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  1. Book ; Conference proceedings: Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences

    Valafar, Faramarz

    METMBS'03 ; Las Vegas, Nevada, USA, June 23 - 26, 2003

    2003  

    Title variant METMBS'03
    Event/congress International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (2003, LasVegasNev.)
    Author's details ed.: Faramarz Valafar
    Language English
    Size 538 S. : Ill., graph. Darst.
    Publisher CSREA Press
    Publishing place Bogart
    Publishing country United States
    Document type Book ; Conference proceedings
    HBZ-ID HT015221149
    ISBN 1-932415-04-1 ; 978-1-932415-04-9
    Database Catalogue ZB MED Medicine, Health

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    Shelf markLoan statusLocation
    2008 A 5662 order for loan Magazin

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  2. Book ; Conference proceedings: Techniques in bioinformatics and medical informatics

    Valafar, Faramarz

    [result of a conference entitled the 2001 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, held on June 25 - 28, 2001, in Las Vegas, Nevada, USA]

    (Annals of the New York Academy of Sciences ; 980)

    2002  

    Event/congress International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (2001, LasVegasNev.)
    Author's details ed. by Faramarz Valafar
    Series title Annals of the New York Academy of Sciences ; 980
    Collection
    Keywords Bioinformatik ; Medizinische Informatik ; Methode
    Subject Methodik ; Verfahren ; Technik ; Methoden ; Medizininformatik
    Language English
    Size 316 S. : Ill., graph. Darst.
    Publisher New York Acad. of Sciences
    Publishing place New York, NY
    Publishing country United States
    Document type Book ; Conference proceedings
    HBZ-ID HT013657449
    ISBN 1-57331-432-3 ; 1-57331-433-1 ; 978-1-57331-432-9 ; 978-1-57331-433-6
    Database Catalogue ZB MED Medicine, Health

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    Se 110 -980- verfügbar in Königswinter Königswinter

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  3. Article ; Online: Pathogenesis of multi drug-resistant and extensively drug-resistant tuberculosis as a determinant of future treatment success.

    Valafar, Faramarz

    International journal of mycobacteriology

    2016  Volume 5 Suppl 1, Page(s) S64–S65

    Language English
    Publishing date 2016-12
    Publishing country Netherlands
    Document type Journal Article
    ISSN 2212-554X
    ISSN (online) 2212-554X
    DOI 10.1016/j.ijmyco.2016.11.017
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  4. Article ; Online: Evaluating impacts of syntenic block detection strategies on rearrangement phylogeny using Mycobacterium tuberculosis isolates.

    Elghraoui, Afif / Mirarab, Siavash / Swenson, Krister M / Valafar, Faramarz

    Bioinformatics (Oxford, England)

    2023  Volume 39, Issue 1

    Abstract: Motivation: The phylogenetic signal of structural variation informs a more comprehensive understanding of evolution. As (near-)complete genome assembly becomes more commonplace, the next methodological challenge for inferring genome rearrangement trees ... ...

    Abstract Motivation: The phylogenetic signal of structural variation informs a more comprehensive understanding of evolution. As (near-)complete genome assembly becomes more commonplace, the next methodological challenge for inferring genome rearrangement trees is the identification of syntenic blocks of orthologous sequences. In this article, we studied 94 reference quality genomes of primarily Mycobacterium tuberculosis (Mtb) isolates as a benchmark to evaluate these methods. The clonal nature of Mtb evolution, the manageable genome sizes, along with substantial levels of structural variation make this an ideal benchmarking dataset.
    Results: We tested several methods for detecting homology and obtaining syntenic blocks and two methods for inferring phylogenies from them, then compared the resulting trees to the standard method's tree, inferred from nucleotide substitutions. We found that, not only the choice of methods, but also their parameters can impact results, and that the tree inference method had less impact than the block determination method. Interestingly, a rearrangement tree based on blocks from the Cactus whole-genome aligner was fully compatible with the highly supported branches of the substitution-based tree, enabling the combination of the two into a high-resolution supertree. Overall, our results indicate that accurate trees can be inferred using genome rearrangements, but the choice of the methods for inferring homology requires care.
    Availability and implementation: Analysis scripts and code written for this study are available at https://gitlab.com/LPCDRP/rearrangement-homology.pub and https://gitlab.com/LPCDRP/syntement.
    Supplementary information: Supplementary data are available at Bioinformatics online.
    MeSH term(s) Phylogeny ; Mycobacterium tuberculosis/genetics ; Genome ; Synteny
    Language English
    Publishing date 2023-01-13
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 1422668-6
    ISSN 1367-4811 ; 1367-4803
    ISSN (online) 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btad024
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    Zs.A 2374: Show issues Location:
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    Jg. 1995 - 2021: Lesesall (2.OG)
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  5. Article: Novel and reported compensatory mutations in

    Conkle-Gutierrez, Derek / Ramirez-Busby, Sarah M / Gorman, Bria M / Elghraoui, Afif / Hoffner, Sven / Elmaraachli, Wael / Valafar, Faramarz

    Frontiers in microbiology

    2024  Volume 14, Page(s) 1265390

    Abstract: Background: Rifampicin (RIF) is a key first-line drug used to treat tuberculosis, a primarily pulmonary disease caused by : Objectives: We performed an association study on a globally representative set of 4,309 whole genome sequenced clinical : ... ...

    Abstract Background: Rifampicin (RIF) is a key first-line drug used to treat tuberculosis, a primarily pulmonary disease caused by
    Objectives: We performed an association study on a globally representative set of 4,309 whole genome sequenced clinical
    Results and conclusions: Of the 1,079 RIF resistant isolates, 638 carried previously reported putative and high-probability compensatory mutations. Our strict criteria identified 46 additional mutations in
    Language English
    Publishing date 2024-01-08
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2023.1265390
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  6. Article ; Online: Pyrazinamide-resistant Tuberculosis Obscured From Common Targeted Molecular Diagnostics.

    Modlin, Samuel J / Mansjö, Mikael / Werngren, Jim / Ejike, Chidera M / Hoffner, Sven E / Valafar, Faramarz

    Drug resistance updates : reviews and commentaries in antimicrobial and anticancer chemotherapy

    2023  Volume 68, Page(s) 100959

    Abstract: Here, we describe a clinical case of pyrazinamide-resistant (PZA-R) tuberculosis (TB) reported as PZA-susceptible (PZA-S) by common molecular diagnostics. Phenotypic susceptibility testing (pDST) indicated PZA-R TB. Targeted Sanger sequencing reported ... ...

    Abstract Here, we describe a clinical case of pyrazinamide-resistant (PZA-R) tuberculosis (TB) reported as PZA-susceptible (PZA-S) by common molecular diagnostics. Phenotypic susceptibility testing (pDST) indicated PZA-R TB. Targeted Sanger sequencing reported wild-type PncA, indicating PZA-S TB. Whole Genome Sequencing (WGS) by PacBio and IonTorrent both detected deletion of a large portion of pncA, indicating PZA-R. Importantly, both WGS methods showed deletion of part of the primer region targeted by Sanger sequencing. Repeating Sanger sequencing from a culture in presence of PZA returned no result, revealing that 1) two minority susceptible subpopulations had vanished, 2) the PZA-R majority subpopulation harboring the pncA deletion could not be amplified by Sanger primers, and was thus obscured by amplification process. This case demonstrates how a small susceptible subpopulation can entirely obscure majority resistant populations from targeted molecular diagnostics and falsely imply homogenous susceptibility, leading to incorrect diagnosis. To our knowledge, this is the first report of a minority susceptible subpopulation masking a majority resistant population, causing targeted molecular diagnostics to call false susceptibility. The consequence of such genomic events is not limited to PZA. This phenomenon can impact molecular diagnostics' sensitivity whenever the resistance-conferring mutation is not fully within primer-targeted regions. This can be caused by structural changes of genomic context with phenotypic consequence as we report here, or by uncommon mechanisms of resistance. Such false susceptibility calls promote suboptimal treatment and spread of strains that challenge targeted molecular diagnostics. This motivates development of molecular diagnostics unreliant on primer conservation, and impels frequent WGS surveillance for variants that evade prevailing molecular diagnostics.
    MeSH term(s) Humans ; Pyrazinamide/pharmacology ; Pyrazinamide/therapeutic use ; Antitubercular Agents/pharmacology ; Antitubercular Agents/therapeutic use ; Mycobacterium tuberculosis/genetics ; Pathology, Molecular ; Amidohydrolases/genetics ; Amidohydrolases/therapeutic use ; Microbial Sensitivity Tests ; Tuberculosis, Multidrug-Resistant/diagnosis ; Tuberculosis, Multidrug-Resistant/drug therapy ; Tuberculosis, Multidrug-Resistant/genetics ; Mutation
    Chemical Substances Pyrazinamide (2KNI5N06TI) ; Antitubercular Agents ; Amidohydrolases (EC 3.5.-)
    Language English
    Publishing date 2023-04-06
    Publishing country Scotland
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 1474513-6
    ISSN 1532-2084 ; 1368-7646
    ISSN (online) 1532-2084
    ISSN 1368-7646
    DOI 10.1016/j.drup.2023.100959
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 5099: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
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  7. Book ; Online: A Comparative study of Artificial Neural Networks Using Reinforcement learning and Multidimensional Bayesian Classification Using Parzen Density Estimation for Identification of GC-EIMS Spectra of Partially Methylated Alditol Acetates

    Valafar, Faramarz / Valafar, Homayoun

    2020  

    Abstract: This study reports the development of a pattern recognition search engine for a World Wide Web-based database of gas chromatography-electron impact mass spectra (GC-EIMS) of partially methylated Alditol Acetates (PMAAs). Here, we also report comparative ... ...

    Abstract This study reports the development of a pattern recognition search engine for a World Wide Web-based database of gas chromatography-electron impact mass spectra (GC-EIMS) of partially methylated Alditol Acetates (PMAAs). Here, we also report comparative results for two pattern recognition techniques that were employed for this study. The first technique is a statistical technique using Bayesian classifiers and Parzen density estimators. The second technique involves an artificial neural network module trained with reinforcement learning. We demonstrate here that both systems perform well in identifying spectra with small amounts of noise. Both system's performance degrades with degrading signal-to-noise ratio (SNR). When dealing with partial spectra (missing data), the artificial neural network system performs better. The developed system is implemented on the world wide web, and is intended to identify PMAAs using submitted spectra of these molecules recorded on any GC-EIMS instrument. The system, therefore, is insensitive to instrument and column dependent variations in GC-EIMS spectra.

    Comment: 5 pages
    Keywords Electrical Engineering and Systems Science - Signal Processing ; Computer Science - Machine Learning ; Computer Science - Neural and Evolutionary Computing ; Quantitative Biology - Biomolecules
    Subject code 006
    Publishing date 2020-07-31
    Publishing country us
    Document type Book ; Online
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  8. Book ; Online: Reduction in the complexity of 1D 1H-NMR spectra by the use of Frequency to Information Transformation

    Valafar, Homayoun / Valafar, Faramarz

    2020  

    Abstract: Analysis of 1H-NMR spectra is often hindered by large variations that occur during the collection of these spectra. Large solvent and standard peaks, base line drift and negative peaks (due to improper phasing) are among some of these variations. ... ...

    Abstract Analysis of 1H-NMR spectra is often hindered by large variations that occur during the collection of these spectra. Large solvent and standard peaks, base line drift and negative peaks (due to improper phasing) are among some of these variations. Furthermore, some instrument dependent alterations, such as incorrect shimming, are also embedded in the recorded spectrum. The unpredictable nature of these alterations of the signal has rendered the automated and instrument independent computer analysis of these spectra unreliable. In this paper, a novel method of extracting the information content of a signal (in this paper, frequency domain 1H-NMR spectrum), called the frequency-information transformation (FIT), is presented and compared to a previously used method (SPUTNIK). FIT can successfully extract the relevant information to a pattern matching task present in a signal, while discarding the remainder of a signal by transforming a Fourier transformed signal into an information spectrum (IS). This technique exhibits the ability of decreasing the inter-class correlation coefficients while increasing the intra-class correlation coefficients. Different spectra of the same molecule, in other words, will resemble more to each other while the spectra of different molecules will look more different from each other. This feature allows easier automated identification and analysis of molecules based on their spectral signatures using computer algorithms.

    Comment: 21 pages
    Keywords Electrical Engineering and Systems Science - Signal Processing ; Computer Science - Computer Vision and Pattern Recognition ; Quantitative Biology - Biomolecules
    Subject code 303
    Publishing date 2020-12-16
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: Atypical Genetic Basis of Pyrazinamide Resistance in Monoresistant Mycobacterium tuberculosis.

    Modlin, Samuel J / Marbach, Tyler / Werngren, Jim / Mansjö, Mikael / Hoffner, Sven E / Valafar, Faramarz

    Antimicrobial agents and chemotherapy

    2021  Volume 65, Issue 6

    Abstract: Pyrazinamide (PZA) is a widely used antitubercular chemotherapeutic. Typically, PZA resistance (PZA-R) emerges ... ...

    Abstract Pyrazinamide (PZA) is a widely used antitubercular chemotherapeutic. Typically, PZA resistance (PZA-R) emerges in
    MeSH term(s) Amidohydrolases/genetics ; Antitubercular Agents/pharmacology ; Antitubercular Agents/therapeutic use ; Drug Resistance, Bacterial/genetics ; Humans ; Microbial Sensitivity Tests ; Mutation ; Mycobacterium tuberculosis/genetics ; Phylogeny ; Pyrazinamide/pharmacology ; Sweden ; Tuberculosis, Multidrug-Resistant/drug therapy
    Chemical Substances Antitubercular Agents ; Pyrazinamide (2KNI5N06TI) ; Amidohydrolases (EC 3.5.-)
    Language English
    Publishing date 2021-05-18
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 217602-6
    ISSN 1098-6596 ; 0066-4804
    ISSN (online) 1098-6596
    ISSN 0066-4804
    DOI 10.1128/AAC.01916-20
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    Zs.A 809: Show issues Location:
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    Einzelsignatur: Show issues

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  10. Book ; Online: Parallel, Self Organizing, Consensus Neural Networks

    Valafar, Homayoun / Valafar, Faramarz / Ersoy, Okan

    2020  

    Abstract: A new neural network architecture (PSCNN) is developed to improve performance and speed of such networks. The architecture has all the advantages of the previous models such as self-organization and possesses some other superior characteristics such as ... ...

    Abstract A new neural network architecture (PSCNN) is developed to improve performance and speed of such networks. The architecture has all the advantages of the previous models such as self-organization and possesses some other superior characteristics such as input parallelism and decision making based on consensus. Due to the properties of this network, it was studied with respect to implementation on a Parallel Processor (Ncube Machine) as well as a regular sequential machine. The architecture self organizes its own modules in a way to maximize performance. Since it is completely parallel, both recall and learning procedures are very fast. The performance of the network was compared to the Backpropagation networks in problems of language perception, remote sensing and binary logic (Exclusive-Or). PSCNN showed superior performance in all cases studied.

    Comment: 4 pages
    Keywords Computer Science - Neural and Evolutionary Computing ; Computer Science - Machine Learning
    Subject code 006
    Publishing date 2020-07-30
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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