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Clinical-pathological and molecular characterization of long-term survivors with advanced non-small cell lung cancer

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Cancer Biology & medicine 2020年第2期17卷 444-457页

作者： Juan moreno-Rubio Santiago Ponce Rosa Alvarez maria Eugenia Olmedo Sandra Falagan Xabier mielgo Fatima Navarro Patricia Cruz Luis Cabezon-Gutierrez Carlos Aguado Gonzalo Colmenarejo marta munoz-Fernandez de Leglaria Ana Belen Enguita maria Cebollero Amparo Benito Isabel Alemany Carolina del castillo Ricardo Ramos Ana Ramirez de molina Enrique Casado maria Sereno Ana Ramirez de molina1 Enrique Casado5Maria Sereno5 XIMDEA Food InstituteCEI UAM+CSICMadrid 28702Spain 12 de Octubre University Hospital Madrid 28041Spain Gregorio maranon University Hospital Madrid 28009Spain Ramon y Cajal University Hospital Madrid 28034Spain Infanta Sofia University Hospital San Sebastian De Los ReyesMadrid 28702Spain Fundacion Alcorcon University Hospital AlcorconMadrid 28922Spain Prlncipe de Asturias University Hospital Alcala De HenaresMadrid 28805Spain La paz University Hospital Madrid 28046Spain University Hospital of Torrejon Torrejon De ArdozMadrid 28850Spain Clinico San Carlos University Hospital Madrid 28040Spain Parque Cientifico de madrid Foundation Madrid 28049Spain

Objective:Long-term survivors(LS)of non-small cell lung cancer(NSCLC)without driver alterations,displaying an overall survival(OS)of more than 3 years,comprise around 10%of cases in several series treated with chemotherapy.There are classical prognosis factors for these cases[stage,Eastern Cooperative Oncology Group(ECOG),etc.],but more data are required in the literature.In this multi-center study,we focused on LS of advanced NSCLC with OS above 36 months to perform a clinical-pathological and molecular characterization.methods:In the first step,we conducted a clinical-pathological characterization of the patients.Afterwards,we carried out a genetic analysis by comparing LS to a sample of short-term survivors(SS)(with an OS less than 9 months).We initially used whole-genome RNA-seq to identify differentiating profiles of LS and SS,and later confirmed these with reverse transcription-polymerase chain reaction(RT-PCR)for the rest of the samples.Results:A total of 94 patients were included,who were mainly men,former smokers,having adenocarcinoma(AC)-type NSCLC with an ECOG of 0-1.We obtained an initial differential transcriptome expression,displaying 5 over-and 33 under-expressed genes involved in different pathways:namely,the secretin receptor,surfactant protein,trefoil factor 1(T FF1),serpin,Ca-channels,and Tolllike receptor(TLRs)families.Finally,RT-PCR analysis of 40(20 LS/20 SS)samples confirmed that four genes(surfactant proteins and SFTP)were significantly down-regulated in SS compared to LS by using an analysis of covariance(ANCOVA)model:SFTPA1(P=0.023),SFTPA2(P=0.027),SFTPB{P=0.02),and SFT PC(P=0.047).Conclusions:We present a sequential genetic analysis of a sample of NSCLCLS with no driver alterations,obtaining a differential RNA-seq/RT-PCR profile showing an abnormal expression of SF genes.

关键词： Long-term survivors non-small cell lung cancer surfactant proteins

Determination of the Taxonomic Diversity of the Intertidal Fish Communities on the Pacific Coast of Baja California Sur, méxico from 2015-2019

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Open Journal of marine Science 2022年第2期12卷 44-60页

作者： Jesús Eduardo Contreras Romero Emelio Barjau González Juan manuel López-Viva José Ángel Armenta Quintana Javier Aguilar Parra Elvia Esthela Aispuro Felix Bruma Rachel castillo-Rosas Departamento Académico de Ciencias marinas y Costeras Universidad Autónoma de Baja California Sur La Paz B.C.S. Departamento Académico de Ciencia Animal y Conservación del Hábitat Universidad Autónoma de Baja California Sur La Paz B.C.S. Departamento Académico de Sistemas Computacionales Universidad Autónoma de Baja California Sur La Paz B.C.S.

The coastal areas of the Baja California peninsula are characterized mainly by rocky areas, where rock pools dominate as important coastal habitats because of the tide cycle, when the water is trapped during the low tide, forming the pools. Environmental parameters like temperature, salinity and dissolved oxygen of the water trapped in the pools are key factors for the flora and fauna that inhabit these areas, particularly during the warmer months when the mean values of these parameters are usually higher than the mean values of the sea surface. The aim of the present study was to determine the variation of the taxonomic diversity of the fish communities that inhabit the rock pools in the common land known as Conquista Agraria in the Pacific coast of Baja California Sur, méxico, from 2015 to 2019. A total of 59 visual censuses were carried out monthly during the second low tide of the full moon. Temperature, salinity, and dissolved oxygen showed variation throughout the study period, with two distinct seasons (warm and cold), which influenced the taxonomic diversity and taxonomic distinctness of the species recorded in the area. There was a higher diversity in the warmer months (summer) and years (2015 and 2016). In addition, according to the mDS analysis, 2017 and 2018 showed high similarity of species.

关键词： Rock Pools Intertidal Zone Taxonomic Diversity Taxonomic Distinctness

Structure of the Community of Dominant Fish Species Associated to Soft-Bottoms in the Lagoon of La paz, B.C.S., méxico

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Open Journal of marine Science 2020年第3期10卷 79-92页

作者： Bruma R. castillo-Rosas Emelio Barjau-González Juan manuel López-Vivas Abril Karim Romo-Piñeda Eleonora Romero-Vadillo Jose Ángel Armenta-Quintana Departamento Académico de Ciencias marinas y Costeras Universidad Autónoma de Baja California Sur La Paz México Departamento Académico de Ciencia Animal y Conservación del Hábitat Universidad Autónoma de Baja California Sur La Paz México

The study of fish communities from coastal lagoons allows a better understanding of role of these organisms in these systems, and the effect of anthropogenic impact. The aim of the present study was to determine the community structure, in particular dominance of fish species associated to soft bottoms in the lagoon of La paz. Six bimonthly samplings were carried out in seven localities from November 2016 to September 2017 and physicochemical parameters were recorded. Analysis of temperature showed differences between two marked seasons, warm and cold. Species richness showed differences between months and localities. Shannon-Weaver index and Pielou’s evenness showed significant differences only between months. Simpson’s index suggests a high diversity. According to the BVI, 15 species from the families Haemulidae, Sciaenidae and Gerreidae, were the most biologically important. Zoogeographic affinity analysis showed that 58% of the species prefer the Province of Cortez. Dominant species recorded in this study play a key role in soft-bottom systems like the lagoon of La paz.

关键词： Coastal Lagoon Lagoon of La paz Diversity Dominance

Variation of Density and Biomass of the Ichthyofauna Associated to Soft Bottoms of a Western Coastal Lagoon of B.C.S., mexico

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Open Journal of marine Science 2021年第4期11卷 169-186页

作者： Bruma Rachel castillo Rosas Emelio Barjau González Juan manuel López Vivas José Ángel Armenta Quintana Javier Aguilar Parra Rodolfo Daniel Acosta Guerrero Rogelio Esquivel Tiscareño Departamento Académico de Ciencias marinas y Costeras Universidad Autónoma de Baja California Sur La Paz B.C.S. Departamento Académico de Ciencia Animal y Conservación del Hábitat Universidad Autónoma de Baja California Sur La Paz B.C.S. Departamento Académico de Sistemas Computacionales Universidad Autónoma de Baja California Sur La Paz B.C.S.

An analysis of the variation of the density and biomass of the fish communities of the lagoon of La paz, mexico was carried out from November 2016 to September 2017. A total of 2763 organisms were collected with a total biomass of 211,422.93 g in an area of 5022 m2, a density and biomass of 0.550 lnd/m2 and 44.091 g/m2. The site with the largest biomass was recorded in Zacatecas (11.179 g/m2) located north of the lagoon, while Grand Plaza recorded the lowest biomass (2.732 g/m2). Regarding the density, the maximum value was recorded in the site Yate Hundido, located northwest of the lagoon (0.129 lnd/m2) and the lowest was Las Palmas (0.036 lnd/m2) located north of the lagoon. The most abundant species was Diapterus peruvianus with 683 individuals and a biomass of 37,507.57 g. The physicochemical variables showed two seasons with significant change where we can observe higher temperatures in the summer (average of 27.45°C) and minimum in winter (average of 22.49°C). The Shannon-Weaver diversity index showed a difference (p = 0.050) between months, with the highest value recorded in April (H' = 2.133 bits/ind) and the lowest in June (H'mal;">mily:;" "=""> = 1.041 bits/ind). The biomass and density values recorded in the lagoon were found to be associated with the spatio-temporal variation of temperature of the lagoon, as well as the resident and transitory species located in the area of study. In addition, the body sizes recorded corresponded to juveni

关键词： Lagoon of La paz Diversity Abundance Dominance

Performance and calibration of quark/gluon-jet taggers using 140 fb^(-1) of pp collisions at √s=13 TeV with the ATLAS detector

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Chinese Physics C 2024年第2期48卷 1-25页

作者： G. Aad B. Abbott K. Abeling N.J. Abicht S.H. Abidi A. Aboulhorma H. Abramowicz H. Abreu Y. Abulaiti B.S. Acharya C. Adam Bourdarios L. Adamczyk S.V. Addepalli m.J. Addison J. Adelman A. Adiguzel T. Adye A.A. Affolder Y. Afik m.N. Agaras J. Agarwala A. Aggarwal C. Agheorghiesei A. Ahmad F. Ahmadov W.S. Ahmed S. Ahuja X. Ai G. Aielli A. Aikot m. Ait Tamlihat B. Aitbenchikh I. Aizenberg m. Akbiyik T.P.A. Åkesson A.V. Akimov D. Akiyama N.N. Akolkar K. Al Khoury G.L. Alberghi J. Albert P. Albicocco G.L. Albouy S. Alderweireldt m. Aleksa I.N. Aleksandrov C. Alexa T. Alexopoulos F. Alfonsi m. Algren m. Alhroob B. Ali H.m.J. Ali S. Ali S.W. Alibocus m. Aliev G. Alimonti W. Alkakhi C. Allaire B.m.m. Allbrooke J.F. Allen C.A. Allendes Flores P.P. Allport A. Aloisio F. Alonso C. Alpigiani m. Alvarez Estevez A. Alvarez Fernandez m. Alves Cardoso m.G. Alviggi m. Aly Y. Amaral Coutinho A. Ambler C. Amelung m. Amerl C.G. Ames D. Amidei S.P. Amor Dos Santos K.R. Amos V. Ananiev C. Anastopoulos T. Andeen J.K. Anders S.Y. Andrean A. Andreazza S. angelidakis A. angerami A.V. Anisenkov A. Annovi C. Antel m.T. Anthony E. Antipov m. Antonelli F. Anulli m. Aoki T. Aoki J.A. Aparisi Pozo m.A. Aparo L. Aperio Bella C. Appelt A. Apyan N. Aranzabal S.J. Arbiol Val C. Arcangeletti A.T.H. Arce E. Arena J-F. Arguin S. Argyropoulos J.-H. Arling O. Arnaez H. Arnold G. Artoni H. Asada K. Asai S. Asai N.A. Asbah J. Assahsah K. Assamagan R. Astalos S. Atashi R.J. Atkin m. Atkinson H. Atmani P.A. Atmasiddha K. Augsten S. Auricchio A.D. Auriol V.A. Austrup G. Avolio K. Axiotis G. Azuelos D. Babal H. Bachacou K. Bachas A. Bachiu F. Backman A. Badea P. Bagnaia m. Bahmani A.J. Bailey V.R. Bailey J.T. Baines L. Baines O.K. Baker E. Bakos D. Bakshi Gupta V. Balakrishnan R. Balasubramanian E.m. Baldin P. Balek E. Ballabene F. Balli L.m. Baltes W.K. Balunas J. Balz E. Banas m. Bandieramonte A. Bandyopadhyay S. Bansal L. Barak m. Barakat E.L. Barberio D. Barberis m. Barbero m.Z. Barel K.N. Barends T. Barillari m-S. Barisits T. Barklow P. Baron D.A. Baron mo The ATLAS Collaboration

The identification of jets originating from quarks and gluons,often referred to as quark/gluon tagging,plays an important role in various analyses performed at the Large Hadron Collider,as Standard model measurements and searches for new particles decaying to quarks often rely on suppressing a large gluon-induced background.This paper describes the measurement of the efficiencies of quark/gluon taggers developed within the ATLAS Collaboration,using √s=13 TeV proton–proton collision data with an integrated luminosity of 140 fb^(-1) collected by the ATLAS experiment.Two taggers with high performances in rejecting jets from gluon over jets from quarks are studied:one tagger is based on requirements on the number of inner-detector tracks associated with the jet,and the other combines several jet substructure observables using a boosted decision tree.A method is established to determine the quark/gluon fraction in data,by using quark/gluon-enriched subsamples defined by the jet pseudorapidity.Differences in tagging efficiency between data and simulation are provided for jets with transverse momentum between 500 GeV and 2 TeV and for multiple tagger working points.

关键词： ATLAS JET QUARK GLUON TAGGING