bluuebunny/crossref_metadata_2025 huggingface dataset:
An Eddy Pair in the Northwestern Bay of Bengal: Characteristics, Dynamics and Interannual Variability
Authors: Zhong Wenjing , Chen Gengxin , Chu Xiaoqing
Published: February 2024

Mesoscale eddies are active in the Bay of Bengal and have profound effects on the dynamic conditions, the transport of heat and salt, and the primary productivity. We report a pair of periodic eddies in the Bay of Bengal and examine their characteristics, dynamic mechanisms and interannual variability based on satellite observations and a nonlinear 1.5‐layer reduced‐gravity model. The eddy pair mainly occupies the northwestern Bay of Bengal from March to May and consists of a cyclonic eddy in the north and an anticyclonic eddy in the south. The anticyclonic eddy is generated by local wind forcing, whereas the cyclonic eddy is significantly contributed by equatorial and coastal Kelvin waves. On an interannual scale, the eddy pair was exceptionally weak in 1999, 2000 and 2008 due to the extreme La Niña events in these years when the westerly wind anomaly over the equatorial Indian Ocean weakened the local wind forcing and coastal Kelvin waves. This study provides new knowledge on periodic eddies in the Bay of Bengal and advances our understanding of the dynamic connections between this marginal sea and the equator.
A CloudSat and CALIPSO‐Based Evaluation of the Effects of Thermodynamic Instability and Aerosol Loading on Amazon Basin Deep Convection and Lightning
Authors: Allen Dale , Pickering Kenneth , Avery Melody , Li Zhanqing , Shan Siyu , Morales Rodriguez Carlos Augusto , Artaxo Paulo
Published: February 2024

The Amazon Basin, which plays a critical role in the carbon and water cycle, is under stress due to changes in climate, agricultural practices, and deforestation. The effects of thermodynamic and microphysical forcing on the strength of thunderstorms in the Basin (75–45°W, 0–15°S) were examined during the pre‐monsoon season (mid‐August through mid‐December), a period with large variations in aerosols, intense convective storms, and plentiful flashes. The analysis used measurements of radar reflectivity, ice water content (IWC), and aerosol type from instruments aboard the CloudSat and CALIPSO satellites, flash rates from the ground‐based Sferics Timing and Ranging Network, and total aerosol optical depth (AOD) from a surface network and a meteorological re‐analysis. After controlling for convective available potential energy (CAPE), it was found that thunderstorms that developed under dirty (high‐AOD) conditions were 1.5 km deeper, had 50% more IWC, and more than two times as many flashes as storms that developed under clean conditions. The sensitivity of flashes to AOD was largest for low values of CAPE where increases of more than a factor of three were observed. The additional ice water indicated that these deeper systems had higher vertical velocities and more condensation nuclei capable of sustaining higher concentrations of water and large hydrometeors in the upper troposphere. Flash rates were also found to be larger during periods when smoke rather than dust was common in the lower troposphere, likely because smoky periods were less stable due to higher values of CAPE and AOD and lower values of mid‐tropospheric relative humidity.
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

There 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

Gasdermin 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

Prion-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

Site-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

Organic 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

We 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

Exploring 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

Whole 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

The 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

Infection 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

Single 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

Short-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

Secondary 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

A 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.
Few-shot concealed object detection in sub-THz security images using improved pseudo-annotations
Authors: Cheng Ran , Lucyszyn Stepan
Published: February 2024

In this research, we explore the few-shot object detection application for identifying concealed objects in sub-terahertz security images, using fine-tuning based frameworks. To adapt these machine learning frameworks for the (sub-)terahertz domain, we propose an innovative pseudo-annotation method to augment the object detector by sourcing high-quality training samples from unlabeled images. This approach employs multiple one-class detectors coupled with a fine-grained classifier, trained on supporting thermal-infrared images, to prevent overfitting. Consequently, our approach enhances the model’s ability to detect challenging objects (e.g., 3D-printed guns and ceramic knives) when few-shot training examples are available, especially in the real-world scenario where images of concealed dangerous items are scarce.
Interpretable predictions of chaotic dynamical systems using dynamical system deep learning
Authors: Wang Mingyu , Li Jianping
Published: February 2024

Making accurate predictions of chaotic dynamical systems is an essential but challenging task with many practical applications in various disciplines. However, the current dynamical methods can only provide short-term precise predictions, while prevailing deep learning techniques with better performances always suffer from model complexity and interpretability. Here, we propose a new dynamic-based deep learning method, namely the dynamical system deep learning (DSDL), to achieve interpretable long-term precise predictions by the combination of nonlinear dynamics theory and deep learning methods. As validated by four chaotic dynamical systems with different complexities, the DSDL framework significantly outperforms other dynamical and deep learning methods. Furthermore, the DSDL also reduces the model complexity and realizes the model transparency to make it more interpretable. We firmly believe that the DSDL framework is a promising and effective method for comprehending and predicting chaotic dynamical systems.
Plutonium mobility and reactivity in a heterogeneous clay rock barrier accented by synchrotron-based microscopic chemical imaging
Authors: Kaplan U. , Amayri S. , Drebert J. , Grolimund D. , Reich T.
Published: February 2024

The long-term safe disposal of radioactive waste corresponds to a challenging responsibility of present societies. Within deep geological waste disposal concepts, host rocks correspond to the ultimate safety barrier towards the environment. To assess the performance of such barriers over extended time scales, mechanistic information on the interaction between the radiotoxic, long-lived radionuclides like plutonium and the host rock is essential. Chemical imaging based on synchrotron microspectroscopic techniques was used to visualize undisturbed reactive transport patterns of Pu within pristine Opalinus Clay rock material. Pu+V is shown to be progressively reduced along its diffusion path to Pu+IV and Pu+III due to interaction with redox-active clay rock constituents. Experimental results and modeling emphasize the dominant role of electron-transfer reactions determining the mobility of Pu in reactive barrier systems. The effective migration velocity of Pu is controlled by the kinetic rates of the reduction to Pu+IV and Pu+III and the redox capacity of the involved electron donor pools. To advance our predictive capabilities further, an improved understanding of the nature and capacity of redox-active components of the reactive barrier material is fundamental. The findings represent an essential contribution to the evaluation of the long-term safety of potential nuclear waste repositories and have implications regarding the development of effective geological disposal strategies.
Altered resting-state functional connectivity in newborns with hypoxic ischemic encephalopathy assessed using high-density functional near-infrared spectroscopy
Authors: Tang Lingkai , Kebaya Lilian M. N. , Altamimi Talal , Kowalczyk Alexandra , Musabi Melab , Roychaudhuri Sriya , Vahidi Homa , Meyerink Paige , de Ribaupierre Sandrine , Bhattacharya Soume , de Moraes Leandro Tristao Abi Ramia , St. Lawrence Keith , Duerden Emma G.
Published: February 2024

Hypoxic-ischemic encephalopathy (HIE) results from a lack of oxygen to the brain during the perinatal period. HIE can lead to mortality and various acute and long-term morbidities. Improved bedside monitoring methods are needed to identify biomarkers of brain health. Functional near-infrared spectroscopy (fNIRS) can assess resting-state functional connectivity (RSFC) at the bedside. We acquired resting-state fNIRS data from 21 neonates with HIE (postmenstrual age [PMA] = 39.96), in 19 neonates the scans were acquired post-therapeutic hypothermia (TH), and from 20 term-born healthy newborns (PMA = 39.93). Twelve HIE neonates also underwent resting-state functional magnetic resonance imaging (fMRI) post-TH. RSFC was calculated as correlation coefficients amongst the time courses for fNIRS and fMRI data, respectively. The fNIRS and fMRI RSFC maps were comparable. RSFC patterns were then measured with graph theory metrics and compared between HIE infants and healthy controls. HIE newborns showed significantly increased clustering coefficients, network efficiency and modularity compared to controls. Using a support vector machine algorithm, RSFC features demonstrated good performance in classifying the HIE and healthy newborns in separate groups. Our results indicate the utility of fNIRS-connectivity patterns as potential biomarkers for HIE and fNIRS as a new bedside tool for newborns with HIE.
Effects of DMT on mental health outcomes in healthy volunteers
Authors: Timmermann Christopher , Zeifman Richard J. , Erritzoe David , Nutt David J. , Carhart-Harris Robin L.
Published: February 2024

Psilocybin, a serotonergic psychedelic, is being increasingly researched in clinical studies for the treatment of psychiatric disorders. The relatively lengthy duration of oral psilocybin’s acute effects (4–6 h) may have pragmatic and cost-effectiveness limitations. Here, we explored the effects of intravenous (IV) N,N-Dimethyltryptamine (DMT), a closely related, but faster-acting psychedelic intervention, on mental health outcomes in healthy volunteers. Data is reported from two separate analyses: (1) A comparison of mental health-related variables 1 week after 7, 14, 18, and 20 mg of IV DMT versus IV saline placebo (n = 13) and, (2) A prospective dataset assessing effects before versus 2 weeks after 20 mg of IV DMT (n = 17). Mental health outcomes included measures of depression severity (QIDS-SR16), trait anxiety (STAI-T), Neuroticism (NEO-FFI), wellbeing (WHO-5), meaning in life (MLQ), optimism (LOT-R), and gratitude (GQ-6). In both the prospective and placebo-controlled datasets, significant improvements in scores of depression were found 1–2 weeks after DMT administration. Significant reductions in trait Neuroticism were only found for the placebo-controlled sample. Finally, changes in depression and trait anxiety correlated with acute peak experiences (assessed via ‘Oceanic Boundlessness’). While the use of two separate cohorts in pooled analysis limits the generalizability of these correlational findings, these results suggest that DMT may reduce depressive symptomatology by inducing peak experiences. The short half-life of IV DMT and its potential for flexible dosing via controlled infusions makes it an appealing candidate for psychedelic medicine. Further research in clinical samples is needed to corroborate the therapeutic potential of DMT.
Magnolol extends lifespan and improves age-related neurodegeneration in Caenorhabditis elegans via increase of stress resistance
Authors: Yu Jing , Gao Xiaoyan , Zhang Lijun , Shi Hang , Yan Yingxuan , Han Yongli , Wu Chengyuan , Liu Ying , Fang Minglv , Huang Cheng , Fan Shengjie
Published: February 2024

Magnolol is a naturally occurring polyphenolic compound in many edible plants, which has various biological effects including anti-aging and alleviating neurodegenerative diseases. However, the underlying mechanism on longevity is uncertain. In this study, we investigated the effect of magnolol on the lifespan of Caenorhabditis elegans and explored the mechanism. The results showed that magnolol treatment significantly extended the  lifespan of nematode and alleviated senescence-related decline in the nematode model. Meanwhile, magnolol enhanced stress resistance to heat shock, hydrogen peroxide (H2O2), mercuric potassium chloride (MeHgCl) and paraquat (PQ) in nematode. In addition, magnolol reduced reactive oxygen species and malondialdehyde (MDA) levels, and increased superoxide dismutase and catalase (CAT) activities in nematodes. Magnolol also up-regulated gene expression of sod-3, hsp16.2, ctl-3, daf-16, skn-1, hsf-1, sir2.1, etc., down-regulated gene expression of daf-2, and promoted intranuclear translocation of daf-16 in nematodes. The lifespan-extending effect of magnolol were reversed in insulin/IGF signaling (IIS) pathway-related mutant lines, including daf-2, age-1, daf-16, skn-1, hsf-1 and sir-2.1, suggesting that IIS signaling is involved in the modulation of longevity by magnolol. Furthermore, magnolol improved the age-related neurodegeneration in PD and AD C. elegans models. These results indicate that magnolol may enhance lifespan and health span through IIS and sir-2.1 pathways. Thus, the current findings implicate magnolol as a potential candidate to ameliorate the symptoms of aging.
Association between alkaline phosphatase to albumin ratio and mortality among patients with sepsis
Authors: Liu Shuyue , Zhao Kai , Shao Chunhong , Xu Lulu , Cui Xianglun , Wang Yong
Published: February 2024

The alkaline phosphatase-to-albumin ratio (APAR) is correlated to worse prognosis in coronary artery disease, cancer, and acute renal failure. However, the relationship between APAR and sepsis prognosis has received little research. The content of this research was to investigate the prognostic relationship between APAR and sepsis. And validate the stability of the correlation in 90-days and 1-year mortality. Retrospective cohort research was conducted basing MIMIC-IV database (version 2.0). The hazard ratio (HR) and 95% confidence interval (Cl) were computed using multivariate Cox regression analysis. In addition, plots of survival curves and subgroup analyzes were conducted. Receiver operating characteristic (ROC) curves were also used. 9741 participants were included in this investigation. The 90-days mortality was 32.8%, and the 1-year mortality was 42.0%. After controlling for confounders, the adjusted HRs (95% CI) for tertile 2 (2.2–3.8) and tertile 3 (> 3.8) were 1.37 (1.25–1.51) and 1.74 (1.58–1.91), respectively. The Kaplan–Meier curve analysis showed a higher probability of 90-days death in the higher APAR group. The area under the curve (AUC) of APAR was 0.674 and could reach 0.709 after combining the Oxford Acute Severity of Illness Score (OASIS). This study demonstrates that APAR is significantly related to bad clinical outcomes in sepsis.
Saddlepoint p-values for a class of location-scale tests under randomized block design
Authors: Mohamed Haidy N. , Abd-Elfattah Ehab F. , Abd-El-Monem Amel , Abd El-Raheem Abd El-Raheem M.
Published: February 2024

This paper deals with a class of nonparametric two-sample location-scale tests. The purpose of this paper is to approximate the exact p-value of the considered class under a randomized block design. The exact p-value of the considered class is approximated by the saddlepoint approximation method, also by the traditional method which is the normal approximation method. The saddlepoint approximation method is more accurate than the normal approximation method in approximating the exact p-value, and does not take a lot of time like the simulation method. This accuracy is proved by applying the mentioned methods to two real data sets and a simulation study.
Prognostic value of Geriatric Nutritional Risk Index and systemic immune-inflammatory index in elderly patients with acute coronary syndromes
Authors: Zhu Xing-Yu , Zhang Kai-Jie , Li Xiao , Su Fei-Fei , Tian Jian-Wei
Published: February 2024

The objective of this study was to evaluate the predictive value of the Geriatric Nutritional Risk Index (GNRI) combined with the Systemic Immunoinflammatory Index (SII) for the risk of major adverse cardiovascular events (MACE) following percutaneous coronary intervention in elderly patients with acute coronary syndrome (ACS). We retrospectively reviewed the medical records of 1202 elderly patients with acute coronary syndromes divided into MACE and non-MACE groups according to whether they had a MACE. The sensitivity analysis utilized advanced machine learning algorithms to preliminarily identify the critical role of GNRI versus SII in predicting MACE risk. We conducted a detailed analysis using a restricted cubic spline approach to investigate the nonlinear relationship between GNRI, SII, and MACE risk further. We constructed a clinical prediction model based on three key factors: GNRI, SII, and Age. To validate the accuracy and usefulness of this model, we compared it to the widely used GRACE score using subject work and recall curves. Additionally, we compared the predictive value of models and GRACE scores in assessing the risk of MACE using the Integrated Discriminant Improvement Index (IDI) and the Net Reclassification Index (NRI). This study included 827 patients. The GNRI scores were lower in the MACE group than in the non-MACE group, while the SII scores were higher in the MACE group (P < 0.001). The multifactorial analysis revealed a low GNRI (OR = 2.863, 95% CI: 2.026–4.047, P = 0.001), High SII (OR = 3.102, 95% CI: 2.213–4.348, P = 0.001). The area under the curve (AUC) for the predictive model was 0.778 (95% CI: 0.744–0.813, P = 0.001), while the AUC for the GRACE score was 0.744 (95% CI: 0.708–0.779, P = 0.001). NRI was calculated to be 0.5569, with NRI + at 0.1860 and NRI- at 0.3708. The IDI was found to be 0.0571, with a P-value of less than 0.001. These results suggest that the newly developed prediction model is more suitable for use with the population in this study than the GRACE score. The model constructed using GNRI and SII demonstrated good standardization and clinical impact, as evidenced by the standard, DCA, and clinical impact curves. The study shows that combining GNRI and SII can be a simple, cost-effective, and valuable way to predict the risk of MACE within one year in elderly acute coronary syndromes.
Identification and validation of a copper homeostasis-related gene signature for the predicting prognosis of breast cancer patients via integrated bioinformatics analysis
Authors: Li Yi , Wei Xiuxian , Wang Yuning , Wang Wenzhuo , Zhang Cuntai , Kong Deguang , Liu Yu
Published: February 2024

The prognostic value of copper homeostasis-related genes in breast cancer (BC) remains largely unexplored. We analyzed copper homeostasis-related gene profiles within The Cancer Genome Atlas Program breast cancer cohorts and performed correlation analysis to explore the relationship between copper homeostasis-related mRNAs (chrmRNA) and lncRNAs. Based on these results, we developed a gene signature-based risk assessment model to predict BC patient outcomes using Cox regression analysis and a nomogram, which was further validated in a cohort of 72 BC patients. Using the gene set enrichment analysis, we identified 139 chrmRNAs and 16 core mRNAs via the Protein–Protein Interaction network. Additionally, our copper homeostasis-related lncRNAs (chrlncRNAs) (PINK1.AS, OIP5.AS1, HID.AS1, and MAPT.AS1) were evaluated as gene signatures of the predictive model. Kaplan–Meier survival analysis revealed that patients with a high-risk gene signature had significantly poorer clinical outcomes. Receiver operating characteristic curves showed that the prognostic value of the chrlncRNAs model reached 0.795 after ten years. Principal component analysis demonstrated the capability of the model to distinguish between low- and high-risk BC patients based on the gene signature. Using the pRRophetic package, we screened out 24 anticancer drugs that exhibited a significant relationship with the predictive model. Notably, we observed higher expression levels of the four chrlncRNAs in tumor tissues than in the adjacent normal tissues. The correlation between our model and the clinical characteristics of patients with BC highlights the potential of chrlncRNAs for predicting tumor progression. This novel gene signature not only predicts the prognosis of patients with BC but also suggests that targeting copper homeostasis may be a viable treatment strategy.
Near-perfect sound absorption using hybrid resonance between subwavelength Helmholtz resonators with non-uniformly partitioned cavities
Authors: Choi Eunji , Jeon Wonju
Published: February 2024

We present near-perfect sound absorption using a metasurface composed of meta-atoms (MAs) which are subwavelength Helmholtz resonators (HRs) with cavities non-uniformly partitioned by membranes. By embedding the membranes at different horizontal locations in the cavities, we break geometrical symmetry between the MAs so as to derive hybrid resonance between the MAs at our target frequency. The resonance frequency of each MA is determined by delicately adjusting the locations of the membranes, resulting in perfect absorption at the target frequency which is different from the resonance frequencies of MAs. The metasurface is designed to satisfy impedance matching conditions with air at one or more target frequencies with the aid of a theoretical model for frequency-dependent effective acoustic impedance. The theoretical model is established with physical reality by considering the higher-order eigenmodes of the membrane, the visco-thermal losses in narrow orifices, and the end corrections of the subwavelength HR. The designed metasurface is fabricated and its absorption performance is verified experimentally in an impedance tube. Near-perfect absorption of sound is achieved at the target frequency of 500 Hz, which is 12.3% lower than that of near-perfect absorption by previous metasurfaces inducing hybrid resonance between HRs without membranes.
Physical strength, body composition, and G-test results of air force cadets based on nutrition knowledge differences
Authors: Sung Jun-Young , Lee Kyu-Lim
Published: February 2024

The Gravitational Acceleration Test (G-test) is a demanding, and sophisticated high-intensity physical activity, greatly influenced by individual body composition and physical strength. This study analyzed the general nutrition knowledge questionnaire (GNKQ) responses of Air Force cadets to identify the relationship between nutrition knowledge, body composition, physical activity, physical strength, and gravity-induced loss of consciousness. Based on the G-test results, 105 fourth-year Air Force cadets were divided into two groups: GP (G-test pass group) and GF (G-test fail group). The analysis items were GNKQ responses, body composition, and physical strength analysis, based on which independent sample t-tests , and logistic regression analysis were conducted. Physical activity according to the G-test results was statistically higher in the GP compared to the GF (vigorous activity reps/week, p = 0.017; mins/day, p = 0.011). The GP Group showed a statistically high GNKQ score compared to the GF Group: Overall (p = 0.003), Section 1 (p < 0.001), and Section 2 (p = 0.002). Based on this study, it can be deduced that analyzing the effect G-test through continuous research over the next years and applying them to physical training will have a greater impact on the cadets’ increased physical strength and their success on the G-test.
Assessment of mycotoxin sequestration efficacy in Saccharomyces cerevisiae by-products cultured in wheat bran and whey protein medium
Authors: Mirseyed Pardis Sadat , Kheirabadi Shahpour , Anbarteh Rojin , H. Ghaffari Morteza
Published: February 2024

Mycotoxins are metabolic products of fungi found in feed for farm animals and pose a major threat to food safety due to their adverse health effects. The development of strategies to reduce their bioavailability is crucial. In this context, the cell wall components of Saccharomyces cerevisiae (YCW), especially β-d-glucans and Mannan-oligosaccharide, have been recognized as potent mycotoxin binders. The objective of this research was to develop a novel culture medium to increase the biomass yield of S. cerevisiae and optimize cell disruption by stepwise physical lysis and hydrolytic preconditioning. This process resulted in a yield of approximately 56% reducing saccharides and 28.54% protein. Subsequently, the β-glucan was extracted after cell wall sequestration. The isolated YCW and extracted β-glucan were characterized both individually and synergistically to evaluate their antibacterial properties and analyze their Fourier transform infrared (FTIR) spectra. In vitro evaluation of antibacterial activity revealed that a concentration greater than 250 μg/mL of YCW-β-glucan blend significantly inhibited the growth of Gram-negative bacteria. In addition, this blend showed good adsorption of various mycotoxins, including Aflatoxin B1, Ochratoxin A, and Zearalenone, the latter of which exhibited a remarkable adsorption rate of 80.85%. This study highlights the promising potential of a combination of YCW and β-glucan as a robust strategy to address the pervasive problem of mycotoxin contamination in feed.