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J H Bates

Publications and source records attributed to J H Bates.

At least 19 recordsLinked to original sources
PubMed2006

Association between Mycobacterium tuberculosis Beijing/W lineage strain infection and extrathoracic tuberculosis: Insights from epidemiologic and clinical characterization of the three principal genetic groups of M. tuberculosis clinical isolates.

Clinical strains of Mycobacterium tuberculosis can be divided into three principal genetic groups based on the single-nucleotide polymorphisms at the katG gene codon 463 and the gyrA gene codon 95. One subgroup of genetic group 1, the Beijing/W lineage, has been widely studied because of its worldwide distribution and association with outbreaks. In order to increase our understanding of the clinical and epidemiological relevance of the genetic grouping of M. tuberculosis clinical strains and the Beijing/W lineage, we investigated the genetic grouping of 679 clinical isolates of M. tuberculosis, representing 96.3% of culture-confirmed tuberculosis cases diagnosed in Arkansas between January 1996 and December 2000 using PCR and DNA sequencing. We assessed the associations of infections by different genetic groups of M. tuberculosis strains and infection by the Beijing/W lineage strains with the clinical and epidemiological characteristics of the patients using chi-square tests and multivariate logistic regression analysis. Of the 679 study isolates, 676 fell into one of the three principal genetic groups, with 63 (9.3%) in group 1, 438 (64.8%) in group 2, and 175 (25.9%) in group 3. After adjusting for potential confounding of age, gender, race/ethnicity, human immunodeficiency virus serostatus, and plcD genotype in a multivariate logistic regression model, patients infected by the Beijing/W lineage isolates were nearly three times as likely as patients infected with the non-Beijing/W lineage isolates to have an extrathoracic involvement (odds ratio [95% confidence interval], 2.85 [1.33, 6.12]). Thus, the Beijing/W lineage strains may have some special biological features that facilitate the development of extrathoracic tuberculosis.

Adolescent↗
PubMed2006

Population-based study of deletions in five different genomic regions of Mycobacterium tuberculosis and possible clinical relevance of the deletions.

Regions of difference (RDs) have been described in clinical isolates of Mycobacterium tuberculosis, but the potential epidemiological and clinical relevance of the genotypes of these RDs remains to be investigated. We screened a population-based sample of 648 isolates for the deletion of five RDs, designated RD105, RD181, RD142, RD150, and RD239, using microarray-based hybridization, PCR, and DNA sequencing and assessed the associations between the RD deletions and the clinical characteristics of the patients using chi-square analysis and multivariate logistic regression model. Of the 648 isolates, 18 (2.8%) had the RD239 deletion and 39 (6.0%) had the RD105 deletion. The deletions of RD142, RD150, and RD181 subdivided the isolates with the RD105 deletion into four groups comprising a group with concurrent deletions of RD105, RD181, and RD142 (n = 13); a group with concurrent deletions of RD105, RD181, and RD150 (n = 5); a group with concurrent deletions of RD105 and RD181 (n = 13); and a group with a deletion of RD105 only (n = 8). Extrathoracic tuberculosis is statistically significantly associated with infection with the isolates with concurrent deletions of RD105, RD181, and RD142 (adjusted odds ratio [OR] = 3.05; 95% confidence interval [CI] = 1.58, 5.90) and the isolates with concurrent deletions of RD105, RD181, and RD150 (adjusted OR = 11.09; 95% CI = 4.27, 28.80), after controlling for the previously identified risk factors for extrathoracic tuberculosis (human immunodeficiency virus serostatus, race, gender, and the genotype of the plcD gene). These two combinations of RD deletions have the potential for predicting the clinical presentation of M. tuberculosis infection in the human host.

Adolescent↗
PubMed2005

Distribution of insertion- and deletion-associated genetic polymorphisms among four Mycobacterium tuberculosis phospholipase C genes and associations with extrathoracic tuberculosis: a population-based study.

The Mycobacterium tuberculosis genome contains four phospholipase C (PLC)-encoding genes, designated plcA, plcB, plcC, and plcD, respectively. Each of the four genes contributes to the overall PLC activity of M. tuberculosis. PLC is hypothesized to contribute to M. tuberculosis virulence. Infection of M. tuberculosis strains carrying a truncated plcD gene is associated with the occurrence of extrathoracic tuberculosis. However, whether the other three plc genes are also associated with extrathoracic tuberculosis remains to be assessed. We investigated the insertion- and deletion-associated genetic diversity in all four plc genes among 682 epidemiologically and clinically well-characterized M. tuberculosis clinical isolates using PCR, DNA sequencing, and Southern hybridization. Two hundred sixty-six (39%) of the 682 isolates had an interruption in at least one of the four plc genes, most often associated with an IS6110 insertion. The plcD gene interruption was the most common: it was observed in 233 (34%) of the isolates, compared to 4.7%, 4.1%, and 5.9% for plcA, plcB, and plcC gene interruption, respectively. The association between the plc gene genotypes and disease presentation was adjusted for clustering using generalized estimating equations for both bivariate and multivariate analyses. After controlling for the genotypes of the plcABC genes and the host-related risk factors, interruption in the plcD gene remained significantly associated with extrathoracic tuberculosis (odds ratio, 3.27; 95% confidence interval, 1.32 to 8.14). The data suggest that the plcD gene might play a more important role in the pathogenesis of thoracic TB than it does in the pathogenesis of extrathoracic TB.

Bacterial Proteins↗
PubMed2004

Persistence of a strain of Mycobacterium tuberculosis in a prison system.

SETTING: A prison system with an average year-end census of 9084 inmates. OBJECTIVE: To determine transmission dynamics of tuberculosis over a long period; to establish whether Mycobacterium tuberculosis strains responsible for disease in a prison system persist; and to determine whether patients in a community whose isolates cluster with those in a prison system are linked. DESIGN: Retrospective epidemiologic analysis was performed on tuberculosis cases reported in a prison system over a 9-year period. In addition, IS6110 RFLP patterns of M. tuberculosis isolates obtained from prisoners were compared with those of other cases from the state at large. The results of the RFLP analysis and the epidemiologic investigation were compared. RESULTS: Approximately 80% of tuberculosis cases in the prison system were clustered. Over 9 years, a single strain of M. tuberculosis accounted for more than 50% of cases. Patients from the community at large who were infected with the same strain were linked to the prison system. CONCLUSION: In spite of intensive tuberculosis control efforts, a single strain of M. tuberculosis has persisted in the prison system. Its persistence is accounted for by activation of latent infection in patients who, prior to being diagnosed and treated, infected other patients, who then sustained the transmission chain.

Adult↗
PubMed2001

Effects of deep inspiration on bronchoconstriction in the rat.

It is important to understand the mechanisms by which a deep inspiration (DI) affects bronchoconstriction in rodents so that their relevance as animal models of asthma can be assessed. We investigated the effect of DI on respiratory input impedance after methacholine inhalation in four groups of rats: a control group, a group receiving DI prior to challenge, and two groups receiving different degrees of DI after challenge. We measured respiratory input impedance for 15 min following a challenge. This provided time-courses approximating the resistance of the conducting airways and the impedance of the respiratory tissues. We found no significant difference in the peak changes in airway resistance comparing the control group and any of the DI groups following challenge. However, the peak increase in tissue impedance was reduced in the group receiving the largest DI after challenge. Our results thus suggest that the DIs that we administered were neither bronchodilatory nor bronchoprotective, but that they were able to reduce the amount of airway closure occurring following bronchoconstriction.

Animals↗
PubMed2001

Fuzzy logic and mechanical ventilation.

Closed-loop control can achieve appropriate ventilation of the lungs in a healthy person by involving the continuous interaction of three components: sensors, controllers, and effectors. The sensors are the chemo-mechanoreceptors, which continuously monitor key bodily functions affected by ventilation. This information is relayed to the controllers, the respiratory centers in the brain, allowing them to determine how actual ventilation compares with that needed by the body. Finally, the controllers direct the effectors, the muscles of respiration, to adjust the ventilation accordingly. When a patient is in respiratory failure, the effector's role is taken over by a mechanical ventilator. The issue that is considered in this article is how the physician might be taken out of the feedback loop.

Algorithms↗
PubMed2001

Secondary typing of Mycobacterium tuberculosis isolates with matching IS6110 fingerprints from different geographic regions of the United States.

Fifty-nine isolates of Mycobacterium tuberculosis obtained from different states in the United States and representing 25 interstate clusters were investigated. These clusters were identified by computer-assisted analysis of DNA fingerprints submitted during 1996 and 1997 by different laboratories participating in the CDC National Genotyping and Surveillance Network. Isolates were fingerprinted with the IS6110 right-hand probe (IS6110-3'), the IS6110 left-hand probe (IS6110-5'), and the probe pTBN12, containing the polymorphic GC-rich sequence (PGRS). Spoligotyping based on the polymorphism in the 36-bp direct-repeat locus was also performed. As a control, 43 M. tuberculosis isolates in 17 clusters obtained from patients in Arkansas during the study period were analyzed. Of the 25 interstate clusters, 19 were confirmed as correctly clustered when all the isolates were analyzed on the same gel using the IS6110-3' probe. Of the 19 true IS6110-3' clusters, 10 (53%) were subdivided by one or more secondary typing methods. Clustering of the control group was virtually identical by all methods. Of the three different secondary typing methods, spoligotyping was the least discriminating. IS6110-5' fingerprinting was as discriminating as PGRS fingerprinting. The data indicate that the IS6110-5' probe not only is a useful secondary typing method but also probably would prove to be a more useful primary typing method for a genotyping network which involves isolates from different geographic regions.

Bacterial Typing Techniques↗
PubMed2001

Airway branching morphology of mature and immature rabbit lungs.

The scheme of Horsfield et al. for describing the pulmonary airway tree (J Appl Physiol 52: 21-26, 1982) catalogs each airway according to its order and the difference in order of its two daughters (denoted Delta). Although this scheme captures the natural asymmetry in the airway tree, it is still deterministic, because it assumes that all airways of a given order are the same; yet such variability is extremely important in determining the overall behavior of the lungs. We therefore analyzed complete lung lobes from three mature and two immature rabbits and determined the Horsfield order and Delta of every airway down to the terminal bronchioles. We also measured the diameter of each airway. This allowed us to determine the average structure of the rabbit airway tree, the variation about this average, and also how the structures of mature and immature airway trees compare. We found some variation in branching asymmetry and airway diameter at a given order between animals but no evidence of systematic differences in structure between mature and immature lungs. We found evidence of a difference in the branching structure of the peripheral vs. the central part of the airway tree (the break point being around order 20). We also determined the nature of the variation in Delta and diameter as a function of order, which should be valuable for the development of computer models seeking to encapsulate the naturally occurring regional variation in airway geometry in the normal rabbit lung.

Animals↗
PubMed2001

Respiratory mechanics and lung development in the rat from early age to adulthood.

The purpose of the present study was to establish how the dependence of respiratory mechanics on lung inflation changes during development. We studied seven groups of rats from 10 days to 3 mo of age at five levels of positive end-expiratory pressure (PEEP) from 0 to 7 hPa (1 hPa = 0.1 kPa approximately 1 cmH(2)O). At each PEEP level, we measured respiratory system resistance and elastance at both 0.9 and 4.8 Hz to partition the mechanical properties into its airway and tissue components. Elastance increased more rapidly with PEEP in the younger animals, which we interpret as reflecting a more pronounced strain stiffening of the younger parenchyma. However, the decrease in airway resistance with PEEP was more pronounced in the older animals. Morphometric analysis showed that mean tissue density decreased and total alveolar surface area increased with age. Our data suggest that the mechanical interdependence between airways and parenchyma is weaker in very young animals compared with mature animals. This may play a role in the hyperresponsiveness of immaturity.

Aging↗
PubMed2001

Mechanical output impedance of the lung determined from cardiogenic oscillations.

The beating heart naturally oscillates the lung because of the close juxtaposition between these organs producing cardiogenic oscillations in flow that can be measured at the mouth when the glottis is open. Correspondingly, if the mouth is occluded, the same phenomenon produces cardiogenic pressure oscillations that can be measured just distal to the site of occlusion. The Fourier-domain ratio of these oscillations in pressure and flow constitutes what we call cardiogenic respiratory impedance (Zc). We calculated Zc between about 1.5 and 10 Hz in relaxed normal subjects at functional residual capacity with open glottis. Zc was insensitive to heart rate changes induced by exercise and had an imaginary part close to zero at all frequencies investigated. Its real part was similar to or smaller than resistance determined by the forced oscillation technique. We speculate that Zc measures the flow resistance of the central and upper airways of the lung. Zc may be useful as a means of obtaining information about lung mechanics without the need for an external source of flow perturbations.

Adult↗
PubMed2001

A clinic-based molecular epidemiologic study of tuberculosis in Monterrey, Mexico.

SETTING: A tuberculosis clinic associated with a university hospital in Monterrey, Mexico, an urban community with high tuberculosis incidence. OBJECTIVE: To determine the diversity of DNA fingerprint patterns and the extent of drug resistance of Mycobacterium tuberculosis isolates from patients who attended the clinic. DESIGN: Isolates of M. tuberculosis obtained from 186 patients during the period from 31 January 1996 to 31 March 1998 were tested for susceptibility to isoniazid, rifampicin, ethambutol and streptomycin. Demographic data and the social history of each patient were obtained prospectively by interview. The IS6110 DNA fingerprints were obtained for 166 of the 186 isolates. Secondary typing was carried out on isolates with fewer than six copies of IS6110. RESULTS: Thirty-two per cent of the tested isolates (60/ 186) were drug-resistant, and 18% (33/186) were multidrug-resistant. Approximately 55% of the resistant isolates (33/60) were attributed to acquired resistance. A total of 106 different IS6110 fingerprint patterns were observed among the 166 fingerprinted isolates. Based on both IS6110 and pTBN12 fingerprinting, 65 (39%) of the 166 isolates were part of 22 DNA fingerprint clusters. Various drug susceptibility patterns were seen in most clusters. CONCLUSION: Fingerprint clustering indicates extensive recent transmission of tuberculosis in patients attending the clinic. The prevalence of drug-resistant tuberculosis is high.

Adult↗
PubMed2000

Tidal breath analysis for infant pulmonary function testing. ERS/ATS Task Force on Standards for Infant Respiratory Function Testing. European Respiratory Society/American Thoracic Society.

The aim of this position paper is to provide recommendations pertaining to software and equipment requirements when analysing tidal breathing measurements in infants. These guidelines cover numerous aspects including terminology and definitions, equipment, data acquisition and analysis, and reporting of results, and highlight areas in which further research is needed before consensus can be reached. When collecting tidal breathing data in infants and children, equipment dead space and resistance must be minimized, all sources of leak eliminated, and a flowmeter with appropriate frequency response and linearity employed. Inspired gases should be corrected to body temperature, barometric pressure and saturated with water vapour conditions and efforts made to eliminate the various sources of drift in volume that can occur. In addition, the analogue-to-digital converter used to sample data must be capable of adequately resolving the highest and lowest flows required by the study. An adequate sampling rate must be used; 50-100 Hz may be sufficient for the determination of timing and volume parameters, especially in older infants, but rates of 200 Hz are recommended for analysis of the tidal breathing flow/volume loop and other sensitive parameters such as time to peak tidal expiratory flow/expiratory time. The potentially most troublesome aspect of tidal breath analysis from the computational point of view is the identification of the beginning and end of inspiration and expiration. Once methods and equipment for the measurement and analysis of tidal breathing in infants have been standardized, there is an urgent need to establish appropriate reference ranges for various key parameters so that they may be used more effectively in the clinical setting. Implementation of these recommendations should help to ensure that such measurements are as accurate as possible and that more meaningful comparisons can be made between data collected in different centres or with different equipment.

Child↗
PubMed2000

A micromechanical model of airway-parenchymal interdependence.

The forces of parenchymal interdependence in the lung are potent inhibitors of airway smooth muscle shortening, as evidenced by the marked dependence of bronchial responsiveness on lung volume. In this study we developed a mathematical-computer model of the effects of parenchymal interdependence on airway smooth muscle shortening. A three-dimensional network of cuboidal alveolar walls was tethered at its boundaries and surrounded a single airway with mechanical properties identical to the alveolar parenchyma. The walls were assigned highly nonlinear properties so that the pressure-volume behavior of the model matched that measured in dogs. Constriction of the airway was achieved by increasing the circumferential tension in the airway wall, and then solving the force-balance equations of the model to calculate the equilibrium configurations of the airway wall and all the interconnecting alveolar walls. The changes in airway resistance predicted by the model at various transpulmonary pressures (P(tp)) were compared to those obtained by the alveolar capsule oscillator technique in dogs during induced bronchoconstriction at various P(tp) (Balassy et al., J. Appl. Physiol. 78:875-880, 1995). The model matched the data reasonably well at P(tp) values above about 0.5 kPa, but was too responsive at lower P(tp). We were able to make the model match the data at all P(tp) by including an additional stiffness term, such as might conceivably arise from the airway wall itself.

Airway Resistance↗
PubMed2000

Spoligotyping and polymorphic GC-rich repetitive sequence fingerprinting of mycobacterium tuberculosis strains having few copies of IS6110.

Several genetic loci have been utilized to genotype isolates of Mycobacterium tuberculosis. A shortcoming of the most commonly used method, IS6110 fingerprinting, is that it does not adequately discriminate between isolates having few copies of IS6110. This study was undertaken to compare pTBN12 fingerprinting of polymorphic GC-rich repetitive sequence genes and spoligotyping of the direct repeat locus as secondary typing procedures for M. tuberculosis isolates having fewer than six copies of IS6110. A total of 88 isolates (100% of the isolates with fewer than six copies of IS6110 isolated in Arkansas during 1996 and 1997) were included in this study. Among the 88 isolates, 34 different IS6110 patterns were observed, 10 of which were shared by more than 1 isolate, involving a total of 64 isolates. The 64 isolates were subdivided into 13 clusters (containing 37 isolates) and 27 unique isolates based on a combination of IS6110 and pTBN12 fingerprinting and into 11 clusters (containing 51 isolates) and 13 unique isolates based on a combination of IS6110 fingerprinting and spoligotyping. Identical spoligotypes were found among isolates having different IS6110 patterns, as well as among isolates showing different pTBN12 patterns. In contrast, all isolates that had different IS6110 patterns were found to be unique by pTBN12 typing. The clustering rate was 73, 58, and 42%, respectively, for IS6110 fingerprinting alone, IS6110 fingerprinting and spoligotyping combined, and IS6110 and pTBN12 combined fingerprinting. The data indicate that the pTBN12 method has greater discriminating power among low-copy-number isolates than does spoligotyping.

Arkansas↗
PubMed2000

Comparative respiratory system mechanics in rodents.

Because of the wide utilization of rodents as animal models in respiratory research and the limited data on measurements of respiratory input impedance (Zrs) in small animals, we measured Zrs between 0.25 and 9.125 Hz at different levels (0-7 hPa) of positive end-expiratory pressure (PEEP) in mice, rats, guinea pigs, and rabbits using a computer-controlled small-animal ventilator (Schuessler TF and Bates JHT, IEEE Trans Biomed Eng 42: 860-866, 1995). Zrs was fitted with a model, including a Newtonian resistance (R) and inertance in series with a constant-phase tissue compartment characterized by tissue damping (Gti) and elastance (Hti) parameters. Inertance was negligible in all cases. R, Gti, and Hti were normalized to body weight, yielding normalized R, Gti, and Hti (NHti), respectively. Normalized R tended to decrease slightly with PEEP and increased with animal size. Normalized Gti had a minimal dependence on PEEP. NHti decreased with increasing PEEP, reaching a minimum at approximately 5 hPa in all species except mice. NHti was also higher in mice and rabbits compared with guinea pigs and rats at low PEEPs, which we conclude is probably due to a relatively smaller air space volume in mice and rabbits. Our data also suggest that smaller rodents have proportionately wider airways than do larger animals. We conclude that a detailed, comparative study of respiratory system mechanics shows some evidence of structural differences among the lungs of various species but that, in general, rodent lungs obey scaling laws similar to those described in other species.

Airway Resistance↗