bluuebunny/crossref_metadata_2025_split huggingface dataset:
Escherichia coli ST155 as a production-host of three different polyvalent phages and their characterisation with a prospect for wastewater disinfection
Authors: Salim Amrita , Madhavan Ajith , Subhash Suja , Prasad Megha , Nair Bipin G. , Pal Sanjay 
Published: November 2022

AbstractBacteriophages are generally specific, and a cocktail of phages is needed to combat different bacterial targets. Their production usually requires pathogenic isolation hosts. We identified a novel strain, Escherichia coli ST155, that could serve as a production host for three different polyvalent phages (ϕPh_SE03, ϕPh_SD01, and ϕPh_EC01), thus superseding the use of individual isolation hosts. Upon propagation in E. coli ST155, the phages demonstrated differential intergeneric infectivity against Salmonella enterica, E. coli OP50, Shigella dysenteriae, E. coli MDR, and Acinetobacter baumannii. Phages were characterised based on morphology, latent period, burst size, the efficiency of plating, and restriction enzyme profile. Survival assay on Caenorhabditis elegans, the absence of Shiga toxin, and enterotoxigenic E. coli virulence genes indicated that E. coli ST155 could be non-pathogenic. Lack of antibiotic resistance and absence of functional prophages rendered the host suitable for environmental applications. As a proof-of-concept, phage ϕPh_SE03 was produced in ST155 by employing a unique Bacteriophage Amplification Reactor-Lytics Broadcasting System and was simultaneously disseminated into S. enterica augmented wastewater, which resulted in a 3-log reduction in 24 h. The study establishes the potential of E. coli ST155 as a phage production host thereby minimising the possibility of accidental release of pathogenic hosts into wastewater.
Association between cholesterol levels and dementia risk according to the presence of diabetes and statin use: a nationwide cohort study
Authors: Lee You-Bin , Kim Min Young , Han Kyungdo , Kim Bongsung , Park Jiyun , Kim Gyuri , Hur Kyu Yeon , Kim Jae Hyeon , Jin Sang-Man 
Published: November 2022

AbstractWe explored the association between cholesterol levels and dementia risk according to the presence of diabetes and statin use. In this population-based longitudinal cohort study, the Korean National Health Insurance Service datasets (2002–2017) were used. Among individuals aged ≥ 40 years who underwent health examinations in 2009 (N = 6,883,494), the hazard of dementia was evaluated according to cholesterol levels. During a median 8.33 years, 263,185 dementia cases were detected. In statin non-users with or without diabetes, the hazards of all-cause dementia were highest for those in the lowest quartile or quintile of low-density lipoprotein-cholesterol (LDL-C) level, showing an inverted J-shaped relationship. Among statin users with or without diabetes, an advance in LDL-C group was associated with an increase in hazards of all-cause dementia. In statin users with diabetes, even very low LDL-C level was not associated with an increased risk of all-cause dementia. Although there was a seemingly paradoxical association between low LDL-C level and dementia risk in statin non-users, the trend was not observed in statin users and is not likely to be clinically relevant. Rather, an advance in LDL-C levels was associated with an increase in the hazard of all-cause dementia in statin users, regardless of the presence of diabetes.
Differences in lung and lobe volumes between supine and upright computed tomography in patients with idiopathic lung fibrosis
Authors: Chubachi Shotaro , Okamori Satoshi , Yamada Yoshitake , Yamada Minoru , Yokoyama Yoichi , Niijima Yuki , Kamata Hirofumi , Ishii Makoto , Fukunaga Koichi , Jinzaki Masahiro 
Published: November 2022

AbstractNo clinical study has compared lung or lobe volumes on computed tomography (CT) between the supine and standing positions in patients with idiopathic lung fibrosis (IPF). This study aimed to compare lung and lobe volumes between the supine and standing positions and evaluate the correlations between the supine/standing lung volumes on CT and pulmonary function in patients with IPF. Twenty-three patients with IPF underwent a pulmonary function test and both low-dose conventional (supine position) and upright CT (standing position) during inspiration breath-holds. The volumes of the total lungs and lobes were larger in the standing than in the supine position in patients with IPF (all p < 0.05). Spearman's correlation coefficients between total lung volumes on chest CT in supine/standing positions and vital capacity (VC) or forced VC (FVC) were 0.61/0.79 or 0.64/0.80, respectively. CT-based volumes on upright CT were better correlated with VC and FVC than those on supine CT. Lung and lobe volumes in the standing position may be useful biomarkers to assess disease severity or therapeutic effect in patients with IPF.
Exploring structure, microbiota, and metagenome functions of epigean and hypogean black deposits by microscopic, molecular and bioinformatic approaches
Authors: Farda Beatrice , Vaccarelli Ilaria , Ercole Claudia , Djebaili Rihab , Del Gallo Maddalena , Pellegrini Marika 
Published: November 2022

AbstractThis study revealed how Bacteria and Archaea communities and their metabolic functions differed between two groups of black deposits identified in gorge and cave environments. Scanning electron microscopy coupled with energy dispersive spectroscopy was used to analyse the presence of microbial biosignatures and the elemental composition of samples. Metabarcoding of the V3–V4 regions of 16S rRNA was used to investigate Bacteria and Archaea communities. Based on 16S rRNA sequencing results, PICRUSt software was used to predict metagenome functions. Micrographs showed that samples presented microbial biosignatures and microanalyses highlighted Mn concretions and layers on Al-Si surfaces. The 16S rRNA metabarcoding alpha-diversity metrics showed similar Simpson's and Shannon indices and different values of the Chao-1 index. The amplicon sequence variants (ASVs) analysis at the different taxonomic levels showed a diverse genera composition. However, the communities of all samples shared the presence of uncultured ASVs belonging to the Gemmatales family (Phylogenesis: Gemmataceae; Planctomycetes; Planctomycetota; Bacteria). The predicted metagenome functions analysis revealed diverse metabolic profiles of the Cave and Gorge groups. Genes coding for essential Mn metabolism were present in all samples. Overall, the findings on structure, microbiota, and predicted metagenome functions showed a similar microbial contribution to epigean and hypogean black deposits Mn metabolism.
High throughput 3D gel-based neural organotypic model for cellular assays using fluorescence biosensors
Authors: Kundu Srikanya , Boutin Molly E. , Strong Caroline E. , Voss Ty , Ferrer Marc 
Published: November 2022

AbstractThree-dimensional (3D) organotypic models that capture native-like physiological features of tissues are being pursued as clinically predictive assays for therapeutics development. A range of these models are being developed to mimic brain morphology, physiology, and pathology of neurological diseases. Biofabrication of 3D gel-based cellular systems is emerging as a versatile technology to produce spatially and cell-type tailored, physiologically complex and native-like tissue models. Here we produce 3D fibrin gel-based functional neural co-culture models with human-iPSC differentiated dopaminergic or glutamatergic neurons and astrocytes. We further introduce genetically encoded fluorescence biosensors and optogenetics activation for real time functional measurements of intracellular calcium and levels of dopamine and glutamate neurotransmitters, in a high-throughput compatible plate format. We use pharmacological perturbations to demonstrate that the drug responses of 3D gel-based neural models are like those expected from in-vivo data, and in some cases, in contrast to those observed in the equivalent 2D neural models.
Gene–gene interaction detection with deep learning
Authors: Cui Tianyu , El Mekkaoui Khaoula , Reinvall Jaakko , Havulinna Aki S. , Marttinen Pekka , Kaski Samuel 
Published: November 2022

AbstractThe extent to which genetic interactions affect observed phenotypes is generally unknown because current interaction detection approaches only consider simple interactions between top SNPs of genes. We introduce an open-source framework for increasing the power of interaction detection by considering all SNPs within a selected set of genes and complex interactions between them, beyond only the currently considered multiplicative relationships. In brief, the relation between SNPs and a phenotype is captured by a neural network, and the interactions are quantified by Shapley scores between hidden nodes, which are gene representations that optimally combine information from the corresponding SNPs. Additionally, we design a permutation procedure tailored for neural networks to assess the significance of interactions, which outperformed existing alternatives on simulated datasets with complex interactions, and in a cholesterol study on the UK Biobank it detected nine interactions which replicated on an independent FINRISK dataset.
Single-cell transcriptome analysis reveals cellular heterogeneity in mouse intra- and extra articular ligaments
Authors: Ishibashi Kyota , Ikegami Kentaro , Shimbo Takashi , Sasaki Eiji , Kitayama Tomomi , Nakamura Yuzuru , Tsushima Takahiro , Ishibashi Yasuyuki , Tamai Katsuto 
Published: November 2022

AbstractLigaments are collagenous connective tissues that connect bones. Injury of knee ligaments, namely anterior cruciate ligament (ACL) and medial collateral ligament (MCL), is common in athletes. Both ligaments have important functions, but distinct regeneration capacities. The capacity for recovery after injury also diminishes with age. However, cellular heterogeneity in the ligaments remains unclear. Here, we profiled the transcriptional signatures of ACL and MCL cells in mice using single-cell RNA sequencing. These ligaments comprise three fibroblast types expressing Col22a1, Col12a1, or Col14a1, but have distinct localizations in the tissue. We found substantial heterogeneity in Col12a1- and Col14a1-positive cells between ACL and MCL. Gene Ontology analysis revealed that angiogenesis- and collagen regulation-related genes were specifically enriched in MCL cells. Furthermore, we identified age-related changes in cell composition and gene expression in the ligaments. This study delineates cellular heterogeneity in ligaments, serving as a foundation for identifying potential therapeutic targets for ligament injuries.
Development of a ternary cyclodextrin–arginine–ciprofloxacin antimicrobial complex with enhanced stability
Authors: Vukomanovic Marija , Gazvoda Lea , Kurtjak Mario , Hrescak Jitka , Jaklic Blaž , Moya-Andérico Laura , Cendra Maria del Mar , Torrents Eduard 
Published: November 2022

AbstractDesigning useful functionalities in clinically validated, old antibiotics holds promise to provide the most economical solution for the global lack of effective antibiotics, as undoubtedly a serious health threat. Here we show that using the surface chemistry of the cyclodextrin (βCD) cycle and arginine (arg) as a linker, provides more stable ternary antibiotic complex (βCD-arg-cpx). In contrast to classical less stable inclusion complexes, which only modify antibiotic solubility, here-presented ternary complex is more stable and controls drug release. The components of the complex intensify interactions with bacterial membranes and increase the drug’s availability inside bacterial cells, thereby improving its antimicrobial efficacy and safety profile. Multifunctional antibiotics, formulated as drug delivery systems per se, that take the drug to the site of action, maximize its efficacy, and provide optical detectability are envisaged as the future in fighting against infections. Their role as a tool against multiresistant strains remains as interesting challenge open for further research.
Biosynthesis of cannabinoid precursor olivetolic acid in genetically engineered Yarrowia lipolytica
Authors: Ma Jingbo , Gu Yang , Xu Peng 
Published: November 2022

AbstractEngineering microbes to produce plant-derived natural products provides an alternate solution to obtain bioactive products. Here we report a systematic approach to sequentially identify the rate-limiting steps and improve the biosynthesis of the cannabinoid precursor olivetolic acid (OLA) inYarrowia lipolytica. We find thatPseudomonas spLvaE encoding a short-chain acyl-CoA synthetase can efficiently convert hexanoic acid to hexanoyl-CoA. The co-expression of the acetyl-CoA carboxylase, the pyruvate dehydrogenase bypass, the NADPH-generating malic enzyme, as well as the activation of peroxisomal β-oxidation pathway and ATP export pathway are effective strategies to redirect carbon flux toward OLA synthesis. Implementation of these strategies led to an 83-fold increase in OLA titer, reaching 9.18 mg/L of OLA in shake flask culture. This work may serve as a baseline for engineering cannabinoids biosynthesis in oleaginous yeast species.
Microfluidic live tracking and transcriptomics of cancer-immune cell doublets link intercellular proximity and gene regulation
Authors: Flores Bianca C. T. , Chawla Smriti , Ma Ning , Sanada Chad , Kujur Praveen Kumar , Yeung Rudy , Bellon Margot B. , Hukari Kyle , Fowler Brian , Lynch Mark , Chinen Ludmilla T. D. , Ramalingam Naveen , Sengupta Debarka , Jeffrey Stefanie S. 
Published: November 2022

AbstractCell–cell communication and physical interactions play a vital role in cancer initiation, homeostasis, progression, and immune response. Here, we report a system that combines live capture of different cell types, co-incubation, time-lapse imaging, and gene expression profiling of doublets using a microfluidic integrated fluidic circuit that enables measurement of physical distances between cells and the associated transcriptional profiles due to cell–cell interactions. We track the temporal variations in natural killer—triple-negative breast cancer cell distances and compare them with terminal cellular transcriptome profiles. The results show the time-bound activities of regulatory modules and allude to the existence of transcriptional memory. Our experimental and bioinformatic approaches serve as a proof of concept for interrogating live-cell interactions at doublet resolution. Together, our findings highlight the use of our approach across different cancers and cell types.
Quantum control of spin qubits using nanomagnets
Authors: Niknam Mohamad , Chowdhury Md. Fahim F. , Rajib Md Mahadi , Misba Walid Al , Schwartz Robert N. , Wang Kang L. , Atulasimha Jayasimha , Bouchard Louis-S. 
Published: November 2022

AbstractSingle-qubit gates are essential components of a universal quantum computer. Without selective addressing of individual qubits, scalable implementation of quantum algorithms is extremely challenging. When the qubits are discrete points or regions on a lattice, selectively addressing magnetic spin qubits at the nanoscale remains a challenge due to the difficulty of localizing and confining a classical divergence-free field to a small volume of space. Herein we propose a technique for addressing spin qubits using voltage-control of nanoscale magnetism, exemplified by the use of voltage control of magnetic anisotropy. We show that by tuning the frequency of the nanomagnet’s electric field drive to the Larmor frequency of the spins confined to a nanoscale volume, and by modulating the phase of the drive, single-qubit quantum gates with fidelities approaching those for fault-tolerant quantum computing can be implemented. Such single-qubit gate operations require only tens of femto-Joules per gate operation and have lossless, purely magnetic field control. Their physical realization is also straightforward using foundry manufacturing techniques.
Emergence and manipulation of non-equilibrium Yu-Shiba-Rusinov states
Authors: Bedow Jasmin , Mascot Eric , Morr Dirk K. 
Published: November 2022

AbstractThe experimental advances in the study of time-dependent phenomena has opened a new path to investigating the complex electronic structure of strongly correlated and topological materials. Yu-Shiba-Rusinov (YSR) states induced by magnetic impurities in s-wave superconductors provide an ideal candidate system to study the response of a system to time-dependent manipulations of the magnetic environment. Here, we show that by imposing a time-dependent change in the magnetic exchange coupling, by changing the relative alignment of magnetic moments in an impurity dimer, or through a periodic drive of the impurity moment, one can tune the system through a time-dependent quantum phase transition, in which the system undergoes a transition from a singlet to a doublet ground state. We show that the electronic response of the system to external perturbations can be imaged through the time-dependent differential conductance, dI(t)/dV, which, in analogy to the equilibrium case, is proportional to a non-equilibrium local density of states. Our results open the path to visualizing the response of complex quantum systems to time-dependent external perturbations.
Activation energy and force fields during topological transitions of fluid lipid vesicles
Authors: Bottacchiari Matteo , Gallo Mirko , Bussoletti Marco , Casciola Carlo Massimo 
Published: November 2022

AbstractTopological transitions of fluid lipid membranes are fundamental processes for cell life. For example, they are required for endo- and exocytosis or to enable neurotransmitters to cross the neural synapses. Here, inspired by the idea that fusion and fission proteins could have evolved in Nature in order to carry out a minimal work expenditure, we evaluate the minimal free energy pathway for the transition between two spherical large unilamellar vesicles and a dumbbell-shaped one. To address the problem, we propose and successfully use a Ginzburg-Landau type of free energy, which allows us to uniquely describe without interruption the whole, full-scale topological change. We also compute the force fields needed to overcome the involved energy barriers. The obtained forces are in excellent agreement, in terms of intensity, scale, and spatial localization with experimental data on typical fission protein systems, whereas they suggest the presence of additional features in fusion proteins.
Suppression of the transition to superconductivity in crystal/glass high-entropy alloy nanocomposites
Authors: Zhang Xiaofu , Shu Rui , Liu Huanlong , Elsukova Anna , Persson Per O. Å. , Schilling Andreas , von Rohr Fabian O. , Eklund Per 
Published: November 2022

AbstractSuperconducting high entropy alloys (HEAs) may combine extraordinary mechanical properties with robust superconductivity. They are suitable model systems for the investigation of the interplay of disorder and superconductivity. Here, we report on the superconductivity in (TaNb)1-x(ZrHfTi)x thin films. Beyond the near-equimolar region, the films comprise hundreds-of-nanometer-sized crystalline grains and show robust bulk superconductivity. However, the superconducting transitions in these nanocomposites are dramatically suppressed in the near-equimolar configurations, i.e., 0.45 < x < 0.64, where elemental distributions are equivalently homogeneous. Crystal/glass high entropy alloy nanocomposite phase separation was observed for the films in the near-equimolar region, which yields a broadened two-step normal to superconducting transition. Furthermore, the diamagnetic shielding in these films is only observed far below the onset temperature of superconductivity. As these unusual superconducting transitions are observed only in the samples with the high mixing entropy, this compositional range influences the collective electronic properties in these materials.
City or hinterland – site potentials for upscaled aquaponics in a Berlin case study
Authors: Baganz Gösta F. M. , Timpe Axel , Baganz Daniela , Staaks Georg , Hunger Bernd , Kloas Werner , Lohrberg Frank 
Published: November 2022

AbstractSustainably feeding the rapidly growing urban populations requires resource-efficient food production solutions, such as aquaponics. To assess its upscaled fruition in city regions, we applied system analysis to depict determinants of aquaponics at a mesoscale. Using Berlin as a case study, site potentials regarding the production of freshwater fish, tomatoes, and lettuce to achieve self-sufficiency were investigated. We analysed planning documents by text mining and applied geographic information system procedures to evaluate this technology’s spatial efficacy in intra- and peri-urban spaces, considering aspects of economy, sustainability and spatial distribution. In a facility-based approach, we contrasted specific intra- and peri-urban site potentials with their different boundary conditions. A thereupon-based scenario allocates approximately 20% of the production volume in Berlin, 80% in its hinterland, and emphasises the crucial use of circular economy resources in both spaces. Policy recommendations and the transferability of this realistic approach will support the implementation of aquaponics.
Point-defect avalanches mediate grain boundary diffusion
Authors: Chesser Ian , Mishin Yuri 
Published: November 2022

AbstractGrain boundary diffusion in polycrystalline materials is a physical phenomenon of great fundamental interest and practical significance. Although accelerated atomic transport along grain boundaries has been known for decades, atomic-level understanding of diffusion mechanisms remains poor. Previous atomistic simulations focused on low temperatures where the grain boundary structure is ordered or high temperatures where it is highly disordered. Here, we conduct molecular dynamics simulations of grain boundary diffusion at intermediate temperatures most relevant to applications. A surprising result of this work is the observation of intermittent GB diffusion behavior and its strong system-size dependence unseen in previous work. Both effects are found to originate from thermally activated point-defect avalanches. We identify the length and time scales of the avalanches and link their formation to dynamic heterogeneity in partially disordered systems. Our findings have implications for future computer modeling of grain boundary diffusion and mass transport in nano-scale materials.
Subpolar gyre decadal variability explains the recent oxygenation in the Irminger Sea
Authors: Feucher Charlène , Portela Esther , Kolodziejczyk Nicolas , Thierry Virginie 
Published: November 2022

AbstractAccurate monitoring of the long-term trend of oxygen content at global scale requires a better knowledge of the regional oxygen variability at interannual to decadal time scale. Here, we combined the Argo dataset and repeated ship-based sections to investigate the drivers of the oxygen variability in the North Atlantic Ocean, a key region for the oxygen supply into the deep ocean. We focus on the Labrador Sea Water in the Irminger Sea over the period 1991–2018 and we show that the oxygen solubility explains less than a third of the oxygen variability. In turn, the main drivers of the oxygen variability are due to changes in vertical mixing, advection, and other processes as revealed by Apparent Oxygen Utilization computation. Our findings revealed the key role of physical processes on the changes in oxygen variability and highlight the need of keeping a sustained monitoring of those processes to disentangle human-induced changes in oxygen from decadal natural variability.