scholarly journals Unique k-mers as Strain-Specific Barcodes for Phylogenetic Analysis and Natural Microbiome Profiling

2020 ◽  
Vol 21 (3) ◽  
pp. 944 ◽  
Author(s):  
Valery V. Panyukov ◽  
Sergey S. Kiselev ◽  
Olga N. Ozoline
Keyword(s):  
Distance Matrix ◽  
Pairwise Distance ◽  
Clinical Samples ◽  
E Coli ◽  
Taxonomic Profiling ◽  
New Methods ◽  
Natural Microflora ◽  
Microbiome Profiling ◽  
Pairwise Distance Matrix

The need for a comparative analysis of natural metagenomes stimulated the development of new methods for their taxonomic profiling. Alignment-free approaches based on the search for marker k-mers turned out to be capable of identifying not only species, but also strains of microorganisms with known genomes. Here, we evaluated the ability of genus-specific k-mers to distinguish eight phylogroups of Escherichia coli (A, B1, C, E, D, F, G, B2) and assessed the presence of their unique 22-mers in clinical samples from microbiomes of four healthy people and four patients with Crohn’s disease. We found that a phylogenetic tree inferred from the pairwise distance matrix for unique 18-mers and 22-mers of 124 genomes was fully consistent with the topology of the tree, obtained with concatenated aligned sequences of orthologous genes. Therefore, we propose strain-specific “barcodes” for rapid phylotyping. Using unique 22-mers for taxonomic analysis, we detected microbes of all groups in human microbiomes; however, their presence in the five samples was significantly different. Pointing to the intraspecies heterogeneity of E. coli in the natural microflora, this also indicates the feasibility of further studies of the role of this heterogeneity in maintaining population homeostasis.

scholarly journals Cluster Analysis Stopping Rules in Stata

2016 ◽  
Author(s):  
Brendan Halpin
Keyword(s):  
Cluster Analysis ◽  
Distance Matrix ◽  
Stopping Rules ◽  
Pairwise Distance ◽  
Optimum Number ◽  
Pairwise Similarity ◽  
Number Of Clusters ◽  
Euclidean Distances ◽  
New Applications ◽  
Pairwise Distance Matrix

AbstractAnalysts doing cluster analysis sometimes want the data to tell them the optimum number of clusters. Common "stopping rules" use the Calinski-Harabasz pseudo-F statistic and Duda-Hart indices, which are based on squared Euclidean distances between cases. Cluster analysis operates on a pairwise matrix of distances between the objects clusters, which are usually created from the observed variables. However, approaches such as expert judgement or algorithmic pattern-recognition (as used for instance in sequence analysis) often output matrices of pairwise similarity or difference whose relationship to the observed variables is much less direct. Built-in Stata utilities allow calculation of the CH and DH indices when cluster analysis starts from variables, but not with cluster analysis that starts from a pairwise distance matrix (unless the distances are squared Euclidean distances defined on variables which are still available). In this note I present two small Stata utilities that will calculate the CH and DH statistics from the distance matrix, if the distances are squared Euclidean. If the distances have another metric, these utilities can be seen as calculating a pseudo-CH pseudo-F or pseudo-DH statistic, potentially extending their use to new applications.-- Brendan Halpin, Head, Department of Sociology, University of Limerick, IrelandTel: w +353-61-213147 f +353-61-202569 h +353-61-338562; Room F1-002 x 3147mailto:[email protected] ULSociology on Facebook: http://on.fb.me/fjIK9thttp://teaching.sociology.ul.ie/bhalpin/wordpress twitter:@ULSociology

Focusing on plasma glycoprotein VI

2012 ◽  
Vol 107 (04) ◽  
pp. 648-655 ◽  
Author(s):  
Jane F. Arthur ◽  
Elizabeth E. Gardiner ◽  
Robert K. Andrews ◽  
Mohammad Al-Tamimi
Keyword(s):  
Experimental Models ◽  
Clinical Samples ◽  
Glycoprotein Vi ◽  
New Methods ◽  
Tumour Metastasis ◽  
Pathophysiological Role ◽  
Plasma Glycoprotein ◽  
Therapeutic Compounds ◽  
Collagen Receptor

SummaryNew methods for analysing both platelet and plasma forms of the platelet-specific collagen receptor, glycoprotein VI (GPVI) in experimental models or human clinical samples, and the development of the first therapeutic compounds based on dimeric soluble GPVI-Fc or anti-GPVI antibody-based constructs, coincide with increased understanding of the potential pathophysiological role of GPVI ligand binding and shedding. Platelet GPVI not only mediates platelet activation at the site of vascular injury where collagen is exposed, but is also implicated in the pathogenesis of other diseases, such as atherosclerosis and coagulopathy, rheumatoid arthritis and tumour metastasis. Here, we describe some of the critical mechanisms for generating soluble GPVI from platelets, and future avenues for exploiting this unique platelet-specific receptor for diagnosis and/or disease prevention.

RAMP based fingerprinting and assessment of relationships among Australian narrow-leafed lupin (Lupinus angustifolius L.) cultivars

2005 ◽  
Vol 56 (12) ◽  
pp. 1339 ◽  
Author(s):  
H. Yuan ◽  
G. Yan ◽  
K. H. M. Siddique ◽  
H. Yang
Keyword(s):  
Cluster Analysis ◽  
Molecular Identification ◽  
Distance Matrix ◽  
Farming System ◽  
Pairwise Distance ◽  
Grain Legume ◽  
Dna Variation ◽  
Legume Crop ◽  
Commercial Cultivars ◽  
Pairwise Distance Matrix

Narrow-leafed lupin is a major winter grain legume crop in the Australian farming system and a number of commercial cultivars are currently available to growers. A significant level of polymorphism was detected in narrow-leafed lupin cultivars by the randomly amplified microsatellite polymorphism (RAMP) approach, suggesting that cultivars harbour considerable DNA variation. Seventy-seven cultivar-specific markers were found among the 23 lupin cultivars examined and a dichotomous fingerprinting key was developed for the molecular identification of lupin cultivars. Cluster analysis of pairwise distance matrix computed from RAMP profiles grouped the 23 cultivars into 4–5 clusters, which generally agreed with their pedigree relationships.

Exploring Evolution of Public Opinions on Tianya Club Using Dynamic Topic Models

2020 ◽  
Vol 8 (4) ◽  
pp. 309-324
Author(s):  
Zhihua Yan ◽  
Xijin Tang
Keyword(s):  
Family Life ◽  
Topic Model ◽  
Distance Matrix ◽  
Pairwise Distance ◽  
Online Media ◽  
Traditional Media ◽  
Public Opinions ◽  
Government Administration ◽  
Media Data ◽  
Pairwise Distance Matrix

AbstractOnline media have brought tremendous changes to civic life, public opinions, and government administration. Compared with traditional media, online media not only allow individuals to browse news and express their views more freely, but also accelerate the transmission of opinions and expand influence. As public opinions may arouse societal unrest, it is worth detecting the primary topics and uncovering the evolution trends of public opinions for societal administration. Various algorithms are developed to deal with the huge volume of unstructured online media data. In this study, dynamic topic model is employed to explore topic content evolution and prevalence evolution using the original posts published from 2013 to 2017 on the Tianya Zatan Board of Tianya Club, which is one of the most popular BBS in China. Based on semantic similarities, topics are grouped into three themes: Family life, societal affairs, and government administration. The evolution of topic prevalence and content are affected by emergent incidents. Topics on family life become popular, while themes “societal affairs” and “government administration” with bigger standard deviations are more likely to be influenced by emergent hot events. Content evolution represented by monthly pairwise distance matrix is very easy to find change points of topic content.

scholarly journals Highly clade-specific biosynthesis of rhamnose: present in all plants and in only 42% of prokaryotes. Only Pseudomonas uses both D- and L-rhamnose

2019 ◽  
Author(s):  
Toshi Mishra ◽  
Petety V. Balaji
Keyword(s):  
Salmonella Enterica ◽  
Physiological Role ◽  
Biosynthesis Pathway ◽  
E Coli ◽  
Taxonomic Profiling ◽  
Physiological Processes ◽  
Commercially Important ◽  
Horseshoe Bat

ABSTRACTRhamnose is a constituent of lipo- and capsular polysaccharides, and cell surface glycoproteins. L-rhamnose is biosynthesized by the rml or udp pathway and D-rhamnose by the gdp pathway. Disruption of its biosynthesis affects survival, colonisation, etc. Rhamnosides are commercially important in pharmaceutical and cosmetics industries. HMM profiles were used to investigate the prevalence of the three pathways in completely sequenced genomes and metagenomes. The three pathways are mutually exclusive except in Pseudomonas which has both rml and gdp pathways. The rml pathway is restricted to bacteria (42% genomes), archaea (21%) and bacteriophages, and absent in eukaryotes and other viruses. The gdp pathway is restricted to Pseudomonas and Aneurinibacillus. The udp pathway is primarily found in plants, fungi and algae, and in human faecal metagenomic samples. The rml pathway is found in >40% genomes of Actinobacteria, Bacteroidetes, Crenarchaeota, Cyanobacteria, Fusobacteria and Proteobacteria but in <20% genomes of Chlamydiae, Euryarchaeota and Tenericutes. The udp pathway is found in all genomes of Streptophyta, <=25% genomes of Ascomycota and Chordata, and none of the genomes of Arthropoda and Basidiomycota. Some genera which lack any of these pathways are Chlamydia, Helicobacter, Listeria, Mycoplasma, Pasteurella, Rickettsia and Staphylococcus. Organisms such as E. coli and Salmonella enterica showed significant strain-specific differences in the presence/absence of rhamnose pathways. Identification of rhamnose biosynthesis genes facilitates profiling their expression pattern, and in turn, better understanding the physiological role of rhamnose. Knowledge of phylogenetic distribution of biosynthesis pathways helps in fine graining the taxonomic profiling of metagenomes.AUTHOR SUMMARYIn the present study, we have investigated the prevalence of rhamnose biosynthesis pathways in completely sequenced genomes and metagenomes. It is observed that the prevalence of rhamnose is highly clade specific: present in all plants but in less than half of all prokaryotes. Among chordates, only the Chinese rufous horseshoe bat has rhamnose biosynthesis pathway and this exclusive presence is quite baffling. The effect of disrupting rhamnose biosynthesis has been reported in a few prokaryotes and all these cases pointed to the essentiality of rhamnose for critical physiological processes such as survival, colonisation, etc. In this background, it is surprising that many of the prokaryotes such as Escherichia coli and Salmonella enterica show significant strain-specific differences in the presence/absence of rhamnose pathway. This study will facilitate the experimental characterization of rhamnose biosynthesis genes in organisms where this pathway has not been characterised yet, eventually leading to the elucidation of the biological role of rhamnose. Phylum-, genus-, species- and strain-level differences found with respect to presence of rhamnose biosynthesis pathway genes can be used as a tool for taxonomic profiling of metagenome samples. This study could also annotate a significant number of orphan proteins in the TrEMBL database.

Are Three Items Sufficient to Measure Sense of Coherence?

2018 ◽  
Vol 34 (4) ◽  
pp. 229-237 ◽  
Author(s):  
Francesca Chiesi ◽  
Andrea Bonacchi ◽  
Caterina Primi ◽  
Alessandro Toccafondi ◽  
Guido Miccinesi
Keyword(s):  
Sense Of Coherence ◽  
Convergent Validity ◽  
Clinical Sample ◽  
Clinical Samples ◽  
Depression Symptoms ◽  
Time Saving ◽  
Positive Role ◽  
Patients With Cancer ◽  
Measure Sense

Abstract. The present study aimed at evaluating if the three-item sense of coherence (SOC) scale developed by Lundberg and Nystrom Peck (1995) can be effectively used for research purpose in both nonclinical and clinical samples. To provide evidence that it represents adequately the measured construct we tested its validity in a nonclinical (N = 658) and clinical sample (N = 764 patients with cancer). Results obtained in the nonclinical sample attested a positive relation of SOC – as measured by the three-item SOC scale – with Antonovsky’s 13-item and 29-item SOC scales (convergent validity), and with dispositional optimism, sense of mastery, anxiety, and depression symptoms (concurrent validity). Results obtained in the clinical sample confirmed the criterion validity of the scale attesting the positive role of SOC – as measured by the three-item SOC scale – on the person’s capacity to respond to illness and treatment. The current study provides evidence that the three-item SOC scale is a valid, low-loading, and time-saving instrument for research purposes on large sample.

The Local Sanarelli-Shwartzman Phenomenon in Rats Induced by Human Leukaemic Cells

1973 ◽  
Vol 29 (02) ◽  
pp. 353-362
Author(s):  
J Lisiewicz ◽  
A Pituch ◽  
J. A Litwin
Keyword(s):  
Chronic Lymphocytic Leukaemia ◽  
Intravenous Injection ◽  
Peripheral Blood ◽  
Lymphocytic Leukaemia ◽  
Acute Myeloblastic Leukaemia ◽  
Demarcation Line ◽  
E Coli ◽  
Leukaemic Cells ◽  
Shwartzman Phenomenon

SummaryThe local Sanarelli-Shwartzman phenomenon (SSP-L) in the skin of 30 rats was induced by an intr a cutaneous sensitizing injection of leukaemic leucocytes isolated from the peripheral blood of patients with chronic lymphocytic leukaemia (CLL), acute myeloblastic leukaemia (AL) and chronic granulocytic leukaemia (CGL) and challenged by an intravenous injection of 100(μ of E. coli endotoxin. SSP-L was observed in 7 rats after injection of CLL lymphocytes and in 6 and 2 rats after AL myeloblasts and the CGL granulocytes, respectively. The lesions in the skin after AL myeloblasts appeared in a shorter time and were of longer duration compared with those observed after CLL lymphocytes and CGL granulocytes. Histologically, the lesions consisted of areas of destruction in the superficial layers of the skin ; the demarcation line showed the presence of neutrophils, macrophages and erythrocytes. Haemorrhages and fibrin deposits near the demarcation line were larger after injection of CLL lymphocytes and AL myeloblasts than after CGL granulocytes. The possible role of leucocyte procoagulative substances in the differences observed have been discussed.

USE OF INNOVATIVE TEACHING METHODS IN RUSSIAN LESSONS IN GROUPS WITH A NON-RUSSIAN TEACHING LANGUAGE

2020 ◽  
Vol 6 (3) ◽  
pp. 204-212
Author(s):  
Nigora Vokhidova ◽  
Keyword(s):  
Foreign Language ◽  
Teaching Methods ◽  
Group Work ◽  
Russian Language ◽  
Interactive Communication ◽  
Innovative Teaching ◽  
Teaching Language ◽  
New Methods ◽  
The Russian Language

The article discusses the effectiveness of innovative approaches in teaching Russian as a foreign language. It is noted that the use of new methods makes it possible to take into account the knowledge already acquired by the student for studying the Russian language and developing creative skills. The role of such a form of training as group work is shown, and some methods of interactive communication between students in practical classes in the Russian language are considered

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