Article
Biochemical Research Methods
Xudong Zhao, Tong Liu, Guohua Wang
Summary: Molecular signatures play a crucial role in cancer diagnosis, but currently there are issues with identifying false positive signatures. Researchers proposed a new feature selection framework and a data transformation process to address these problems, and experimental results demonstrated the effectiveness of their method.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Genetics & Heredity
Chengdong Wang, Feng Li, Linhua Deng, Mingzhou Li, Ming Wei, Bo Zeng, Kai Wu, Zhongxian Xu, Rongping Wei, Limin Wei, Weiping Liu, Siyuan Zhang, Lin Xu, Yan Huang, Desheng Li, Ying Li, Hemin Zhang
Summary: The study provided miRNA profiles of the heart, liver, spleen, lung, and kidney of giant pandas using high-throughput sequencing technology, revealing miRNA expression differences between these tissues and offering valuable genetic resources for further genetic research.
Article
Biochemistry & Molecular Biology
Austin J. Van Asselt, Jeffrey J. Beck, Casey T. Finnicum, Brandon N. Johnson, Noah Kallsen, Jouke Jan Hottenga, Eco J. C. de Geus, Dorret I. Boomsma, Erik A. Ehli, Jenny van Dongen
Summary: The field of DNA methylation research is rapidly evolving, focusing on studying disease and phenotype changes over time using methylation measurements from diverse tissue sources and multiple array platforms. This study identified longitudinal, inter-tissue, and inter-platform variation in DNA methylation, and identified a set of shared CpGs associated with aging, ancestry, and mQTLs.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Developmental Biology
Stephanie H. Nowotarski, Erin L. Davies, Sofia M. C. Robb, Eric J. Ross, Nicolas Matentzoglu, Viraj Doddihal, Mol Mir, Melainia McClain, Alejandro Sanchez Alvarado
Summary: PLANA is a relational framework containing over 850 terms describing planarian anatomy, with imported terms from other anatomy ontologies to promote interoperability. In addition to serving as a data curation tool, PLANA includes resources for planarian embryogenesis and gene expression. It is an open-source tool built using FAIR principles, providing a platform for community-led growth and evolution of the resource.
Article
Chemistry, Multidisciplinary
Menna Maged Kamel, Alberto Gil-Solla, Luis Fernando Guerrero-Vasquez, Yolanda Blanco-Fernandez, Jose Juan Pazos-Arias, Martin Lopez-Nores
Summary: Cultural heritage has undergone a significant digital transformation, but a lack of accurate metadata affects the usability and discoverability of digital content. Crowdsourcing can play a significant role in enriching the metadata quality of digital cultural content. This paper presents an image annotation recommendation system for cultural heritage platforms.
APPLIED SCIENCES-BASEL
(2023)
Article
Computer Science, Artificial Intelligence
Yingying Xue, Jiahui Jin, Aibo Song, Yingxue Zhang, Yangyang Liu, Kaixuan Wang
Summary: This study addresses the challenges in ontology-enhanced knowledge graph embedding and proposes a multi-type aware KG embedding model, achieving substantial improvements in link prediction and multi-type classification tasks.
Article
Geochemistry & Geophysics
Ying Zhang, Puhong Duan, Jianxu Mao, Xudong Kang, Leyuan Fang, Pedram Ghamisi
Summary: This paper proposes an edge-aware feature extractor to address the problem of over-smoothing in hyperspectral image classification. The proposed method extracts discriminative features through contour structural profiles and multiscale structural profiles, and obtains the final classification map through fusion and a classifier.
IEEE TRANSACTIONS ON GEOSCIENCE AND REMOTE SENSING
(2022)
Article
Computer Science, Hardware & Architecture
Ching-Chi Lin, Junjie Shi, Niklas Ueter, Mario Guenzel, Jan Reineke, Jian-Jia Chen
Summary: In order to exploit the performance benefits of heterogeneous multicore platforms in real-time systems, task models that expose the parallelism and heterogeneity of the workload, as well as scheduling algorithms that effectively utilize this information, are needed. This article introduces type-aware federated scheduling algorithms for sporadic typed DAG tasks with implicit deadlines on a heterogeneous multicore platform with two types of cores. The algorithms achieve better schedulability, especially for task sets with skewed workload, compared to the state of the art.
IEEE TRANSACTIONS ON COMPUTERS
(2023)
Article
Biochemistry & Molecular Biology
Gemma Arderiu, Guiomar Mendieta, Alex Gallinat, Carmen Lambert, Alberto Diez-Caballero, Carlos Ballesta, Lina Badimon
Summary: Obesity is linked to metabolic disorders and increased cardiovascular risk. The presence of type 2 diabetes mellitus (T2DM) affects the protein composition in adipose tissue and serum, leading to changes in systemic markers and dysregulation of metabolic pathways in visceral adipose tissue (VAT).
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemical Research Methods
Xuan Liu, Wenbo Chen, Yu Fang, Siqi Yang, Liuping Chang, Xingyu Chen, Haidong Ye, Xinyu Tang, Shan Zhong, Wen Zhang, Zhiqiang Dong, Leng Han, Chunjiang He
Summary: Gene expression and immune status in human tissues change with aging. A platform named ADEIP has been developed to integrate age-dependent gene expression and immune profiles across tissues, providing a powerful tool for studying immune regulation in organogenesis and infectious or genetic diseases related to aging.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Business
Supratim Kundu, Swapnajit Chakraborti
Summary: This study aims to investigate the differences in online consumer reviews across different review platforms on the internet. By applying mixed methods of quantitative and qualitative analysis, the researchers identified the topics and characteristics of reviews on various platforms, ultimately creating a typology of reviews for each platform. The findings can help managers tailor their online review strategies according to the platform of interest.
ELECTRONIC COMMERCE RESEARCH
(2022)
Article
Engineering, Electrical & Electronic
Mayukh Roy Chowdhury, Swades De
Summary: The paper proposes a delay-aware priority access classification (DPAC) based ACB scheme to address congestion issues caused by the increasing number of devices in mMTC. The proposed scheme increases successful preamble transmissions by up to 75% while ensuring that the access delay is well within the delay budget.
IEEE TRANSACTIONS ON VEHICULAR TECHNOLOGY
(2021)
Article
Biochemical Research Methods
Xiang Zhou, Hua Chai, Yuansong Zeng, Huiying Zhao, Yuedong Yang
Summary: The study developed a virtual adversarial domain adaptation network called scAdapt to transfer cell labels between datasets with batch effects. scAdapt utilized both the labeled source and unlabeled target data to train an enhanced classifier, aligning centroids to create a joint embedding. The scAdapt outperformed existing methods for classification in various datasets and showed superior capabilities in preserving cluster structure.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Hospitality, Leisure, Sport & Tourism
Raffaele Filieri, Elisabetta Raguseo, Francesco Galati
Summary: Scholars have investigated factors that enhance the performance of Airbnb hosts but there is limited research on negative signals like host cancellation messages. This study focuses on the impact of cancellation signals on host occupancy and how it is moderated by the level of involvement associated with the accommodation type. Using a dataset of 31,778 reviews of 6384 Airbnb listings, the results show that cancellations have a stronger impact on higher involvement accommodations (entire apartments) compared to lower involvement ones (shared rooms). This study contributes to the understanding of negative signals and helps P2P managers comprehend the effects of cancellations on their revenues.
INTERNATIONAL JOURNAL OF HOSPITALITY MANAGEMENT
(2023)
Article
Biotechnology & Applied Microbiology
Edoardo Spairani, Beniamino Daniele, Maria Gabriella Signorini, Giovanni Magenes
Summary: This study proposes a hybrid approach based on a neural network for classifying healthy and pathological fetuses by combining quantitative parameters and image representations of the fetal heart rate signal. After training, the proposed neural network achieves an overall accuracy of 80.1% on a large dataset.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Urology & Nephrology
Catherine R. Butler, Paul S. Appelbaum, Heather Ascani, Mark Aulisio, Catherine E. Campbell, Ian H. de Boer, Ashveena L. Dighe, Daniel E. Hall, Jonathan Himmelfarb, Richard Knight, Karla Mehl, Raghavan Murugan, Sylvia E. Rosas, John R. Sedor, John F. O'Toole, Katherine R. Tuttle, Sushrut S. Waikar, Michael Freeman
Summary: This article emphasizes the importance of critically examining the ethical basis of human subjects research involving some risks without anticipated clinical benefits. It provides a comprehensive conceptualization of the types of benefits that may be important to research participants and proposes a model to better respect and support participants in future research.
AMERICAN JOURNAL OF KIDNEY DISEASES
(2022)
Correction
Biochemical Research Methods
Jian Zhou, Olga G. Troyanskaya
Article
Oncology
Abhinav Jaiswal, Akanksha Verma, Ruth Dannenfelser, Marit Melssen, Itay Tirosh, Benjamin Izar, Tae-Gyun Kim, Christopher J. Nirschl, K. Sanjana P. Devi, Walter C. Olson, Craig L. Slingluff, Victor H. Engelhard, Levi Garraway, Aviv Regev, Kira Minkis, Charles H. Yoon, Olga Troyanskaya, Olivier Elemento, Mayte Suarez-Farinas, Niroshana Anandasabapathy
Summary: Better classification and understanding of tumor-infiltrating lymphocytes (TILs) is needed. This study found enrichment of T memory/resident memory programs in solid tumors compared to other T cell states. Single-cell analysis of melanoma CD8(+) TILs revealed a high proportion of memory/resident memory-scoring TILs in responders to anti-PD-1 therapy. TILs scoring highly for early T cell activation, but not exhaustion, were associated with non-response. Late/persistent activation signatures were predictive of melanoma survival and co-expressed with dendritic cell and IFN-gamma response programs.
Article
Urology & Nephrology
Rachel Sealfon, Laura Mariani, Carmen Avila-Casado, Viji Nair, Rajasree Menon, Julien Funk, Aaron Wong, Gabriel Lerner, Norifumi Hayashi, Olga Troyanskaya, Matthias Kretzler, Laurence H. Beck
Summary: Using gene expression data from the kidney tissue, MN patients can be accurately distinguished from other kidney disease patients. By analyzing the gene expression differences between MN patients and other glomerulonephropathy patients, specific gene modules related to MN can be identified in a kidney-specific functional network, indicating upregulation of podocyte-expressed genes in MN.
JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY
(2022)
Article
Urology & Nephrology
Rajasree Menon, Andrew S. Bomback, Blue B. Lake, Christy Stutzke, Stephanie M. Grewenow, Steven Menez, Vivette D. D'Agati, Sanjay Jain
KIDNEY INTERNATIONAL
(2022)
Article
Cell Biology
Zidong Zhang, Michel Zamojski, Gregory R. Smith, Thea L. Willis, Val Yianni, Natalia Mendelev, Hanna Pincas, Nitish Seenarine, Mary Anne S. Amper, Mital Vasoya, Wan Sze Cheng, Elena Zaslavsky, Venugopalan D. Nair, Judith L. Turgeon, Daniel J. Bernard, Olga G. Troyanskaya, Cynthia L. Andoniadou, Stuart C. Sealfon, Frederique Ruf-Zamojski
Summary: This study characterizes the gene expression and chromatin accessibility of human pituitary stem cells (PSCs) using single nucleus RNA-seq and ATAC-seq. The researchers identified uncommitted PSCs, committing progenitor cells, and sex differences, as well as distinct mechanisms contributing to heterogeneous marker expression within PSCs.
Article
Immunology
Alessandra Soares-Schanoski, Natalie Sauerwald, Carl W. Goforth, Sivakumar Periasamy, Dawn L. Weir, Stephen Lizewski, Rhonda Lizewski, Yongchao Ge, Natalia A. Kuzmina, Venugopalan D. Nair, Sindhu Vangeti, Nada Marjanovic, Antonio Cappuccio, Wan Sze Cheng, Sagie Mofsowitz, Clare M. Miller, Xuechen B. Yu, Mary-Catherine George, Elena Zaslavsky, Alexander Bukreyev, Olga G. Troyanskaya, Stuart C. Sealfon, Andrew G. Letizia, Irene Ramos
Summary: Research has shown that asymptomatic and mild symptomatic COVID-19 infections in young adults have similar viral loads and specific antibody responses, but there are differences in inflammatory protein profiles. Some analytes in asymptomatic infections are associated with tissue repair and may contribute to symptom control.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Public, Environmental & Occupational Health
Rhonda A. Lizewski, Rachel S. G. Sealfon, Sang Woo Park, Gregory R. Smith, Chad K. Porter, Ana S. Gonzalez-Reiche, Yongchao Ge, Clare M. Miller, Carl W. Goforth, Hanna Pincas, Michael S. Termini, Irene Ramos, Venugopalan D. Nair, Stephen E. Lizewski, Hala Alshammary, Regina Z. Cer, Hua Wei Chen, Mary-Catherine George, Catherine E. Arnold, Lindsay A. Glang, Kyle A. Long, Francisco Malagon, Jan J. Marayag, Edgar Nunez, Gregory K. Rice, Ernesto Santa Ana, Megan A. Schilling, Darci R. Smith, Victor A. Sugiharto, Peifang Sun, Adriana van de Guchte, Zenab Khan, Jayeeta Dutta, Sindhu Vangeti, Logan J. Voegtly, Dawn L. Weir, C. Jessica E. Metcalf, Olga G. Troyanskaya, Kimberly A. Bishop-Lilly, Bryan T. Grenfell, Harm van Bakel, Andrew G. Letizia, Stuart C. Sealfon
Summary: Marine recruits training at Parris Island experienced a high rate of SARS-CoV-2 infection, which was twice that seen in the community. The transmission of the virus was mainly due to multiple introductions and spread within companies. Frequent testing and case isolation may help minimize outbreaks.
Article
Genetics & Heredity
Kathleen M. Chen, Aaron K. Wong, Olga G. Troyanskaya, Jian Zhou
Summary: Sei is a new framework for integrating human genetics data with a sequence-based mapping of predicted regulatory activities to elucidate mechanisms contributing to complex traits and diseases.
Article
Biochemistry & Molecular Biology
Christine A. Roden, Yifan Dai, Catherine A. Giannetti, Ian Seim, Myungwoon Lee, Rachel Sealfon, Grace A. McLaughlin, Mark A. Boerneke, Christiane Iserman, Samuel A. Wey, Joanne L. Ekena, Olga G. Troyanskaya, Kevin M. Weeks, Lingchong You, Ashutosh Chilkoti, Amy S. Gladfelter
Summary: The nucleocapsid protein (N-protein) plays a crucial role in the replication of betacoronaviruses. In this study, researchers identify two separate double-stranded RNA motifs that promote the condensation of N-protein, mediated by its two RNA binding domains (RBDs), which have distinct preferences for different types of RNA sequences. These interactions between N-protein and RNA motifs have specific physical properties that support various viral functions. The findings suggest that SARS-CoV-2 achieves biochemical complexity and performs multiple functions in the same cytoplasm using minimal protein components, by utilizing multiple distinct RNA motifs that control N-protein interactions.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Weiguang Mao, Clare M. Miller, Venugopalan D. Nair, Yongchao Ge, Mary Anne S. Amper, Antonio Cappuccio, Mary-Catherine George, Carl W. Goforth, Kristy Guevara, Nada Marjanovic, German Nudelman, Hanna Pincas, Irene Ramos, Rachel S. G. Sealfon, Alessandra Soares-Schanoski, Sindhu Vangeti, Mital Vasoya, Dawn L. Weir, Elena Zaslavsky, Seunghee Biobank Team, Seunghee Kim-Schulze, Sacha Gnjatic, Miriam Merad, Andrew G. Letizia, Olga G. Troyanskaya, Stuart C. Sealfon, Maria Chikina
Summary: DNA methylation is a cumulative record of lifetime exposures and genetic markers. This study investigated the dynamics of blood epigenetic remodeling following asymptomatic and mildly symptomatic SARS-CoV-2 infection. Differential methylation persisted for months after infection and resembled autoimmune or inflammatory disease. Machine learning models based on methylation accurately distinguished different infection time periods and predicted time since infection. The clinical trajectory of young adults and a diverse cohort with severe outcomes was predicted based on the similarity of methylation before or early after SARS-CoV-2 infection to the postinfection state defined by the model. The postacute SARS-CoV-2 epigenetic landscape identified in this study is antiprotective.
MOLECULAR SYSTEMS BIOLOGY
(2023)
Article
Cell Biology
Camille Brewer, Tobias Lanz, Caryn R. Hale, Gregory D. Sepich-Poore, Cameron Martino, Austin D. Swafford, Thomas S. Carroll, Sarah Kongpachith, Lisa K. Blum, Serra E. Elliott, Nathalie E. Blachere, Salina Parveen, John Fak, Vicky Yao, Olga Troyanskaya, Mayu O. Frank, Michelle S. Bloom, Shaghayegh Jahanbani, Alejandro M. Gomez, Radhika Iyer, Nitya S. Ramadoss, Orr Sharpe, Sangeetha Chandrasekaran, Lindsay B. Kelmenson, Qian Wang, Heidi Wong, Holly L. Torres, Mark Wiesen, Dana T. Graves, Kevin D. Deane, V. Michael Holers, Rob Knight, Robert B. Darnell, William H. Robinson, Dana E. Orange
Summary: This study found that periodontal disease is more common in individuals with rheumatoid arthritis (RA) who have detectable anticitrullinated protein antibodies (ACPAs), suggesting a link between oral mucosal inflammation and RA pathogenesis. The researchers also discovered that RA patients with periodontal disease experienced repeated oral bacteremias associated with transcriptional signatures of specific monocyte subsets observed in inflamed RA synovia and blood during RA flares. The bacteremia was caused by citrullinated oral bacteria and resulted in activation of ACPA B cells, promoting affinity maturation and epitope spreading to citrullinated human antigens.
SCIENCE TRANSLATIONAL MEDICINE
(2023)
Article
Biochemical Research Methods
Zijun Zhang, Natalie Sauerwald, Antonio Cappuccio, Irene Ramos, Venugopalan D. Nair, German Nudelman, Elena Zaslavsky, Yongchao Ge, Angelo Gaitas, Hui Ren, Joel Brockman, Jennifer Geis, Naveen Ramalingam, David King, Micah T. McClain, Christopher W. Woods, Ricardo Henao, Thomas W. Burke, Ephraim L. Tsalik, Carl W. Goforth, Rhonda A. Lizewski, Stephen E. Lizewski, Dawn L. Weir, Andrew G. Letizia, Stuart C. Sealfon, Olga G. Troyanskaya
Summary: Assays detecting blood transcriptome changes are studied for infectious disease diagnosis. Blood-based RNA alternative splicing (AS) events have the potential to be better diagnostic biomarkers compared to gene expression. This study presents a computational framework for developing AS diagnostic biomarkers using SARS-CoV-2 infection data and identifies a major functional AS program switch upon viral infection. AS-based biomarkers are more accurate for SARS-CoV-2 diagnosis compared to transcriptome signatures, and microfluidic PCR diagnostic assays achieve nearly perfect test accuracy.
CELL REPORTS METHODS
(2023)
Article
Biochemical Research Methods
Renming Liu, Matthew Hirn, Arjun Krishnan
Summary: This paper presents a network embedding method called node2vec+ that takes into account edge weights during the biased random walk generation process, showing higher robustness and superior performance compared to node2vec in weighted graphs.
Article
Biotechnology & Applied Microbiology
Kayla A. Johnson, Arjun Krishnan
Summary: This study provides a comprehensive benchmarking and analysis of 36 different workflows for constructing coexpression networks from RNA-seq datasets. The results demonstrate that between-sample normalization has the biggest impact, with counts adjusted by size factors producing networks that most accurately recapitulate known gene functional relationships. The findings provide researchers with concrete recommendations for building accurate coexpression networks from RNA-seq datasets.