346 research outputs found
The disruption of proteostasis in neurodegenerative diseases
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- Publication venue
- 'American Institute of Mathematical Sciences (AIMS)'
- Publication date
- 01/01/2015
- Field of study
Cells count on surveillance systems to monitor and protect the cellular proteome which, besides being highly heterogeneous, is constantly being challenged by intrinsic and environmental factors. In this context, the proteostasis network (PN) is essential to achieve a stable and functional proteome. Disruption of the PN is associated with aging and can lead to and/or potentiate the occurrence of many neurodegenerative diseases (ND). This not only emphasizes the importance of the PN in health span and aging but also how its modulation can be a potential target for intervention and treatment of human diseases.info:eu-repo/semantics/publishedVersio
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)
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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- Thomsen LA
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- Tikhonov YA
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- Tisserant S
- Tobon CAM
- Todome K
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- Tolley E
- Tomiwa KG
- Tomoto M
- Tompkins L
- Tong B
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- Toro RC
- Torrence E
- Torres H
- Torres RET
- Tosciri C
- Toth J
- Tovey DR
- Traeet A
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- Tricoli A
- Trigger IM
- Trincaz-Duvoid S
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- Trischuk W
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- Trofymov A
- Troncon C
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- Truong L
- Trzebinski M
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- Tsai F
- Tseng JC-L
- Tsiareshka P
- Tsirigotis A
- Tsiskaridze V
- Tskhadadze EG
- Tsopoulou M
- Tsukerman II
- Tsulaia V
- Tsuno S
- Tsybychev D
- Tu Y
- Tudorache A
- Tudorache V
- Tulbure TT
- Tuna AN
- Turchikhin S
- Turgeman D
- Turner RJ
- Turra RT
- Tuts PM
- Tzamarias S
- Tzovara E
- Ucchielli G
- Uchida K
- Ukegawa F
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- Undrus A
- Unel G
- Ungaro FC
- Unno Y
- Uno K
- Urban J
- Urquijo P
- Usai G
- Uysal Z
- Vacek V
- Vachon B
- Vadla KOH
- Vaidya A
- Valderanis C
- Vale MAB
- Valente M
- Valentinetti S
- Valero A
- Valery L
- Vallance RA
- Vallier A
- Van Daalen TR
- Van Gemmeren P
- Van Vulpen I
- Vanadia M
- Vandelli W
- Vandenbroucke M
- Vandewall ER
- Vaniachine A
- Vannicola D
- Vari R
- Varnes EW
- Varni C
- Varol T
- Varouchas D
- Varvell KE
- Vasile ME
- Vasquez GA
- Vazeille F
- Vazquez Furelos D
- Vazquez CJB
- Vazquez JGP
- Veatch J
- Vecchio V
- Veen MJ
- Veloce LM
- Veloso F
- Veneziano S
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- Venturi N
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- Verbytskyi A
- Vercesi V
- Verducci M
- Vergara JCR
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- Verkerke W
- Vermeulen AT
- Vermeulen JC
- Verzini MJA
- Vetterli MC
- Viaux Maira N
- Vickey T
- Viehhauser GHA
- Vigani L
- Villa M
- Vilucchi E
- Vincter MG
- Virdee GS
- Vishwakarma A
- Vittori C
- Vivarelli I
- Vogel M
- Vokac P
- von Buddenbrock SE
- Von Toerne E
- Vorobel V
- Vorobev K
- Vos M
- Vossebeld JH
- Vozak M
- Vranjes N
- Vrba V
- Vreeswijk M
- Vuillermet R
- Vukotic I
- Wagner P
- Wagner W
- Wagner-Kuhr J
- Wahdan S
- Wahlberg H
- Walbrecht VM
- Walder J
- Walker R
- Walker SD
- Walkowiak W
- Wallangen V
- Wang AM
- Wang AZ
- Wang C
- Wang F
- Wang H
- Wang J
- Wang P
- Wang Q
- Wang R
- Wang R-J
- Wang SM
- Wang W
- Wang WT
- Wang WX
- Wang Y
- Wang Z
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- Warburton A
- Ward CP
- Wardrope DR
- Warrack N
- Washbrook A
- Watson AT
- Watson MF
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- Webb AF
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- Weber SA
- Weber SM
- Weidberg AR
- Weingarten J
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- Wengler T
- Wenig S
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- Werner MD
- Wessels M
- Weston TD
- Whalen K
- Whallon NL
- Wharton AM
- White A
- White AS
- White MJ
- Whiteson D
- Whitmore BW
- Wiedenmann W
- Wiel C
- Wielers M
- Wieseotte N
- Wiglesworth C
- Wiik-Fuchs LAM
- Wilkens HG
- Wilkins LJ
- Williams HH
- Williams S
- Willis C
- Willocq S
- Wingerter-Seez I
- Winkels E
- Winklmeier F
- Winston OJ
- Winter BT
- Wittgen M
- Wobisch M
- Wolf A
- Wolf TMH
- Wolff R
- Wolker R
- Wollrath J
- Wolter MW
- Wolters H
- Wong VWS
- Woods NL
- Worm SD
- Wosiek BK
- Wozniak KW
- Wraight K
- Wu SL
- Wu X
- Wu Y
- Wyatt TR
- Wynne BM
- Xella S
- Xi Z
- Xia L
- Xiao X
- Xiotidis I
- Xu D
- Xu H
- Xu L
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- Xu Z
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- Yacoob S
- Yajima K
- Yallup DP
- Yamaguchi N
- Yamaguchi Y
- Yamamoto A
- Yamatani M
- Yamazaki T
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- Yao W-M
- Yap YC
- Yasu Y
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- Yexley MR
- Yigitbasi E
- Yildiz HD
- Yorita K
- Yoshihara K
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- Yue X
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- Zabinski B
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- Zahreddine J
- Zaitsev AM
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- Zanzi D
- Zaripovas DR
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- Zemaityte G
- Zeng JC
- Zenin O
- Zenis T
- Zerwas D
- Zgubic M
- Zhang B
- Zhang DF
- Zhang G
- Zhang H
- Zhang J
- Zhang L
- Zhang M
- Zhang R
- Zhang S
- Zhang X
- Zhang Y
- Zhang Z
- Zhao P
- Zhao Z
- Zhemchugov A
- Zheng Z
- Zhong D
- Zhou B
- Zhou C
- Zhou M
- Zhou MS
- Zhou N
- Zhou Y
- Zhu C
- Zhu CG
- Zhu H
- Zhu HL
- Zhu J
- Zhu Y
- Zhuang X
- Zhukov K
- Zhulanov V
- Zieminska D
- Zimine N
- Zimmermann S
- Zinonos Z
- Ziolkowski M
- Zivkovic L
- Zobernig G
- Zoccoli A
- Zoch K
- Zorbas TG
- Zou R
- Zu Theenhausen HM
- 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
A second generation human haplotype map of over 3.1 million SNPs
- Author
- Abecasis GR
- Adebamowo CA
- Adewole IF
- Ajayi I
- Altshuler D
- Altshuler D
- Altshuler D
- An D
- Aniagwu T
- Auton A
- Ballinger DG
- Barrett J
- Barry R
- Bellemare G
- Belmont JW
- Belmont JW
- Bentley DR
- Bird CP
- Birren BW
- Blumenstiel B
- Bottolo L
- Boudreau A
- Brooks LD
- Burton J
- Cai D
- Camargo A
- Cardin N
- Cardon LR
- Carter NP
- Chagnon F
- Chakravarti A
- Chee MS
- Chen PE
- Chen Z
- Chretien YR
- Chu X
- Clarke G
- Clayton EW
- Clee CM
- Collins FS
- Cox DR
- Cutler DJ
- Daly MJ
- Daly MJ
- de Bakker PI
- Defelice M
- Delgado M
- Deloukas P
- Dermitzakis ET
- Dixon M
- Donnelly P
- Evans DM
- Eyheramendy S
- Faggart M
- Fan JB
- Feolo M
- Ferretti V
- Foster MW
- Frazer KA
- Freeman C
- Fu H
- Fukushima Y
- Fulton LL
- Gabriel SB
- Gabriel SB
- Galver LM
- Gao Y
- Gibbs RA
- Gibbs RA
- Godbout M
- Goyette M
- Griffiths M
- Guan W
- Gunderson K
- Gupta S
- Guyer MS
- Gwilliam R
- Han H
- Hardenbol P
- He Y
- Hinds DA
- Holden AL
- Hu H
- Hu W
- Huang W
- Hudson TJ
- Hunt S
- Jamieson R
- Jin L
- Jones MC
- Kang L
- Kashuk CS
- Kato K
- Kawaguchi T
- Kennedy K
- Kent A
- Kitamoto T
- Knoppers BM
- Koboldt DC
- Krishnan L
- Kwok PY
- L'Archevêque P
- Leal SM
- Leboeuf M
- Leppert MF
- Li C
- Li Q
- Li Y
- Lin S
- Lin W
- Liu S
- Liu Y
- Macer DR
- Mak W
- Maller J
- Marchini J
- Marshall PA
- Matsuda I
- McCarroll S
- McEwen JE
- McLay K
- McVean G
- Miller RD
- Montpetit A
- Moore J
- Morizono T
- Morris AP
- Morrison J
- Mullikin JC
- Munro HM
- Murray SS
- Muzny D
- Myers S
- Nagashima A
- Nakamura Y
- Nazareth L
- Nguyen H
- Niikawa N
- Nkwodimmah C
- Ohnishi Y
- Oliphant AR
- Olivier JF
- Onofrio RC
- Onofrio RC
- Pan H
- Parkin M
- Pasternak S
- Patterson N
- Pawlikowska L
- Pe'er I
- Peiffer A
- Peterson JL
- Phillips MS
- Plumb RW
- Powell D
- Price A
- Purcell S
- Qin ZS
- Qiu R
- Richter DJ
- Richter DJ
- Rogers J
- Ross MT
- Rotimi CN
- Roumy S
- Roy J
- Royal CD
- Sabeti P
- Saeki K
- Sallée C
- Saxena R
- Schaffner SF
- Sekine A
- Sham PC
- Shen Y
- Shen Y
- Sherry ST
- Shi M
- Sims SK
- Skol A
- Smith AV
- Sodergren E
- Song YQ
- Spencer C
- Spiegel J
- Stahl E
- Stein LD
- Stephens M
- Stewart J
- Stranger BE
- Stuve LL
- Suda E
- Sun W
- Sung LM
- Taillon-Miller P
- Tam PK
- Tanaka T
- Tang X
- 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
- Wang W
- Wang Y
- Wang Y
- Wang Z
- Watkin J
- Waye MM
- Weinstock GM
- Weir BS
- Wheeler DA
- Wheeler DA
- 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
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
- H Harlin
- H Kida
- H Li
- H Liu
- H Miyake
- H Nemoto
- H Ostrer
- H Pilch
- H Rangaswami
- H Rangaswami
- H Rangaswami
- H Ren
- H Roca
- H Roca
- H Samaratunga
- H Savli
- H Schlechte
- H Schoder
- H Sheng
- H Sunwoo
- H Then
- H Wang
- H Wang
- HC Lee
- HG Thomas
- HJ Worman
- HL Winfield
- HS Leff
- HT Quan
- HY Vu
- HZ Zhang
- I Agalliu
- I Bae
- I Ben-Porath
- I Grosse
- I Haritoglou
- I Leav
- I Marinescu
- I Moll
- I Sakai
- IE Wertz
- IK Lim
- IL Tourkova
- IM Bachmann
- IM Shih
- IW Reiniger
- IY Dodin
- J Bartkova
- J Edwards
- J Fellenberg
- J Gille
- J Graells
- J Jaeger
- J Johnson
- J Lammerding
- J Laoukili
- J Lapointe
- J Linden
- J Luo
- J Luo
- J Luo
- J Mandelin
- J Melamed
- J Moser
- J Rangel
- J Rapley
- J Reimand
- J Ruiz-Ederra
- J Schmitz
- J Schultz
- J Soikkeli
- J Stewart
- J Suh
- J Walter-Yohrling
- J Wang
- J Wang
- J Weiske
- J Xu
- J Yang
- J Yang
- J Zheng
- JA Camargo
- JA Douglas
- JA Hackett
- JA Karam
- JA McGrath
- JA McGrath
- JA McGrath
- JA McGrath
- JA Mobley
- JA Pettus
- JB Roche
- JC Cheville
- JD French
- JD Licchesi
- JD Owen
- JE Lai-Cheong
- JE Sleeman
- JE Wilusz
- JG Wen
- JH Lee
- JH Luo
- JJ Brey
- JJ Park
- JJ Raffoul
- JJ Tseng
- JJ Van den Oord
- JK Wahl 3rd
- JL Broers
- JL Herrmann
- JL Phillips
- JM Brandner
- JM Bridger
- JM Cummins
- JM Gonzalez
- JM Lizcano
- JM Muller
- JM Muller
- JM Parrondo
- JM Saffin
- JN Hutchinson
- JN Mubiru
- JN Mubiru
- JN Mubiru
- JP Arbitrario
- JP Clark
- JP Ehlers
- JP Fruehauf
- JP Struewing
- JR Cansino Alcaide
- JR McMillan
- JS Butler
- JS Butler
- JS Fang
- JS Hub
- JS Lee
- JS Mattick
- JS Mattick
- JS Mattick
- JT Bishoff
- JT Chang
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- X Liu
- X Meng
- X Ouyang
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- XQ Wang
- Y Bu
- Y Cai
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- YB Lim
- YC Chao
- YJ Ko
- YL Liu
- YN Liu
- 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
Pan-cancer analysis of whole genomes
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- The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium View Correspondence (jump link)
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- Zou
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- Publication venue
- Publication date
- 11/12/2019
- Field of study
Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe
Invasive cells in animals and plants: searching for LECA machineries in later eukaryotic life
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- A Berken
- A Das
- A Geitmann
- A Geitmann
- A Gupta
- A Hall
- A Hall
- A Hendrix
- A Kodama
- A Li
- A Lovy-Wheeler
- A Schwarz
- A Tabuchi
- AA Woollard
- AG Simpson
- AH Hutagalung
- AI Prokhnevsky
- AJ Molendijk
- AJ Ridley
- AK Mongiu
- AL Szumlanski
- AM Craig
- AM Pooler
- AM Weaver
- AP Barnes
- AR Strohmaier
- AS Howell
- AY Cheung
- AY Cheung
- B Diaz
- B Kost
- B Kost
- B Leitinger
- BC Gibbon
- BH de Graaf
- BJ Sieberer
- BK McMichael
- BL Goode
- C Albertinazzi
- C Viotti
- CD Moore
- CD Nobes
- CG Dotti
- CG Koh
- CH Woo
- CL Leung
- CL Wymer
- CM Yoo
- CM Yoo
- CW Pak
- D Basu
- D Gianni
- D Gianni
- D Goryunov
- D Lingwood
- D Pommereit
- D Vignjevic
- DA Murphy
- Daniel Rösel
- DB Szymanski
- DB Szymanski
- DH Schott
- DJ Hernandez-Deviez
- DJ Hernandez-Deviez
- E Forster
- E Giannoni
- E Gouin
- E Michard
- E Mucha
- ED Goley
- EE Govek
- EL Ojangu
- EM Lord
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- M Schoumacher
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- M Valiente
- MA del Pozo
- MA Tischfield
- Margaret Nikolič
- ME Nielsen
- MF Hanzal-Bayer
- MF Olson
- MJ Allen
- MJ Deeks
- MJ Deeks
- MJ Kwon
- ML Preuss
- ML Preuss
- N Arimura
- N Asada
- N Balasubramanian
- N Gupta
- N Kebdani
- N Sorek
- N Thapa
- N Xu
- NG Pasteris
- NR Jog
- O Gossot
- O Hazak
- O Reiner
- O Tolde
- P Caroni
- P Liu
- P Niethammer
- P Novick
- PC Coelho
- PT Caswell
- Q Duan
- R Ahuja
- R Buccione
- R Harel
- R Janostiak
- R Pleskot
- R Poincloux
- RA Arkowitz
- RA Cole
- RJ Carol
- RJ Carol
- Roberto Buccione
- S Cappello
- S Corbetta
- S Cudmore
- S Dupraz
- S Etienne-Manneville
- S Hakeda-Suzuki
- S Hashimoto
- S Katoh
- S Katoh
- S Li
- S Linder
- S Linder
- S Locke
- S Muallem
- S Nagawa
- S Rakic
- S Robert
- S Swanson
- S Tahirovic
- S Takeda
- S Wang
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- SC Mueller
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- SC Noctor
- SC Noctor
- SD Harris
- SE Tague
- SH Shiu
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- T Chen
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- V Zarsky
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- Publication venue
- 'Springer Science and Business Media LLC'
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- Field of study
Alternative splicing: the pledge, the turn, and the prestige
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- A Aartsma-Rus
- A Berger
- A DeMicco
- A Goren
- A Haraga
- A Ivanov
- A Kalsotra
- A Krämer
- A Malamitsi-Puchner
- A Mankodi
- A Pawellek
- A Peri
- A Sureau
- A Sveen
- A Zaghlool
- A. C. Leote
- AA Melton
- AD Norris
- AG Matera
- AGL Douglas
- AJ Linares
- AJ Ward
- AJ Westermann
- AJ Westermann
- AL Shaffer
- AM Muise
- AN Brooks
- AN Kuhn
- AR Grosso
- AR Grosso
- AR Krainer
- AR Krainer
- AV Chee
- B Chabot
- B Hu
- B Ng
- B Raj
- B Raj
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- B Ruskin
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- B Treutlein
- BD Berkovits
- BJ Albert
- BJ Blencowe
- BJG Baaten
- BK Dredge
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- C Gao
- C Ghigna
- C Holland
- C Karakaya
- C Kress
- C Liu
- C Vernet
- C Wei
- C Zhu
- CA Opitz
- CA Turner Jr
- CH George
- CJ David
- CJ David
- CK Vuong
- CM Koh
- CR Rothrock
- CV Clower
- D Ahmadi Rastegar
- D Dominguez
- D Hanahan
- D Kumar
- D Lipscombe
- D Memon
- D Sakamuro
- DD Licatalosi
- DD Licatalosi
- DG Nowak
- DJ Elliott
- DO Bates
- DP Hughes
- DW Seol
- DW Walke
- E Brody
- E Lara-Pezzi
- E Lara-Pezzi
- E Sebestyén
- E Sebestyén
- EJ Love
- EL Heinzen
- ES Goers
- ET Wang
- ET Wang
- EY Osman
- F Melchers
- F Wang
- FALM Eskens
- G Lamson
- G Lev-Maor
- G Magistrelli
- G McClorey
- G Pintucci
- G Yeo
- H Bierne
- H Cheng
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- H Dvinge
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- H Gallinaro
- H Jung
- H Maatz
- H Wang
- H Yong
- H-Y Wang
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- HE Bryant
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- MA Havens
- MA Havens
- MA Jensen
- MB Coelho
- MB Warf
- MD Diaz-Muñoz
- MF Krummel
- MG Rosenfeld
- MG Rosenfeld
- MJ Benson
- MJ Mallory
- MJ Moore
- MK Oaks
- MK O’Bryan
- MM Scotti
- MP Paronetto
- MP Paronetto
- MR Cookson
- MR Lerner
- MS Anderson
- N Charlet-B
- N Droin
- N Hamada
- N Iwamori
- N Keppetipola
- N Martínez-Montiel
- N-T Chiou
- N. L. Barbosa-Morais
- N. Saraiva-Agostinho
- NA Olshavsky
- NL Barbosa-Morais
- NM Martinez
- NN Singh
- NS Foulkes
- O Anczuków
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- O Kelemen
- O Muhlemann
- O Rossbach
- P Early
- P Early
- P Tucker
- PA Merwe van der
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- R Spellman
- R Sperling
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- RW Ching
- S Alsafadi
- S Berto
- S Bonomi
- S Carpenter
- S Fletcher
- S Gueroussov
- S Leu
- S Oberdoerffer
- S Oltean
- S Ramalingam
- S Rosenberger
- S Shen
- S Zheng
- SD Wagner
- SE Butcher
- SF Nagueh
- SM Berget
- SM Dehm
- SM Rueter
- SM Weyn-Vanhentenryck
- SP Wongpalee
- SV Graham
- SV Kozyrev
- T Fukuhara
- T Hermann
- T Iijima
- T Iijima
- T Nojima
- T Stiewe
- TH Ho
- TM Miller
- TR Webb
- TY-T Hsu
- U Rosani
- V Cognata La
- V Gonçalves
- V Runfola
- VR Moulton
- W Gilbert
- W Guo
- W Liu
- W Xia
- W Zhong
- WR Jeck
- X-D Fu
- Y Barash
- Y Kanemori
- Y Kanemori
- Y Ohshima
- Y Onouchi
- Y Wang
- Y Xue
- Y Zhang
- Y-H Goo
- Y-S Lin
- YS Tsai
- Z Xu
- ZM Zheng
- Publication venue
- 'Springer Science and Business Media LLC'
- Publication date
- Field of study
Measurements of differential cross-sections in top-quark pair events with a high transverse momentum top quark and limits on beyond the Standard Model contributions to top-quark pair production with the ATLAS detector at √s = 13 TeV
- Author
- Aad G
- Abbott B
- Abbott DC
- Abeling K
- Abhayasinghe DK
- Abidi SH
- Aboulhorma A
- Abramowicz H
- Abreu H
- Abud AA
- Abulaiti Y
- Acharya BS
- Achkar B
- Adam L
- Adamczyk L
- Adamek L
- Addepalli SV
- Adelman J
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- Aggarwal A
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- Akesson TPA
- Akimov AV
- Al Khoury K
- Alberghi GL
- Albert J
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- Ali B
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- Zhemchugov A
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- Zwalinski L
- Publication venue
- 'Springer Science and Business Media LLC'
- Publication date
- 01/01/2022
- Field of study
Cross-section measurements of top-quark pair production where the hadronically decaying top quark has transverse momentum greater than 355 GeV and the other top quark decays into ℓνb are presented using 139 fb−1 of data collected by the ATLAS experiment during proton-proton collisions at the LHC. The fiducial cross-section at s = 13 TeV is measured to be σ = 1.267 ± 0.005 ± 0.053 pb, where the uncertainties reflect the limited number of data events and the systematic uncertainties, giving a total uncertainty of 4.2%. The cross-section is measured differentially as a function of variables characterising the tt¯ system and additional radiation in the events. The results are compared with various Monte Carlo generators, including comparisons where the generators are reweighted to match a parton-level calculation at next-to-next-to-leading order. The reweighting improves the agreement between data and theory. The measured distribution of the top-quark transverse momentum is used to search for new physics in the context of the effective field theory framework. No significant deviation from the Standard Model is observed and limits are set on the Wilson coefficients of the dimension-six operators OtG and Otq(8), where the limits on the latter are the most stringent to date. [Figure not available: see fulltext.]
Measurements of differential cross-sections in four-lepton events in 13 TeV proton-proton collisions with the ATLAS detector
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- Zhemchugov A
- Zheng Z
- Zhong D
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- Zieminska D
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- Publication venue
- 'Springer Fachmedien Wiesbaden GmbH'
- Publication date
- 02/07/2021
- Field of study
Measurements of four-lepton differential and integrated fiducial cross-sections in events with two same-flavour, opposite-charge electron or muon pairs are presented. The data correspond to 139 fb−1 of s√ = 13 TeV proton-proton collisions, collected by the ATLAS detector during Run 2 of the Large Hadron Collider (2015–2018). The final state has contributions from a number of interesting Standard Model processes that dominate in different four-lepton invariant mass regions, including single Z boson production, Higgs boson production and on-shell ZZ production, with a complex mix of interference terms, and possible contributions from physics beyond the Standard Model. The differential cross-sections include the four-lepton invariant mass inclusively, in slices of other kinematic variables, and in different lepton flavour categories. Also measured are dilepton invariant masses, transverse momenta, and angular correlation variables, in four regions of four-lepton invariant mass, each dominated by different processes. The measurements are corrected for detector effects and are compared with state-of-the-art Standard Model calculations, which are found to be consistent with the data. The Z → 4ℓ branching fraction is extracted, giving a value of (4.41 ± 0.30) × 10−6. Constraints on effective field theory parameters and a model based on a spontaneously broken B − L gauge symmetry are also evaluated. Further reinterpretations can be performed with the provided information
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