Negative / Null Result ReportOpen accessBiochemistry, Genetics and Molecular Biology
Fernanda Marcondes de Rezende, M. Haile‐Mariam, J.E. Pryce et al. · 2020 · Journal of Dairy Science
The use of information across populations is an attractive approach to increase the accuracy of genomic predictions for numerically small breeds and traits that are time-consuming and difficult to measure, such as male fertility in cattle.…
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Ayca Gucalp, Tiffany A. Traina · 2017 · Cancer
Patients with triple-negative breast cancer (TNBC) generally are considered a single clinical subgroup, defined by the lack of receptor expression, and are uniformly treated with cytotoxic chemotherapy. However, the advent of molecular…
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Zhiyu Yang, Fanny‐Dhelia Pajuste, Kristina Zguro et al. · 2025 · Nature Genetics
Abstract Understanding disease progression is of high biological and clinical interest. Unlike disease susceptibility, whose genetic basis has been abundantly studied, less is known about the genetics of disease progression and its overlap with disease susceptibility. Considering nine common diseases ( n cases ranging from 11,980 to 124,682) across seven biobanks, we systematically compared genetic architectures of susceptibility and progression, defined as disease-specific mortality. We identified only one locus substantially associated with disease-specific mortality and showed that, at a si
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Harkeran K. Jandu, Colin Veal, Laura Fachal et al. · 2023 · Radiotherapy and Oncology
Background and purpose Up to a quarter of breast cancer patients treated by surgery and radiotherapy experience clinically significant toxicity. If patients at high risk of adverse effects could be identified at diagnosis, their treatment could be tailored accordingly. This study was designed to identify common single nucleotide polymorphisms (SNPs) associated with toxicity two years following whole breast radiotherapy. Materials and Methods A genome-wide association study (GWAS) was performed in 1,640 breast cancer patients with complete SNP, clinical, treatment and toxicity data, recruited a
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Isaac Shiri, Sebastian Balzer, Giovanni Baj et al. · 2024 · European Journal of Nuclear Medicine and Molecular Imaging
PURPOSE: Transthyretin amyloid cardiomyopathy (ATTR-CM) is a frequent concomitant condition in patients with severe aortic stenosis (AS), yet it often remains undetected. This study aims to comprehensively evaluate artificial intelligence-based models developed based on preprocedural and routinely collected data to detect ATTR-CM in patients with severe AS planned for transcatheter aortic valve implantation (TAVI). METHODS: Tc]-DPD) for the presence of ATTR-CM. Clinical, laboratory, electrocardiogram, echocardiography, invasive measurements, 4-dimensional cardiac CT (4D-CCT) strain data, and C
View details →Negative / Null Result ReportOpen accessBiochemistry, Genetics and Molecular Biology
Mireia M. Ginesta, Zamira V. Díaz‐Riascos, Juli Busquets et al. · 2016 · Oncology Letters
Early detection of pancreatic and periampullary neoplasms is critical to improve their clinical outcome. The present authors previously demonstrated that DNA hypermethylation of adenomatous polyposis coli (APC), histamine receptor H2…
View details →Negative / Null Result ReportBiochemistry, Genetics and Molecular Biology
Kaneen Gomez-Hixson, Ericka Biagioni, Melissa Brown · 2020 · Journal of American College Health
Objective: This study evaluated dietary intake patterns of NCAA Division III soccer players compared to recommended levels. Participants: NCAA Division III soccer players (n = 75). Methods: Actual dietary intake was determined by the…
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Jacqueline Ramı́rez, Tae Won Kim, Wanqing Liu et al. · 2013 · Pharmacogenetics and Genomics
XK469 (NSC 697887) is a selective topoisomerase II β inhibitor eliminated mainly by aldehyde oxidase I (AOX1). We performed a candidate gene study to investigate whether AOX1 genetic variation contributes to interindividual variability in…
View details →Negative / Null Result ReportOpen accessBiochemistry, Genetics and Molecular Biology
Nicolás Fragoso-Bargas, Hannah R. Elliott, Sindre Lee-Ødegård et al. · 2022 · Diabetes
Although there are some epigenome-wide association studies (EWAS) of insulin resistance, for most of them authors did not replicate their findings, and most are focused on populations of European ancestry, limiting the generalizability. In…
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Jiayi Liu, Weichen Hong, Zhendong Sun et al. · 2026 · Frontiers in Immunology
The proposal of the gut-lung axis has profoundly reshaped our understanding of the mechanisms underlying respiratory diseases. As a crucial component of this axis, the gut microbiota plays a central role in pulmonary immune regulation through inter-organ communication mediated by metabolic products. However, a systematic integration of mechanisms explaining how gut microbes achieve precise cross-organ immune regulation remains elusive. Existing research predominantly focuses on descriptive observations, such as the association between early-life microbiota dysbiosis and an increased risk of as
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Miki Takemura, Rio Nakamura, Merime Ota et al. · 2023 · Antimicrobial Agents and Chemotherapy
ABSTRACT Achromobacter spp. and Burkholderia cepacia complex (Bcc) are rare but diverse opportunistic pathogens associated with serious infections, which are often multidrug resistant. This study compared the in vitro antibacterial activity of the siderophore antibiotic cefiderocol against Achromobacter spp. and Bcc isolates with that of other approved antibacterial drugs, including ceftazidime-avibactam, ciprofloxacin, colistin, imipenem-relebactam, and meropenem-vaborbactam. Isolates were collected in the SIDERO multinational surveillance program. Among 334 Achromobacter spp. isolates [76.6%
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Aras Fahrettin Korkmaz, Fatih Ekinci, Şehmus Altaş et al. · 2025 · Biology
This study presents a novel approach for classifying Discomycetes species using deep learning and explainable artificial intelligence (XAI) techniques. The EfficientNet-B0 model achieved the highest performance, reaching 97% accuracy, a 97% F1-score, and a 99% AUC, making it the most effective model. MobileNetV3-L followed closely, with 96% accuracy, a 96% F1-score, and a 99% AUC, while ShuffleNet also showed strong results, reaching 95% accuracy and a 95% F1-score. In contrast, the EfficientNet-B4 model exhibited lower performance, achieving 89% accuracy, an 89% F1-score, and a 93% AUC. These
View details →Negative / Null Result ReportOpen accessBiochemistry, Genetics and Molecular Biology
Mohamad Saad, Ayman El‐Menyar, Khalid Kunji et al. · 2022 · Circulation Genomic and Precision Medicine
Background: Enthusiasm for using polygenic risk scores (PRSs) in clinical practice is tempered by concerns about their portability to diverse ancestry groups, thus motivating genome-wide association studies in non-European ancestry…
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Guadalupe Nibeyro, Verónica M. Baronetto, Juan I. Folco et al. · 2023 · Frontiers in Immunology
Introduction: Identification of tumor specific neoantigen (TSN) immunogenicity is crucial to develop peptide/mRNA based anti-tumoral vaccines and/or adoptive T-cell immunotherapies; thus, accurate in-silico classification/prioritization proves critical for cost-effective clinical applications. Several methods were proposed as TSNs immunogenicity predictors; however, comprehensive performance comparison is still lacking due to the absence of well documented and adequate TSN databases. Methods: Here, by developing a new curated database having 199 TSNs with experimentally-validated MHC-I present
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Xuan Xu, Penghao Zhen, Fuchao Yu et al. · 2022 · Frontiers in Cardiovascular Medicine
Obstructive sleep apnea (OSA) accelerates the progression of chronic heart failure (CHF). OSA is characterized by chronic intermittent hypoxia (CIH), and CIH exposure accelerates cardiac systolic dysfunction and cardiac remodeling in a cardiac afterload stress mouse model. Mechanistic experiments showed that long-term CIH exposure activated hypoxia-inducible factor 1α (HIF-1α) expression in the mouse heart and upregulated miR-29c expression and that both HIF-1α and miR-29c simultaneously inhibited sarco-/endoplasmic reticulum calcium ATPase 2a (SERCA2a) expression in the mouse heart. Cardiac H
View details →Negative / Null Result ReportBiochemistry, Genetics and Molecular Biology
Liang Chih Liu, Su Chen, Hwei Chung Wang et al. · 2011 · PubMed
AIM: Japanese and American groups reported that single nucleotide variation of caveolin-1 gene (CAV1) plays an important role in breast cancer risk. The aim of this study was to evaluate the association of six polymorphic genotypes of…
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Waylon J. Hastings, Laura Etzel, Christine M. Heim et al. · 2022 · Aging
Various approaches exist to assess population differences in biological aging. Telomere length (TL) is one such measure, and is associated with disease, disability and early mortality. Yet, issues surrounding precision and reproducibility are a concern for TL measurement. An alternative method to estimate TL using DNA methylation (DNAmTL) was recently developed. Although DNAmTL has been characterized in adult and elderly cohorts, its utility in pediatric populations remains unknown. We examined the comparability of leukocyte TL measurements generated using qPCR (absolute TL; aTL) to those esti
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Rasit Dinc, Nurittin Ardıç · 2026 · Cells
Exosomes and other extracellular vesicles (EVs) carry microRNAs, proteins, and lipids that reflect cardiovascular pathophysiology and can enable minimally invasive biomarker discovery. However, EV datasets are highly dimensional and heterogeneous, strongly influenced by pre-analytic variables and non-standardized isolation/characterization workflows, limiting reproducibility across studies. Artificial intelligence (AI), including machine learning (ML), deep learning (DL), and network-based approaches, can support EV biomarker development by integrating multi-omics profiles with clinical metada
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Wil Biddle, David G. Schwark, Margaret A. Schmitt et al. · 2022 · Frontiers in Chemistry
The expansion of the genetic code beyond a single type of noncanonical amino acid (ncAA) is hindered by inefficient machinery for reassigning the meaning of sense codons. A major obstacle to using directed evolution to improve the efficiency of sense codon reassignment is that fractional sense codon reassignments lead to heterogeneous mixtures of full-length proteins with either a ncAA or a natural amino acid incorporated in response to the targeted codon. In stop codon suppression systems, missed incorporations lead to truncated proteins; improvements in activity may be inferred from increase
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Burooj Ghani, Vincent J. Kalkman, Bob Planqué et al. · 2025 · Scientific Reports
Animal sounds can be recognised automatically by machine learning, and this has an important role to play in biodiversity monitoring. Yet despite increasingly impressive capabilities, bioacoustic species classifiers still exhibit imbalanced performance across species and habitats, especially in complex soundscapes. In this study, we explore the effectiveness of transfer learning in large-scale bird sound classification across various conditions, including single- and multi-label scenarios, and across different model architectures such as CNNs and Transformers. Our experiments demonstrate that
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Raya Kh. Yashooa, Ari Q. Nabi, Shukur Wasman Smail et al. · 2026 · Frontiers in Neurology
CRISPR-Cas genome-editing technologies have emerged as powerful tools for precise DNA and RNA modulation, offering promising therapeutic strategies for neurodegenerative disorders such as Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD), and amyotrophic lateral sclerosis (ALS). This review critically evaluates current CRISPR/Cas applications in neurodegeneration, with emphasis on mechanistic insights, therapeutic outcomes, and translational feasibility. Preclinical and early translational studies demonstrate that CRISPR-Cas platforms can correct pathogenic mutation
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Raissa Relator, Aika Terada, Jun Sese · 2018 · BMC Medical Genomics
BACKGROUND: Survival analysis methods have been widely applied in different areas of health and medicine, spanning over varying events of interest and target diseases. They can be utilized to provide relationships between the survival time of individuals and factors of interest, rendering them useful in searching for biomarkers in diseases such as cancer. However, some disease progression can be very unpredictable because the conventional approaches have failed to consider multiple-marker interactions. An exponential increase in the number of candidate markers requires large correction factor
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M Hayat, Wenlong Carl Chen, Chantal Babb de Villiers et al. · 2025 · Nature Communications
Abstract Genome-wide association studies (GWAS) have characterized the contribution of common variants to breast cancer (BC) risk in populations of European ancestry, however GWAS have not been reported in resident African populations. This GWAS included 2485 resident African BC cases and 1101 population matched controls. Two risk loci were identified, located between UNC13C and RAB27A on chromosome 15 (rs7181788, p = 1.01 × 10 −08 ) and in USP22 on chromosome 17 (rs899342, p = 4.62 × 10 −08 ). Several genome-wide significant signals were also detected in hormone receptor subtype analysis. The
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Stella Aslibekyan, Hassan S. Dashti, Toshiko Tanaka et al. · 2014 · Chronobiology International
Sunlight exposure has been shown to alter DNA methylation patterns across several human cell-types, including T-lymphocytes. Since epigenetic changes establish gene expression profiles, changes in DNA methylation induced by sunlight…
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Maria Nikogհosyan, Siras Hakobyan, Anahit Hovhannisyan et al. · 2019 · Frontiers in Genetics
Background: During last decades a number of genome-wide association studies (GWAS) has identified numerous single nucleotide polymorphisms (SNPs) associated with different complex diseases. However, associations reported in one population are often conflicting and did not replicate when studied in other populations. One of the reasons could be that most of GWAS employ case-control design in one or a limited number of populations, but little attention was paid to global distribution of disease associated alleles across different populations. Moreover, the majority of GWAS have been performed on
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Luca‐Cesare Blawitzki, Nina Bartels, Lorand Bonda et al. · 2024 · Biomacromolecules
The glycocalyx, a complex carbohydrate layer on cell surfaces, plays a crucial role in various biological processes. Understanding native glycocalyces' complexity is challenging due to their intricate and dynamic nature. Simplified mimics…
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Sandra Waaijenborg, Oksana Korobko, Ko Willems van Dijk et al. · 2018 · PLoS ONE
Combining different metabolomics platforms can contribute significantly to the discovery of complementary processes expressed under different conditions. However, analysing the fused data might be hampered by the difference in their quality. In metabolomics data, one often observes that measurement errors increase with increasing measurement level and that different platforms have different measurement error variance. In this paper we compare three different approaches to correct for the measurement error heterogeneity, by transformation of the raw data, by weighted filtering before modelling
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Celia Sequera, Margherita Grattarola, Floriane Cannet et al. · 2025 · Nature Communications
Histone deacetylases (HDACs) are epigenetic regulators frequently altered in cancer. Here we report that overexpression of HDAC1/2 occurs in Hepatocellular Carcinoma (HCC) patients, correlating with poor prognosis. We show that romidepsin,…
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Guangfu Hu, Guangxia Hu, Chengjiao Zhang et al. · 2020 · BMC Cancer
BACKGROUND: The benefit of adjuvant chemotherapy in invasive lobular carcinoma (ILC) is still unclear. The objective of the current study was to elucidate the effectiveness of adjuvant chemotherapy in hormone receptor (HR)-positive, human epidermal growth factor receptor 2 (HER2)-negative, pT1b-c/N0-1/M0 ILC. METHODS: Based on Surveillance, Epidemiology, and End-Results (SEER) database, we identified original 12,334 HR-positive, HER2-negative, pT1b-c/N0-1/M0 ILC patients, who were then divided into adjuvant chemotherapy group and control group. End-points were overall survival (OS) and breast
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Yukun Kuang, Weiping Tan, Chaohui Hu et al. · 2024 · Frontiers in Cellular and Infection Microbiology
Background: Targeted next-generation sequencing (tNGS) has become a trending tool in the field of infection diagnosis, but concerns are also raising about its performance compared with metagenomic next-generation sequencing (mNGS). This study aims to explore the clinical feasibility of a tNGS panel for respiratory tract infection diagnosis and compare it with mNGS in the same cohort of inpatients. Methods: 180 bronchoalveolar lavage fluid samples were collected and sent to two centers for mNGS and tNGS blinded tests, respectively. The concordance between pathogen reports of both methods and th
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