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3. LASIGE and UNICAGE solution to the NASA LitCoin NLP Competition

Author

Ruas, Pedro, Sousa, Diana F., Neves, André, Cruz, Carlos, and Couto, Francisco M.

Subjects
Computer Science - Computation and Language, Computer Science - Information Retrieval, Computer Science - Performance
Abstract

Biomedical Natural Language Processing (NLP) tends to become cumbersome for most researchers, frequently due to the amount and heterogeneity of text to be processed. To address this challenge, the industry is continuously developing highly efficient tools and creating more flexible engineering solutions. This work presents the integration between industry data engineering solutions for efficient data processing and academic systems developed for Named Entity Recognition (LasigeUnicage\_NER) and Relation Extraction (BiOnt). Our design reflects an integration of those components with external knowledge in the form of additional training data from other datasets and biomedical ontologies. We used this pipeline in the 2022 LitCoin NLP Challenge, where our team LasigeUnicage was awarded the 7th Prize out of approximately 200 participating teams, reflecting a successful collaboration between the academia (LASIGE) and the industry (Unicage). The software supporting this work is available at \url{https://github.com/lasigeBioTM/Litcoin-Lasige_Unicage}.

Published
2023

6. The platelet transcriptome and proteome in Alzheimers disease and aging: an exploratory cross-sectional study.

Author

de Sousa, Diana, Poupardin, Rodolphe, Villeda, Saul, Fröhlich, Thomas, Frey, Vanessa, Staffen, Wolfgang, Mrowetz, Heike, Altendorfer, Barbara, Unger, Michael, Iglseder, Bernhard, Paulweber, Bernhard, Trinka, Eugen, Cadamuro, Janne, Drerup, Martin, Schallmoser, Katharina, Aigner, Ludwig, Kniewallner, Kathrin, and Schroer, Adam

Subjects
Alzheimer’s disease, aging, platelets, proteomics, transcriptomics
Abstract

Introduction: Alzheimers disease (AD) and aging are associated with platelet hyperactivity. However, the mechanisms underlying abnormal platelet function in AD and aging are yet poorly understood. Methods: To explore the molecular profile of AD and aged platelets, we investigated platelet activation (i.e., CD62P expression), proteome and transcriptome in AD patients, non-demented elderly, and young individuals as controls. Results: AD, aged and young individuals showed similar levels of platelet activation based on CD62P expression. However, AD and aged individuals had a proteomic signature suggestive of increased platelet activation compared with young controls. Transcriptomic profiling suggested the dysregulation of proteolytic machinery involved in regulating platelet function, particularly the ubiquitin-proteasome system in AD and autophagy in aging. The functional implication of these transcriptomic alterations remains unclear and requires further investigation. Discussion: Our data strengthen the evidence of enhanced platelet activation in aging and provide a first glimpse of the platelet transcriptomic changes occurring in AD.

Published
2023

7. Outcome Prediction in Cerebral Venous Thrombosis: The IN-REvASC Score.

Author

Klein, Piers, Shu, Liqi, Nguyen, Thanh, Siegler, James, Omran, Setareh, Simpkins, Alexis, Heldner, Mirjam, Havenon, Adam, Aparicio, Hugo, Abdalkader, Mohamad, Psychogios, Marios, Vedovati, Maria, Paciaroni, Maurizio, Martial, Rascha, Liebeskind, David, Sousa, Diana, Coutinho, Jonathan, and Yaghi, Shadi

Subjects
Prognosis, Sinus thrombosis, intracranial, Stroke
Abstract

BACKGROUND: We identified risk factors, derived and validated a prognostic score for poor neurological outcome and death for use in cerebral venous thrombosis (CVT). METHODS: We performed an international multicenter retrospective study including consecutive patients with CVT from January 2015 to December 2020. Demographic, clinical, and radiographic characteristics were collected. Univariable and multivariable logistic regressions were conducted to determine risk factors for poor outcome, mRS 3-6. A prognostic score was derived and validated. RESULTS: A total of 1,025 patients were analyzed with median 375 days (interquartile range [IQR], 180 to 747) of follow-up. The median age was 44 (IQR, 32 to 58) and 62.7% were female. Multivariable analysis revealed the following factors were associated with poor outcome at 90- day follow-up: active cancer (odds ratio [OR], 11.20; 95% confidence interval [CI], 4.62 to 27.14; P

Published
2022

15. Generating Biomedical Question Answering Corpora from Q&A forums

Author

Lamurias, Andre, Sousa, Diana, and Couto, Francisco M.

Subjects
Computer Science - Information Retrieval
Abstract

Question Answering (QA) is a natural language processing task that aims at obtaining relevant answers to user questions. While some progress has been made in this area, biomedical questions are still a challenge to most QA approaches, due to the complexity of the domain and limited availability of training sets. We present a method to automatically extract question-article pairs from Q\&A web forums, which can be used for document retrieval, a crucial step of most QA systems. The proposed framework extracts from selected forums the questions and the respective answers that contain citations. This way, QA systems based on document retrieval can be developed and evaluated using the question-article pairs annotated by users of these forums. We generated the BiQA corpus by applying our framework to three forums, obtaining 7,453 questions and 14,239 question-article pairs. We evaluated how the number of articles associated with each question and the number of votes on each answer affects the performance of baseline document retrieval approaches. Also, we demonstrated that the articles given as answers are significantly similar to the questions and trained a state-of-the-art deep learning model that obtained similar performance to using a dataset manually annotated by experts. The proposed framework can be used to update the BiQA corpus from the same forums as new posts are made, and from other forums that support their answers with documents. The BiQA corpus and the framework used to generate it are available at \url{https://github.com/lasigeBioTM/BiQA}.

Published
2020
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16. BiOnt: Deep Learning using Multiple Biomedical Ontologies for Relation Extraction

Author

Sousa, Diana and Couto, Francisco M.

Subjects
Computer Science - Information Retrieval
Abstract

Successful biomedical relation extraction can provide evidence to researchers and clinicians about possible unknown associations between biomedical entities, advancing the current knowledge we have about those entities and their inherent mechanisms. Most biomedical relation extraction systems do not resort to external sources of knowledge, such as domain-specific ontologies. However, using deep learning methods, along with biomedical ontologies, has been recently shown to effectively advance the biomedical relation extraction field. To perform relation extraction, our deep learning system, BiOnt, employs four types of biomedical ontologies, namely, the Gene Ontology, the Human Phenotype Ontology, the Human Disease Ontology, and the Chemical Entities of Biological Interest, regarding gene-products, phenotypes, diseases, and chemical compounds, respectively. We tested our system with three data sets that represent three different types of relations of biomedical entities. BiOnt achieved, in F-score, an improvement of 4.93 percentage points for drug-drug interactions (DDI corpus), 4.99 percentage points for phenotype-gene relations (PGR corpus), and 2.21 percentage points for chemical-induced disease relations (BC5CDR corpus), relatively to the state-of-the-art. The code supporting this system is available at https://github.com/lasigeBioTM/BiOnt., Comment: ECIR 2020

Published
2020
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17. Global Impact of COVID-19 on Stroke Care and IV Thrombolysis.

Author

Nogueira, Raul, Qureshi, Muhammad, Abdalkader, Mohamad, Martins, Sheila, Yamagami, Hiroshi, Qiu, Zhongming, Mansour, Ossama, Sathya, Anvitha, Czlonkowska, Anna, Tsivgoulis, Georgios, Aguiar de Sousa, Diana, Demeestere, Jelle, Mikulik, Robert, Vanacker, Peter, Siegler, James, Kõrv, Janika, Biller, Jose, Liang, Conrad, Sangha, Navdeep, Zha, Alicia, Czap, Alexandra, Holmstedt, Christine, Turan, Tanya, Ntaios, George, Malhotra, Konark, Tayal, Ashis, Loochtan, Aaron, Ranta, Annamarei, Mistry, Eva, Alexandrov, Anne, Huang, David, Yaghi, Shadi, Raz, Eytan, Sheth, Sunil, Mohammaden, Mahmoud, Frankel, Michael, Bila Lamou, Eric, Aref, Hany, Elbassiouny, Ahmed, Hassan, Farouk, Menecie, Tarek, Mustafa, Wessam, Shokri, Hossam, Roushdy, Tamer, Sarfo, Fred, Alabi, Tolulope, Arabambi, Babawale, Nwazor, Ernest, Sunmonu, Taofiki, Wahab, Kolawole, Yaria, Joseph, Mohammed, Haytham, Adebayo, Philip, Riahi, Anis, Sassi, Samia, Gwaunza, Lenon, Ngwende, Gift, Sahakyan, David, Rahman, Aminur, Ai, Zhibing, Bai, Fanghui, Duan, Zhenhui, Hao, Yonggang, Huang, Wenguo, Li, Guangwen, Li, Wei, Liu, Ganzhe, Luo, Jun, Shang, Xianjin, Sui, Yi, Tian, Ling, Wen, Hongbin, Wu, Bo, Yan, Yuying, Yuan, Zhengzhou, Zhang, Hao, Zhang, Jun, Zhao, Wenlong, Zi, Wenjie, Leung, Thomas, Chugh, Chandril, Huded, Vikram, Menon, Bindu, Pandian, Jeyaraj, Sylaja, P, Usman, Fritz, Farhoudi, Mehdi, Hokmabadi, Elyar, Horev, Anat, Reznik, Anna, Sivan Hoffmann, Rotem, Ohara, Nobuyuki, Sakai, Nobuyuki, Watanabe, Daisuke, Yamamoto, Ryoo, Doijiri, Ryosuke, Tokuda, Naoki, Yamada, Takehiro, Terasaki, Tadashi, and Yazawa, Yukako

Subjects
COVID-19, Cross-Sectional Studies, Hospitalization, Humans, Pandemics, Retrospective Studies, SARS-CoV-2, Stroke, Thrombolytic Therapy
Abstract

OBJECTIVE: To measure the global impact of COVID-19 pandemic on volumes of IV thrombolysis (IVT), IVT transfers, and stroke hospitalizations over 4 months at the height of the pandemic (March 1 to June 30, 2020) compared with 2 control 4-month periods. METHODS: We conducted a cross-sectional, observational, retrospective study across 6 continents, 70 countries, and 457 stroke centers. Diagnoses were identified by their ICD-10 codes or classifications in stroke databases. RESULTS: There were 91,373 stroke admissions in the 4 months immediately before compared to 80,894 admissions during the pandemic months, representing an 11.5% (95% confidence interval [CI] -11.7 to -11.3, p < 0.0001) decline. There were 13,334 IVT therapies in the 4 months preceding compared to 11,570 procedures during the pandemic, representing a 13.2% (95% CI -13.8 to -12.7, p < 0.0001) drop. Interfacility IVT transfers decreased from 1,337 to 1,178, or an 11.9% decrease (95% CI -13.7 to -10.3, p = 0.001). Recovery of stroke hospitalization volume (9.5%, 95% CI 9.2-9.8, p < 0.0001) was noted over the 2 later (May, June) vs the 2 earlier (March, April) pandemic months. There was a 1.48% stroke rate across 119,967 COVID-19 hospitalizations. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection was noted in 3.3% (1,722/52,026) of all stroke admissions. CONCLUSIONS: The COVID-19 pandemic was associated with a global decline in the volume of stroke hospitalizations, IVT, and interfacility IVT transfers. Primary stroke centers and centers with higher COVID-19 inpatient volumes experienced steeper declines. Recovery of stroke hospitalization was noted in the later pandemic months.

Published
2021

20. Genome-guided analysis allows the identification of novel physiological traits in Trichococcus species

Author

Strepis, Nikolaos, Naranjo, Henry D, Meier-Kolthoff, Jan, Göker, Markus, Shapiro, Nicole, Kyrpides, Nikos, Klenk, Hans-Peter, Schaap, Peter J, Stams, Alfons JM, and Sousa, Diana Z

Subjects
Microbiology, Biological Sciences, Genetics, Biotechnology, Infection, Bacterial Typing Techniques, Carnobacteriaceae, Phenotype, Phylogeny, Propylene Glycols, RNA, Ribosomal, 16S, Sequence Analysis, DNA, Comparative genomics, Protein domains, Halophilic, Psychrophilic, 1, 3-propanediol, 1, 3-propanediol, Information and Computing Sciences, Medical and Health Sciences, Bioinformatics, Biological sciences, Biomedical and clinical sciences
Abstract

BackgroundThe genus Trichococcus currently contains nine species: T. flocculiformis, T. pasteurii, T. palustris, T. collinsii, T. patagoniensis, T. ilyis, T. paludicola, T. alkaliphilus, and T. shcherbakoviae. In general, Trichococcus species can degrade a wide range of carbohydrates. However, only T. pasteurii and a non-characterized strain of Trichococcus, strain ES5, have the capacity of converting glycerol to mainly 1,3-propanediol. Comparative genomic analysis of Trichococcus species provides the opportunity to further explore the physiological potential and uncover novel properties of this genus.ResultsIn this study, a genotype-phenotype comparative analysis of Trichococcus strains was performed. The genome of Trichococcus strain ES5 was sequenced and included in the comparison with the other nine type strains. Genes encoding functions related to e.g. the utilization of different carbon sources (glycerol, arabinan and alginate), antibiotic resistance, tolerance to low temperature and osmoregulation could be identified in all the sequences analysed. T. pasteurii and Trichococcus strain ES5 contain a operon with genes encoding necessary enzymes for 1,3-PDO production from glycerol. All the analysed genomes comprise genes encoding for cold shock domains, but only five of the Trichococcus species can grow at 0 °C. Protein domains associated to osmoregulation mechanisms are encoded in the genomes of all Trichococcus species, except in T. palustris, which had a lower resistance to salinity than the other nine studied Trichococcus strains.ConclusionsGenome analysis and comparison of ten Trichococcus strains allowed the identification of physiological traits related to substrate utilization and environmental stress resistance (e.g. to cold and salinity). Some substrates were used by single species, e.g. alginate by T. collinsii and arabinan by T. alkaliphilus. Strain ES5 may represent a subspecies of Trichococcus flocculiformis and contrary to the type strain (DSM 2094T), is able to grow on glycerol with the production of 1,3-propanediol.

Published
2020

21. Using Neural Networks for Relation Extraction from Biomedical Literature

Author

Sousa, Diana, Lamurias, Andre, and Couto, Francisco M.

Subjects
Computer Science - Computation and Language, Computer Science - Machine Learning, Statistics - Machine Learning
Abstract

Using different sources of information to support automated extracting of relations between biomedical concepts contributes to the development of our understanding of biological systems. The primary comprehensive source of these relations is biomedical literature. Several relation extraction approaches have been proposed to identify relations between concepts in biomedical literature, namely, using neural networks algorithms. The use of multichannel architectures composed of multiple data representations, as in deep neural networks, is leading to state-of-the-art results. The right combination of data representations can eventually lead us to even higher evaluation scores in relation extraction tasks. Thus, biomedical ontologies play a fundamental role by providing semantic and ancestry information about an entity. The incorporation of biomedical ontologies has already been proved to enhance previous state-of-the-art results., Comment: Artificial Neural Networks book (Springer) - Chapter 14

Published
2019
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22. A Silver Standard Corpus of Human Phenotype-Gene Relations

Author

Sousa, Diana, Lamurias, Andre, and Couto, Francisco M.

Subjects
Computer Science - Computation and Language
Abstract

Human phenotype-gene relations are fundamental to fully understand the origin of some phenotypic abnormalities and their associated diseases. Biomedical literature is the most comprehensive source of these relations, however, we need Relation Extraction tools to automatically recognize them. Most of these tools require an annotated corpus and to the best of our knowledge, there is no corpus available annotated with human phenotype-gene relations. This paper presents the Phenotype-Gene Relations (PGR) corpus, a silver standard corpus of human phenotype and gene annotations and their relations. The corpus consists of 1712 abstracts, 5676 human phenotype annotations, 13835 gene annotations, and 4283 relations. We generated this corpus using Named-Entity Recognition tools, whose results were partially evaluated by eight curators, obtaining a precision of 87.01%. By using the corpus we were able to obtain promising results with two state-of-the-art deep learning tools, namely 78.05% of precision. The PGR corpus was made publicly available to the research community., Comment: NAACL 2019

Published
2019
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23. Medical Management Versus Endovascular Treatment for Large-Vessel Occlusion Anterior Circulation Stroke With Low NIHSS

Author

Safouris, Apostolos, Palaiodimou, Lina, Nardai, Sándor, Kargiotis, Odysseas, Magoufis, George, Psychogios, Klearchos, Matusevicius, Marius, Feil, Katharina, Ahmed, Niaz, Kellert, Lars, Spiliopoulos, Stavros, Brountzos, Elias, Szikora, István, Sarraj, Amrou, Goyal, Nitin, Aguiar de Sousa, Diana, Strbian, Daniel, Caso, Valeria, Alexandrov, Andrei V., and Tsivgoulis, Georgios

Published
2023
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24. Study of Rivaroxaban for Cerebral Venous Thrombosis: A Randomized Controlled Feasibility Trial Comparing Anticoagulation With Rivaroxaban to Standard-of-Care in Symptomatic Cerebral Venous Thrombosis

Author

Field, Thalia S., Dizonno, Vanessa, Almekhlafi, Mohammed A., Bala, Fouzi, Alhabli, Ibrahim, Wong, Hubert, Norena, Monica, Villaluna, Maria Karina, King-Azote, Princess, Ratnaweera, Namali, Mancini, Steven, Van Gaal, Stephen C., Wilson, Laura K., Graham, Brett R., Sposato, Luciano A., Blacquiere, Dylan, Dewar, Brian M., Boulos, Mark I., Buck, Brian H., Odier, Celine, Perera, Kanjana S., Pikula, Aleksandra, Tkach, Aleksander, Medvedev, George, Canfield, Carolyn, Mortenson, W. Ben, Nadeau, Janel O., Alshimemeri, Sohaila, Benavente, Oscar R., Demchuk, Andrew M., Dowlatshahi, Dar, Lanthier, Sylvain, Lee, Agnes Y.Y., Mandzia, Jennifer, Suryanarayan, Deepa, Weitz, Jeffrey I., Hill, Michael D., Hill, Michael, Villaluna Murray, Karina, Jones, Andrea, Matsubara, Lauren, O’Neill, Zoe, Park, Sarah, Yuan, Michelle, Saluzzi, Marina, Dueck, Ashley, McKibben, K. Ingrid, Zhang, Qiao, Benavente (chair), Oscar, Butcher (chair), Ken, Bushnell, Cheryl, de Sousa, Diana Aguiar, Hill, Michael, Benavente, Oscar, Wilson, Dr Laura, Benavente, Oscar, Lloret, Mar, Lau, Hsien Lee, Maclean, Genoveva, Mann, Sharanpal, Murphy, Colleen, Smith, Jonathan, Teal, Philip, Tse, Ming Yin (Dominic), Yip, Samuel, Naidoo, VIshaya, Brar, Jaskiran, Chen, Shuo, Horton, Myles, Hill, Michael, Save, Supriya, Althubait, Shorog, Bogiatzi, Chrysi, Boyko, Matthew, Chatuverdi, Surbhi, Coutts, Shelagh, Ganesh, Aravind, Ghavami, Kimia, Harrison, Emme, Hu, Sherry, Jambula, Anitha, Joundi, Raed, Kenney, Carol, Klein, Gary, Lin, Katie, Mansoor, Salman, Marko, Martha, Ryckborst, Karla, Sage, Kayla, Singh, Nishita, Tse, Ming Yin (Dominic), Wadhwa, Ankur, Wasiliw, Sanchea, Graham, Brett, Bhavsar, Shrijal, Bold, Kala, Maley, Sharleen, Urroz, Lilian, Foster, Kaitlyn, Junk, Emily, Corley, Scott, Gardner, Aaron, McMullen, Jennifer, Whelan, Ruth, Duff, Whitney, Tyson, Cassandra, Cooley, Regan, Hunter, Gary, Magee, Fergall, Wasyliw, Sanchea, Beauchamp, Meribeth-Ann (Beth), Lambourn, Lindsay, Ayan, Diana, Khaw, Aleksander, Mai, Lauren, Bullrich, Maria Bres, Fridman, Sebastian, Daham, Zeinab, Fahad, Robert, Shamy, Michel, Stotts, Grant, Fatadawala, Idris, Lopes, Kaitlyn, Southwell, Alisia, Bhandari, Vinaya, Fitzpatrick, Tess, Gladstone, David, Hopyan, Julia, Kamra, Maneesha, Khosravani, Houman, Liddy, Anne-Marie, Liu, Zhongyu, Popel, Najla, Sivakumar, Keith, Swartz, Richard, Yu, Amy, Fairall, Paige, Ahmed, Farhat, Jabs, Juline, White, Leah, Piquette, Lori, Shepherd, Rekha, Ishaque, Noman, Odier, Céline, Simon, Nandy-Shelwine, Lapierre, Marlene, Bereznyakova, Olena, Caporuscio, Casey Boudreau, Cauchon, Francois, Côté, Valerie, Denault, Nicole, Desciantre, Yan, Gauthier, Lyne, Gioia, Laura, Jaquin, Grégory, Jadil, Nadia, Lim, Sothun, Poppe, Alexandra, Rodriguez, Caludia, Rodriguez, Marie-Christine, Stapf, Christian, Vandervelde, Cheyenne, Ng, Kuan Huei (Kelvin), Oczkowski, Wes, Lourenco, Diane, Moreau, Cathay, Jolie, Amber, Bhagraith, Vinai, Katsanos, Aristeidis, de Sa Boasquevisque, Danielle, Ratnayake, Kanchana, McLelland, Marie, Adderly, Coleen, Elamin, Elsadig, Galloway, Camille, Smith, Michelle, Topor, Tess, Singh, Shobha, To, William, Akthar, Farhana, Casaubon, Leanne, Cayley, Anne, Crelling, Lisa, Del Campo, Martin, Gao, Mingyang, Hanna, Cresti, Khalid, Muhammad, Pham, Nga, Schaafsma, Joanna, Silver, Frank, Stewart, TIm, Tiopanas, Patricia, Wigner, Rely, and Williams, Janice

Published
2023
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29. Wheat genotypes selection via multi-trait for abiotic stresses.

Author

Oliveira Ribeiro, João Paulo, Palheta de Sousa, Diana Jhulia, Gomes de Carvalho, Chainheny, Oliveira Willmann, Guilherme, Fernandes dos Santos Dias, Denise Cunha, and Nardino, Maicon

Subjects
*ABIOTIC stress, *WHEAT, *WHEAT seeds, *GERMINATION, *CROP development
Abstract

Abiotic stresses, such as heat, drought and salinity, affect the development of wheat crop and hinder its expansion to the central region of Brazil. The identification of genotypes tolerant to these conditions is important for improving yield performance. The present research evaluated the impact of different abiotic stresses on germination and seedling development and selected wheat genotypes tolerant to these stresses, using multi-trait analysis. Heat, drought and salinity stresses were induced in seeds of 23 wheat genotypes. Seed germination, seedling length and dry mass were evaluated. An adaptability and stability model and a multi-trait selection index were applied to the data. Drought and salinity negatively affected the development of seedlings of the 23 evaluated genotypes. However, the VI 14055, ORS Madre Pérola and BRS 404 genotypes conferred the best adaptability and stability results and were selected by the MGIDI, which revealed that great performance can be achieved in regions with potential for abiotic stress, in the early stages of development. [ABSTRACT FROM AUTHOR]

Published
2024
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30. Risk of major adverse cardiovascular events and stroke associated with treatment with GLP-1 or the dual GIP/GLP-1 receptor agonist tirzepatide for type 2 diabetes: A systematic review and meta-analysis.

Author

Stefanou, Maria-Ioanna, Theodorou, Aikaterini, Malhotra, Konark, Aguiar de Sousa, Diana, Katan, Mira, Palaiodimou, Lina, Katsanos, Aristeidis H, Koutroulou, Ioanna, Lambadiari, Vaia, Lemmens, Robin, Giannopoulos, Sotirios, Alexandrov, Andrei V, Siasos, Gerasimos, and Tsivgoulis, Georgios

Published
2024
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31. Primary stroke prevention worldwide: translating evidence into action

Author

Abanto, Carlos, Abera, Semaw Ferede, Addissie, Adamu, Adebayo, Oluwadamilola, Adeleye, Amos Olufemi, Adilbekov, Yerzhan, Adilbekova, Bibigul, Adoukonou, Thierry Armel, Aguiar de Sousa, Diana, Ajagbe, Temitope, Akhmetzhanova, Zauresh, Akpalu, Albert, Álvarez Ahlgren, Jhon, Ameriso, Sebastián, Andonova, Silva, Awoniyi, Foloruso Emmanuel, Bakhiet, Moiz, Barboza, Miguel, Basri, Hamidon, Bath, Philip, Bello, Olamide, Bereczki, Dániel, Beretta, Simone, Berkowitz, Aaron, Bernabé-Ortiz, Antonio, Bernhardt, Julie, Berzina, Guna, Bisharyan, Mher, Bovet, Pascal, Budincevic, Hrvoje, Cadilhac, Dominique, Caso, Valeria, Chen, Christopher, Chin, Jerome, Chwojnicki, Kamil, Conforto, Adriana, Cruz, Vitor Tedim, D'Amelio, Marco, Danielyan, Kristine, Davis, Stephen, Demarin, Vida, Dempsey, Robert, Dichgans, Martin, Dokova, Klara, Donnan, Geoffrey, Elkind, Mitchell S., Endres, Matthias, Fischer, Urs, Gankpé, Fortuné, Gaye Saavedra, Andrés, Gil, Artyom, Giroud, Maurice, Gnedovskaya, Elena, Hachinski, Vladimir, Hafdi, Melanie, Hamadeh, Randah, Hamzat, T. Kolapo, Hankey, Graeme, Heldner, Mirjam, Ibrahim, Etedal Ahmed, Ibrahim, Norlinah Mohamed, Inoue, Manabu, Jee, Sungju, Jeng, Jiann-Shing, Kalkonde, Yogesh, Kamenova, Saltanat, Karaszewski, Bartosz, Kelly, Peter, Khan, Taskeen, Kiechl, Stefan, Kondybayeva, Aida, Kõrv, Janika, Kravchenko, Michael, Krishnamurthi, Rita V., Kruja, Jera, Lakkhanaloet, Mongkol, Langhorne, Peter, Lavados, Pablo M., Law, Zhe Kang, Lawal, Abisola, Lazo-Porras, Maria, Lebedynets, Dmytro, Lee, Tsong-Hai, Leung, Thomas, Liebeskind, David S., Lindsay, Patrice, López-Jaramillo, Patricio, Lotufo, Paulo Andrade, Machline-Carrion, Julia, Makanjuola, Akintomiwa, Markus, Hugh Stephen, Marquez-Romero, Juan Manuel, Medina, Marco, Medukhanova, Sabina, Mehndiratta, Man Mohan, Merkin, Alexandr, Mirrakhimov, Erkin, Mohl, Stephanie, Moscoso-Porras, Miguel, Müller-Stierlin, Annabel, Murphy, Sean, Musa, Kamarul Imran, Nasreldein, Ahmed, Nogueira, Raul Gomes, Nolte, Christian, Noubiap, Jean Jacques, Novarro-Escudero, Nelson, Ogun, Yomi, Oguntoye, Richard Ayobami, Oraby, Mohammed Ibrahim, Osundina, Morenike, Ovbiagele, Bruce, Orken, Dilek Necioglu, Ozdemir, Atilla Özcan, Ozturk, Serefnur, Paccot, Melanie, Phromjai, Jurairat, Piradov, Piradov, Platz, Thomas, Potpara, Tatjana, Ranta, Annemarei, Rathore, Farooq, Richard, Edo, Sacco, Ralph L., Sahathevan, Ramesh, Santos Carquín, Irving, Saposnik, Gustavo, Sarfo, Fred Stephen, Sharma, Mike, Sheth, Kevin, Shobhana, A., Suwanwela, Nijasri, Svyato, Irina, Sylaja, P.N., Tao, Xuanchen, Thakur, Kiran T., Toni, Danilo, Topcuoglu, Mehmet Akif, Torales, Julio, Towfighi, Amytis, Truelsen, Thomas Clement, Tsiskaridze, Alexander, Tulloch-Reid, Marshall, Useche, Nicolás, Vanacker, Peter, Vassilopoulou, Sophia, Vukorepa, Gorana, Vuletic, Vladimira, Wahab, Kolawole W., Wang, Wenzhi, Wijeratne, Tissa, Wolfe, Charles, Yifru, Yared Mamushet, Yock-Corrales, Adriana, Yonemoto, Naohiro, Yperzeele, Laetitia, Zhang, Puhong, Owolabi, Mayowa O, Thrift, Amanda G, Mahal, Ajay, Ishida, Marie, Martins, Sheila, Johnson, Walter D, Pandian, Jeyaraj, Abd-Allah, Foad, Yaria, Joseph, Phan, Hoang T, Roth, Greg, Gall, Seana L, Beare, Richard, Phan, Thanh G, Mikulik, Robert, Akinyemi, Rufus O, Norrving, Bo, Brainin, Michael, and Feigin, Valery L

Published
2022
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32. Timing of oral anticoagulants initiation for atrial fibrillation after acute ischemic stroke: A systematic review and meta-analysis

Author

Palaiodimou, Lina, primary, Stefanou, Maria-Ioanna, additional, Katsanos, Aristeidis H, additional, De Marchis, Gian Marco, additional, Aguiar De Sousa, Diana, additional, Dawson, Jesse, additional, Katan, Mira, additional, Karapanayiotides, Theodore, additional, Toutouzas, Konstantinos, additional, Paciaroni, Maurizio, additional, Seiffge, David J, additional, and Tsivgoulis, Georgios, additional

Published
2024
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35. Coma in adult cerebral venous thrombosis: The BEAST study

Author

Neurologen, Brain, Circulatory Health, Ranjan, Redoy, Ken-Dror, Gie, Martinelli, Ida, Grandone, Elvira, Hiltunen, Sini, Lindgren, Erik, Margaglione, Maurizio, Duchez, Veronique Le Cam, Triquenot Bagan, Aude, Zedde, Marialuisa, Giannini, Nicola, Ruigrok, Ynte M., Worrall, Bradford B., Majersik, Jennifer J., Putaala, Jukka, Haapaniemi, Elena, Zuurbier, Susanna M., Brouwer, Matthijs C., Passamonti, Serena M., Abbattista, Maria, Bucciarelli, Paolo, Lemmens, Robin, Pappalardo, Emanuela, Costa, Paolo, Colombi, Marina, Aguiar de Sousa, Diana, Rodrigues, Sofia, Canhão, Patrícia, Tkach, Aleksander, Santacroce, Rosa, Favuzzi, Giovanni, Arauz, Antonio, Colaizzo, Donatella, Spengos, Kostas, Hodge, Amanda, Ditta, Reina, Pezzini, Alessandro, Coutinho, Jonathan M., Thijs, Vincent, Jood, Katarina, Tatlisumak, Turgut, Ferro, José M., Sharma, Pankaj, Neurologen, Brain, Circulatory Health, Ranjan, Redoy, Ken-Dror, Gie, Martinelli, Ida, Grandone, Elvira, Hiltunen, Sini, Lindgren, Erik, Margaglione, Maurizio, Duchez, Veronique Le Cam, Triquenot Bagan, Aude, Zedde, Marialuisa, Giannini, Nicola, Ruigrok, Ynte M., Worrall, Bradford B., Majersik, Jennifer J., Putaala, Jukka, Haapaniemi, Elena, Zuurbier, Susanna M., Brouwer, Matthijs C., Passamonti, Serena M., Abbattista, Maria, Bucciarelli, Paolo, Lemmens, Robin, Pappalardo, Emanuela, Costa, Paolo, Colombi, Marina, Aguiar de Sousa, Diana, Rodrigues, Sofia, Canhão, Patrícia, Tkach, Aleksander, Santacroce, Rosa, Favuzzi, Giovanni, Arauz, Antonio, Colaizzo, Donatella, Spengos, Kostas, Hodge, Amanda, Ditta, Reina, Pezzini, Alessandro, Coutinho, Jonathan M., Thijs, Vincent, Jood, Katarina, Tatlisumak, Turgut, Ferro, José M., and Sharma, Pankaj

Published
2024

36. Gene-Gene Interaction Between Factor-XI and ABO Genes in Cerebral Venous Thrombosis: The BEAST Study

Author

Neurologen, Brain, Circulatory Health, Ken-Dror, Gie, Martinelli, Ida, Grandone, Elvira, Hiltunen, Sini, Lindgren, Erik, Margaglione, Maurizio, Le Cam Duchez, Veronique, Triquenot, Aude B., Zedde, Marialuisa, Mancuso, Michelangelo, Ruigrok, Ynte M., Worrall, Bradford B., Majersik, Jennifer J., Putaala, Jukka, Haapaniemi, Elena, Zuurbier, Susanna, Brouwer, Matthijs C., Passamonti, Serena M., Abbattista, Maria, Bucciarelli, Paolo, Lemmens, Robin, Pappalardo, Emanuela, Costa, Paolo, Colombi, Marina, De Sousa, Diana Aguiar, Rodrigues, Sofia G., Canhao, Patrícia, Tkach, Aleksander, Santacroce, Rosa, Favuzzi, Giovanni, Arauz, Antonio, Colaizzo, Donatella, Spengos, Konstantinos, Hodge, Amanda, Ditta, Reina, Pezzini, Alessandro, Coutinho, Jonathan M., Thijs, Vincent N., Jood, Katarina, Pare, Guillaume, Tatlisumak, Turgut, Ferro, José M., Sharma, Pankaj, Neurologen, Brain, Circulatory Health, Ken-Dror, Gie, Martinelli, Ida, Grandone, Elvira, Hiltunen, Sini, Lindgren, Erik, Margaglione, Maurizio, Le Cam Duchez, Veronique, Triquenot, Aude B., Zedde, Marialuisa, Mancuso, Michelangelo, Ruigrok, Ynte M., Worrall, Bradford B., Majersik, Jennifer J., Putaala, Jukka, Haapaniemi, Elena, Zuurbier, Susanna, Brouwer, Matthijs C., Passamonti, Serena M., Abbattista, Maria, Bucciarelli, Paolo, Lemmens, Robin, Pappalardo, Emanuela, Costa, Paolo, Colombi, Marina, De Sousa, Diana Aguiar, Rodrigues, Sofia G., Canhao, Patrícia, Tkach, Aleksander, Santacroce, Rosa, Favuzzi, Giovanni, Arauz, Antonio, Colaizzo, Donatella, Spengos, Konstantinos, Hodge, Amanda, Ditta, Reina, Pezzini, Alessandro, Coutinho, Jonathan M., Thijs, Vincent N., Jood, Katarina, Pare, Guillaume, Tatlisumak, Turgut, Ferro, José M., and Sharma, Pankaj

Published
2024

37. External validation of the SI2NCAL2C score for outcomes following cerebral venous thrombosis

Author

MS Interne Geneeskunde, Klein, Piers, Shu, Liqi, Lindgren, Erik, de Winter, Maria A., Siegler, James E., Simpkins, Alexis N., Omran, Satareh Salehi, Heldner, Mirjam R., de Havenon, Adam, Abdalkader, Mohamad, al Kasab, Sami, Stretz, Christoph, Wu, Teddy Y., Wilson, Duncan, Asad, Syed Daniyal, Almallouhi, Eyad, Frontera, Jennifer, Kuohn, Lindsey, Rothstein, Aaron, Bakradze, Ekaterina, Henninger, Nils, Zubair, Adeel S., Sharma, Richa, Kerrigan, Deborah, Aziz, Yasmin, Mistry, Eva A., van Kammen, Mayte Sanchez, Tatlisumak, Turgut, Krzywicka, Katarzyna, Aguiar de Sousa, Diana, Jood, Katarina, Field, Thalia S., Yaghi, Shadi, Coutinho, Jonathan M., Nguyen, Thanh N., MS Interne Geneeskunde, Klein, Piers, Shu, Liqi, Lindgren, Erik, de Winter, Maria A., Siegler, James E., Simpkins, Alexis N., Omran, Satareh Salehi, Heldner, Mirjam R., de Havenon, Adam, Abdalkader, Mohamad, al Kasab, Sami, Stretz, Christoph, Wu, Teddy Y., Wilson, Duncan, Asad, Syed Daniyal, Almallouhi, Eyad, Frontera, Jennifer, Kuohn, Lindsey, Rothstein, Aaron, Bakradze, Ekaterina, Henninger, Nils, Zubair, Adeel S., Sharma, Richa, Kerrigan, Deborah, Aziz, Yasmin, Mistry, Eva A., van Kammen, Mayte Sanchez, Tatlisumak, Turgut, Krzywicka, Katarzyna, Aguiar de Sousa, Diana, Jood, Katarina, Field, Thalia S., Yaghi, Shadi, Coutinho, Jonathan M., and Nguyen, Thanh N.

Published
2024

38. Transcriptomic evidence for an energetically advantageous relationship between Syntrophomonas wolfei and Methanothrix soehngenii

Author

Besteman, Maaike S., Doloman, Anna, Sousa, Diana Z., Besteman, Maaike S., Doloman, Anna, and Sousa, Diana Z.

Abstract

Syntrophic interactions are key in anaerobic food chains, facilitating the conversion of complex organic matter into methane. A typical example involves acetogenic bacteria converting fatty acids (e.g., butyrate and propionate), a process thermodynamically reliant on H2 consumption by microorganisms such as methanogens. While most studies focus on H2-interspecies transfer between these groups, knowledge on acetate cross-feeding in anaerobic systems is lacking. This study investigated butyrate oxidation by co-cultures of Syntrophomonas wolfei and Methanospirillum hungatei, both with and without the addition of the acetate scavenger Methanothrix soehngenii. Growth and gene expression patterns of S. wolfei and M. hungatei were followed in the two conditions. Although butyrate consumption rates remained constant, genes in the butyrate degradation pathway of S. wolfei were less expressed in the presence of M. soehngenii, including genes involved in reverse electron transport. Higher expression of a type IV-pili operon in S. wolfei hints to the potential for direct interspecies electron transfer between S. wolfei and M. soehngenii and an energetically advantageous relationship between the two microorganisms. Overall, the presence of the acetate scavenger M. soehngenii positively influenced the energy metabolism of S. wolfei and highlighted the relevance of including acetate scavengers when investigating syntrophic fatty acid degradation.

Published
2024

39. Mechanisms of microbial co-aggregation in mixed anaerobic cultures

Author

Doloman, Anna, Sousa, Diana Z., Doloman, Anna, and Sousa, Diana Z.

Abstract

Co-aggregation of anaerobic microorganisms into suspended microbial biofilms (aggregates) serves ecological and biotechnological functions. Tightly packed aggregates of metabolically interdependent bacteria and archaea play key roles in cycling of carbon and nitrogen. Additionally, in biotechnological applications, such as wastewater treatment, microbial aggregates provide a complete metabolic network to convert complex organic material. Currently, experimental data explaining the mechanisms behind microbial co-aggregation in anoxic environments is scarce and scattered across the literature. To what extent does this process resemble co-aggregation in aerobic environments? Does the limited availability of terminal electron acceptors drive mutualistic microbial relationships, contrary to the commensal relationships observed in oxygen-rich environments? And do co-aggregating bacteria and archaea, which depend on each other to harvest the bare minimum Gibbs energy from energy-poor substrates, use similar cellular mechanisms as those used by pathogenic bacteria that form biofilms? Here, we provide an overview of the current understanding of why and how mixed anaerobic microbial communities co-aggregate and discuss potential future scientific advancements that could improve the study of anaerobic suspended aggregates. Key points: • Metabolic dependency promotes aggregation of anaerobic bacteria and archaea • Flagella, pili, and adhesins play a role in the formation of anaerobic aggregates • Cyclic di-GMP/AMP signaling may trigger the polysaccharides production in anaerobes.

Published
2024

40. Correction to: Physiological and stoichiometric characterization of ethanol-based chain elongation in the absence of short-chain carboxylic acids

Author

Allaart, Maximilienne Toetie, Fox, Bartholomeus B., Nettersheim, Ingo H.M.S., Pabst, Martin, Sousa, Diana Z., Kleerebezem, Robbert, Allaart, Maximilienne Toetie, Fox, Bartholomeus B., Nettersheim, Ingo H.M.S., Pabst, Martin, Sousa, Diana Z., and Kleerebezem, Robbert

Abstract

The original version of this Article contained errors in the Discussion section, where reference 34 was incorrectly cited as reference 25. Consequently, “Spirito et al.25 also observed a decreased conversion rate when feeding a chain-elongating reactor microbiome with mainly ethanol. This could explain why previous studies with shorter incubation times reported no metabolic activity in the absence of acetate25,35. The mechanism that underlies this change in rate remains elusive. Spirito et al.25 proposed a thermodynamic constraint on the rate due to increased hydrogen partial pressures, but in our experiments pH2 was low due to continuous sparging and we still observed low rates.” now reads: “Spirito et al.34 also observed a decreased conversion rate when feeding a chain-elongating reactor microbiome with mainly ethanol. This could explain why previous studies with shorter incubation times reported no metabolic activity in the absence of acetate34,35. The mechanism that underlies this change in rate remains elusive. Spirito et al.34 proposed a thermodynamic constraint on the rate due to increased hydrogen partial pressures, but in our experiments pH2 was low due to continuous sparging and we still observed low rates.” The original Article has been corrected.

Published
2024

41. A novel experimental method to determine substrate uptake kinetics of gaseous substrates applied to the carbon monoxide-fermenting Clostridium autoethanogenum

Author

Allaart, M.T. (author), Korkontzelos, Charilaos (author), Sousa, Diana Z. (author), Kleerebezem, R. (author), Allaart, M.T. (author), Korkontzelos, Charilaos (author), Sousa, Diana Z. (author), and Kleerebezem, R. (author)

Abstract

Syngas fermentation has gained momentum over the last decades. The cost-efficient design of industrial-scale bioprocesses is highly dependent on quantitative microbial growth data. Kinetic and stoichiometric models for syngas-converting microbes exist, but accurate experimental validation of the derived parameters is lacking. Here, we describe a novel experimental approach for measuring substrate uptake kinetics of gas-fermenting microbes using the model microorganism Clostridium autoethanogenum. One-hour disturbances of a steady-state chemostat bioreactor with increased CO partial pressures (up to 1.2 bar) allowed for measurement of biomass-specific CO uptake- and CO2 production rates ((Formula presented.), (Formula presented.)) using off-gas analysis. At a pCO of 1.2 bar, a (Formula presented.) of −119 ± 1 mmol g−1X h−1 was measured. This value is 1.8–3.5-fold higher than previously reported experimental and kinetic modeling results for syngas fermenters. Analysis of the catabolic flux distribution reveals a metabolic shift towards ethanol production at the expense of acetate at pCO (Formula presented.) 0.6 atm, likely to be mediated by acetate availability and cellular redox state. We characterized this metabolic shift as acetogenic overflow metabolism. These results provide key mechanistic understanding of the factors steering the product spectrum of CO fermentation in C. autoethanogenum and emphasize the importance of dedicated experimental validation of kinetic parameters., BT/Environmental Biotechnology

Published
2024
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42. A novel experimental method to determine substrate uptake kinetics of gaseous substrates applied to the carbon monoxide-fermenting Clostridium autoethanogenum

Author

Allaart, Maximilienne T., Korkontzelos, Charilaos, Sousa, Diana Z., Kleerebezem, Robbert, Allaart, Maximilienne T., Korkontzelos, Charilaos, Sousa, Diana Z., and Kleerebezem, Robbert

Abstract

Syngas fermentation has gained momentum over the last decades. The cost-efficient design of industrial-scale bioprocesses is highly dependent on quantitative microbial growth data. Kinetic and stoichiometric models for syngas-converting microbes exist, but accurate experimental validation of the derived parameters is lacking. Here, we describe a novel experimental approach for measuring substrate uptake kinetics of gas-fermenting microbes using the model microorganism Clostridium autoethanogenum. One-hour disturbances of a steady-state chemostat bioreactor with increased CO partial pressures (up to 1.2 bar) allowed for measurement of biomass-specific CO uptake- and CO2 production rates ((Formula presented.), (Formula presented.)) using off-gas analysis. At a pCO of 1.2 bar, a (Formula presented.) of −119 ± 1 mmol g−1X h−1 was measured. This value is 1.8–3.5-fold higher than previously reported experimental and kinetic modeling results for syngas fermenters. Analysis of the catabolic flux distribution reveals a metabolic shift towards ethanol production at the expense of acetate at pCO (Formula presented.) 0.6 atm, likely to be mediated by acetate availability and cellular redox state. We characterized this metabolic shift as acetogenic overflow metabolism. These results provide key mechanistic understanding of the factors steering the product spectrum of CO fermentation in C. autoethanogenum and emphasize the importance of dedicated experimental validation of kinetic parameters.

Published
2024

43. Accelerate acetogenic bioproduction : Acetogens as sustainable producers of biocommodities

Author

Flaiz, Maximilian, Sousa, Diana Z., Flaiz, Maximilian, and Sousa, Diana Z.

Abstract

Gas fermentation using autotrophic acetogenic bacteria has been industrialized, however, its full potential remains untapped, with only native products like ethanol being produced thus far. Advancements in synthetic biology have enabled the recombinant production of diverse biocommodities to broaden their limited natural product spectrum from C1-gases. Additionally, co-culturing acetogens with other microorganisms holds the potential for expanding the product spectrum further. However, commercialization remains challenging due to complex pathway and (co)culturing optimizations. To address this, novel synthetic biology tools, including the use of high throughput biopart screenings using reporter proteins, the deployment of cell-free systems to combine best-performing enzymes, and the identification and elimination of competing pathways, can be employed. Incorporating genetically engineered strains in co-cultures improves dependencies, directs product formation, and increases resilience, enhancing bioproduction efficiency. This review emphasizes using these tools to enhance the recombinant production of biocommodities, offering promising solutions to overcome existing challenges.

Published
2024

44. Coupling extracellular glycan composition with metagenomic data in papermill and brewery anaerobic granular sludges

Author

Doloman, Anna, de Bruin, Stefan, van Loosdrecht, Mark C.M., Sousa, Diana Z., Lin, Yuemei, Doloman, Anna, de Bruin, Stefan, van Loosdrecht, Mark C.M., Sousa, Diana Z., and Lin, Yuemei

Abstract

Glycans are crucial for the structure and function of anaerobic granular sludge in wastewater treatment. Yet, there is limited knowledge regarding the microorganisms and biosynthesis pathways responsible for glycan production. In this study, we analysed samples from anaerobic granular sludges treating papermill and brewery wastewater, examining glycans composition and using metagenome-assembled genomes (MAGs) to explore potential biochemical pathways associated with their production. Uronic acids were the predominant constituents of the glycans in extracellular polymeric substances (EPS) produced by the anaerobic granular sludges, comprising up to 60 % of the total polysaccharide content. MAGs affiliated with Anaerolineacae, Methanobacteriaceae and Methanosaetaceae represented the majority of the microbial community (30–50 % of total reads per MAG). Based on the analysis of MAGs, it appears that Anaerolinea sp. and members of the Methanobacteria class are involved in the production of exopolysaccharides within the analysed granular sludges. These findings shed light on the functional roles of microorganisms in glycan production in industrial anaerobic wastewater treatment systems.

Published
2024

45. Acetic acid stress response of the acidophilic sulfate reducer Acididesulfobacillus acetoxydans

Author

Egas, Reinier A., Sahonero-Canavesi, Diana X., Bale, Nicole J., Koenen, Michel, Yildiz, Çağlar, Villanueva, Laura, Sousa, Diana Z., Sánchez-Andrea, Irene, Egas, Reinier A., Sahonero-Canavesi, Diana X., Bale, Nicole J., Koenen, Michel, Yildiz, Çağlar, Villanueva, Laura, Sousa, Diana Z., and Sánchez-Andrea, Irene

Abstract

Acid mine drainage (AMD) waters are a severe environmental threat, due to their high metal content and low pH (pH <3). Current technologies treating AMD utilize neutrophilic sulfate-reducing microorganisms (SRMs), but acidophilic SRM could offer advantages. As AMDs are low in organics these processes require electron donor addition, which is often incompletely oxidized into organic acids (e.g., acetic acid). At low pH, acetic acid is undissociated and toxic to microorganisms. We investigated the stress response of the acetotrophic Acididesulfobacillus acetoxydans to acetic acid. A. acetoxydans was cultivated in bioreactors at pH 5.0 (optimum). For stress experiments, triplicate reactors were spiked until 7.5 mM of acetic acid and compared with (non-spiked) triplicate reactors for physiological, transcriptomic, and membrane lipid changes. After acetic acid spiking, the optical density initially dropped, followed by an adaptation phase during which growth resumed at a lower growth rate. Transcriptome analysis revealed a downregulation of genes involved in glutamate and aspartate synthesis following spiking. Membrane lipid analysis revealed a decrease in iso and anteiso fatty acid relative abundance; and an increase of acetyl-CoA as a fatty acid precursor. These adaptations allow A. acetoxydans to detoxify acetic acid, creating milder conditions for other microorganisms in AMD environments.

Published
2024

46. Alcohol dehydrogenase system acts as the sole pathway for methanol oxidation in Desulfofundulus kuznetsovii strain TPOSR

Author

Friedeheim, Lukas, Boeren, Sjef, Sánchez-Andrea, Irene, Stams, Fons, Sousa, Diana Z., Friedeheim, Lukas, Boeren, Sjef, Sánchez-Andrea, Irene, Stams, Fons, and Sousa, Diana Z.

Abstract

Desulfofundulus kuznetsovii is a thermophilic, spore-forming sulphate-reducing bacterium in the family Peptococcaceae. In this study, we describe a newly isolated strain of D. kuznetsovii, strain TPOSR, and compare its metabolism to the type strain D. kuznetsovii 17T. Both strains grow on a large variety of alcohols, such as methanol, ethanol and propane-diols, coupled to the reduction of sulphate. Strain 17T metabolizes methanol via two routes, one involving a cobalt-dependent methyl transferase and the other using a cobalt-independent alcohol dehydrogenase. However, strain TPOSR, which shares 97% average nucleotide identity with D. kuznetsovii strain 17T, lacks several genes from the methyl transferase operon found in strain 17T. The gene encoding the catalytically active methyl transferase subunit B is missing, indicating that strain TPOSR utilizes the alcohol dehydrogenase pathway exclusively. Both strains grew with methanol during cobalt starvation, but growth was impaired. Strain 17T was more sensitive to cobalt deficiency, due to the repression of its methyl transferase system. Our findings shed light on the metabolic diversity of D. kuznetsovii and their metabolic differences of encoding one or two routes for the conversion of methanol.

Published
2024

47. Coupling extracellular glycan composition with metagenomic data in papermill and brewery anaerobic granular sludges

Author

Doloman, Anna (author), de Bruin, S. (author), van Loosdrecht, Mark C.M. (author), Sousa, Diana Z. (author), Lin, Y. (author), Doloman, Anna (author), de Bruin, S. (author), van Loosdrecht, Mark C.M. (author), Sousa, Diana Z. (author), and Lin, Y. (author)

Abstract

Glycans are crucial for the structure and function of anaerobic granular sludge in wastewater treatment. Yet, there is limited knowledge regarding the microorganisms and biosynthesis pathways responsible for glycan production. In this study, we analysed samples from anaerobic granular sludges treating papermill and brewery wastewater, examining glycans composition and using metagenome-assembled genomes (MAGs) to explore potential biochemical pathways associated with their production. Uronic acids were the predominant constituents of the glycans in extracellular polymeric substances (EPS) produced by the anaerobic granular sludges, comprising up to 60 % of the total polysaccharide content. MAGs affiliated with Anaerolineacae, Methanobacteriaceae and Methanosaetaceae represented the majority of the microbial community (30–50 % of total reads per MAG). Based on the analysis of MAGs, it appears that Anaerolinea sp. and members of the Methanobacteria class are involved in the production of exopolysaccharides within the analysed granular sludges. These findings shed light on the functional roles of microorganisms in glycan production in industrial anaerobic wastewater treatment systems., BT/Environmental Biotechnology

Published
2024
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48. Outcomes of Cerebral Venous Thrombosis due to Vaccine-Induced Immune Thrombotic Thrombocytopenia After the Acute Phase

Author

van de Munckhof, Anita, Lindgren, Erik, Kleinig, Timothy J., Field, Thalia S., Cordonnier, Charlotte, Krzywicka, Katarzyna, Poli, Sven, Sánchez van Kammen, Mayte, Borhani-Haghighi, Afshin, Lemmens, Robin, Scutelnic, Adrian, Ciccone, Alfonso, Gattringer, Thomas, Wittstock, Matthias, Dizonno, Vanessa, Devroye, Annemie, Elkady, Ahmed, Günther, Albrecht, Cervera, Alvaro, Mengel, Annerose, Chew, Beng Lim Alvin, Buck, Brian, Zanferrari, Carla, Garcia-Esperon, Carlos, Jacobi, Christian, Soriano, Cristina, Michalski, Dominik, Zamani, Zohreh, Blacquiere, Dylan, Johansson, Elias, Cuadrado-Godia, Elisa, Vuillier, Fabrice, Bode, Felix J., Caparros, François, Maier, Frank, Tsivgoulis, Georgios, Katzberg, Hans D., Duan, Jiangang, Burrow, Jim, Pelz, Johann, Mbroh, Joshua, Oen, Joyce, Schouten, Judith, Zimmermann, Julian, Ng, Karl, Garambois, Katia, Petruzzellis, Marco, Carvalho Dias, Mariana, Ghiasian, Masoud, Romoli, Michele, Miranda, Miguel, Wronski, Miriam, Skjelland, Mona, Almasi-Dooghaee, Mostafa, Cuisenier, Pauline, Murphy, Seán, Timsit, Serge, Coutts, Shelagh B., Schönenberger, Silvia, Nagel, Simon, Hiltunen, Sini, Chatterton, Sophie, Cox, Thomas, Bartsch, Thorsten, Shaygannejad, Vahid, Mirzaasgari, Zahra, Middeldorp, Saskia, Levi, Marcel M., Kremer Hovinga, Johanna A., Jood, Katarina, Tatlisumak, Turgut, Putaala, Jukka, Heldner, Mirjam R., Arnold, Marcel, Aguiar de Sousa, Diana, Ferro, José M., and Coutinho, Jonathan M.

Published
2022
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50. Comparative International Testing of Early Childhood Education: The Democratic Deficit and the Case of Portugal

Author

Sousa, Diana, Grey, Sue, and Oxley, Laura

Abstract

The Organisation for Economic Co-operation and Development (OECD) has a key role in driving educational discourse and global educational governance. Its comparative 'Programme of International School Assessment' (PISA) has explicitly linked the knowledge and skills of young people with the economic potential of countries. Through the International Early Learning and Child Well-Being Study (IELS), the OECD plans to extend its reach to early childhood education (ECE) by developing metrics to measure 'quality' in ECE. This focus gives weight to discourses centred around ideas of 'what works'. The rhetoric derives from the principles that standards of learning and well-being can be improved by emulating notions of 'best practice' identified through comparative data. This article uses the case of Portugal to illustrate the significant disconnect between the aims and pedagogies of ECE and the increasingly influential de-contextualised discourses concerning ranking, performance and outcomes, as espoused by the OECD IELS project. Using evidence from three diverse Portuguese ECE settings, we illustrate how conceptual understandings of democracy in each school closely reflected the individual school philosophies. We discuss how the dampening of localised realities, for example, through standardisation and de-contextualisation, could lead to a democratic deficit enabled by discourses which displace the purpose, complexity and subjectivity of ECE policy and practice.

Published
2019
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