44 research outputs found
What's in your next-generation sequence data? An exploration of unmapped DNA and RNA sequence reads from the bovine reference individual.
- Author
- Publication venue
- eScholarship, University of California
- Publication date
- 01/12/2015
- Field of study
BackgroundNext-generation sequencing projects commonly commence by aligning reads to a reference genome assembly. While improvements in alignment algorithms and computational hardware have greatly enhanced the efficiency and accuracy of alignments, a significant percentage of reads often remain unmapped.ResultsWe generated de novo assemblies of unmapped reads from the DNA and RNA sequencing of the Bos taurus reference individual and identified the closest matching sequence to each contig by alignment to the NCBI non-redundant nucleotide database using BLAST. As expected, many of these contigs represent vertebrate sequence that is absent, incomplete, or misassembled in the UMD3.1 reference assembly. However, numerous additional contigs represent invertebrate species. Most prominent were several species of Spirurid nematodes and a blood-borne parasite, Babesia bigemina. These species are either not present in the US or are not known to infect taurine cattle and the reference animal appears to have been host to unsequenced sister species.ConclusionsWe demonstrate the importance of exploring unmapped reads to ascertain sequences that are either absent or misassembled in the reference assembly and for detecting sequences indicative of parasitic or commensal organisms
Thermal response to firefighting activities in residential structure fires: impact of job assignment and suppression tactic
- Author
- Publication venue
- 'Informa UK Limited'
- Publication date
- 31/07/2017
- Field of study
Firefighters’ thermal burden is generally attributed to high heat loads from the fire and metabolic heat generation, which may vary between job assignments and suppression tactic employed. Utilising a full-sized residential structure, firefighters were deployed in six job assignments utilising two attack tactics (1. Water applied from the interior, or 2. Exterior water application before transitioning to the interior). Environmental temperatures decreased after water application, but more rapidly with transitional attack. Local ambient temperatures for inside operation firefighters were higher than other positions (average ~10–30 °C). Rapid elevations in skin temperature were found for all job assignments other than outside command. Neck skin temperatures for inside attack firefighters were ~0.5 °C lower when the transitional tactic was employed. Significantly higher core temperatures were measured for the outside ventilation and overhaul positions than the inside positions (~0.6–0.9 °C). Firefighters working at all fireground positions must be monitored and relieved based on intensity and duration.
Practitioner Summary: Testing was done to characterise the thermal burden experienced by firefighters in different job assignments who responded to controlled residential fires (with typical furnishings) using two tactics. Ambient, skin and core temperatures varied based on job assignment and tactic employed, with rapid elevations in core temperature in many roles.This work was supported by the Department of Homeland Security Fire Prevention and Safety Grant [#EMW-2013-FP-00766].Ope
Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle
- Author
- A Achilli
- A Achilli
- A Esteve-Codina
- A Gotherstrom
- A Seguin-Orlando
- A Vaysse
- A Winter
- AE Minoche
- AJ Amaral
- Alison Murphy
- Amanda J. Lohan
- Andrew T. Chamberlain
- AV Zimin
- B Grisart
- B Grisart
- BP Lewis
- Brendan J. Loftus
- C Gamba
- C Glaser
- Ceiridwen J. Edwards
- CG Elsik
- Charles Spillane
- CJ Edwards
- CJ Edwards
- CJ Edwards
- CJ Rubin
- CJ Stevens
- CM Leu
- CS Troy
- D Reich
- Daniel G. Bradley
- David A. Magee
- David E. MacHugh
- DE MacHugh
- DG Bradley
- DM Larkin
- DP Toews
- E Palkopoulou
- E Svensson
- EJ McTavish
- EY Durand
- H Jonsson
- H Jonsson
- H Li
- H Zhang
- HD Daetwyler
- J Clutton-Brock
- J Diamond
- J Kantanen
- J Lenstra
- J Schibler
- JA Guerra-Assuncao
- JD Vigne
- JE Decker
- JK Pickrell
- JK Pritchard
- JS Pedersen
- K Prufer
- KA Moutou
- Kévin Rue-Albrecht
- L Orlando
- L Perez-Pardal
- LK Matukumalli
- M Gautier
- M Hofreiter
- M Li
- M Meyer
- M Raghavan
- M Rasmussen
- M Schubert
- MA DePristo
- MA Greagg
- MA Groenen
- Mark T. Donoghue
- Martin Braud
- Matthew D. Teasdale
- MJ Montague
- N Murakami
- N Patterson
- NA Rosenberg
- O Smith
- Paul A. McGettigan
- R Bollongino
- R Chen
- RA Gibbs
- RE Green
- RE Green
- RH Meadow
- RR Hudson
- RT Loftus
- S Bonfiglio
- S Bonfiglio
- S Bonfiglio
- S Guindon
- S Koks
- S Paabo
- S Qanbari
- S Sawyer
- Shuaishuai Tai
- Stephen D E Park
- Steven Schroeder
- Tad S. Sonstegard
- TH Lee
- W McLaren
- Y Benjamini
- Yuan Liu
- Publication venue
- 'Springer Science and Business Media LLC'
- Publication date
- 01/01/2015
- Field of study
Background
Domestication of the now-extinct wild aurochs, Bos primigenius, gave rise to the two major domestic extant cattle taxa, B. taurus and B. indicus. While previous genetic studies have shed some light on the evolutionary relationships between European aurochs and modern cattle, important questions remain unanswered, including the phylogenetic status of aurochs, whether gene flow from aurochs into early domestic populations occurred, and which genomic regions were subject to selection processes during and after domestication. Here, we address these questions using whole-genome sequencing data generated from an approximately 6,750-year-old British aurochs bone and genome sequence data from 81 additional cattle plus genome-wide single nucleotide polymorphism data from a diverse panel of 1,225 modern animals.
Results
Phylogenomic analyses place the aurochs as a distinct outgroup to the domestic B. taurus lineage, supporting the predominant Near Eastern origin of European cattle. Conversely, traditional British and Irish breeds share more genetic variants with this aurochs specimen than other European populations, supporting localized gene flow from aurochs into the ancestors of modern British and Irish cattle, perhaps through purposeful restocking by early herders in Britain. Finally, the functions of genes showing evidence for positive selection in B. taurus are enriched for neurobiology, growth, metabolism and immunobiology, suggesting that these biological processes have been important in the domestication of cattle.
Conclusions
This work provides important new information regarding the origins and functional evolution of modern cattle, revealing that the interface between early European domestic populations and wild aurochs was significantly more complex than previously thought
An atlas of bovine gene expression reveals novel distinctive tissue characteristics and evidence for improving genome annotation
- Author
- A Chang
- A Mortazavi
- A Sakudo
- AS Siddiqui
- AS Siddiqui
- AV Zimin
- C Keime
- Cathy R Gresham
- CG Elsik
- Christian D Haudenschild
- Curtis P Van Tassell
- DG Lemay
- E Vidal
- ES Lein
- G Miele
- Gregory P Harhay
- H Li
- H Wickham
- I Schomburg
- JM Dubinsky
- John W Keele
- KD Pruitt
- Lakshmi K Matukumalli
- LD Stein
- Leeson J Alexander
- R Development Core Team
- RR Wilcox
- S Harris
- Shane C Burgess
- Steven G Schroeder
- Susan M Bridges
- Tad S Sonstegard
- Timothy PL Smith
- TS Sonstegard
- TT Torres
- Vencio
- Y He
- Z Wang
- Publication venue
- BioMed Central
- Publication date
- 01/01/2012
- Field of study
A Systems Approach for Tumor Pharmacokinetics
- Author
- A Flynn
- A Garg
- A Pluen
- A Pugachev
- AI Minchinton
- AM Wu
- AR Pries
- AR Tzafriri
- C. Andrew Boswell
- CD Eggleton
- CS Patlak
- CY Wang
- D Breimer
- D Goldman
- DG Levitt
- DJ Chaplin
- DM Goldenberg
- E Gounaris
- F Castell
- FB Pruijn
- G Frykholm
- G Thurber
- GM Thurber
- GM Thurber
- GM Thurber
- GM Thurber
- Greg Michael Thurber
- GZ Ferl
- H Hurwitz
- H Wildiers
- I Tannock
- IP Torres
- J Tol
- J van der Greef
- JN Patton
- JR Hecht
- JW Baish
- K Fujimori
- K Fujimori
- K McLarty
- KB Bischoff
- L Aloj
- L Baxter
- L Gerlowski
- LT Baxter
- M Heijn
- MJ Mattes
- MM Schmidt
- MW Dewhirst
- NA Mullani
- P Poulin
- P Vaupel
- PH Hinderling
- PS Tofts
- R Sutherland
- Ralph Weissleder
- RK Jain
- RK Jain
- RK Jain
- RM Sharkey
- S Middleman
- SRB Allerheiligen
- T Schroeder
- TAD Smith
- TW Secomb
- V Tolmachev
- W Deen
- WJ Jusko
- Y Noguchi
- ZS Yao
- Publication venue
- 'Public Library of Science (PLoS)'
- Publication date
- 01/01/2011
- Field of study
Recent advances in genome inspired target discovery, small molecule screens, development of biological and nanotechnology have led to the introduction of a myriad of new differently sized agents into the clinic. The differences in small and large molecule delivery are becoming increasingly important in combination therapies as well as the use of drugs that modify the physiology of tumors such as anti-angiogenic treatment. The complexity of targeting has led to the development of mathematical models to facilitate understanding, but unfortunately, these studies are often only applicable to a particular molecule, making pharmacokinetic comparisons difficult. Here we develop and describe a framework for categorizing primary pharmacokinetics of drugs in tumors. For modeling purposes, we define drugs not by their mechanism of action but rather their rate-limiting step of delivery. Our simulations account for variations in perfusion, vascularization, interstitial transport, and non-linear local binding and metabolism. Based on a comparison of the fundamental rates determining uptake, drugs were classified into four categories depending on whether uptake is limited by blood flow, extravasation, interstitial diffusion, or local binding and metabolism. Simulations comparing small molecule versus macromolecular drugs show a sharp difference in distribution, which has implications for multi-drug therapies. The tissue-level distribution differs widely in tumors for small molecules versus macromolecular biologic drugs, and this should be considered in the design of agents and treatments. An example using antibodies in mouse xenografts illustrates the different in vivo behavior. This type of transport analysis can be used to aid in model development, experimental data analysis, and imaging and therapeutic agent design.National Institutes of Health (U.S.) (grant T32 CA079443
Multi-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysis
- Author
- A Ferrer-Admetlla
- A Heger
- A Mosig
- A Phillippy
- A. J Gentles
- A. J Vilella
- A. L Price
- Albert J. Vilella
- Aleksey V. Zimin
- Andrew Jiang
- Audrey P. McElroy
- B Paten
- B. F Benkel
- B. T Sherman
- C Ender
- C Iseli
- C Kosiol
- C Lottaz
- C. A Reynaud
- C. G Elsik
- C. M Wade
- Carl J. Schmidt
- Chantel Scheuring
- Clive Evans
- Curtis P. Van Tassell
- Cédric Notredame
- D Higgins
- D Pan
- D. A Hosack
- D. E Dimcheff
- D. J Laird
- D. K Griffin
- D. W Burt
- Dan Qioa
- Daniela Puiu
- David Langenberger
- David W. Burt
- Dennis Prickett
- E Axelsson
- E. K Kruithof
- E. M McCarthy
- E. W Myers
- Edward J. Smith
- Emanuele Raineri
- G Denisov
- G. K Wong
- G. M Cooper
- G. W Glenney
- Geo Pertea
- Guillaume Marcais
- H Ellegren
- H Kerstens
- H Zhao
- Hakim Tafer
- Heebal Kim
- Hendrik-Jan Megens
- Hong-Bin Zhang
- I Hellmann
- I Korf
- I. L Hofacker
- Ian R. Paton
- J Kaufman
- J. A Bailey
- J. C Dohm
- J. C Roach
- J. E Allen
- J. E Mank
- J. E Stajich
- J. O Korbel
- J. R Miller
- Jacqueline Smith
- James A. Yorke
- Javier Herrero
- Jennifer J. Dong
- Jerry B. Dodgson
- Julie A. Long
- K. J Laing
- K. M Kim
- K. M Reed
- Karin M. Frederickson
- Kathryn Beal
- Kelly P. Williams
- Kent M. Reed
- Kristal Cooper
- Kyu-Won Kim
- L Goodstadt
- L Gordon
- L Lestrade
- L. D Chaves
- L. D Chaves
- L. W Hillier
- L. W Hillier
- Le Ann Blomberg
- Liliana Florea
- Liqing Zhang
- Luqman Aslam
- M Margulies
- M Rehmsmeier
- M Shibusawa
- M Suyama
- M van Tuinen
- M-K Lee
- M. A Larkin
- M. N Romanov
- M. R Lerner
- M. V Han
- Magali Ruffier
- Manja Marz
- Martien A. M. Groenen
- Mary E. Delany
- Mi-Kyung Lee
- Michael C. Schatz
- Mikhail Nefedov
- N. D Temperley
- N. H Ruddle
- O Harismendy
- Oswald Crasta
- Otto Folkerts
- P Bloomer
- P Kaiser
- P Shao
- P. M Murphy
- Pascal Bouffard
- Paul Flicek
- Pete Kaiser
- Peter F. Stadler
- Pieter de Jong
- Q Zheng
- R Li
- R. A Gibbs
- R. A Gibbs
- R. A Sunde
- R. C Edgar
- R. H Waterston
- R. T Kimball
- Rami A. Dalloul
- Richard J. Roberts
- Richard P. M. A. Crooijmans
- Roger A. Coulombe
- S Griffiths-Jones
- S Griffiths-Jones
- S Huse
- S Levy
- S Mukherjee
- S Rautenschlein
- S Schwartz
- S. B Hedges
- S. F Altschul
- S. V Drovetski
- Shrinivasrao Mane
- Stephen M. J. Searle
- Steve Hoffmann
- Steven L. Salzberg
- Steven Schroeder
- Sungwon Kim
- Supriyo De
- T Wicker
- T. M Crowe
- Tad S. Sonstegard
- Taeheon Lee
- Thero Modise
- Tim T. Harkins
- V Curwen
- V Fillon
- W. C Warren
- W. G Hill
- W. H Majoros
- W. J Kent
- William S. Payne
- Xiaojun Zhang
- Y Benjamini
- Yang Zhang
- Z Yang
- Zhijian (Jake) Tu
- Publication venue
- Public Library of Science
- Publication date
- 01/01/2010
- Field of study
The combined application of next-generation sequencing platforms has provided an economical approach to unlocking the potential of the turkey genome
Muon reconstruction and identification efficiency in ATLAS using the full Run 2 pp collision data set at \sqrt{s}=13 TeV
- Author
- Aad G
- Abbott B
- Abbott DC
- Abeling K
- Abhayasinghe DK
- Abidi SH
- AbouZeid OS
- Abraham NL
- Abramowicz H
- Abreu H
- Abud AA
- Abulaiti Y
- Acharya BS
- Achkar B
- Adam L
- Adamczyk L
- Adamek L
- Adelman J
- Adiguzel A
- Adorni S
- Adye T
- Affolder AA
- Afik Y
- Agapopoulou C
- Agaras MN
- Aggarwal A
- Agheorghiesei C
- Aguilar-Saavedra JA
- Agullo PM
- Ahmad A
- Ahmadov F
- Ahmed WS
- Ahnen JV
- Ai X
- Aielli G
- Akatsuka S
- Akbiyik M
- Akesson TPA
- Akilli E
- Akimov AV
- Alberghi GL
- Albert J
- Alderweireldt S
- Aleksa M
- Aleksandrov IN
- Alexa C
- Alexopoulos T
- Alfonsi A
- Alfonsi F
- Alhroob M
- Ali B
- Ali S
- Aliev M
- Alimonti G
- Allaire C
- Allbrooke BMM
- Allen BW
- Allport PP
- Aloisio A
- Alonso F
- Alpigiani C
- Alves FLL
- Alviggi MG
- Ambler A
- Ambroz L
- Amelung C
- Amidei D
- Amoroso S
- Amrouche CS
- An F
- Anastopoulos C
- Andari N
- Andeen T
- Anders JK
- Andrean SY
- Andreazza A
- Andrei V
- Anelli CR
- Angelidakis S
- Angerami A
- Anisenkov AV
- Annovi A
- Antel C
- Anthony MT
- Antipov E
- Antonelli M
- Antrim DJA
- Anulli F
- Aoki M
- Aparo MA
- Aranda CP
- Aranzabal N
- Araya ST
- Arcangeletti C
- Arce ATH
- Arguin J-F
- Argyropoulos S
- Arling J-H
- Armbruster AJ
- Armstrong A
- Arnaez O
- Arnold H
- Artoni G
- Asada H
- Asai K
- Asai S
- Asawatavonvanich T
- Asbah NA
- Asimakopoulou EM
- Asquith L
- Assahsah J
- Assamagan K
- Astalos R
- Astigarraga MEP
- Atkin RJ
- Atkinson M
- Atlay NB
- Atmani H
- Atmasiddha PA
- Augsten K
- Austrup VA
- Avolio G
- Ayoub MK
- Azuelos G
- Babal D
- Bachacou H
- Bachas K
- Backman F
- Bagnaia P
- Bahilo JJL
- Bahrasemani H
- Bailey AJ
- Bailey VR
- Baines JT
- Bakalis C
- Baker OK
- Bakker PJ
- Bakos E
- Balaji S
- Balasubramanian R
- Baldin EM
- Balek P
- Balli F
- Balunas WK
- Balz J
- Banas E
- Bandieramonte M
- Bandyopadhyay A
- Banerjee S
- Barak L
- Barbe WM
- Barberio EL
- Barberis D
- Barbero M
- Barbour G
- Barillari T
- Barisits M-S
- Barkeloo J
- Barklow T
- Barnea R
- Barnett BM
- Barnett RM
- Barnovska-Blenessy Z
- Baroncelli A
- Barone G
- Barr AJ
- Barreiro F
- Barron U
- Barsov S
- Bartels F
- Bartoldus R
- Bartolini G
- Barton AE
- Bartos P
- Basalaev A
- Basan A
- Bassalat A
- Basso MJ
- Bates RL
- Batlamous S
- Batley JR
- Batool B
- Battaglia M
- Bauce M
- Bauer F
- Bauer P
- Bawa HS
- Bayirli A
- Beacham JB
- Beau T
- Beauchemin PH
- Becherer F
- Bechtle P
- Beck HC
- Beck HP
- Becker K
- Becot C
- Beddall A
- Beddall AJ
- Bednyakov VA
- Bedognetti M
- Bee CP
- Beermann TA
- Begalli M
- Begel M
- Behera A
- Behr JK
- Beisiegel F
- Belfkir M
- Bell AS
- Bella G
- Bella LA
- Bellagamba L
- Bellerive A
- Bellos P
- Beloborodov K
- Belotskiy K
- Belyaev NL
- Benchekroun D
- Benekos N
- Benhammou Y
- Benjamin DP
- Benoit M
- Bensinger JR
- Bentvelsen S
- Beresford L
- Beretta M
- Berge D
- Berger N
- Bergmann B
- Bergsten LJ
- Beringer J
- Berlendis S
- Berlingen JM
- Bernardi G
- Bernius C
- Bernlochner FU
- Berry T
- Berta P
- Berthold A
- Bertram IA
- Besson N
- Bethke S
- Betti A
- Bevan AJ
- Beyer J
- Bhatta S
- Bhattacharya DS
- Bhattarai P
- Bhopatkar VS
- Bi R
- Bianchi RM
- Biebel O
- Biedermann D
- Bielski R
- Bierwagen K
- Biesuz NV
- Biglietti M
- Billoud TRV
- Bindi M
- Bingul A
- Bini C
- Biondi S
- Birch-sykes CJ
- Birman M
- Bisanz T
- Biswal JP
- Biswas D
- Bitadze A
- Bittrich C
- Bjorke K
- Blazek T
- Bloch I
- Blocker C
- Blue A
- Blumenschein U
- Bobbink GJ
- Bobrovnikov VS
- Bocchetta SS
- Boeriu OEV
- Bogavac D
- Bogdanchikov AG
- Bohm C
- Boisvert V
- Bokan P
- Bolanos GR
- Bold T
- Bolz AE
- Bomben M
- Bona M
- Bonilla JS
- Boonekamp M
- Booth CD
- Borbely AG
- Borecka-Bielska HM
- Borgna LS
- Borisov A
- Borissov G
- Bortoletto D
- Bosca SR
- Boscherini D
- Bosman M
- Bostanabad MG
- Bouaouda K
- Boudreau J
- Bouhova-Thacker EV
- Boumediene D
- Bourdarios CA
- Boveia A
- Boyd J
- Boye D
- Boyko IR
- Bozson AJ
- Bracinik J
- Brahimi N
- Brandt G
- Brandt O
- Braren F
- Brau B
- Brau JE
- Brendlinger K
- Brener R
- Brenner L
- Brenner R
- Bressler S
- Bret MC
- Brickwedde B
- Briglin DL
- Britton D
- Britzger D
- Brock I
- Brock R
- Brooijmans G
- Brooks WK
- Brost E
- Brueers B
- Bruncko D
- Bruni A
- Bruni G
- Bruschi M
- Bruscino N
- Bryngemark L
- Buanes T
- Buat Q
- Buchholz P
- Buckley AG
- Budagov IA
- Buescher V
- Bugge MK
- Bulekov O
- Bullard BA
- Burch TJ
- Burdin S
- Burgard CD
- Burger AM
- Burghgrave B
- Burr JTP
- Burton CD
- Burzynski JC
- Buschmann E
- Bussey PJ
- Butler JM
- Buttar CM
- Butterworth JM
- Butti P
- Buttinger W
- Buzatu A
- Buzykaev AR
- Bylund OB
- Cabras G
- Caforio D
- Cai H
- Cairo VMM
- Cakir IT
- Cakir O
- Calace N
- Calafiura P
- Calderini G
- Calfayan P
- Callea G
- Caloba LP
- Caltabiano A
- Calvet D
- Calvet S
- Calvet TP
- Calvetti M
- Camarda S
- Camarri P
- Camelia EA
- Camerlingo MT
- Cameron D
- Camincher C
- Campana S
- Campanelli M
- Camplani A
- Canale V
- Canesse A
- Cantero J
- Cao T
- Cao Y
- Capriles FGD
- Capua M
- Cardarelli R
- Cardillo F
- Carducci G
- Carli I
- Carli T
- Carlino G
- Carlson BT
- Carlson EM
- Carminati L
- Carney RMD
- Caron S
- Carquin E
- Carra S
- Carratta G
- Carter JWS
- Carter TM
- Casado MP
- Casha AF
- Castiglia EG
- Castillo FL
- Castillo LRF
- Castro NF
- Catinaccio A
- Catmore JR
- Cattai A
- Cavaliere V
- Cavasinni V
- Celebi E
- Celli F
- Cerny K
- Cerqueira AS
- Cerri A
- Cerrito L
- Cerutti F
- Cervelli A
- Cetin SA
- Chadi Z
- Chakraborty D
- Chan J
- Chan WS
- Chan WY
- Chapman JD
- Chargeishvili B
- Charlton DG
- Charman TP
- Chatterjee M
- Chau CC
- Che S
- Chekanov S
- Chekulaev SV
- Chelkov GA
- Chen B
- Chen C
- Chen CH
- Chen H
- Chen H
- Chen J
- Chen J
- Chen J
- Chen S
- Chen SJ
- Chen X
- Chen Y
- Chen Y-H
- Cheng HC
- Cheng HJ
- Cheplakov A
- Cheremushkina E
- Cheu E
- Cheung K
- Chevalerias TJA
- Chevalier L
- Chiarella V
- Chiarelli G
- Chiodini G
- Chisholm AS
- Chitan A
- Chiu I
- Chiu YH
- Chizhov MV
- Choi K
- Chomont AR
- Chou Y
- Chow YS
- Christopher LD
- Chu MC
- Chu X
- Chudoba J
- Chwastowski JJ
- Chytka L
- Cieri D
- Ciesla KM
- Cindro V
- Cioara IA
- Ciocio A
- Cirotto F
- Citron ZH
- Citterio M
- Ciubotaru DA
- Ciungu BM
- Clark A
- Clark PJ
- Clawson SE
- Clement C
- Coadou Y
- Cobal M
- Coccaro A
- Cochran J
- Codina EP
- Cohen H
- Coimbra AEC
- Cole B
- Colijn AP
- Collot J
- Connell SH
- Connelly IA
- Constantinescu S
- Conventi F
- Cooper-Sarkar AM
- Cormier F
- Cormier KJR
- Cornell SD
- Corpe LD
- Corradi M
- Correia AMH
- Corrigan EE
- Corriveau F
- Costa MJ
- Costanza F
- Costanzo D
- Coutinho YA
- Cowan G
- Cowley JW
- Crane J
- Cranmer K
- Creager RA
- Crepe-Renaudin S
- Crescioli F
- Cristinziani M
- Croft V
- Crosetti G
- Cueto A
- Cui H
- Cukierman AR
- Cunningham WR
- Czekierda S
- Czodrowski P
- Czurylo MM
- D'amen G
- D'Amico V
- D'Auria S
- D'Eramo L
- D'onofrio A
- D'Onofrio M
- D'uffizi M
- Da Costa AMMJ
- da Costa JBG
- Da Fonseca Pinto JV
- Da Via C
- Dabrowski W
- Dachs F
- Dado T
- Dahbi S
- Dai T
- Dallapiccola C
- Dam M
- Damazio DO
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- Zhemchugov A
- Zheng Z
- Zhong D
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- Zimmermann S
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- Zivkovic L
- Zobernig G
- Zoccoli A
- Zoch K
- Zorbas TG
- Zou R
- Zwalinski L
- Publication venue
- 'Springer Fachmedien Wiesbaden GmbH'
- Publication date
- 01/01/2021
- Field of study
This article documents the muon reconstruction and identification efficiency obtained by the ATLAS experiment for 139 \hbox {fb}^{-1} of pp collision data at \sqrt{s}=13 TeV collected between 2015 and 2018 during Run 2 of the LHC. The increased instantaneous luminosity delivered by the LHC over this period required a reoptimisation of the criteria for the identification of prompt muons. Improved and newly developed algorithms were deployed to preserve high muon identification efficiency with a low misidentification rate and good momentum resolution. The availability of large samples of Z\rightarrow \mu \mu and J/\psi \rightarrow \mu \mu decays, and the minimisation of systematic uncertainties, allows the efficiencies of criteria for muon identification, primary vertex association, and isolation to be measured with an accuracy at the per-mille level in the bulk of the phase space, and up to the percent level in complex kinematic configurations. Excellent performance is achieved over a range of transverse momenta from 3 GeV to several hundred GeV, and across the full muon detector acceptance of |\eta |<2.7
The ATLAS inner detector trigger performance in pp collisions at 13 TeV during LHC Run 2
- Author
- Aad G
- Abbott B
- Abbott DC
- Abeling K
- Abhayasinghe DK
- Abidi SH
- AbouZeid OS
- Abraham NL
- Abramowicz H
- Abreu H
- Abud AA
- Abulaiti Y
- Acharya BS
- Achkar B
- Adam L
- Adamczyk L
- Adamek L
- Adelman J
- Adiguzel A
- Adorni S
- Adye T
- Aenis T
- Affolder AA
- Afik Y
- Agapopoulou C
- Agaras MN
- Aggarwal A
- Agheorghiesei C
- Aguilar-Saavedra JA
- Agullo PM
- Ahmad A
- Ahmadov F
- Ahmed WS
- Ahnen JV
- Ai X
- Aielli G
- Aivkovic L
- Akatsuka S
- Akbiyik M
- Akesson TPA
- Akilli E
- Akimov AV
- Alberghi GL
- Albert J
- Alderweireldt S
- Aleksa M
- Aleksandrov IN
- Alexa C
- Alexopoulos T
- Alfonsi A
- Alfonsi F
- Alhroob M
- Ali B
- Ali S
- Aliev M
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- Allaire C
- Allbrooke BMM
- Allport PP
- Aloisio A
- Alonso F
- Alpigiani C
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- Alviggi MG
- Ambler A
- Ambroz L
- Amelung C
- Amidei D
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- Asimakopoulou EM
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- Beisiegel F
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- Bellerive A
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- Beloborodov K
- Belotskiy K
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- Benchekroun D
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- Bloch I
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- Blue A
- Blumenschein U
- Blumenthal J
- Bobbink GJ
- Bobrovnikov VS
- Boeriu OEV
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- Bohm C
- Boisvert V
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- Bold T
- Bomben M
- Bona M
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- Boonekamp M
- Booth CD
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- Borecka-Bielska HM
- Borgna LS
- Borisov A
- Borissov G
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- Bosca SR
- Boscherini D
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- Briglin DL
- Britton D
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- Buanes T
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- Buckley AG
- Budagov IA
- Buddenbrock SEV
- Bugge MK
- Bulekov O
- Bullard BA
- Burch TJ
- Burdin S
- Burgard CD
- Burger AM
- Burghgrave B
- Burr JTP
- Burton CD
- Burzynski JC
- Buscher V
- Buschmann E
- Bussey PJ
- Butler JM
- Buttar CM
- Butterworth JM
- Buttinger W
- Buzykaev AR
- Bylund OB
- Cabras G
- Caforio D
- Cai H
- Cairo VMM
- Cakir IT
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- Calace N
- Calafiura P
- Calderini G
- Calfayan P
- Callea G
- Caloba LP
- Caltabiano A
- Calvet D
- Calvet S
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- Calvetti M
- Camarda S
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- Camerlingo MT
- Cameron D
- Camincher C
- Campanelli M
- Camplani A
- Canale V
- Canesse A
- Cantero J
- Cao Y
- Capriles FGD
- Capua M
- Cardarelli R
- Cardillo F
- Carducci G
- Carli T
- Carlino G
- Carlson BT
- Carlson EM
- Carminati L
- Carney RMD
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- Casha AF
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- Castillo FL
- Castillo LRF
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- Catinaccio A
- Catmore JR
- Cattai A
- Cavaliere V
- Cavasinni V
- Celebi E
- Celli F
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- Chen X
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- Cheng HC
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- Cheplakov A
- Cheremushkina E
- Cheu E
- Cheung K
- Chevalerias TJA
- Chevalier L
- Chiarella V
- Chiarelli G
- Chiodini G
- Chisholm AS
- Chitan A
- Chiu I
- Chiu YH
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- Choi K
- Chomont AR
- Chou Y
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- Christopher LD
- Chu MC
- Chu X
- Chudoba J
- Chwastowski JJ
- Ciaccio AD
- Ciaccio LD
- Cieri D
- Ciesla KM
- Cindro V
- Cioara IA
- Ciocio A
- Cirotto F
- Citron ZH
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- Ciubotaru DA
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- Cornell SD
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- D'Auria S
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- Da Costa AMMJ
- da Costa JBG
- Da Via C
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- Dachs F
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- Damazio DO
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- de Renstrom PAB
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- Dedovich DV
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- Dodsworth D
- Doglioni C
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- Dominguez LP
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- Donaldson CP
- Donato CD
- Donell DMM
- Dong B
- Donini J
- Donszelmann TC
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- Doria A
- Dova MT
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- Drechsler E
- Dreyer E
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- Du D
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- Dubreuil A
- Duchovni E
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- Ducu OA
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- Dudarev A
- Dudder AC
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- Dumitriu AE
- Dunford M
- Dungs S
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- Dutta B
- Duvnjak D
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- Dyndal M
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- Dziedzic BS
- Eggleston MG
- Eifert T
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- Enari Y
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- Ereditato A
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- Escobar C
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- Fabiani V
- Facini G
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- Fang Y
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- Farrington SM
- Farthouat P
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- Fawcett WJ
- Fayard L
- Fedin OL
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- Feligioni L
- Fell A
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- Fenyuk AB
- Ferguson SW
- Fernandez SG
- Ferrando J
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- Filthaut F
- Finelli KD
- Fiolhais MCN
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- Fischer F
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- Fitschen T
- Fleck I
- Fleischmann P
- Flick T
- Flierl BM
- Flores L
- Follega FM
- Fomin N
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- Forland BC
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- Fusayasu T
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- Garonne V
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- Gingrich DM
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- Girolamo AD
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- Giuli F
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- Gkialas I
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- Publication venue
- Publication date
- 01/01/2022
- Field of study
The design and performance of the inner detector trigger for the high level trigger of the ATLAS experiment at the Large Hadron Collider during the 2016-2018 data taking period is discussed. In 2016, 2017, and 2018 the ATLAS detector recorded 35.6 fb(-1), 46.9 fb(-1), and 60.6 fb(-1) respectively of proton-proton collision data at a centre-of-mass energy of 13TeV. In order to deal with the very high interaction multiplicities per bunch crossing expected with the 13TeV collisions the inner detector trigger was redesigned during the long shutdown of the Large Hadron Collider from 2013 until 2015. An overview of these developments is provided and the performance of the tracking in the trigger for the muon, electron, tau and b-jet signatures is discussed. The high performance of the inner detector trigger with these extreme interaction multiplicities demonstrates how the inner detector tracking continues to lie at the heart of the trigger performance and is essential in enabling the ATLAS physics programme
Observation of electroweak production of two jets in association with an isolated photon and missing transverse momentum, and search for a Higgs boson decaying into invisible particles at 13 TeV with the ATLAS detector
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- Zhemchugov A
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- Åkesson TPA
- Öncel ÖO
- Ženiš T
- Živković L
- Publication venue
- EUROPEAN PHYSICAL JOURNAL C
- Publication date
- 01/01/2022
- Field of study
This paper presents the measurement of the electroweak production of two jets
in association with a Zγ pair with the Z boson decaying into two
neutrinos. It also presents the search for invisible or partially invisible
decays of a Higgs boson with a mass of 125 GeV produced through vector-boson
fusion with a photon in the final state. These results use data from LHC
proton-proton collisions at s = 13 TeV collected with the ATLAS
detector corresponding to an integrated luminosity of 139 fb−1. The event
signature, shared by all benchmark processes considered for measurements and
searches, is characterized by a significant amount of unbalanced transverse
momentum and a photon in the final state, in addition to a pair of forward
jets. For electroweak production of Zγ in association with two jets, the
background-only hypothesis is rejected with an observed (expected) significance
of 5.2 (5.1) standard deviations. The measured fiducial cross-section for this
process is 1.31±0.29 fb. Observed (expected) upper limit of 0.37 (0.34) at
95% confidence level is set on the branching ratio of a 125 GeV Higgs boson to
invisible particles, assuming the Standard Model production cross-section. The
signature is also interpreted in the context of decays of a Higgs boson to a
photon and a dark photon. An observed (expected) 95% CL upper limit on the
branching ratio for this decay is set at 0.018 (0.017), assuming the 125 GeV
Standard Model Higgs boson production cross-section
Recommended from our members
What's in your next-generation sequence data? An exploration of unmapped DNA and RNA sequence reads from the bovine reference individual.
- Author
- Publication venue
- eScholarship, University of California
- Publication date
- 01/12/2015
- Field of study
BackgroundNext-generation sequencing projects commonly commence by aligning reads to a reference genome assembly. While improvements in alignment algorithms and computational hardware have greatly enhanced the efficiency and accuracy of alignments, a significant percentage of reads often remain unmapped.ResultsWe generated de novo assemblies of unmapped reads from the DNA and RNA sequencing of the Bos taurus reference individual and identified the closest matching sequence to each contig by alignment to the NCBI non-redundant nucleotide database using BLAST. As expected, many of these contigs represent vertebrate sequence that is absent, incomplete, or misassembled in the UMD3.1 reference assembly. However, numerous additional contigs represent invertebrate species. Most prominent were several species of Spirurid nematodes and a blood-borne parasite, Babesia bigemina. These species are either not present in the US or are not known to infect taurine cattle and the reference animal appears to have been host to unsequenced sister species.ConclusionsWe demonstrate the importance of exploring unmapped reads to ascertain sequences that are either absent or misassembled in the reference assembly and for detecting sequences indicative of parasitic or commensal organisms