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

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.

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.

TNDP: Tensor-based Network Distance Prediction with Confidence Intervals

2021 ◽  
pp. 1-1
Author(s):  
Haojun Huang ◽  
Li Li ◽  
Geyong Min ◽  
Wang Miao ◽  
Yingying Zhu ◽  
...  
Keyword(s):  
Confidence Intervals ◽  
Network Distance ◽  
Distance Prediction

Network distance estimation with dynamic landmark triangles

2008 ◽  
Vol 36 (1) ◽  
pp. 433-434
Author(s):  
Zhihua Wen ◽  
Michael Rabinovich
Keyword(s):  
Distance Estimation ◽  
Network Distance

scholarly journals Phylogenetic relationships between European and Chinese truffles based on parsimony and distance analysis of ITS sequences

1999 ◽  
Vol 180 (2) ◽  
pp. 147-155 ◽  
Author(s):  
Christophe Roux ◽  
Nathalie Séjalon-Delmas ◽  
Monique Martins ◽  
Agnès Parguey-Leduc ◽  
Robert Dargent ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Its Sequences ◽  
Distance Analysis

scholarly journals Multiple Origins of a Mitochondrial Mutation Conferring Deafness

Genetics ◽  
1997 ◽  
Vol 145 (3) ◽  
pp. 771-776 ◽  
Author(s):  
Timothy P Hutchin ◽  
Gino A Cortopassi
Keyword(s):  
Phylogenetic Analysis ◽  
Genetic Distance ◽  
Ribosomal Subunit ◽  
Sensorineural Deafness ◽  
Nucleotide Substitutions ◽  
Mitochondrial Mutation ◽  
Distance Analysis ◽  
Multiple Origins ◽  
Mtdna Haplotypes ◽  
Mtdna Sequence

A point mutation (1555G) in the smaller ribosomal subunit of the mitochondrial DNA (mtDNA) has been associated with maternally inherited traits of hypersensitivity to streptomycin and sensorineural deafness in a number of families from China, Japan, Israel, and Africa. To determine whether this distribution was the result of a single or multiple mutational events, we carried out genetic distance analysis and phylogenetic analysis of 10 independent mtDNA D-loop sequences from Africa and Asia. The mtDNA sequence diversity was high (2.21%). Phylogenetic analysis assigned 1555G-bearing haplotypes at very divergent points in the human mtDNA evolutionary tree, and the 1555G mutations occur in many cases on race-specific mtDNA haplotypes, both facts are inconsistent with a recent introgression of the mutation into these races. The simplest interpretation of the available data is that there have been multiple origins of the 1555G mutation. The genetic distance among mtDNAs bearing the pathogenic 1555G mutation is much larger than among mtDNAs bearing either evolutionarily neutral or weakly deleterious nucleotide substitutions (such as the 4336G mutation). These results are consistent with the view that pathogenic mtDNA haplotypes such as 1555G arise on disparate mtDNA lineages which because of negative natural selection leave relatively few related descendants. The co-existence of the same mutation with deafness in individuals with very different nuclear and mitochondrial genetic backgrounds confirms the pathogenicity of the 1555G mutation.

Sign in / Sign up

Export Citation Format

Share Document