scholarly journals NDAMDA: Network distance analysis for MiRNA-disease association prediction

2018 ◽  
Vol 22 (5) ◽  
pp. 2884-2895 ◽  
Author(s):  
Xing Chen ◽  
Le-Yi Wang ◽  
Li Huang
Keyword(s):  
Disease Association ◽  
Network Distance ◽  
Distance Analysis

scholarly journals Phylogeography of msp4 genotypes of Anaplasma marginale in beef cattle from the Brazilian Pantanal

2019 ◽  
Vol 28 (3) ◽  
pp. 451-457 ◽  
Author(s):  
Inalda Angélica de Souza Ramos ◽  
Heitor Miraglia Herrera ◽  
Natália Serra Mendes ◽  
Simone de Jesus Fernandes ◽  
João Bosco Vilela Campos ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Conventional Pcr ◽  
Network Distance ◽  
Msp4 Gene ◽  
Distance Analysis ◽  
Network Analyses ◽  
Breeding Farms ◽  
Brazilian Pantanal ◽  
Extensive Breeding

Abstract The msp4 gene of A. marginale is unicodon, stable and mostly homogeneous, being considered as a useful marker for phylogeographic characterization of this bacterium. The objective of this work was to analyze the phylogeography of A. marginale based on the msp4 gene in beef cattle from the Brazilian Pantanal, compared to those found in other regions worldwide. The blood samples investigated were collected from 400 animals (200 cows and 200 calves) reared in five extensive breeding farms in this region. The results indicated that of the evaluated samples, 56.75% (227/400) were positive for A. marginale based on the msp1β gene by quantitatitve PCR (qPCR), while 8.37% (19/227) were positive for the msp4 gene in the conventional PCR. In the Network distance analysis, 14 sequences from the Brazilian Pantanal were grouped into a single group with those from Thailand, India, Spain, Colombia, Parana (Brazil), Mexico, Portugal, Argentina, China, Venezuela, Australia, Italy and Minas Gerais (Brazil). Among 68 sequences from Brazil and the world, 15 genotypes were present while genotype number one (#1) was the most distributed worldwide. Both Splitstree and network analyses showed that the A. marginale msp4 sequences detected in beef cattle from the Brazilian Pantanal showed low polymorphism, with the formation of one genogroup phylogenetically related to those found in ruminants from South and Central America, Europe, and Asia.

Walking accessibility to neighbourhood open space in a multi-level urban environment of Hong Kong

2020 ◽  
pp. 239980832093257 ◽  
Author(s):  
Bo-Sin Tang ◽  
Kenneth KH Wong ◽  
Kenneth SS Tang ◽  
Siu Wai Wong
Keyword(s):  
Hong Kong ◽  
Urban Environment ◽  
Land Use Planning ◽  
Open Space ◽  
Residential Buildings ◽  
Public Facility ◽  
Local Planning ◽  
Network Distance ◽  
Distance Analysis ◽  
Multi Level

This study presents the spatial analysis of walking accessibility to a public facility in a hilly, multi-level urban environment. Our spatial database includes street topography, physical impedances, formal crossings, and designated access points in assessing the network distance of all private residential buildings to public open space in Hong Kong. Pedestrian movement of uneven speed on walkways of varying gradients is assessed. The study concludes that, compared with our method, conventional buffer analysis and network distance analysis over-estimate the walking accessibility of private housing to neighbourhood open space in Hong Kong by about 2–8%. Despite Hong Kong’s compact built environment, about 15% of the total number of residential blocks cannot reach a neighbourhood open space within 5 minutes of walking (equivalent to the local planning standard of 400 metres of walking on a flat terrain). These open space-deficient neighbourhoods comprise mostly the affluent or middle-class households in gated housing estates and in low-rise housing, but also some neighbourhoods of underprivileged families in old urban tenement buildings. Our assessment reveals the spatial bias of land use planning policy leading to these blackspots of open space shortfall in the territory. It requires urban planners to pay attention to the geographical barriers of a pedestrian network in redressing the inequitable distribution and achieving a pedestrian-friendly 3D city.

Using Network Distance Analysis to Predict lncRNA–miRNA Interactions

2021 ◽  
Author(s):  
Li Zhang ◽  
Pengyu Yang ◽  
Huawei Feng ◽  
Qi Zhao ◽  
Hongsheng Liu
Keyword(s):  
Network Distance ◽  
Distance Analysis

Computational Evidences of Phytochemical Mediated Disruption of PLpro Driven Replication of SARS-CoV-2: A Therapeutic Approach Against COVID-19

2020 ◽  
Vol 21 ◽  
Author(s):  
Acharya Balkrishna ◽  
Rashmi Mittal ◽  
Vedpriya Arya
Keyword(s):  
Molecular Docking ◽  
Md Simulation ◽  
Bond Distance ◽  
Immunological Response ◽  
Docking Study ◽  
Receptor Interaction ◽  
Molecular Docking Study ◽  
Replication Process ◽  
Stable Conformation ◽  
Distance Analysis

Background:: COVID-19 caused by SARS-CoV-2 has been declared as global pandemic by WHO. Comprehensive analysis of this unprecedented outbreak may help to fight against the disease and may play a pivotal role in decreasing the mortality rate linked with it. Papain like protease (PLpro), a multifunctional polyprotein facilitates the replication of SARS-CoV-2 and evades it from the host immunological response by antagonizing cytokines, interferons and may be considered as potential drug target to combat the current pandemic. Methods:: Natural moieties obtained from medicinal plants were analysed for their potency to target PLpro of SARS-CoV-2 by molecular docking study and were compared with synthetic analogs named as remdesivir, chloroquine and favipiravir. The stability of complexes of top hits was analysed by MD Simulation and interaction energy was calculated. Furthermore, average RMSD values were computed and deepsite ligand binding pockets were predicted using Play Molecule. Drug like abilities of these moieties were determined using ADMET and bond distance between the ligand and active site was assessed to predict the strength of interaction. Results:: Nimbocinol (-7.6 Kcal/mol) and sage (-7.3 Kcal/mol) exhibited maximum BA against PLpro SARS-CoV-2 as evident from molecular docking study which was found to be even better than remdesivir (-6.1 Kcal/mol), chloroquine (-5.3 Kcal/mol) and favipiravir (-5.7 Kcal/mol). Both nimbocinol-PLpro and sage-PLpro SARS-CoV-2 complex exhibited stable conformation during MD Simulation of 101ns at 310 K and potential, kinetic and electrostatic interaction energies were computed which was observed to be concordant with results of molecular docking study. RMSD average values were found to be 0.496 ± 0.015 Å and 0.598 ± 0.023 Å for nimbocinol and sage respectively thus revealing that both the deviation and fluctuations during MD Simulation were observed to be least. Deepsite prediction disclosed that both compounds occupied cryptic pockets in receptor and non-bond distance analysis revealed the formation of hydrogen bonds during ligand-receptor interaction. ADMET exploration further validated the drug like properties of these compounds. Conclusion:: Present study revealed that active constituents of Azadirachta indica and Salvia officinalis can be potentially used to target SARS-CoV-2 by hindering its replication process.

EHAI: Enhanced Human Microbe-Disease Association Identification

2020 ◽  
Vol 21 (11) ◽  
pp. 1078-1084
Author(s):  
Ruizhi Fan ◽  
Chenhua Dong ◽  
Hu Song ◽  
Yixin Xu ◽  
Linsen Shi ◽  
...  
Keyword(s):  
Microbial Community ◽  
Human Health ◽  
Complex Diseases ◽  
Disease Association ◽  
Computational Results ◽  
Computational Approaches ◽  
Disease Diagnostics ◽  
Disease Associations ◽  
Association Discovery ◽  
Biological Tool

: Recently, an increasing number of biological and clinical reports have demonstrated that imbalance of microbial community has the ability to play important roles among several complex diseases concerning human health. Having a good knowledge of discovering potential of microbe-disease relationships, which provides the ability to having a better understanding of some issues, including disease pathology, further boosts disease diagnostics and prognostics, has been taken into account. Nevertheless, a few computational approaches can meet the need of huge scale of microbe-disease association discovery. In this work, we proposed the EHAI model, which is Enhanced Human microbe- disease Association Identification. EHAI employed the microbe-disease associations, and then Gaussian interaction profile kernel similarity has been utilized to enhance the basic microbe-disease association. Actually, some known microbe-disease associations and a large amount of associations are still unavailable among the datasets. The ‘super-microbe’ and ‘super-disease’ were employed to enhance the model. Computational results demonstrated that such super-classes have the ability to be helpful to the performance of EHAI. Therefore, it is anticipated that EHAI can be treated as an important biological tool in this field.

scholarly journals VTRNA2-1: Genetic Variation, Heritable Methylation and Disease Association

2021 ◽  
Vol 22 (5) ◽  
pp. 2535
Author(s):  
Pierre-Antoine Dugué ◽  
Chenglong Yu ◽  
Timothy McKay ◽  
Ee Ming Wong ◽  
Jihoon Eric Joo ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Dna Methylation ◽  
Genetic Variation ◽  
Genetic Factors ◽  
Disease Association ◽  
Country Of Birth ◽  
Cpg Site ◽  
Multiple Case ◽  
Metastable Epiallele ◽  
Methylation Quantitative Trait Loci

VTRNA2-1 is a metastable epiallele with accumulating evidence that methylation at this region is heritable, modifiable and associated with disease including risk and progression of cancer. This study investigated the influence of genetic variation and other factors such as age and adult lifestyle on blood DNA methylation in this region. We first sequenced the VTRNA2-1 gene region in multiple-case breast cancer families in which VTRNA2-1 methylation was identified as heritable and associated with breast cancer risk. Methylation quantitative trait loci (mQTL) were investigated using a prospective cohort study (4500 participants with genotyping and methylation data). The cis-mQTL analysis (334 variants ± 50 kb of the most heritable CpG site) identified 43 variants associated with VTRNA2-1 methylation (p < 1.5 × 10−4); however, these explained little of the methylation variation (R2 < 0.5% for each of these variants). No genetic variants elsewhere in the genome were found to strongly influence VTRNA2-1 methylation. SNP-based heritability estimates were consistent with the mQTL findings (h2 = 0, 95%CI: −0.14 to 0.14). We found no evidence that age, sex, country of birth, smoking, body mass index, alcohol consumption or diet influenced blood DNA methylation at VTRNA2-1. Genetic factors and adult lifestyle play a minimal role in explaining methylation variability at the heritable VTRNA2-1 cluster.

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