bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Internal Waves Data Set From Sentinel‐1 Synthetic Aperture Radar Imagery and Preliminary Detection
Authors: Tao Mingkai , Xu Chengji , Guo Lingxi , Wang Xiaoqing , Xu Yanlang 
Published: November 2022

AbstractInternal waves (IWs) are a widely occurring phenomenon in the global oceans. They have significant impacts on marine environments through their propagation mechanisms. In this study, we collect 390 satellite images with 775 labels from Sentinel‐1 Synthetic Aperture Radar (SAR) from 2014 to 2021 to construct a data set containing IW packets in Andaman Sea, South China Sea, Sulu Sea, and Celebes Sea, respectively. All the SAR images acquired are pre‐processed to provide clear IW packets for better visualization. To better detect IWs in global oceans automatically, a machine‐learning based model is proposed to focus on different channels and the spatial information. The precision, recall, and mean average precision of our improved model applied on the IW data set is up to 98.7%, 96.9%, and 98.9%, respectively. Various cases of IWs images are analyzed to illustrate detection quality in different stripes, scales, and propagation directions of IWs. The experimental results indicate that our data set is helpful to better detect IWs, and proposed network can accurately detect IWs in SAR images under various conditions.
Thermo‐Compositional Structure of the South American Platform Lithosphere: Evidence of Stability, Modification, and Erosion
Authors: Altoe Isabella , Goes Saskia , Assumpção Marcelo 
Published: November 2022

AbstractConstraints on the structure of cratonic lithosphere are essential to improve our understanding of craton formation, evolution and long‐term stability. Here, we perform a joint inversion for the thermal and compositional structure of the mantle lithosphere below the South America Platform, using Rayleigh wave group velocities, elevation, and geoid height. Thick thermal lithosphere (200–300 km) is found below the southern Amazonian and São Francisco Cratons and adjoining Parecis and eastern Paraná Basins. The southern Rio de la Plata Craton also retains a 200–250 km thick keel. Compositionally, Amazonian, São Francisco, and Rio de la Plata lithosphere has a metasomatic and possibly eclogite signature similar to that of North American Proterozoic collision belts. Parecis and eastern Paraná lithosphere has likely been altered by Mesozoic plume activity throughout most of its depth, while the rest of the Paraná Basin and the Chaco and Pantanal Basins appear to have lost the lithospheric root below ∼100 km depth that was there during intracratonic basin formation. The low elevation and high geoid of the western Paraná Basin requires a dense (eclogite) layer within the crust/shallow lithosphere, possibly associated with the NeoProterozoic Western Paraná Suture Zone and/or Mesozoic plume activity, while topography and geoid of the basins further west and of the western Rio de la Plata craton seem affected by dynamic (subduction‐related) topography. Thus, the variable geophysical structure of the platform lithosphere reflects a history that involves besides some stable keels, significant modification and thinning.
Using Seafloor Geodesy to Detect Vertical Deformation at the Hikurangi Subduction Zone: Insights From Self‐Calibrating Pressure Sensors and Ocean General Circulation Models
Authors: Woods K. , Webb S. C. , Wallace L. M. , Ito Y. , Collins C. , Palmer N. , Hino R. , Savage M. K. , Saffer D. M. , Davis E. E. , Barker D. H. N. 
Published: November 2022

AbstractSeafloor pressure sensor data is emerging as a promising approach to resolve vertical displacement of the seafloor in the offshore reaches of subduction zones, particularly in response to slow slip events (SSEs), although such signals are challenging to resolve due to sensor drift and oceanographic signals. Constraining offshore SSE slip distribution is of key importance to understanding earthquake and tsunami hazards posed by subduction zones. We processed seafloor pressure data from January to October 2019 acquired at the Hikurangi subduction zone, offshore New Zealand, to estimate vertical displacement associated with a large SSE that occurred beneath the seafloor array. The experiment included three self‐calibrating sensors designed to remove sensor drift, which, together with ocean general circulation models, were essential to the identification and correction of long‐period ocean variability remaining in the data after applying traditional processing techniques. We estimate that long‐period oceanographic signals that were not synchronous between pressure sensors and reference sites influenced our inferred displacements by 0.3–2.6 cm, suggesting that regionally deployed reference sites alone may not provide sufficient ocean noise correction. After incorporating long‐period ocean variability corrections into the processing, we calculate 1.0–3.3 cm of uplift during the SSE offshore Gisborne at northern Hikurangi, and 1.1–2.7 cm of uplift offshore the Hawke's Bay area at central Hikurangi. Some Hawke Bay displacements detected by pressure sensors near the trench were delayed by 6 weeks compared to the timing of slip onset detected by onshore Global Navigation Satellite System sites, suggesting updip migration of the SSE.
Mutant p53 in cancer: from molecular mechanism to therapeutic modulation
Authors: Chen Xiaohua , Zhang Taotao , Su Wei , Dou Zhihui , Zhao Dapeng , Jin Xiaodong , Lei Huiwen , Wang Jing , Xie Xiaodong , Cheng Bo , Li Qiang , Zhang Hong , Di Cuixia 
Published: November 2022

AbstractTP53, a crucial tumor suppressor gene, is the most commonly mutated gene in human cancers. Aside from losing its tumor suppressor function, mutant p53 (mutp53) often acquires inherent, novel oncogenic functions, which is termed “gain-of-function”. Emerging evidence suggests that mutp53 is highly associated with advanced malignancies and poor prognosis, which makes it a target for development of novel cancer therapies. Herein, we provide a summary of our knowledge of the mutp53 types and mutp53 spectrum in cancers. The mechanisms of mutp53 accumulation and gain-of-function are also summarized. Furthermore, we discuss the gain-of-function of mutp53 in cancers: genetic instability, ferroptosis, microenvironment, and stemness. Importantly, the role of mutp53 in the clinic is also discussed, particularly with regard to chemotherapy and radiotherapy. Last, emphasis is given to emerging strategies on how to target mutp53 for tumor therapy. Thus, this review will contribute to better understanding of the significance of mutp53 as a target for therapeutic strategies.
Perovskite quantum dot-induced monochromatization for broadband photodetection of wafer-scale molybdenum disulfide
Authors: Kim Minji , Bae Garam , Kim Kyeong Nam , Jo Hyeong-ku , Song Da Som , Ji Seulgi , Jeon Dohyun , Ko Semin , Lee Seon Joo , Choi Sungho , Yim Soonmin , Song Wooseok , Myung Sung , Yoon Dae Ho , An Ki-Seok , Lee Sun Sook 
Published: November 2022

AbstractTwo-dimensional transition metal dichalcogenide (2D TMD) crystals are versatile platforms for realizing emergent optoelectronic devices. However, the ability to produce large-area 2D TMDs with spatial homogeneity and to accomplish broadband photodetection by tuning the operating wavelengths in photodetectors are two paramount prerequisites for practical applications of 2D TMD-based photodetectors. Here, we demonstrated all-solution-processed broadband photodetectors based on the wafer-scale perovskite quantum dots (PQDs)/MoS2 through light management via the monochromatization effect of the PQDs. The photodetectors exhibited broadband photodetection behavior that retained high photocurrents over a wide spectral range (254, 365, and 532 nm) by enhancing the photoresponse in the UV region through light management via the monochromatization effect of the PQDs. This intriguing strategy was proven with (i) electrical isolation realized by inserting an Al2O3 insulator between the PQDs and MoS2 and (ii) alteration of the PQD density. The rational nanohybrid-based photodetectors also exhibited superb air stability and exceptional bending durability.
Bowing-alleviated continuous bandgap engineering of wafer-scale WS2xSe2(1-x) monolayer alloys and their assembly into hetero-multilayers
Authors: Kang Hee Seong , Kang Jung Hoon , Lee Sol , Lee Kihyun , Koo Do Hyoung , Kim Yong-Sung , Hong Young Joon , Kim Yong-Jin , Kim Kwanpyo , Lee Donghun , Lee Chul-Ho 
Published: November 2022

AbstractBandgap engineering of compound semiconductors and the fabrication of bandgap-modulated heterostructures are important for enabling the development of modern optoelectronics. However, these engineering processes are challenging for two-dimensional (2D) semiconductors of transition metal dichalcogenides, particularly on a large scale. Herein, we report the wafer-scale homogeneous growth of composition-modulated WS2xSe2(1-x) alloys with a continuously tunable bandgap using metal–organic chemical vapor deposition. Well-optimized growth produces monolayer films with excellent homogeneity over the entire wafer. The substitutional atomic chalcogen (S, Se) concentration in WS2xSe2(1-x) alloys is precisely controlled by varying the flow rate of the metal–organic precursors, leading to a bandgap modulation from 1.67 to 2.05 eV, as determined from absorbance spectra. Notably, the optical bandgap of WS2xSe2(1-x) alloys exhibits a nearly linear relationship with the chalcogen composition, implying a low bowing effect. This bowing-alleviated bandgap modulation is attributed to the small lattice mismatch, strain relaxation, and thermodynamic miscibility in the WS2xSe2(1-x) alloys, as confirmed by density-functional theory calculations. Furthermore, the fabrication of hetero-multilayers by stacking differently alloyed films is demonstrated. The produced heterostructure film exhibits a broad spectral absorbance distinct from that of the individual layers. The findings of this study provide insights for the advancement of versatile design of functional 2D optoelectronics.
Sea-level rise will likely accelerate rock coast cliff retreat rates
Authors: Shadrick Jennifer R. , Rood Dylan H. , Hurst Martin D. , Piggott Matthew D. , Hebditch Bethany G. , Seal Alexander J. , Wilcken Klaus M. 
Published: November 2022

AbstractCoastal response to anthropogenic climate change is of central importance to the infrastructure and inhabitants in these areas. Despite being globally ubiquitous, the stability of rock coasts has been largely neglected, and the expected acceleration of cliff erosion following sea-level rise has not been tested with empirical data, until now. We have optimised a coastal evolution model to topographic and cosmogenic radionuclide data to quantify cliff retreat rates for the past 8000 years and forecast rates for the next century. Here we show that rates of cliff retreat will increase by up to an order of magnitude by 2100 according to current predictions of sea-level rise: an increase much greater than previously predicted. This study challenges conventional coastal management practices by revealing that even historically stable rock coasts are highly sensitive to sea-level rise and should be included in future planning for global climate change response.
Prioritizing autoimmunity risk variants for functional analyses by fine-mapping mutations under natural selection
Authors: Pankratov Vasili , Yunusbaeva Milyausha , Ryakhovsky Sergei , Zarodniuk Maksym ,   Estonian Biobank Research Team, Metspalu Andres , Nelis Mari , Milani Lili , Mägi Reedik , Esko Tõnu , Yunusbayev Bayazit 
Published: November 2022

AbstractPathogen-driven selection shaped adaptive mutations in immunity genes, including those contributing to inflammatory disorders. Functional characterization of such adaptive variants can shed light on disease biology and past adaptations. This popular idea, however, was difficult to test due to challenges in pinpointing adaptive mutations in selection footprints. In this study, using a local-tree-based approach, we show that 28% of risk loci (153/535) in 21 inflammatory disorders bear footprints of moderate and weak selection, and part of them are population specific. Weak selection footprints allow partial fine-mapping, and we show that in 19% (29/153) of the risk loci under selection, candidate disease variants are hitchhikers, and only in 39% of cases they are likely selection targets. We predict function for a subset of these selected SNPs and highlight examples of antagonistic pleiotropy. We conclude by offering disease variants under selection that can be tested functionally using infectious agents and other stressors to decipher the poorly understood link between environmental stressors and genetic risk in inflammatory conditions.
Biological effects of the loss of homochirality in a multicellular organism
Authors: Banreti Agnes , Bhattacharya Shayon , Wien Frank , Matsuo Koichi , Réfrégiers Matthieu , Meinert Cornelia , Meierhenrich Uwe , Hudry Bruno , Thompson Damien , Noselli Stéphane 
Published: November 2022

AbstractHomochirality is a fundamental feature of all known forms of life, maintaining biomolecules (amino-acids, proteins, sugars, nucleic acids) in one specific chiral form. While this condition is central to biology, the mechanisms by which the adverse accumulation of non-l-α-amino-acids in proteins lead to pathophysiological consequences remain poorly understood. To address how heterochirality build-up impacts organism’s health, we use chiral-selective in vivo assays to detect protein-bound non-l-α-amino acids (focusing on aspartate) and assess their functional significance in Drosophila. We find that altering the in vivo chiral balance creates a ‘heterochirality syndrome’ with impaired caspase activity, increased tumour formation, and premature death. Our work shows that preservation of homochirality is a key component of protein function that is essential to maintain homeostasis across the cell, tissue and organ level.
An atlas of amyloid aggregation: the impact of substitutions, insertions, deletions and truncations on amyloid beta fibril nucleation
Authors: Seuma Mireia , Lehner Ben , Bolognesi Benedetta 
Published: November 2022

AbstractMultiplexed assays of variant effects (MAVEs) guide clinical variant interpretation and reveal disease mechanisms. To date, MAVEs have focussed on a single mutation type—amino acid (AA) substitutions—despite the diversity of coding variants that cause disease. Here we use Deep Indel Mutagenesis (DIM) to generate a comprehensive atlas of diverse variant effects for a disease protein, the amyloid beta (Aβ) peptide that aggregates in Alzheimer’s disease (AD) and is mutated in familial AD (fAD). The atlas identifies known fAD mutations and reveals that many variants beyond substitutions accelerate Aβ aggregation and are likely to be pathogenic. Truncations, substitutions, insertions, single- and internal multi-AA deletions differ in their propensity to enhance or impair aggregation, but likely pathogenic variants from all classes are highly enriched in the polar N-terminal region of Aβ. This comparative atlas highlights the importance of including diverse mutation types in MAVEs and provides important mechanistic insights into amyloid nucleation.
Accessing chiral sulfones bearing quaternary carbon stereocenters via photoinduced radical sulfur dioxide insertion and Truce–Smiles rearrangement
Authors: Huang Jiapian , Liu Fei , Zeng Ling-Hui , Li Shaoyu , Chen Zhiyuan , Wu Jie 
Published: November 2022

AbstractFrom the viewpoint of synthetic accessibility and functional group compatibility, photoredox-catalyzed sulfur dioxide insertion strategy enables in situ generation of functionalized sulfonyl radicals from easily accessible starting materials under mild conditions, thereby conferring broader application potential. Here we present two complementary photoinduced sulfur dioxide insertion systems to trigger radical asymmetric Truce–Smiles rearrangements for preparing a variety of chiral sulfones that bear a quaternary carbon stereocenter. This protocol features broad substrate scope and excellent stereospecificity. Aside from scalability, the introduction of a quaternary carbon stereocenter at position β to bioactive molecule-derived sulfones further demonstrates the practicality and potential of this methodology.
A comprehensive update to the Mycobacterium tuberculosis H37Rv reference genome
Authors: Chitale Poonam , Lemenze Alexander D. , Fogarty Emily C. , Shah Avi , Grady Courtney , Odom-Mabey Aubrey R. , Johnson W. Evan , Yang Jason H. , Eren A. Murat , Brosch Roland , Kumar Pradeep , Alland David 
Published: November 2022

AbstractH37Rv is the most widely usedMycobacterium tuberculosisstrain, and its genome is globally used as theM. tuberculosisreference sequence. Here, we present Bact-Builder, a pipeline that uses consensus building to generate complete and accurate bacterial genome sequences and apply it to three independently cultured and sequenced H37Rv aliquots of a single laboratory stock. Two of the 4,417,942 base-pair long H37Rv assemblies are 100% identical, with the third differing by a single nucleotide. Compared to the existing H37Rv reference, the new sequence contains ~6.4 kb additional base pairs, encoding ten new regions that include insertions in PE/PPE genes and new paralogs ofesxNandesxJ, which are differentially expressed compared to the reference genes. New sequencing and de novo assemblies with Bact-Builder confirm that all 10 regions, plus small additional polymorphisms, are also present in the commonly used H37Rv strains NR123, TMC102, and H37Rv1998. Thus, Bact-Builder shows promise as an improved method to perform accurate and reproducible de novo assemblies of bacterial genomes, and our work provides important updates to the primaryM. tuberculosisreference genome.
A Myb enhancer-guided analysis of basophil and mast cell differentiation
Authors: Matsumura Takayoshi , Totani Haruhito , Gunji Yoshitaka , Fukuda Masahiro , Yokomori Rui , Deng Jianwen , Rethnam Malini , Yang Chong , Tan Tze King , Karasawa Tadayoshi , Kario Kazuomi , Takahashi Masafumi , Osato Motomi , Sanda Takaomi , Suda Toshio 
Published: November 2022

AbstractThe transcription factor MYB is a crucial regulator of hematopoietic stem and progenitor cells. However, the nature of lineage-specific enhancer usage of the Myb gene is largely unknown. We identify the Myb −68 enhancer, a regulatory element which marks basophils and mast cells. Using the Myb −68 enhancer activity, we show a population of granulocyte-macrophage progenitors with higher potential to differentiate into basophils and mast cells. Single cell RNA-seq demonstrates the differentiation trajectory is continuous from progenitors to mature basophils in vivo, characterizes bone marrow cells with a gene signature of mast cells, and identifies LILRB4 as a surface marker of basophil maturation. Together, our study leads to a better understanding of how MYB expression is regulated in a lineage-associated manner, and also shows how a combination of lineage-related reporter mice and single-cell transcriptomics can overcome the rarity of target cells and enhance our understanding of gene expression programs that control cell differentiation in vivo.
An enantioselective four-component reaction via assembling two reaction intermediates
Authors: Yu Sifan , Chang Wenju , Hua Ruyu , Jie Xiaoting , Zhang Mengchu , Zhao Wenxuan , Chen Jinzhou , Zhang Dan , Qiu Huang , Liang Yong , Hu Wenhao 
Published: November 2022

AbstractA reaction intermediate is a key molecular entity that has been used in explaining how starting materials converts into the final products in the reaction, and it is usually unstable, highly reactive, and short-lived. Extensive efforts have been devoted in identifying and characterizing such species via advanced physico-chemical analytical techniques. As an appealing alternative, trapping experiments are powerful tools in this field. This trapping strategy opens an opportunity to discover multicomponent reactions. In this work, we report various highly diastereoselective and enantioselective four-component reactions (containing alcohols, diazoesters, enamines/indoles and aldehydes) which involve the coupling of in situ generated intermediates (iminium and enol). The reaction conditions presented herein to produce over 100 examples of four-component reaction products proceed under mild reaction conditions and show high functional group tolerance to a broad range of substrates. Based on experimental and computational analyses, a plausible mechanism of this multicomponent reaction is proposed.
Accurate discharge and water level forecasting using ensemble learning with genetic algorithm and singular spectrum analysis-based denoising
Authors: Nguyen Anh Duy , Le Nguyen Phi , Vu Viet Hung , Pham Quoc Viet , Nguyen Viet Huy , Nguyen Minh Hieu , Nguyen Thanh Hung , Nguyen Kien 
Published: November 2022

AbstractForecasting discharge (Q) and water level (H) are essential factors in hydrological research and flood prediction. In recent years, deep learning has emerged as a viable technique for capturing the non-linear relationship of historical data to generate highly accurate prediction results. Despite the success in various domains, applying deep learning in Q and H prediction is hampered by three critical issues: a shortage of training data, the occurrence of noise in the collected data, and the difficulty in adjusting the model’s hyper-parameters. This work proposes a novel deep learning-based Q–H prediction model that overcomes all the shortcomings encountered by existing approaches. Specifically, to address data scarcity and increase prediction accuracy, we design an ensemble learning architecture that takes advantage of multiple deep learning techniques. Furthermore, we leverage the Singular-Spectrum Analysis (SSA) to remove noise and outliers from the original data. Besides, we exploit the Genetic Algorithm (GA) to propose a novel mechanism that can automatically determine the prediction model’s optimal hyper-parameters. We conducted extensive experiments on two datasets collected from Vietnam’s Red and Dakbla rivers. The results show that our proposed solution outperforms current techniques across a wide range of metrics, including NSE, MSE, MAE, and MAPE. Specifically, by exploiting the ensemble learning technique, we can improve the NSE by at least $$2\%$$

2
%

. Moreover, with the aid of the SSA-based data preprocessing technique, the NSE is further enhanced by more than $$5\%$$

5
%

. Finally, thanks to GA-based optimization, our proposed model increases the NSE by at least $$6\%$$

6
%

and up to $$40\%$$

40
%

in the best case.