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Single-base mismatch profiles for NGS samples [article]

Marco Chierici and Giuseppe Jurman and Marco Roncador and Cesare Furlanello
2011 arXiv   pre-print
Within the preprocessing pipeline of a Next Generation Sequencing sample, its set of Single-Base Mismatches is one of the first outcomes, together with the number of correctly aligned reads. The union of these two sets provides a 4x4 matrix (called Single Base Indicator, SBI in what follows) representing a blueprint of the sample and its preprocessing ingredients such as the sequencer, the alignment software, the pipeline parameters. In this note we show that, under the same technological
more » ... ions, there is a strong relation between the SBI and the biological nature of the sample. To reach this goal we need to introduce a similarity measure between SBIs: we also show how two measures commonly used in machine learning can be of help in this context.
arXiv:1109.1108v1 fatcat:hkqs35artrg7rdnd2vpubd3iee

A PRÁXIS DA CULTURA UCRANIANA NO ESPAÇO URBANO DE RONCADOR (PR), BRASIL: análise das categorias forma, função, estrutura e processo

Marcos Clair Bovo, Elaine Cristina Zavadovski Kalinovski, Ricardo Luiz Töws
2014 Raega - O Espaço Geográfico em Análise  
O estudo versa sobre a cultura ucraniana na imagem da cidade de Roncador (PR), destacando, nesse prisma, a contribuição do grupo étnico no processo de colonização e formação do núcleo urbano.  ...  Nesse sentido, a partir dos referenciais teórico, empírico e técnico, evidenciamos que as formas culturais impressas pelo grupo ucraíno no espaço urbano de Roncador não sucumbiram frente ao processo de  ...  Chamamos a atenção do poder público municipal para a elaboração de políticas públicas consistentes, voltadas para a conservação dos marcos culturais do espaço urbano de Roncador, assegurando a preservação  ... 
doi:10.5380/raega.v32i0.32173 fatcat:mqukspj7jbgzpnsk5j6ov4sydq

Physical attributes of the river basin of Roncador river associated to the landscape change in the municipality of Magé, Rio de Janeiro-Brazil

Raquel de Oliveira Santos, Rafael Coll Delgado, Marcos Gervasio Pereira, Leonardo Paula de Souza
2018 Bioscience Journal  
The objective of this study was to conduct a temporal analysis of biophysical attributes of the river basin of Rio Roncador, located in the municipality of Magé, Rio de Janeiro.  ...  Thus, the main channel of the Roncador River will not simultaneously receive contributions from all channels, thus reducing the risk of overflow.  ...  Table 1 . 1 Characteristics of the river basin of Roncador River. Geometric Features Table 2 . 2 Quantification of soil cover classes for 1986 and 2010 at BHRR.  ... 
doi:10.14393/bj-v34n3a2018-36716 fatcat:z47s5swc7vhupa4paxpxk3f3am

Microbial community structure in vineyard soils across altitudinal gradients and in different seasons

Paola E. Corneo, Alberto Pellegrini, Luca Cappellin, Marco Roncador, Marco Chierici, Cesare Gessler, Ilaria Pertot
2013 FEMS Microbiology Ecology  
Microbial communities living in nine vineyards distributed over three altitudinal transects were studied over 2 years. Fungal and bacterial community dynamics were explored using automated ribosomal intergenic spacer analysis (ARISA) and by determining bacterial cells and fungal colony-forming units (CFUs). Moreover, extensive chemical and physical analyses of the soils were carried out. Multivariate analyses demonstrated that bacterial and fungal communities are affected by altitude, which
more » ... as a complex physicochemical gradient. In fact, soil moisture, Al, Mg, Mn and clay content are changing with altitude and influencing the bacterial genetic structure, while in the case of fungi, soil moisture, B and clay content are found to be the main drivers of the community. Moreover, other exchangeable cations and heavy metals, not correlating with altitude, are involved in the ordination of the sites, especially Cu. Qualitative ARISA revealed the presence of a stable core microbiome of operational taxonomic units (OTUs) within each transect, which ranged between 57% and 68% of total OTUs in the case of fungi and between 63% and 72% for bacteria. No seasonal effect on the composition of microbial communities was found, demonstrating that bacterial and fungal communities in vineyards are mostly stable over the considered seasons.
doi:10.1111/1574-6941.12087 pmid:23398556 fatcat:lagry6nc5zhiva6ulos2oxzhzy

Space-time variability of the Roncador river basin in the change of land use and cover and its correlation with climatic variables

Raquel de Oliveira Santos, Rafael Coll Delgado, Marcos Gervasio Pereira, Leonardo Paula de Souza, Paulo Eduardo Teodoro, Carlos Antonio da Silva Junior, Giovani Glaucio de Oliveira Costa
2019 Bioscience Journal  
The objective of this study was to evaluate the space-time dynamics of the soil use and occupation of the Rio Roncador river basin between 1985 and 2010.  ...  These results confirm that the Roncador River Basin is undergoing transformation in its landscape, with an average reduction of -49% in native vegetation areas due to the increase in urban areas (25%)  ...  O. et al evapotranspiration) may be caused by the landscape dynamics in the Roncador river basin.  ... 
doi:10.14393/bj-v35n4a2019-39486 fatcat:73d66jf5ojgwfk5lafadwy5ebi

DROSHA associates to DNA damage sites and is required for DNA repair [article]

Matteo Cabrini, Marco Roncador, Alessandro Galbiati, Lina Cipolla, Fabio Iannelli, Simone Sabbioneda, Fabrizio d'Adda di Fagagna, Sofia Francia
2018 bioRxiv   pre-print
The DNA damage response (DDR) is the signaling cascade through which a cell recognizes DNA lesions, and promotes their resolution via the repair pathways of Non-Homologous End Joining (NHEJ), or Homologous Recombination (HR). We recently demonstrated that DROSHA boosts DDR signaling by processing damage-induced long non-coding RNAs into smaller DNA damage response RNAs (DDRNAs). However, the location at which DROSHA exerts its DDR functions, relative to sites of DNA damage, remains unknown. To
more » ... nvestigate DROSHA's localization during DDR activation, we used the DiVA cellular system, which allows the controlled induction of several DNA double strand breaks (DSBs) in the human genome. Indeed, by genome wide chromatin immunoprecipitation followed by next generation sequencing, we demonstrate that DROSHA associates with DSBs. In support of this, DSB-recruitment of DROSHA is detectable at the single-cell level by Proximity Ligation Assay between DROSHA and known DDR markers, and by DNA damage in situ ligation followed by Proximity Ligation Assay (DI-PLA), which demonstrates proximity of DROSHA to DNA ends. DROSHA recruitment occurs at both genic and inter-genic DSBs, suggesting that its recruitment is independent from ongoing transcription preceding damage generation. DROSHA's recruitment to DNA lesions occurs throughout the cell cycle, and with a preference for NHEJ-prone DSBs. Consistently, inhibition of the HR pathway increases DROSHA recruitment, and DROSHA knock down strongly impairs NHEJ efficiency in a GFP-reporter cellular system for monitoring NHEJ DNA repair. Overall, these results demonstrate that DROSHA acts locally at sites of DNA damage to promote NHEJ DNA repair.
doi:10.1101/261289 fatcat:jn4o6wikjvf4tff54wsvgmd2wq

From the Body with the Body: Performing with a Genome-Based Musical Instrument

Francesco Rì, Raul Masu, Mauro Graziani, Marco Roncador
2018 EAI Endorsed Transactions on Creative Technologies  
INTRODUCTION: In this paper we present Silico, a new Digital Musical Instrument which ideally represents the performer itself. This instrument is composed by two parts: an interface (a sensor glove), which relies on the movements of the performer's hand, and a computational engine (a set of patches developed in Max 7), which generates sound events based on the genomic data of the performer. OBJECTIVES: We want to propose a new reflection on the relation between the body and musical instruments.
more » ... Moreover, we aim to investigate the voluntary and involuntary aspects of our body, intended as a starting point for a musical performance. As a metaphor of these two layers, we used here the hand and the genome of the performer. METHODS: We have investigated our objectives through the whole design process of a Digital Musical Instrument, using a practice-based approach. RESULTS: Our system is a multilayered composed instrument which maps its computational part and its interface on the performer's body. Silico can be used as a standalone musical instrument to generate music in real time. CONCLUSION: Our works shows a new path about the use of genomic data in a musical way, as a new perspective of human-computer interaction in a performative contexts.
doi:10.4108/eai.13-7-2018.163993 fatcat:ve2nr3odibe5blmvngngfa3i6u

Reduced mortality and shorten ICU stay in SARS-COV-2 pneumonia: a low PEEP strategy [article]

Samuele Ceruti, Marco Roncador, Olivier Gie, Giovanni Bona, Martina Iattoni, Maira Biggiogero, Pier Andrea Maida, Christian Garzoni, Romano Mauri, COVID-19 Clinical Management Team
2020 medRxiv   pre-print
Intensive Care Unit (ICU) management of COVID-19 patients with severe hypoxemia is associated with high mortality. We implemented a "care map", as a standardized multidisciplinary approach to improve patients monitoring using: uniform patient selection for ICU admission, a low-PEEP strategy and a pharmacologic strategic thromboembolism management. Methods A standardized protocol for managing COVID-19 patients and ICU admissions was implemented through accurate Early Warning Score (EWS)
more » ... g and thromboembolism prophylaxis at hospital admission. Dyspnea, mental confusion or SpO2 less than 85% were criteria for ICU admission. Ventilation approach employed low PEEP values (about 10 cmH2O in presence of lung compliance > 40 mL/cmH2O) and FiO2 as needed. In presence of lower lung compliance (< 40 mL/cmH2O) PEEP value was increased to about 14 cmH2O. Results From March 16th to April 12nd 2020, 41 COVID-19 patients were admitted to our ICU from a total of 310 patients. 83% (34) of them needed mechanical ventilation. The ventilation approach chosen employed low PEEP value based on BMI (PEEP 11+/- 3.8 (10-12) cmH2O if BMI < 30 Kg/m2; PEEP 15+/- 3.26 (12-18) cmH2O if BMI >30 Kg/m2). To date, ten patients (24%) died, four (9.7%) received mechanical ventilation, two were transferred to another hospital and 25 (60.9%) were discharged from ICU after a median of nine days. Discussion A multimodal approach for COVID-19 patients is mandatory. The knowledge of this multi-organ disease is growing rapidly, requiring improvements in the standard of care. Our approach implements an accurate pre-ICU monitoring and strict selection for ICU admission, and allows to reduce mechanical ventilation, ICU stay and mortality. Funding No funding has been required.
doi:10.1101/2020.05.03.20089318 fatcat:lr7ghynnqrdgrayxbrapvjsima

Integrated genomics and comprehensive validation reveal drivers of genomic evolution in esophageal adenocarcinoma

Subodh Kumar, Leutz Buon, Srikanth Talluri, Marco Roncador, Chengcheng Liao, Jiangning Zhao, Jialan Shi, Chandraditya Chakraborty, Gabriel Gonzalez, Yu-Tzu Tai, Rao Prabhala, Mehmet K. Samur (+2 others)
2021 Communications Biology  
AbstractEsophageal adenocarcinoma (EAC) is associated with a marked genomic instability, which underlies disease progression and development of resistance to treatment. In this study, we used an integrated genomics approach to identify a genomic instability signature. Here we show that elevated expression of this signature correlates with poor survival in EAC as well as three other cancers. Knockout and overexpression screens establish the relevance of these genes to genomic instability.
more » ... evaluation of three genes (TTK, TPX2 and RAD54B) confirms their role in genomic instability and tumor growth. Mutational signatures identified by whole genome sequencing and functional studies demonstrate that DNA damage and homologous recombination are common mechanisms of genomic instability induced by these genes. Our data suggest that the inhibitors of TTK and possibly other genes identified in this study have potential to inhibit/reduce growth and spontaneous as well as chemotherapy-induced genomic instability in EAC and possibly other cancers.
doi:10.1038/s42003-021-02125-x pmid:34031527 fatcat:c7abj47thfgytnu7zxeuaqnkmi

MAP17 and SGLT1 Protein Expression Levels as Prognostic Markers for Cervical Tumor Patient Survival

Marco Perez, Juan M. Praena-Fernandez, Blanca Felipe-Abrio, Maria A. Lopez-Garcia, Antonio Lucena-Cacace, Angel Garcia, Matilde Lleonart, Guiovanna Roncador, Juan J. Marin, Amancio Carnero, Matthew L. Anderson
2013 PLoS ONE  
MAP17 is a membrane-associated protein that is overexpressed in human tumors. Because the expression of MAP17 increases reactive oxygen species (ROS) generation through SGLT1 in cancer cells, in the present work, we investigated whether MAP17 and/or SGLT1 might be markers for the activity of treatments involving oxidative stress, such as cisplatin or radiotherapy. First, we confirmed transcriptional alterations in genes involved in the oxidative stress induced by MAP17 expression in HeLa
more » ... l tumor cells and found that Hela cells expressing MAP17 were more sensitive to therapies that induce ROS than were parental cells. Furthermore, MAP17 increased glucose uptake through SGLT receptors. We then analyzed MAP17 and SGLT1 expression levels in cervical tumors treated with cisplatin plus radiotherapy and correlated the expression levels with patient survival. MAP17 and SGLT1 were expressed in approximately 70% and 50% of cervical tumors of different types, respectively, but they were not expressed in adenoma tumors. Furthermore, there was a significant correlation between MAP17 and SGLT1 expression levels. High levels of either MAP17 or SGLT1 correlated with improved patient survival after treatment. However, the patients with high levels of both MAP17 and SGLT1 survived through the end of this study. Therefore, the combination of high MAP17 and SGLT1 levels is a marker for good prognosis in patients with cervical tumors after cisplatin plus radiotherapy treatment. These results also suggest that the use of MAP17 and SGLT1 markers may identify patients who are likely to exhibit a better response to treatments that boost oxidative stress in other cancer types. Citation: Perez M, Praena-Fernandez JM, Felipe-Abrio B, Lopez-Garcia MA, Lucena-Cacace A, et al. (2013) MAP17 and SGLT1 Protein Expression Levels as Prognostic Markers for Cervical Tumor Patient Survival. PLoS ONE 8(2): e56169.
doi:10.1371/journal.pone.0056169 pmid:23418532 pmcid:PMC3572015 fatcat:fsshqlxrkvferolof6z5s37dsm

A damaged genome's transcriptional landscape through multilayered expression profiling around in situ-mapped DNA double-strand breaks

Fabio Iannelli, Alessandro Galbiati, Ilaria Capozzo, Quan Nguyen, Brian Magnuson, Flavia Michelini, Giuseppina D'Alessandro, Matteo Cabrini, Marco Roncador, Sofia Francia, Nicola Crosetto, Mats Ljungman (+2 others)
2017 Nature Communications  
Supplementary Figure 2. (a) Number of predicted AsiSI sites upon in silico digestion of the GRCh37/hg19 human genome assembly. The number of sites has been normalized by the length of each chromosome. (b) Top-ranked AsiSI-induced cleavage site. The AsiSI recognition site with the highest γH2AX rank score is depicted. The panel represents a 20-fold zoom out, centered on the ~100 Kb window across which individual z-scores were averaged to calculate the score. The LOESS curves represent average
more » ... cores. Absence of dots indicates that no positive z-scores were calculated for the respective windows (no or negative enrichment over background). Supplementary Figure 3. (a) Venn diagram plot showing intersection of the 214 sites detected by BLISS (blue) and the 100 top sites detected according to γH2AX ChIP-seq (red).
doi:10.1038/ncomms15656 pmid:28561034 pmcid:PMC5499205 fatcat:c26g4xveabdl5ny45h7q5c7sd4

NOTCH pathway inactivation promotes bladder cancer progression

Antonio Maraver, Pablo J. Fernandez-Marcos, Timothy P. Cash, Marinela Mendez-Pertuz, Marta Dueñas, Paolo Maietta, Paola Martinelli, Maribel Muñoz-Martin, Mónica Martínez-Fernández, Marta Cañamero, Giovanna Roncador, Jorge L. Martinez-Torrecuadrada (+6 others)
2015 Journal of Clinical Investigation  
doi:10.1172/jci78185 pmid:25574842 pmcid:PMC4319408 fatcat:4uhoc2ofvravleu4ots4yy7odi

Genomic landscape and chronological reconstruction of driver events in multiple myeloma [article]

Francesco Maura, Niccolo Bolli, Nicos Angelopoulos, Kevin J. Dawson, Daniel Leongamornlert, Inigo Martincorena, Thomas J. Mitchell, Anthony Fullam, Santiago Gonzalez, Raphael Szalat, Bernardo Rodriguez-Martin, Mehmet K. Samur (+15 others)
2018 bioRxiv   pre-print
Multiple myeloma (MM) has a heterogeneous genome, evolving through both pre-clinical and post-diagnosis phases. Here, using sequences from 67 MM genomes serially collected from 30 patients together with public datasets, we establish a hierarchy of driver lesions. Point mutations, structural variants and copy number aberrations define at least 7 genomic subgroups of MM, each with distinct sets of co-operating driver mutations. Complex structural events are major drivers of MM, including
more » ... ipsis, chromoplexy and a replication-based mechanism of templated insertions: these typically occur early. Hyperdiploidy also occurs early, with individual chromosomes often gained in more than one chronological epoch of MM evolution, showing a preferred order of acquisition. Positively selected point mutations frequently occur in later phases of disease development, as do structural variants involving MYC. Thus, initiating driver events of MM, drawn from a limited repertoire of structural and numerical chromosomal changes, shape preferred trajectories of subsequent evolution.
doi:10.1101/388611 fatcat:u5bqlfwvnjccdjqf3r7vmwbnjy

Lineage-restricted function of the pluripotency factor NANOG in stratified epithelia

Daniela Piazzolla, Adelaida R. Palla, Cristina Pantoja, Marta Cañamero, Ignacio Perez de Castro, Sagrario Ortega, Gonzalo Gómez-López, Orlando Dominguez, Diego Megías, Giovanna Roncador, Jose L. Luque-Garcia, Beatriz Fernandez-Tresguerres (+9 others)
2014 Nature Communications  
NANOG is a pluripotency transcription factor in embryonic stem cells; however, its role in adult tissues remains largely unexplored. Here we show that mouse NANOG is selectively expressed in stratified epithelia, most notably in the oesophagus where the Nanog promoter is hypomethylated. Interestingly, inducible ubiquitous overexpression of NANOG in mice causes hyperplasia selectively in the oesophagus, in association with increased cell proliferation. NANOG transcriptionally activates the
more » ... c programme, including Aurora A kinase (Aurka), in stratified epithelia, and endogenous NANOG directly binds to the Aurka promoter in primary keratinocytes. Interestingly, overexpression of Nanog or Aurka in mice increased proliferation and aneuploidy in the oesophageal basal epithelium. Finally, inactivation of NANOG in cell lines from oesophageal or head and neck squamous cell carcinomas (ESCCs or HNSCCs, respectively) results in lower levels of AURKA and decreased proliferation, and NANOG and AURKA expression are positively correlated in HNSCCs. Together, these results indicate that NANOG has a lineage-restricted mitogenic function in stratified epithelia.
doi:10.1038/ncomms5226 pmid:24979572 fatcat:crcjey4ivjbx7m643atf6o4jrq

ANÁLISE DA PERMANÊNCIA DA PRÁXIS DA CULTURA UCRANIANA NO ESPAÇO URBANO DE RONCADOR-PR¹ THE PERMANENCE OF THE UKRAINIAN CULTURE PRAXIS IN THE URBAN SPACE OF RONCADOR-PR

Elaine Kalinovski, Zavadovski², Marcos Bovo, Clair³, Töws, Ricardo Luiz
unpublished
Palavras-chave: Roncador; cultura ucraniana; rugosidades.  ...  um projeto de pesquisa que se encontra no presente momento em construção, cujo enfoque analítico é entender a inserção e a permanência dos traços da cultura ucraniana no espaço urbano do município de Roncador-Pr  ...  A cultura ucraniana na imagem da cidade: a conservação dos marcos culturais Doravante, passaremos a analisar as formas impressas pelo povo ucraniano no espaço urbano de Roncador e que representam a sua  ... 
fatcat:5hmbnl47orf4zipvbwzwzaxpaq
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