Review
Urology & Nephrology
Chava L. Ramspek, Kitty J. Jager, Friedo W. Dekker, Carmine Zoccali, Merel van Diepen
Summary: This article highlights the importance of external validation studies for improving prediction models' reproducibility and generalizability. Various methodological considerations and statistical analyses are crucial for designing and interpreting external validation studies.
CLINICAL KIDNEY JOURNAL
(2021)
Article
Computer Science, Artificial Intelligence
Amit Sheth, Kaushik Roy, Manas Gaur
Summary: Humans interact with the environment by transforming perception into symbols and mapping symbols to knowledge for abstraction, reasoning, and planning. Machine perception in AI refers to pattern recognition from data trained using self-supervised learning, while machine cognition involves more complex computations based on knowledge of the environment. Humans can control and explain their cognitive functions, requiring retention of symbolic mappings from perception to environment knowledge. This is important in safety-critical applications like healthcare, criminal justice, and autonomous driving.
IEEE INTELLIGENT SYSTEMS
(2023)
Review
Plant Sciences
Jonas Hilty, Bertrand Muller, Florent Pantin, Sebastian Leuzinger
Summary: Growth is a widely used term in plant science and ecology, with different meanings depending on context and scale. It can refer to cell production, tissue expansion, biomass increase, or net primary production. Understanding the different aspects of plant growth is essential for unraveling genetic and environmental effects on phenotype.
Article
Computer Science, Information Systems
Xiaofei Wang, Xiaoxu Ren, Chao Qiu, Zehui Xiong, Haipeng Yao, Victor C. M. Leung
Summary: This paper investigates the integration of edge intelligence (EI) and blockchain (BC), summarizes the latest research efforts, and explores how blockchain can benefit EI in terms of computing power management, data administration, and model optimization. It also presents methods to tailor blockchain to EI and discusses future research directions.
IEEE COMMUNICATIONS SURVEYS AND TUTORIALS
(2022)
Article
Engineering, Industrial
Bart L. MacCarthy, Wafaa A. H. Ahmed, Guven Demirel
Summary: There is a growing recognition of the important role played by supply chains in the global economy. This paper discusses the reasons for mapping supply chains, the diversity of mapping exercises, and the development of a hierarchy to define the unit of analysis for mapping studies. It also highlights emerging commercial solutions for capturing, mapping, and analyzing supply systems.
INTERNATIONAL JOURNAL OF PRODUCTION ECONOMICS
(2022)
Review
Biochemistry & Molecular Biology
Jung Woo Park, Philip N. P. Lagniton, Yu Liu, Ren-He Xu
Summary: The COVID-19 pandemic caused by SARS-CoV-2 has led to significant impact on human lives, with mRNA vaccines emerging as promising candidates due to their rapid development time, cost-effectiveness, versatility in design, and proven ability to induce immune response.
INTERNATIONAL JOURNAL OF BIOLOGICAL SCIENCES
(2021)
Article
Neurosciences
Ann Kennedy
Summary: Advances in machine learning have led to the growth of descriptive and generative models of animal behavior, offering higher levels of detail and granularity. These methods help us understand the governing principles behind complex and naturalistic behavior.
CURRENT OPINION IN NEUROBIOLOGY
(2022)
Article
Medicine, General & Internal
Isaac K. S. Ng, Norman H. Y. Lin, Wilson G. W. Goh, Desmond B. Teo, Li Feng Tan, Kenneth H. K. Ban
Summary: Insight is of great importance in clinical practice, as it affects patient compliance, clinical outcomes, and the learning and clinical competencies of medical trainees. Cultivating insight in medical training can promote lifelong clinical learning, improve clinical competencies and person-centered care, and enhance physician mental health. Educational pedagogies are helpful in creating a medical eco-system that promotes the cultivation of insight. Poor insight can be addressed through psychological and non-psychological interventions.
POSTGRADUATE MEDICAL JOURNAL
(2023)
Review
Microbiology
Sofia Esteves, Ines Costa, Sara Luelmo, Nuno Santarem, Anabela Cordeiro-da-Silva
Summary: Leishmaniasis is an important neglected tropical disease without vaccines, and the available chemotherapy is suboptimal. Understanding parasite biology is essential for developing new strategies for disease control. Studies on the exoproteome, especially extracellular vesicles, have provided valuable information on parasite survival, pathogenesis, and relevant processes.
Review
Physiology
Shah-Abas Muhamad, Azizah Ugusman, Jaya Kumar, Dominik Skiba, Adila A. Hamid, Amilia Aminuddin
Summary: Observational studies globally have shown that most COVID-19 patients have preexisting hypertension, raising questions about the potential relationship between COVID-19 and hypertension. This review summarizes the current understanding of the link between hypertension and COVID-19, as well as its underlying mechanisms.
FRONTIERS IN PHYSIOLOGY
(2021)
Review
Medicine, General & Internal
Francesca Ingegnoli, Lavinia Agra Coletto, Isabella Scotti, Riccardo Compagnoni, Pietro Simone Randelli, Roberto Caporali
Summary: Synovial tissue analysis plays a crucial role in the diagnosis and research of joint diseases, aiding in disease classification and patient stratification. Effective dialogue between clinicians and pathologists is essential for proper sample handling and identifying histological patterns.
FRONTIERS IN MEDICINE
(2021)
Review
Environmental Studies
David C. Wang, M. Elizabeth Lewis Hall, Laura R. Shannonhouse, Mary Chase Breedlove Mize, Jamie D. Aten, Edward B. Davis, Daryl R. Van Tongeren, Kent Annan
Summary: Humility is seen as a crucial trait in organizational leadership, as it has predictive positive outcomes, represents good character, and aligns with the essence of humanitarian aid.
Review
Chemistry, Multidisciplinary
Arvind Rajendran, Sai Gokul Subraveti, Kasturi Nagesh Pai, Vinay Prasad, Zukui Li
Summary: Adsorption using solid sorbents is becoming a serious competitor to liquid absorption for CO2 capture. Significant efforts have been made in developing new adsorbents for this application, but identifying the right adsorbent remains a challenge. This article discusses the development of computational methods for process-based evaluation and highlights the need for collaboration between chemists and chemical engineers.
ACCOUNTS OF CHEMICAL RESEARCH
(2023)
Review
Urology & Nephrology
R. Gulsah Dilaver, T. Alp Ikizler
Summary: Personalized hemodialysis prescriptions can reduce the burden on maintenance hemodialysis patients and prevent complications. Tailoring dialysate electrolyte concentrations based on individual factors is crucial, but comprehensive patient data collection, technological advancements, and patient involvement are also important.
CLINICAL KIDNEY JOURNAL
(2023)
Article
Green & Sustainable Science & Technology
Elsa Diez-Busto, Lidia Sanchez-Ruiz, Ana Fernandez-Laviada
Summary: The B Corp certification is a means to measure the impact of companies on social, environmental, and economic factors. However, there is a lack of research on the B Corp certification process itself. To address this gap, this study aims to design and propose a questionnaire based on companies' experiences. The final questionnaire, named B Corp Certification Process Survey (BCCPS), consists of motivations, barriers, and effects. Having a common questionnaire allows for comparisons and promotes the development of research in this field.
JOURNAL OF CLEANER PRODUCTION
(2022)
Article
Biochemistry & Molecular Biology
Saqib Mir, Younes Alhroub, Stephen Anyango, David R. Armstrong, John M. Berrisford, Alice R. Clark, Matthew J. Conroy, Jose M. Dana, Mandar Deshpande, Deepti Gupta, Aleksandras Gutmanas, Pauline Haslam, Lora Mak, Abhik Mukhopadhyay, Nurul Nadzirin, Typhaine Paysan-Lafosse, David Sehnal, Sanchayita Sen, Oliver S. Smart, Mihaly Varadi, Gerard J. Kleywegt, Sameer Velankar
NUCLEIC ACIDS RESEARCH
(2018)
Article
Biochemistry & Molecular Biology
Stephen K. Burley, Helen M. Berman, Charmi Bhikadiya, Chunxiao Bi, Li Chen, Luigi Di Costanzo, Cole Christie, Jose M. Duarte, Shuchismita Dutta, Zukang Feng, Sutapa Ghosh, David S. Goodsell, Rachel Kramer Green, Vladimir Guranovic, Dmytro Guzenko, Brian P. Hudson, Yuhe Liang, Robert Lowe, Ezra Peisach, Irina Periskova, Chris Randle, Alexander Rose, Monica Sekharan, Chenghua Shao, Yi-Ping Tao, Yana Valasatava, Maria Voigt, John Westbrook, Jasmine Young, Christine Zardecki, Marina Zhuravleva, Genji Kurisu, Haruki Nakamura, Yumiko Kengaku, Hasumi Cho, Junko Sato, Ju Yaen Kim, Yasuyo Ikegawa, Atsushi Nakagawa, Reiko Yamashita, Takahiro Kudou, Gert-Jan Bekker, Hirofumi Suzuki, Takeshi Iwata, Masashi Yokochi, Naohiro Kobayashi, Toshimichi Fujiwara, Sameer Velankar, Gerard J. Kleywegt, Stephen Anyango, David R. Armstrong, John M. Berrisford, Matthew J. Conroy, Jose M. Dana, Mandar Deshpande, Paul Gane, Romana Gaborova, Deepti Gupta, Aleksandras Gutmanas, Jaroslav Koca, Lora Mak, Saqib Mir, Abhik Mukhopadhyay, Nurul Nadzirin, Sreenath Nair, Ardan Patwardhan, Typhaine Paysan-Lafosse, Lukas Pravda, Osman Salih, David Sehnal, Mihaly Varadi, Radka Varekova, John L. Markley, Jeffrey C. Hoch, Pedro R. Romero, Kumaran Baskaran, Dimitri Maziuk, Eldon L. Ulrich, Jonathan R. Wedell, Hongyang Yao, Miron Livny, Yannis E. Ioannidis
NUCLEIC ACIDS RESEARCH
(2019)
Article
Biochemistry & Molecular Biology
David R. Armstrong, John M. Berrisford, Matthew J. Conroy, Aleksandras Gutmanas, Stephen Anyango, Preeti Choudhary, Alice R. Clark, Jose M. Dana, Mandar Deshpande, Roisin Dunlop, Paul Gane, Romana Gaborova, Deepti Gupta, Pauline Haslam, Jaroslav Koca, Lora Mak, Saqib Mir, Abhik Mukhopadhyay, Nurul Nadzirin, Sreenath Nair, Typhaine Paysan-Lafosse, Lukas Pravda, David Sehnal, Osman Salih, Oliver Smart, James Tolchard, Mihaly Varadi, Radka Svobodova-Varekova, Hossam Zaki, Gerard J. Kleywegt, Sameer Velankar
NUCLEIC ACIDS RESEARCH
(2020)
Article
Multidisciplinary Sciences
Kathryn Tunyasuvunakool, Jonas Adler, Zachary Wu, Tim Green, Michal Zielinski, Augustin Zidek, Alex Bridgland, Andrew Cowie, Clemens Meyer, Agata Laydon, Sameer Velankar, Gerard J. Kleywegt, Alex Bateman, Richard Evans, Alexander Pritzel, Michael Figurnov, Olaf Ronneberger, Russ Bates, Simon A. A. Kohl, Anna Potapenko, Andrew J. Ballard, Bernardino Romera-Paredes, Stanislav Nikolov, Rishub Jain, Ellen Clancy, David Reiman, Stig Petersen, Andrew W. Senior, Koray Kavukcuoglu, Ewan Birney, Pushmeet Kohli, John Jumper, Demis Hassabis
Summary: Using the AlphaFold method, the structural coverage of the proteome has been significantly expanded, covering 98.5% of human proteins with 58% of residues having confident predictions and 36% having very high confidence. Introducing new metrics to interpret the dataset and identify disordered regions, this study aims to provide high-quality predictions for generating biological hypotheses.
Editorial Material
Biochemical Research Methods
Ugis Sarkans, Wah Chiu, Lucy Collinson, Michele C. Darrow, Jan Ellenberg, David Grunwald, Jean-Karim Heriche, Andrii Iudin, Gabriel G. Martins, Terry Meehan, Kedar Narayan, Ardan Patwardhan, Matthew Robert Geoffrey Russell, Helen R. Saibil, Caterina Strambio-De-Castillia, Jason R. Swedlow, Christian Tischer, Virginie Uhlmann, Paul Verkade, Mary Barlow, Omer Bayraktar, Ewan Birney, Cesare Catavitello, Christopher Cawthorne, Stephan Wagner-Conrad, Elizabeth Duke, Perrine Paul-Gilloteaux, Emmanuel Gustin, Maria Harkiolaki, Pasi Kankaanpaa, Thomas Lemberger, Jo McEntyre, Josh Moore, Andrew W. Nicholls, Shuichi Onami, Helen Parkinson, Maddy Parsons, Marina Romanchikova, Nicholas Sofroniew, Jim Swoger, Nadine Utz, Lenard M. Voortman, Frances Wong, Peijun Zhang, Gerard J. Kleywegt, Alvis Brazma
Summary: The study proposes draft metadata guidelines to address the needs of diverse communities within light and electron microscopy, with the hope of stimulating discussions about their implementation and future extension.
Article
Chemistry, Applied
Laura Okmane, Gustav Nestor, Emma Jakobsson, Bingze Xu, Kiyohiko Igarashi, Mats Sandgren, Gerard J. Kleywegt, Jerry Stahlberg
Summary: In this study, the enzymatic hydrolysis of barley beta-glucan, konjac glucomannan, and carboxymethyl cellulose by MeCel45A from blue mussel was compared with GH45 members from different subfamilies, showing that subfamily B and C enzymes exhibited mannanase activity while the subfamily A member was uniquely able to produce monomeric glucose. MeCel45A appears to be cold adapted and maintained higher activity at 4 degrees Celsius compared to other enzymes.
CARBOHYDRATE POLYMERS
(2022)
Article
Biochemistry & Molecular Biology
Matthew Hartley, Gerard J. Kleywegt, Ardan Patwardhan, Ugis Sarkans, Jason R. Swedlow, Alvis Brazma
Summary: The BioImage Archive is a new data resource designed to centralize biological imaging data and facilitate scientists' research. It accepts bioimaging data from different imaging modalities and enables scientists to generate new insights by reusing existing data to answer new biological questions. It also provides training and benchmarking data for the development of image analysis tools.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Editorial Material
Biochemical Research Methods
Sriram Subramaniam, Gerard J. Kleywegt
Article
Biochemistry & Molecular Biology
Mihaly Varadi, Stephen Anyango, Mandar Deshpande, Sreenath Nair, Cindy Natassia, Galabina Yordanova, David Yuan, Oana Stroe, Gemma Wood, Agata Laydon, Augustin Zidek, Tim Green, Kathryn Tunyasuvunakool, Stig Petersen, John Jumper, Ellen Clancy, Richard Green, Ankur Vora, Mira Lutfi, Michael Figurnov, Andrew Cowie, Nicole Hobbs, Pushmeet Kohli, Gerard Kleywegt, Ewan Birney, Demis Hassabis, Sameer Velankar
Summary: AlphaFold DB is an openly accessible database with high-accuracy protein-structure predictions, powered by DeepMind's AlphaFold v2.0. It provides programmatic access to a vast number of predicted structures and is expanding to cover more sequences.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemical Research Methods
Zhe Wang, Ardan Patwardhan, Gerard J. Kleywegt
Summary: The Electron Microscopy Data Bank (EMDB) is a central archive for cryo-EM volume maps and tomograms. It has developed new resources for validating cryo-EM structures, with a three-tiered system based on community input. These resources are useful for both experts and non-specialists to better understand and evaluate the quality of cryo-EM structures.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2022)
Editorial Material
Chemistry, Multidisciplinary
Gerard J. Kleywegt, Sameer Velankar
Article
Biochemistry & Molecular Biology
Mihaly Varadi, Stephen Anyango, Sri Devan Appasamy, David Armstrong, Marcus Bage, John Berrisford, Preeti Choudhary, Damian Bertoni, Mandar Deshpande, Grisell Diaz Leines, Joseph Ellaway, Genevieve Evans, Romana Gaborova, Deepti Gupta, Aleksandras Gutmanas, Deborah Harrus, Gerard J. Kleywegt, Weslley Morellato Bueno, Nurul Nadzirin, Sreenath Nair, Lukas Pravda, Marcelo Querino Lima Afonso, David Sehnal, Ahsan Tanweer, James Tolchard, Charlotte Abrams, Roisin Dunlop, Sameer Velankar
Summary: The archiving and dissemination of protein and nucleic acid structures are crucial for impactful research in life sciences. The Protein Data Bank in Europe (PDBe) provides databases, web services, and visualizations to facilitate basic and applied research and education.
Article
Biochemistry & Molecular Biology
Andrii Iudin, Paul K. Korir, Sriram Somasundharam, Simone Weyand, Cesare Cattavitello, Neli Fonseca, Osman Salih, Gerard J. Kleywegt, Ardan Patwardhan
Summary: Public archiving in structural biology has been well established with the Protein Data Bank (PDB) and the Electron Microscopy Data Bank (EMDB). EMPIAR, as a public archive, has become an important resource for storing cryo-EM image data and 3D reconstructions, meeting the increasing demand for archiving such data from cryo-EM experiments, as well as from volume EM and X-ray tomography experiments.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Matthew Thakur, Alex Bateman, Cath Brooksbank, Mallory Freeberg, Melissa Harrison, Matthew Hartley, Thomas Keane, Gerard Kleywegt, Andrew Leach, Mariia Levchenko, Sarah Morgan, Ellen M. McDonagh, Sandra Orchard, Irene Papatheodorou, Sameer Velankar, Juan Antonio Vizcaino, Rick Witham, Barbara Zdrazil, Johanna McEntyre
Summary: EMBL-EBI is one of the world's leading sources of public biomolecular data, offering sustainable, high-quality data that can serve as training sets for deep learning and artificial intelligence applications. The open availability of their extensive curated databases makes them ideal for research in the life sciences.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Jack Turner, Sanja Abbott, Neli Fonseca, Lucas Carrijo, Amudha Kumari Duraisamy, Osman Salih, Zhe Wang, Gerard J. Kleywegt, Kyle L. Morris, Ardan Patwardhan, Stephen K. Burley, Gregg Crichlow, Zukang Feng, Justin W. Flatt, Sutapa Ghosh, Brian P. Hudson, Catherine L. Lawson, Yuhe Liang, Ezra Peisach, Irina Persikova, Monica Sekharan, Chenghua Shao, Jasmine Young, Sameer Velankar, David Armstrong, Marcus Bage, Wesley Morellato Bueno, Genevieve Evans, Romana Gaborova, Sudakshina Ganguly, Deepti Gupta, Deborah Harrus, Ahsan Tanweer, Manju Bansal, Vetriselvi Rangannan, Genji Kurisu, Hasumi Cho, Yasuyo Ikegawa, Yumiko Kengaku, Ju Yaen Kim, Satomi Niwa, Junko Sato, Ayako Takuwa, Jian Yu, Jeffrey C. Hoch, Kumaran Baskaran, Wenqing Xu, Weizhe Zhang, Xiaodan Ma
Summary: This article provides an overview of the Electron Microscopy Data Bank (EMDB), its significance as a global public archive, and its current holdings, recent updates, and future plans.
NUCLEIC ACIDS RESEARCH
(2023)
