Article
Geography, Physical
Guillaume Jouvet, Guillaume Cordonnier, Byungsoo Kim, Martin Luthi, Andreas Vieli, Andy Aschwanden
Summary: This paper introduces a model called Instructed Glacier Model (IGM), which simulates ice dynamics using a Convolutional Neural Network and a cheap emulator trained from data. It can predict the evolution of glaciers accurately and efficiently.
JOURNAL OF GLACIOLOGY
(2022)
Article
Computer Science, Information Systems
Alistair Moffat
Summary: This paper proposes the buying power metric for assessing the quality of product rankings on e-commerce sites. It discusses the relationship between the buying power metric and user reactions, and introduces an alternative product ranking effectiveness metric.
INFORMATION PROCESSING & MANAGEMENT
(2024)
Article
Biochemistry & Molecular Biology
Alexander H. van Asbeck, Jurgen Dieker, Rik Oude Egberink, Lennard van den Berg, Johan van der Vlag, Roland Brock
Summary: The study found a linear correlation between dose, uptake, and expression under different delivery vehicles, cell lines, and incubation times, and differences in expression levels can be explained by the number of mRNAs packaged per delivery vehicle. Using mRNA provides excellent quantitative control over protein expression over extended periods of time.
Article
Materials Science, Multidisciplinary
Zhiyu Zhu, Hang Qu, Yaorong Chen, Chengyang Zhang, Ruihao Li, Yi Zhao, Yu Zhou, Zhixin Chen, Junyang Liu, Zongyuan Xiao, Wenjing Hong
Summary: By designing molecules with multiple anchoring sites, mechanical switching of single-molecule conductance and multiple transmission pathways can be achieved, leading to a four-order-of-magnitude change in conductance. This finding provides a reliable strategy for investigating single-molecule electronic devices.
JOURNAL OF MATERIALS CHEMISTRY C
(2021)
Article
Chemistry, Physical
Paul L. Houston, Chen Qu, Apurba Nandi, Riccardo Conte, Qi Yu, Joel M. Bowman
Summary: Researchers have recently made further improvements to permutationally invariant polynomial (PIP) regression, including compacting purified basis and speeding up gradient evaluation using reverse differentiation method. They found that PIP computation time for energy and force evaluation is significantly faster than other machine-learning methods, and have introduced a new PIP potential energy surface (PES) for ethanol.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Computer Science, Theory & Methods
Mordecai Golin, Elfarouk Harb
Summary: AIFV-2 codes are a new method for constructing lossless codes for memoryless sources that provide better worst-case redundancy than Huffman codes. By using two code trees and allowing some bounded delay in the decoding process, they achieve this improvement.
THEORETICAL COMPUTER SCIENCE
(2021)
Article
Engineering, Electrical & Electronic
Tsai-Sheng Gau, Po-Hsiung Chen, Burn J. J. Lin, Fu-Hsiang Ko, Chun-Kung Chen, Anthony Yen
Summary: An ultra-fast image simulation algorithm is developed using full fast-Fourier-transform (FFT). The algorithm scales the mask and calculates its diffraction spectrum using FFT. It then inverse transforms the diffraction spectrum to the aerial image. Compared to the original FT, this algorithm improves computation speed by 4000-5000 times with only about 3% intensity deviation. It provides an efficient engine for lithography optimization.
JOURNAL OF MICRO-NANOPATTERNING MATERIALS AND METROLOGY-JM3
(2023)
Article
Information Science & Library Science
Su Golder, Kelly Farrah, Monika Mierzwinski-Urban, Beth Barker, Anna Rama
Summary: This study developed and validated search filters for retrieving evidence on adverse drug effects from Ovid medline and Ovid Embase. The results showed that the search filters achieved high recall rates in retrieving adverse drug effects data. The study also found that adding specific adverse effects terms improved the recall rate of the search.
HEALTH INFORMATION AND LIBRARIES JOURNAL
(2023)
Proceedings Paper
Computer Science, Artificial Intelligence
Yosi Mass, Doron Cohen, Asaf Yehudai, David Konopnicki
Summary: This paper presents a method for dealing with conversational search scenarios, where user queries are under-specified or ambiguous. The method utilizes a mixed-initiative setup, where user-asks and system-answers, as well as system-asks and user response, are used to clarify information needs. The method leverages passage retrieval and fine-tuned deep-learning models to rank candidate clarification questions, and it performs well in two different use-cases.
PROCEEDINGS OF THE SECOND DIALDOC WORKSHOP ON DOCUMENT-GROUNDED DIALOGUE AND CONVERSATIONAL QUESTION ANSWERING (DIALDOC 2022)
(2022)
Article
Immunology
Sean Wei Xiang Ong, Calvin J. Chiew, Li Wei Ang, Tze-Minn Mak, Lin Cui, Matthias Paul H. S. Toh, Yi Ding Lim, Pei Hua Lee, Tau Hong Lee, Po Ying Chia, Sebastian Maurer-Stroh, Raymond T. P. Lin, Yee-Sin Leo, Vernon J. Lee, David Chien Lye, Barnaby Edward Young
Summary: The study revealed an association between infection with the B.1.617.2 variant and increased disease severity, higher viral loads, and prolonged duration of viral shedding. Vaccination remained protective against severe outcomes.
CLINICAL INFECTIOUS DISEASES
(2022)
Article
Medicine, Research & Experimental
Matthew Zirui Tay, Angeline Rouers, Siew-Wai Fong, Yun Shan Goh, Yi-Hao Chan, Zi Wei Chang, Weili Xu, Chee Wah Tan, Wan Ni Chia, Anthony Torres-Ruesta, Siti Naqiah Amrun, Yuling Huang, Pei Xiang Hor, Chiew Yee Loh, Nicholas Kim-Wah Yeo, Bei Wang, Eve Zi Xian Ngoh, Siti Nazihah Mohd Salleh, Jean-Marc Chavatte, Alicia Jieling Lim, Sebastian Maurer-Stroh, Lin-Fa Wang, Raymond Valentine Tzer Pin Lin, Cheng- Wang, Seow-Yen Tan, Barnaby Edward Young, Yee-Sin Leo, David C. Lye, Laurent Renia, Lisa F. P. Ng
Summary: The study found that the Delta variant of the SARS-CoV-2 virus can infect vaccinated individuals. Vaccine breakthrough cases showed lower memory B cell frequencies against the SARS-CoV-2 receptor-binding domain, but antibodies secreted by memory B cells retained neutralizing properties against the Delta variant. Inflammatory cytokines were lower in vaccine breakthrough infections compared to primary infections, highlighting the importance of vaccination in preventing inflammation.
EMBO MOLECULAR MEDICINE
(2022)
Article
Genetics & Heredity
Emmanuelle Szenker-Ravi, Tim Ott, Muznah Khatoo, Anne Moreau de Bellaing, Wei Xuan Goh, Yan Ling Chong, Anja Beckers, Darshini Kannesan, Guillaume Louvel, Priyanka Anujan, Vydianathan Ravi, Carine Bonnard, Sebastien Moutton, Patric Schoen, Melanie Fradin, Estelle Colin, Andre Megarbane, Linda Daou, Ghassan Chehab, Sylvie Di Filippo, Caroline Rooryck, Jean-Francois Deleuze, Anne Boland, Nicolas Arribard, Rukiye Eker, Sumanty Tohari, Alvin Yu-Jin Ng, Marlene Rio, Chun Teck Lim, Birgit Eisenhaber, Frank Eisenhaber, Byrappa Venkatesh, Jeanne Amiel, Hugues Roest Crollius, Christopher T. Gordon, Achim Gossler, Sudipto Roy, Tania Attie-Bitach, Martin Blum, Patrice Bouvagnet, Bruno Reversade
Summary: Phylogenomic and genetic analyses have identified an ancestral module of genes expressed specifically in ciliated left-right organizer tissue, which is essential for left-right axis specification in humans and certain vertebrates. CIROP, a newly discovered gene encoding an extracellular protein, is shown to be specifically expressed in ciliated LROs and plays a crucial role in distinguishing left from right in vertebrates. Mutations in the CIROP gene have been found in human patients with recessive situs anomalies, highlighting the importance of this gene in determining left-right asymmetry.
Editorial Material
Biochemistry & Molecular Biology
Frank Eisenhaber, Chandra Verma, Tom Blundell
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2022)
Editorial Material
Biotechnology & Applied Microbiology
Frank Eisenhaber, Juilee Thakar, Alicia Ponte-Sucre, Thomas Dandekar
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Medicine, General & Internal
Junxiong Pang, Huei Nuo Tan, Tze Minn Mak, Sophie Octavia, Sebastian Maurer-Stroh, Fernanda L. Sirota, Mark Peng Chew Chan, Ian Yi Onn Leong, Valerie T. J. Koh, Peng Lim Ooi, Shawn Vasoo, Dale Fisher, Lin Cui, Heidi Rafman, Jeffery Cutter, Vernon J. Lee
Summary: This study aims to determine the potential sources of SARS-CoV-2 transmission in the first nursing home facility in Singapore. The findings suggest that household transmission is a possible source of introduction into the nursing home. Among residents, a higher proportion of non-survivors were asymptomatic and had hypertension.
FRONTIERS IN MEDICINE
(2022)
Correction
Genetics & Heredity
Emmanuelle Szenker-Ravi, Tim Ott, Muznah Khatoo, Anne Moreau de Bellaing, Wei Xuan Goh, Yan Ling Chong, Anja Beckers, Darshini Kannesan, Guillaume Louvel, Priyanka Anujan, Vydianathan Ravi, Carine Bonnard, Sebastien Moutton, Patric Schoen, Melanie Fradin, Estelle Colin, Andre Megarbane, Linda Daou, Ghassan Chehab, Sylvie Di Filippo, Caroline Rooryck, Jean-Francois Deleuze, Anne Boland, Nicolas Arribard, Rukiye Eker, Sumanty Tohari, Alvin Yu-Jin Ng, Marlene Rio, Chun Teck Lim, Birgit Eisenhaber, Frank Eisenhaber, Byrappa Venkatesh, Jeanne Amiel, Hugues Roest Crollius, Christopher T. Gordon, Achim Gossler, Sudipto Roy, Tania Attie-Bitach, Martin Blum, Patrice Bouvagnet, Bruno Reversade
Article
Biochemistry & Molecular Biology
Minh N. Nguyen, Nora L. Krutz, Vachiranee Limviphuvadh, Andreas L. Lopata, G. Frank Gerberick, Sebastian Maurer-Stroh
Summary: AllerCatPro 2.0 is a web server for predicting the allergenic potential of proteins with better accuracy than other methods, and new features to help assessors make informed decisions. It predicts protein similarity using amino acid sequences and predicted 3D structures.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Cell Biology
Jovian Lin Jing, Trishia Cheng Yi Ning, Federica Natali, Frank Eisenhaber, Mohammad Alfatah
Summary: Aging is a global challenge, but iron supplementation can delay aging and increase cellular lifespan by upregulating mitochondrial genes and increasing ATP levels. Additionally, iron supplementation has anti-aging effects in AMPK knockout mutants. Thus, iron supplementation has potential therapeutic applications for delaying aging and prolonging healthy lifespan.
Article
Biology
Erwin Tantoso, Birgit Eisenhaber, Miles Kirsch, Vladimir Shitov, Zhiya Zhao, Frank Eisenhaber
Summary: This study systematically analyzed the pangenome of E. coli and explored the biological characteristics of different subtypes. The findings indicate that the softcore genome can define the genome of a bacterial species, providing insights into evolutionarily important gene families.
Article
Geriatrics & Gerontology
Mohammad Alfatah, Frank Eisenhaber
Summary: Although aging is a major risk factor for chronic diseases, there are limited interventions directly targeting aging. Cellular aging is the basis for aging processes, and yeast serves as a model for studying human cellular aging. Researchers have developed a fast and high-throughput method for measuring yeast cell lifespan and used it to identify a compound with anti-aging potential.
Article
Immunology
Hui Chen, Junqiu Wang, Yunsong Liu, Ivy Quek Ee Ling, Chih Chuan Shih, Dafei Wu, Zhiyan Fu, Raphael Tze Chuen Lee, Miao Xu, Vincent T. Chow, Sebastian Maurer-Stroh, Da Zhou, Jianjun Liu, Weiwei Zhai
Summary: This study aims to develop a computational tool for selecting the best candidate vaccine virus (CVV) based on the negative correlation between egg passage adaptation and vaccine effectiveness (VE). They characterized the pattern of sequence evolution driven by egg passage adaptation and developed a new metric known as the adaptive distance (AD) which measures the overall strength of egg passage adaptation. They found that AD is negatively correlated with influenza H3N2 vaccine effectiveness (VE) and developed a computational package called MADE to measure the adaptive distance and predict vaccine effectiveness.
Article
Biology
Erwin Tantoso, Birgit Eisenhaber, Swati Sinha, Lars Juhl Jensen, Frank Eisenhaber
Summary: This study aims to quantify the impact of scientific literature on the E. coli gene function space and assess our progress towards a complete list of E. coli gene functions. The results show that the coverage of scientific literature for E. coli genes is extremely uneven, with a few elite genes receiving the majority of the research attention. Most genes have at least one mention in a dedicated scientific article, but there are still some genes that remain completely unstudied. The growth rate of literature for uncharacterized or understudied genes was highest until 2005-2010 and has since become negative. Once a gene reaches a literature threshold of 10 full publication equivalents (FPEs), most of the critical fundamental research risks seem to be overcome.
Article
Medical Informatics
Arsen Batagov, Rinkoo Dalan, Andrew Wu, Wenbin Lai, Colin S. Tan, Frank Eisenhaber
Summary: Chronic metabolic diseases are caused by accumulated changes in metabolic fluxes and gene networks over an individual's lifetime. Computational models, such as GMFA, are necessary to understand the pathological disturbances in biomolecular processes and achieve personalized insights into disease progression. By grouping metabolites/fluxes into pools and mapping clinical modalities onto the network, GMFA simplifies analysis and allows for prediction of disease dynamics and the evolution of metabolic health state.
HEALTH INFORMATION SCIENCE AND SYSTEMS
(2023)
Article
Immunology
Yun Shan Goh, Siew-Wai Fong, Pei Xiang Hor, Chiew Yee Loh, Bei Wang, Siti Nazihah Mohd Salleh, Eve Zi Xian Ngoh, Raphael Tze Chuen Lee, Xuan Ying Poh, Suma Rao, Po Ying Chia, Sean W. X. Ong, Tau Hong Lee, Clarissa Lim, Jefanie Teo, Surinder Pada, Louisa Jin Sun, Desmond Luan Seng Ong, Jyoti Somani, Eng Sing Lee, Sebastian Maurer-Stroh, Cheng- Wang, Yee-Sin Leo, David C. Lye, Barnaby Edward Young, Lisa F. P. Ng, Laurent Renia
Summary: This study found that individuals with a higher variant-specific IgA antibody response one month after booster vaccination were associated with a lower risk of infection. Individuals who remained uninfected for at least 8 months had higher variant-specific IgA levels compared to those who became infected.
JOURNAL OF INFECTIOUS DISEASES
(2023)
