Memory Clinic of Dr. Sardjito General Hospital Yogyakarta, Indonesia from January 2020 until December 2022. The cut-off value of MTA and Koedam score was set with Receiver Operating Curve. Multivariate analysis was performed to investigate the association between MTA and Koedam score with cognitive function. Of 61 patients, 22.95% had probable AD, 59.01% vascular dementia, and 18.03% mixed dementia. Correlation test showed that MTA and Koedam score were negatively associated with Montreal Cognitive Assessment-Indonesian Version (MoCA-INA) score. MTA score ≥ 3 (AUC 0.69) and Koedam score ≥ 2 (AUC 0.67) were independently associated with higher risk of poor cognitive function (OR 13.54, 95% CI 1.77–103.43, p = 0.01 and OR 5.52, 95% CI 1.08–28.19, p = 0.04). Higher MTA and Koedam score indicate worse cognitive function in dementia. Future study is needed to delineate these findings as prognostic markers of dementia severity.
Quantifying sources of subseasonal prediction skill in CESM2
Authors: Richter Jadwiga H. , Glanville Anne A. , King Teagan , Kumar Sanjiv , Yeager Stephen G. , Davis Nicholas A. , Duan Yanan , Fowler Megan D. , Jaye Abby , Edwards Jim , Caron Julie M. , Dirmeyer Paul A. , Danabasoglu Gokhan , Oleson Keith 
Published: March 2024

AbstractSubseasonal prediction fills the gap between weather forecasts and seasonal outlooks. There is evidence that predictability on subseasonal timescales comes from a combination of atmosphere, land, and ocean initial conditions. Predictability from the land is often attributed to slowly varying changes in soil moisture and snowpack, while predictability from the ocean is attributed to sources such as the El Niño Southern Oscillation. Here we use a set of subseasonal reforecast experiments with CESM2 to quantify the respective roles of atmosphere, land, and ocean initial conditions on subseasonal prediction skill over land. These reveal that the majority of prediction skill for global surface temperature in weeks 3–4 comes from the atmosphere, while ocean initial conditions become important after week 4, especially in the Tropics. In the CESM2 subseasonal prediction system, the land initial state does not contribute to surface temperature prediction skill in weeks 3–6 and climatological land conditions lead to higher skill, disagreeing with our current understanding. However, land-atmosphere coupling is important in week 1. Subseasonal precipitation prediction skill also comes primarily from the atmospheric initial condition, except for the Tropics, where after week 4 the ocean state is more important.
Adaptive Darwinian off-target resistance mechanisms to selective RET inhibition in RET driven cancer
Authors: Subbiah Vivek , Gouda Mohamed A. , Iorgulescu J. Bryan , Dadu Ramona , Patel Keyur , Sherman Steven , Cabanillas Maria , Hu Mimi , Castellanos Luz E. , Amini Behrang , Meric-Bernstam Funda , Shen Tao , Wu Jie 
Published: March 2024

AbstractPatients treated with RET protein tyrosine kinase inhibitors (TKIs) selpercatinib or pralsetinib develop RET TKI resistance by secondary RET mutations or alterative oncogenes, of which alterative oncogenes pose a greater challenge for disease management because of multiple potential mechanisms and the unclear tolerability of drug combinations. A patient with metastatic medullary thyroid carcinoma (MTC) harboring a RET activation loop D898_E901del mutation was treated with selpercatinib. Molecular alterations were monitored with tissue biopsies and cfDNA during the treatment. The selpercatinib-responsive MTC progressed with an acquired ETV6::NTRK3 fusion, which was controlled by selpercatinib plus the NTRK inhibitor larotrectinib. Subsequently, tumor progressed with an acquired EML4::ALK fusion. Combination of selpercatinib with the dual NTRK/ALK inhibitor entrectinib reduced the tumor burden, which was followed by appearance of NTRK3 solvent-front G623R mutation. Preclinical experiments validated selpercatinib plus larotrectinib or entrectinib inhibited RET/NTRK3 dependent cells, whereas selpercatinib plus entrectinib was necessary to inhibit cells with RET/NTRK3/ALK triple alterations or a mixture of cell population carrying these genetic alterations. Thus, RET-altered MTC adapted to selpercatinib and larotrectinib with acquisition of ETV6::NTRK3 and EML4::ALK oncogenes can be managed by combination of selpercatinib and entrectinib providing proof-of-concept of urgency of incorporating molecular profiling in real-time and personalized N-of-1 care transcending one-size-fits-all approach.
ScLinear predicts protein abundance at single-cell resolution
Authors: Hanhart Daniel , Gossi Federico , Rapsomaniki Maria Anna , Kruithof-de Julio Marianna , Chouvardas Panagiotis 
Published: March 2024

AbstractSingle-cell multi-omics have transformed biomedical research and present exciting machine learning opportunities. We present scLinear, a linear regression-based approach that predicts single-cell protein abundance based on RNA expression. ScLinear is vastly more efficient than state-of-the-art methodologies, without compromising its accuracy. ScLinear is interpretable and accurately generalizes in unseen single-cell and spatial transcriptomics data. Importantly, we offer a critical view in using complex algorithms ignoring simpler, faster, and more efficient approaches.
On the need for a multi-dimensional framework to measure accessibility to urban green
Authors: Battiston Alice , Schifanella Rossano 
Published: March 2024

AbstractWith the recent expansion of urban greening interventions, the definition of spatial indicators to measure the provision of urban greenery has become pivotal in informing the policy-design process. By analyzing the stability of the population and area rankings induced by several indicators of green accessibility for over 1000 cities worldwide, we investigate the extent to which using a single metric provides a reliable assessment of green accessibility in a city. The results suggest that, due to the complex interaction between the spatial distribution of greenspaces in an urban center and its population distribution, a single indicator may inadequately differentiate across areas or subgroups of the population, even when focusing on one form of green accessibility. From a policy standpoint, this indicates the need to switch toward a multi-dimensional framework capable of organically evaluating a range of indicators at once.
Identification of reliable locations for wind power generation through a global analysis of wind droughts
Authors: Antonini Enrico G. A. , Virgüez Edgar , Ashfaq Sara , Duan Lei , Ruggles Tyler H. , Caldeira Ken 
Published: March 2024

AbstractWind droughts, or prolonged periods of low wind speeds, pose challenges for electricity systems largely reliant on wind generation. Using weather reanalysis data, we analyzed the global distribution of and trends in wind droughts using an energy deficit metric that integrates the depth and duration of wind droughts. We identified regions with high power densities, low seasonal variability, and limited weather fluctuations that favor wind power generation, such as the American Midwest, Australia, the Sahara, Argentina, Central Asia, and Southern Africa. Northwestern Europe has high power densities but experiences more frequent and prolonged wind droughts due to higher weather variability. We found little evidence for strong trends in wind droughts over recent decades in most places. Rather, the most severe wind droughts in many places occurred before wind power substantially penetrated power systems, which suggests that historical weather data can be useful in designing reliable wind-reliant electricity systems.
Complete transition from mantle plume to mantle exhumation on the Central Atlantic Guyana/Suriname margin
Authors: Kilsdonk Bill , Trude James , Grow Tim , Ott Bryan , Manatschal Gianreto 
Published: March 2024

AbstractModern data are clarifying tectonic transitions from continents to oceans. The importance of magmatic additions relative to mechanical extension varies between cases and through time based on observations of isolated margins and ridges. Magma poor spreading centers and magma rich continental margins are both well known. Here we present data to document the complete and continuous evolution from a magma rich Central Atlantic margin to a magma-starved ocean floor. Tectonic changes correlate with separation rate changes. Early Jurassic hotspot volcanism initially overwhelmed slow extension to build the Demerara Plateau at the eastern edge of the margin, but hotspot activity waned near the end of the Middle Jurassic. Normal spreading rates and normal thickness oceanic crust prevailed through most of the Oxfordian. Spreading slowed in the Kimmeridgian but magmatic addition slowed even more, evidenced by normal faults that offset the full oceanic crust and by outboard exhumed mantle.