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At least 1,693 records · Page 94Linked to original sources
PubMed1999

Multicenter evaluation of the Abbott LCx Mycobacterium tuberculosis ligase chain reaction assay.

Four Australian hospital laboratories evaluated the performance of the Abbott LCx Mycobacterium tuberculosis assay with 2,347 specimens (2,083 respiratory and 264 nonrespiratory specimens) obtained from 1, 411 patients. A total of 152 specimens (6.5%) were culture positive for Mycobacterium tuberculosis complex (MTBC); of these, 79 (52%) were smear positive. After resolution of discrepant data, the overall sensitivity, specificity, and positive and negative predictive values for the LCx assay were 69.7, 99.9, 99.1, and 97.7% respectively. For smear-positive respiratory specimens that were culture positive for MTBC, the values were 98.5, 100, 100, and 98.4%, respectively, while the values for smear-negative respiratory specimens were 41.5, 99.9, 96.4, and 98%, respectively. Relative operating characteristic curves were constructed to demonstrate the relationship between sensitivity and specificity for a range of possible cutoff values in the LCx assay. These graphs suggested that the assay sensitivity for respiratory samples could be increased from 70.2 to 78.6%, while the specificity would be reduced from 99.9 to 99.4% by inclusion of a grey zone (i.e., LCx assay values of between 0.2 and 0.99). An algorithm is presented for the handling of specimens with LCx assay values within this grey zone.

DNA Ligases↗
PubMed2026

Mannheimia haemolytica strain-level diversity in cattle populations.

High-resolution genomic characterization is essential for understanding diversity, pathogenicity, and transmission dynamics of bacterial pathogens. Mannheimia haemolytica (Mh) is the most consequential bacterial agent associated with bovine respiratory disease (BRD) in cattle, as a leading cause of morbidity, mortality, and antimicrobial use. Historically, BRD pathogens, including Mh, have been studied using culture or PCR approaches that provided limited ability to characterize fine-scale genomic variation across communities. Here, we evaluated target-enriched (TE) shotgun sequencing, a culture-independent method capable of strain-level resolution within metagenomic data, for detecting and characterizing Mh in comparison with qPCR and 16S rRNA gene sequencing. Nasal swabs (10 individual and 2 composited DNA samples per pen) and environmental samples (three ropes hung on pen rails and three water bowl swabs per pen) were collected from four pens in each of five distinct cattle populations. DNA was extracted for TE sequencing to identify Mh at both species and genomic sequence variant (GSV) levels, and to characterize antimicrobial resistance genes across the bacterial communities. qPCR was performed to quantify Mh genome copies, and 16S rRNA gene sequencing was used to assess the broader respiratory microbiome. TE sequencing identified Mh in 100% of TE-tested samples and classified multiple GSVs in all but 3 of 121 samples. GSV profiles clustered within housing groups and varied across cattle populations, indicating structured strain-level diversity. In contrast, Mannheimia spp. were detected in only 47.7% of samples by 16S rRNA sequencing. These findings demonstrate that TE sequencing enables sensitive, strain-level characterization of Mh in cattle and environmental samples and reveals substantial within-population genomic diversity not captured by conventional approaches.IMPORTANCETarget-enriched shotgun sequencing enabled sensitive, strain-level detection of Mannheimia haemolytica (Mh), revealing multiple co-circulating genomic sequence variants (GSVs) within and among cattle groups. This demonstrates greater genetic variability of Mh populations in beef cattle than has been previously recognized. The clustering of GSVs within housing groups, together with the overlap between respiratory and environmental samples, is consistent with the hypothesis that contagious transmission contributes to Mh ecology. These results highlight the potential utility of composite nasal swab and environmental samples for future studies evaluating relationships between Mh genomic variation and disease risk.

Animals↗
PubMed1999

The proteasome.

Proteasomes are large multisubunit proteases that are found in the cytosol, both free and attached to the endoplasmic reticulum, and in the nucleus of eukaryotic cells. Their ubiquitous presence and high abundance in these compartments reflects their central role in cellular protein turnover. Proteasomes recognize, unfold, and digest protein substrates that have been marked for degradation by the attachment of a ubiquitin moiety. Individual subcomplexes of the complete 26S proteasome are involved in these different tasks: The ATP-dependent 19S caps are believed to unfold substrates and feed them to the actual protease, the 20S proteasome. This core particle appears to be more ancient than the ubiquitin system. Both prokaryotic and archaebacterial ancestors have been identified. Crystal structures are now available for the E. coli proteasome homologue and the T. acidophilum and S. cerevisiae 20S proteasomes. All three enzymes are cylindrical particles that have their active sites on the inner walls of a large central cavity. They share the fold and a novel catalytic mechanism with an N-terminal nucleophilic threonine, which places them in the family of Ntn (N terminal nucleophile) hydrolases. Evolution has added complexity to the comparatively simple prokaryotic prototype. This minimal proteasome is a homododecamer made from two hexameric rings stacked head to head. Its heptameric version is the catalytic core of archaebacterial proteasomes, where it is sandwiched between two inactive antichambers that are made up from a different subunit. In eukaryotes, both subunits have diverged into seven different subunits each, which are present in the particle in unique locations such that a complex dimer is formed that has six active sites with three major specificities that can be attributed to individual subunits. Genetic, biochemical, and high-resolution electron microscopy data, but no crystal structures, are available for the 19S caps. A first step toward a mechanistic understanding of proteasome activation and regulation has been made with the elucidation of the X-ray structure of the alternative, mammalian proteasome activator PA28.

Adenosine Triphosphatases↗
PubMedDate not supplied

Nontraumatic emergent abdominal vascular conditions: advantages of multi-detector row CT and three-dimensional imaging.

In the past decade, great strides have been made in the development of helical computed tomography (CT) that have led to shorter scanning time and higher spatial resolution. A wide range of traumatic and nontraumatic emergent conditions may be quickly and accurately diagnosed with multi-detector row CT. Multi-detector row CT angiography is the preferred method for imaging in emergent abdominal vascular conditions because it enables the acquisition of high-spatial-resolution volumetric image data during a single breath hold. Unlike catheter angiography, multi-detector row CT angiography not only depicts the vessels but also allows assessment of perfusion in adjacent organs. To make the most effective diagnostic use of multi-detector row CT angiography and three-dimensional image postprocessing, radiologists must be familiar with the optimal CT angiographic protocols and with the typical CT findings in various emergent vascular conditions. This article describes the protocols used in 11 patients with conditions including ruptured abdominal aortic aneurysm, secondary aortoduodenal fistula, splanchnic segmental arterial mediolysis, and Wegener-type vasculitis with visceral involvement. All of the diagnoses in these 11 cases were made in the emergency department, and the delay between imaging and diagnosis was decreased considerably by avoiding the transfer of patients for catheter angiography.

Abdomen, Acute↗
PubMed2002

Counting channels: a tutorial guide on ion channel fluctuation analysis.

Ion channels open and close in a stochastic fashion, following the laws of probability. However, distinct from tossing a coin or a die, the probability of finding the channel closed or open is not a fixed number but can be modified (i.e., we can cheat) by some external stimulus, such as the voltage. Single-channel records can be obtained using the appropriate electrophysiological technique (e.g., patch clamp), and from these records the open probability and the channel conductance can be calculated. Gathering these parameters from a membrane containing many channels is not straightforward, as the macroscopic current I = iNP(o), where i is the single-channel current, N the number of channels, and P(o) the probability of finding the channel open, cannot be split into its individual components. In this tutorial, using the probabilistic nature of ion channels, we discuss in detail how i, N, and P(o max) (the maximum open probability) can be obtained using fluctuation (nonstationary noise) analysis (Sigworth FJ. G Gen Physiol 307: 97-129, 1980). We also analyze the sources of possible artifacts in the determination of i and N, such as channel rundown, inadequate filtering, and limited resolution of digital data acquisition by use of a simulation computer program (available at www.cecs.cl).

Animals↗
PubMed2004

Microarray analysis reveals differences in gene expression of circulating CD8(+) T cells in melanoma patients and healthy donors.

Circulating T cells from many cancer patients are known to be dysfunctional and undergo spontaneous apoptosis. We used microarray technology to determine whether gene expression differences exist in T cells from melanoma patients versus healthy subjects, which may underlie these abnormalities. To maximize the resolution of our data, we sort purified CD8(+) subsets and amplified the extracted RNA for microarray analysis. These analyses show subtle but statistically significant expression differences for 10 genes in T cells from melanoma patients versus healthy controls, which were additionally confirmed by quantitative real-time PCR analysis. Whereas none of these genes are members of the classical apoptosis pathways, several may be linked to apoptosis. To additionally investigate the significance of these 10 genes, we combined them into a classifier and found that they provide a much better discrimination between melanoma and healthy T cells as compared with a classifier built uniquely with classical apoptosis-related genes. These results suggest the possible engagement of an alternative apoptosis pathway in circulating T cells from cancer patients.

Cluster Analysis↗
PubMed2004

A thallium-sensitive, fluorescence-based assay for detecting and characterizing potassium channel modulators in mammalian cells.

Potassium channels have been identified as targets for a large number of therapeutic indications. The ability to use a high-throughput functional assay for the detection and characterization of small-molecule modulators of potassium channels is very desirable. However, present techniques capable of screening very large chemical libraries are limited in terms of data quality, temporal resolution, ease of use, and requirements for specialized instrumentation. To address these issues, the authors have developed a fluorescence-based thallium flux assay. This assay is capable of detecting modulators of both voltage and ligand-gated potassium channels expressed in mammalian cells. The thallium flux assay can use instruments standard to most high-throughput screening laboratories, and using such equipment has been successfully employed to screen large chemical libraries consisting of hundreds of thousands of compounds.

Biological Assay↗
PubMed1979

Progress report of the TUDAB project for automated cancer cell detection.

Two methods for high resolution cell image data acquisition are applied routinely. Cells are either scanned by a computer controlled fast scanning microscope photometer (SMP) or a TV-camera. The software system for digital image analysis was completely revised and implemented on the PR 330 minicomputer. The system contains codes for primary cell data acquisition, segmentation of cells, cell feature extraction and statistical cell analysis. With this system, SMP and TV scanned cell data bases of PAP stained cells in vaginal smears, grouped into several classes, have been built up. Each data base contains 34 primary features and 20 feature combinations for each cell. A linear discriminant analysis is applied routinely for cell classification. The present state of the system and its operation are described, cell features and classification results are shown, and future steps for a prescreening strategy are discussed.

Computers↗
PubMed2003

Correlates of gay and lesbian couples' relationship satisfaction and relationship dissolution.

A sample of committed gay and lesbian cohabiting couples engaged in two conversations after being apart for at least 8 hours: (a) an events of the day conversation and (b) a conflict resolution conversation. Physiological data were collected during the conversations and a videotape record was made. Couples viewed the videotapes and rated their affect during the interaction. The video records were coded with a system that categorized specific affects displayed. Models derived from physiology, from the perception of interaction, and from specific affective behavior were related to relationship satisfaction, and to the prediction of relationship dissolution over a 12-year period. Results supported previous findings that satisfaction and stability in gay and lesbian relationships are related to similar emotional qualities as in heterosexual relationships.

Adult↗
PubMed2005

Undersampling correction for array detector-based satellite spectrometers.

Array detector-based instruments are now fundamental to measurements of ozone and other atmospheric trace gases from space in the ultraviolet, visible, and infrared. The present generation of such instruments suffers, to a greater or lesser degree, from undersampling of the spectra, leading to difficulties in the analysis of atmospheric radiances. We provide extended analysis of the undersampling suffered by modern satellite spectrometers, which include the Global Ozone Monitoring Experiment, Scanning Imaging Absorption Spectrometer for Atmospheric Chartography, Ozone Monitoring Instrument, and Ozone Mapping and Profiler Suite. The analysis includes basic undersampling, the effects of binning into separate detector pixels, and the application of high-resolution Fraunhofer spectral data to correct for undersampling in many useful cases.

Journal Article↗
PubMed2003

An automated approach to quantitative air trapping measurements in mild cystic fibrosis.

PURPOSE: To automatically derive the degree of air trapping in mild cystic fibrosis (CF) disease from high-resolution CT (HRCT) data, and to evaluate the discriminating power of the measurement. MATERIALS AND METHODS: The data consist of six pairs of anatomically matched tomographic slices, obtained during breath-holding in triggered HRCT acquisitions. The pairs consist of an inspiratory slice, at > or = 95% of slow vital capacity, and an expiratory slice at near residual volume (nRV). The subjects are 25 patients with mild CF and 10 age-matched, normal control subjects. SUBJECTS: Lung segmentation is automatic. The limits defining air trapping in the expiratory slices are determined by the distribution of densities in the expanded lung. They are modulated by density changes between expiration and inspiration. Air trapping defects consist of contiguous low-density voxels. The difference between patients and control subjects was evaluated in comparison to pulmonary function test (PFT) results and lung density distribution descriptors (global density descriptors). RESULTS: In mild CF, air trapping does not correlate with global PFT results, except for the ratio of residual volume (RV) to total lung capacity (TLC); however, the size of air trapping defects was the best discriminator between patients and control subjects (p < 0.005). Of PFT results, only RV/TLC reached significance at p < 0.05. The global density descriptors reached near significance in the nRV images only. CONCLUSION: Air trapping defined as defect size and measured in an objective automated manner is a powerful discriminator for mild CF.

Adolescent↗
PubMed2005

Paired inspiratory/expiratory volumetric thin-slice CT scan for emphysema analysis: comparison of different quantitative evaluations and pulmonary function test.

PURPOSES: The aim of the study was to use three-dimensional high-resolution CT scan data sets in inspiration and expiration for the quantitative evaluation of emphysema. Using an advanced dedicated semiautomatic analysis tool, the functional inspiratory/expiratory shifts of emphysema volume and clusters were quantified. The pulmonary function test (PFT) served as the clinical "gold standard." MATERIALS AND METHODS: Thirty-one patients (9 women and 22 men; mean [+/- SD] age, 60 +/- 8 years) who had severe emphysema due to COPD (Global Initiative for Chronic Obstructive Lung Disease [GOLD] class III and IV) were included in the study. All patients underwent paired inspiratory/expiratory multidetector CT scans (slice thickness, 1/0.8 mm) and pulmonary function tests (PFTs). CT scan data were analyzed with self-written emphysema detection solftware. It provides lung volume (LV), emphysema volume (EV), emphysema index (EI), and four clusters of emphysema with different volumes (from 2, 8, 65, and 120 mm(3)). These results were correlated with total lung capacity (TLC), intrathoracic gas volume (ITGV), and residual volume (RV) derived from PFT results. RESULTS: Inspiratory LV correlated with TLC (r = 0.9), expiratory LV with ITGV (r = 0.87), and RV (r = 0.83). Expiratory EV correlated better with ITGV (r = 0.88) and RV (r = 0.93) than with inspiratory EV (r = 0.83 and 0.88, respectively). The mean inspiratory EI was 54 +/- 13%, and it decreased to 43 +/- 15% in expiration. However, the individuals showed a broad spectrum of changes of EI (mean, 11%; range, 1 to 28%), and no differences in inspiratory/expiratory EI and changes in EI or LV were found between GOLD III and GOLD IV patients. In expiration, there was a change from the large emphysema cluster (-37%) to the intermediate cluster (+15%) and small cluster (+13% and +11%, respectively). The change of volume of the large emphysema cluster after expiration correlated well with the changes in LV (r = 0.9), EV (r = 0.99), EI (r = 0.85), and MLD (r = 0.76). CONCLUSION: Emphysema volumes measured from expiratory MDCT scans better reflect PFT abnormalities in patients with severe emphysema than those from inspiratory scans. Volumetric cluster analysis provided deeper insights into the local hyperinflation and expiratory obstruction of large emphysematous clusters.

Adult↗
PubMedDate not supplied

Organosulfur compounds from garlic (Allium sativum) oxidizing canine erythrocytes.

The sulfurous acid ester, trans-sulfurous acid allyl ester 3-allylsulfanyl-allyl ester 8, along with two known thiosulfinates was isolated from the aqueous ethanol extract of garlic (Allium sativum). The chemical structure of 8 was determined on the basis of spectroscopic data including high resolution mass and two-dimensional NMR techniques. All of these compounds induced methemoglobin formation in a canine erythrocyte suspension in vitro resulting in the oxidation of canine erythrocytes. This is the first report of sulfurous acid ester showing oxidant activity in canine erythrocytes.

Alkanesulfonates↗
PubMed2006

Molecular composition of the endocannabinoid system at glutamatergic synapses.

Endocannabinoids play central roles in retrograde signaling at a wide variety of synapses throughout the CNS. Although several molecular components of the endocannabinoid system have been identified recently, their precise location and contribution to retrograde synaptic signaling is essentially unknown. Here we show, by using two independent riboprobes, that principal cell populations of the hippocampus express high levels of diacylglycerol lipase alpha (DGL-alpha), the enzyme involved in generation of the endocannabinoid 2-arachidonoyl-glycerol (2-AG). Immunostaining with two independent antibodies against DGL-alpha revealed that this lipase was concentrated in heads of dendritic spines throughout the hippocampal formation. Furthermore, quantification of high-resolution immunoelectron microscopic data showed that this enzyme was highly compartmentalized into a wide perisynaptic annulus around the postsynaptic density of axospinous contacts but did not occur intrasynaptically. On the opposite side of the synapse, the axon terminals forming these excitatory contacts were found to be equipped with presynaptic CB1 cannabinoid receptors. This precise anatomical positioning suggests that 2-AG produced by DGL-alpha on spine heads may be involved in retrograde synaptic signaling at glutamatergic synapses, whereas CB1 receptors located on the afferent terminals are in an ideal position to bind 2-AG and thereby adjust presynaptic glutamate release as a function of postsynaptic activity. We propose that this molecular composition of the endocannabinoid system may be a general feature of most glutamatergic synapses throughout the brain and may contribute to homosynaptic plasticity of excitatory synapses and to heterosynaptic plasticity between excitatory and inhibitory contacts.

Animals↗
PubMed1997

Overview of periodontal clinical trials utilizing anti-infective or host modulating agents.

Issues in periodontal trials designed to evaluate anti-infective or host modulating agents for the prevention and treatment of periodontal diseases are reviewed in this paper. Clinical trial designs, prevention versus treatment, disease activity, utility of new measurement technologies, ethical and safety issues, selection of outcome variables, and clinical significance are discussed. In general, randomized parallel arm, double-blinded, controlled clinical trials are most appropriate for testing anti-infective and host modulating agents. New measurement technologies may offer increased measurement resolution and automated data capture; but, depending on their specific application and level of examiner reproducibility, these technologies may or may not result in lowered thresholds for declaring change. Mechanical therapy for common plaque-associated gingivitis and adult periodontitis is effective, has low risk, and is widely accepted as a minimum standard of care. New agents for treatment of these diseases must carry minimal risk and have equal or greater effectiveness than this standard of care. Outcome variables for gingivitis trials should include a visual index of gingival inflammation and a separate or component index of gingival bleeding. Prevention studies of periodontitis require a longer duration than treatment studies. Maintenance of mean clinical attachment level should be a primary outcome measure for all prevention studies of adult periodontitis. Maintenance of alveolar bone support is an essential additional outcome for agents specifically acting on bone. The design and conduct of clinical trials for anti-infective and host modulating agents depend on the specific hypothesis to be tested and the ethical demands of providing safe and effective care for all study volunteers.

Anti-Infective Agents↗
PubMed1992

Measurement of attachment level in clinical trials: probing methods.

Measurement of clinical attachment level has become a standard for judging clinical response in periodontal therapy. A number of probing methods and instruments have been developed in an attempt to address limitations in obtaining this measurement. First generation instruments include conventional periodontal probes; second generation probes utilize controlled forces; and third generation probes incorporate automated measurement, controlled forces, and computerized data capture. Various types of stents have been used and repeated measurement techniques have been proposed to reduce examiner error. Controlled force probes appear to have their greatest advantage in increasing inter-examiner repeatability. The use of measurement stents increases inter- and intra-examiner reliability. However, use of such stents may be limited to small sample studies of limited duration. Third generation instruments offer advantages in terms of automated measurement and data capture, increased resolution, and a more continuous measurement scale, but do not necessarily result in increased intra- or inter-examiner reliability. Examiner training and calibration are essential for any measurement instrument. Decisions for or against use of a particular instrument must be made on the basis of the needs of each clinical trial. At the present time, no commercially available instrument resolves all of the inherent limitations of clinical measurement of attachment.

Clinical Trials as Topic↗
PubMed1992

Three-dimensional structure of recombinant human muscle fatty acid-binding protein.

The three-dimensional structure of recombinant human muscle fatty acid-binding protein with a bound fatty acid has been solved and refined with x-ray diffraction data to 2.1 A resolution. The refined model has a crystallographic R factor of 19.5% for data between 9.0 and 2.1 A (7243 unique reflections) and root-mean-square deviations in bond length and bond angle of 0.013 A and 2.7 degrees. The protein contains 10 antiparallel beta-strands and two short alpha-helices which are arranged into two approximately orthogonal beta-sheets. Difference electron density maps and a multiple isomorphous derivative electron density map showed the presence of a single bound molecule of a long chain fatty acid within the interior core of the protein. The hydrocarbon tail of the fatty acid was found to be in a "U-shaped" conformation. Seven ordered water molecules were also identified within the interior of the protein in a pocket on the pseudo-si face of the fatty acid's bent hydrocarbon tail. The methylene tail of the fatty acid forms van der Waals interactions with atoms from 13 residues and three ordered waters. The carboxylate of the fatty acid is located in the interior of the protein where it forms hydrogen bonds with the side chains of Tyr128 and Arg126 and two ordered water molecules. A comparison of the three-dimensional structure of human muscle fatty acid-binding protein and rat intestinal fatty acid-binding protein shows strong similarity. Both proteins bind a single fatty acid within their interior cores, but the bound fatty acids are very different in their conformations and interactions. These findings suggest that the intestinal and muscle fatty acid-binding proteins have evolved distinct binding sites in order to satisfy different requirements within the tissues where they are expressed.

Amino Acid Sequence↗
PubMed1996

Decreasing period-length of the endogenous circadian rhythm of oxygen evolution in Acetabularia and its possible relation to aging.

Endogenous circadian rhythms observed under constant conditions normally show period length variations. However, a general trend is difficult to identify when cells or organisms are entrained with the usual 24-h-period light/dark cycles. Therefore, these variations in time have been considered as fluctuations. In order to gain more insight into this phenomenon, individual Acetabularia cells were exposed to light/dark cycles of 16 h (LD 8:8) and 33.6 h (LD 16.8:16.8), respectively, i.e., periods which lie distinctly outside the range of the normal circadian entrainment. Employing a high-resolution procedure for data analysis, decreasing period lengths could consistently be detected when cells were kept under constant conditions for several weeks. Possible causes of this decrease are discussed.

Acetabularia↗