bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Acinetobacter baumannii disinfectant resistance protein, AmvA, is a spermidine and spermine efflux pump
Authors: Short Francesca L. , Liu Qi , Shah Bhumika , Clift Heather E. , Naidu Varsha , Li Liping , Prity Farzana T. , Mabbutt Bridget C. , Hassan Karl A. , Paulsen Ian T. 
Published: September 2021

AbstractAntimicrobial resistance genes, including multidrug efflux pumps, evolved long before the ubiquitous use of antimicrobials in medicine and infection control. Multidrug efflux pumps often transport metabolites, signals and host-derived molecules in addition to antibiotics or biocides. Understanding their ancestral physiological roles could inform the development of strategies to subvert their activity. In this study, we investigated the response of Acinetobacter baumannii to polyamines, a widespread, abundant class of amino acid-derived metabolites, which led us to identify long-chain polyamines as natural substrates of the disinfectant efflux pump AmvA. Loss of amvA dramatically reduced tolerance to long-chain polyamines, and these molecules induce expression of amvA through binding to its cognate regulator AmvR. A second clinically-important efflux pump, AdeABC, also contributed to polyamine tolerance. Our results suggest that the disinfectant resistance capability that allows A. baumannii to survive in hospitals may have evolutionary origins in the transport of polyamine metabolites.
The development of tumour vascular networks
Authors: Fouladzadeh Anahita , Dorraki Mohsen , Min Kay Khine Myo , Cockshell Michaelia P. , Thompson Emma J. , Verjans Johan W. , Allison Andrew , Bonder Claudine S. , Abbott Derek 
Published: September 2021

AbstractThe growth of solid tumours relies on an ever-increasing supply of oxygen and nutrients that are delivered via vascular networks. Tumour vasculature includes endothelial cell lined angiogenesis and the less common cancer cell lined vasculogenic mimicry (VM). To study and compare the development of vascular networks formed during angiogenesis and VM (represented here by breast cancer and pancreatic cancer cell lines) a number of in vitro assays were utilised. From live cell imaging, we performed a large-scale automated extraction of network parameters and identified properties not previously reported. We show that for both angiogenesis and VM, the characteristic network path length reduces over time; however, only endothelial cells increase network clustering coefficients thus maintaining small-world network properties as they develop. When compared to angiogenesis, the VM network efficiency is improved by decreasing the number of edges and vertices, and also by increasing edge length. Furthermore, our results demonstrate that angiogenic and VM networks appear to display similar properties to road traffic networks and are also subject to the well-known Braess paradox. This quantitative measurement framework opens up new avenues to potentially evaluate the impact of anti-cancer drugs and anti-vascular therapies.
Computational modeling and experimental validation of the EPI-X4/CXCR4 complex allows rational design of small peptide antagonists
Authors: Sokkar Pandian , Harms Mirja , Stürzel Christina , Gilg Andrea , Kizilsavas Gönül , Raasholm Martina , Preising Nico , Wagner Manfred , Kirchhoff Frank , Ständker Ludger , Weidinger Gilbert , Mayer Benjamin , Münch Jan , Sanchez-Garcia Elsa 
Published: September 2021

AbstractEPI-X4, a 16-mer fragment of albumin, is a specific endogenous antagonist and inverse agonist of the CXC-motif-chemokine receptor 4 (CXCR4) and thus a key regulator of CXCR4 function. Accordingly, activity-optimized synthetic derivatives of EPI-X4 are promising leads for the therapy of CXCR4-linked disorders such as cancer or inflammatory diseases. We investigated the binding of EPI-X4 to CXCR4, which so far remained unclear, by means of biomolecular simulations combined with experimental mutagenesis and activity studies. We found that EPI-X4 interacts through its N-terminal residues with CXCR4 and identified its key interaction motifs, explaining receptor antagonization. Using this model, we developed shortened EPI-X4 derivatives (7-mers) with optimized receptor antagonizing properties as new leads for the development of CXCR4 inhibitors. Our work reveals the molecular details and mechanism by which the first endogenous peptide antagonist of CXCR4 interacts with its receptor and provides a foundation for the rational design of improved EPI-X4 derivatives.
Emerging SARS-CoV-2 variants follow a historical pattern recorded in outgroups infecting non-human hosts
Authors: Katoh Kazutaka , Standley Daron M. 
Published: September 2021

AbstractThe ability to predict emerging variants of SARS-CoV-2 would be of enormous value, as it would enable proactive design of vaccines in advance of such emergence. We estimated diversity of each site on a multiple sequence alignment (MSA) of the Spike (S) proteins from close relatives of SARS-CoV-2 that infected bat and pangolin before the pandemic. Then we compared the locations of high diversity sites in this MSA and those of mutations found in multiple emerging lineages of human-infecting SARS-CoV-2. This comparison revealed a significant correspondence, which suggests that a limited number of sites in this protein are repeatedly substituted in different lineages of this group of viruses. It follows, therefore, that the sites of future emerging mutations in SARS-CoV-2 can be predicted by analyzing their relatives (outgroups) that have infected non-human hosts. We discuss a possible evolutionary basis for these substitutions and provide a list of frequently substituted sites that potentially include future emerging variants in SARS-CoV-2.
X-ray scattering from light-driven spin fluctuations in a doped Mott insulator
Authors: Wang Yao , Chen Yuan , Devereaux Thomas P. , Moritz Brian , Mitrano Matteo 
Published: September 2021

AbstractManipulating spin fluctuations with ultrafast laser pulses is a promising route to dynamically control collective phenomena in strongly correlated materials. However, understanding how photoexcited spin degrees of freedom evolve at a microscopic level requires a momentum- and energy-resolved characterization of their nonequilibrium dynamics. Here, we study the photoinduced dynamics of finite-momentum spin excitations in two-dimensional Mott insulators on a square lattice. By calculating the time-resolved resonant inelastic x-ray scattering cross-section, we show that an ultrafast pump above the Mott gap induces a prompt softening of the spin excitation energy, compatible with a transient renormalization of the exchange interaction. While spin fluctuations in a hole-doped system (paramagnons) are well described by Floquet theory, magnons at half filling are found to deviate from this picture. Furthermore, we show that the paramagnon softening is accompanied by an ultrafast suppression of d-wave pairing correlations, indicating a link between the transient spin excitation dynamics and superconducting pairing far from equilibrium.
Reduced subgenomic RNA expression is a molecular indicator of asymptomatic SARS-CoV-2 infection
Authors: Wong Chee Hong , Ngan Chew Yee , Goldfeder Rachel L. , Idol Jennifer , Kuhlberg Chris , Maurya Rahul , Kelly Kevin , Omerza Gregory , Renzette Nicholas , De Abreu Francine , Li Lei , Browne Frederick A. , Liu Edison T. , Wei Chia-Lin 
Published: September 2021

Abstract
Background
It is estimated that up to 80% of infections caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are asymptomatic and asymptomatic patients can still effectively transmit the virus and cause disease. While much of the effort has been placed on decoding single nucleotide variation in SARS-CoV-2 genomes, considerably less is known about their transcript variation and any correlation with clinical severity in human hosts, as defined here by the presence or absence of symptoms.

Methods
To assess viral genomic signatures of disease severity, we conducted a systematic characterization of SARS-CoV-2 transcripts and genetic variants in 81 clinical specimens collected from symptomatic and asymptomatic individuals using multi-scale transcriptomic analyses including amplicon-seq, short-read metatranscriptome and long-read Iso-seq.

Results
Here we show a highly coordinated and consistent pattern of sgRNA expression from individuals with robust SARS-CoV-2 symptomatic infection and their expression is significantly repressed in the asymptomatic infections. We also observe widespread inter- and intra-patient variants in viral RNAs, known as quasispecies frequently found in many RNA viruses. We identify unique sets of deletions preferentially found primarily in symptomatic individuals, with many likely to confer changes in SARS-CoV-2 virulence and host responses. Moreover, these frequently occurring structural variants in SARS-CoV-2 genomes serve as a mechanism to further induce SARS-CoV-2 proteome complexity.

Conclusions
Our results indicate that differential sgRNA expression and structural mutational burden are highly correlated with the clinical severity of SARS-CoV-2 infection. Longitudinally monitoring sgRNA expression and structural diversity could further guide treatment responses, testing strategies, and vaccine development.
Selective HIF stabilization alleviates hepatocellular steatosis and ballooning in a rodent model of 70% liver resection
Authors: Iesari Samuele , Leclercq Isabelle , Joudiou Nicolas , Komuta Mina , Daumerie Aurélie , Ambroise Jérôme , Dili Alexandra , Feza-Bingi Natacha , Xhema Daela , Bouzin Caroline , Gallez Bernard , Pisani Francesco , Bonaccorsi-Riani Eliano , Gianello Pierre 
Published: September 2021

Abstract
Background: Small-for-size syndrome (SFSS) looms over patients needing liver resection or living-donor transplantation. Hypoxia has been shown to be crucial for the successful outcome of liver resection in the very early postoperative phase. While poorly acceptable as such in real-world clinical practice, hypoxia responses can still be simulated by pharmacologically raising levels of its transducers, the hypoxia-inducible factors (HIFs).
We aimed to assess the potential role of a selective inhibitor of HIF degradation in 70% hepatectomy (70%Hx).
Methods: In a pilot study, we tested the required dose of roxadustat to stabilize liver HIF1α. We then performed 70%Hx in 8-week-old male Lewis rats and administered 25 mg/kg of roxadustat (RXD25) at the end of the procedure. Regeneration was assessed: ki67 and 5-ethynyl-2′-deoxyuridine (EdU) immunofluorescent labeling, and histological parameters. We also assessed liver function via a blood panel and functional gadoxetate-enhanced magnetic resonance imaging (MRI), up to 47 h after the procedure. Metabolic results were analyzed by means of RNA sequencing (RNAseq).
Results: Roxadustat effectively increased early HIF1α transactivity. Liver function did not appear to be improved nor liver regeneration to be accelerated by the experimental compound. However, treated livers showed a mitigation in hepatocellular steatosis and ballooning, known markers of cellular stress after liver resection. RNAseq confirmed that roxadustat unexpectedly increases lipid breakdown and cellular respiration.
Conclusions: Selective HIF stabilization did not result in an enhanced liver function after standard liver resection, but it induced interesting metabolic changes that are worth studying for their possible role in extended liver resections and fatty liver diseases.
Incremental multi‐view correlated feature learning based on non‐negative matrix factorisation
Authors: Zhao Liang , Yang Tao , Zhang Jie , Chen Zhikui 
Published: September 2021

AbstractIn real‐world applications, large amounts of data from multiple sources come in the form of streams. This makes multi‐view feature learning cost much time when new instances rise incrementally. Dealing with these growing multi‐view data becomes a challenging problem. Some single‐view methods focus on processing the data dynamically, but they are not suitable for multi‐view data. Some online multi‐view methods are proposed to tackle it, but they ignore the influence of uncorrelated items in each view. Therefore, in this study, the authors propose a new algorithm, called Incremental Multi‐view Correlated Feature Learning (IMCFL) based on non‐negative matrix factorisation, to learn the common feature across views. By separating uncorrelated items of new instances and constructing incremental joint learning of correlated and uncorrelated features, the proposed IMCFL can eliminate the influence of uncorrelated information in the individual view and improve the effectiveness of incremental multi‐view common feature learning. Extensive experiments on real‐world datasets confirm its superiority by comparing it with other state‐of‐the‐art incremental and non‐incremental methods.
Learning spatial self‐attention information for visual tracking
Authors: Li Shengwu , Zhang Xuande , Xiong Jing , Ning Chenjing , Zhang Mingke 
Published: September 2021

AbstractVisual object tracking has been a fundamental topic in computer vision and many convolutional neural network (CNN) based trackers proposed in recent years have achieved state‐of‐the‐art performance, multi‐domain convolutional neural network (MDNet) is one of the most representative CNN‐based algorithms with high performance. In order to significantly improve the robustness and accuracy of the MDNet algorithm, a multi‐domain convolutional neural network based on spatial self‐attention information learning (SAMDNet) is proposed in this study. The authors use the spatial self‐attention module for the spatial information learning of the model. The spatial self‐attention module selectively aggregates the feature at each position by a weighted sum of the features at all positions. Under the control of self‐learning parameters in this module, spatial attention information can be flexibly acquired. The authors also propose a novel interval loss term to solve the problem of different classes with the same semantics in the training data. Finally, an anomaly detection module is carefully designed for relocation after the algorithm completely lost the target. Extensive experiments on the object tracking benchmark (OTB) and the visual object tracking challenge (VOT) benchmarks show that the proposed tracker outperforming most of the state‐of‐art trackers.
To wish you well: the biopolitical subjectivities of medical crowdfunders during and after Aotearoa New Zealand’s COVID-19 lockdown
Authors: Wardell Susan 
Published: September 2021

AbstractCrowdfunding platforms apply a marketized, competitive logic to healthcare, increasingly functioning as generative spaces in which worthy citizens and biopolitical subjects are produced. Using a lens of biopower, this article considers what sort of biopolitical subjectivities were produced in and through New Zealand crowdfunding campaigns during the 2020 COVID-19 lockdown. It focuses on a discursive and dialogical analysis of 59 online medical crowdfunding campaigns that were active during lockdown and chose to mention the pandemic. These pages pointed to interrelated biological, social and economic precarities, speaking to questions about how citizens navigate uneven needs during uncertain times. Findings showed that crowdfunders referred to the pandemic in order to narrate their own situation in culturally coherent ways and to establish context-specific relations of care. This included contextualising their needs through establishing shared crisis narratives that also made the infrastructural contexts of healthcare visible and performing relational labour in ways that aligned with nationally specific affective regimes. By highlighting their own vulnerability, crowdfunders strategically mobilised broader lockdown discourses of self-sacrifice on behalf of vulnerable people. In this way, New Zealand’s lockdown produced subjectivities both drawing on wider neoliberal moral regimes and specific to the nuanced and emergent moral systems of pandemic citizenship.
Phase lag index-based graph attention networks for detecting driving fatigue
Authors: Wang Zhongmin , Zhao Yupeng , He Yan , Zhang Jie 
Published: September 2021

It is important to understand the changes in the characteristics of the brain network in the state of driving fatigue and to reveal the pattern of functional connectivity between brain regions when fatigue occurs. This paper proposes a method for the detection of driving fatigue based on electroencephalogram (EEG) signals using a phase lag index graph attention network (PLI-GAT). Phase synchronization between EEG signals is a key attribute for establishing communication links among different regions of the brain, and so, the PLI is used to construct a functional brain network reflecting the relationship between EEG signals from different channels. Multi-channel EEG time–frequency features are then modeled as graph data, and the driving fatigue monitoring model is trained using a GAT. Compared with traditional graph neural networks, the GAT applies an aggregation operation to adjacent EEG channel features through the attention mechanism. This enables the adaptive assignment of different neighbor weights, which greatly improves the expressiveness of the graph neural network model. The proposed method is validated on the publicly available SEED-VIG dataset, and the accuracy of fatigue state recognition is found to reach 85.53%. The results show that the functional connectivity among different channels is significantly enhanced in the fatigue state.
High-speed 2D and 3D mid-IR imaging with an InGaAs camera
Authors: Potma Eric O. , Knez David , Ettenberg Martin , Wizeman Matthew , Nguyen Hai , Sudol Tom , Fishman Dmitry A. 
Published: September 2021

Recent work on mid-infrared (MIR) detection through the process of non-degenerate two-photon absorption (NTA) in semiconducting materials has shown that wide-field MIR imaging can be achieved with standard Si cameras. While this approach enables MIR imaging at high pixel densities, the low nonlinear absorption coefficient of Si prevents fast NTA-based imaging at lower illumination doses. Here, we overcome this limitation by using InGaAs as the photosensor. Taking advantage of the much higher nonlinear absorption coefficient of this direct bandgap semiconductor, we demonstrate high-speed MIR imaging up to 500 fps with under 1 ms exposure per frame, enabling 2D or 3D mapping without pre- or post-processing of the image.
Emotion metaphors in an awakening language
Authors: Amery Rob 
Published: September 2021

AbstractKaurna, the language of the Adelaide Plains, is an awakening language undergoing revival since 1989 (Amery 2016). Though little knowledge of Kaurna remains in the oral tradition and no sound recordings of the language as it was spoken in the nineteenth century exist, a surprising number and range of emotion terms were documented. A great many of these involve thetangka‘liver’ followed bykuntu‘chest’,wingku‘lungs’,yurni‘throat’ andyurlu‘forehead’, whilstmukamuka‘brain’ andyuri‘ear’ are involved in cognition. The role ofpultha‘heart’ is minimal. But these are not the only means to talk about emotions.Muiyu‘pit of the stomach’, a more elusive term, which may or may not be located in a body part andyitpi‘seed’ are also central to emotions. These three termstangka‘liver’,muiyu‘pit of the stomach’ andyitpi‘seed’, appear to be viewed byTeichelmann & Schürmann (1840)and especiallyTeichelmann (1857)as seats of emotion. In addition, there are a range of other means to express emotion, simple verbs and interjections.This paper will discuss in detail the historical documentation, its interpretation and the ways in which this documentation is used today. In the context of re-introducing a reclaimed language, such as Kaurna, how to talk about emotions can become the topic of serious and sometimes unresolved debate. The title of a book of poetry (Proctor & Gale 1997) ended up having two translations, one involvingtangka‘liver’ and the otherpultha‘heart’. Historical phrases expressing emotions are often co-opted in names, speeches, poetry and written texts.
Relationship between 316L steel powder characteristics and residual stress in additive manufactured builds
Authors: Hodek J , Vavřík J , Brázda M 
Published: September 2021

Abstract
This investigation involved cube samples created by an Additive Manufacturing (AM) process. Four commercially available AISI 316L powders with a particle size range of 50-150 μm were used to produce four cube-shapes samples using Direct Energy Deposition (DED) in the industrial metal 3D printer InssTek MX-600. The contour method (CM), a destructive stress relaxation method, was used to determine the residual stress distribution on the cross-section. The results illustrate the impact of the powders on residual stress distribution after DED additive process.
Analysis of the relationship between changes in mechanical properties and precipitation in SUPER 304H steel during its exposure
Authors: Horváth J , Horváthová M , Pilsová L , Smola V , Chvostová E , Janovec J 
Published: September 2021

Abstract
Aim of the article is to provide properties comparison between initial state and two thermally exposed states of creep resistant steel SUPER 304H by usage of conventional and miniaturised tensile test specimens. Tests were performed at room temperature. Thermally exposed material was aged by 15 and 30 thousand hours at 675°C. This exposition which simulated accelerated operation exposition caused precipitation of intermetallic phases which affect mechanical properties like ultimate strength and elongation. The performed tests showed a decrease in elongation and ultimate strength between the first exposed state and initial state followed by partial increase of both tested values for the second exposed state. Sigma phase precipitation was confirmed for the exposed samples. The presence of the sigma phase also led to a change in the fracture morphology from full ductile (initial state) to combined ductile with the presence of brittle particle cleavage (exposed states). A comparison of the tests performed on classical and miniaturized test samples proved the possibilities of using miniaturized samples both for the basic material and for the exposed ones.
Material Properties of Steel with NiCr-Cold Spray Coating
Authors: Chocholousek M , Spirit Z , Brom J 
Published: September 2021

Abstract
The work is aimed on the NiCr-Cold spray coating applied on GOST 08CH18N10T steel and GOST 22K steel. Cold spray coating shows a high cohesion even as a few millimeter thick layer, therefore it has potential for the repairs not only of the energy industry components. Applied on the steel substrate, the cold spray can be considered as a bimetallic material for the purpose of the mechanical properties evaluation. Performed comparison based on tensile mechanical properties at room temperature and at 350 °C of separate steels and cold spray versus bimetallic combination is discussed. The main goal is to find the optimal approach of bimetallic material evaluation. Additional metallographic and microstructural analysis is attached to show the differences between the used combinations. Influence of possible heat treatment on the mechanical and adhesive properties is also included.