bluuebunny/crossref_metadata_2025 huggingface dataset:
Vitrification-enabled enhancement of proton conductivity in hydrogen-bonded organic frameworks
Authors: Yang Feng-Fan , Wang Xiao-Lu , Tian Jiayue , Yin Yang , Liang Linfeng
Published: May 2024

Hydrogen-bonded organic frameworks (HOFs) are versatile materials with potential applications in proton conduction. Traditional approaches involve incorporating humidity control to address grain boundary challenges for proton conduction. This study finds vitrification as an alternative strategy to eliminate grain boundary effect in HOFs by rapidly melt quenching the kinetically stable HOF-SXU-8 to glassy state HOF-g. Notably, a remarkable enhancement in proton conductivity without humidity was achieved after vitrification, from 1.31 × 10−7 S cm−1 to 5.62× 10−2 S cm−1 at 100 °C. Long term stability test showed negligible performance degradation, and even at 30 °C, the proton conductivity remained at high level of 1.2 × 10−2 S cm−1. Molecule dynamics (MD) simulations and X-ray total scattering experiments reveal the HOF-g system is consisted of three kinds of clusters, i.e., 1,5-Naphthalenedisulfonic acid (1,5-NSA) anion clusters, N,N-dimethylformamide (DMF) molecule clusters, and H+-H2O clusters. In which, the H+ plays an important role to bridge these clusters and the high conductivity is mainly related to the H+ on H3O+. These findings provide valuable insights for optimizing HOFs, enabling efficient proton conduction, and advancing energy conversion and storage devices.
5′UTR G-quadruplex structure enhances translation in size dependent manner
Authors: Lee Chun-Ying , Joshi Meera , Wang Ashley , Myong Sua
Published: May 2024

Translation initiation in bacteria is frequently regulated by various structures in the 5′ untranslated region (5′UTR). Previously, we demonstrated that G-quadruplex (G4) formation in non-template DNA enhances transcription. In this study, we aim to explore how G4 formation in mRNA (RG4) at 5′UTR impacts translation using a T7-based in vitro translation system and in E. coli. We show that RG4 strongly promotes translation efficiency in a size-dependent manner. Additionally, inserting a hairpin upstream of the RG4 further enhances translation efficiency, reaching up to a 12-fold increase. We find that the RG4-dependent effect is not due to increased ribosome affinity, ribosome binding site accessibility, or mRNA stability. We propose a physical barrier model in which bulky structures in 5′UTR biases ribosome movement toward the downstream start codon, thereby increasing the translation output. This study provides biophysical insights into the regulatory role of 5′UTR structures in in vitro and bacterial translation, highlighting their potential applications in tuning gene expression.
Multiplexed bulk and single-cell RNA-seq hybrid enables cost-efficient disease modeling with chimeric organoids
Authors: Cheng Chen , Wang Gang , Zhu Yuqing , Wu Hangdi , Zhang Li , Liu Zhihong , Huang Yuanhua , Zhang Jin
Published: May 2024

Disease modeling with isogenic Induced Pluripotent Stem Cell (iPSC)-differentiated organoids serves as a powerful technique for studying disease mechanisms. Multiplexed coculture is crucial to mitigate batch effects when studying the genetic effects of disease-causing variants in differentiated iPSCs or organoids, and demultiplexing at the single-cell level can be conveniently achieved by assessing natural genetic barcodes. Here, to enable cost-efficient time-series experimental designs via multiplexed bulk and single-cell RNA-seq of hybrids, we introduce a computational method in our Vireo Suite, Vireo-bulk, to effectively deconvolve pooled bulk RNA-seq data by genotype reference, and thereby quantify donor abundance over the course of differentiation and identify differentially expressed genes among donors. Furthermore, with multiplexed scRNA-seq and bulk RNA-seq, we demonstrate the usefulness and necessity of a pooled design to reveal donor iPSC line heterogeneity during macrophage cell differentiation and to model rare WT1 mutation-driven kidney disease with chimeric organoids. Our work provides an experimental and analytic pipeline for dissecting disease mechanisms with chimeric organoids.
Molecular basis of bacterial DSR2 anti-phage defense and viral immune evasion
Authors: Huang Jiafeng , Zhu Keli , Gao Yina , Ye Feng , Li Zhaolong , Ge Yao , Liu Songqing , Yang Jing , Gao Ang
Published: May 2024

Defense-associated sirtuin 2 (DSR2) systems are widely distributed across prokaryotic genomes, providing robust protection against phage infection. DSR2 recognizes phage tail tube proteins and induces abortive infection by depleting intracellular NAD+, a process that is counteracted by another phage-encoded protein, DSR Anti Defense 1 (DSAD1). Here, we present cryo-EM structures of Bacillus subtilis DSR2 in its apo, Tube-bound, and DSAD1-bound states. DSR2 assembles into an elongated tetramer, with four NADase catalytic modules clustered in the center and the regulatory-sensing modules distributed at four distal corners. Interestingly, monomeric Tube protein, rather than its oligomeric states, docks at each corner of the DSR2 tetramer to form a 4:4 DSR2-Tube assembly, which is essential for DSR2 NADase activity. DSAD1 competes with Tube for binding to DSR2 by occupying an overlapping region, thereby inhibiting DSR2 immunity. Thus, our results provide important insights into the assembly, activation and inhibition of the DSR2 anti-phage defense system.
Strain engineering the spin-valley coupling of the R-stacking sliding ferroelectric bilayer 2H-VX2 (X = S, Se, Te)
Authors: Ma Jiayu , Luo Xin , Zheng Yue
Published: May 2024

The emergence of magnetic transition metal dichalcogenides has significantly advanced the development of valleytronics due to the spontaneous breaking of time-reversal symmetry and space-inversion symmetry. However, the lack of regulation methods has prevented researchers from exploring their potential applications. Herein, we propose to use strain engineering to control the spin-valley coupling in the sliding ferroelectric bilayer 2H-VX2 (X = S, Se, Te). Four multiferroic states are constructed by combining the sliding ferroelectricity and antiferromagnetism in the R-stacking bilayer VX2, where the spin and valley polarizations are coupled together from the layer-dependent spin-polarized band structures. By applying a small external strain or pressure on the out-of-plane van der Waals direction, we predicted that there is an antiferromagnetic to magnetic transition in the bilayer VX2, leading to the interesting spin-polarized and chiral circularly polarized radiation at K+ and K- valleys, similar to those found in the magnetic monolayer. To comprehend the coupling between various degrees of freedom in these multiferroic systems, we have developed an effective k·p model. This model unveils a linear relationship between the electric polarization generated by interlayer sliding and the energy difference of the valence band maximum at K+ and K- valleys. Thus, providing an alternate method to measure the electric polarization in the sliding ferroelectrics. Based on the strong coupling between the strain, spin-valley, and electric polarization, it is likely to use the strain to control the interesting emerging properties of 2H-VX2 such as the anomalous valley Hall effect.
Localized corrosion in selective laser melted SS316L in CO2 and H2S brines at elevated temperatures
Authors: Narayanan Deeparekha , Martinez Alan , Martin Ulises , Mansoor Bilal , Case Raymundo , Castaneda Homero
Published: May 2024

In this work, the passivation and localized corrosion of selective laser melted (SLM) stainless steel 316 L when exposed to high pressures of CO2 with the presence of H2S and Cl− at 25 °C and 125 °C were studied. Depletion of Cr/Mo was observed at the cell interiors and melt-pool boundaries (MPBs) compared to the cell boundaries. Volta potential differences obtained from scanning Kelvin probe force microscopy (SKPFM) showed that the MPBs were 8–20 mV lower than the matrix, while the cell interiors were 20–50 mV lower than the cell boundaries. Electrochemical impedance spectroscopy (EIS) and Mott–Schottky tests indicated a more defective passive film at 125 °C, and X-ray photoelectron spectroscopy (XPS) confirmed the formation of a less protective film with an increased S/O ratio at 125 °C than 25 °C. Initiation of localized corrosion was observed at the MPBs and pits formed after a week of immersion were wider by an order of magnitude at 125 °C than 25 °C, with evidence of cell-interior dissolution. While passivity was observed even at elevated temperatures, local chemical heterogeneities compromised the stability of the film and contributed to localized corrosion in SLM SS316L.
Untargeted serum metabolic profiling of diabetes mellitus among Parkinson’s disease patients
Authors: Li Shiwen , Lin Yuyuan , Jones Dean , Walker Douglas I. , Duarte Folle Aline , Del Rosario Irish , Yu Yu , Zhang Keren , Keener Adrienne M. , Bronstein Jeff , Ritz Beate , Paul Kimberly C.
Published: May 2024

Type 2 diabetes mellitus (T2DM) is a common comorbidity among Parkinson’s disease (PD) patients. Yet, little is known about dysregulated pathways that are unique in PD patients with T2DM. We applied high-resolution metabolomic profiling in serum samples of 636 PD and 253 non-PD participants recruited from Central California. We conducted an initial discovery metabolome-wide association and pathway enrichment analysis. After adjusting for multiple testing, in positive (or negative) ion mode, 30 (25) metabolic features were associated with T2DM in both PD and non-PD participants, 162 (108) only in PD participants, and 32 (7) only in non-PD participants. Pathway enrichment analysis identified 17 enriched pathways associated with T2DM in both the PD and non-PD participants, 26 pathways only in PD participants, and 5 pathways only in non-PD participants. Several amino acid, nucleic acids, and fatty acid metabolisms were associated with T2DM only in the PD patient group suggesting a possible link between PD and T2DM.
Rhizobia–diatom symbiosis fixes missing nitrogen in the ocean
Authors: Tschitschko Bernhard , Esti Mertcan , Philippi Miriam , Kidane Abiel T. , Littmann Sten , Kitzinger Katharina , Speth Daan R. , Li Shengjie , Kraberg Alexandra , Tienken Daniela , Marchant Hannah K. , Kartal Boran , Milucka Jana , Mohr Wiebke , Kuypers Marcel M. M.
Published: May 2024

Nitrogen (N2) fixation in oligotrophic surface waters is the main source of new nitrogen to the ocean1 and has a key role in fuelling the biological carbon pump2. Oceanic N2 fixation has been attributed almost exclusively to cyanobacteria, even though genes encoding nitrogenase, the enzyme that fixes N2 into ammonia, are widespread among marine bacteria and archaea3–5. Little is known about these non-cyanobacterial N2 fixers, and direct proof that they can fix nitrogen in the ocean has so far been lacking. Here we report the discovery of a non-cyanobacterial N2-fixing symbiont, ‘Candidatus Tectiglobus diatomicola’, which provides its diatom host with fixed nitrogen in return for photosynthetic carbon. The N2-fixing symbiont belongs to the order Rhizobiales and its association with a unicellular diatom expands the known hosts for this order beyond the well-known N2-fixing rhizobia–legume symbioses on land6. Our results show that the rhizobia–diatom symbioses can contribute as much fixed nitrogen as can cyanobacterial N2 fixers in the tropical North Atlantic, and that they might be responsible for N2 fixation in the vast regions of the ocean in which cyanobacteria are too rare to account for the measured rates.
An electrochemical, and surface studies of synthesized Gemini ionic liquid as corrosion inhibitor for carbon steel in petroleum field
Authors: Selim Yousef A. , Abd-El-Raouf M. , Zakaria K. , Sayed Ahmed Z. , Moustafa Yasser M. , Ashmawy Ashraf M.
Published: May 2024

In this work, we study the efficiency ofN1,N3-dibenzyl-N1, N1,N3,N3-tetramethylpropane-1,3-diaminium chloride, as anticorrosion. This compound exhibits potential as a prospective remedy to stop the deterioration of carbon steel caused by corrosion in 1.0 M HCl. The synthesis of this compound is described in a comprehensive manner, and its composition is supported by a range of precise analytical approaches such as elemental analysis, and mass spectroscopy. Based on the findings of the investigation, the synthesized Gemini ionic liquid demonstrates a robust capacity to slow down the rate at which the metal corrodes. The Prepared compound was evaluation by electrochemical and morphology study. Our results revealed that elevating the inhibitor concentration led to an augmentation in inhibition effectiveness, reaching up to 94.8% at 200 ppm of the synthesized compound at 298 K. It is crucial to emphasize that the recently prepared Gemini ionic liquid is consistent with the Langmuir adsorption model and function as a mixed inhibitor, participating in the physio-chemisorption process of adsorption.
Exact solitary wave propagations for the stochastic Burgers’ equation under the influence of white noise and its comparison with computational scheme
Authors: Baber Muhammad Zafarullah , Mohammed Wael W. , Ahmed Nauman , Iqbal Muhammad Sajid
Published: May 2024

In this manuscript, the well-known stochastic Burgers’ equation in under investigation numerically and analytically. The stochastic Burgers’ equation plays an important role in the fields of applied mathematics such as fluid dynamics, gas dynamics, traffic flow, and nonlinear acoustics. This study is presented the existence, approximate, and exact stochastic solitary wave results. The existence of results is shown by the help of Schauder fixed point theorem. For the approximate results the proposed stochastic finite difference scheme is constructed. The analysis of the proposed scheme is analyzed by presented the consistency and stability of scheme. The consistency is checked under the mean square sense while the stability condition is gained by the help of Von-Neumann criteria. Meanwhile, the stochastic exact solutions are constructed by using the generalized exponential rational function method. These exact stochastic solutions are obtained in the form of hyperbolic, trigonometric and exponential functions. Mainly, the comparison of both numerical and exact solutions are analyzed via simulations. The unique physical problems are constructed from the newly constructed soliton solutions to compare the numerical results with exact solutions under the presence of randomness. The 3D and line plots are dispatched that are shown the similar behavior by choosing the different values of parameters. These results are the main innovation of this study under the noise effects.
Research on coupling optimization of carbon emissions and carbon leakage in international construction projects
Authors: Zhou Zhiwu , Wang Ying , Alcalá Julián , Yepes Víctor
Published: May 2024

Due to the rapid economic development of globalization and the intensification of economic and trade exchanges, cross-international and regional carbon emissions have become increasingly severe. Governments worldwide establish laws and regulations to protect their countries' environmental impact. Therefore, selecting robustness evaluation models and metrics is an urgent research topic. This article proves the reliability and scientific of the assessment data through literature coupling evaluation, multidisciplinary coupling mathematical model and international engineering case analysis. The innovation of this project's research lies in the comprehensive analysis of the complex coupling effects of various discrete data and uncertainty indicators on the research model across international projects and how to model and evaluate interactive effects accurately. This article provides scientific measurement standards and data support for governments worldwide to formulate carbon tariffs and carbon emission policies. Case analysis data shows that the carbon emission ratio of exporting and importing countries is 0.577:100; the carbon trading quota ratio is 32.50:100.
Application of advanced causal analyses to identify processes governing secondary organic aerosols
Authors: Sinha S. , Sharma H. , Shrivastava M.
Published: May 2024

Understanding how different physical and chemical atmospheric processes affect the formation of fine particles has been a persistent challenge. Inferring causal relations between the various measured features affecting the formation of secondary organic aerosol (SOA) particles is complicated since correlations between variables do not necessarily imply causality. Here, we apply a state-of-the-art information transfer measure coupled with the Koopman operator framework to infer causal relations between isoprene epoxydiol SOA (IEPOX-SOA) and different chemistry and meteorological variables derived from detailed regional model predictions over the Amazon rainforest. IEPOX-SOA represents one of the most complex SOA formation pathways and is formed by the interactions between natural biogenic isoprene emissions and anthropogenic emissions affecting sulfate, acidity and particle water. Since the regional model captures the known relations of IEPOX-SOA with different chemistry and meteorological features, their simulated time series implicitly include their causal relations. We show that our causal model successfully infers the known major causal relations between total particle phase 2-methyl tetrols (the dominant component of IEPOX-SOA over the Amazon) and input features. We provide the first proof of concept that the application of our causal model better identifies causal relations compared to correlation and random forest analyses performed over the same dataset. Our work has tremendous implications, as our methodology of causal discovery could be used to identify unknown processes and features affecting fine particles and atmospheric chemistry in the Earth’s atmosphere.
3SAT on an all-to-all-connected CMOS Ising solver chip
Authors: Cılasun Hüsrev , Zeng Ziqing , S Ramprasath , Kumar Abhimanyu , Lo Hao , Cho William , Moy William , Kim Chris H. , Karpuzcu Ulya R. , Sapatnekar Sachin S.
Published: May 2024

This work solves 3SAT, a classical NP-complete problem, on a CMOS-based Ising hardware chip with all-to-all connectivity. The paper addresses practical issues in going from algorithms to hardware. It considers several degrees of freedom in mapping the 3SAT problem to the chip—using multiple Ising formulations for 3SAT; exploring multiple strategies for decomposing large problems into subproblems that can be accommodated on the Ising chip; and executing a sequence of these subproblems on CMOS hardware to obtain the solution to the larger problem. These are evaluated within a software framework, and the results are used to identify the most promising formulations and decomposition techniques. These best approaches are then mapped to the all-to-all hardware, and the performance of 3SAT is evaluated on the chip. Experimental data shows that the deployed decomposition and mapping strategies impact SAT solution quality: without our methods, the CMOS hardware cannot achieve 3SAT solutions on SATLIB benchmarks. Under the assumption of some hardware improvements, our chip-based 3SAT solver demonstrates a remarkable 250$$\times$$
×
acceleration compared to Tabu search in dwave-hybrid on a CPU.
The prognostic significance and potential mechanism of DBF4 zinc finger in hepatocellular carcinoma
Authors: Wu Zhongkai , Zhang Lilong , Li Xinyi , Liu Li , Kuang Tianrui , Qiu Zhendong , Deng Wenhong , Wang Weixing
Published: May 2024

DBF4 zinc finger (DBF4) is a critical component involved in DNA replication and cell proliferation. It acts as a positive regulator of the cell division cycle 7 kinase. In this study, our investigation encompassed the impact of DBF4 on hepatocellular carcinoma (HCC) progression and delved into the potential mechanisms. We utilized open-access databases like TCGA and GEO to analyze the association between DBF4 and 33 different tumor types. We also conducted immunohistochemistry experiments to validate the expression of DBF4 in HCC, STAD, COAD, READ, PAAD, and LGG. Furthermore, we employed lentiviral transduction to knockdown DBF4 in HLF and SMMC cells, as well as to overexpress DBF4 in Huh7 cells. Subsequently, we evaluated the impact of DBF4 on proliferation, migration, and invasion of hepatocellular carcinoma cells. RNA sequencing and KEGG pathway enrichment analysis were also conducted to identify potential pathways, which were further validated through WB experiments. Finally, pathway inhibitor was utilized in rescue experiments to confirm whether DBF4 exerts its effects on tumor cells via the implicated pathway. Our findings revealed that DBF4 exhibited significant expression levels in nearly all examined tumors, which were further substantiated by the results of immunohistochemistry analysis. High DBF4 expression was correlated with poor overall survival (OS), disease-specific survival (DSS), progression-free interval (PFI), disease-free interval (DFI), relapse-free interval (RFI) in majority of tumor types, particularly in patients with HCC. In vitro experiments demonstrated that inhibition of DBF4 impaired the proliferative, migratory, and invasive abilities of HCC cells, whereas overexpression of DBF4 promoted these phenotypes. Sequencing results indicated that DBF4 may induce these changes through the ERBB signaling pathway. Further experimental validation revealed that DBF4 activates the ERBB signaling pathway, leading to alterations in the JNK/STAT, MAPK, and PI3K/AKT signaling pathways, thereby impacting the proliferative, migratory, and invasive abilities of tumor cells. Lastly, treatment of Huh7 cells overexpressing DBF4 with the ERBB2 inhibitor dacomitinib demonstrated the ability of ERBB2 inhibition to reverse the promoting effect of DBF4 overexpression on the proliferative, migratory, and invasive abilities of HCC cells. DBF4 plays a pivotal oncogenic role in HCC by promoting the ERBB signaling pathway and activating its downstream PI3K/AKT, JNK/STAT3, and MAPK signaling pathways. DBF4 may serve as a prognostic biomarker for patients with HCC.
Benefits of tropical peatland rewetting for subsidence reduction and forest regrowth: results from a large-scale restoration trial
Authors: Hooijer A. , Vernimmen R. , Mulyadi D. , Triantomo V. , Hamdani  , Lampela M. , Agusti R. , Page S. E. , Doloksaribu J. , Setiawan I. , Suratmanto B. , Swarup S.
Published: May 2024

Drainage and deforestation of tropical peat swamp forests (PSF) in Southeast Asia cause carbon emissions and biodiversity loss of global concern. Restoration efforts to mitigate these impacts usually involve peatland rewetting by blocking canals. However, there have been no studies to date of the optimal rewetting approach that will reduce carbon emission whilst also promoting PSF regeneration. Here we present results of a large-scale restoration trial in Sumatra (Indonesia), monitored for 7.5 years. Water levels in a former plantation were raised over an area of 4800 ha by constructing 257 compacted peat dams in canals. We find peat surface subsidence rates in the rewetted restoration area and adjoining PSF to be halved where water tables were raised from ~ − 0.6 m to ~ − 0.3 m, demonstrating the success of rewetting in reducing carbon emission. A total of 57 native PSF tree species were found to spontaneously grow in the most rewetted conditions and in high densities, indicating that forest regrowth is underway. Based on our findings we propose that an effective PSF restoration strategy should follow stepwise rewetting to achieve substantial carbon emission reduction alongside unassisted regrowth of PSF, thereby enabling the peat, forest and canal vegetation to establish a new nature-based ecosystem balance.
Noise-induced hearing loss alters potassium-chloride cotransporter KCC2 and GABA inhibition in the auditory centers
Authors: Parameshwarappa V. , Siponen M. I. , Watabe I. , Karkaba A. , Galazyuk A. , Noreña A. J.
Published: May 2024

Homeostatic plasticity, the ability of neurons to maintain their averaged activity constant around a set point value, is thought to account for the central hyperactivity after hearing loss. Here, we investigated the putative role of GABAergic neurotransmission in this mechanism after a noise-induced hearing loss larger than 50 dB in high frequencies in guinea pigs. The effect of GABAergic inhibition is linked to the normal functioning of K + –Cl– co-transporter isoform 2 (KCC2) which maintains a low intracellular concentration of chloride. The expression of membrane KCC2 were investigated before and after noise trauma in the ventral and dorsal cochlear nucleus (VCN and DCN, respectively) and in the inferior colliculus (IC). Moreover, the effect of gabazine (GBZ), a GABA antagonist, was also studied on the neural activity in IC. We show that KCC2 is downregulated in VCN, DCN and IC 3 days after noise trauma, and in DCN and IC 30 days after the trauma. As expected, GBZ application in the IC of control animals resulted in an increase of spontaneous and stimulus-evoked activity. In the noise exposed animals, on the other hand, GBZ application decreased the stimulus-evoked activity in IC neurons. The functional implications of these central changes are discussed.
In-vitro and in-vivo assessment of nirmatrelvir penetration into CSF, central nervous system cells, tissues, and peripheral blood mononuclear cells
Authors: Avedissian Sean N. , Malik Johid R. , Podany Anthony T. , Neely Michael , Rhodes Nathaniel J. , Scarsi Kimberly K. , Scheetz Marc H. , Duryee Michael J. , Modebelu Ukamaka O. , Mykris Timothy M. , Winchester Lee C. , Byrareddy Siddappa N. , Fletcher Courtney V.
Published: May 2024

Three years after SARS-CoV-2 emerged as a global infectious threat, the virus has become endemic. The neurological complications such as depression, anxiety, and other CNS complications after COVID-19 disease are increasing. The brain, and CSF have been shown as viral reservoirs for SARS-CoV-2, yielding a potential hypothesis for CNS effects. Thus, we investigated the CNS pharmacology of orally dosed nirmatrelvir/ritonavir (NMR/RTV). Using both an in vitro and an in vivo rodent model, we investigated CNS penetration and potential pharmacodynamic activity of NMR. Through pharmacokinetic modeling, we estimated the median CSF penetration of NMR to be low at 18.11% of plasma with very low accumulation in rodent brain tissue. Based on the multiples of the 90% maximal effective concentration (EC90) for SARS-CoV-2, NMR concentrations in the CSF and brain do not achieve an exposure level similar to that of plasma. A median of only 16% of all the predicted CSF concentrations in rats were > 3xEC90 (unadjusted for protein binding). This may have implications for viral persistence and neurologic post-acute sequelae of COVID-19 if increased NMR penetration in the CNS leads to decreased CNS viral loads and decreased CNS inflammation.
Adolescents’ trajectories of depression and anxiety symptoms prior to and during the COVID-19 pandemic and their association with healthy sleep patterns
Authors: Bauducco Serena , Gardner Lauren A. , Smout Scarlett , Champion Katrina E. , Chapman Cath , Gamble Amanda , Teesson Maree , Gradisar Michael , Newton Nicola C.
Published: May 2024

The COVID-19 pandemic has seen a rise in anxiety and depression among adolescents. This study aimed to investigate the longitudinal associations between sleep and mental health among a large sample of Australian adolescents and examine whether healthy sleep patterns were protective of mental health in the context of the COVID-19 pandemic. We used three waves of longitudinal control group data from the Health4Life cluster-randomized trial (N = 2781, baseline Mage = 12.6, SD =  0.51; 47% boys and 1.4% ‘prefer not to say’). Latent class growth analyses across the 2 years period identified four trajectories of depressive symptoms: low-stable (64.3%), average-increasing (19.2%), high-decreasing (7.1%), moderate-increasing (9.4%), and three anxiety symptom trajectories: low-stable (74.8%), average-increasing (11.6%), high-decreasing (13.6%). We compared the trajectories on sociodemographic and sleep characteristics. Adolescents in low-risk trajectories were more likely to be boys and to report shorter sleep latency and wake after sleep onset, longer sleep duration, less sleepiness, and earlier chronotype. Where mental health improved or worsened, sleep patterns changed in the same direction. The subgroups analyses uncovered two important findings: (1) the majority of adolescents in the sample maintained good mental health and sleep habits (low-stable trajectories), (2) adolescents with worsening mental health also reported worsening sleep patterns and vice versa in the improving mental health trajectories. These distinct patterns of sleep and mental health would not be seen using mean-centred statistical approaches.
Diagnostic biomarker discovery from brain EEG data using LSTM, reservoir-SNN, and NeuCube methods in a pilot study comparing epilepsy and migraine
Authors: Saeedinia Samaneh Alsadat , Jahed-Motlagh Mohammad Reza , Tafakhori Abbas , Kasabov Nikola Kirilov
Published: May 2024

The study introduces a new online spike encoding algorithm for spiking neural networks (SNN) and suggests new methods for learning and identifying diagnostic biomarkers using three prominent deep learning neural network models: deep BiLSTM, reservoir SNN, and NeuCube. EEG data from datasets related to epilepsy, migraine, and healthy subjects are employed. Results reveal that BiLSTM hidden neurons capture biological significance, while reservoir SNN activities and NeuCube spiking dynamics identify EEG channels as diagnostic biomarkers. BiLSTM and reservoir SNN achieve 90 and 85% classification accuracy, while NeuCube achieves 97%, all methods pinpointing potential biomarkers like T6, F7, C4, and F8. The research bears implications for refining online EEG classification, analysis, and early brain state diagnosis, enhancing AI models with interpretability and discovery. The proposed techniques hold promise for streamlined brain-computer interfaces and clinical applications, representing a significant advancement in pattern discovery across the three most popular neural network methods for addressing a crucial problem. Further research is planned to study how early can these diagnostic biomarkers predict an onset of brain states.
Pulmonary arteries in coelacanths shed light on the vasculature evolution of air-breathing organs in vertebrates
Authors: Cupello Camila , Clément Gaël , Herbin Marc , Meunier François J. , Brito Paulo M.
Published: May 2024

To date, the presence of pulmonary organs in the fossil record is extremely rare. Among extant vertebrates, lungs are described in actinopterygian polypterids and in all sarcopterygians, including coelacanths and lungfish. However, vasculature of pulmonary arteries has never been accurately identified neither in fossil nor extant coelacanths due to the paucity of fossil preservation of pulmonary organs and limitations of invasive studies in extant specimens. Here we present the first description of the pulmonary vasculature in both fossil and extant actinistian, a non-tetrapod sarcopterygian clade, contributing to a more in-depth discussion on the morphology of these structures and on the possible homology between vertebrate air-filled organs (lungs of sarcopterygians, lungs of actinopterygians, and gas bladders of actinopterygians).
Tree growth potential and its relationship with soil moisture conditions across a heterogeneous boreal forest landscape
Authors: Larson Johannes , Vigren Carl , Wallerman Jörgen , Ågren Anneli M. , Appiah Mensah Alex , Laudon Hjalmar
Published: May 2024

Forest growth varies across landscapes due to the intricate relationships between various environmental drivers and forest management. In this study, we analysed the variation of tree growth potential across a landscape scale and its relation to soil moisture. We hypothesised that soil moisture conditions drive landscape-level variation in site quality and that intermediate soil moisture conditions demonstrate the highest potential forest production. We used an age-independent difference model to estimate site quality in terms of maximum achievable tree height by measuring the relative change in Lorey’s mean height for a five year period across 337 plots within a 68 km2 boreal landscape. We achieved wall-to-wall estimates of site quality by extrapolating the modelled relationship using repeated airborne laser scanning data collected in connection to the field surveys. We found a clear decrease in site quality under the highest soil moisture conditions. However, intermediate soil moisture conditions did not demonstrate clear site quality differences; this is most likely a result of the nature of the modelled soil moisture conditions and limitations connected to the site quality estimation. There was considerable unexplained variation in the modelled site quality both on the plot and landscape levels. We successfully demonstrated that there is a significant relationship between soil moisture conditions and site quality despite limitations associated with a short study period in a low productive region and the precision of airborne laser scanning measurements of mean height.
Immigration documentation statuses evoke racialized faceism in mental representations
Authors: Martinez Joel E. , Oh DongWon , Todorov Alexander
Published: May 2024

U.S. immigration discourse has spurred interest in characterizing who illegalized immigrants are or perceived to be. What are the associated visual representations of migrant illegality? Across two studies with undergraduate and online samples (N = 686), we used face-based reverse correlation and similarity sorting to capture and compare mental representations of illegalized immigrants, native-born U.S. citizens, and documented immigrants. Documentation statuses evoked racialized imagery. Immigrant representations were dark-skinned and perceived as non-white, while citizen representations were light-skinned, evaluated positively, and perceived as white. Legality further differentiated immigrant representations: documentation conjured trustworthy representations, illegality conjured threatening representations. Participants spontaneously sorted unlabeled faces by documentation status in a spatial arrangement task. Faces’ spatial similarity correlated with their similarity in pixel luminance and “American” ratings, confirming racialized distinctions. Representations of illegalized immigrants were uniquely racialized as dark-skinned un-American threats, reflecting how U.S. imperialism and colorism set conditions of possibility for existing representations of migrant illegalization.
Microscopic behavior of nano-water droplets on a silica glass surface
Authors: Araki Yuki , Minato Taketoshi , Arai Toyoko
Published: May 2024

Recent advancements in computational science and interfacial measurements have sparked interest in microscopic water droplets and their diverse behaviors. A previous study using nonlinear spectroscopy revealed the heterogeneous wetting phenomenon of silica glass in response to humidity. Building on this premise, we employed high-resolution atomic force microscopy to investigate the wetting dynamics of silica glass surfaces at various humidity levels. Our observations revealed the spontaneous formation of nano-water droplets at a relative humidity of 50%. In contrast to the conventional model, which predicts the spreading of nanodroplets to form a uniform water film, our findings demonstrate the coexistence of nano-water droplets and the liquid film. Moreover, the mobility of the nano-water droplets suggests their potential in inducing the transport of adsorbates on solid surfaces. These results may contribute to the catalytic function of solid materials.
The relationship between oxidative balance score and erectile dysfunction in the U.S. male adult population
Authors: Chen Mutong , Zhang Zhongfu , Zhou Rui , Li Baizhi , Jiang Jiahao , Shi Bentao
Published: May 2024

Oxidative stress strongly influences the pathophysiology of erectile dysfunction (ED). In this study, we used the oxidative balance score (OBS), a composite index, to measure the effects of oxidative stress triggered by diet and lifestyle factors. Here, we conducted a cross-sectional study to determine the statistical relationship between OBS and ED among adult males in the U.S. The data from 3318 participants in the National Health and Nutrition Examination Survey (NHANES) 2001–2004 were analyzed. Weighted logistic regression was used to correct for confounding factors and acquire nationwide representative estimates. Generalized additive modeling was used to explore the nonlinear relationship. We also supplemented subgroup and sensitivity analysis to examine the robustness of the main results. Multivariate logistic regression indicated a consistent negative linear association between OBS and ED across all participants [OR (95% CI) = 0.96 (0.94, 0.98)]. After categorizing OBS into tertiles, participants in the highest tertile had 43% lower odds of having ED than those in the lowest tertile [OR (95% CI) = 0.57 (0.37, 0.87)]. The generalized additive model also visualized the linear trend of this association. Furthermore, this linear relationship remained relatively consistent, regardless of whether subgroup or sensitivity analyses were performed. Our findings suggest that adopting a lifestyle and diet pattern that promotes favorable OBS may effectively protect against the development of ED, regardless of the underlying causes.
Establishment and validation of an artificial intelligence-based model for real-time detection and classification of colorectal adenoma
Authors: Zhao Luqing , Wang Nan , Zhu Xihan , Wu Zhenyu , Shen Aihua , Zhang Lihong , Wang Ruixin , Wang Dianpeng , Zhang Shengsheng
Published: May 2024

Colorectal cancer (CRC) prevention requires early detection and removal of adenomas. We aimed to develop a computational model for real-time detection and classification of colorectal adenoma. Computationally constrained background based on real-time detection, we propose an improved adaptive lightweight ensemble model for real-time detection and classification of adenomas and other polyps. Firstly, we devised an adaptive lightweight network modification and effective training strategy to diminish the computational requirements for real-time detection. Secondly, by integrating the adaptive lightweight YOLOv4 with the single shot multibox detector network, we established the adaptive small object detection ensemble (ASODE) model, which enhances the precision of detecting target polyps without significantly increasing the model's memory footprint. We conducted simulated training using clinical colonoscopy images and videos to validate the method's performance, extracting features from 1148 polyps and employing a confidence threshold of 0.5 to filter out low-confidence sample predictions. Finally, compared to state-of-the-art models, our ASODE model demonstrated superior performance. In the test set, the sensitivity of images and videos reached 87.96% and 92.31%, respectively. Additionally, the ASODE model achieved an accuracy of 92.70% for adenoma detection with a false positive rate of 8.18%. Training results indicate the effectiveness of our method in classifying small polyps. Our model exhibits remarkable performance in real-time detection of colorectal adenomas, serving as a reliable tool for assisting endoscopists.
Exploring the virulence potential of Staphylococcus aureus CC121 and CC152 lineages related to paediatric community-acquired bacteraemia in Manhiça, Mozambique
Authors: Garrine Marcelino , Andrade Mariana , Neves Joana , Mandomando Inácio , Couto Isabel , Costa Sofia Santos
Published: May 2024

Staphylococcus aureus is a frequent agent of bacteraemia. This bacterium has a variety of virulence traits that allow the establishment and maintenance of infection. This study explored the virulence profile of S. aureus strains causing paediatric bacteraemia (SAB) in Manhiça district, Mozambique. We analysed 336 S. aureus strains isolated from blood cultures of children younger than 5 years admitted to the Manhiça District Hospital between 2001 and 2019, previously characterized for antibiotic susceptibility and clonality. The strains virulence potential was evaluated by PCR detection of the Panton-Valentine leucocidin (PVL) encoding genes, lukS-PV/lukF-PV, assessment of the capacity for biofilm formation and pathogenicity assays in Galleria mellonella. The overall carriage of PVL-encoding genes was over 40%, although reaching ~ 70 to 100% in the last years (2014 to 2019), potentially linked to the emergence of CC152 lineage. Strong biofilm production was a frequent trait of CC152 strains. Representative CC152 and CC121 strains showed higher virulence potential in the G. mellonella model when compared to reference strains, with variations within and between CCs. Our results highlight the importance of monitoring the emergent CC152-MSSA-PVL+ and other lineages, as they display important virulence traits that may negatively impact the management of SAB paediatric patients in Manhiça district, Mozambique.
Diagnostic implications of ubiquitination-related gene signatures in Alzheimer's disease
Authors: Xu Fei , Gao Wei , Zhang Miao , Zhang Fuyue , Sun XiaoFei , Wu Bao , Liu Yali , Li Xue , Li Honglin
Published: May 2024

The purpose of this study was to explore the diagnostic implications of ubiquitination-related gene signatures in Alzheimer's disease. In this study, we first collected 161 samples from the GEO database (including 87 in the AD group and 74 in the normal group). Subsequently, through differential expression analysis and the iUUCD 2.0 database, we obtained 3450 Differentially Expressed Genes (DEGs) and 806 Ubiquitin-related genes (UbRGs). After taking the intersection, we obtained 128 UbR-DEGs. Secondly, by conducting GO and KEGG enrichment analysis on these 128 UbR-DEGs, we identified the main molecular functions and biological pathways related to AD. Furthermore, through the utilization of GSEA analysis, we have gained insight into the enrichment of functions and pathways within both the AD and normal groups. Further, using lasso regression analysis and cross-validation techniques, we identified 22 characteristic genes associated with AD. Subsequently, we constructed a logistic regression model and optimized it, resulting in the identification of 6 RUbR-DEGs: KLHL21, WDR82, DTX3L, UBTD2, CISH, and ATXN3L. In addition, the ROC result showed that the diagnostic model we built has excellent accuracy and reliability in identifying AD patients. Finally, we constructed a lncRNA-miRNA-mRNA (competing endogenous RNA, ceRNA) regulatory network for AD based on six RUbR-DEGs, further elucidating the interaction between UbRGs and lncRNA, miRNA. In conclusion, our findings will contribute to further understanding of the molecular pathogenesis of AD and provide a new perspective for AD risk prediction, early diagnosis and targeted therapy in the population.
Tunable electronic and photoelectric properties of Janus group-III chalcogenide monolayers and based heterostructures
Authors: Zhao Yipeng , Tan Qiaolai , Li Honglai , Li Zhiqiang , Wang Yicheng , Ma Liang
Published: May 2024

Janus group-III chalcogenide monolayers and based heterostructures with breaking vertical structural symmetry offer additional prospects in the upcoming high-performance photoelectric devices. We studied the geometrical, electronic, and photoelectric properties of Janus group-III chalcogenide monolayers and heterostructures. The most energy favorable stacking design of ten vertical heterostructures are considered. The results showed that the Janus Se-In-Ga-S and S-In-Ga-Se monolayers exhibit semiconducting characteristics with the band gaps of 1.295 eV and 1.752 eV, respectively. Furthermore, the different stacking configurations and surface termination at interface can realize the transition of band alignment between type I and type II due to the interlayer coupling. Moreover, we systematically investigated the photoelectric properties of Janus group-III chalcogenide heterostructures and predicated an optimized power conversion efficiency of 16.2%. These findings can aid in comprehending the customized characteristics of Janus group-III chalcogenide heterostructures, offering theoretical guidance for creating innovative photoelectric devices.
Klotho is highly expressed in the chief sites of regulated potassium secretion, and it is stimulated by potassium intake
Authors: Jung Hyun Jun , Pham Truyen D. , Su Xiao-Tong , Grigore Teodora Veronica , Hoenderop Joost G. , Olauson Hannes , Wall Susan M. , Ellison David H. , Welling Paul A. , Al-Qusairi Lama
Published: May 2024

Klotho regulates many pathways in the aging process, but it remains unclear how it is physiologically regulated. Because Klotho is synthesized, cleaved, and released from the kidney; activates the chief urinary K+ secretion channel (ROMK) and stimulates urinary K+ secretion, we explored if Klotho protein is regulated by dietary K+ and the potassium-regulatory hormone, Aldosterone. Klotho protein along the nephron was evaluated in humans and in wild-type (WT) mice; and in mice lacking components of Aldosterone signaling, including the Aldosterone-Synthase KO (AS-KO) and the Mineralocorticoid-Receptor KO (MR-KO) mice. We found the specific cells of the distal nephron in humans and mice that are chief sites of regulated K+ secretion have the highest Klotho protein expression along the nephron. WT mice fed K+-rich diets increased Klotho expression in these cells. AS-KO mice exhibit normal Klotho under basal conditions but could not upregulate Klotho in response to high-K+ intake in the K+-secreting cells. Similarly, MR-KO mice exhibit decreased Klotho protein expression. Together, i) Klotho is highly expressed in the key sites of regulated K+ secretion in humans and mice, ii) In mice, K+-rich diets increase Klotho expression specifically in the potassium secretory cells of the distal nephron, iii) Aldosterone signaling is required for Klotho response to high K+ intake.
Early nutrition is safe and does not increase complications after upper gastrointestinal bleeding—a systematic review and meta-analysis of randomized controlled trials
Authors: Obeidat Mahmoud , Teutsch Brigitta , Floria Diana-Elena , Veres Dániel Sándor , Hegyi Péter , Erőss Bálint
Published: May 2024

Despite a lack of evidence, patients are often not fed for 48–96 h after upper gastrointestinal bleeding (UGIB); however, many trials have demonstrated the benefits of early nutrition (EN). We conducted a meta-analysis of randomized controlled trials (RTCs) to evaluate the outcomes of EN compared to delayed nutrition (DN) after UGIB. The protocol was registered on PROSPERO (CRD42022372306). PubMed, Embase, CENTRAL, Scopus, and Web of Science were searched on the 27th of April 2024 to identify eligible RCTs. The primary outcomes were early (within 7 days) and late (within 30–42 days) mortality and rebleeding. Pooled risk ratios (RR), mean differences (MD), and corresponding 95% confidence intervals (CI) were calculated using a random-effects model. A total of 10 trials with 1051 patients were included in the analysis. Early mortality was not significantly different between the two groups (RR 1.20, CI 0.85–1.71, I2 = 0%), whereas late mortality was reduced to a clinically relevant extent in the EN group (RR 0.61, CI 0.35–1.06, I2 = 0%). When comparing the two groups, we found no significant difference in terms of early and late rebleeding (RR 1.04, CI 0.66–1.63, I2 = 0% and RR 1.16, CI 0.63–2.13, I2 = 0%, respectively). Our analysis also showed that the length of hospital stay was reduced in the EN group compared to the DN group (MD −1.22 days, CI: −2.43 to −0.01, I2 = 94%). In conclusion, compared with DN, EN (within 24 h) appears to be a safe intervention and could reduce the length of hospital stay without increasing the risk of complications after UGIB.