Mechanistic information on the copper-catalysed autoxidation of mercaptosuccinic acid in aqueous solutionElectronic supplementary information (ESI) available: Spectral changes during reaction. See http://www.rsc.org/suppdata/dt/b3/b311053b/

2004 ◽  
pp. 292 ◽  
Author(s):  
Marek Pawelec ◽  
Gra?yna Stochel ◽  
Rudi van Eldik
Keyword(s):  
Supplementary Information ◽  
Spectral Changes ◽  
Mercaptosuccinic Acid

scholarly journals ccNetViz: a WebGL-based JavaScript library for visualization of large networks

2020 ◽  
Vol 36 (16) ◽  
pp. 4527-4529
Author(s):  
Ales Saska ◽  
David Tichy ◽  
Robert Moore ◽  
Achilles Rasquinha ◽  
Caner Akdas ◽  
...  
Keyword(s):  
Systems Biology ◽  
Complex Networks ◽  
Open Source ◽  
High Speed ◽  
A Priori ◽  
Supplementary Information ◽  
Network Visualization ◽  
Supplementary Data ◽  
Web Based ◽  
Flow Of Information

Abstract Summary Visualizing a network provides a concise and practical understanding of the information it represents. Open-source web-based libraries help accelerate the creation of biologically based networks and their use. ccNetViz is an open-source, high speed and lightweight JavaScript library for visualization of large and complex networks. It implements customization and analytical features for easy network interpretation. These features include edge and node animations, which illustrate the flow of information through a network as well as node statistics. Properties can be defined a priori or dynamically imported from models and simulations. ccNetViz is thus a network visualization library particularly suited for systems biology. Availability and implementation The ccNetViz library, demos and documentation are freely available at http://helikarlab.github.io/ccNetViz/. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals MODER2: first-order Markov modeling and discovery of monomeric and dimeric binding motifs

2020 ◽  
Vol 36 (9) ◽  
pp. 2690-2696
Author(s):  
Jarkko Toivonen ◽  
Pratyush K Das ◽  
Jussi Taipale ◽  
Esko Ukkonen
Keyword(s):  
Markov Models ◽  
Expectation Maximization Algorithm ◽  
Software Tool ◽  
Specific Weight ◽  
Training Data ◽  
Supplementary Information ◽  
Markov Modeling ◽  
Binding Motifs ◽  
The Difference ◽  
Probability Matrices

Abstract Motivation Position-specific probability matrices (PPMs, also called position-specific weight matrices) have been the dominating model for transcription factor (TF)-binding motifs in DNA. There is, however, increasing recent evidence of better performance of higher order models such as Markov models of order one, also called adjacent dinucleotide matrices (ADMs). ADMs can model dependencies between adjacent nucleotides, unlike PPMs. A modeling technique and software tool that would estimate such models simultaneously both for monomers and their dimers have been missing. Results We present an ADM-based mixture model for monomeric and dimeric TF-binding motifs and an expectation maximization algorithm MODER2 for learning such models from training data and seeds. The model is a mixture that includes monomers and dimers, built from the monomers, with a description of the dimeric structure (spacing, orientation). The technique is modular, meaning that the co-operative effect of dimerization is made explicit by evaluating the difference between expected and observed models. The model is validated using HT-SELEX and generated datasets, and by comparing to some earlier PPM and ADM techniques. The ADM models explain data slightly better than PPM models for 314 tested TFs (or their DNA-binding domains) from four families (bHLH, bZIP, ETS and Homeodomain), the ADM mixture models by MODER2 being the best on average. Availability and implementation Software implementation is available from https://github.com/jttoivon/moder2. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Returning to dialysis after kidney allograft failure: the experience of the Italian Registry of Paediatric Chronic Dialysis

2021 ◽  
Author(s):  
Edoardo La Porta ◽  
Ester Conversano ◽  
Daniela Zugna ◽  
Roberta Camilla ◽  
Raffaella Labbadia ◽  
...  
Keyword(s):  
Kidney Transplantation ◽  
Chronic Dialysis ◽  
Supplementary Information ◽  
Dialysis Modality ◽  
Specific Population ◽  
Kidney Allograft ◽  
Allograft Failure ◽  
Younger Age ◽  
Complicated Course ◽  
Significant Mortality

Abstract Background The need for dialysis after kidney allograft failure (DAGF) is among the top five reasons for dialysis initiation, making this an important topic in clinical nephrology. However, data are scarce on dialysis choice after transplantation and clinical outcomes for DAGF in children. Methods Patients receiving chronic dialysis < 18 years were recorded from January 1991 to January 2019 by the Italian Registry of Pediatric Chronic Dialysis (IRPCD). We investigated factors influencing choice of dialysis modality, patient outcome in terms of mortality, switching dialysis modality, and kidney transplantation. Results Among 118 patients receiving DAGF, 41 (35%) were treated with peritoneal dialysis (PD), and 77 (65%) with haemodialysis (HD). Significant predictors for treatment with PD were younger age at dialysis start (OR 0.85 per year increase [95%CI 0.72–1.00]) and PD use before kidney transplantation (OR 8.20 [95%CI 1.82–37.01]). Patients entering DAGF in more recent eras (OR 0.87 per year increase [95%CI 0.80–0.94]) and with more than one dialysis modality before kidney transplantation (OR 0.56 for being treated with PD [0.12–2.59]) were more likely to be initiated on HD. As compared to patients on HD, those treated with PD exhibited increased but non-significant mortality risk (HR 2.15 [95%CI 0.54–8.6]; p = 0.28) and higher prevalence of dialysis-related complications during DAGF (p = 0.002) Conclusions Patients entering DAGF in more recent years are more likely to be initiated on HD. In this specific population of children, use of PD seems associated with a more complicated course. Graphical abstract A higher resolution version of the Graphical abstract is available as Supplementary information

scholarly journals How the Multiplicity of Suggested Information Affects the Behavior of a User in a Recommender System

Electronics ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 741
Author(s):  
Yuseok Ban ◽  
Kyungjae Lee
Keyword(s):  
High Precision ◽  
Recommender System ◽  
Visual Information ◽  
Experimental Results ◽  
Supplementary Information ◽  
Digital Platform ◽  
Different Types ◽  
Types Of Information

Many researchers have suggested improving the retention of a user in the digital platform using a recommender system. Recent studies show that there are many potential ways to assist users to find interesting items, other than high-precision rating predictions. In this paper, we study how the diverse types of information suggested to a user can influence their behavior. The types have been divided into visual information, evaluative information, categorial information, and narrational information. Based on our experimental results, we analyze how different types of supplementary information affect the performance of a recommender in terms of encouraging users to click more items or spend more time in the digital platform.

TIGER: inferring DNA replication timing from whole-genome sequence data

2021 ◽  
Author(s):  
Amnon Koren ◽  
Dashiell J Massey ◽  
Alexa N Bracci
Keyword(s):  
Dna Replication ◽  
Genome Sequence ◽  
Genomic Dna ◽  
Sequence Data ◽  
Replication Timing ◽  
Whole Genome Sequence ◽  
Supplementary Information ◽  
Whole Genome ◽  
Genome Sequence Data ◽  
Dna Replication Timing

Abstract Motivation Genomic DNA replicates according to a reproducible spatiotemporal program, with some loci replicating early in S phase while others replicate late. Despite being a central cellular process, DNA replication timing studies have been limited in scale due to technical challenges. Results We present TIGER (Timing Inferred from Genome Replication), a computational approach for extracting DNA replication timing information from whole genome sequence data obtained from proliferating cell samples. The presence of replicating cells in a biological specimen leads to non-uniform representation of genomic DNA that depends on the timing of replication of different genomic loci. Replication dynamics can hence be observed in genome sequence data by analyzing DNA copy number along chromosomes while accounting for other sources of sequence coverage variation. TIGER is applicable to any species with a contiguous genome assembly and rivals the quality of experimental measurements of DNA replication timing. It provides a straightforward approach for measuring replication timing and can readily be applied at scale. Availability and Implementation TIGER is available at https://github.com/TheKorenLab/TIGER. Supplementary information Supplementary data are available at Bioinformatics online

scholarly journals Color-tuning of natural variants of heliorhodopsin

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Se-Hwan Kim ◽  
Kimleng Chuon ◽  
Shin-Gyu Cho ◽  
Ahreum Choi ◽  
Seanghun Meas ◽  
...  
Keyword(s):  
3D Structure ◽  
Site Directed Mutagenesis ◽  
Type I ◽  
Transmembrane Helices ◽  
Color Tuning ◽  
Tuning Mechanism ◽  
Spectral Changes ◽  
His Tag ◽  
Natural Variants ◽  
Retinal Chromophore

AbstractMicrobial rhodopsins are distributed through many microorganisms. Heliorhodopsins are newly discovered but have an unclear function. They have seven transmembrane helices similar to type-I and type-II rhodopsins, but they are different in that the N-terminal region of heliorhodopsin is cytoplasmic. We chose 13 representative heliorhodopsins from various microorganisms, expressed and purified with an N-terminal His tag, and measured the absorption spectra. The 13 natural variants had an absorption maximum (λmax) in the range 530–556 nm similar to proteorhodopsin (λmax = 490–525 nm). We selected several candidate residues that influence rhodopsin color-tuning based on sequence alignment and constructed mutants via site-directed mutagenesis to confirm the spectral changes. We found two important residues located near retinal chromophore that influence λmax. We also predict the 3D structure via homology-modeling of Thermoplasmatales heliorhodopsin. The results indicate that the color-tuning mechanism of type-I rhodopsin can be applied to understand the color-tuning of heliorhodopsin.

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