Genetic Evolution and Molecular Selection of the HE Gene of Influenza C Virus

Influenza C virus (ICV) was first identified in humans and swine, but recently also in cattle, indicating a wider host range and potential threat to both the livestock industry and public health than was originally anticipated. The ICV hemagglutinin-esterase (HE) glycoprotein has multiple functions in the viral replication cycle and is the major determinant of antigenicity. Here, we developed a comparative approach integrating genetics, molecular selection analysis, and structural biology to identify the codon usage and adaptive evolution of ICV. We show that ICV can be classified into six lineages, consistent with previous studies. The HE gene has a low codon usage bias, which may facilitate ICV replication by reducing competition during evolution. Natural selection, dinucleotide composition, and mutation pressure shape the codon usage patterns of the ICV HE gene, with natural selection being the most important factor. Codon adaptation index (CAI) and relative codon deoptimization index (RCDI) analysis revealed that the greatest adaption of ICV was to humans, followed by cattle and swine. Additionally, similarity index (SiD) analysis revealed that swine exerted a stronger evolutionary pressure on ICV than humans, which is considered the primary reservoir. Furthermore, a similar tendency was also observed in the M gene. Of note, we found HE residues 176, 194, and 198 to be under positive selection, which may be the result of escape from antibody responses. Our study provides useful information on the genetic evolution of ICV from a new perspective that can help devise prevention and control strategies

Through Skull Fluorescence Imaging of the Brain in a New Near-Infrared Window

To date, brain imaging has largely relied on X-ray computed tomography and magnetic resonance angiography with limited spatial resolution and long scanning times. Fluorescence-based brain imaging in the visible and traditional near-infrared regions (400-900 nm) is an alternative but currently requires craniotomy, cranial windows and skull thinning techniques, and the penetration depth is limited to 1-2 mm due to light scattering. Here, we report through-scalp and through-skull fluorescence imaging of mouse cerebral vasculature without craniotomy utilizing the intrinsic photoluminescence of single-walled carbon nanotubes in the 1.3-1.4 micrometre near-infrared window. Reduced photon scattering in this spectral region allows fluorescence imaging reaching a depth of >2 mm in mouse brain with sub-10 micrometre resolution. An imaging rate of ~5.3 frames/s allows for dynamic recording of blood perfusion in the cerebral vessels with sufficient temporal resolution, providing real-time assessment of blood flow anomaly in a mouse middle cerebral artery occlusion stroke model.Comment: 38 pages, 4 main figures and 11 Supplementary figures. published in Nature Photonics, 201

Investigating inner Galactic Bulge stars through the near infrared

Context: The formation of the Galactic Bulge is a topic of active research. There are many scenarios based on observations and Galactic evolution models. The key properties which need to be well constrained observationally are the metallicity distributions of stars and the spatial metallicity gradients. The metallicity distribution of stars in the inner Galactic Bulge (|b| 0.1 dex) end of the distribution, depending on the methodology. Considering the low sample size and uncertainties, the presence of a metal poor population ([Fe/H] ~ -1.0dex), as claimed in Schultheis et al. (2015), is weakened based on the results of this study.Sedan mänsklighetens början har det alltid funnits de som dragits till natthimlen och förundrats över vad som kan finnas bortom det mörkaste av mörker. Funderingarna om att vi människor endast är en del av något mycket större började gro ordentligt i samband med teleskopet som verktyg, och när personer som Galileo Galileis och William Herschels började observera himlen med nya tekniker. Det visade sig till slut att de oräkneliga antal stjärnor som de observerade utgjorde ett diskliknande system, det vi idag kallar Vintergatan, vår galax. En av de mest fängslande frågorna som uppstått efter denna upptäckt är ”Hur blev Vintergatan till?”. Denna fråga har fascinerat astronomer sedan långt tillbaka i historien. Trots flera århundrande av forskning och försök att besvara frågan är det fortfarande ett väl studerat ämne. Det finns många teorier om möjliga mekanismer som ligger bakom Vintergatans tillblivelse men trots detta har vi ännu inte en fullständig bild. Det här projektet har som mål att kunna bidra till att besvara frågan, detta genom att använda stjärnor i den inre ”utbuktnigen”, eller som det heter på engelska ”bulge”, för att finna begränsningar i de teoretiska modellerna om hur Vintergatan formades. Utifrån observationer kan man dela in Vintergatan i komponenter, så som ”the disk”, ”the halo” och ”the bulge”. The bulge är särskilt intressant eftersom extragalactic studier visar att inte alla galaxer har liknande strukturer och därför kan sakna en ”bulge”. Hur det kommer sig att Vintergatan har en ”bulge” är fortfarande inte utrett, för att besvara det behövs fler observationer av de inre regionerna av galaxens centrum. Dock är observationer med hjälp av optiskt ljus svåra att genomföra på grund av den stora mängden gas och damm som finns i the bulge som absorberar ljuset. Inte förrän nyligen har nya tekniker gjort det möjlig att göra observationer med infrarött ljus, som enkelt kan färdas genom gas och damm så att spektroskopi kan göras. Spektroskopi är en metod där man avgör ett material eller provs kemisk sammansättning genom att använda ljus. På liknande sätt som ett prisma sprider ljus i olika färger, fungerar spektroskopi genom att man splittrar ljuset genom ett prov och observerar de olika våglängderna som ljuset har. När fotoner skapas i en stjärna genom nukleär bränning måste de fara genom stjärnans alla lager innan de kan observeras. Under tiden kan fotonerna bli absorberade av ämnen som skapas i en nukleär fusion, men bara vid särskilda våglängder. Dessa absorptioner lämnar distinkta mönster i observationerna som kan liknas vid fingeravtryck och på så sätt kan man avgöra strukturers kemiska sammansättning utifrån vilka våglängder som kan observeras. Genom att experimentera med ett flertal ämnen i ett laboratorium och hitta våglängdsfingeravtryck och sedan jämföra med observationer kan man avgöra vilka ämnen som bygger upp en stjärna. Genom att ta reda på vilka kemiska sammansättningar som bygger upp stjärnor inom en region kan vi börja förstå hur dess stjärnor en gång blev till. Detta är ett avgörande steg för att förstå hur the bulge, och senare Vintergatan, skapades

A census of stellar structures in the Fornax cluster

AbstractIt is well known that galaxies in the Universe tend to be found in either clusters, groups, or in the field, and that the hierarchical growth of structure dictates that galaxies can first aggregate in groups before falling into cluster. The difference in properties between environments (e.g. mass, velocity dispersion, gravitational potential) means that some mechanisms (e.g. ram pressure stripping, harassment, galaxy–cluster tidal interactions) dominate in certain environments. The main aim of this thesis is to study the effects of the environment on the properties of galaxies, particularly between the group and cluster environment, where galaxies can be transformed in groups before entering clusters. To this end, in this thesis I present a detailed view of the stellar structures hosted by galaxies in the Fornax cluster.To study the structures in detail, we use data from the Fornax Deep Survey (FDS), a deep multi-band imaging survey covering 26 deg2 around the Fornax cluster. We use the catalogue of likely Fornax members from Venhola et al. (2018) and split the sample into the Fornax main cluster and the Fornax A group. To extract and quantify the stellar structures of galaxies, we conduct structural decompositions with models of varying complexity (single Sérsic, Sérsic+PSF, and multi-component) and calculate non-parametric morphological indices, which provide a global measure of morphology. Additionally, we apply aperture photometry to derive surface brightness profiles in order to study the faint outskirts of galaxies, as well as to measure the integrated and radial colour properties.From the quantities derived from structural decompositions: g − r and r − i colours; effective radius (re); Sérsic index (n); mean effective surface brightness (μe,r), and non-parametric morphological indices: concentration (C); asymmetry (A); clumpiness (S); Gini (G); brightest second order moment of light (M20), we find significantly (KS test p-value g − r, bluer in r − i, larger in re, fainter in μe,r, less asymmetric (lower A), and less clumpy (lower S) than their Fornax A group counterparts. Furthermore, we find significant correlations (Spearman’s ρ p-value r − i, re, μe,r, A, S, G, and M20. This implies that as galaxies fall deeper towards the Fornax main cluster centre, they become bluer in r − i, more extended ((re), fainter (μe,r), less asymmetric (lower A), less clumpy (lower S), possess higher equality in terms of the light distribution (lower G), and have larger spatial distribution in the brightest 20% of pixels (higher M20). In contrast, we did not find significant group-centric trends for the Fornax A group galaxies, which is potentially due to the low sample size.In terms of hosting large scale stellar structures (i.e. bulges, bars), we find that the vast majority of structures are hosted by massive galaxies (M∗ ≳ 109M⊙). As such, the fraction of galaxies hosting these stellar structures closely follows the galaxy stellar ass. This relation appears to be consistent across different environments, as we find similar fractions at a fixed galaxy stellar mass in the Virgo cluster and in the field. This suggests that the formation and/or maintenance of stellar structures is primarily reliant on the galaxy (stellar) mass, rather than from environmental influences.The most prevalent structure is the nucleus, which corresponds to the unresolved nuclear star cluster (NSC). We use a combination of visual inspection and the model selection statistic Bayesian information criterion (BIC) to detect nuclei, and also explore the use of the BIC as an unsupervised method for nucleus detection. We find that the overall nucleation fraction for the Fornax main cluster is much higher (0.29) than in the Fornax A group (0.14), which alludes to the importance of the environment in the nucleation of galaxies. Overall we find a dichotomy in the nucleus properties for host galaxies with stellar masses above and below M∗,galaxy ≈ 108.5M⊙: the nuclei of lower mass galaxies tend to be bluer than their host and follow a mass scaling relation of M∗,nuc ∝ M∗,galaxy0.5, whereas higher mass galaxies tend to have redder nuclei compared to their host and follow M∗,nuc ∝ M∗,galaxy. Comparing the host properties of the nucleated and non-nucleated galaxies, we find significant difference in the distributions such that nucleated galaxies tend to be redder in g – r, less asymmetric (lower A), have redder outer regions (relative to itself; Δ(g – r)), and show less scatter in M20 than their non-nucleated counterparts.To test whether cluster galaxies show signs of quenching (e.g. due to the removal of gas via ram pressure stripping), we compare the colours and mean effective surface brightnesses of galaxies in the Fornax and Virgo cluster to predictions from stellar population models. We find that late-type dwarfs show properties consistent with a fading and reddening stellar population, but not for the early-type dwarfs, even though they must be passively evolving. This is possibly due to a quenching of star formation very early on, which is supported by the fact that ETGs which appear to be recently additions to the Virgo cluster show signs of fading and reddening. Additionally, the sizes of ETGs and LTGs of a given stellar mass below M∗ ≲ 108M⊙ are consistent with each other, which further supports the fading and reddening scenario.We also investigated the bright (mB re, whereas Fornax A group LTGs tend to have break radius beyond 1re. The dichotomy of disk break properties likely reflects the higher efficiency of environmental mechanisms (e.g. ram pressure stripping, tidal effects) and the longer time spent in the Fornax main cluster than the Fornax A group.Original papersOriginal papers are not included in the electronic version of the dissertation.Su, A. H., Salo, H., Janz, J., Laurikainen, E., Venhola, A., Peletier, R. F., Iodice, E., Hilker, M., Cantiello, M., Napolitano, N., Spavone, M., Raj, M. A., van de Ven, G., Mieske, Steffen., Paolillo, M., Capaccioli, M., Valentijn, E. A., & Watkins, A. E. (2021). The Fornax Deep Survey (FDS) with the VST: XI. The search for signs of preprocessing between the Fornax main cluster and Fornax A group. https://doi.org/10.48550/ARXIV.2101.05699Su, A. H., Salo, H., Janz, J., Venhola, A., & Peletier, R. F. (2022). Photometric properties of nuclear star clusters and their host galaxies in the Fornax cluster. Astronomy & Astrophysics, 664, A167. https://doi.org/10.1051/0004-6361/202142593Self-archived versionJanz, J., Salo, H., Su, A. H., & Venhola, A. (2021). Signatures of quenching in dwarf galaxies in local galaxy clusters: A comparison of the galaxy populations in the Virgo and Fornax clusters. Astronomy & Astrophysics, 647, A80. https://doi.org/10.1051/0004-6361/202039408Self-archived versionRaj, M. A., Iodice, E., Napolitano, N. R., Spavone, M., Su, H.-S., Peletier, R. F., Davis, T. A., Zabel, N., Hilker, M., Mieske, S., Falcon Barroso, J., Cantiello, M., van de Ven, G., Watkins, A. E., Salo, H., Schipani, P., Capaccioli, M., & Venhola, A. (2019). The Fornax Deep Survey with the VST: VII. Evolution and structure of late type galaxies inside the virial radius of the Fornax cluster. Astronomy & Astrophysics, 628, A4. https://doi.org/10.1051/0004-6361/201935433Self-archived versionRaj, M. A., Iodice, E., Napolitano, N. R., Hilker, M., Spavone, M., Peletier, R. F., Su, H.-S., Falcón-Barroso, J., van de Ven, G., Cantiello, M., Kleiner, D., Venhola, A., Mieske, S., Paolillo, M., Capaccioli, M., & Schipani, P. (2020). The Fornax Deep Survey with VST: X. The assembly history of the bright galaxies and intra-group light in the Fornax A subgroup. Astronomy & Astrophysics, 640, A137. https://doi.org/10.1051/0004-6361/202038043Self-archived versionOsajulkaisutOsajulkaisut eivät sisälly väitöskirjan elektroniseen versioon.Su, A. H., Salo, H., Janz, J., Laurikainen, E., Venhola, A., Peletier, R. F., Iodice, E., Hilker, M., Cantiello, M., Napolitano, N., Spavone, M., Raj, M. A., van de Ven, G., Mieske, Steffen., Paolillo, M., Capaccioli, M., Valentijn, E. A., & Watkins, A. E. (2021). The Fornax Deep Survey (FDS) with the VST: XI. The search for signs of preprocessing between the Fornax main cluster and Fornax A group. https://doi.org/10.48550/ARXIV.2101.05699Su, A. H., Salo, H., Janz, J., Venhola, A., & Peletier, R. F. (2022). Photometric properties of nuclear star clusters and their host galaxies in the Fornax cluster. Astronomy & Astrophysics, 664, A167. https://doi.org/10.1051/0004-6361/202142593Rinnakkaistallennettu versioJanz, J., Salo, H., Su, A. H., & Venhola, A. (2021). Signatures of quenching in dwarf galaxies in local galaxy clusters: A comparison of the galaxy populations in the Virgo and Fornax clusters. Astronomy & Astrophysics, 647, A80. https://doi.org/10.1051/0004-6361/202039408Rinnakkaistallennettu versioRaj, M. A., Iodice, E., Napolitano, N. R., Spavone, M., Su, H.-S., Peletier, R. F., Davis, T. A., Zabel, N., Hilker, M., Mieske, S., Falcon Barroso, J., Cantiello, M., van de Ven, G., Watkins, A. E., Salo, H., Schipani, P., Capaccioli, M., & Venhola, A. (2019). The Fornax Deep Survey with the VST: VII. Evolution and structure of late type galaxies inside the virial radius of the Fornax cluster. Astronomy & Astrophysics, 628, A4. https://doi.org/10.1051/0004-6361/201935433Rinnakkaistallennettu versioRaj, M. A., Iodice, E., Napolitano, N. R., Hilker, M., Spavone, M., Peletier, R. F., Su, H.-S., Falcón-Barroso, J., van de Ven, G., Cantiello, M., Kleiner, D., Venhola, A., Mieske, S., Paolillo, M., Capaccioli, M., & Schipani, P. (2020). The Fornax Deep Survey with VST: X. The assembly history of the bright galaxies and intra-group light in the Fornax A subgroup. Astronomy & Astrophysics, 640, A137. https://doi.org/10.1051/0004-6361/202038043Rinnakkaistallennettu versioAcademic Dissertation to be presented with the assent of the Faculty of Science, University of Oulu, for public discussion in the Auditorium L6, on September 23rd, 2022, at 12 o’clock noonAbstract It is well known that galaxies in the Universe tend to be found in either clusters, groups, or in the field, and that the hierarchical growth of structure dictates that galaxies can first aggregate in groups before falling into cluster. The difference in properties between environments (e.g. mass, velocity dispersion, gravitational potential) means that some mechanisms (e.g. ram pressure stripping, harassment, galaxy–cluster tidal interactions) dominate in certain environments. The main aim of this thesis is to study the effects of the environment on the properties of galaxies, particularly between the group and cluster environment, where galaxies can be transformed in groups before entering clusters. To this end, in this thesis I present a detailed view of the stellar structures hosted by galaxies in the Fornax cluster. To study the structures in detail, we use data from the Fornax Deep Survey (FDS), a deep multi-band imaging survey covering 26 deg2 around the Fornax cluster. We use the catalogue of likely Fornax members from Venhola et al. (2018) and split the sample into the Fornax main cluster and the Fornax A group. To extract and quantify the stellar structures of galaxies, we conduct structural decompositions with models of varying complexity (single Sérsic, Sérsic+PSF, and multi-component) and calculate non-parametric morphological indices, which provide a global measure of morphology. Additionally, we apply aperture photometry to derive surface brightness profiles in order to study the faint outskirts of galaxies, as well as to measure the integrated and radial colour properties. From the quantities derived from structural decompositions: g − r and r − i colours; effective radius (re); Sérsic index (n); mean effective surface brightness (μe,r), and non-parametric morphological indices: concentration (C); asymmetry (A); clumpiness (S); Gini (G); brightest second order moment of light (M20), we find significantly (KS test p-value e,r, less asymmetric (lower A), and less clumpy (lower S) than their Fornax A group counterparts. Furthermore, we find significant correlations (Spearman’s ρ p-value e, μe,r, A, S, G, and M20. This implies that as galaxies fall deeper towards the Fornax main cluster centre, they become bluer in r − i, more extended ((re), fainter (μe,r), less asymmetric (lower A), less clumpy (lower S), possess higher equality in terms of the light distribution (lower G), and have larger spatial distribution in the brightest 20% of pixels (higher M20). In contrast, we did not find significant group-centric trends for the Fornax A group galaxies, which is potentially due to the low sample size. In terms of hosting large scale stellar structures (i.e. bulges, bars), we find that the vast majority of structures are hosted by massive galaxies (M∗ ≳ 109M⊙). As such, the fraction of galaxies hosting these stellar structures closely follows the galaxy stellar ass. This relation appears to be consistent across different environments, as we find similar fractions at a fixed galaxy stellar mass in the Virgo cluster and in the field. This suggests that the formation and/or maintenance of stellar structures is primarily reliant on the galaxy (stellar) mass, rather than from environmental influences. The most prevalent structure is the nucleus, which corresponds to the unresolved nuclear star cluster (NSC). We use a combination of visual inspection and the model selection statistic Bayesian information criterion (BIC) to detect nuclei, and also explore the use of the BIC as an unsupervised method for nucleus detection. We find that the overall nucleation fraction for the Fornax main cluster is much higher (0.29) than in the Fornax A group (0.14), which alludes to the importance of the environment in the nucleation of galaxies. Overall we find a dichotomy in the nucleus properties for host galaxies with stellar masses above and below M∗,galaxy ≈ 108.5M⊙: the nuclei of lower mass galaxies tend to be bluer than their host and follow a mass scaling relation of M∗,nuc ∝ M∗,galaxy0.5, whereas higher mass galaxies tend to have redder nuclei compared to their host and follow M∗,nuc ∝ M∗,galaxy. Comparing the host properties of the nucleated and non-nucleated galaxies, we find significant difference in the distributions such that nucleated galaxies tend to be redder in g – r, less asymmetric (lower A), have redder outer regions (relative to itself; Δ(g – r)), and show less scatter in M20 than their non-nucleated counterparts. To test whether cluster galaxies show signs of quenching (e.g. due to the removal of gas via ram pressure stripping), we compare the colours and mean effective surface brightnesses of galaxies in the Fornax and Virgo cluster to predictions from stellar population models. We find that late-type dwarfs show properties consistent with a fading and reddening stellar population, but not for the early-type dwarfs, even though they must be passively evolving. This is possibly due to a quenching of star formation very early on, which is supported by the fact that ETGs which appear to be recently additions to the Virgo cluster show signs of fading and reddening. Additionally, the sizes of ETGs and LTGs of a given stellar mass below M∗ ≲ 108M⊙ are consistent with each other, which further supports the fading and reddening scenario. We also investigated the bright (mB e, whereas Fornax A group LTGs tend to have break radius beyond 1re. The dichotomy of disk break properties likely reflects the higher efficiency of environmental mechanisms (e.g. ram pressure stripping, tidal effects) and the longer time spent in the Fornax main cluster than the Fornax A group

An Introduction and Characterisation of Non-identical Digital Twins in Manufacturing Systems

The digital twin (DT) has become a key component for the digitalisation, monitoring, and improvement of manufacturing systems. This has led to the development of various DTs for distinct workpieces, processes, and tools. While beneficial, these individual components need to be configured to form a system of DTs that represents the overall manufacturing system, a task that is nontrivial but necessary to realise a truly smart manufacturing system. This paper proposes an identification scheme to distinguish each unique DT within a system of DTs (Digital Twin System) from three aspects: the physical entity, the digital representation and connections. Based on it, non-identical DTs are proposed as different digital representations of the same element or elements in a manufacturing system. They are sorted into three classes, including homologous DTs, heterologous DTs, and exclusive DTs, based on their context and behaviour. Definitions and characterisations of three types of non-identical DTs are then discussed. Lastly, a case study of in-situ failure detection for material extrusion(MEX) additive manufacturing is demonstrated to explore affordances, challenges, and potential applications of non-identical DTs