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    <title>Paper on MillironX</title>
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    <description>Recent content in Paper on MillironX</description>
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    <lastBuildDate>Mon, 23 Oct 2023 00:00:00 +0000</lastBuildDate>
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      <title>nf-core/taxprofiler: highly parallelised and flexible pipeline for metagenomic taxonomic classification and profiling</title>
      <link>http://localhost:1313/academia/taxprofiler/</link>
      <pubDate>Mon, 23 Oct 2023 00:00:00 +0000</pubDate>
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      <description>&lt;p&gt;Metagenomic classification tackles the problem of characterising the taxonomic&#xA;source of all DNA sequencing reads in a sample. A common approach to address the&#xA;differences and biases between the many different taxonomic classification tools&#xA;is to run metagenomic data through multiple classification tools and databases.&#xA;This, however, is a very time-consuming task when performed manually -&#xA;particularly when combined with the appropriate preprocessing of sequencing&#xA;reads before the classification. Here we present nf-core/taxprofiler, a highly&#xA;parallelised read-processing and taxonomic classification pipeline. It is&#xA;designed for the automated and simultaneous classification and/or profiling of&#xA;both short- and long-read metagenomic sequencing libraries against a 11&#xA;taxonomic classifiers and profilers as well as databases within a single&#xA;pipeline run. Implemented in Nextflow and as part of the nf-core initiative, the&#xA;pipeline benefits from high levels of scalability and portability, accommodating&#xA;from small to extremely large projects on a wide range of computing&#xA;infrastructure. It has been developed following best-practise software&#xA;development practises and community support to ensure longevity and adaptability&#xA;of the pipeline, to help keep it up to date with the field of metagenomics.&lt;/p&gt;</description>
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      <title>Investigation of Hydronium Diffusion in Poly(vinyl alcohol) Hydrogels: A Critical First Step to Describe Acid Transport for Encapsulated Bioremediation</title>
      <link>http://localhost:1313/academia/hydronium-pva/</link>
      <pubDate>Fri, 02 Sep 2022 00:00:00 +0000</pubDate>
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      <description>&lt;p&gt;Bioremediation of chlorinated aliphatic hydrocarbon-contaminated aquifers can be&#xA;hindered by high contaminant concentrations and acids generated during&#xA;remediation. Encapsulating microbes in hydrogels may provide a protective,&#xA;tunable environment from inhibiting compounds; however, current approaches to&#xA;formulate successful encapsulated systems rely on trial and error rather than&#xA;engineering approaches because fundamental information on mass-transfer&#xA;coefficients is lacking. To address this knowledge gap, hydronium ion&#xA;mass-transfer rates through two commonly used hydrogel materials, poly(vinyl&#xA;alcohol) and alginic acid, under two solidification methods (chemical and&#xA;cryogenic) were measured. Variations in hydrogel crosslinking conditions,&#xA;polymer composition, and solvent ionic strength were investigated to understand&#xA;how each influenced hydronium ion diffusivity. A three-way ANOVA indicated that&#xA;the ionic strength, membrane type, and crosslinking method significantly (&lt;em&gt;p&lt;/em&gt; &amp;lt;&#xA;0.001) contributed to changes in hydronium ion mass transfer. Hydronium ion&#xA;diffusion increased with ionic strength, counter to what is observed in&#xA;aqueous-only (no polymer) solutions. Co-occurring mechanisms correlated to&#xA;increased hydronium ion diffusion with ionic strength included an increased&#xA;water fraction within hydrogel matrices and hydrogel contraction. Measured&#xA;diffusion rates determined in this study provide first principal design&#xA;information to further optimize encapsulating hydrogels for bioremediation.&lt;/p&gt;</description>
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      <title>Assessment of Porcine Rotavirus-associated virome variations in pigs with enteric disease</title>
      <link>http://localhost:1313/academia/rotavirus-virome/</link>
      <pubDate>Wed, 27 Apr 2022 00:00:00 +0000</pubDate>
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      <description>&lt;p&gt;Enteric disease is the predominant cause of morbidity and mortality in young&#xA;mammals including pigs. Viral species involved in porcine enteric disease&#xA;complex (PEDC) include rotaviruses, coronaviruses, picornaviruses, astroviruses&#xA;and pestiviruses among others. The virome of three groups of swine samples&#xA;submitted to the Kansas State University Veterinary Diagnostic Laboratory for&#xA;routine testing were assessed, namely, a Rotavirus A positive (RVA) group, a&#xA;Rotavirus co-infection (RV) group and a Rotavirus Negative (RV Neg) group. All&#xA;groups were designated by qRT-PCR results testing for Porcine Rotavirus A, B, C&#xA;and H such that samples positive for RVA only went in the RVA group, samples&#xA;positive for &amp;gt;1 rotavirus went in the RV group and samples negative for all were&#xA;grouped in the RVNeg group. All of the animals had clinical enteric disease&#xA;resulting in scours and swollen joints/lameness, enlarged heart and/or a cough.&#xA;All samples were metagenomic sequenced and analyzed for viral species&#xA;composition that identified 14 viral species and eight bacterial viruses/phages.&#xA;Sapovirus and Escherichia coli phages were found at a high prevalence in RVA and&#xA;RV samples but were found at low or no prevalence in the RV Neg samples.&#xA;Picobirnavirus was identified at a high proportion and prevalence in RV Neg and&#xA;RV samples but at a low prevalence in the RVA group. A sequence analysis of the&#xA;possible host of Picobirnaviruses revealed fungi as the most likely host.&#xA;Non-rotaviral diversity was highest in RVA samples followed by RV then RV Neg&#xA;samples. Various sequences were extracted from the sample reads and a&#xA;phylogenetic update was provided showing a high prevalence of G9 and P[23] RVA&#xA;genotypes. These data are important for pathogen surveillance and control&#xA;measures&lt;/p&gt;</description>
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