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Cluster Analysis (2):
Recent article
Cluster Analysis
Abstract
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Abstract
We describe sequencing of the Yoka poxvirus genome using a combination of Roche/454 and Illumina next-generation sequencing technologies. A single consensus contig of ∼175 kb in length that encodes 186 predicted genes was generated. Multiple methods were used to show that Yoka poxvirus is most clo...
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PMID: 21813608
PDF is available here.
PDF is available here.
Abstract
We hypothesize that cell-scaffold interaction and mechanical deformation results in upregulation of genes related to osteogenic/chondrogenic differentiation and thus changes extracellular matrix (ECM) composition in human bone marrow mesenchymal stem cell (hBMSC)-derived tissue-engineered grafts. hB...
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PMID: 21554191
PDF is available here.
PDF is available here.
Abstract
Three dsRNA segments, two similarly sized at 9.5kbp and a third one of approximately 3.6kbp, were extracted from a hypovirulent strain SZ-150 of Sclerotinia sclerotiorum. The complete cDNA sequence of one of the two large dsRNA segment (10398bp, excluding the poly (A) tail) reveals a single ORF that...
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PMID: 21813149
PDF is available here.
PDF is available here.
Abstract
Changes in eating habits could potentially be contributing to vitamin D insufficiency among US adults.
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PMID: 21872696
PDF is available here.
PDF is available here.
Abstract
The purpose of this study was to evaluate and analyze statistical shapes of the outer mandible contour of Caucasian and Chinese people, offering data for the production of preformed mandible reconstruction plates.
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PMID: 21094050
PDF is available here.
PDF is available here.
Biocontrol Science (16)3 2011
Abstract
We attempted to define the connection between chlorine resistance and the geno-cluster. The average CT value of group I was 0.89 mg•min/l and the average of group II was 0.69 mg•min/l. No remarkable differences in the CT values for the groups were found....
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PMID: 21946320
PDF is available here.
PDF is available here.
Abstract
Although oligoarticular juvenile idiopathic arthritis (oJIA) is considered to carry the best prognosis among the JIA subtypes, many children evolve to a chronic course. A few studies have identified clinical risk factors for disease extension, and recent studies have evaluated synovial fluid markers....
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PMID: 21813070
PDF is available here.
PDF is available here.
Abstract
African American women have disproportionately higher rates of breast cancer mortality than all other ethnic groups, thus highlighting the importance of promoting early detection.
African American women (N = 984) from San Diego, California, participated in a randomize...
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PMID: 22046851
PDF is available here.
PDF is available here.
Abstract
We therefore report the development of a markedly improved approach combining fluorescence-based miRNA-in situ hybridization (miRNA-ISH) with immunohistochemistry (IHC). We have applied this protocol to differentiating embryoid bodies (EBs) as well as embryonic and adult mouse hearts, to detect miRN...
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PMID: 21643937
PDF is available here.
PDF is available here.
Abstract
To assess the degree of relationship among individuals with hemangiomas and to evaluate the relative risk (RR) for family members of individuals with hemangiomas.
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PMID: 21844408
PDF is available here.
PDF is available here.
Abstract
We analyzed transcriptional profiles from four independent Shh-medulloblastoma expression datasets (n = 66). Unsupervised clustering analyses demonstrated a clear distinction between infant and adult Shh-medulloblastomas, which was reliably replicated across datasets. Comparison of transcriptomes fr...
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PMID: 21681522
PDF is available here.
PDF is available here.
Abstract
We also re-analysed data from the Four Area Project in Ireland, a large-scale intervention study aimed at assessing the effect of proactive badger culling on bovine TB incidence in cattle herds, taking possible spatial correlation into account. We established that infected herds are spatially correl...
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PMID: 20950513
PDF is available here.
PDF is available here.
Abstract
We have developed a sparse Bayesian factor analysis model in which the observed expression diversity of among a large set of high-dimensional images is modeled by a small number of hidden common factors. We apply this approach on embryonic expression patterns from a Drosophila RNA in situ image data...
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PMID: 21814502
PDF is available here.
PDF is available here.
Abstract
We perform complete proteome level comparisons between M. tuberculosis, mycobacteria, other prokaryotes and available eukaryotes based on protein domains, local sequence similarities and protein disorder. We show that the enrichment of certain domains in the genome can indicate an important function...
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PMID: 21814507
PDF is available here.
PDF is available here.
Abstract
We have described physical activity in the context of clustering patterns of health-promoting behaviors. Laying the groundwork for physical activity in the lifestyle is important for establishing health-promotion strategies to increase physical activity....
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PMID: 21721968
PDF is available here.
PDF is available here.
ISME Journal (5)7 2011
Abstract
We characterize previously undetected microbial metabolic capabilities concealed within the genomes of uncultured marine viral communities. A total of 34 microbial gene families were detected on 452 viral GOS scaffolds. The majority of auxiliary metabolic genes found on these scaffolds have never be...
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PMID: 21307954
PDF is available here.
PDF is available here.
Abstract
We evaluated the effect of different sample preservation strategies (eg, cryopreservation of peripheral blood mononuclear cells or freezing of PAXgene-stabilized whole blood samples) on gene expression profiles. Expression profiles obtained from cryopreserved peripheral blood mononuclear cells diffe...
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PMID: 21704280
PDF is available here.
PDF is available here.
Abstract
We found that several miRs have altered expression levels in osteosarcoma cell lines and tumor tissues when compared to normal human osteoblasts. Three miRs, miR-199a-3p, miR-127-3p, and miR-376c were significantly decreased in osteosarcoma cell lines, while miR-151-3p and miR-191 were increased in...
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PMID: 21666078
PDF is available here.
PDF is available here.
Abstract
We represent molecular evidence supporting the identification of at least two major lineages (subspecies) within the species of R. opimus in Iran. Analysis of the mitochondrial cytochrome b (cyt b) gene, revealed a range of 1-10% genetic variation among populations, which were well associated with b...
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PMID: 21683054
PDF is available here.
PDF is available here.
Abstract
We used 12 polymorphic microsatellite markers. A low level of genetic diversity was found among collections from China and higher levels were seen in Southeast Asia collections. Three genetically distinct groups, Southeast Asia, southwest China, and southeast China, were recovered by Bayesian model-...
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PMID: 21735930
PDF is available here.
PDF is available here.
Abstract
We used gene expression data sets from the analysis of primary and metastatic melanomas to develop a molecular description of the heterogeneity that characterizes this disease. Unsupervised hierarchical clustering, gene set enrichment analyses, and pathway activity analyses were used to describe the...
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PMID: 21641377
PDF is available here.
PDF is available here.
Abstract
We document here the association of a human trafficking route and new world CL. Clinicians and public health officials should be aware of this emerging infectious disease risk....
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PMID: 21633017
PDF is available here.
PDF is available here.
Abstract
The essential oils extracted from the leaves and the shoots of five Abies species (Pinaceae) growing in Japan, i.e., A. firma, A. homolepis, A. veitchii, A. mariesii, and A. sachalinensis, were characterized by GC-FID and GC/MS analyses. The yields of the essential oils extracted fro...
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PMID: 21674785
PDF is available here.
PDF is available here.
Abstract
We utilized a proteomics strategy to characterize proteome-wide alterations between MP-treated MKN28 lines and their untreated counterparts. A total of 97 spots were positively identified as differentially expressed, and of these 62 proteins were up-regulated, whereas 35 proteins were down-regulated...
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PMID: 21574062
PDF is available here.
PDF is available here.
Abstract
These results underscore the utility of considering synergistic issues in the examination of the tripartite efficacy framework....
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PMID: 21659670
PDF is available here.
PDF is available here.
Abstract
We propose a deterministic data mining approach for a distribution of a data set (input/output data) into two representative and balanced sets of roughly equal size taking the variability of the data set into consideration with the purpose of allowing both a fair evaluation of learning's accuracy an...
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PMID: 21656926
PDF is available here.
PDF is available here.
Clinical Cancer Research (17)13 2011
Abstract
These studies define a signal transduction pathway downstream of FGFR-4 Arg388 that acts via ERK and SRF to promote prostate cancer progression....
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PMID: 21622724
PDF is available here.
PDF is available here.
Proteomics (11)12 2011
Abstract
We also found differences at post-translational level. The results indicated that late embryogenesis abundant Rab21 was more strongly phosphorylated in the embryos of the sensitive varieties than in the embryos of the tolerant ones. We propose that the differences found in the phosphorylation status...
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PMID: 21595035
PDF is available here.
PDF is available here.
Sports Biomechanics (10)2 2011
Abstract
One important extrinsic factor that causes foot deformity and pain in women is footwear. Women's sports shoes are designed as smaller versions of men's shoes. Based on this, the current study aims to identify foot shape in 1,236 Chinese young adult men and 1,085 Chinese young adult women. Three-dimen...
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PMID: 21834393
PDF is available here.
PDF is available here.
Abstract
We investigated the relationship between disease-associated proteins and their subcellular localizations, based on the assumption that protein pairs associated with phenotypically similar diseases are more likely to be connected via subcellular localization. The spatial constraints from subcellular...
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PMID: 21613983
PDF is available here.
PDF is available here.
Abstract
This study reports a combined analysis of mitochondrial and ribosomal DNA target regions of phlebotomine sand flies (Diptera: Psychodidae) from the Mediterranean region. A ∼900bp long fragment of the mitochondrial DNA encompassing regions within cytb and nd1 gene and the complete ITS2 ribosomal reg...
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PMID: 21635869
PDF is available here.
PDF is available here.
Abstract
We employed structured sampling to explore the population structure of B. henselae in the United Kingdom and to determine the distribution of strains associated with zoonotic disease within this structure. A total of 118 B. henselae strains were delineated into 12 sequence types (STs) using multiloc...
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PMID: 21471345
PDF is available here.
PDF is available here.
Abstract
Molecular epidemiologic studies may use genotypic clustering of isolates as an indicator of recent transmission. It has been shown that missing cases lead to underestimating clustering, and modelling studies suggested that they may also lead to underestimating odds ratios for clustering. Using a nati...
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PMID: 21606233
PDF is available here.
PDF is available here.
Abstract
The Neolithic site of Çatalhöyük, Turkey (7400-5600 cal BC) is widely acknowledged for its role in the study of early farming communities. To better understand the social and community structure of this setting, an intracemetery biological distance analysis was conducted. Metric and nonmetric obse...
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PMID: 21590748
PDF is available here.
PDF is available here.
Abstract
Scrub typhus, caused by antigenically disparate isolates of Orientia tsutsugamushi, is a widely distributed mite-borne human disease in the Asia Pacific region. Information regarding the heterogeneity of the immunodominant 56-kDa type-specific antigen (TSA) gene is crucial for the design and evaluati...
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PMID: 21593255
PDF is available here.
PDF is available here.
Abstract
To investigate the extent to which authors of cluster randomised trials adhered to two basic requirements of the World Medical Association's Declaration of Helsinki and the International Committee of Medical Journal Editors' uniform requirements for manuscripts (namely, reporting of research ethics r...
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PMID: 21562003
PDF is available here.
PDF is available here.
Abstract
Childhood pilocytic astrocytoma is the most frequent brain tumor affecting children. Proteomics analysis is currently considered a powerful tool for global evaluation of protein expression and has been widely applied in the field of cancer research. In the present study, a series of...
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PMID: 21466243
PDF is available here.
PDF is available here.
Abstract
We used an iTRAQ reference data on hepatocellular carcinoma (HCC) to design a two-stage functional analysis pipeline to widen and improve the proteome coverage and, subsequently, to unveil the molecular changes that occur during HCC progression in human tumorous tissue. The first involved functional...
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PMID: 21410269
PDF is available here.
PDF is available here.
Abstract
Cold acclimation is the phenomenon in which plants are exposed to low, but nonfreezing, temperatures before exposure to drastic temperatures. To investigate how sunflower plants adjust their metabolism during cold treatment, a comparative proteomic approach, based on spectral countin...
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PMID: 21341810
PDF is available here.
PDF is available here.
Abstract
We performed MLST to investigate the genetic relatedness among bloodstream infection (BSI) isolates of C. albicans recovered from 10 Korean hospitals over a 12-month period. The 156 isolates yielded 112 unique diploid sequence types (DSTs). While 95 DSTs were each derived from a single isolate, 17 D...
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PMID: 21562112
PDF is available here.
PDF is available here.
Abstract
Originally composed of the single family Chlamydiaceae, the Chlamydiales order has extended considerably over the last several decades. Chlamydia-related bacteria were added and classified into six different families and family-level lineages: the Criblamydiaceae, Parachlamydiaceae, Piscichlamydiacea...
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PMID: 21562107
PDF is available here.
PDF is available here.
Genetika (Moskva) (47)5 2011
Abstract
Using five SSR markers, polymorphism ofmicrosatellite loci was examined in 46 cultivars and five species of pear (Pyrus ussuriensis, P. bretscgneideri, P. pyraster, and P. elaegnifolia). Most of the accessions examined demonstrated the presence of unique allele sets. The degree of relationship betwee...
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PMID: 21786670
PDF is available here.
PDF is available here.
Abstract
Two sets of Sham and infarcted rats were studied. The first was used to perform cluster analysis and the second to prospectively validate the results. Six months after inducing myocardial infarction (MI), rats were subjected to transthoracic echocardiography. Infarct size was measured by histologica...
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PMID: 21617080
PDF is available here.
PDF is available here.
Abstract
We propose to use an incremental fuzzy mining technique called incremental fuzzy mining (IFM). By transforming quantitative expression values into linguistic terms, such as highly or lowly expressed, IFM can effectively capture heterogeneity in expression data for pattern discovery. It does so using...
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PMID: 20403777
PDF is available here.
PDF is available here.
Abstract
In this paper, an automatic and unsupervised snore detection algorithm is proposed. The respiratory sound signals of 30 patients with different levels of airway obstruction were recorded by two microphones: one placed over the trachea (the tracheal microphone), and the other was a freestanding microp...
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PMID: 20679022
PDF is available here.
PDF is available here.
Abstract
We revisit the PCA procedure to analyze its weaknesses and describe an improved feature extraction method. This paper proposes a linear feature extraction technique that we call graph-Laplacian features, which simultaneously minimizes the graph Laplacian and maximizes variance. The algorithm's perfo...
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PMID: 21047707
PDF is available here.
PDF is available here.
Abstract
We provide a novel implementation, demonstrate its potential and practicability, and provide a web-based service for public usage. Evaluation with published data sets mimicking varyingly complex habitats resulted into classification specificities and sensitivities of close to 100% to above 90% from...
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PMID: 21160538
PDF is available here.
PDF is available here.
Abstract
Understanding the epidemiology of human H5N1 cases in Indonesia is important. The question of whether cases are clustered or not is unclear. An increase in clustered cases suggests greater transmissibility. In the present study, 107 confirmed and 302 suspected human H5N1 cases in Indonesia during 200...
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PMID: 21706937
PDF is available here.
PDF is available here.
Abstract
Gene expression analysis is a valuable tool for determining the risk of disease recurrence and overall survival of an individual patient with breast cancer. The purpose of this study was to create and validate a robust prognostic algorithm and implement it within an online analysis e...
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PMID: 21458382
PDF is available here.
PDF is available here.
Abstract
Familial clustering has been reported in gastric cancer (GC). However, the mechanism of the intrafamilial aggregation of GC remains unclear.
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PMID: 21502924
PDF is available here.
PDF is available here.
Abstract
Coxsackievirus (CV) strains CVA2, CVA4, CVA5, and CVA10 were isolated from patients with hand, foot, and mouth disease during a 2009 outbreak in China. Full genome sequences for four representative strains, CVA2/SD/CHN/09 (A2SD09), CVA4/SZ/CHN/09 (A4SZ09), CVA5/SD/CHN/09 (A5SD09), and CVA10/SD/CHN/09...
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PMID: 21543560
PDF is available here.
PDF is available here.
Abstract
We focused on the characterization of GI-3, studying its organization and the genetic conservation of the GI-3 sequence using techniques such as tiling-path PCR (TP-PCR) and restriction fragment length polymorphism-PCR (RFLP-PCR). Our results, after PFGE was performed on 69 field isolates of B. abor...
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PMID: 21543580
PDF is available here.
PDF is available here.
Abstract
Several of the more recently proposed new species of Enterococcus are nearly identical based on 16S rRNA gene sequence analysis and phenotypic traits. In the present study, DNA-DNA reassociation experiments, in conjunction with sequencing of the 16S rRNA and rpoB genes, provided evidence that "Entero...
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PMID: 21543565
PDF is available here.
PDF is available here.
Abstract
Acinetobacter soli is a new bacterial species described from forest soil. Five cases of bloodstream infection caused by A. soli clonal isolates are reported here for the first time. The patients were neonates admitted to an intensive care unit. This is a new neonatal pathogen with the potential to ca...
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PMID: 21525230
PDF is available here.
PDF is available here.
Abstract
A total of 222 urinary Escherichia coli isolates from 20 tertiary hospitals in 15 different provinces and 4 municipalities in mainland China were characterized by antimicrobial susceptibility, phylogrouping, and the presence of plasmid-mediated quinolone resistance genes. A subset of 138 suspected ex...
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PMID: 21525216
PDF is available here.
PDF is available here.
Abstract
Two fatal cases of infantile rotavirus enteritis occurred in northern Italy in 2005. Both children were severely dehydrated, and death was related to severe cerebral edema. Histological examination demonstrated extensive damage of the intestinal epithelium, villous atrophy or blunting, and macrophage...
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PMID: 21525221
PDF is available here.
PDF is available here.
Abstract
Numerous studies with conflicting results have tried to prove the influence of seasonal variations or different meteorological factors on the occurrence of aneurysmal subarachnoidal hemorrhage (SAH). The aim of this study was to establish a mathematical model of a series of aneurysmal rupture dates i...
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PMID: 21499961
PDF is available here.
PDF is available here.
Abstract
To investigate whether PALSA PLUS, an on-site educational outreach programme of non-didactic, case based, iterative clinical education of staff, led by a trainer, can increase access to and comprehensiveness of care for patients with HIV/AIDS.
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PMID: 21511783
PDF is available here.
PDF is available here.
Abstract
Actinobaculum schaalii, which belongs to the group of Gram-positive rods, is difficult to culture. Using molecular genetics, Actinobaculum schaalii could be identified as a causing microorganism in a case of Fournier's gangrene.
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PMID: 21508151
PDF is available here.
PDF is available here.