Hierarchical Cluster Analysis

Köhn, Hans-Friedrich; Hubert, Lawrence

doi:10.1002/9781118445112.stat02449.pub2

Cited by 78 publications

(49 citation statements)

References 38 publications

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“…Here, pair-wise differential COG-count for two functional categories was placed in two rows (with a degree of freedom = 1) in the 2x2 contingency table and the Chi Square significance test performed for the two individual communities. Furthermore, hierarchical clustering 94 was carried out to quantitatively decipher the relatedness between the mat communities in terms of their enrichment of various COG categories. Heat map depicting the results of hierarchical cluster analysis was drawn with an in house R script (Supplementary Note 3) using complete linkage method (Johnson's maximum method) 95 .…”

Section: Methodsmentioning

confidence: 99%

Microbiome and ecology of a hot spring-microbialite system on the Trans-Himalayan Plateau

Roy

Rameez

Haldar

et al. 2020

Sci Rep

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Little is known about life in the boron-rich hot springs of trans-Himalayas. Here, we explore the geomicrobiology of a 4438-m-high spring which emanates ~70 °C-water from a boratic microbialite called Shivlinga. Due to low atmospheric pressure, the vent-water is close to boiling point so can entropically destabilize biomacromolecular systems. Starting from the vent, Shivlinga's geomicrobiology was revealed along the thermal gradients of an outflow-channel and a progressivelydrying mineral matrix that has no running water; ecosystem constraints were then considered in relation to those of entropically comparable environments. the spring-water chemistry and sinter mineralogy were dominated by borates, sodium, thiosulfate, sulfate, sulfite, sulfide, bicarbonate, and other macromolecule-stabilizing (kosmotropic) substances. Microbial diversity was high along both of the hydrothermal gradients. Bacteria, eukarya and Archaea constituted >98%, ~1% and <1% of Shivlinga's microbiome, respectively. Temperature constrained the biodiversity at ~50 °C and ~60 °C, but not below 46 °C. Along each thermal gradient, in the vent-to-apron trajectory, communities were dominated by Aquificae/Deinococcus-Thermus, then Chlorobi/Chloroflexi/Cyanobacteria, and finally Bacteroidetes/Proteobacteria/Firmicutes. interestingly, sites of >45 °C were inhabited by phylogenetic relatives of taxa for which laboratory growth is not known at >45 °C. Shivlinga's geomicrobiology highlights the possibility that the system's kosmotrope-dominated chemistry mitigates against the biomacromolecule-disordering effects of its thermal water. The microbial ecologies of habitats that are hydrothermal, or hypersaline, have been well-characterized, and can give insights into the origins of early life on Earth 1-3. Both chaotrope-rich hypersaline brines and high-temperature freshwater systems can entropically disorder the macromolecules of cellular systems, and are in this way analogous as microbial habitats 4-7. Indeed, highly-chaotropic and hydrothermal habitats are comparable at various scales of biology: the biomacromolecule, cellular system, and functional ecosystem 8,9. Chaotropic, hypersaline habitats include the MgCl 2-constrained ecosystems located at the interfaces of some of the stratified deep-sea hypersaline brines and their overlying seawater. Biophysical, culture-based, and metagenomic studies of the steep haloclines found at these interfaces have revealed that macromolecule-disordering (chaotropic) activities of MgCl 2 not only determine microbial community composition, but also limit Earth's functional biosphere 5,7,10 in such locations, as in situ microbial communities stop functioning at 2.2-2.4 M MgCl 2

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Section: Methodsmentioning

confidence: 99%

Microbiome and ecology of a hot spring-microbialite system on the Trans-Himalayan Plateau

Roy

Rameez

Haldar

et al. 2020

Sci Rep

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“…We also used multiple linear regression analysis to show the relative effect of both harvest amount and awareness of diseases on the presence or absence of applied control practices. Moreover, hierarchical cluster analysis [25] was performed to classify sites into groups according to their mean harvest quantity, percentage of respondents that applied control, the average number of known diseases and the average income.…”

Section: The Results Of Interviews With Householdsmentioning

confidence: 99%

Socioeconomic Perspectives on Household Chestnut Fruit Utilization and Chestnut Blight Prevention Efforts in Turkey

2017

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Exotic pathogens, within the center of genetic diversity for the species, compromise European chestnut populations in Turkey. In Turkey today, the species is of tremendous economic, ecological and cultural importance. At this time of severe exotic pathogenic pressure on a highly-valued forest species, we ask, how does awareness of diseases and treatments as well as value for chestnut trees affect the efforts of households to manage pests and diseases of chestnut trees in Turkey? We conducted 96 surveys in 34 villages in 10 provinces across Turkey to investigate awareness of diseases and other challenges to the chestnut population, chestnut harvesting habits, family value for chestnuts and efforts to mitigate pest and disease pressure. We analyze our results using cluster and regression analysis. Our results show that based on analysis of all observed characteristics, our research sites in Turkey break cleanly into groups based on production level. Further, results demonstrate significant correlation between amount of chestnut-derived income and awareness of pests and diseases as well as the likelihood of households enacting disease mitigation measures. These results also demonstrate correlation between observed awareness of diseases and pests and the likelihood of households enacting disease mitigation measures.

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“…The hierarchical clustering method [119] was used to group amino acids, as well as inhibitors, based on the interaction similarity expressed in binary form (1 means interaction, 0 means no interaction). A cluster package from SciPy library was used to perform hierarchical clustering.…”

Section: Clusteringmentioning

confidence: 99%

Novel Potential Binding Sites for Selective Inhibitor Design of Human Soluble Epoxide Hydrolase

Bzówka

Mitusińska

Góra

2020

Preprint

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Human soluble epoxide hydrolase (hsEH) has been known to be involved in the hydrolysis of epoxyeicosatrienoic acids (EETs), which are anti-inflammatory and cardioprotective signalling molecules. Since the conversion of EETs into the corresponding diols generates non-bioactive molecules, the enzyme’s inhibition would be beneficial. hsEH quickly became the molecular target, however, the proposed inhibitors directed toward this enzyme have not undergone clinical trials, mostly due to their low solubility in water. Our goal is to indicate new regions, distinct from those already investigated, that could be considered during the development of novel and perhaps more soluble inhibitors of hsEH. To fulfil this goal, we used a combination of classical and mixed-solvent molecular dynamics (cMD and MixMD) simulations and a ligand tracking approach. Such a strategy, considers conformational changes in the interior of the enzyme, extends conformational space of binding cavities, and provides insight into different sets of potential binding modes. By analysis of the local distribution of different molecular probes (water and organic cosolvent molecules), we were able to identify potential binding sites (hot-spots), which can indicate the location of the most important functional groups for the binding of designed inhibitors. The uniqueness of the binding spots was examined by superpositioning the indicated hot-spots with a map of chemical interactions between the known inhibitors and hsEH. We analysed all available crystal structures of hsEHs with inhibitors deposited in the PDB database to gain insight into the binding modes of the known inhibitors and to find similarities and dissimilarities between them. By comparing the results obtained based on the map of chemical interactions, with the regions identified by using cMD and MixMD, we were able to identify regions that have not been targeted by ligands until now and which are promising possible binding sites for polar groups that would be beneficial for inhibitors solubility.

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Hierarchical Cluster Analysis

Cited by 78 publications

References 38 publications

Microbiome and ecology of a hot spring-microbialite system on the Trans-Himalayan Plateau

Microbiome and ecology of a hot spring-microbialite system on the Trans-Himalayan Plateau

Socioeconomic Perspectives on Household Chestnut Fruit Utilization and Chestnut Blight Prevention Efforts in Turkey

Novel Potential Binding Sites for Selective Inhibitor Design of Human Soluble Epoxide Hydrolase

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