Growth of individual hydrogen-bonded nanostructures on gold monolayersElectronic supplementary information (ESI) available: Characterization of compound 2, assemblies 13·(DEB)6, 12·2·(DEB)6 and preparation of monolayers. See http://www.rsc.org/suppdata/cc/b2/b210996d/

2003 ◽  
pp. 352-353 ◽  
Author(s):  
Juan J. Garcia-Lopez ◽  
Szczepan Zapotoczny ◽  
Peter Timmerman ◽  
Frank C. J. M. van Veggel ◽  
G. Julius Vancso ◽  
...  
Keyword(s):  
Supplementary Information ◽  
Hydrogen Bonded

scholarly journals CSMD: a computational subtraction-based microbiome discovery pipeline for species-level characterization of clinical metagenomic samples

2019 ◽  
Author(s):  
Yu Liu ◽  
Paul W Bible ◽  
Bin Zou ◽  
Qiaoxing Liang ◽  
Cong Dong ◽  
...  
Keyword(s):  
Species Level ◽  
Supplementary Information ◽  
Clinical Samples ◽  
Plasma Dna ◽  
Bioinformatics Pipeline ◽  
Microbial Identification ◽  
Reference Databases ◽  
Microbial Dna ◽  
Higher Sensitivity

Abstract Motivation Microbiome analyses of clinical samples with low microbial biomass are challenging because of the very small quantities of microbial DNA relative to the human host, ubiquitous contaminating DNA in sequencing experiments and the large and rapidly growing microbial reference databases. Results We present computational subtraction-based microbiome discovery (CSMD), a bioinformatics pipeline specifically developed to generate accurate species-level microbiome profiles for clinical samples with low microbial loads. CSMD applies strategies for the maximal elimination of host sequences with minimal loss of microbial signal and effectively detects microorganisms present in the sample with minimal false positives using a stepwise convergent solution. CSMD was benchmarked in a comparative evaluation with other classic tools on previously published well-characterized datasets. It showed higher sensitivity and specificity in host sequence removal and higher specificity in microbial identification, which led to more accurate abundance estimation. All these features are integrated into a free and easy-to-use tool. Additionally, CSMD applied to cell-free plasma DNA showed that microbial diversity within these samples is substantially broader than previously believed. Availability and implementation CSMD is freely available at https://github.com/liuyu8721/csmd. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Jasmine: a Java pipeline for isomiR characterization in miRNA-Seq data

2019 ◽  
Author(s):  
Xiangfu Zhong ◽  
Albert Pla ◽  
Simon Rayner
Keyword(s):  
Population Structure ◽  
Software Tool ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Analysis Pipeline ◽  
Detailed Characterization ◽  
Fasta Format ◽  
Java Application

Abstract Motivation The existence of complex subpopulations of miRNA isoforms, or isomiRs, is well established. While many tools exist for investigating isomiR populations, they differ in how they characterize an isomiR, making it difficult to compare results across different tools. Thus, there is a need for a more comprehensive and systematic standard for defining isomiRs. Such a standard would allow investigation of isomiR population structure in progressively more refined sub-populations, permitting the identification of more subtle changes between conditions and leading to an improved understanding of the processes that generate these differences. Results We developed Jasmine, a software tool that incorporates a hierarchal framework for characterizing isomiR populations. Jasmine is a Java application that can process raw read data in fastq/fasta format, or mapped reads in SAM format to produce a detailed characterization of isomiR populations. Thus, Jasmine can reveal structure not apparent in a standard miRNA-Seq analysis pipeline. Availability and implementation Jasmine is implemented in Java and R and freely available at bitbucket https://bitbucket.org/bipous/jasmine/src/master/. Contact [email protected] Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Network-based characterization of disease–disease relationships in terms of drugs and therapeutic targets

2020 ◽  
Vol 36 (Supplement_1) ◽  
pp. i516-i524
Author(s):  
Midori Iida ◽  
Michio Iwata ◽  
Yoshihiro Yamanishi
Keyword(s):  
Large Scale ◽  
Expression Patterns ◽  
Therapeutic Targets ◽  
Molecular Networks ◽  
Supplementary Information ◽  
New Associations ◽  
Disease States ◽  
Molecular Features ◽  
Novel Approach

Abstract Motivation Disease states are distinguished from each other in terms of differing clinical phenotypes, but characteristic molecular features are often common to various diseases. Similarities between diseases can be explained by characteristic gene expression patterns. However, most disease–disease relationships remain uncharacterized. Results In this study, we proposed a novel approach for network-based characterization of disease–disease relationships in terms of drugs and therapeutic targets. We performed large-scale analyses of omics data and molecular interaction networks for 79 diseases, including adrenoleukodystrophy, leukaemia, Alzheimer's disease, asthma, atopic dermatitis, breast cancer, cystic fibrosis and inflammatory bowel disease. We quantified disease–disease similarities based on proximities of abnormally expressed genes in various molecular networks, and showed that similarities between diseases could be explained by characteristic molecular network topologies. Furthermore, we developed a kernel matrix regression algorithm to predict the commonalities of drugs and therapeutic targets among diseases. Our comprehensive prediction strategy indicated many new associations among phenotypically diverse diseases. Supplementary information Supplementary data are available at Bioinformatics online.

Self-Assembly and Characterization of A Novel Hydrogen-Bonded Nanostructure

2004 ◽  
Vol 108 (20) ◽  
pp. 6256-6260 ◽  
Author(s):  
Yang Liu ◽  
Shengqiang Xiao ◽  
Hongmei Li ◽  
Yuliang Li ◽  
Huibiao Liu ◽  
...  
Keyword(s):  
Self Assembly ◽  
Hydrogen Bonded

Crystal structure and characterization of the novel hydrogen bonded polar crystal

2012 ◽  
Vol 187 ◽  
pp. 35-44 ◽  
Author(s):  
M. Wojtaś ◽  
A. Ga¸gor ◽  
O. Czupiński ◽  
W. Medycki ◽  
R. Jakubas
Keyword(s):  
Crystal Structure ◽  
The Novel ◽  
Polar Crystal ◽  
Hydrogen Bonded

scholarly journals Reflection Absorption Infrared Spectroscopy Characterization of SAM Formation from 8-Mercapto-N-(phenethyl)octanamide Thiols with Phe Ring and Amide Groups

Molecules ◽  
2020 ◽  
Vol 25 (23) ◽  
pp. 5633
Author(s):  
Zenonas Kuodis ◽  
Ieva Matulaitienė ◽  
Marija Špandyreva ◽  
Linas Labanauskas ◽  
Sigitas Stončius ◽  
...  
Keyword(s):  
Infrared Spectroscopy ◽  
Self Assembled Monolayers ◽  
Trans Conformation ◽  
Band Frequency ◽  
Reflection Absorption Infrared Spectroscopy ◽  
Assembled Monolayers ◽  
Vibrational Bands ◽  
Induced Changes ◽  
Hydrogen Bonded

Multifunctional amide-containing self-assembled monolayers (SAMs) provide prospects for the construction of interfaces with required physicochemical properties and distinctive stability. In this study, we report the synthesis of amide-containing thiols with terminal phenylalanine (Phe) ring functionality (HS(CH2)7CONH(CH2)2C6H5) and the characterization of the formation of SAMs from these thiols on gold by reflection absorption infrared spectroscopy (RAIRS). For reliable assignments of vibrational bands, ring deuterated analogs were synthesized and studied as well. Adsorption time induced changes in Amide-II band frequency and relative intensity of Amide-II/Amide-I bands revealed two-state sigmoidal form dependence with a transition inflection points at 2.2 ± 0.5 and 4.7 ± 0.5 min, respectively. The transition from initial (disordered) to final (hydrogen-bonded, ordered) structure resulted in increased Amide-II frequency from 1548 to 1557 cm−1, which is diagnostic for a strongly hydrogen-bonded amide network in trans conformation. However, the lateral interactions between the alkyl chains were found to be somewhat reduced when compared with well-ordered alkane thiol monolayers.

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