519 research outputs found
Approaches in biotechnological applications of natural polymers
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- Publication venue
- 'American Institute of Mathematical Sciences (AIMS)'
- Publication date
- 01/01/2016
- Field of study
Natural polymers, such as gums and mucilage, are biocompatible, cheap, easily available and non-toxic materials of native origin. These polymers are increasingly preferred over synthetic materials for industrial applications due to their intrinsic properties, as well as they are considered alternative sources of raw materials since they present characteristics of sustainability, biodegradability and biosafety. As definition, gums and mucilages are polysaccharides or complex carbohydrates consisting of one or more monosaccharides or their derivatives linked in bewildering variety of linkages and structures. Natural gums are considered polysaccharides naturally occurring in varieties of plant seeds and exudates, tree or shrub exudates, seaweed extracts, fungi, bacteria, and animal sources. Water-soluble gums, also known as hydrocolloids, are considered exudates and are pathological products; therefore, they do not form a part of cell wall. On the other hand, mucilages are part of cell and physiological products. It is important to highlight that gums represent the largest amounts of polymer materials derived from plants. Gums have enormously large and broad applications in both food and non-food industries, being commonly used as thickening, binding, emulsifying, suspending, stabilizing agents and matrices for drug release in pharmaceutical and cosmetic industries. In the food industry, their gelling properties and the ability to mold edible films and coatings are extensively studied. The use of gums depends on the intrinsic properties that they provide, often at costs below those of synthetic polymers. For upgrading the value of gums, they are being processed into various forms, including the most recent nanomaterials, for various biotechnological applications. Thus, the main natural polymers including galactomannans, cellulose, chitin, agar, carrageenan, alginate, cashew gum, pectin and starch, in addition to the current researches about them are reviewed in this article.. }To the Conselho Nacional de Desenvolvimento Cientfíico e Tecnológico (CNPq) for fellowships (LCBBC and MGCC) and the Coordenação de Aperfeiçoamento de Pessoal de Nvíel Superior (CAPES) (PBSA). This study was supported by the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469/2013 unit, the Project RECI/BBB-EBI/0179/2012 (FCOMP-01-0124-FEDER-027462) and COMPETE 2020 (POCI-01-0145-FEDER-006684) (JAT)
Perspectives on the use of transcriptomics to advance biofuels
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- Ahn J-M Mitchell RJ, Gu MB
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- Publication venue
- 'American Institute of Mathematical Sciences (AIMS)'
- Publication date
- 01/01/2015
- Field of study
As a field within the energy research sector, bioenergy is continuously expanding. Although much has been achieved and the yields of both ethanol and butanol have been improved, many avenues of research to further increase these yields still remain. This review covers current research related with transcriptomics and the application of this high-throughput analytical tool to engineer both microbes and plants with the penultimate goal being better biofuel production and yields. The initial focus is given to the responses of fermentative microbes during the fermentative production of acids, such as butyric acid, and solvents, including ethanol and butanol. As plants offer the greatest natural renewable source of fermentable sugars within the form of lignocellulose, the second focus area is the transcriptional responses of microbes when exposed to plant hydrolysates and lignin-related compounds. This is of particular importance as the acid/base hydrolysis methods commonly employed to make the plant-based cellulose available for enzymatic hydrolysis to sugars also generates significant amounts of lignin-derivatives that are inhibitory to fermentative bacteria and microbes. The article then transitions to transcriptional analyses of lignin-degrading organisms, such as Phanerochaete chrysosporium, as an alternative to acid/base hydrolysis. The final portion of this article will discuss recent transcriptome analyses of plants and, in particular, the genes involved in lignin production. The rationale behind these studies is to eventually reduce the lignin content present within these plants and, consequently, the amount of inhibitors generated during the acid/base hydrolysis of the lignocelluloses. All four of these topics represent key areas where transcriptomic research is currently being conducted to identify microbial genes and their responses to products and inhibitors as well as those related with lignin degradation/formation.clos
Transcriptome sequencing and analysis of major genes involved in calcium signaling pathways in pear plants (Pyrus calleryana Decne.)
- Author
- A Canovas
- A Conesa
- AJ Matlin
- AK Parida
- AL Li
- AN Dodd
- BJ Chen
- C Dubos
- C Trapnell
- C Vannini
- CY Shi
- DL Black
- E McCormack
- ET Wang
- F Liu
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- LL Huang
- M Kanehisa
- M Okubo
- M Xie
- M Zhang
- MA Harris
- N Tuteja
- O Batistič
- P Cingolani
- PG Engström
- Q Guan
- Q Yu
- Qingsong Yang
- QS Wu
- R Li
- R Li
- R Munns
- R Weikard
- S Bai
- S Luan
- S Ma
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- S Weinl
- SA Filichkin
- SH Cheng
- T Urao
- U Kolukisaoglu
- X Kang
- Xiaogang Li
- Y Liao
- Y Liu
- Y Saijo
- Y Xu
- Y Zhao
- Y Zhou
- YH Chang
- Youhong Chang
- Yuanyuan Xu
- ZH Dang
- Zhonghua Wang
- Publication venue
- 'Springer Science and Business Media LLC'
- Publication date
- Field of study
A second generation human haplotype map of over 3.1 million SNPs
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- Abecasis GR
- Adebamowo CA
- Adewole IF
- Ajayi I
- Altshuler D
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- Tello-Ruiz MK
- Thomas DJ
- Thorisson GA
- Tsui LC
- Tsui SK
- Tsunoda T
- Tsunoda T
- Varilly P
- Verner A
- Wallenburg JC
- Wang H
- Wang H
- Wang J
- Wang R
- Wang VO
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- Wang Z
- Watkin J
- Waye MM
- Weinstock GM
- Weir BS
- Wheeler DA
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- Whittaker P
- Willey DL
- Willis TD
- Wilson RK
- Winchester E
- Wong JT
- Xiao M
- Xiong X
- Xu L
- Xue H
- Yakub I
- Yang H
- Yao Z
- Yu F
- Yu J
- Zacharia LF
- Zeng C
- Zeng C
- Zhang B
- Zhang H
- Zhang Q
- Zhao H
- Zhao H
- Zhao H
- Zhou J
- Ziaugra L
- Ziaugra L
- Publication venue
- 'Springer Science and Business Media LLC'
- Publication date
- 01/01/2007
- Field of study
We describe the Phase II HapMap, which characterizes over 3.1 million human single nucleotide polymorphisms (SNPs) genotyped in 270 individuals from four geographically diverse populations and includes 25-35% of common SNP variation in the populations surveyed. The map is estimated to capture untyped common variation with an average maximum r(2) of between 0.9 and 0.96 depending on population. We demonstrate that the current generation of commercial genome-wide genotyping products captures common Phase II SNPs with an average maximum r(2) of up to 0.8 in African and up to 0.95 in non-African populations, and that potential gains in power in association studies can be obtained through imputation. These data also reveal novel aspects of the structure of linkage disequilibrium. We show that 10-30% of pairs of individuals within a population share at least one region of extended genetic identity arising from recent ancestry and that up to 1% of all common variants are untaggable, primarily because they lie within recombination hotspots. We show that recombination rates vary systematically around genes and between genes of different function. Finally, we demonstrate increased differentiation at non-synonymous, compared to synonymous, SNPs, resulting from systematic differences in the strength or efficacy of natural selection between populations.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/62863/1/nature06258.pd
Search for new phenomena in final states with an energetic jet and large missing transverse momentum in pp collisions at √ s = 8 TeV with the ATLAS detector
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- Zwalinski L
- Publication venue
- 'Springer Science and Business Media LLC'
- Publication date
- 01/01/2015
- Field of study
Results of a search for new phenomena in final states with an energetic jet and large missing transverse momentum are reported. The search uses 20.3 fb−1 of √ s = 8 TeV data collected in 2012 with the ATLAS detector at the LHC. Events are required to have at least one jet with pT > 120 GeV and no leptons. Nine signal regions are considered with increasing missing transverse momentum requirements between Emiss T > 150 GeV and Emiss T > 700 GeV. Good agreement is observed between the number of events in data and Standard Model expectations. The results are translated into exclusion limits on models with either large extra spatial dimensions, pair production of weakly interacting dark matter candidates, or production of very light gravitinos in a gauge-mediated supersymmetric model. In addition, limits on the production of an invisibly decaying Higgs-like boson leading to similar topologies in the final state are presente
Search for the neutral Higgs bosons of the minimal supersymmetric standard model in pp collisions at root s=7 TeV with the ATLAS detector
- Author
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- Publication venue
- Publication date
- 01/02/2013
- Field of study
A search for neutral Higgs bosons of the Minimal Supersymmetric Standard Model (MSSM) is reported. The analysis is based on a sample of proton-proton collisions at a centre-of-mass energy of 7TeV recorded with the ATLAS detector at the Large Hadron Collider. The data were recorded in 2011 and correspond to an integrated luminosity of 4.7 fb-1 to 4.8 fb-1. Higgs boson decays into oppositely-charged muon or τ lepton pairs are considered for final states requiring either the presence or absence of b-jets. No statistically significant excess over the expected background is observed and exclusion limits at the 95% confidence level are derived. The exclusion limits are for the production cross-section of a generic neutral Higgs boson, φ, as a function of the Higgs boson mass and for h/A/H production in the MSSM as a function of the parameters mA and tan β in the mhmax scenario for mA in the range of 90GeV to 500 GeV. Copyright CERN
Jet energy measurement with the ATLAS detector in proton-proton collisions at root s=7 TeV
- Author
- Aad G
- Abbott B
- Abdallah J
- Abdelalim AA
- Abdesselam A
- Abdinov O
- Abi B
- Abolins M
- Abramowicz H
- Abreu H
- Acerbi E
- Acharya BS
- Adams DL
- Addy TN
- Adelman J
- Aderholz M
- Adomeit S
- Adragna P
- Adye T
- Aefsky S
- Aguilar-Saavedra JA
- Aharrouche M
- Ahlen SP
- Ahles F
- Ahmad A
- Ahsan M
- Aielli G
- Akdogana T
- Akesson TPA
- Akimoto G
- Akimov AV
- Akiyama A
- Aktas A
- Alam MA
- Alam MS
- Albert J
- Albrand S
- Aleksa M
- Aleksandrov IN
- Alessandria F
- Alexa C
- Alexander G
- Alexandre G
- Alexopoulos T
- Alhroob M
- Aliev M
- Alimonti G
- Alison J
- Aliyev M
- Allport PP
- Allwood-Spiers SE
- Almenar CC
- Almond J
- Aloisio A
- Alon R
- Alonso A
- Alviggi MG
- Amako K
- Amaral P
- Amelung C
- Ammosov VV
- Amorim A
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- Ancu LS
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- Anders G
- Anderson KJ
- Andreazza A
- Andrei V
- Andrieux M-L
- Anduaga XS
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- Antonaki A
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- Baker MD
- Baker OK
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- Strube J
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- Succurro A
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- Sundermann JE
- Suruliz K
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- Susinno G
- Sutton MR
- Suzuki Y
- Suzuki Y
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- Sviridov YM
- Swedish S
- Sykora I
- Sykora T
- Szeless B
- Ta D
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- Taffard A
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- Taiblum N
- Takahashi Y
- Takai H
- Takashima R
- Takeda H
- Takeshita T
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- Thompson RJ
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- Van der Leeuw R
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- Van Huysduynen LH
- Van Kesteren Z
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- Vannucci F
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- Varnes EW
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- Vassilakopouloss VI
- Vazeille F
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- Veillet JJ
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- Vinogradov VB
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- Vitells O
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- Vivarelli I
- Vlachos S
- Vladoiu D
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- Von Radziewski H
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- Voss TT
- Vossebeld JH
- Vranjes N
- Vrba V
- Vreeswijk M
- Vuillermet R
- Vujicic M
- Vukotic I
- Wagner P
- Wagner W
- Wahlen H
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- Walbersloh J
- Walch S
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- Walkowiak W
- Wall R
- Waller P
- Wang C
- Wang H
- Wang H
- Wang J
- Wang J
- Wang JC
- Wang R
- Wang SM
- Warburton A
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- Wastie R
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- Watson AT
- Watson MF
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- Waugh BM
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- Weber MS
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- Weidberg AR
- Weigell P
- Weingarten J
- Weiser C
- Wellenstein H
- Wells PS
- Wen M
- Wenaus T
- Wendler S
- Weng Z
- Wenglers T
- Wenig S
- Wermes N
- Werner M
- Werner P
- Werth M
- Wessels M
- Weydert C
- Whalen K
- Wheeler-Ellis SJ
- Whitaker SP
- White A
- White MJ
- White S
- Whitehead SR
- Whiteson D
- Whittington D
- Wicek F
- Wicke D
- Wickens FJ
- Wiedenmann W
- Wielersis M
- Wienemann P
- Wiglesworth C
- Wiik-Fuchs LAM
- Wijeratne PA
- Wildauer A
- Wildt MA
- Wilhelm I
- Wilkens HG
- Will JZ
- Williams E
- Williams HH
- Willis W
- Willocq S
- Wilson A
- Wilson JA
- Wilson MG
- Wingerter-Seez I
- Winkelmann S
- Winklmeier F
- Wittgen M
- Wolter MW
- Wolters H
- Wong WC
- Wooden G
- Wosiek BK
- Wotschack J
- Woudstra MJ
- Wraight K
- Wright C
- Wright D
- Wright M
- Wrona B
- Wu SL
- Wu X
- Wu Y
- Wulf E
- Wunstorf R
- Wynne BM
- Xaplanteris L
- Xella S
- Xie S
- Xie Y
- Xu C
- Xu D
- Xu G
- Yabsley B
- Yacoobb S
- Yagci KD
- Yamada M
- Yamaguchi H
- Yamamoto A
- Yamamoto K
- Yamamoto S
- Yamamura T
- Yamanaka T
- Yamaoka J
- Yamazaki T
- Yamazaki Y
- Yan Z
- Yang H
- Yang UK
- Yang Y
- Yang Y
- Yang Z
- Yanush S
- Yao Y
- Yasu Y
- Ye J
- Ye S
- Yildizb HD
- Yilmaz M
- Yoosootiniya R
- Yorita K
- Yoshida R
- Young C
- Youssef S
- Yu D
- Yu J
- Yu J
- Yuan L
- Yurkewicz A
- Zaets VG
- Zaidan R
- Zaitsev AM
- Zajacova Z
- Zalite YK
- Zanello L
- Zarzhitsky P
- Zaytsev A
- Zeitnitz C
- Zeller M
- Zeman M
- Zemla A
- Zendler C
- Zenin O
- Zenonos Z
- Zenz S
- Zerwas D
- Zhan Z
- Zhang D
- Zhang H
- Zhang J
- Zhang Q
- Zhang X
- Zhang Z
- Zhao L
- Zhao T
- Zhao Z
- Zhemchugov A
- Zheng S
- Zhong J
- Zhou B
- Zhou N
- Zhou Y
- Zhu CG
- Zhu H
- Zhu J
- Zhu Y
- Zhuang X
- Zhuravlov V
- Zieminska D
- Zimmermann R
- Zimmermann S
- Zimmermann S
- Zinonos Z
- Ziolkowski M
- Zitoun R
- Zivkovic L
- Zmouchko VV
- Zobernig G
- Zoccoli A
- Zolnierowski Y
- Zsenei A
- Zutshi V
- Zwalinski L
- Publication venue
- 'Springer Science and Business Media LLC'
- Publication date
- 01/03/2013
- Field of study
The jet energy scale and its systematic uncertainty are determined for jets measured with the ATLAS detector at the LHC in proton-proton collision data at a centre-of-mass energy of √s = 7TeV corresponding to an integrated luminosity of 38 pb-1. Jets are reconstructed with the anti-kt algorithm with distance parameters R=0. 4 or R=0. 6. Jet energy and angle corrections are determined from Monte Carlo simulations to calibrate jets with transverse momenta pT≥20 GeV and pseudorapidities {pipe}η{pipe}<4. 5. The jet energy systematic uncertainty is estimated using the single isolated hadron response measured in situ and in test-beams, exploiting the transverse momentum balance between central and forward jets in events with dijet topologies and studying systematic variations in Monte Carlo simulations. The jet energy uncertainty is less than 2. 5 % in the central calorimeter region ({pipe}η{pipe}<0. 8) for jets with 60≤pT<800 GeV, and is maximally 14 % for pT<30 GeV in the most forward region 3. 2≤{pipe}η{pipe}<4. 5. The jet energy is validated for jet transverse momenta up to 1 TeV to the level of a few percent using several in situ techniques by comparing a well-known reference such as the recoiling photon pT, the sum of the transverse momenta of tracks associated to the jet, or a system of low-pT jets recoiling against a high-pT jet. More sophisticated jet calibration schemes are presented based on calorimeter cell energy density weighting or hadronic properties of jets, aiming for an improved jet energy resolution and a reduced flavour dependence of the jet response. The systematic uncertainty of the jet energy determined from a combination of in situ techniques is consistent with the one derived from single hadron response measurements over a wide kinematic range. The nominal corrections and uncertainties are derived for isolated jets in an inclusive sample of high-pT jets. Special cases such as event topologies with close-by jets, or selections of samples with an enhanced content of jets originating from light quarks, heavy quarks or gluons are also discussed and the corresponding uncertainties are determined. © 2013 CERN for the benefit of the ATLAS collaboration
Whole transcriptome sequencing identifies tumor-specific mutations in human oral squamous cell carcinoma
- Author
- A Alexa
- A Canovas
- A Jemal
- A Mortazavi
- A Vaezi
- AE Al Moustafa
- AI Zavras
- B Vogelstein
- BB Tuch
- C Garnis
- C Greenman
- C Gregg
- C Gregg
- C Leethanakul
- DM Parkin
- EA Gibb
- ET Cirulli
- GJ Thomas
- H Li
- Hong Jin
- I Alevizos
- I Chepelev
- IF Tsui
- IF Tsui
- J Califano
- Jun Zhang
- K Kozaki
- L Mao
- LD Wood
- LQ Zhang
- M Ashburner
- M Kanehisa
- M Kanehisa
- MP Rosin
- N Cloonan
- N Homer
- ND Dees
- P Kumar
- Qu Zhang
- R Kridel
- R Morin
- R Moslehi
- S Anders
- S Jones
- S Mukherjee
- S Myllykangas
- SA Liu
- SC Hung
- Sitong Sheng
- ST Sherry
- T Sjoblom
- TJ Belbin
- Y Benjamini
- YH Yu
- Z Wang
- Publication venue
- 'Springer Science and Business Media LLC'
- Publication date
- Field of study
Emerging concepts in biomarker discovery; The US-Japan workshop on immunological molecular markers in oncology
- Author
- A Abati
- A Dash
- A Hiasa
- A Hildesheim
- A Hubel
- A Jemal
- A Karolina Palucka
- A Malyguine
- A Mantovani
- A Mantovani
- A Paun
- A Player
- A Ribas
- A Ribas
- A Shanker
- A Worschech
- A Worschech
- A Zobywalski
- AG Heriot
- AH Zea
- AK Kurian
- Akira Kanamoto
- AL Fields
- AL Harzstark
- AL Landay
- AL McDermott
- AM Wu
- AN Houghton
- Anatoli Malyguine
- Antoni Ribas
- AT Chan
- ATC Chan
- B Bhattacharya
- B Comin-Anduix
- B Comin-Anduix
- B Namjou
- B Piqueras
- B Rubinfeld
- BE Stranger
- BE Stranger
- Benjamin Zeskind
- Bernard A Fox
- BJ Feng
- C Badoual
- C Doehn
- C Haqq
- C Kudo-Saito
- C Lengauer
- C Longo
- C Monteagudo
- C Sarrazin
- C Schindler
- C Soubrane
- C Soubrane
- C Volpers
- C-L Lin
- CA Sarkar
- CB Bigger
- CB Bigger
- CC Lu
- CG Clemente
- CG Fraser
- CG Fraser
- CG Radu
- Craig L Slingluff
- CS Karapetis
- D Chaussabel
- D Chaussabel
- D Chua
- D Leibovici
- D Liu
- DA Casciano
- Damien Chaussabel
- David F Stroncek
- DB Goldsmith
- DF Stroncek
- DF Stroncek
- DG Bowen
- DN Martin
- DR Budiani
- E Sato
- E von Euw
- E Wang
- E Wang
- E Wang
- E Wang
- E Wang
- E Wang
- E Wang
- E Wang
- E Wang
- E Wang
- E Wang
- E Wang
- EA Engels
- EA Heller
- EB Walker
- EB Walker
- EB Walker
- EL Korn
- Emanuel F Petricoin
- Ena Wang
- ET Hawk
- F Balkwill
- F Balkwill
- F Benencia
- F Pages
- F Pages
- F Pages
- FDA
- FDA
- FM Marincola
- FM Marincola
- Francesco M Marincola
- FS Hodi
- FW Frueh
- G Ahlenstiel
- Giuseppe Masucci
- GP Nolan
- GQ Phan
- H Gogas
- H Harlin
- H Lu
- H Suzuki
- H Wada
- H Yamaguchi
- Hideaki Tahara
- Hiroshi Shiku
- Hiroya Takeuchi
- Hiroyoshi Nishikawa
- Hisahiro Matsubara
- Hisashi Wada
- Howard Streicher
- HS Conjeevaram
- HT Maecker
- HT Maecker
- I Hoshino
- IM Mullins
- iSBTc
- J Galon
- J Galon
- J Han
- J Ma
- J Ren
- J Salk
- JA Kelly
- James Jacobson
- JD Wulfkuhle
- JD Wulfkuhle
- JD Wulfkuhle
- JF Apgar
- JK Habermann
- JM Kirkwood
- JM Kirkwood
- John M Kirkwood
- Jon M Wigginton
- JP Ioannidis
- JS Burgos
- Julia Wulfkuhle
- JW Shin
- K Honda
- K Lassi
- K Shafer-Weaver
- K Shafer-Weaver
- Kazunori Kato
- KC Straathof
- KE De Visser
- Kiminori Nakamura
- KK Dobbin
- KK Dobbin
- KK Fleming
- KM Lally
- KM Marks
- Kohzoh Imai
- KW Lo
- L Bennett
- L Rivino
- L Rossi
- L Shen
- L Shi
- L Shi
- L Zaritskaya
- L Zhang
- LA Norian
- Lance Liotta
- LC Platanias
- LG Salazar
- LH Butterfield
- LH Butterfield
- LH Butterfield
- LH Butterfield
- Licia Rivoltini
- Lisa H Butterfield
- LM Coussens
- M Berg
- M Bittner
- M Camus
- M Inokuma
- M Jinushi
- M Jinushi
- M Jinushi
- M Kashani-Sabet
- M Kunz
- M Morley
- M Sabatino
- M Sabatino
- M Sarwal
- MA Chaudry
- MA Cheever
- MA Cheever
- Magdalena Thurin
- Mai-Britt Zocca
- Marimo Sato
- Mary L Disis
- Masahisa Jinushi
- MB Atkins
- MC Dieu-Nosjean
- MC Panelli
- MC Panelli
- MC Panelli
- MC Panelli
- MC Panelli
- MC Yu
- ME Dudley
- MH Tsai
- Michael T Lotze
- Michele Maio
- Minoru Toyota
- MJ Simons
- MJ Simons
- ML Disis
- ML Disis
- MM Aloysius
- MM Davis
- Mohammed Kashani-Sabet
- MS Pepe
- MS Pepe
- MS Pepe
- N Mokni-Baizig
- N Sato
- Noriyuki Sato
- Oleg Eremin
- P Dubey
- P Jin
- P Jin
- P Kalinski
- P Salama
- PA Ascierto
- Paul V Lehmann
- PC Rodriguez
- PC Tumeh
- Peter P Lee
- PF Robbins
- PJ Gaglio
- PP Lee
- PV Lehmann
- R Aebersold
- R Muthuswamy
- R Shippy
- R Simon
- R Simon
- R Simon
- R Simon
- R Simon
- RB Mailliard
- RD Canales
- RJ Critchley-Thorne
- RJ Critchley-Thorne
- RL Grubb
- RR Weichselbaum
- RS Huang
- RT Calado
- S Deola
- S Gnjatic
- S Halabi
- S Kaur
- S Kuerten
- S Mandruzzato
- S Mocellin
- S Mocellin
- S Mocellin
- S Selleri
- S Ugurel
- SA Ghanekar
- SA Tishkoff
- SA Tishkoff
- Samir N Khleif
- Shawmarie Mayrand-Chung
- SJ Moschos
- SM Kaech
- SP Lee
- SP Mankoff
- Stefan Ambs
- T Tatsumi
- TA Patterson
- TA Wallace
- TF Gajewski
- TH Han
- Thomas O Kleen
- TL Hocker
- TL Sorensen
- TM Nowacki
- Tomonori Yaguchi
- TR Schlingmann
- U Keilholz
- V Espina
- V Monsurro'
- V Monsurro'
- V Monsurro'
- V Monsurro'
- V Pascual
- VG Brichard
- VG Brichard
- W Fang
- W Zhang
- WD Stein
- WJ Leonard
- Wolf Hervé Fridman
- WW Hancock
- X Li
- X Li
- X Su
- Xifeng Wu
- XS He
- Y Huang
- Y Kawakami
- Y Luo
- Y Naito
- Y Xu
- Yasunori Akutsu
- YH Li
- Yingdong Zhao
- Yoshihiko Hirohashi
- Yuichiro Doki
- Yutaka Kawakami
- Z Huang
- Z Zhang
- Zoltan Pos
- ZR Yurkovetsky
- ZT Xin
- Publication venue
- BioMed Central
- Publication date
- 01/01/2009
- Field of study
Supported by the Office of International Affairs, National Cancer Institute (NCI), the "US-Japan Workshop on Immunological Biomarkers in Oncology" was held in March 2009. The workshop was related to a task force launched by the International Society for the Biological Therapy of Cancer (iSBTc) and the United States Food and Drug Administration (FDA) to identify strategies for biomarker discovery and validation in the field of biotherapy. The effort will culminate on October 28th 2009 in the "iSBTc-FDA-NCI Workshop on Prognostic and Predictive Immunologic Biomarkers in Cancer", which will be held in Washington DC in association with the Annual Meeting. The purposes of the US-Japan workshop were a) to discuss novel approaches to enhance the discovery of predictive and/or prognostic markers in cancer immunotherapy; b) to define the state of the science in biomarker discovery and validation. The participation of Japanese and US scientists provided the opportunity to identify shared or discordant themes across the distinct immune genetic background and the diverse prevalence of disease between the two Nations
Cancer Biomarker Discovery: The Entropic Hallmark
- Author
- A Alcaraz
- A Arabzadeh
- A Bagri
- A Balbin
- A Bantis
- A Ben-Naim
- A Bolander
- A Buhmeida
- A Burykin
- A Chetcuti
- A de Baey
- A Efeyan
- A Eroglu
- A Fabarius
- A Forget
- A Fujita
- A Geirsson
- A Geirsson
- A Geirsson
- A Guffanti
- A Hugel
- A Inoue
- A Isidoro
- A Jang
- A Kollara
- A Kuzmanov
- A Lundqvist
- A Maria McCrohan
- A Marreiros
- A Mendes
- A Mitra
- A Nassar
- A Petitjean
- A Petitjean
- A Pinzon-Charry
- A Richmond
- A Roesch
- A Santinelli
- A Schmidt
- A Shapiro
- A Sreekumar
- A Takeno
- A Urbanucci
- A Winter
- A Yemelyanov
- AA Babiker
- AA Babiker
- AA Tarhini
- AC Dudley
- AD Judge
- AD Ortega
- AG Puebla-Mora
- AH Fox
- AH Fox
- AI Riker
- AJ Liu
- AK Meeker
- AK Panigrahi
- AK Witkiewicz
- AL Cheung
- AL Fachin
- AL Gartel
- AL Okorokov
- AM Craig
- AM Lena
- AM Levin
- AM Tokes
- AP South
- AS Payne
- AS Verkman
- AS Verkman
- AS Verkman
- AS Wierzbicki
- AV Skamrov
- AW Maniccia
- B Cinar
- B Gao
- B Ouyang
- B Ren
- B Ryu
- B Tycko
- B Vukovic
- B Wu
- B Wu
- BD Dimitrov
- BF Gilmore
- BF Goncalves
- BF Skinnider
- BK Zehentner
- BL Adamsen
- BL de Groot
- BR Johnson
- BR Middleman
- BS Strauss
- C Adami
- C Bastide
- C Cao
- C Cybulski
- C Haqq
- C Hayashi
- C Hornig
- C Ivorra
- C Kumar-Sinha
- C Langner
- C Magi-Galluzzi
- C Magi-Galluzzi
- C Muller-Tidow
- C Nessler-Menardi
- C Nunez
- C Pequeux
- C Rajesh
- C Xu
- C Yuli
- CD Sturgis
- CD Truong
- CG Pham
- CG Rogers
- CG Rogers
- CJ Hutchison
- CJ Pronk
- CK Mavis
- CL Stewart
- CL Wu
- CM Caves
- CM Caves
- CM Clemson
- CM Perou
- CP Gray
- CP Gray
- CP Gray
- CR Mangahas
- CS Bond
- D Acehan
- D Bonn
- D Denhardt
- D Fu
- D Gilley
- D Gisselsson
- D Hanahan
- D Javelaud
- D Kroepfl
- D Lodygin
- D Maraldo
- D Ouazia
- D Scadden
- D Wang
- D Wang
- D Wang
- D Weckermann
- D Wodarz
- DA Shoskes
- DA Tennant
- DE Hansel
- DF Gleason
- DG Albertson
- DG Tenen
- DH Palmer
- DJ Darley
- DJ Grignon
- DJ Smit
- DJ Son
- DJ Wong
- DJC MacKay
- DK Koynova
- DK Lee
- DM Kube
- DM Peehl
- DR Wonsey
- DS Perez
- DV Makarov
- DV Makarov
- E Beitz
- E Beitz
- E Cabuy
- E Fagiani
- E Flannery
- E Geissinger
- E Kikuchi
- E Kruse
- E Sbisa
- E Sprecher
- E Tajkhorshid
- EA Ostrander
- EH Feng
- EH Feng
- EM Rosen
- EM Rosen
- EM Schaeffer
- EO Kehinde
- ET Canepa
- EV Vykhovanets
- EY Lin
- EY Tan
- F Bai
- F Bonetto
- F Boralevi
- F Buback
- F Colotta
- F Langer
- F Saad
- F Tas
- F Yang
- FS Krause
- G Benga
- G Bhanot
- G Blandino
- G Buchanan
- G Kaic
- G Kristiansen
- G Kristiansen
- G Kroemer
- G Murugaiyan
- G Petrovics
- G Pirtskhalaishvili
- G Russo
- G Sardana
- G Stirling
- G Tscheudschilsuren
- G Untergasser
- G Venkataraman
- G von Figura
- GA Jarvis
- GE Crooks
- GF Azzone
- GF Ding
- GL Shen-Ong
- GP Bienert
- GQ Daley
- GR Ribeiro
- GS Palapattu
- GV Glinsky
- GV Glinsky
- H Chang-zheng
- H Chen
- H Dzojic
- H Gronberg
- H Haghnegahdar
- H Harant
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- William C. S. Cho
- WK Kaufmann
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- X Chen
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- X Liu
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- Y Bu
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- YJ Ko
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- YT Sasaki
- YT Sasaki
- YU Katagiri
- Z Jiang
- Z Jiang
- Z Jiang
- Z Jiang
- Z Jiang
- Z Rudzki
- ZA Dotan
- ZR Yurkovetsky
- Publication venue
- Public Library of Science
- Publication date
- 01/01/2010
- Field of study
Background: It is a commonly accepted belief that cancer cells modify their transcriptional state during the progression of the disease. We propose that the progression of cancer cells towards malignant phenotypes can be efficiently tracked using high-throughput technologies that follow the gradual changes observed in the gene expression profiles by employing Shannon's mathematical theory of communication. Methods based on Information Theory can then quantify the divergence of cancer cells' transcriptional profiles from those of normally appearing cells of the originating tissues. The relevance of the proposed methods can be evaluated using microarray datasets available in the public domain but the method is in principle applicable to other high-throughput methods. Methodology/Principal Findings: Using melanoma and prostate cancer datasets we illustrate how it is possible to employ Shannon Entropy and the Jensen-Shannon divergence to trace the transcriptional changes progression of the disease. We establish how the variations of these two measures correlate with established biomarkers of cancer progression. The Information Theory measures allow us to identify novel biomarkers for both progressive and relatively more sudden transcriptional changes leading to malignant phenotypes. At the same time, the methodology was able to validate a large number of genes and processes that seem to be implicated in the progression of melanoma and prostate cancer. Conclusions/Significance: We thus present a quantitative guiding rule, a new unifying hallmark of cancer: the cancer cell's transcriptome changes lead to measurable observed transitions of Normalized Shannon Entropy values (as measured by high-throughput technologies). At the same time, tumor cells increment their divergence from the normal tissue profile increasing their disorder via creation of states that we might not directly measure. This unifying hallmark allows, via the the Jensen-Shannon divergence, to identify the arrow of time of the processes from the gene expression profiles, and helps to map the phenotypical and molecular hallmarks of specific cancer subtypes. The deep mathematical basis of the approach allows us to suggest that this principle is, hopefully, of general applicability for other diseases
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