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953 results on '"Vodicka, P"'

1. Phylogenetic degrees for Jukes-Cantor model

Author

Dinu, Rodica Andreea and Vodička, Martin

Subjects
Mathematics - Algebraic Geometry, Mathematics - Combinatorics, Quantitative Biology - Populations and Evolution
Abstract

Jukes-Cantor model is one of the most meaningful statistical models from a biological perspective. We are interested in computing the algebraic degrees for phylogenetic varieties, which we call phylogenetic degrees, associated to the Jukes-Cantor model and any tree. As these varieties are toric, their geometry is hidden in the associated polytopes. For this reason, we provide two different combinatorial approaches to compute the volume for these polytopes.

Published
2024

2. Genome-wide meta-analyses of restless legs syndrome yield insights into genetic architecture, disease biology and risk prediction

Author

Schormair, Barbara, Zhao, Chen, Bell, Steven, Didriksen, Maria, Nawaz, Muhammad S., Schandra, Nathalie, Stefani, Ambra, Högl, Birgit, Dauvilliers, Yves, Bachmann, Cornelius G., Kemlink, David, Sonka, Karel, Paulus, Walter, Trenkwalder, Claudia, Oertel, Wolfgang H., Hornyak, Magdolna, Teder-Laving, Maris, Metspalu, Andres, Hadjigeorgiou, Georgios M., Polo, Olli, Fietze, Ingo, Ross, Owen A., Wszolek, Zbigniew K., Ibrahim, Abubaker, Bergmann, Melanie, Kittke, Volker, Harrer, Philip, Dowsett, Joseph, Chenini, Sofiene, Ostrowski, Sisse Rye, Sørensen, Erik, Erikstrup, Christian, Pedersen, Ole B., Topholm Bruun, Mie, Nielsen, Kaspar R., Butterworth, Adam S., Soranzo, Nicole, Ouwehand, Willem H., Roberts, David J., Danesh, John, Burchell, Brendan, Furlotte, Nicholas A., Nandakumar, Priyanka, Earley, Christopher J., Ondo, William G., Xiong, Lan, Desautels, Alex, Perola, Markus, Vodicka, Pavel, Dina, Christian, Stoll, Monika, Franke, Andre, Lieb, Wolfgang, Stewart, Alexandre F. R., Shah, Svati H., Gieger, Christian, Peters, Annette, Rye, David B., Rouleau, Guy A., Berger, Klaus, Stefansson, Hreinn, Ullum, Henrik, Stefansson, Kari, Hinds, David A., Di Angelantonio, Emanuele, Oexle, Konrad, and Winkelmann, Juliane

Published
2024
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3. Classification of normal phylogenetic varieties for tripods

Author

Dinu, Rodica Andreea and Vodička, Martin

Subjects
Mathematics - Algebraic Geometry, Mathematics - Combinatorics
Abstract

We provide a complete classification of normal phylogenetic varieties coming from tripods, and more generally, from trivalent trees. Let $G$ be an abelian group. We prove that the group-based phylogenetic variety $X_{G,\mathcal{T}}$, for any trivalent tree $\mathcal{T}$, is projectively normal if and only if $G\in \{\mathbb{Z}_2, \mathbb{Z}_3, \mathbb{Z}_2\times\mathbb{Z}_2, \mathbb{Z}_4, \mathbb{Z}_5, \mathbb{Z}_7\}$.

Published
2023

4. The cost of care for children hospitalized with respiratory syncytial virus (RSV) associated lower respiratory infection in Kenya

Author

Joyce U. Nyiro, Bryan O. Nyawanda, Martin Mutunga, Nickson Murunga, D. James Nokes, Godfrey Bigogo, Nancy A. Otieno, Shirley Lidechi, Bilali Mazoya, Mark Jit, Cheryl Cohen, Jocelyn Moyes, Clint Pecenka, Ranju Baral, Clayton Onyango, Patrick K. Munywoki, and Elisabeth Vodicka

Subjects
Respiratory syncytial virus, Hospitalization, Cost, Households, Health System, Public aspects of medicine, RA1-1270
Abstract

Abstract Background Respiratory syncytial virus (RSV) is one of the main causes of hospitalization for lower respiratory tract infection in children under five years of age globally. Maternal vaccines and monoclonal antibodies for RSV prevention among infants are approved for use in high income countries. However, data are limited on the economic burden of RSV disease from low- and middle-income countries (LMIC) to inform decision making on prioritization and introduction of such interventions. This study aimed to estimate household and health system costs associated with childhood RSV in Kenya. Methods A structured questionnaire was administered to caregivers of children aged

Published
2024
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5. Haplotype analysis identifies functional elements in monoclonal gammopathy of unknown significance

Author

Hauke Thomsen, Subhayan Chattopadhyay, Niels Weinhold, Pavel Vodicka, Ludmila Vodickova, Per Hoffmann, Markus M. Nöthen, Karl-Heinz Jöckel, Börge Schmidt, Roman Hajek, Göran Hallmans, Ulrika Pettersson-Kymmer, Florentin Späth, Hartmut Goldschmidt, Kari Hemminki, and Asta Försti

Subjects
Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

Abstract Genome-wide association studies (GWASs) based on common single nucleotide polymorphisms (SNPs) have identified several loci associated with the risk of monoclonal gammopathy of unknown significance (MGUS), a precursor condition for multiple myeloma (MM). We hypothesized that analyzing haplotypes might be more useful than analyzing individual SNPs, as it could identify functional chromosomal units that collectively contribute to MGUS risk. To test this hypothesis, we used data from our previous GWAS on 992 MGUS cases and 2910 controls from three European populations. We identified 23 haplotypes that were associated with the risk of MGUS at the genome-wide significance level (p

Published
2024
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6. Deciphering the genetics and mechanisms of predisposition to multiple myeloma

Author

Molly Went, Laura Duran-Lozano, Gisli H. Halldorsson, Andrea Gunnell, Nerea Ugidos-Damboriena, Philip Law, Ludvig Ekdahl, Amit Sud, Gudmar Thorleifsson, Malte Thodberg, Thorunn Olafsdottir, Antton Lamarca-Arrizabalaga, Caterina Cafaro, Abhishek Niroula, Ram Ajore, Aitzkoa Lopez de Lapuente Portilla, Zain Ali, Maroulio Pertesi, Hartmut Goldschmidt, Lilja Stefansdottir, Sigurdur Y. Kristinsson, Simon N. Stacey, Thorvardur J. Love, Saemundur Rognvaldsson, Roman Hajek, Pavel Vodicka, Ulrika Pettersson-Kymmer, Florentin Späth, Carolina Schinke, Frits Van Rhee, Patrick Sulem, Egil Ferkingstad, Grimur Hjorleifsson Eldjarn, Ulf-Henrik Mellqvist, Ingileif Jonsdottir, Gareth Morgan, Pieter Sonneveld, Anders Waage, Niels Weinhold, Hauke Thomsen, Asta Försti, Markus Hansson, Annette Juul-Vangsted, Unnur Thorsteinsdottir, Kari Hemminki, Martin Kaiser, Thorunn Rafnar, Kari Stefansson, Richard Houlston, and Björn Nilsson

Subjects
Science
Abstract

Abstract Multiple myeloma (MM) is an incurable malignancy of plasma cells. Epidemiological studies indicate a substantial heritable component, but the underlying mechanisms remain unclear. Here, in a genome-wide association study totaling 10,906 cases and 366,221 controls, we identify 35 MM risk loci, 12 of which are novel. Through functional fine-mapping and Mendelian randomization, we uncover two causal mechanisms for inherited MM risk: longer telomeres; and elevated levels of B-cell maturation antigen (BCMA) and interleukin-5 receptor alpha (IL5RA) in plasma. The largest increase in BCMA and IL5RA levels is mediated by the risk variant rs34562254-A at TNFRSF13B. While individuals with loss-of-function variants in TNFRSF13B develop B-cell immunodeficiency, rs34562254-A exerts a gain-of-function effect, increasing MM risk through amplified B-cell responses. Our results represent an analysis of genetic MM predisposition, highlighting causal mechanisms contributing to MM development.

Published
2024
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7. A mixed-mode dependent interface and phase-field damage model for solids with inhomogeneities

Author

Vodička, Roman

Subjects
Computer Science - Computational Engineering, Finance, and Science, Mathematics - Numerical Analysis, 74R10, 74S05, 65K15
Abstract

The developed computational approach is capable of initiating and propagating cracks inside materials and along material interfaces of general multi-domain structures under quasi-static conditions. Special attention is paid to particular situation of a solid with inhomogeneities. Description of the fracture processes are based on the theory of material damage. It introduces two independent damage parameters to distinguish between interface and internal cracks. The parameter responsible for interface cracks is defined in a thin adhesive layer of the interface and renders relation between stress and strain quantities in fashion of cohesive zone models.The second parameter is defined inside material domains and it is founded on the theory of phase-field fracture guaranteeing the material damage to occur in a thin material strip introducing a regularised model of internal cracks. Additional property of both interface and phase-field damage is their capability to distinguish between fracture modes which is useful if the structures is subjected to combined loading. The solution methodology is based on a variational approach which allows implementation of non-linear programming optimisation into standard methods of finite-element discretisation and time stepping method.Computational implementation is prepared in MATLAB whose numerical data validate developed formulation for analysis of problems of fracture in multi-domain elements of structures., Comment: 24 pages, 19 figures, to be published in Theoretical and Applied Fracture Mechanics

Published
2023
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10. Deciphering the genetics and mechanisms of predisposition to multiple myeloma

Author

Went, Molly, Duran-Lozano, Laura, Halldorsson, Gisli H., Gunnell, Andrea, Ugidos-Damboriena, Nerea, Law, Philip, Ekdahl, Ludvig, Sud, Amit, Thorleifsson, Gudmar, Thodberg, Malte, Olafsdottir, Thorunn, Lamarca-Arrizabalaga, Antton, Cafaro, Caterina, Niroula, Abhishek, Ajore, Ram, Lopez de Lapuente Portilla, Aitzkoa, Ali, Zain, Pertesi, Maroulio, Goldschmidt, Hartmut, Stefansdottir, Lilja, Kristinsson, Sigurdur Y., Stacey, Simon N., Love, Thorvardur J., Rognvaldsson, Saemundur, Hajek, Roman, Vodicka, Pavel, Pettersson-Kymmer, Ulrika, Späth, Florentin, Schinke, Carolina, Van Rhee, Frits, Sulem, Patrick, Ferkingstad, Egil, Hjorleifsson Eldjarn, Grimur, Mellqvist, Ulf-Henrik, Jonsdottir, Ingileif, Morgan, Gareth, Sonneveld, Pieter, Waage, Anders, Weinhold, Niels, Thomsen, Hauke, Försti, Asta, Hansson, Markus, Juul-Vangsted, Annette, Thorsteinsdottir, Unnur, Hemminki, Kari, Kaiser, Martin, Rafnar, Thorunn, Stefansson, Kari, Houlston, Richard, and Nilsson, Björn

Published
2024
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11. Fine-mapping analysis including over 254,000 East Asian and European descendants identifies 136 putative colorectal cancer susceptibility genes

Author

Chen, Zhishan, Guo, Xingyi, Tao, Ran, Huyghe, Jeroen R., Law, Philip J., Fernandez-Rozadilla, Ceres, Ping, Jie, Jia, Guochong, Long, Jirong, Li, Chao, Shen, Quanhu, Xie, Yuhan, Timofeeva, Maria N., Thomas, Minta, Schmit, Stephanie L., Díez-Obrero, Virginia, Devall, Matthew, Moratalla-Navarro, Ferran, Fernandez-Tajes, Juan, Palles, Claire, Sherwood, Kitty, Briggs, Sarah E. W., Svinti, Victoria, Donnelly, Kevin, Farrington, Susan M., Blackmur, James, Vaughan-Shaw, Peter G., Shu, Xiao-Ou, Lu, Yingchang, Broderick, Peter, Studd, James, Harrison, Tabitha A., Conti, David V., Schumacher, Fredrick R., Melas, Marilena, Rennert, Gad, Obón-Santacana, Mireia, Martín-Sánchez, Vicente, Oh, Jae Hwan, Kim, Jeongseon, Jee, Sun Ha, Jung, Keum Ji, Kweon, Sun-Seog, Shin, Min-Ho, Shin, Aesun, Ahn, Yoon-Ok, Kim, Dong-Hyun, Oze, Isao, Wen, Wanqing, Matsuo, Keitaro, Matsuda, Koichi, Tanikawa, Chizu, Ren, Zefang, Gao, Yu-Tang, Jia, Wei-Hua, Hopper, John L., Jenkins, Mark A., Win, Aung Ko, Pai, Rish K., Figueiredo, Jane C., Haile, Robert W., Gallinger, Steven, Woods, Michael O., Newcomb, Polly A., Duggan, David, Cheadle, Jeremy P., Kaplan, Richard, Kerr, Rachel, Kerr, David, Kirac, Iva, Böhm, Jan, Mecklin, Jukka-Pekka, Jousilahti, Pekka, Knekt, Paul, Aaltonen, Lauri A., Rissanen, Harri, Pukkala, Eero, Eriksson, Johan G., Cajuso, Tatiana, Hänninen, Ulrika, Kondelin, Johanna, Palin, Kimmo, Tanskanen, Tomas, Renkonen-Sinisalo, Laura, Männistö, Satu, Albanes, Demetrius, Weinstein, Stephanie J., Ruiz-Narvaez, Edward, Palmer, Julie R., Buchanan, Daniel D., Platz, Elizabeth A., Visvanathan, Kala, Ulrich, Cornelia M., Siegel, Erin, Brezina, Stefanie, Gsur, Andrea, Campbell, Peter T., Chang-Claude, Jenny, Hoffmeister, Michael, Brenner, Hermann, Slattery, Martha L., Potter, John D., Tsilidis, Kostas K., Schulze, Matthias B., Gunter, Marc J., Murphy, Neil, Castells, Antoni, Castellví-Bel, Sergi, Moreira, Leticia, Arndt, Volker, Shcherbina, Anna, Bishop, D. Timothy, Giles, Graham G., Southey, Melissa C., Idos, Gregory E., McDonnell, Kevin J., Abu-Ful, Zomoroda, Greenson, Joel K., Shulman, Katerina, Lejbkowicz, Flavio, Offit, Kenneth, Su, Yu-Ru, Steinfelder, Robert, Keku, Temitope O., van Guelpen, Bethany, Hudson, Thomas J., Hampel, Heather, Pearlman, Rachel, Berndt, Sonja I., Hayes, Richard B., Martinez, Marie Elena, Thomas, Sushma S., Pharoah, Paul D. P., Larsson, Susanna C., Yen, Yun, Lenz, Heinz-Josef, White, Emily, Li, Li, Doheny, Kimberly F., Pugh, Elizabeth, Shelford, Tameka, Chan, Andrew T., Cruz-Correa, Marcia, Lindblom, Annika, Hunter, David J., Joshi, Amit D., Schafmayer, Clemens, Scacheri, Peter C., Kundaje, Anshul, Schoen, Robert E., Hampe, Jochen, Stadler, Zsofia K., Vodicka, Pavel, Vodickova, Ludmila, Vymetalkova, Veronika, Edlund, Christopher K., Gauderman, W. James, Shibata, David, Toland, Amanda, Markowitz, Sanford, Kim, Andre, Chanock, Stephen J., van Duijnhoven, Franzel, Feskens, Edith J. M., Sakoda, Lori C., Gago-Dominguez, Manuela, Wolk, Alicja, Pardini, Barbara, FitzGerald, Liesel M., Lee, Soo Chin, Ogino, Shuji, Bien, Stephanie A., Kooperberg, Charles, Li, Christopher I., Lin, Yi, Prentice, Ross, Qu, Conghui, Bézieau, Stéphane, Yamaji, Taiki, Sawada, Norie, Iwasaki, Motoki, Le Marchand, Loic, Wu, Anna H., Qu, Chenxu, McNeil, Caroline E., Coetzee, Gerhard, Hayward, Caroline, Deary, Ian J., Harris, Sarah E., Theodoratou, Evropi, Reid, Stuart, Walker, Marion, Ooi, Li Yin, Lau, Ken S., Zhao, Hongyu, Hsu, Li, Cai, Qiuyin, Dunlop, Malcolm G., Gruber, Stephen B., Houlston, Richard S., Moreno, Victor, Casey, Graham, Peters, Ulrike, Tomlinson, Ian, and Zheng, Wei

Published
2024
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14. Phylogenetic degrees for claw trees

Author

Dinu, Rodica Andreea and Vodička, Martin

Subjects
Mathematics - Algebraic Geometry, Mathematics - Combinatorics
Abstract

Group-based models appear in algebraic statistics as mathematical models coming from evolutionary biology, respectively the study of mutations of organisms. Both theoretically and in terms of applications, we are interested in determining the algebraic degrees of the phylogenetic varieties coming from these models. These algebraic degrees are called phylogenetic degrees. In this paper, we compute the phylogenetic degree of the variety $X_{G, n}$ with $G\in\{\mathbb{Z}_2,\mathbb{Z}_2\times\mathbb{Z}_2, \mathbb{Z}_3\}$ and any $n$-claw tree. As these varieties are toric, computing their phylogenetic degree relies on computing the volume of their associated polytopes $P_{G,n}$. We apply combinatorial methods and we give concrete formulas for them.

Published
2023

15. Fine-mapping analysis including over 254,000 East Asian and European descendants identifies 136 putative colorectal cancer susceptibility genes

Author

Zhishan Chen, Xingyi Guo, Ran Tao, Jeroen R. Huyghe, Philip J. Law, Ceres Fernandez-Rozadilla, Jie Ping, Guochong Jia, Jirong Long, Chao Li, Quanhu Shen, Yuhan Xie, Maria N. Timofeeva, Minta Thomas, Stephanie L. Schmit, Virginia Díez-Obrero, Matthew Devall, Ferran Moratalla-Navarro, Juan Fernandez-Tajes, Claire Palles, Kitty Sherwood, Sarah E. W. Briggs, Victoria Svinti, Kevin Donnelly, Susan M. Farrington, James Blackmur, Peter G. Vaughan-Shaw, Xiao-Ou Shu, Yingchang Lu, Peter Broderick, James Studd, Tabitha A. Harrison, David V. Conti, Fredrick R. Schumacher, Marilena Melas, Gad Rennert, Mireia Obón-Santacana, Vicente Martín-Sánchez, Jae Hwan Oh, Jeongseon Kim, Sun Ha Jee, Keum Ji Jung, Sun-Seog Kweon, Min-Ho Shin, Aesun Shin, Yoon-Ok Ahn, Dong-Hyun Kim, Isao Oze, Wanqing Wen, Keitaro Matsuo, Koichi Matsuda, Chizu Tanikawa, Zefang Ren, Yu-Tang Gao, Wei-Hua Jia, John L. Hopper, Mark A. Jenkins, Aung Ko Win, Rish K. Pai, Jane C. Figueiredo, Robert W. Haile, Steven Gallinger, Michael O. Woods, Polly A. Newcomb, David Duggan, Jeremy P. Cheadle, Richard Kaplan, Rachel Kerr, David Kerr, Iva Kirac, Jan Böhm, Jukka-Pekka Mecklin, Pekka Jousilahti, Paul Knekt, Lauri A. Aaltonen, Harri Rissanen, Eero Pukkala, Johan G. Eriksson, Tatiana Cajuso, Ulrika Hänninen, Johanna Kondelin, Kimmo Palin, Tomas Tanskanen, Laura Renkonen-Sinisalo, Satu Männistö, Demetrius Albanes, Stephanie J. Weinstein, Edward Ruiz-Narvaez, Julie R. Palmer, Daniel D. Buchanan, Elizabeth A. Platz, Kala Visvanathan, Cornelia M. Ulrich, Erin Siegel, Stefanie Brezina, Andrea Gsur, Peter T. Campbell, Jenny Chang-Claude, Michael Hoffmeister, Hermann Brenner, Martha L. Slattery, John D. Potter, Kostas K. Tsilidis, Matthias B. Schulze, Marc J. Gunter, Neil Murphy, Antoni Castells, Sergi Castellví-Bel, Leticia Moreira, Volker Arndt, Anna Shcherbina, D. Timothy Bishop, Graham G. Giles, Melissa C. Southey, Gregory E. Idos, Kevin J. McDonnell, Zomoroda Abu-Ful, Joel K. Greenson, Katerina Shulman, Flavio Lejbkowicz, Kenneth Offit, Yu-Ru Su, Robert Steinfelder, Temitope O. Keku, Bethany van Guelpen, Thomas J. Hudson, Heather Hampel, Rachel Pearlman, Sonja I. Berndt, Richard B. Hayes, Marie Elena Martinez, Sushma S. Thomas, Paul D. P. Pharoah, Susanna C. Larsson, Yun Yen, Heinz-Josef Lenz, Emily White, Li Li, Kimberly F. Doheny, Elizabeth Pugh, Tameka Shelford, Andrew T. Chan, Marcia Cruz-Correa, Annika Lindblom, David J. Hunter, Amit D. Joshi, Clemens Schafmayer, Peter C. Scacheri, Anshul Kundaje, Robert E. Schoen, Jochen Hampe, Zsofia K. Stadler, Pavel Vodicka, Ludmila Vodickova, Veronika Vymetalkova, Christopher K. Edlund, W. James Gauderman, David Shibata, Amanda Toland, Sanford Markowitz, Andre Kim, Stephen J. Chanock, Franzel van Duijnhoven, Edith J. M. Feskens, Lori C. Sakoda, Manuela Gago-Dominguez, Alicja Wolk, Barbara Pardini, Liesel M. FitzGerald, Soo Chin Lee, Shuji Ogino, Stephanie A. Bien, Charles Kooperberg, Christopher I. Li, Yi Lin, Ross Prentice, Conghui Qu, Stéphane Bézieau, Taiki Yamaji, Norie Sawada, Motoki Iwasaki, Loic Le Marchand, Anna H. Wu, Chenxu Qu, Caroline E. McNeil, Gerhard Coetzee, Caroline Hayward, Ian J. Deary, Sarah E. Harris, Evropi Theodoratou, Stuart Reid, Marion Walker, Li Yin Ooi, Ken S. Lau, Hongyu Zhao, Li Hsu, Qiuyin Cai, Malcolm G. Dunlop, Stephen B. Gruber, Richard S. Houlston, Victor Moreno, Graham Casey, Ulrike Peters, Ian Tomlinson, and Wei Zheng

Subjects
Science
Abstract

Abstract Genome-wide association studies (GWAS) have identified more than 200 common genetic variants independently associated with colorectal cancer (CRC) risk, but the causal variants and target genes are mostly unknown. We sought to fine-map all known CRC risk loci using GWAS data from 100,204 cases and 154,587 controls of East Asian and European ancestry. Our stepwise conditional analyses revealed 238 independent association signals of CRC risk, each with a set of credible causal variants (CCVs), of which 28 signals had a single CCV. Our cis-eQTL/mQTL and colocalization analyses using colorectal tissue-specific transcriptome and methylome data separately from 1299 and 321 individuals, along with functional genomic investigation, uncovered 136 putative CRC susceptibility genes, including 56 genes not previously reported. Analyses of single-cell RNA-seq data from colorectal tissues revealed 17 putative CRC susceptibility genes with distinct expression patterns in specific cell types. Analyses of whole exome sequencing data provided additional support for several target genes identified in this study as CRC susceptibility genes. Enrichment analyses of the 136 genes uncover pathways not previously linked to CRC risk. Our study substantially expanded association signals for CRC and provided additional insight into the biological mechanisms underlying CRC development.

Published
2024
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16. Cost of illness due to respiratory syncytial virus acute lower respiratory tract infection among infants hospitalized in Argentina

Author

Julia Dvorkin, Emiliano Sosa, Elizabeth Vodicka, Ranju Baral, Andrea Sancilio, Karina Dueñas, Andrea Rodriguez, Carlos Rojas-Roque, Patricia B. Carruitero, Fernando P. Polack, Clint Pecenka, Romina Libster, and Mauricio T. Caballero

Subjects
Cost of illness, Direct medical cost, Respiratory syncytial virus, Acute lower respiratory tract infection, Public aspects of medicine, RA1-1270
Abstract

Abstract Background Information is scarce regarding the economic burden of respiratory syncytial virus (RSV) disease in low-resource settings. This study aimed to estimate the cost per episode of hospital admissions due to RSV severe disease in Argentina. Methods This is a prospective cohort study that collected information regarding 256 infants under 12 months of age with acute lower respiratory tract infection (ALRTI) due to RSV in two public hospitals of Buenos Aires between 2014 and 2016. Information on healthcare resource use was collected from the patient’s report and its associated costs were estimated based on the financial database and account records of the hospitals. We estimated the total cost per hospitalization due to RSV using the health system perspective. The costs were estimated in US dollars as of December 2022 (1 US dollar = 170 Argentine pesos). Results The mean costs per RSV hospitalization in infants was US$587.79 (95% confidence interval [CI] $535.24 – $640.33). The mean costs associated with pediatric intensive care unit (PICU) admission more than doubled from those at regular pediatric wards ($1,556.81 [95% CI $512.21 – $2,601.40] versus $556.53 [95% CI $514.59 – $598.48]). Conclusions This study shows the direct economic impact of acute severe RSV infection on the public health system in Argentina. The estimates obtained from this study could be used to inform cost-effectiveness analyses of new preventive RSV interventions being developed.

Published
2024
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17. European Aerosol Phenomenology -- 8: Harmonised Source Apportionment of Organic Aerosol using 22 Year-long ACSM/AMS Datasets

Author

Chen, Gang, Canonaco, Francesco, Tobler, Anna, Aas, Wenche, Alastuey, Andres, Allan, James, Atabakhsh, Samira, Aurela, Minna, Baltensperger, Urs, Bougiatioti, Aikaterini, De Brito, Joel F., Ceburnis, Darius, Chazeau, Benjamin, Chebaicheb, Hasna, Daellenbach, Kaspar R., Ehn, Mikael, Haddad, Imad El, Eleftheriadis, Konstantinos, Favez, Olivier, Flentje, Harald, Font, Anna, Fossum, Kirsten, Freney, Evelyn, Gini, Maria, Green, David C, Heikkinen, Liine, Herrmann, Hartmut, Kalogridis, Athina-Cerise, Keernik, Hannes, Lhotka, Radek, Lin, Chunshui, Lunder, Chris, Maasikmets, Marek, Manousakas, Manousos I., Marchand, Nicolas, Marin, Cristina, Marmureanu, Luminita, Mihalopoulos, Nikolaos, Močnik, Griša, Nęcki, Jaroslaw, O'Dowd, Colin, Ovadnevaite, Jurgita, Peter, Thomas, Petit, Jean-Eudes, Pikridas, Michael, Platt, Stephen Matthew, Pokorná, Petra, Poulain, Laurent, Priestman, Max, Riffault, Véronique, Rinaldi, Matteo, Różański, Kazimierz, Schwarz, Jaroslav, Sciare, Jean, Simon, Leïla, Skiba, Alicja, Slowik, Jay G., Sosedova, Yulia, Stavroulas, Iasonas, Styszko, Katarzyna, Teinemaa, Erik, Timonen, Hilkka, Tremper, Anja, Vasilescu, Jeni, Via, Marta, Vodička, Petr, Wiedensohler, Alfred, Zografou, Olga, Minguillón, María Cruz, and Prévôt, André S. H.

Subjects
Physics - Atmospheric and Oceanic Physics
Abstract

Organic aerosol (OA) is a key component to total submicron particulate matter (PM1), and comprehensive knowledge of OA sources across Europe is crucial to mitigate PM1 levels. Europe has a well-established air quality research infrastructure from which yearlong datasets using 21 aerosol chemical speciation monitors (ACSMs) and 1 aerosol mass spectrometer (AMS) were gathered during 2013-2019. It includes 9 non-urban and 13 urban sites. This study developed a state-of-the-art source apportionment protocol to analyse long-term OA mass spectrum data by applying the most advanced source apportionment strategies (i.e., rolling PMF, ME-2, and bootstrap). This harmonised protocol enables the quantifications of the most common OA components such as hydrocarbon-like OA (HOA), biomass burning OA (BBOA), cooking-like OA (COA), more oxidised-oxygenated OA (MO-OOA), and less oxidised-oxygenated OA (LO-OOA). Other components such as coal combustion OA (CCOA), solid fuel OA (SFOA: mainly mixture of coal and peat combustion), cigarette smoke OA (CSOA), sea salt (mostly inorganic but part of the OA mass spectrum), coffee OA, and ship industry OA could also be separated at a few specific sites. Oxygenated OA (OOA) components make up most of the submicron OA mass (average = 71.1%, a range of 43.7-100%). Solid fuel combustion-related OA components (i.e., BBOA, CCOA, and SFOA) are still considerable with in total 16.0% yearly contribution to the OA, yet mainly during winter months (21.4%). Overall, this comprehensive protocol works effectively across all sites governed by different sources and generates robust and consistent source apportionment results. Our work presents a comprehensive overview of OA sources in Europe with a unique combination of high time resolution and long-term data coverage (9-36 months), providing essential information to improve/validate air quality, health impact, and climate models.

Published
2022
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18. Endemic parkinsonism: clusters, biology and clinical features

Author

Menšíková, Katerina, Steele, John C., Rosales, Raymond, Colosimo, Carlo, Spencer, Peter, Lannuzel, Annie, Ugawa, Yoshikazu, Sasaki, Ryogen, Giménez-Roldán, Santiago, Matej, Radoslav, Tuckova, Lucie, Hrabos, Dominik, Kolarikova, Kristyna, Vodicka, Radek, Vrtel, Radek, Strnad, Miroslav, Hlustik, Petr, Otruba, Pavel, Prochazka, Martin, Bares, Martin, Boluda, Susana, Buee, Luc, Ransmayr, Gerhard, and Kaňovský, Petr

Published
2023
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19. Probing the diabetes and colorectal cancer relationship using gene – environment interaction analyses

Author

Dimou, Niki, Kim, Andre E., Flanagan, Orlagh, Murphy, Neil, Diez-Obrero, Virginia, Shcherbina, Anna, Aglago, Elom K., Bouras, Emmanouil, Campbell, Peter T., Casey, Graham, Gallinger, Steven, Gruber, Stephen B., Jenkins, Mark A., Lin, Yi, Moreno, Victor, Ruiz-Narvaez, Edward, Stern, Mariana C., Tian, Yu, Tsilidis, Kostas K., Arndt, Volker, Barry, Elizabeth L., Baurley, James W., Berndt, Sonja I., Bézieau, Stéphane, Bien, Stephanie A., Bishop, D. Timothy, Brenner, Hermann, Budiarto, Arif, Carreras-Torres, Robert, Cenggoro, Tjeng Wawan, Chan, Andrew T., Chang-Claude, Jenny, Chanock, Stephen J., Chen, Xuechen, Conti, David V., Dampier, Christopher H., Devall, Matthew, Drew, David A., Figueiredo, Jane C., Giles, Graham G., Gsur, Andrea, Harrison, Tabitha A., Hidaka, Akihisa, Hoffmeister, Michael, Huyghe, Jeroen R., Jordahl, Kristina, Kawaguchi, Eric, Keku, Temitope O., Larsson, Susanna C., Le Marchand, Loic, Lewinger, Juan Pablo, Li, Li, Mahesworo, Bharuno, Morrison, John, Newcomb, Polly A., Newton, Christina C., Obon-Santacana, Mireia, Ose, Jennifer, Pai, Rish K., Palmer, Julie R., Papadimitriou, Nikos, Pardamean, Bens, Peoples, Anita R., Pharoah, Paul D. P., Platz, Elizabeth A., Potter, John D., Rennert, Gad, Scacheri, Peter C., Schoen, Robert E., Su, Yu-Ru, Tangen, Catherine M., Thibodeau, Stephen N., Thomas, Duncan C., Ulrich, Cornelia M., Um, Caroline Y., van Duijnhoven, Franzel J. B., Visvanathan, Kala, Vodicka, Pavel, Vodickova, Ludmila, White, Emily, Wolk, Alicja, Woods, Michael O., Qu, Conghui, Kundaje, Anshul, Hsu, Li, Gauderman, W. James, Gunter, Marc J., and Peters, Ulrike

Published
2023
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20. Geometry of the Gaussian graphical model of the cycle

Author

Dinu, Rodica Andreea, Michałek, Mateusz, and Vodička, Martin

Subjects
Mathematics - Algebraic Geometry
Abstract

We prove a conjecture due to Sturmfels and Uhler concerning the degree of the projective variety associated to the Gaussian graphical model of the cycle. We involve new methods based on the intersection theory in the space of complete quadrics.

Published
2021

21. Reply to: Questioning the cycad theory of Kii ALS–PDC causation

Author

Menšíková, Katerina, Rosales, Raymond, Colosimo, Carlo, Spencer, Peter, Lannuzel, Annie, Ugawa, Yoshikazu, Sasaki, Ryogen, Giménez-Roldán, Santiago, Matej, Radoslav, Tuckova, Lucie, Hrabos, Dominik, Kolarikova, Kristyna, Vodicka, Radek, Vrtel, Radek, Strnad, Miroslav, Hlustik, Petr, Otruba, Pavel, Prochazka, Martin, Bares, Martin, Boluda, Susana, Buee, Luc, Ransmayr, Gerhard, and Kaňovský, Petr

Published
2024
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22. Genome-wide association studies and Mendelian randomization analyses provide insights into the causes of early-onset colorectal cancer

Author

Laskar, R.S., Qu, C., Huyghe, J.R., Harrison, T., Hayes, R.B., Cao, Y., Campbell, P.T., Steinfelder, R., Talukdar, F.R., Brenner, H., Ogino, S., Brendt, S., Bishop, D.T., Buchanan, D.D., Chan, A.T., Cotterchio, M., Gruber, S.B., Gsur, A., van Guelpen, B., Jenkins, M.A., Keku, T.O., Lynch, B.M., Le Marchand, L., Martin, R.M., McCarthy, K., Moreno, V., Pearlman, R., Song, M., Tsilidis, K.K., Vodička, P., Woods, M.O., Wu, K., Hsu, L., Gunter, M.J., Peters, U., and Murphy, N.

Published
2024
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23. Continuous short-term acclimation to moderate cold elicits cardioprotection in rats, and alters β-adrenergic signaling and immune status

Author

Marvanova, Aneta, Kasik, Petr, Elsnicova, Barbara, Tibenska, Veronika, Galatik, František, Hornikova, Daniela, Zvolska, Veronika, Vebr, Pavel, Vodicka, Petr, Hejnova, Lucie, Matous, Petr, Szeiff Bacova, Barbara, Sykora, Matus, Novotny, Jiri, Neuzil, Jiri, Kolar, Frantisek, Novakova, Olga, and Zurmanova, Jitka M.

Published
2023
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24. Combining Asian and European genome-wide association studies of colorectal cancer improves risk prediction across racial and ethnic populations

Author

Thomas, Minta, Su, Yu-Ru, Rosenthal, Elisabeth A., Sakoda, Lori C., Schmit, Stephanie L., Timofeeva, Maria N., Chen, Zhishan, Fernandez-Rozadilla, Ceres, Law, Philip J., Murphy, Neil, Carreras-Torres, Robert, Diez-Obrero, Virginia, van Duijnhoven, Franzel J. B., Jiang, Shangqing, Shin, Aesun, Wolk, Alicja, Phipps, Amanda I., Burnett-Hartman, Andrea, Gsur, Andrea, Chan, Andrew T., Zauber, Ann G., Wu, Anna H., Lindblom, Annika, Um, Caroline Y., Tangen, Catherine M., Gignoux, Chris, Newton, Christina, Haiman, Christopher A., Qu, Conghui, Bishop, D. Timothy, Buchanan, Daniel D., Crosslin, David R., Conti, David V., Kim, Dong-Hyun, Hauser, Elizabeth, White, Emily, Siegel, Erin, Schumacher, Fredrick R., Rennert, Gad, Giles, Graham G., Hampel, Heather, Brenner, Hermann, Oze, Isao, Oh, Jae Hwan, Lee, Jeffrey K., Schneider, Jennifer L., Chang-Claude, Jenny, Kim, Jeongseon, Huyghe, Jeroen R., Zheng, Jiayin, Hampe, Jochen, Greenson, Joel, Hopper, John L., Palmer, Julie R., Visvanathan, Kala, Matsuo, Keitaro, Matsuda, Koichi, Jung, Keum Ji, Li, Li, Le Marchand, Loic, Vodickova, Ludmila, Bujanda, Luis, Gunter, Marc J., Matejcic, Marco, Jenkins, Mark A., Slattery, Martha L., D’Amato, Mauro, Wang, Meilin, Hoffmeister, Michael, Woods, Michael O., Kim, Michelle, Song, Mingyang, Iwasaki, Motoki, Du, Mulong, Udaltsova, Natalia, Sawada, Norie, Vodicka, Pavel, Campbell, Peter T., Newcomb, Polly A., Cai, Qiuyin, Pearlman, Rachel, Pai, Rish K., Schoen, Robert E., Steinfelder, Robert S., Haile, Robert W., Vandenputtelaar, Rosita, Prentice, Ross L., Küry, Sébastien, Castellví-Bel, Sergi, Tsugane, Shoichiro, Berndt, Sonja I., Lee, Soo Chin, Brezina, Stefanie, Weinstein, Stephanie J., Chanock, Stephen J., Jee, Sun Ha, Kweon, Sun-Seog, Vadaparampil, Susan, Harrison, Tabitha A., Yamaji, Taiki, Keku, Temitope O., Vymetalkova, Veronika, Arndt, Volker, Jia, Wei-Hua, Shu, Xiao-Ou, Lin, Yi, Ahn, Yoon-Ok, Stadler, Zsofia K., Van Guelpen, Bethany, Ulrich, Cornelia M., Platz, Elizabeth A., Potter, John D., Li, Christopher I., Meester, Reinier, Moreno, Victor, Figueiredo, Jane C., Casey, Graham, Lansdorp Vogelaar, Iris, Dunlop, Malcolm G., Gruber, Stephen B., Hayes, Richard B., Pharoah, Paul D. P., Houlston, Richard S., Jarvik, Gail P., Tomlinson, Ian P., Zheng, Wei, Corley, Douglas A., Peters, Ulrike, and Hsu, Li

Published
2023
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27. Assessing the long-term economic impact of wheezing episodes after severe RSV disease in children from Argentina: a cost of illness analysis

Author

Ranju Baral, Clint Pecenka, Elisabeth Vodicka, Andrea Rodríguez, Julia Dvorkin, Emiliano M Sosa, Andrea Sancilio, Karina Dueñas, Carlos Rojas-Roque, Patricia B Carruitero, Fernando P Polack, and Mauricio T Caballero

Subjects
Public aspects of medicine, RA1-1270
Abstract

Introduction There is lack of available data on the economic burden of wheezing episodes after severe respiratory syncytial virus (RSV) infection. This study aimed to assess the cost incurred for wheezing episodes after a severe RSV infection in children from Argentina, considering both the public health system and societal perspectives.Methods A prospective cohort was conducted from 2014 to 2022 to assess the cost of illness of wheezing episodes after severe RSV disease in children from Buenos Aires, Argentina. Direct medical and non-medical costs were estimated, along with indirect costs per episode and patient. Data pertaining to healthcare resource utilisation, indirect expenses and parental out-of-pocket costs were obtained. The overall cost per hospitalisation and health visits was calculated. Costs were quantified in US dollars using the average exchange rate on the specific date of data collection.Results A total of 256 infants experienced severe RSV disease during their first year of life and were followed over a 5-year period in Buenos Aires. Overall, 150 children between 12 and 60 months presented 429 wheezing episodes. The median number of wheezing episodes per patient was 5 (IQR 3–7). The mean cost per wheezing episode was US$191.01 (95% CI 166.37 to 215.64). The total cost per episode of wheezing was significantly higher (p

Published
2024
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28. The leading coefficient of Lascoux polynomials

Author

Borzí, Alessio, Chen, Xiangying, Motwani, Harshit J., Venturello, Lorenzo, and Vodička, Martin

Subjects
Mathematics - Algebraic Geometry, Mathematics - Combinatorics, Mathematics - Optimization and Control, Mathematics - Statistics Theory, Primary: 62R01, 14N10, Secondary: 05E05, 14Q15, 60G15
Abstract

Lascoux polynomials have been recently introduced to prove polynomiality of the maximum-likelihood degree of linear concentration models. We find the leading coefficient of the Lascoux polynomials (type C) and their generalizations to the case of general matrices (type A) and skew symmetric matrices (type D). In particular, we determine the degrees of such polynomials. As an application, we find the degree of the polynomial $\delta(m,n,n-s)$ of the algebraic degree of semidefinite programming, and when $s=1$ we find its leading coefficient for types C, A and D.

Published
2021

29. Grounded Framework for Culturally Relevant and Responsive Music Teaching

Author

Palmer, Elizabeth S., Vodicka, Jason, Huynh, Tina, D'Alexander, Christine, and Crawford, Lisa

Abstract

Building upon the work of Ladson-Billings, Lind and McKoy, and Shaw, our proposed framework takes into consideration the depth and breadth of musical experiences and contexts, musical content, and the diversity of musical cultures. The proposed framework includes four quadrants: (a) teacher competencies, (b) informed choices, (c) authenticity, and (d) holistic and comparative lessons. The framework provides K-16 teachers with tangible, accessible, and actionable methods for implementing a teaching pedagogy that has often been misunderstood or implemented without fidelity, and therefore ineffective. Each quadrant's description and detail provide educators with guidance, supporting their individual musical growth, facilitating authentic relationships with students, authentic performances, and careful idea development for lesson planning that is inclusive of multiple musical perspectives and origins. Muñiz and Richards et al. acknowledged that community support and teacher capacity are essential for culturally relevant pedagogy to be implemented effectively, thus increasing students' academic growth.

Published
2022
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30. Continuous short-term acclimation to moderate cold elicits cardioprotection in rats, and alters β-adrenergic signaling and immune status

Author

Aneta Marvanova, Petr Kasik, Barbara Elsnicova, Veronika Tibenska, František Galatik, Daniela Hornikova, Veronika Zvolska, Pavel Vebr, Petr Vodicka, Lucie Hejnova, Petr Matous, Barbara Szeiff Bacova, Matus Sykora, Jiri Novotny, Jiri Neuzil, Frantisek Kolar, Olga Novakova, and Jitka M. Zurmanova

Subjects
Medicine, Science
Abstract

Abstract Moderate cold acclimation (MCA) is a non-invasive intervention mitigating effects of various pathological conditions including myocardial infarction. We aim to determine the shortest cardioprotective regimen of MCA and the response of β1/2/3-adrenoceptors (β-AR), its downstream signaling, and inflammatory status, which play a role in cell-survival during myocardial infarction. Adult male Wistar rats were acclimated (9 °C, 1–3-10 days). Infarct size, echocardiography, western blotting, ELISA, mitochondrial respirometry, receptor binding assay, and quantitative immunofluorescence microscopy were carried out on left ventricular myocardium and brown adipose tissue (BAT). MultiPlex analysis of cytokines and chemokines in serum was accomplished. We found that short-term MCA reduced myocardial infarction, improved resistance of mitochondria to Ca2+-overload, and downregulated β1-ARs. The β2-ARs/protein kinase B/Akt were attenuated while β3-ARs translocated on the T-tubular system suggesting its activation. Protein kinase G (PKG) translocated to sarcoplasmic reticulum and phosphorylation of AMPKThr172 increased after 10 days. Principal component analysis revealed a significant shift in cytokine/chemokine serum levels on day 10 of acclimation, which corresponds to maturation of BAT. In conclusion, short-term MCA increases heart resilience to ischemia without any negative side effects such as hypertension or hypertrophy. Cold-elicited cardioprotection is accompanied by β1/2-AR desensitization, activation of the β3-AR/PKG/AMPK pathways, and an immunomodulatory effect.

Published
2023
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31. Combining Asian and European genome-wide association studies of colorectal cancer improves risk prediction across racial and ethnic populations

Author

Minta Thomas, Yu-Ru Su, Elisabeth A. Rosenthal, Lori C. Sakoda, Stephanie L. Schmit, Maria N. Timofeeva, Zhishan Chen, Ceres Fernandez-Rozadilla, Philip J. Law, Neil Murphy, Robert Carreras-Torres, Virginia Diez-Obrero, Franzel J. B. van Duijnhoven, Shangqing Jiang, Aesun Shin, Alicja Wolk, Amanda I. Phipps, Andrea Burnett-Hartman, Andrea Gsur, Andrew T. Chan, Ann G. Zauber, Anna H. Wu, Annika Lindblom, Caroline Y. Um, Catherine M. Tangen, Chris Gignoux, Christina Newton, Christopher A. Haiman, Conghui Qu, D. Timothy Bishop, Daniel D. Buchanan, David R. Crosslin, David V. Conti, Dong-Hyun Kim, Elizabeth Hauser, Emily White, Erin Siegel, Fredrick R. Schumacher, Gad Rennert, Graham G. Giles, Heather Hampel, Hermann Brenner, Isao Oze, Jae Hwan Oh, Jeffrey K. Lee, Jennifer L. Schneider, Jenny Chang-Claude, Jeongseon Kim, Jeroen R. Huyghe, Jiayin Zheng, Jochen Hampe, Joel Greenson, John L. Hopper, Julie R. Palmer, Kala Visvanathan, Keitaro Matsuo, Koichi Matsuda, Keum Ji Jung, Li Li, Loic Le Marchand, Ludmila Vodickova, Luis Bujanda, Marc J. Gunter, Marco Matejcic, Mark A. Jenkins, Martha L. Slattery, Mauro D’Amato, Meilin Wang, Michael Hoffmeister, Michael O. Woods, Michelle Kim, Mingyang Song, Motoki Iwasaki, Mulong Du, Natalia Udaltsova, Norie Sawada, Pavel Vodicka, Peter T. Campbell, Polly A. Newcomb, Qiuyin Cai, Rachel Pearlman, Rish K. Pai, Robert E. Schoen, Robert S. Steinfelder, Robert W. Haile, Rosita Vandenputtelaar, Ross L. Prentice, Sébastien Küry, Sergi Castellví-Bel, Shoichiro Tsugane, Sonja I. Berndt, Soo Chin Lee, Stefanie Brezina, Stephanie J. Weinstein, Stephen J. Chanock, Sun Ha Jee, Sun-Seog Kweon, Susan Vadaparampil, Tabitha A. Harrison, Taiki Yamaji, Temitope O. Keku, Veronika Vymetalkova, Volker Arndt, Wei-Hua Jia, Xiao-Ou Shu, Yi Lin, Yoon-Ok Ahn, Zsofia K. Stadler, Bethany Van Guelpen, Cornelia M. Ulrich, Elizabeth A. Platz, John D. Potter, Christopher I. Li, Reinier Meester, Victor Moreno, Jane C. Figueiredo, Graham Casey, Iris Lansdorp Vogelaar, Malcolm G. Dunlop, Stephen B. Gruber, Richard B. Hayes, Paul D. P. Pharoah, Richard S. Houlston, Gail P. Jarvik, Ian P. Tomlinson, Wei Zheng, Douglas A. Corley, Ulrike Peters, and Li Hsu

Subjects
Science
Abstract

Abstract Polygenic risk scores (PRS) have great potential to guide precision colorectal cancer (CRC) prevention by identifying those at higher risk to undertake targeted screening. However, current PRS using European ancestry data have sub-optimal performance in non-European ancestry populations, limiting their utility among these populations. Towards addressing this deficiency, we expand PRS development for CRC by incorporating Asian ancestry data (21,731 cases; 47,444 controls) into European ancestry training datasets (78,473 cases; 107,143 controls). The AUC estimates (95% CI) of PRS are 0.63(0.62-0.64), 0.59(0.57-0.61), 0.62(0.60-0.63), and 0.65(0.63-0.66) in independent datasets including 1681-3651 cases and 8696-115,105 controls of Asian, Black/African American, Latinx/Hispanic, and non-Hispanic White, respectively. They are significantly better than the European-centric PRS in all four major US racial and ethnic groups (p-values

Published
2023
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32. Cohen-Macaulay and Gorenstein tangential varieties of the Segre-Veronese Varieties

Author

Khadam, M. Azeem and Vodička, Martin

Subjects
Mathematics - Algebraic Geometry, 14M25, 14M17, 13P25
Abstract

We classify the tangential varieties of the Segre-Veronese varieties which are Cohen-Macaulay or Gorenstein., Comment: Accepted for publication in Bulletin of the London Mathematical Society

Published
2020

33. Complete quadrics: Schubert calculus for Gaussian models and semidefinite programming

Author

Manivel, Laurent, Michałek, Mateusz, Monin, Leonid, Seynnaeve, Tim, and Vodička, Martin

Subjects
Mathematics - Algebraic Geometry, Mathematics - Combinatorics, Mathematics - Representation Theory, Mathematics - Statistics Theory, Primary: 62R01, 14M17, 14N10, Secondary: 05E05, 14C17, 14E05, 14M15, 14Q15, 60G15
Abstract

We establish connections between: the maximum likelihood degree (ML-degree) for linear concentration models, the algebraic degree of semidefinite programming (SDP), and Schubert calculus for complete quadrics. We prove a conjecture by Sturmfels and Uhler on the polynomiality of the ML-degree. We also prove a conjecture by Nie, Ranestad and Sturmfels providing an explicit formula for the degree of SDP. The interactions between the three fields shed new light on the asymptotic behaviour of enumerative invariants for the variety of complete quadrics. We also extend these results to spaces of general matrices and of skew-symmetric matrices., Comment: 35 pages, comments welcome

Published
2020

34. Targeted mass spectrometry for monitoring of neural differentiation

Author

Sucha, Rita, Kubickova, Martina, Cervenka, Jakub, Hruska-Plochan, Marian, Bohaciakova, Dasa, Kepkova, Katerina Vodickova, Novakova, Tereza, Budkova, Katerina, Susor, Andrej, Marsala, Martin, Motlik, Jan, Kovarova, Hana, and Vodicka, Petr

Subjects
Stem Cell Research - Nonembryonic - Human, Stem Cell Research, Regenerative Medicine, Biotechnology, Neurosciences, Generic health relevance, Biomarkers, Cell Differentiation, Cell Line, Cell Lineage, Gene Expression Profiling, Gene Expression Regulation, Developmental, Humans, Immunohistochemistry, Mass Spectrometry, Neural Stem Cells, Neuroglia, Neurons, Neural stem cell, Neural differentiation, Selected reaction monitoring, Mass spectrometry, Cell line characterization, Protein marker, Other Biological Sciences
Abstract

Human multipotent neural stem cells could effectively be used for the treatment of a variety of neurological disorders. However, a defining signature of neural stem cell lines that would be expandable, non-tumorigenic, and differentiate into desirable neuronal/glial phenotype after in vivo grafting is not yet defined. Employing a mass spectrometry approach, based on selected reaction monitoring, we tested a panel of well-described culture conditions, and measured levels of protein markers routinely used to probe neural differentiation, i.e. POU5F1 (OCT4), SOX2, NES, DCX, TUBB3, MAP2, S100B, GFAP, GALC, and OLIG1. Our multiplexed assay enabled us to simultaneously identify the presence of pluripotent, multipotent, and lineage-committed neural cells, thus representing a powerful tool to optimize novel and highly specific propagation and differentiation protocols. The multiplexing capacity of this method permits the addition of other newly identified cell type-specific markers to further increase the specificity and quantitative accuracy in detecting targeted cell populations. Such an expandable assay may gain the advantage over traditional antibody-based assays, and represents a method of choice for quality control of neural stem cell lines intended for clinical use.

Published
2021

35. Postdischarge nausea and vomiting (PDNV) in children: A review and observational study

Author

Michal Frelich, Vojtech Vodicka, Ondrej Jor, Filip Bursa, Martin Formanek, Peter Sklienka, and Vaclav Prochazka

Subjects
postoperative nausea, postoperative vomiting, postdischarge nausea, postdischarge vomiting, antiemetics, setrons, Medicine
Abstract

Postdischarge nausea and vomiting (PDNV) cause substantial pediatric morbidity with potentially serious postoperative complications. However, few studies have addressed PDNV prevention and treatment in pediatric patients. Here we searched the literature and processed it in a narrative review describing PDNV incidence, risk factors, and management in pediatric patients.. A successful strategy for reducing PDNV considers both the pharmacokinetics of the antiemetic agents and the principle of multimodal prophylaxis, utilizing agents of different pharmacologic classes. Since many highly effective antiemetic agents have relatively short half-lives, a different approach must be used to prevent PDNV. A combination of oral and intravenous medications with longer half-lives, such as palonosetron or aprepitant, can be used. In addition, we designed a prospective observational study with the primary objective of determining PDNV incidence. In our study group of 205 children, the overall PDNV incidence was 14.6% (30 of 205), including 21 children suffering from nausea and 9 suffering from vomiting.

Published
2023
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36. The dynamics of telomere length in primary and metastatic colorectal cancer lesions

Author

Michal Kroupa, Ondrej Kubecek, Kristyna Tomasova, Petr Hanak, Marketa Krupova, Klara Cervena, Anna Siskova, Jachym Rosendorf, Petr Hosek, Ludmila Vodickova, Pavel Vodicka, Vaclav Liska, Stanislav John, Veronika Vymetalkova, and Jiri Petera

Subjects
Medicine, Science
Abstract

Abstract Telomeric sequences, the structures comprised of hexanucleotide repeats and associated proteins, play a pivotal role in chromosome end protection and preservation of genomic stability. Herein we address telomere length (TL) dynamics in primary colorectal cancer (CRC) tumour tissues and corresponding liver metastases. TL was measured by multiplex monochrome real-time qPCR in paired samples of primary tumours and liver metastases along with non-cancerous reference tissues obtained from 51 patients diagnosed with metastatic CRC. Telomere shortening was observed in the majority of primary tumour tissues compared to non-cancerous mucosa (84.1%, p

Published
2023
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37. Gorenstein property for phylogenetic trivalent trees

Author

Dinu, Rodica and Vodička, Martin

Subjects
Mathematics - Combinatorics, Mathematics - Algebraic Geometry
Abstract

We study the Gorenstein property for phylogenetic group-based models. We prove that for the groups $\mathbb Z_3$ and $\mathbb Z_2\times \mathbb Z_2$ and trivalent trees the associated polytopes are always Gorenstein extending the results of Buczy\'nska and Wi\'sniewski for the group $\mathbb Z_2$.

Published
2020

38. Estimates of the national burden of respiratory syncytial virus in Kenyan children aged under 5 years, 2010–2018

Author

Bryan O. Nyawanda, Nickson Murunga, Nancy A. Otieno, Godfrey Bigogo, Joyce U. Nyiro, Elisabeth Vodicka, Marc Bulterys, D. James Nokes, Patrick K. Munywoki, and Gideon O. Emukule

Subjects
Burden, Epidemiology, National estimates, Pneumonia, Respiratory syncytial virus, Medicine
Abstract

Abstract Background Respiratory syncytial virus (RSV) is among the leading childhood causes of viral pneumonia worldwide. Establishing RSV-associated morbidity and mortality is important in informing the development, delivery strategies, and evaluation of interventions. Methods Using data collected during 2010–2018 from base regions (population-based surveillance studies in western Kenya and the Kilifi Health and Demographic Surveillance Study), we estimated age-specific rates of acute respiratory illness (ARI), severe acute respiratory illness (SARI—defined as hospitalization with cough or difficulty breathing with onset within the past 10 days), and SARI-associated deaths. We extrapolated the rates from the base regions to other regions of Kenya, while adjusting for risk factors of ARI and healthcare seeking behavior, and finally applied the proportions of RSV-positive cases identified from various sentinel and study facilities to the rates to obtain regional age-specific rates of RSV-associated outpatient and non-medically attended ARI and hospitalized SARI and severe ARI that was not hospitalized (non-hospitalized SARI). We applied age-specific RSV case fatality ratios to SARI to obtain estimates of RSV-associated in- and out-of-hospital deaths. Results Among Kenyan children aged

Published
2023
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39. Estimating the economic burden of respiratory syncytial virus infections in infants in Vietnam: a cohort study

Author

Lien Anh Ha Do, Elisabeth Vodicka, An Nguyen, Thi Ngoc Kim Le, Thi Thanh Hai Nguyen, Quang Tung Thai, Van Quang Pham, Thanh Uyen Pham, Thu Ngoc Nguyen, Kim Mulholland, Minh Thang Cao, Nguyen Thanh Nhan Le, Anh Tuan Tran, and Clinton Pecenka

Subjects
Respiratory syncytial virus, Lower respiratory tract infections, Direct cost, Indirect cost, Cost of illness, Infectious and parasitic diseases, RC109-216
Abstract

Abstract Background Little information is available on the costs of respiratory syncytial virus (RSV) in Vietnam or other low- and middle-income countries. Our study estimated the costs of LRTIs associated with RSV infection among children in southern Vietnam. Methods We conducted a prospective cohort study evaluating household and societal costs associated with LRTIs stratified by RSV status and severity among children under 2 years old who sought care at a major pediatric referral hospital in southern Vietnam. Enrollment periods were September 2019–December 2019, October 2020–June 2021 and October 2021–December 2021. RSV status was confirmed by a validated RT-PCR assay. RSV rapid detection antigen (RDA) test performance was also evaluated. Data on resource utilization, direct medical and non-medical costs, and indirect costs were collected from billing records and supplemented by patient-level questionnaires. All costs are reported in 2022 US dollars. Results 536 children were enrolled in the study, with a median age of 7 months (interquartile range [IQR] 3–12). This included 210 (39.2%) children from the outpatient department, 318 children (59.3%) from the inpatient respiratory department (RD), and 8 children (1.5%) from the intensive care unit (ICU). Nearly 20% (105/536) were RSV positive: 3.9 percent (21/536) from the outpatient department, 15.7% (84/536) from the RD, and none from the ICU. The median total cost associated with LRTI per patient was US$52 (IQR 32–86) for outpatients and US$184 (IQR 109–287) for RD inpatients. For RSV-associated LRTIs, the median total cost per infection episode per patient was US$52 (IQR 32–85) for outpatients and US$165 (IQR 95–249) for RD inpatients. Total out-of-pocket costs of one non-ICU admission of RSV-associated LRTI ranged from 32%-70% of the monthly minimum wage per person (US$160) in Ho Chi Minh City. The sensitivity and the specificity of RSV RDA test were 88.2% (95% CI 63.6–98.5%) and 100% (95% CI 93.3–100%), respectively. Conclusion These are the first data reporting the substantial economic burden of RSV-associated illness in young children in Vietnam. This study informs policymakers in planning health care resources and highlights the urgency of RSV disease prevention.

Published
2023
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40. Deciphering colorectal cancer genetics through multi-omic analysis of 100,204 cases and 154,587 controls of European and east Asian ancestries

Author

Fernandez-Rozadilla, Ceres, Timofeeva, Maria, Chen, Zhishan, Law, Philip, Thomas, Minta, Schmit, Stephanie, Díez-Obrero, Virginia, Hsu, Li, Fernandez-Tajes, Juan, Palles, Claire, Sherwood, Kitty, Briggs, Sarah, Svinti, Victoria, Donnelly, Kevin, Farrington, Susan, Blackmur, James, Vaughan-Shaw, Peter, Shu, Xiao-ou, Long, Jirong, Cai, Qiuyin, Guo, Xingyi, Lu, Yingchang, Broderick, Peter, Studd, James, Huyghe, Jeroen, Harrison, Tabitha, Conti, David, Dampier, Christopher, Devall, Mathew, Schumacher, Fredrick, Melas, Marilena, Rennert, Gad, Obón-Santacana, Mireia, Martín-Sánchez, Vicente, Moratalla-Navarro, Ferran, Oh, Jae Hwan, Kim, Jeongseon, Jee, Sun Ha, Jung, Keum Ji, Kweon, Sun-Seog, Shin, Min-Ho, Shin, Aesun, Ahn, Yoon-Ok, Kim, Dong-Hyun, Oze, Isao, Wen, Wanqing, Matsuo, Keitaro, Matsuda, Koichi, Tanikawa, Chizu, Ren, Zefang, Gao, Yu-Tang, Jia, Wei-Hua, Hopper, John, Jenkins, Mark, Win, Aung Ko, Pai, Rish, Figueiredo, Jane, Haile, Robert, Gallinger, Steven, Woods, Michael, Newcomb, Polly, Duggan, David, Cheadle, Jeremy, Kaplan, Richard, Maughan, Timothy, Kerr, Rachel, Kerr, David, Kirac, Iva, Böhm, Jan, Mecklin, Lukka-Pekka, Jousilahti, Pekka, Knekt, Paul, Aaltonen, Lauri, Rissanen, Harri, Pukkala, Eero, Eriksson, Johan, Cajuso, Tatiana, Hänninen, Ulrika, Kondelin, Johanna, Palin, Kimmo, Tanskanen, Tomas, Renkonen-Sinisalo, Laura, Zanke, Brent, Männistö, Satu, Albanes, Demetrius, Weinstein, Stephanie, Ruiz-Narvaez, Edward, Palmer, Julie, Buchanan, Daniel, Platz, Elizabeth, Visvanathan, Kala, Ulrich, Cornelia, Siegel, Erin, Brezina, Stefanie, Gsur, Andrea, Campbell, Peter, Chang-Claude, Jenny, Hoffmeister, Michael, Brenner, Hermann, Slattery, Martha, Potter, John, Tsilidis, Konstantinos, Schulze, Matthias, Gunter, Marc, Murphy, Neil, Castells, Antoni, Castellví-Bel, Sergi, Moreira, Leticia, Arndt, Volker, Shcherbina, Anna, Stern, Mariana, Pardamean, Bens, Bishop, Timothy, Giles, Graham, Southey, Melissa, Idos, Gregory, McDonnell, Kevin, Abu-Ful, Zomoroda, Greenson, Joel, Shulman, Katerina, Lejbkowicz, Flavio, Offit, Kenneth, Su, Yu-Ru, Steinfelder, Robert, Keku, Temitope, van Guelpen, Bethany, Hudson, Thomas, Hampel, Heather, Pearlman, Rachel, Berndt, Sonja, Hayes, Richard, Martinez, Marie Elena, Thomas, Sushma, Corley, Douglas, Pharoah, Paul, Larsson, Susanna, Yen, Yun, Lenz, Heinz-Josef, White, Emily, Li, Li, Doheny, Kimberly, Pugh, Elizabeth, Shelford, Tameka, Chan, Andrew, Cruz-Correa, Marcia, Lindblom, Annika, Hunter, David, Joshi, Amit, Schafmayer, Clemens, Scacheri, Peter, Kundaje, Anshul, Nickerson, Deborah, Schoen, Robert, Hampe, Jochen, Stadler, Zsofia, Vodicka, Pavel, Vodickova, Ludmila, Vymetalkova, Veronika, Papadopoulos, Nickolas, Edlund, Chistopher, Gauderman, William, Thomas, Duncan, Shibata, David, Toland, Amanda, Markowitz, Sanford, Kim, Andre, Chanock, Stephen, van Duijnhoven, Franzel, Feskens, Edith, Sakoda, Lori, Gago-Dominguez, Manuela, Wolk, Alicja, Naccarati, Alessio, Pardini, Barbara, FitzGerald, Liesel, Lee, Soo Chin, Ogino, Shuji, Bien, Stephanie, Kooperberg, Charles, Li, Christopher, Lin, Yi, Prentice, Ross, Qu, Conghui, Bézieau, Stéphane, Tangen, Catherine, Mardis, Elaine, Yamaji, Taiki, Sawada, Norie, Iwasaki, Motoki, Haiman, Christopher, Le Marchand, Loic, Wu, Anna, Qu, Chenxu, McNeil, Caroline, Coetzee, Gerhard, Hayward, Caroline, Deary, Ian, Harris, Sarah, Theodoratou, Evropi, Reid, Stuart, Walker, Marion, Ooi, Li Yin, Moreno, Victor, Casey, Graham, Gruber, Stephen, Tomlinson, Ian, Zheng, Wei, Dunlop, Malcolm, Houlston, Richard, and Peters, Ulrike

Published
2023
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42. A monolithic model for phase-field fracture and waves in solid-fluid media towards earthquakes

Author

Roubíček, Tomáš and Vodička, Roman

Subjects
Physics - Geophysics, 74F10, 74J10, 74R20, 74S05, 86-08
Abstract

Coupling of rupture processes in solids with waves also propagating in fluids is a prominent phenomenon arising during tectonic earthquakes. It is executed here in a single `monolithic' model which can asymptotically capture both damageable solids (rocks) and (visco-)elastic fluids (outer core or oceans). Both ruptures on pre-existing lithospheric faults and a birth of new faults in compact rocks are covered by this model, together with emission and propagation of seismic waves, including, e.g., reflection of S-waves and refraction of P-waves on the solid-fluid interfaces. A robust, energy conserving, and convergent staggered FEM discretisation is devised. Using a rather simplified variant of such models for rupture, three computational experiments documenting the applicability of this approach are presented. Some extensions of the model towards more realistic geophysical modelling are outlined, too.

Published
2019
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43. Gorenstein graphic matroids

Author

Hibi, Takayuki, Lasoń, Michał, Matsuda, Kazunori, Michałek, Mateusz, and Vodička, Martin

Subjects
Mathematics - Combinatorics, Mathematics - Commutative Algebra, 05B35, 05C75, 13H10, 14M25
Abstract

The toric variety of a matroid is projectively normal, and therefore it is Cohen-Macaulay. We provide a complete graph-theoretic classification when the toric variety of a graphic matroid is Gorenstein.

Published
2019
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44. Normality of the Kimura 3-parameter model

Author

Vodička, Martin

Subjects
Mathematics - Algebraic Geometry
Abstract

The Kimura 3-parameter model is one of the most fundamental phylogenetic models in algebraic statistics. We prove that all algebraic varieties associated to this model are projectively normal, confirming a conjecture of Michalek.

Published
2019

45. Diffuse Large B-Cell Lymphoma (DLBCL): Early Patient Management and Emerging Treatment Options

Author

Vodicka P, Klener P, and Trneny M

Subjects
diffuse large b-cell lymphoma, first-line therapy, r-chop, agnostic therapy, tailored therapy, polatuzumab vedotin, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

Prokop Vodicka, Pavel Klener, Marek Trneny First Department of Medicine, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech RepublicCorrespondence: Marek Trneny, First Department of Medicine, First Faculty of Medicine, Charles University and General University Hospital, U Nemocnice 499/2, Prague, 128 08, Czech Republic, Tel +420 224 96 25 27, Fax +420 224 96 35 56, Email trneny@cesnet.czAbstract: Diffuse large B-cell lymphoma (DLBCL) represents a curable disease with a 60– 70% chance of cure with current R-CHOP chemoimmunotherapy. However, 30– 40% of patients are refractory or relapsing. Many attempts failed to improve the outcome of DLBCL patients, including the intensification of R-CHOP regimen, consolidation, or maintenance therapy since the introduction of R-CHOP in 2000. Better understanding of both molecular biology of lymphoma cells and the tumor microenvironment raised the hope for future improvement of DLBCL patients’ survival. Novel molecular findings have initiated clinical trials exploring targeted therapy based on driver genetic alterations with an intent to improve survival of high-risk subsets of patients. But the preliminary results remain ambiguous. The approach “agnostic” to specific molecular alterations of lymphoma cell includes antibody-drug conjugates (especially polatuzumab vedotin), immunotherapy comprising different antibodies with immunomodulatory effect (tafasitamab, lenalidomide), and T-cell engaging therapy (bispecific antibodies, early use of CAR T-cell). This approach could increase the cure rates and change the current therapeutic paradigm. However, better prognostic stratification, smarter designs of clinical trials, modification of endpoints including the use of ctDNA are needed. This review covers the complexity of DLBCL management.Keywords: diffuse large B-cell lymphoma, first-line therapy, R-CHOP, agnostic therapy, tailored therapy, polatuzumab vedotin

Published
2022

46. Experimental investigation of combustion engine with novel jacket and flue gas heat recovery

Author

Jan Spale, Jan Pavlicko, Vaclav Vodicka, Jakub Mascuch, and Vaclav Novotny

Subjects
Internal combustion engine, Waste heat recovery, Organic Rankine cycle, ORC, Experimental, Biomass, Electrical engineering. Electronics. Nuclear engineering, TK1-9971
Abstract

Internal combustion engines (ICE) are utilized in a number of energy and transportation systems and with the prospect of synthetic green fuels have also secured a place in the future low emission systems. Still, aiming at the effective utilization of the fuel suggests an addition of waste heat recovery systems such as organic Rankine cycle (ORC) to boost electric efficiency. Greater widespread of the ORC integration into the ICE systems is however limited from multiple aspects. Furthermore, when these systems are employed, they are typically applied only for flue gas waste heat utilization, while the large amounts of lower temperature jacket cooling heat remain unutilized, or at the cost of high system complexity. Direct cooling of the ICE jacket by the ORC working fluid has been previously theoretically proposed to tackle some of them. Complexity of the system can be reduced while more waste heat can be effectively transferred from the ICE jacket cooling to the ORC. Here we propose further configuration of ICE waste heat sources integration into a biomass fired ORC unit, creating a multi-fuel system. Such system offers the possibility to increase the electricity demand while reducing biomass consumption. This system has been experimentally explored on a case of a 3 kWe/50 kWth micro-cogeneration ORC and an 8 kWeICE. The experimental data are evaluated in comparison to the theoretically predicted operation. A specific control system has been developed for this system to be easily operated. The results, experience and operation verification from the ICE jacket cooling with the ORC fluid can be also utilized in the construction for waste heat recovery ORC integrated to ICE for higher electrical efficiency. Integration of combined direct jacket and flue gas heat recovery increased the overall electrical efficiency of the system from about 5% for operation of standalone ORC to over 20% for full ICE power.

Published
2022
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47. Fidelity varies in the symbiosis between a gutless marine worm and its microbial consortium

Author

Yui Sato, Juliane Wippler, Cecilia Wentrup, Rebecca Ansorge, Miriam Sadowski, Harald Gruber-Vodicka, Nicole Dubilier, and Manuel Kleiner

Subjects
Microbiome, Animal-bacterial symbiosis, Symbiont transmission, Phylosymbiosis, Intraspecific genetic variation, Microbial ecology, QR100-130
Abstract

Abstract Background Many animals live in intimate associations with a species-rich microbiome. A key factor in maintaining these beneficial associations is fidelity, defined as the stability of associations between hosts and their microbiota over multiple host generations. Fidelity has been well studied in terrestrial hosts, particularly insects, over longer macroevolutionary time. In contrast, little is known about fidelity in marine animals with species-rich microbiomes at short microevolutionary time scales, that is at the level of a single host population. Given that natural selection acts most directly on local populations, studies of microevolutionary partner fidelity are important for revealing the ecological and evolutionary processes that drive intimate beneficial associations within animal species. Results In this study on the obligate symbiosis between the gutless marine annelid Olavius algarvensis and its consortium of seven co-occurring bacterial symbionts, we show that partner fidelity varies across symbiont species from strict to absent over short microevolutionary time. Using a low-coverage sequencing approach that has not yet been applied to microbial community analyses, we analysed the metagenomes of 80 O. algarvensis individuals from the Mediterranean and compared host mitochondrial and symbiont phylogenies based on single-nucleotide polymorphisms across genomes. Fidelity was highest for the two chemoautotrophic, sulphur-oxidizing symbionts that dominated the microbial consortium of all O. algarvensis individuals. In contrast, fidelity was only intermediate to absent in the sulphate-reducing and spirochaetal symbionts with lower abundance. These differences in fidelity are likely driven by both selective and stochastic forces acting on the consistency with which symbionts are vertically transmitted. Conclusions We hypothesize that variable degrees of fidelity are advantageous for O. algarvensis by allowing the faithful transmission of their nutritionally most important symbionts and flexibility in the acquisition of other symbionts that promote ecological plasticity in the acquisition of environmental resources. Video Abstract

Published
2022
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48. Sugars dominate the seagrass rhizosphere

Author

Sogin, E. Maggie, Michellod, Dolma, Gruber-Vodicka, Harald R., Bourceau, Patric, Geier, Benedikt, Meier, Dimitri V., Seidel, Michael, Ahmerkamp, Soeren, Schorn, Sina, D’Angelo, Grace, Procaccini, Gabriele, Dubilier, Nicole, and Liebeke, Manuel

Published
2022
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