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At least 469 records · Page 26

Quantum Davidson algorithm for excited states

Abstract Excited state properties play a pivotal role in various chemical and physical phenomena, such as charge separation and light emission. However, the primary focus of most existing quantum algorithms has been the ground state, as seen in quantum phase estimation and the variational quantum eigensolver (VQE). Although VQE-type methods have been extended to explore excited states, these methods grapple with optimization challenges. In contrast, the quantum Krylov subspace (QKS) method has been introduced to address both ground and excited states, positioning itself as a cost-effective alternative to quantum phase estimation. However, conventional QKS methodologies depend on a pre-generated subspace through real or imaginary-time evolutions. This subspace is inherently expansive and can be plagued with issues like slow convergence or numerical instabilities, often leading to relatively deep circuits. Our research presents an economic QKS algorithm, which we term the quantum Davidson (QDavidson) algorithm. This innovation hinges on the iterative expansion of the Krylov subspace and the incorporation of a pre-conditioner within the Davidson framework. By using the residues of eigenstates to expand the Krylov subspace, we manage to formulate a compact subspace that aligns closely with the exact solutions. This iterative subspace expansion paves the way for a more rapid convergence in comparison to other QKS techniques, such as the quantum Lanczos. Using quantum simulators, we employ the novel QDavidson algorithm to delve into the excited state properties of various systems, spanning from the Heisenberg spin model to real molecules. Compared to the existing QKS methods, the QDavidson algorithm not only converges swiftly but also demands a significantly shallower circuit. This efficiency establishes the QDavidson method as a pragmatic tool for elucidating both ground and excited state properties on quantum computing platforms.

97 MATHEMATICS AND COMPUTING↗

Uncovering obscured phonon dynamics from powder inelastic neutron scattering using machine learning

The study of phonon dynamics is pivotal for understanding material properties, yet it faces challenges due to the irreversible information loss inherent in powder inelastic neutron scattering spectra and the limitations of traditional analysis methods. In this study, we present a machine learning framework designed to reveal obscured phonon dynamics from powder spectra. Using a variational autoencoder, we obtain a disentangled latent representation of spectra and successfully extract force constants for reconstructing phonon dispersions. Notably, our model demonstrates effective applicability to experimental data even when trained exclusively on physics-based simulations. The fine-tuning with experimental spectra further mitigates issues arising from domain shift. Analysis of latent space underscores the model’s versatility and generalizability, affirming its suitability for complex system applications. Furthermore, our framework’s two-stage design is promising for developing a universal pre-trained feature extractor. This approach has the potential to revolutionize neutron measurements of phonon dynamics, offering researchers a potent tool to decipher intricate spectra and gain valuable insights into the intrinsic physics of materials.

domain adaptation↗

Current and future directions in network biology

Network biology is an interdisciplinary field bridging computational and biological sciences that has proved pivotal in advancing the understanding of cellular functions and diseases across biological systems and scales. Although the field has been around for two decades, it remains nascent. It has witnessed rapid evolution, accompanied by emerging challenges. These stem from various factors, notably the growing complexity and volume of data together with the increased diversity of data types describing different tiers of biological organization. We discuss prevailing research directions in network biology, focusing on molecular/cellular networks but also on other biological network types such as biomedical knowledge graphs, patient similarity networks, brain networks, and social/contact networks relevant to disease spread. In more detail, we highlight areas of inference and comparison of biological networks, multimodal data integration and heterogeneous networks, higher-order network analysis, machine learning on networks, and network-based personalized medicine. Following the overview of recent breakthroughs across these five areas, we offer a perspective on future directions of network biology. Additionally, we discuss scientific communities, educational initiatives, and the importance of fostering diversity within the field. This article establishes a roadmap for an immediate and long-term vision for network biology.

59 BASIC BIOLOGICAL SCIENCES↗

EpitopeVec: linear epitope prediction using deep protein sequence embeddings

Motivation: B-cell epitopes (BCEs) play a pivotal role in the development of peptide vaccines, immuno-diagnostic reagents and antibody production, and thus in infectious disease prevention and diagnostics in general. Experimental methods used to determine BCEs are costly and time-consuming. Therefore, it is essential to develop computational methods for the rapid identification of BCEs. Although several computational methods have been developed for this task, generalizability is still a major concern, where cross-testing of the classifiers trained and tested on different datasets has revealed accuracies of 51–53%. Results: We describe a new method called EpitopeVec, which uses a combination of residue properties, modified antigenicity scales, and protein language model-based representations (protein vectors) as features of peptides for linear BCE predictions. Extensive benchmarking of EpitopeVec and other state-of-the-art methods for linear BCE prediction on several large and small datasets, as well as cross-testing, demonstrated an improvement in the performance of EpitopeVec over other methods in terms of accuracy and area under the curve. As the predictive performance depended on the species origin of the respective antigens (viral, bacterial and eukaryotic), we also trained our method on a large viral dataset to create a dedicated linear viral BCE predictor with improved cross-testing performance.

59 BASIC BIOLOGICAL SCIENCES↗

Reference-free structural variant detection in microbiomes via long-read co-assembly graphs

Motivation: The study of bacterial genome dynamics is vital for understanding the mechanisms underlying microbial adaptation, growth, and their impact on host phenotype. Structural variants (SVs), genomic alterations of 50 base pairs or more, play a pivotal role in driving evolutionary processes and maintaining genomic heterogeneity within bacterial populations. While SV detection in isolate genomes is relatively straightforward, metagenomes present broader challenges due to the absence of clear reference genomes and the presence of mixed strains. In response, our proposed method rhea, forgoes reference genomes and metagenome-assembled genomes (MAGs) by encompassing all metagenomic samples in a series (time or other metric) into a single co-assembly graph. The log fold change in graph coverage between successive samples is then calculated to call SVs that are thriving or declining. Results: We show rhea to outperform existing methods for SV and horizontal gene transfer (HGT) detection in two simulated mock metagenomes, particularly as the simulated reads diverge from reference genomes and an increase in strain diversity is incorporated. We additionally demonstrate use cases for rhea on series metagenomic data of environmental and fermented food microbiomes to detect specific sequence alterations between successive time and temperature samples, suggesting host advantage. Our approach leverages previous work in assembly graph structural and coverage patterns to provide versatility in studying SVs across diverse and poorly characterized microbial communities for more comprehensive insights into microbial gene flux.

59 BASIC BIOLOGICAL SCIENCES↗

Conserved white-rot enzymatic mechanism for wood decay in the Basidiomycota genus Pycnoporus

White-rot (WR) fungi are pivotal decomposers of dead organic matter in forest ecosystems and typically use a large array of hydrolytic and oxidative enzymes to deconstruct lignocellulose. However, the extent of lignin and cellulose degradation may vary between species and wood type. Here, we combined comparative genomics, transcriptomics and secretome proteomics to identify conserved enzymatic signatures at the onset of wood-decaying activity within the Basidiomycota genus Pycnoporus. We observed a strong conservation in the genome structures and the repertoires of protein-coding genes across the four Pycnoporus species described to date, despite the species having distinct geographic distributions. We further analysed the early response of P. cinnabarinus, P. coccineus and P. sanguineus to diverse (ligno)-cellulosic substrates. We identified a conserved set of enzymes mobilized by the three species for breaking down cellulose, hemicellulose and pectin. The co-occurrence in the exo-proteomes of H 2 O 2 -producing enzymes with H 2 O 2 -consuming enzymes was a common feature of the three species, although each enzymatic partner displayed independent transcriptional regulation. Finally, cellobiose dehydrogenase-coding genes were systematically co-regulated with at least one AA9 lytic polysaccharide monooxygenase gene, indicative of enzymatic synergy in vivo. This study highlights a conserved core white-rot fungal enzymatic mechanism behind the wood-decaying process.

59 BASIC BIOLOGICAL SCIENCES↗

Divergent Evolution of Early Terrestrial Fungi Reveals the Evolution of Mucormycosis Pathogenicity Factors

Abstract Fungi have evolved over millions of years and their species diversity is predicted to be the second largest on the earth. Fungi have cross-kingdom interactions with many organisms that have mutually shaped their evolutionary trajectories. Zygomycete fungi hold a pivotal position in the fungal tree of life and provide important perspectives on the early evolution of fungi from aquatic to terrestrial environments. Phylogenomic analyses have found that zygomycete fungi diversified into two separate clades, the Mucoromycota which are frequently associated with plants and Zoopagomycota that are commonly animal-associated fungi. Genetic elements that contributed to the fitness and divergence of these lineages may have been shaped by the varied interactions these fungi have had with plants, animals, bacteria, and other microbes. To investigate this, we performed comparative genomic analyses of the two clades of zygomycetes in the context of Kingdom Fungi, benefiting from our generation of a new collection of zygomycete genomes, including nine produced for this study. We identified lineage-specific genomic content that may contribute to the disparate biology observed in these zygomycetes. Our findings include the discovery of undescribed diversity in CotH, a Mucormycosis pathogenicity factor, which was found in a broad set of zygomycetes. Reconciliation analysis identified multiple duplication events and an expansion of CotH copies throughout the Mucoromycotina, Mortierellomycotina, Neocallimastigomycota, and Basidiobolus lineages. A kingdom-level phylogenomic analysis also identified new evolutionary relationships within the subphyla of Mucoromycota and Zoopagomycota, including supporting the sister-clade relationship between Glomeromycotina and Mortierellomycotina and the placement of Basidiobolus as sister to other Zoopagomycota lineages.

59 BASIC BIOLOGICAL SCIENCES↗

The Unified Phenotype Ontology : a framework for cross-species integrative phenomics

Phenotypic data are critical for understanding biological mechanisms and consequences of genomic variation, and are pivotal for clinical use cases such as disease diagnostics and treatment development. For over a century, vast quantities of phenotype data have been collected in many different contexts covering a variety of organisms. The emerging field of phenomics focuses on integrating and interpreting these data to inform biological hypotheses. A major impediment in phenomics is the wide range of distinct and disconnected approaches to recording the observable characteristics of an organism. Phenotype data are collected and curated using free text, single terms or combinations of terms, using multiple vocabularies, terminologies, or ontologies. Integrating these heterogeneous and often siloed data enables the application of biological knowledge both within and across species. Existing integration efforts are typically limited to mappings between pairs of terminologies; a generic knowledge representation that captures the full range of cross-species phenomics data is much needed. We have developed the Unified Phenotype Ontology (uPheno) framework, a community effort to provide an integration layer over domain-specific phenotype ontologies, as a single, unified, logical representation. uPheno comprises (1) a system for consistent computational definition of phenotype terms using ontology design patterns, maintained as a community library; (2) a hierarchical vocabulary of species-neutral phenotype terms under which their species-specific counterparts are grouped; and (3) mapping tables between species-specific ontologies. This harmonized representation supports use cases such as cross-species integration of genotype-phenotype associations from different organisms and cross-species informed variant prioritization.

59 BASIC BIOLOGICAL SCIENCES↗

Proteome-wide association study and functional validation identify novel protein markers for pancreatic ductal adenocarcinoma

Pancreatic ductal adenocarcinoma (PDAC) remains a lethal malignancy, largely due to the paucity of reliable biomarkers for early detection and therapeutic targeting. Existing blood protein biomarkers for PDAC often suffer from replicability issues, arising from inherent limitations such as unmeasured confounding factors in conventional epidemiologic study designs. To circumvent these limitations, we use genetic instruments to identify proteins with genetically predicted levels to be associated with PDAC risk. Leveraging genome and plasma proteome data from the INTERVAL study, we established and validated models to predict protein levels using genetic variants. By examining 8,275 PDAC cases and 6,723 controls, we identified 40 associated proteins, of which 16 are novel. Functionally validating these candidates by focusing on 2 selected novel protein-encoding genes, GOLM1 and B4GALT1, we demonstrated their pivotal roles in driving PDAC cell proliferation, migration, and invasion. Furthermore, we also identified potential drug repurposing opportunities for treating PDAC.

60 APPLIED LIFE SCIENCES↗

Trends and drivers of marine fish landings in Portugal since its entrance in the European Union

Abstract Marine landings in Portugal have decreased at a higher rate than fishing effort in the last 20 years. Identifying the variables driving the quantity and composition of landings is pivotal to understand the dynamics of the fisheries sector, which entails complex social and environmental aspects. In this study, we investigate the main drivers of marine fish landings in continental Portugal between 1989 and 2014. To identify common trends in time series, and quantify the importance of environmental factors, we applied a dynamic factor analysis considering four regions and three types of gear (trawling, purse-seine, and a multi-gear fishery). Our results show the importance of fishing effort as the most relevant factor driving marine landings in Portugal, both at the long and short terms. In addition, the effect of environmental factors such as the winter river discharge and the spring East Atlantic Teleconnection index should not be neglected, probably through mechanisms affecting coastal productivity. We provide a comprehensive amount of information that permits to improve our understanding of the trends of the most important commercial species in Portugal during the period of study.

Bueno-Pardo, Juan↗

Metabolite release by nitrifiers facilitates metabolic interactions in the ocean

Microbial chemoautotroph-heterotroph interactions may play a pivotal role in the cycling of carbon in the deep ocean, reminiscent of phytoplankton-heterotroph associations in surface waters. Nitrifiers are the most abundant chemoautotrophs in the global ocean, yet very little is known about nitrifier metabolite production, release, and transfer to heterotrophic microbial communities. To elucidate which organic compounds are released by nitrifiers and potentially available to heterotrophs, we characterized the exo- and endometabolomes of the ammonia-oxidizing archaeon Nitrosopumilus adriaticus CCS1 and the nitrite-oxidizing bacterium Nitrospina gracilis Nb-211. Nitrifier endometabolome composition was not a good predictor of exometabolite availability, indicating that metabolites were predominately released by mechanisms other than cell death/lysis. Although both nitrifiers released labile organic compounds, N. adriaticus preferentially released amino acids, particularly glycine, suggesting that its cell membranes might be more permeable to small, hydrophobic amino acids. We further initiated co-culture systems between each nitrifier and a heterotrophic alphaproteobacterium, and compared exometabolite and transcript patterns of nitrifiers grown axenically to those in co-culture. In particular, B vitamins exhibited dynamic production and consumption patterns in nitrifier-heterotroph co-cultures. We observed an increased production of vitamin B 2 and the vitamin B 12 lower ligand dimethylbenzimidazole by N. adriaticus and N. gracilis, respectively. In contrast, the heterotroph likely produced vitamin B 5 in co-culture with both nitrifiers and consumed the vitamin B 7 precursor dethiobiotin when grown with N. gracilis. Our results indicate that B vitamins and their precursors could play a particularly important role in governing specific metabolic interactions between nitrifiers and heterotrophic microbes in the ocean.

54 ENVIRONMENTAL SCIENCES↗

Variations in pharmacokinetic-pharmacodynamic target values across MICs and their potential impact on determination of susceptibility test interpretive criteria

Abstract Background An antibacterial drug’s susceptibility test interpretive criteria (STIC) are determined by integrating clinical, microbiological and pharmacokinetic-pharmacodynamic (PK-PD) data. PTA analysis plays a pivotal or supportive role in STIC determination and is heavily dependent on the PK-PD target values determined from animal PK-PD studies. Therefore, variations in PK-PD target values may impact STIC determination. Factors contributing to variation in the PK-PD target values include the number of and MICs for bacterial isolates used in animal PK-PD studies. Objectives To analyse the relationship between PK-PD target values and MICs, describe the variations in PK-PD target values of isolates and evaluate whether the proposed/target STICs were within the ranges of the MICs for isolates used in animal PK-PD studies. Methods A database was compiled for this research by screening animal PK-PD study reports submitted to the FDA from 10 new drug applications (NDAs). Results A relationship evaluation between PK-PD target values and MICs for tested isolates for seven drugs (that used AUC/MIC ratio as the PK-PD index) showed that, generally, the AUC/MIC values decreased with an increase in MIC. These target values were highly variable, with the percentage coefficient of variation ranging between 1% and 132% for isolates having the same MIC. For 16/27 (59%) drug/bacteria combinations from all 10 drugs, the proposed/target STICs were higher than the highest MIC for bacteria isolates evaluated, while 6/27 (22.5%) were lower. Conclusions This research suggests that careful considerations related to selection of bacterial isolates for animal PK-PD studies could strengthen the STIC determination process.

Waack, Ursula↗

The overlooked interaction of emerging contaminants and microbial communities: a threat to ecosystems and public health

Abstract Context and aims Emerging contaminants (ECs) and microbial communities should not be viewed in isolation, but through the One Health perspective. Both ECs and microorganisms lie at the core of this interconnected framework, as they directly influence the health of humans, animals, and the environment. The interactions between ECs and microbial communities can have profound implications for public health, affecting all three domains. However, these ECs-microorganism interactions remain underexplored, potentially leaving significant public health and ecological risks unrecognized. Therefore, this article seeks to alert the scientific community to the overlooked interactions between ECs and microbial communities, emphasizing the pivotal role these interactions may play in the management of ‘One Health.’ Results The most extensively studied interaction between ECs and microbial communities is biodegradation. However, other more complex and concerning interactions demand attention, such as the impact of ECs on microbial ecology (disruptions in ecosystem balance affecting nutrient and energy cycles) and the rise and spread of antimicrobial resistance (a growing global health crisis). Although these ECs-microbial interactions had not been extensively studied, there are scientific evidence that ECs impact on microbial communities may be concerning for public health and ecosystem balance. Conclusions So, this perspective summarizes the impact of ECs through a One Health lens and underscores the urgent need to understand their influence on microbial communities, while highlighting the key challenges researchers must overcome. Tackling these challenges is vital to mitigate potential long-term consequences for both ecosystems and public health.

Gomes, Inês B. (ORCID:0000000207313662)↗

Purple non-sulfur bacteria for biotechnological applications

Abstract In this review, we focus on how purple non-sulfur bacteria can be leveraged for sustainable bioproduction to support the circular economy. We discuss the state of the field with respect to the use of purple bacteria for energy production, their role in wastewater treatment, as a fertilizer, and as a chassis for bioplastic production. We explore their ability to serve as single-cell protein and production platforms for fine chemicals from waste materials. We also introduce more Avant-Garde technologies that leverage the unique metabolisms of purple bacteria, including microbial electrosynthesis and co-culture. These technologies will be pivotal in our efforts to mitigate climate change and circularize the economy in the next two decades. One-sentence summary Purple non-sulfur bacteria are utilized for a range of biotechnological applications, including the production of bio-energy, single cell protein, fertilizer, bioplastics, fine chemicals, in wastewater treatment and in novel applications like co-cultures and microbial electrosynthesis.

Morrison, Hailee M. (ORCID:0000000225121824)↗

The turbulence driving parameter of molecular clouds in disc galaxies

ABSTRACT Supersonic turbulence plays a pivotal role during the formation of molecular clouds and stars in galaxies. However, little is known about how the fraction of compressive and solenoidal modes in the velocity field evolves over time and how it depends on properties of the molecular cloud or the galactic environment. In this work, we carry out magnetohydrodynamical simulations of disc galaxies and study the time evolution of the turbulence driving parameter for an ensemble of clouds. We find that the time-averaged turbulence driving parameter is insensitive to the position of the cloud within the galaxy. The ensemble-averaged driving parameter is found to be rather compressive with b ∼ 0.5–0.7, indicating almost time-independent global star formation properties. However, each individual cloud shows a highly fluctuating driving parameter, which would strongly affect the cloud’s star formation rate. We find that the mode of turbulence driving can rapidly change within only a few Myr, both from solenoidal to compressive and vice versa. We attribute these changes to cloud collisions and to tidal interactions with clouds or overdensities in the environment. Last, we find no significant differences in the average driving parameter between hydrodynamic and initially strongly magnetized galaxies. However, the magnetic field tends to reduce the overall fluctuation of the driving parameter. The average driving and its uncertainty are seen to be in agreement with recent constraints on the turbulence driving mode for solar neighbourhood clouds.

Körtgen, Bastian↗

Mass calibration of the CODEX cluster sample using SPIDERS spectroscopy – II. The X-ray luminosity–mass relation

ABSTRACT We perform the calibration of the X-ray luminosity–mass scaling relation on a sample of 344 CODEX clusters with z < 0.66 using the dynamics of their member galaxies. Spectroscopic follow-up measurements have been obtained from the SPIDERS survey, leading to a sample of 6658 red member galaxies. We use the Jeans equation to calculate halo masses, assuming an NFW mass profile and analysing a broad range of anisotropy profiles. With a scaling relation of the form $L_{\rm {X}} \propto \text{A}_{\rm {X}}M_{\text{200c}}^{\text{B}_{\rm {X}}} E(z)^2 (1+z)^{\gamma _{\rm {X}}}$, we find best-fitting parameters $\text{A}_{\rm {X}}=0.62^{+0.05}_{-0.06} (\pm 0.06)\times 10^{44}\, \mathrm{erg\, s^{-1}}$, $\text{B}_{\rm {X}}=2.35^{+0.21}_{-0.18}(\pm 0.09)$, $\gamma _{\rm {X}}=-2.77^{+1.06}_{-1.05}(\pm 0.79)$, where we include systematic uncertainties in parentheses and for a pivot mass and redshift of $3\times 10^{14}\, \mathrm{M}_\odot$ and 0.16, respectively. We compare our constraints with previous results, and we combine our sample with the SPT SZE-selected cluster subsample observed with XMM–Newton extending the validity of our results to a wider range of redshifts and cluster masses.

Capasso, R.↗

Mass calibration of distant SPT galaxy clusters through expanded weak-lensing follow-up observations with HST, VLT, & Gemini-South

Expanding from previous work, we present weak-lensing (WL) measurements for a total sample of 30 distant (z median = 0.93) massive galaxy clusters from the South Pole Telescope Sunyaev–Zel’dovich (SPT-SZ) Survey, measuring galaxy shapes in Hubble Space Telescope (HST) Advanced Camera for Surveys images. We remove cluster members and preferentially select z ≳ 1.4 background galaxies via V - I colour, employing deep photometry from VLT/FORS2 and Gemini-South/GMOS. We apply revised calibrations for the WL shape measurements and the source redshift distribution to estimate the cluster masses. In combination with earlier Magellan/Megacam results for lower-redshifts clusters, we infer refined constraints on the scaling relation between the SZ detection significance and the cluster mass, in particular regarding its redshift evolution. The mass scale inferred from the WL data is lower by a factor $0.76^{+0.10}_{-0.14}$ (at our pivot redshift z = 0.6) compared to what would be needed to reconcile a flat Planck νΛCDM cosmology (in which the sum of the neutrino masses is a free parameter) with the observed SPT-SZ cluster counts. In order to sensitively test the level of (dis-)agreement between SPT clusters and Planck, further expanded WL follow-up samples are needed.

79 ASTRONOMY AND ASTROPHYSICS↗

Spectral analysis of ultra-cool white dwarfs polluted by planetary debris

ABSTRACT We identify two ultra-cool (${T_\mathrm{eff}}\lt 4000$ K) metal-polluted (DZ) white dwarfs WD J2147−4035 and WD J1922+0233 as the coolest and second coolest DZ stars known to date with ${T_\mathrm{eff}}\approx 3050$ K and ${T_\mathrm{eff}}\approx 3340$ K, respectively. Strong atmospheric collision-induced absorption (CIA) causes the suppression of red optical and infrared flux in WD J1922+0233, resulting in an unusually blue colour given its low temperature. WD J2147−4035 has moderate infrared CIA yet has the reddest optical colours known for a DZ white dwarf. Microphysics improvements to the non-ideal effects and CIA opacities in our model atmosphere code yields reasonable solutions to observations of these ultra-cool stars. WD J2147−4035 has a cooling age of over 10 Gyr which is the largest known for a DZ white dwarf, whereas WD J1922+0233 is slightly younger with a cooling age of 9 Gyr. Galactic kinematics calculations from precise Gaia EDR3 astrometry reveal these ultra-cool DZ stars as likely members of the Galactic disc thus they could be pivotal objects in future studies constraining an upper age limit for the disc of the Milky Way. We present intermediate-resolution spectroscopy for both objects, which provides the first spectroscopic observations of WD J2147−4035. Detections of sodium and potassium are made in both white dwarfs, in addition to calcium in WD J1922+0233 and lithium in WD J2147−4035. We identify the magnetic nature of WD J2147−4035 from Zeeman splitting in the lithium line and also make a tentative detection of carbon, so we classify this star as DZQH. WD J1922+0233 likely accreted planetary crust debris, while the debris composition that polluted WD J2147−4035 remains unconstrained.

Elms, Abbigail K. (ORCID:0000000176667416)↗