bluuebunny/crossref_metadata_2025_split huggingface dataset:
Oceanic Regime Shift to a Warmer Continental Shelf Adjacent to the Shackleton Ice Shelf, East Antarctica
Authors: Ribeiro Natalia , Herraiz‐Borreguero Laura , Rintoul Stephen R. , Williams Guy , McMahon Clive R. , Hindell Mark , Guinet Christophe 
Published: November 2023

AbstractThe long‐held view that the East Antarctic margin is isolated from warm offshore waters has been challenged by recent observations showing incursions of warm modified Circumpolar Deep Water (mCDW) reaching several East Antarctic ice shelves. However, large areas of the East Antarctic continental shelf remain poorly observed, making it challenging to determine if the supply of oceanic heat to the ice shelves is changing. Here, we use temperature and salinity profiles to the west of the Shackleton Ice Shelf (SIS; ≈100°E) spanning 60 years to assess the variability of the water masses in the context of a changing climate. We document warming and freshening of shelf waters. Prior to 1996, cold mCDW water (θ < −1.6°C) was found below the surface mixed layer and cold Dense Shelf Water (DSW) with a salinity of >34.5 dominated the water column. After 2010, warm mCDW (≥−1.0°C) was widespread over the continental shelf and DSW with salinity over 34.5 was no longer present. The mixing ratio of glacial meltwater indicates that warm mCDW observed in 2011 caused basal melting of the SIS, possibly reducing the salinity of DSW. Increased access of warm waters to the continental shelf may have also occurred on the eastern side of the ice shelf, where glaciological evidence shows the grounding line has retreated. These observations suggest a shift occurred prior to 2011 that has increased the ocean heat supply to the continental shelf and to the SIS, increasing basal melt and reducing DSW formation.
Wave Velocities and Poisson Ratio in a Loose Sandy Martian Regolith Simulant Under Low Stresses: 2. Theoretical Analysis
Authors: Caicedo B. , Castillo Betancourt J. P. , Delage P. , Lognonné P. , Banerdt B. 
Published: November 2023

AbstractThis paper presents a theoretical analysis of the data on wave velocity measurements at small stresses presented in a companion paper describing the experimental results on a Martian regolith loose sandy simulant (Fontainebleau sand) of the soil at the InSight landing site on Mars (Elysium Planitia). Experimental data of wave velocities and Poisson's ratio are interpreted in the light of a granular contact mechanics theory and completed accounting for rugosity effects that are suspected to have stronger effects in sands under low stresses. The asperities of a grain of Fontainebleau sand were investigated through Atomic Force Microscopy, but larger asperities had to be adopted so as to better fit the model prediction with experimental data. A good agreement between the experimental data and the model predictions is obtained for stress above 10 kPa. Below 5 kPa, an area in which asperities are suspected to have a stronger influence, the model is not fully satisfactory, showing that further experimental and theoretical investigation is necessary in a stress zone particularly relevant to surface soils in planets, with probably enhanced effects of asperities on the intergrain contact mechanics.
Post-CMOS processing challenges and design developments of CMOS-MEMS microheaters for local CNT synthesis
Authors: Roy Avisek , Ta Bao Q. , Azadmehr Mehdi , Aasmundtveit Knut E. 
Published: November 2023

AbstractCarbon nanotubes (CNTs) can be locally grown on custom-designed CMOS microheaters by a thermal chemical vapour deposition (CVD) process to utilize the sensing capabilities of CNTs in emerging micro- and nanotechnology applications. For such a direct CMOS-CNT integration, a key requirement is the development of necessary post-processing steps on CMOS chips for fabricating CMOS-MEMS polysilicon heaters that can locally generate the required CNT synthesis temperatures (~650–900 °C). In our post-CMOS processing, a subtractive fabrication technique is used for micromachining the polysilicon heaters, where the passivation layers in CMOS are used as masks to protect the electronics. For dielectric etching, it is necessary to achieve high selectivity, uniform etching and a good etch rate to fully expose the polysilicon layers without causing damage. We achieved successful post-CMOS processing by developing two-step reactive ion etching (RIE) of the SiO2 dielectric layer and making design improvements to a second-generation CMOS chip. After the dry etching process, CMOS-MEMS microheaters are partially suspended by SiO2 wet etching with minimum damage to the exposed aluminium layers, to obtain high thermal isolation. The fabricated microheaters are then successfully utilized for synthesizing CNTs by a local thermal CVD process. The CMOS post-processing challenges and design aspects to fabricate CMOS-MEMS polysilicon microheaters for such high-temperature applications are detailed in this article. Our developed process for heterogeneous monolithic integration of CMOS-CNT shows promise for wafer-level manufacturing of CNT-based sensors by incorporating additional steps in an already existing foundry CMOS process.
C-MEMS-derived glassy carbon electrochemical biosensors for rapid detection of SARS-CoV-2 spike protein
Authors: Mandal Naresh , Mitra Raja , Pramanick Bidhan 
Published: November 2023

AbstractAccording to a World Health Organization (WHO) report, the world has experienced more than 766 million cases of positive SARS-CoV-2 infection and more than 6.9 million deaths due to COVID through May 2023. The WHO declared a pandemic due to the rapid spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, and the fight against this pandemic is not over yet. Important reasons for virus spread include the lack of detection kits, appropriate detection techniques, delay in detection, asymptomatic cases and failure in mass screening. In the last 3 years, several researchers and medical companies have introduced successful test kits to detect the infection of symptomatic patients in real time, which was necessary to monitor the spread. However, it is also important to have information on asymptomatic cases, which can be obtained by antibody testing for the SARS-CoV-2 virus. In this work, we developed a simple, advantageous immobilization procedure for rapidly detecting the SARS-CoV-2 spike protein. Carbon-MEMS-derived glassy carbon (GC) is used as the sensor electrode, and the detection is based on covalently linking the SARS-CoV-2 antibody to the GC surface. Glutaraldehyde was used as a cross-linker between the antibody and glassy carbon electrode (GCE). The binding was investigated using Fourier transform infrared spectroscopy (FTIR) characterization and cyclic voltammetric (CV) analysis. Electrochemical impedance spectroscopy (EIS) was utilized to measure the change in total impedance before and after incubation of the SARS-CoV-2 antibody with various concentrations of SARS-CoV-2 spike protein. The developed sensor can sense 1 fg/ml to 1 µg/ml SARS-CoV-2 spike protein. This detection is label-free, and the chances of false positives are minimal. The calculated LOD was ~31 copies of viral RNA/mL. The coefficient of variation (CV) number is calculated from EIS data at 100 Hz, which is found to be 0.398%. The developed sensor may be used for mass screening because it is cost-effective.
Phenotypic similarity-based approach for variant prioritization for unsolved rare disease: a preliminary methodological report
Authors: Lagorce David , Lebreton Emeline , Matalonga Leslie , Hongnat Oscar , Chahdil Maroua , Piscia Davide , Paramonov Ida , Ellwanger Kornelia , Köhler Sebastian , Robinson Peter , Graessner Holm , Beltran Sergi , Lucano Caterina , Hanauer Marc , Rath Ana 
Published: November 2023

AbstractRare diseases (RD) have a prevalence of not more than 1/2000 persons in the European population, and are characterised by the difficulty experienced in obtaining a correct and timely diagnosis. According to Orphanet, 72.5% of RD have a genetic origin although 35% of them do not yet have an identified causative gene. A significant proportion of patients suspected to have a genetic RD receive an inconclusive exome/genome sequencing. Working towards the International Rare Diseases Research Consortium (IRDiRC)’s goal for 2027 to ensure that all people living with a RD receive a diagnosis within one year of coming to medical attention, the Solve-RD project aims to identify the molecular causes underlying undiagnosed RD. As part of this strategy, we developed a phenotypic similarity-based variant prioritization methodology comparing submitted cases with other submitted cases and with known RD in Orphanet. Three complementary approaches based on phenotypic similarity calculations using the Human Phenotype Ontology (HPO), the Orphanet Rare Diseases Ontology (ORDO) and the HPO-ORDO Ontological Module (HOOM) were developed; genomic data reanalysis was performed by the RD-Connect Genome-Phenome Analysis Platform (GPAP). The methodology was tested in 4 exemplary cases discussed with experts from European Reference Networks. Variants of interest (pathogenic or likely pathogenic) were detected in 8.8% of the 725 cases clustered by similarity calculations. Diagnostic hypotheses were validated in 42.1% of them and needed further exploration in another 10.9%. Based on the promising results, we are devising an automated standardized phenotypic-based re-analysis pipeline to be applied to the entire unsolved cases cohort.
Recent research progress on the passivation and selective oxidation for the 3d-transition-metal and refractory multi-principal element alloys
Authors: Wang Zening , Yan Yu , Wu Yuan , Zhang Yi , Zhao Xinpeng , Su Yanjing , Qiao Lijie 
Published: November 2023

AbstractThe wide range of alloy composition controllability for multi-principal element alloys (MPEAs) may provide a great opportunity for discovering special forms of surface oxides to improve the corrosion and oxidation resistance in extreme environments. Changing the type and content of promoting passivation elements would not only change the microstructure of the alloy but also significantly affect the composition and structure of the surface passive film, resulting in a strong impact on the corrosion and oxidation resistance of the alloy. This article reviews recent research on the effects of alloying elements on the passivation properties, the contribution of each alloying element, and the synergistic effect between the elements on the passivation mechanisms and electrochemical dissolution characteristics of surface passive films that form on some MPEAs. In addition, the composition and structural characteristics of surface oxides relevant to the selective oxidation of elements are elaborated upon. Finally, several open questions and recommendations for research directions regarding the passivation and selective oxidation of MPEAs were provided to guide future exploration.
Pseudogap behavior in charge density wave kagome material ScV6Sn6 revealed by magnetotransport measurements
Authors: DeStefano Jonathan M. , Rosenberg Elliott , Peek Olivia , Lee Yongbin , Liu Zhaoyu , Jiang Qianni , Ke Liqin , Chu Jiun-Haw 
Published: November 2023

AbstractOver the last few years, significant attention has been devoted to studying the kagome materialsAV3Sb5(A = K, Rb, Cs) due to their unconventional superconductivity and charge density wave (CDW) ordering. Recently$${{{{\rm{ScV}}}}}_{6}{{{{\rm{Sn}}}}}_{6}$$ScV6Sn6was found to host a CDW below ≈ 90 K, and, likeAV3Sb5, it contains a kagome lattice comprised only of V ions. Here we present a comprehensive magnetotransport study on$${{{{\rm{ScV}}}}}_{6}{{{{\rm{Sn}}}}}_{6}$$ScV6Sn6. We discovered several anomalous transport phenomena above the CDW ordering temperature, including insulating behavior in interlayer resistivity, a strongly temperature-dependent Hall coefficient, and a violation of Kohler’s rule. All these anomalies can be consistently explained by a progressive decrease in carrier densities with decreasing temperature, suggesting the formation of a pseudogap. Our findings suggest that high-temperature CDW fluctuations play a significant role in determining the normal state electronic properties of$${{{{\rm{ScV}}}}}_{6}{{{{\rm{Sn}}}}}_{6}$$ScV6Sn6.
Identification of the flavivirus conserved residues in the envelope protein hinge region for the rational design of a candidate West Nile live-attenuated vaccine
Authors: Maloney Bailey E. , Carpio Kassandra L. , Bilyeu Ashley N. , Saunders Danielle R. D. , Park So Lee , Pohl Adrienne E. , Ball Natalia Costa , Raetz Janae L. , Huang Claire Y. , Higgs Stephen , Barrett Alan D. T. , Roman-Sosa Gleyder , Kenney Joanie L. , Vanlandingham Dana L. , Huang Yan-Jang S. 
Published: November 2023

AbstractThe flavivirus envelope protein is a class II fusion protein that drives flavivirus-cell membrane fusion. The membrane fusion process is triggered by the conformational change of the E protein from dimer in the virion to trimer, which involves the rearrangement of three domains, EDI, EDII, and EDIII. The movement between EDI and EDII initiates the formation of the E protein trimer. The EDI-EDII hinge region utilizes four motifs to exert the hinge effect at the interdomain region and is crucial for the membrane fusion activity of the E protein. Using West Nile virus (WNV) NY99 strain derived from an infectious clone, we investigated the role of eight flavivirus-conserved hydrophobic residues in the EDI-EDII hinge region in the conformational change of E protein from dimer to trimer and viral entry. Single mutations of the E-A54, E-I130, E-I135, E-I196, and E-Y201 residues affected infectivity. Importantly, the E-A54I and E-Y201P mutations fully attenuated the mouse neuroinvasive phenotype of WNV. The results suggest that multiple flavivirus-conserved hydrophobic residues in the EDI-EDII hinge region play a critical role in the structure–function of the E protein and some contribute to the virulence phenotype of flaviviruses as demonstrated by the attenuation of the mouse neuroinvasive phenotype of WNV. Thus, as a proof of concept, residues in the EDI-EDII hinge region are proposed targets to engineer attenuating mutations for inclusion in the rational design of candidate live-attenuated flavivirus vaccines.
Genetics and epidemiology of mutational barcode-defined clonal hematopoiesis
Authors: Stacey Simon N. , Zink Florian , Halldorsson Gisli H. , Stefansdottir Lilja , Gudjonsson Sigurjon A. , Einarsson Gudmundur , Hjörleifsson Grimur , Eiriksdottir Thjodbjorg , Helgadottir Anna , Björnsdottir Gyda , Thorgeirsson Thorgeir E. , Olafsdottir Thorunn A. , Jonsdottir Ingileif , Gretarsdottir Solveig , Tragante Vinicius , Magnusson Magnus K. , Jonsson Hakon , Gudmundsson Julius , Olafsson Sigurgeir , Holm Hilma , Gudbjartsson Daniel F. , Sulem Patrick , Helgason Agnar , Thorsteinsdottir Unnur , Tryggvadottir Laufey , Rafnar Thorunn , Melsted Pall , Ulfarsson Magnus Ö. , Vidarsson Brynjar , Thorleifsson Gudmar , Stefansson Kari 
Published: November 2023

AbstractClonal hematopoiesis (CH) arises when a substantial proportion of mature blood cells is derived from a single hematopoietic stem cell lineage. Using whole-genome sequencing of 45,510 Icelandic and 130,709 UK Biobank participants combined with a mutational barcode method, we identified 16,306 people with CH. Prevalence approaches 50% in elderly participants. Smoking demonstrates a dosage-dependent impact on risk of CH. CH associates with several smoking-related diseases. Contrary to published claims, we find no evidence that CH is associated with cardiovascular disease. We provide evidence that CH is driven by genes that are commonly mutated in myeloid neoplasia and implicate several new driver genes. The presence and nature of a driver mutation alters the risk profile for hematological disorders. Nevertheless, most CH cases have no known driver mutations. A CH genome-wide association study identified 25 loci, including 19 not implicated previously in CH. Splicing, protein and expression quantitative trait loci were identified for CD164 and TCL1A.
Harnessing CD3 diversity to optimize CAR T cells
Authors: Velasco Cárdenas Rubí M.-H. , Brandl Simon M. , Meléndez Ana Valeria , Schlaak Alexandra Emilia , Buschky Annabelle , Peters Timo , Beier Fabian , Serrels Bryan , Taromi Sanaz , Raute Katrin , Hauri Simon , Gstaiger Matthias , Lassmann Silke , Huppa Johannes B. , Boerries Melanie , Andrieux Geoffroy , Bengsch Bertram , Schamel Wolfgang W. , Minguet Susana 
Published: November 2023

AbstractCurrent US Food and Drug Administration-approved chimeric antigen receptor (CAR) T cells harbor the T cell receptor (TCR)-derived ζ chain as an intracellular activation domain in addition to costimulatory domains. The functionality in a CAR format of the other chains of the TCR complex, namely CD3δ, CD3ε and CD3γ, instead of ζ, remains unknown. In the present study, we have systematically engineered new CD3 CARs, each containing only one of the CD3 intracellular domains. We found that CARs containing CD3δ, CD3ε or CD3γ cytoplasmic tails outperformed the conventional ζ CAR T cells in vivo. Transcriptomic and proteomic analysis revealed differences in activation potential, metabolism and stimulation-induced T cell dysfunctionality that mechanistically explain the enhanced anti-tumor performance. Furthermore, dimerization of the CARs improved their overall functionality. Using these CARs as minimalistic and synthetic surrogate TCRs, we have identified the phosphatase SHP-1 as a new interaction partner of CD3δ that binds the CD3δ–ITAM on phosphorylation of its C-terminal tyrosine. SHP-1 attenuates and restrains activation signals and might thus prevent exhaustion and dysfunction. These new insights into T cell activation could promote the rational redesign of synthetic antigen receptors to improve cancer immunotherapy.
Genetically encoded multimeric tags for subcellular protein localization in cryo-EM
Authors: Fung Herman K. H. , Hayashi Yuki , Salo Veijo T. , Babenko Anastasiia , Zagoriy Ievgeniia , Brunner Andreas , Ellenberg Jan , Müller Christoph W. , Cuylen-Haering Sara , Mahamid Julia 
Published: November 2023

AbstractCryo-electron tomography (cryo-ET) allows for label-free high-resolution imaging of macromolecular assemblies in their native cellular context. However, the localization of macromolecules of interest in tomographic volumes can be challenging. Here we present a ligand-inducible labeling strategy for intracellular proteins based on fluorescent, 25-nm-sized, genetically encoded multimeric particles (GEMs). The particles exhibit recognizable structural signatures, enabling their automated detection in cryo-ET data by convolutional neural networks. The coupling of GEMs to green fluorescent protein-tagged macromolecules of interest is triggered by addition of a small-molecule ligand, allowing for time-controlled labeling to minimize disturbance to native protein function. We demonstrate the applicability of GEMs for subcellular-level localization of endogenous and overexpressed proteins across different organelles in human cells using cryo-correlative fluorescence and cryo-ET imaging. We describe means for quantifying labeling specificity and efficiency, and for systematic optimization for rare and abundant protein targets, with emphasis on assessing the potential effects of labeling on protein function.
Unravelling the hidden diversity of cave mycobiota in Thailand’s Satun Geopark
Authors: Suetrong Satinee , Preedanon Sita , Kobmoo Noppol , Srihom Charisa , Somrithipol Sayanh , Saengkaewsuk Supicha , Srikitikulchai Prasert , Klaysuban Anupong , Nuankaew Salilaporn , Chuaseeharonnachai Charuwan , Chainuwong Boonchuai , Muangsong Chotika , Malimart Kittapha , Rungjindamai Nattawut , Siripornpibul Chaiyaporn , Chareonkunnatum Umapon , Ploydam Bumrungrat , Thungprue Narongrit , Tongsima Sissades , Zhang Zhi-Feng , Cai Lei , Boonyuen Nattawut 
Published: November 2023

AbstractKarst caves are distinctive ecosystems that have limited nutrients, darkness, low to moderate temperatures, and high moisture levels, which allow for a diverse range of fungal communities to thrive. Despite their significance, little is understood about the fungi found in karst caves in Thailand. In 2019, we studied the cultured mycobiota from five substrate types (air, water, rock, soil/sediment, and organic debris) in two karst caves (Le Stegodon and Phu Pha Phet Caves) of the Satun UNESCO Global Geopark, southern Thailand. A cumulative count of 829 distinct fungal morphological types was identified, encompassing 319 fungal culturable were observed. Based on preliminary analyses of the internal transcribed spacer (ITS) sequence using BLAST searches, the most common phylum among the fungal morphotypes was Ascomycota, harboring 282 species in 91 genera, 93.4% of which were distributed in the classes Eurotiomycetes, Sordariomycetes, and Dothideomycetes. The most common fungal genera identified in the two karst caves were Aspergillus, Penicillium, Cladosporium, Talaromyces, Xylaria, and Trichoderma, with 45, 41, 24, 14, 14, and 6 species identified, respectively. Discovering fungi in Thai karst caves highlights the extensive fungal diversity in the Satun UNESCO Global Geopark, implying undiscovered species, and emphasizing the need for comprehensive investigations in other unexplored Thai karst caves.
Dynamic analysis of cylindrical foundations under torsional loading via generic discrete-element models simulating soil stratum
Authors: Chen Shi-Shuenn , Kao Chi-Jou , Shi Jun-Yang 
Published: November 2023

AbstractTorsional vibration, considering soil-structure interaction, is essential to the dynamic response of most irregular structures. A systematic method is developed to seek the optimal simplified model among multiple model candidates for uniform soil on rigid base regarding dynamic soil-foundation interactions. A generic model is identified by the proposed method to simulate the cylindrical foundation resting on or embedded in the soil stratum under torsional vibrations. Various soil-foundation parameters, mainly including embedment depth, layer depth, and mass ratios, are considered in the simplified analysis. The frequency-magnification curves and resonant responses of the foundation using the generic model agree well with theoretical solutions. The resultant resonant magnification factors against mass ratios clearly illustrate the impacts of the whipping effect resulting from the soil-foundation interactions. The generic model performs better and adopts fewer parameters than the existing model to simulate the soil-foundation interactions. In addition, dimensionless parametric charts are presented to estimate foundation responses for engineering applications quickly. The proposed charts also significantly overcome the limitations of the Wolf and Paronesso model. The generic model shows efficiency and accuracy in simulating the soil stratum. This research could contribute to the foundation vibration analysis for torsional responses.