Three-dimensional Cluster Analysis Research Articles

Investigation on the clinical efficacy and mechanism of compound kushen injection in treating esophageal cancer based on multi-dimensional network meta-analysis and in vitro experiment

Ethnopharmacological relevanceEsophageal cancer, as a high incidence of gastrointestinal cancer, has an indelible impact on human life and health. The combination of Chinese herbal injections and chemotherapy is commonly applied in the treatment of Esophageal cancer. Aim of the studyThis study aimed to confirm the clinical advantage of Compound Kushen Injection to treat esophageal cancer and explore its molecular mechanism. MethodsThe network meta-analysis method was used for the clinical evaluation of anti-tumor Chinese herbal injections. Initially, several electronic databases were searched to identify randomized controlled trials regarding Chinese herbal injections to treat esophageal cancer from their inception to September 5, 2020. Then, WinBugs and Stata software was used to calculate and analyze the outcome indicators, including total clinical efficiency, improvement of quality of life and adverse reactions. Furthermore, the surface under the cumulative ranking curve and three-dimensional cluster analysis were used to rank the efficacy and safety of Chinese herbal injections about each outcome. Cell Counting Kit-8 assay was used to observe the effect of Compound Kushen Injection on the proliferation of esophageal cancer cells. Real-Time Quantitative PCR and Western Blot analysis were used to detect the mRNA and protein expression of EGFR and AURKA in ESCA cells. ResultsThe surface under the cumulative ranking curve of Compound Kushen Injection combined with chemotherapy in total clinical efficiency, quality of life, reduction of nausea and vomiting were ranking at 89.1%, 81.8% and 92.4%, respectively. Compound Kushen Injection was determined as the dominant variety in the treatment of esophageal cancer which can inhibit the proliferation of esophageal cancer cells and downregulate the overexpression of EGFR and AURKA mRNA and protein. ConclusionIn this study, network meta-analysis was applied to confirm that Compound Kushen Injection has a curative effect on esophageal cancer and is superior to other anti-tumor Chinese herbal injections. Combined with the network pharmacology and in vitro experiment, the mechanism of Compound Kushen Injection inhibiting the proliferation of esophageal cancer cells by regulating the abnormal expression of EGFR and AURKA was revealed.

Oil Users, Air Polluters, and Forest Abusers: Macro-Level Segmentation of 121 Countries Based on Resource Usage Efficiency Per Capita

This paper makes a vital contribution to the fields of sustainability studies and environmental policy making by presenting evidence that contradicts widely accepted conventional wisdom about the relative environmental efficiency of countries.Significant findings include the existence of clusters of relative resource usage efficiency that are not entirely explained by geography, stages of economic development, or other conventional theories.To the best knowledge of the authors, this is the first time that a model-based three-dimensional cluster analysis has been used to address this question of ranking the relative environmental efficiency of countries.

Compact groups of galaxies (CGs) from the SDSS Data Release 6

Abstract From the volume-limited MAIN galaxy sample of the SDSS Data Release 6 (SDSS6), we have identified 1298 compact groups of galaxies (CGs) at the neighbourhood radius of R = 1.2 Mpc by three-dimensional cluster analysis. In order to compile the CG catalog, we also estimated velocity dispersion, virial radius, virial mass and crossing time of CGs. In addition, our results show that properties of galaxies may not correlate with merging frequencies.

Modulation of Activity in Swallowing Motor Cortex Following Esophageal Acidification: A Functional Magnetic Resonance Imaging Study

Esophageal acid exposure induces sensory and motility changes in the upper gastrointestinal tract; however, the mechanisms involved and the effects on activity in the brain regions that control swallowing are unknown. The aim of this study was to examine functional changes in the cortical swallowing network as a result of esophageal acidification using functional magnetic resonance imaging (fMRI). Seven healthy volunteers (3 female, age range=20-30 years) were randomized to receive either a 0.1 M hydrochloric acid or (control) saline infusion for 30 min into the distal esophagus. Postinfusion, subjects underwent four 8 min blocks of fMRI over 1 h. These alternated between 1 min swallowing water boluses and 1 min rest. Three-dimensional cluster analysis for group brain activation during swallowing was performed together with repeated-measures ANOVA for differences between acid and saline. After acid infusion, swallowing-induced activation was seen predominantly in postcentral gyrus (p<0.004). ANOVA comparison of acid with saline showed a significant relative reduction in activation during swallowing of the precentral gyrus (M1) BA 4 (p<0.008) in response to acid infusion. No areas of increased cortical activation were identified with acid vs. saline during swallowing. Esophageal acidification inhibits motor and association cortical areas during a swallowing task, probably via changes in vagal afferent or nociceptive input from the esophagus. This mechanism may play a protective role, facilitating acid clearance by reduced descending central motor inhibition of enteric/spinal reflexes, or by preventing further ingestion of injurious agents.

Isolated Main Galaxy Pairs from the SDSS Data Release 4

From the Main galaxy data of the SDSS Data Release 4 (SDSS4), we have iden- tified close galaxy pairs at neighbourhood radius R = 100kpc by three-dimensional cluster analysis. Using the criterion that an galaxy must be separated from its nearest neighborby more than 500kpc, we constructed an isolated galaxy pair sample of 1158 pairs. We also constructed a random pair sample by randomly selecting 1158 galaxy pairs from the Main galaxy sample, which has the same redshift distribution as the isolated galaxy pair sample, and in which the two components of any pair have the same redshifts. Comparative studies of luminosity and size between the members of the galaxy pairs are performed. We find and further confirm there is no tendency for paired galaxies to have similar luminosities or sizes. From the isolated pair sample we also selected a subsample with the magnitude limit of the primary raised by 2 magnitudes,so as to include pairs in which the secondary is 2 mag- nitudes fainter than the primary. This subsample contains 82 pairs. A random pair sample is similarly constructed.

The properties of isolated Main galaxies in different redshift bins

In order to decrease the effect of radial selection function, we have constructed a volume-limited sample that extends to Z max = 0.12, and limits the absolute magnitude region: −22.40 ⩽ M ⩽ −20.97. It contains 55,054 galaxies. By three-dimensional cluster analysis, two isolated galaxy samples are extracted from volume-limited sample at the dimensionless neighbourhood radii r = 1.2 and r = 1.4. We analyse the basic properties of isolated galaxies identified at r = 1.2 in different redshift bins, and compare these properties of isolated galaxies with that of volume-limited sample in different redshift bins. It turns out that isolated galaxies have the same basic properties as volume-limited sample in different redshift bins. This indicates that these basic properties of galaxies have no correlation with environment around galaxies. When comparing basic properties of isolated galaxy sample identified at r = 1.2 with that of isolated galaxy sample identified at r = 1.4, we find that isolated galaxy samples identified at different radii have the same properties. This demonstrates that isolated galaxies identified at neighbourhood radii r ⩾ 1.2 by cluster analysis have definite basic properties and can be considered good isolated galaxy samples.

Computational methods for functional site identification suggest a substrate access channel in transaldolase.

The homozygous deletion of Serine 171 results in the catalytic inactivation of the human transaldolase. Since Ser171 is in an outside loop, whereas the catalytic site is inside of the alpha/beta-barrel of the protein at least 15 A away, the loss of activity is difficult to explain. Two distinct computational methods are used to elucidate the potential origin of inactivation. Computational solvent mapping, which moves small organic molecules as probes around a protein surface and finds favorable binding positions, identifies the region around Ser171 as an important binding site. Three-dimensional cluster analysis, based both on a reference structure and multiple sequence alignment, shows that a patch of functionally important residues extends from Ser171 toward the catalytic site. Based on the findings of these two methods, we propose a novel ligand access path connecting these specific sites to the enzyme's active site. We also suggest that this mechanism may be aided by a significant conformational change involving the separation of two helices, alphaD and alphaG, in order to create an easy-access channel between the Ser171-related site and the active site. Further experimental procedures will be necessary to examine the biological feasibility of this proposed ligand shuttling path.

Searching for Potential Drug Targets in Two-component and Phosphorelay Signal-transduction Systems using Three-dimensional Cluster Analysis

Two-component and phosphorelay signal transduction systems are central components in the virulence and antimicrobial resistance responses of a number of bacterial and fungal pathogens; in some cases, these systems are essential for bacterial growth and viability. Herein, we analyze in detail the conserved surface residue clusters in the phosphotransferase domain of histidine kinases and the regulatory domain of response regulators by using complex structure-based three-dimensional cluster analysis. We also investigate the protein-protein interactions that these residue clusters participate in. The Spo0B-Spo0F complex structure was used as the reference structure, and the multiple aligned sequences of phosphotransferases and response regulators were paired correspondingly. The results show that a contiguous conserved residue cluster is formed around the active site, which crosses the interface of histidine kinases and response regulators. The conserved residue clusters of phosphotransferase and the regulatory domains are directly involved in the functional implementation of two-component signal transduction systems and are good targets for the development of novel antimicrobial agents.

Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins.

Three-dimensional cluster analysis offers a method for the prediction of functional residue clusters in proteins. This method requires a representative structure and a multiple sequence alignment as input data. Individual residues are represented in terms of regional alignments that reflect both their structural environment and their evolutionary variation, as defined by the alignment of homologous sequences. From the overall (global) and the residue-specific (regional) alignments, we calculate the global and regional similarity matrices, containing scores for all pairwise sequence comparisons in the respective alignments. Comparing the matrices yields two scores for each residue. The regional conservation score (C(R)(x)) defines the conservation of each residue x and its neighbors in 3D space relative to the protein as a whole. The similarity deviation score (S(x)) detects residue clusters with sequence similarities that deviate from the similarities suggested by the full-length sequences. We evaluated 3D cluster analysis on a set of 35 families of proteins with available cocrystal structures, showing small ligand interfaces, nucleic acid interfaces and two types of protein-protein interfaces (transient and stable). We present two examples in detail: fructose-1,6-bisphosphate aldolase and the mitogen-activated protein kinase ERK2. We found that the regional conservation score (C(R)(x)) identifies functional residue clusters better than a scoring scheme that does not take 3D information into account. C(R)(x) is particularly useful for the prediction of poorly conserved, transient protein-protein interfaces. Many of the proteins studied contained residue clusters with elevated similarity deviation scores. These residue clusters correlate with specificity-conferring regions: 3D cluster analysis therefore represents an easily applied method for the prediction of functionally relevant spatial clusters of residues in proteins.

Assumptions and validations of statistical tests for functional neuroimaging.

We contrast two statistical methods: three-dimensional cluster analysis and statistical parametric mapping. We show that three-dimensional cluster analysis is based on a neurobiological theory of the regulation of blood flow and, unlike statistical parametric mapping, carries a minimum of assumptions that are tested. Statistical parametric mapping is a formal approach, which is based on a multitude of assumptions of which the majority have not been validated. We also demonstrate that in practice three-dimensional cluster analysis has a reasonable balance between sensitivity and the probability of false positives, giving high reproducibility with data on e.g. colour discrimination.