Article
Chemistry, Analytical
Andras Guttman, Csenge Filep, Barry L. Karger
Summary: Recent advancements in protein therapeutics necessitate high-resolution bioseparation techniques, such as SDS-CGE using a borate cross-linked dextran matrix. By adjusting the dextran and borate concentration ratios, optimal separation for specific biopharmaceutical modalities can be achieved with excellent reproducibilities.
ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Basab Kanti Das, Raju Samanta, Sahnawaz Ahmed, Bapan Pramanik
Summary: A peptide hydrogelator containing a C-terminal cysteine can form insoluble hydrogel through non-covalent and covalent interactions, exhibiting thixotropic and injectable properties. It has been utilized for the removal of organic dyes from wastewater, offering a reliable, straightforward, nontoxic, cheap, and environmentally friendly adsorbent.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Biochemical Research Methods
Rong Huang, Wei Zhu, Zili Xu, Jiakang Chen, Biao Jiang, Hongli Chen, Wenzhang Chen
Summary: The study found that monolinked peptides carry information on the retention time of corresponding cross-linked pairs, enabling accurate prediction of retention time for cross-linked peptide pairs. By using retention time as an additional filter, false positive rate can be reduced significantly. The T-DTSS method not only improves identification confidence for protein-protein interactions but also increases the number of inter-cross-links identified.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2021)
Article
Biochemistry & Molecular Biology
Kelti A. Smith, Mickael Dang, Alexander E. G. Baker, Tobias Fuehrmann, Ana Fokina, Molly S. Shoichet
Summary: Detachment of fragile cell types cultured on 2D surfaces has been shown to be detrimental to their viability. A reversible cross-linked hydrogel was synthesized for cell culture and differentiation, which is stable and can be cleaved by an external stimulus for injection. The hydrogel demonstrated good stability, enzyme-sensitive degradation, and cytocompatibility with iPSC-derived neural progenitor cells, laying the foundation for broad applicability.
Article
Biochemistry & Molecular Biology
Taj Muhammad, Adam A. A. Stromstedt, Sunithi Gunasekera, Ulf Goransson
Summary: By designing backbone-cyclized dimers cross-linked via a disulfide bond, the structural stability and biological activity of truncated antimicrobial peptide KR-12 derived from LL-37 were improved. One of the cross-linked dimers showed significantly increased antimicrobial activity against human pathogens and retained activity under physiologically relevant conditions. This study provides insight into the structure-activity relationship of KR-12 and demonstrates its potential as a potent antimicrobial peptide drug lead.
Article
Economics
Zifeng Zhao, Peng Shi, Zhengjun Zhang
Summary: This article introduces a novel multivariate time series model named CuDvine, which models both temporal and cross-sectional dependence simultaneously. By linking multiple uDvines, CuDvine provides a flexible model that can handle complex time series dependency issues.
JOURNAL OF BUSINESS & ECONOMIC STATISTICS
(2022)
Article
Mathematics, Applied
Fatemeh Keshavarz-Kohjerdi, Alireza Bagheri
Summary: This paper solves the problem for a special class of solid grid graphs, i.e. truncated rectangular grid graphs, in linear time.
APPLIED MATHEMATICS AND COMPUTATION
(2023)
Article
Biochemistry & Molecular Biology
Jana Dvorakova, Jiri Trousil, Bohumila Podhorska, Zuzana Miksovska, Olga Janouskova, Vladimir Proks
Summary: Injectable hydrogel scaffolds combined with stem cell therapy offer a promising approach for tissue repair. The developed synthetic hydrogel was modified with an integrin-binding peptide, showing long-term survival of encapsulated cells and providing a suitable microenvironment for stem cell therapy. The study highlights the importance of optimizing mechanical properties and gelation time for successful application in 3D cell culture.
Article
Energy & Fuels
Tejavathu Ramesh, Kandipati Rajani, Anup Kumar Panda
Summary: This paper introduces a novel PV array configuration that outperforms traditional configurations in terms of power extraction under partial shading conditions.
CSEE JOURNAL OF POWER AND ENERGY SYSTEMS
(2021)
Article
Computer Science, Artificial Intelligence
Lunshan Gao
Summary: This paper proposes a new randomized algorithm that uses fuzzy logic to solve the local Max-Cut problem in graphs. The paper proves the computational complexity and effectiveness of the algorithm and demonstrates its superiority over IBM CPLEX solvers, especially in signed graphs.
Article
Computer Science, Artificial Intelligence
Joel Honkamaa, Umair Khan, Sonja Koivukoski, Mira Valkonen, Leena Latonen, Pekka Ruusuvuori, Pekka Marttinen
Summary: This work proposes a generic solution for cross-modality image synthesis with paired but non-aligned data by introducing new deformation equivariance encouraging loss functions. The method involves joint training of an image synthesis network and separate registration networks, allowing adversarial training even with misaligned data. It lowers the barriers for training cross-modality image synthesis networks for more difficult data sets.
MEDICAL IMAGE ANALYSIS
(2023)
Article
Multidisciplinary Sciences
Xuesong Xie, Jingjing Li, Zhengyue Xing, Bingan Lu, Shuquan Liang, Jiang Zhou
Summary: This study proposes a green and programmable electro-cross-linking strategy to synthesize highly hierarchical Zn-alginate electrolytes via superionic binding between carboxylate groups and Zn2+. The resulting electrolyte exhibits high reversibility, long-time stability, and high biocompatibility, making it suitable for modern wearable and implantable devices.
NATIONAL SCIENCE REVIEW
(2023)
Article
Mathematics, Applied
Francesco Leonetti, Marta Macri, Pier Vincenzo Petricca
Summary: In the framework of nonlinear elasticity, the study focuses on a mapping problem under constraints, with positive results obtained when certain conditions are met.
JOURNAL OF MATHEMATICAL ANALYSIS AND APPLICATIONS
(2021)
Article
Economics
Xuan Liang, Jiti Gao, Xiaodong Gong
Summary: This article examines a semiparametric spatial autoregressive (SAR) panel data model with fixed effects and time-varying coefficients, proposing a local linear quasi-maximum likelihood estimation method. It reveals significant spatial dependence among Chinese cities, with the impacts of capital, investment, and the economy's structure on labor compensation changing over time.
JOURNAL OF BUSINESS & ECONOMIC STATISTICS
(2022)
Article
Polymer Science
Iris G. Mercer, Angelina N. Italiano, Irina G. Gazaryan, Aaron B. Steiner, Sergey V. Kazakov
Summary: This study investigates the kinetics of degradation and drug release of biodegradable microgels. The results show that degradation occurs through the cleavage of disulfide bonds, leading to swelling and erosion processes. The kinetics of swelling and erosion are dependent on the concentration of the reducing agent glutathione. These findings suggest that drug release profiles can be different in cancer cells compared to normal cells.
Article
Genetics & Heredity
Shuang Song, Wei Jiang, Yiliang Zhang, Lin Hou, Hongyu Zhao
Summary: Heritability is a crucial concept in genetic studies, and LD eigenvalue regression (LDER) is an extended method that utilizes LD information to estimate genetic contributions more accurately and differentiate between polygenicity and confounding effects.
AMERICAN JOURNAL OF HUMAN GENETICS
(2022)
Article
Biotechnology & Applied Microbiology
Assaf Kacen, Aaron Javitt, Matthias P. Kramer, David Morgenstern, Tomer Tsaban, Merav D. Shmueli, Guo Ci Teo, Felipe da Veiga Leprevost, Eilon Barnea, Fengchao Yu, Arie Admon, Lea Eisenbach, Yardena Samuels, Ora Schueler-Furman, Yishai Levin, Alexey Nesvizhskii, Yifat Merbl
Summary: This study describes an antigen discovery pipeline that analyzes different post-translational modifications (PTMs) of antigens, expands the antigen landscape, and reveals disease-specific modified targets, which have important implications for T cell-mediated therapies in cancer and other fields.
NATURE BIOTECHNOLOGY
(2023)
Article
Respiratory System
Ming Chen, Yiliang Zhang, Taylor Adams, Dingjue Ji, Wei Jiang, Louise Wain, Michael Cho, Naftali Kaminski, Hongyu Zhao
Summary: Our study identified new genes associated with IPF susceptibility through integrative analysis, expanding the understanding of the complex genetic architecture and disease mechanism of IPF.
Article
Chemistry, Analytical
Junho Park, Fengchao Yu, James M. Fulcher, Sarah M. Williams, Kristin Engbrecht, Ronald J. Moore, Geremy C. Clair, Vladislav Petyuk, Alexey I. Nesvizhskii, Ying Zhu
Summary: To overcome the issue of ratio compression in isobaric labeling-based multiplexed single-cell proteomics, we developed an improved MS3-based method using a linear ion trap. This method increased proteome coverage for single-cell-level peptides and was applied to study immune activation in single macrophages.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Wenxuan Deng, Bolun Li, Jiawei Wang, Wei Jiang, Xiting Yan, Ningshan Li, Milica Vukmirovic, Naftali Kaminski, Jing Wang, Hongyu Zhao
Summary: Computational cell type deconvolution can reveal cell type proportion heterogeneity in samples. This study introduces tranSig, a novel Bayesian framework, to improve signature matrix inference from single-cell RNA sequencing data. The simulations and applications show that tranSig is accurate and robust in defining gene expression signatures of different cell types, facilitating improved in silico cell type deconvolutions.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemical Research Methods
Daniel A. Polasky, Daniel J. Geiszler, Fengchao Yu, Kai Li, Guo Ci Teo, Alexey I. Nesvizhskii
Summary: Posttranslational modifications of proteins play crucial roles in defining and regulating protein functions. Traditional methods for identifying these modifications using mass spectrometry-based proteomics have limitations, as they treat modifications as static attachments to peptide sequences. However, many modifications undergo fragmentation during mass spectrometry experiments, offering opportunities for improved searches. In this study, a new labile mode in the MSFragger search engine was developed to incorporate modification-specific fragment ions, resulting in significant improvements in identifying phosphopeptides, RNA-crosslinked peptides, and ADP-ribosylated peptides.
MOLECULAR & CELLULAR PROTEOMICS
(2023)
Article
Biochemistry & Molecular Biology
Shuaijian Dai, Shichang Liu, Chen Zhou, Fengchao Yu, Guang Zhu, Wenhao Zhang, Haiteng Deng, Al Burlingame, Weichuan Yu, Tingliang Wang, Ning Li
Summary: In this study, the researchers used cross-linking mass spectrometry to analyze the nuclear proteins in soybean seedlings, and identified 1297 nuclear protein-protein interactions. They also constructed a network model for these interactions, and discovered several ethylene-specific module variants.
Article
Multidisciplinary Sciences
Georges Bedran, Daniel A. Polasky, Yi Hsiao, Fengchao Yu, Felipe da Veiga Leprevost, Javier A. Alfaro, Marcin Cieslik, Alexey I. Nesvizhskii
Summary: In this study, a fast computational workflow merging the MSFragger-Glyco search algorithm with a false discovery rate control is introduced for analyzing glycopeptides from mass spectrometry-based immunopeptidome data. The authors analyze eight large-scale publicly available studies and find that glycosylated MHC-associated peptides are predominantly presented by MHC class II. They present a comprehensive resource, HLA-Glyco, which contains over 3,400 human leukocyte antigen (HLA) class II N-glycopeptides from 1,049 distinct protein glycosylation sites. This resource provides valuable insights into glycosylation properties in antigen recognition and immune modulation.
NATURE COMMUNICATIONS
(2023)
Article
Biochemical Research Methods
Ruizhi Zhu, Han Chen, Meiyan Liu, Yanqun Xu, Wei Jiang, Xiaoxi Si, Lunzhao Yi, Ying Gu, Dabing Ren, Juan Wang
Summary: A chemical isotope labeling strategy coupled with ultra-high performance liquid chromatography-high resolution mass spectrometry (UHPLC-HRMS) was developed for the capture and detection of aldehydes and ketones. A post-acquisition data processing method called MSFilter was proposed to facilitate the screening and identification of these compounds in complex matrices.
JOURNAL OF CHROMATOGRAPHY A
(2023)
Article
Health Care Sciences & Services
Yuhan Xie, Song Zhai, Wei Jiang, Hongyu Zhao, Devan Mehrotra, Judong Shen
Summary: In the era of precision medicine, biomarkers associated with drug efficacy and safety responses are used for patient stratification and drug response prediction. Meta-analysis is commonly used to identify prognostic and predictive biomarkers, but it is challenging to find independent studies for replication, limiting the impact of discovered biomarkers.
STATISTICAL METHODS IN MEDICAL RESEARCH
(2023)
Article
Multidisciplinary Sciences
Fengchao Yu, Guo Ci Teo, Andy T. T. Kong, Klemens Froehlich, Ginny Xiaohe Li, Vadim Demichev, Alexey I. Nesvizhskii
Summary: MSFragger-DIA is a fast and sensitive tool for direct peptide identification from DIA spectra, demonstrating excellent performance in applications such as large-scale tumor studies and single-cell proteomics.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Kevin L. Yang, Fengchao Yu, Guo Ci Teo, Kai Li, Vadim Demichev, Markus Ralser, Alexey I. Nesvizhskii
Summary: This article presents an accessible method to improve peptide spectrum match rescoring using deep learning predictions in bottom-up proteomics. The authors demonstrate significant improvements in peptide/protein identifications across various experiments, including single-cell proteomics and immunopeptidomics. They introduce a new tool called MSBooster, which incorporates deep learning-based predictions of peptide properties to rescore peptide-to-spectrum matches, and show its utility in different workflows, such as immunopeptidomics and single-cell proteomics.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Daniel J. Geiszler, Daniel A. Polasky, Fengchao Yu, Alexey I. Nesvizhskii
Summary: Post-translational modifications are important in proteomics, but can complicate searches for modified peptides. The authors present an automated method to find diagnostic spectral features for any modification, improving peptide recovery and localization. They demonstrate the utility of this approach for various modifications and analyze the interactions between ion intensity and statistical properties. This method has been incorporated into PTM-Shepherd and FragPipe.
NATURE COMMUNICATIONS
(2023)
Review
Biochemical Research Methods
Chen Lin, Wei Liu, Wei Jiang, Hongyu Zhao
Summary: Genetic association signals are commonly found in noncoding regions, highlighting the importance of gene expression regulation in human diseases and traits. However, it has been challenging to colocalize expression quantitative trait loci (eQTL) with disease-associated variants. Mediated expression score regression (MESC) is a method that quantifies the proportion of trait heritability mediated by genetically regulated gene expressions (GReX). However, MESC may lead to biased estimates of mediated heritability due to misspecifications of gene and SNP annotations, as well as errors in eQTL effect estimates.
BIOLOGY METHODS & PROTOCOLS
(2023)
Meeting Abstract
Biochemistry & Molecular Biology
Daniel Polasky, Fengchao Yu, Daniel Geislzer, Kai Li, Alexey Nesvizhskii