Applied and environmental microbiology, Feb 16, 2016
An estimated 1.5B microbial infections occur globally each year and result in ∼4.6M deaths. A tec... more An estimated 1.5B microbial infections occur globally each year and result in ∼4.6M deaths. A technology gap associated with commercially available diagnostic tests in remote and underdeveloped regions prevents timely pathogen identification for effective antibiotic chemotherapies for infected patients. The result is a trial-and-error approach that is limited in effectiveness and increases risk for patients while contributing to antimicrobial drug resistance and reduces the lifetime of antibiotics. This manuscript addresses this important diagnostic technology gap by describing a low cost, portable, rapid, and easy-to-use microfluidic cartridge-based system for detecting the ESKAPE bacterial pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp) that are most commonly associated with antibiotic resistance. The point-of-care molecular diagnostic system consists of a vacuum-degassed microflu...
The past decade has seen considerable development in the diagnostic application of nonculture met... more The past decade has seen considerable development in the diagnostic application of nonculture methods, including nucleic acid amplification-based methods and mass spectrometry, for the diagnosis of infectious diseases. The implications of these new culture-independent diagnostic tests (CIDTs) include bypassing the need to culture organisms, thus potentially affecting public health surveillance systems, which continue to use isolates as the basis of their surveillance programs and to assess phenotypic resistance to antimicrobial agents. CIDTs may also affect the way public health practitioners detect and respond to a bioterrorism event. In response to a request from the Department of Homeland Security, Los Alamos National Laboratory and the Centers for Disease Control and Prevention cosponsored a workshop to review the impact of CIDTs on the rapid detection and identification of biothreat agents. Four panel discussions were held that covered nucleic acid amplification-based diagnosti...
To analyse the dimensions of interantral bone available for dental implant placement in the fully... more To analyse the dimensions of interantral bone available for dental implant placement in the fully edentulous maxilla. Interantral bone height (IBH) was measured using panoramic radiography and computed tomography (CT). Interantral bone width (IBW) was measured by means of CT. The difference between both imaging methods in IBH assessment was highly statistically significant (p < 0.001) in the canine area, whereas in other areas it was found not to be significant. Measured in the CT scans, bone is significantly higher in the canine area compared to the area of central and lateral incisors (p < 0.001). Significant variations in IBW were found in all three locations; bone in the central incisor area is the widest, in the area of the lateral incisor, the narrowest (p < 0.001). Panoramic radiography is a sufficiently accurate method for IBH imaging in the incisor area, but not in the canine area.
Journal of clinical and experimental dentistry, 2014
Oral lichen planus is chronic inflammatory disease with a high prevalence in the population. This... more Oral lichen planus is chronic inflammatory disease with a high prevalence in the population. This study describes the epidemiological and clinical characteristics of group of patients with oral lichen planus in the Czech Republic. Data was taken from the medical records of 171 patients referred to the Oral Medicine Unit at the University Hospital in Hradec Králové with histologically confirmed clinical diagnosis of oral lichen planus in the period 2003 - 2013. The data were retrospectively reviewed. Of the 171 patients, 116 (67.8%) were women and 55 (32.2%) were men. The mean age was 55.2 ± 12.4 years (range of 85.0 - 20.9). The reticular form was the most frequent 93.6% (160 pts.), desquamative gingivitis was 12.9% (22). The buccal mucosa was the site most affected 89.5% (153 pts.). The lesions were asymptomatic in 52 patients (30.4%). Extraoral lesions were observed in 20.5% (35 pts.) of the patients, skin involvement was in 16.4% (28 pts.). Smokers were 29 patients. Local treatme...
Efforts are underway at numerous sites around the world to construct physical maps of all human c... more Efforts are underway at numerous sites around the world to construct physical maps of all human chromosomes. These maps will enable researchers to locate, characterize, and eventually understand the genes that control human structure and function. The volume and complexity of the data already generated requires a sophisticated array of computational support to collect, store, analyze, integrate and display data in biologically meaningful ways. The Human Genome Center at Livermore has spent the past 6 years constructing a database system to support its physical mapping efforts on human chromosome 19. Our computational support team is composed of experienced computer professionals who share a common pragmatic primary goal of rapidly supplying tools that meet the ever-changing needs of the biologists. In this paper, we concentrate on the design issues, tradeoffs, and consequences from the point of view of building a complex database system to support leading-edge genomic research. We i...
We report on a 13-month-old girl showing dysmorphic features and a delay in psychomotor developme... more We report on a 13-month-old girl showing dysmorphic features and a delay in psychomotor development. She was diagnosed with a balancedde novo translocation 46, X, t(X;13)(p11. 2;p13) and non-random inactivation of the X chromosome. FISH analysis, employing the X chromosome centromere andXIST-region-specific probes, showed that theXIST locus was not involved in the translocation. Selective inactivation of paternal X, which was
A high-throughput multiplexed assay was developed for the differential laboratory detection of fo... more A high-throughput multiplexed assay was developed for the differential laboratory detection of foot-and- mouth disease virus (FMDV) from viruses that cause clinically similar diseases of livestock. This assay simultaneously screens for five RNA and two DNA viruses by using multiplexed reverse transcription-PCR (mRT-PCR) amplification coupled with a microsphere hybridization array and flow-cytometric detection. Two of the 17 primer-probe sets included
Background Identifying the bacteria and viruses present in a complex sample is useful in disease ... more Background Identifying the bacteria and viruses present in a complex sample is useful in disease diagnostics, product safety, environmental characterization, and research. Array-based methods have proven utility to detect in a single assay at a reasonable cost any microbe from the thousands that have been sequenced. Methods We designed a pan-Microbial Detection Array (MDA) to detect all known viruses (including phages), bacteria and plasmids and developed a novel statistical analysis method to identify mixtures of organisms from complex samples hybridized to the array. The array has broader coverage of bacterial and viral targets and is based on more recent sequence data and more probes per target than other microbial detection/discovery arrays in the literature. Family-specific probes were selected for all sequenced viral and bacterial complete genomes, segments, and plasmids. Probes were designed to tolerate some sequence variation to enable detection of divergent species with hom...
Background MannDB was created to meet a need for rapid, comprehensive automated protein sequence ... more Background MannDB was created to meet a need for rapid, comprehensive automated protein sequence analyses to support selection of proteins suitable as targets for driving the development of reagents for pathogen or protein toxin detection. Because a large number of open-source tools were needed, it was necessary to produce a software system to scale the computations for whole-proteome analysis. Thus, we built a fully automated system for executing software tools and for storage, integration, and display of automated protein sequence analysis and annotation data. Description MannDB is a relational database that organizes data resulting from fully automated, high-throughput protein-sequence analyses using open-source tools. Types of analyses provided include predictions of cleavage, chemical properties, classification, features, functional assignment, post-translational modifications, motifs, antigenicity, and secondary structure. Proteomes (lists of hypothetical and known proteins) a...
Applied and environmental microbiology, Feb 16, 2016
An estimated 1.5B microbial infections occur globally each year and result in ∼4.6M deaths. A tec... more An estimated 1.5B microbial infections occur globally each year and result in ∼4.6M deaths. A technology gap associated with commercially available diagnostic tests in remote and underdeveloped regions prevents timely pathogen identification for effective antibiotic chemotherapies for infected patients. The result is a trial-and-error approach that is limited in effectiveness and increases risk for patients while contributing to antimicrobial drug resistance and reduces the lifetime of antibiotics. This manuscript addresses this important diagnostic technology gap by describing a low cost, portable, rapid, and easy-to-use microfluidic cartridge-based system for detecting the ESKAPE bacterial pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp) that are most commonly associated with antibiotic resistance. The point-of-care molecular diagnostic system consists of a vacuum-degassed microflu...
The past decade has seen considerable development in the diagnostic application of nonculture met... more The past decade has seen considerable development in the diagnostic application of nonculture methods, including nucleic acid amplification-based methods and mass spectrometry, for the diagnosis of infectious diseases. The implications of these new culture-independent diagnostic tests (CIDTs) include bypassing the need to culture organisms, thus potentially affecting public health surveillance systems, which continue to use isolates as the basis of their surveillance programs and to assess phenotypic resistance to antimicrobial agents. CIDTs may also affect the way public health practitioners detect and respond to a bioterrorism event. In response to a request from the Department of Homeland Security, Los Alamos National Laboratory and the Centers for Disease Control and Prevention cosponsored a workshop to review the impact of CIDTs on the rapid detection and identification of biothreat agents. Four panel discussions were held that covered nucleic acid amplification-based diagnosti...
To analyse the dimensions of interantral bone available for dental implant placement in the fully... more To analyse the dimensions of interantral bone available for dental implant placement in the fully edentulous maxilla. Interantral bone height (IBH) was measured using panoramic radiography and computed tomography (CT). Interantral bone width (IBW) was measured by means of CT. The difference between both imaging methods in IBH assessment was highly statistically significant (p < 0.001) in the canine area, whereas in other areas it was found not to be significant. Measured in the CT scans, bone is significantly higher in the canine area compared to the area of central and lateral incisors (p < 0.001). Significant variations in IBW were found in all three locations; bone in the central incisor area is the widest, in the area of the lateral incisor, the narrowest (p < 0.001). Panoramic radiography is a sufficiently accurate method for IBH imaging in the incisor area, but not in the canine area.
Journal of clinical and experimental dentistry, 2014
Oral lichen planus is chronic inflammatory disease with a high prevalence in the population. This... more Oral lichen planus is chronic inflammatory disease with a high prevalence in the population. This study describes the epidemiological and clinical characteristics of group of patients with oral lichen planus in the Czech Republic. Data was taken from the medical records of 171 patients referred to the Oral Medicine Unit at the University Hospital in Hradec Králové with histologically confirmed clinical diagnosis of oral lichen planus in the period 2003 - 2013. The data were retrospectively reviewed. Of the 171 patients, 116 (67.8%) were women and 55 (32.2%) were men. The mean age was 55.2 ± 12.4 years (range of 85.0 - 20.9). The reticular form was the most frequent 93.6% (160 pts.), desquamative gingivitis was 12.9% (22). The buccal mucosa was the site most affected 89.5% (153 pts.). The lesions were asymptomatic in 52 patients (30.4%). Extraoral lesions were observed in 20.5% (35 pts.) of the patients, skin involvement was in 16.4% (28 pts.). Smokers were 29 patients. Local treatme...
Efforts are underway at numerous sites around the world to construct physical maps of all human c... more Efforts are underway at numerous sites around the world to construct physical maps of all human chromosomes. These maps will enable researchers to locate, characterize, and eventually understand the genes that control human structure and function. The volume and complexity of the data already generated requires a sophisticated array of computational support to collect, store, analyze, integrate and display data in biologically meaningful ways. The Human Genome Center at Livermore has spent the past 6 years constructing a database system to support its physical mapping efforts on human chromosome 19. Our computational support team is composed of experienced computer professionals who share a common pragmatic primary goal of rapidly supplying tools that meet the ever-changing needs of the biologists. In this paper, we concentrate on the design issues, tradeoffs, and consequences from the point of view of building a complex database system to support leading-edge genomic research. We i...
We report on a 13-month-old girl showing dysmorphic features and a delay in psychomotor developme... more We report on a 13-month-old girl showing dysmorphic features and a delay in psychomotor development. She was diagnosed with a balancedde novo translocation 46, X, t(X;13)(p11. 2;p13) and non-random inactivation of the X chromosome. FISH analysis, employing the X chromosome centromere andXIST-region-specific probes, showed that theXIST locus was not involved in the translocation. Selective inactivation of paternal X, which was
A high-throughput multiplexed assay was developed for the differential laboratory detection of fo... more A high-throughput multiplexed assay was developed for the differential laboratory detection of foot-and- mouth disease virus (FMDV) from viruses that cause clinically similar diseases of livestock. This assay simultaneously screens for five RNA and two DNA viruses by using multiplexed reverse transcription-PCR (mRT-PCR) amplification coupled with a microsphere hybridization array and flow-cytometric detection. Two of the 17 primer-probe sets included
Background Identifying the bacteria and viruses present in a complex sample is useful in disease ... more Background Identifying the bacteria and viruses present in a complex sample is useful in disease diagnostics, product safety, environmental characterization, and research. Array-based methods have proven utility to detect in a single assay at a reasonable cost any microbe from the thousands that have been sequenced. Methods We designed a pan-Microbial Detection Array (MDA) to detect all known viruses (including phages), bacteria and plasmids and developed a novel statistical analysis method to identify mixtures of organisms from complex samples hybridized to the array. The array has broader coverage of bacterial and viral targets and is based on more recent sequence data and more probes per target than other microbial detection/discovery arrays in the literature. Family-specific probes were selected for all sequenced viral and bacterial complete genomes, segments, and plasmids. Probes were designed to tolerate some sequence variation to enable detection of divergent species with hom...
Background MannDB was created to meet a need for rapid, comprehensive automated protein sequence ... more Background MannDB was created to meet a need for rapid, comprehensive automated protein sequence analyses to support selection of proteins suitable as targets for driving the development of reagents for pathogen or protein toxin detection. Because a large number of open-source tools were needed, it was necessary to produce a software system to scale the computations for whole-proteome analysis. Thus, we built a fully automated system for executing software tools and for storage, integration, and display of automated protein sequence analysis and annotation data. Description MannDB is a relational database that organizes data resulting from fully automated, high-throughput protein-sequence analyses using open-source tools. Types of analyses provided include predictions of cleavage, chemical properties, classification, features, functional assignment, post-translational modifications, motifs, antigenicity, and secondary structure. Proteomes (lists of hypothetical and known proteins) a...
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Papers by Roy Slezak