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Mar 2023 DOI 10.14302/issn.2768-0207.jbr-23-4478
FAKIR YoussefCorresponding author
Spatial data mining (SDM) is searching important relationships and characteristics that can clearly exist in spatial databases. This content aims to compare object clustering algorithms for spatial data mining, before identifying the most efficient algorithm. To this end, this paper compare k-means, Partionning Around Medoids (PAM) and Clustering Large Applications based on RANdomized Search (CLARANS) algorithms based on computing time. Experimental results indicate that, CLARANS is very efficient and effective.
Apr 2016 DOI 10.14302/issn.2575-7881.jdrr-15-863
A. Fuertes MiguelCorresponding author
Centro de Biología Molecular ‘‘Severo Ochoa’’ (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain.
It was, previously, reported that the specific pattern of the compositional features of particular human-mouse orthologs defining in human two clusters, named C2 and C5, are present in different clusters in mouse. Since, thus, these orthologs can harbor a significant number of nucleotide differences a large sample of human-mouse orthologs having in human the C2 and C5 compositional features were collected in order to identify the orthologs that have been conserved or diverged during speciation. From the collection, 945 and 1051 orthologs had in human the C2 and C5 profile, respectively, while in mouse only 77 and 125, respectively, had these profiles. We further analyzed whether or not the frequency-usage of trinucleotides having the same gross composition computed from the reading of all nearest-neighbors of the DNA sequence might convey a layer of biological information in terms of chromosomal topology and function. In human, more than 50% of the C2 and C5 genes were found distributed in six chromosomes and preferentially located in GC-rich bands of chromosomes 11, 16 and 19. It was, also, found that 80% of the entire set of genes of band 19p13.3 had the C2 and C5 profile. The data shown also indicate that the proteins codified by the C5 genes have a bias towards nucleus and cytoplasm and specific post-translational modifications while the proteins codified by the C2 genes are mainly located in the cellular membrane or secreted to the external cellular milieu and particular post-transcriptional modifications
May 2024 DOI 10.14302/issn.2998-4122.jlr-24-4992
Nater HankCorresponding author
A few assertions made by Gloria Mellesmoen (2021) in an Optimality Theory-based article on obstruent clustering in Bella Coola (Nuχalk) are disputed. At issue are: (i) failure to cite all-stop and all-fricative words; (ii) exclusion of stops as potential nuclei and ambiguous views on the status of affricates; (iii) absence of a procedure to determine nuclearity of fricatives in certain environments. It is also shown that (iv) obstruent clustering is an areal trait shared with Rivers Inlet (Oowekyala). Agreeing with Newman (1947), I maintain that Bella Coola is non-syllabic.
Mar 2020 DOI 10.14302/issn.2379-7835.ijn-20-3175
Cyril Abang AgborCorresponding author
Department of Anatomy, Collage of Basic Medical Sciences, University of Calabar, Nigeria
Local Nigerian men have been using AuriculariaPolytricha as a treatment for sexual dysfunction without supporting evidence from scientific experiments. This study was to investigate the effect of ethanolic extract of A. Polytricha on testicular DNA expression and some oxidative stress markers using STZ-Induced diabetic rats as a model. The experiment included six groups, Group A (Normal Control, treated with normal saline), Group B (treated with 65mg/kg.bw of STZ), Groups C, D, and E (treated with 250mg/kg.bw, 500mg/kg.bw, 1000mg/kg.bw AP after inducing diabetics), and Group F (treated with 40mg/kg.bw metformin after inducing diabetics). The experiment lasted for 35 days. After termination of the experiment, Fuelgen nuclear reaction was used for DNA demonstration to assess testicular DNA distribution while serum Superoxide Dimutase (SOD), Catalase and Melondialdehyde where evaluated using reagent based antioxidant enzyme assay. Results reveals that SOD and Melondialdehyde activities were remarkably (p<0.05) higher in diabetic control animals when compared with the normal control group. Values in Groups C, D and F that were administered with 250, 500mg/kg.bw A. polytricha and metformin respectively were also significantly (p<0.05) increased when compared with the normal control group. However, diabetic animals placed on 1000mg/kg.bw A. polytrichadid not show any statistical significance in comparison with normal control group but was remarkably (p<0.01) decreased when compared to the diabetic group that received low dose A. polytricha, an indication that the reversal is dose dependent. Catalase concentration in diabetic control animals was remarkably (p<0.05) higher when compared to the normal control but was not significantly (p<0.05) different in groups D (DM+500mg/kg.bw A. polytricha) and E (DM+1000mg/kg.bw A. polytricha) when compared with the normal control group. Diabetic control animals showed reduced magenta colour intensity of DNA and increased clustering and cross linking of DNA strands when compared with the normal control. However the degree of cross link in DNA strands was reduced in the diabetic animals placed on 1000mg/kg.bw A. polytrichawhen compared with the diabetic control group. Reversal in DNA damage and values of serum oxidative stress markers following administration of graded doses of A. polytricha could be attributed to essential phytochemical and therapeutic constituents in A. polytricha like polyphenol and flavonoid which can be found useful in prevention and treatment of diabetes induced testicular dysfunction. In summary, AP can contribute to a reversal in DNA damage and levels of serum oxidative stress markers in treating diabetes-induced testicular dysfunction.
Jan 2019 DOI 10.14302/issn.2643-6655.jcap-18-2541
S.O OyamakinCorresponding author
Department of Statistics, University of Ibadan, Nigeria
Many researchers have devoted considerable attention to the impact of individual-level factors on child mortality, but little is known about how family and community characteristics affect health of children. Trend in child mortality as well as its determinants, has long been the subject of academic and policy debates. In spite of this, the problem of child mortality remains as daunting as ever. In fact, advancement in medical sciences and the upsurge in information and telecommunication technology equipment have not significantly reduced child mortality in the country, unlike in the West. The Multilevel proportional hazards model for data that are hierarchically clustered at three levels was applied to the study of covariates of child mortality in Nigeria. This study merges two parallel developments of statistical tools for data analysis: statistical methods known as hazard models that are used for analyzing event-duration data and statistical methods for analyzing hierarchically clustered data known as multilevel models. These developments have rarely been integrated in research practice and the formalization and estimation of models for hierarchically clustered survival data remain largely uncharted. The model was estimated using the Newton-Raphsons numerical search approach. The model accounts for hierarchical clustering with three random effects or frailty effects. We assume that the random effects are independent and follow the Exponential and Weibull distribution. The results indicate that bio-demographic factors are more important in infancy while socioeconomic factors and household and environmental conditions have a greater effect in childhood. Furthermore, there is significant variation in child mortality risks even after controlling for measured determinants of mortality. Also, factors that fall under family and community level are more significant indicating that child survival is most controlled or determined by family and community factors and variables at the child level is not weighty. This suggests that there may exits unobserved or unobservable factors related to mortality.
Oct 2018 DOI 10.14302/issn.2641-9467.jgrc-18-2339
Sarmah PrabaleeCorresponding author
Jr. Scientist-S2 (PBG), AICRP on Vegetable Crops, Department of Horticulture, AAU, Jorhat, Assam, India.
We evaluated a set of 37 chilli genotypes collected and maintained at Assam Agricultural University, Jorhat for 27 different traits related to plant habit (5), leaf (6), flower (2), fruit (13) and biotic stress (1). The variation in fruit yield among the genotypes could be attributed to high coefficients of variability for component traits viz., number of fruits per plant (91.7%), plant height (80.8%), leaf breadth (55.9 %), fruit weight (49.7%), leaf length (45.4%) fruit length (35.8%), fruit breadth (35.5%) and number of branches per plant (22.2%). Maximum phenotypic variants were observed for fruit traits followed by leaf characteristics. Phylogenetic analysis revealed Euclidean distances varying from a minimum of 2.065 and a maximum of 13.311 indicating the diverse nature of the genotypes. UPGMA clustering grouped the genotypes into 5 distinct clusters. The largest one, cluster I, had 26 genotypes belonging to Capsicum annuum var. acuminatum. Cluster II consisted of Capsicum annuum var. conoides with cone-shaped fruits. Cluster III included Moni Jolokia, a perennial shrub with cone-shaped globose erect fruits which clustered in between the other local C. annuum sp. Bireek and Mem Jolokia. The fourth cluster (IV) included the local chilli genotypes - Mem Jolokia, Bhekuri Jolokia and Haitha Jolokia which were perennial, with green stem and leaves. Cluster V included the C. chinense genotypes consisting of Manipuri Bhut, Bor Bhut and Lota Bhut. The first principal component explained 34.93% of the total variation contributed by mostly leaf and fruit characteristics. The fruit characters in this component showed significant positive correlation with leaf length, breadth and plant height indicating their importance in the morphological characterization of the chilli genotypes.
Feb 2016 DOI 10.14302/issn.2575-7881.jdrr-15-849
BOULILA MoncefCorresponding author
Professor, Université de Sfax- Institut de l’Olivier- B.P. 14, 4061 Sousse Ibn Khaldoun, Tunisia.
Reverse Transcription Polymerase Chain Reaction (RT-PCR) using new designed primers pair for Heat Shock Protein70 homologue (HSP70h) of Olive leaf yellowing-associated virus revealed 667 amplified product of 10 olive accessions collected from various olive-growing regions in Tunisia. Amplicons were cloned and sequenced. The sequences were deposited in the international databases. Pairwise sequence comparisons among 10 Tunisian isolates along with a reference sequence (AJ440010) extracted from GenBank revealed a nucleotide identity of 86.06-99.40 and an amino acid similarity of 91.89-99.55. Sequence multiple alignments were searched for evidence of recombination using three methods, ie. Differences of Sums of Squares (DSS) implemented in TOPALi v2.5 software and Single Breakpoint (SBP) along with GARD, a genetic algorithm, both incorporated in HyPhy package. All used methods pointed out the presence of putative breaking points in partially sequenced HSP70h-coding gene. Since failing to account for recombination can mislead the phylogeny inference and can elevate the false positive error rate in positive selection assessment, the use of GARD resulted in the reconstruction of different phylogenies on the left as well as on the right sides of putative recombination breaking points, and the 11 accessions were distributed into at least three clusters compared to MEGA6 software which delineated only two clades. Nonetheless, by dividing the aligned sequences at breakpoints into separate sequence sets, MEGA6 delineated a clustering pattern different from the former two. As a result, recombination reshuffled the affiliation of the different accessions to the clusters. Analysis of selection pressures exerted on HSP70h encoded protein using different models (SLAC, IFEL, FEL, REL, PARRIS, FUBAR, MEME, GA Branch, and PRIME) taking into account recombination, and implemented in HyPhy package, revealed that it underwent predominantly purifying selection as confirmed by Tajima’s D, Fu and Li’s D and F tests, and SNAP algorithm. However, a few sites were also under positive selection as assessed by various models such as FEL, IFEL, REL, MEME, and PRIME.
May 2015 DOI 10.14302/issn.2572-3030.jcgb-14-495
Khan AshrafCorresponding author
Departments of Pathology, UMass Memorial Medical Center, University of Massachusetts Medical School, Worcester, MA 01605, USA
Thyroid carcinomas encompass a wide spectrum ranging from differentiated thyroid carcinoma (DTC) to poorly differentiated (PDC) and anaplastic thyroid carcinoma (ATC). DTC of both follicular (FTC) and papillary (PTC) types can progress to PDC and AC. The aim of our study was to evaluate if there is differential microRNA (miRNA) expression in various tumor subtypes during this progression. The miRNA profile of differentiated carcinomas (Follicular and Papillary) and ATC were compared with that of PDCs either by itself or in a background of differentiated carcinomas and anaplastic carcinomas. Unsupervised hierarchical clustering analysis revealed that FTC and PDC tend to cluster together in the absence of ATC. Interestingly, in cases with presence of all components i.e. FTC, PDC and ATC, the miRNA profile of poorly differentiated component clusters with that of the Anaplastic carcinoma component. miR-494 and miR-125a-5p were found to be differentially regulated in tumors with an anaplastic component and even the well-differentiated component (FTC) of these tumors were found to be aligned with the anaplastic profile. In addition, we also discovered some differentially regulated miRNAs in follicular variant of papillary thyroid carcinoma as compared to follicular thyroid carcinoma (miR-486-5p and miR-31).