bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rupture Dynamics of Cascading Earthquakes in a Multiscale Fracture Network
Authors: Palgunadi Kadek Hendrawan , Gabriel Alice‐Agnes , Garagash Dmitry Igor , Ulrich Thomas , Mai Paul Martin 
Published: March 2024

AbstractFault‐damage zones comprise multiscale fracture networks that may slip dynamically and interact with the main fault during earthquake rupture. Using 3D dynamic rupture simulations and scale‐dependent fracture energy, we examine dynamic interactions of more than 800 intersecting multiscale fractures surrounding a listric fault, emulating a major listric fault and its damage zone. We investigate 10 distinct orientations of maximum horizontal stress, probing the conditions necessary for sustained slip within the fracture network or activating the main fault. Additionally, we assess the feasibility of nucleating dynamic rupture earthquake cascades from a distant fracture and investigate the sensitivity of fracture network cascading rupture to the effective normal stress level. We model either pure cascades or main fault rupture with limited off‐fault slip. We find that cascading ruptures within the fracture network are dynamically feasible under certain conditions, including: (a) the fracture energy scales with fracture and fault size, (b) favorable relative pre‐stress of fractures within the ambient stress field, and (c) close proximity of fractures. We find that cascading rupture within the fracture network discourages rupture on the main fault. Our simulations suggest that fractures with favorable relative pre‐stress, embedded within a fault damage zone, may lead to cascading earthquake rupture that shadows main fault slip. We find that such off‐fault events may reach moment magnitudes up to Mw ≈ 5.5, comparable to magnitudes that can be otherwise hosted by the main fault. Our findings offer insights into physical processes governing cascading earthquake dynamic rupture within multiscale fracture networks.
The Contribution of Aeolus Wind Observations to ECMWF Sea Surface Wind Forecasts
Authors: Zuo Haichen , Stoffelen Ad , Rennie Michael , Hasager Charlotte Bay 
Published: March 2024

AbstractAeolus is the first satellite mission focusing on wind profile detection from near the surface to about 30 km in height on a global scale. This study evaluates the contribution of Aeolus winds to sea surface wind forecasts geographically by further analyzing the Observing System Experiments from the European Centre for Medium‐Range Weather Forecasts (ECMWF) with scatterometer winds from the meteorological operational satellites (assimilated into the model) and the Haiyang‐2B satellite (not assimilated into the model). The findings indicate that Aeolus has the ability to reduce the root‐mean‐square difference between scatterometer winds and background forecasts (short‐range) by about 0.05%–0.16% on average for climatic regions, except for the meridional wind component in the tropics. Also, Aeolus can generally reduce zonal biases of the background forecasts, while its beneficial impact on meridional biases mainly occurs in the Northern Hemisphere extratropics and tropics. For medium‐range forecast assessments, as the forecast step extends up to day 5, the positive impact of Aeolus on sea surface wind forecasts becomes more evident and is even greater than 3%, especially for extratropical ocean regions in the Southern Hemisphere. Furthermore, the impact of Aeolus shows seasonal variation, with a substantial positive impact from September 2019 to February 2020 and a negative impact mainly in March, April, and May 2020.
Cognitive function based on theta-gamma coupling vs. clinical diagnosis in older adults with mild cognitive impairment with or without major depressive disorder
Authors: Brooks Heather , Wang Wei , Zomorrodi Reza , Blumberger Daniel M. , Bowie Christopher R. , Daskalakis Zafiris J. , Fischer Corinne E. , Flint Alastair J. , Herrmann Nathan , Kumar Sanjeev , Lanctôt Krista L. , Mah Linda , Mulsant Benoit H. , Pollock Bruce G. , Voineskos Aristotle N. , Rajji Tarek K. ,   the PACt-MD Study Group, Mulsant Benoit H. , Rajji Tarek K. , Herrmann Nathan , Pollock Bruce G. , Blumberger Daniel M. , Bowie Christopher R. , Butters Meryl A. , Fischer Corinne E. , Flint Alastair J. , Golas Angela , Graff Ariel , Kennedy James L. , Kumar Sanjeev , Lanctôt Krista L. , Lourenco Lillian , Mah Linda , Ovaysikia Shima , Rapoport Mark , Thorpe Kevin E. , Verhoeff Nicolaas P. L. G. , Voineskos Aristotle 
Published: March 2024

AbstractWhether individuals with mild cognitive impairment (MCI) and a history of major depressive disorder (MDD) are at a higher risk for cognitive decline than those with MCI alone is still not clear. Previous work suggests that a reduction in prefrontal cortical theta phase-gamma amplitude coupling (TGC) is an early marker of cognitive impairment. This study aimed to determine whether using a TGC cutoff is better at separating individuals with MCI or MCI with remitted MDD (MCI+rMDD) on cognitive performance than their clinical diagnosis. Our hypothesis was that global cognition would differ more between TGC-based groups than diagnostic groups. We analyzed data from 128 MCI (mean age: 71.8, SD: 7.3) and 85 MCI+rMDD (mean age: 70.9, SD: 4.7) participants. Participants completed a comprehensive neuropsychological battery; TGC was measured during the N-back task. An optimal TGC cutoff was determined during the performance of the 2-back. This TGC cutoff was used to classify participants into low vs. high-TGC groups. We then compared Cohen’s d of the difference in global cognition between the high and low TGC groups to Cohen’s d between the MCI and MCI+rMDD groups. We used bootstrapping to determine 95% confidence intervals for Cohen’s d values using the whole sample. As hypothesized, Cohen’s d for the difference in global cognition between the TGC groups was larger (0.64 [0.32, 0.88]) than between the diagnostic groups (0.10 [0.004, 0.37]) with a difference between these two Cohen’s d’s of 0.54 [0.10, 0.80]. Our findings suggest that TGC is a useful marker to identify individuals at high risk for cognitive decline, beyond clinical diagnosis. This could be due to TGC being a sensitive marker of prefrontal cortical dysfunction that would lead to an accelerated cognitive decline.
Performance of self-cured versus light-cured universal adhesive in patients with non-carious cervical lesions: 18-month randomized clinical trial
Authors: Ashour Aya Gamal , Abd ElAziz Rawda Hesham , Yassen Asmaa Ali 
Published: March 2024

Abstract
Objective
To evaluate the clinical performance of self versus light-cured universal adhesive in non-carious cervical lesions (NCCLs) after 18 months.

Materials and methods
Sixty-eight NCCLs in 28 patients were divided into two equal groups; G1: self-cured universal adhesive (Palfique,Tokuyama,Japan) and G2: light-cured universal adhesive (Single Bond Universal,3 M ESPE,USA). Nanohybrid resin composite (Z350XT, 3 M ESPE, USA) was used as a final restoration. Evaluation for fracture, loss of retention, marginal adaptation and discoloration were done after 1 week, 6,12, and 18 months using FDI criteria. Postoperative sensitivity was assessed after 1 week. Chi-Square and Mann-Whitney tests with statistical significance at (P ≤ 0.05) were used for intergroup comparison,while the intragroup one was performed using the Cochran’s Q and Friedman’s tests. Survival rate was analyzed using Kaplan-meier and Log-rank test.

Results
Both groups exhibited fracture and retention loss, however, there was statistically significant difference favoring the control group at 6 months (p = 0.0114,0.0016). For secondary outcomes, marginal adaptation and discoloration revealed no significant differences. For postoperative sensitivity, there was a significant difference favoring the control group (p = 0.0007, 0.0011). Palfique had 1.5 Relative-Risk (RR) after 6 months (95% CI 0.5659–4.2617; P = 0.3928) and 20% less risk of failure after 18 months (RR 0.8) (95% CI 0.4618–1.3858; P = 0.4260). Tested adhesives showed equal survival rate (P = 0.5685).

Conclusions
Both adhesives revealed similar clinical performance in restoring the NCCLs after 18 m, however, the early failure was more frequent in the self-cured universal adhesive.
Piplartine eliminates CD34 + AML stem/progenitor cells by inducing oxidative stress and suppressing NF-κB signalling
Authors: Rodrigues Ana Carolina B. da C. , Silva Suellen L. R. , Dias Ingrid R. S. B. , Costa Rafaela G. A. , Oliveira Maiara de S. , Soares Milena B. P. , Dias Rosane B. , Valverde Ludmila F. , Rocha Clarissa A. G. , Johnson Emily M. , Pina Cristina , Bezerra Daniel P. 
Published: March 2024

AbstractAcute myeloid leukaemia (AML) is a haematological malignancy characterised by the accumulation of transformed myeloid progenitors in the bone marrow. Piplartine (PL), also known as piperlongumine, is a pro-oxidant small molecule extracted from peppers that has demonstrated antineoplastic potential in solid tumours and other haematological malignancies. In this work, we explored the potential of PL to treat AML through the use of a combination of cellular and molecular analyses of primary and cultured leukaemia cells in vitro and in vivo. We showed that PL exhibits in vitro cytotoxicity against AML cells, including CD34+ leukaemia-propagating cells, but not healthy haematopoietic progenitors, suggesting anti-leukaemia selectivity. Mechanistically, PL treatment increased reactive oxygen species (ROS) levels and induced ROS-mediated apoptosis in AML cells, which could be prevented by treatment with the antioxidant scavenger N-acetyl-cysteine and the pancaspase inhibitor Z-VAD(OMe)-FMK. PL treatment reduced NFKB1 gene transcription and the level of NF-κB p65 (pS536), which was depleted from the nucleus of AML cells, indicating suppression of NF-κB p65 signalling. Significantly, PL suppressed AML development in a mouse xenograft model, and its combination with current AML treatments (cytarabine, daunorubicin and azacytidine) had synergistic effects, indicating translational therapeutic potential. Taken together, these data position PL as a novel anti-AML candidate drug that can target leukaemia stem/progenitors and is amenable to combinatorial therapeutic strategies.
Structure of prolylrapamycin: confirmation through a revised and detailed NMR assignment study
Authors: Mortoni Annalisa , Castelli Eugenio , Recca Teresa , Quadrelli Paolo 
Published: March 2024

AbstractA complete and detailed characterization of Rapamycin (1) and Prolylrapamycin (2) has been conducted by homo- and hetero-nuclear NMR experiments in DMSO-d6 along with HRMS and FT-IR spectra and DSCs analyses. The NMR experiments allowed the assignment of every single proton and carbon atom belonging to the two structures and the definitive confirm of the presence of a pyrrolidine ring in Prolylrapamycin (2) in place of the piperidine ring that characterizes the structure of Sirolimus.
Single cell atlas of Xenoturbella bocki highlights limited cell-type complexity
Authors: Robertson Helen E. , Sebé-Pedrós Arnau , Saudemont Baptiste , Loe-Mie Yann , Zakrzewski Anne-C. , Grau-Bové Xavier , Mailhe Marie-Pierre , Schiffer Philipp , Telford Maximilian J. , Marlow Heather 
Published: March 2024

AbstractPhylogenetic analyses over the last two decades have united a few small, and previously orphan clades, the nematodermatids, acoels and xenoturbelids, into the phylum Xenacoelomorpha. Some phylogenetic analyses support a sister relationship between Xenacoelomorpha and Ambulacraria (Xenambulacraria), while others suggest that Xenacoelomorpha may be sister to the rest of the Bilateria (Nephrozoa). An understanding of the cell type complements of Xenacoelomorphs is essential to assessing these alternatives as well as to our broader understanding of bilaterian cell type evolution. Employing whole organism single-cell RNA-seq in the marine xenacoelomorph worm Xenoturbella bocki, we show that Xenambulacrarian nerve nets share regulatory features and a peptidergic identity with those found in cnidarians and protostomes and more broadly share muscle and gland cell similarities with other metazoans. Taken together, these data are consistent with broad homologies of animal gland, muscle, and neurons as well as more specific affinities between Xenoturbella and acoel gut and epidermal tissues, consistent with the monophyly of Xenacoelomorpha.
SCGB1D2 inhibits growth of Borrelia burgdorferi and affects susceptibility to Lyme disease
Authors: Strausz Satu , Abner Erik , Blacker Grace , Galloway Sarah , Hansen Paige , Feng Qingying , Lee Brandon T. , Jones Samuel E. , Haapaniemi Hele , Raak Sten , Nahass George Ronald , Sanders Erin ,   FinnGen,   Estonian Genome Centre,   Estonian Biobank Research Team, Soodla Pilleriin , Võsa Urmo , Esko Tõnu , Sinnott-Armstrong Nasa , Weissman Irving L. , Daly Mark , Aivelo Tuomas , Tal Michal Caspi , Ollila Hanna M. 
Published: March 2024

AbstractLyme disease is a tick-borne disease caused by bacteria of the genus Borrelia. The host factors that modulate susceptibility for Lyme disease have remained mostly unknown. Using epidemiological and genetic data from FinnGen and Estonian Biobank, we identify two previously known variants and an unknown common missense variant at the gene encoding for Secretoglobin family 1D member 2 (SCGB1D2) protein that increases the susceptibility for Lyme disease. Using live Borrelia burgdorferi (Bb) we find that recombinant reference SCGB1D2 protein inhibits the growth of Bb in vitro more efficiently than the recombinant protein with SCGB1D2 P53L deleterious missense variant. Finally, using an in vivo murine infection model we show that recombinant SCGB1D2 prevents infection by Borrelia in vivo. Together, these data suggest that SCGB1D2 is a host defense factor present in the skin, sweat, and other secretions which protects against Bb infection and opens an exciting therapeutic avenue for Lyme disease.
Genetic imputation of kidney transcriptome, proteome and multi-omics illuminates new blood pressure and hypertension targets
Authors: Xu Xiaoguang , Khunsriraksakul Chachrit , Eales James M. , Rubin Sebastien , Scannali David , Saluja Sushant , Talavera David , Markus Havell , Wang Lida , Drzal Maciej , Maan Akhlaq , Lay Abigail C. , Prestes Priscilla R. , Regan Jeniece , Diwadkar Avantika R. , Denniff Matthew , Rempega Grzegorz , Ryszawy Jakub , Król Robert , Dormer John P. , Szulinska Monika , Walczak Marta , Antczak Andrzej , Matías-García Pamela R. , Waldenberger Melanie , Woolf Adrian S. , Keavney Bernard , Zukowska-Szczechowska Ewa , Wystrychowski Wojciech , Zywiec Joanna , Bogdanski Pawel , Danser A. H. Jan , Samani Nilesh J. , Guzik Tomasz J. , Morris Andrew P. , Liu Dajiang J. , Charchar Fadi J. ,   Human Kidney Tissue Resource Study Group, Tomaszewski Maciej 
Published: March 2024

AbstractGenetic mechanisms of blood pressure (BP) regulation remain poorly defined. Using kidney-specific epigenomic annotations and 3D genome information we generated and validated gene expression prediction models for the purpose of transcriptome-wide association studies in 700 human kidneys. We identified 889 kidney genes associated with BP of which 399 were prioritised as contributors to BP regulation. Imputation of kidney proteome and microRNAome uncovered 97 renal proteins and 11 miRNAs associated with BP. Integration with plasma proteomics and metabolomics illuminated circulating levels of myo-inositol, 4-guanidinobutanoate and angiotensinogen as downstream effectors of several kidney BP genes (SLC5A11,AGMAT,AGT, respectively). We showed that genetically determined reduction in renal expression may mimic the effects of rare loss-of-function variants on kidney mRNA/protein and lead to an increase in BP (e.g.,ENPEP). We demonstrated a strong correlation (r = 0.81) in expression of protein-coding genes between cells harvested from urine and the kidney highlighting a diagnostic potential of urinary cell transcriptomics. We uncovered adenylyl cyclase activators as a repurposing opportunity for hypertension and illustrated examples of BP-elevating effects of anticancer drugs (e.g. tubulin polymerisation inhibitors). Collectively, our studies provide new biological insights into genetic regulation of BP with potential to drive clinical translation in hypertension.
Genetic gains underpinning a little-known strawberry Green Revolution
Authors: Feldmann Mitchell J. , Pincot Dominique D. A. , Cole Glenn S. , Knapp Steven J. 
Published: March 2024

AbstractThe annual production of strawberry has increased by one million tonnes in the US and 8.4 million tonnes worldwide since 1960. Here we show that the US expansion was driven by genetic gains from Green Revolution breeding and production advances that increased yields by 2,755%. Using a California population with a century-long breeding history and phenotypes of hybrids observed in coastal California environments, we estimate that breeding has increased fruit yields by 2,974-6,636%, counts by 1,454-3,940%, weights by 228-504%, and firmness by 239-769%. Using genomic prediction approaches, we pinpoint the origin of the Green Revolution to the early 1950s and uncover significant increases in additive genetic variation caused by transgressive segregation and phenotypic diversification. Lastly, we show that the most consequential Green Revolution breeding breakthrough was the introduction of photoperiod-insensitive, PERPETUAL FLOWERING hybrids in the 1970s that doubled yields and drove the dramatic expansion of strawberry production in California.
Face and context integration in emotion inference is limited and variable across categories and individuals
Authors: Goel Srishti , Jara-Ettinger Julian , Ong Desmond C. , Gendron Maria 
Published: March 2024

AbstractThe ability to make nuanced inferences about other people’s emotional states is central to social functioning. While emotion inferences can be sensitive to both facial movements and the situational context that they occur in, relatively little is understood about when these two sources of information are integrated across emotion categories and individuals. In a series of studies, we use one archival and five empirical datasets to demonstrate that people could be integrating, but that emotion inferences are just as well (and sometimes better) captured by knowledge of the situation alone, while isolated facial cues are insufficient. Further, people integrate facial cues more for categories for which they most frequently encounter facial expressions in everyday life (e.g.,happiness). People are also moderately stable over time in their reliance on situational cues and integration of cues and those who reliably utilize situation cues more also have better situated emotion knowledge. These findings underscore the importance of studying variability in reliance on and integration of cues.
Fibroblast-specific PRMT5 deficiency suppresses cardiac fibrosis and left ventricular dysfunction in male mice
Authors: Katanasaka Yasufumi , Yabe Harumi , Murata Noriyuki , Sobukawa Minori , Sugiyama Yuga , Sato Hikaru , Honda Hiroki , Sunagawa Yoichi , Funamoto Masafumi , Shimizu Satoshi , Shimizu Kana , Hamabe-Horiike Toshihide , Hawke Philip , Komiyama Maki , Mori Kiyoshi , Hasegawa Koji , Morimoto Tatsuya 
Published: March 2024

AbstractProtein arginine methyltransferase 5 (PRMT5) is a well-known epigenetic regulatory enzyme. However, the role of PRMT5-mediated arginine methylation in gene transcription related to cardiac fibrosis is unknown. Here we show that fibroblast-specific deletion of PRMT5 significantly reduces pressure overload-induced cardiac fibrosis and improves cardiac dysfunction in male mice. Both the PRMT5-selective inhibitor EPZ015666 and knockdown of PRMT5 suppress α-smooth muscle actin (α-SMA) expression induced by transforming growth factor-β (TGF-β) in cultured cardiac fibroblasts. TGF-β stimulation promotes the recruitment of the PRMT5/Smad3 complex to the promoter site of α-SMA. It also increases PRMT5-mediated H3R2 symmetric dimethylation, and this increase is inhibited by Smad3 knockdown. TGF-β stimulation increases H3K4 tri-methylation mediated by the WDR5/MLL1 methyltransferase complex, which recognizes H3R2 dimethylation. Finally, treatment with EPZ015666 significantly improves pressure overload-induced cardiac fibrosis and dysfunction. These findings suggest that PRMT5 regulates TGF-β/Smad3-dependent fibrotic gene transcription, possibly through histone methylation crosstalk, and plays a critical role in cardiac fibrosis and dysfunction.
VCF1 is a p97/VCP cofactor promoting recognition of ubiquitylated p97-UFD1-NPL4 substrates
Authors: Mirsanaye Ann Schirin , Hoffmann Saskia , Weisser Melanie , Mund Andreas , Lopez Mendez Blanca , Typas Dimitris , van den Boom Johannes , Benedict Bente , Hendriks Ivo A. , Nielsen Michael Lund , Meyer Hemmo , Duxin Julien P. , Montoya Guillermo , Mailand Niels 
Published: March 2024

AbstractThe hexameric AAA+ ATPase p97/VCP functions as an essential mediator of ubiquitin-dependent cellular processes, extracting ubiquitylated proteins from macromolecular complexes or membranes by catalyzing their unfolding. p97 is directed to ubiquitylated client proteins via multiple cofactors, most of which interact with the p97 N-domain. Here, we discover that FAM104A, a protein of unknown function also named VCF1 (VCP/p97 nuclear Cofactor Family member 1), acts as a p97 cofactor in human cells. Detailed structure-function studies reveal that VCF1 directly binds p97 via a conserved α-helical motif that recognizes the p97 N-domain with unusually high affinity, exceeding that of other cofactors. We show that VCF1 engages in joint p97 complex formation with the heterodimeric primary p97 cofactor UFD1-NPL4 and promotes p97-UFD1-NPL4-dependent proteasomal degradation of ubiquitylated substrates in cells. Mechanistically, VCF1 indirectly stimulates UFD1-NPL4 interactions with ubiquitin conjugates via its binding to p97 but has no intrinsic affinity for ubiquitin. Collectively, our findings establish VCF1 as an unconventional p97 cofactor that promotes p97-dependent protein turnover by facilitating p97-UFD1-NPL4 recruitment to ubiquitylated targets.
Prediction of glycopeptide fragment mass spectra by deep learning
Authors: Yang Yi , Fang Qun 
Published: March 2024

AbstractDeep learning has achieved a notable success in mass spectrometry-based proteomics and is now emerging in glycoproteomics. While various deep learning models can predict fragment mass spectra of peptides with good accuracy, they cannot cope with the non-linear glycan structure in an intact glycopeptide. Herein, we present DeepGlyco, a deep learning-based approach for the prediction of fragment spectra of intact glycopeptides. Our model adopts tree-structured long-short term memory networks to process the glycan moiety and a graph neural network architecture to incorporate potential fragmentation pathways of a specific glycan structure. This feature is beneficial to model explainability and differentiation ability of glycan structural isomers. We further demonstrate that predicted spectral libraries can be used for data-independent acquisition glycoproteomics as a supplement for library completeness. We expect that this work will provide a valuable deep learning resource for glycoproteomics.