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243 results on '"Carrato P"'

1. The best linear unbiased prediction (BLUP) method as a tool to estimate the lifetime risk of pancreatic ductal adenocarcinoma in high-risk individuals with no known pathogenic germline variants

Author

Cristina-Marianini-Rios, Sanchez, María E. Castillo, de Paredes, Ana García García, Rodríguez, Mercedes, Barreto, Emma, López, Jorge Villalón, Fuentes, Raquel, Beltrán, María Muñoz, Sanjuanbenito, Alfonso, Lobo, Eduardo, Caminoa, Alejandra, Ruz-Caracuel, Ignacio, Durán, Sergio López, Olcina, José Ramón Foruny, Blázquez, Javier, Sequeros, Enrique Vázquez, Carrato, Alfredo, Ávila, Jose Carlos Martínez, and Earl, Julie

Published
2024
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2. The Spanish Familial Pancreatic Cancer Registry (PANGENFAM): a decade follow-up of individuals at high-risk for pancreatic cancer

Author

Earl, Julie, Fuentes, Raquel, Sanchez, María E. Castillo, de Paredes, Ana García García, Muñoz, María, Sanjuanbenito, Alfonso, Lobo, Eduardo, Caminoa, Alejandra, Rodríguez, Mercedes, Barreto, Emma, López, Jorge Villalón, Ruz-Caracuel, Ignacio, Durán, Sergio López, Olcina, José Ramón Foruny, Sánchez, Bárbara Luna, Páez, Sonia Camaño, Torres, Ana, Blázquez, Javier, Sequeros, Enrique Vázquez, and Carrato, Alfredo

Published
2024
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3. Phase Ib study of talimogene laherparepvec in combination with atezolizumab in patients with triple negative breast cancer and colorectal cancer with liver metastases

Author

Hecht, JR, Raman, SS, Chan, A, Kalinsky, K, Baurain, J-F, Jimenez, MM, Garcia, MM, Berger, MD, Lauer, UM, Khattak, A, Carrato, A, Zhang, Y, Liu, K, Cha, E, Keegan, A, Bhatta, S, Strassburg, CP, and Roohullah, A

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Oncology and Carcinogenesis, Immunology, Liver Disease, Colo-Rectal Cancer, Patient Safety, Digestive Diseases, Breast Cancer, Clinical Research, Cancer, Clinical Trials and Supportive Activities, Good Health and Well Being, Adult, Humans, Melanoma, Triple Negative Breast Neoplasms, Cohort Studies, Oncolytic Virotherapy, Liver Neoplasms, Colorectal Neoplasms, breast neoplasms, drug therapy combination, gastrointestinal neoplasms, virotherapy, viral immunotherapy, Oncology and carcinogenesis
Abstract

BackgroundTalimogene laherparepvec (T-VEC), a first-in-class oncolytic viral immunotherapy, enhances tumor-specific immune activation. T-VEC combined with atezolizumab, which blocks inhibitor T-cell checkpoints, could provide greater benefit than either agent alone. Safety/efficacy of the combination was explored in patients with triple negative breast cancer (TNBC) or colorectal cancer (CRC) with liver metastases.MethodsIn this phase Ib, multicenter, open-label, parallel cohort study of adults with TNBC or CRC with liver metastases, T-VEC (106 then 108 PFU/ml; ≤4 ml) was administered into hepatic lesions via image-guided injection every 21 (±3) days. Atezolizumab 1200 mg was given on day 1 and every 21 (±3) days thereafter. Treatment continued until patients experienced dose-limiting toxicity (DLT), had complete response, progressive disease, needed alternative anticancer treatment, or withdrew due to an adverse event (AE). The primary endpoint was DLT incidence, and secondary endpoints included efficacy and AEs.ResultsBetween 19 March 2018 and 6 November 2020, 11 patients with TNBC were enrolled (safety analysis set: n = 10); between 19 March 2018 and 16 October 2019, 25 patients with CRC were enrolled (safety analysis set: n = 24). For the 5 patients in the TNBC DLT analysis set, no patient had DLT; for the 18 patients in the CRC DLT analysis set, 3 (17%) had DLT, all serious AEs. AEs were reported by 9 (90%) TNBC and 23 (96%) CRC patients, the majority with grade ≥3 [TNBC, 7 (70%); CRC, 13 (54%)], and 1 was fatal [CRC, 1 (4%)]. Evidence of efficacy was limited. Overall response rate was 10% (95% confidence interval 0.3-44.5) for TNBC; one (10%) patient had a partial response. For CRC, no patients had a response; 14 (58%) were unassessable.ConclusionsThe safety profile reflected known risks with T-VEC including risks of intrahepatic injection; no unexpected safety findings from addition of atezolizumab to T-VEC were observed. Limited evidence of antitumor activity was observed.

Published
2023

5. A modular software framework for the design and implementation of ptychography algorithms

Author

Guzzi, Francesco, Kourousias, George, Billè, Fulvio, Pugliese, Roberto, Gianoncelli, Alessandra, and Carrato, Sergio

Subjects
Computer Science - Computer Vision and Pattern Recognition, Physics - Applied Physics, Physics - Computational Physics, Physics - Data Analysis, Statistics and Probability
Abstract

Computational methods are driving high impact microscopy techniques such as ptychography. However, the design and implementation of new algorithms is often a laborious process, as many parts of the code are written in close-to-the-hardware programming constructs to speed up the reconstruction. In this paper, we present SciComPty, a new ptychography software framework aiming at simulating ptychography datasets and testing state-of-the-art and new reconstruction algorithms. Despite its simplicity, the software leverages GPU accelerated processing through the PyTorch CUDA interface. This is essential to design new methods that can readily be employed. As an example, we present an improved position refinement method based on Adam and a new version of the rPIE algorithm, adapted for partial coherence setups. Results are shown on both synthetic and real datasets. The software is released as open-source.

Published
2022
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6. A parameter refinement method for Ptychography based on Deep Learning concepts

Author

Guzzi, Francesco, Kourousias, George, Billè, Fulvio, Pugliese, Roberto, Gianoncelli, Alessandra, and Carrato, Sergio

Subjects
Electrical Engineering and Systems Science - Image and Video Processing, Computer Science - Computer Vision and Pattern Recognition, Mathematics - Numerical Analysis, 68U10, 94A08, 92C55
Abstract

X-ray Ptychography is an advanced computational microscopy technique which is delivering exceptionally detailed quantitative imaging of biological and nanotechnology specimens. However coarse parametrisation in propagation distance, position errors and partial coherence frequently menaces the experiment viability. In this work we formally introduced these actors, solving the whole reconstruction as an optimisation problem. A modern Deep Learning framework is used to correct autonomously the setup incoherences, thus improving the quality of a ptychography reconstruction. Automatic procedures are indeed crucial to reduce the time for a reliable analysis, which has a significant impact on all the fields that use this kind of microscopy. We implemented our algorithm in our software framework, SciComPty, releasing it as open-source. We tested our system on both synthetic datasets and also on real data acquired at the TwinMic beamline of the Elettra synchrotron facility.

Published
2021
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7. Visible pump -- mid infrared pump -- broadband probe: development and characterization of a three-pulse setup for single-shot ultrafast spectroscopy at 50 kHz

Author

Montanaro, Angela, Giusti, Francesca, Colja, Matija, Brajnik, Gabriele, Marciniak, Alexandre M. A., Sergo, Rudi, De Angelis, Dario, Glerean, Filippo, Sparapassi, Giorgia, Jarc, Giacomo, Carrato, Sergio, Cautero, Giuseppe, and Fausti, Daniele

Subjects
Physics - Optics, Condensed Matter - Superconductivity, Physics - Chemical Physics, Physics - Instrumentation and Detectors
Abstract

We report here an experimental setup to perform three-pulse pump-probe measurements over a wide wavelength and temperature range. By combining two pump pulses in the visible (650-900 nm) and mid-IR (5-20 $\mu$m) range, with a broadband supercontinuum white-light probe, our apparatus enables both the combined selective excitation of different material degrees of freedom and a full time-dependent reconstruction of the non-equilibrium dielectric function of the sample. We describe here the optical setup, the cryogenic sample environment and the custom-made acquisition electronics capable of referenced single-pulse detection of broadband spectra at the maximum repetition rate of 50 kHz, achieving a sensitivity of the order of 10$^{-4}$ over an integration time of 1 s. We demonstrate the performance of the setup by reporting data on mid-IR pump, optical push and broadband probe in a single-crystal of Bi$_2$Sr$_2$Y$_{0.08}$Ca$_{0.92}$Cu$_2$O$_{8+\delta}$ across the superconducting and pseudogap phases., Comment: 12 pages, 7 figures

Published
2020
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10. In silico validation of RNA-Seq results can identify gene fusions with oncogenic potential in glioblastoma

Author

Hernandez, Ainhoa, Muñoz-Mármol, Ana Maria, Esteve-Codina, Anna, Alameda, Francesc, Carrato, Cristina, Pineda, Estela, Arpí-Lluciá, Oriol, Martinez-García, Maria, Mallo, Mar, Gut, Marta, del Barco, Sonia, Gallego, Oscar, Dabad, Marc, Mesia, Carlos, Bellosillo, Beatriz, Domenech, Marta, Vidal, Noemí, Aldecoa, Iban, de la Iglesia, Nuria, and Balana, Carmen

Published
2022
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11. Data mining analyses for precision medicine in acromegaly: a proof of concept

Author

Gil, Joan, Marques-Pamies, Montserrat, Sampedro, Miguel, Webb, Susan M., Serra, Guillermo, Salinas, Isabel, Blanco, Alberto, Valassi, Elena, Carrato, Cristina, Picó, Antonio, García-Martínez, Araceli, Martel-Duguech, Luciana, Sardon, Teresa, Simó-Servat, Andreu, Biagetti, Betina, Villabona, Carles, Cámara, Rosa, Fajardo-Montañana, Carmen, Álvarez-Escolá, Cristina, Lamas, Cristina, Alvarez, Clara V., Bernabéu, Ignacio, Marazuela, Mónica, Jordà, Mireia, and Puig-Domingo, Manel

Published
2022
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13. Personalized Medicine in Acromegaly: The ACROFAST Study

Author

Marques-Pamies, Montserrat, Gil, Joan, Sampedro-Nuñez, Miguel, Valassi, Elena, Biagetti, Betina, Giménez-Palop, Olga, Hernández, Marta, Martínez, Silvia, Carrato, Cristina, Villar-Taibo, Rocío, Araujo-Castro, Marta, Blanco, Concepción, Simón-Muela, Inmaculada, Simó-Servat, Andreu, Xifra, Gemma, Vázquez, Federico, Pavón, Isabel, Rosado, José Antonio, García-Centeno, Rogelio, Zavala, Roxana, Hanzu, Felicia Alexandra, Mora, Mireia, Aulinas, Anna, Vilarrasa, Nuria, Librizzi, Soledad, Calatayud, María, de Miguel, Paz, Alvarez-Escola, Cristina, Picó, Antonio, Salinas, Isabel, Fajardo-Montañana, Carmen, Cámara, Rosa, Bernabéu, Ignacio, Jordà, Mireia, Webb, Susan M, Marazuela, Mónica, and Puig-Domingo, Manel

Published
2025
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14. Gamma/Neutron Online Discrimination Based on Machine Learning With CLYC Detectors

Author

Morales, Ivan Rene, Soledad Molina, Romina, Bogovac, Mladen, Jovalekic, Nikola, Liz Crespo, Maria, Kanaki, Kalliopi, Ramponi, Giovanni, and Carrato, Sergio

Abstract

An embedded system (ES) for gamma and neutron discrimination in mixed radiation environments is proposed, validated with an off-the-shelf detector consisting of a Cs2LiYCl6:Ce (CLYC) crystal coupled to a silicon photomultiplier (SiPM) cell array. This solution employs a machine learning classification model based on a multilayer perceptron (MLP) running on a commercial field-programmable gate array (FPGA), providing online single-event identification with 98.2% overall accuracy at rates higher than 200 kilocounts/s. Thermal neutrons and fast neutrons up to 5 MeV can be detected and discriminated from gamma events, even under pile-up scenarios with a dead-time lower than $2.5~\mu $ s. The system exhibits excellent size, weight, and power consumption (SWaP) characteristics, packed in a volume smaller than 0.6 l and weighing less than 0.5 kg, while ensuring continuous operation with only 1.5 W. These features render our proposal suitable for embedded applications where low SWaP is critical and radiation levels manifest large count rates variability, such as space exploration, portable dosimeters, radiation surveillance on uncrewed aerial vehicles (UAVs), and soil moisture monitoring.

Published
2024
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15. Development and tests of a new prototype detector for the XAFS beamline at Elettra Synchrotron in Trieste

Author

Fabiani, S, Ahangarianabhari, M, Baldazzi, G, Bellutti, P, Bertuccio, G, Bruschi, M, Bufon, J, Carrato, S, Castoldi, A, Cautero, G, Ciano, S, Cicuttin, A, Crespo, M L, Santos, M Dos, Gandola, M, Giacomini, G, Giuressi, D, Guazzoni, C, Menk, R H, Niemela, J, Olivi, L, Picciotto, A, Piemonte, C, Rashevskaya, I, Rachevski, A, Rignanese, L P, Sbrizzi, A, Schillani, S, Vacchi, A, Garcia, V Villaverde, Zampa, G, Zampa, N, and Zorzi, N

Subjects
Physics - Instrumentation and Detectors
Abstract

The XAFS beamline at Elettra Synchrotron in Trieste combines X-ray absorption spectroscopy and X-ray diffraction to provide chemically specific structural information of materials. It operates in the energy range 2.4-27 keV by using a silicon double reflection Bragg monochromator. The fluorescence measurement is performed in place of the absorption spectroscopy when the sample transparency is too low for transmission measurements or the element to study is too diluted in the sample. We report on the development and on the preliminary tests of a new prototype detector based on Silicon Drift Detectors technology and the SIRIO ultra low noise front-end ASIC. The new system will be able to reduce drastically the time needed to perform fluorescence measurements, while keeping a short dead time and maintaining an adequate energy resolution to perform spectroscopy. The custom-made silicon sensor and the electronics are designed specifically for the beamline requirements., Comment: Proceeding of the 6YRM 12th-14th Oct 2015 - L'Aquila (Italy). Accepted for publication on Journal of Physics: Conference Series

Published
2016
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20. Analysis of Heritability and Shared Heritability Based on Genome-Wide Association Studies for 13 Cancer Types

Author

Sampson, Joshua N, Wheeler, William A, Yeager, Meredith, Panagiotou, Orestis, Wang, Zhaoming, Berndt, Sonja I, Lan, Qing, Abnet, Christian C, Amundadottir, Laufey T, Figueroa, Jonine D, Landi, Maria Teresa, Mirabello, Lisa, Savage, Sharon A, Taylor, Philip R, De Vivo, Immaculata, McGlynn, Katherine A, Purdue, Mark P, Rajaraman, Preetha, Adami, Hans-Olov, Ahlbom, Anders, Albanes, Demetrius, Amary, Maria Fernanda, An, She-Juan, Andersson, Ulrika, Andriole, Gerald, Andrulis, Irene L, Angelucci, Emanuele, Ansell, Stephen M, Arici, Cecilia, Armstrong, Bruce K, Arslan, Alan A, Austin, Melissa A, Baris, Dalsu, Barkauskas, Donald A, Bassig, Bryan A, Becker, Nikolaus, Benavente, Yolanda, Benhamou, Simone, Berg, Christine, Van Den Berg, David, Bernstein, Leslie, Bertrand, Kimberly A, Birmann, Brenda M, Black, Amanda, Boeing, Heiner, Boffetta, Paolo, Boutron-Ruault, Marie-Christine, Bracci, Paige M, Brinton, Louise, Brooks-Wilson, Angela R, Bueno-de-Mesquita, H Bas, Burdett, Laurie, Buring, Julie, Butler, Mary Ann, Cai, Qiuyin, Cancel-Tassin, Geraldine, Canzian, Federico, Carrato, Alfredo, Carreon, Tania, Carta, Angela, Chan, John KC, Chang, Ellen T, Chang, Gee-Chen, Chang, I-Shou, Chang, Jiang, Chang-Claude, Jenny, Chen, Chien-Jen, Chen, Chih-Yi, Chen, Chu, Chen, Chung-Hsing, Chen, Constance, Chen, Hongyan, Chen, Kexin, Chen, Kuan-Yu, Chen, Kun-Chieh, Chen, Ying, Chen, Ying-Hsiang, Chen, Yi-Song, Chen, Yuh-Min, Chien, Li-Hsin, Chirlaque, María-Dolores, Choi, Jin Eun, Choi, Yi Young, Chow, Wong-Ho, Chung, Charles C, Clavel, Jacqueline, Clavel-Chapelon, Françoise, Cocco, Pierluigi, Colt, Joanne S, Comperat, Eva, Conde, Lucia, Connors, Joseph M, Conti, David, Cortessis, Victoria K, Cotterchio, Michelle, Cozen, Wendy, Crouch, Simon, Crous-Bou, Marta, Cussenot, Olivier, and Davis, Faith G

Subjects
Tobacco, Clinical Research, Urologic Diseases, Lung, Genetics, Rare Diseases, Lung Cancer, Human Genome, Hematology, Cancer, Tobacco Smoke and Health, Prevention, Lymphoma, Adult, Aged, Asian People, Bone Neoplasms, Female, Genetic Predisposition to Disease, Genome-Wide Association Study, Humans, Kidney Neoplasms, Leukemia, Lymphocytic, Chronic, B-Cell, Lung Neoplasms, Lymphoma, Large B-Cell, Diffuse, Male, Middle Aged, Neoplasms, Osteosarcoma, Polymorphism, Single Nucleotide, Smoking, Testicular Neoplasms, Tissue Array Analysis, Urinary Bladder Neoplasms, White People, Oncology and Carcinogenesis, Oncology & Carcinogenesis
Abstract

BackgroundStudies of related individuals have consistently demonstrated notable familial aggregation of cancer. We aim to estimate the heritability and genetic correlation attributable to the additive effects of common single-nucleotide polymorphisms (SNPs) for cancer at 13 anatomical sites.MethodsBetween 2007 and 2014, the US National Cancer Institute has generated data from genome-wide association studies (GWAS) for 49 492 cancer case patients and 34 131 control patients. We apply novel mixed model methodology (GCTA) to this GWAS data to estimate the heritability of individual cancers, as well as the proportion of heritability attributable to cigarette smoking in smoking-related cancers, and the genetic correlation between pairs of cancers.ResultsGWAS heritability was statistically significant at nearly all sites, with the estimates of array-based heritability, hl (2), on the liability threshold (LT) scale ranging from 0.05 to 0.38. Estimating the combined heritability of multiple smoking characteristics, we calculate that at least 24% (95% confidence interval [CI] = 14% to 37%) and 7% (95% CI = 4% to 11%) of the heritability for lung and bladder cancer, respectively, can be attributed to genetic determinants of smoking. Most pairs of cancers studied did not show evidence of strong genetic correlation. We found only four pairs of cancers with marginally statistically significant correlations, specifically kidney and testes (ρ = 0.73, SE = 0.28), diffuse large B-cell lymphoma (DLBCL) and pediatric osteosarcoma (ρ = 0.53, SE = 0.21), DLBCL and chronic lymphocytic leukemia (CLL) (ρ = 0.51, SE =0.18), and bladder and lung (ρ = 0.35, SE = 0.14). Correlation analysis also indicates that the genetic architecture of lung cancer differs between a smoking population of European ancestry and a nonsmoking Asian population, allowing for the possibility that the genetic etiology for the same disease can vary by population and environmental exposures.ConclusionOur results provide important insights into the genetic architecture of cancers and suggest new avenues for investigation.

Published
2015

21. Analysis of Heritability and Shared Heritability Based on Genome-Wide Association Studies for Thirteen Cancer Types.

Author

Sampson, Joshua N, Wheeler, William A, Yeager, Meredith, Panagiotou, Orestis, Wang, Zhaoming, Berndt, Sonja I, Lan, Qing, Abnet, Christian C, Amundadottir, Laufey T, Figueroa, Jonine D, Landi, Maria Teresa, Mirabello, Lisa, Savage, Sharon A, Taylor, Philip R, De Vivo, Immaculata, McGlynn, Katherine A, Purdue, Mark P, Rajaraman, Preetha, Adami, Hans-Olov, Ahlbom, Anders, Albanes, Demetrius, Amary, Maria Fernanda, An, She-Juan, Andersson, Ulrika, Andriole, Gerald, Andrulis, Irene L, Angelucci, Emanuele, Ansell, Stephen M, Arici, Cecilia, Armstrong, Bruce K, Arslan, Alan A, Austin, Melissa A, Baris, Dalsu, Barkauskas, Donald A, Bassig, Bryan A, Becker, Nikolaus, Benavente, Yolanda, Benhamou, Simone, Berg, Christine, Van Den Berg, David, Bernstein, Leslie, Bertrand, Kimberly A, Birmann, Brenda M, Black, Amanda, Boeing, Heiner, Boffetta, Paolo, Boutron-Ruault, Marie-Christine, Bracci, Paige M, Brinton, Louise, Brooks-Wilson, Angela R, Bueno-de-Mesquita, H Bas, Burdett, Laurie, Buring, Julie, Butler, Mary Ann, Cai, Qiuyin, Cancel-Tassin, Geraldine, Canzian, Federico, Carrato, Alfredo, Carreon, Tania, Carta, Angela, Chan, John KC, Chang, Ellen T, Chang, Gee-Chen, Chang, I-Shou, Chang, Jiang, Chang-Claude, Jenny, Chen, Chien-Jen, Chen, Chih-Yi, Chen, Chu, Chen, Chung-Hsing, Chen, Constance, Chen, Hongyan, Chen, Kexin, Chen, Kuan-Yu, Chen, Kun-Chieh, Chen, Ying, Chen, Ying-Hsiang, Chen, Yi-Song, Chen, Yuh-Min, Chien, Li-Hsin, Chirlaque, María-Dolores, Choi, Jin Eun, Choi, Yi Young, Chow, Wong-Ho, Chung, Charles C, Clavel, Jacqueline, Clavel-Chapelon, Françoise, Cocco, Pierluigi, Colt, Joanne S, Comperat, Eva, Conde, Lucia, Connors, Joseph M, Conti, David, Cortessis, Victoria K, Cotterchio, Michelle, Cozen, Wendy, Crouch, Simon, Crous-Bou, Marta, Cussenot, Olivier, and Davis, Faith G

Subjects
Humans, Neoplasms, Osteosarcoma, Bone Neoplasms, Testicular Neoplasms, Lung Neoplasms, Kidney Neoplasms, Genetic Predisposition to Disease, Tissue Array Analysis, Smoking, Polymorphism, Single Nucleotide, Adult, Aged, Middle Aged, Asian Continental Ancestry Group, European Continental Ancestry Group, Female, Male, Urinary Bladder Neoplasms, Leukemia, Lymphocytic, Chronic, B-Cell, Lymphoma, Large B-Cell, Diffuse, Genome-Wide Association Study, Polymorphism, Single Nucleotide, Leukemia, Lymphocytic, Chronic, B-Cell, Lymphoma, Large B-Cell, Diffuse, Oncology And Carcinogenesis, Oncology & Carcinogenesis, Oncology and Carcinogenesis
Abstract

BackgroundStudies of related individuals have consistently demonstrated notable familial aggregation of cancer. We aim to estimate the heritability and genetic correlation attributable to the additive effects of common single-nucleotide polymorphisms (SNPs) for cancer at 13 anatomical sites.MethodsBetween 2007 and 2014, the US National Cancer Institute has generated data from genome-wide association studies (GWAS) for 49 492 cancer case patients and 34 131 control patients. We apply novel mixed model methodology (GCTA) to this GWAS data to estimate the heritability of individual cancers, as well as the proportion of heritability attributable to cigarette smoking in smoking-related cancers, and the genetic correlation between pairs of cancers.ResultsGWAS heritability was statistically significant at nearly all sites, with the estimates of array-based heritability, hl (2), on the liability threshold (LT) scale ranging from 0.05 to 0.38. Estimating the combined heritability of multiple smoking characteristics, we calculate that at least 24% (95% confidence interval [CI] = 14% to 37%) and 7% (95% CI = 4% to 11%) of the heritability for lung and bladder cancer, respectively, can be attributed to genetic determinants of smoking. Most pairs of cancers studied did not show evidence of strong genetic correlation. We found only four pairs of cancers with marginally statistically significant correlations, specifically kidney and testes (ρ = 0.73, SE = 0.28), diffuse large B-cell lymphoma (DLBCL) and pediatric osteosarcoma (ρ = 0.53, SE = 0.21), DLBCL and chronic lymphocytic leukemia (CLL) (ρ = 0.51, SE =0.18), and bladder and lung (ρ = 0.35, SE = 0.14). Correlation analysis also indicates that the genetic architecture of lung cancer differs between a smoking population of European ancestry and a nonsmoking Asian population, allowing for the possibility that the genetic etiology for the same disease can vary by population and environmental exposures.ConclusionOur results provide important insights into the genetic architecture of cancers and suggest new avenues for investigation.

Published
2015

23. A high dynamic Micro Strips Ionization Chamber featuring Embedded Multi DSP Processing

Author

Voltolina, Francesco, Menk, Ralf H., and Carrato, Sergio

Subjects
Physics - Instrumentation and Detectors
Abstract

An X-ray detector will be presented that is the combination of a segmented ionization chamber featuring one-dimensional spatial resolution integrated with an intelligent ADC front-end, multi DSP processing and embedded PC platform. This detector is optimized to fan beam geometry with an active area of 192 mm (horizontal) and a vertical acceptance of 6 mm. Spatial resolution is obtained by subdividing the anode into readout strips, having pitch of 150 micrometers, which are connected to 20 custom made integrating VLSI chips (each capable of 64-channel read-out and multiplexing) and read out by 14 bits 10 MHz ADCs and fast adaptive PGAs into DSP boards. A bandwidth reaching 3.2Gbit/s of raw data, generated from the real time sampling of the 1280 micro strips, is cascaded processed with FPGA and DSP to allow data compression resulting in several days of uninterrupted acquisition capability. Fast acquisition rates reaching 10 kHz are allowed due to the MicroCAT structure utilized not only as a shielding grid in ionization chamber mode but also to provide active electron amplification in the gas., Comment: 5 pages, 7 figures, distilled by AFPL Ghostscript 7.04

Published
2010
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24. Imputation and subset-based association analysis across different cancer types identifies multiple independent risk loci in the TERT-CLPTM1L region on chromosome 5p15.33

Author

Wang, Zhaoming, Zhu, Bin, Zhang, Mingfeng, Parikh, Hemang, Jia, Jinping, Chung, Charles C, Sampson, Joshua N, Hoskins, Jason W, Hutchinson, Amy, Burdette, Laurie, Ibrahim, Abdisamad, Hautman, Christopher, Raj, Preethi S, Abnet, Christian C, Adjei, Andrew A, Ahlbom, Anders, Albanes, Demetrius, Allen, Naomi E, Ambrosone, Christine B, Aldrich, Melinda, Amiano, Pilar, Amos, Christopher, Andersson, Ulrika, Andriole, Gerald, Andrulis, Irene L, Arici, Cecilia, Arslan, Alan A, Austin, Melissa A, Baris, Dalsu, Barkauskas, Donald A, Bassig, Bryan A, Beane Freeman, Laura E, Berg, Christine D, Berndt, Sonja I, Bertazzi, Pier Alberto, Biritwum, Richard B, Black, Amanda, Blot, William, Boeing, Heiner, Boffetta, Paolo, Bolton, Kelly, Boutron-Ruault, Marie-Christine, Bracci, Paige M, Brennan, Paul, Brinton, Louise A, Brotzman, Michelle, Bueno-de-Mesquita, H Bas, Buring, Julie E, Butler, Mary Ann, Cai, Qiuyin, Cancel-Tassin, Geraldine, Canzian, Federico, Cao, Guangwen, Caporaso, Neil E, Carrato, Alfredo, Carreon, Tania, Carta, Angela, Chang, Gee-Chen, Chang, I-Shou, Chang-Claude, Jenny, Che, Xu, Chen, Chien-Jen, Chen, Chih-Yi, Chen, Chung-Hsing, Chen, Constance, Chen, Kuan-Yu, Chen, Yuh-Min, Chokkalingam, Anand P, Chu, Lisa W, Clavel-Chapelon, Francoise, Colditz, Graham A, Colt, Joanne S, Conti, David, Cook, Michael B, Cortessis, Victoria K, Crawford, E David, Cussenot, Olivier, Davis, Faith G, De Vivo, Immaculata, Deng, Xiang, Ding, Ti, Dinney, Colin P, Di Stefano, Anna Luisa, Diver, W Ryan, Duell, Eric J, Elena, Joanne W, Fan, Jin-Hu, Feigelson, Heather Spencer, Feychting, Maria, Figueroa, Jonine D, Flanagan, Adrienne M, Fraumeni, Joseph F, Freedman, Neal D, Fridley, Brooke L, Fuchs, Charles S, Gago-Dominguez, Manuela, Gallinger, Steven, Gao, Yu-Tang, Gapstur, Susan M, and Garcia-Closas, Montserrat

Subjects
Biological Sciences, Genetics, Human Genome, Cancer, Prevention, 2.1 Biological and endogenous factors, Alleles, Chromosomes, Human, Pair 5, Computational Biology, DNA Methylation, Epigenesis, Genetic, Female, Gene Expression Regulation, Neoplastic, Gene Frequency, Genetic Loci, Genetic Predisposition to Disease, Genome-Wide Association Study, Humans, Male, Membrane Proteins, Neoplasm Proteins, Neoplasms, Odds Ratio, Polymorphism, Single Nucleotide, Risk, Telomerase, Medical and Health Sciences, Genetics & Heredity
Abstract

Genome-wide association studies (GWAS) have mapped risk alleles for at least 10 distinct cancers to a small region of 63 000 bp on chromosome 5p15.33. This region harbors the TERT and CLPTM1L genes; the former encodes the catalytic subunit of telomerase reverse transcriptase and the latter may play a role in apoptosis. To investigate further the genetic architecture of common susceptibility alleles in this region, we conducted an agnostic subset-based meta-analysis (association analysis based on subsets) across six distinct cancers in 34 248 cases and 45 036 controls. Based on sequential conditional analysis, we identified as many as six independent risk loci marked by common single-nucleotide polymorphisms: five in the TERT gene (Region 1: rs7726159, P = 2.10 × 10(-39); Region 3: rs2853677, P = 3.30 × 10(-36) and PConditional = 2.36 × 10(-8); Region 4: rs2736098, P = 3.87 × 10(-12) and PConditional = 5.19 × 10(-6), Region 5: rs13172201, P = 0.041 and PConditional = 2.04 × 10(-6); and Region 6: rs10069690, P = 7.49 × 10(-15) and PConditional = 5.35 × 10(-7)) and one in the neighboring CLPTM1L gene (Region 2: rs451360; P = 1.90 × 10(-18) and PConditional = 7.06 × 10(-16)). Between three and five cancers mapped to each independent locus with both risk-enhancing and protective effects. Allele-specific effects on DNA methylation were seen for a subset of risk loci, indicating that methylation and subsequent effects on gene expression may contribute to the biology of risk variants on 5p15.33. Our results provide strong support for extensive pleiotropy across this region of 5p15.33, to an extent not previously observed in other cancer susceptibility loci.

Published
2014

25. Epigenetic loss of RNA-methyltransferase NSUN5 in glioma targets ribosomes to drive a stress adaptive translational program

Author

Janin, Maxime, Ortiz-Barahona, Vanessa, de Moura, Manuel Castro, Martínez-Cardús, Anna, Llinàs-Arias, Pere, Soler, Marta, Nachmani, Daphna, Pelletier, Joffrey, Schumann, Ulrike, Calleja-Cervantes, Maria E., Moran, Sebastian, Guil, Sonia, Bueno-Costa, Alberto, Piñeyro, David, Perez-Salvia, Montserrat, Rosselló-Tortella, Margalida, Piqué, Laia, Bech-Serra, Joan J., De La Torre, Carolina, Vidal, August, Martínez-Iniesta, María, Martín-Tejera, Juan F., Villanueva, Alberto, Arias, Alexandra, Cuartas, Isabel, Aransay, Ana M., La Madrid, Andres Morales, Carcaboso, Angel M., Santa-Maria, Vicente, Mora, Jaume, Fernandez, Agustin F., Fraga, Mario F., Aldecoa, Iban, Pedrosa, Leire, Graus, Francesc, Vidal, Noemi, Martínez-Soler, Fina, Tortosa, Avelina, Carrato, Cristina, Balañá, Carme, Boudreau, Matthew W., Hergenrother, Paul J., Kötter, Peter, Entian, Karl-Dieter, Hench, Jürgen, Frank, Stephan, Mansouri, Sheila, Zadeh, Gelareh, Dans, Pablo D., Orozco, Modesto, Thomas, George, Blanco, Sandra, Seoane, Joan, Preiss, Thomas, Pandolfi, Pier Paolo, and Esteller, Manel

Published
2019
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26. A phase 2 study of panitumumab with irinotecan as salvage therapy in chemorefractory KRAS exon 2 wild-type metastatic colorectal cancer patients

Author

Elez, Elena, Pericay, Carles, Valladares-Ayerbes, Manuel, Bando, Inmaculada, Safont, Maria Jose, Gallego, Javier, Grávalos, Cristina, Arrivi, Antonio, Carrato, Alfredo, Conde, Verónica, Ortiz, Maria José, López, Carlos, Alonso, Beatriz, Ruiz de Mena, Inmaculada, Díaz-Rubio, Eduardo, Tabernero, Josep, and Aranda, Enrique

Published
2019
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27. Tumor-associated macrophage-secreted 14-3-3ζ signals via AXL to promote pancreatic cancer chemoresistance

Author

D’Errico, Gabriele, Alonso-Nocelo, Marta, Vallespinos, Mireia, Hermann, Patrick C., Alcalá, Sonia, García, Coral Pedrero, Martin-Hijano, Laura, Valle, Sandra, Earl, Julie, Cassiano, Chiara, Lombardia, Luis, Feliu, Jaime, Monti, Maria Chiara, Seufferlein, Thomas, García-Bermejo, Laura, Martinelli, Paola, Carrato, Alfredo, and Sainz, Jr., Bruno

Published
2019
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31. A phase II Study Evaluating Combined Neoadjuvant Cetuximab and Chemotherapy Followed by Chemoradiotherapy and Concomitant Cetuximab in Locoregional Oesophageal Cancer Patients

Author

Alsina, Maria, Rivera, Fernando, Ramos, Francisco Javier, Galán, Maica, López, Rafael, García-Alfonso, Pilar, Alés-Martinez, José Enrique, Queralt, Bernardo, Antón, Antonio, Carrato, Alfredo, Grávalos, Cristina, Méndez-Vidal, Maria José, López, Carlos, de Mena, Inmaculada Ruiz, Tabernero, Josep, Giralt, Jordi, Aranda, Enrique, and on behalf of the Spanish Cooperative Group for the Treatment of Digestive Tumors (TTD) and Grupo de Investigación Clínica en Oncología Radioterápica (GICOR)

Published
2018
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32. Gamma/neutron classification with SiPM CLYC detectors using frequency-domain analysis for embedded real-time applications

Author

Morales, Iván René, Crespo, Maria Liz, Bogovac, Mladen, Cicuttin, Andres, Kanaki, Kalliopi, and Carrato, Sergio

Abstract

A method for gamma/neutron event classification based on frequency-domain analysis for mixed radiation environments is proposed. In contrast to the traditional charge comparison method for pulse-shape discrimination, which requires baseline removal and pulse alignment, our method does not need any preprocessing of the digitized data, apart from removing saturated traces in sporadic pile-up scenarios. It also features the identification of neutron events in the detector’s full energy range with a single device, from thermal neutrons to fast neutrons, including low-energy pulses, and still provides a superior figure-of-merit for classification.

Published
2024
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34. First-line single-agent regorafenib in frail patients with metastatic colorectal cancer: a pilot phase II study of the Spanish Cooperative Group for the Treatment of Digestive Tumours (TTD)

Author

Carrato, A., Benavides, M., Massutí, B., Ferreiro-Monteagudo, R., García Alfonso, P., Falcó, E., Reboredo, M., Cano, T., Gallego, J., Viéitez, J. M., Layos, L., Salud, A., Polo, E., Dotor, E., Durán-Ogalla, G., Rodriguez-Garrote, M., Calvo, A., Grande, E., and Aranda, E.

Published
2019
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41. Consensus guidelines for diagnosis, treatment and follow-up of patients with pancreatic cancer in Spain

Author

Hidalgo, M., Álvarez, R., Gallego, J., Guillén-Ponce, C., Laquente, B., Macarulla, T., Muñoz, A., Salgado, M., Vera, R., Adeva, J., Alés, I., Arévalo, S., Blázquez, J., Calsina, A., Carmona, A., de Madaria, E., Díaz, R., Díez, L., Fernández, T., de Paredes, B. G., Gallardo, M. E., González, I., Hernando, O., Jiménez, P., López, A., López, C., López-Ríos, F., Martín, E., Martínez, J., Martínez, A., Montans, J., Pazo, R., Plaza, J. C., Peiró, I., Reina, J. J., Sanjuanbenito, A., Yaya, R., and Carrato, Alfredo

Published
2017
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44. Balloon-Targeted Extra-Anatomic Sharp Recanalization Technique to Re-establish Supraclavicular Vascular Access.

Author

Choi, Taedo J., Carrato, Kaitlin A., Sabri, Saher S., Tabori, Nora E., and Sivananthan, Gajan

Abstract

A balloon-targeted extra-anatomic sharp recanalization (BEST) technique was investigated to re-establish supraclavicular vascular access in patients with central venous occlusion. Query of the authors' institution's database yielded 130 patients who underwent central venous recanalization. Of these, a retrospective review of 5 patients with concurrent thoracic central venous and bilateral internal jugular vein occlusions who underwent sharp recanalization using the BEST technique from May 2018 to August 2022 was performed. Technical success was achieved in all cases without major adverse events. Four (80%) of the 5 patients underwent hemodialysis reliable outflow (HeRO) graft placement using the newly established supraclavicular vascular access. [Display omitted] [ABSTRACT FROM AUTHOR]

Published
2023
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45. Endothelial cell activation on 3D-matrices derived from PDGF-BB-stimulated fibroblasts is mediated by Snail1

Author

Herrera, Alberto, Herrera, Mercedes, Guerra-Perez, Natalia, Galindo-Pumariño, Cristina, Larriba, María Jesús, García-Barberán, Vanesa, Gil, Beatriz, Giménez-Moyano, Sara, Ferreiro-Monteagudo, Reyes, Veguillas, Pilar, Candia, Antonio, Peña, Raúl, Pinto, Jesús, García-Bermejo, Mª Laura, Muñoz, Alberto, García de Herreros, Antonio, Bonilla, Félix, Carrato, Alfredo, and Peña, Cristina

Published
2018
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47. The Peptidoglycan Recognition Protein 1 confers immune evasive properties on pancreatic cancer stem cells

Author

López-Gil, Juan Carlos, García-Silva, Susana, Ruiz-Cañas, Laura, Navarro, Diego, Palencia-Campos, Adrián, Giráldez-Trujillo, Antonio, Earl, Julie, Dorado, Jorge, Gómez-López, Gonzalo, Monfort-Vengut, Ana, Alcalá, Sonia, Gaida, Matthias M, García-Mulero, Sandra, Cabezas-Sáinz, Pablo, Batres-Ramos, Sandra, Barreto, Emma, Sánchez-Tomero, Patricia, Vallespinós, Mireia, Ambler, Leah, Lin, Meng-Lay, Aicher, Alexandra, García García de Paredes, Ana, de la Pinta, Carolina, Sanjuanbenito, Alfonso, Ruz-Caracuel, Ignacio, Rodríguez-Garrote, Mercedes, Guerra, Carmen, Carrato, Alfredo, de Cárcer, Guillermo, Sánchez, Laura, Nombela-Arrieta, César, Espinet, Elisa, Sanchez-Arevalo Lobo, Víctor Javier, Heeschen, Christopher, and Sainz, Bruno

Abstract

ObjectivePancreatic ductal adenocarcinoma (PDAC) has limited therapeutic options, particularly with immune checkpoint inhibitors. Highly chemoresistant ‘stem-like’ cells, known as cancer stem cells (CSCs), are implicated in PDAC aggressiveness. Thus, comprehending how this subset of cells evades the immune system is crucial for advancing novel therapies.DesignWe used the KPC mouse model (LSL-KrasG12D/+; LSL-Trp53R172H/+; Pdx-1-Cre) and primary tumour cell lines to investigate putative CSC populations. Transcriptomic analyses were conducted to pinpoint new genes involved in immune evasion. Overexpressing and knockout cell lines were established with lentiviral vectors. Subsequent in vitrococulture assays, in vivomouse and zebrafish tumorigenesis studies, and in silicodatabase approaches were performed.ResultsUsing the KPC mouse model, we functionally confirmed a population of cells marked by EpCAM, Sca-1 and CD133 as authentic CSCs and investigated their transcriptional profile. Immune evasion signatures/genes, notably the gene peptidoglycan recognition protein 1 (PGLYRP1), were significantly overexpressed in these CSCs. Modulating PGLYRP1 impacted CSC immune evasion, affecting their resistance to macrophage-mediated and T-cell-mediated killing and their tumourigenesis in immunocompetent mice. Mechanistically, tumour necrosis factor alpha (TNFα)-regulated PGLYRP1 expression interferes with the immune tumour microenvironment (TME) landscape, promoting myeloid cell-derived immunosuppression and activated T-cell death. Importantly, these findings were not only replicated in human models, but clinically, secreted PGLYRP1 levels were significantly elevated in patients with PDAC.ConclusionsThis study establishes PGLYRP1 as a novel CSC-associated marker crucial for immune evasion, particularly against macrophage phagocytosis and T-cell killing, presenting it as a promising target for PDAC immunotherapy.

Published
2024
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48. Bevacizumab and temozolomide versus temozolomide alone as neoadjuvant treatment in unresected glioblastoma: the GENOM 009 randomized phase II trial

Author

Balana, Carmen, De Las Penas, Ramon, Sepúlveda, Juan Manuel, Gil-Gil, Miguel J., Luque, Raquel, Gallego, Oscar, Carrato, Cristina, Sanz, Carolina, Reynes, Gaspar, Herrero, Ana, Ramirez, Jose Luis, Pérez-Segura, Pedro, Berrocal, Alfonso, Vieitez, Jose Maria, Garcia, Almudena, Vazquez-Estevez, Sergio, Peralta, Sergi, Fernandez, Isaura, Henriquez, Ivan, Martinez-Garcia, Maria, De la Cruz, Juan Jose, Capellades, Jaume, Giner, Pilar, and Villà, Salvador

Published
2016
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49. Prognostic Value of BRAF, PI3K, PTEN, EGFR Copy Number, Amphiregulin and Epiregulin Status in Patients with KRAS Codon 12 Wild-Type Metastatic Colorectal Cancer Receiving First-Line Chemotherapy with Anti-EGFR Therapy

Author

Llovet, Patricia, Sastre, Javier, Ortega, Julián Sanz, Bando, Inmaculada, Ferrer, Milagros, García-Alfonso, Pilar, Donnay, Olga, Carrato, Alfredo, Jiménez, Ana, Aranda, Enrique, León, Ana, Grávalos, Cristina, Cámara, Juan Carlos, Feliú, Jaime, Sanchíz, Bárbara, Caldés, Trinidad, and Díaz-Rubio, Eduardo

Published
2015
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