Article
Multidisciplinary Sciences
Wei-Ching Liang, Jianping Yin, Patrick Lupardus, Jianhuan Zhang, Kelly M. Loyet, Jawahar Sudhamsu, Yan Wu
Summary: Our study revealed unexpected differences in activity between two variants of humanized 4A11 with identical CDRs, suggesting that framework residue variations could convert an antibody's activity. This suggests that in addition to CDRs, framework residues and interactions between Fabs in an antibody could be engineered to modulate activity.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Zihao Liu, Xingxing Li, Hiroshi Masai, Xinyi Huang, Susumu Tsuda, Jun Terao, Jinlong Yang, Xuefeng Guo
Summary: By utilizing a single-molecule electrical methodology based on stable graphene-molecule-graphene structures, amino acids can be efficiently discriminated by varying pH values. Experimental results demonstrate the ability to identify amino acids based on different host-guest interactions, enabling accurate measurements within nanoseconds.
Article
Business, Finance
Samuele Bibi, Rosa Canelli
Summary: Central bank digital currency (CBDC) has gained increasing attention from policymakers and academics. This paper aims to enhance understanding of CBDC through the use of Endogenous Money Theory (EMT). By examining the balance sheets of central banks, commercial banks, and the non-financial private sector, the paper explores the asset and liability relationships involved in the introduction of CBDC. It also amends the four quadrants model proposed by post-Keynesian scholars to explain the chain of relationships starting from bank loans, transforming into deposits, and ultimately converting into CBDC.
RESEARCH IN INTERNATIONAL BUSINESS AND FINANCE
(2023)
Article
Chemistry, Multidisciplinary
Guoxiu Wang, Wenjuan Lv, Congjie Pan, Hongli Chen, Xingguo Chen
Summary: A novel chiral COF, DA-TD COF, was synthesized and used as a chiral stationary phase for open-tubular capillary electrochromatography, showing excellent enantioseparation efficiency and stability. The enantioseparation mechanism was also studied in this work.
CHEMICAL COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Leqi Tian, Tianwei Yu
Summary: Untargeted metabolomics has wide applications, but the problem of matching uncertainty between data features and known metabolites is not well-addressed. The current approach is to match the mass-to-charge ratio (m/z) of data features to theoretical values of known metabolites. However, the matching uncertainty caused by metabolites with the same molecular composition and the generation of various adduct ions affects the reliability of the results. In this study, an integrated deep learning framework is proposed to consider the matching uncertainty, which can simultaneously evaluate metabolite importance, infer feature-metabolite matching likelihood, and select disease sub-networks.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
David Baux, Charles Van Goethem, Olivier Ardouin, Thomas Guignard, Anne Bergougnoux, Michel Koenig, Anne-Francoise Roux
Summary: MobiDetails is an expert tool that gathers useful data for interpreting DNA variants, crucial for patient care and familial outcomes. It is designed to help medical staff quickly submit and annotate DNA variants related to over 18,000 human genes.
EUROPEAN JOURNAL OF HUMAN GENETICS
(2021)
Article
Multidisciplinary Sciences
Diego del Alamo, Lillian DeSousa, Rahul M. Nair, Suhaila Rahman, Jens Meiler, Hassane S. Mchaourab
Summary: The APC transporter GadC plays a role in the survival of pathogenic bacteria under extreme acid stress. Through studying its conformational dynamics using DEER spectroscopy, researchers discovered acid-induced conformational changes in GadC, enabling isomerization between inward- and outward-facing states. The substrate glutamate modulates the dynamics of an extracellular gate. This study provides insights into the conformational cycle of GadC and highlights the divergence in dynamics among different families in the LeuT-fold.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemical Research Methods
Jian He, Rongao Yuan, Lei Xu, Yanzhi Guo, Menglong Li
Summary: This study constructed prediction models for disease-associated SAPs from protein sequences based on Random Forest (RF) principle, achieving higher than 90% accuracy and Area Under the Curve (AUC) of over 0.9 by optimizing feature selection and SAP peptide lengths. The method using only protein sequence information proved to be more universal and performed well on independent test sets.
CURRENT BIOINFORMATICS
(2021)
Review
Oncology
Maurizio Ragni, Claudia Fornelli, Enzo Nisoli, Fabio Penna
Summary: Cancer metabolism offers new insights into identifying vulnerabilities of cancer cells, targeting alterations in amino acid metabolism to limit tumor growth can impact the cancer-host metabolism and patient outcome; Cachexia, a common syndrome in cancer patients, may be improved by appropriate amino acid interventions to enhance nutritional status and anti-cancer treatment effectiveness.
Article
Multidisciplinary Sciences
Shu Wen Lim, Kennet JunKai Tan, Osman Mohd Azuraidi, Maran Sathiya, Ee Chen Lim, Kok Song Lai, Wai-Sum Yap, Nik Abd Rahman Nik Mohd Afizan
Summary: MYB proteins are highly conserved DNA-binding domains, and mutations in MYB oncoproteins can lead to aberrant cancer progression. A biomarker discovery pipeline was employed to investigate deleterious nsSNPs in the MYB family, which may alter protein stability and DNA-binding specificity. Results suggest potential implications for pharmacogenomic and cancer therapy.
SCIENTIFIC REPORTS
(2021)
Article
Chemistry, Inorganic & Nuclear
Chengfeng Zhu, Hongzhao Wang, Yongfei Mu, Ziwei Zhang, Lanjun Cheng, Tianfu Li, Yanming Fu, Xiang Wu, Yougui Li
Summary: The chiral metal-organic framework constructed from camphoric acid and a dipyridyl ligand has open chiral channels and multiple recognition sites, making it an efficient chiral solid adsorbent capable of separating racemic alcohols and epoxides with excellent enantioselectivities.
DALTON TRANSACTIONS
(2022)
Article
Automation & Control Systems
Tie Li, Gang Kou, Yi Peng, Philip S. Yu
Summary: The goal of this study is to develop an integrated approach to detect clusters in financial data and optimize their scope for easy interpretation. The proposed algorithm efficiently finds a reasonable number of clusters and is suitable for large-scale financial datasets and financial mining tasks.
IEEE TRANSACTIONS ON CYBERNETICS
(2022)
Article
Chemistry, Multidisciplinary
Judith Juvin, Victor Malherbe, Marie-Charlotte Belhomme, Stephanie Castex, Agathe Martinez, Hassan Khartabil, Arnaud Haudrechy
Summary: The Overman rearrangement is a useful C-N bond forming reaction, but the existing modified approaches suffer from elevated temperatures, long reaction times, and sometimes disappointing yields. This combined experimental and theoretical study aims to elucidate the structures and reactivities of orthoamides to bridge this gap. The study identifies the reactive species and investigates the reactivity of orthoamides using density functional theory. Molecular simulation helps to understand the temperature requirements and reaction time in the orthoamide Overman rearrangement.
NEW JOURNAL OF CHEMISTRY
(2022)
Article
Chemistry, Organic
Stephen G. Davies, Ai M. Fletcher, Sean M. Linsdall, Paul M. Roberts, James E. Thomson
Summary: The synthesis of various loline alkaloids was achieved through a series of reactions. The C(7) and C(7a) stereogenic centers were formed by conjugate addition and subsequent oxidation and exchange reactions. The remaining C(1) and C(2) stereogenic centers were formed through a Mannich-type reaction. The synthesis was completed by forming the 2,7-ether bridge and further manipulations.
JOURNAL OF ORGANIC CHEMISTRY
(2023)
Article
Biology
Maria Ganopoulou, Theodoros Moysiadis, Anastasios Gounaris, Nikolaos Mittas, Fani Chatzopoulou, Dimitrios Chatzidimitriou, Georgios Sianos, Ioannis S. Vizirianakis, Lefteris Angelis
Summary: Due to recent technological progress, a large amount of accumulated data has emerged in various scientific fields, posing new challenges in leveraging this data for valuable insights. Causal models are effective tools for revealing the causal relationships between variables, enabling experts to better understand these relationships and potentially uncover new knowledge. A study on 963 patients with coronary artery disease examined the robustness of the causal structure of single nucleotide polymorphisms, taking into account the Syntax Score, which evaluates the complexity of the disease. The study found that the causal structure was more robust under milder interventions, but the impact increased with stronger interventions, and the local causal structure around the Syntax Score remained resilient even under strong interventions.
Article
Biochemistry & Molecular Biology
Miguel Vazquez, Martin Krallinger, Florian Leitner, Martin Kuiper, Alfonso Valencia, Astrid Laegreid
Summary: This article describes a method to construct a knowledge graph of transcription factor-target gene relationships using text mining tools, with an accuracy close to 75%. It covers 80% of the relationships annotated in existing databases and adds around 11,000 potential interactions.
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS
(2022)
Article
Biochemistry & Molecular Biology
Sarah J. Stock, Jade Carruthers, Clara Calvert, Cheryl Denny, Jack Donaghy, Anna Goulding, Lisa E. M. Hopcroft, Leanne Hopkins, Terry McLaughlin, Jiafeng Pan, Ting Shi, Bob Taylor, Utkarsh Agrawal, Bonnie Auyeung, Srinivasa Vittal Katikireddi, Colin McCowan, Josie Murray, Colin R. Simpson, Chris Robertson, Eleftheria Vasileiou, Aziz Sheikh, Rachael Wood
Summary: Population-level data on COVID-19 vaccine uptake in pregnancy and SARS-CoV-2 infection outcomes are lacking. However, this study reveals low levels of vaccination uptake by pregnant women compared to women in the general population and that not being vaccinated is associated with increased risk of severe complications of COVID-19 in pregnancy, including perinatal mortality.
Correction
Biochemistry & Molecular Biology
Sarah J. Stock, Jade Carruthers, Clara Calvert, Cheryl Denny, Jack Donaghy, Anna Goulding, Lisa E. M. Hopcroft, Leanne Hopkins, Terry McLaughlin, Jiafeng Pan, Ting Shi, Bob Taylor, Utkarsh Agrawal, Bonnie Auyeung, Srinivasa Vittal Katikireddi, Colin McCowan, Josie Murray, Colin R. Simpson, Chris Robertson, Eleftheria Vasileiou, Aziz Sheikh, Rachael Wood
Article
Biochemical Research Methods
Carlos A. Garcia-Prieto, Francisco Martinez-Jimenez, Alfonso Valencia, Eduard Porta-Pardo
Summary: This study highlights the significant impact of variant calling decisions on key analyses of cancer genomic data, such as the identification of cancer driver genes, quantification of mutational signatures, and detection of clinically actionable variants. The choice of somatic variant caller or strategy to combine them can lead to important differences in results, potentially impacting treatment decisions for patients. The widely used Consensus of three calling strategy may result in the loss of important cancer driver genes and actionable mutations, emphasizing the importance of careful consideration in variant calling for critical analyses of tumor sequencing data.
Article
Computer Science, Artificial Intelligence
Charilaos Akasiadis, Miguel Ponce-de-Leon, Arnau Montagud, Evangelos Michelioudakis, Alexia Atsidakou, Elias Alevizos, Alexander Artikis, Alfonso Valencia, Georgios Paliouras
Summary: Computational systems and methods play an important role in biological research, particularly in the understanding and treatment of cancer. This study combines a simulator for tumor cell growth and a genetic algorithm to find effective parameter configurations for drug treatments. Experimental results demonstrate the effectiveness and computational efficiency of the approach.
COMPUTATIONAL INTELLIGENCE
(2022)
Article
Medicine, General & Internal
Ferran Catala-Lopez, Jane A. Driver, Matthew J. Page, Brian Hutton, Manuel Ridao, Clara Berrozpe-Villabona, Adolfo Alonso-Arroyo, Cristina A. Fraga-Medin, Enrique Bernal-Delgado, Alfonso Valencia, Rafael Tabares-Seisdedos
Summary: This study aims to evaluate the design, methods, and reporting of studies conducted using routine health data to investigate the link between cancer and neurodegenerative diseases. The study will search electronic databases and use standardized data extraction forms. The findings will be summarized using tables and graphs. No ethical approval is required, and the full study will be published in an open access journal.
Article
Microbiology
Ferran Tarres-Freixas, Benjamin Trinite, Anna Pons-Grifols, Miguel Romero-Durana, Eva Riveira-Munoz, Carlos avila-Nieto, Monica Perez, Edurne Garcia-Vidal, Daniel Perez-Zsolt, Jordana Munoz-Basagoiti, Dalia Raich-Regue, Nuria Izquierdo-Useros, Cristina Andres, Andres Anton, Tomas Pumarola, Ignacio Blanco, Marc Noguera-Julian, Victor Guallar, Rosalba Lepore, Alfonso Valencia, Victor Urrea, Julia Vergara-Alert, Bonaventura Clotet, Ester Ballana, Jorge Carrillo, Joaquim Segales, Julia Blanco
Summary: The study found that the emerging SARS-CoV-2 variants show heterogeneous infectivity and pathogenesis in mice models, with B.1.351/Beta variant being the most pathogenic and BA.1.1/Omicron leading to lower viral RNA levels.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Medicine, General & Internal
Amelia Green, Helen Curtis, William Hulme, Elizabeth Williamson, Helen McDonald, Krishnan Bhaskaran, Christopher Rentsch, Anna Schultze, Brian MacKenna, Viyaasan Mahalingasivam, Laurie Tomlinson, Alex Walker, Louis Fisher, Jon Massey, Colm Andrews, Lisa Hopcroft, Caroline Morton, Richard Croker, Jessica Morley, Amir Mehrkar, Seb Bacon, David Evans, Peter Inglesby, George Hickman, Tom Ward, Simon Davy, Rohini Mathur, John Tazare, Rosalind Eggo, Kevin Wing, Angel Wong, Harriet Forbes, Chris Bates, Jonathan Cockburn, John Parry, Frank Hester, Sam Harper, Ian Douglas, Stephen Evans, Liam Smeeth, Ben Goldacre
Summary: While the majority of COVID-19 vaccine breakthrough cases in England were mild, some differences in rates of breakthrough cases have been identified in several clinical groups. Further analysis is needed to assess vaccine waning and rates of breakthrough COVID-19 between different variants in order to identify individuals at higher risk.
Article
Oncology
Grant D. Stewart, Sarah J. Welsh, Stephan Ursprung, Ferdia A. Gallagher, James O. Jones, Jacqui Shields, Christopher G. Smith, Thomas J. Mitchell, Anne Y. Warren, Axel Bex, Ekaterini Boleti, Jade Carruthers, Tim Eisen, Kate Fife, Abdel Hamid, Alexander Laird, Steve Leung, Jahangeer Malik, Iosif A. Mendichovszky, Faiz Mumtaz, Grenville Oades, Andrew N. Priest, Antony C. P. Riddick, Balaji Venugopal, Michelle Welsh, Kathleen Riddle, Lisa E. M. Hopcroft, Robert J. Jones
Summary: The study demonstrates that axitinib can reduce the level of VTT in patients, leading to a reduction in the extent of surgery for a significant proportion of patients. However, some patients show poor response to axitinib.
BRITISH JOURNAL OF CANCER
(2022)
Article
Medicine, Research & Experimental
James Sweet-Jones, Maham Ahmad, Andrew C. R. Martin
Summary: This article introduces a new notation language called AbML specifically for complex multi-specific antibodies (MsAbs). AbML overcomes the limitations of existing languages and can annotate all current and future antibody formats. The authors have also developed a tool, abYdraw, to assist users in visualizing and generating AbML strings.
Article
Medicine, General & Internal
Elsie M. F. Horne, William J. Hulme, Ruth H. Keogh, Tom M. Palmer, Elizabeth J. Williamson, Edward P. K. Parker, Amelia Green, Venexia Walker, Alex J. Walker, Helen Curtis, Louis Fisher, Brian MacKenna, Richard Croker, Lisa Hopcroft, Robin Y. Park, Jon Massey, Jessica Morley, Amir Mehrkar, Sebastian Bacon, David Evans, Peter Inglesby, Caroline E. Morton, George Hickman, Simon Davy, Tom Ward, Iain Dillingham, Ben Goldacre, Miguel A. Hernan, Jonathan A. C. Sterne
Summary: This study aimed to evaluate the waning of COVID-19 vaccine effectiveness after the second dose over a period of six months. The findings showed similar trends of declining vaccine effectiveness for both BNT162b2 and ChAdOx1 vaccines, and across different age and clinical vulnerability subgroups. Despite the waning effectiveness, rates of COVID-19-related hospital admission and death remained significantly lower among vaccinated individuals compared to unvaccinated individuals up to 26 weeks after the second dose. The estimated vaccine effectiveness was above 80% for BNT162b2 and above 75% for ChAdOx1. However, in the 23-26 week period, rates of positive SARS-CoV-2 tests in vaccinated individuals were similar to or higher than those in unvaccinated individuals.
BMJ-BRITISH MEDICAL JOURNAL
(2022)
Article
Multidisciplinary Sciences
Clara Calvert, Jade Carruthers, Cheryl Denny, Jack Donaghy, Sam Hillman, Lisa E. M. Hopcroft, Leanne Hopkins, Anna Goulding, Laura Lindsay, Terry McLaughlin, Emily Moore, Jiafeng Pan, Bob Taylor, Fatima Almaghrabi, Bonnie Auyeung, Krishnan Bhaskaran, Cheryl L. Gibbons, Srinivasa Vittal Katikireddi, Colin McCowan, Josie Murray, Maureen O'Leary, Lewis D. Ritchie, Syed Ahmar Shah, Colin R. Simpson, Chris Robertson, Aziz Sheikh, Sarah J. Stock, Rachael Wood
Summary: This study found no association between COVID-19 vaccination during early pregnancy and miscarriage or ectopic pregnancy. The findings support the current recommendations that vaccination remains the safest way for pregnant women to protect themselves and their babies from COVID-19.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Clara Calvert, Jade Carruthers, Cheryl Denny, Jack Donaghy, Lisa E. M. Hopcroft, Leanne Hopkins, Anna Goulding, Laura Lindsay, Terry McLaughlin, Emily Moore, Bob Taylor, Maria Loane, Helen Dolk, Joan Morris, Bonnie Auyeung, Krishnan Bhaskaran, Cheryl L. Gibbons, Srinivasa Vittal Katikireddi, Maureen O'Leary, David McAllister, Ting Shi, Colin R. Simpson, Chris Robertson, Aziz Sheikh, Sarah J. Stock, Rachael Wood
Summary: This study using electronic health records from Scotland found no increased risk of congenital anomalies associated with COVID-19 vaccination or SARS-CoV-2 infection during early pregnancy.
NATURE COMMUNICATIONS
(2023)
Article
Medical Informatics
Brian MacKenna, Helen J. Curtis, Lisa E. M. Hopcroft, Alex J. Walker, Richard Croker, Orla Macdonald, Stephen J. W. Evans, Peter Inglesby, David Evans, Jessica Morley, Sebastian C. J. Bacon, Ben Goldacre
Summary: This study develops a hypothesis-free approach to identify unusual prescribing behavior in primary care data. The approach provides rankings for candidates and allows for audit and review in clinical practice. Two examples of highly unusual antipsychotics used disproportionately in specific geographic areas are provided to illustrate the effectiveness of the approach.
JMIR MEDICAL INFORMATICS
(2022)
Article
Medical Informatics
Lisa E. M. Hopcroft, Jon Massey, Helen J. Curtis, Brian Mackenna, Richard Croker, Andrew Brown, Thomas O'Dwyer, Orla Macdonald, David Evans, Peter Inglesby, Sebastian C. J. Bacon, Ben Goldacre, Alex J. Walker
Summary: This study developed and applied a hypothesis-free algorithm to identify unusual prescribing behavior in primary care data in England. The results were visualized using interactive dashboards, demonstrating the potential of data-driven approaches in identifying targets for improved healthcare delivery.
JMIR MEDICAL INFORMATICS
(2023)
