ZnII-induced conformational control of amphiphilic cavitands in Langmuir monolayersElectronic supplementary information (ESI) available: characterization of 1 and 2; protocol of Langmuir experiments performed on the water subphase at different pH; Job plot analysis. See http://www.rsc.org/suppdata/cc/b4/b405331a/

2004 ◽  
pp. 1362 ◽  
Author(s):  
Markus Frei ◽  
Federica Marotti ◽  
Fran�ois Diederich
Keyword(s):  
Supplementary Information ◽  
Conformational Control ◽  
Plot Analysis

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.

Conformational control via sequence for a heteropeptoid in water: coupled NMR and Rosetta modelling

2021 ◽  
Author(s):  
Trideep Rajale ◽  
Jacob Carlson Miner ◽  
Ryszard Michalczyk ◽  
M. Lisa Phipps ◽  
Jurgen Schmidt ◽  
...  
Keyword(s):  
Microwave Assisted Synthesis ◽  
Side Chains ◽  
Conformational Control ◽  
Microwave Assisted

We report a critical advance in the generation and characterization of peptoid hetero-oligomers. A library of sub-monomers with amine and carboxylate side-chains are combined in different sequences using microwave-assisted synthesis....

scholarly journals Characterization of Tar Deposits, Extraction and Sorption Properties

2016 ◽  
Vol 62 (2) ◽  
pp. 1-4
Author(s):  
Adrian Pryszcz ◽  
Barbora Grycová ◽  
Ivan Koutník ◽  
Veronika Blahůšková
Keyword(s):  
Storage Tank ◽  
Potassium Hydroxide ◽  
Surface Characterization ◽  
External Surface ◽  
Single Point ◽  
Experimental Part ◽  
Surface Areas ◽  
Plot Analysis ◽  
Bet Method

Abstract The main goal of this paper was to characterize and find a useful solution for the decomposition of tar deposits. For the experimental part, tar deposits, formed by polymerization and condensation reactions, were chosen from a storage tank for tars. At first the initial analyses of tar deposits (elemental, thermogravimetric, and calorimetric analyses) were performed. After the characterization, the tar deposits were extracted in the Soxhlet extractor by acetone, toluene, and quinolone and activated with potassium hydroxide. As the final step of this work, the sorption characterization on the 3Flex Surface Characterization Analyzer (Micromeritics) was performed. The specific surface area of the samples was evaluated using two methods - a single point measurement at p/p0=0.2 and BET method. Micropore and external surface areas were calculated based on a t-plot analysis (carbon black model).

Characterization of HRV by Poincare Plot Analysis among the Female Tea Garden Workers of Northern Hilly Regions of West Bengal

2012 ◽  
pp. 206-215
Author(s):  
Somsirsa Chatterjee ◽  
Ankur Ganguly ◽  
Saugat Bhattacharya
Keyword(s):  
Heart Rate ◽  
Heart Rate Variability ◽  
Standard Deviation ◽  
West Bengal ◽  
Mean Value ◽  
Short Term ◽  
Poincaré Plot ◽  
Plot Analysis ◽  
Tea Garden

Recent research on Heart Rate Variability (HRV) has proven that Poincare Plot is a powerful tool to mark Short Term and Long Term Heart Rate Variability. This study focuses a comprehensive characterization of HRV among the Tea Garden Workers of the Northern Hilly Regions of West Bengal. The characterization, as available from the data sets, projects the average values of SD1 characteristics, that is, Short Term HRV in females as 58.265ms and SD2 as 149.474. The SDRR shows a mean value of 87.298 with a standard deviation of 119.669 and the S Characterization as 16505.99 ms and Standard deviation of 45882.31 ms. The SDRR shows a mean value of 87.298 with a standard deviation of 119.669 and the S Characterization as 16505.99 ms and Standard deviation of 45882.31 ms. ApEn Characterization showed mean value of 0.961 and standard deviation of 0.274.

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.

CHARACTERIZATION OF THE FUNCTIONAL ADHESION PROPERTY OF THE MONOCYTE FIBRINOGEN RECEPTOR WITH A MONOCLONAL ANTIBODY (Mab) DIRECTED TO THE ACTIVATED STATE OF THE PLATELET GLYCOPROTEIN (GP) IIb/IIIa

1987 ◽  
Author(s):  
Dario C Altieri ◽  
Rossella Bader ◽  
Pier M Mannucci
Keyword(s):  
Surface Antigen ◽  
Platelet Glycoprotein ◽  
Blood Monocytes ◽  
Adhesion Properties ◽  
Fibrinogen Receptor ◽  
Plot Analysis ◽  
Straight Line ◽  
Platelet Receptor ◽  
Activated State

We recently showed that human blood monocytes bind fibrinogen through a genuine surface antigen only in part similar to the platelet GP Ilb/IIIa. Moreover, some anti-GP IIb/IIIa Mabs cross-react with monocytes. In this study we used the 7E3 Mab which preferentially binds to the activated conformation of the platelet GP IIb/IIIa to characterize the dynamic mechanism of "exposure" of the monocyte fibrinogen receptor. 7E3 Mab (25 μg/ml) completely suppressed the binding of i25I-fibrinogen to ADP (10μM)-stimulated monocytes. However, differently from the platelet GP IIb/IIIa, 125I-7E3 binding to unstimulated monocytes was a non-specific and non-saturable reaction. In contrast, after stimulation with ADP (10 μM), suspensions of human monocytes bound 125I-7E3 with saturation of 25-30 μg/ml of added Mab. Scatchard plot analysis was a single-affinity straight line revealing 97,400 binding sites/monocyte with a dissociation constant of 5.2×10−8 M. The monocyte surface antigen uniquely expressed after ADP-activation recognized by 7E3 was visualized by immunoprecipitation studies. Surface iodinated platelet lysate subjected to immunoprecipitation with 7E3 revealed a single band with molecular weight (Mr) of 116,000 corresponding to the platelet GP IIb/IIIa. In contrast, monocytes showed a dimeric surface antigen precipitated by 7E3 in two subunits with Mr=l55,000 and 95,000 respectively. These data indicate that the adhesion properties of the monocyte fibrinogen receptor defined by an anti-platelet GP IIb/IIIa cross-reacting Mab are structurally and functionally distinct from those of the platelet receptor.

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