Article
Operations Research & Management Science
Nicolas Boutet, Rob Haelterman, Joris Degroote
Summary: This paper proposes a new update formula for the estimate of the Hessian matrix in optimization, called generalised PSB (gPSB), which combines the Powell-Symetric-Broyden formula with information from previous optimization steps. The study provides a novel interpretation of the non-existence of gPSB and compares it with other methods to show its advantages in estimating the Hessian matrix.
COMPUTATIONAL OPTIMIZATION AND APPLICATIONS
(2021)
Article
Environmental Studies
Shiquan Dou, Chen Yue, Deyi Xu, Yi Wei, Hang Li
Summary: This article examines the impact of natural resource utilization on economic development, arguing that there is heterogeneity in this relationship. By combining mineral location data with nighttime light data, the study finds that natural resource utilization has a significant positive effect on the county economy in Guangxi Province, China, with no evidence of a resource curse. The study suggests that improving institutional quality can enhance the sustainability of mining-led development.
Article
Environmental Studies
Roger F. Auch, Danika F. Wellington, Janis L. Taylor, Stephen V. Stehman, Heather J. Tollerud, Jesslyn F. Brown, Thomas R. Loveland, Bruce W. Pengra, Josephine A. Horton, Zhe Zhu, Alemayehu A. Midekisa, Kristi L. Sayler, George Xian, Christopher P. Barber, Ryan R. Reker
Summary: This study used sample-based estimates and complete coverage land-cover maps to analyze and describe the patterns of annual land-cover change in the contiguous United States (CONUS) from 1985 to 2016. The results showed that while most of the land cover remained stable over the period, there were significant changes in natural resource cycles, urbanization, and surface-water dynamics. The study also revealed a reduction in the rate of urban expansion after 2006, new growth in cropland after 2007, a net decline in cropland since 1985, and two periods of net tree cover loss.
Article
Agronomy
Fangfang Huang, Yingru Jiang, Tiantian Chen, Haoran Li, Mengjia Fu, Yazhou Wang, Yufang Xu, Yang Li, Zhengfu Zhou, Lihua Jia, Yidan Ouyang, Wen Yao
Summary: This article summarizes the updates and new features of the funRiceGenes database, highlighting its importance in rice functional genomics studies.
Article
Environmental Sciences
Shi Bai, Jie Zhao
Summary: Geochemical data is widely used in mineral exploration, environmental assessment, and resource potential analysis. However, the spatial accuracy of geochemical data often limits decision-making. Harsh natural and geographic conditions make geochemical sampling difficult in some areas, resulting in medium/low-precision survey data that may not be adequate for regional mapping and exploration. The use of remote sensing technology can help address this issue.
Article
Energy & Fuels
Ziyu Gu, Shuwei Pang, Wenxiang Zhou, Yuchen Li, Qiuhong Li
Summary: This paper proposes an online data-driven LPV modeling method based on online sequential extreme learning machine. By inserting an additional multiplying layer between the hidden layer and the output layer, the input and output of the LPV model are multiplied, improving the accuracy and efficiency of the modeling.
Article
Geosciences, Multidisciplinary
Ylenia Saretta, Luca Sbrogi, Maria Rosa Valluzzi
Summary: The study assigned vulnerability classes to strengthened buildings in Italy by considering factors such as masonry quality, diaphragm stiffness, and type of interventions. Improving interventions led to improved building performance similar to modern constructions, while rubble stone buildings with downgrading interventions behaved like their original conditions.
INTERNATIONAL JOURNAL OF DISASTER RISK REDUCTION
(2021)
Article
Mathematics, Applied
Xiaolin Zhou, Gang Cai, Prasit Cholamjiak, Suparat Kesornprom
Summary: This paper investigates a generalized proximal method with a new step size update for solving the variational inequality problem in Hilbert spaces. Weak convergence of the proposed scheme is proven under certain assumptions on the operators and parameters, with an additional R-linear convergence rate when the operator is strongly monotone. Numerical experiments are conducted to demonstrate the efficacy of the proposed iterative algorithm, and it is noted that several existing methods in the literature are special cases of the proposed method.
JOURNAL OF COMPUTATIONAL AND APPLIED MATHEMATICS
(2024)
Article
Engineering, Electrical & Electronic
Itai E. Berman, Tirza Routtenberg
Summary: The paper explores the performance optimization of the linear minimum mean-squared error estimator under a mixed-resolution model, proposing a linear Gaussian orthonormal measurement model and optimizing resource allocation and dithering strategies. It attempts to address the impact of quantized signals on data estimation performance.
IEEE TRANSACTIONS ON SIGNAL PROCESSING
(2021)
Article
Chemistry, Multidisciplinary
Karen Manalastas-Cantos, Petr Konarev, Nelly R. Hajizadeh, Alexey G. Kikhney, Maxim Petoukhov, Dmitry S. Molodenskiy, Alejandro Panjkovich, Haydyn D. T. Mertens, Andrey Gruzinov, Clemente Borges, Cy M. Jeffries, Dmitri Svergun, Daniel Franke
Summary: ATSAS 3.0 introduces new programs and technical updates for processing small-angle scattering data from biological macromolecules. It includes features like simulating scattering patterns, resampling methods, pair distance distribution calculation, and adding new analysis tools. The package also includes improvements for maintainability, compatibility, and is freely available for academic users.
JOURNAL OF APPLIED CRYSTALLOGRAPHY
(2021)
Article
Economics
Prasad Buddhavarapu, Prateek Bansal, Jorge A. Prozzi
Summary: Recent crash frequency studies have limitations in addressing temporal variation in model parameters and convergence issues in Gibbs sampler due to non-conjugacy. A new count data model is proposed to identify temporal patterns of regression parameters and allow for time-varying spatial correlation and heterogeneity in non-temporal parameters. Improvement is made by deriving a Gibbs sampler with conditionally conjugate posterior updates for all model parameters.
TRANSPORTATION RESEARCH PART B-METHODOLOGICAL
(2021)
Article
Automation & Control Systems
Zefeng Chen, Abhishek Gupta, Lei Zhou, Yew-Soon Ong
Summary: In this article, a method is proposed to quickly optimize large datasets using auxiliary source tasks. A computational resource allocation strategy is designed to effectively utilize these auxiliary tasks. Experimental results show that the proposed algorithm achieves higher speedup compared to existing methods, demonstrating its efficiency in handling real-world multiobjective optimization problems involving large datasets.
IEEE TRANSACTIONS ON CYBERNETICS
(2022)
Review
Business
Yucheng Zhang, Shan Xu, Long Zhang, Mengxi Yang
Summary: The lack of sufficient big data-based approaches hinders the advancement of HRM research and practices. Scholars are aware of the importance of applying big data approaches, but there is a need for clear guidance on integration. This study provides a framework for conducting big data research in HRM and proposes a future research agenda and challenges in the era of big data.
JOURNAL OF BUSINESS RESEARCH
(2021)
Article
Hematology
Laurie H. Sehn, Mark Hertzberg, Stephen Opat, Alex F. Herrera, Sarit Assouline, Christopher R. Flowers, Tae Min Kim, Andrew McMillan, Muhit Ozcan, Violaine Safar, Gilles Salles, Grace Ku, Jamie Hirata, Yi Meng Chang, Lisa Musick, Matthew J. Matasar
Summary: Polatuzumab vedotin plus bendamustine and rituximab (pola + BR) has been approved for the treatment of relapsed/refractory diffuse large B-cell lymphoma (R/R DLBCL) based on the results of the GO29365 study. The study reported updated results from the randomized arms and the extension cohort, showing that pola + BR is an effective treatment option with a well-characterized safety profile.
Article
Automation & Control Systems
Yanling Wei, Hamid Reza Karimi, Shichun Yang
Summary: This article presents a novel sampled-data static output-feedback control technique for continuous-time linear parameter-varying systems. By introducing the input-delay approach and parameter-dependent Lyapunov-Krasovskii functional, a bounded real lemma is achieved. Moreover, the controller synthesis problem is transformed into a group of parameterized matrix inequalities with convex optimization techniques, and it is shown that the controller can depend on time-varying parameters.
INTERNATIONAL JOURNAL OF ROBUST AND NONLINEAR CONTROL
(2022)
Article
Physiology
Sophie L. Dahl, Svende Pfundstein, Rico Hunkeler, Xingtong Dong, Thomas Knoepfel, Patrick Spielmann, Carsten C. Scholz, Karen A. Nolan, Roland H. Wenger
Summary: Fibroblast-like renal erythropoietin (Epo) producing (REP) cells respond to tissue hypoxia and play a role in erythropoiesis. However, during fibrotic tissue remodelling, Epo expression is inhibited. This study found that REP cells do not die, proliferate, migrate, or differentiate into myofibroblasts. Instead, there is a transient repression of Epo transcription. Additionally, REP cells can be repeatedly recruited by tissue hypoxia, and a pharmacological hypoxia-inducible factor (HIF) stabilizer can rescue dormant REP cells and restore Epo expression. These findings demonstrate the persistence and functionality of REP cells during Epo suppression.
Article
Chemistry, Medicinal
Melanie Schneider, Vanessa Delfosse, Muriel Gelin, Marina Grimaldi, Meritxell Granell, Laurene Heriaud, Jean-Luc Pons, Martin Cohen Gonsaud, Patrick Balaguer, William Bourguet, Gilles Labesse
Summary: By determining the crystal structure of dabrafenib bound to PXR and analyzing its mode of binding to both PXR and its primary target, B-Raf-V600E, new compounds with nanomolar activity against B-Raf and no detectable affinity for PXR were derived. The crystal structure of B-Raf in complex with the lead compound revealed a subdomain swapping of the activation loop with potentially important functional implications for prolonged inhibition of B-Raf-V600E.
JOURNAL OF MEDICINAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Caroline Benz, Muhammad Ali, Izabella Krystkowiak, Leandro Simonetti, Ahmed Sayadi, Filip Mihalic, Johanna Kliche, Eva Andersson, Per Jemth, Norman E. Davey, Ylva Ivarsson
Summary: Specific protein-protein interactions are crucial for cell physiology, but many interactions are yet to be discovered. This study introduces an optimized peptide-phage display library that allows for the screening of numerous peptides in a single binding assay, aiding the discovery of SLiM-based interactions.
MOLECULAR SYSTEMS BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Manjeet Kumar, Sushama Michael, Jesus Alvarado-Valverde, Balint Meszaros, Hugo Samano-Sanchez, Andras Zeke, Laszlo Dobson, Tamas Lazar, Mihkel Ord, Anurag Nagpal, Nazanin Farahi, Melanie Kaser, Ramya Kraleti, Norman E. Davey, Rita Pancsa, Lucia B. Chemes, Toby J. Gibson
Summary: The Eukaryotic Linear Motif (ELM) resource remains a crucial source of information for motif-mediated protein-protein interactions, with the current update adding new motif classes focused on various cellular processes. The resource continues to face challenges in keeping up-to-date due to the increasing number of SLiM-mediated interactions being discovered.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Federica Quaglia, Balint Meszaros, Edoardo Salladini, Andras Hatos, Rita Pancsa, Lucia B. Chemes, Matyas Pajkos, Tamas Lazar, Samuel Pena-Diaz, Jaime Santos, Veronika Acs, Nazanin Farahi, Erzsebet Ficho, Maria Cristina Aspromonte, Claudio Bassot, Anastasia Chasapi, Norman E. Davey, Radoslav Davidovic, Laszlo Dobson, Arne Elofsson, Gabor Erdos, Pascale Gaudet, Michelle Giglio, Juliana Glavina, Javier Iserte, Valentin Iglesias, Zsofia Kalman, Matteo Lambrughi, Emanuela Leonardi, Sonia Longhi, Sandra Macedo-Ribeiro, Emiliano Maiani, Julia Marchetti, Cristina Marino-Buslje, Attila Meszaros, Alexander Miguel Monzon, Giovanni Minervini, Suvarna Nadendla, Juliet F. Nilsson, Marian Novotny, Christos A. Ouzounis, Nicolas Palopoli, Elena Papaleo, Pedro Jose Barbosa Pereira, Gabriele Pozzati, Vasilis J. Promponas, Jordi Pujols, Alma Carolina Sanchez Rocha, Martin Salas, Luciana Rodriguez Sawicki, Eva Schad, Aditi Shenoy, Tamas Szaniszlo, Konstantinos D. Tsirigos, Nevena Veljkovic, Gustavo Parisi, Salvador Ventura, Zsuzsanna Dosztanyi, Peter Tompa, Silvio C. E. Tosatto, Damiano Piovesan
Summary: The latest update of DisProt version 9 includes a restyled web interface, refactored IDPO, improvements in curation process, and around 30% content growth. The newly implemented reviewing process and curator training aim to provide higher quality and more consistent annotations. Integration with APICURON and adoption of MIADE standard, along with collaborations with GO and ECO consortia and support from ELIXIR infrastructure, enhance interoperability.
NUCLEIC ACIDS RESEARCH
(2022)
Editorial Material
Biochemistry & Molecular Biology
Norman E. Davey, Leandro Simonetti, Ylva Ivarsson
TRENDS IN BIOCHEMICAL SCIENCES
(2022)
Article
Biology
Marta Ripamonti, Andrea Lamarca, Norman E. Davey, Diletta Tonoli, Sara Surini, Ivan de Curtis
Summary: Scaffold protein liprin-alpha 1 plays an important role in assembling plasma membrane-associated platforms (PMAPs) at the front of migrating breast cancer cells. It interacts with B56 regulatory subunits and mediates the interaction between liprin-alpha 1 and the heterotrimeric PP2A holoenzyme. B56 gamma/PP2A is a novel component of the PMAPs machinery regulating tumor cell motility.
COMMUNICATIONS BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Priyanka Madhu, Norman E. Davey, Ylva Ivarsson
Summary: Viruses exploit the host cellular machinery to replicate through interactions with host proteins, including recognition of host globular domains by short linear motifs or intrinsically disordered domains. This review focuses on the strategies used by viruses to bind to the disordered regions of human or viral ligands, including the use of viral domains and proteins. Protein-protein interactions are crucial for viral replication and may be targets for inhibitor design.
ESSAYS IN BIOCHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Mehmet Akdel, Douglas E. Pires, Eduard Porta Pardo, Jurgen Janes, Arthur O. Zalevsky, Balint Meszaros, Patrick Bryant, Lydia L. Good, Roman A. Laskowski, Gabriele Pozzati, Aditi Shenoy, Wensi Zhu, Petras Kundrotas, Victoria Ruiz Serra, Carlos H. M. Rodrigues, Alistair S. Dunham, David Burke, Neera Borkakoti, Sameer Velankar, Adam Frost, Jerome Basquin, Kresten Lindorff-Larsen, Alex Bateman, Andrey Kajava, Alfonso Valencia, Sergey Ovchinnikov, Janani Durairaj, David B. Ascher, Janet M. Thornton, Norman E. Davey, Amelie Stein, Arne Elofsson, Tristan Croll, Pedro Beltrao
Summary: This study evaluates the performance of AlphaFold2 in structural biology applications and finds that it performs well and can partially replace experimentally determined structures, which is of great significance for life science research.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2022)
Article
Microbiology
Steffen Klein, Gonen Golani, Fabio Lolicato, Carmen Lahr, Daniel Beyer, Alexia Herrmann, Moritz Wachsmuth-Melm, Nina Reddmann, Romy Brecht, Mehdi Hosseinzadeh, Androniki Kolovou, Jana Makroczyova, Sarah Peterl, Martin Schorb, Yannick Schwab, Britta Bruegger, Walter Nickel, Ulrich S. Schwarz, Petr Chlanda
Summary: Interferon-induced transmembrane protein 3 (IFITM3) inhibits virus entry through lipid sorting to stabilize hemifusion and prevent fusion pore formation, ultimately leading to viral degradation in lysosomes. In situ cryo-electron tomography confirms the arrest of viral membrane fusion by IFITM3 and identifies hemifusion stabilization as the molecular mechanism. The presence of post-fusion conformation of the influenza fusion protein hemagglutinin near hemifusion sites further suggests that IFITM3 does not interfere with viral fusion machinery.
CELL HOST & MICROBE
(2023)
Article
Biochemistry & Molecular Biology
Elizabeth Martinez-Perez, Matyas Pajkos, Silvio C. E. Tosatto, Toby J. Gibson, Zsuzsanna Dosztanyi, Cristina Marino-Buslje
Summary: DisProt is a curated database of Intrinsically Disordered Proteins (IDPs) with strong experimental support. Transferring annotations regarding disorder state and functions to homologous proteins in other species is important for understanding their biological roles. With the use of a pipeline, it is possible to transfer annotations from DisProt proteins to their orthologs, resulting in a large number of transferred terms by homology.
Article
Oncology
Artem Baranovskii, Irem B. Guenduez, Vedran Franke, Bora Uyar, Altuna Akalin
Summary: Cancer is a complex disease with heterogeneous subtypes, and the current genomic analysis panels only partially reflect the tumor's response to cancer drugs. This study demonstrates that incorporating transcriptome information on top of genomic aberrations significantly improves the prediction of drug response.
Article
Gastroenterology & Hepatology
Annika Behrendt, Pegah Golchin, Filip Koenig, Daniel Mulnaes, Amelie Stalke, Carola Droege, Verena Keitel, Holger Gohlke
Summary: The article introduces a machine learning-based model called Vasor for predicting the benign or pathogenic classification of missense variants in MDR3. Vasor outperforms other prediction tools and covers the entire sequence space of MDR3. Vasor provides a fast and reliable assessment of the impact of single-site variants on their substitution sites.
HEPATOLOGY COMMUNICATIONS
(2022)
