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Jiang W, Song S, Hou L, Zhao H. A Set of Efficient Methods to Generate High-Dimensional Binary Data With Specified Correlation Structures. AM STAT 2020. [DOI: 10.1080/00031305.2020.1816213] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Wei Jiang
- Department of Biostatistics, School of Public Health, Yale University, New Haven, CT
| | - Shuang Song
- Center for Statistical Science, Tsinghua University, Beijing, China
- Department of Industrial Engineering, Tsinghua University, Beijing, China
| | - Lin Hou
- Center for Statistical Science, Tsinghua University, Beijing, China
- Department of Industrial Engineering, Tsinghua University, Beijing, China
| | - Hongyu Zhao
- Department of Biostatistics, School of Public Health, Yale University, New Haven, CT
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2
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Guo L, Modarres R. Interpoint Distance Classification of High Dimensional Discrete Observations. Int Stat Rev 2018. [DOI: 10.1111/insr.12281] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lingzhe Guo
- Department of Statistics; The George Washington University; Washington 20052 DC USA
| | - Reza Modarres
- Department of Statistics; The George Washington University; Washington 20052 DC USA
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Santamans AC, Boluda R, Picazo A, Gil C, Ramos-Miras J, Tejedo P, Pertierra LR, Benayas J, Camacho A. Soil features in rookeries of Antarctic penguins reveal sea to land biotransport of chemical pollutants. PLoS One 2017; 12:e0181901. [PMID: 28813428 PMCID: PMC5558944 DOI: 10.1371/journal.pone.0181901] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 07/10/2017] [Indexed: 11/29/2022] Open
Abstract
The main soil physical-chemical features, the concentrations of a set of pollutants, and the soil microbiota linked to penguin rookeries have been studied in 10 selected sites located at the South Shetland Islands and the Antarctic Peninsula (Maritime Antarctica). This study aims to test the hypothesis that biotransport by penguins increases the concentration of pollutants, especially heavy metals, in Antarctic soils, and alters its microbiota. Our results show that penguins do transport certain chemical elements and thus cause accumulation in land areas through their excreta. Overall, a higher penguin activity is associated with higher organic carbon content and with higher concentrations of certain pollutants in soils, especially cadmium, cooper and arsenic, as well as zinc and selenium. In contrast, in soils that are less affected by penguins’ faecal depositions, the concentrations of elements of geochemical origin, such as iron and cobalt, increase their relative weighted contribution, whereas the above-mentioned pollutants maintain very low levels. The concentrations of pollutants are far higher in those penguin rookeries that are more exposed to ship traffic. In addition, the soil microbiota of penguin-influenced soils was studied by molecular methods. Heavily penguin-affected soils have a massive presence of enteric bacteria, whose relative dominance can be taken as an indicator of penguin influence. Faecal bacteria are present in addition to typical soil taxa, the former becoming dominant in the microbiota of penguin-affected soils, whereas typical soil bacteria, such as Actinomycetales, co-dominate the microbiota of less affected soils. Results indicate that the continuous supply by penguin faeces, and not the selectivity by increased pollutant concentrations is the main factor shaping the soil bacterial community. Overall, massive penguin influence results in increased concentrations of certain pollutants and in a strong change in taxa dominance in the soil bacterial community.
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Affiliation(s)
- Anna C. Santamans
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de Valencia, Paterna, Spain
- Departament de Biologia Vegetal, Facultat de Farmàcia, Universitat de València, Burjassot, València, Spain
| | - Rafael Boluda
- Departament de Biologia Vegetal, Facultat de Farmàcia, Universitat de València, Burjassot, València, Spain
| | - Antonio Picazo
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de Valencia, Paterna, Spain
| | - Carlos Gil
- Escuela Politécnica Superior, Departamento de Agronomía, Universidad de Almería, Almería, Spain
| | - Joaquín Ramos-Miras
- Escuela Politécnica Superior, Departamento de Agronomía, Universidad de Almería, Almería, Spain
| | - Pablo Tejedo
- Departamento de Ecología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Luis R. Pertierra
- Departamento de Biogeografía y Cambio Global, Museo Nacional de Ciencias Naturales, Madrid, Spain
| | - Javier Benayas
- Departamento de Ecología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Antonio Camacho
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de Valencia, Paterna, Spain
- * E-mail:
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Yao XF, Zhang JM, Tian L, Guo JH. The effect of heavy metal contamination on the bacterial community structure at Jiaozhou Bay, China. Braz J Microbiol 2016; 48:71-78. [PMID: 27751665 PMCID: PMC5220637 DOI: 10.1016/j.bjm.2016.09.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 07/14/2016] [Indexed: 11/24/2022] Open
Abstract
In this study, determination of heavy metal parameters and microbiological characterization of marine sediments obtained from two heavily polluted sites and one low-grade contaminated reference station at Jiaozhou Bay in China were carried out. The microbial communities found in the sampled marine sediments were studied using PCR-DGGE (denaturing gradient gel electrophoresis) fingerprinting profiles in combination with multivariate analysis. Clustering analysis of DGGE and matrix of heavy metals displayed similar occurrence patterns. On this basis, 17 samples were classified into two clusters depending on the presence or absence of the high level contamination. Moreover, the cluster of highly contaminated samples was further classified into two sub-groups based on the stations of their origin. These results showed that the composition of the bacterial community is strongly influenced by heavy metal variables present in the sediments found in the Jiaozhou Bay. This study also suggested that metagenomic techniques such as PCR-DGGE fingerprinting in combination with multivariate analysis is an efficient method to examine the effect of metal contamination on the bacterial community structure.
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Affiliation(s)
- Xie-Feng Yao
- Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, China
| | - Jiu-Ming Zhang
- First Institute of Oceanography, State Oceanic Administration, Qingdao, China; Qingdao University of Science & Technology, Qingdao, China
| | - Li Tian
- First Institute of Oceanography, State Oceanic Administration, Qingdao, China; Qingdao University of Science & Technology, Qingdao, China.
| | - Jian-Hua Guo
- Nanjing Agricultural University, College of Plant Protection, Department of Plant Pathology, Nanjing, China.
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Yan H, Lu H, Almeida VV, Ward MG, Adeola O, Nakatsu CH, Ajuwon KM. Effects of dietary resistant starch content on metabolic status, milk composition, and microbial profiling in lactating sows and on offspring performance. J Anim Physiol Anim Nutr (Berl) 2016; 101:190-200. [PMID: 26848026 DOI: 10.1111/jpn.12440] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 10/27/2015] [Indexed: 01/20/2023]
Abstract
In the present study, the effects of dietary resistant starch (RS) content on serum metabolite and hormone concentrations, milk composition, and faecal microbial profiling in lactating sows, as well as on offspring performance was investigated. Sixteen sows were randomly allotted at breeding to two treatments containing low- and high-RS contents from normal and high-amylose corn varieties, respectively, and each treatment had eight replicates (sows). Individual piglet body weight (BW) and litter size were recorded at birth and weaning. Milk samples were obtained on day 10 after farrowing for composition analysis. On day 2 before weaning, blood and faecal samples were collected to determine serum metabolite and hormone concentrations and faecal microbial populations, respectively. Litter size at birth and weaning were not influenced (p > 0.05) by the sow dietary treatments. Although feeding the RS-rich diet to sows reduced (p = 0.004) offspring birth BW, there was no difference in piglet BW at weaning (p > 0.05). High-RS diet increased (p < 0.05) serum triacylglycerol and nonesterified fatty acid concentrations and milk total solid content, and tended (p = 0.09) to increase milk fat content in lactating sows. Feeding the RS-rich diet to sows increased (p < 0.01) faecal bacterial population diversity. These results indicate that high-RS diets induce fatty acid mobilization and a greater intestinal bacterial richness in lactating sows, as well as a greater nutrient density in maternal milk, without affecting offspring performance at weaning.
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Affiliation(s)
- H Yan
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
| | - H Lu
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
| | - V V Almeida
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
| | - M G Ward
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
| | - O Adeola
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
| | - C H Nakatsu
- Department of Agronomy, Purdue University, West Lafayette, IN, USA
| | - K M Ajuwon
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
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Gibb S, Strimmer K. Differential protein expression and peak selection in mass spectrometry data by binary discriminant analysis. Bioinformatics 2015; 31:3156-62. [PMID: 26026136 DOI: 10.1093/bioinformatics/btv334] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 05/26/2015] [Indexed: 02/05/2023] Open
Abstract
MOTIVATION Proteomic mass spectrometry analysis is becoming routine in clinical diagnostics, for example to monitor cancer biomarkers using blood samples. However, differential proteomics and identification of peaks relevant for class separation remains challenging. RESULTS Here, we introduce a simple yet effective approach for identifying differentially expressed proteins using binary discriminant analysis. This approach works by data-adaptive thresholding of protein expression values and subsequent ranking of the dichotomized features using a relative entropy measure. Our framework may be viewed as a generalization of the 'peak probability contrast' approach of Tibshirani et al. (2004) and can be applied both in the two-group and the multi-group setting. Our approach is computationally inexpensive and shows in the analysis of a large-scale drug discovery test dataset equivalent prediction accuracy as a random forest. Furthermore, we were able to identify in the analysis of mass spectrometry data from a pancreas cancer study biological relevant and statistically predictive marker peaks unrecognized in the original study. AVAILABILITY AND IMPLEMENTATION The methodology for binary discriminant analysis is implemented in the R package binda, which is freely available under the GNU General Public License (version 3 or later) from CRAN at URL http://cran.r-project.org/web/packages/binda/. R scripts reproducing all described analyzes are available from the web page http://strimmerlab.org/software/binda/. CONTACT k.strimmer@imperial.ac.uk.
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Affiliation(s)
- Sebastian Gibb
- Anesthesiology and Intensive Care Medicine, University Hospital Greifswald, Ferdinand-Sauerbruch-Straße, D-17475 Greifswald, Germany and
| | - Korbinian Strimmer
- Epidemiology and Biostatistics, School of Public Health, Imperial College London, Norfolk Place, London, W2 1PG, UK
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Role of RNase on microbial community analysis in the rice and wheat plants soil by 16S rDNA-DGGE. ACTA ACUST UNITED AC 2014. [DOI: 10.1007/s12892-014-0071-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Javed K, Babri HA, Saeed M. Impact of a metric of association between two variables on performance of filters for binary data. Neurocomputing 2014. [DOI: 10.1016/j.neucom.2014.05.066] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Hyodo M, Kubokawa T. A variable selection criterion for linear discriminant rule and its optimality in high dimensional and large sample data. J MULTIVARIATE ANAL 2014. [DOI: 10.1016/j.jmva.2013.10.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Boz B, Mizanur Rahman M, Bottegal M, Basaglia M, Squartini A, Gumiero B, Casella S. Vegetation, soil and hydrology management influence denitrification activity and the composition of nirK-type denitrifier communities in a newly afforested riparian buffer. N Biotechnol 2013; 30:675-84. [DOI: 10.1016/j.nbt.2013.03.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2012] [Revised: 03/15/2013] [Accepted: 03/18/2013] [Indexed: 11/15/2022]
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Yan H, Potu R, Lu H, Vezzoni de Almeida V, Stewart T, Ragland D, Armstrong A, Adeola O, Nakatsu CH, Ajuwon KM. Dietary fat content and fiber type modulate hind gut microbial community and metabolic markers in the pig. PLoS One 2013; 8:e59581. [PMID: 23573202 PMCID: PMC3616062 DOI: 10.1371/journal.pone.0059581] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Accepted: 02/15/2013] [Indexed: 12/27/2022] Open
Abstract
Obesity leads to changes in the gut microbial community which contribute to the metabolic dysregulation in obesity. Dietary fat and fiber affect the caloric density of foods. The impact of dietary fat content and fiber type on the microbial community in the hind gut is unknown. Effect of dietary fat level and fiber type on hindgut microbiota and volatile fatty acid (VFA) profiles was investigated. Expression of metabolic marker genes in the gut, adipose tissue and liver was determined. A 2×2 experiment was conducted in pigs fed at two dietary fat levels (5% or 17.5% swine grease) and two fiber types (4% inulin, fermentable fructo-oligosaccharide or 4% solka floc, non-fermentable cellulose). High fat diets (HFD) resulted in a higher (P<0.05) total body weight gain, feed efficiency and back fat accumulation than the low fat diet. Feeding of inulin, but not solka floc, attenuated (P<0.05) the HFD-induced higher body weight gain and fat mass accumulation. Inulin feeding tended to lead to higher total VFA production in the cecum and resulted in a higher (P<0.05) expression of acyl coA oxidase (ACO), a marker of peroxisomal β-oxidation. Inulin feeding also resulted in lower expression of sterol regulatory element binding protein 1c (SREBP-1c), a marker of lipid anabolism. Bacteria community structure characterized by DGGE analysis of PCR amplified 16S rRNA gene fragments showed that inulin feeding resulted in greater bacterial population richness than solka floc feeding. Cluster analysis of pairwise Dice similarity comparisons of the DGGE profiles showed grouping by fiber type but not the level of dietary fat. Canonical correspondence analysis (CCA) of PCR- DGGE profiles showed that inulin feeding negatively correlated with back fat thickness. This study suggests a strong interplay between dietary fat level and fiber type in determining susceptibility to obesity.
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Affiliation(s)
- Hui Yan
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, United States of America
| | - Ramesh Potu
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, United States of America
| | - Hang Lu
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, United States of America
| | | | - Terry Stewart
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, United States of America
| | - Darryl Ragland
- Food Animal Production Medicine, School of Veterinary Medicine, Purdue University, Indiana, United States of America
| | - Arthur Armstrong
- Department of Agronomy, Purdue University, West Lafayette, Indiana, United States of America
| | - Olayiwola Adeola
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, United States of America
| | - Cindy H. Nakatsu
- Department of Agronomy, Purdue University, West Lafayette, Indiana, United States of America
| | - Kolapo M. Ajuwon
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, United States of America
- * E-mail:
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Raginsky M, Silva JG, Lazebnik S, Willett R. A recursive procedure for density estimation on the binary hypercube. Electron J Stat 2013. [DOI: 10.1214/13-ejs787] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Park J, Ghosh JK. Guided random walk through some high dimensional problems. SANKHYA-SERIES A-MATHEMATICAL STATISTICS AND PROBABILITY 2010. [DOI: 10.1007/s13171-010-0017-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Park J, Ghosh JK. Persistence of plug-in rule in classification of high dimensional multivariate binary data. J Stat Plan Inference 2007. [DOI: 10.1016/j.jspi.2007.03.043] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Park J, Wilbur JD, Ghosh JK, Nakatsu CH, Ackerman C. Selection of Binary Variables and Classification by Boosting. COMMUN STAT-SIMUL C 2007. [DOI: 10.1080/03610910701419729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Chakrabarti A, Ghosh JK. A generalization of BIC for the general exponential family. J Stat Plan Inference 2006. [DOI: 10.1016/j.jspi.2005.01.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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