Supplementary Information File Research Articles

Publisher Correction: Parallel genome reduction in symbionts descended from closely related free-living bacteria.

The Supplementary Information file originally published with this Article was missing Supplementary Figs 1-7. This has now been corrected.

Author Correction: The link between magnetic field orientations and star formation rates

In the Supplementary Information file originally published, Supplementary Table 1 was mistakenly omitted. This has now been corrected.

Publisher Correction: Measuring progress from nationally determined contributions to mid-century strategies

In the version of this Article previously published, technical problems led to the wrong summary appearing on the homepage, and an incorrect Supplementary Information file being uploaded. Both errors have now been corrected.

Author Correction: Earth’s early O2 cycle suppressed by primitive continents

In the Supplementary Information file originally published, notes were mistakenly omitted from Supplementary Table 4. This has now been corrected.

Enterovirus-associated changes in blood transcriptomic profiles of children with genetic susceptibility to type 1 diabetes

Aims/hypothesisEnterovirus infections have been associated with the development of type 1 diabetes in multiple studies, but little is known about enterovirus-induced responses in children at risk for developing type 1 diabetes. Our aim was to use genome-wide transcriptomics data to characterise enterovirus-associated changes in whole-blood samples from children with genetic susceptibility to type 1 diabetes.MethodsLongitudinal whole-blood samples (356 samples in total) collected from 28 pairs of children at increased risk for developing type 1 diabetes were screened for the presence of enterovirus RNA. Seven of these samples were detected as enterovirus-positive, each of them collected from a different child, and transcriptomics data from these children were analysed to understand the individual-level responses associated with enterovirus infections. Transcript clusters with peaking or dropping expression at the time of enterovirus positivity were selected as the enterovirus-associated signals.ResultsStrong signs of activation of an interferon response were detected in four children at enterovirus positivity, while transcriptomic changes in the other three children indicated activation of adaptive immune responses. Additionally, a large proportion of the enterovirus-associated changes were specific to individuals. An enterovirus-induced signature was built using 339 genes peaking at enterovirus positivity in four of the children, and 77 of these genes were also upregulated in human peripheral blood mononuclear cells infected in vitro with different enteroviruses. These genes separated the four enterovirus-positive samples clearly from the remaining 352 blood samples analysed.Conclusions/interpretationWe have, for the first time, identified enterovirus-associated transcriptomic profiles in whole-blood samples from children with genetic susceptibility to type 1 diabetes. Our results provide a starting point for understanding the individual responses to enterovirus infections in blood and their potential connection to the development of type 1 diabetes.Data availabilityThe datasets analysed during the current study are included in this published article and its supplementary information files (www.btk.fi/research/computational-biomedicine/1234-2) or are available from the Gene Expression Omnibus (GEO) repository (accession GSE30211).

Erratum: Acetate-mediated novel survival strategy against drought in plants

This corrects the article DOI: 10.1038/nplants.2017.97.

Correction: Corrigendum: Megafaunal isotopes reveal role of increased moisture on rangeland during late Pleistocene extinctions

Nature Ecology & Evolution 1, 0125 (2017); published 18 April 2017; corrected 5 June 2017. The Supplementary Information files that were originally published with the Article were not the intended final files. Both files have been updated.

Supporting precision medicine by data mining across multi-disciplines: an integrative approach for generating comprehensive linkages between single nucleotide variants (SNVs) and drug-binding sites.

Genetic variants in drug targets and metabolizing enzymes often have important functional implications, including altering the efficacy and toxicity of drugs. Identifying single nucleotide variants (SNVs) that contribute to differences in drug response and understanding their underlying mechanisms are fundamental to successful implementation of the precision medicine model. This work reports an effort to collect, classify and analyze SNVs that may affect the optimal response to currently approved drugs. An integrated approach was taken involving data mining across multiple information resources including databases containing drugs, drug targets, chemical structures, protein-ligand structure complexes, genetic and clinical variations as well as protein sequence alignment tools. We obtained 2640 SNVs of interest, most of which occur rarely in populations (minor allele frequency < 0.01). Clinical significance of only 9.56% of the SNVs is known in ClinVar, although 79.02% are predicted as deleterious. The examples here demonstrate that even if the mapped SNVs predicted as deleterious may not result in significant structural modifications, they can plausibly modify the protein-drug interactions, affecting selectivity and drug-binding affinity. Our analysis identifies potentially deleterious SNVs present on drug-binding residues that are relevant for further studies in the context of precision medicine. Data are available from Supplementary information file. yanli.wang@nih.gov. Supplementary Tables S1-S5 are available at Bioinformatics online.

ChemEngine: harvesting 3D chemical structures of supplementary data from PDF files.

Digital access to chemical journals resulted in a vast array of molecular information that is now available in the supplementary material files in PDF format. However, extracting this molecular information, generally from a PDF document format is a daunting task. Here we present an approach to harvest 3D molecular data from the supporting information of scientific research articles that are normally available from publisher’s resources. In order to demonstrate the feasibility of extracting truly computable molecules from PDF file formats in a fast and efficient manner, we have developed a Java based application, namely ChemEngine. This program recognizes textual patterns from the supplementary data and generates standard molecular structure data (bond matrix, atomic coordinates) that can be subjected to a multitude of computational processes automatically. The methodology has been demonstrated via several case studies on different formats of coordinates data stored in supplementary information files, wherein ChemEngine selectively harvested the atomic coordinates and interpreted them as molecules with high accuracy. The reusability of extracted molecular coordinate data was demonstrated by computing Single Point Energies that were in close agreement with the original computed data provided with the articles. It is envisaged that the methodology will enable large scale conversion of molecular information from supplementary files available in the PDF format into a collection of ready- to- compute molecular data to create an automated workflow for advanced computational processes. Software along with source codes and instructions available at https://sourceforge.net/projects/chemengine/files/?source=navbar.Graphical abstract. Electronic supplementary materialThe online version of this article (doi:10.1186/s13321-016-0175-x) contains supplementary material, which is available to authorized users.

Erratum: Is the detection of accelerated sea level rise imminent?

Scientific Reports 6: Article number: 31245; published online: 10 August 2016; updated: 10 November 2016 In the Supplementary Information file originally published with this Article, there was a typographical error in the legend of Figure S2 where “El Chichón” was incorrectly given as “El Chicón”. In addition, Figure S3 and its accompanying Figure legend were incorrect.

Corrigendum: Automated Axon Counting in Rodent Optic Nerve Sections with AxonJ.

Scientific Reports 6: Article number: 26559; published online: 26 May 2016; updated: 19 October 2016 In the Supplementary Information file originally published with this Article, Supplemental Figure 1 was omitted. In addition, “Supplemental Software” was incorrectly given as “Software Legend” These errors have now been corrected in the Supplementary Information that now accompanies the Article.

Corrigendum: From Allergens to Battery Anodes: Nature-Inspired, Pollen Derived Carbon Architectures for Room- and Elevated- Temperature Li-ion Storage.

Scientific Reports 6: Article number: 20290; published online: 05 February 2016; updated: 02 September 2016 Vinodkumar Etacheri was omitted from the author list in the original version of this Article. This has now been corrected in the PDF and HTML versions of the Article, as well as the Supplementary Information file that now accompanies the Article.

Corrigendum: ACT-PRESTO: Rapid and consistent tissue clearing and labeling method for 3-dimensional (3D) imaging.

Scientific Reports 6: Article number: 18631; published online: 11 January 2016; updated: 01 September 2016. In this Article and Supplementary Information file, some instances of ‘0.001M PBS’ and ‘0.01M PBS’ are incorrectly written as ‘0.01M PBS’ and ‘0.1M PBS’ respectively. With the exception of thefollowing:

Correction: Corrigendum: Towards combinatorial mixing devices without any pumps by open-capillary channels: fundamentals and applications

Scientific Reports 5: Article number: 10263; published online: 23 June 2015; updated: 07 September 2016 In the Supplementary Information file originally published with this Article, Figures S1 and S2 were omitted. These errors have been corrected in the Supplementary Information that now accompaniesthe Article.

Corrigendum: Assisted reproduction causes placental maldevelopment and dysfunction linked to reduced fetal weight in mice.

Scientific Reports 5: Article number: 10596; published online: 18 June 2015; updated: 20 July 2016 In the Supplementary Information file originally published with this Article, Tables S1–S3 were omitted. These errors have been corrected in the Supplementary Information that now accompanies the Article.

Erratum: Rate-dependent interface capture beyond the coffee-ring effect.

Scientific Reports 6: Article number: 24628; published online: 19 April 2016; updated: 27 June 2016. An incorrect Supplementary Information file was inadvertently published with this Article. In addition, Supplementary Movies 1–5 were omitted. The correct Supplementary Information and Supplementary Movies now accompany the Article.

Erratum: Membrane-proximal TRAIL species are incapable of inducing short circuit apoptosis signaling: Implications for drug development and basic cytokine biology.

Scientific Reports 6: Article number: 22661; published online: 03 March 2016; updated: 04 May 2016 In the Supplementary Information file originally published with this Article, references 32, 33 and 37 were incorrectly given as references 25, 26 and 35 respectively. These errors have been corrected in the Supplementary Information that now accompanies the Article.

Erratum: Kallikrein-related peptidase 8 is expressed in myocardium and induces cardiac hypertrophy.

Scientific Reports 6: Article number: 20024; published online: 29 January 2016; updated: 29 April 2016. The original version of this Article contained a typographical error in the spelling of the author Binhai Cong, which was incorrectly given as Binghai Cong. This has now been corrected in the PDF and HTML versions of the Article, as well as the Supplementary Information file that now accompanies the Article.

Erratum: Involvement of hormones in olfactory imprinting and homing in chum salmon.

Scientific Reports 6: Article number: 21102; published online: 16 February 2016; updated: 22 April 2016 In the Supplementary Information file originally published with this Article, the lower part of Fig. S1 ‘sGnRH-II’ was incorrectly labelled ‘GnRH-II’. This error has been corrected in the Supplementary Information that now accompanies the Article.

Erratum: Host Stress Drives Salmonella Recrudescence.

Scientific Reports 6: Article number: 20849; published online: 09 February 2016; updated: 15 April 2016. In the Supplementary Information file originally published with this Article, Figures S1-4, Tables S1, S2, S4 and S5 were omitted. This error has been corrected in the Supplementary Information that now accompanies the Article.