Browsing Brage INN by Author "Ahmad, Rafi"
Now showing items 1-20 of 23
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AMR-Diag: Neural network based genotype-to-phenotype prediction of resistance towards β-lactams in Escherichia coli and Klebsiella pneumoniae
Avershina, Ekaterina; Sharma, Priyanka; Taxt, Arne Michael; Singh, Harpreet; Frye, Stephan Alfons; Paul, Kolin; Kapil, Arti; Naseer, Mohammed Umaer; Kaur, Punit; Ahmad, Rafi (Peer reviewed; Journal article, 2021)Antibiotic resistance poses a major threat to public health. More effective ways of the antibiotic prescription are needed to delay the spread of antibiotic resistance. Employment of sequencing technologies coupled with ... -
Chronic obstructive pulmonary disease does not impair responses to resistance training
Mølmen, Knut Sindre; Hammarström, Jens Konrad Daniel; Falch, Gunnar Slettaløkken; Grundtvig, Morten; Koll, Lise; Hanestadhaugen, Marita; Khan, Yusuf; Ahmad, Rafi; Malerbakken, Bente; Rødølen, Tore Jørgen; Lien, Roger; Rønnestad, Bent; Raastad, Truls; Ellefsen, Stian (Peer reviewed; Journal article, 2021) -
Chronic obstructive pulmonary disease does not impair responses to resistance training
Mølmen, Knut Sindre; Hammarström, Jens Konrad Daniel; Falch, Gunnar Slettaløkken; Grundtvig, Morten; Koll, Lise; Hanestadhaugen, Marita; Khan, Yusuf; Ahmad, Rafi; Malerbakken, Bente; Rødølen, Tore J.; Lien, Roger; Rønnestad, Bent; Raastad, Truls; Ellefsen, Stian (Peer reviewed; Journal article, 2021)Background: Subjects with chronic obstructive pulmonary disease (COPD) are prone to accelerated decay of muscle strength and mass with advancing age. This is believed to be driven by disease-inherent systemic pathophysiologies, ... -
Clinical Diagnostics of Bacterial Infections and Their Resistance to Antibiotics—Current State and Whole Genome Sequencing Implementation Perspectives
Avershina, Ekaterina; Khezri, Abdolrahman; Ahmad, Rafi (Peer reviewed; Journal article, 2023)Antimicrobial resistance (AMR), defined as the ability of microorganisms to withstand antimicrobial treatment, is responsible for millions of deaths annually. The rapid spread of AMR across continents warrants systematic ... -
A culture-, amplification-independent, and rapid method for identification of pathogens and antibiotic resistance profile in bovine mastitis milk
Ahmadi, Asal; Khezri, Abdolrahman; Nørstebø, Håvard; Ahmad, Rafi (Peer reviewed; Journal article, 2023)Introduction: Rapid and accurate diagnosis of causative pathogens in mastitis would minimize the imprudent use of antibiotics and, therefore, reduce the spread of antimicrobial resistance. Whole genome sequencing offers a ... -
Developing a hybrid antimicrobial resistance surveillance system in India: Needs & challenges
Kaur, Jasmine; Sharma, Arun; Dhama, Ajay Singh; Buttolia, Harish; Ohri, V.C.; Walia, Kamini; Sharma, Amitesh Kumar; Yahara, Koji; Ahmad, Rafi; Singh, Harpreet (Peer reviewed; Journal article, 2019) -
Distribution of siderophore gene systems on a Vibrionaceae phylogeny: Database searches, phylogenetic analyses and evolutionary perspectives
Thode, Sunniva Katharina; Rojek, Ewelina; Kozlowski, Mikolaj; Ahmad, Rafi; Haugen, Peik (Peer reviewed; Journal article, 2018) -
DNA methylation patterns vary in boar sperm cells with different levels of DNA fragmentation
Narud, Birgitte; Stenseth, Else-Berit; Johannisson, Anders; Myromslien, Frøydis Deinboll; Gaustad, Ann Helen; Wilson, Robert Charles; Lyle, Robert; Morrell, Jane; Kommisrud, Elisabeth; Ahmad, Rafi (Peer reviewed; Journal article, 2019) -
Enhanced Raman techniques for infection diagnostics
Hanrahan, Niall; Lister, Adam; Highmore, Callum; Rajith, Leena; Avershina, Ekaterina; Ali, Jawad; Ahmad, Rafi; Webb, Jeremy; Mahajan, Sumeet (Peer reviewed; Journal article, 2022)In this paper we describe our recent work in multi-excitation surface enhanced Raman spectroscopy (MX-SERS), and its application for robust strain-level bacteria identification. The development of MX-SERS follows directly ... -
Highly sensitive quantitative phase microscopy and deep learning aided with whole genome sequencing for rapid detection of infection and antimicrobial resistance
Ahmad, Azeem; Hettiarachchi, Ramith; Khezri, Abdolrahman; Ahluwalia, Balpreet Singh; Wadduwage, Dushan; Ahmad, Rafi (Peer reviewed; Journal article, 2023)Current state-of-the-art infection and antimicrobial resistance (AMR) diagnostics are based on culture-based methods with a detection time of 48–96 h. Therefore, it is essential to develop novel methods that can do real-time ... -
Hybrid Assembly Provides Improved Resolution of Plasmids, Antimicrobial Resistance Genes, and Virulence Factors in Escherichia coli and Klebsiella pneumoniae Clinical Isolates
Khezri, Abdolrahman; Avershina, Ekaterina; Ahmad, Rafi (Peer reviewed; Journal article, 2021)Emerging new sequencing technologies have provided researchers with a unique opportunity to study factors related to microbial pathogenicity, such as antimicrobial resistance (AMR) genes and virulence factors. However, the ... -
Increased biological relevance of transcriptome analyses in human skeletal muscle using a model-specific pipeline
Khan, Yusuf; Hammarström, Jens Konrad Daniel; Rønnestad, Bent; Ellefsen, Stian; Ahmad, Rafi (Peer reviewed; Journal article, 2020)Abstract Background: Human skeletal muscle responds to weight-bearing exercise with signifcant inter-individual diferences. Investigation of transcriptome responses could improve our understanding of this variation. ... -
Increased growth temperature and vitamin B12 supplementation reduces the lag time for rapid pathogen identification in BHI agar and blood cultures
Ali, Jawad; Joshi, Mukund; Ahmadi, Asal; Strætkvern, Knut Olav; Ahmad, Rafi (Peer reviewed; Journal article, 2023)Background: The rapid diagnostics of pathogens is essential to prescribe appropriate and early antibiotic therapy. The current methods for pathogen detection require the bacteria to grow in a culture medium, which is ... -
The new COST Action European Venom Network (EUVEN)—synergy and future perspectives of modern venomics
Modica, Maria Vittoria; Ahmad, Rafi; Ainsworth, Stuart; Anderluh, Gregor; Antunes, Agostinho; Beis, Dimitris; Caliskan, Figen; Serra, Mauro Dalla; Dutertre, Sebastien; Moran, Yehu; Nalbantsoy, Ayse; Oukkache, Naoual; Pekar, Stano; Remm, Maido; von Reumont, Bjoern Marcus; Sarigiannis, Yiannis; Tarallo, Andrea; Tytgat, Jan; Undheim, Eivind Andreas Baste; Utkin, Yuri; Verdes, Aida; Violette, Aude; Zancolli, Giulia (Peer reviewed; Journal article, 2021)Venom research is a highly multidisciplinary field that involves multiple subfields of biology, informatics, pharmacology, medicine, and other areas. These different research facets are often technologically challenging ... -
The new COST Action European Venom Network (EUVEN)—synergy and future perspectives of modern venomics
Modica, Maria Vittoria; Ahmad, Rafi; Ainsworth, Stuart; Anderluh, Gregor; Antunes, Agostinho; Beis, Dimitris; Caliskan, Figen; Serra, Mauro Dalla; Dutertre, Sebastien; Moran, Yehu; Nalbantsoy, Ayse; Oukkache, Naoual; Pekar, Stano; Remm, Maido; von Reumont, Bjoern Marcus; Sarigiannis, Yiannis; Tarallo, Andrea; Tytgat, Jan; Undheim, Eivind Andreas Baste; Utkin, Yuri; Verdes, Aida; Violette, Aude; Zancolli, Giulia (Peer reviewed; Journal article, 2021)Venom research is a highly multidisciplinary field that involves multiple subfields of biology, informatics, pharmacology, medicine, and other areas. These different research facets are often technologically challenging ... -
Normalization of gene expression data revisited: the three viewpoints of the transcriptome in human skeletal muscle undergoing load-induced hypertrophy and why they matter
Khan, Yusuf; Hammarström, Daniel; Ellefsen, Stian; Ahmad, Rafi (Peer reviewed; Journal article, 2022)The biological relevance and accuracy of gene expression data depend on the adequacy of data normalization. This is both due to its role in resolving and accounting for technical variation and errors, and its defining role ... -
Plasmid Identification and Plasmid-Mediated Antimicrobial Gene Detection in Norwegian Isolates
Khezri, Abdolrahman; Avershina, Ekaterina; Ahmad, Rafi (Peer reviewed; Journal article, 2020)Norway is known for being one of the countries with the lowest levels of antimicrobial resistance (AMR). AMR, through acquired genes located on transposons or conjugative plasmids, is the horizontal transmission of genes ... -
Rapid identification of antimicrobial drug resistance strains of E-coli using SERS nanowire chip
Das, Sathi; saxena, kanchan; Khezri, Abdolrahman; Dubey, Vishesh Kumar; Ahmad, Azeem; jean-claude, Tinguely; mehta, dalip singh; Ahmad, Rafi; Ahluwalia, Balpreet Singh (Peer reviewed; Journal article, 2023)We have investigated the enhanced Raman spectra of AMR bacteria strains of E. coli using silver coated silicon nanowires SERS assay. Three different E. coli strains, E. coli CCUG17620, NCTC 13441, and A239, were detected ... -
Rapid identification of pathogens, antibiotic resistance genes and plasmids in blood cultures by nanopore sequencing
Taxt, Arne Michael; Avershina, Ekaterina; Frye, Stephan Alfons; Naseer, Mohammed Umaer; Ahmad, Rafi (Peer reviewed; Journal article, 2020)Bloodstream infections (BSI) and sepsis are major causes of morbidity and mortality worldwide. Blood culture-based diagnostics usually requires 1–2 days for identification of bacterial agent and an additional 2–3 days for ... -
SERS Nanowire Chip and Machine Learning-Enabled Classification of Wild-Type and Antibiotic-Resistant Bacteria at Species and Strain Levels
Das, Sathi; Saxena, Kanchan; Tinguely, Jean-Claude; Pal, Arijit; Wickramasinghe, Nima L.; Khezri, Abdolrahman; Dubey, Vishesh Kumar; Ahmad, Azeem; Perumal, Vivekanandan; Ahmad, Rafi; Wadduwage, Dushan N.; Ahluwalia, Balpreet Singh; Mehta, Dalip Singh (Peer reviewed; Journal article, 2023)Antimicrobial resistance (AMR) is a major health threat worldwide and the culture-based bacterial detection methods are slow. Surface-enhanced Raman spectroscopy (SERS) can be used to identify target analytes in real time ...