Search

The concept of steady-state solutions to the Navier–Stokes equation is defined. Such solutions extend the notion of stationary ones, diminish exponentially over time, and have a fixed spatial field of velocities and constant pressure in the absence of external fields. A way of constructing these solutions is considered, and the problem of Taylor vortices is solved. A mathematical model of a tornado is proposed, within which a steady-state solution is obtained as an eigenfunction of the problem in the form of a vortex. A model for the formation of the structure of a gas cloud is proposed, based on the Navier–Stokes equation. It is shown that spiral arms arise from flows of gas moving outward, due to the Coriolis force. It is proved that the number of arms is even and their structure is independent of the angular velocity of rotation. We obtain a formula for the twist angle of the spirals, depending on the cloud parameters for when . [ABSTRACT FROM AUTHOR]

Very recently, a straightforward method was proposed to understand galaxies and galactic clusters without using the very elusive dark matter concept. This method is called the κ -model. The main idea is to maintain the form of the usual physical laws, especially Newton's laws of motion when gravity is weak, but only by applying a local scaling procedure for the related lengths, distances, and velocities. This local scaling appears as a correspondence principle in the κ -model. In this model, the fundamental physical constants remain universal, i.e., they are independent of a point in space and of time. The κ -model is Newtonian in its essence, but there is a relativistic extension that can easily be built. The aim of the present paper is to detail the mathematical formalism supporting it. [ABSTRACT FROM AUTHOR]

Galaxies are observed to host magnetic fields with a typical total strength of around 15 μ G. A coherent large-scale field constitutes up to a few microgauss of the total, while the rest is built from strong magnetic fluctuations over a wide range of spatial scales. This represents sufficient magnetic energy for it to be dynamically significant. Several questions immediately arise: What is the physical mechanism that gives rise to such magnetic fields? How do these magnetic fields affect the formation and evolution of galaxies? In which physical processes do magnetic fields play a role, and how can that role be characterized? Numerical modelling of magnetized flows in galaxies is playing an ever-increasing role in finding those answers. We review major techniques used for these models. Current results strongly support the conclusion that field growth occurs during the formation of the first galaxies on timescales shorter than their accretion timescales due to small-scale turbulent dynamos. The saturated small-scale dynamo maintains field strengths at only a few percent of equipartition with turbulence. This is in contradiction with the observed magnitude of turbulent fields, but may be reconciled by the further contribution to the turbulent field of the large-scale dynamo. The subsequent action of large-scale dynamos in differentially rotating discs produces field strengths observed in low redshift galaxies, where it reaches equipartition with the turbulence and has substantial power at large scales. The field structure resulting appears consistent with observations including Faraday rotation and polarisation from synchrotron and dust thermal emission. Major remaining challenges include scaling numerical models toward realistic scale separations and Prandtl and Reynolds numbers. [ABSTRACT FROM AUTHOR]

FungiDB (https://fungidb.org) serves as a valuable online resource that seamlessly integrates genomic and related large-scale data for a wide range of fungal and oomycete species. As an integral part of the VEuPathDB Bioinformatics Resource Center (https://veupathdb.org), FungiDB continually integrates both published and unpublished data addressing various aspects of fungal biology. Established in early 2011, the database has evolved to support 674 datasets. The datasets include over 300 genomes spanning various taxa (e.g. Ascomycota, Basidiomycota, Blastocladiomycota, Chytridiomycota, Mucoromycota, as well as Albuginales, Peronosporales, Pythiales, and Saprolegniales). In addition to genomic assemblies and annotation, over 300 extra datasets encompassing diverse information, such as expression and variation data, are also available. The resource also provides an intuitive web-based interface, facilitating comprehensive approaches to data mining and visualization. Users can test their hypotheses and navigate through omics-scale datasets using a built-in search strategy system. Moreover, FungiDB offers capabilities for private data analysis via the integrated VEuPathDB Galaxy platform. FungiDB also permits genome improvements by capturing expert knowledge through the User Comments system and the Apollo genome annotation editor for structural and functional gene curation. FungiDB facilitates data exploration and analysis and contributes to advancing research efforts by capturing expert knowledge for fungal and oomycete species. [ABSTRACT FROM AUTHOR]

This white paper explores the detectability of intermediate-mass black holes (IMBHs) wandering in the Milky Way (MW) and massive local galaxies, with a particular emphasis on the role of AXIS. IMBHs, ranging within 10 3 − 6 M ⊙ , are commonly found at the centers of dwarf galaxies and may exist, yet undiscovered, in the MW. By using model spectra for advection-dominated accretion flows (ADAFs), we calculated the expected fluxes emitted by a population of wandering IMBHs with masses of 10 5 M ⊙ in various MW environments and extrapolated our results to massive local galaxies. Around 40 % of the potential population of wandering IMBHs in the MW can be detected in an AXIS deep field. We proposed criteria to aid with selecting IMBH candidates using already available optical surveys. We also showed that IMBHs wandering in >200 galaxies within 10 Mpc can be easily detected with AXIS when passing within dense galactic environments (e.g., molecular clouds and cold neutral medium). In summary, we highlighted the potential X-ray detectability of wandering IMBHs in local galaxies and provided insights for guiding future surveys. Detecting wandering IMBHs is crucial for understanding their demographics and evolution and the merging history of galaxies. This white paper is part of a series commissioned for the AXIS Probe Concept Mission; additional AXIS white papers can be found at the AXIS website. [ABSTRACT FROM AUTHOR]

We study the metallicity distribution and evolution in the galactic disk based on the largest sample of open star clusters in the galaxy. From the catalog of 1,879 open clusters in the range of galactocentric distance (RGC) from 4 to 20 kpc, we investigate the variation in metallicity in the galactic disk as functions of RGC, vertical distance (Z), and ages of the clusters. In the direction perpendicular to the galactic plane, the variation in metallicity is found to follow a stepped linear relation. We estimate a vertical metallicity gradient?????H" of -0.545 ± 0.046 dex kpc-1 for |Z| < 0.487 kpc and -0.075 ± 0.093 dex kpc-1 for 0.487 < |Z| < 1.8 kpc. On average, metallicity variations above and below the galactic plane are found to change at similar rates. The change in metallicity in the radial direction is also found to follow a two-function linear relation. We obtain a radial metallicity gradient ^^ of -0.070 ± 0.002 dex kpc-1 for 4.0 < RGC < 12.8 dRGC kpc and -0.005 ± 0.018 dex kpc-1 for 12.8 < RGC < 20.5 kpc, which clearly shows a strong variation in the metallicity gradient when moving from the inner to the outer galactic disk. The age-metallicity relation (AMR) is found to follow a steeper negative slope of -0.031 ± 0.006 dex Gyr-1 for clusters older than 240 Myr; however, there is some hint of positive metallicity age gradient for younger clusters. [ABSTRACT FROM AUTHOR]

Our main goal here is to conduct a comparative analysis between the well-known MOND theory and a more recent model called the κ -model. An additional connection, between the κ -model and two other novel MOND-type theories, Newtonian Fractional-Dimension Gravity (NFDG) and Refracted Gravity (RG), is likewise presented. All these models are built to overtake the DM paradigm, or at least to strongly reduce the dark matter content. Whereas they rely on different formalisms, however, all four seem to suggest that the universal parameter, a 0 , appearing in MOND theory could intrinsically be correlated to either the sole baryonic mean mass density (RG and κ -model) and/or to the dimension of the object under consideration (NFDG and κ -model). We then confer to parameter a 0 a more flexible status of multiscale parameter, as required to explain the dynamics together in galaxies and in galaxy clusters. Eventually, the conformal gravity theory (CFT) also seems to have some remote link with the κ -model, even though the first one is an extension of general relativity, and the second one is Newtonian in essence. The κ -model has been tested on a small sample of spiral galaxies and in galaxy clusters. Now, we test this model on a large sample of galaxies issued from the SPARC database. [ABSTRACT FROM AUTHOR]

The Scalar Field Dark Matter model has been known in various ways throughout its history; Fuzzy, BEC, Wave, Ultralight, Axion-like Dark Matter, etc. All of them consist in proposing that dark matter of the universe is a spinless field Φthat follows the Klein-Gordon (KG) equation of motion □Φ-dV/dΦ=0, for a given scalar field potential V. The difference between different models is sometimes the choice of the scalar field potential V. In the literature we find that people usually work in the non-relativistic, weak-field limit of the Klein- Gordon equation, where it transforms into the Schrödinger equation and the Einstein equations into the Poisson equation, reducing the KG-Einstein system, to the Schrödinger-Poisson system. In this paper, we review some of the most interesting achievements of this model from the historical point of view and its comparison with observations, showing that this model could be the last answer to the question about the nature of dark matter in the universe. [ABSTRACT FROM AUTHOR]

Abstract Background Not changing the native constitution of genes prior to their expression by a heterologous host can affect the amount of proteins synthesized as well as their folding, hampering their activity and even cell viability. Over the past decades, several strategies have been developed to optimize the translation of heterologous genes by accommodating the difference in codon usage between species. While there have been a handful of studies assessing various codon optimization strategies, to the best of our knowledge, no research has been performed towards the evaluation and comparison of codon harmonization algorithms. To highlight their importance and encourage meaningful discussion, we compared different open-source codon harmonization tools pertaining to their in silico performance, and we investigated the influence of different gene-specific factors. Results In total, 27 genes were harmonized with four tools toward two different heterologous hosts. The difference in %MinMax values between the harmonized and the original sequences was calculated (ΔMinMax), and statistical analysis of the obtained results was carried out. It became clear that not all tools perform similarly, and the choice of tool should depend on the intended application. Almost all biological factors under investigation (GC content, RNA secondary structures and choice of heterologous host) had a significant influence on the harmonization results and thus must be taken into account. These findings were substantiated using a validation dataset consisting of 8 strategically chosen genes. Conclusions Due to the size of the dataset, no complex models could be developed. However, this initial study showcases significant differences between the results of various codon harmonization tools. Although more elaborate investigation is needed, it is clear that biological factors such as GC content, RNA secondary structures and heterologous hosts must be taken into account when selecting the codon harmonization tool.

Abstract Background Galaxy is a web-based open-source platform for scientific analyses. Researchers use thousands of high-quality tools and workflows for their respective analyses in Galaxy. Tool recommender system predicts a collection of tools that can be used to extend an analysis. In this work, a tool recommender system is developed by training a transformer on workflows available on Galaxy Europe and its performance is compared to other neural networks such as recurrent, convolutional and dense neural networks. Results The transformer neural network achieves two times faster convergence, has significantly lower model usage (model reconstruction and prediction) time and shows a better generalisation that goes beyond training workflows than the older tool recommender system created using RNN in Galaxy. In addition, the transformer also outperforms CNN and DNN on several key indicators. It achieves a faster convergence time, lower model usage time, and higher quality tool recommendations than CNN. Compared to DNN, it converges faster to a higher precision@k metric (approximately 0.98 by transformer compared to approximately 0.9 by DNN) and shows higher quality tool recommendations. Conclusion Our work shows a novel usage of transformers to recommend tools for extending scientific workflows. A more robust tool recommendation model, created using a transformer, having significantly lower usage time than RNN and CNN, higher precision@k than DNN, and higher quality tool recommendations than all three neural networks, will benefit researchers in creating scientifically significant workflows and exploratory data analysis in Galaxy. Additionally, the ability to train faster than all three neural networks imparts more scalability for training on larger datasets consisting of millions of tool sequences. Open-source scripts to create the recommendation model are available under MIT licence at https://github.com/anuprulez/galaxy_tool_recommendation_transformers

Galaxies are one of the most interesting and complex astronomical objects statistically due to their continuous diversification caused mainly due to incidents such as accretion, action, or mergers. Multivariate studies are one of the most useful tools to analyze these type of data and to understand various components of them. We study a sample of the local universe of Orlando 509 galaxies, imputed with a Predictive Mean Matching (PMM) multiple imputation algorithm, with the aim of classifying the galaxies into distinct clusters through k-medoids and k-mean algorithms and, in turn, performing a heuristic evaluation of the two partitioning algorithms through the percentage of misclassification observed. From the clustering algorithms, it was observed that there were four distinct clusters of the galaxies with misclassification of about 1.96 % . Also, comparing the percentage of misclassification heuristically k-means is a superior algorithm to k-medoids under fixed optimal sizes when the said category of galaxy datasets is concerned. By considering that galaxies are continuously evolving complex objects and using appropriate statistical tools, we are able to derive an explanatory classification of galaxies, based on the physical diverse properties of galaxies, and also establish a better method of partitioning when working on the galaxies. [ABSTRACT FROM AUTHOR]

Background: Galaxy is a web-based open-source platform for scientific analyses. Researchers use thousands of high-quality tools and workflows for their respective analyses in Galaxy. Tool recommender system predicts a collection of tools that can be used to extend an analysis. In this work, a tool recommender system is developed by training a transformer on workflows available on Galaxy Europe and its performance is compared to other neural networks such as recurrent, convolutional and dense neural networks. Results: The transformer neural network achieves two times faster convergence, has significantly lower model usage (model reconstruction and prediction) time and shows a better generalisation that goes beyond training workflows than the older tool recommender system created using RNN in Galaxy. In addition, the transformer also outperforms CNN and DNN on several key indicators. It achieves a faster convergence time, lower model usage time, and higher quality tool recommendations than CNN. Compared to DNN, it converges faster to a higher precision@k metric (approximately 0.98 by transformer compared to approximately 0.9 by DNN) and shows higher quality tool recommendations. Conclusion: Our work shows a novel usage of transformers to recommend tools for extending scientific workflows. A more robust tool recommendation model, created using a transformer, having significantly lower usage time than RNN and CNN, higher precision@k than DNN, and higher quality tool recommendations than all three neural networks, will benefit researchers in creating scientifically significant workflows and exploratory data analysis in Galaxy. Additionally, the ability to train faster than all three neural networks imparts more scalability for training on larger datasets consisting of millions of tool sequences. Open-source scripts to create the recommendation model are available under MIT licence at https://github.com/anuprulez/galaxy_tool_recommendation_transformers [ABSTRACT FROM AUTHOR]

Genetic modifiers are variants modulating phenotypic outcomes of a primary detrimental variant. They contribute to rare diseases phenotypic variability, but their identification is challenging. Genetic screening with model organisms is a widely used method for demystifying genetic modifiers. Forward genetics screening followed by whole genome sequencing allows the detection of variants throughout the genome but typically produces thousands of candidate variants making the interpretation and prioritization process very time-consuming and tedious. Despite whole genome sequencing is more time and cost-efficient, usage of computational pipelines specific to modifier identification remains a challenge for biological-experiment-focused laboratories doing research with model organisms. To facilitate a broader implementation of whole genome sequencing in genetic screens, we have developed Model Organism Modifier or MOM, a pipeline as a user-friendly Galaxy workflow. Model Organism Modifier analyses raw short-read whole genome sequencing data and implements tailored filtering to provide a Candidate Variant List short enough to be further manually curated. We provide a detailed tutorial to run the Galaxy workflow Model Organism Modifier and guidelines to manually curate the Candidate Variant Lists. We have tested Model Organism Modifier on published and validated Caenorhabditis elegans modifiers screening datasets. As whole genome sequencing facilitates high-throughput identification of genetic modifiers in model organisms, Model Organism Modifier provides a user-friendly solution to implement the bioinformatics analysis of the short-read datasets in laboratories without expertise or support in Bioinformatics. [ABSTRACT FROM AUTHOR]

We study the metallicity distribution and evolution in the galactic disk based on the largest sample of open star clusters in the galaxy. From the catalog of 1,879 open clusters in the range of galactocentric distance (RGC) from 4 to 20 kpc, we investigate the variation in metallicity in the galactic disk as functions of RGC, vertical distance (Z), and ages of the clusters. In the direction perpendicular to the galactic plane, the variation in metallicity is found to follow a stepped linear relation. We estimate a vertical metallicity gradient d[Fe/H]d|Z| of −0.545 ± 0.046 dex kpc−1 for |Z| < 0.487 kpc and −0.075 ± 0.093 dex kpc−1 for 0.487 < |Z| < 1.8 kpc. On average, metallicity variations above and below the galactic plane are found to change at similar rates. The change in metallicity in the radial direction is also found to follow a two-function linear relation. We obtain a radial metallicity gradient d[Fe/H]dRGC of −0.070 ± 0.002 dex kpc−1 for 4.0 ≲ RGC ≲ 12.8 kpc and −0.005 ± 0.018 dex kpc−1 for 12.8 ≲ RGC ≲ 20.5 kpc, which clearly shows a strong variation in the metallicity gradient when moving from the inner to the outer galactic disk. The age–metallicity relation (AMR) is found to follow a steeper negative slope of −0.031 ± 0.006 dex Gyr−1 for clusters older than 240 Myr; however, there is some hint of positive metallicity age gradient for younger clusters.

The Scalar Field Dark Matter model has been known in various ways throughout its history; Fuzzy, BEC, Wave, Ultralight, Axion-like Dark Matter, etc. All of them consist in proposing that dark matter of the universe is a spinless field Φ that follows the Klein-Gordon (KG) equation of motion □Φ − dV/dΦ = 0, for a given scalar field potential V. The difference between different models is sometimes the choice of the scalar field potential V. In the literature we find that people usually work in the non-relativistic, weak-field limit of the Klein-Gordon equation, where it transforms into the Schrödinger equation and the Einstein equations into the Poisson equation, reducing the KG-Einstein system, to the Schrödinger-Poisson system. In this paper, we review some of the most interesting achievements of this model from the historical point of view and its comparison with observations, showing that this model could be the last answer to the question about the nature of dark matter in the universe.

Abstract Background Cells orchestrate histone biogenesis with strict temporal and quantitative control. To efficiently regulate histone biogenesis, the repetitive Drosophila melanogaster replication-dependent histone genes are arrayed and clustered at a single locus. Regulatory factors concentrate in a nuclear body known as the histone locus body (HLB), which forms around the locus. Historically, HLB factors are largely discovered by chance, and few are known to interact directly with DNA. It is therefore unclear how the histone genes are specifically targeted for unique and coordinated regulation. Results To expand the list of known HLB factors, we performed a candidate-based screen by mapping 30 publicly available ChIP datasets of 27 unique factors to the Drosophila histone gene array. We identified novel transcription factor candidates, including the Drosophila Hox proteins Ultrabithorax (Ubx), Abdominal-A (Abd-A), and Abdominal-B (Abd-B), suggesting a new pathway for these factors in influencing body plan morphogenesis. Additionally, we identified six other factors that target the histone gene array: JIL-1, hormone-like receptor 78 (Hr78), the long isoform of female sterile homeotic (1) (fs(1)h) as well as the general transcription factors TBP associated factor 1 (TAF-1), Transcription Factor IIB (TFIIB), and Transcription Factor IIF (TFIIF). Conclusions Our foundational screen provides several candidates for future studies into factors that may influence histone biogenesis. Further, our study emphasizes the powerful reservoir of publicly available datasets, which can be mined as a primary screening technique.

Very recently, a straightforward method was proposed to understand galaxies and galactic clusters without using the very elusive dark matter concept. This method is called the κ-model. The main idea is to maintain the form of the usual physical laws, especially Newton’s laws of motion when gravity is weak, but only by applying a local scaling procedure for the related lengths, distances, and velocities. This local scaling appears as a correspondence principle in the κ-model. In this model, the fundamental physical constants remain universal, i.e., they are independent of a point in space and of time. The κ-model is Newtonian in its essence, but there is a relativistic extension that can easily be built. The aim of the present paper is to detail the mathematical formalism supporting it.

This white paper explores the detectability of intermediate-mass black holes (IMBHs) wandering in the Milky Way (MW) and massive local galaxies, with a particular emphasis on the role of AXIS. IMBHs, ranging within 103−6M⊙, are commonly found at the centers of dwarf galaxies and may exist, yet undiscovered, in the MW. By using model spectra for advection-dominated accretion flows (ADAFs), we calculated the expected fluxes emitted by a population of wandering IMBHs with masses of 105M⊙ in various MW environments and extrapolated our results to massive local galaxies. Around 40% of the potential population of wandering IMBHs in the MW can be detected in an AXIS deep field. We proposed criteria to aid with selecting IMBH candidates using already available optical surveys. We also showed that IMBHs wandering in >200 galaxies within 10 Mpc can be easily detected with AXIS when passing within dense galactic environments (e.g., molecular clouds and cold neutral medium). In summary, we highlighted the potential X-ray detectability of wandering IMBHs in local galaxies and provided insights for guiding future surveys. Detecting wandering IMBHs is crucial for understanding their demographics and evolution and the merging history of galaxies. This white paper is part of a series commissioned for the AXIS Probe Concept Mission; additional AXIS white papers can be found at the AXIS website.

Abstract Background ‘Omics methods have empowered scientists to tackle the complexity of microbial communities on a scale not attainable before. Individually, omics analyses can provide great insight; while combined as “meta-omics”, they enhance the understanding of which organisms occupy specific metabolic niches, how they interact, and how they utilize environmental nutrients. Here we present three integrative meta-omics workflows, developed in Galaxy, for enhanced analysis and integration of metagenomics, metatranscriptomics, and metaproteomics, combined with our newly developed web-application, ViMO (Visualizer for Meta-Omics) to analyse metabolisms in complex microbial communities. Results In this study, we applied the workflows on a highly efficient cellulose-degrading minimal consortium enriched from a biogas reactor to analyse the key roles of uncultured microorganisms in complex biomass degradation processes. Metagenomic analysis recovered metagenome-assembled genomes (MAGs) for several constituent populations including Hungateiclostridium thermocellum , Thermoclostridium stercorarium and multiple heterogenic strains affiliated to Coprothermobacter proteolyticus. The metagenomics workflow was developed as two modules, one standard, and one optimized for improving the MAG quality in complex samples by implementing a combination of single- and co-assembly, and dereplication after binning. The exploration of the active pathways within the recovered MAGs can be visualized in ViMO, which also provides an overview of the MAG taxonomy and quality (contamination and completeness), and information about carbohydrate-active enzymes (CAZymes), as well as KEGG annotations and pathways, with counts and abundances at both mRNA and protein level. To achieve this, the metatranscriptomic reads and metaproteomic mass-spectrometry spectra are mapped onto predicted genes from the metagenome to analyse the functional potential of MAGs, as well as the actual expressed proteins and functions of the microbiome, all visualized in ViMO. Conclusion Our three workflows for integrative meta-omics in combination with ViMO presents a progression in the analysis of ‘omics data, particularly within Galaxy, but also beyond. The optimized metagenomics workflow allows for detailed reconstruction of microbial community consisting of MAGs with high quality, and thus improves analyses of the metabolism of the microbiome, using the metatranscriptomics and metaproteomics workflows.

Modern investigations in biology often require the efforts of one or more groups of researchers. Often these are groups of specialists from various scientific fields who generate and share data of different formats and sizes. Without modern approaches to work automation and data versioning (where data from different collaborators are stored at different points in time), teamwork quickly devolves into unmanageable confusion. In this review, we present a number of information systems designed to solve these problems. Their application to the organization of scientific activity helps to manage the flow of actions and data, allowing all participants to work with relevant information and solving the issue of reproducibility of both experimental and computational results. The article describes methods for organizing data flows within a team, principles for organizing metadata and ontologies. The information systems Trello, Git, Redmine, SEEK, OpenBIS and Galaxy are considered. Their functionality and scope of use are described. Before using any tools, it is important to understand the purpose of implementation, to define the set of tasks they should solve, and, based on this, to formulate requirements and finally to monitor the application of recommendations in the field. The tasks of creating a framework of ontologies, metadata, data warehousing schemas and software systems are key for a team that has decided to undertake work to automate data circulation. It is not always possible to implement such systems in their entirety, but one should still strive to do so through a step­by­step introduction of principles for organizing data and tasks with the mastery of individual software tools. It is worth noting that Trello, Git, and Redmine are easier to use, customize, and support for small research groups. At the same time, SEEK, OpenBIS, and Galaxy are more specific and their use is advisable if the capabilities of simple systems are no longer sufficient.

The fertility of female cows is the main factor for the survival of dairy farming. This study was performed to determine the differentially expressed genes in fertility in Holstein cows using phenotypic data and next-generation sequencing (NGS) technology. Corpus luteum samples from 18 Holstein cows at up to two parturitions were used in two high and low fertility groups, three samples from each group were pooled together and a total of three biological samples from each were submitted for whole genome sequencing. The preparation and analysis steps were performed on the Galaxy 22.01 platform. DAVID (2021) database were used for gene ontology. The results of differential gene expression analysis in luteal tissue showed that 19 genes out of 13049 expressed transcripts had a significant difference in expression between high and low-fertility cows with an FDR-adjusted p-value (q-value) of less than 0.05. UBE3B, NIF3L1 and ORC2 genes were three functional marker genes that were more highly expressed in the corpus luteum of high-fertility cows. The UBE3B gene is involved in biological processes as a protein involved in the catabolic process of ubiquitin-dependent protein. NIF3L1 is involved in the biological process of neuronal differentiation, positive transcriptional regulation, DNA pattern, and negative transcriptional regulation by nucleic acid pattern. The ORC2 gene plays a role in the biological process of DNA replication. The genes KRT8, PHLDB3, PPT2, LOC787628, PPYR1, TOX, TP73, DHX8, KCNN1, CLEC6A, PXMP4, LRRC26, SLC34A3, and OR13C7 have been shown to be more highly expressed in the corpus luteum in low fertility cows. Among these genes, three genes PPT2, PPYR1 and CLEC6A were functional indicators. The loci UBE3B, NIF3L1 and ORC2, which were expressed more strongly in the corpus luteum of highly fertile cows, can be used as functional indicator genes in the genetic selection of dairy cows. [ABSTRACT FROM AUTHOR]

Background: Cells orchestrate histone biogenesis with strict temporal and quantitative control. To efficiently regulate histone biogenesis, the repetitive Drosophila melanogaster replication-dependent histone genes are arrayed and clustered at a single locus. Regulatory factors concentrate in a nuclear body known as the histone locus body (HLB), which forms around the locus. Historically, HLB factors are largely discovered by chance, and few are known to interact directly with DNA. It is therefore unclear how the histone genes are specifically targeted for unique and coordinated regulation. Results: To expand the list of known HLB factors, we performed a candidate-based screen by mapping 30 publicly available ChIP datasets of 27 unique factors to the Drosophila histone gene array. We identified novel transcription factor candidates, including the Drosophila Hox proteins Ultrabithorax (Ubx), Abdominal-A (Abd-A), and Abdominal-B (Abd-B), suggesting a new pathway for these factors in influencing body plan morphogenesis. Additionally, we identified six other factors that target the histone gene array: JIL-1, hormone-like receptor 78 (Hr78), the long isoform of female sterile homeotic (1) (fs(1)h) as well as the general transcription factors TBP associated factor 1 (TAF-1), Transcription Factor IIB (TFIIB), and Transcription Factor IIF (TFIIF). Conclusions: Our foundational screen provides several candidates for future studies into factors that may influence histone biogenesis. Further, our study emphasizes the powerful reservoir of publicly available datasets, which can be mined as a primary screening technique. [ABSTRACT FROM AUTHOR]

Our main goal here is to conduct a comparative analysis between the well-known MOND theory and a more recent model called the κ-model. An additional connection, between the κ-model and two other novel MOND-type theories, Newtonian Fractional-Dimension Gravity (NFDG) and Refracted Gravity (RG), is likewise presented. All these models are built to overtake the DM paradigm, or at least to strongly reduce the dark matter content. Whereas they rely on different formalisms, however, all four seem to suggest that the universal parameter, a0, appearing in MOND theory could intrinsically be correlated to either the sole baryonic mean mass density (RG and κ-model) and/or to the dimension of the object under consideration (NFDG and κ-model). We then confer to parameter a0 a more flexible status of multiscale parameter, as required to explain the dynamics together in galaxies and in galaxy clusters. Eventually, the conformal gravity theory (CFT) also seems to have some remote link with the κ-model, even though the first one is an extension of general relativity, and the second one is Newtonian in essence. The κ-model has been tested on a small sample of spiral galaxies and in galaxy clusters. Now, we test this model on a large sample of galaxies issued from the SPARC database.

Background: 'Omics methods have empowered scientists to tackle the complexity of microbial communities on a scale not attainable before. Individually, omics analyses can provide great insight; while combined as "meta-omics", they enhance the understanding of which organisms occupy specific metabolic niches, how they interact, and how they utilize environmental nutrients. Here we present three integrative meta-omics workflows, developed in Galaxy, for enhanced analysis and integration of metagenomics, metatranscriptomics, and metaproteomics, combined with our newly developed web-application, ViMO (Visualizer for Meta-Omics) to analyse metabolisms in complex microbial communities. Results: In this study, we applied the workflows on a highly efficient cellulose-degrading minimal consortium enriched from a biogas reactor to analyse the key roles of uncultured microorganisms in complex biomass degradation processes. Metagenomic analysis recovered metagenome-assembled genomes (MAGs) for several constituent populations including Hungateiclostridium thermocellum, Thermoclostridium stercorarium and multiple heterogenic strains affiliated to Coprothermobacter proteolyticus. The metagenomics workflow was developed as two modules, one standard, and one optimized for improving the MAG quality in complex samples by implementing a combination of single- and co-assembly, and dereplication after binning. The exploration of the active pathways within the recovered MAGs can be visualized in ViMO, which also provides an overview of the MAG taxonomy and quality (contamination and completeness), and information about carbohydrate-active enzymes (CAZymes), as well as KEGG annotations and pathways, with counts and abundances at both mRNA and protein level. To achieve this, the metatranscriptomic reads and metaproteomic mass-spectrometry spectra are mapped onto predicted genes from the metagenome to analyse the functional potential of MAGs, as well as the actual expressed proteins and functions of the microbiome, all visualized in ViMO. Conclusion: Our three workflows for integrative meta-omics in combination with ViMO presents a progression in the analysis of 'omics data, particularly within Galaxy, but also beyond. The optimized metagenomics workflow allows for detailed reconstruction of microbial community consisting of MAGs with high quality, and thus improves analyses of the metabolism of the microbiome, using the metatranscriptomics and metaproteomics workflows. [ABSTRACT FROM AUTHOR]

Oort constants and local kinematics are vital parameters with which to study the structure and dynamics of the Milky Way. When GCNS was published, it provided a clean sample of stars in the solar vicinity, which gives us an ideal tool with which to determine these parameters. Our aim was to calculate the reliable Oort constants with GCNS. We determined the Oort constants using the GCNS from Gaia EDR3 with d < 100 pc . The proper motions and radial velocities were fitted with a maximum likelihood model. The uncertainties were obtained with an MCMC method. The sample was carefully selected to obtain a reliable result. The result yields the Oort constants A = 15.6 ± 1.6 km s − 1 kpc − 1 , B = − 15.8 ± 1.7 km s − 1 kpc − 1 , C = − 3.5 ± 1.6 km s − 1 kpc − 1 , and K = 2.7 ± 1.5 km s − 1 kpc − 1 . The non-zero C and K imply that the local disc is in a non-asymmetric potential. With the Oort constants, we derived the local angular velocity Ω 0 ≈ A − B = 31.4 ± 2.3 km s − 1 kpc − 1 . The solar motion ( U ⊙ , V ⊙ , W ⊙ ) was calculated as ( 10.1 ± 0.1 , 22.8 ± 0.1 , 7.8 ± 0.1 ) km s − 1 . [ABSTRACT FROM AUTHOR]

In this work, we investigate the possibility of observing quasars, particularly lensed quasars, by the Nancy Grace Roman Space Telescope (Roman). To this aim, based on the capabilities of the Roman Space Telescope and the results from the quasar luminosity function (QLF) in the infrared band of the Spitzer Space Telescope imaging survey, we calculated the number of quasars expected to be in its field of view. In order to estimate the number of lensed quasars, we develop a Monte Carlo simulation to estimate the probability that a quasar is lensed once or more times by foreground galaxies. Using the mass–luminosity distribution function of galaxies and the redshift distributions of galaxies and quasars, we find that 1 per 180 observed quasars will be lensed by foreground galaxies. Further on, adopting a singular isothermal sphere (SIS) model for lens galaxies, we calculate the time delay between lensed images for single and multiple lensing systems and present their distributions. We emphasize that detailed studies of these lensing systems will provide a powerful probe of the physical properties of quasars and may allow testing the mass distribution models of galaxies in addition to being extremely helpful for constraining the cosmological parameters. [ABSTRACT FROM AUTHOR]

Aims. The goal of this study is to present the development of a machine learning based approach that utilizes phase space alone to separate the Gaia DR2 stars into two categories: those accreted onto the Milky Way from those that are in situ. Traditional selection methods that have been used to identify accreted stars typically rely on full 3D velocity, metallicity information, or both, which significantly reduces the number of classifiable stars. The approach advocated here is applicable to a much larger portion of Gaia DR2. Methods. A method known as "transfer learning" is shown to be effective through extensive testing on a set of mock Gaia catalogs that are based on the FIRE cosmological zoom-in hydrodynamic simulations of Milky Way-mass galaxies. The machine is first trained on simulated data using only 5D kinematics as inputs and is then further trained on a cross-matched Gaia/RAVE data set, which improves sensitivity to properties of the real Milky Way. Results. The result is a catalog that identifies ∼767 000 accreted stars within Gaia DR2. This catalog can yield empirical insights into the merger history of the Milky Way and could be used to infer properties of the dark matter distribution.

Photometric techniques are one of the fundamentals and of great importance in the study of astronomical phenomena, including galaxies, and have witnessed a wide development during the last 100 years in equipment, sensitivity and accuracy in data analysis, especially after the direction toward space telescopes and the widespread use of a CCD camera. Therefore, in this research, an analytical study is made to compare two types of galaxies, which are spiral and lenticular galaxies, using photometric techniques and compare the photometric parameters of each type with tables and illustrations. An analysis of the morphological of the two galaxies is done by using the Least Square Fitting Method, and it is fully explained in the research. The results show the clear difference between the structure of spiral and lenticular galaxies. [ABSTRACT FROM AUTHOR]

Can high-energy transient events affect life on a planet? We provide a review of the works that have tried to answer this question. It is argued that that gamma ray bursts, specifically those of the long class, are among the most dangerous astrophysical sources for biotic life and may exert evolutionary pressure on possible life forms in the universe. Their radiation can be directly lethal for biota or induce extinction by removing most of the protective atmospheric ozone layer on terrestrial planets. Since the rate of long gamma ray bursts is proportional to the birth rate of stars but is reduced in metal rich regions, the evolution of the "safest place" to live in our galaxy depended on the past 12 billion years of evolution of the star formation rate and relative metal pollution of the interstellar medium. Until 6 billion years ago, the outskirts of the galaxy were the safest places to live, despite the relatively low density of terrestrial planets. In the last 5 billion years, regions between 2 and 8 kiloparsecs from the center, featuring a higher density of terrestrial planets, gradually became the best places for safe biotic life growth. [ABSTRACT FROM AUTHOR]

In this study, the morphological galaxy classification process was carried out with a hybrid approach. Since the Galaxy classification process may contain detailed information about the universe's formation, it remains the current research topic. Researchers divided more than 100 billion galaxies into ten different classes. It is not always possible to understand which class the galaxy types belong. However, Artificial Intelligence (AI) can be used for successful classification. There are studies on the automatic classification of galaxies into a small number of classes. As the number of classes increases, the success of the used methods decreases. Based on the literature, the classification using Convolutional Neural Network (CNN) is better. Three metaheuristic algorithms are used to obtain the optimum architecture of CNN. These are Grey Wolf Optimizer (GWO), Particle Swarm Optimization (PSO) and Artificial Bee Colony (ABC) algorithms. A CNN architecture with nine hidden layers and two full connected layers was used. The number of neurons in the hidden layers and the fully connected layers, the learning coefficient and the batch size values were optimized. The classification accuracy of my model was 85%. The best results were obtained usingGWO. Manual optimization of CNN is difficult. It was carried out with the help of the GWO meta-heuristic algorithm. [ABSTRACT FROM AUTHOR]

MicroRNAs (miRNAs) are important regulators of gene expression. The large-scale detection and profiling of miRNAs have been accelerated with the development of high-throughput small RNA sequencing (sRNA-Seq) techniques and bioinformatics tools. However, generating high-quality comprehensive miRNA annotations remains challenging due to the intrinsic complexity of sRNA-Seq data and inherent limitations of existing miRNA prediction tools. Here, we present iwa-miRNA, a Galaxy-based framework that can facilitate miRNA annotation in plant species by combining computational analysis and manual curation. iwa-miRNA is specifically designed to generate a comprehensive list of miRNA candidates, bridging the gap between already annotated miRNAs provided by public miRNA databases and new predictions from sRNA-Seq datasets. It can also assist users in selecting promising miRNA candidates in an interactive mode, contributing to the accessibility and reproducibility of genome-wide miRNA annotation. iwa-miRNA is user-friendly and can be easily deployed as a web application for researchers without programming experience. With flexible, interactive, and easy-to-use features, iwa-miRNA is a valuable tool for the annotation of miRNAs in plant species with reference genomes. We also illustrate the application of iwa-miRNA for miRNA annotation using data from plant species with varying genomic complexity. The source codes and web server of iwa-miRNA are freely accessible at http://iwa-miRNA.omicstudio.cloud/.

BackgroundComplex microbial communities are an area of growing interest in biology. Metatranscriptomics allows researchers to quantify microbial gene expression in an environmental sample via high-throughput sequencing. Metatranscriptomic experiments are computationally intensive because the experiments generate a large volume of sequence data and each sequence must be compared with reference sequences from thousands of organisms.ResultsSAMSA2 is an upgrade to the original Simple Annotation of Metatranscriptomes by Sequence Analysis (SAMSA) pipeline that has been redesigned for standalone use on a supercomputing cluster. SAMSA2 is faster due to the use of the DIAMOND aligner, and more flexible and reproducible because it uses local databases. SAMSA2 is available with detailed documentation, and example input and output files along with examples of master scripts for full pipeline execution.ConclusionsSAMSA2 is a rapid and efficient metatranscriptome pipeline for analyzing large RNA-seq datasets in a supercomputing cluster environment. SAMSA2 provides simplified output that can be examined directly or used for further analyses, and its reference databases may be upgraded, altered or customized to fit the needs of any experiment.

Plant genome-scale resources are being generated at an increasing rate as sequencing technologies continue to improve and raw data costs continue to fall; however, the cost of downstream analyses remains large. This has resulted in a considerable range of genome assembly and annotation qualities across plant genomes due to their varying sizes, complexity, and the technology used for the assembly and annotation. To effectively work across genomes, researchers increasingly rely on comparative genomic approaches that integrate across plant community resources and data types. Such efforts have aided the genome annotation process and yielded novel insights into the evolutionary history of genomes and gene families, including complex non-model organisms. The essential tools to achieve these insights rely on gene family analysis at a genome-scale, but they are not well integrated for rapid analysis of new data, and the learning curve can be steep. Here we present PlantTribes2, a scalable, easily accessible, highly customizable, and broadly applicable gene family analysis framework with multiple entry points including user provided data. It uses objective classifications of annotated protein sequences from existing, high-quality plant genomes for comparative and evolutionary studies. PlantTribes2 can improve transcript models and then sort them, either genome-scale annotations or individual gene coding sequences, into pre-computed orthologous gene family clusters with rich functional annotation information. Then, for gene families of interest, PlantTribes2 performs downstream analyses and customizable visualizations including, (1) multiple sequence alignment, (2) gene family phylogeny, (3) estimation of synonymous and non-synonymous substitution rates among homologous sequences, and (4) inference of large-scale duplication events. We give examples of PlantTribes2 applications in functional genomic studies of economically important plant families, namely transcriptomics in the weedy Orobanchaceae and a core orthogroup analysis (CROG) in Rosaceae. PlantTribes2 is freely available for use within the main public Galaxy instance and can be downloaded from GitHub or Bioconda. Importantly, PlantTribes2 can be readily adapted for use with genomic and transcriptomic data from any kind of organism. [ABSTRACT FROM AUTHOR]