Synthesis, Characterisation and Antifungal Activity of Copper(II)-Functionalised Silicone Polymers and Silicone-Coated Magnetic Nanoparticles

Two families of amine-functionalised silicone polymers were prepared using monomeric (3-aminopropyl)triethoxysilane (APTES) and (3-trimethoxysilylpropyl)diethylene triamine (TMSPDT). Schiff base derivatives of these polymers were synthesised using salicylaldehyde. The same suite of polymers were also formed as a surface coating on magnetite nanoparticles (Fe3O4-MNPs). Copper(II) ions were coordinated to the pendant amine groups of all of the polymers. In vitro tests using the fungal pathogen, Candida albicans, revealed that the silicone polymers, their Cu(II) complexes and the Schiff base salicylate derivatives inhibited cell growth. None of the silicone-coated Fe3O4-MNPs were bioactive

Exploring the importance of cell-type-specific gene expression regulation and splicing in Parkinson’s disease

Parkinson’s disease (PD) is defined primarily as a movement disorder, but its symptoms extend beyond the diagnosis-defining motor symptoms. Among non-motor symptoms, dementia is one of the most common and debilitating, yet it remains relatively understudied in comparison to motor symptoms, in part due to the considerable clinical, genetic and pathologic overlap between Parkinson’s disease with dementia (PDD) and dementia with Lewy bodies (DLB). Common to all three diseases is a lack of disease-modifying therapies, the development of which requires knowledge of the genes, cell types and biological pathways affected in disease. In this thesis, publicly available brain-relevant functional genomic annotations were used to identify PD-relevant pathways and cell types in silico. PD heritability was not found enriched in a specific cell type or state; however, PD heritability was found significantly enriched in a lysosomal and loss-of-function-intolerant gene set, with the former highly expressed in astrocytic, microglial, and oligodendrocyte subtypes and the latter highly expressed in almost all tested cellular subtypes. In addition, new annotations were generated by applying bulk-tissue and single-nucleus RNA-sequencing to anterior cingulate cortex samples derived from individuals with PD, PDD and DLB. This pairing permitted cellular deconvolution of bulk-tissue gene expression; estimation of bulk-tissue cell-type abundances; and in-depth splicing analyses. These analyses found that PD, PDD and DLB were associated not just with one, but several cell types, including neuronal, glial and vascular cell types, suggesting that these are disorders of global pathways working across various cell types. Furthermore, these analyses illustrated the commonalities and differences between the three diseases in terms of associated pathways, cell types, and upstream regulators of splicing, observations that can be used to begin building a biological basis on which to distinguish these disorders

The World of ISSN—Standards Revisions and Related Projects

There are several ongoing projects that will be of interest to the library, publisher, and vendor communities, including the International ISSN Centre-Ulrich’s ISSN project, the revision of ISO-8, and the revision of the ISSN Standard (ISO-3297). The national centers that are participating in the ISSN IC-Ulrich’s project and how that project benefits the greater community of scholarly publishers and users of scholarly information, the project plan and progress of the ISO-8 revision (presentation of periodicals) that is related to ISSN and the NISO PIE-J recommended practice, and the status of and details about the proposed ISSN standard revision are outlined

Everything old is new again: ISSN in the digital environment

Abstract Abstract: If the International Standard Serial Number (ISSN) did not exist, someone would have to invent it. It’s that simple. In the current environment where databases contain many millions of records, unique identifiers are crucial. Most databases, indexes, and registries of journals require the use of the ISSN. ISSN is now a key element of OpenURL link resolution services that connect users to article content. New types of resources that require ISSN for identification continue to be created. New needs for ISSN, such as its role in identifying titles for print and digital archiving, continue to emerge. In a future world of linked data for libraries, identifiers—including the ISSN—will play an essential role. Dodds and Davis, authors of Linked Data Patterns, state that the single most important part of the Linked Data approach is the adoption of web-scale identifiers (URIs) to identify things of interest. This case study will provide background on the ISSN; describe ISSN traditional uses in the library, publishing, and information communities; discuss the enlarging scope of resources that are assigned ISSN; and elaborate on ISSN uses in the current digital environment including ROAD, a new ISSN database of open access scholarly resources. The case study will conclude with an exploration of ISSN potential in the future linked data environment. Keywords: ISSN. Digital environment. Data environment. Linked data. Semantic web. Tudo velho é novo outra vez: o ISSN no ambiente digital Resumo Se o Número Internacional Normalizado para Publicações Seriadas (ISSN) não existisse, alguém teria que inventá-lo. Simples assim. No atual ambiente onde bases de dados contêm muitos milhões de registros, identificadores únicos são cruciais. A maioria das bases, índices e registros de periódicos exigem o uso do ISSN. O ISSN é hoje um elemento-chave nos serviços de resolução de links OpenURL que conectam usuários ao conteúdo dos artigos. Novos tipos de recursos que exigem o ISSN para identificação continuam a ser criados. Novas necessidades para o ISSN, como seu papel na identificação de títulos para arquivamento impresso e digital, continuam a surgir. Em um mundo futuro de dados conectados para bibliotecas, identificadores – incluindo o ISSN – terão um papel essencial. Dodds e Davis, autores de Padrões de Dados Conectados, afirmam que a parte mais importante da abordagem de Dados Conectados é a adoção de identificadores em escala Web (URIs) para identificar coisas de interesse. Este estudo de caso oferece um histórico do ISSN; descreve os usos tradicionais do ISSN em bibliotecas, publicações e comunidades informacionais; discute o escopo crescente de recursos que recebem atribuição de ISSN; e elabora nos usos do ISSN no ambiente digital atual, incluindo ROAD, uma nova base de dados do ISSN de recursos acadêmicos de acesso aberto. Conclui com uma exploração do potencial do ISSN em ambientes futuros de dados conectados. Palavras-chave: ISSN. Ambiente digital. Ambiente de dados. Todo lo viejo es nuevo otra vez: el ISSN en el ambiente digital Resumen Si no existiera el Número Internacional Normalizado para Publicaciones Seriadas (ISSN), alguien tendría que inventarlo. Es así de simple. En el ambiente actual donde bases de datos contiene muchos millones de registros, identificadores únicos son cruciales. La mayoría de bases, índices y registros de periódicos requieren el uso del ISSN. El ISSN es hoy un elemento clave en servicios de resolución de enlaces OpenURL que conectan usuarios al contenido de los artículos. Nuevos tipos de recursos que requieren el ISSN para identificación continúan a ser creados. Nuevas necesidades para el ISSN, como su papel en la identificación de títulos para archivamiento impreso y digital, continúan a aparecer. En un mundo futuro de datos conectados para bibliotecas, identificadores – incluyendo el ISSN – tendrán un papel fundamental. Dodds y Davis, autores de Linkded Data Patterns, afirman que la parte más importante del abordaje de Datos Conectados es la adopción de identificadores en escala Web (URIs) para identificar cosas de interés. Este estudio de caso ofrece un histórico del ISSN; describe los usos tradicionales del ISSN en bibliotecas, publicaciones y comunidades informacionales; discute el alcance creciente de recursos que reciben asignación de ISSN; y elabora en los usos del ISSN en el ambiente digital actual, incluyendo ROAD, una nueva base de datos del ISSN de recursos académicos de acceso abierto. Concluye con una exploración del potencial del ISSN en ambientes futuros de datos conectados. Palabras clave: ISSN. Ambiente digital. Ambiente de dados

Formally calling the CoPs for staff working with first year students

Drawing on both Community of Practice (CoP) and First Year in Higher Education (FYHE) literature this nuts and bolts session will explore whether the FYHE community may be identified as a CoP. This discussion will be used as a springboard to a presentation on the development of CoPs that support the FYHE teaching community in other Australian universities and the establishment of the CoP for staff who work with first year students at Flinders University. The presentation will outline why a CoP was established to support first year teaching and how the initiative is progressing. Participants will be provided with time to either consider the CoPs at their own institutions or to consider whether investing in one is an appropriate strategy to support staff who work with first year students

ensemblQueryR: fast, flexible and high-throughput querying of Ensembl LD API endpoints in R

We present ensemblQueryR, a package providing an R interface to the Ensembl REST API that facilitates flexible, fast, user-friendly and R workflow integrable querying of Ensembl REST API linkage disequilibrium (LD) endpoints, optimised for high-throughput querying. ensemblQueryR achieves this through functions that are intuitive and amenable to custom code integration, use of familiar R object types as inputs and outputs, code optimisation and optional parallelisation functionality. For each LD endpoint, ensemblQueryR provides two functions, permitting both single-query and multi-query modes of operation. The multi-query functions are optimised for large query sizes and provide optional parallelisation to leverage available computational resources and minimise processing time. We demonstrate that ensemblQueryR has improved performance in terms of random access memory (RAM) usage and speed, delivering a 10-fold speed increase over analogous software whilst using a third of the RAM. Finally, ensemblQueryR is near-agnostic to operating system and computational architecture through availability of Docker and singularity images, making this tool widely accessible to the scientific community

ensemblQueryR: fast, flexible and high-throughput querying of Ensembl LD API endpoints in R

We present ensemblQueryR, an R package for querying Ensembl linkage disequilibrium (LD) endpoints. This package is flexible, fast and user-friendly, and optimised for high-throughput querying. ensemblQueryR uses functions that are intuitive and amenable to custom code integration, familiar R object types as inputs and outputs as well as providing parallelisation functionality. For each Ensembl LD endpoint, ensemblQueryR provides two functions, permitting both single- and multi-query modes of operation. The multi-query functions are optimised for large query sizes and provide optional parallelisation to leverage available computational resources and minimise processing time. We demonstrate improved computational performance of ensemblQueryR over an exisiting tool in terms of random access memory (RAM) usage and speed, delivering a 10-fold speed increase whilst using a third of the RAM. Finally, ensemblQueryR is near-agnostic to operating system and computational architecture through Docker and singularity images, making this tool widely accessible to the scientific community

ggtranscript: an R package for the visualization and interpretation of transcript isoforms using ggplot2

MOTIVATION: The advent of long-read sequencing technologies has increased demand for the visualisation and interpretation of transcripts. However, tools that perform such visualizations remain inflexible and lack the ability to easily identify differences between transcript structures. Here, we introduce ggtranscript, an R package that provides a fast and flexible method to visualize and compare transcripts. As a ggplot2 extension, ggtranscript inherits the functionality and familiarity of ggplot2 making it easy to use. AVAILABILITY: ggtranscript is an R package available at https://github.com/dzhang32/ggtranscript (DOI: https://doi.org/10.5281/zenodo.6374061) via an open-source MIT license. Further is available at https://dzhang32.github.io/ggtranscript/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online

Regional genetic correlations highlight relationships between neurodegenerative disease loci and the immune system

Neurodegenerative diseases, including Alzheimer’s and Parkinson’s disease, are devastating complex diseases resulting in physical and psychological burdens on patients and their families. There have been important efforts to understand their genetic basis leading to the identification of disease risk-associated loci involved in several molecular mechanisms, including immune-related pathways. Regional, in contrast to genome-wide, genetic correlations between pairs of immune and neurodegenerative traits have not been comprehensively explored, but could uncover additional immune-mediated risk-associated loci. Here, we systematically assess the role of the immune system in five neurodegenerative diseases by estimating regional genetic correlations between these diseases and immune-cell-derived single-cell expression quantitative trait loci (sc-eQTLs). We also investigate correlations between diseases and protein levels. We observe significant (FDR < 0.01) correlations between sc-eQTLs and neurodegenerative diseases across 151 unique genes, spanning both the innate and adaptive immune systems, across most diseases tested. With Parkinson’s, for instance, RAB7L1 in CD4+ naïve T cells is positively correlated and KANSL1-AS1 is negatively correlated across all adaptive immune cell types. Follow-up colocalization highlight candidate causal risk genes. The outcomes of this study will improve our understanding of the immune component of neurodegeneration, which can warrant repurposing of existing immunotherapies to slow disease progression