Article
Veterinary Sciences
Sayed Haidar Abbas Raza, Chengcheng Liang, Wang Guohua, Sameer D. Pant, Zuhair M. Mohammedsaleh, Abdullah F. Shater, Mashael Alhumaidi Alotaibi, Rajwali Khan, Nicola Schreurs, Gong Cheng, Chugang Mei, Linsen Zan
Summary: In this study, differentially expressed genes specific to multiple muscle tissues in mice were identified using bioinformatics techniques, providing potential candidate genes for studying the regulatory mechanisms of muscle development. The genes were found to be associated with myofibril, cytoskeletal protein binding, and metabolic pathways, offering important insights for further research on muscle development.
FRONTIERS IN VETERINARY SCIENCE
(2021)
Article
Biochemical Research Methods
Rachisan Djiake Tihagam, Sanchita Bhatnagar
Summary: Transcriptomic profiling is widely used in cancer research to identify subtypes, predict survival, and find therapeutic targets. Integration of multiple datasets increases sample size and improves statistical power, but also introduces variations that need to be adjusted through normalization. This study used meta-analysis to investigate the expression of TRIM37 across different cancer types.
Review
Medicine, General & Internal
Gioia Mastromoro, Nader Khaleghi Hashemian, Daniele Guadagnolo, Maria Grazia Giuffrida, Barbara Torres, Laura Bernardini, Flavia Ventriglia, Gerardo Piacentini, Antonio Pizzuti
Summary: Cardiovascular malformations are common structural anomalies. Prenatal investigation with fetal echocardiography and genetic counseling is important for CVM. Chromosomal microarray analysis can improve the diagnostic yield in fetuses with isolated CVM, with varying detection rates for different types of heart diseases.
Article
Computer Science, Artificial Intelligence
Anurup Naskar, Rishav Pramanik, S. K. Sabbir Hossain, Seyedali Mirjalili, Ram Sarkar
Summary: In the era of data-driven digital society, there is a need for optimized solutions that can reduce operation costs and increase productivity. Machine learning and data mining algorithms have limitations when processing large amounts of data, especially when dealing with redundant and non-important information. Researchers have developed feature selection algorithms to address this issue, and metaheuristic based optimization algorithms have proven to be effective in solving feature selection problems.
EXPERT SYSTEMS WITH APPLICATIONS
(2023)
Article
Biology
Shyam Marjit, Trinav Bhattacharyya, Bitanu Chatterjee, Ram Sarkar
Summary: This paper proposes a meta-heuristic approach called SAGA, which combines simulated annealing and genetic algorithm to identify informative genes from high-dimensional datasets. SAGA outperforms other algorithms by utilizing a clustering-based population generation and a score-based filter approach.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Biochemistry & Molecular Biology
Cui-Xiang Lin, Hong-Dong Li, Chao Deng, Yuanfang Guan, Jianxin Wang
Summary: TissueNexus is a database containing 49 human tissue/cell line FGNs constructed by integrating 1,341 RNA-seq datasets. Extensive hand-curation was performed to improve quality. It can be used for network search, visualization, functional analysis, and prioritizing disease genes.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Genetics & Heredity
Kimia Sadat Hashemi, Mohadese Koohi Aliabadi, Arian Mehrara, Elham Talebi, Ali Akbar Hemmati, Radin Dabbagh Rezaeiye, Mohammad Javad Ghanbary, Maryam Motealleh, Behnaz Dayeri, Shayan Khalili Alashti
Summary: This study utilized microarray bioinformatic analysis to identify potential biomarkers of AD by analyzing six microarray datasets of AD patients and control groups. The results identified CXCR4, TGFB1, ITGB1, MYH11, and SELE genes as hub genes in this study. These genes were significantly enriched in actin cytoskeleton regulation, ECM-receptor interaction, and hypertrophic cardiomyopathy. Additionally, multiple miRNAs exhibited significant interactions with most of the hub genes.
FRONTIERS IN GENETICS
(2023)
Review
Engineering, Industrial
Jing Lin, Yuhang Cai, Qinyuan Li
Summary: The construction industry has a high accident rate, making safety training for construction workers increasingly important. This study provides a comprehensive summary of the development of construction safety training, evaluates the effectiveness of current training methods, and analyzes potential improvements for the future. The findings reveal that prevention and hazard recognition are key research topics, current safety training methods are generally effective but less so in field studies, personalized safety training is a foreseeable trend, and safety training methods should be revised and optimized for intelligent construction and prefabricated construction.
JOURNAL OF MANAGEMENT IN ENGINEERING
(2023)
Article
Gastroenterology & Hepatology
Xinxing Tantai, Yi Liu, Yee Hui Yeo, Michael Praktiknjo, Ezequiel Mauro, Yuhei Hamaguchi, Cornelius Engelmann, Peng Zhang, Jae Yoon Jeong, Jeroen Laurens Ad van Vugt, Huijuan Xiao, Huan Deng, Xu Gao, Qing Ye, Jiayuan Zhang, Longbao Yang, Yaqin Cai, Yixin Liu, Na Liu, Zongfang Li, Tao Han, Toshimi Kaido, Joo Hyun Sohn, Christian Strassburg, Thomas Berg, Jonel Trebicka, Yao-Chun Hsu, Jan Nicholaas Maria Ijzermans, Jinhai Wang, Grace L. Su, Fanpu Ji, Mindie H. Nguyen
Summary: There is a significant association between sarcopenia and increased mortality risk in patients with cirrhosis, especially in male patients, those with alcohol-associated liver disease, and those with Child-Pugh C cirrhosis. The severity and duration of sarcopenia are correlated with higher mortality rates. Raising awareness about the importance of sarcopenia in patients with cirrhosis is crucial.
JOURNAL OF HEPATOLOGY
(2022)
Article
Pharmacology & Pharmacy
Haiyan Cao, Xiaosheng Rao, Junya Jia, Tiekun Yan, Dong Li
Summary: This study reveals the molecular pathogenesis of diabetic kidney disease (DKD) through microarray data analysis. The results show the importance of inflammation response, immune-related pathways, and extracellular matrix-related pathways in the development of DKD. Additionally, 15 hub genes associated with the disease were identified.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Caitlin A. Finney, Fabien Delerue, Wendy A. Gold, David A. Brown, Artur Shvetcov
Summary: Alzheimer's disease is the most common form of dementia with no effective treatment. Thousands of dysregulated genes have been identified in the brains of patients with Alzheimer’s disease. A study using meta-analysis and artificial intelligence techniques suggests that mitochondrial dysfunction may play a crucial role in Alzheimer's disease.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Environmental Sciences
Ying Ma, Jianli Wang, Jingying Wu, Chuxuan Tong, Ting Zhang
Summary: This study conducted a meta-analysis of published data on the cytotoxicity of graphene and developed models to predict graphene cytotoxicity based on cell viability, IC50, and LDH release as toxicity endpoints. The most influential attributes influencing graphene cytotoxicity were identified, providing guidance for future studies of graphene toxicity. The results highlight the importance of data mining and machine learning in predicting graphene toxicity.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Engineering, Chemical
Seong-Beom Cho
Summary: This study analyzed muscle samples from PCOS patients to identify androgen-responsive genes (ARGs) and found that a broad range of cellular processes is affected by androgen administration. These findings provide valuable information for the identification of ARGs.
Article
Medicine, General & Internal
Yan Sun, Weiyuan Zhang, Zhiwen Wang, Likui Guo, Shaowen Shi
Summary: This study calculated the incidence of chromosomal abnormalities and incremental yield of chromosomal microarray analysis (CMA) in ventriculomegaly (VM). The results showed that applying CMA in VM improved the detection rate of abnormalities, and obstetricians should recommend fetal karyotype analysis to exclude chromosomal abnormalities.
CHINESE MEDICAL JOURNAL
(2022)
Review
Allergy
Margarete Arrais, Tiago Maricoto, Bright I. Nwaru, Philip J. Cooper, Jorge M. R. Gama, Miguel Brito, Luis Taborda-Barata
Summary: Helminth infections may increase the risk of bronchial hyperreactivity in children and atopy in adults, but the overall strength of the evidence is low.
JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY
(2022)
Article
Genetics & Heredity
Steven Laurie, Davide Piscia, Leslie Matalonga, Alberto Corvo, Marcos Fernandez-Callejo, Carles Garcia-Linares, Carles Hernandez-Ferrer, Cristina Luengo, Ines Martinez, Anastasios Papakonstantinou, Daniel Pico-Amador, Joan Protasio, Rachel Thompson, Raul Tonda, Monica Bayes, Gemma Bullich, Jordi Camps-Puchadas, Ida Paramonov, Jean-Remi Trotta, Angel Alonso, Marcella Attimonelli, Christophe Beroud, Virginie Bros-Facer, Orion J. Buske, Andres Canada-Pallares, Jose M. Fernandez, Mats G. Hansson, Rita Horvath, Julius O. B. Jacobsen, Rajaram Kaliyaperumal, Severine Lair-Preterre, Luana Licata, Pedro Lopes, Estrella Lopez-Martin, Deborah Mascalzoni, Lucia Monaco, Luis A. Perez-Jurado, Manuel Posada de la Paz, Jordi Rambla, Ana Rath, Olaf Riess, Peter N. Robinson, David Salgado, Damian Smedley, Dylan Spalding, Peter A. C. 't Hoen, Ana Topf, Irina Zaharieva, Holm Graessner, Ivo G. Gut, Hanns Lochmuller, Sergi Beltran
Summary: Rare disease patients are now more likely to receive rapid molecular diagnosis, but some cases still remain undiagnosed. The RD-Connect GPAP provides a standardized platform for data collection, sharing, and analysis to aid in diagnosing cases and discovering new disease causing genes.
Article
Genetics & Heredity
Vanessa Luiza Romanelli Tavares, Sofia Ligia Guimaraes-Ramos, Yan Zhou, Cibele Masotti, Suzana Ezquina, Danielle de Paula Moreira, Henk Buermans, Renato S. Freitas, Johan T. Den Dunnen, Stephen R. F. Twigg, Maria Rita Passos-Bueno
Summary: The study identified a fourth locus causative of ARCND in a family, represented by a tandem duplication of 430 kb in a candidate region on chromosome 7. The findings support the hypothesis that deregulation of TWIST1 expression during craniofacial development can contribute to the phenotype.
JOURNAL OF MEDICAL GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Sylvia Nieuwenhuis, Joanna Widomska, Paul Blom, Peter-Bram A. C. 't Hoen, Baziel G. M. van Engelen, Jeffrey C. Glennon
Summary: The blood transcriptome was examined in relation to disease severity in type I myotonic dystrophy (DM1) patients. It was found that changes in transcriptome, particularly in innate and adaptive immunity associated with muscle-wasting, were linked to symptom severity in DM1. Further studies should investigate the role of immunity in DM1.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Immunology
Dario F. Marzella, Farzaneh M. Parizi, Derek Van Tilborg, Nicolas Renaud, Daan Sybrandi, Rafaella Buzatu, Daniel T. Rademaker, Peter A. C. 't Hoen, Li C. Xue
Summary: A deeper understanding of T-cell-mediated adaptive immune responses is crucial for cancer immunotherapy and antiviral vaccine design. Researchers have developed PANDORA, a generic modelling pipeline for pMHC-I and pMHC-II, which shows excellent performance in pMHC-I modelling.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Multidisciplinary Sciences
K. Joeri van der Velde, Gurnoor Singh, Rajaram Kaliyaperumal, Xiaofeng Liao, Sander de Ridder, Susanne Rebers, Hindrik H. D. Kerstens, Fernanda de Andrade, Jeroen van Reeuwijk, Fini E. De Gruyter, Saskia Hiltemann, Maarten Ligtvoet, Marjan M. Weiss, Hanneke W. M. van Deutekom, Anne M. L. Jansen, Andrew P. Stubbs, Lisenka E. L. M. Vissers, Jeroen F. J. Laros, Esther van Enckevort, Daphne Stemkens, Peter A. C. t Hoen, Jeroen A. M. Belien, Marielle E. van Gijn, Morris A. Swertz
Summary: FAIR Genomes aims to facilitate the reuse of genomic data by developing metadata standards and providing templates for data entry and programmatic interfaces. It addresses the challenge of storing and sharing genomic data by offering a semantic schema for data descriptions. With FAIR Genomes, rare disease diagnosis and personalized medicine research can be enhanced.
Article
Mathematical & Computational Biology
Renee X. de Menezes, Armin Rauschenberger, Bios Consortium, Peter A. C. 't Hoen, Marianne A. Jonker
Summary: This article introduces a score-based test method that takes into account the effects of all exons and all SNPs on exon inclusion simultaneously. The test method is computationally efficient and can be used when the number of SNPs is larger than the number of samples. It is also more robust to exon-SNP pair-specific effects.
BIOMETRICAL JOURNAL
(2023)
Article
Biotechnology & Applied Microbiology
Anna Niehues, Daniele Bizzarri, Marcel J. T. Reinders, P. Eline Slagboom, Alain J. van Gool, Erik B. van den Akker, Peter A. C. 't Hoen
Summary: Population-scale expression profiling studies provide valuable insights into biological and disease mechanisms. Missing or incomplete phenotypic information can hinder data analysis. Metabolomics-based surrogates can be used as predictors for clinical phenotypes. In this study, metabolomic surrogates were evaluated for 17 traits using expression profiling data. The results showed that metabolomic surrogates performed similarly to reported phenotypes.
Editorial Material
Genetics & Heredity
Andreas Laner, Ales Maver, Johan T. den Dunnen
Summary: The journal Human Mutation focuses on variants in the human genome and aims to understand the consequences of carrying a variant for individual health. This article collection provides insights into the advancements and limitations in variant effect prediction, aiming to improve our understanding of genotype-phenotype relationships.
Article
Biology
Tooba Abbassi-Daloii, Salma el Abdellaoui, Lenard M. Voortman, Thom T. J. Veeger, Davy Cats, Hailiang Mei, Duncan E. Meuffels, Ewoud van Arkel, Peter Bram 't Hoen, Hermien Kan, Vered Raz
Summary: We constructed a large atlas of RNA-seq profiles from leg muscles, identifying differential expression patterns and cellular composition across different tissues. The muscle samples were clustered into three groups based on anatomical location, which were associated with oxidative metabolism and fast- or slow-twitch myofibers. Expression profiles of Homeobox transcription factors differed between the three groups. Our study provides a novel resource to study muscle-specific molecular features and their potential links to physiological processes.
Article
Biochemical Research Methods
Casper van Bavel, Wim Thiels, Rob Jelier
Summary: The shape of a cell is important for understanding various cellular processes, but current cell shape descriptors only capture simple geometric features. This study proposes a new framework called FlowShape, which represents cell shape by measuring curvature and mapping it onto a sphere. The framework allows for various shape analyses, including alignment and statistical comparison.
Article
Biophysics
Maxim Cuvelier, Jef Vangheel, Wim Thiels, Herman Ramon, Rob Jelier, Bart Smeets
Summary: Cell division during early embryogenesis is influenced by the mechanical and geometrical environment, and this study presents a computational model that can accurately predict the volume ratio of daughter cells during the cleavage phase of development. The model also demonstrates how the orientation of confinement relative to the division axis and the properties of the cell cortex affect cell division and shape. Additionally, the model suggests that compression can affect spindle positioning and cell volume in asymmetric cell divisions.
BIOPHYSICAL JOURNAL
(2023)
Article
Biology
Ellen Geens, Pieter Van de Walle, Francesca Caroti, Rob Jelier, Christian Steuwe, Liliane Schoofs, Liesbet Temmerman
Summary: Oviparous animals support reproduction with yolk as a nutrient source. However, in Caenorhabditis elegans, yolk proteins don't affect fecundity, despite being the majority of embryonic protein pool and carriers for nutrient-rich lipids. Yolk provisioning in C. elegans provides temporal advantage during embryogenesis, increases early juvenile body size, and promotes competitive fitness. Unlike other species, C. elegans relies on yolk as a fail-safe for offspring survival rather than maintaining offspring numbers.
LIFE SCIENCE ALLIANCE
(2023)
Meeting Abstract
Biochemistry & Molecular Biology
Tabea V. Riepe, Mubeen Khan, Susanne Roosing, Frans P. M. Cremers, Peter A. C. t Hoen
EUROPEAN JOURNAL OF HUMAN GENETICS
(2022)
Meeting Abstract
Biochemistry & Molecular Biology
Isabel Spier, Xiaoyu Sherry Yin, John-Paul Plazzer, Andreas Laner, Ian M. Frayling, Deborah Ritter, Sharon Plon, Marc Greenblatt, Johan T. den Dunnen, Finlay A. Macrae, Stefan Aretz
EUROPEAN JOURNAL OF HUMAN GENETICS
(2022)
Article
Genetics & Heredity
Max J. F. Degener, Remco T. P. van Cruchten, Brittney A. Otero, Eric T. Wang, Derick G. Wansink, Peter A. C. 't Hoen
Summary: In patients with myotonic dystrophy type 1 (DM1), dysregulation of RNA-binding proteins leads to alternative splicing patterns similar to fetal ones, and this dysregulation is associated with changes in mRNA expression of splice regulators MBNL1, MBNL2 and CELF1.
NAR GENOMICS AND BIOINFORMATICS
(2022)