Review
Neurosciences
Julie Smeyers, Elena-Gaia Banchi, Morwena Latouche
Summary: The non-coding repeat expansion in the C9ORF72 gene is the most common cause of frontotemporal dementia and amyotrophic lateral sclerosis. After a decade of research, it has been found that the toxic accumulation of gain-of-function products and the loss of function may both contribute to the disease.
FRONTIERS IN CELLULAR NEUROSCIENCE
(2021)
Article
Economics
Shuai Liu, Guowei Hua, Yuxuan Kang, T. C. Edwin Cheng, Yadong Xu
Summary: This study examines the role of blockchain in imported fresh food supply chains. The findings indicate that blockchain can help increase profits for manufacturers and retailers when it does not alleviate consumers' safety concerns; otherwise, its value is not significant. Additionally, risk-averse manufacturers and retailers decrease prices in response to demand fluctuations, while the blockchain platform benefits from risk-averse manufacturers and retailers but suffers from risk-averse consumers.
TRANSPORTATION RESEARCH PART E-LOGISTICS AND TRANSPORTATION REVIEW
(2022)
Article
Mathematics
Alma Maciulyte-Sniukiene, Mindaugas Butkus, Renata Macaitiene, Vida Davidaviciene
Summary: This study aims to provide recommendations for policymakers regarding infrastructure investment allocation by assessing the non-linear relationships between transport and ICT infrastructure development and convergence of EU MS NUTS2 regions. The results indicate a diminishing marginal effect of infrastructure development on convergence, and a tipping point after which infrastructure development slows down convergence.
Review
Clinical Neurology
Letizia Maria Cupini, Ilenia Corbelli, Paola Sarchelli
Summary: Menstrual migraine (MM) diagnostic criteria are considered research criteria in need of validation; The relationship between MM and hormonal factors is a key focus in literature; Understanding mechanisms behind neuroendocrine vulnerability may lead to targeted treatment options for MM.
JOURNAL OF NEUROLOGY
(2021)
Article
Statistics & Probability
Stephen Bates, Trevor Hastie, Robert Tibshirani
Summary: Cross-validation is a widely used technique for estimating prediction error, but its behavior is not fully understood. It does not estimate the prediction error of the model trained on the data used for cross-validation, but rather the average prediction error of models trained on unseen data from the same population. The standard confidence intervals derived from cross-validation may have lower coverage than desired, due to correlations among the measured accuracies within each fold. A nested cross-validation scheme is introduced to estimate variance more accurately and improve coverage of confidence intervals.
JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION
(2023)
Review
Oncology
Jules Tianyu Zhang-Yin, Antoine Girard, Marc Bertaux
Summary: This article provides a review of the current place and perspectives of positron emission tomography (PET) imaging in the diagnosis and follow-up of primary and secondary brain tumors. Different PET radiotracers are used to accurately depict brain tumors and provide unique metabolic and biologic information. PET imaging is increasingly used to supplement MRI in the clinical management of brain tumors. The main radiotracers implemented in clinical practice include [F-18]FDG, radiolabeled amino acids, and [Ga-68]Ga-DOTA-SSTR.
Editorial Material
Multidisciplinary Sciences
Jeff Tollefson, Elizabeth Gibney
Summary: Researchers at the US National Ignition Facility achieved a reaction that resulted in a net energy gain.
Article
Agronomy
Zichun Zhu, Congsheng Fu, Huawu Wu, Haohao Wu, Haixia Zhang, Yang Cao, Ye Xia
Summary: The study found that non-intensive grazing is beneficial for water management and nutrient control in alpine-meadow watersheds. Hydrological, water-quality, and meteorological variables have significant impacts on nutrient flux variations, with dissolved oxygen, soluble phosphorus, precipitation, overland flow, and water temperature each explaining over 5% of the nitrogen flux variations.
AGRICULTURAL WATER MANAGEMENT
(2023)
Article
Business, Finance
Bo Wang, Yunjun Yu, Ziying Yang, Xiaomei Zhang
Summary: This study finds that expansion of local microfinance institutions enhances availability of loans in P2P lending, but also increases default risk. Microfinance competition has positive externalities in improving borrowers' bargaining power, strengthening the substitution effect between MFIs and P2P lending.
PACIFIC-BASIN FINANCE JOURNAL
(2021)
Article
Psychology, Multidisciplinary
Meshandren Naidoo
Summary: The study proposes a practical approach to better regulate new AI technologies by considering factors such as predictive ability, semantic information, and self-referential logic. It offers a method for ranking and evaluating AI systems, and is adaptable to current and future developments in AI technologies and society.
FRONTIERS IN PSYCHOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Ji Wang, Claire Toffano-Nioche, Florence Lorieux, Daniel Gautheret, Jean Lehmann
Summary: In RNA high-throughput sequencing, modifications on tRNA transcripts can hinder their conversion into cDNA libraries. By optimizing experimental conditions and utilizing suitable RT enzymes, it is possible to highlight all modifications that affect transcription without the need for demethylation procedures.
Article
Biotechnology & Applied Microbiology
Yingdan Yuan, Mengting Zu, Jiajia Zuo, Runze Li, Jun Tao
Summary: Plastic film mulching can increase crop yield, but long-term mulching may have adverse effects on plant growth. By studying the bacterial communities in the root-associated compartments of P. ostii, it was found that long-term mulching reduced enzyme activities and available nutrients in the soil, and also affected the abundance and diversity of bacterial communities in different root-associated compartments. This may be related to the decrease of litter content and the serious degradation of the plastic film, resulting in the entry of microplastics and harmful substances into the soil.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Article
Computer Science, Artificial Intelligence
Abhijit Guha Roy, Jie Ren, Shekoofeh Azizi, Aaron Loh, Vivek Natarajan, Basil Mustafa, Nick Pawlowski, Jan Freyberg, Yuan Liu, Zach Beaver, Nam Vo, Peggy Bui, Samantha Winter, Patricia MacWilliams, Greg S. Corrado, Umesh Telang, Yun Liu, Taylan Cemgil, Alan Karthikesalingam, Balaji Lakshminarayanan, Jim Winkens
Summary: Supervised deep learning models have shown great effectiveness in classifying dermatological conditions, but there is a need for better detection of rare diseases that are not easily classified using supervised learning.
MEDICAL IMAGE ANALYSIS
(2022)
Review
Biochemistry & Molecular Biology
Adriana Buskin, Emma Scott, Ryan Nelson, Luke Gaughan, Craig N. Robson, Rakesh Heer, Anastasia C. Hepburn
Summary: A key challenge in the management of prostate cancer is its heterogeneity, and there is an urgent need for models that can reflect clinical diversity and resistant phenotypes. The three-dimensional organoid model has revolutionized cancer research, providing opportunities for disease modeling, drug screening, and precision medicine. However, there are limitations in emulating the tumor microenvironment and metastasis process, as well as the epigenome profile, which need to be addressed to maximize the translational relevance of organoids.
Article
Biology
Daniela M. Perez, Cristian L. Klunk, Sabrina B. L. Araujo
Summary: This study investigates imperfect courtship synchrony in fiddler crabs and finds that courtship effort is not directly related to male size, while a faster wave rate is correlated with both leadership and synchrony.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Immunology
Daniel Neumeier, Alessandro Pedrioli, Alessandro Genovese, Ioana Sandu, Roy Ehling, Kai-Lin Hong, Chrysa Papadopoulou, Andreas Agrafiotis, Raphael Kuhn, Danielle Shlesinger, Damiano Robbiani, Jiami Han, Laura Hauri, Lucia Csepregi, Victor Greiff, Doron Merkler, Sai T. Reddy, Annette Oxenius, Alexander Yermanos
Summary: The study conducted single-cell transcriptome and antibody repertoire sequencing of plasma cells following chronic viral infection in mice, revealing that chronic infection can lead to increased levels of clonal expansion, class-switching, and somatic variants in plasma cells, generating cross-reactive antibodies.
EUROPEAN JOURNAL OF IMMUNOLOGY
(2022)
Review
Pharmacology & Pharmacy
Kyrin R. Hanning, Mason Minot, Annmaree K. Warrender, William Kelton, Sai T. Reddy
Summary: Deep mutational scanning (DMS), a method combining protein mutagenesis, functional screening, deep sequencing, and bioinformatics, has significantly improved the properties of monoclonal antibody (mAb) drug candidates. It has been successfully applied in mapping antibody-binding epitopes, profiling viral escape potential, and advancing computational screening and engineering of therapeutic antibodies.
TRENDS IN PHARMACOLOGICAL SCIENCES
(2022)
Article
Multidisciplinary Sciences
Fortunato Ferrara, M. Frank Erasmus, Sara D'Angelo, Camila Leal-Lopes, Andre A. Teixeira, Alok Choudhary, William Honnen, David Calianese, Deli Huang, Linghan Peng, James E. Voss, David Nemazee, Dennis R. Burton, Abraham Pinter, Andrew R. M. Bradbury
Summary: This study demonstrates that highly potent human neutralizing antibodies against the SARS-CoV-2 spike protein can be generated directly from a semisynthetic naive antibody library. These antibodies have comparable affinities, developability properties, and neutralization activities to those from immune sources, providing a potential alternative to traditional immunization methods.
NATURE COMMUNICATIONS
(2022)
Article
Cell Biology
Roy A. Ehling, Cedric R. Weber, Derek M. Mason, Simon Friedensohn, Bastian Wagner, Florian Bieberich, Edo Kapetanovic, Rodrigo Vazquez-Lombardi, Raphael B. Di Roberto, Kai-Lin Hong, Camille Wagner, Michele Pataia, Max D. Overath, Daniel J. Sheward, Ben Murrell, Alexander Yermanos, Andreas P. Cuny, Miodrag Savic, Fabian Rudolf, Sai T. Reddy
Summary: This study presents a technology pipeline that combines single-cell antibody repertoire sequencing and mammalian display to investigate the specificity of plasma cells from convalescent COVID-19 patients. The results reveal specific antibodies targeting SARS-CoV-2 antigens, including those with high affinity and broad binding to the receptor binding domain (RBD) of SARS-CoV-2 variants.
Article
Immunology
Raphael Kuhn, Ioana Sandu, Andreas Agrafiotis, Kai-Lin Hong, Danielle Shlesinger, Daniel Neimeier, Doron Merkler, Annette Oxenius, Sai T. Reddy, Alexander Yermanos
Summary: CD8+ T cells play a crucial role in viral infections and exhibit diverse phenotypes and effector functions. By analyzing the TCR repertoire and transcriptome of virus-specific CD8 T cells in murine models, we identified infection-specific populations corresponding to different phenotypes. Chronic and latent infections resulted in a higher proportion of clonally expanded T cells compared to acute infection. We also observed a relationship between transcriptional heterogeneity and clonal expansion.
FRONTIERS IN IMMUNOLOGY
(2022)
Correction
Multidisciplinary Sciences
Fortunato Ferrara, M. Frank Erasmus, Sara D'Angelo, Camila Leal-Lopes, Andre A. Teixeira, Alok Choudhary, William Honnen, David Calianese, Deli Huang, Linghan Peng, James E. Voss, David Nemazee, Dennis R. Burton, Abraham Pinter, Andrew R. M. Bradbury
NATURE COMMUNICATIONS
(2022)
Article
Medicine, Research & Experimental
Andre A. R. Teixeira, Sara D'Angelo, M. Frank Erasmus, Camila Leal-Lopes, Fortunato Ferrara, Laura P. Spector, Leslie Naranjo, Esteban Molina, Tamara Max, Ashley DeAguero, Katherine Perea, Shaun Stewart, Rebecca A. Buonpane, Horacio G. Nastri, Andrew R. M. Bradbury
Summary: This article presents a sequence agnostic method to improve antibody affinities while simultaneously eliminating sequence liabilities and retaining the same epitope binding as the parental antibody.
Article
Multidisciplinary Sciences
Andreas Agrafiotis, Daniel Neumeier, Kai-Lin Hong, Tasnia Chowdhury, Roy Ehling, Raphael Kuhn, Ioana Sandu, Victor Kreiner, Tudor-Stefan Cotet, Danielle Shlesinger, Daria Laslo, Stine Anzbock, Dale Starkie, Daniel J. Lightwood, Annette Oxenius, Sai T. Reddy, Alexander Yermanos
Summary: By performing single-cell sequencing and transcriptome analysis on mouse B cells, the relationship between antibody diversity, gene expression, and antigen specificity was investigated. The study discovered the presence of clonally expanded and class-switched antigen-specific B cells, which were more common in young mice. Several features, including IgG subtype and sequence composition, correlated with antigen specificity, while other features like germline gene usage and transcriptional signatures did not.
Article
Multidisciplinary Sciences
Nileena Velappan, Fortunato Ferrara, Sara R. D'Angelo, Devin C. Close, Leslie B. Naranjo, Madeline R. K. Bolding, Sarah C. Mozden, Camille B. Troup, Donna K. McCullough, Analyssa Gomez, Marijo Kedge, Andrew R. M. Bradbury
Summary: Antibodies play a crucial role in research, diagnostics, and therapeutics. A high throughput method based on yeast display is described to select antibodies suitable for conversion to fluorescent chimeras. This method allows for the direct identification of functional antibodies in the single chain TGP format, which exhibit higher protein expression, easier purification, and one-step binding assays.
Editorial Material
Oncology
Florian Bieberich, Sai T. Reddy
Summary: The cross-reactivity of T-cell receptors has a positive impact on cancer cell eradication and holds potential advantages for targeted cancer immunotherapies.
Article
Biochemistry & Molecular Biology
Manuel Lisetto, Mariagiulia Fattorini, Andrea Lanza, Marco Gerdol, Martin Griffin, Zhuo Wang, Fortunato Ferrara, Daniele Sblattero
Summary: Transglutaminase 2 (TG2) is a multifunctional protein involved in various physiological and pathological processes. Its role in these processes is controversial due to different effects depending on localization, cell type, or experimental conditions. This study characterized the enzymatic and functional properties of TG2 proteins in zebrafish and demonstrated their similarities to the human ortholog.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemical Research Methods
Camila Leal-Lopes, Sara 'Angelo, M. Frank Erasmus, Andre A. R. Teixeira, Graham Temples, Jinxiang Zhou, Andrew R. M. Bradbury, Fortunato Ferrara
Summary: The therapeutic use of monoclonal antibodies (mAbs) is diverse, ranging from cancer treatment to immune-mediated conditions, covering infectious and cardiovascular disorders, among others. This work describes a new high-throughput mAb expression and purification method for rapid validation of potential mAb leads, enabling efficient functional validation.
Article
Multidisciplinary Sciences
Aerin Yang, Kevin M. Jude, Ben Lai, Mason Minot, Anna M. Kocyla, Caleb R. Glassman, Daisuke Nishimiya, Yoon Seok Kim, Sai T. Reddy, Aly A. Khan, K. Christopher Garcia
Summary: This article presents a synthetic protein-protein coevolution platform that can isolate matched pairs of interacting muteins from complex libraries. The large dataset of coevolved complexes enables a systems-level analysis of molecular recognition and the prediction of remodeled interfaces beyond the reach of the experimental library. The integration of these approaches allows for simulating protein coevolution and generating protein complexes with diverse molecular recognition properties.
Article
Genetics & Heredity
Danielle Shlesinger, Kai-Lin Hong, Ghazal Shammas, Nicolas Page, Ioana Sandu, Andreas Agrafiotis, Victor Kreiner, Nicolas Fonta, Ilena Vincenti, Ingrid Wagner, Margot Piccinno, Alexandre Mariotte, Bogna Klimek, Raphael Dizerens, Marcos Manero-Carranza, Raphael Kuhn, Roy Ehling, Lester Frei, Keywan Khodaverdi, Camilla Panetti, Nicole Joller, Annette Oxenius, Doron Merkler, Sai T. Reddy, Alexander Yermanos
Summary: This study utilized single-cell sequencing to obtain transcriptome and immune repertoire information related to immune responses. The researchers found correlations between cell phenotypes and factors such as clonal expansion, gene usage, and clonal convergence.
GENES AND IMMUNITY
(2022)
Article
Biochemical Research Methods
Erik Aznauryan, Alexander Yermanos, Elvira Kinzina, Anna Devaux, Edo Kapetanovic, Denitsa Milanova, George M. Church, Sai T. Reddy
Summary: Existing approaches to therapeutic gene transfer have limitations in terms of transient gene expression and safety concerns. This study identified two human genomic sites that allow for stable expression of integrated genes without malignant changes. These sites have wide applicability for tissue engineering, protein biomanufacturing, and cancer therapy.
CELL REPORTS METHODS
(2022)