bluuebunny/crossref_metadata_2025 huggingface dataset:
Performing Distributed Quantum Calculations in a Multi-cloud Architecture Secured by the Quantum Key Distribution Protocol
Authors: Huang Jose Luis Lo , Emeakaroha Vincent C.
Published: April 2024

Quantum computing (QC) is an emerging area that yearly improves and develops more advances in the number of qubits and the available infrastructure for public users. Nowadays, the main cloud service providers (CSP) are implementing different mechanisms to support access to their quantum computers, which can be used to perform small experiments, test hybrid algorithms and prove quantum theories. Recent research work have discussed the low capacity of using quantum computers in a single CSP to perform quantum computation that are needed to solve different experiments for real world problems. Thus, there are needs for computing powers in the form of qubits from multi-cloud environment. Quantum computing in a multi-cloud environment requires security of the communicating channels. A well known algorithm in quantum cryptography for this purpose is the quantum key distribution (QKD) protocol. This enables the sender and receiver of a message to know when a third party eavesdropped any data from the insecure quantum channel. To address the low capacity issue, this research develops and tests the use of heterogeneous quantum computers located on different CSP to distribute quantum calculations between them by leveraging the channel security provided by the QKD protocol. The achieved results show over 88.1% of correct distributed quantum computation results without error correction methods, 96.8% of correct distributed quantum computation results using error correction methods and over 98.8% correct authorisation detection in multi-cloud environments. This demonstrates that quantum calculations can be distributed between different CSP while securing the channel with the QKD protocol at the same time.
Surface and bulk acoustic wave resonators based on aluminum nitride for bandpass filters
Authors: Zha Xian-Hu , Luo Jing-Ting , Tao Ran , Fu Chen
Published: April 2024

Bandpass filters with high frequency and wide bandwidth are indispensable parts of the fifth-generation telecommunication technologies, and currently, they are mainly based on surface and bulk acoustic wave resonators. Owing to its high mechanical strength, excellent stability at elevated temperatures, good thermal conductivity, and compatibility with complementary metal-oxide-semiconductor technology, aluminum nitride (AlN) becomes the primary piezoelectric material for high-frequency resonators. This review briefly introduces the structures and key performance parameters of the acoustic resonators. The common filter topologies are also discussed. In particular, research progresses in the piezoelectric AlN layer, electrodes, and substrates of the resonators are elaborated. Increasing the electromechanical coupling constant is the main concern for the AlN film. To synthesize AlN in single-crystalline or poly-crystalline with a high intensity of (0002) orientation, and alloy the AlN with other elements are two effective approaches. For the substrates and bottom electrodes, lattice and thermal expansion mismatch, and surface roughness are critical for the synthesis of a high-crystal-quality piezoelectric layer. The electrodes with low electrical resistance, large acoustic-impedance mismatch to the piezoelectric layer, and low density are ideal to reduce insertion loss. Based on the research progress, several possible research directions in the AlN-based filters are suggested at the end of the paper.
The obscure politics of artificial intelligence: a Marxian socio-technical critique of the AI alignment problem thesis
Authors: Cugurullo Federico
Published: April 2024

There is a growing feeling that artificial intelligence (AI) is getting out of control. Many AI experts worldwide stress that great care must be taken on the so-called alignment problem, broadly understood as the challenge of developing AIs whose actions are in line with human values and goals. The story goes that ever more powerful AI systems are escaping human control and might soon operate in a manner that is no longer guided by human purposes. This is what we call the AI-out-of-control discourse which, in this paper, we critically examine and debunk. Drawing on complementary insights from political theory, socio-technical studies and Marxian political economy, we critique the supposed animistic and autonomous nature of AI, and the myth of the uncontrollability of AI. The problem is not that humanity has lost control over AI, but that only a minority of powerful stakeholders are controlling its creation and diffusion, through politically undemocratic processes of decision-making. In these terms, we reframe the alignment problem thesis with an emphasis on citizen engagement and public political participation. We shed light on the existing politics of AI and contemplate alternative political expressions whereby citizens steer AI development or stop it in the first place.
TrajectoFormer: Transformer-Based Trajectory Prediction of Autonomous Vehicles with Spatio-temporal Neighborhood Considerations
Authors: Amin Farhana , Gharami Kanchon , Sen Barshon
Published: April 2024

Accurate trajectory prediction of autonomous vehicles is crucial for ensuring road safety. Predicting precise and accurate trajectories is still considered a challenging problem because of the intricate spatio-temporal dependencies among the vehicles. Our study primarily focuses on resolving this issue by introducing a comprehensive system called “TrajectoFormer”, which can effectively represent the spatio-temporal dependency between vehicles. In this system, we have conducted preprocessing on the NGSIM dataset by constructing an 8-neighborhood for each vehicle that represents the spatio-temporal dependency between vehicles effectively. Second, we have deployed a transformer network that captures dependencies between the target vehicle and its neighbor from the constructed neighborhood and predicts future trajectories for the target vehicle with notably reduced training times and significant accuracy compared to existing methods. Experiments on both NGSIM US-101 and US-I80 show that our proposed approach outperforms the other benchmarks in terms of showing low RMSE value for the 5-s prediction horizon of trajectory prediction. Our conducted ablation study also underscores the effectiveness of each component of our proposed TrajectoFormer model relative to traditional time-series prediction models.
The Etiology of Advanced Chronic Kidney Disease in Southeast Asia: A Meta-analysis
Authors: Hustrini Ni Made , Susalit Endang , Widjaja Felix Firyanto , Khumaedi Anandhara Indriani , Dekkers Olaf M. , van Diepen Merel , Rotmans Joris I.
Published: April 2024

Introduction

Chronic kidney disease (CKD) etiology varies greatly between developed and developing countries. In addition, differences in underlying pathogenesis and therapeutic options affect the progression towards advanced-CKD. This meta-analysis aims to identify the etiology of advanced-CKD in Southeast Asia.

Methods

A systematic search in four electronic-databases and complementary search on national kidney registries and repository libraries was conducted until July 20, 2023. The risk of bias was assessed using Newcastle–Ottawa Scale for observational studies and Version-2 of Cochrane for intervention studies. A random-effects model was used to estimate pooled prevalence. The protocol is registered in the International Prospective Register of Systematic Reviews PROSPERO; Registration ID:CRD42022300786.

Results

We analyzed 81 studies involving 32,834 subjects. The pooled prevalence of advanced-CKD etiologies are diabetic kidney disease (DKD) 29.2% (95%CI 23.88–34.78), glomerulonephritis 20.0% (95%CI 16.84–23.38), hypertension 16.8% (95%CI 14.05–19.70), other 8.6% (95%CI 6.97–10.47), unknown 7.5% (95%CI 4.32–11.50), and polycystic kidney disease 0.7% (95%CI 0.40–1.16). We found a significant increase in DKD prevalence from 21% (9.2%, 95%CI 0.00–33.01) to 30% (95%CI 24.59–35.97) before and after the year 2000. Among upper-middle-income and high-income countries, DKD is the most prevalent (26.8%, 95%CI 21.42–32.60 and 38.9%, 95%CI 29.33–48.79, respectively), while glomerulonephritis is common in lower-middle-income countries (33.8%, 95%CI 15.62–54.81).

Conclusion

The leading cause of advanced-CKD in Southeast Asia is DKD, with a substantial proportion of glomerulonephritis. An efficient screening program targeting high-risk populations (diabetes mellitus and glomerulonephritis) is needed, with the aim to delay CKD progression.
Substreetutions and more on trees
Authors: BARAVIERA ALEXANDRE , LEPLAIDEUR RENAUD
Published: April 2024

We define a notion of substitution on colored binary trees that we call substreetution. We show that a point fixed by a substreetution may (or not) be almost periodic, and thus the closure of the orbit under the
$\mathbb {F}_{2}^{+}$
-action may (or not) be minimal. We study one special example: we show that it belongs to the minimal case and that the number of preimages in the minimal set increases just exponentially fast, whereas it could be expected a super-exponential growth. We also give examples of periodic trees without invariant measures on their orbit. We use our construction to get quasi-periodic colored tilings of the hyperbolic disk.
Sub-filter-scale shear stress analysis in hypersonic turbulent Couette flow
Authors: Toki Takahiko , Sousa Victor C.B. , Chen Yongkai , Scalo Carlo
Published: April 2024

Direct numerical simulations of hypersonic turbulent Couette flows are performed for top-wall Mach numbers of 6, 7 and 8, inspired by non-reactive high-enthalpy wind tunnel free-stream conditions, with the goal of analysing the physical processes driving the sub-filter-scale (SFS) stresses to inform development of large-eddy simulation techniques for hypersonic wall-bounded flows. Semi-local scaling laws collapse mean profiles and second-order turbulent statistics well, in spite of the strong wall-normal gradients of temperature and density. On the other hand, the SFS shear stresses exhibit an unexpected profile characterized by a region of pronounced shear stress deficit, which becomes more pronounced for higher Mach numbers. Instantaneous visualizations suggest that the SFS shear stress deficit is induced by the counter-gradient resolved momentum transport driven by residual velocity motions at the interface between high-density low-speed streaks being ejected away from the wall, and low-density high-speed ones replacing the displaced fluid, qualifying this as a compressibility effect. It is shown that the SFS shear stresses are primarily driven by second-order interactions between residual velocities, in spite of their triply nonlinear nature. This, in turn, motivated a statistical quadrant analysis revealing the presence of a SFS shear stress deficit, that is, SFS processes driving momentum transport of the resolved field towards the top wall. Additionally, higher-Reynolds-number simulations reveal that there is an upper limit of spatial filter widths to resolve large-scale structures, and such deficit is observable at any Reynolds number when a reasonable spatial filter is applied.
Mirrors of Death, Images of God: Likeness and Difference in Gregory of Nyssa’s Social Ethics
Authors: Breedlove Thomas , Fogleman Alex
Published: April 2024

Gregory of Nyssa’s critiques of various forms of social injustice hinge on his rigorous theological anthropology. For Gregory, slavery, the accumulation of wealth, and the mistreatment of the poor are evil because they deny the freedom proper to human creatures created according to the divine Image. However, Gregory’s anthropology also contains, we will argue, a distinct account of the ways in which humanity’s difference from God – particularly its poverty and limitation – reveals important aspects of the particular and ultimately Christological mode in which finite humans imitate the infinitude God. The aim of this present essay is to articulate how both likeness and unlikeness to God – mirrors of God and mirrors of death – are integral to Gregory’s theological anthropology as it pertains to various forms of social critique.
Isolation, identification, and antibacterial activity of endophytic fungus from Acanthus ilicifolius
Authors: Sruthi V. P. , Sreenath K. R. , Sumithra T. G. , Anusree V. N. , Sainamole Kurian P.
Published: April 2024

Antimicrobial-resistant bacteria pose serious public health risks, necessitating bioprospecting for novel antimicrobial drugs. The endophytic fungi of the mangrove ecosystem are hotspots for discovering new bioactive chemical compounds. In this context, an investigation was designed to determine the isolation of the major endophytic fungi inhabiting the leaves of Acanthus ilicifolius, a mangrove plant with a long history of traditional use in the Chinese and Indian medical systems. Based on the morphological characterizations and molecular analysis of internal transcribed spacer rDNA sequence data, the study identified three unique endophytic fungal species, namely, Periconia macrospinosa, Coprinopsis cinerea, and Alternaria sp. Of these, P. macrospinosa was identified as the most dominant one, with the highest relative frequency (35.22%). The antibacterial activity of P. macrospinosa isolate (CMFRI/fPM-01) was evaluated by the well and diffusion method against six human pathogens, viz., Escherichia coli, Klebsiella pneumoniae, Staphylococcus aureus, Vibrio cholerae, Vibrio parahaemolyticus, and Vibrio vulnificus. The results demonstrated a high and wide spectrum of antimicrobial action of the isolate against all the tested human pathogens, with no significant difference (P > 0.05) in the activity between the pathogens. The antibacterial activity was further confirmed by determining the fungal culture supernatant's minimum inhibitory concentration and minimum bactericidal concentration. Although the studied fungi are known from other sources, this is the first report of P. macrospinosa and C. cinerea as endophytes in A. ilicifolius leaves. The outcomes also showed that the P. macrospinosa isolate could be used to discover effective antibacterial drugs against various human diseases.
Critical Size of Silver Iodide Containing Glaciogenic Cloud Seeding Particles
Authors: Chen Jie , Rösch Carolin , Rösch Michael , Shilin Aleksei , Kanji Zamin A.
Published: April 2024

Cloud seeding is considered a practical but unproved method to enhance precipitation or suppress hail, due to insufficient knowledge of ice formation and evolution after seeding clouds with ice nucleating particles. This study investigates the size effects on the immersion freezing of aerosol produced from commercial silver iodide (AgI) containing flares at mixed‐phase cloud temperatures from 243 to 267 K. Flare‐generated aerosol exhibited comparable ice nucleation ability (INA) to pure AgI particles in the size range of 200 and 400 nm. Non‐AgI impurities reduced the INA of flare‐generated particles ≤90 nm, which is lower than pure AgI particles ≤40 nm. The critical mass ice‐active site density of the generated aerosols (critical‐nm) was derived, indicating the minimum mass of AgI particles required for efficient ice nucleation. The new parameterization to predict critical‐nm can serve as a reference to optimize the effectiveness of cloud‐seeding materials for practical use.
Forecasting Tropical Annual Maximum Wet‐Bulb Temperatures Months in Advance From the Current State of ENSO
Authors: Zhang Yi , Boos William R. , Held Isaac , Paciorek Christopher J. , Fueglistaler Stephan
Published: April 2024

Humid heatwaves, characterized by high temperature and humidity combinations, challenge tropical societies. Extreme wet‐bulb temperatures (TW) over tropical land are coupled to the warmest sea surface temperatures by atmospheric convection and wave dynamics. Here, we harness this coupling for seasonal forecasts of the annual maximum of daily maximum TW (TWmax). We develop a multiple linear regression model that explains 80% of variance in tropical mean TWmax and significant regional TWmax variances. The model considers warming trends and El Niño and Southern Oscillation indices. Looking ahead, the strong‐to‐very‐strong El Niño at the end of 2023, with an Oceanic Niño Index of ∼2.0, suggests a 2024 tropical land mean TWmax of 26.2°C (25.9–26.4°C), and a 68% chance (24%–94%) of breaking existing records. This method also predicts regional TWmax in specific areas.
Quantification of H2O in Amorphous and Crystalline Ferric Sulfates Relevant to Mars
Authors: Meng Fan , Shi Erbin , Liu Changqing , Ling Zongcheng
Published: April 2024

Crystalline ferric sulfates (e.g., ferricopiapite and Fe(OH)SO4) have been proposed at multiple locations on Mars by the orbiter. While at Meridiani Planum and Gale Crater by rover missions, amorphous ferric sulfates were also suggested to exist in soils and sedimentary rocks. Ferric sulfates with different hydration degrees may play a key role in the water cycle on Mars. In order to understand the role of the hydrated ferric sulfates in the water cycle and their exact hydration states on Mars, five crystalline ferric sulfates and seven amorphous ferric sulfates with different hydration states were synthesized in the laboratory. The water content (number of H2O molecules per ferric sulfate molecule) was quantified by Raman spectroscopy and Laser‐induced breakdown spectroscopy (LIBS), respectively. It was found that the amorphous ferric sulfates water content has a good relationship with the SO4 tetrahedron main Raman feature position around 1,000 cm−1, shown as the intensity and area of water feature around 3,500 cm−1 over SO4 tetrahedron main Raman feature around 1,000 cm−1, respectively. Twelve ferric sulfates' Hα emission line area at 656.7 nm was normalized by the O emission line area at 778 nm in LIBS spectra. The crystalline and amorphous ferric sulfates all showed a good relationship between the values of normalized results and the water content. These results will aid us in precisely constraining the exact phases of hydrated ferric sulfates, provide a better reference for ChemCam, SuperCam, and Scanning Habitable Environments with Raman and Luminescence for Organics and Chemicals data interpretation and their use to quantify the water content in detected targets.
Olfactory genes affect major depression in highly educated, emotionally stable, lean women: a bridge between animal models and precision medicine
Authors: Eszlari Nora , Hullam Gabor , Gal Zsofia , Torok Dora , Nagy Tamas , Millinghoffer Andras , Baksa Daniel , Gonda Xenia , Antal Peter , Bagdy Gyorgy , Juhasz Gabriella
Published: April 2024

Most current approaches to establish subgroups of depressed patients for precision medicine aim to rely on biomarkers that require highly specialized assessment. Our present aim was to stratify participants of the UK Biobank cohort based on three readily measurable common independent risk factors, and to investigate depression genomics in each group to discover common and separate biological etiology. Two-step cluster analysis was run separately in males (n = 149,879) and females (n = 174,572), with neuroticism (a tendency to experience negative emotions), body fat percentage, and years spent in education as input variables. Genome-wide association analyses were implemented within each of the resulting clusters, for the lifetime occurrence of either a depressive episode or recurrent depressive disorder as the outcome. Variant-based, gene-based, gene set-based, and tissue-specific gene expression test were applied. Phenotypically distinct clusters with high genetic intercorrelations in depression genomics were found. A two-cluster solution was the best model in each sex with some differences including the less important role of neuroticism in males. In females, in case of a protective pattern of low neuroticism, low body fat percentage, and high level of education, depression was associated with pathways related to olfactory function. While also in females but in a risk pattern of high neuroticism, high body fat percentage, and less years spent in education, depression showed association with complement system genes. Our results, on one hand, indicate that alteration of olfactory pathways, that can be paralleled to the well-known rodent depression models of olfactory bulbectomy, might be a novel target towards precision psychiatry in females with less other risk factors for depression. On the other hand, our results in multi-risk females may provide a special case of immunometabolic depression.
The broad impact of cell death genes on the human disease phenome
Authors: Rich Abigail L. , Lin Phillip , Gamazon Eric R. , Zinkel Sandra S.
Published: April 2024

Cell death mediated by genetically defined signaling pathways influences the health and dynamics of all tissues, however the tissue specificity of cell death pathways and the relationships between these pathways and human disease are not well understood. We analyzed the expression profiles of an array of 44 cell death genes involved in apoptosis, necroptosis, and pyroptosis cell death pathways across 49 human tissues from GTEx, to elucidate the landscape of cell death gene expression across human tissues, and the relationship between tissue-specific genetically determined expression and the human phenome. We uncovered unique cell death gene expression profiles across tissue types, suggesting there are physiologically distinct cell death programs in different tissues. Using summary statistics-based transcriptome wide association studies (TWAS) on human traits in the UK Biobank (n ~ 500,000), we evaluated 513 traits encompassing ICD-10 defined diagnoses and laboratory-derived traits. Our analysis revealed hundreds of significant (FDR < 0.05) associations between genetically regulated cell death gene expression and an array of human phenotypes encompassing both clinical diagnoses and hematologic parameters, which were independently validated in another large-scale DNA biobank (BioVU) at Vanderbilt University Medical Center (n = 94,474) with matching phenotypes. Cell death genes were highly enriched for significant associations with blood traits versus non-cell-death genes, with apoptosis-associated genes enriched for leukocyte and platelet traits. Our findings are also concordant with independently published studies (e.g. associations between BCL2L11/BIM expression and platelet & lymphocyte counts). Overall, these results suggest that cell death genes play distinct roles in their contribution to human phenotypes, and that cell death genes influence a diverse array of human traits.
A live attenuated vaccine to prevent severe neonatal Escherichia coli K1 infections
Authors: Sereme Youssouf , Schrimp Cécile , Faury Helène , Agapoff Maeva , Lefebvre-Wloszczowski Esther , Chang Marchand Yunhua , Ageron-Ardila Elisabeth , Panafieu Emilie , Blec Frank , Coureuil Mathieu , Frapy Eric , Tsatsaris Vassilis , Bonacorsi Stephane , Skurnik David
Published: April 2024

Preterm birth is currently the leading cause of neonatal morbidity and mortality. Genetic, immunological and infectious causes are suspected. Preterm infants have a higher risk of severe bacterial neonatal infections, most of which are caused by Escherichia coli an in particular E. coli K1strains. Women with history of preterm delivery have a high risk of recurrence and therefore constitute a target population for the development of vaccine against E. coli neonatal infections. Here, we characterize the immunological, microbiological and protective properties of a live attenuated vaccine candidate in adult female mice and their pups against after a challenge by K1 and non-K1 strains of E. coli. Our results show that the E. coli K1 E11 ∆aroA vaccine induces strong immunity, driven by polyclonal bactericidal antibodies. In our model of meningitis, mothers immunized prior to mating transfer maternal antibodies to pups, which protect newborn mice against various K1 and non-K1 strains of E. coli. Given the very high mortality rate and the neurological sequalae associated with neonatal E. coli K1 meningitis, our results constitute preclinical proof of concept for the development of a live attenuated vaccine against severe E. coli infections in women at risk of preterm delivery.
Engineering an artificial catch bond using mechanical anisotropy
Authors: Liu Zhaowei , Liu Haipei , Vera Andrés M. , Yang Byeongseon , Tinnefeld Philip , Nash Michael A.
Published: April 2024

Catch bonds are a rare class of protein-protein interactions where the bond lifetime increases under an external pulling force. Here, we report how modification of anchor geometry generates catch bonding behavior for the mechanostable Dockerin G:Cohesin E (DocG:CohE) adhesion complex found on human gut bacteria. Using AFM single-molecule force spectroscopy in combination with bioorthogonal click chemistry, we mechanically dissociate the complex using five precisely controlled anchor geometries. When tension is applied between residue #13 on CohE and the N-terminus of DocG, the complex behaves as a two-state catch bond, while in all other tested pulling geometries, including the native configuration, it behaves as a slip bond. We use a kinetic Monte Carlo model with experimentally derived parameters to simulate rupture force and lifetime distributions, achieving strong agreement with experiments. Single-molecule FRET measurements further demonstrate that the complex does not exhibit dual binding mode behavior at equilibrium but unbinds along multiple pathways under force. Together, these results show how mechanical anisotropy and anchor point selection can be used to engineer artificial catch bonds.
Large-volume focus control at 10 MHz refresh rate via fast line-scanning amplitude-encoded scattering-assisted holography
Authors: Shibukawa Atsushi , Higuchi Ryota , Song Gookho , Mikami Hideharu , Sudo Yuki , Jang Mooseok
Published: April 2024

The capability of focus control has been central to optical technologies that require both high temporal and spatial resolutions. However, existing varifocal lens schemes are commonly limited to the response time on the microsecond timescale and share the fundamental trade-off between the response time and the tuning power. Here, we propose an ultrafast holographic focusing method enabled by translating the speed of a fast 1D beam scanner into the speed of the complex wavefront modulation of a relatively slow 2D spatial light modulator. Using a pair of a digital micromirror device and a resonant scanner, we demonstrate an unprecedented refresh rate of focus control of 31 MHz, which is more than 1,000 times faster than the switching rate of a digital micromirror device. We also show that multiple micrometer-sized focal spots can be independently addressed in a range of over 1 MHz within a large volume of 5 mm × 5 mm × 5.5 mm, validating the superior spatiotemporal characteristics of the proposed technique – high temporal and spatial precision, high tuning power, and random accessibility in a three-dimensional space. The demonstrated scheme offers a new route towards three-dimensional light manipulation in the 100 MHz regime.
Optics miniaturization strategy for demanding Raman spectroscopy applications
Authors: Ilchenko Oleksii , Pilhun Yurii , Kutsyk Andrii , Slobodianiuk Denys , Goksel Yaman , Dumont Elodie , Vaut Lukas , Mazzoni Chiara , Morelli Lidia , Boisen Sofus , Stergiou Konstantinos , Aulin Yaroslav , Rindzevicius Tomas , Andersen Thomas Emil , Lassen Mikael , Mundhada Hemanshu , Jendresen Christian Bille , Philipsen Peter Alshede , Hædersdal Merete , Boisen Anja
Published: April 2024

Raman spectroscopy provides non-destructive, label-free quantitative studies of chemical compositions at the microscale as used on NASA’s Perseverance rover on Mars. Such capabilities come at the cost of high requirements for instrumentation. Here we present a centimeter-scale miniaturization of a Raman spectrometer using cheap non-stabilized laser diodes, densely packed optics, and non-cooled small sensors. The performance is comparable with expensive bulky research-grade Raman systems. It has excellent sensitivity, low power consumption, perfect wavenumber, intensity calibration, and 7 cm−1resolution within the 400–4000 cm−1range using a built-in reference. High performance and versatility are demonstrated in use cases including quantification of methanol in beverages, in-vivo Raman measurements of human skin, fermentation monitoring, chemical Raman mapping at sub-micrometer resolution, quantitative SERS mapping of the anti-cancer drug methotrexate and in-vitro bacteria identification. We foresee that the miniaturization will allow realization of super-compact Raman spectrometers for integration in smartphones and medical devices, democratizing Raman technology.
Metabolic plasticity, essentiality and therapeutic potential of ribose-5-phosphate synthesis in Toxoplasma gondii
Authors: Guo Xuefang , Ji Nuo , Guo Qinghong , Wang Mengting , Du Huiyu , Pan Jiajia , Xiao Lihua , Gupta Nishith , Feng Yaoyu , Xia Ningbo
Published: April 2024

Ribose-5-phosphate (R5P) is a precursor for nucleic acid biogenesis; however, the importance and homeostasis of R5P in the intracellular parasite Toxoplasma gondii remain enigmatic. Here, we show that the cytoplasmic sedoheptulose-1,7-bisphosphatase (SBPase) is dispensable. Still, its co-deletion with transaldolase (TAL) impairs the double mutant’s growth and increases 13C-glucose-derived flux into pentose sugars via the transketolase (TKT) enzyme. Deletion of the latter protein affects the parasite’s fitness but is not lethal and is correlated with an increased carbon flux via the oxidative pentose phosphate pathway. Further, loss of TKT leads to a decline in 13C incorporation into glycolysis and the TCA cycle, resulting in a decrease in ATP levels and the inability of phosphoribosyl-pyrophosphate synthetase (PRPS) to convert R5P into 5′-phosphoribosyl-pyrophosphate and thereby contribute to the production of AMP and IMP. Likewise, PRPS is essential for the lytic cycle. Not least, we show that RuPE-mediated metabolic compensation is imperative for the survival of the ΔsbpaseΔtal strain. In conclusion, we demonstrate that multiple routes can flexibly supply R5P to enable parasite growth and identify catalysis by TKT and PRPS as critical enzymatic steps. Our work provides novel biological and therapeutic insights into the network design principles of intracellular parasitism in a clinically-relevant pathogen.
Comparative characterization of the infant gut microbiome and their maternal lineage by a multi-omics approach
Authors: Barker-Tejeda Tomás Clive , Zubeldia-Varela Elisa , Macías-Camero Andrea , Alonso Lola , Martín-Antoniano Isabel Adoración , Rey-Stolle María Fernanda , Mera-Berriatua Leticia , Bazire Raphaëlle , Cabrera-Freitag Paula , Shanmuganathan Meera , Britz-McKibbin Philip , Ubeda Carles , Francino M. Pilar , Barber Domingo , Ibáñez-Sandín María Dolores , Barbas Coral , Pérez-Gordo Marina , Villaseñor Alma
Published: April 2024

The human gut microbiome establishes and matures during infancy, and dysregulation at this stage may lead to pathologies later in life. We conducted a multi-omics study comprising three generations of family members to investigate the early development of the gut microbiota. Fecal samples from 200 individuals, including infants (0-12 months old; 55% females, 45% males) and their respective mothers and grandmothers, were analyzed using two independent metabolomics platforms and metagenomics. For metabolomics, gas chromatography and capillary electrophoresis coupled to mass spectrometry were applied. For metagenomics, both 16S rRNA gene and shotgun sequencing were performed. Here we show that infants greatly vary from their elders in fecal microbiota populations, function, and metabolome. Infants have a less diverse microbiota than adults and present differences in several metabolite classes, such as short- and branched-chain fatty acids, which are associated with shifts in bacterial populations. These findings provide innovative biochemical insights into the shaping of the gut microbiome within the same generational line that could be beneficial in improving childhood health outcomes.
Single-cell multiomics reveals the interplay of clonal evolution and cellular plasticity in hepatoblastoma
Authors: Roehrig Amélie , Hirsch Theo Z. , Pire Aurore , Morcrette Guillaume , Gupta Barkha , Marcaillou Charles , Imbeaud Sandrine , Chardot Christophe , Gonzales Emmanuel , Jacquemin Emmanuel , Sekiguchi Masahiro , Takita Junko , Nagae Genta , Hiyama Eiso , Guérin Florent , Fabre Monique , Aerts Isabelle , Taque Sophie , Laithier Véronique , Branchereau Sophie , Guettier Catherine , Brugières Laurence , Fresneau Brice , Zucman-Rossi Jessica , Letouzé Eric
Published: April 2024

Hepatoblastomas (HB) display heterogeneous cellular phenotypes that influence the clinical outcome, but the underlying mechanisms are poorly understood. Here, we use a single-cell multiomic strategy to unravel the molecular determinants of this plasticity. We identify a continuum of HB cell states between hepatocytic (scH), liver progenitor (scLP) and mesenchymal (scM) differentiation poles, with an intermediate scH/LP population bordering scLP and scH areas in spatial transcriptomics. Chromatin accessibility landscapes reveal the gene regulatory networks of each differentiation pole, and the sequence of transcription factor activations underlying cell state transitions. Single-cell mapping of somatic alterations reveals the clonal architecture of each tumor, showing that each genetic subclone displays its own range of cellular plasticity across differentiation states. The most scLP subclones, overexpressing stem cell and DNA repair genes, proliferate faster after neo-adjuvant chemotherapy. These results highlight how the interplay of clonal evolution and epigenetic plasticity shapes the potential of HB subclones to respond to chemotherapy.
Thermodiffusive desalination
Authors: Xu Shuqi , Hutchinson Alice J. , Taheri Mahdiar , Corry Ben , Torres Juan F.
Published: April 2024

Desalination could solve the grand challenge of water scarcity, but materials-based and conventional thermal desalination methods generally suffer from scaling, fouling and materials degradation. Here, we propose and assess thermodiffusive desalination (TDD), a method that operates entirely in the liquid phase and notably excludes evaporation, freezing, membranes, or ion-adsorbing materials. Thermodiffusion is the migration of species under a temperature gradient and can be driven by thermal energy ubiquitous in the environment. Experimentally, a 450 ppm concentration drop was achieved by thermodiffusive separation when passing a NaCl/H2O solution through a single channel. This was further increased through re-circulation as a proof of concept for TDD. We also demonstrate via molecular dynamics and experiments that TDD in multi-component seawater is more amenable than in binary NaCl/H2O solutions. Numerically, we show that a scalable cascaded channel structure can further amplify thermodiffusive separation, achieving a concentration drop of 25000 ppm with a recovery rate of 10%. The minimum electric power consumption in this setup can be as low as 3 Whe m−3, which is only 1% of the theoretical minimum energy for desalination. TDD has potential in areas with abundant thermal energy but limited electrical power resources and can contribute to alleviating global freshwater scarcity.
Multicore fiber optic imaging reveals that astrocyte calcium activity in the mouse cerebral cortex is modulated by internal motivational state
Authors: Gau Yung-Tian A. , Hsu Eric T. , Cha Richard J. , Pak Rebecca W. , Looger Loren L. , Kang Jin U. , Bergles Dwight E.
Published: April 2024

Astrocytes are a direct target of neuromodulators and can influence neuronal activity on broad spatial and temporal scales in response to a rise in cytosolic calcium. However, our knowledge about how astrocytes are recruited during different animal behaviors remains limited. To measure astrocyte activity calcium in vivo during normative behaviors, we utilize a high-resolution, long working distance multicore fiber optic imaging system that allows visualization of individual astrocyte calcium transients in the cerebral cortex of freely moving mice. We define the spatiotemporal dynamics of astrocyte calcium changes during diverse behaviors, ranging from sleep-wake cycles to the exploration of novel objects, showing that their activity is more variable and less synchronous than apparent in head-immobilized imaging conditions. In accordance with their molecular diversity, individual astrocytes often exhibit distinct thresholds and activity patterns during explorative behaviors, allowing temporal encoding across the astrocyte network. Astrocyte calcium events were induced by noradrenergic and cholinergic systems and modulated by internal state. The distinct activity patterns exhibited by astrocytes provides a means to vary their neuromodulatory influence in different behavioral contexts and internal states.
A chromosomal-scale genome assembly of modern cultivated hybrid sugarcane provides insights into origination and evolution
Authors: Bao Yixue , Zhang Qing , Huang Jiangfeng , Zhang Shengcheng , Yao Wei , Yu Zehuai , Deng Zuhu , Yu Jiaxin , Kong Weilong , Yu Xikai , Lu Shan , Wang Yibin , Li Ru , Song Yuhan , Zou Chengwu , Xu Yuzhi , Liu Zongling , Yu Fan , Song Jiaming , Huang Youzong , Zhang Jisen , Wang Haifeng , Chen Baoshan , Zhang Xingtan , Zhang Muqing
Published: April 2024

Sugarcane is a vital crop with significant economic and industrial value. However, the cultivated sugarcane’s ultra-complex genome still needs to be resolved due to its high ploidy and extensive recombination between the two subgenomes. Here, we generate a chromosomal-scale, haplotype-resolved genome assembly for a hybrid sugarcane cultivar ZZ1. This assembly contains 10.4 Gb genomic sequences and 68,509 annotated genes with defined alleles in two sub-genomes distributed in 99 original and 15 recombined chromosomes. RNA-seq data analysis shows that sugar accumulation-associated gene families have been primarily expanded from the ZZSO subgenome. However, genes responding to pokkah boeng disease susceptibility have been derived dominantly from the ZZSS subgenome. The region harboring the possible smut resistance genes has expanded significantly. Among them, the expansion of WAK and FLS2 families is proposed to have occurred during the breeding of ZZ1. Our findings provide insights into the complex genome of hybrid sugarcane cultivars and pave the way for future genomics and molecular breeding studies in sugarcane.
Spin-orbit coupling induced Van Hove singularity in proximity to a Lifshitz transition in Sr4Ru3O10
Authors: Marques Carolina A. , Murgatroyd Philip A. E. , Fittipaldi Rosalba , Osmolska Weronika , Edwards Brendan , Benedičič Izidor , Siemann Gesa-R. , Rhodes Luke C. , Buchberger Sebastian , Naritsuka Masahiro , Abarca-Morales Edgar , Halliday Daniel , Polley Craig , Leandersson Mats , Horio Masafumi , Chang Johan , Arumugam Raja , Lettieri Mariateresa , Granata Veronica , Vecchione Antonio , King Phil D. C. , Wahl Peter
Published: April 2024

Van Hove singularities (VHss) in the vicinity of the Fermi energy often play a dramatic role in the physics of strongly correlated electron materials. The divergence of the density of states generated by VHss can trigger the emergence of phases such as superconductivity, ferromagnetism, metamagnetism, and density wave orders. A detailed understanding of the electronic structure of these VHss is therefore essential for an accurate description of such instabilities. Here, we study the low-energy electronic structure of the trilayer strontium ruthenate Sr4Ru3O10, identifying a rich hierarchy of VHss using angle-resolved photoemission spectroscopy and millikelvin scanning tunneling microscopy. Comparison of k-resolved electron spectroscopy and quasiparticle interference allows us to determine the structure of the VHss and demonstrate the crucial role of spin-orbit coupling in shaping them. We use this to develop a minimal model from which we identify a mechanism for driving a field-induced Lifshitz transition in ferromagnetic metals.
Temperature optima of a natural diatom population increases as global warming proceeds
Authors: Hattich G. S. I. , Jokinen S. , Sildever S. , Gareis M. , Heikkinen J. , Junghardt N. , Segovia M. , Machado M. , Sjöqvist C.
Published: April 2024

Studies in laboratory-based experimental evolution have demonstrated that phytoplankton species can rapidly adapt to higher temperatures. However, adaptation processes and their pace remain largely unknown under natural conditions. Here, by comparing resurrected Skeletonema marinoi strains from the Baltic Sea during the past 60 years, we show that modern S. marinoi have increased their temperature optima by 1 °C. With the increasing ability to grow in higher temperatures, growth rates in cold water decreased. Modern S. marinoi modified their valve:girdle ratio under warmer temperatures, which probably increases nutrient uptake ability. This was supported by the upregulation of several genes related to nitrate metabolism in modern strains grown under high temperatures. Our approach using resurrected strains demonstrates the adaptation potential of naturally occurring marine diatoms to increasing temperatures as global warming proceeds and exemplifies a realistic pace of evolution, which is an order of magnitude slower than estimated by experimental evolution.
Spike sorting with Kilosort4
Authors: Pachitariu Marius , Sridhar Shashwat , Pennington Jacob , Stringer Carsen
Published: April 2024

Spike sorting is the computational process of extracting the firing times of single neurons from recordings of local electrical fields. This is an important but hard problem in neuroscience, made complicated by the nonstationarity of the recordings and the dense overlap in electrical fields between nearby neurons. To address the spike-sorting problem, we have been openly developing the Kilosort framework. Here we describe the various algorithmic steps introduced in different versions of Kilosort. We also report the development of Kilosort4, a version with substantially improved performance due to clustering algorithms inspired by graph-based approaches. To test the performance of Kilosort, we developed a realistic simulation framework that uses densely sampled electrical fields from real experiments to generate nonstationary spike waveforms and realistic noise. We found that nearly all versions of Kilosort outperformed other algorithms on a variety of simulated conditions and that Kilosort4 performed best in all cases, correctly identifying even neurons with low amplitudes and small spatial extents in high drift conditions.
Ancient DNA indicates a century of overhunting did not reduce genetic diversity in Pacific Walruses (Odobenus rosmarus divergens)
Authors: Mills Kendall K. , Hildebrandt Kyndall P. B. , Everson Kathryn M. , Horstmann Lara , Misarti Nicole , Olson Link E.
Published: April 2024

Pacific Walruses (Odobenus rosmarus divergens [Illiger 1815]) are gregarious marine mammals considered to be sentinels of the Arctic because of their dependence on sea ice for feeding, molting, and parturition. Like many other marine mammal species, their population sizes were decimated by historical overhunting in the nineteenth and twentieth centuries. Although they have since been protected from nearly all commercial hunting pressure, they now face rapidly accelerating habitat loss as global warming reduces the extent of summer sea ice in the Arctic. To investigate how genetic variation was impacted by overhunting, we obtained mitochondrial DNA sequences from historic Pacific Walrus samples in Alaska that predate the period of overhunting, as well as from extant populations. We found that genetic variation was unchanged over this period, suggesting Pacific Walruses are resilient to genetic attrition in response to reduced population size, and that this may be related to their high vagility and lack of population structure. Although Pacific Walruses will almost certainly continue to decline in number as the planet warms and summer sea ice is further reduced, they may be less susceptible to the ratcheting effects of inbreeding that typically accompany shrinking populations.
Volcanic soil gas 4He/CO2 ratio: a useful geochemical tool for real-time eruption forecasting
Authors: Pérez Nemesio M. , Padrón Eleazar , Melián Gladys , Hernández Pedro A. , Padilla German , Barrancos José , Rodríguez Fátima , D’Auria Luca , Calvo David
Published: April 2024

At many dormant volcanoes, magmatic gases are not channeled through preferential degassing routes as fumaroles and only percolate through the flanks of the volcano in a diffuse way. This type of volcanic gas emission provides valuable information, even though the soil matrix contains an important atmospheric component. This study aimed to demonstrate that chemical ratios such as He/CO2 in soil gases provide excellent information on the evolution of volcanic unrest episodes and help forecast the volcanic eruption onset. Before and during the occurrence of the October 2011–March 2012 submarine of El Hierro, Canary Islands, more than 8500 soil He analyses and diffuse CO2 emission measurements were performed. The results show that the soil He/CO2 emission ratio began increasing drastically one month before eruption onset, reaching the maximum value 10 days before. During the eruptive period, this ratio also showed a maximum value several days before the period with the highest magma emission rate. The He/CO2 ratio was also helpful in forecasting the eruption onset. We demonstrate that this tool can be applied in real-time during volcanic emergencies. Our results also encourage a reevaluation of the global He emission from the subaerial volcanism.
Bone mineral density in adults with arthrogryposis multiplex congenita: a retrospective cohort analysis
Authors: Romand X. , Gastaldi R. , Pérennou D. , Baillet A. , Dieterich K.
Published: April 2024

The primary objective of this study was to evaluate the prevalence of low femoral and lumbar spine bone mineral density (BMD) in adults with arthrogryposis multiplex congenita (AMC). We performed a retrospective cohort analysis of adults with AMC who were enrolled in the French Reference Center for AMC and in the Pediatric and Adult Registry for Arthrogryposis (PARART, NCT05673265). Patients who had undergone dual-energy X-ray absorptiometry (DXA) and/or vitamin D testing were included in the analysis. Fifty-one patients (mean age, 32.9 ± 12.6 years) were included; 46 had undergone DXA. Thirty-two (32/51, 62.7%) patients had Amyoplasia, and 19 (19/51, 37.3%) had other types of AMC (18 distal arthrogryposis, 1 Larsen). Six patients (6/42, 14.3%) had a lumbar BMD Z score less than − 2. The mean lumbar spine Z score (− 0.03 ± 1.6) was not significantly lower than the expected BMD Z score in the general population. Nine (9/40, 22.5%) and 10 (10/40, 25.0%) patients had femoral neck and total hip BMD Z scores less than − 2, respectively. The mean femoral neck (− 1.1 ± 1.1) and total hip (− 1.2 ± 1.2) BMD Z scores in patients with AMC were significantly lower than expected in the general population (p < 0.001). Femoral neck BMD correlated with height (rs = 0.39, p = 0.01), age (rs = − 0.315, p = 0.48); total hip BMD correlated with height (rs = 0.331, p = 0.04) and calcium levels (rs = 0.41, p = 0.04). Twenty-five patients (25/51, 49.0%) reported 39 fractures. Thirty-one (31/36, 86.1%) patients had 25-hydroxyvitamin D levels less than 75 nmol/l, and 6 (6/36, 16.7%) had 25-hydroxyvitamin D levels less than 75 nmol/l. Adults with AMC had lower hip BMD than expected for their age, and they more frequently showed vitamin D insufficiency. Screening for low BMD by DXA and adding vitamin D supplementation when vitamin D status is insufficient should be considered in adults with AMC, especially if there is a history of falls or fractures.