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443 results on '"Marc Jacobs"'

1. Current state of data stewardship tools in life science

Author

Anna Aksenova, Anoop Johny, Tim Adams, Phil Gribbon, Marc Jacobs, and Martin Hofmann-Apitius

Subjects
data stewardship tools, FAIR, research data repositories, data sharing, literature review, data interoperability, Information technology, T58.5-58.64
Abstract

In today's data-centric landscape, effective data stewardship is critical for facilitating scientific research and innovation. This article provides an overview of essential tools and frameworks for modern data stewardship practices. Over 300 tools were analyzed in this study, assessing their utility, relevance to data stewardship, and applicability within the life sciences domain.

Published
2024
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2. Rationalism in the face of GPT hypes: Benchmarking the output of large language models against human expert-curated biomedical knowledge graphs

Author

Negin Sadat Babaiha, Sathvik Guru Rao, Jürgen Klein, Bruce Schultz, Marc Jacobs, and Martin Hofmann-Apitius

Subjects
Large language models (LLMs), Natural language processing (NLP), Biomedical text mining, Biomedical knowledge graphs, Biological expression language (BEL), Science (General), Q1-390
Abstract

Biomedical knowledge graphs (KGs) hold valuable information regarding biomedical entities such as genes, diseases, biological processes, and drugs. KGs have been successfully employed in challenging biomedical areas such as the identification of pathophysiology mechanisms or drug repurposing. The creation of high-quality KGs typically requires labor-intensive multi-database integration or substantial human expert curation, both of which take time and contribute to the workload of data processing and annotation. Therefore, the use of automatic systems for KG building and maintenance is a prerequisite for the wide uptake and utilization of KGs. Technologies supporting the automated generation and updating of KGs typically make use of Natural Language Processing (NLP), which is optimized for extracting implicit triples described in relevant biomedical text sources. At the core of this challenge is how to improve the accuracy and coverage of the information extraction module by utilizing different models and tools. The emergence of pre-trained large language models (LLMs), such as ChatGPT which has grown in popularity dramatically, has revolutionized the field of NLP, making them a potential candidate to be used in text-based graph creation as well. So far, no previous work has investigated the power of LLMs on the generation of cause-and-effect networks and KGs encoded in Biological Expression Language (BEL). In this paper, we present initial studies towards one-shot BEL relation extraction using two different versions of the Generative Pre-trained Transformer (GPT) models and evaluate its performance by comparing the extracted results to a highly accurate, manually curated BEL KG curated by domain experts.

Published
2024
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3. Effects of mobile phone electromagnetic fields on brain waves in healthy volunteers

Author

Johan N. van der Meer, Yke B. Eisma, Ronald Meester, Marc Jacobs, and Aart J. Nederveen

Subjects
Medicine, Science
Abstract

Abstract The interaction between biological tissue and electromagnetic fields (EMF) is a topic of increasing interest due to the rising prevalence of background EMF in the past decades. Previous studies have attempted to measure the effects of EMF on brainwaves using EEG recordings, but are typically hampered by experimental and environmental factors. In this study, we present a framework for measuring the impact of EMF on EEG while controlling for these factors. A Bayesian statistical approach is employed to provide robust statistical evidence of the observed EMF effects. This study included 32 healthy participants in a double-blinded crossover counterbalanced design. EEG recordings were taken from 63 electrodes across 6 brain regions. Participants underwent a measurement protocol comprising two 18-min sessions with alternating blocks of eyes open (EO) and eyes closed (EC) conditions. Group 1 (n = 16) had EMF during the first session and sham during the second session; group 2 (n = 16) had the opposite. Power spectral density plots were generated for all sessions and brain regions. The Bayesian analysis provided statistical evidence for the presence of an EMF effect in the alpha band power density in the EO condition. This measurement protocol holds potential for future research on the impact of novel transmission protocols.

Published
2023
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4. A natural language processing system for the efficient updating of highly curated pathophysiology mechanism knowledge graphs

Author

Negin Sadat Babaiha, Hassan Elsayed, Bide Zhang, Abish Kaladharan, Priya Sethumadhavan, Bruce Schultz, Jürgen Klein, Bruno Freudensprung, Vanessa Lage-Rupprecht, Alpha Tom Kodamullil, Marc Jacobs, Stefan Geissler, Sumit Madan, and Martin Hofmann-Apitius

Subjects
Knowledge graphs, Relation extraction, Natural language processing, Biomedical text mining, Biological expression language (BEL), Human brain pharmacome (HBP), Science (General), Q1-390
Abstract

Background: Biomedical knowledge graphs (KG) have become crucial for describing biological findings in a structured manner. To keep up with the constantly changing flow of knowledge, their embedded information must be regularly updated with the latest findings. Natural language processing (NLP) has created new possibilities for automating this upkeep by facilitating information extraction from free text. However, due to annotated and labeled biomedical data limitations, the development of completely autonomous information extraction systems remains a substantial scientific and technological hurdle. This study aims to explore methodologies best suited to support the automatic extraction of causal relationships from biomedical literature with the aim of regular and rapid updating of disease-specific pathophysiology mechanism KGs. Methods: Our proposed approach first searches and retrieves PubMed abstracts using the desired terms and keywords. The extension corpora are then passed through the NLP pipeline for automatic information extraction. We then identify triples representing cause-and-effect relationships and encode this content using the Biological Expression Language (BEL). Finally, domain experts perform an analysis of the completeness, relevance, accuracy, and novelty of the extracted triples. Results: In our test scenario, which is focused on the KG regarding the phosphorylation of the Tau protein, our pipeline successfully contributed novel data, which was then subsequently used to update the KG leading to the identification of six additional upstream regulators of Tau phosphorylation. Conclusion: Here, it is demonstrated that the NLP-based workflow we created is capable of rapidly updating pathophysiology mechanism graphs. As a result, production-scale, semi-automated updating of pre-existing, curated mechanism graphs is enabled.

Published
2023
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5. Curating, Collecting, and Cataloguing Global COVID-19 Datasets for the Aim of Predicting Personalized Risk

Author

Sepehr Golriz Khatami, Astghik Sargsyan, Maria Francesca Russo, Daniel Domingo-Fernández, Andrea Zaliani, Abish Kaladharan, Priya Sethumadhavan, Sarah Mubeen, Yojana Gadiya, Reagon Karki, Stephan Gebel, Ram Kumar Ruppa Surulinathan, Vanessa Lage-Rupprecht, Saulius Archipovas, Geltrude Mingrone, Marc Jacobs, Carsten Claussen, Martin Hofmann-Apitius, and Alpha Tom Kodamullil

Subjects
COVID-19, data catalogue, personalized risk model, predictive models, Bibliography. Library science. Information resources
Abstract

Although hundreds of datasets have been published since the beginning of the coronavirus pandemic, there is a lack of centralized resources where these datasets are listed and harmonized to facilitate their applicability and uptake by predictive modeling approaches. Firstly, such a centralized resource provides information about data owners to researchers who are searching datasets to develop their predictive models. Secondly, the harmonization of the datasets supports simultaneously taking advantage of several similar datasets. This, in turn, does not only ease the imperative external validation of data-driven models but can also be used for virtual cohort generation, which helps to overcome data sharing impediments. Here, we present that the COVID-19 data catalogue is a repository that provides a landscape view of COVID-19 studies and datasets as a putative source to enable researchers to develop personalized COVID-19 predictive risk models. The COVID-19 data catalogue currently contains over 400 studies and their relevant information collected from a wide range of global sources such as global initiatives, clinical trial repositories, publications, and data repositories. Further, the curated content stored in this data catalogue is complemented by a web application, providing visualizations of these studies, including their references, relevant information such as measured variables, and the geographical locations of where these studies were performed. This resource is one of the first to capture, organize, and store studies, datasets, and metadata related to COVID-19 in a comprehensive repository. We believe that our work will facilitate future research and development of personalized predictive risk models for COVID-19.

Published
2024
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6. Automated pose estimation reveals walking characteristics associated with lameness in broilers

Author

István Fodor, Malou van der Sluis, Marc Jacobs, Britt de Klerk, Aniek C. Bouwman, and Esther D. Ellen

Subjects
computer vision, gait score, broiler, DeepLabCut, precision phenotyping, Animal culture, SF1-1100
Abstract

ABSTRACT: Walking ability of broilers can be improved by selective breeding, but large-scale phenotypic records are required. Currently, gait of individual broilers is scored by trained experts, however, precision phenotyping tools could offer a more objective and high-throughput alternative. We studied whether specific walking characteristics determined through pose estimation are linked to gait in broilers. We filmed male broilers from behind, walking through a 3 m × 0.4 m (length × width) corridor one by one, at 3 time points during their lifetime (at 14, 21, and 33 d of age). We used a deep learning model, developed in DeepLabCut, to detect and track 8 keypoints (head, neck, left and right knees, hocks, and feet) of broilers in the recorded videos. Using the keypoints of the legs, 6 pose features were quantified during the double support phase of walking, and 1 pose feature was quantified during steps, at maximum leg lift. Gait was scored on a scale from 0 to 5 by 4 experts, using the videos recorded on d 33, and the broilers were further classified as having either good gait (mean gait score ≤2) or suboptimal gait (mean gait score >2). The relationship of pose features on d 33 with gait was analyzed using the data of 84 broilers (good gait: 57.1%, suboptimal gait: 42.9%). Birds with suboptimal gait had sharper hock joint lateral angles and lower hock-feet distance ratios during double support on d 33, on average. During steps, relative step height was lower in birds with suboptimal gait. Step height and hock-feet distance ratio showed the largest mean deviations in broilers with suboptimal gait compared to those with good gait. We demonstrate that pose estimation can be used to assess walking characteristics during a large part of the productive life of broilers, and to phenotype and monitor broiler gait. These insights can be used to understand differences in the walking patterns of lame broilers, and to build more sophisticated gait prediction models.

Published
2023
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7. Association of body mass index with outcomes in patients with newly diagnosed atrial fibrillation: GARFIELD-AF

Author

Daniela Poli, Sophie Testa, Corrado Lodigiani, Toon Wei Lim, Kevin Jones, Kangning Chen, Hui Li, Hilary Pinnock, Grzegorz Bilo, Hack-Lyoung Kim, Andrew Murray, Bernard J Gersh, Kurt Huber, Robin Fox, Sarah Davies, James Rogers, Morten Schou, Xin Li, Vira Tseluyko, Sergey Popov, Rajeev Gupta, Grzegorz Opolski, Preeti Pandya, Bronte Ayres, Milan Gupta, Peter Hutchinson, Phil Simmons, Andrew Gallagher, Michel Galinier, Franck Paganelli, Jens Kilian, Adam Blenkhorn, Mohamed Ibrahim, Fernando Lanas, Karen Pieper, Eivind Berge, M Clark, Agneta Andersson, Karim Ladha, Bijoy Sinha, Torstein Hole, Dan Atar, Hywel Jones, R Smith, Andrew Ross, Emmanuel Ellie, Paul Evans, Yong Wang, Hiroshi Ono, Tadashi Nakamura, Paul MacDonald, Stephen Rogers, Igor Sibon, Simon Dobson, David Fitzmaurice, Jiyan Chen, Neil Roberts, Pierre Amarenco, Nigel Hart, Giancarlo Agnelli, Georges Mairesse, Pekka Raatikainen, Oleg Sychov, Yasuyuki Suzuki, Bo Liu, Mathieu Zuber, John French, Yuejin Yang, Myeong-Chan Cho, Julian Thompson, Michael Stokes, John W Eikelboom, Mark Richardson, John Matthews, Will Murdoch, Jean-Philippe Neau, Freek Verheugt, Ajay K Kakkar, Giuseppe Ambrosio, Marcin Gruchała, Keith A A Fox, Sunil Kumar, Ruiping Zhao, Patrick Carroll, Masanori Kaneko, Thanh Phan, Ping Yang, Sung-Won Jang, Claire Jones, Mårten Rosenqvist, Johan Engdahl, Debabrata Roy, John Cairns, Ping Chen, Michael Olsen, Paul Angaran, David Russell, Helena Dominguez, Béla Merkely, Joseph Berlingieri, James Bennett, Hugo ten Cate, Hiroshi Yamaguchi, Masahiro Minamoto, Hiroyuki Oda, Toshihiko Shiraiwa, Jonathan Webster, Yukihiro Koretsune, Kotaro Obunai, R Thompson, Yong Seog Oh, Giuliana Guazzaloca, Giuliana Martini, Marc Bonnefoy, Michael Cox, András Nagy, Kazuki Sato, Richard Davies, Daisuke Ikeda, Susumu Suzuki, Hiroki Teragawa, Koji Matsushita, Ying Guo, Catherine Neden, Mark Pugsley, Simon Cartwright, Polly Jacobs, Xiaoshu Cheng, Daniel Nishijima, Sylvia Haas, Vinay Kumar, Saverio Virdone, Jean-Pierre Bassand, Samuel Z Goldhaber, Shinya Goto, Frank Misselwitz, Alexander G G Turpie, Alison Macleod, Karen Forshaw, Mark Boon, Stephen Miller, Simon Wetherell, Moustafa Moustafa, Gaetano Serviddio, Renato Lopes, Kazuo Takei, Hiroaki Nishioka, Mykola Stanislavchuk, C Ramesh, R Kamath, Stuart J Connolly, Nooshin Bazargani, Kevin Douglas, Werner Hacke, Gloria Kayani, Ali Oto, Hiroshi Watanabe, Walter Hermans, Kazuya Murata, Christian Fielder Camm, Marco Moia, Niraj Sharma, Jaeyoung Kim, Walter Abhayaratna, Andriy Yagensky, Hosen Kiat, Wilhelm Haverkamp, Yang Jiao, Hitoshi Kato, Jindrich Spinar, Daniel Theodoro, Philip Cooke, Paolo Golino, Tetsuro Yoshida, Prakash Chandwani, Christine A'Court, Brian Ramjattan, Torbjørn Øien, Toshiyuki Kobayashi, Richard West, Petr Jansky, Seil Oh, Jan Steffel, Martin van Eickels, Hyung-Wook Park, Nam-Ho Kim, Søren Rasmussen, Kazuo Suzuki, David Colquhoun, Hiroshi Ando, Simon Franklin, Tae-Joon Cha, Sang Cheol Bae, Guosheng Fu, Yoshihiro Saito, Heinz Drexel, Michel Martelet, Joseph Mouallem, Nicolas Delarche, Sylvain Destrac, Neil Macey, Andreas Kopf, Masayuki Nakano, Olga Barbarash, Takeshi Inoue, Taro Minagawa, Weihua Li, John Eikelboom, Hiroshi Kubo, Lars Andersson, D Burns, Andrea Podczeck-Schweighofer, Megumi Okada, Massimo Volpe, Takuma Aoyama, Karsten Mueller, Carlos Astudillo, Hiroshi Takeda, Peter Mayer, Jung Hoon Sung, Dinesh Jain, Jung Han Yoon, Alessandro Capucci, Dongryeol Ryu, Kelvin Wong, Hong Euy Lim, Xiaowei Yan, Yusheng Zhao, Yuehui Yin, YUKIHIRO SETA, Taek Jong Hong, MASAKI SHIMOYAMA, Dayi Hu, Junichi Minami, Yuriy Mostovoy, David Foo, Ramazan Topsakal, Zhi-Cheng Jing, Dipen Shah, Kenichi Yamamoto, David Coulshed, Olivier Piot, Ramón Corbalán, Silva Severi, Waldemar Myszka, Mehmet Birhan Yilmaz, Gi-Byoung Nam, Jun Kim, Harald Darius, Jan-Erik Karlsson, PETER VANDERGOTEN, Nasser Taha, Shuta Toru, Jörn Nielsen, Tsutomu Takagi, Koji Higuchi, Steen Husted, Tomohiro Katsuya, Frank Cools, Iveta Petrova, Songkwan Silaruks, GÜNTER LEHMANN, Frederic Casassus, Bernard Crousillat, Bernard Doucet, Jean-Joseph Muller, Grzegorz Raczak, Kazuyuki Saito, Anders Ostrem, Chi Keong Ching, KUNIHIKO YAMAMOTO, John Camm, Carmine Mazzone, Jaemin Shim, Jadwiga Nessler, Jan Vercammen, Marc Delforge, Chong-Jin Kim, Pierre Nazeyrollas, Louise Lumley, Paul Roome, Helen Stoddart, Mark Rickenbach, Paul Mullen, Noriyuki Nakanishi, Gordon Irvine, Paul Conn, Kurt Lenz, Richard Coates, E Fisher, Warwick Coulson, Jiri Lastuvka, Pablo García Pavía, P Jhittay, Philip Saunders, Peter Bernhardt, Wanwarang Wongcharoen, Kentaro Yamamoto, Hector Lucas Luciardi, Harry Gibbs, Marianne Brodmann, Jørn Dalsgaard Nielsen, Hany Ragy, Matyas Keltai, Jitendra Pal Singh Sawhney, Janina Stepinska, Elizaveta Panchenko, Barry Jacobson, Xavier Viñolas, Pantep Angchaisuksiri, Alex Parkhomenko, Huaiqin Zhang, Shiping Cao, Daowen Wang, Guizhou Tao, Yingmin Chen, Shenghu He, Tongguo Wu, Moshui Chen, Longgen Xiong, Praveen Jadhavm, Raghava Sarma, Govind Kulkarni, Rasesh Atulbhai Pothiwala, Mohanan Padinhare Purayil, Kamaldeep Chawla, Veerappa Annasaheb Kothiwale, Bagirath Raghuraman, Vinod Madan Vijan, Jitendra Sawhney, Ganapathi Bantwal, Aziz Khan, Ramdhan Meena, Manojkumar Chopada, Sunitha Abraham, Vikas Bisne, Govindan Vijayaraghavan, Rajashekhar Durgaprasad, Kartikeya Bhargava, Udigala Madappa Nagamalesh, Rajeeve Kumar Rajput, Seishu Kanamori, Koichiro Kumagai, Yosuke Katsuda, Keiki Yoshida, Fumitoshi Toyota, Yuji Mizuno, Ikuo Misumi, Hiroo Noguchi, Shinichi Ando, Tetsuro Suetsugu, Susumu Adachi, Kei Chiba, Hiroaki Norita, Makoto Tsuruta, Takeshi Koyanagi, Takayuki Higashi, Shiro Azakami, Shinichiro Komaki, Kenshi Kumeda, Takashi Murayama, Jun Matsumura, Yurika Oba, Ryuji Sonoda, Kazuo Goto, Kotaro Minoda, Yoshikuni Haraguchi, Hisakazu Suefuji, Hiroo Miyagi, Tsugihiro Nakamura, Hidekazu Nandate, Ryuji Zaitsu, Yoshihisa Fujiura, Akira Yoshimura, Hiroyuki Numata, Jun Ogawa, Yasuyuki Kamogawa, Kinshiro Murakami, Yutaka Wakasa, Masanori Yamasawa, Hiromitsu Maekawa, Sumihisa Abe, Hajime Kihara, Satoru Tsunoda, Katsumi Saito, Hiroki Tachibana, Ichiro Oba, Takashi Kuwahata, Satoshi Higa, Masamichi Gushiken, Takuma Eto, Hidetoshi Chibana, Kazuaki Fujisawa, Yuhei Shiga, Hirokuni Sumi, Toshihisa Nagatomo, Yoshihiko Atsuchi, Toshiro Nagoshi, Kazuhisa Sanno, Fumihiro Hoshino, Naoto Yokota, Masahiro Kameko, Toshifumi Tabuchi, Munesumi Ishizawa, Yoshitake Fujiura, Taku Seto, Tetsu Iwao, Norio Ishioka, Koichi Oshiro, Keizo Tsuchida, Yutaka Hatori, Motoshi Takeuchi, Hiroto Takezawa, Shinjiro Nagano, Masaaki Iwaki, Yuichiro Nakamura, Naomasa Miyamoto, Toshifumi Taguchi, Ko Ashida, Naoto Yoshizawa, Jun Agata, Seishiro Matsukawa, Osamu Arasaki, Shuji Fukuoka, Hirofumi Murakami, Kazuya Mishima, Yoshiki Hata, Ichiro Sakuma, Ichiro Takamura, Mitsuyuki Akutsu, Toshihide Unoki, Yoshinori Go, Makoto Ikemura, Shoji Morii, Shigeru Marusaki, Hideo Doi, Mitsuru Tanaka, Takaaki Kusumoto, Shigeo Kakinoki, Chiga Ogurusu, Masami Nakatsuka, Yutaka Kitami, Yoichi Nakamura, Hiroshi Oda, Rikimaru Oyama, Masato Ageta, Teruaki Mita, Kazuhiko Nagao, Takafumi Mito, Mitsunori Abe, Masako Fujii, Makoto Okawa, Tsuneo Fujito, Toshiya Taniguchi, Tenei Ko, Mizuho Imamaki, Masahiro Akiyama, Takashi Ueda, Hironori Odakura, Masahiko Inagaki, Yoshiki Katsube, Atsuyuki Nakata, Shinobu Tomimoto, Mitsuhiro Shibuya, Kenichiro Ito, Masahiro Matsuta, Motoyuki Ishiguro, Masamichi Wada, Hiroaki Mukawa, Masato Mizuguchi, Fumio Okuda, Teruaki Kimura, Kuniaki Taga, Masaaki Techigawara, Morio Igarashi, Toshihiko Seo, Shinya Hiramitsu, Hiroaki Hosokawa, Mitsumoto Hoshiai, Michitaka Hibino, Koichi Miyagawa, Hideki Horie, Nobuyoshi Sugishita, Yukio Shiga, Akira Soma, Kazuo Neya, Kunio Akahane, Saori Matsui, Hirofumi Kanda, Shiro Nagasaka, Atsushi Taguchi, Akiko Miyashita, Hiroki Sasaguri, Jin Nariyama, Taketo Hatsuno, Takash Iwase, Kazuya Kawai, Tomobumi Kotani, Tsuyoshi Tsuji, Hirosumi Sakai, Kiyoshi Nishino, Kenichi Ikeda, Kazuo Maeda, Tomohiro Shinozuka, Koichi Kawakami, Hiromichi Kitazumi, Mamoru Hamaoka, Jisho Kojima, Akitoshi Sasaki, Yoshihiro Tsuchiya, Tetsuo Betsuyaku, Masaaki Honda, Koichi Hasegawa, Takao Baba, Kazuaki Mineoi, Toshihiko Koeda, Kunihiko Hirasawa, Toshihide Kumazaki, Akira Nakagomi, Eiji Otaki, Takashi Shindo, Hiroyoshi Hirayama, Chikako Sugimoto, Takashi Yamagishi, Ichiro Mizuguchi, Kazunori Sezaki, Isamu Niwa, Ken Takenaka, Osamu Iiji, Koichi Taya, Hitoshi Kitazawa, Samu Ueda, Hirokazu Kakuda, Takuya Ono, Seizo Oriso, Junya Kamata, Toshihiko Nanke, Itaru Maeda, Yoshifusa Matsuura, Yasuyuki Maruyama, Hajime Horie, Tetsutaro Kito, Hiroshi Asano, Masaichi Nakamura, Takashi Washizuka, Tomoki Yoshida, Masato Sawano, Shinichi Arima, Hidekazu Arai, Hisanori Shinohara, Hiroyuki Takai, Nobufusa Furukawa, Akira Ota, Kenji Aoki, Taku Yamamoto, Takeaki Kasai, Shunji Suzuki, Shu Suzuki, Nitaro Shibata, Masayuki Watanabe, Yosuke Nishihata, Toru Arino, Masaki Okuyama, Tetsushi Wakiyama, Tomoko Kato, Yasuo Sasagawa, Takeshi Tana, Yoshihito Hayashi, Shinichi Hirota, Yukihiko Abe, Hirohide Uchiyama, Shuichi Tohyo, Naoto Hanazono, Seiichi Miyajima, Hisashi Shimono, Yasunobu Shozawa, Yawara Niijima, Osamu Murai, Hideko Inaba, Katsumasa Nomura, Masatsugu Nozoe, Toshiyuki Furukawa, Nobuhisa Ito, Shunichi Nagai, Kiyoharu Sato, Shiro Nakahara, Yujin Shimoyama, Naoko Ohara, Teruhiko Kozuka, Hideaki Okita, Masato Endo, Tsutomu Goto, Makoto Hirose, Emiko Nagata, Toshizumi Mori, Shuichi Seki, Katsuhiro Okamoto, Osamu Moriai, Yoko Emura, Tsuyoshi Fukuda, Haruhiko Date, Shuichi Kawakami, Sho Nagai, Yuya Ueyama, Tetsuro Fudo, Mitsuru Imaizumi, Takuo Ogawa, Shunsuke Take, Hideo Ikeda, Norihiko Sakamoto, Kiyomitsu Ikeoka, Nobuo Wakaki, Masatake Abe, Junji Doiuchi, Tetsuya Kira, Masato Tada, Ken Tsuzaki, Naoya Miura, Yasuaki Fujisawa, Wataru Furumoto, Akinori Fujisawa, Ryosai Nakamura, Hiroyasu Komatsu, Rei Fujiki, Shuichi Kawano, Keijiro Nishizawa, Yoji Kato, Junya Azuma, Kiyoshi Yasui, Toshio Amano, Yasuhiro Sekine, Tatsuo Honzawa, Yuichiro Koshibu, Yasuhide Sakamoto, Shingo Miyaguchi, Kojuro Morishita, Yasuko Samejima, Toyoshi Sasaki, Fumiko Iseki, Hiroshi Kano, Yoichi Takagi, Yoko Onuki Pearce, Takayuki Fukui, Toru Nakayama, Hideaki Kanai, Yoshiyuki Kawano, Tetsuji Ino, Hironori Miyoshi, Yasufumi Miyamoto, Masahito Shigekiyo, Shimato Ono, Yutaka Okamoto, Satoshi Ubukata, Kojiro Kodera, Tatsuo Oriuchi, Naoki Matsumoto, Koichi Inagaki, Atsushi Iseki, Tomohiro Yoshida, Toshihiro Goda, Tsukasa Katsuki, Atsushi Sato, Etsuo Mori, Toshio Tsubokura, Hiroshi Shudo, Shunichi Fujimoto, Yoshiyuki Furukawa, Hiroshi Hosokawa, Jun Narumi, Kiichiro Yamamoto, Masaki Owari, Takuya Inakura, Takafumi Anno, Kazuyuki Shirakawa, Tan Yuyang, Hui Nam Park, Woo-Shik Kim, HyeYoung Lee, Dae Hyeok Kim, Dae-Kyeong Kim, Dong Ju Choi, Hui-Kyung Jeon, Dong-Gu Shin, Sang Weon Park, Hoon Ki Park, Sang-Jin Han, Young Keun On, JaeJin Kwak, Seong Hoon Park, Kee-Sik Kim, Byung Chun Jung, Gyo-Seung Hwang, Sakda Rungaramsin, Peerapat Katekangplu, Porames Khunrong, Thanita Bunyapipat, Pinij Kaewsuwanna, Khanchai Siriwattana, Waraporn Tiyanon, Supalerk Pattanaprichakul, Khanchit Likittanasombat, Doungrat Cholsaringkarl, Warangkana Boonyapisit, Sirichai Cheewatanakornkul, Pisit Hutayanon, Seksan Chawanadelert, Pairoj Chattranukulchai, Boonsert Chatlaong, Yingsak Santanakorn, Khompiya Kanokphatcharakun, Piya Mongkolwongroj, Sasivimon Jai-Aue, Ongkarn Komson, Armagan Altun, Ali Aydinlar, Zeki Ongen, Sadik Acikel, Durmus Yildiray Sahin, Ozcan Yilmaz, Hasan Pekdemir, Mesut Demir, Murat Sucu, Levent Sahiner, Murat Ersanli, Ertugrul Okuyan, Dursun Aras, Florencia Rolandi, Adrian Cesar Ingaramo, Gustavo Alberto Sambadaro, Vanina Fernandez Caputi, Hector Luciardi, Sofia Graciela Berman, Pablo Dragotto, Andres Javier Kleiban, Nestor Centurion, Ricardo Dario Dran, Javier Egido, Matias Jose Fosco, Victor Alfredo Sinisi, Luis Rodolfo Cartasegna, Oscar Gomez Vilamajo, Jose Luis Ramos, Sonia Sassone, Gerardo Zapata, Diego Conde, Guillermo Giacomi, Alberto Alfredo Fernandez, Mario Alberto Berli, Fabian Ferroni, Jefferson Jaber, Luciana Vidal Armaganijan, André Steffens, José Márcio Ribeiro, Marcelo Silveira Teixeira, Paulo Rossi, Leonardo Pires, Daniel Moreira, Luiz Bodanese, Marcelo Westerlund Montera, Jamil Abdalla Saad, Euler Roberto Manenti, Alexandre Negri, Carlos Moncada, Dalton Precoma, Fernando Roquette, Gilmar Reis, Estêvão Lanna Figueiredo, Roberto Vieira Botelho, Helius Carlos Finimundi, Adriano Kochi, Fábio Alban, Rogério Tadeu Tumelero, Lilia Maia, Humberto Montecinos, Martín Larico Gómez, Carlos Conejeros, Patricio Marin Cuevas, Alejandro Forero, Claudio Bugueño Gutiérrez, Juan Aguilar, Sergio Potthoff Cardenas, German Eggers, Cesar Houzvic, Carlos Rey, Germán Arriagada, Gustavo Charme Vilches, Raul Leal Cantu, Ricardo Cabrera Jardines, Nilda Espinola Zavaleta, Enrique Lopez Rosas, Gerardo Pozas, Ernesto Cardona Muñoz, Norberto Matadamas Hernandez, Adolfo Leyva Rendon, Norberto Garcia Hernandez, David Lopez Villezca, Carlos Hernandez Herrera, Rodolfo Gaona Rodriguez, Efrain Villeda Espinosa, David Flores Martinez, Jose Velasco Barcena, Omar Fierro Fierro, Ignacio Rodriguez Briones, Humberto Alvarez Lopez, Rafael Olvera Ruiz, Roxana Reyes Sanchez, Roberto Arriaga Nava, Pedro Fajardo Campos, Mario Benavides Gonzalez, Claus Hagn, Johannes Foechterle, Michael Winkler, Bruno Schneeweiss, Alfons Gegenhuber, Wilfried Lang, Sabine Eichinger-Hasenauer, Peter Kaserer, Josef Sykora, Heribert Rasch, Bernhard Strohmer, Luc Capiau, Geert Vervoort, Bart Wollaert, Geert Hollanders, Dirk Faes, Yohan Balthazar, Olivier Xhaet, Harry Striekwold, John Thoeng, Kurt Hermans, Wim Anné, Ivan Blankoff, Michel Beutels, Stefan Verstraete, Philippe Purnode, Pascal Godart, Tim Boussy, Philippe Desfontaines, Alex Heyse, Joeri Voet, Eva Zidkova, Rudolf Spacek, Vilma Machova, Ondrej Ludka, Josef Olsr, Lubos Kotik, Blazej Racz, Richard Ferkl, Jan Hubac, Ilja Kotik, Zdenek Monhart, Hana Burianova, Ondrej Jerabek, Jana Pisova, Vratislav Dedek, Michaela Honkova, Petr Podrazil, Petr Reichert, Miroslav Novak, Vaclav Durdil, Katarina Plocova, Ulrik Hintze, Næstved Sygehus, Arne Bremmelgaard, John Markenvard, Jan Børger, Jorgen Solgaard, Ebbe Eriksen, Thomas Løkkegaard, Michael Bruun, Jacob Mertz, Joël Ohayon, Yannick Gottwalles, Philippe Loiselet, Mohamed Bassel Koujan, André Marquand, Jean-Pierre Cebron, Maxime Guenoun, Dominique Guedj-Meynier, A G Lokesh, James Kadouch, Pierre-Yves Fournier, Jean-Pierre Huberman, Nestor Lemaire, Gilles Rodier, Xavier Vandamme, Marie Hélène Mahagne, Antoine Mielot, Jean-Baptiste Churet, Vincent Navarre, Frederic Sellem, Gilles Monniot, Jean-Paul Boyes, Désiré Obadia, Etienne Bearez, Jean Philippe Brugnaux, Alain Fedorowsky, Jean-Baptiste Berneau, Frédéric Chemin, Sebastien Schellong, Georg Koeniger, Uwe Gerbaulet, Bernd-Thomas Kellner, Thomas Schaefer, Jan Purr, Enno Eißfeller, Heinz-Dieter Zauzig, Peter Riegel, Christoph Axthelm, Gerd-Ulrich Heinz, Holger Menke, Andreas Pustelnik, Stefan Zutz, Wolfgang Eder, Guenter Rehling, Dirk Glatzel, Norbert Ludwig, Petra Sandow, Henning Wiswedel, Cosmas Wildenauer, Steffen Schoen, Toralf Schwarz, Adyeri Babyesiza, Maximilian Kropp, Hans-Hermann Zimny, Friedhelm Kahl, Andreas Caspar, Sabine Omankowsky, Torsten Laessig, Hermann-Josef Hartmann, Hans-Walter Bindig, Gunter Hergdt, Dietrich Reimer, Joachim Hauk, Holger Michel, Praxis Dres, Werner Erdle, Wilfried Dorsch, Janna Dshabrailov, Karl-Albrecht Rapp, Reinhold Vormann, Thomas Mueller, Uwe Horstmeier, Volker Eissing, Heinz Hey, Heinz Leuchtgens, Volker Lilienweiss, Heiner Mueller, Christian Schubert, Herrmann Lauer, Thomas Buchner, Gunter Brauer, Susanne Kamin, Sylvia Baumbach, Muwafeg Abdel-Qader, Hans-Holger Ebert, Carsten Schwencke, Laszlo Karolyi, Britta Sievers, Jens-Uwe Roehnisch, Andras Vertes, Gabor Szantai, Andras Matoltsy, Nikosz Kanakaridisz, Zoltan Boda, Erno Kis, Balazs Gaszner, Ferenc Juhasz, Gizella Juhasz, Sandor Kancz, Zoltan Laszlo, Zsolt May, Ebrahim Noori, Tamas Habon, Peter Polgar, Gabriella Szalai, Sandor Vangel, Gabriella Engelthaler, Judit Ferenczi, Mihaly Egyutt, Leone Maria Cristina, Eros Tiraferri, Rita Santoro, Teresa Maria Caimi, Maria Tessitori, Roberto Cappelli, Roberto Quintavalla, Franco Cosmi, Raffaele Fanelli, Vincenzo Oriana, Raffaele Reggio, Roberto Santi, Leonardo Pancaldi, Jorge Salerno Uriate, Flavia Lillo, Enrico Maria Pogliani, Michele Accogli, Antonio Mariani, Mauro Feola, Arturo Raisaro, Luciano Fattore, Andrea Mauric, Fabrizio Germini, Luca Tedeschi, Maria Settimi, Sergio Nicoli, Paolo Ricciarini, Antonio Argena, Paolo Ronchini, Claudio Bulla, Filippo Tradati, Maria Grazia Bongiorni, Enrico Salomone, Claudio Tondo, Saverio Iacopino, Andreas Lucassen, Henk Adriaansen, Maarten Bongaerts, Mathijs Pieterse, Johannes Herrman, Pieter Hoogslag, Cees Buiks, Per Anton Sirnes, Erik Gjertsen, Knut Erga, Arne Hallaråker, Gunnar Skjelvan, Beraki Ghezai, Arne Svilaas, Peter Christersson, Svein Høegh Henrichsen, Jan Erik Otterstad, Jan Berg-Johansen, Andrzej Gieroba, Malgorzata Biedrzycka, Michal Ogorek, Beata Wozakowska-Kaplon, Krystyna Loboz-Grudzien, Jerzy Kuzniar, Roman Zaluska, Jaroslaw Hiczkiewicz, Lucyna Swiatkowska-Byczynska, Lech Kucharski, Piotr Minc, Maciej Olszewski, Grzegorz Kania, Malgorzata Krzciuk, Zbigniew Lajkowski, Bozenna Ostrowska-Pomian, Jerzy Lewczuk, Elzbieta Zinka, Agnieszka Karczmarczyk, Malgorzata Chmielnicka-Pruszczynska, Iwona Wozniak-Skowerska, Marek Bronisz, Marcin Ogorek, Grazyna Glanowska, Piotr Ruszkowski, Grzegorz Skonieczny, Ryszard Sciborski, Boguslaw Okopien, Piotr Kukla, Krzysztof Galbas, Krzysztof Cymerman, Jaroslaw Jurowiecki, Pawel Miekus, Stanislaw Mazur, Roman Lysek, Jacek Baszak, Teresa Rusicka-Piekarz, Ewa Domanska, Jozef Lesnik, Gadel Kamalov, Dmitry Belenky, Liudmila Egorova, Alexander Khokhlov, Eduard Yakupov, Dmitry Zateyshchikov, Olga Miller, Evgeniy Mazur, Konstantin Zrazhevskiy, Tatyana Novikova, Yulia Moiseeva, Elena Polkanova, Konstantin Sobolev, Maria Rossovskaya, Yulia Shapovalova, Alla Kolesnikova, Konstantin Nikolaev, Oksana Zemlianskaia, Anna Zateyshchikova, Victor Kostenko, Maria Poltavskaya, Anton Edin, Elena Aleksandrova, Oksana Drapkina, Alexander Vishnevsky, Oleg Nagibovich, Petr Chizhov, Svetlana Rachkova, Mikhail Sergeev, Borys Kurylo, Alexey Ushakov, Pere Alvarez Garcia, Luis Tercedor Sanchez, Salvador Tranche Iparraguirre, Pere Toran Monserrat, Emilio Marquez Contreras, Jordi Isart Rafecas, Juan Motero Carrasco, Casimiro Gomez Pajuelo, Angel Grande Ruiz, Jordi Merce Klein, Ines Monte Collado, Herminia Palacin Piquero, Carles Brotons Cuixart, Esther Fernandez Escobar, Cecilia Corros Vicente, Manuel Vida Gutierrez, Francisco Epelde Gonzalo, Encarnacion Martinez Navarro, Maria Barreda Gonzalez, Jose Iglesias Sanmartin, Mercedes Jimenez Gonzalez, Juan Herreros Melenchon, Tomas Ripoll Vera, Manuel Jimenez Navarro, Maria Vazquez Caamano, Gonzalo Marcos Gomez, Andres Iniguez Romo, Alexander Wirdby, Kerstin Henriksson, Micael Elmersson, Arnor Egilsson, Ulf Börjesson, Gunnar Svärd, Anders Lindh, Lars-Bertil Olsson, Mikael Gustavsson, Lars Benson, Claes Bothin, Ali Hajimirsadeghi, Björn Martinsson, Marianne Ericsson, Åke Ohlsson, Håkan Lindvall, Peter Svensson, Katarina Thörne, Hans Händel, Pyotr Platonov, Fredrik Bernsten, Ingar Timberg, Milita Crisby, Lennart Malmqvist, Jörgen Thulin, Aida Hot-Bjelak, Steen Jensen, Per Stalby, Johann Debrunner, Iurii Rudyk, Oleksandr Karpenko, Svitlana Zhurba, Igor Kraiz, Oleksandr Parkhomenko, Iryna Kupnovytska, Nestor Seredyuk, Oleksiy Ushakov, Olena Koval, Igor Kovalskiy, Yevgeniya Svyshchenko, Susanna Tykhonova, Ivan Fushtey, Naresh Chauhan, Daryl Goodwin, Ramila Patel, Bennett Wong, Alex Cameron, Niranjan Patel, M S Kainth, Gill Pickavance, Joanna McDonnell, Laura Handscombe, Trevor Gooding, Helga Wagner, Catherine Bromham, Shoeb Suryani, Bhupinder Sarai, W Willcock, S Sircar, A Gilliand, Roman Bilas, E Strieder, Anne Wakeman, Graham Kirby, Bhaskhar Vishwanathan, Nigel Bird, John Bisatt, Jennifer Litchfield, Tim Fooks, Richard Kelsall, Neil Paul, Elizabeth Alborough, Michael Aziz, Pete Wilson, Sue Fairhead, Hasan Chowan, Gary Taylor, Dawn Tragen, Matt Parfitt, Claire Seamark, Carolyn Paul, Angus Jefferies, Helen Sharp, Claire Giles, Matthew Bramley, Philip Williams, Jehad Aldegather, William Lumb, Phil Evans, Frances Scouller, Yvette Stipp, Philip Pinney, Paul Wadeson, T Railton, Emyr Davies, Jonathan McClure, Marc Jacobs, Claire Hutton, Keith Butter, Susan Barrow, Helen Little, Ulka Choudhary, Ikram Haq, Paul Ainsworth, Phil Weeks, Jane Eden, Lisa Gibbons, Janet Glencross, K Poland, Conor Mulolland, A Warke, Ian Hodgins, Stephen Vercoe, Jayesh Patel, Amar Ali, Nigel De-Sousa, Mark Danielsen, Purnima Sharma, Sophia Galloway, Charlotte Hawkins, Raife Oliver, Martin Aylward, Mira Pattni, Shahid Ahmad, Catherine Rothwell, Fiaz Choudhary, Sabrina Khalaque, Stephanie Short, Sharon Peters, Amy Butler, Steven Coates, Steve Walton, Diane Shepherd, Toh Wong, Melanie Deacon, David Cornelius, Henry Choi, Jon Sumner, Tim Myhill, Salah Estifanos, Diane Geatch, Justin Wilkinson, Richard Veale, Rob Hirst, Kashif Zaman, Catherine Liley, Rebecca Wastling, Paul McEleny, Andre Beattie, Mike Wong, Chaminda Dooldeniya, Greg Rogers, Rajesh Muvva, Matthew Adam, Nicolas Thomas, Rory Reed, Simon Randfield, Ann Flynn, Andrew Halpin, Louise Lomax, Minnal Nadaph, Iain Munro, Jane Goram, John Shewring, Emma Bowen-Simpkins, Bhuwanendu Singh, Penny Astridge, Philip Thomson, Ron Lehman, Andrei Catanchin, David Eccleston, Peter Blombery, Greg Starmer, Margaret Arstall, Maurits Binnekamp, Astin Lee, Robert Luton, Amritanshu Shekhar Pandey, Stephen Cheung, Rolland Leader, Philippe Beaudry, Félix Ayala-Paredes, John Heath, Germain Poirier, Bradley Schweitzer, Reginald Nadeau, Ripple Dhillon, Tomasz Hruczkowski, Andrea Lavoie, Ratika Parkash, James Cha, Benoit Coutu, Jorge Bonet, Saul Vizel, Sameh Fikry, Ahmed Mowafy, Azza Katta, Mazen Tawfik, Moustafa Nawar, Mohamed Sobhy, Tarek Khairy, Ahmed Abd El-Aziz, Ashraf Reda, Atef Elbahry, Mohamed Setiha, Magdi Elkhadem, Adel El-Etreby, David Kettles, Junaid Bayat, Heidi Siebert, Adrian Horak, Ynez Kelfkens, Riaz Garda, Thayabran Pillay, Michele Guerra, Hendrik Theron, Rikus Louw, Deon Greyling, Pindile Mntla, Siddique Ismail, Fayzal Ahmed, Johannes Engelbrecht, Shambu Maharajh, Veronica Ueckermann, Ghazi Yousef, Munther AlOmairi, Rajan Maruthanayagam, Rupesh Singh, Ahmed Naguib, Amrish Agrawal, Mukesh Nathani, Adel Wassef, Scott Beach, Peter Duffy, Stephen Falkowski, Kevin Ferrick, Miguel Franco, Annette Quick, Vance Wilson, Mark Alberts, Edwin Blumberg, Roddy Canosa, Ted Gutowski, Rodney Ison, Jorge Garcia, Howard Noveck, Pamela Rama, Rajneesh Reddy, Marcus Williams, Keith Ferdinand, Ihsan Haque, Robert Mendelson, Sridevi Pitta, Charles Treasure, Cas Cader, Walter Pharr, Alisha Oropallo, George Platt, Jaspal Gujral, James Welker, Firas Koura, Ajay K. Kakkar, A. John Camm, David A. Fitzmaurice, Keith A.A. Fox, Bernard J. Gersh, Samuel Z. Goldhaber, Lorenzo G. Mantovani, Karen S. Pieper, Alexander G.G. Turpie, Freek W.A. Verheugt, Antonio Carlos PereiraBarretto, Stuart J. Connolly, Jean-Yves Le Heuzey, Jitendra Pal SinghSawhney, Carlos JerjesSánchez Díaz, Hugo Ten Cate, Wael Al Mahmeed, Zhiming Yang Li Xue, A.G. Ravi Shankar, Chiei Takanaka Sen Adachi, Rodolfo AndresAhuad Guerrero, Leonel Adalberto Di Paola, DárioCelestino Sobral Filho, Costantino RobertoFrack Costantini, Weimar Kunz SebbaBarrosodeSouzaem, João David deSouzaNeto, José Carlos MouraJorge, Adalberto MenezesLorga Filho, Carlos Henrique DelCarlo, FernandoAugustoAlves da Costa, Gilson Robertode Araújo, Jose FranciscoKerr Saraiva, João CarlosFerreira Braga, Roberto Álvaro RamosFilho, Cláudio MunhozdaFontoura Tavares, CésarCássio Broilo França, Guido BernardoAranha Rosito, João BatistadeMouraXavierMoraes Junior, Roberto Simõesde Almeida, Ney CarterdoCarmo Borges, LuísGustavo Gomes Ferreira, Benjamin AleckJosehStockins Fernandez, CarlosJerjes Sanchez Diaz, Jesus JaimeIllescas Diaz, Maria GuadalupeRamos Zavala, GuillermoAntonio Llamas Esperón, Manuel delosRios Ibarra, LuisRamon Virgen Carrillo, JuanJose Lopez Prieto, Jose LuisLeiva Pons, Carlos GerardoCantu Brito, EduardoJulianJose Roberto ChuquiureValenzuela, Alberto EstebanBazzoni Ruiz, Oscar MartinLopez Ruiz, Jesus DavidMorales Cerda, Axel De Wolf, Carmela Viitanen, Giovanni Di Minno, Raimondo De Cristofaro, Angelo De Blasio, Maria D'Avino, J.H. Ruiter, Coen van Guldener, P.R. Nierop S.H.K., B.E. Groenemeijer, W. Terpstra, L.V.A. Boersma, Wieslaw Supinski Jaroslaw, Roman Libis Vera Eltishcheva, Maria FernandaLopez Fernandez, Luis MiguelRincon Diaz, Luis FernandoIglesias Alonso, Jose RamonGonzalez Juanatey, Joan Bayo iLlibre, Carlos AlexandreAlmeida Fernandez, Juan JoseMontero Alia, Maria AngelsMoleiro Oliva, Maria delMarRodriguez Alvarez, Maria FeArcocha Torres, Miguel AngelPrieto Diaz, Jan Lindén Centrumkliniken, Juerg H. Beer, Colin Bradshaw Cumberlidge, Daniel Jackson Ben Ward, Nick Hargreaves Ben Frankel, William van Gaal, David O'Donnell, Miranda du Preez, Seif Kamal Abou Seif, Mohamed Gamal El Din, Louis van Zyl, Rehana Loghdey Wessel Oosthuysen, Abdullah Al Naeemi, Ehab M. Esheiba, and W. Michael Kutayli

Subjects
Diseases of the circulatory (Cardiovascular) system, RC666-701
Abstract

Objective While greater body mass index (BMI) is associated with increased risk of developing atrial fibrillation (AF), the impact of BMI on outcomes in newly diagnosed AF is unclear. We examine the influence of BMI on outcomes and whether this is modified by sex and evaluate the effect of non-vitamin K oral anticoagulants (NOACs) in patients with high BMI.Methods GARFIELD-AF is a prospective registry of 52 057 newly diagnosed AF patients. The study population comprised 40 482 participants: 703 underweight (BMI

Published
2022
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8. A method for the rational selection of drug repurposing candidates from multimodal knowledge harmonization

Author

Bruce Schultz, Andrea Zaliani, Christian Ebeling, Jeanette Reinshagen, Denisa Bojkova, Vanessa Lage-Rupprecht, Reagon Karki, Sören Lukassen, Yojana Gadiya, Neal G. Ravindra, Sayoni Das, Shounak Baksi, Daniel Domingo-Fernández, Manuel Lentzen, Mark Strivens, Tamara Raschka, Jindrich Cinatl, Lauren Nicole DeLong, Phil Gribbon, Gerd Geisslinger, Sandra Ciesek, David van Dijk, Steve Gardner, Alpha Tom Kodamullil, Holger Fröhlich, Manuel Peitsch, Marc Jacobs, Julia Hoeng, Roland Eils, Carsten Claussen, and Martin Hofmann-Apitius

Subjects
Medicine, Science
Abstract

Abstract The SARS-CoV-2 pandemic has challenged researchers at a global scale. The scientific community’s massive response has resulted in a flood of experiments, analyses, hypotheses, and publications, especially in the field of drug repurposing. However, many of the proposed therapeutic compounds obtained from SARS-CoV-2 specific assays are not in agreement and thus demonstrate the need for a singular source of COVID-19 related information from which a rational selection of drug repurposing candidates can be made. In this paper, we present the COVID-19 PHARMACOME, a comprehensive drug-target-mechanism graph generated from a compilation of 10 separate disease maps and sources of experimental data focused on SARS-CoV-2/COVID-19 pathophysiology. By applying our systematic approach, we were able to predict the synergistic effect of specific drug pairs, such as Remdesivir and Thioguanosine or Nelfinavir and Raloxifene, on SARS-CoV-2 infection. Experimental validation of our results demonstrate that our graph can be used to not only explore the involved mechanistic pathways, but also to identify novel combinations of drug repurposing candidates.

Published
2021
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9. Soft document clustering using a novel graph covering approach

Author

Jens Dörpinghaus, Sebastian Schaaf, and Marc Jacobs

Subjects
Document clustering, Information retrieval, Graph theory, Computer applications to medicine. Medical informatics, R858-859.7, Analysis, QA299.6-433
Abstract

Abstract Background In text mining, document clustering describes the efforts to assign unstructured documents to clusters, which in turn usually refer to topics. Clustering is widely used in science for data retrieval and organisation. Results In this paper we present and discuss a novel graph-theoretical approach for document clustering and its application on a real-world data set. We will show that the well-known graph partition to stable sets or cliques can be generalized to pseudostable sets or pseudocliques. This allows to perform a soft clustering as well as a hard clustering. The software is freely available on GitHub. Conclusions The presented integer linear programming as well as the greedy approach for this NP $\mathcal {NP}$-complete problem lead to valuable results on random instances and some real-world data for different similarity measures. We could show that PS-Document Clustering is a remarkable approach to document clustering and opens the complete toolbox of graph theory to this field.

Published
2018
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10. Abstract: Development of Injectable Allograft Adipose Matrix for Soft Tissue Filling: From Conception to Clinical Trial

Author

Francesco M. Egro, MBChB, MSc, MRCS, Lauren Kokai, PhD, Wesley Sivak, MD, Mark Asher Schusterman, MD, Benjamin Schilling, BS, Evangelia Chnari, PhD, Yen-Chen Huang, PhD, Emily Imming, PhD, Heather Brennan, PhD, Marc Jacobs, PhD, Sydney Coleman, MD, Patsy Simon, Kacey Marra, PhD, and J. Peter Rubin, MD

Subjects
Surgery, RD1-811
Published
2018
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14. Common data model for COVID-19 datasets.

Author

Philipp Wegner, Geena Mariya Jose, Vanessa Lage-Rupprecht, Sepehr Golriz Khatami, Bide Zhang, Stephan Springstubbe, Marc Jacobs 0001, Thomas Linden, Cindy Ku, Bruce Schultz, Martin Hofmann-Apitius, and Alpha Tom Kodamullil

Published
2022
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16. The COVID-19 Ontology.

Author

Astghik Sargsyan, Alpha Tom Kodamullil, Shounak Baksi, Johannes Darms, Sumit Madan, Stephan Gebel, Oliver Keminer, Geena Mariya Jose, Helena Balabin, Lauren Nicole Delong, Manfred Kohler, Marc Jacobs 0001, and Martin Hofmann-Apitius

Published
2021
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23. Anticoagulation and Antiplatelet Therapy for Prevention of Venous and Arterial Thrombotic Events in Critically Ill Patients With COVID-19: COVID-PACT

Author

Erin A. Bohula, David D. Berg, Mathew S. Lopes, Jean M. Connors, Ijlal Babar, Christopher F. Barnett, Sunit-Preet Chaudhry, Amit Chopra, Wilson Ginete, Michael H. Ieong, Jason N. Katz, Edy Y. Kim, Julia F. Kuder, Emilio Mazza, Dalton McLean, Jarrod M. Mosier, Ari Moskowitz, Sabina A. Murphy, Michelle L. O’Donoghue, Jeong-Gun Park, Rajnish Prasad, Christian T. Ruff, Mohamad N. Shahrour, Shashank S. Sinha, Stephen D. Wiviott, Sean Van Diepen, Mark Zainea, Vivian Baird-Zars, Marc S. Sabatine, David A. Morrow, Kyung Ah Im, Retu Saxena, Brandon Wiley, Carina Benson, Roman Delamed, Nedaa Skeik, Ami Chopra, Marc Judson, Scott Beegle, Boris Shkolnik, Anupama Tiwari, Gregory Wu, Abhijit Raval, Emerald Branch, Franz Rischard, Cameron Hypes, Billie Bixby, Christian Bime, Madhan Sundaram, Nancy Sweitzer, Alfredo Vazquez Sandoval, Heath White, Katherine Berg, Shahzad Shaefi, Michael Donnino, Brett Carroll, Michael Ieong, Kimberly Ackerbauer, Jaime Murphy, Ankeet Bhatt, Alexander Blood, Siddharth Patel, Victor Luu, Shraddha Narechania, Austin Lorganger, Robert Plambeck, Ali Nayfeh, Michael Sanley, Michel Del Cor, AJ Hegg, Winston Nara, Michael Snyder, Faisal Khan, Imad Shawa, Joshua Larned, Elias Collado, Mohammed Al Faiyumi, Rajeev Mehta, Sudarshan Komanapalli, Vijayadershan Muppidi, Mehul Desai, Casey Flanagan, Leonard Genovese, Tariq Haddad, Christopher King, Amber Peterson, Thane Htun, Elizabeth Pionk, Nicolas Mouawad, Chintalapudi Kumar, Kevin Nguyen, Majid Mughal, Ryan Malek, Akarsh Parekh, Christopher Provenzano, Melissa Ianitelli, Nicole Prentice-Gaytan, Adam Bykowski, Don Tait, Shelley Schendel, Varun Yalamanchili, Vasim Lala, Victor Hunyadi, Alexander Papolos, Benjamin Kenigsberg, Aarthi Shenoy, Thomas Stuckey, Douglas McQuaid, Praveen Mannam, Jeffrey McClung, Kent Nilsson, Andrew McKown, Jason Wells, David Hotchkin, Marc Jacobs, Wayne Strauss, Rick Balestra, Vikram Sahni, R. Jeffrey Snell, Hussam Suradi, Sarah Sungurlu, Jessica Kuppy, Eileen Gajo, Foster Adams, Abbas Shehadeh, Addi Suleiman, Harish Nandigam, Jihad Slim, Sardar Ijlal Babar, Dipti Baral, Talha Nawaz, Syed Abdullah Waheed, Randy Roth, Subhas Sitaula, Shahid Hayat, Jooby Babu, Jason Caberto, Victor Hsu, Robert Chang, Markian Bochan, Rafael Garcia-Cortes, Hal Skopicki, On Chen, Lauren Pilato, Paul Richman, Alexander Adler, Praveen Sudhindra, Jamie Beversdorf, Ravindra Kashyap, Parth Mehta, Borna Mehrad, Ali Ataya, Jorge Lascano, Mark Brantly, Adam Austin, Eduard Koman, Thomas Galski, Vijaya Kumar, Ayman Soubani, Nicolas Harrison, Vineet Reddy, and Audrey Fonkam

Subjects
Venous Thrombosis, Treatment Outcome, Critical Illness, Physiology (medical), Humans, COVID-19, Anticoagulants, Thrombosis, Hemorrhage, Cardiology and Cardiovascular Medicine, Platelet Aggregation Inhibitors, Clopidogrel
Abstract

Background: The efficacy and safety of prophylactic full-dose anticoagulation and antiplatelet therapy in critically ill COVID-19 patients remain uncertain. Methods: COVID-PACT (Prevention of Arteriovenous Thrombotic Events in Critically-ill COVID-19 Patients Trial) was a multicenter, 2×2 factorial, open-label, randomized-controlled trial with blinded end point adjudication in intensive care unit–level patients with COVID-19. Patients were randomly assigned to a strategy of full-dose anticoagulation or standard-dose prophylactic anticoagulation. Absent an indication for antiplatelet therapy, patients were additionally randomly assigned to either clopidogrel or no antiplatelet therapy. The primary efficacy outcome was the hierarchical composite of death attributable to venous or arterial thrombosis, pulmonary embolism, clinically evident deep venous thrombosis, type 1 myocardial infarction, ischemic stroke, systemic embolic event or acute limb ischemia, or clinically silent deep venous thrombosis, through hospital discharge or 28 days. The primary efficacy analyses included an unmatched win ratio and time-to-first event analysis while patients were on treatment. The primary safety outcome was fatal or life-threatening bleeding. The secondary safety outcome was moderate to severe bleeding. Recruitment was stopped early in March 2022 (≈50% planned recruitment) because of waning intensive care unit–level COVID-19 rates. Results: At 34 centers in the United States, 390 patients were randomly assigned between anticoagulation strategies and 292 between antiplatelet strategies (382 and 290 in the on-treatment analyses). At randomization, 99% of patients required advanced respiratory therapy, including 15% requiring invasive mechanical ventilation; 40% required invasive ventilation during hospitalization. Comparing anticoagulation strategies, a greater proportion of wins occurred with full-dose anticoagulation (12.3%) versus standard-dose prophylactic anticoagulation (6.4%; win ratio, 1.95 [95% CI, 1.08–3.55]; P =0.028). Results were consistent in time-to-event analysis for the primary efficacy end point (full-dose versus standard-dose incidence 19/191 [9.9%] versus 29/191 [15.2%]; hazard ratio, 0.56 [95% CI, 0.32–0.99]; P =0.046). The primary safety end point occurred in 4 (2.1%) on full dose and in 1 (0.5%) on standard dose ( P =0.19); the secondary safety end point occurred in 15 (7.9%) versus 1 (0.5%; P =0.002). There was no difference in all-cause mortality (hazard ratio, 0.91 [95% CI, 0.56–1.48]; P =0.70). There were no differences in the primary efficacy or safety end points with clopidogrel versus no antiplatelet therapy. Conclusions: In critically ill patients with COVID-19, full-dose anticoagulation, but not clopidogrel, reduced thrombotic complications with an increase in bleeding, driven primarily by transfusions in hemodynamically stable patients, and no apparent excess in mortality. Registration: URL: https://www.clinicaltrials.gov ; Unique identifier: NCT04409834.

Published
2022

27. The Epilepsy Ontology: a community-based ontology tailored for semantic interoperability and text mining

Author

Astghik Sargsyan, Philipp Wegner, Stephan Gebel, Abish Kaladharan, Priya Sethumadhavan, Vanessa Lage-Rupprecht, Johannes Darms, Bruce Schultz, Jürgen Klein, Marc Jacobs, Sumit Madan, Martin Hofmann-Apitius, and Alpha Tom Kodamullil

Subjects
General Medicine
Abstract

Motivation Epilepsy is a multifaceted complex disorder that requires a precise understanding of the classification, diagnosis, treatment and disease mechanism governing it. Although scattered resources are available on epilepsy, comprehensive and structured knowledge is missing. In contemplation to promote multidisciplinary knowledge exchange and facilitate advancement in clinical management, especially in pre-clinical research, a disease-specific ontology is necessary. The presented ontology is designed to enable better interconnection between scientific community members in the epilepsy domain. Results The Epilepsy Ontology (EPIO) is an assembly of structured knowledge on various aspects of epilepsy, developed according to Basic Formal Ontology (BFO) and Open Biological and Biomedical Ontology (OBO) Foundry principles. Concepts and definitions are collected from the latest International League against Epilepsy (ILAE) classification, domain-specific ontologies and scientific literature. This ontology consists of 1879 classes and 28 151 axioms (2171 declaration axioms, 2219 logical axioms) from several aspects of epilepsy. This ontology is intended to be used for data management and text mining purposes. Availability and implementation The current release of the ontology is publicly available under a Creative Commons 4.0 License and shared via http://purl.obolibrary.org/obo/epso.owl and is a community-based effort assembling various facets of the complex disease. The ontology is also deposited in BioPortal at https://bioportal.bioontology.org/ontologies/EPIO. Supplementary information Supplementary data are available at Bioinformatics Advances online.

Published
2023

33. Antwerp’s museums response to super diversity. A study of multiperspective cultural education for secondary school students: learning revisited

Author

Wil Meeus, Marc Jacobs, Lore Suls, Indra Wolfaert, Paul Janssenswillen, History, Archeology, Arts, Philosophy and Ethics, and Brussels Heritage Lab

Subjects
Cultural Studies, History, Museology, media_common.quotation_subject, Geography, Planning and Development, Heritage, Conservation, superdiversity, Education, multiperspectivity, Sociology, Comparative research, 0502 economics and business, Agency (sociology), Pedagogy, learing, 0601 history and archaeology, Student learning, media_common, Educational sciences, 060102 archaeology, Visitor pattern, 05 social sciences, Cultural education, Superdiversity, 06 humanities and the arts, Tourism, Leisure and Hospitality Management, museums, Antwerp, Art, 050212 sport, leisure & tourism, Diversity (politics)
Abstract

The recent publication of Emotional Heritage resulting from the study of visitor agency in Heritage Sites and Museums opens the way for comparative research and case studies in other contexts than the former British Commonwealth. In this article, the evolution of super-diversity in the Low Countries, and Antwerp in particular, in the twenty-first century is such a case study to urge to move away from that crude concept of visitors and to differentiate more. In European urban contexts, museums face the challenge of connecting the ‘dominant’ ‘culture’/’identity’ represented in their collections with the different ‘cultures’ or ‘identities’ of their target audience. The project team formed a multidisciplinary learning community that created a synergy between art, heritage and education. Three important Antwerp museums participated, providing lessons to secondary students. The museum lessons were developed using the HEM matrix as a multiperspective frame of reference. They were found to appeal to all students in general, and in some respects, the effect of the museum lessons was found to be more positive as the background of the students became more diverse. The project shows that the concept of multiperspectivity is of value to museum strategies addressing an ever more superdiverse urban context.

Published
2021

35. The Epilepsy Ontology: a community-based ontology tailored for semantic interoperability and text-mining

Author

Astghik Sargsyan, Philipp Wegner, Stephan Gebel, Shounak Baksi, Geena Mariya Jose, Vanessa Lange-Rupprecht, Johannes Darms, Bruce Schultz, Jürgen Klein, Marc Jacobs, Philippe Ryvlin, Sumit Madan, Martin Hofmann-Apitius, and Alpha Tom Kodamullil

Subjects
ComputingMethodologies_PATTERNRECOGNITION
Abstract

Motivation: Epilepsy is a multi-faceted complex disorder that requires a precise understanding of the classification, diagnosis, treatment, and disease mechanism governing it. Although scattered resources are available on epilepsy, comprehensive and structured knowledge is missing. In contemplation to promote multidisciplinary knowledge exchange and facilitate advancement in clinical management, especially in pre-clinical research, a disease-specific ontology is necessary. The presented ontology is designed to enable better interconnection between scientific community members in the epilepsy domain.Results: The Epilepsy Ontology (EPIO) is an assembly of structured knowledge on various aspects of epilepsy, developed according to Basic Formal Ontology (BFO) and Open Biological and Biomedical Ontology (OBO) Foundry principles. Concepts and definitions are collected from the latest International League against Epilepsy (ILAE) classification, domain-specific ontologies, and scientific literature. This ontology consists of 1,879 classes and 28,151 axioms (2,171 declaration axioms, 2,219 logical axioms) from several aspects of epilepsy. This ontology is intended to be used for data management and text mining purposes.

Published
2022

36. The crime of witchcraft, a straw figure in slave trade and the robbers gang of Jan de Lichte among the ancestors : dealing with dark heritage and the potential of contemporary genealogical resources

Author

Dirk Jacobs, Marc Jacobs, and History, Archeology, Arts, Philosophy and Ethics

Subjects
History, controversies, witch trials, Sociology, familiy history, Witchcraft, Documentation and information, Heritage, genealogy, slavery, Art, controversial heritage
Abstract

The World Wide Web and digitization have strongly improved the possibilities to search and find. What happens if applying these tools to your family history, leads to the discovery of several ancestors with controversial stories? Think for instance about unexpected stories, ranging from connections to the slave trade in the 18th century, an ancestor connected to a famous gang of 18th-century highway robbers like Jan de Lichte, or a woman condemned and executed after accusations of witchcraft. It raises many questions, but also the challenge for your family or heritage (project): if you do your homework and research, and look far enough, you will find many shades of heritage or genealogies.

Published
2022

37. ASAS-NANP Symposium: Mathematical Modeling in Animal Nutrition: Opportunities and challenges of confined and extensive precision livestock production

Author

Hector M Menendez, Jameson R Brennan, Charlotte Gaillard, Krista Ehlert, Jaelyn Quintana, Suresh Neethirajan, Aline Remus, Marc Jacobs, Izabelle A M A Teixeira, Benjamin L Turner, and Luis O Tedeschi

Subjects
Farms, Livestock, Extensive, Sensors, Confined, Modeling, Agriculture, General Medicine, Models, Theoretical, Livestock production, Genetics, WIAS, Animals, Adaptation Physiology, Animal Science and Zoology, Animal Nutritional Physiological Phenomena, Adaptatiefysiologie, Digital monitoring, Food Science
Abstract

Modern animal scientists, industry, and managers have never faced a more complex world. Precision livestock technologies have altered management in confined operations to meet production, environmental, and consumer goals. Applications of precision technologies have been limited in extensive systems such as rangelands due to lack of infrastructure, electrical power, communication, and durability. However, advancements in technology have helped to overcome many of these challenges. Investment in precision technologies is growing within the livestock sector, requiring the need to assess opportunities and challenges associated with implementation to enhance livestock production systems. In this review, precision livestock farming and digital livestock farming are explained in the context of a logical and iterative five-step process to successfully integrate precision livestock measurement and management tools, emphasizing the need for precision system models (PSMs). This five-step process acts as a guide to realize anticipated benefits from precision technologies and avoid unintended consequences. Consequently, the synthesis of precision livestock and modeling examples and key case studies help highlight past challenges and current opportunities within confined and extensive systems. Successfully developing PSM requires appropriate model(s) selection that aligns with desired management goals and precision technology capabilities. Therefore, it is imperative to consider the entire system to ensure that precision technology integration achieves desired goals while remaining economically and managerially sustainable. Achieving long-term success using precision technology requires the next generation of animal scientists to obtain additional skills to keep up with the rapid pace of technology innovation. Building workforce capacity and synergistic relationships between research, industry, and managers will be critical. As the process of precision technology adoption continues in more challenging and harsh, extensive systems, it is likely that confined operations will benefit from required advances in precision technology and PSMs, ultimately strengthening the benefits from precision technology to achieve short- and long-term goals.Interest and investment in precision technologies are growing within the livestock sector. Though these technologies offer many promises of increased efficiency and reduced inputs, there is a need to assess the opportunities and challenges associated with precision technology implementation in livestock production systems. In this review, precision livestock measurement and management tools are explained in the context of a logical and iterative five-step process that highlights the need for systems computer modeling to realize anticipated benefits from these technologies and avoid unintended consequences. This review includes key case studies to highlight past challenges and current opportunities within operations that house animals in a central area or building with sufficient infrastructure (confined livestock production systems) and other operation settings that utilize large grasslands that contain far less infrastructure (extensive livestock production systems). The key to precision livestock management success is training the next generation of animal scientists in computer modeling, precision technologies, computer programming, and data science while still being grounded in traditional animal science principles.

Published
2022

38. Contact zones, participation, agonism and difficult heritage : the impulses from the field of new museology

Author

Vic Bervoets, Hélène Verreyke, Marc Jacobs, and History, Archeology, Arts, Philosophy and Ethics

Subjects
museum studies, new museology, History, difficult heritage, agonism, Heritage, museums, Art
Abstract

In this review article, we first investigate the impact of a volume edited by Peter Vergo, New Museology, on the discourse and practice of museums and the role they can play in society. Are museums already or still contact zones as James Clifford proposed? How far can this metaphor be pushed, as Robin Boast advocated? Critical changes are needed, according to Bruno Brulon Soares. Furthermore, the handbook, understand website, The participatory museum by Nina Simon had a major impact in promoting be!er use of museums as community spaces and participatory models. Graham Black added emphasis on conversation and social interaction: facilitating taking part, corrective response, belonging, empowering and taking action. Agonism is the path recommended by Chantal Mouffe. Moreover, this proposal was further developed and operationalized by Anna Cento Bull and Hans Lauge Hansen in the model of agonistic memory.

Published
2022

39. Critical assessment of transformer-based AI models for German clinical notes

Author

Manuel Lentzen, Sumit Madan, Vanessa Lage-Rupprecht, Lisa Kühnel, Juliane Fluck, Marc Jacobs, Mirja Mittermaier, Martin Witzenrath, Peter Brunecker, Martin Hofmann-Apitius, Joachim Weber, and Holger Fröhlich

Subjects
transformer-based models, Health Informatics, clinical concept extraction, natural language processing
Abstract

Lay Summary In 2022, the majority of clinical documents are still written as free text. Assuming that these records are consistently and correctly transformed into structured data, they present an opportunity for optimized health-economic purposes as well as personalized patient care. Deep-learning methods, particularly transformer-based models, have recently received much attention as they excel in a variety of fields; however, the majority of applications are currently only available in English. Although there are general-language models in German, none have been developed specifically for biomedical or clinical documents. In this context, this study systematically compared 8 previously published general-language models and 3 newly trained biomedical domain models in information extraction and document classification tasks. Our findings show that while training entirely new models with currently available data has proven ineffective, adapting existing models for biomedical language holds a lot of promise. Furthermore, we found out that even models that have not been specifically developed for biomedical applications can achieve excellent results in the specified fields. Objective Healthcare data such as clinical notes are primarily recorded in an unstructured manner. If adequately translated into structured data, they can be utilized for health economics and set the groundwork for better individualized patient care. To structure clinical notes, deep-learning methods, particularly transformer-based models like Bidirectional Encoder Representations from Transformers (BERT), have recently received much attention. Currently, biomedical applications are primarily focused on the English language. While general-purpose German-language models such as GermanBERT and GottBERT have been published, adaptations for biomedical data are unavailable. This study evaluated the suitability of existing and novel transformer-based models for the German biomedical and clinical domain. Materials and Methods We used 8 transformer-based models and pre-trained 3 new models on a newly generated biomedical corpus, and systematically compared them with each other. We annotated a new dataset of clinical notes and used it with 4 other corpora (BRONCO150, CLEF eHealth 2019 Task 1, GGPONC, and JSynCC) to perform named entity recognition (NER) and document classification tasks. Results General-purpose language models can be used effectively for biomedical and clinical natural language processing (NLP) tasks, still, our newly trained BioGottBERT model outperformed GottBERT on both clinical NER tasks. However, training new biomedical models from scratch proved ineffective. Discussion The domain-adaptation strategy's potential is currently limited due to a lack of pre-training data. Since general-purpose language models are only marginally inferior to domain-specific models, both options are suitable for developing German-language biomedical applications. Conclusion General-purpose language models perform remarkably well on biomedical and clinical NLP tasks. If larger corpora become available in the future, domain-adapting these models may improve performances.

Published
2022

40. Heritage and sustainability : regulating participation

Author

Marc Jacobs, Ana Pereira Roders, Rosana Albuquerque, Clara Bertrand Cabral, Ilaria Rosetti, and History, Archeology, Arts, Philosophy and Ethics

Subjects
Geography, Planning and Development, TJ807-830, heritability, Management, Monitoring, Policy and Law, TD194-195, Renewable energy sources, heritage, forms of participation, sustainable development, international regulatory frameworks, COE, ICOM, ICOMOS, UN-HABITAT III, UNESCO, GE1-350, Biology, Environmental effects of industries and plants, Renewable Energy, Sustainability and the Environment, Documentation and information, Participation, Environmental sciences, Chemistry, Sustainability, Engineering sciences. Technology
Abstract

In the past three decades, there has been increasing research carried out on the role of heritage and its processes in achieving broader sustainable development objectives beyond heritage conservation. As part of this movement, people-centered approaches and participation have been widely integrated into international regulations and guidelines on heritage management, stimulating the implementation of case studies-based research worldwide. Despite the wide advocacy of participatory heritage practices’ contributions to more inclusive and culturally sensitive local development in a great variety of projects, there is limited research into the roles these practices can have in addressing sustainability objectives. How are these roles addressed in international heritage regulatory frameworks, and what forms of participation are promoted for their fulfillment? This paper seeks to answer this research question through a content analysis of international declarations, conventions, guidelines, and policy documents focused on the roles and forms of participation that are promoted. A crossed-matched analysis of results reveals that active forms of participation are those most used to promote all roles and subcategories of participation, as a right, as a driver, and as an enabler of sustainable development. However, fewer active forms are presented as complementary at different stages of sustainability-oriented heritage practices. Moreover, a higher incidence of generic forms of participation can be observed in documents addressing international stakeholders, while partnership and intervention are to be found in those targeting regional and local actors. Nevertheless, the low incidence of decisional forms of participation confirms the challenges of power-sharing at all scales. Trends and influences are highlighted, informing heritage research, governance, and policymaking, but also revealing gaps and ambiguities in current regulations that further research encompassing a larger number of documents might confirm.

Published
2022

43. Green Well Stimulation Fluids for Enhanced Oil Recovery from Tight Sand Formations: Field Wide 70+ Wells Study Over 4 Years

Author

Shumway Martin R, Anthony Nerris, D. Marc Jacobs, Janaina I. S. Aguiar, Mcgonagle Ryan, and Amir Mahmoudkhani

Subjects
Petroleum engineering, Field (physics), Well stimulation, Enhanced oil recovery, Geology
Abstract

Legacy oil production from Appalachian basin has been in a decline mode since 2013. With more than 80% of wells producing less than 15 bbl/day, there is a growing interest in economically and environmentally viable options for well stimulation treatments. Analysis of formation mineralogy and reservoir fluids along with history of well interventions indicated formation damage in many wells due precipitation of organics and a change in wettability being partially responsible for production decline rates in excess of forecasts. The development and properties of a novel cost-effective biosurfactant based well-stimulation fluid are described here along lessons learned from several field trials in wells completed in the Upper Devonian Bradford Group. This group of 74 wells, completed in siltstone and sandstone reservoirs were presenting more than 12 well failures annually across the field, which was attributed to the accumulation of organic deposits in the tubulars. Based on these cases, batch stimulation treatments using a novel fluid comprising biosurfactants were proposed and implemented field wide. The treatments effectively removed organic deposits, changed formation wettability from oil to water wet and resulted in a sustained oil production increase. Well failures were significantly reduced as a result of this program and the group of 74 wells did not have a paraffin-related well failure for 18 months. Results from this program demonstrates the efficiency of the green well stimulation fluids in mitigating formation damage, reducing organics deposition and in increasing oil production as a promising method to stimulate tight formations.

Published
2021

44. Benchmarking Table Recognition Performance on Biomedical Literature on Neurological Disorders

Author

Tim Adams, Marcin Namysl, Alpha Tom Kodamullil, Sven Behnke, Marc Jacobs, and Publica

Subjects
Statistics and Probability, Computational Mathematics, Computational Theory and Mathematics, Molecular Biology, Biochemistry, Computer Science Applications
Abstract

Motivation Table recognition systems are widely used to extract and structure quantitative information from the vast amount of documents that are increasingly available from different open sources. While many systems already perform well on tables with a simple layout, tables in the biomedical domain are often much more complex. Benchmark and training data for such tables are however very limited. Results To address this issue, we present a novel, highly curated benchmark dataset based on a hand-curated literature corpus on neurological disorders, which can be used to tune and evaluate table extraction applications for this challenging domain. We evaluate several state-of-the-art table extraction systems based on our proposed benchmark and discuss challenges that emerged during the benchmark creation as well as factors that can impact the performance of recognition methods. For the evaluation procedure, we propose a new metric as well as several improvements that result in a better performance evaluation. Availability and implementation The resulting benchmark dataset (https://zenodo.org/record/5549977) as well as the source code to our novel evaluation approach can be openly accessed. Supplementary information Supplementary data are available at Bioinformatics online.

Published
2021

45. Diversity of Culicoides in the middle belt of Ghana with Implications on the transmission of Mansonella perstans; a molecular approach

Author

Linda Batsa Debrah, Joseph F. Arthur, Augustine Yeboah, Dorcas O. Owusu, Ernest Adankwah, Isaac Acheampong, Difery Minadzi, Millicent Lamptey, Vera Serwaa Opoku, Wilfred Aniagyei, Monika M. Vivekanandan, Mohammed K. Abass, Amidu Gawusu, Samuel Wanji, Alexander Y. Debrah, Marc Jacobsen, and Richard O. Phillips

Subjects
Culicoides species, Culicoides grahamii, Mansonella perstans, Microfilariae, Infectious and parasitic diseases, RC109-216
Abstract

Abstract Background Culicoides, also known as biting midges, carry pathogens which include Mansonella perstans. Mansonella perstans is a nematode parasite implicated in a number of disease outcomes. Even though a high prevalence of about 75% M. perstans infection has been recorded in some communities in the middle belt of Ghana, and a wide diversity of Culicoides species has been identified, the exact Culicoides species transmitting M. perstans in Ghana has not yet been deciphered. This study therefore aimed at assessing the species diversity of Culicoides and their role in the transmission of M. perstans in the middle belt of Ghana. Methods Culicoides species were sampled from 11 communities in the Asante-Akim North and Sene West districts in the middle belt of Ghana. Centre for Disease Control (CDC) UV light traps, as well as human bait (i.e. human landing catch and engorged catch) methods were used to assess the species abundance and diversity of Culicoides in the study communities in the wet and dry season. A colorimetric Loop-Mediated Isothermal Amplification (LAMP) assay was performed to assess the vector competence of the various Culicoides species. Results A total of 4810 Culicoides from 6 species were sampled. These included Culicoides inornatipennis, C. milnei, C. schultzei, C. grahamii, C. neavei, and C. imicola. Culicoides imicola was the most abundant species (56%) followed by C. grahamii (16%). Light traps sampled the most diverse species (6 species). Human landing catch and engorged catch methods identified three anthropophilic species, C. grahamii, C. milnei, and C. inornatipennis, with C. grahamii being the most anthropophilic with a peak biting time between the hours of 5 p.m. to 6 p.m. Generally, there was relatively higher species abundance in the wet than dry season. LAMP assay identified C. grahamii as the potential vector for M. perstans transmission in the middle belt of Ghana. Conclusions For the first time, we have demonstrated that C. grahamii is the potential competent vector for M. perstans transmission in the middle belt of Ghana. It is more abundant in the rainy season and has a peak biting time between the hours of 5 and 6 p.m. Graphical Abstract

Published
2024
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46. The COVID-19 Ontology

Author

Martin Hofmann-Apitius, Johannes Darms, Stephan Gebel, Sumit Madan, Oliver Keminer, Lauren Nicole DeLong, Marc Jacobs, Astghik Sargsyan, Helena Balabin, Geena Mariya Jose, Alpha Tom Kodamullil, Manfred Kohler, Shounak Baksi, and Publica

Subjects
Statistics and Probability, AcademicSubjects/SCI01060, Computer science, MEDLINE, interoperability, Context (language use), text mining, Ontology (information science), Biochemistry, World Wide Web, 03 medical and health sciences, Text mining, Development (topology), semantic search, Molecular Biology, 030304 developmental biology, 0303 health sciences, semantic integration, business.industry, ontology and terminology, 030302 biochemistry & molecular biology, semantic interoperability, Computer Science Applications, Applications Note, Computational Mathematics, Computational Theory and Mathematics, Ontology, business, Scope (computer science)
Abstract

Motivation The COVID-19 pandemic has prompted an impressive, worldwide response by the academic community. In order to support text mining approaches as well as data description, linking and harmonization in the context of COVID-19, we have developed an ontology representing major novel coronavirus (SARS-CoV-2) entities. The ontology has a strong scope on chemical entities suited for drug repurposing, as this is a major target of ongoing COVID-19 therapeutic development. Results The ontology comprises 2270 classes of concepts and 38 987 axioms (2622 logical axioms and 2434 declaration axioms). It depicts the roles of molecular and cellular entities in virus-host interactions and in the virus life cycle, as well as a wide spectrum of medical and epidemiological concepts linked to COVID-19. The performance of the ontology has been tested on Medline and the COVID-19 corpus provided by the Allen Institute. Availabilityand implementation COVID-19 Ontology is released under a Creative Commons 4.0 License and shared via https://github.com/covid-19-ontology/covid-19. The ontology is also deposited in BioPortal at https://bioportal.bioontology.org/ontologies/COVID-19. Supplementary information Supplementary data are available at Bioinformatics online.

Published
2020

48. De kinderen van Linda en Amanda

Author

Marc Jacobs and History, Archeology, Arts, Philosophy and Ethics

Subjects
craftsmanship, publicity campaign, crafts, apprenticeship
Abstract

reflection about campaign for crafts and apprenticeship

Published
2021

49. The effect of hydroxychloride trace minerals on the growth performance and carcass quality of grower/finisher pigs: a meta-analysis

Author

Marc Jacobs, Sandra J.A. van Kuijk, Yanming Han, and Coen H M Smits

Subjects
Male, Swine, Non Ruminant Nutrition, Body weight, Animal science, Genetics, Animals, Mineral Sources, growth performance, Chemistry, Back fat, Body Weight, General Medicine, sulfate trace minerals, Animal Feed, carcass characteristics, Diet, Trace Elements, grow-finishing pigs, meta-analysis, Europe, Red Meat, Zinc, Trace Minerals, hydroxychloride trace minerals, Body Composition, Female, Animal Science and Zoology, Copper, Food Science, Lean meat
Abstract

The current study compared the effect of hydroxychloride trace minerals (HTM) with the effect of inorganic trace minerals (ITM) on growth performance and carcass quality in grower-finisher pigs. The results of 6 studies conducted throughout Europe were combined into one meta-analysis. All included studies were performed using pigs from about 19 kg of body weight until slaughter. In all studies, 2 different mineral sources were compared, HTM and sulfates as ITM. Zn from either HTM or ITM was added at a level of 80 ppm to the diet, and Cu was added at a level of 15 ppm from the same source as Zn. In most studies, an additional treatment was included in which 20 ppm Zn was used from either source in combination with 15 ppm Cu from the same source. Diets were fed in 3 phases according to local commercial standards. The body weight, average daily gain, average daily feed intake, and gain:feed ratio were measured at the end of each phase. At the end of each study, the carcass yield, back fat thickness, and lean meat percentage were measured at commercial slaughterhouses. The meta-analysis was conducted using a MIXED model in SAS taking into account the within-study and between-study variation. The comparison was done only between HTM and ITM added at the same Zn level. No statistical differences were observed for growth performance or carcass characteristics between the mineral sources in pigs fed 20 ppm Zn. When 80 ppm Zn was used, a significant improvement in lean meat percentage was observed in pigs fed HTM compared with pigs fed ITM. In the overall study period, there was a tendency towards an increased gain:feed ratio in pigs fed 80 ppm Zn from HTM. In the last feeding phase, before slaughter gain:feed ratio and average daily gain were both significantly improved by 3.9%. In conclusion, HTM addition improved growth performance and lean meat percentage in grower-finisher pigs.

Published
2019

50. Core Set of Patient-reported Outcomes in Pancreatic Cancer (COPRAC)

Author

Sun Whe Kim, Olivier R. Busch, Ammar A. Javed, Laura Maggino, Silvia Pellegrini, Suriya Umesh Dalvi, Johanna W. Wilmink, Carlos Fernandez-del Castillo, Inge Henselmans, Mirjam A. G. Sprangers, Jin-Young Jang, Nita Nandkumar Chavan, Marc G. Besselink, Claudio Bassi, Arja Gerritsen, Abhishek Mitra, Shailesh V. Shrikhande, Jin He, Hanneke W. M. van Laarhoven, Lennart B. van Rijssen, Christopher L. Wolfgang, Marc Jacobs, Zhi Ven Fong, Vikas Ostwal, Ear, Nose and Throat, Graduate School, AGEM - Digestive immunity, AGEM - Endocrinology, metabolism and nutrition, AGEM - Re-generation and cancer of the digestive system, CCA - Cancer Treatment and Quality of Life, Surgery, Medical Psychology, APH - Personalized Medicine, APH - Quality of Care, APH - Mental Health, Oncology, and APH - Aging & Later Life

Subjects
Adult, Male, medicine.medical_specialty, Asia, Delphi Technique, Health Personnel, pancreatic cancer, education, Delphi method, MEDLINE, patient reported outcomes, 03 medical and health sciences, patient reported outcomes, pancreatic surgery, pancreatic cancer, 0302 clinical medicine, Quality of life (healthcare), Pancreatic cancer, Health care, medicine, Humans, pancreatic surgery, Patient Reported Outcome Measures, 030212 general & internal medicine, Aged, computer.programming_language, Core set, business.industry, Middle Aged, medicine.disease, United States, humanities, Europe, Pancreatic Neoplasms, 030220 oncology & carcinogenesis, Family medicine, Female, Surgery, Patient-reported outcome, business, computer, Delphi
Abstract

OBJECTIVE: To establish an international core set of patient-reported outcomes (PROs) selected by both patients and healthcare providers (HCPs) from the United States (US), Europe, and Asia. SUMMARY BACKGROUND DATA: PROs are increasingly recognized in pancreatic cancer studies. There is no consensus on which of the many available PROs are most important. METHODS: A multicenter Delphi study among patients with pancreatic cancer (curative- and palliative-setting) and HCPs in 6 pancreatic centers in the US (Baltimore, Boston), Europe (Amsterdam, Verona), and Asia (Mumbai, Seoul) was performed. In round 1, participants rated the importance of 56 PROs on a 1 to 9 Likert scale. PROs rated as very important (scores 7-9) by the majority (≥80%) of curative- and/or palliative-patients as well as HCPs were included in the core set. PROs not fulfilling these criteria were presented again in round 2, together with feedback on individual and group ratings. Remaining PROs were ranked based on the importance ratings. RESULTS: In total 731 patients and HCPs were invited, 501 completed round 1, and 420 completed both rounds. This included 204 patients in curative-setting, 74 patients in palliative-setting, and 142 HCPs. After 2 rounds, 8 PROs were included in the core set: general quality of life, general health, physical ability, ability to work/do usual activities, fear of recurrence, satisfaction with services/care organization, abdominal complaints, and relationship with partner/family. CONCLUSIONS: This international Delphi study among patients and HCPs established a core set of PROs in pancreatic cancer, which should facilitate the design of future pancreatic cancer trials and outcomes research.

Published
2019

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