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Acetylated and butyrylated high amylose starch (HAMS-AB) is a prebiotic shown to be effective in type 1 diabetes (T1D) prevention in mouse models and is safe in adults with established T1D. HAMS-AB alters the gut microbiome profile with increased bacterial fermenters that produce short chain fatty acids (SCFAs) with anti-inflammatory and immune-modulatory effects. We performed a pilot study using a cross-over design to assess the safety and efficacy of 4 weeks of oral HAMS-AB consumption by recently diagnosed (< 2 years of diagnosis) youths with T1D. Seven individuals completed the study. The mean±SD age was 15.0±1.2 years, diabetes duration 19.5±6.3 months, 5/7 were female and 4/7 were White, all with a BMI of < 85th%. The prebiotic was safe. Following prebiotic intake, gut microbiome changes were seen, including a notable increase in the relative abundance of fermenters such as Bifidobacterium and Faecalibacterium. Treatment was also associated with changes in bacterial functional pathways associated with either improved energy metabolism (upregulation of tyrosine metabolism) or anti-inflammatory effects (reduced geraniol degradation). There were no differences in stool SCFA levels. Plasma metabolites associated with improved glycemia, such as hippurate, were significantly increased after treatment and there were positive and significant changes in the immune regulatory function of mucosal associated invariant T cells. There was a significant decrease in the area under the curve glucose but not C-peptide, as measured during a mixed meal tolerance testing, following the prebiotic consumption. In summary, the prebiotic HAMS-AB was safe in adolescents with T1D and showed promising effects on the gut microbiome composition, function and immune regulatory function.

[3.1] - 2021-05-13 :warning: Major enhancements Samplesheet format has changed from <code>group,replicate,fastq_1,fastq_2,strandedness</code> to <code>sample,fastq_1,fastq_2,strandedness</code> This gives users the flexibility to name their samples however they wish (see #550) PCA generated by DESeq2 will now be monochrome and will not be grouped by using the replicate id Updated Nextflow version to <code>v21.04.0</code> (see nextflow#572) Restructure pipeline scripts into <code>modules/</code>, <code>subworkflows/</code> and <code>workflows/</code> directories Enhancements &amp; fixes Updated pipeline template to nf-core/tools <code>1.14</code> Initial implementation of a standardised samplesheet JSON schema to use with user interfaces and for validation Only FastQ files that require to be concatenated will be passed to <code>CAT_FASTQ</code> process [#449] - <code>--genomeSAindexNbases</code> will now be auto-calculated before building STAR indices [#460] - Auto-detect and bypass featureCounts execution if biotype doesn't exist in GTF [#544] - Update test-dataset for pipeline [#553] - Make tximport output files using all the samples; identified by @j-andrews7 [#561] - Add gene symbols to merged output; identified by @grst [#563] - samplesheet.csv merge error [#567] - Update docs to mention trimgalore core usage nuances [#568] - <code>--star_index</code> argument is ignored with <code>--aligner star_rsem</code> option [#569] - nextflow edge release documentation for running 3.0 [#575] - Remove duplicated salmon output files [#576] - umi_tools dedup : Run before salmon to dedup counts [#582] - Generate a separate bigwig tracks for each strand [#583] - Samtools error during run requires use of BAM CSI index [#585] - Clarify salmon uncertainty for some transcripts [#604] - Additional fasta with GENCODE annotation results in biotype error [#610] - save R objects as RDS [#619] - implicit declaration of the workflow in main [#629] - Add and fix EditorConfig linting in entire pipeline [nf-core/modules#423] - Replace <code>publish_by_id</code> module option to <code>publish_by_meta</code> [nextflow#2060] - Pipeline execution hang when native task fail to be submitted Parameters Old parameter New parameter <code>--hisat_build_memory</code> <code>--hisat2_build_memory</code> <code>--gtf_count_type</code> <code>--featurecounts_feature_type</code> <code>--gtf_group_features_type</code> <code>--featurecounts_group_type</code> <code>--bam_csi_index</code> <code>--schema_ignore_params</code> <code>--show_hidden_params</code> <code>--validate_params</code> <code>--clusterOptions</code> <strong>NB:</strong> Parameter has been <strong>updated</strong> if both old and new parameter information is present. <strong>NB:</strong> Parameter has been <strong>added</strong> if just the new parameter information is present. <strong>NB:</strong> Parameter has been <strong>removed</strong> if parameter information isn't present. Software dependencies Note, since the pipeline is now using Nextflow DSL2, each process will be run with its own Biocontainer. This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference. Dependency Old version New version <code>bedtools</code> 2.29.2 2.30.0 <code>multiqc</code> 1.9 1.10.1 <code>preseq</code> 2.0.3 3.1.2 <strong>NB:</strong> Dependency has been <strong>updated</strong> if both old and new version information is present. <strong>NB:</strong> Dependency has been <strong>added</strong> if just the new version information is present. <strong>NB:</strong> Dependency has been <strong>removed</strong> if version information isn't present.

The chiral tetradentate N4-donor ligand, 1-methyl-2-({(S)-2-[(S)-1-(1-methylbenzimidazol-2-yl methyl)pyrrolidin-2-yl]pyrrolidin-1-yl}methyl) benzimidazole (S,S-PDBzL), based on a chiral dipyrrolidine backbone, has been synthesized and its corresponding Fe(ii) complex has been prepared and characterized. The X-ray structure of the complex reveals that the Fe(ii) ion is in a distorted octahedral coordination environment with two cis-oriented coordination sites occupied by (labile) triflate anions. The ability of the iron complex to catalyze asymmetric epoxidation reactions of olefins with H2O2 was investigated, using 2-cyclohexen-1-one, 2-cyclopenten-1-one, cis-β-methylstyrene, isophorone, chalcones and tetralones as substrates. Different carboxylic acids were used as additives to enhance yields and enantioselectivities, and 2-ethylhexanoic acid was found to give the best results. The catalysis results indicate that the Fe(ii) complex is capable of effecting comparatively high enantioselectivities (>80%) in the epoxidation reactions.

Abstract Using Genome Wide Association Studies (GWAS), we and others have previously identified and replicated genetic variations in chromosome 5p12, 8q24 and 11q13. Interestingly, the majority of risk-associated variations map to non-coding regions of the genome and thus, the molecular mechanism of single nucleotide polymorphisms (SNPs) underlying increased cancer risk remains unknown. To assess whether these SNPs could affect the biogenesis and function of non-coding RNA species, such as microRNAs (miRNA), here we assessed miRNA gene polymorphisms in these cancer susceptibility loci. We catalogued two miRNA genes in 5p12, sixteen miRNA genes in 8q24, and seven miRNA genes in 11q13. We re-sequenced the pri- and pre-miRNA genomic sequences in these loci using HapMap DNA samples. As a result, in 8q24 miRNA genes, we identified three new SNPs and confirmed two previously reported SNPs. In 11q13, we identified four genetic variations within different miRNA genes. However, linkage disequilibrium plot analysis of both loci didn't show any statistically significant association of any of these SNPs with their corresponding GWAS signals. Thus, we consider it unlikely that miRNA in these regions are direct downstream effectors of cancer-associated genetic variations. Nevertheless, because these risk loci are prone to genomic instability, we assessed whether the SNPs could affect miRNA gene expression since indirect associations with increased cancer susceptibility can't be excluded. To address this question, we cloned pre-miRNA genes from these loci, with or without genetic variations, into miRNA expression vectors and determined their relative expression in transfected 293T cells. We tested for an 8q24-encoded miRNA (miR-1206) or an 11q13 encoded-miRNA (miR-612) expression using miRNA TaqMan assays, and we found that the G allele polymorphism (rs2114358) in miR-1206 significantly downregulated miRNA expression levels compared to the reference A allele. On the other hand, an rs550894 (C/A) in miR-612 significantly upregulated miRNA expression levels compared to that of the reference C allele. These data indicate that the miRNA SNPs in these loci have indeed functional consequences that lead to dysregulation of miRNA biogenesis. Whether such changes in miRNA expression could also result in increased cancer risk needs to be assessed in future studies by identifying the downstream target genes of these miRNAs. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 1170. doi:10.1158/1538-7445.AM2011-1170

Social insects—ants, bees, wasps, and termites—and the distributed problem-solving, multi-agent paradigm that they represent, have been enormously influential in nature-inspired computing. Insect societies have been a source of inspiration and amazement for centuries, but only in the last 25 years or so have we made significant inroads to both understanding just how various collective phenomena arise and are governed, and how we can use the lessons and insights garnered from sociobiological research for more practical purposes. In this chapter, we provide a very brief history of the field, detailing some of the key phenomena, mechanisms, and lessons learned, and a quick tour of some of the different types of applications to which this knowledge has been put to use, including but certainly not limited to distributed problem solving, task allocation, search, and collective robotics.