scholarly journals RecRWR: A Recursive Random Walk Method for Improved Identification of Diseases

2015 ◽  
Vol 2015 ◽  
pp. 1-7
Author(s):  
Joel Perdiz Arrais ◽  
José Luís Oliveira
Keyword(s):  
Random Walk ◽  
Dna Microarrays ◽  
Physical Interaction ◽  
Biomedical Data ◽  
Biological Processes ◽  
Biological Noise ◽  
Random Walk With Restarts ◽  
Generation Sequencing ◽  
Selection Of ◽  
Best Disease

High-throughput methods such as next-generation sequencing or DNA microarrays lack precision, as they return hundreds of genes for a single disease profile. Several computational methods applied to physical interaction of protein networks have been successfully used in identification of the best disease candidates for each expression profile. An open problem for these methods is the ability to combine and take advantage of the wealth of biomedical data publicly available. We propose an enhanced method to improve selection of the best disease targets for a multilayer biomedical network that integrates PPI data annotated with stable knowledge from OMIM diseases and GO biological processes. We present a comprehensive validation that demonstrates the advantage of the proposed approach, Recursive Random Walk with Restarts (RecRWR). The obtained results outline the superiority of the proposed approach, RecRWR, in identifying disease candidates, especially with high levels of biological noise and benefiting from all data available.

An Insight into Oligopeptide Transporter 3 (OPT3) family proteins

2020 ◽  
Vol 27 ◽  
Author(s):  
Fırat Kurt
Keyword(s):  
Stress Responses ◽  
Chelating Agent ◽  
Biological Processes ◽  
Biotic And Abiotic Stress ◽  
Oligopeptide Transporter ◽  
Binding Residues ◽  
Fe Homeostasis ◽  
Proteins Interactions ◽  
Insight Into ◽  
Selection Of

: Oligopeptide transporter 3 (OPT3) proteins are one of the subsets of OPT clade, yet little is known about these transporters. Therefore, homolog OPT3 proteins in several plant species were investigated and characterized using bioinformatical tools. Motif and co-expression analyses showed that OPT3 proteins may be involved in both biotic and abiotic stress responses as well as growth and developmental processes. AtOPT3 usually seemed to take part in Fe homeostasis whereas ZmOPT3 putatively interacted with proteins involved in various biological processes from plant defense system to stress responses. Glutathione (GSH), as a putative alternative chelating agent, was used in the AtOPT3 and ZmOPT3 docking analyses to identify their putative binding residues. The information given in this study will contribute to the understanding of OPT3 proteins’ interactions in various pathways and to the selection of potential ligands for OPT3s.

scholarly journals Incorporating radiomics into clinical trials: expert consensus on considerations for data-driven compared to biologically driven quantitative biomarkers

2021 ◽  
Author(s):  
Laure Fournier ◽  
Lena Costaridou ◽  
Luc Bidaut ◽  
Nicolas Michoux ◽  
Frederic E. Lecouvet ◽  
...  
Keyword(s):  
Clinical Trials ◽  
Quantitative Imaging ◽  
A Priori ◽  
External Validation ◽  
Data Driven ◽  
Imaging Biomarkers ◽  
Clinical Validation ◽  
Biological Processes ◽  
Imaging Data ◽  
Selection Of

Abstract Existing quantitative imaging biomarkers (QIBs) are associated with known biological tissue characteristics and follow a well-understood path of technical, biological and clinical validation before incorporation into clinical trials. In radiomics, novel data-driven processes extract numerous visually imperceptible statistical features from the imaging data with no a priori assumptions on their correlation with biological processes. The selection of relevant features (radiomic signature) and incorporation into clinical trials therefore requires additional considerations to ensure meaningful imaging endpoints. Also, the number of radiomic features tested means that power calculations would result in sample sizes impossible to achieve within clinical trials. This article examines how the process of standardising and validating data-driven imaging biomarkers differs from those based on biological associations. Radiomic signatures are best developed initially on datasets that represent diversity of acquisition protocols as well as diversity of disease and of normal findings, rather than within clinical trials with standardised and optimised protocols as this would risk the selection of radiomic features being linked to the imaging process rather than the pathology. Normalisation through discretisation and feature harmonisation are essential pre-processing steps. Biological correlation may be performed after the technical and clinical validity of a radiomic signature is established, but is not mandatory. Feature selection may be part of discovery within a radiomics-specific trial or represent exploratory endpoints within an established trial; a previously validated radiomic signature may even be used as a primary/secondary endpoint, particularly if associations are demonstrated with specific biological processes and pathways being targeted within clinical trials. Key Points • Data-driven processes like radiomics risk false discoveries due to high-dimensionality of the dataset compared to sample size, making adequate diversity of the data, cross-validation and external validation essential to mitigate the risks of spurious associations and overfitting. • Use of radiomic signatures within clinical trials requires multistep standardisation of image acquisition, image analysis and data mining processes. • Biological correlation may be established after clinical validation but is not mandatory.

scholarly journals Nanometre-Scale Visualization of Chemical Parameter Changes by T1-Weighted ODMR Imaging Using a Fluorescent Nanodiamond

Chemosensors ◽  
2020 ◽  
Vol 8 (3) ◽  
pp. 68
Author(s):  
Takahiro Fujisaku ◽  
Ryuji Igarashi ◽  
Masahiro Shirakawa
Keyword(s):  
Magnetic Resonance ◽  
Laser Pulse ◽  
Real Time ◽  
Physical Parameters ◽  
Biological Processes ◽  
Chemical Parameter ◽  
Ph Conditions ◽  
Optically Detected ◽  
Life Phenomena ◽  
Selection Of

The dynamics of physical parameters in cells is strongly related to life phenomena; thus, a method to monitor and visualize them on a single-organelle scale would be useful to reveal unknown biological processes. We demonstrate real-time nanometre-scale T1-weighted imaging using a fluorescent nanodiamond. We explored optically detected magnetic resonance (ODMR) contrast at various values of interval laser pulse (τ), showing that sufficient contrast is obtained by appropriate selection of τ. By this method, we visualized nanometre-scale pH changes using a functionalized nanodiamond whose T1 has a dependence on pH conditions.

scholarly journals Global transcriptional differences in myokine and inflammatory genes in muscle of mature steer progeny are related to maternal lactation diet and muscle composition

2018 ◽  
Vol 50 (10) ◽  
pp. 884-892
Author(s):  
T. M. Casey ◽  
J. F. Walker ◽  
K. Bhide ◽  
J. Thimmapuram ◽  
J. P. Schoonmaker
Keyword(s):  
Inflammatory Cytokines ◽  
Control Diet ◽  
Muscle Composition ◽  
Dried Distillers Grains ◽  
Maintenance Factors ◽  
Transcriptomic Signature ◽  
Lactation Phase ◽  
Differentiation Pathways ◽  
Generation Sequencing ◽  
Selection Of

Steer progeny suckled by cows fed a dried distillers grains and solubles (DDGS) diet the first 3 mo of lactation were heavier during feedlot finishing and had significantly lower marbling and larger longissimus muscles than steers suckled by cows fed a control diet (CON). These differences were profound in that progeny were managed and fed identically from weaning until finishing, and findings suggest that the suckling period established the developmental program of muscle composition. Here transcriptomes of longissimus muscle were measured by next-generation sequencing to investigate whether there were any developmental clues to the differences in marbling scores and muscle content between steers suckled by DDGS ( n = 5) vs. control (CON; n = 5) diet-fed cows during lactation. There were 809 genes differentially expressed ( P-adj<0.1) between CON and DDGS muscle. Of these 636 were upregulated and 173 downregulated in DDGS relative to CON. Overall the DDGS vs. CON muscle transcriptomic signature was promyogenic and antiadipogenic. In particular, myokines/satellite cell maintenance factors were found among upregulated (LIF, CNTF, FGFB1, EPHB1) genes. The antiadipogenic signature was typified by the upregulation of anti-inflammatory cytokines and receptors (IL1RAP, IL1RL2, IL13RA2, IL1F10), and downregulation of expression of inflammation/inflammatory cytokines and receptor (TNF, IL6R, CXCL9), which suggests a selection of differentiation pathways away from adipogenic line. The upregulation of TGFB, SPP1, and INHBA supports selection of fibroblast lineage of cells. Thus, the lactation phase of production can effect meat quality by affecting transcriptional signatures that favor myogenesis and depress inflammation.

scholarly journals Development of KASP Markers for Germplasm Characterization and Fingerprinting Identification of Broccoli in China

2020 ◽  
Author(s):  
Yusen Shen ◽  
Jiansheng Wang ◽  
Huifang Yu ◽  
Xiaoguang Sheng ◽  
Zhenqing Zhao ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Marker Assisted Selection ◽  
Genetic Relationships ◽  
Cost Effective ◽  
Germplasm Characterization ◽  
2D Barcode ◽  
New Type ◽  
Generation Sequencing ◽  
Kasp Markers ◽  
Selection Of

Abstract Background: Broccoli (Brassica oleracea var. italica) is a vegetable widely cultivated in China. Many new-type broccoli cultivars were bred and developed by Chinese breeders during the recent three decades. However, the broccoli cultivar nomenclature and detailed information of genetic relationships among broccoli germplasms are unclear. Results: The present study identified millions of SNPs by next-generation sequencing of 23 representative broccoli lines. Through several steps of selection, 100 SNPs were successfully converted into KASP markers, and used to evaluate the genetic diversity, genetic relationship, and population structure of 392 broccoli accessions, which represent the mainly broccoli breeding materials in China. The initial, introduced and improved accessions were well clustered, though some accessions were overlapped between groups, probably reflecting the fact that breeding activities led to genetic similarities. To make the KASP genotyping more efficient and cost-effective, 25 of the 100 KASPs were selected for fingerprinting of all accessions, and the 2D barcode contained fingerprinting information were generated for elite varieties. Conclusion: The KASP markers developed in this study provided an efficient way for germplasm characterization, DNA fingerprinting, seed purity identification, and marker-assisted selection of broccoli in China.

scholarly journals Between Access and Privacy: Challenges in Sharing Health Data

2018 ◽  
Vol 27 (01) ◽  
pp. 055-059 ◽  
Author(s):  
Bradley Malin ◽  
Kenneth Goodman ◽  
Keyword(s):  
Data Sharing ◽  
Digital Library ◽  
Selection Process ◽  
Data Access ◽  
Biomedical Data ◽  
Game Theoretic ◽  
Privacy Risks ◽  
Cryptographic Techniques ◽  
Selection Of

Objective: To summarize notable research contributions published in 2017 on data sharing and privacy issues in medical informatics. Methods: An extensive search of PubMed/Medline, Web of Science, ACM Digital Library, IEEE Xplore, and AAAI Digital Library was conducted to uncover the scientific contributions published in 2017 that addressed issues of biomedical data sharing, with a focus on data access and privacy. The selection process was based on three steps: (i) a selection of candidate best papers, (ii) the review of the candidate best papers by a team of international experts with respect to six predefined criteria, and (iii) the selection of the best papers by the editorial board of the Yearbook. Results: Five best papers were selected. They cover the lifecycle of biomedical data collection, use, and sharing. The papers introduce 1) consenting strategies for emerging environments, 2) software for searching and retrieving datasets in organizationally distributed environments, 3) approaches to measure the privacy risks of sharing new data increasingly utilized in research and the clinical setting (e.g., genomic), 4) new cryptographic techniques for querying clinical data for cohort discovery, and 5) novel game theoretic strategies for publishing summary information about genome-phenome studies that balance the utility of the data with potential privacy risks to the participants of such studies. Conclusion: The papers illustrated that there is no one-size-fitsall solution to privacy while working with biomedical data. At the same time, the papers show that there are opportunities for leveraging newly emerging technologies to enable data use while minimizing privacy risks.

scholarly journals Multimodal Approach to Assessment of Fecal Microbiota Donors based on Three Complementary Methods

2020 ◽  
Vol 9 (7) ◽  
pp. 2036
Author(s):  
Jaroslaw Bilinski ◽  
Mikolaj Dziurzynski ◽  
Pawel Grzesiowski ◽  
Edyta Podsiadly ◽  
Anna Stelmaszczyk-Emmel ◽  
...  
Keyword(s):  
Flow Cytometry ◽  
Fecal Microbiota ◽  
Dead Cell ◽  
Series Of Experiments ◽  
Multi Method Approach ◽  
The Stability ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data ◽  
Generation Sequencing ◽  
Selection Of

Methods of stool assessment are mostly focused on next-generation sequencing (NGS) or classical culturing, but only rarely both. We conducted a series of experiments using a multi-method approach to trace the stability of gut microbiota in various donors over time, to find the best method for the proper selection of fecal donors and to find “super-donor” indicators. Ten consecutive stools donated by each of three donors were used for the experiments (30 stools in total). The experiments assessed bacterial viability measured by flow cytometry, stool culturing on different media and in various conditions, and NGS (90 samples in total). There were no statistically significant differences between live and dead cell numbers; however, we found a group of cells classified as not-dead-not-alive, which may be possibly important in selection of “good” donors. Donor C, being a regular stool donor, was characterized by the largest number of cultivable species (64). Cultivable core microbiota (shared by all donors) was composed of only 16 species. ANCOM analysis of NGS data highlighted particular genera to be more abundant in one donor vs. the others. There was a correlation between the not-dead-not-alive group found in flow cytometry and Anaeroplasma found by NGS, and we could distinguish a regular stool donor from the others. In this work, we showed that combining various methods of microbiota assessment gives more information than each method separately.

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