Weighted Pair Group Method Research Articles

Range maps and waterbody occupancy data for 1158 freshwater macroinvertebrate genera in the contiguous USA

Range maps are used to estimate the geographic extent of taxa, providing valuable information for biodiversity and conservation research and management. Freshwater macroinvertebrates are not well-represented in the range map literature relative to freshwater vertebrates. To address this knowledge gap, we provide range maps for 1158 freshwater macroinvertebrate genera based on two decades of publicly available occurrence data from the USEPA National Aquatic Resource Surveys, which included 11,628 sites and 6,906,990 organisms across the contiguous USA. Maps were created by applying unweighted and weighted pair group method with arithmetic mean clustering and single-linkage clustering algorithms to the occurrence data and creating three layers of polygons from the minimum convex hulls of clusters. A total of 25 freshwater macroinvertebrate classes are represented in the range map dataset. Most mapped genera were insects (394/1158), followed by malacostracans (242/1158), polychaetes (182/1158), and bivalves (121/1158). Additionally, we provide waterbody type percent occupancy data for all genera, detailing how genera are partitioned between boatable streams, wadeable streams, inland lakes, Laurentian Great Lakes, and coastal estuaries.

High-throughput single nucleotide polymorphism genotyping reveals population structure and genetic diversity of tall fescue (

Single nucleotide polymorphisms (SNPs) are the most abundant form of genetic variation in eukaryote genomes and may be useful for selection of genetically distant parents for crossing in breeding programs. In this study, genome-wide SNPs of tall fescue (Festuca arundinacea Schreb.) were genotyped by using double-digest restriction-site-associated DNA sequencing to determine the genetic variation and differentiation among and within forage, turf and hybrid populations. After filtering, 16 036 SNPs were used to investigate genetic diversity and for structure analysis. SNP markers clearly differentiated the populations from each other. However, the hybrid population had a higher genetic similarity with the turf population than with the forage population. The results were confirmed by genetic differentiation (fixation index, Fst) and gene flow (Nm) statistics, so that low Fst and high Nm were observed between turf and hybrid groups, indicating less genetic distance and a high similarity between them. Based on the results of the weighted pair group method with arithmetic mean clustering, discriminant analysis of principal components and analysis of molecular variance, greater genetic differentiations were found among diverse turf, forage and hybrid populations, especially between turf and forage ones. In conclusion, numerous informative SNPs, natural allelic diversity-led domestication patterns, basic genetic variation statistics (e.g. Fst and heterozygosity) and population structures have multidimensional applicability for tall fescue genomics-assisted breeding.

Tradeoff between compression ratio and decoding delay of distributed source coding for uplink transmissions in machine-type communication

Rapid growth of machine-type communications devices challenges the future network with a significant aggregated data traffic. Distributed source coding is a promising technique that compresses data sources and decreases required aggregated data transmission rate. In this article, we discuss the merits and demerits of deploying distributed source coding in machine-type communications uplink transmissions. We analyze how the decoding delay and storage consumption scale with the number of users and prove that the average decoding delay grows linearly with the user number under some assumptions. A machine-type communications uplink transmission scheme adopting clustered distributed source coding is proposed to balance the compression ratio and decoding delay of distributed source coding where users are divided into independently encoded and decoded clusters. We evaluate three clustering algorithms, grid dividing, Weighted Pair Group Method with Arithmetic Mean, and K-medoids in our system model. The grid dividing algorithm clusters users based on their locations, while Weighted Pair Group Method with Arithmetic Mean and K-medoids cluster users using the correlation intensity between them. Our simulation results show that Weighted Pair Group Method with Arithmetic Mean and K-medoids outperform grid dividing on compression ratio and K-medoids and grid dividing have a more balanced delay distribution among different clusters than Weighted Pair Group Method with Arithmetic Mean.

Molecular dissection of genetic diversity in pigeonpea [Cajanus cajan (L) Millsp.] minicore collection

The present investigation was carried out using 191genotypes as mini core collections of pigeonpea along with 5 check varieties to know the genetic diversity at molecular level. Significant variation was observed by the way of analysis of variance for nine characters viz., days to 50 % flowering, days to maturity, plant height, number of branches per plant, pod bearing length, number of pods per plant, number of seeds per pod, seed yield per plant and hundred seed weight. Molecular diversity using 18 polymorphic simple sequence repeat (SSR) markers divided genotypes into 15 clusters, of which ICP-11059 and AK-101 were solitary, indicating their distinctiveness among all genotypes. Similarly, BSMR-533, JKM-7, RVK-285, ICP-1126, ICP-348, ICP-6859 and ICP-7869 were found distinct among the genotypes. Geographical origin based diversity separated Indian and non Indian genotypes. The Un weighted Pair Group Method with Arithmetic mean (UPGMA) based dendrogram indicated distinctiveness of ICP-13633 and Bennur local, as they formed solitary cluster. The SSR marker CcM 602, as it could differentiate 4 genotypes at different base pair size can be used for identification and finger printing of genotypes.

Assessment of Genetic Diversity in Wheat (<i>Triticum aestivum</i> L.) under Elevated Yellow Rust Pressure

The research work was carried out at national agriculture research center Islamabad (NARC) and Pakistan council of scientific and industrial research (PCSIR) Peshawar. The research was comprised of biochemical characterization SDS page and PCA to estimate the genetic diversity. The cultivar were consisted of cultivated varieties, elite varieties and advance line of (30) genotypes. To absorb Fe, Cr, Ca, Mn, Zn, Pb, Cu, Na, K, protein, moisture, concentration. Sodium Dodeceylsulphate Poly Acraylamide Gel Electrophoresis of wheat genotypes was conducted. The data was collected and subjected to analysis of un weighted pair group method with arithmetic averages (UPGMA) with statistica software package 0.5. In multivariate data analysis have 11 variables which have maximum variability. The more variation was observed among Inqilab-91, Bars-2009, Shafaq-2006, NARC-2009, Wc-24, and Sahakar-95. To produce more diverse genotypes we should cross among these varieties.

Differences in the Biodiversity of the Fecal Microbiota of Infants With Rotaviral Diarrhea and Healthy Infants.

BackgroundRotaviral diarrhea (RD) has been associated with the biodiversity of the fecal microbiota in infants; however, the differences in the biodiversity of the fecal microbiota between infants with RD and healthy (H) infants have not been clearly elucidated.ObjectivesThis study aimed to reveal the changes in the biodiversity of the fecal microbiota of infants with RD.Patients and MethodsFor this study, 30 fecal samples from 15 RD infants and 15 H infants were collected. The biodiversity of the fecal microbiota from the two groups was compared via polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and gene sequencing.ResultsThe Shannon-Weaver index showed that the biodiversity of the fecal microbiota from the RD infants was significantly lower (P < 0.05) than that from the H infants. All fifteen RD infants were grouped into one cluster and were separated from the H infants by the un weighted-pair group method, with the arithmetic average (UPGMA) clustering algorithm. In addition, when compared with the healthy infants, the communities of the dominant microbes, Lactobacillus and Bifidobacterium, in the fecal microbiota from the RD infants have obviously changed.ConclusionsWith regard to improving the understanding of the differences in the biodiversity of the fecal microbiota between RD infants and H infants, the findings of this study can provide a possible basis to reveal the relationship between RD and intestinal microbiota.

An Effective Approach for Clustering InhA Molecular Dynamics Trajectory Using Substrate-Binding Cavity Features.

Protein receptor conformations, obtained from molecular dynamics (MD) simulations, have become a promising treatment of its explicit flexibility in molecular docking experiments applied to drug discovery and development. However, incorporating the entire ensemble of MD conformations in docking experiments to screen large candidate compound libraries is currently an unfeasible task. Clustering algorithms have been widely used as a means to reduce such ensembles to a manageable size. Most studies investigate different algorithms using pairwise Root-Mean Square Deviation (RMSD) values for all, or part of the MD conformations. Nevertheless, the RMSD only may not be the most appropriate gauge to cluster conformations when the target receptor has a plastic active site, since they are influenced by changes that occur on other parts of the structure. Hence, we have applied two partitioning methods (k-means and k-medoids) and four agglomerative hierarchical methods (Complete linkage, Ward’s, Unweighted Pair Group Method and Weighted Pair Group Method) to analyze and compare the quality of partitions between a data set composed of properties from an enzyme receptor substrate-binding cavity and two data sets created using different RMSD approaches. Ensembles of representative MD conformations were generated by selecting a medoid of each group from all partitions analyzed. We investigated the performance of our new method for evaluating binding conformation of drug candidates to the InhA enzyme, which were performed by cross-docking experiments between a 20 ns MD trajectory and 20 different ligands. Statistical analyses showed that the novel ensemble, which is represented by only 0.48% of the MD conformations, was able to reproduce 75% of all dynamic behaviors within the binding cavity for the docking experiments performed. Moreover, this new approach not only outperforms the other two RMSD-clustering solutions, but it also shows to be a promising strategy to distill biologically relevant information from MD trajectories, especially for docking purposes.

Software refactoring at the function level using new Adaptive K-Nearest Neighbor algorithm

Improving the quality of software is a vital target of software engineering. Constantly evolving requirements force software developers to enhance, modify, or adapt software. Thus, increasing internal complexity, maintenance effort, and ultimately cost. In trying to balance between the needs to change software, maintain high quality, and keep the maintenance effort and cost low, refactoring comes up as a solution. Refactoring aims to improve a number of quality factors, among which is understandability. Enhancing understandability of ill-structured software decreases the maintenance effort and cost. To improve understandability, designers need to maximize cohesion and minimize coupling, which becomes more difficult to achieve as software evolves and internal complexity increases. In this paper, we propose a new Adaptive K-Nearest Neighbor (A-KNN) algorithm to perform clustering with different attribute weights. The technique is used to assist software developers in refactoring at the function/method level. This is achieved by identifying ill-structured software entities and providing suggestions to improve cohesion of such entities. We also compare the proposed technique with three function-level clustering techniques Single Linkage algorithm (SLINK), Complete Linkage algorithm (CLINK) and Weighted Pair-Group Method using Arithmetic averages (WPGMA). A-KNN showed competitive performance with the other three algorithms and required less computational complexity.

Influence of Sungun copper mine on groundwater quality, NW Iran

Sungun mine is the largest open-cast copper mine in northwest of Iran and is in the primary stages of extraction. The influence of mining activity on the quality of regional groundwater has been taken in to consideration in this study. Accordingly, sampling was done from 22 springs in the study area. The concentrations of major anions and cations as well as Al, Cu, Cd, Cr, Fe, Mn, and Zn were determined for all 22 spring samples in mid-August 2005. The results showed that the concentrations of most of these elements were below the USA Environmental Protection Agency (EPA) limits; however, Al and Fe concentrations are considered to be more than limits in a couple of samples. Despite the fact that geological formations are highly weathered and fractured, the dissolution of minerals within the study area is low. This may be justified by the relatively high alkalinity of local underground water which keeps metals in solid phase and does not let them enter dissolved phase. Additionally, this may be attributed to the high velocity of groundwater flows, which do not give enough time for minerals to dissolve. Correlation coefficients among water chemistry components were determined and the weighted-pair group method was chosen for cluster analysis. Accordingly, high correlation among Al, Fe and Cr, Cd ,and Cu, sodium absorption ratio (SAR) and Na as well as total hardness (TH), Ca, and Mg were observed. The chemical characteristics of water compositions on the basis of major ion concentrations were evaluated on a Schoeller and Piper diagram. Accordingly, the dominant type of water in the region is considered to be Ca-HCO3 (calcium-bicarbonate type). However, this type of water is also rich in Na, K, and especially Mg. Regarding Schoeller diagram, the current status of local underground water is good for drinking purposes. By commencing mining excavation with designed capacity in near future, the minerals will come into contact with air and water resulting in dissolution, especially in ponds, which, in turn, will increase the concentration of toxic metals in groundwater. Considering future uses of this water including for drinking, irrigation, industrial purposes, etc., precautions must be taken in to consideration.

Dissimilar or orthogonal reversed-phase chromatographic systems: A comparison of selection techniques

Developing an analytical separation procedure for an unknown mixture is a challenging issue. An important example is the separation and quantification of a new drug and its impurities. One approach to start method development is the screening of the mixture on dissimilar chromatographic systems, i.e. systems with large selectivity differences. After screening, the most suited system is retained for further method development. In a step prior to such strategy dissimilar chromatographic systems need to be selected. In this paper the performance of different chemometric selection approaches, described in the literature, was visually evaluated and compared. Additionally, orthogonal projection approach (OPA) was tested as another potential selection method. All techniques, including the OPA method, were able to select (a set of) dissimilar chromatographic systems and many similarities between the selections were observed. However, the Kennard and Stone algorithm performed best in selecting the most dissimilar systems in the earliest steps of the selection procedure. The generalized pairwise correlation method (GPCM) and the auto-associative multivariate regression trees (AAMRT) were also performing well. OPA and weighted pair group method using arithmetic averages (WPGMA) are less preferable.

Molecular markers indicate that the narrow Québec endemicsRosa rousseauiorumandRosa williamsiiare synonymous with the widespreadRosa blanda

Rosa rousseauiorum Boivin and Rosa williamsii Fern. are two rare roses in eastern Québec, whose taxonomic status is controversial. Morphological characters alone do not clearly differentiate these two taxa from each other or from the morphologically variable and widespread Rosa blanda Ait. We evaluated the taxonomic status of these two taxa, and of two other R. blanda segregates, Rosa subblanda Rydb. and Rosa johannensis Fern., through an analysis of RAPD, ISSR, and AFLP markers. We surveyed 86 individuals from 36 populations in eastern North America. Despite a high degree of polymorphism, principal coordinate analyses and the weighted pair group method with arithmetic averaging suggest no clustering of individuals that correspond to taxonomic boundaries. However, the closely related Rosa palustris Marsh. is clearly differentiated from the R. blanda s.l. taxa. When populations of R. blanda west of Québec are included, the principal coordinate analyses and Mantel tests indicate the presence of a significant east–west geographic gradient. Analyses of molecular variation suggest that most of the observed variation occurs within taxa, rather than among taxa. A weak inter-taxon variation is nonetheless significant for RAPD and ISSR data, and a weak pattern dependent on geographical location is evident within the province of Québec. In accordance with studies based on morphological characters, molecular data indicate that R. rousseauiorum and R. williamsii should not be considered as species distinct from R. blanda.Key words: Rosa blanda, Rosa rousseauiorum, Rosa williamsii, Rosa johannensis, Rosa subblanda, RAPD, ISSR, AFLP, endangered plants, taxonomic status.

Identification of Direct Genomic Targets Downstream of the Nuclear Factor-κB Transcription Factor Mediating Tumor Necrosis Factor Signaling

Tumor necrosis factor (TNF) is a pro-inflammatory cytokine that controls expression of inflammatory genetic networks. Although the nuclear factor-kappaB (NF-kappaB) pathway is crucial for mediating cellular TNF responses, the complete spectrum of NF-kappaB-dependent genes is unknown. In this study, we used a tetracycline-regulated cell line expressing an NF-kappaB inhibitor to systematically identify NF-kappaB-dependent genes. A microarray data set generated from a time course of TNF stimulation in the presence or absence of NF-kappaB signaling was analyzed. We identified 50 unique genes that were regulated by TNF (Pr(F)<0.001) and demonstrated a change in signal intensity of+/-3-fold relative to control. Of these, 28 were NF-kappaB-dependent, encoding proteins involved in diverse cellular activities. Quantitative real-time PCR assays of eight characterized NF-kappaB-dependent genes and five genes not previously known to be NF-kappaB-dependent (Gro-beta and-gamma, IkappaBepsilon, interleukin (IL)-7R, and Naf-1) were used to determine whether they were directly or indirectly NF-kappaB regulated. Expression of constitutively active enhanced green fluorescent.NF-kappaB/Rel A fusion protein transactivated all but IL-6 and IL-7R in the absence of TNF stimulation. Moreover, TNF strongly induced all 12 genes in the absence of new protein synthesis. High probability NF-kappaB sites in novel genes were predicted by binding site analysis and confirmed by electrophoretic mobility shift assay. Chromatin immunoprecipitation assays show the endogenous IkappaBalpha/epsilon, Gro-beta/gamma, and Naf-1 promoters directly bound NF-kappaB/Rel A in TNF-stimulated cells. Together, these studies systematically identify the direct NF-kappaB-dependent gene network downstream of TNF signaling, extending our knowledge of biological processes regulated by this pathway.

Spatial Distribution of Holocene Benthic Foraminifera, Northeastern Aegean Sea

The distribution of Holocene benthic foraminifera in the Gokceada-Bozcaada-Canakkale triangle was investigated in 31 surface-sediment samples. The sediments can be classified as muddy to gravelly-muddy sand with rare occurrences of muddy gravel and gravelly sand. The fauna exhibits high diversity and richness, and the populations increase in diversity and richness depending on the number of specimens. One hundred sixty (160) species were found. Eight benthic fossil assemblages, comprising only calcareous species, were identified in the region: Porosononion subgranosum (Egger), Ammonia compacta Hofker, Asterigerinata mamilla (Williamson), Rosalina bradyi Cushman, Elphidium crispum. (Linne), Cassidulina carinata Silvestri, Brizalina spathulata (Williamson) and Valvulineria bradyana (Fornasini). In order to analyze the samples statistically, the main foraminiferal parameters were calculated, namely, species richness (d'), Shannon-Wiener diversity (H) and evenness (J'). Finally, Q-mode cluster analysis was applied to the Bray-Curtis measure of similarity using the weighted pair-group method, and the ordination of the samples was plotted using an MDS plot. Eight benthic fossil assemblages, dominated by calcareous, hyaline-wall-bearing species, characterize the northeastern Aegean Sea.

Comparative fruit studies in a group of tribe Peucedaneae (Umbelliferae)

Comparative fruit studies (macro- and micro-morphology and anatomy) have been undertaken in a group of tribe Peucedaneae (Umbelliferae) (Malabaila Hoffm.,Pastinaca L., Heracleum L., Stenotaenia Boiss., Opopanax W.D.J. Koch, andGrafia Rchb.). A multivariate analysis was carried out using Simple Matching Coefficient and UPGMA (unweighted pair group method using arithmetic averages)and WPGMA (weighted pair group method using arithmetic averages) clustering methods. Two types of dorsal mericarp surface and margin sufaces were detected:(1) reticulate with a smooth surface, (2) reticulate with a striate surface. On the dorsal surface of the mericarps, three hair shapes and four hair surface types were seen. These hairs are treated as having systematic significance. For instance, a very short triangular hair with a papillose surface is unique to Pastinaca. The shapes of the mericarp and mericarp apex at the base of stylopodium are significant features for generic delimitation. Malabaila is distinguished by its c...

Verification of the health care region in Fukuoka Prefecture.

Because the change in the location of industries, if comprehensive health care is to be promoted, there is need to derive a methodology for finding the life cycle patterns of the residents and to set up health care regions from these results. Formally, health care had evolved within the prefecture or the Health Center administrative districts with each spectrum of health promotion, "disease prevention" and "diagnosis, treatment and rehabilitation" using fragmented and unrelated methods. However, there is need to designate the region for health care planning aside from the present units for administrative purposes. With this object in mind, Fukuoka Prefecture, which has experienced a dramatic change in industrial structure, was selected as an example. Regions were designated centering around the analysis of "socio-economic aspects" and "demographic characteristics". From the viewpoint of the relationship with the life style, the geographical extent of the activity of the residents was studied through the commuting areas. Based on this activity range and the geographical distribution of the industrial locations, a reasonable "Region for health care" was designated. The first quantitative approach to verify the results was made by using the weighted pair-group method and principal component analysis. And from the vantage of the Fuzzy Sets-theory, a multivariate technique centering around clustering analysis was next utilized to analyse.(ABSTRACT TRUNCATED AT 250 WORDS)

年齢段階別にみた日常動作の主観的運動強度の分析

Psychological problems inherent to physical activities and efforts have had much less prominence until the last few years. But the most recent decade has witnessed an increasing in problems concerning this field. The purpose of this work is to investigate of the age differences in the worker's activities of daily living from the view point of perceived exertion. The answers to the questions including about perceived exertions during daily activities, subjective symptoms of fatigue and aging, self perceptions of fitness and obesity rate etc. were collected from1, 801 male workers(including 952 job applicants)aged from 16 to 76 years. This data was analyzed by the quantification method by C. Hayashi and by the cluster analysis(weighted pair group method and re-arrangement method). Increasing in perceived exertion during daily activitieseems to appear on the surface at the age of 45-54 years and to become great from the age of 65-76 years. While sublective fatigue seems to decrease with advancing of age.

Comparison of Numerical Taxonomic Methods Used to Estimate Flavonoid Similarities in the Limnanthaceae

The Limnanthaceae is a small family of North American herbs with uncertain internal relationships. Taxa of the family were compared on the basis of 46 flavonol glycosides occurring in all plant tissues or in petals only. The flavonoid data were analyzed by 3 numerical taxonomic techniques: 1) clustering by the Weighted Pair Group method considering positive and negative matches (Using Simple Matching coefficient) ; 2) clustering by the Weighted Pair Group method considering only positive matches (using Jaccard coefficient) ; 3) Varimax Factor Analysis with rotation. No significantly different results were produced by the two clustering methods. Factor analysis provided a clearer indication of relationships among taxa of the Limnanthaceae than did conventional clustering analysis. Apparently, ordination of taxa in three dimensions is necessary to accurately express relationships between divergent evolutionary lines of the family since much of the expressed variation in flavonoids cannot be accounted for by a one-dimensional clustering technique.

Binary coefficients: A theoretical and empirical study

Binary coefficients can be assigned to several categories on the basis of algebraic and conceptual properties. The phi coefficient of association is related algebraically to the chi-square statistic for 2-by-2 contingency tables, and use of this coefficient in cluster analysis permits the objective, nonarbitrary partitioning of objects among groups on the basis of previously selected levels of significant, positive association. Similarity, matching, and distance coefficients possess neither conceptual nor operational statistical meaning for many geological data sets. The weighted pair group method and flexible clustering strategy may give an overly conservative partitioning of objects among groups. Clustering by the unweighted pair group method, using the phi coefficient, is recommended for the analysis of biostratigraphic and paleoecologic presence—absence data.

A Numerical Study of the Common Narrow-Leaved Taxa of Chenopodium Occurring in the Western United States

A numerical taxonomic study was conducted on the common narrow-leaved members of the genusChenopodium that occur in the western United States. As many as six and as few as two species have been recognized. Thirty-five individual popu lations were used as OTU’s, and 35 characters were considered. The data were subjected to cluster (both the weighted-pair group method and the within-group dispersion method) and principal component analysis. The results of both analyses are in general agreement and suggest phenetic relationships that differ from current interpretations in the literature. It is concluded thatC. desiccatum var.leptophylloides is much more closely related phenetically toC. atrovirens (and may not be distinct from it) than it is toC. desiccatum var.desiccatum. Chenopodium hians andC. leptophyllum appear to be phenetically distinct despite the fact that they have sometimes been viewed as conspecific.Cheno podium subglabrum is not very similar toC. leptophyllum, and should probably be treated as a separate species rather than as a variety of the latter. Popu lations referable toC. incognitum form a rather loose cluster that appears some what intermediate between populations ofC. desiccatum var.leptophylloides,C. atrovirens, C. hians, andC. leptophyllum.

An Osteological Analysis of Holarctic Tree Frogs, Family Hylidae

Holarctic hylids are currently grouped into 4 genera: Hyla, Acris, Pseudacris, and Limnaeodus. A complete osteological analysis of 32 species of holarctic hylids was performed to discover if systematic skeletal differences supported recognition of these taxonomic groups. Detailed examinations of their skeletons revealed that the species differed in 20 osteological characters. Simple matching similarity coefficients were calculated for all of the species and a phenogram was constructed using the weighted pair group method of averages. The osteological analysis suggests that the 32 species form 5 clusters: 1) 7 species of Pseudacris; 2) two species of Acris; 3) Limnaeodus ocularis; 4) Hyla crucifer; and, 5) 21 species of Hyla. Both Acris and Limnaeodus are distinctive osteologically, and both genera appear to be valid. Osteologically, Hyla crucifer appears to be a connecting link between Pseudacris and other Hyla, and literature reports of hydridization studies also suggest that H. crucifer is equally related to both Pseudacris and other holarctic Hyla. Present data, then, suggest that the recognition of Pseudacris as a separate genus is unwarranted, and the species so designated probably represent species within the genus Hyla.