bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gravity‐Driven Differences in Fluvial Sediment Transport on Mars and Earth
Authors: Braat Lisanne , Brückner Muriel Z. M. , Sefton‐Nash Elliot , Lamb Michael P. 
Published: February 2024

AbstractThere is abundant evidence from fluvial landforms and deposits that Mars had rivers that actively transported sediment and shaped its surface. Sediment transport equations are playing a key role in quantifying river processes from these observations, which continue to increase in quality and quantity. In this study, we review sediment transport equations developed on Earth and isolate the effect of gravity for the case of an alluvial channel. We compare 33 formulas used to calculate the sediment transport rate, under transport‐limited conditions, for grain sizes that range from silt to boulders and a lognormal sediment distribution. Results indicate that for a given discharge, channel morphology and grain size, the lower gravity on Mars compared to Earth results in: (a) larger grains mobilized on Mars and transported in suspension, and (b) larger suspended sediment transport rates on Mars and therefore larger total transport rates. Importantly, the effect of gravity is different for bed load and suspended load, with nonlinearity at the bed load‐suspended load transition zone. Therefore, typical total‐load transport relations that do not distinguish between bedload and suspended load are not appropriate for other planets as they simplify the effect of gravity. Gravity‐driven differences in fluvial sediment transport should produce differences in sediment sorting, morphology and stratigraphy between Earth and Mars. Additionally, our results show how Earth‐derived fluvial sediment transport theory can be applied beyond Mars to other planets and moons.
Crosstalk of HDAC4, PP1, and GSDMD in controlling pyroptosis
Authors: Xu Weilv , Jin Qiao , Li Xinyue , Li Danyue , Fu Xinyu , Chen Nan , Lv Qian , Shi Yuhua , He Suhui , Dong Lu , Yang Yang , Yan Yuqi , Shi Fushan 
Published: February 2024

AbstractGasdermin D (GSDMD) functions as a pivotal executor of pyroptosis, eliciting cytokine secretion following cleavage by inflammatory caspases. However, the role of posttranslational modifications (PTMs) in GSDMD-mediated pyroptosis remains largely unexplored. In this study, we demonstrate that GSDMD can undergo acetylation at the Lysine 248 residue, and this acetylation enhances pyroptosis. We identify histone deacetylase 4 (HDAC4) as the specific deacetylase responsible for mediating GSDMD deacetylation, leading to the inhibition of pyroptosis both in vitro and in vivo. Deacetylation of GSDMD impairs its ubiquitination, resulting in the inhibition of pyroptosis. Intriguingly, phosphorylation of HDAC4 emerges as a critical regulatory mechanism promoting its ability to deacetylate GSDMD and suppress GSDMD-mediated pyroptosis. Additionally, we implicate Protein phosphatase 1 (PP1) catalytic subunits (PP1α and PP1γ) in the dephosphorylation of HDAC4, thereby nullifying its deacetylase activity on GSDMD. This study reveals a complex regulatory network involving HDAC4, PP1, and GSDMD. These findings provide valuable insights into the interplay among acetylation, ubiquitination, and phosphorylation in the regulation of pyroptosis, offering potential targets for further investigation in the field of inflammatory cell death.
Heterotypic interactions can drive selective co-condensation of prion-like low-complexity domains of FET proteins and mammalian SWI/SNF complex
Authors: Davis Richoo B. , Supakar Anushka , Ranganath Aishwarya Kanchi , Moosa Mahdi Muhammad , Banerjee Priya R. 
Published: February 2024

AbstractPrion-like domains (PLDs) are low-complexity protein sequences enriched within nucleic acid-binding proteins including those involved in transcription and RNA processing. PLDs of FUS and EWSR1 play key roles in recruiting chromatin remodeler mammalian SWI/SNF (mSWI/SNF) complex to oncogenic FET fusion protein condensates. Here, we show that disordered low-complexity domains of multiple SWI/SNF subunits are prion-like with a strong propensity to undergo intracellular phase separation. These PLDs engage in sequence-specific heterotypic interactions with the PLD of FUS in the dilute phase at sub-saturation conditions, leading to the formation of PLD co-condensates. In the dense phase, homotypic and heterotypic PLD interactions are highly cooperative, resulting in the co-mixing of individual PLD phases and forming spatially homogeneous condensates. Heterotypic PLD-mediated positive cooperativity in protein-protein interaction networks is likely to play key roles in the co-phase separation of mSWI/SNF complex with transcription factors containing homologous low-complexity domains.
Orthogonal LoxPsym sites allow multiplexed site-specific recombination in prokaryotic and eukaryotic hosts
Authors: Cautereels Charlotte , Smets Jolien , De Saeger Jonas , Cool Lloyd , Zhu Yanmei , Zimmermann Anna , Steensels Jan , Gorkovskiy Anton , Jacobs Thomas B. , Verstrepen Kevin J. 
Published: February 2024

AbstractSite-specific recombinases such as the Cre-LoxP system are routinely used for genome engineering in both prokaryotes and eukaryotes. Importantly, recombinases complement the CRISPR-Cas toolbox and provide the additional benefit of high-efficiency DNA editing without generating toxic DNA double-strand breaks, allowing multiple recombination events at the same time. However, only a handful of independent, orthogonal recombination systems are available, limiting their use in more complex applications that require multiple specific recombination events, such as metabolic engineering and genetic circuits. To address this shortcoming, we develop 63 symmetrical LoxP variants and test 1192 pairwise combinations to determine their cross-reactivity and specificity upon Cre activation. Ultimately, we establish a set of 16 orthogonal LoxPsym variants and demonstrate their use for multiplexed genome engineering in both prokaryotes (E. coli) and eukaryotes (S. cerevisiae and Z. mays). Together, this work yields a significant expansion of the Cre-LoxP toolbox for genome editing, metabolic engineering and other controlled recombination events, and provides insights into the Cre-LoxP recombination process.
Visualizing the interfacial-layer-based epitaxial growth process toward organic core-shell architectures
Authors: Zhuo Ming-Peng , Wei Xiao , Li Yuan-Yuan , Shi Ying-Li , He Guang-Peng , Su Huixue , Zhang Ke-Qin , Guan Jin-Ping , Wang Xue-Dong , Wu Yuchen , Liao Liang-Sheng 
Published: February 2024

AbstractOrganic heterostructures (OHTs) with the desired geometry organization on micro/nanoscale have undergone rapid progress in nanoscience and nanotechnology. However, it is a significant challenge to elucidate the epitaxial-growth process for various OHTs composed of organic units with a lattice mismatching ratio of > 3%, which is unimaginable for inorganic heterostructures. Herein, we have demonstrated a vivid visualization of the morphology evolution of epitaxial-growth based on a doped interfacial-layer, which facilitates the comprehensive understanding of the hierarchical self-assembly of core-shell OHT with precise spatial configuration. Significantly, the barcoded OHT with periodic shells obviously illustrate the shell epitaxial-growth from tips to center parts along the seeded rods for forming the core-shell OHT. Furthermore, the diameter, length, and number of periodic shells were modulated by finely tuning the stoichiometric ratio, crystalline time, and temperature, respectively. This epitaxial-growth process could be generalized to organic systems with facile chemical/structural compatibility for forming the desired OHTs.
Two-edge-resolved three-dimensional non-line-of-sight imaging with an ordinary camera
Authors: Czajkowski Robinson , Murray-Bruce John 
Published: February 2024

AbstractWe introduce an approach for three-dimensional full-colour non-line-of-sight imaging with an ordinary camera that relies on a complementary combination of a new measurement acquisition strategy, scene representation model, and tailored reconstruction method. From an ordinary photograph of a matte line-of-sight surface illuminated by the hidden scene, our approach reconstructs a three-dimensional image of the scene hidden behind an occluding structure by exploiting two orthogonal edges of the structure for transverse resolution along azimuth and elevation angles and an information orthogonal scene representation for accurate range resolution. Prior demonstrations beyond two-dimensional reconstructions used expensive, specialized optical systems to gather information about the hidden scene. Here, we achieve accurate three-dimensional imaging using inexpensive, and ubiquitous hardware, without requiring a calibration image. Thus, our system may find use in indoor situations like reconnaissance and search-and-rescue.
Tracing back primed resistance in cancer via sister cells
Authors: Dai Jun , Zheng Shuyu , Falco Matías M. , Bao Jie , Eriksson Johanna , Pikkusaari Sanna , Forstén Sofia , Jiang Jing , Wang Wenyu , Gao Luping , Perez-Villatoro Fernando , Dufva Olli , Saeed Khalid , Wang Yinyin , Amiryousefi Ali , Färkkilä Anniina , Mustjoki Satu , Kauppi Liisa , Tang Jing , Vähärautio Anna 
Published: February 2024

AbstractExploring non-genetic evolution of cell states during cancer treatments has become attainable by recent advances in lineage-tracing methods. However, transcriptional changes that drive cells into resistant fates may be subtle, necessitating high resolution analysis. Here, we present ReSisTrace that uses shared transcriptomic features of sister cells to predict the states priming treatment resistance. Applying ReSisTrace in ovarian cancer cells perturbed with olaparib, carboplatin or natural killer (NK) cells reveals pre-resistant phenotypes defined by proteostatic and mRNA surveillance features, reflecting traits enriched in the upcoming subclonal selection. Furthermore, we show that DNA repair deficiency renders cells susceptible to both DNA damaging agents and NK killing in a context-dependent manner. Finally, we leverage the obtained pre-resistance profiles to predict and validate small molecules driving cells to sensitive states prior to treatment. In summary, ReSisTrace resolves pre-existing transcriptional features of treatment vulnerability, facilitating both molecular patient stratification and discovery of synergistic pre-sensitizing therapies.
A cost-effective sequencing method for genetic studies combining high-depth whole exome and low-depth whole genome
Authors: Bhérer Claude , Eveleigh Robert , Trajanoska Katerina , St-Cyr Janick , Paccard Antoine , Nadukkalam Ravindran Praveen , Caron Elizabeth , Bader Asbah Nimara , McClelland Peyton , Wei Clare , Baumgartner Iris , Schindewolf Marc , Döring Yvonne , Perley Danielle , Lefebvre François , Lepage Pierre , Bourgey Mathieu , Bourque Guillaume , Ragoussis Jiannis , Mooser Vincent , Taliun Daniel 
Published: February 2024

AbstractWhole genome sequencing (WGS) at high-depth (30X) allows the accurate discovery of variants in the coding and non-coding DNA regions and helps elucidate the genetic underpinnings of human health and diseases. Yet, due to the prohibitive cost of high-depth WGS, most large-scale genetic association studies use genotyping arrays or high-depth whole exome sequencing (WES). Here we propose a cost-effective method which we call “Whole Exome Genome Sequencing” (WEGS), that combines low-depth WGS and high-depth WES with up to 8 samples pooled and sequenced simultaneously (multiplexed). We experimentally assess the performance of WEGS with four different depth of coverage and sample multiplexing configurations. We show that the optimal WEGS configurations are 1.7–2.0 times cheaper than standard WES (no-plexing), 1.8–2.1 times cheaper than high-depth WGS, reach similar recall and precision rates in detecting coding variants as WES, and capture more population-specific variants in the rest of the genome that are difficult to recover when using genotype imputation methods. We apply WEGS to 862 patients with peripheral artery disease and show that it directly assesses more known disease-associated variants than a typical genotyping array and thousands of non-imputable variants per disease-associated locus.
Characterizing ATP processing by the AAA+ protein p97 at the atomic level
Authors: Shein Mikhail , Hitzenberger Manuel , Cheng Tat Cheung , Rout Smruti R. , Leitl Kira D. , Sato Yusuke , Zacharias Martin , Sakata Eri , Schütz Anne K. 
Published: February 2024

AbstractThe human enzyme p97 regulates various cellular pathways by unfolding hundreds of protein substrates in an ATP-dependent manner, making it an essential component of protein homeostasis and an impactful pharmacological target. The hexameric complex undergoes substantial conformational changes throughout its catalytic cycle. Here we elucidate the molecular motions that occur at the active site in the temporal window immediately before and after ATP hydrolysis by merging cryo-EM, NMR spectroscopy and molecular dynamics simulations. p97 populates a metastable reaction intermediate, the ADP·Pi state, which is poised between hydrolysis and product release. Detailed snapshots reveal that the active site is finely tuned to trap and eventually discharge the cleaved phosphate. Signalling pathways originating at the active site coordinate the action of the hexamer subunits and couple hydrolysis with allosteric conformational changes. Our multidisciplinary approach enables a glimpse into the sophisticated spatial and temporal orchestration of ATP handling by a prototype AAA+ protein.
Genome-wide association study identifies human genetic variants associated with fatal outcome from Lassa fever
Authors: Kotliar Dylan , Raju Siddharth , Tabrizi Shervin , Odia Ikponmwosa , Goba Augustine , Momoh Mambu , Sandi John Demby , Nair Parvathy , Phelan Eric , Tariyal Ridhi , Eromon Philomena E. , Mehta Samar , Robles-Sikisaka Refugio , Siddle Katherine J. , Stremlau Matt , Jalloh Simbirie , Gire Stephen K. , Winnicki Sarah , Chak Bridget , Schaffner Stephen F. , Pauthner Matthias , Karlsson Elinor K. , Chapin Sarah R. , Kennedy Sharon G. , Branco Luis M. , Kanneh Lansana , Vitti Joseph J. , Broodie Nisha , Gladden-Young Adrianne , Omoniwa Omowunmi , Jiang Pan-Pan , Yozwiak Nathan , Heuklom Shannon , Moses Lina M. , Akpede George O. , Asogun Danny A. , Rubins Kathleen , Kales Susan , Happi Anise N. , Iruolagbe Christopher O. , Dic-Ijiewere Mercy , Iraoyah Kelly , Osazuwa Omoregie O. , Okonkwo Alexander K. , Kunz Stefan , McCormick Joseph B. , Khan S. Humarr , Honko Anna N. , Lander Eric S. , Oldstone Michael B. A. , Hensley Lisa , Folarin Onikepe A. , Okogbenin Sylvanus A. , Günther Stephan , Ollila Hanna M. , Tewhey Ryan , Okokhere Peter O. , Schieffelin John S. , Andersen Kristian G. , Reilly Steven K. , Grant Donald S. , Garry Robert F. , Barnes Kayla G. , Happi Christian T. , Sabeti Pardis C. 
Published: February 2024

AbstractInfection with Lassa virus (LASV) can cause Lassa fever, a haemorrhagic illness with an estimated fatality rate of 29.7%, but causes no or mild symptoms in many individuals. Here, to investigate whether human genetic variation underlies the heterogeneity of LASV infection, we carried out genome-wide association studies (GWAS) as well as seroprevalence surveys, human leukocyte antigen typing and high-throughput variant functional characterization assays. We analysed Lassa fever susceptibility and fatal outcomes in 533 cases of Lassa fever and 1,986 population controls recruited over a 7 year period in Nigeria and Sierra Leone. We detected genome-wide significant variant associations with Lassa fever fatal outcomes near GRM7 and LIF in the Nigerian cohort. We also show that a haplotype bearing signatures of positive selection and overlapping LARGE1, a required LASV entry factor, is associated with decreased risk of Lassa fever in the Nigerian cohort but not in the Sierra Leone cohort. Overall, we identified variants and genes that may impact the risk of severe Lassa fever, demonstrating how GWAS can provide insight into viral pathogenesis.
High-fidelity initialization and control of electron and nuclear spins in a four-qubit register
Authors: Reiner J. , Chung Y. , Misha S. H. , Lehner C. , Moehle C. , Poulos D. , Monir S. , Charde K. J. , Macha P. , Kranz L. , Thorvaldson I. , Thorgrimsson B. , Keith D. , Hsueh Y. L. , Rahman R. , Gorman S. K. , Keizer J. G. , Simmons M. Y. 
Published: February 2024

AbstractSingle electron spins bound to multi-phosphorus nuclear spin registers in silicon have demonstrated fast (0.8 ns) two-qubit $$\sqrt{\mathrm{SWAP}}$$

SWAP

gates and long spin relaxation times (~30 s). In these spin registers, when the donors are ionized, the nuclear spins remain weakly coupled to their environment, allowing exceptionally long coherence times. When the electron is present, the hyperfine interaction allows coupling of the spin and charge degrees of freedom for fast qubit operation and control. Here we demonstrate the use of the hyperfine interaction to enact electric dipole spin resonance to realize high-fidelity ($$F=10{0}_{-6}^{+0}$$

F
=
10

0

−
6

+
0

%) initialization of all the nuclear spins within a four-qubit nuclear spin register. By controllably initializing the nuclear spins to $$\left\vert \Downarrow \Downarrow \Downarrow \right\rangle$$

⇓
⇓
⇓

, we achieve single-electron qubit gate fidelities of F = 99.78 ± 0.07% (Clifford gate fidelities of 99.58 ± 0.14%), above the fault-tolerant threshold for the surface code with a coherence time of $${T}_{2}^{\,* }=12\,\upmu {{{\rm{s}}}}$$

T

2

*

=
12

μ
s

.
Functional brain responses to emotional faces after three to five weeks of intake of escitalopram in healthy individuals: a double-blind, placebo-controlled randomised study
Authors: Armand Sophia , Langley Christelle , Johansen Annette , Ozenne Brice , Overgaard-Hansen Oliver , Larsen Kristian , Jensen Peter Steen , Knudsen Gitte Moos , Sahakian Barbara Jacquelyn , Stenbæk Dea Siggard , Fisher Patrick MacDonald 
Published: February 2024

AbstractShort-term intake of selective serotonin reuptake inhibitors (SSRIs) modulates threat-related amygdala responses in healthy individuals. However, how SSRI intake over a clinically relevant time period modulates threat-related amygdala responses is less clear. In a semi-randomised, double-blind, placebo-controlled study of 64 healthy individuals (SSRI n = 32, placebo n = 32), we examined the effect of 3–5 weeks of SSRI escitalopram (20 mg daily) on brain response to angry, fearful and neutral faces using BOLD fMRI. Data was analysed using a whole-brain region-wise approach extracting standardised effects (i.e., Cohen’s D). The study was conducted at the Copenhagen University Hospital. A priori, we hypothesised that SSRI would attenuate amygdala responses to angry and fearful faces but not to neutral ones. Whether SSRI modulates correlations between amygdala responses to emotional faces and negative mood states was also explored. Compared to placebo, 3–5 weeks of SSRI intake did not significantly affect the amygdala response to angry, fearful, or neutral faces (|Cohen’s D|< 0.2, PFWER = 1). Whole-brain, region-wise analyses revealed significant differences in frontal (|Cohen’s D|< 0.6, PFWER < .01) and occipital regions (|Cohen’s D|< 0.5, PFWER < .01). SSRI did not modulate correlations between amygdala responses to emotional faces and negative mood states. Our findings indicate that a 3–5 week SSRI intake impacts cortical responses to emotional stimuli, an effect possibly involved in SSRI’s therapeutic efficacy.Trial registration Clinical Trials NCT04239339.
Antioxidant, antibacterial, and molecular docking of methyl ferulate and oleic acid produced by Aspergillus pseudodeflectus AUMC 15761 utilizing wheat bran
Authors: Ramadan Ahmed Mohamed Ahmed Ali , Zidan Sabry Ahmed Hussein , Shehata Reda Mohamed , EL-Sheikh Hussein Hosny , Ameen Fuad , Stephenson Steven L. , Al-Bedak Osama Abdel-Hafeez Mohamed 
Published: February 2024

AbstractSecondary metabolites (SMs) are the primary source of therapeutics and lead chemicals in medicine. They have been especially important in the creation of effective cures for conditions such as cancer, malaria, bacterial and fungal infections, neurological and cardiovascular problems, and autoimmune illnesses. In the present study, Aspergillus pseudodeflectus AUMC 15761 was demonstrated to use wheat bran in solid state fermentation (SSF) at optimum conditions (pH 7.0 at 30 °C after 10 days of incubation and using sodium nitrate as a nitrogen source) to produce methyl ferulate and oleic acid with significant antioxidant and antibacterial properties. Gas chromatography-mass spectrometry (GC–MS) analysis of the crude methanol extract revealed eleven peaks that indicated the most common chemical components. Purification of methyl ferulate and oleic acid was carried out by column chromatography, and both compounds were identified by in-depth spectroscopic analysis, including 1D and 2D NMR and HR-ESI–MS. DPPH activity increased as the sample concentration increased. IC50 values of both compounds obtained were 73.213 ± 11.20 and 104.178 ± 9.53 µM, respectively. Also, the MIC value for methyl ferulate against Bacillus subtilis and Staphylococcus aureus was 0.31 mg/mL, while the corresponding MIC values for oleic acid were 1.25 mg/mL and 0.62 mg/mL for both bacterial strains, respectively. Molecular modeling calculations were carried out to reveal the binding mode of methyl ferulate and oleic acid within the binding site of the crucial proteins of Staphylococcus aureus. The docking results were found to be well correlated with the experimental data.
Combined laser-activated SVF and PRP remodeled spinal sclerosis via activation of Olig-2, MBP, and neurotrophic factors and inhibition of BAX and GFAP
Authors: Farid Mariam F. , Yasin Noha A. E. , Al-Mokaddem Asmaa K. , Ibrahim Marwa A. , Abouelela Yara S. , rizk Hamdy 
Published: February 2024

AbstractA single injection of platelet-rich plasma (PRP) or stromal vascular fraction (SVF) in treating neurological ailments suggests promise; however, there is limited evidence of the efficacy of combination therapy. This trial aimed to determine whether combining SVF and PRP could provide further therapeutic effects in treating multiple sclerosis (MS). Fifteen Persian cats were separated into three groups (n = 5): group I (control negative), and group II (control positive); EB was injected intrathecally into the spinal cord and then treated 14 days later with intrathecal phosphate buffered saline injection, and group III (SVF + PRP), cats were injected intrathecally with EB through the spinal cord, followed by a combination of SVF and PRP 14 days after induction. Therapeutic effects were evaluated using the Basso–Beattie–Bresnahan scale throughout the treatment timeline and at the end. Together with morphological, MRI scan, immunohistochemical, transmission electron microscopy, and gene expression investigations. The results demonstrated that combining SVF and PRP successfully reduced lesion intensity on gross inspection and MRI. In addition to increased immunoreactivity to Olig2 and MBP and decreased immunoreactivity to Bax and GFAP, there was a significant improvement in BBB scores and an increase in neurotrophic factor (BDNF, NGF, and SDF) expression when compared to the positive control group. Finally, intrathecal SVF + PRP is the most promising and safe therapy for multiple sclerosis, resulting in clinical advantages such as functional recovery, MRI enhancement, and axonal remyelination.