bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evidence of Reflected Internal Solitary Waves in the Strait of Gibraltar
Authors: Roustan Jean‐Baptiste , Bordois Lucie , Garciá‐Lafuente Jesús , Dumas Franck , Auclair Francis , Carton Xavier 
Published: February 2024

AbstractLarge‐amplitude internal solitary waves (ISWs) propagating eastward toward the Alboran Sea have long been known in the Strait of Gibraltar. New in‐situ data and satellite images evidence northwestward propagating ISWs. These waves are probably the reflection of the well‐known eastward propagating wave along the Moroccan shelf. A simple 2D‐vertical section, run with the compressible non‐hydrostatic Coastal and Regional Ocean COmmunity model, illustrates that the Moroccan slope is conducive to reflection of incident solitary waves of amplitude observed in the Strait of Gibraltar. A clear signature of these waves in the Tarifa high‐frequency sea level oscillations is depicted that paves the way to studies of the seasonality of ISWs in the Strait of Gibraltar with the long‐time series of sea level at Tarifa. The polarity of the reflected waves, observed with Acoustic Doppler Current Profilers/Conductivity‐Temperature‐Depth array moorings, presents a slight variability possibly due to the internal tide oscillations. The reflected ISWs arrives at the mooring location in phase with the peak of the internal tide. For the strongest tide, the pynocline approaches a critical point where the polarity of the ISWs might reverse.
Depositional and Diagenetic Sulfates of Hogwallow Flats and Yori Pass, Jezero Crater: Evaluating Preservation Potential of Environmental Indicators and Possible Biosignatures From Past Martian Surface Waters and Groundwaters
Authors: Benison Kathleen C. , Gill Karena K. , Sharma Sunanda , Siljeström Sandra , Zawaski Mike , Bosak Tanja , Broz Adrian , Clark Benton C. , Cloutis Edward , Czaja Andrew D. , Flannery David , Fornaro Teresa , Gómez Felipe , Hand Kevin , Herd Chris D. K. , Johnson Jeffrey R. , Madariaga Juan Manuel , Madsen Morten B. , Martinez‐Frías Jesús , Nachon Marion , Núñez Jorge I. , Pedersen David A. K. , Randazzo Nicholas , Shuster David L. , Simon Justin , Steele Andrew , Tate Christian , Treiman Allan , Uckert Kyle , Williams Amy J. , Yanchilina Anastasia 
Published: February 2024

AbstractThe Mars 2020 Perseverance rover has examined and sampled sulfate‐rich clastic rocks from the Hogwallow Flats member at Hawksbill Gap and the Yori Pass member at Cape Nukshak. Both strata are located on the Jezero crater western fan front, are lithologically and stratigraphically similar, and have been assigned to the Shenandoah formation. In situ analyses demonstrate that these are fine‐grained sandstones composed of phyllosilicates, hematite, Ca‐sulfates, Fe‐Mg‐sulfates, ferric sulfates, and possibly chloride salts. Sulfate minerals are found both as depositional grains and diagenetic features, including intergranular cement and vein‐ and vug‐cements. Here, we describe the possibility of various sulfate phases to preserve potential biosignatures and the record of paleoenvironmental conditions in fluid and solid inclusions, based on findings from analog sulfate‐rich rocks on Earth. The samples collected from these outcrops, Hazeltop and Bearwallow from Hogwallow Flats, and Kukaklek from Yori Pass, should be examined for such potential biosignatures and environmental indicators upon return to Earth.
An Efficient and Robust Estimation of Spatio‐Temporally Distributed Parameters in Dynamic Models by an Ensemble Kalman Filter
Authors: Sawada Yohei , Duc Le 
Published: February 2024

AbstractThe accuracy of Earth system models is compromised by unknown and/or unresolved dynamics, making the quantification of systematic model errors essential. While a model parameter estimation, which allows parameters to change spatio‐temporally, shows promise in quantifying and mitigating systematic model errors, the estimation of the spatio‐temporally distributed model parameters has been practically challenging. Here we present an efficient and practical method to estimate time‐varying parameters in high‐dimensional spaces. In our proposed method, Hybrid Offline and Online Parameter Estimation with ensemble Kalman filtering (HOOPE‐EnKF), model parameters estimated by EnKF are constrained by results of offline batch optimization, in which the posterior distribution of model parameters is obtained by comparing simulated and observed climatological variables. HOOPE‐EnKF outperforms the original EnKF in synthetic experiments using a two‐scale Lorenz96 model and a simple global general circulation model. One advantage of HOOPE‐EnKF over traditional EnKFs is that its performance is not greatly affected by inflation factors for model parameters, thus eliminating the need for extensive tuning of inflation factors. We thoroughly discuss the potential of HOOPE‐EnKF as a practical method for improving parameterizations of process‐based models and prediction in real‐world applications such as numerical weather prediction.
High‐Resolution Terrestrial Water Storage Estimates From GRACE and Land Surface Models
Authors: Kim Jae‐Seung , Seo Ki‐Weon , Kim Byeong‐Hoon , Ryu Dongryeol , Chen Jianli , Wilson Clark 
Published: February 2024

AbstractTerrestrial Water Storage (TWS) changes have been estimated at basin to continental scales from gravity variations using data from the Gravity Recovery and Climate Experiment (GRACE) satellites since 2002. The relatively low spatial resolution (∼300 km) of GRACE observations has been a main limitation in such studies. Various data processing strategies, including mascons, forward modeling, and constrained linear deconvolution (CLD), have been employed to address this limitation. Here we develop a revised CLD method to obtain a TWS estimate that combines GRACE observations with much higher spatial resolution land surface models. The revised CLD constrains model estimates to agree with GRACE TWS when smoothed. As an example, we apply the method to obtain a high spatial resolution TWS estimate in Australia. We assess the accuracy of the approach using synthetic GRACE data.
Ultracompact mirror device for forming 20-nm achromatic soft-X-ray focus toward multimodal and multicolor nanoanalyses
Authors: Shimamura Takenori , Takeo Yoko , Moriya Fumika , Kimura Takashi , Shimura Mari , Senba Yasunori , Kishimoto Hikaru , Ohashi Haruhiko , Shimba Kenta , Jimbo Yasuhiko , Mimura Hidekazu 
Published: February 2024

AbstractNanoscale soft-X-ray microscopy is a powerful analysis tool in biological, chemical, and physical sciences. To enhance its probe sensitivity and leverage multimodal soft-X-ray microscopy, precise achromatic focusing devices, which are challenging to fabricate, are essential. Here, we develop an ultracompact Kirkpatrick-Baez (ucKB) mirror, which is ideal for the high-performance nanofocusing of broadband-energy X-rays. We apply our advanced fabrication techniques and short-focal-length strategy to realize diffraction-limited focusing over the entire soft-X-ray range. We achieve a focus size of 20.4 nm at 2 keV, which represents a significant improvement in achromatic soft-X-ray focusing. The ucKB mirror extends soft-X-ray fluorescence microscopy by producing a bicolor nanoprobe with a 1- or 2-keV photon energy. We propose a subcellular chemical mapping method that allows a comprehensive analysis of specimen morphology and the distribution of light elements and metal elements. ucKB mirrors will improve soft-X-ray nanoanalyses by facilitating photon-hungry, multimodal, and polychromatic methods, even with table-top X-ray sources.
Delayed increase in stone tool cutting-edge productivity at the Middle-Upper Paleolithic transition in southern Jordan
Authors: Kadowaki Seiji , Wakano Joe Yuichiro , Tamura Toru , Watanabe Ayami , Hirose Masato , Suga Eiki , Tsukada Kazuhiro , Tarawneh Oday , Massadeh Sate 
Published: February 2024

AbstractAlthough the lithic cutting-edge productivity has long been recognized as a quantifiable aspect of prehistoric human technological evolution, there remains uncertainty how the productivity changed during the Middle-to-Upper Paleolithic transition. Here we present the cutting-edge productivity of eight lithic assemblages in the eastern Mediterranean region that represent a chrono-cultural sequence including the Late Middle Paleolithic, Initial Upper Paleolithic, the Early Upper Paleolithic, and the Epipaleolithic. The results show that a major increase in the cutting-edge productivity does not coincide with the conventional Middle-Upper Paleolithic boundary characterized by the increase in blades in the Initial Upper Paleolithic, but it occurs later in association with the development of bladelet technology in the Early Upper Paleolithic. Given increasing discussions on the complexity of Middle-Upper Paleolithic cultural changes, it may be fruitful to have a long-term perspective and employ consistent criteria for diachronic comparisons to make objective assessment of how cultural changes proceeded across conventional chrono-cultural boundaries.
Structural basis for lysophosphatidylserine recognition by GPR34
Authors: Izume Tamaki , Kawahara Ryo , Uwamizu Akiharu , Chen Luying , Yaginuma Shun , Omi Jumpei , Kawana Hiroki , Hou Fengjue , Sano Fumiya K. , Tanaka Tatsuki , Kobayashi Kazuhiro , Okamoto Hiroyuki H. , Kise Yoshiaki , Ohwada Tomohiko , Aoki Junken , Shihoya Wataru , Nureki Osamu 
Published: February 2024

AbstractGPR34 is a recently identified G-protein coupled receptor, which has an immunomodulatory role and recognizes lysophosphatidylserine (LysoPS) as a putative ligand. Here, we report cryo-electron microscopy structures of human GPR34-Gi complex bound with one of two ligands bound: either the LysoPS analogue S3E-LysoPS, or M1, a derivative of S3E-LysoPS in which oleic acid is substituted with a metabolically stable aromatic fatty acid surrogate. The ligand-binding pocket is laterally open toward the membrane, allowing lateral entry of lipidic agonists into the cavity. The amine and carboxylate groups of the serine moiety are recognized by the charged residue cluster. The acyl chain of S3E-LysoPS is bent and fits into the L-shaped hydrophobic pocket in TM4-5 gap, and the aromatic fatty acid surrogate of M1 fits more appropriately. Molecular dynamics simulations further account for the LysoPS-regioselectivity of GPR34. Thus, using a series of structural and physiological experiments, we provide evidence that chemically unstable 2-acyl LysoPS is the physiological ligand for GPR34. Overall, we anticipate the present structures will pave the way for development of novel anticancer drugs that specifically target GPR34.
ASPSCR1-TFE3 reprograms transcription by organizing enhancer loops around hexameric VCP/p97
Authors: Pozner Amir , Li Li , Verma Shiv Prakash , Wang Shuxin , Barrott Jared J. , Nelson Mary L. , Yu Jamie S. E. , Negri Gian Luca , Colborne Shane , Hughes Christopher S. , Zhu Ju-Fen , Lambert Sydney L. , Carroll Lara S. , Smith-Fry Kyllie , Stewart Michael G. , Kannan Sarmishta , Jensen Bodrie , John Cini M. , Sikdar Saif , Liu Hongrui , Dang Ngoc Ha , Bourdage Jennifer , Li Jinxiu , Vahrenkamp Jeffery M. , Mortenson Katelyn L. , Groundland John S. , Wustrack Rosanna , Senger Donna L. , Zemp Franz J. , Mahoney Douglas J. , Gertz Jason , Zhang Xiaoyang , Lazar Alexander J. , Hirst Martin , Morin Gregg B. , Nielsen Torsten O. , Shen Peter S. , Jones Kevin B. 
Published: February 2024

AbstractThe t(X,17) chromosomal translocation, generating the ASPSCR1::TFE3 fusion oncoprotein, is the singular genetic driver of alveolar soft part sarcoma (ASPS) and some Xp11-rearranged renal cell carcinomas (RCCs), frustrating efforts to identify therapeutic targets for these rare cancers. Here, proteomic analysis identifies VCP/p97, an AAA+ ATPase with known segregase function, as strongly enriched in co-immunoprecipitated nuclear complexes with ASPSCR1::TFE3. We demonstrate that VCP is a likely obligate co-factor of ASPSCR1::TFE3, one of the only such fusion oncoprotein co-factors identified in cancer biology. Specifically, VCP co-distributes with ASPSCR1::TFE3 across chromatin in association with enhancers genome-wide. VCP presence, its hexameric assembly, and its enzymatic function orchestrate the oncogenic transcriptional signature of ASPSCR1::TFE3, by facilitating assembly of higher-order chromatin conformation structures demonstrated by HiChIP. Finally, ASPSCR1::TFE3 and VCP demonstrate co-dependence for cancer cell proliferation and tumorigenesis in vitro and in ASPS and RCC mouse models, underscoring VCP’s potential as a novel therapeutic target.
Non-Abelian Floquet braiding and anomalous Dirac string phase in periodically driven systems
Authors: Slager Robert-Jan , Bouhon Adrien , Ünal F. Nur 
Published: February 2024

AbstractWhile a significant fraction of topological materials has been characterized using symmetry requirements1–4, the past two years have witnessed the rise of novel multi-gap dependent topological states5–9, the properties of which go beyond these approaches and are yet to be fully explored. Although already of active interest at equilibrium10–15, we show that the combination of out-of-equilibrium processes and multi-gap topological insights galvanize a new direction within topological phases of matter. We show that periodic driving can induce anomalous multi-gap topological properties that have no static counterpart. In particular, we identify Floquet-induced non-Abelian braiding, which in turn leads to a phase characterized by an anomalous Euler class, being the prime example of a multi-gap topological invariant. Most strikingly, we also retrieve the first example of an ‘anomalous Dirac string phase’. This gapped out-of-equilibrium phase features an unconventional Dirac string configuration that physically manifests itself via anomalous edge states on the boundary. Our results not only provide a stepping stone for the exploration of intrinsically dynamical and experimentally viable multi-gap topological phases, but also demonstrate periodic driving as a powerful way to observe these non-Abelian braiding processes notably in quantum simulators.
Androgen drives melanoma invasiveness and metastatic spread by inducing tumorigenic fucosylation
Authors: Liu Qian , Adhikari Emma , Lester Daniel K. , Fang Bin , Johnson Joseph O. , Tian Yijun , Mockabee-Macias Andrea T. , Izumi Victoria , Guzman Kelly M. , White Michael G. , Koomen John M. , Wargo Jennifer A. , Messina Jane L. , Qi Jianfei , Lau Eric K. 
Published: February 2024

AbstractMelanoma incidence and mortality rates are historically higher for men than women. Although emerging studies have highlighted tumorigenic roles for the male sex hormone androgen and its receptor (AR) in melanoma, cellular and molecular mechanisms underlying these sex-associated discrepancies are poorly defined. Here, we delineate a previously undisclosed mechanism by which androgen-activated AR transcriptionally upregulates fucosyltransferase 4 (FUT4) expression, which drives melanoma invasiveness by interfering with adherens junctions (AJs). Global phosphoproteomic and fucoproteomic profiling, coupled with in vitro and in vivo functional validation, further reveal that AR-induced FUT4 fucosylates L1 cell adhesion molecule (L1CAM), which is required for FUT4-increased metastatic capacity. Tumor microarray and gene expression analyses demonstrate that AR-FUT4-L1CAM-AJs signaling correlates with pathological staging in melanoma patients. By delineating key androgen-triggered signaling that enhances metastatic aggressiveness, our findings help explain sex-associated clinical outcome disparities and highlight AR/FUT4 and its effectors as potential prognostic biomarkers and therapeutic targets in melanoma.
Cryo-EM structure of the extracellular domain of murine Thrombopoietin Receptor in complex with Thrombopoietin
Authors: Sarson-Lawrence Kaiseal T. G. , Hardy Joshua M. , Iaria Josephine , Stockwell Dina , Behrens Kira , Saiyed Tamanna , Tan Cyrus , Jebeli Leila , Scott Nichollas E. , Dite Toby A. , Nicola Nicos A. , Leis Andrew P. , Babon Jeffrey J. , Kershaw Nadia J. 
Published: February 2024

AbstractThrombopoietin (Tpo) is the primary regulator of megakaryocyte and platelet numbers and is required for haematopoetic stem cell maintenance. Tpo functions by binding its receptor (TpoR, a homodimeric Class I cytokine receptor) and initiating cell proliferation or differentiation. Here we characterise the murine Tpo:TpoR signalling complex biochemically and structurally, using cryo-electron microscopy. Tpo uses opposing surfaces to recruit two copies of receptor, forming a 1:2 complex. Although it binds to the same, membrane-distal site on both receptor chains, it does so with significantly different affinities and its highly glycosylated C-terminal domain is not required. In one receptor chain, a large insertion, unique to TpoR, forms a partially structured loop that contacts cytokine. Tpo binding induces the juxtaposition of the two receptor chains adjacent to the cell membrane. The therapeutic agent romiplostim also targets the cytokine-binding site and the characterisation presented here supports the future development of improved TpoR agonists.
Programming crack patterns with light in colloidal plasmonic films
Authors: Thorimbert Fanny , Odziomek Mateusz , Chateau Denis , Parola Stéphane , Faustini Marco 
Published: February 2024

AbstractCrack formation observed across diverse fields like geology, nanotechnology, arts, structural engineering or surface science, is a chaotic and undesirable phenomenon, resulting in random patterns of cracks generally leading to material failure. Limiting the formation of cracks or “programming” the path of cracks is a great technological challenge since it holds promise to enhance material durability or even to develop low cost patterning methods. Drawing inspiration from negative phototropism in plants, we demonstrate the capability to organize, guide, replicate, or arrest crack propagation in colloidal films through remote light manipulation. The key consists in using plasmonic photothermal absorbers to generate “virtual” defects enabling controlled deviation of cracks. We engineer a dip-coating process coupled with selective light irradiation enabling simultaneous deposition and light-directed crack patterning. This approach represents a rare example of a robust self-assembly process with long-range order that can be programmed in both space and time.
Structural basis for the oligomerization-facilitated NLRP3 activation
Authors: Yu Xiaodi , Matico Rosalie E. , Miller Robyn , Chauhan Dhruv , Van Schoubroeck Bertrand , Grauwen Karolien , Suarez Javier , Pietrak Beth , Haloi Nandan , Yin Yanting , Tresadern Gary John , Perez-Benito Laura , Lindahl Erik , Bottelbergs Astrid , Oehlrich Daniel , Van Opdenbosch Nina , Sharma Sujata 
Published: February 2024

AbstractThe NACHT-, leucine-rich-repeat-, and pyrin domain-containing protein 3 (NLRP3) is a critical intracellular inflammasome sensor and an important clinical target against inflammation-driven human diseases. Recent studies have elucidated its transition from a closed cage to an activated disk-like inflammasome, but the intermediate activation mechanism remains elusive. Here we report the cryo-electron microscopy structure of NLRP3, which forms an open octamer and undergoes a ~ 90° hinge rotation at the NACHT domain. Mutations on open octamer’s interfaces reduce IL-1β signaling, highlighting its essential role in NLRP3 activation/inflammasome assembly. The centrosomal NIMA-related kinase 7 (NEK7) disrupts large NLRP3 oligomers and forms NEK7/NLRP3 monomers/dimers which is a critical step preceding the assembly of the disk-like inflammasome. These data demonstrate an oligomeric cooperative activation of NLRP3 and provide insight into its inflammasome assembly mechanism.
A mediator of OsbZIP46 deactivation and degradation negatively regulates seed dormancy in rice
Authors: Guo Naihui , Tang Shengjia , Wang Yakun , Chen Wei , An Ruihu , Ren Zongliang , Hu Shikai , Tang Shaoqing , Wei Xiangjin , Shao Gaoneng , Jiao Guiai , Xie Lihong , Wang Ling , Chen Ying , Zhao Fengli , Sheng Zhonghua , Hu Peisong 
Published: February 2024

AbstractPreharvest sprouting (PHS) is a deleterious phenotype that occurs frequently in rice-growing regions where the temperature and precipitation are high. It negatively affects yield, quality, and downstream grain processing. Seed dormancy is a trait related to PHS. Longer seed dormancy is preferred for rice production as it can prevent PHS. Here, we map QTLs associated with rice seed dormancy and clone Seed Dormancy 3.1 (SDR3.1) underlying one major QTL. SDR3.1 encodes a mediator of OsbZIP46 deactivation and degradation (MODD). We show that SDR3.1 negatively regulates seed dormancy by inhibiting the transcriptional activity of ABIs. In addition, we reveal two critical amino acids of SDR3.1 that are critical for the differences in seed dormancy between the Xian/indica and Geng/japonica cultivars. Further, SDR3.1 has been artificially selected during rice domestication. We propose a two-line model for the process of rice seed dormancy domestication from wild rice to modern cultivars. We believe the candidate gene and germplasm studied in this study would be beneficial for the genetic improvement of rice seed dormancy.
Diffusible fraction of niche BMP ligand safeguards stem-cell differentiation
Authors: Ridwan Sharif M. , Twillie Autumn , Poursaeid Samaneh , Beard Emma Kristine , Bener Muhammed Burak , Antel Matthew , Cowan Ann E. , Matsuda Shinya , Inaba Mayu 
Published: February 2024

AbstractDrosophila male germline stem cells (GSCs) reside at the tip of the testis and surround a cluster of niche cells. Decapentaplegic (Dpp) is one of the well-established ligands and has a major role in maintaining stem cells located in close proximity. However, the existence and the role of the diffusible fraction of Dpp outside of the niche have been unclear. Here, using genetically-encoded nanobodies called Morphotraps, we physically block Dpp diffusion without interfering with niche-stem cell signaling and find that a diffusible fraction of Dpp is required to ensure differentiation of GSC daughter cells, opposite of its role in maintenance of GSC in the niche. Our work provides an example in which a soluble niche ligand induces opposed cellular responses in stem cells versus in differentiating descendants to ensure spatial control of the niche. This may be a common mechanism to regulate tissue homeostasis.
Chemical, rheological, and sensorial properties of Baladi bread supplemented with buckwheat flour produced in Egypt
Authors: Hussein Ahmed M. S. , El-Aal Hala A. Abd , Morsy Nahla M. , Hassona Mohamed M. 
Published: February 2024

AbstractThis research aimed to enhance the nutritional and sensory qualities of Balady bread by adding locally Egyptian buckwheat flours, Fagopyrum esculentum (FE) and Fagopyrum tataricum (FT), to Hard Wheat Flour (HWF) 82% extraction at three levels (10%, 20%, and 30%). The chemical composition, rheological properties, color, sensory evaluation and stalling of the balady bread were determined. The chemical composition of raw materials revealed that FE was significantly (P ≤ 0.05) higher in protein and fat contents compared to HWF and FT. While FT was higher in fiber and ash contents. The findings show that a 30% replacement with FE or FT significantly enhances the bread's nutritional profile, notably increasing protein, fiber, ash, and moisture content. Rheological analysis revealed that FE and FT alter dough handling, with a notable improvement in dough stability and mixing tolerance at 30% FT. Sensory evaluation indicated acceptable qualities even at higher substitution levels, although 30% FE showed slight declines in certain attributes. Furthermore, bread supplemented with 30% FT demonstrated slower staling and potentially extended shelf life. These results highlight the potential of FE and FT as nutritional enhancers in bread formulations, with 30% FT emerging as the optimal replacement level for balancing nutritional benefits and sensory acceptance.