Volume 4; Issue 1

Main
Microbiome
Volume 4; Issue 1

Microbiome

Volume 4; Issue 1

1

Human milk microbiota profiles in relation to birthing method, gestation and infant gender

Urbaniak, Camilla, Angelini, Michelle, Gloor, Gregory B., Reid, Gregor

Journal:

Year:

2016

Language:

english

File:

PDF, 722 KB

english, 2016

2

Towards a functional hypothesis relating anti-islet cell autoimmunity to the dietary impact on microbial communities and butyrate production

Endesfelder, David, Engel, Marion, Davis-Richardson, Austin G., Ardissone, Alexandria N., Achenbach, Peter, Hummel, Sandra, Winkler, Christiane, Atkinson, Mark, Schatz, Desmond, Triplett, Eric, Ziegle

Journal:

Year:

2016

Language:

english

File:

PDF, 962 KB

english, 2016

3

Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality

Jiang, Yue, Xiong, Xuejian, Danska, Jayne, Parkinson, John

Journal:

Year:

2016

Language:

english

File:

PDF, 5.05 MB

english, 2016

4

Erratum to: The first microbial environment of infants born by C-section: the operating room microbes

Shin, Hakdong, Pei, Zhiheng, Martinez, Keith A., Rivera-Vinas, Juana I., Mendez, Keimari, Cavallin, Humberto, Dominguez-Bello, Maria G.

Journal:

Year:

2016

Language:

english

File:

PDF, 335 KB

english, 2016

5

Erratum to: Linear growth faltering in infants is associated with Acidaminococcus sp. and community-level changes in the gut microbiota

Gough, Ethan K., Stephens, David A., Moodie, Erica E.M., Prendergast, Andrew J., Stoltzfus, Rebecca J., Humphrey, Jean H., Manges, Amee R.

Journal:

Year:

2016

Language:

english

File:

PDF, 806 KB

english, 2016

6

Composition and dynamics of the respiratory tract microbiome in intubated patients

Kelly, Brendan J., Imai, Ize, Bittinger, Kyle, Laughlin, Alice, Fuchs, Barry D., Bushman, Frederic D., Collman, Ronald G.

Journal:

Year:

2016

Language:

english

File:

PDF, 1.93 MB

english, 2016

7

ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses

Fouquier, Jennifer, Rideout, Jai Ram, Bolyen, Evan, Chase, John, Shiffer, Arron, McDonald, Daniel, Knight, Rob, Caporaso, J Gregory, Kelley, Scott T.

Journal:

Year:

2016

Language:

english

File:

PDF, 1.46 MB

english, 2016

8

Bloom and bust: intestinal microbiota dynamics in response to hospital exposures andClostridium difficilecolonization or infection

Vincent, Caroline, Miller, Mark A., Edens, Thaddeus J., Mehrotra, Sudeep, Dewar, Ken, Manges, Amee R.

Journal:

Year:

2016

Language:

english

File:

PDF, 1.13 MB

english, 2016

9

Erratum to: Prolonged use of a proton pump inhibitor reduces microbial diversity: implications for Clostridium difficile susceptibility

Seto, Charlie T., Jeraldo, Patricio, Orenstein, Robert, Chia, Nicholas, DiBaise, John K.

Journal:

Year:

2016

Language:

english

File:

PDF, 336 KB

english, 2016

10

InterpretingPrevotellaandBacteroidesas biomarkers of diet and lifestyle

Gorvitovskaia, Anastassia, Holmes, Susan P., Huse, Susan M.

Journal:

Year:

2016

Language:

english

File:

PDF, 1.58 MB

english, 2016

11

Bacterial communities in penile skin, male urethra, and vaginas of heterosexual couples with and without bacterial vaginosis

Zozaya, Marcela, Ferris, Michael J., Siren, Julia D., Lillis, Rebecca, Myers, Leann, Nsuami, M. Jacques, Eren, A. Murat, Brown, Jonathan, Taylor, Christopher M., Martin, David H.

Journal:

Year:

2016

Language:

english

File:

PDF, 951 KB

english, 2016

12

Marker genes that are less conserved in their sequences are useful for predicting genome-wide similarity levels between closely related prokaryotic strains

Lan, Yemin, Rosen, Gail, Hershberg, Ruth

Journal:

Year:

2016

Language:

english

File:

PDF, 2.52 MB

english, 2016

13

Effect of room temperature transport vials on DNA quality and phylogenetic composition of faecal microbiota of elderly adults and infants

Hill, Cian J., Brown, Jillian R. M., Lynch, Denise B., Jeffery, Ian B., Ryan, C. Anthony, Ross, R. Paul, Stanton, Catherine, O’Toole, Paul W.

Journal:

Year:

2016

Language:

english

File:

PDF, 1.42 MB

english, 2016

14

Microbial succession in an inflated lunar/Mars analog habitat during a 30-day human occupation

Mayer, Teresa, Blachowicz, Adriana, Probst, Alexander J., Vaishampayan, Parag, Checinska, Aleksandra, Swarmer, Tiffany, de Leon, Pablo, Venkateswaran, Kasthuri

Journal:

Year:

2016

Language:

english

File:

PDF, 2.27 MB

english, 2016

15

Correlation of the lung microbiota with metabolic profiles in bronchoalveolar lavage fluid in HIV infection

Cribbs, Sushma K., Uppal, Karan, Li, Shuzhao, Jones, Dean P., Huang, Laurence, Tipton, Laura, Fitch, Adam, Greenblatt, Ruth M., Kingsley, Lawrence, Guidot, David M., Ghedin, Elodie, Morris, Alison

Journal:

Year:

2016

Language:

english

File:

PDF, 1.43 MB

english, 2016

16

Making microbiology of the built environment relevant to design

Brown, G. Z., Kline, Jeff, Mhuireach, Gwynne, Northcutt, Dale, Stenson, Jason

Journal:

Year:

2016

Language:

english

File:

PDF, 323 KB

english, 2016

17

Recovering complete and draft population genomes from metagenome datasets

Sangwan, Naseer, Xia, Fangfang, Gilbert, Jack A.

Journal:

Year:

2016

Language:

english

File:

PDF, 720 KB

english, 2016

18

Presence of pathogenic Escherichia coli is correlated with bacterial community diversity and composition on pre-harvest cattle hides

Chopyk, Jessica, Moore, Ryan M., DiSpirito, Zachary, Stromberg, Zachary R., Lewis, Gentry L., Renter, David G., Cernicchiaro, Natalia, Moxley, Rodney A., Wommack, K. Eric

Journal:

Year:

2016

Language:

english

File:

PDF, 1.04 MB

english, 2016

19

Colitis susceptibility in p47phox−/−mice is mediated by the microbiome

Falcone, E. Liana, Abusleme, Loreto, Swamydas, Muthulekha, Lionakis, Michail S., Ding, Li, Hsu, Amy P., Zelazny, Adrian M., Moutsopoulos, Niki M., Kuhns, Douglas B., Deming, Clay, Quiñones, Mariam, Se

Journal:

Year:

2016

Language:

english

File:

PDF, 3.34 MB

english, 2016

20

The roles of the outdoors and occupants in contributing to a potential pan-microbiome of the built environment: a review

Leung, Marcus H. Y., Lee, Patrick K. H.

Journal:

Year:

2016

Language:

english

File:

PDF, 1.04 MB

english, 2016

21

Toward a microbial Neolithic revolution in buildings

Thaler, David S.

Journal:

Year:

2016

Language:

english

File:

PDF, 618 KB

english, 2016

22

Reduced diversity and altered composition of the gut microbiome in individuals with myalgic encephalomyelitis/chronic fatigue syndrome

Ludovic Giloteaux,Julia K. Goodrich,William A. Walters,Susan M. Levine…

Journal:

Year:

2016

Language:

english

File:

PDF, 1.55 MB

english, 2016

23

MetaPro-IQ: a universal metaproteomic approach to studying human and mouse gut microbiota

Zhang, Xu, Ning, Zhibin, Mayne, Janice, Moore, Jasmine I., Li, Jennifer, Butcher, James, Deeke, Shelley Ann, Chen, Rui, Chiang, Cheng-Kang, Wen, Ming, Mack, David, Stintzi, Alain, Figeys, Daniel

Journal:

Year:

2016

Language:

english

File:

PDF, 2.07 MB

english, 2016

24

Research on the human virome: where are we and what is next

Zou, Shimian, Caler, Lis, Colombini-Hatch, Sandra, Glynn, Simone, Srinivas, Pothur

Journal:

Year:

2016

Language:

english

File:

PDF, 381 KB

english, 2016

25

Genomic characterization of the unculturedBacteroidalesfamilyS24-7inhabiting the guts of homeothermic animals

Ormerod, Kate L., Wood, David L. A., Lachner, Nancy, Gellatly, Shaan L., Daly, Joshua N., Parsons, Jeremy D., Dal’Molin, Cristiana G. O., Palfreyman, Robin W., Nielsen, Lars K., Cooper, Matthew A., Mo

Journal:

Year:

2016

Language:

english

File:

PDF, 2.67 MB

english, 2016

26

The microbiota in bronchoalveolar lavage from young children with chronic lung disease includes taxa present in both the oropharynx and nasopharynx

Marsh, R. L., Kaestli, M., Chang, A. B., Binks, M. J., Pope, C. E., Hoffman, L. R., Smith-Vaughan, H. C.

Journal:

Year:

2016

Language:

english

File:

PDF, 2.29 MB

english, 2016

27

Longitudinal analysis of the lung microbiota of cynomolgous macaques during long-term SHIV infection

Morris, Alison, Paulson, Joseph N., Talukder, Hisham, Tipton, Laura, Kling, Heather, Cui, Lijia, Fitch, Adam, Pop, Mihai, Norris, Karen A., Ghedin, Elodie

Journal:

Year:

2016

Language:

english

File:

PDF, 1.88 MB

english, 2016

28

Latitude in sample handling and storage for infant faecal microbiota studies: the elephant in the room?

Shaw, Alexander G., Sim, Kathleen, Powell, Elizabeth, Cornwell, Emma, Cramer, Teresa, McClure, Zoë E., Li, Ming-Shi, Kroll, J. Simon

Journal:

Year:

2016

Language:

english

File:

PDF, 3.24 MB

english, 2016

29

Post-translational modifications are enriched within protein functional groups important to bacterial adaptation within a deep-sea hydrothermal vent environment

Zhang, Weipeng, Sun, Jin, Cao, Huiluo, Tian, Renmao, Cai, Lin, Ding, Wei, Qian, Pei-Yuan

Journal:

Year:

2016

Language:

english

File:

PDF, 1.54 MB

english, 2016

30

Mungo bean sprout microbiome and changes associated with culture based enrichment protocols used in detection of Gram-negative foodborne pathogens

Margot, Heike, Stephan, Roger, Tasara, Taurai

Journal:

Year:

2016

Language:

english

File:

PDF, 1.05 MB

english, 2016

31

Cardiorespiratory fitness as a predictor of intestinal microbial diversity and distinct metagenomic functions

Estaki, Mehrbod, Pither, Jason, Baumeister, Peter, Little, Jonathan P., Gill, Sandeep K., Ghosh, Sanjoy, Ahmadi-Vand, Zahra, Marsden, Katelyn R., Gibson, Deanna L.

Journal:

Year:

2016

Language:

english

File:

PDF, 1.40 MB

english, 2016

32

Intestinal microbiota in pediatric patients with end stage renal disease: a Midwest Pediatric Nephrology Consortium study

Crespo-Salgado, Janice, Vehaskari, V. Matti, Stewart, Tyrus, Ferris, Michael, Zhang, Qiang, Wang, Guangdi, Blanchard, Eugene E., Taylor, Christopher M., Kallash, Mahmoud, Greenbaum, Larry A., Aviles,

Journal:

Year:

2016

Language:

english

File:

PDF, 1.16 MB

english, 2016

33

Picodroplet partitioned whole genome amplification of low biomass samples preserves genomic diversity for metagenomic analysis

Hammond, Maria, Homa, Felix, Andersson-Svahn, Helene, Ettema, Thijs J. G., Joensson, Haakan N.

Journal:

Year:

2016

Language:

english

File:

PDF, 1.18 MB

english, 2016

34

Rapid change of fecal microbiome and disappearance ofClostridium difficilein a colonized infant after transition from breast milk to cow milk

Davis, Manli Y., Zhang, Husen, Brannan, Lera E., Carman, Robert J., Boone, James H.

Journal:

Year:

2016

Language:

english

File:

PDF, 1.25 MB

english, 2016

35

Diet may influence the oral microbiome composition in cats

Adler, Christina J., Malik, Richard, Browne, Gina V., Norris, Jacqueline M.

Journal:

Year:

2016

Language:

english

File:

PDF, 1.79 MB

english, 2016

36

The structure and diversity of human, animal and environmental resistomes

Pal, Chandan, Bengtsson-Palme, Johan, Kristiansson, Erik, Larsson, D. G. Joakim

Journal:

Year:

2016

Language:

english

File:

PDF, 1.35 MB

english, 2016

37

Skin fungal community and its correlation with bacterial community of urban Chinese individuals

Leung, Marcus H. Y., Chan, Kelvin C. K., Lee, Patrick K. H.

Journal:

Year:

2016

Language:

english

File:

PDF, 3.27 MB

english, 2016

38

Nasopharyngeal microbiota composition of children is related to the frequency of upper respiratory infection and acute sinusitis

Santee, Clark A., Nagalingam, Nabeetha A., Faruqi, Ali A., DeMuri, Gregory P., Gern, James E., Wald, Ellen R., Lynch, Susan V.

Journal:

Year:

2016

Language:

english

File:

PDF, 1.04 MB

english, 2016

39

Rumen metagenome and metatranscriptome analyses of low methane yield sheep reveals aSharpea-enriched microbiome characterised by lactic acid formation and utilisation

Kamke, Janine, Kittelmann, Sandra, Soni, Priya, Li, Yang, Tavendale, Michael, Ganesh, Siva, Janssen, Peter H., Shi, Weibing, Froula, Jeff, Rubin, Edward M., Attwood, Graeme T.

Journal:

Year:

2016

Language:

english

File:

PDF, 1.98 MB

english, 2016

40

Adjusting microbiome profiles for differences in microbial load by spike-in bacteria

Stämmler, Frank, Gläsner, Joachim, Hiergeist, Andreas, Holler, Ernst, Weber, Daniela, Oefner, Peter J., Gessner, André, Spang, Rainer

Journal:

Year:

2016

Language:

english

File:

PDF, 1.39 MB

english, 2016

41

The vaginal microbiota, human papillomavirus infection and cervical intraepithelial neoplasia: what do we know and where are we going next?

Mitra, Anita, MacIntyre, David A., Marchesi, Julian R., Lee, Yun S., Bennett, Phillip R., Kyrgiou, Maria

Journal:

Year:

2016

Language:

english

File:

PDF, 772 KB

english, 2016

42

Environment shapes the fecal microbiome of invasive carp species

Eichmiller, Jessica J., Hamilton, Matthew J., Staley, Christopher, Sadowsky, Michael J., Sorensen, Peter W.

Journal:

Year:

2016

Language:

english

File:

PDF, 1.47 MB

english, 2016

43

The lung microbiota in early rheumatoid arthritis and autoimmunity

Scher, Jose U., Joshua, Vijay, Artacho, Alejandro, Abdollahi-Roodsaz, Shahla, Öckinger, Johan, Kullberg, Susanna, Sköld, Magnus, Eklund, Anders, Grunewald, Johan, Clemente, Jose C., Ubeda, Carles, Seg

Journal:

Year:

2016

Language:

english

File:

PDF, 1.26 MB

english, 2016

44

Fat and vitamin intakes during pregnancy have stronger relations with a pro-inflammatory maternal microbiota than does carbohydrate intake

Mandal, Siddhartha, Godfrey, Keith M., McDonald, Daniel, Treuren, Will V., Bjørnholt, Jørgen V., Midtvedt, Tore, Moen, Birgitte, Rudi, Knut, Knight, Rob, Brantsæter, Anne Lise, Peddada, Shyamal D., Eg

Journal:

Year:

2016

Language:

english

File:

PDF, 1.16 MB

english, 2016

45

Extending colonic mucosal microbiome analysis—assessment of colonic lavage as a proxy for endoscopic colonic biopsies

Watt, Euan, Gemmell, Matthew R., Berry, Susan, Glaire, Mark, Farquharson, Freda, Louis, Petra, Murray, Graeme I., El-Omar, Emad, Hold, Georgina L.

Journal:

Year:

2016

Language:

english

File:

PDF, 2.16 MB

english, 2016

46

Two sampling methods yield distinct microbial signatures in the nasopharynges of asthmatic children

Pérez-Losada, Marcos, Crandall, Keith A., Freishtat, Robert J.

Journal:

Year:

2016

Language:

english

File:

PDF, 855 KB

english, 2016

47

Transmission of viruses via our microbiomes

Ly, Melissa, Jones, Marcus B., Abeles, Shira R., Santiago-Rodriguez, Tasha M., Gao, Jonathan, Chan, Ivan C., Ghose, Chandrabali, Pride, David T.

Journal:

Year:

2016

Language:

english

File:

PDF, 1.26 MB

english, 2016

48

The impact of sequence database choice on metaproteomic results in gut microbiota studies

Tanca, Alessandro, Palomba, Antonio, Fraumene, Cristina, Pagnozzi, Daniela, Manghina, Valeria, Deligios, Massimo, Muth, Thilo, Rapp, Erdmann, Martens, Lennart, Addis, Maria Filippa, Uzzau, Sergio

Journal:

Year:

2016

Language:

english

File:

PDF, 1.63 MB

english, 2016

49

Staphylococcal species heterogeneity in the nasal microbiome following antibiotic prophylaxis revealed bytufgene deep sequencing

McMurray, Claire L., Hardy, Katherine J., Calus, Szymon T., Loman, Nicholas J., Hawkey, Peter M.

Journal:

Year:

2016

Language:

english

File:

PDF, 628 KB

english, 2016

50

DNA from fecal immunochemical test can replace stool for detection of colonic lesions using a microbiota-based model

Baxter, Nielson T., Koumpouras, Charles C., Rogers, Mary A. M., Ruffin, Mack T., Schloss, Patrick D.

Journal:

Year:

2016

Language:

english

File:

PDF, 1.11 MB

english, 2016

51

Large-scale benchmarking reveals false discoveries and count transformation sensitivity in 16S rRNA gene amplicon data analysis methods used in microbiome studies

Thorsen, Jonathan, Brejnrod, Asker, Mortensen, Martin, Rasmussen, Morten A., Stokholm, Jakob, Al-Soud, Waleed Abu, Sørensen, Søren, Bisgaard, Hans, Waage, Johannes

Journal:

Year:

2016

Language:

english

File:

PDF, 1.27 MB

english, 2016

52

The developing hypopharyngeal microbiota in early life

Mortensen, Martin Steen, Brejnrod, Asker Daniel, Roggenbuck, Michael, Abu Al-Soud, Waleed, Balle, Christina, Krogfelt, Karen Angeliki, Stokholm, Jakob, Thorsen, Jonathan, Waage, Johannes, Rasmussen, M

Journal:

Year:

2016

Language:

english

File:

PDF, 1.72 MB

english, 2016

53

The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report

Journal:

Year:

2016

Language:

english

File:

PDF, 1.35 MB

english, 2016

54

Influence of maternal breast milk ingestion on acquisition of the intestinal microbiome in preterm infants

Gregory, Katherine E., Samuel, Buck S., Houghteling, Pearl, Shan, Guru, Ausubel, Frederick M., Sadreyev, Ruslan I., Walker, W. Allan

Journal:

Year:

2016

Language:

english

File:

PDF, 1.74 MB

english, 2016

55

Resilient microorganisms in dust samples of the International Space Station—survival of the adaptation specialists

Mora, Maximilian, Perras, Alexandra, Alekhova, Tatiana A., Wink, Lisa, Krause, Robert, Aleksandrova, Alina, Novozhilova, Tatiana, Moissl-Eichinger, Christine

Journal:

Year:

2016

Language:

english

File:

PDF, 1.88 MB

english, 2016

56

The gut microbiota in conventional and serrated precursors of colorectal cancer

Peters, Brandilyn A., Dominianni, Christine, Shapiro, Jean A., Church, Timothy R., Wu, Jing, Miller, George, Yuen, Elizabeth, Freiman, Hal, Lustbader, Ian, Salik, James, Friedlander, Charles, Hayes, R

Journal:

Year:

2016

Language:

english

File:

PDF, 3.72 MB

english, 2016

57

Temporal bacterial and metabolic development of the preterm gut reveals specific signatures in health and disease

Stewart, Christopher J., Embleton, Nicholas D., Marrs, Emma C. L., Smith, Daniel P., Nelson, Andrew, Abdulkadir, Bashir, Skeath, Tom, Petrosino, Joseph F., Perry, John D., Berrington, Janet E., Cummin

Journal:

Year:

2016

Language:

english

File:

PDF, 1.55 MB

english, 2016

58

Disruption of the microbiota across multiple body sites in critically ill children

Rogers, Matthew B., Firek, Brian, Shi, Min, Yeh, Andrew, Brower-Sinning, Rachel, Aveson, Victoria, Kohl, Brittany L., Fabio, Anthony, Carcillo, Joseph A., Morowitz, Michael J.

Journal:

Year:

2016

Language:

english

File:

PDF, 1.01 MB

english, 2016

59

Comparison of faecal microbiota inBlastocystis-positive andBlastocystis-negative irritable bowel syndrome patients

Nagel, Robyn, Traub, Rebecca J., Allcock, Richard J. N., Kwan, Marcella M. S., Bielefeldt-Ohmann, Helle

Journal:

Year:

2016

Language:

english

File:

PDF, 1.17 MB

english, 2016

60

A comprehensive method for amplicon-based and metagenomic characterization of viruses, bacteria, and eukaryotes in freshwater samples

Uyaguari-Diaz, Miguel I., Chan, Michael, Chaban, Bonnie L., Croxen, Matthew A., Finke, Jan F., Hill, Janet E., Peabody, Michael A., Van Rossum, Thea, Suttle, Curtis A., Brinkman, Fiona S. L., Isaac-Re

Journal:

Year:

2016

Language:

english

File:

PDF, 1.63 MB

english, 2016

61

Host species identity, site and time drive temperate tree phyllosphere bacterial community structure

Laforest-Lapointe, Isabelle, Messier, Christian, Kembel, Steven W.

Journal:

Year:

2016

Language:

english

File:

PDF, 1.18 MB

english, 2016

62

Unusual sub-genus associations of faecalPrevotellaandBacteroideswith specific dietary patterns

Francesca De Filippis,Nicoletta Pellegrini,Luca Laghi,Marco Gobbetti…

Journal:

Year:

2016

Language:

english

File:

PDF, 1.68 MB

english, 2016

63

Variable responses of human microbiomes to dietary supplementation with resistant starch

A. Venkataraman,J. R. Sieber,A. W. Schmidt,C. Waldron,K. R. Theis…

Journal:

Year:

2016

Language:

english

File:

PDF, 615 KB

english, 2016

64

Erratum to: Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires

Eugen Bauer,Cedric Christian Laczny,Stefania Magnusdottir,Paul Wilmes…

Journal:

Year:

2016

Language:

english

File:

PDF, 332 KB

english, 2016

65

Erratum to: The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium Inaugural Meeting Report

Journal:

Year:

2016

Language:

english

File:

PDF, 359 KB

english, 2016

66

Altered gut microbiota in Rett syndrome

Francesco Strati,Duccio Cavalieri,Davide Albanese,Claudio De Felice…

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Year:

2016

Language:

english

File:

PDF, 1.70 MB

english, 2016

67

Reviewer acknowledgement 2015

Jacques Ravel,Eric Wommack

Journal:

Year:

2016

Language:

english

File:

PDF, 281 KB

english, 2016

68

Comparison of placenta samples with contamination controls does not provide evidence for a distinct placenta microbiota

Abigail P. Lauder,Aoife M. Roche,Scott Sherrill-Mix,Aubrey Bailey…

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Year:

2016

Language:

english

File:

PDF, 1.83 MB

english, 2016

69

Effect of postnatal low-dose exposure to environmental chemicals on the gut microbiome in a rodent model

Jianzhong Hu,Vincent Raikhel,Kalpana Gopalakrishnan…

Journal:

Year:

2016

Language:

english

File:

PDF, 2.10 MB

english, 2016

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