Author: "Minna, M." / Publication Type: Electronic Resources - Searchworks@Jio Institute Digital Library Search Results

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Start Over Author "Minna, M." Publication Type Electronic Resources

101 results on '"Minna, M."'

1. Doxing ethics

Author: Naskali, Juhani, Rantanen, Minna M., Rottenkolber, Maria, K. Kimppa, Kai, Naskali, Juhani, Rantanen, Minna M., Rottenkolber, Maria, and K. Kimppa, Kai
Published: 2024

2. Acquisition of complement clause constructions by English-speaking children : a corpus investigation

Author: Kirjavainen, Minna M.
Subjects: 420.1
Abstract: The acquisition of complement clause constructions in English, like in other languages, has received relatively little attention from researchers, even though the development of these complex sentence structures can shed light on the language acquisition process, and can hence inform us about the accurateness of suggestions put forward by different theoretical stances. The previous corpus research that has been conducted in this field has been based on relatively sparsely collected datasets, while a large majority of experimental studies have focused on sentences with to-infinitive clauses as control structures often ignoring other aspects of development and other construction types. Due to the need for a detailed investigation, the present thesis first investigated the development of all finite and non-finite complement clause constructions in one English-speaking child's densely collected data (5h/week). This analysis showed that many complement clause constructions appear within a relatively short period of time during the latter half of the third year of life. We suggest that input, cognitive/functional salience, and semantic and pragmatic factors are likely to play an important role in the development and appearance of these constructions. The effect of input was then investigated further by looking at (1) complementizer omission errors produced with certain non-finite complement clauses, and (2) ACC-for- NOM lpsg sentence subject errors in 14-17 children's speech. These errors were found to be tightly linked to the competition between different forms in the input that the children were exposed to. The complementizer omissions were shown to be related to children learning one- (want-X, going-X) and two-word chunks (want-to-X, going-to-X), which were competing for output. The ACC-for-NOM errors were linked to the input and competition of I-verb sequences in simple sentences and me-verb sequences in non-finite complement clause constructions (e. g. Let me do that). Finally, the effect of input was investigated through a narrower window by analysing how input in the immediate discourse context affects one child's production of that- and to-infinitive complement constructions in naturalistic conversation between 2;9 - 3;11. The two constructions were found to differ in the amounts of lexical and structural overlap with adult utterances in prior discourse, suggesting that (a) they developed at a different pace despite emerging very closely together in the child's speech and (b) close-proximity-input may aid the production of difficult sentence structures early in development. The present research largely supports the Constructivist view of language acquisition. In particular, it adds to the previous research suggesting that input plays a major role in children's adult and non-adult-like language knowledge.
Published: 2007

3. Four principles to establish a universal virus taxonomy

Author: Simmonds, Peter, Adriaenssens, Evelien M, Zerbini, F Murilo, Abrescia, Nicola G A, Aiewsakun, Pakorn, Alfenas-Zerbini, Poliane, Bao, Yiming, Barylski, Jakub, Drosten, Christian, Duffy, Siobain, Duprex, W Paul, Dutilh, Bas E, Elena, Santiago F, García, Maria Laura, Junglen, Sandra, Katzourakis, Aris, Koonin, Eugene V, Krupovic, Mart, Kuhn, Jens H, Lambert, Amy J, Lefkowitz, Elliot J, Łobocka, Małgorzata, Lood, Cédric, Mahony, Jennifer, Meier-Kolthoff, Jan P, Mushegian, Arcady R, Oksanen, Hanna M, Poranen, Minna M, Reyes-Muñoz, Alejandro, Robertson, David L, Roux, Simon, Rubino, Luisa, Sabanadzovic, Sead, Siddell, Stuart, Skern, Tim, Smith, Donald B, Sullivan, Matthew B, Suzuki, Nobuhiro, Turner, Dann, Van Doorslaer, Koenraad, Vandamme, Anne-Mieke, Varsani, Arvind, Vasilakis, Nikos, Simmonds, Peter, Adriaenssens, Evelien M, Zerbini, F Murilo, Abrescia, Nicola G A, Aiewsakun, Pakorn, Alfenas-Zerbini, Poliane, Bao, Yiming, Barylski, Jakub, Drosten, Christian, Duffy, Siobain, Duprex, W Paul, Dutilh, Bas E, Elena, Santiago F, García, Maria Laura, Junglen, Sandra, Katzourakis, Aris, Koonin, Eugene V, Krupovic, Mart, Kuhn, Jens H, Lambert, Amy J, Lefkowitz, Elliot J, Łobocka, Małgorzata, Lood, Cédric, Mahony, Jennifer, Meier-Kolthoff, Jan P, Mushegian, Arcady R, Oksanen, Hanna M, Poranen, Minna M, Reyes-Muñoz, Alejandro, Robertson, David L, Roux, Simon, Rubino, Luisa, Sabanadzovic, Sead, Siddell, Stuart, Skern, Tim, Smith, Donald B, Sullivan, Matthew B, Suzuki, Nobuhiro, Turner, Dann, Van Doorslaer, Koenraad, Vandamme, Anne-Mieke, Varsani, Arvind, and Vasilakis, Nikos
Abstract: A universal taxonomy of viruses is essential for a comprehensive view of the virus world and for communicating the complicated evolutionary relationships among viruses. However, there are major differences in the conceptualisation and approaches to virus classification and nomenclature among virologists, clinicians, agronomists, and other interested parties. Here, we provide recommendations to guide the construction of a coherent and comprehensive virus taxonomy, based on expert scientific consensus. Firstly, assignments of viruses should be congruent with the best attainable reconstruction of their evolutionary histories, i.e., taxa should be monophyletic. This fundamental principle for classification of viruses is currently included in the International Committee on Taxonomy of Viruses (ICTV) code only for the rank of species. Secondly, phenotypic and ecological properties of viruses may inform, but not override, evolutionary relatedness in the placement of ranks. Thirdly, alternative classifications that consider phenotypic attributes, such as being vector-borne (e.g., "arboviruses"), infecting a certain type of host (e.g., "mycoviruses," "bacteriophages") or displaying specific pathogenicity (e.g., "human immunodeficiency viruses"), may serve important clinical and regulatory purposes but often create polyphyletic categories that do not reflect evolutionary relationships. Nevertheless, such classifications ought to be maintained if they serve the needs of specific communities or play a practical clinical or regulatory role. However, they should not be considered or called taxonomies. Finally, while an evolution-based framework enables viruses discovered by metagenomics to be incorporated into the ICTV taxonomy, there are essential requirements for quality control of the sequence data used for these assignments. Combined, these four principles will enable future development and expansion of virus taxonomy as the true evolutionary diversity of viruses becomes a
Published: 2023

4. Abolishment of morphology-based taxa and change to binomial species names: 2022 taxonomy update of the ICTV bacterial viruses subcommittee

Author: Turner, Dann, Shkoporov, Andrey N, Lood, Cédric, Millard, Andrew D, Dutilh, Bas E, Alfenas-Zerbini, Poliane, van Zyl, Leonardo J, Aziz, Ramy K, Oksanen, Hanna M, Poranen, Minna M, Kropinski, Andrew M, Barylski, Jakub, Brister, J Rodney, Chanisvili, Nina, Edwards, Rob A, Enault, François, Gillis, Annika, Knezevic, Petar, Krupovic, Mart, Kurtböke, Ipek, Kushkina, Alla, Lavigne, Rob, Lehman, Susan, Lobocka, Malgorzata, Moraru, Cristina, Moreno Switt, Andrea, Morozova, Vera, Nakavuma, Jesca, Reyes Muñoz, Alejandro, Rūmnieks, Jānis, Sarkar, B L, Sullivan, Matthew B, Uchiyama, Jumpei, Wittmann, Johannes, Yigang, Tong, Adriaenssens, Evelien M, Turner, Dann, Shkoporov, Andrey N, Lood, Cédric, Millard, Andrew D, Dutilh, Bas E, Alfenas-Zerbini, Poliane, van Zyl, Leonardo J, Aziz, Ramy K, Oksanen, Hanna M, Poranen, Minna M, Kropinski, Andrew M, Barylski, Jakub, Brister, J Rodney, Chanisvili, Nina, Edwards, Rob A, Enault, François, Gillis, Annika, Knezevic, Petar, Krupovic, Mart, Kurtböke, Ipek, Kushkina, Alla, Lavigne, Rob, Lehman, Susan, Lobocka, Malgorzata, Moraru, Cristina, Moreno Switt, Andrea, Morozova, Vera, Nakavuma, Jesca, Reyes Muñoz, Alejandro, Rūmnieks, Jānis, Sarkar, B L, Sullivan, Matthew B, Uchiyama, Jumpei, Wittmann, Johannes, Yigang, Tong, and Adriaenssens, Evelien M
Abstract: This article summarises the activities of the Bacterial Viruses Subcommittee of the International Committee on Taxonomy of Viruses for the period of March 2021-March 2022. We provide an overview of the new taxa proposed in 2021, approved by the Executive Committee, and ratified by vote in 2022. Significant changes to the taxonomy of bacterial viruses were introduced: the paraphyletic morphological families Podoviridae, Siphoviridae, and Myoviridae as well as the order Caudovirales were abolished, and a binomial system of nomenclature for species was established. In addition, one order, 22 families, 30 subfamilies, 321 genera, and 862 species were newly created, promoted, or moved.
Published: 2023

5. Abolishment of morphology-based taxa and change to binomial species names: 2022 taxonomy update of the ICTV bacterial viruses subcommittee

Author: UCL - SST/ELI/ELIM - Applied Microbiology, Turner, Dann, Shkoporov, Andrey N., Lood, Cédric, Millard, Andrew D., Dutilh, Bas E., Alfenas-Zerbini, Poliane, van Zyl, Leonardo J., Aziz, Ramy K., Oksanen, Hanna M., Poranen, Minna M., Kropinski, Andrew M., Barylski, Jakub, Brister, J Rodney, Chanisvili, Nina, Edwards, Rob A., Enault, François, Gillis, Annika, Knezevic, Petar, Krupovic, Mart, Kurtböke, Ipek, Kushkina, Alla, Lavigne, Rob, Lehman, Susan, Lobocka, Malgorzata, Moraru, Cristina, Moreno Switt, Andrea, Morozova, Vera, Nakavuma, Jesca, Reyes Muñoz, Alejandro, Rūmnieks, Jānis, Sarkar, BL, Sullivan, Matthew B., Uchiyama, Jumpei, Wittmann, Johannes, Yigang, Tong, Adriaenssens, Evelien M., UCL - SST/ELI/ELIM - Applied Microbiology, Turner, Dann, Shkoporov, Andrey N., Lood, Cédric, Millard, Andrew D., Dutilh, Bas E., Alfenas-Zerbini, Poliane, van Zyl, Leonardo J., Aziz, Ramy K., Oksanen, Hanna M., Poranen, Minna M., Kropinski, Andrew M., Barylski, Jakub, Brister, J Rodney, Chanisvili, Nina, Edwards, Rob A., Enault, François, Gillis, Annika, Knezevic, Petar, Krupovic, Mart, Kurtböke, Ipek, Kushkina, Alla, Lavigne, Rob, Lehman, Susan, Lobocka, Malgorzata, Moraru, Cristina, Moreno Switt, Andrea, Morozova, Vera, Nakavuma, Jesca, Reyes Muñoz, Alejandro, Rūmnieks, Jānis, Sarkar, BL, Sullivan, Matthew B., Uchiyama, Jumpei, Wittmann, Johannes, Yigang, Tong, and Adriaenssens, Evelien M.
Abstract: This article summarises the activities of the Bacterial Viruses Subcommittee of the International Committee on Taxonomy of Viruses for the period of March 2021−March 2022. We provide an overview of the new taxa proposed in 2021, approved by the Executive Committee, and ratified by vote in 2022. Significant changes to the taxonomy of bacterial viruses were introduced: the paraphyletic morphological families Podoviridae, Siphoviridae, and Myoviridae as well as the order Caudovirales were abolished, and a binomial system of nomenclature for species was established. In addition, one order, 22 families, 30 subfamilies, 321 genera, and 862 species were newly created, promoted, or moved.
Published: 2023

6. Consistent centennial-scale change in European sub-Arctic peatland vegetation toward Sphagnum dominance—Implications for carbon sink capacity

Author: Piilo, Sanna R., Väliranta, Minna M., Amesbury, Matt J., Aquino-López, Marco A., Charman, Dan J., Gallego-Sala, Angela, Garneau, Michelle, Koroleva, Natalia, Kärppä, Mai, Laine, Anna M., Sannel, A. Britta K., Tuittila, Eeva-Stiina, Zhang, Hui, Piilo, Sanna R., Väliranta, Minna M., Amesbury, Matt J., Aquino-López, Marco A., Charman, Dan J., Gallego-Sala, Angela, Garneau, Michelle, Koroleva, Natalia, Kärppä, Mai, Laine, Anna M., Sannel, A. Britta K., Tuittila, Eeva-Stiina, and Zhang, Hui
Abstract: Climate warming is leading to permafrost thaw in northern peatlands, and current predictions suggest that thawing will drive greater surface wetness and an increase in methane emissions. Hydrology largely drives peatland vegetation composition, which is a key element in peatland functioning and thus in carbon dynamics. These processes are expected to change. Peatland carbon accumulation is determined by the balance between plant production and peat decomposition. But both processes are expected to accelerate in northern peatlands due to warming, leading to uncertainty in future peatland carbon budgets. Here, we compile a dataset of vegetation changes and apparent carbon accumulation data reconstructed from 33 peat cores collected from 16 sub-arctic peatlands in Fennoscandia and European Russia. The data cover the past two millennia that has undergone prominent changes in climate and a notable increase in annual temperatures toward present times. We show a pattern where European sub-Arctic peatland microhabitats have undergone a habitat change where currently drier habitats dominated by Sphagnum mosses replaced wetter sedge-dominated vegetation and these new habitats have remained relatively stable over the recent decades. Our results suggest an alternative future pathway where sub-arctic peatlands may at least partly sustain dry vegetation and enhance the carbon sink capacity of northern peatlands.
Published: 2023
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7. Four principles to establish a universal virus taxonomy

Author: Theoretical Biology and Bioinformatics, Sub Bioinformatics, Simmonds, Peter, Adriaenssens, Evelien M, Zerbini, F Murilo, Abrescia, Nicola G A, Aiewsakun, Pakorn, Alfenas-Zerbini, Poliane, Bao, Yiming, Barylski, Jakub, Drosten, Christian, Duffy, Siobain, Duprex, W Paul, Dutilh, Bas E, Elena, Santiago F, García, Maria Laura, Junglen, Sandra, Katzourakis, Aris, Koonin, Eugene V, Krupovic, Mart, Kuhn, Jens H, Lambert, Amy J, Lefkowitz, Elliot J, Łobocka, Małgorzata, Lood, Cédric, Mahony, Jennifer, Meier-Kolthoff, Jan P, Mushegian, Arcady R, Oksanen, Hanna M, Poranen, Minna M, Reyes-Muñoz, Alejandro, Robertson, David L, Roux, Simon, Rubino, Luisa, Sabanadzovic, Sead, Siddell, Stuart, Skern, Tim, Smith, Donald B, Sullivan, Matthew B, Suzuki, Nobuhiro, Turner, Dann, Van Doorslaer, Koenraad, Vandamme, Anne-Mieke, Varsani, Arvind, Vasilakis, Nikos, Theoretical Biology and Bioinformatics, Sub Bioinformatics, Simmonds, Peter, Adriaenssens, Evelien M, Zerbini, F Murilo, Abrescia, Nicola G A, Aiewsakun, Pakorn, Alfenas-Zerbini, Poliane, Bao, Yiming, Barylski, Jakub, Drosten, Christian, Duffy, Siobain, Duprex, W Paul, Dutilh, Bas E, Elena, Santiago F, García, Maria Laura, Junglen, Sandra, Katzourakis, Aris, Koonin, Eugene V, Krupovic, Mart, Kuhn, Jens H, Lambert, Amy J, Lefkowitz, Elliot J, Łobocka, Małgorzata, Lood, Cédric, Mahony, Jennifer, Meier-Kolthoff, Jan P, Mushegian, Arcady R, Oksanen, Hanna M, Poranen, Minna M, Reyes-Muñoz, Alejandro, Robertson, David L, Roux, Simon, Rubino, Luisa, Sabanadzovic, Sead, Siddell, Stuart, Skern, Tim, Smith, Donald B, Sullivan, Matthew B, Suzuki, Nobuhiro, Turner, Dann, Van Doorslaer, Koenraad, Vandamme, Anne-Mieke, Varsani, Arvind, and Vasilakis, Nikos
Published: 2023

8. Abolishment of morphology-based taxa and change to binomial species names: 2022 taxonomy update of the ICTV bacterial viruses subcommittee

Author: Theoretical Biology and Bioinformatics, Sub Bioinformatics, Turner, Dann, Shkoporov, Andrey N, Lood, Cédric, Millard, Andrew D, Dutilh, Bas E, Alfenas-Zerbini, Poliane, van Zyl, Leonardo J, Aziz, Ramy K, Oksanen, Hanna M, Poranen, Minna M, Kropinski, Andrew M, Barylski, Jakub, Brister, J Rodney, Chanisvili, Nina, Edwards, Rob A, Enault, François, Gillis, Annika, Knezevic, Petar, Krupovic, Mart, Kurtböke, Ipek, Kushkina, Alla, Lavigne, Rob, Lehman, Susan, Lobocka, Malgorzata, Moraru, Cristina, Moreno Switt, Andrea, Morozova, Vera, Nakavuma, Jesca, Reyes Muñoz, Alejandro, Rūmnieks, Jānis, Sarkar, B L, Sullivan, Matthew B, Uchiyama, Jumpei, Wittmann, Johannes, Yigang, Tong, Adriaenssens, Evelien M, Theoretical Biology and Bioinformatics, Sub Bioinformatics, Turner, Dann, Shkoporov, Andrey N, Lood, Cédric, Millard, Andrew D, Dutilh, Bas E, Alfenas-Zerbini, Poliane, van Zyl, Leonardo J, Aziz, Ramy K, Oksanen, Hanna M, Poranen, Minna M, Kropinski, Andrew M, Barylski, Jakub, Brister, J Rodney, Chanisvili, Nina, Edwards, Rob A, Enault, François, Gillis, Annika, Knezevic, Petar, Krupovic, Mart, Kurtböke, Ipek, Kushkina, Alla, Lavigne, Rob, Lehman, Susan, Lobocka, Malgorzata, Moraru, Cristina, Moreno Switt, Andrea, Morozova, Vera, Nakavuma, Jesca, Reyes Muñoz, Alejandro, Rūmnieks, Jānis, Sarkar, B L, Sullivan, Matthew B, Uchiyama, Jumpei, Wittmann, Johannes, Yigang, Tong, and Adriaenssens, Evelien M
Published: 2023

9. SUCCOR cone study: conization before radical hysterectomy

Author: Chacon, Enrique Manzour, Nabil Zanagnolo, Vanna Querleu, Denis Nunez-Cordoba, Jorge M. Martin-Calvo, Nerea Capilna, Mihai Emil Fagotti, Anna Kucukmetin, Ali Mom, Constantijne and Chakalova, Galina Shamistan, Aliyev Gil Moreno, Antonio and Malzoni, Mario Narducci, Fabrice Arencibia, Octavio and Raspagliesi, Francesco Toptas, Tayfun Cibula, David and Kaidarova, Dilyara Meydanli, Mehmet Mutlu Tavares, Mariana and Golub, Dmytro Perrone, Anna Myriam Poka, Robert Tsolakidis, Dimitrios Vujic, Goran Jedryka, Marcin A. Zusterzeel, Petra L. M. Beltman, Jogchum Jan Goffin, Frederic Haidopoulos, Dimitrios Haller, Herman Jach, Robert Yezhova, Iryna and Berlev, Igor Bernardino, Margarida Bharathan, Rasiah Lanner, Maximilian Maenpaa, Minna M. Sukhin, Vladyslav Feron, Jean-Guillaume Fruscio, Robert Kukk, Kersti Ponce, Jordi and Angel Minguez, Jose Vazquez-Vicente, Daniel Castellanos, Teresa and Boria, Felix Luis Alcazar, Juan Chiva, Luis SUCCOR Study Grp and Chacon, Enrique Manzour, Nabil Zanagnolo, Vanna Querleu, Denis Nunez-Cordoba, Jorge M. Martin-Calvo, Nerea Capilna, Mihai Emil Fagotti, Anna Kucukmetin, Ali Mom, Constantijne and Chakalova, Galina Shamistan, Aliyev Gil Moreno, Antonio and Malzoni, Mario Narducci, Fabrice Arencibia, Octavio and Raspagliesi, Francesco Toptas, Tayfun Cibula, David and Kaidarova, Dilyara Meydanli, Mehmet Mutlu Tavares, Mariana and Golub, Dmytro Perrone, Anna Myriam Poka, Robert Tsolakidis, Dimitrios Vujic, Goran Jedryka, Marcin A. Zusterzeel, Petra L. M. Beltman, Jogchum Jan Goffin, Frederic Haidopoulos, Dimitrios Haller, Herman Jach, Robert Yezhova, Iryna and Berlev, Igor Bernardino, Margarida Bharathan, Rasiah Lanner, Maximilian Maenpaa, Minna M. Sukhin, Vladyslav Feron, Jean-Guillaume Fruscio, Robert Kukk, Kersti Ponce, Jordi and Angel Minguez, Jose Vazquez-Vicente, Daniel Castellanos, Teresa and Boria, Felix Luis Alcazar, Juan Chiva, Luis SUCCOR Study Grp
Abstract: Objective To evaluate disease-free survival of cervical conization prior to radical hysterectomy in patients with stage IB1 cervical cancer (International Federation of Gynecology and Obstetrics (FIGO) 2009). Methods A multicenter retrospective observational cohort study was conducted including patients from the Surgery in Cervical Cancer Comparing Different Surgical Aproaches in Stage IB1 Cervical Cancer (SUCCOR) database with FIGO 2009 IB1 cervical carcinoma treated with radical hysterectomy between January 1, 2013, and December 31, 2014. We used propensity score matching to minimize the potential allocation biases arising from the retrospective design. Patients who underwent conization but were similar for other measured characteristics were matched 1:1 to patients from the non-cone group using a caliper width <= 0.2 standard deviations of the logit odds of the estimated propensity score. Results We obtained a weighted cohort of 374 patients (187 patients with prior conization and 187 non-conization patients). We found a 65% reduction in the risk of relapse for patients who had cervical conization prior to radical hysterectomy (hazard ratio (HR) 0.35, 95% confidence interval (CI) 0.16 to 0.75, p=0.007) and a 75% reduction in the risk of death for the same sample (HR 0.25, 95% CI 0.07 to 0.90, p=0.033). In addition, patients who underwent minimally invasive surgery without prior conization had a 5.63 times higher chance of relapse compared with those who had an open approach and previous conization (HR 5.63, 95% CI 1.64 to 19.3, p=0.006). Patients who underwent minimally invasive surgery with prior conization and those who underwent open surgery without prior conization showed no differences in relapse rates compared with those who underwent open surgery with prior cone biopsy (reference) (HR 1.94, 95% CI 0.49 to 7.76, p=0.349 and HR 2.94, 95% CI 0.80 to 10.86, p=0.106 respectively). Conclusions In this retrospective study, patients undergoing cervical conizati
Published: 2022

10. Norway spruce postglacial recolonization of Fennoscandia

Author: Nota, Kevin, Klaminder, Jonatan, Milesi, Pascal, Bindler, Richard, Nobile, Alessandro, van Steijn, Tamara, Bertilsson, Stefan, Svensson, Brita, Hirota, Shun K., Matsuo, Ayumi, Gunnarsson, Urban, Seppä, Heikki, Väliranta, Minna M., Wohlfarth, Barbara, Suyama, Yoshihisa, Parducci, Laura, Nota, Kevin, Klaminder, Jonatan, Milesi, Pascal, Bindler, Richard, Nobile, Alessandro, van Steijn, Tamara, Bertilsson, Stefan, Svensson, Brita, Hirota, Shun K., Matsuo, Ayumi, Gunnarsson, Urban, Seppä, Heikki, Väliranta, Minna M., Wohlfarth, Barbara, Suyama, Yoshihisa, and Parducci, Laura
Abstract: Contrasting theories exist regarding how Norway spruce (Picea abies) recolonized Fennoscandia after the last glaciation and both early Holocene establishments from western microrefugia and late Holocene colonization from the east have been postulated. Here, we show that Norway spruce was present in southern Fennoscandia as early as 14.7 ± 0.1 cal. kyr BP and that the millennia-old clonal spruce trees present today in central Sweden likely arrived with an early Holocene migration from the east. Our findings are based on ancient sedimentary DNA from multiple European sites (N = 15) combined with nuclear and mitochondrial DNA analysis of ancient clonal (N = 135) and contemporary spruce forest trees (N = 129) from central Sweden. Our other findings imply that Norway spruce was present shortly after deglaciation at the margins of the Scandinavian Ice Sheet, and support previously disputed finds of pollen in southern Sweden claiming spruce establishment during the Lateglacial.
Published: 2022
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11. Cognitive performance at time of AD diagnosis:a clinically augmented register-based study

Author: Alenius, M. (Minna), Hokkanen, L. (Laura), Koskinen, S. (Sanna), Hallikainen, I. (Ilona), Hänninen, T. (Tuomo), Karrasch, M. (Mira), Raivio, M. M. (Minna M.), Laakkonen, M.-L. (Marja-Liisa), Krüger, J. (Johanna), Suhonen, N.-M. (Noora-Maria), Kivipelto, M. (Miia), Ngandu, T. (Tiia), Alenius, M. (Minna), Hokkanen, L. (Laura), Koskinen, S. (Sanna), Hallikainen, I. (Ilona), Hänninen, T. (Tuomo), Karrasch, M. (Mira), Raivio, M. M. (Minna M.), Laakkonen, M.-L. (Marja-Liisa), Krüger, J. (Johanna), Suhonen, N.-M. (Noora-Maria), Kivipelto, M. (Miia), and Ngandu, T. (Tiia)
Abstract: We aimed to evaluate the feasibility of using real-world register data for identifying persons with mild Alzheimer’s disease (AD) and to describe their cognitive performance at the time of diagnosis. Patients diagnosed with AD during 2010–2013 (aged 60–81 years) were identified from the Finnish national health registers and enlarged with a smaller private sector sample (total n = 1,268). Patients with other disorders impacting cognition were excluded. Detailed clinical and cognitive screening data (the Consortium to Establish a Registry for Alzheimer’s Disease neuropsychological battery [CERAD-nb]) were obtained from local health records. Adequate cognitive data were available for 389 patients with mild AD (31%) of the entire AD group. The main reasons for not including patients in analyses of cognitive performance were AD diagnosis at a moderate/severe stage (n = 266, 21%), AD diagnosis given before full register coverage (n = 152, 12%), and missing CERAD-nb data (n = 139, 11%). The cognitive performance of persons with late-onset AD (n = 284), mixed cerebrovascular disease and AD (n = 51), and other AD subtypes (n = 54) was compared with that of a non-demented sample (n = 1980) from the general population. Compared with the other AD groups, patients with late-onset AD performed the worst in word list recognition, while patients with mixed cerebrovascular disease and AD performed the worst in constructional praxis and clock drawing tests. A combination of national registers and local health records can be used to collect data relevant for cognitive screening; today, the process is laborious, but it could be improved in the future with refined search algorithms and electronic data.
Published: 2022

12. SUCCOR cone study: conization before radical hysterectomy

Author: Chacon, E, Manzour, N, Zanagnolo, V, Querleu, D, Núñez-Córdoba, J, Martin-Calvo, N, Căpîlna, M, Fagotti, A, Kucukmetin, A, Mom, C, Chakalova, G, Shamistan, A, Gil Moreno, A, Malzoni, M, Narducci, F, Arencibia, O, Raspagliesi, F, Toptas, T, Cibula, D, Kaidarova, D, Meydanli, M, Tavares, M, Golub, D, Perrone, A, Poka, R, Tsolakidis, D, Vujić, G, Jedryka, M, Zusterzeel, P, Beltman, J, Goffin, F, Haidopoulos, D, Haller, H, Jach, R, Yezhova, I, Berlev, I, Bernardino, M, Bharathan, R, Lanner, M, Maenpaa, M, Sukhin, V, Feron, J, Fruscio, R, Kukk, K, Ponce, J, Minguez, J, Vázquez-Vicente, D, Castellanos, T, Boria, F, Alcazar, J, Chiva, L, Chacon, Enrique, Manzour, Nabil, Zanagnolo, Vanna, Querleu, Denis, Núñez-Córdoba, Jorge M, Martin-Calvo, Nerea, Căpîlna, Mihai Emil, Fagotti, Anna, Kucukmetin, Ali, Mom, Constantijne, Chakalova, Galina, Shamistan, Aliyev, Gil Moreno, Antonio, Malzoni, Mario, Narducci, Fabrice, Arencibia, Octavio, Raspagliesi, Francesco, Toptas, Tayfun, Cibula, David, Kaidarova, Dilyara, Meydanli, Mehmet Mutlu, Tavares, Mariana, Golub, Dmytro, Perrone, Anna Myriam, Poka, Robert, Tsolakidis, Dimitrios, Vujić, Goran, Jedryka, Marcin A, Zusterzeel, Petra L M, Beltman, Jogchum Jan, Goffin, Frederic, Haidopoulos, Dimitrios, Haller, Herman, Jach, Robert, Yezhova, Iryna, Berlev, Igor, Bernardino, Margarida, Bharathan, Rasiah, Lanner, Maximilian, Maenpaa, Minna M, Sukhin, Vladyslav, Feron, Jean-Guillaume, Fruscio, Robert, Kukk, Kersti, Ponce, Jordi, Minguez, Jose Angel, Vázquez-Vicente, Daniel, Castellanos, Teresa, Boria, Felix, Alcazar, Juan Luis, Chiva, Luis, Chacon, E, Manzour, N, Zanagnolo, V, Querleu, D, Núñez-Córdoba, J, Martin-Calvo, N, Căpîlna, M, Fagotti, A, Kucukmetin, A, Mom, C, Chakalova, G, Shamistan, A, Gil Moreno, A, Malzoni, M, Narducci, F, Arencibia, O, Raspagliesi, F, Toptas, T, Cibula, D, Kaidarova, D, Meydanli, M, Tavares, M, Golub, D, Perrone, A, Poka, R, Tsolakidis, D, Vujić, G, Jedryka, M, Zusterzeel, P, Beltman, J, Goffin, F, Haidopoulos, D, Haller, H, Jach, R, Yezhova, I, Berlev, I, Bernardino, M, Bharathan, R, Lanner, M, Maenpaa, M, Sukhin, V, Feron, J, Fruscio, R, Kukk, K, Ponce, J, Minguez, J, Vázquez-Vicente, D, Castellanos, T, Boria, F, Alcazar, J, Chiva, L, Chacon, Enrique, Manzour, Nabil, Zanagnolo, Vanna, Querleu, Denis, Núñez-Córdoba, Jorge M, Martin-Calvo, Nerea, Căpîlna, Mihai Emil, Fagotti, Anna, Kucukmetin, Ali, Mom, Constantijne, Chakalova, Galina, Shamistan, Aliyev, Gil Moreno, Antonio, Malzoni, Mario, Narducci, Fabrice, Arencibia, Octavio, Raspagliesi, Francesco, Toptas, Tayfun, Cibula, David, Kaidarova, Dilyara, Meydanli, Mehmet Mutlu, Tavares, Mariana, Golub, Dmytro, Perrone, Anna Myriam, Poka, Robert, Tsolakidis, Dimitrios, Vujić, Goran, Jedryka, Marcin A, Zusterzeel, Petra L M, Beltman, Jogchum Jan, Goffin, Frederic, Haidopoulos, Dimitrios, Haller, Herman, Jach, Robert, Yezhova, Iryna, Berlev, Igor, Bernardino, Margarida, Bharathan, Rasiah, Lanner, Maximilian, Maenpaa, Minna M, Sukhin, Vladyslav, Feron, Jean-Guillaume, Fruscio, Robert, Kukk, Kersti, Ponce, Jordi, Minguez, Jose Angel, Vázquez-Vicente, Daniel, Castellanos, Teresa, Boria, Felix, Alcazar, Juan Luis, and Chiva, Luis
Abstract: OBJECTIVE: To evaluate disease-free survival of cervical conization prior to radical hysterectomy in patients with stage IB1 cervical cancer (International Federation of Gynecology and Obstetrics (FIGO) 2009). METHODS: A multicenter retrospective observational cohort study was conducted including patients from the Surgery in Cervical Cancer Comparing Different Surgical Aproaches in Stage IB1 Cervical Cancer (SUCCOR) database with FIGO 2009 IB1 cervical carcinoma treated with radical hysterectomy between January 1, 2013, and December 31, 2014. We used propensity score matching to minimize the potential allocation biases arising from the retrospective design. Patients who underwent conization but were similar for other measured characteristics were matched 1:1 to patients from the non-cone group using a caliper width ≤0.2 standard deviations of the logit odds of the estimated propensity score. RESULTS: We obtained a weighted cohort of 374 patients (187 patients with prior conization and 187 non-conization patients). We found a 65% reduction in the risk of relapse for patients who had cervical conization prior to radical hysterectomy (hazard ratio (HR) 0.35, 95% confidence interval (CI) 0.16 to 0.75, p=0.007) and a 75% reduction in the risk of death for the same sample (HR 0.25, 95% CI 0.07 to 0.90, p=0.033). In addition, patients who underwent minimally invasive surgery without prior conization had a 5.63 times higher chance of relapse compared with those who had an open approach and previous conization (HR 5.63, 95% CI 1.64 to 19.3, p=0.006). Patients who underwent minimally invasive surgery with prior conization and those who underwent open surgery without prior conization showed no differences in relapse rates compared with those who underwent open surgery with prior cone biopsy (reference) (HR 1.94, 95% CI 0.49 to 7.76, p=0.349 and HR 2.94, 95% CI 0.80 to 10.86, p=0.106 respectively). CONCLUSIONS: In this retrospective study, patients undergoing cervical conizatio
Published: 2022

13. Structural Insight into CVB3-VLP Non-Adjuvanted Vaccine.

Author: Hankaniemi, Minna M, Hankaniemi, Minna M, Baikoghli, Mo A, Stone, Virginia M, Xing, Li, Väätäinen, Outi, Soppela, Saana, Sioofy-Khojine, Amirbabak, Saarinen, Niila VV, Ou, Tingwei, Anson, Brandon, Hyöty, Heikki, Marjomäki, Varpu, Flodström-Tullberg, Malin, Cheng, R Holland, Hytönen, Vesa P, Laitinen, Olli H, Hankaniemi, Minna M, Hankaniemi, Minna M, Baikoghli, Mo A, Stone, Virginia M, Xing, Li, Väätäinen, Outi, Soppela, Saana, Sioofy-Khojine, Amirbabak, Saarinen, Niila VV, Ou, Tingwei, Anson, Brandon, Hyöty, Heikki, Marjomäki, Varpu, Flodström-Tullberg, Malin, Cheng, R Holland, Hytönen, Vesa P, and Laitinen, Olli H
Abstract: Coxsackievirus B (CVB) enteroviruses are common pathogens that can cause acute and chronic myocarditis, dilated cardiomyopathy, aseptic meningitis, and they are hypothesized to be a causal factor in type 1 diabetes. The licensed enterovirus vaccines and those currently in clinical development are traditional inactivated or live attenuated vaccines. Even though these vaccines work well in the prevention of enterovirus diseases, new vaccine technologies, like virus-like particles (VLPs), can offer important advantages in the manufacturing and epitope engineering. We have previously produced VLPs for CVB3 and CVB1 in insect cells. Here, we describe the production of CVB3-VLPs with enhanced production yield and purity using an improved purification method consisting of tangential flow filtration and ion exchange chromatography, which is compatible with industrial scale production. We also resolved the CVB3-VLP structure by Cryo-Electron Microscopy imaging and single particle reconstruction. The VLP diameter is 30.9 nm on average, and it is similar to Coxsackievirus A VLPs and the expanded enterovirus cell-entry intermediate (the 135s particle), which is ~2 nm larger than the mature virion. High neutralizing and total IgG antibody levels, the latter being a predominantly Th2 type (IgG1) phenotype, were detected in C57BL/6J mice immunized with non-adjuvanted CVB3-VLP vaccine. The structural and immunogenic data presented here indicate the potential of this improved methodology to produce highly immunogenic enterovirus VLP-vaccines in the future.
Published: 2020

14. Radical hysterectomy in early cervical cancer in Europe: characteristics, outcomes and evaluation of ESGO quality indicators

Author: Boria, Felix Chiva, Luis Zanagnolo, Vanna Querleu, Denis and Martin-Calvo, Nerea Capilna, Mihai Emil Fagotti, Anna and Kucukmetin, Ali Mom, Constantijne Chakalova, Galina and Shamistan, Aliyev Malzoni, Mario Narducci, Fabrice and Arencibia, Octavio Raspagliesi, Francesco Toptas, Tayfun and Cibula, David Kaidarova, Dilyara Meydanli, Mehmet Mutlu and Tavares, Mariana Golub, Dmytro Perrone, Anna Myriam Poka, Robert Tsolakidis, Dimitrios Vujic, Goran Jedryka, Marcin A. and Zusterzeel, Petra L. M. Beltman, Jogchum Jan Goffin, Frederic Haidopoulos, Dimitrios Haller, Herman Jach, Robert and Yezhova, Iryna Berlev, Igor Bernardino, Margarida and Bharathan, Rasiah Lanner, Maximilian Maenpaa, Minna M. and Sukhin, Vladyslav Feron, Jean-Guillaume Fruscio, Robert and Kukk, Kersti Ponce, Jordi Alonso-Espias, Maria Angel Minguez, Jose Vazquez-Vicente, Daniel Manzour, Nabil Jurado, Matias Castellanos, Teresa Chacon, Enrique Luis Alcazar, Juan and Boria, Felix Chiva, Luis Zanagnolo, Vanna Querleu, Denis and Martin-Calvo, Nerea Capilna, Mihai Emil Fagotti, Anna and Kucukmetin, Ali Mom, Constantijne Chakalova, Galina and Shamistan, Aliyev Malzoni, Mario Narducci, Fabrice and Arencibia, Octavio Raspagliesi, Francesco Toptas, Tayfun and Cibula, David Kaidarova, Dilyara Meydanli, Mehmet Mutlu and Tavares, Mariana Golub, Dmytro Perrone, Anna Myriam Poka, Robert Tsolakidis, Dimitrios Vujic, Goran Jedryka, Marcin A. and Zusterzeel, Petra L. M. Beltman, Jogchum Jan Goffin, Frederic Haidopoulos, Dimitrios Haller, Herman Jach, Robert and Yezhova, Iryna Berlev, Igor Bernardino, Margarida and Bharathan, Rasiah Lanner, Maximilian Maenpaa, Minna M. and Sukhin, Vladyslav Feron, Jean-Guillaume Fruscio, Robert and Kukk, Kersti Ponce, Jordi Alonso-Espias, Maria Angel Minguez, Jose Vazquez-Vicente, Daniel Manzour, Nabil Jurado, Matias Castellanos, Teresa Chacon, Enrique Luis Alcazar, Juan
Abstract: Introduction Comprehensive updated information on cervical cancer surgical treatment in Europe is scarce. Objective To evaluate baseline characteristics of women with early cervical cancer and to analyze the outcomes of the ESGO quality indicators after radical hysterectomy in the SUCCOR database. Methods The SUCCOR database consisted of 1272 patients who underwent radical hysterectomy for stage IB1 cervical cancer (FIGO 2009) between January 2013 and December 2014. After exclusion criteria, the final sample included 1156 patients. This study first described the clinical, surgical, pathological, and follow-up variables of this population and then analyzed the outcomes (disease-free survival and overall survival) after radical hysterectomy. Surgical-related ESGO quality indicators were assessed and the accomplishment of the stated recommendations was verified. Results The mean age of the patients was 47.1 years (SD 10.8), with a mean body mass index of 25.4 kg/m(2) (SD 4.9). A total of 423 (36.6%) patients had a previous cone biopsy. Tumor size (clinical examination) <2 cm was observed in 667 (57.7%) patients. The most frequent histology type was squamous carcinoma (794 (68.7%) patients), and positive lymph nodes were found in 143 (12.4%) patients. A total of 633 (54.8%) patients were operated by open abdominal surgery. Intra-operative complications occurred in 108 (9.3%) patients, and post-operative complications during the first month occurred in 249 (21.5%) patients, with bladder dysfunction as the most frequent event (119 (10.3%) patients). Clavien-Dindo grade III or higher complication occurred in 56 (4.8%) patients. A total of 510 (44.1%) patients received adjuvant therapy. After a median follow-up of 58 months (range 0-84), the 5-year disease-free survival was 88.3%, and the overall survival was 94.9%. In our population, 10 of the 11 surgical-related quality indicators currently recommended by ESGO were fully fulfilled 5 years before its implementation. Con
Published: 2021

15. Bacterial Viruses Subcommittee and Archaeal Viruses Subcommittee of the ICTV: update of taxonomy changes in 2021

Author: Krupovic, Mart, Turner, Dann, Morozova, Vera, Dyall-Smith, Mike, Oksanen, Hanna M., Edwards, Rob, Dutilh, Bas E., Lehman, Susan M., Reyes, Alejandro, Baquero, Diana P., Sullivan, Matthew B., Uchiyama, Jumpei, Nakavuma, Jesca, Barylski, Jakub, Young, Mark J., Du, Shishen, Alfenas-Zerbini, Poliane, Kushkina, Alla, Kropinski, Andrew M., Kurtboke, Ipek, Brister, J. Rodney, Lood, Cedric, Sarkar, B. L., Yigang, Tong, Liu, Ying, Huang, Li, Wittmann, Johannes, Chanishvili, Nina, van Zyl, Leonardo J., Rumnieks, Janis, Mochizuki, Tomohiro, Jalasvuori, Matti, Aziz, Ramy K., Lobocka, Malgorzata, Stedman, Kenneth M., Shkoporov, Andrey N., Gillis, Annika, Peng, Xu, Enault, Francois, Knezevic, Petar, Lavigne, Rob, Rhee, Sung-Keun, Cvirkaite-Krupovic, Virginija, Moraru, Cristina, Moreno Switt, Andrea I., Poranen, Minna M., Millard, Andrew, Prangishvili, David, Adriaenssens, Evelien M., Krupovic, Mart, Turner, Dann, Morozova, Vera, Dyall-Smith, Mike, Oksanen, Hanna M., Edwards, Rob, Dutilh, Bas E., Lehman, Susan M., Reyes, Alejandro, Baquero, Diana P., Sullivan, Matthew B., Uchiyama, Jumpei, Nakavuma, Jesca, Barylski, Jakub, Young, Mark J., Du, Shishen, Alfenas-Zerbini, Poliane, Kushkina, Alla, Kropinski, Andrew M., Kurtboke, Ipek, Brister, J. Rodney, Lood, Cedric, Sarkar, B. L., Yigang, Tong, Liu, Ying, Huang, Li, Wittmann, Johannes, Chanishvili, Nina, van Zyl, Leonardo J., Rumnieks, Janis, Mochizuki, Tomohiro, Jalasvuori, Matti, Aziz, Ramy K., Lobocka, Malgorzata, Stedman, Kenneth M., Shkoporov, Andrey N., Gillis, Annika, Peng, Xu, Enault, Francois, Knezevic, Petar, Lavigne, Rob, Rhee, Sung-Keun, Cvirkaite-Krupovic, Virginija, Moraru, Cristina, Moreno Switt, Andrea I., Poranen, Minna M., Millard, Andrew, Prangishvili, David, and Adriaenssens, Evelien M.
Abstract: In this article, we – the Bacterial Viruses Subcommittee and the Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) – summarise the results of our activities for the period March 2020 – March 2021. We report the division of the former Bacterial and Archaeal Viruses Subcommittee in two separate Subcommittees, welcome new members, a new Subcommittee Chair and Vice Chair, and give an overview of the new taxa that were proposed in 2020, approved by the Executive Committee and ratified by vote in 2021. In particular, a new realm, three orders, 15 families, 31 subfamilies, 734 genera and 1845 species were newly created or redefined (moved/promoted).
Published: 2021

16. Black box of phage-bacterium interactions: exploring alternative phage infection strategies.

Author: Mäntynen, Sari, Mäntynen, Sari, Laanto, Elina, Oksanen, Hanna M, Poranen, Minna M, Díaz-Muñoz, Samuel L, Mäntynen, Sari, Mäntynen, Sari, Laanto, Elina, Oksanen, Hanna M, Poranen, Minna M, and Díaz-Muñoz, Samuel L
Abstract: The canonical lytic-lysogenic binary has been challenged in recent years, as more evidence has emerged on alternative bacteriophage infection strategies. These infection modes are little studied, and yet they appear to be more abundant and ubiquitous in nature than previously recognized, and can play a significant role in the ecology and evolution of their bacterial hosts. In this review, we discuss the extent, causes and consequences of alternative phage lifestyles, and clarify conceptual and terminological confusion to facilitate research progress. We propose distinct definitions for the terms 'pseudolysogeny' and 'productive or non-productive chronic infection', and distinguish them from the carrier state life cycle, which describes a population-level phenomenon. Our review also finds that phages may change their infection modes in response to environmental conditions or the physiological state of the host cell. We outline known molecular mechanisms underlying the alternative phage-host interactions, including specific genetic pathways and their considerable biotechnological potential. Moreover, we discuss potential implications of the alternative phage lifestyles for microbial biology and ecosystem functioning, as well as applied topics such as phage therapy.
Published: 2021

17. Bacterial Viruses Subcommittee and Archaeal Viruses Subcommittee of the ICTV: update of taxonomy changes in 2021

Author: Sub Bioinformatics, Theoretical Biology and Bioinformatics, Krupovic, Mart, Turner, Dann, Morozova, Vera, Dyall-Smith, Mike, Oksanen, Hanna M., Edwards, Rob, Dutilh, Bas E., Lehman, Susan M., Reyes, Alejandro, Baquero, Diana P., Sullivan, Matthew B., Uchiyama, Jumpei, Nakavuma, Jesca, Barylski, Jakub, Young, Mark J., Du, Shishen, Alfenas-Zerbini, Poliane, Kushkina, Alla, Kropinski, Andrew M., Kurtboke, Ipek, Brister, J. Rodney, Lood, Cedric, Sarkar, B. L., Yigang, Tong, Liu, Ying, Huang, Li, Wittmann, Johannes, Chanishvili, Nina, van Zyl, Leonardo J., Rumnieks, Janis, Mochizuki, Tomohiro, Jalasvuori, Matti, Aziz, Ramy K., Lobocka, Malgorzata, Stedman, Kenneth M., Shkoporov, Andrey N., Gillis, Annika, Peng, Xu, Enault, Francois, Knezevic, Petar, Lavigne, Rob, Rhee, Sung-Keun, Cvirkaite-Krupovic, Virginija, Moraru, Cristina, Moreno Switt, Andrea I., Poranen, Minna M., Millard, Andrew, Prangishvili, David, Adriaenssens, Evelien M., Sub Bioinformatics, Theoretical Biology and Bioinformatics, Krupovic, Mart, Turner, Dann, Morozova, Vera, Dyall-Smith, Mike, Oksanen, Hanna M., Edwards, Rob, Dutilh, Bas E., Lehman, Susan M., Reyes, Alejandro, Baquero, Diana P., Sullivan, Matthew B., Uchiyama, Jumpei, Nakavuma, Jesca, Barylski, Jakub, Young, Mark J., Du, Shishen, Alfenas-Zerbini, Poliane, Kushkina, Alla, Kropinski, Andrew M., Kurtboke, Ipek, Brister, J. Rodney, Lood, Cedric, Sarkar, B. L., Yigang, Tong, Liu, Ying, Huang, Li, Wittmann, Johannes, Chanishvili, Nina, van Zyl, Leonardo J., Rumnieks, Janis, Mochizuki, Tomohiro, Jalasvuori, Matti, Aziz, Ramy K., Lobocka, Malgorzata, Stedman, Kenneth M., Shkoporov, Andrey N., Gillis, Annika, Peng, Xu, Enault, Francois, Knezevic, Petar, Lavigne, Rob, Rhee, Sung-Keun, Cvirkaite-Krupovic, Virginija, Moraru, Cristina, Moreno Switt, Andrea I., Poranen, Minna M., Millard, Andrew, Prangishvili, David, and Adriaenssens, Evelien M.
Published: 2021

18. Joining European Scientific Forces to Face Pandemics

Author: Vasconcelos, M Helena, Vasconcelos, M Helena, Alcaro, Stefano, Arechavala-Gomeza, Virginia, Baumbach, Jan, Borges, Fernanda, Brevini, Tiziana A L, Rivas, Javier De Las, Devaux, Yvan, Hozak, Pavel, Keinänen-Toivola, Minna M, Lattanzi, Giovanna, Mohr, Thomas, Murovska, Modra, Prusty, Bhupesh K, Quinlan, Roy A, Pérez-Sala, Dolores, Scheibenbogen, Carmen, Schmidt, Harald H H W, Silveira, Isabel, Tieri, Paolo, Tolios, Alexander, Riganti, Chiara, Vasconcelos, M Helena, Vasconcelos, M Helena, Alcaro, Stefano, Arechavala-Gomeza, Virginia, Baumbach, Jan, Borges, Fernanda, Brevini, Tiziana A L, Rivas, Javier De Las, Devaux, Yvan, Hozak, Pavel, Keinänen-Toivola, Minna M, Lattanzi, Giovanna, Mohr, Thomas, Murovska, Modra, Prusty, Bhupesh K, Quinlan, Roy A, Pérez-Sala, Dolores, Scheibenbogen, Carmen, Schmidt, Harald H H W, Silveira, Isabel, Tieri, Paolo, Tolios, Alexander, and Riganti, Chiara
Abstract: Despite the international guidelines on the containment of the coronavirus disease 2019 (COVID-19) pandemic, the European scientific community was not sufficiently prepared to coordinate scientific efforts. To improve preparedness for future pandemics, we have initiated a network of nine European-funded Cooperation in Science and Technology (COST) Actions that can help facilitate inter-, multi-, and trans-disciplinary communication and collaboration.
Published: 2021

19. Bacterial Viruses Subcommittee and Archaeal Viruses Subcommittee of the ICTV: update of taxonomy changes in 2021

Author: UCL - SST/ELI/ELIM - Applied Microbiology, Krupovic, Mart, Turner, Dann, Morozova, Vera, Dyall-Smith, Mike, Oksanen, Hanna M., Edwards, Rob, Dutilh, Bas E., Lehman, Susan M., Reyes, Alejandro, Baquero, Diana P., Sullivan, Matthew B., Uchiyama, Jumpei, Nakavuma, Jesca, Barylski, Jakub, Young, Mark J., Du, Shishen, Alfenas-Zerbini, Poliane, Kushkina, Alla, Kropinski, Andrew M., Kurtböke, Ipek, Brister, J. Rodney, Lood, Cédric, Sarkar, B. L., Yigang, Tong, Liu, Ying, Huang, Li, Wittmann, Johannes, Chanishvili, Nina, van Zyl, Leonardo J., Rumnieks, Janis, Mochizuki, Tomohiro, Jalasvuori, Matti, Aziz, Ramy K., Łobocka, Małgorzata, Stedman, Kenneth M., Shkoporov, Andrey N., Gillis, Annika, Peng, Xu, Enault, François, Knezevic, Petar, Lavigne, Rob, Rhee, Sung-Keun, Cvirkaite-Krupovic, Virginija, Moraru, Cristina, Moreno Switt, Andrea I., Poranen, Minna M., Millard, Andrew, Prangishvili, David, Adriaenssens, Evelien M., UCL - SST/ELI/ELIM - Applied Microbiology, Krupovic, Mart, Turner, Dann, Morozova, Vera, Dyall-Smith, Mike, Oksanen, Hanna M., Edwards, Rob, Dutilh, Bas E., Lehman, Susan M., Reyes, Alejandro, Baquero, Diana P., Sullivan, Matthew B., Uchiyama, Jumpei, Nakavuma, Jesca, Barylski, Jakub, Young, Mark J., Du, Shishen, Alfenas-Zerbini, Poliane, Kushkina, Alla, Kropinski, Andrew M., Kurtböke, Ipek, Brister, J. Rodney, Lood, Cédric, Sarkar, B. L., Yigang, Tong, Liu, Ying, Huang, Li, Wittmann, Johannes, Chanishvili, Nina, van Zyl, Leonardo J., Rumnieks, Janis, Mochizuki, Tomohiro, Jalasvuori, Matti, Aziz, Ramy K., Łobocka, Małgorzata, Stedman, Kenneth M., Shkoporov, Andrey N., Gillis, Annika, Peng, Xu, Enault, François, Knezevic, Petar, Lavigne, Rob, Rhee, Sung-Keun, Cvirkaite-Krupovic, Virginija, Moraru, Cristina, Moreno Switt, Andrea I., Poranen, Minna M., Millard, Andrew, Prangishvili, David, and Adriaenssens, Evelien M.
Abstract: In this article, we – the Bacterial Viruses Subcommittee and the Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) – summarise the results of our activities for the period March 2020 – March 2021. We report the division of the former Bacterial and Archaeal Viruses Subcommittee in two separate Subcommittees, welcome new members, a new Subcommittee Chair and Vice Chair, and give an overview of the new taxa that were proposed in 2020, approved by the Executive Committee and ratified by vote in 2021. In particular, a new realm, three orders, 15 families, 31 subfamilies, 734 genera and 1845 species were newly created or redefined (moved/promoted).
Published: 2021

20. Root-type ferredoxin-NADP+ oxidoreductase isoforms in Arabidopsis thaliana:Expression patterns, location and stress responses

Author: Grabsztunowicz, Magda, Rantala, Marjaana, Ivanauskaite, Aiste, Blomster, Tiina, Koskela, Minna M., Vuorinen, Katariina, Tyystjarvi, Esa, Burow, Meike, Overmyer, Kirk, Mahonen, Ari P., Mulo, Paula, Grabsztunowicz, Magda, Rantala, Marjaana, Ivanauskaite, Aiste, Blomster, Tiina, Koskela, Minna M., Vuorinen, Katariina, Tyystjarvi, Esa, Burow, Meike, Overmyer, Kirk, Mahonen, Ari P., and Mulo, Paula
Abstract: In Arabidopsis, two leaf-type ferredoxin-NADP(+) oxidoreductase (LFNR) isoforms function in photosynthetic electron flow in reduction of NADP(+), while two root-type FNR (RFNR) isoforms catalyse reduction of ferredoxin in non-photosynthetic plastids. As the key to understanding, the function of RFNRs might lie in their spatial and temporal distribution in different plant tissues and cell types, we examined expression of RFNR1 and RFNR2 genes using beta-glucuronidase (GUS) reporter lines and investigated accumulation of distinct RFNR isoforms using a GFP approach and Western blotting upon various stresses. We show that while RFNR1 promoter is active in leaf veins, root tips and in the stele of roots, RFNR2 promoter activity is present in leaf tips and root stele, epidermis and cortex. RFNR1 protein accumulates as a soluble protein within the plastids of root stele cells, while RFNR2 is mainly present in the outer root layers. Ozone treatment of plants enhanced accumulation of RFNR1, whereas low temperature treatment specifically affected RFNR2 accumulation in roots. We further discuss the physiological roles of RFNR1 and RFNR2 based on characterization of rfnr1 and rfnr2 knock-out plants and show that although the function of these proteins is partly redundant, the RFNR proteins are essential for plant development and survival.
Published: 2021

21. Bacterial Viruses Subcommittee and Archaeal Viruses Subcommittee of the ICTV:update of taxonomy changes in 2021

Author: Krupovic, Mart, Turner, Dann, Morozova, Vera, Dyall-Smith, Mike, Oksanen, Hanna M., Edwards, Rob, Dutilh, Bas E., Lehman, Susan M., Reyes, Alejandro, Baquero, Diana P., Sullivan, Matthew B., Uchiyama, Jumpei, Nakavuma, Jesca, Barylski, Jakub, Young, Mark J., Du, Shishen, Alfenas-Zerbini, Poliane, Kushkina, Alla, Kropinski, Andrew M., Kurtböke, Ipek, Brister, J. Rodney, Lood, Cédric, Sarkar, B. L., Yigang, Tong, Liu, Ying, Huang, Li, Wittmann, Johannes, Chanishvili, Nina, van Zyl, Leonardo J., Rumnieks, Janis, Mochizuki, Tomohiro, Jalasvuori, Matti, Aziz, Ramy K., Łobocka, Małgorzata, Stedman, Kenneth M., Shkoporov, Andrey N., Gillis, Annika, Peng, Xu, Enault, François, Knezevic, Petar, Lavigne, Rob, Rhee, Sung Keun, Cvirkaite-Krupovic, Virginija, Moraru, Cristina, Moreno Switt, Andrea I., Poranen, Minna M., Millard, Andrew, Prangishvili, David, Adriaenssens, Evelien M., Krupovic, Mart, Turner, Dann, Morozova, Vera, Dyall-Smith, Mike, Oksanen, Hanna M., Edwards, Rob, Dutilh, Bas E., Lehman, Susan M., Reyes, Alejandro, Baquero, Diana P., Sullivan, Matthew B., Uchiyama, Jumpei, Nakavuma, Jesca, Barylski, Jakub, Young, Mark J., Du, Shishen, Alfenas-Zerbini, Poliane, Kushkina, Alla, Kropinski, Andrew M., Kurtböke, Ipek, Brister, J. Rodney, Lood, Cédric, Sarkar, B. L., Yigang, Tong, Liu, Ying, Huang, Li, Wittmann, Johannes, Chanishvili, Nina, van Zyl, Leonardo J., Rumnieks, Janis, Mochizuki, Tomohiro, Jalasvuori, Matti, Aziz, Ramy K., Łobocka, Małgorzata, Stedman, Kenneth M., Shkoporov, Andrey N., Gillis, Annika, Peng, Xu, Enault, François, Knezevic, Petar, Lavigne, Rob, Rhee, Sung Keun, Cvirkaite-Krupovic, Virginija, Moraru, Cristina, Moreno Switt, Andrea I., Poranen, Minna M., Millard, Andrew, Prangishvili, David, and Adriaenssens, Evelien M.
Abstract: In this article, we – the Bacterial Viruses Subcommittee and the Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) – summarise the results of our activities for the period March 2020 – March 2021. We report the division of the former Bacterial and Archaeal Viruses Subcommittee in two separate Subcommittees, welcome new members, a new Subcommittee Chair and Vice Chair, and give an overview of the new taxa that were proposed in 2020, approved by the Executive Committee and ratified by vote in 2021. In particular, a new realm, three orders, 15 families, 31 subfamilies, 734 genera and 1845 species were newly created or redefined (moved/promoted).
Published: 2021

22. Sultan Muhammad Bello and his intellectual contribution to the Sokoto Caliphate

Author: Minna, M. T. M.
Subjects: 900, Hausaland, Jihad, African Islamic history
Published: 1982

23. Taxonomy of prokaryotic viruses: 2018-2019 update from the ICTV Bacterial and Archaeal Viruses Subcommittee

Author: Adriaenssens, Evelien M, Sullivan, Matthew B, Knezevic, Petar, van Zyl, Leonardo J, Sarkar, B L, Dutilh, Bas E, Alfenas-Zerbini, Poliane, Łobocka, Małgorzata, Tong, Yigang, Brister, James Rodney, Moreno Switt, Andrea I, Klumpp, Jochen, Aziz, Ramy Karam, Barylski, Jakub, Uchiyama, Jumpei, Kropinski, Andrew M, Petty, Nicola K, Clokie, Martha R J, Kushkina, Alla I, Morozova, Vera V, Duffy, Siobain, Gillis, Annika, Rumnieks, Janis, Kurtböke, İpek, Chanishvili, Nina, Goodridge, Lawrence, Wittmann, Johannes, Lavigne, Rob, Jang, Ho Bin, Prangishvili, David, Enault, Francois, Turner, Dann, Poranen, Minna M, Oksanen, Hanna M, Krupovic, Mart, Adriaenssens, Evelien M, Sullivan, Matthew B, Knezevic, Petar, van Zyl, Leonardo J, Sarkar, B L, Dutilh, Bas E, Alfenas-Zerbini, Poliane, Łobocka, Małgorzata, Tong, Yigang, Brister, James Rodney, Moreno Switt, Andrea I, Klumpp, Jochen, Aziz, Ramy Karam, Barylski, Jakub, Uchiyama, Jumpei, Kropinski, Andrew M, Petty, Nicola K, Clokie, Martha R J, Kushkina, Alla I, Morozova, Vera V, Duffy, Siobain, Gillis, Annika, Rumnieks, Janis, Kurtböke, İpek, Chanishvili, Nina, Goodridge, Lawrence, Wittmann, Johannes, Lavigne, Rob, Jang, Ho Bin, Prangishvili, David, Enault, Francois, Turner, Dann, Poranen, Minna M, Oksanen, Hanna M, and Krupovic, Mart
Abstract: This article is a summary of the activities of the ICTV's Bacterial and Archaeal Viruses Subcommittee for the years 2018 and 2019. Highlights include the creation of a new order, 10 families, 22 subfamilies, 424 genera and 964 species. Some of our concerns about the ICTV's ability to adjust to and incorporate new DNA- and protein-based taxonomic tools are discussed.
Published: 2020

24. Temperature controlled high-throughput magnetic tweezers show striking difference in activation energies of replicating viral RNA-dependent RNA polymerases

Author: Seifert, Mona (author), van Nies, Pauline (author), Papini, Flávia S. (author), Arnold, Jamie J. (author), Poranen, Minna M. (author), Cameron, Craig E. (author), Depken, S.M. (author), Dulin, D. (author), Seifert, Mona (author), van Nies, Pauline (author), Papini, Flávia S. (author), Arnold, Jamie J. (author), Poranen, Minna M. (author), Cameron, Craig E. (author), Depken, S.M. (author), and Dulin, D. (author)
Abstract: RNA virus survival depends on efficient viral genome replication, which is performed by the viral RNA dependent RNA polymerase (RdRp). The recent development of high throughput magnetic tweezers has enabled the simultaneous observation of dozens of viral RdRp elongation traces on kilobases long templates, and this has shown that RdRp nucleotide addition kinetics is stochastically interrupted by rare pauses of 1-1000 s duration, of which the short-lived ones (1-10 s) are the temporal signature of a low fidelity catalytic pathway. We present a simple and precise temperature controlled system for magnetic tweezers to characterize the replication kinetics temperature dependence between 25°C and 45°C of RdRps from three RNA viruses, i.e. the double-stranded RNA bacteriophage Φ6, and the positive-sense single-stranded RNA poliovirus (PV) and human rhinovirus C (HRV-C). We found that Φ6 RdRp is largely temperature insensitive, while PV and HRV-C RdRps replication kinetics are activated by temperature. Furthermore, the activation energies we measured for PV RdRp catalytic state corroborate previous estimations from ensemble pre-steady state kinetic studies, further confirming the catalytic origin of the short pauses and their link to temperature independent RdRp fidelity. This work will enable future temperature controlled study of biomolecular complex at the single molecule level., BN/Martin Depken Lab, BN/Nynke Dekker Lab
Published: 2020
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25. Taxonomy of prokaryotic viruses: 2018-2019 update from the ICTV Bacterial and Archaeal Viruses Subcommittee

Author: Sub Bioinformatics, Theoretical Biology and Bioinformatics, Adriaenssens, Evelien M, Sullivan, Matthew B, Knezevic, Petar, van Zyl, Leonardo J, Sarkar, B L, Dutilh, Bas E, Alfenas-Zerbini, Poliane, Łobocka, Małgorzata, Tong, Yigang, Brister, James Rodney, Moreno Switt, Andrea I, Klumpp, Jochen, Aziz, Ramy Karam, Barylski, Jakub, Uchiyama, Jumpei, Kropinski, Andrew M, Petty, Nicola K, Clokie, Martha R J, Kushkina, Alla I, Morozova, Vera V, Duffy, Siobain, Gillis, Annika, Rumnieks, Janis, Kurtböke, İpek, Chanishvili, Nina, Goodridge, Lawrence, Wittmann, Johannes, Lavigne, Rob, Jang, Ho Bin, Prangishvili, David, Enault, Francois, Turner, Dann, Poranen, Minna M, Oksanen, Hanna M, Krupovic, Mart, Sub Bioinformatics, Theoretical Biology and Bioinformatics, Adriaenssens, Evelien M, Sullivan, Matthew B, Knezevic, Petar, van Zyl, Leonardo J, Sarkar, B L, Dutilh, Bas E, Alfenas-Zerbini, Poliane, Łobocka, Małgorzata, Tong, Yigang, Brister, James Rodney, Moreno Switt, Andrea I, Klumpp, Jochen, Aziz, Ramy Karam, Barylski, Jakub, Uchiyama, Jumpei, Kropinski, Andrew M, Petty, Nicola K, Clokie, Martha R J, Kushkina, Alla I, Morozova, Vera V, Duffy, Siobain, Gillis, Annika, Rumnieks, Janis, Kurtböke, İpek, Chanishvili, Nina, Goodridge, Lawrence, Wittmann, Johannes, Lavigne, Rob, Jang, Ho Bin, Prangishvili, David, Enault, Francois, Turner, Dann, Poranen, Minna M, Oksanen, Hanna M, and Krupovic, Mart
Published: 2020

26. Taxonomy of prokaryotic viruses: 2018-2019 update from the ICTV Bacterial and Archaeal Viruses Subcommittee

Author: UCL - SST/ELI/ELIM - Applied Microbiology, Adriaenssens, Evelien M., Sullivan, Matthew B., Knezevic, Petar, van Zyl, Leonardo J., Sarkar, B. L., Dutilh, Bas E., Alfenas-Zerbini, Poliane, Łobocka, Małgorzata, Tong, Yigang, Brister, James Rodney, Moreno Switt, Andrea I., Klumpp, Jochen, Aziz, Ramy Karam, Barylski, Jakub, Uchiyama, Jumpei, Edwards, Rob A., Kropinski, Andrew M., Petty, Nicola K., Clokie, Martha R. J., Kushkina, Alla I., Morozova, Vera V., Duffy, Siobain, Gillis, Annika, Rumnieks, Janis, Kurtböke, İpek, Chanishvili, Nina, Goodridge, Lawrence, Wittmann, Johannes, Lavigne, Rob, Jang, Ho Bin, Prangishvili, David, Enault, Francois, Turner, Dann, Poranen, Minna M., Oksanen, Hanna M., Krupovic, Mart, UCL - SST/ELI/ELIM - Applied Microbiology, Adriaenssens, Evelien M., Sullivan, Matthew B., Knezevic, Petar, van Zyl, Leonardo J., Sarkar, B. L., Dutilh, Bas E., Alfenas-Zerbini, Poliane, Łobocka, Małgorzata, Tong, Yigang, Brister, James Rodney, Moreno Switt, Andrea I., Klumpp, Jochen, Aziz, Ramy Karam, Barylski, Jakub, Uchiyama, Jumpei, Edwards, Rob A., Kropinski, Andrew M., Petty, Nicola K., Clokie, Martha R. J., Kushkina, Alla I., Morozova, Vera V., Duffy, Siobain, Gillis, Annika, Rumnieks, Janis, Kurtböke, İpek, Chanishvili, Nina, Goodridge, Lawrence, Wittmann, Johannes, Lavigne, Rob, Jang, Ho Bin, Prangishvili, David, Enault, Francois, Turner, Dann, Poranen, Minna M., Oksanen, Hanna M., and Krupovic, Mart
Abstract: This article is a summary of the activities of the ICTV's Bacterial and Archaeal Viruses Subcommittee for the years 2018 and 2019. Highlights include the creation of a new order, 10 families, 22 subfamilies, 424 genera and 964 species. Some of our concerns about the ICTV's ability to adjust to and incorporate new DNA- and protein-based taxonomic tools are discussed.
Published: 2020

27. Spatially varying peatland initiation, Holocene development, carbon accumulation patterns and radiative forcing within a subarctic fen

Author: Piilo, S. R. (Sanna R.), Korhola, A. (Atte), Heiskanen, L. (Lauri), Tuovinen, J.-P. (Juha-Pekka), Aurela, M. (Mika), Juutinen, S. (Sari), Marttila, H. (Hannu), Saari, M. (Markus), Tuittila, E.-S. (Eeva-Stiina), Turunen, J. (Jukka), Väliranta, M. M. (Minna M.), Piilo, S. R. (Sanna R.), Korhola, A. (Atte), Heiskanen, L. (Lauri), Tuovinen, J.-P. (Juha-Pekka), Aurela, M. (Mika), Juutinen, S. (Sari), Marttila, H. (Hannu), Saari, M. (Markus), Tuittila, E.-S. (Eeva-Stiina), Turunen, J. (Jukka), and Väliranta, M. M. (Minna M.)
Abstract: High latitude peatlands act as globally important carbon (C) sinks and are in constant interaction with the atmosphere. Their C storage formed during the Holocene. In the course of time, the aggregate effect of the C fluxes on radiative forcing (RF) typically changes from warming to cooling, but the timing of this shift varies among different peatlands. Here we investigated Holocene peatland development, including vegetation history, vertical peat growth and the lateral expansion of a patterned subarctic fen in northern Finland by means of multiple sampling points. We modelled the Holocene RF by combining knowledge on past vegetation communities based on plant macrofossil stratigraphies and present in situ C flux measurements. The peatland initiated at ca. 9500 calibrated years Before Present (cal yr BP), and its lateral expansion was greatest between ca. 9000 and 7000 cal yr BP. After the early expansion, vertical peat growth proceeded very differently in different parts of the peatland, regulated by internal and external factors. The pronounced surface microtopography, with high strings and wet flarks, started to form only after ca. 1000 cal yr BP. C accumulation within the peatland recorded a high degree of spatial variability throughout its history, including the recent past. We applied two flux scenarios with different interpretation of the initial peatland development phases to estimate the RF induced by C fluxes of the fen. After ca. 4000 cal yr BP, at the latest, the peatland RF has been negative (cooling), mainly driven by C uptake and biomass production, while methane emissions had a lesser role in the total RF. Interestingly, these scenarios suggest that the greatest cooling effect took place around ca. 1000 cal yr BP, after which the surface microtopography established. The study demonstrated that despite the high spatial heterogeneity and idiosyncratic behaviour of the peatland, the RF of the studied fen followed the general development pattern
Published: 2020

28. SUCCOR study: an international European cohort observational study comparing minimally invasive surgery versus open abdominal radical hysterectomy in patients with stage IB1 cervical cancer

Author: Chiva, L, Zanagnolo, V, Querleu, D, Martin-Calvo, N, Arévalo-Serrano, J, Căpîlna, M, Fagotti, A, Kucukmetin, A, Mom, C, Chakalova, G, Aliyev, S, Malzoni, M, Narducci, F, Arencibia, O, Raspagliesi, F, Toptas, T, Cibula, D, Kaidarova, D, Meydanli, M, Tavares, M, Golub, D, Perrone, A, Poka, R, Tsolakidis, D, Vujić, G, Jedryka, M, Zusterzeel, P, Beltman, J, Goffin, F, Haidopoulos, D, Haller, H, Jach, R, Yezhova, I, Berlev, I, Bernardino, M, Bharathan, R, Lanner, M, Maenpaa, M, Sukhin, V, Feron, J, Fruscio, R, Kukk, K, Ponce, J, Minguez, J, Vázquez-Vicente, D, Castellanos, T, Chacon, E, Alcazar, J, Chiva, Luis, Zanagnolo, Vanna, Querleu, Denis, Martin-Calvo, Nerea, Arévalo-Serrano, Juan, Căpîlna, Mihai Emil, Fagotti, Anna, Kucukmetin, Ali, Mom, Constantijne, Chakalova, Galina, Aliyev, Shamistan, Malzoni, Mario, Narducci, Fabrice, Arencibia, Octavio, Raspagliesi, Francesco, Toptas, Tayfun, Cibula, David, Kaidarova, Dilyara, Meydanli, Mehmet Mutlu, Tavares, Mariana, Golub, Dmytro, Perrone, Anna Myriam, Poka, Robert, Tsolakidis, Dimitrios, Vujić, Goran, Jedryka, Marcin A, Zusterzeel, Petra L M, Beltman, Jogchum Jan, Goffin, Frederic, Haidopoulos, Dimitrios, Haller, Herman, Jach, Robert, Yezhova, Iryna, Berlev, Igor, Bernardino, Margarida, Bharathan, Rasiah, Lanner, Maximilian, Maenpaa, Minna M, Sukhin, Vladyslav, Feron, Jean-Guillaume, Fruscio, Robert, Kukk, Kersti, Ponce, Jordi, Minguez, Jose Angel, Vázquez-Vicente, Daniel, Castellanos, Teresa, Chacon, Enrique, Alcazar, Juan Luis, Chiva, L, Zanagnolo, V, Querleu, D, Martin-Calvo, N, Arévalo-Serrano, J, Căpîlna, M, Fagotti, A, Kucukmetin, A, Mom, C, Chakalova, G, Aliyev, S, Malzoni, M, Narducci, F, Arencibia, O, Raspagliesi, F, Toptas, T, Cibula, D, Kaidarova, D, Meydanli, M, Tavares, M, Golub, D, Perrone, A, Poka, R, Tsolakidis, D, Vujić, G, Jedryka, M, Zusterzeel, P, Beltman, J, Goffin, F, Haidopoulos, D, Haller, H, Jach, R, Yezhova, I, Berlev, I, Bernardino, M, Bharathan, R, Lanner, M, Maenpaa, M, Sukhin, V, Feron, J, Fruscio, R, Kukk, K, Ponce, J, Minguez, J, Vázquez-Vicente, D, Castellanos, T, Chacon, E, Alcazar, J, Chiva, Luis, Zanagnolo, Vanna, Querleu, Denis, Martin-Calvo, Nerea, Arévalo-Serrano, Juan, Căpîlna, Mihai Emil, Fagotti, Anna, Kucukmetin, Ali, Mom, Constantijne, Chakalova, Galina, Aliyev, Shamistan, Malzoni, Mario, Narducci, Fabrice, Arencibia, Octavio, Raspagliesi, Francesco, Toptas, Tayfun, Cibula, David, Kaidarova, Dilyara, Meydanli, Mehmet Mutlu, Tavares, Mariana, Golub, Dmytro, Perrone, Anna Myriam, Poka, Robert, Tsolakidis, Dimitrios, Vujić, Goran, Jedryka, Marcin A, Zusterzeel, Petra L M, Beltman, Jogchum Jan, Goffin, Frederic, Haidopoulos, Dimitrios, Haller, Herman, Jach, Robert, Yezhova, Iryna, Berlev, Igor, Bernardino, Margarida, Bharathan, Rasiah, Lanner, Maximilian, Maenpaa, Minna M, Sukhin, Vladyslav, Feron, Jean-Guillaume, Fruscio, Robert, Kukk, Kersti, Ponce, Jordi, Minguez, Jose Angel, Vázquez-Vicente, Daniel, Castellanos, Teresa, Chacon, Enrique, and Alcazar, Juan Luis
Abstract: Background: Minimally invasive surgery in cervical cancer has demonstrated in recent publications worse outcomes than open surgery. The primary objective of the SUCCOR study, a European, multicenter, retrospective, observational cohort study was to evaluate disease-free survival in patients with stage IB1 (FIGO 2009) cervical cancer undergoing open vs minimally invasive radical hysterectomy. As a secondary objective, we aimed to investigate the association between protective surgical maneuvers and the risk of relapse. Methods: We obtained data from 1272 patients that underwent a radical hysterectomy by open or minimally invasive surgery for stage IB1 cervical cancer (FIGO 2009) from January 2013 to December 2014. After applying all the inclusion-exclusion criteria, we used an inverse probability weighting to construct a weighted cohort of 693 patients to compare outcomes (minimally invasive surgery vs open). The first endpoint compared disease-free survival at 4.5 years in both groups. Secondary endpoints compared overall survival among groups and the impact of the use of a uterine manipulator and protective closure of the colpotomy over the tumor in the minimally invasive surgery group. Results: Mean age was 48.3 years (range; 23-83) while the mean BMI was 25.7 kg/m2 (range; 15-49). The risk of recurrence for patients who underwent minimally invasive surgery was twice as high as that in the open surgery group (HR, 2.07; 95% CI, 1.35 to 3.15; P=0.001). Similarly, the risk of death was 2.42-times higher than in the open surgery group (HR, 2.45; 95% CI, 1.30 to 4.60, P=0.005). Patients that underwent minimally invasive surgery using a uterine manipulator had a 2.76-times higher hazard of relapse (HR, 2.76; 95% CI, 1.75 to 4.33; P<0.001) and those without the use of a uterine manipulator had similar disease-free-survival to the open surgery group (HR, 1.58; 95% CI, 0.79 to 3.15; P=0.20). Moreover, patients that underwent minimally invasive surgery with protective va
Published: 2020

29. Joining European Scientific Forces to Face Pandemics

Author: European Commission, Instituto de Salud Carlos III, Ikerbasque Basque Foundation for Science, Carraresi Foundation, Regione Lombardia, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Consejo Superior de Investigaciones Científicas (España), Fundação para a Ciência e a Tecnologia (Portugal), Associazione Italiana per la Ricerca sul Cancro, PharmaMar, Fonds National de la Recherche Luxembourg, Ministère de l’Enseignement Supérieur et de la Recherche (Luxembourg), Fondation Coeur - Daniel Wagner, Vasconcelos, M. Helena, Alcaro, Stefano, Arechavala-Gameza, Virginia, Baumbach, Jan, Borges, Fernanda, Brevini, Tiziana A. L., De Las Rivas, Javier, Devaux, Yvan, Hozak, Pavel, Keinänen-Toivola, Minna M., Lattanzi, Giovanna, Mohr, Thomas, Murovska, Modra, Prusty, Bhupesh K., Quinlan, Roy A., Pérez-Sala, Dolores, Scheibenbogen, Carmen, Schmidt, Harald H.H.W., Silveira, Isabel, Tieri, Paolo, Tolios, Alexander, Riganti, Chiara, European Commission, Instituto de Salud Carlos III, Ikerbasque Basque Foundation for Science, Carraresi Foundation, Regione Lombardia, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Consejo Superior de Investigaciones Científicas (España), Fundação para a Ciência e a Tecnologia (Portugal), Associazione Italiana per la Ricerca sul Cancro, PharmaMar, Fonds National de la Recherche Luxembourg, Ministère de l’Enseignement Supérieur et de la Recherche (Luxembourg), Fondation Coeur - Daniel Wagner, Vasconcelos, M. Helena, Alcaro, Stefano, Arechavala-Gameza, Virginia, Baumbach, Jan, Borges, Fernanda, Brevini, Tiziana A. L., De Las Rivas, Javier, Devaux, Yvan, Hozak, Pavel, Keinänen-Toivola, Minna M., Lattanzi, Giovanna, Mohr, Thomas, Murovska, Modra, Prusty, Bhupesh K., Quinlan, Roy A., Pérez-Sala, Dolores, Scheibenbogen, Carmen, Schmidt, Harald H.H.W., Silveira, Isabel, Tieri, Paolo, Tolios, Alexander, and Riganti, Chiara
Abstract: Despite the international guidelines on the containment of the coronavirus disease 2019 (COVID-19) pandemic, the European scientific community was not sufficiently prepared to coordinate scientific efforts. To improve preparedness for future pandemics, we have initiated a network of nine European-funded Cooperation in Science and Technology (COST) Actions that can help facilitate inter-, multi-, and trans-disciplinary communication and collaboration.
Published: 2020

30. Shotgun Environmental DNA, Pollen, and Macrofossil Analysis of Lateglacial Lake Sediments From Southern Sweden

Author: Parducci, Laura, Alsos, Inger Greve, Unneberg, Per, Pedersen, Mikkel W., Han, Lu, Lammers, Youri, Salonen, J. Sakari, Valiranta, Minna M., Slotte, Tanja, Wohlfarth, Barbara, Parducci, Laura, Alsos, Inger Greve, Unneberg, Per, Pedersen, Mikkel W., Han, Lu, Lammers, Youri, Salonen, J. Sakari, Valiranta, Minna M., Slotte, Tanja, and Wohlfarth, Barbara
Abstract: The lake sediments of Hasseldala Port in south-east Sweden provide an archive of local and regional environmental conditions similar to 14.5-9.5 ka BP (thousand years before present) and allow testing DNA sequencing techniques to reconstruct past vegetation changes. We combined shotgun sequencing with plant micro- and macrofossil analyses to investigate sediments dating to the Allerod (14.1-12.7 ka BP), Younger Dryas (12.7-11.7 ka BP), and Preboreal (<11.7 ka BP). Number of reads and taxa were not associated with sample age or organic content. This suggests that, beyond the initial rapid degradation, DNA is still present. The proportion of recovered plant DNA was low, but allowed identifying an important number of plant taxa, thus adding valid information on the composition of the local vegetation. Importantly, DNA provides a stronger signal of plant community changes than plant micro- and plant macrofossil analyses alone, since a larger number of new taxa were recorded in Younger Dryas samples. A comparison between the three proxies highlights differences and similarities and supports earlier findings that plants growing close to or within a lake are recorded by DNA. Plant macrofossil remains moreover show that tree birch was present close to the ancient lake since the Allerod; together with the DNA results, this indicates that boreal to subarctic climatic conditions also prevailed during the cold Younger Dryas interval. Increasing DNA reference libraries and enrichment strategies prior to sequencing are necessary to improve the potential and accuracy of plant identification using the shotgun metagenomic approach.
Published: 2019
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31. Reflux aspiration in lungs of dogs with respiratory disease and in healthy West Highland White Terriers

Author: Määttä, OL Merita, Määttä, OL Merita, Laurila, Henna P, Holopainen, Saila, Lilja‐Maula, Liisa, Melamies, Marika, Viitanen, Sanna J, Johnson, LR, Koho, Ninna, Neuvonen, Mikko, Niemi, Mikko, Rajamäki, Minna M, Määttä, OL Merita, Määttä, OL Merita, Laurila, Henna P, Holopainen, Saila, Lilja‐Maula, Liisa, Melamies, Marika, Viitanen, Sanna J, Johnson, LR, Koho, Ninna, Neuvonen, Mikko, Niemi, Mikko, and Rajamäki, Minna M
Published: 2018

32. Taxonomy of prokaryotic viruses: 2017 update from the ICTV Bacterial and Archaeal Viruses Subcommittee

Author: Adriaenssens, Evelien M, Wittmann, Johannes, Kuhn, Jens H, Turner, Dann, Sullivan, Matthew B., Dutilh, Bas E, Jang, Ho Bin, van Zyl, Leonardo J, Klumpp, Jochen, Lobocka, Malgorzata, Moreno Switt, Andrea I, Rumnieks, Janis, Edwards, Robert A, Uchiyama, Jumpei, Alfenas-Zerbini, Poliane, Petty, Nicola K, Kropinski, Andrew M, Barylski, Jakub, Gillis, Annika, Clokie, Martha R C, Prangishvili, David, Lavigne, Rob, Aziz, Ramy Karam, Duffy, Siobain, Krupovic, Mart, Poranen, Minna M., Knezevic, Petar, Enault, Francois, Tong, Yigang, Oksanen, Hanna M., Rodney Brister, J, Adriaenssens, Evelien M, Wittmann, Johannes, Kuhn, Jens H, Turner, Dann, Sullivan, Matthew B., Dutilh, Bas E, Jang, Ho Bin, van Zyl, Leonardo J, Klumpp, Jochen, Lobocka, Malgorzata, Moreno Switt, Andrea I, Rumnieks, Janis, Edwards, Robert A, Uchiyama, Jumpei, Alfenas-Zerbini, Poliane, Petty, Nicola K, Kropinski, Andrew M, Barylski, Jakub, Gillis, Annika, Clokie, Martha R C, Prangishvili, David, Lavigne, Rob, Aziz, Ramy Karam, Duffy, Siobain, Krupovic, Mart, Poranen, Minna M., Knezevic, Petar, Enault, Francois, Tong, Yigang, Oksanen, Hanna M., and Rodney Brister, J
Published: 2018

33. Macrocycles containing 1,1’-ferrocenyldiselenolato ligands on group 4 metallocenes

Author: Sanchez-Perez, C. (Clara), Knapp, C. E. (Caroline E.), Karjalainen, M. M. (Minna M.), Oilunkaniemi, R. (Raija), Carmalt, C. J. (Claire J.), Laitinen, R. S. (Risto S.), Sanchez-Perez, C. (Clara), Knapp, C. E. (Caroline E.), Karjalainen, M. M. (Minna M.), Oilunkaniemi, R. (Raija), Carmalt, C. J. (Claire J.), and Laitinen, R. S. (Risto S.)
Abstract: Macrocyclic [Fe(η⁵-C₅H₄Se)₂M(η⁵-C₅H₄R)₂]₂ [M = Ti (1), Zr (2), Hf (3), R = H; and M = Zr (4), Hf (5), R = tBu] were prepared and characterized by ⁷⁷Se NMR spectroscopy and the crystal structures of 1–3 and 5 were determined by single-crystal X-ray diffraction. The crystal structure of 4 is known and the complex is isomorphous with 5. 1–5 form mutually similar macrocyclic tetranuclear complexes in which the alternating Fe(C₅H₄Se)₂ and M(C₅H₄R)₂ centers are linked by selenium bridges. The thermogravimetric analysis (TGA) of 1–3 under a helium atmosphere indicated that the complexes undergo a two-step decomposition upon heating. The final products were identified using powder X-ray diffraction as FexMSe₂, indicating their potential as single-source precursors for functional materials.
Published: 2018

34. Genome Evolution of Bartonellaceae Symbionts of Ants at the Opposite Ends of the Trophic Scale

Author: Bisch, Gaelle, Neuvonen, Minna M., Pierce, Naomi E., Russell, Jacob A., Koga, Ryuichi, Sanders, Jon G., Lukasik, Piotr, Andersson, Siv G. E., Bisch, Gaelle, Neuvonen, Minna M., Pierce, Naomi E., Russell, Jacob A., Koga, Ryuichi, Sanders, Jon G., Lukasik, Piotr, and Andersson, Siv G. E.
Abstract: Many insects rely on bacterial symbionts to supply essential amino acids and vitamins that are deficient in their diets, but metabolic comparisons of closely related gut bacteria in insects with different dietary preferences have not been performed. Here, we demonstrate that herbivorous ants of the genus Dolichoderus from the Peruvian Amazon host bacteria of the family Bartonellaceae, known for establishing chronic or pathogenic infections in mammals. We detected these bacteria in all studied Dolichoderus species, and found that they reside in the midgut wall, that is, the same location as many previously described nutritional endosymbionts of insects. The genomic analysis of four divergent strains infecting different Dolichoderus species revealed genes encoding pathways for nitrogen recycling and biosynthesis of several vitamins and all essential amino acids. In contrast, several biosynthetic pathways have been lost, whereas genes for the import and conversion of histidine and arginine to glutamine have been retained in the genome of a closely related gut bacterium of the carnivorous ant Harpegnathos saltator. The broad biosynthetic repertoire in Bartonellaceae of herbivorous ants resembled that of gut bacteria of honeybees that likewise feed on carbohydrate-rich diets. Taken together, the broad distribution of Bartonellaceae across Dolichoderus ants, their small genome sizes, the specific location within hosts, and the broad biosynthetic capability suggest that these bacteria are nutritional symbionts in herbivorous ants. The results highlight the important role of the host nutritional biology for the genomic evolution of the gut microbiota-and conversely, the importance of the microbiota for the nutrition of hosts.
Published: 2018
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35. Origin and evolution of the Bartonella Gene Transfer Agent

Author: Tamarit, Daniel, Neuvonen, Minna M., Engel, Philipp, Guy, Lionel, Andersson, Siv G. E., Tamarit, Daniel, Neuvonen, Minna M., Engel, Philipp, Guy, Lionel, and Andersson, Siv G. E.
Abstract: Gene transfer agents (GTAs) are domesticated bacteriophages that have evolved into molecular machines for the transferof bacterial DNA. Despite their widespread nature and their biological implications, the mechanisms and selective forcesthat drive the emergence of GTAs are still poorly understood. Two GTAs have been identifiedintheAlphaproteobacteria:the RcGTA, which is widely distributed in a broad range of species; and the BaGTA, which has a restricted host range thatincludes vector-borne intracellular bacteria of the genusBartonella. The RcGTA packages chromosomal DNA randomly,whereas the BaGTA particles contain a relatively higher fraction of genes for host interaction factors that are amplifiedfrom a nearby phage-derived origin of replication. In this study, we compare the BaGTA genes with homologous bac-teriophage genes identified in the genomes ofBartonellaspecies and close relatives. Unlike the BaGTA, the prophagegenes are neither present in all species, nor inserted into homologous genomic sites. Phylogenetic inferences and sub-stitution frequency analyses confirm codivergence of the BaGTA with the host genome, as opposed to multiple integra-tion and recombination events in the prophages. Furthermore, the organizationof segments flanking the BaGTA differsfrom that of the prophages by a few rearrangement events,which have abolished the normal coordination betweenphage genome replication and phage gene expression. Based on the results of our comparative analysis, we propose amodel for how a prophage may be transformed into a GTA that transfers amplified bacterial DNA segments.
Published: 2018
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36. Taxonomy of prokaryotic viruses: 2017 update from the ICTV Bacterial and Archaeal Viruses Subcommittee.

Author: UCL - SST/ELI/ELIM - Applied Microbiology, Adriaenssens, Evelien M, Wittmann, Johannes, Kuhn, Jens H, Turner, Dann, Sullivan, Matthew B, Dutilh, Bas E, Jang, Ho Bin, van Zyl, Leonardo J, Klumpp, Jochen, Lobocka, Malgorzata, Moreno Switt, Andrea I, Rumnieks, Janis, Edwards, Robert A, Uchiyama, Jumpei, Alfenas-Zerbini, Poliane, Petty, Nicola K, Kropinski, Andrew M, Barylski, Jakub, Gillis, Annika, Clokie, Martha R C, Prangishvili, David, Lavigne, Rob, Aziz, Ramy Karam, Duffy, Siobain, Krupovic, Mart, Poranen, Minna M, Knezevic, Petar, Enault, Francois, Tong, Yigang, Oksanen, Hanna M, Rodney Brister, J, UCL - SST/ELI/ELIM - Applied Microbiology, Adriaenssens, Evelien M, Wittmann, Johannes, Kuhn, Jens H, Turner, Dann, Sullivan, Matthew B, Dutilh, Bas E, Jang, Ho Bin, van Zyl, Leonardo J, Klumpp, Jochen, Lobocka, Malgorzata, Moreno Switt, Andrea I, Rumnieks, Janis, Edwards, Robert A, Uchiyama, Jumpei, Alfenas-Zerbini, Poliane, Petty, Nicola K, Kropinski, Andrew M, Barylski, Jakub, Gillis, Annika, Clokie, Martha R C, Prangishvili, David, Lavigne, Rob, Aziz, Ramy Karam, Duffy, Siobain, Krupovic, Mart, Poranen, Minna M, Knezevic, Petar, Enault, Francois, Tong, Yigang, Oksanen, Hanna M, and Rodney Brister, J
Abstract: The prokaryotic virus community is represented at the International Committee on Taxonomy of Viruses (ICTV) by the Bacterial and Archaeal Viruses Subcommittee. Since our last report [5], the committee composition has changed, and a large number of taxonomic proposals (TaxoProps) were submitted to the ICTV Executive Committee (EC) for approval.
Published: 2018

37. Taxonomy of prokaryotic viruses: 2017 update from the ICTV Bacterial and Archaeal Viruses Subcommittee

Author: Sub Bioinformatics, Theoretical Biology and Bioinformatics, Adriaenssens, Evelien M, Wittmann, Johannes, Kuhn, Jens H, Turner, Dann, Sullivan, Matthew B., Dutilh, Bas E, Jang, Ho Bin, van Zyl, Leonardo J, Klumpp, Jochen, Lobocka, Malgorzata, Moreno Switt, Andrea I, Rumnieks, Janis, Edwards, Robert A, Uchiyama, Jumpei, Alfenas-Zerbini, Poliane, Petty, Nicola K, Kropinski, Andrew M, Barylski, Jakub, Gillis, Annika, Clokie, Martha R C, Prangishvili, David, Lavigne, Rob, Aziz, Ramy Karam, Duffy, Siobain, Krupovic, Mart, Poranen, Minna M., Knezevic, Petar, Enault, Francois, Tong, Yigang, Oksanen, Hanna M., Rodney Brister, J, Sub Bioinformatics, Theoretical Biology and Bioinformatics, Adriaenssens, Evelien M, Wittmann, Johannes, Kuhn, Jens H, Turner, Dann, Sullivan, Matthew B., Dutilh, Bas E, Jang, Ho Bin, van Zyl, Leonardo J, Klumpp, Jochen, Lobocka, Malgorzata, Moreno Switt, Andrea I, Rumnieks, Janis, Edwards, Robert A, Uchiyama, Jumpei, Alfenas-Zerbini, Poliane, Petty, Nicola K, Kropinski, Andrew M, Barylski, Jakub, Gillis, Annika, Clokie, Martha R C, Prangishvili, David, Lavigne, Rob, Aziz, Ramy Karam, Duffy, Siobain, Krupovic, Mart, Poranen, Minna M., Knezevic, Petar, Enault, Francois, Tong, Yigang, Oksanen, Hanna M., and Rodney Brister, J
Published: 2018

38. Specialised cleaning associated with antimicrobial coatings for reduction of hospital acquired infection. Opinion of the COST Action Network AMiCI (CA15114)

Author: European Cooperation in Science and Technology Programme, Dunne, Suzanne S., Ahonen, Merja, Modic, Martina, Crijns, Francy R.L., Keinänen-Toivola, Minna M., Meinke, Ruth, Keevil, William C., Gray, Jim, O'Connell, Nuala H., Dunne, Colum P., European Cooperation in Science and Technology Programme, Dunne, Suzanne S., Ahonen, Merja, Modic, Martina, Crijns, Francy R.L., Keinänen-Toivola, Minna M., Meinke, Ruth, Keevil, William C., Gray, Jim, O'Connell, Nuala H., and Dunne, Colum P.
Abstract: peer-reviewed, Recognized issues with poor hand hygiene compliance among healthcare workers and reports of recontamination of previously chemically disinfected surfaces through hand contact emphasize the need for novel hygiene methods in addition to those currently available. One such approach involves antimicrobial (nano) coatings (AMCs), whereby integrated active ingredients are responsible for elimination of micro-organisms that come into contact with treated surfaces. While widely studied under laboratory conditions with promising results, studies under real-life healthcare conditions are scarce. The views of 75 contributors from 30 European countries were collated regarding specialized cleaning associated with AMCs for reduction of healthcare-associated infection. There was unanimous agreement that generation of scientific guidelines for cleaning of AMCs, using traditional or new processes, is needed. Specific topics included: understanding mechanisms of action of cleaning materials and their physical interactions with conventional coatings and AMCs; that assessments mimic the life cycle of coatings to determine the impact of repetitive cleaning and other aspects of ageing (e.g. exposure to sunlight); determining concentrations of AMC-derived biocides in effluents; and development of effective de-activation and sterilization treatments for cleaning effluents. Further, the consensus opinion was that, prior to widespread implementation of AMCs, there is a need for clarification of the varying responsibilities of involved clinical, healthcare management, cleaning services and environmental safety stakeholders., peer-reviewed
Published: 2018

39. Surface modifications for antimicrobial effects in the healthcare setting : a critical overview

Author: Adlhart, Christian, Verran, Joanna, Azevedo, Nuno F., Olmez, Hulya, Keinänen-Toivola, Minna M., Gouveia, Isabel, Melo, Luis F., Crijns, Francy, Adlhart, Christian, Verran, Joanna, Azevedo, Nuno F., Olmez, Hulya, Keinänen-Toivola, Minna M., Gouveia, Isabel, Melo, Luis F., and Crijns, Francy
Abstract: The spread of infections in health care environments is a persistent and growing problem in most countries, aggravated by the development of microbial resistance to antibiotics and disinfectants. In addition to indwelling medical devices (implants, catheters, etc.), such infections may also result from adhesion of microbes either to external solid-water interfaces such as shower caps, taps, drains, etc, or to external solid-gas interfaces such as door handles, clothes, curtains, computer keyboards, etc. The latter are the main focus of the present work, where an overview of antimicrobial coatings for such applications is presented. The paper addresses well-established and novel methodologies, including chemical and physical functional modification of surfaces to reduce microbial contamination, as well as the potential risks associated to the implementation of such anti-contamination measures. Different chemistry-based approaches are discussed, in particular anti-adhesive surfaces (e.g., superhydrophobic, zwitterions, etc.) contact-killing surfaces (e.g., polymer brushes, phages, etc.) and biocide-releasing surfaces (e.g., triggered release, quorum sensing-based systems, etc.). The paper also assesses the impact of topographical modifications at distinct dimensions (micrometre and nanometre orders of magnitude) and the importance of applying safe-by-design criteria (toxicity, contribution for unwanted acquisition of antimicrobial resistance, long-term stability, etc.) when developing and implementing antimicrobial surfaces.
Published: 2018

40. Anti-microbial coating innovations to prevent infectious diseases (AMiCI) : cost action ca15114

Author: Dunne, Colum P., Keinänen-Toivola, Minna M., Kahru, Anne, Teunissen, Birgit, Olmez, Hulya, Gouveia, Isabel, Melo, Luis, Murzyn, Kazimierz, Modic, Martina, Ahonen, Merja, Askew, Pete, Papadopoulos, Theofilos, Adlhart, Christian, Crijns, Francy R. L., Dunne, Colum P., Keinänen-Toivola, Minna M., Kahru, Anne, Teunissen, Birgit, Olmez, Hulya, Gouveia, Isabel, Melo, Luis, Murzyn, Kazimierz, Modic, Martina, Ahonen, Merja, Askew, Pete, Papadopoulos, Theofilos, Adlhart, Christian, and Crijns, Francy R. L.
Abstract: Worldwide, millions of patients are affected annually by healthcare-associated infection (HCAI), impacting up to 80,000 patients in European Hospitals on any given day. This represents not only public health risk, but also an economic burden. Complementing routine hand hygiene practices, cleaning and disinfection, antimicrobial coatings hold promise based, in essence, on the application of materials and chemicals with persistent bactericidal or -static properties onto surfaces or in textiles used in healthcare environments.
Published: 2018

41. Taxonomy of prokaryotic viruses: 2016 update from the ICTV bacterial and archaeal viruses subcommittee

Author: Adriaenssens, Evelien M., Krupovic, Mart, Knezevic, Petar, Ackermann, Hans Wolfgang, Barylski, Jakub, Brister, J. Rodney, Clokie, Martha R C, Duffy, Siobain, Dutilh, Bas E., Edwards, Robert A, Enault, Francois, Jang, Ho Bin, Klumpp, Jochen, Kropinski, Andrew M., Lavigne, Rob, Poranen, Minna M., Prangishvili, David, Rumnieks, Janis, Sullivan, Matthew B., Wittmann, Johannes, Oksanen, Hanna M., Gillis, Annika, Kuhn, Jens H., Adriaenssens, Evelien M., Krupovic, Mart, Knezevic, Petar, Ackermann, Hans Wolfgang, Barylski, Jakub, Brister, J. Rodney, Clokie, Martha R C, Duffy, Siobain, Dutilh, Bas E., Edwards, Robert A, Enault, Francois, Jang, Ho Bin, Klumpp, Jochen, Kropinski, Andrew M., Lavigne, Rob, Poranen, Minna M., Prangishvili, David, Rumnieks, Janis, Sullivan, Matthew B., Wittmann, Johannes, Oksanen, Hanna M., Gillis, Annika, and Kuhn, Jens H.
Abstract: The prokaryotic virus community is represented at the International Committee on Taxonomy of Viruses (ICTV) by the Bacterial and Archaeal Viruses Subcommittee. Since our last report [8], the committee composition has changed, and a large number of taxonomic proposals (TaxoProps) were submitted to the ICTV Executive Committee (EC) for approval.
Published: 2017

42. Competitive Te-Te and C-Te bond cleavage in the oxidative addition of diaryl and dialkyl ditellurides to Pt(0) centers

Author: Karjalainen, M. M. (Minna M.), Wiegand, T. (Torben), Rautiainen, J. M. (J. Mikko), Wagner, A. (Andreas), Görls, H. (Helmar), Weigand, W. (Wolfgang), Oilunkaniemi, R. (Raija), Laitinen, R. S. (Risto S.), Karjalainen, M. M. (Minna M.), Wiegand, T. (Torben), Rautiainen, J. M. (J. Mikko), Wagner, A. (Andreas), Görls, H. (Helmar), Weigand, W. (Wolfgang), Oilunkaniemi, R. (Raija), and Laitinen, R. S. (Risto S.)
Abstract: The oxidative addition reaction of ditellurides R₂Te₂ [R = ⁿBu, Ph, Th (2-thienyl, C4H3S)] to [Pt(η²-nb)(dppn)] (nb = norbornene, dppn = 1,2-bis(diphenylphosphano)naphthalene) was found to afford [Pt(TeR)₂(dppn)] [R = ⁿBu (1), Ph (2), Th (3)] and [Pt(TeR)(R)(dppn)] [R = Ph (4), Th (5)] as a result of the cleavage of the Te-Te or C-Te bond, respectively. The reactions and the product distributions were monitored by 31P{1H} NMR spectroscopy. The spectral interpretation was assisted by the high-yield preparation of [Pt(TePh)₂(dppn)] (2) and [Pt(TeTh)₂(dppn)] (3) by ligand exchange reactions from [PtCl₂(dppn)], and by the crystal structure determinations and spectral characterizations of 2 and 3. Two series of reactions were carried out both at room temperature and at −80 °C. One involved the addition of the toluene solution of R₂Te₂ to that of [Pt(η²-nb)(dppn)], and the other the addition of [Pt(η²-nb)(dppn)] solution to the R₂Te₂ solution. The oxidative addition of ⁿBu₂Te₂ to [Pt(η²-nb)(dppn)] yielded solely [Pt(TenBu)₂(dppn)]. In case of Ph₂Te₂ and Th₂Te₂, the reaction of equimolar amounts of ditelluride and [Pt(η²-nb)(dppn)] afforded only [Pt(TeR)(R)(dppn)] (R = Ph, Th), but when an excess of R₂Te₂ was used, the addition of [Pt(η²-nb)(dppn)] to the ditelluride resulted in the formation of a mixture of [Pt(TeR)₂(dppn)] and [Pt(TeR)(R)(dppn)] with the latter the main component. An excess of R₂Te₂ and the lowering of the temperature favoured the formation of [Pt(TeR)₂(dppn)]. The reaction energetics in toluene was calculated at revPBE/def2-TZVP(-f) level of theory. The increase of the electron withdrawing nature of the organic substituent rendered [Pt(TeR)(R)(dppn)] increasingly stable with respect to [Pt(TeR)₂(dppn)]. The computation of the energy profiles of the likely pathways of the oxidative addition indicated that concurrent formation of [Pt(TeR)₂(dppn)] and [Pt(TeR)(R)(dppn)] (R = Ph, Th) may be more likely than the formation of the latter due to the de
Published: 2017

43. Taxonomy of prokaryotic viruses: 2016 update from the ICTV bacterial and archaeal viruses subcommittee.

Author: UCL - SST/ELI/ELIM - Applied Microbiology, Adriaenssens, Evelien M, Krupovic, Mart, Knezevic, Petar, Ackermann, Hans-Wolfgang, Barylski, Jakub, Brister, J Rodney, Clokie, Martha R C, Duffy, Siobain, Dutilh, Bas E, Edwards, Robert A, Enault, Francois, Jang, Ho Bin, Klumpp, Jochen, Kropinski, Andrew M, Lavigne, Rob, Poranen, Minna M, Prangishvili, David, Rumnieks, Janis, Sullivan, Matthew B, Wittmann, Johannes, Oksanen, Hanna M, Gillis, Annika, Kuhn, Jens H, UCL - SST/ELI/ELIM - Applied Microbiology, Adriaenssens, Evelien M, Krupovic, Mart, Knezevic, Petar, Ackermann, Hans-Wolfgang, Barylski, Jakub, Brister, J Rodney, Clokie, Martha R C, Duffy, Siobain, Dutilh, Bas E, Edwards, Robert A, Enault, Francois, Jang, Ho Bin, Klumpp, Jochen, Kropinski, Andrew M, Lavigne, Rob, Poranen, Minna M, Prangishvili, David, Rumnieks, Janis, Sullivan, Matthew B, Wittmann, Johannes, Oksanen, Hanna M, Gillis, Annika, and Kuhn, Jens H
Published: 2017

44. Taxonomy of prokaryotic viruses: 2016 update from the ICTV bacterial and archaeal viruses subcommittee

Author: Sub Bioinformatics, Theoretical Biology and Bioinformatics, Adriaenssens, Evelien M., Krupovic, Mart, Knezevic, Petar, Ackermann, Hans Wolfgang, Barylski, Jakub, Brister, J. Rodney, Clokie, Martha R C, Duffy, Siobain, Dutilh, Bas E., Edwards, Robert A, Enault, Francois, Jang, Ho Bin, Klumpp, Jochen, Kropinski, Andrew M., Lavigne, Rob, Poranen, Minna M., Prangishvili, David, Rumnieks, Janis, Sullivan, Matthew B., Wittmann, Johannes, Oksanen, Hanna M., Gillis, Annika, Kuhn, Jens H., Sub Bioinformatics, Theoretical Biology and Bioinformatics, Adriaenssens, Evelien M., Krupovic, Mart, Knezevic, Petar, Ackermann, Hans Wolfgang, Barylski, Jakub, Brister, J. Rodney, Clokie, Martha R C, Duffy, Siobain, Dutilh, Bas E., Edwards, Robert A, Enault, Francois, Jang, Ho Bin, Klumpp, Jochen, Kropinski, Andrew M., Lavigne, Rob, Poranen, Minna M., Prangishvili, David, Rumnieks, Janis, Sullivan, Matthew B., Wittmann, Johannes, Oksanen, Hanna M., Gillis, Annika, and Kuhn, Jens H.
Published: 2017

45. Anti-microbial coating innovations to prevent healthcare-associated infection

Author: COST, Crijns, Francy R.L., Keinänen-Toivola, Minna M., Dunne, Colum P., COST, Crijns, Francy R.L., Keinänen-Toivola, Minna M., and Dunne, Colum P.
Abstract: peer-reviewed, Worldwide, millions of patients are affected annually by healthcare-associated infection (HCAI), impacting up to 80,000 patients in European hospitals on any given day.1 This represents not only a public health risk, but also an economic burden., PUBLISHED, peer-reviewed
Published: 2017

46. The genome of Rhizobiales bacteria in predatory ants indicates a role for urease in lifestyle switches

Author: Neuvonen, Minna M., Tamarit, Daniel, Näslund, Kristina, Liebig, Juergen, Feldhaar, Heike, Moran, Nancy A., Guy, Lionel, Andersson, Siv G.E., Neuvonen, Minna M., Tamarit, Daniel, Näslund, Kristina, Liebig, Juergen, Feldhaar, Heike, Moran, Nancy A., Guy, Lionel, and Andersson, Siv G.E.
Abstract: Bacterial symbionts provide amino acids to herbivorous ants, but their role in carnivores is a puzzle. The most prevalent bacterial lineage in ants belongs to the order Rhizobiales. Sequence reads with similarity to Bartonella, a member of the Rhizobiales, were identified in the data collected in a genome project of the carnivorous ant Harpegnatos saltator. Here, we present an analysis of the closed 1.86 Mb genome of the Bartonella-like bacterium, here abbreviated Bhsal. A phylogenetic study showed that Bhsal diverged prior to the radiation of the Bartonella species. Uniquely present in the Bhsal genome is a gene for a giant protein of 6,177 amino acids with a repeated domain structure. We also identified genes for a multi- subunit urease protein complex, potentially involved in the hydrolysis of urea into ammonium. We hypothesize that the urease function protects Bhsal from the acidic environment of the ant gut. The urease genes are also present in Brucella, which has a fecal-oral transmission pathway, but they have been lost in Bartonella species, which use blood-borne transmission pathways. Taken together, the results suggest that the urease function has served an important role for transmission strategies and lifestyle changes in the host-associated members of the Rhizobiales.
Published: 2016

47. The genome of Rhizobiales bacteria in predatory ants reveals urease gene functions but no genes for nitrogen fixation

Author: Neuvonen, Minna M., Tamarit, Daniel, Näslund, Kristina, Liebig, Juergen, Feldhaar, Heike, Moran, Nancy A., Guy, Lionel, Andersson, Siv G. E., Neuvonen, Minna M., Tamarit, Daniel, Näslund, Kristina, Liebig, Juergen, Feldhaar, Heike, Moran, Nancy A., Guy, Lionel, and Andersson, Siv G. E.
Abstract: Gut-associated microbiota of ants include Rhizobiales bacteria with affiliation to the genus Bartonella. These bacteria may enable the ants to fix atmospheric nitrogen, but no genomes have been sequenced yet to test the hypothesis. Sequence reads from a member of the Rhizobiales were identified in the data collected in a genome project of the ant Harpegnathos saltator. We present an analysis of the closed 1.86 Mb genome of the ant-associated bacterium, for which we suggest the species name Candidatus Tokpelaia hoelldoblerii. A phylogenetic analysis reveals a relationship to Bartonella and Brucella, which infect mammals. Novel gene acquisitions include a gene for a putative extracellular protein of more than 6,000 amino acids secreted by the type I secretion system, which may be involved in attachment to the gut epithelium. No genes for nitrogen fixation could be identified, but genes for a multi-subunit urease protein complex are present in the genome. The urease genes are also present in Brucella, which has a fecal-oral transmission pathway, but not in Bartonella, which use blood-borne transmission pathways. We hypothesize that the gain and loss of the urease function is related to transmission strategies and lifestyle changes in the host-associated members of the Rhizobiales., Title in thesis list of papers: The genome of Rhizobiales bacteria in predatory ants indicates a role for urease in lifestyle switches
Published: 2016
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48. S100A12 concentrations and myeloperoxidase activity in the intestinal mucosa of healthy dogs

Author: University of Helsinki, Faculty of Veterinary Medicine, University of Helsinki, Departments of Dermatology, Allergology and Venereology, Hanifeh, Mohsen, Heilmann, Romy M., Sankari, Satu, Rajamäki, Minna M., Mäkitalo, Laura, Syrjä, Pernilla, Kilpinen, Susanne, Suchodolski, Jan S., Steiner, Jörg M., Spillmann, Thomas, University of Helsinki, Faculty of Veterinary Medicine, University of Helsinki, Departments of Dermatology, Allergology and Venereology, Hanifeh, Mohsen, Heilmann, Romy M., Sankari, Satu, Rajamäki, Minna M., Mäkitalo, Laura, Syrjä, Pernilla, Kilpinen, Susanne, Suchodolski, Jan S., Steiner, Jörg M., and Spillmann, Thomas
Abstract: Background: Relatively few laboratory markers have been evaluated for the detection or monitoring of intestinal inflammation in canine chronic enteropathies, including inflammatory bowel disease (IBD). Previous research found that the intestinal mucosal levels of S100A12 and myeloperoxidase (MPO), as biomarkers of gut inflammation, were elevated in human patients with IBD. To date, the S100A12 and MPO levels in intestinal mucosal samples from either healthy dogs or from dogs suffering from IBD remain unreported. Therefore, this study aimed to evaluate the mucosal S100A12 and MPO levels in four different parts of the intestine (duodenum, jejunum, ileum and colon) in 12 healthy laboratory Beagle dogs using the ELISA and spectrophotometric methods, respectively. Results: Based on histological examinations, the recorded findings for all the samples were considered normal. The mucosal concentration of S100A12 in the ileum was significantly higher than in all other segments of the intestine (p <0.05). MPO activity was significantly higher in the ileal, jejunal and duodenal than in colonic mucosal samples (p <0.05). Moreover, its concentration was higher in the jejunum than in the duodenum. Conclusions: This study showed that S100A12 and MPO are reliably detectable in canine intestinal mucosa. The assays used appeared to be sufficient to further evaluate the role of S100A12 and MPO in the pathogenesis of canine chronic enteropathies, including IBD. These biomarkers may play a role in the initial detection of gut inflammation suggesting the need for further investigations to confirm IBD or to differentiate between IBD subtypes. Understanding the role of S100A12 and MPO in the pathogenesis of chronic intestinal inflammation in future may result in an improved understanding of canine chronic intestinal inflammation.
Published: 2015

49. Tumor-Associated Macrophages Provide Significant Prognostic Information in Urothelial Bladder Cancer

Author: University of Helsinki, Institute for Molecular Medicine Finland (FIMM), Bostrom, Minna M., Irjala, Heikki, Mirtti, Tuomas, Taimen, Pekka, Kauko, Tommi, Algars, Annika, Jalkanen, Sirpa, Bostrom, Peter J., University of Helsinki, Institute for Molecular Medicine Finland (FIMM), Bostrom, Minna M., Irjala, Heikki, Mirtti, Tuomas, Taimen, Pekka, Kauko, Tommi, Algars, Annika, Jalkanen, Sirpa, and Bostrom, Peter J.
Abstract: Inflammation is an important feature of carcinogenesis. Tumor-associated macrophages (TAMs) can be associated with either poor or improved prognosis, depending on their properties and polarization. Current knowledge of the prognostic significance of TAMs in bladder cancer is limited and was investigated in this study. We analyzed 184 urothelial bladder cancer patients undergoing transurethral resection of a bladder tumor or radical cystectomy. CD68 (pan-macrophage marker), MAC387 (polarized towards type 1 macrophages), and CLEVER-1/Stabilin-1 (type 2 macrophages and lymphatic/blood vessels) were detected immunohistochemically. The median follow-up time was 6.0 years. High macrophage counts associated with a higher pT category and grade. Among patients undergoing transurethral resection, all studied markers apart from CLEVER-1/Stabilin-1 were associated with increased risk of progression and poorer disease-specific and overall survival in univariate analyses. High levels of two macrophage markers (CD68/MAC387(+/+) or CD68/CLEVER-1(+/+) groups) had an independent prognostic role after transurethral resection in multivariate analyses. In the cystectomy cohort, MAC387, alone and in combination with CD68, was associated with poorer survival in univariate analyses, but none of the markers were independent predictors of outcome in multivariate analyses. In conclusion, this study demonstrates that macrophage phenotypes provide significant independent prognostic information, particularly in bladder cancers undergoing transurethral resection.
Published: 2015

50. Effects of Easy-to-Use Protein-Rich Energy Bar on Energy Balance, Physical Activity and Performance during 8 Days of Sustained Physical Exertion

Author: University of Helsinki, Clinicum, Tanskanen, Minna M., Westerterp, Klaas R., Uusitalo, Arja L., Atalay, Mustafa, Hakkinen, Keijo, Kinnunen, Hannu O., Kyrolainen, Heikki, University of Helsinki, Clinicum, Tanskanen, Minna M., Westerterp, Klaas R., Uusitalo, Arja L., Atalay, Mustafa, Hakkinen, Keijo, Kinnunen, Hannu O., and Kyrolainen, Heikki
Published: 2012

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