cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Flexible and scalable particle-in-cell methods for massively parallel computations
Creators: name: Gassmoeller, R.
name: Heien, E.
name: Puckett, E. G.
name: Bangerth, W.
Publisher: name: arXiv
Year: 2016
Subjects: subject: Numerical Analysis (math.NA)
subject: Computational Physics (physics.comp-ph)
subject: FOS: Mathematics
subject: FOS: Physical sciences

description: Particle-in-cell methods couple mesh-based methods for the solution of continuum mechanics problems, with the ability to advect and evolve particles. They have a long history and many applications in scientific computing. However, they have most often only been implemented for either sequential codes, or parallel codes with static meshes that are statically partitioned. In contrast, many mesh-based codes today use adaptively changing, dynamically partitioned meshes, and can scale to thousands or tens of thousands of processors. Consequently, there is a need to revisit the data structures and algorithms necessary to use particle methods with modern, mesh-based methods. Here we review commonly encountered requirements of particle-in-cell methods, and describe efficient ways to implement them in the context of large-scale parallel finite-element codes that use dynamically changing meshes. We also provide practical experience for how to address bottlenecks that impede the efficient implementation of these algorithms and demonstrate with numerical tests both that our algorithms can be implemented with optimal complexity and that they are suitable for very large-scale, practical applications. We provide a reference implementation in ASPECT, an open source code for geodynamic mantle-convection simulations built on the deal.II library.
Anti-virulence strategy of diaryl chalcogenide compounds against Candida albicans infection
Creators: name: Song, Shihao
name: Zhao, Shuo
name: Sun, Xiuyun
name: Meng, Lili
name: Wang, Zijie
name: Tan, Huihui
name: Liu, Jingyun
name: Zhang, Min
name: Deng, Yinyue
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Pharmacology
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: Candida albicans is an important opportunistic pathogenic fungus that frequently causes serious systemic infection in humans. Due to the vital roles of biofilm formation and the yeast-to-hypha transition in the infection process, we have selected a series of diaryl chalcogenides and tested their efficacy against C. albicans SC5314 pathogenicity by the inhibition of biofilm formation and the yeast-to-hypha transition. The compounds 5-sulfenylindole and 5-selenylindole were found to have excellent abilities to inhibit both biofilm formation and hyphal formation in C. albicans SC5314. Intriguingly, the two leading compounds also markedly attenuated C. albicans SC5314 virulence in human cell lines and mouse infection models at micromolar levels. Furthermore, our results showed that the presence of the compounds at 100 µM resulted in a marked decrease in the expression of genes involved in the cAMP-PKA and MAPK pathways in C. albicans SC5314. Intriguingly, the compounds 5-sulfenylindole and 5-selenylindole not only attenuated the cytotoxicity of Candida species strains but also showed excellent synergistic effects with antifungal agents against the clinical drug-resistant C. albicans strain HCH12. The compound 5-sulfenylindole showed an obvious advantage over fluconazole as it could also restore the composition and richness of the intestinal microbiota in mice infected by C. albicans. Together, these results suggest that diaryl chalcogenides can potentially be designed as novel clinical therapeutic agents against C. albicans infection. The diaryl chalcogenides of 5-sulfenylindole and 5-selenylindole discovered in this study can provide new direction for developing antifungal agents against C. albicans infection.
The Sequential Normal Scores Transformation
Creators: name: Conover, W. J.
name: Tercero, Victor G.
name: Cordero-Franco, Alvaro E.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Statistics Theory (math.ST)
subject: FOS: Mathematics
subject: 62L10, 62Gxx

description: The sequential analysis of series often requires nonparametric procedures, where the most powerful ones frequently use rank transformations. Re-ranking the data sequence after each new observation can become too intensive computationally. This led to the idea of sequential ranks, where only the most recent observation is ranked. However, difficulties finding, or approximating, the null distribution of the statistics may have contributed to the lack of popularity of these methods. In this paper, we propose transforming the sequential ranks into sequential normal scores which are independent, and asymptotically standard normal random variables. Thus original methods based on the normality assumption may be used. A novel approach permits the inclusion of a priori information in the form of quantiles. It is developed as a strategy to increase the sensitivity of the scoring statistic. The result is a powerful convenient method to analyze non-normal data sequences. Also, four variations of sequential normal scores are presented using examples from the literature. Researchers and practitioners might find this approach useful to develop nonparametric procedures to address new problems extending the use of parametric procedures when distributional assumptions are not met. These methods are especially useful with large data streams where efficient computational methods are required.
description: 39 pages, 8 figures
Additional file 1 of Duplex-specific nuclease and Exo-III enzyme-assisted signal amplification cooperating DNA-templated silver nanoclusters for label-free and sensitive miRNA detection
Creators: name: Liu, Hongli
name: Zhu, Changqiong
name: Mou, Chunyan
Publisher: name: figshare
Year: 2022
Subjects: subject: Biochemistry
subject: Space Science
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Additional file 1. Table S1. Details of the nucleic acids used in this research. Fig S1. Optimization of incubation time. (A) Fluorescence signal of the approach with different concentrations of Exo-III enzyme. (B) Fluorescence intensity of the approach with different incubation time of Exo-III enzyme. Fig S2. Fluorescence intensity of the approach when detecting 10 technical duplicates.
A connection between MAX $κ$-CUT and the inhomogeneous Potts spin glass in the large degree limit
Creators: name: Jagannath, Aukosh
name: Ko, Justin
name: Sen, Subhabrata
Publisher: name: arXiv
Year: 2017
Subjects: subject: Probability (math.PR)
subject: Combinatorics (math.CO)
subject: FOS: Mathematics

description: We study the asymptotic behavior of the Max $κ$-cut on a family of sparse, inhomogeneous random graphs. In the large degree limit, the leading term is a variational problem, involving the ground state of a constrained inhomogeneous Potts spin glass. We derive a Parisi type formula for the free energy of this model, with possible constraints on the proportions, and derive the limiting ground state energy by a suitable zero temperature limit.
Efficient FPGA implementation of elliptic curve scalar multiplication over the binary field
Creators: name: Ruangsantikorakul, Kuntapong
Publisher: name: Macquarie University
Year: 2022
Subjects: Other education not elsewhere classified

description: Elliptic curve cryptography (ECC) is the more efficient alternative to the widely used Ron Rivest, Adi Shamir and Leonard Adleman (RSA) cryptosystem since 283 bit ECC provides the same security per bit as 3072 bit RSA. This makes it useful for resource constrained portable devices since smaller operands can be used. For practical use of ECC, an efficient hardware implementation must be achieved in terms of area and time. Elliptic curve scalar multiplication (ECSM) is the crucial operation required for ECC processors. The goal of this research is the implementation of area efficient and high speed ECSM over a binary field in in field-programmable gate array (FGPA) technology.
The role of couple variables in modulating the relationship between patient's psychological traits or states and the experience of chronic pain: protocol of a mapping review
Creators: name: Giusti, Emanuele Maria
name: Fratini, Giulia
name: Varallo, Giorgia
name: Manna, Chiara
name: Mosti, Cristian
name: Confalonieri, Alessia
name: Castelnuovo, Gianluca
Publisher: name: Zenodo
Year: 2022

description: Protocol of the mapping review "The role of couple variables in modulating the relationship between patient’s psychological traits or states and the experience of chronic pain: a mapping review"
Preventable ADRs leading to hospitalization — results of a long-term prospective safety study with 6,427 ADR cases focusing on elderly patients
Creators: name: S Schmiedl
name: M Rottenkolber
name: J Szymanski
name: B Drewelow
name: W Siegmund
name: M Hippius
name: K Farker
name: I R Guenther
name: J Hasford
name: P A Thuermann
Publisher: name: Taylor & Francis
Year: 2017
Subjects: subject: Medicine
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Cancer
subject: Science Policy
subject: 111714 Mental Health
subject: FOS: Health sciences

description: Background: Studies evaluating the impact of age and potentially inappropriate medication (PIM) on avoidable adverse drug reactions (ADRs) are scarce. Methods: In this prospective, multi-center, long-term (8.5 years) observational study, we analysed ADRs leading to hospitalization in departments of internal medicine. ADRs causality and preventability were assessed using standardised algorithms. PIM was defined based on the PRISCUS-list. Multivariate analyses and estimation of ADR incidence rates were conducted. Results: Of all 6,427 ADR patients, a preventable ADR was present in 1,253 (19.5%) patients (elderly patients ≥70 years: 828). Risk factors for preventable ADRs in elderly patients were multimorbidity, two to four ADR-causative drugs, and intake of particular compounds (e.g. spironolactone) but not sex, PIM usage, or the total number of drugs. Regarding particular compounds associated with preventable ADRs, highest incidence rates for preventable ADRs were found for patients aged ≥70 years for spironolactone (3.3 per 1,000 exposed persons (95% CI: 1.4–6.6)) and intermediate-acting insulin (3.3 per 1,000 exposed persons (95% CI: 1.6–6.1)). Conclusion: Avoiding PIM usage seems to be of limited value in increasing safety in elderly patients whereas our results underline the importance of an individualized medication review of the most commonly implicated drugs in preventable ADRs (supported by BfArM FoNr: V-11337/68605/2008–2010).
Additional file 4 of Nonlinear association between changes in fasting plasma glucose and the incidence of diabetes in a nondiabetic Chinese cohort
Creators: name: Huang, Chenghu
name: Ren, Chenhong
name: Xuan, Xiuping
name: Luo, Yi
name: Peng, Caibi
Publisher: name: figshare
Year: 2022
Subjects: Biochemistry
Medicine
Biotechnology
Chemical Sciences not elsewhere classified
Biological Sciences not elsewhere classified
Developmental Biology
Science Policy

description: Additional file 4: Table S1. Baseline characteristic of participants according to sex.
Gender reshaping genre in Aurora Leigh
Creators: name: Rooney, Melissa
Publisher: name: Macquarie University
Year: 2022
Subjects: Other education not elsewhere classified

description: Elizabeth Barrett Browning’s Aurora Leigh is an important nineteenth-century, female-authored epic that has had a significant impact on the way gender is defined within the epic genre. Before the publication of Aurora Leigh, gender representations in epic were defined by the seminal work of the genre, Homer’s Iliad, which focuses on stereotypically masculine concerns such as war, nationhood and male relationships in a world where status is gained through competitiveness. Aurora Leigh reconfigures these epic and heroic conventions into a form more suited to her female protagonist. This research responds to the current lack of dedicated analysis into the broader influence of gender on the epic tradition and will show how gender representations in Aurora Leigh deviate from the traditional epic model as defined by The Iliad. Aurora Leigh reframes the epic in three significant ways that make female representation and discourse more viable. Barratt Browning reshapes the heart of the epic by inserting into it her female protagonist; by the reframing of the locale to the domestic and wider world of nineteenth-century English social politics; and through the personalisation of the narration from the third person omniscient bard to an internalised individualistic first-person narrative. Through these processes of feminisation, Barrett Browning challenges and remodels the widely held belief that the epic is a genre that is inherently and exclusively equipped to sing of arms and the man, or of the ways of God and man.
Type 1,1-operators defined by vanishing frequency modulation
Creators: name: Johnsen, Jon
Publisher: name: arXiv
Year: 2017
Subjects: subject: Analysis of PDEs (math.AP)
subject: FOS: Mathematics
subject: 35S05

description: This paper presents a general definition of pseudo-differential operators of type $1,1$; the definition is shown to be the largest one that is both compatible with negligible operators and stable under vanishing frequency modulation. Elaborating counter-examples of Ching, Hörmander and Parenti--Rodino, type $1,1$-operators with unclosable graphs are proved to exist; others are shown to lack the microlocal property as they flip the wavefront set of an almost nowhere differentiable function. In contrast the definition is shown to imply the pseudo-local property, so type 1,1-operators cannot create singularities but only change their nature. The familiar rule that the support of the argument is transported by the support of the distribution kernel is generalised to arbitrary type $1,1$-operators. A similar spectral support rule is also proved. As no restrictions appear for classical type $1,0$-operators, this is a new result which in many cases makes it unnecessary to reduce to elementary symbols. As an important tool, a convergent sequence of distributions is said to converge regularly if it moreover converges as smooth functions outside the singular support of the limit. This notion is shown to allow limit processes in extended versions of the formula relating operators and kernels.
description: 41 pages. Accepted version, with a few minor misprints corrected. Appeared in 2008, New development in pseudo-differential operators (eds. L. Rodino, M. W. Wong). Operator theory: Advances and applications, vol. 189, 201-246. Birkh\"auser 2008
Resistin secreted by porcine alveolar macrophages leads to endothelial cell dysfunction during Haemophilus parasuis infection
Creators: name: Hua, Kexin
name: Li, Tingting
name: He, Yanling
name: Guan, Aohan
name: Chen, Liying
name: Gao, Yuan
name: Xu, Qianshuan
name: Wang, Haoyu
name: Luo, Rui
name: Zhao, Ling
name: Jin, Hui
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Space Science
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Physiology
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Haemophilus parasuis (H. parasuis) causes exudative inflammation, implying endothelial dysfunction during pathogen infection. However, so far, the molecular mechanism of endothelial dysfunction caused by H. parasuis has not been clarified. By using the transwell-based cell co-culture system, we demonstrate that knocking out resistin in porcine alveolar macrophages (PAMs) dramatically attenuated endothelial monolayer damage caused by H. parasuis. The resistin secreted by PAMs inhibited the expression of the tight junction proteins claudin-5 and occludin rather than the adherens junction protein VE-cadherin in co-cultured porcine aortic endothelial cells (PAECs). Furthermore, we demonstrate that resistin regulated claudin-5 and occludin expression and monolayer PAEC permeability in an LKB1/AMPK/mTOR pathway-dependent manner. Additionally, we reveal that the outer membrane lipoprotein gene lppA in H. parasuis induced resistin expression in PAMs, as deleting lppA reduced resistin expression in H. parasuis-infected PAMs, causing a significant change in LKB1/AMPK/mTOR pathway activity in co-cultured PAECs, thereby restoring tight junction protein levels and endothelial monolayer permeability. Thus, we postulate that the H. parasuis lppA gene enhances resistin production in PAMs, disrupting tight junctions in PAECs and causing endothelial barrier dysfunction. These findings elucidate the pathogenic mechanism of exudative inflammation caused by H. parasuis for the first time and provide a more profound angle of acute exudative inflammation caused by bacteria.
Verilog-A modelling of transistor
Creators: name: Yang, Zhili
Publisher: name: Macquarie University
Year: 2022
Subjects: Other education not elsewhere classified

description: Industry standard transistor models used for computer aided circuit design are not always accurately predicting transistor performance under all circuit conditions ,include RF and analog circuit behavior. Transistor model are expected not only circuit performance but also reliability and accuracy. Improved accuracy may need concern access to the internal currents and voltages of the transistor or add extra internal features such as low-frequency noise sources. Circuits that have very stringent accuracy requirements require modeling techniques with higher accuracy. In contrast, Verilog-A enables full control of transistor model and can be integrated with the circuit design software. This document report present show effective approach to investigate and implement our transistor model in two different environments - AWR and Verilog-A. This is useful for circuit-level design purposes to allow the designer manipulates transistor models have direct access to model equation sets and program structure. A comparison of results between simulation and measurements to transistor model has been illustrated in details.
Additional file 5 of Nonlinear association between changes in fasting plasma glucose and the incidence of diabetes in a nondiabetic Chinese cohort
Creators: name: Huang, Chenghu
name: Ren, Chenhong
name: Xuan, Xiuping
name: Luo, Yi
name: Peng, Caibi
Publisher: name: figshare
Year: 2022
Subjects: Biochemistry
Medicine
Biotechnology
Chemical Sciences not elsewhere classified
Biological Sciences not elsewhere classified
Developmental Biology
Science Policy

description: Additional file 5: Supplemental Table 2. The proportion of diagnosed diabetics in different stages of FPG changes and different genders.
Bayesian model combining linkage and linkage disequilibrium analysis for low density-based genomic selection in animal breeding
Creators: name: Fabyano Fonseca Silva
name: Elcer Albenis Zamora Jerez
name: Resende, Marcos Deon Vilela De
name: Viana, José Marcelo Soriano
name: Azevedo, Camila Ferreira
name: Lopes, Paulo Sávio
name: Moysés Nascimento
name: Lima, Rodrigo Oliveira De
name: Guimarães, Simone Eliza Facioni
Publisher: name: Taylor & Francis
Year: 2017
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics

description: We combined linkage (LA) and linkage disequilibrium (LDA) analyses (emerging the term ‘LALDA’) for genomic selection (GS) purposes. The models were fitted to a simulated dataset and to a real data of feed conversion ratio in pigs. Firstly, the significant QTLs (quantitative trait locus) were identified through LA-based mixed models considering the QTL-genotypes as random effects by means of genotypic identity by descent matrix. This matrix was calculated at the positions of significant QTLs (based on LA) allowing to include the QTL-genotype effects additionally to SNP (single nucleotide polymorphism) markers (based on LDA) and additive polygenic effects in several GS models (Bayesian Ridge Regression – BRR; Bayes A – BA; Bayes B – BB; Bayes C – BC and Bayesian LASSO – BL). These models combing all mentioned effects were denominated LALDA. Goodness-of-fit and predictive ability analyses were performed to evaluate the efficiency of these models. For the real data, although slightly, the superiority of the LALDA models was verified in comparison to traditional LDA models for GS. For the simulated dataset, the models presented similar results. For both LDA and LALDA frameworks, BA showed the best fitting through Deviance Information Criterion and higher predictive ability in the simulated and real datasets.
The relationship between personality, individual differences and the experience of emotions evoked by music that elicits visual mental imagery: project thesis
Creators: name: Day, Robina Anne
Publisher: name: Macquarie University
Year: 2022
Subjects: Other education not elsewhere classified

description: Investigators suggest that there are at least eight possible mechanisms underlying the emotional responses that many individuals experience when listening to music. One proposed mechanism is visual imagery. It is thought that due to the contiguity of visual and auditory information, strong associations develop between these two modalities so that musical sounds may evoke visual mental images, which in turn may arouse certain feelings such as happiness and surprise. As individuals vary in their ability to experience visual mental imagery, it follows that these individual differences are evident when people listen to music. The aim of this project was to explore individual differences that may predict visual mental imagery while listening to music that induces a variety of emotions in the listener. One hundred and twenty first-year psychology participants completed a battery of self-report questionnaires which were designed to assess current mood and specific personality traits such as absorption and empathy and trait visual imagery. Participants also listened to four musical excerpts previously rated as representing Happy, Scary, Sad and Angry discrete emotions and recorded responses after each excerpt. Qualitative data for visual imagery experiences were collected. Regression analyses indicated that Absorption was predictive of Intensity of Visual Imagery for Happy, Scary and Angry music, while Fantasy (Interpersonal Reactivity Index; Davis, 1980);, NA (PANAS; Watson, Clark & Tellegen,1988) and rBAS (revised Behavioural Activation Scale; Jackson, 2009), predicted Intensity of Emotion Felt for these stimuli. However a different pattern emerged for Sad music as Trait Imagery, along with Fantasy and Absorption were predictive of the two DVs. Results for the Sad stimulus also contrasted with those for the other three stimuli in the repeated-measures ANOVAs that were conducted. Finally, the qualitative data indicated that subjective visual imagery experiences of the participants were most detailed and vivid for the Sad 3 music condition. Therefore the results of this study provide support for the view that sad music elicits more complex and aesthetic feelings and also provide tentative support for the hypothesis that visual imagery may be one of the psychological mechanisms involved in the musical elicitation of emotions.
Geometrically finite amalgamations of hyperbolic 3-manifold groups are not LERF
Creators: name: Sun, Hongbin
Publisher: name: arXiv
Year: 2017
Subjects: subject: Geometric Topology (math.GT)
subject: Group Theory (math.GR)
subject: FOS: Mathematics
subject: 20E26, 57M05, 57M50, 22E40

description: We prove that, for any two finite volume hyperbolic $3$-manifolds, the amalgamation of their fundamental groups along any nontrivial geometrically finite subgroup is not LERF. This generalizes the author's previous work on nonLERFness of amalgamations of hyperbolic $3$-manifold groups along abelian subgroups. A consequence of this result is that closed arithmetic hyperbolic $4$-manifolds have nonLERF fundamental groups. Along with the author's previous work, we get that, for any arithmetic hyperbolic manifold with dimension at least $4$, with possible exceptions in $7$-dimensional manifolds defined by the octonion, its fundamental group is not LERF.
description: 29 pages
Vocalisations of captive Sumatran tigers (Panthera tigris sumatrae)
Creators: name: Rose, Shanna J.
Publisher: name: Macquarie University
Year: 2022
Subjects: Other education not elsewhere classified

description: Wild tigers (Panthera tigris) are endangered with populations continuing to decline primarily due to humans. Acoustic communication research is a recommended enhancement to current tiger conservation efforts. Tiger acoustic communication research is extremely limited with a solitary study quantifying a single tiger call. This study investigated the acoustic characteristics and behavioural context of tiger vocalisations. Remote audio recordings of five captive Sumatran tigers (Panthera tigris sumatrae) in two separate enclosures at Taronga Zoo, NSW Australia were obtained March-July 2014 and reviewed with sound analysis software. Tigers were most vocal between 0100-1100 hours. From peak vocalisation times, 547 high quality recordings of tiger vocalisations were separated into seven vocalisation types (‘moan’, ‘arf’, ‘mrr’, ‘chuff’, ‘growl’, ‘roar’, and ‘hiss’). Tiger experts provided suggested contexts and functions for these vocalisations. Classification of frequent laryngeal sounds including moan, arf, and mrr were verified with a multinomial logistic regression based on peak frequency (Hz), fundamental frequency (Hz) and duration (s) measurements. This research represents the first quantitative study of multiple tiger vocalisations. Descriptive literature on tiger communication lacks ‘mrr’ and ‘arf’ descriptions and acoustic characteristics of tiger vocalisations. Future research is needed to standardize vocalisation terms and further quantify the tiger vocal repertoire.
Patterns of hepatitis b virus immune escape and pol/rt mutations across clinical cohorts of patients with genotypes a, e and occult hepatitis b infection in Nigeria: A multi-centre study
Creators: name: Osasona, Oluwadamilola G.
name: Oguntoye, Oluwatosin O.
name: Arowosaye, Abiola O.
name: Abdulkareem, Lukman O.
name: Adewumi, Moses O.
name: Happi, Christian
name: Folarin, Onikepe
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: Hepatitis B virus (HBV) immune escape and Pol/RT mutations account for HBV immunoprophylactic, therapeutic, and diagnostic failure globally. Little is known about circulating HBV immune escape and Pol/RT mutants in Nigeria. This study focused on narrowing the knowledge gap of the pattern and prevalence of the HBV mutants across clinical cohorts of infected patients in southwestern Nigeria. Ninety-five enrollees were purposively recruited across clinical cohorts of HBV-infected patients with HBsAg or anti-HBc positive serological outcome and occult HBV infection. Total DNA was extracted from patients’ sera. HBV S and Pol gene-specific nested PCR amplification was carried out. The amplicons were further sequenced for serotypic, genotypic, phylogenetic, and mutational analysis. HBV S and Pol genes were amplified in 60 (63.2%) and 19 (20%) of HBV isolates, respectively. All the sixty HBV S gene and 14 of 19 Pol gene sequences were exploitable. The ayw4 serotype was predominant (95%) while ayw1 serotype was identified in 5% of isolates. Genotype E predominates in 95% of sequences, while genotype A, sub-genotype A3 was observed in 5%. Prevalence of HBV IEMs in the “a” determinant region was 29%. Commonest HBV IEM was S113T followed by G145A and D144E. The Pol/RT mutations rtV214A and rtI163V among others were identified in this study. This study provided data on the occurrence of existing and new HBV IEMs and Pol gene mutations in Nigeria.
Vegetation and soil seed bank in a 23-year grazing exclusion chronosequence in a Mediterranean dry grassland
Creators: name: A. Saatkamp
name: F. Henry
name: T. Dutoit
Publisher: name: Taylor & Francis
Year: 2017
Subjects: subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: FOS: Biological sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Plant Biology
subject: 60506 Virology

description: Long-term grazing shaped plant diversity in dry Mediterranean grasslands. Abandonment of grazing affects plant diversity especially in the northern Mediterranean. Considerable efforts are, therefore, under way for grassland conservation and restoration. Yet, we do not know at which temporal scales impacts of grazing abandonment appear and in particular how soil seed banks evolve after longer grazing abandonment. Here, we provide detailed data from one of the very few long-term experiments available. These experiments provide data for up to 23 years (1982–2005) of grazing exclusion built in 1982, 1989, 2000 and 2001. Grazing exclusion decreased species richness, modified vegetation structure and changed soil parameters. Decline in species richness appears in communities that experienced 16 and 23 years of grazing exclusion. Only four to nine plant species of this Mediterranean grassland built persistent soil seed banks appearing after grazing exclusion, compared to 40–50 species in the established vegetation of grazed plots. Hence, similarity between vegetation and soil seed bank decreased with time of grazing exclusion. Even 23 years after abandonment, no woody plants colonised the experiments. We conclude that vegetation will recover fast from grazing abandonment in the short-term. Nevertheless, longer abandonment will impact diversity due to reduced soil seed banks.
Substrate engineering for high quality emission of free and localized excitons from atomic monolayers in hybrid architectures
Creators: name: Iff, Oliver
name: He, Yu-Ming
name: Lundt, Nils
name: Stoll, Sebastian
name: Baumann, Vasilij
name: Höfling, Sven
name: Schneider, Christian
Publisher: name: arXiv
Year: 2017
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Atomic monolayers represent a novel class of materials to study localized and free excitons in two dimensions and to engineer optoelectronic devices based on their significant optical response. Here, we investigate the role of the substrate on the photoluminescense response of MoSe$_2$ and WSe$_2$ monolayers exfoliated either on SiO$_2$ or epitaxially grown InGaP substrates. In the case of MoSe$_2$, we observe a significant qualitative modification of the emission spectrum, which is widely dominated by the trion resonance on InGaP substrates. However, the effects of inhomogeneous broadening of the emission features are strongly reduced. Even more strikingly, in sheets of WSe$_2$, we could routinely observe emission lines from localized excitons with linewidths down to the resolution limit of 70\,$μ$ eV. This is in stark contrast to reference samples featuring WSe$_2$ monolayers on SiO$_2$ surfaces, where the emission spectra from localized defects are widely dominated by spectral diffusion and blinking behaviour. Our experiment outlines the enormous potential of III-V-monolayer hybrid architectures to obtain high quality emission signals from atomic monolayers, which are straight forward to integrate into nanophotonic and integrated optoelectronic devices.
Investigating different typologies for the synthesis of evidence: a scoping review protocol
Creators: name: Pollock, danielle
name: Munn, Zachary
Publisher: name: Open Science Framework
Year: 2022

description: Abstract Objective: The objective of this scoping review is to identify evidence synthesis types and previously proposed classification systems, typologies or taxonomies that have guided evidence synthesis. Introduction Evidence synthesis is a constantly evolving field. There is now a plethora of evidence synthesis approaches used across many different disciplines. Historically there have been numerous attempts to organize the types and methods of evidence synthesis in the form of classification systems, typologies or taxonomies. This scoping review will seek to identify all the available classification systems, typologies or taxonomies, how they were developed, their characteristics, and the types of evidence synthesis included within them. Inclusion Criteria This scoping review will include discussion papers, commentaries, books, editorials, manuals, handbooks, and guidance from major organizations that describe multiple approaches to evidence synthesis. Methods: The Evidence Synthesis Taxonomy Initiative will support this scoping review. The search strategy will aim to locate both published and unpublished documents utilizing a three-step search strategy. An exploratory search of MEDLINE (Ovid) has identified key words and MeSH terms. A second search of MEDLINE (Ovid); Embase (Elsevier); CINAHL with full text (EBSCO); ERIC (EBSCO); Scopus (Elsevier); Compendex (Elsevier) and JSTOR will be conducted. Relevant evidence synthesis organisations will be searched. Identified documents will be independently screened, selected, and extracted by two researchers and the data will be presented in tables and summarized descriptively.
Life in the big city: identifying bandicoot presence in the urban matrix
Creators: name: Elwood, Sonja
Publisher: name: Macquarie University
Year: 2022
Subjects: Other education not elsewhere classified

description: The greater Sydney region provides habitat for two species of Peramelidae, the southern brown (Isoodon obesulus obesulus) and long-nosed bandicoot (Perameles nasuta). Both species have suffered significant range contraction since colonisation, yet little is known of their ecology and behavior. The endangered southern brown bandicoot is found only in Sydney's northern national parks and is rarely sighted. The long-nosed bandicoot is listed as endangered in Sydney's inner west and Manly's North Head yet is a common exploiter of lawns and parks in other suburbs adjoining national parks. This study used GIS mapping and statistical analyses to examine five urban land use and four demographic variables likely influencing bandicoot presence in the Sydney urban matrix. Datasets include previously unused wildlife rescue and Council records mapped in five-year time slices over the past twenty-five years. The quality of datasets proved insufficient to establish significant relationships with all but one land-use variable, agricultural and rural lands, which showed a strongly negative association with bandicoot observations. This study demonstrates greater quality, larger scale datasets and the principles of ecologically sustainable development are necessary to make informed policy and planning decisions if longnosed bandicoots are to be sustained within the intensifying Sydney urban landscape.
Mechanical performance of 3D- printed Ti-6Al-4V
Creators: name: Yu, Yuefeng
Publisher: name: Macquarie University
Year: 2022
Subjects: Other education not elsewhere classified

description: Titanium alloys have a wide range of applications in industry, especially in the aerospace industry and biomechanical applications. Ti-6Al-4V is an α-β phase titanium alloy with high strength, low weight ratio and high corrosive resistance. The traditional manufacturing of such an alloy takes plenty of time and money to achieve required features when compared to the 3D-printed method. 3D printing is famous for the efficiency as well as the geometry shape it can create, but there are lots of settings when manufacturing it, such as the thickness of the layer and the moving speed of the nozzle. In this paper, samples with 60μm layer thickness and 1029mm/s scanning speed using the selective laser melting (SLM) method will be studies, and focus on the harness mapping along the building direction before and after heat treatment as well as the microstructure. The connection between the dimensions of the samples and their related mechanical features will be discussed as well.
An ALMA survey of submillimetre galaxies in the Extended Chandra Deep Field South: Spectroscopic redshifts
Creators: name: Danielson, Alice
name: Swinbank, Mark
name: Smail, Ian
name: Simpson, James
name: Casey, Catlin
name: Chapman, Scott
name: Da Cunha, Elisabete
name: Hodge, Jackie
name: Walter, Fabian
name: Wardlow, Julie
name: Alexander, Dave
name: Brandt, Niel
name: de Breuck, Carlos
name: Coppin, Kristen
name: Dannerbauer, Helmut
name: Dickinson, Mark
name: Edge, Alastair
name: Gawiser, Eric
name: Ivison, Rob
name: Karim, Alex
name: Kovacs, Attila
name: Lutz, Dieter
name: Menten, Karl
name: Schinnerer, Eva
name: Weiss, Axel
name: van der Werf, Paul
Publisher: name: arXiv
Year: 2017
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We present spectroscopic redshifts of S(870)>2mJy submillimetre galaxies (SMGs) which have been identified from the ALMA follow-up observations of 870um detected sources in the Extended Chandra Deep Field South (the ALMA-LESS survey). We derive spectroscopic redshifts for 52 SMGs, with a median of z=2.4+/-0.1. However, the distribution features a high redshift tail, with ~25% of the SMGs at z>3. Spectral diagnostics suggest that the SMGs are young starbursts, and the velocity offsets between the nebular emission and UV ISM absorption lines suggest that many are driving winds, with velocity offsets up to 2000km/s. Using the spectroscopic redshifts and the extensive UV-to-radio photometry in this field, we produce optimised spectral energy distributions (SEDs) using Magphys, and use the SEDs to infer a median stellar mass of M*=(6+/-1)x10^{10}Msol for our SMGs with spectroscopic redshifts. By combining these stellar masses with the star-formation rates (measured from the far-infrared SEDs), we show that SMGs (on average) lie a factor ~5 above the main-sequence at z~2. We provide this library of 52 template fits with robust and well-sampled SEDs available as a resource for future studies of SMGs, and also release the spectroscopic catalog of ~2000 (mostly infrared-selected) galaxies targeted as part of the spectroscopic campaign.
description: 26 pages; 15 figures. Accepted for publication in ApJ. Redshift catalogs, spectra and SED templates available from: http://astro.dur.ac.uk/~ams/zLESS/
Potential for conservation use for the Minas Gerais State, Brazil
Creators: name: Gorgens, Eric Bastos
name: Mucida, Danielle Piuzana
name: Silva, Ricardo Siqueira
name: Matozinhos, Cristiano Christófaro
name: Costa, Adriana Monteiro
name: Morais, Marcelino Santos
name: Pereira, Israel Marinho
Publisher: name: Zenodo
Year: 2021
Subjects: agriculture
soil conservation
water recharge

description: [en] To compute the potential for conservation use, we implemented the methodology PUC which assigns to the lithology levels, soil class, and slope a score between 1 and 5. The score reflects the potential for water recharge, agricultural use, and resistance to erosion (Costa et al., 2017). The potential for agricultural use is associated with drainage, fertility, and effective soil depth. Drainage is related to the capacity of supplying water and oxygen to the soil; fertility is related to the natural availability of the soil to provide nutrients, and the effective depth is related to space for the development of the root system and internal drainage of the profile. The water recharge and the erosion resistance took into account the runoff rate and the opportunity time to water infiltration. [pt] Para realizar o diagnóstico do potencial de uso conservacionista foi utilizado o método PUC que classifica o terreno atribuindo uma nota que varia entre 1 e 5 com base em informações de litologia, classe de solo e declividade. Esta nota reflete o potencial de recarga hídrica, o potencial para uso agropecuário e a resistência à erosão. O potencial de uso agropecuário é associado à drenagem, fertilidade e profundidade efetiva. A drenagem, por sua vez, está relacionada à capacidade de suprimento de água e de oxigênio para o solo; a fertilidade está relacionada à disponibilidade natural de nutrientes; e a profundidade efetiva está relacionada ao espaço para o desenvolvimento do sistema radicular e drenagem interna do perfil. A recarga hídrica e a resistência à erosão levaram em consideração a velocidade de escoamento e o tempo de oportunidade de infiltração de água.
description: Funding was provided by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior Brasil (CAPES; Finance Code 001); Conselho Nacional de Desenvolvimento Científico e Tecnológico (Process 301661/2019-7); FAPEMIG, UFMG and UFVJM.
Credit Valuation Adjustment of Credit Default Swaps by Lévy Structural Models
Creators: name: MARK JOHN BENTLEY
Publisher: name: Monash University
Year: 2018
Subjects: subject: 10205 Financial Mathematics
subject: FOS: Mathematics

description: This thesis seeks to extend mathematical models for default based on first passage times that were found to be insufficient in the Global Financial Crisis.
Are Over-massive Haloes of Ultra Diffuse Galaxies Consistent with Extended MOND?
Creators: name: Hodson, Alistair O
name: Zhao, Hongsheng
Publisher: name: arXiv
Year: 2017
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: A sample of Coma cluster ultra-diffuse galaxies (UDGs) are modelled in the context of Extended Modified Newtonian Dynamics (EMOND) with the aim to explain the large dark matter-like effect observed in these cluster galaxies. We first build a model of the Coma cluster in the context of EMOND using gas and galaxy mass profiles from the literature. Then assuming the dynamical mass of the UDGs satisfies the fundamental manifold of other ellipticals, and that the UDG stellar mass-to-light matches their colour, we can verify the EMOND formulation by comparing two predictions of the baryonic mass of UDGs. We find that EMOND can explain the UDG mass, within the expected modelling errors, if they lie on the fundamental manifold of ellipsoids, however, given that measurements show one UDG lying off the fundamental manifold, observations of more UDGs are needed to confirm this assumption.
description: 13 figures, 12 pages, Submitted to A&A
A core UPS molecular complement implicates unique endocytic compartments at the parasite–host interface in Giardia lamblia
Creators: name: Balmer, Erina A.
name: Wirdnam, Corina D.
name: Faso, Carmen
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biochemistry
subject: Physical Sciences not elsewhere classified
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Physiology
subject: Evolutionary Biology
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology
subject: Computational Biology

description: Unconventional protein secretion (UPS) plays important roles in cell physiology. In contrast to canonical secretory routes, UPS does not generally require secretory signal sequences and often bypasses secretory compartments such as the ER and the Golgi apparatus. Giardia lamblia is a protist parasite with reduced subcellular complexity which releases several proteins, some of them virulence factors, without canonical secretory signals. This implicates UPS at the parasite–host interface. No dedicated machinery nor mechanism(s) for UPS in Giardia are currently known, although speculations on the involvement of endocytic organelles called PV/PECs, have been put forth. To begin to address the question of whether PV/PECs are implicated in virulence-associated UPS and to define the composition of molecular machinery involved in protein release, we employed affinity purification and mass spectrometry, coupled to microscopy-based subcellular localization and signal correlation quantification to investigate the interactomes of 11 reported unconventionally secreted proteins, all predicted to be cytosolic. A subset of these are associated with PV/PECs. Extended and validated interactomes point to a core PV/PECs-associated UPS machinery, which includes uncharacterized and Giardia-specific coiled-coil proteins and NEK kinases. Finally, a subset of the alpha-giardin protein family was enriched in all PV/PECs-associated protein interactomes, highlighting a previously unappreciated role for these proteins at PV/PECs and in UPS. Taken together, our results provide the first characterization of a virulence-associated UPS protein complex in Giardia lamblia at PV/PECs, suggesting a novel link between these primarily endocytic and feeding organelles and UPS at the parasite–host interface.
Additional file 1 of Lipidomic identification of urinary extracellular vesicles for non-alcoholic steatohepatitis diagnosis
Creators: name: Zhu, Qingfu
name: Li, Hengrui
name: Ao, Zheng
name: Xu, Hao
name: luo, Jiaxin
name: Kaurich, Connor
name: Yang, Rui
name: Zhu, Pei-Wu
name: Chen, Sui-Dan
name: Wang, Xiao-Dong
name: Tang, Liang-Jie
name: Li, Gang
name: Huang, Ou-Yang
name: Zheng, Ming-Hua
name: Li, Hui-Ping
name: Liu, Fei
Publisher: name: figshare
Year: 2022
Subjects: subject: Biochemistry
subject: Physical Sciences not elsewhere classified
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Cancer

description: Additional file 1: Figure S1. Typical EV morphology of TEM analysis from (a) NAFL patient and (b) NASH patient. The scale bar is 200nm. Figure S2. (a) OPLS-DA analysis of the group of NAFL and NASH. The VIP values of blue points are below 1, and VIP of red points are above 1. (b) Volcano plot showing the differential lipids. Figure S3. Enrichment analysis of the differential lipids between the groups of NAFL and NASH. The percentages of pathway classifications are based on KEGG annotations. Figure S4. Receiver operating characteristic (ROC) curves of differential lipids. Figure S5. Heatmap of hierarchical cluster analysis of differential lipids at different degrees of liver fibrosis. Figure S6. Correlation analysis between concentration levels of putative markers and degrees of liver fibrosis. Table S4. Comparison of EV lipidomic marker-based NASH detection method to the existing methods.