PCR detection of bacteria in seven minutes.
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Bacteria↗
Biomedical subjects
D Hadley
Publications and source records attributed to D Hadley.
Racial differences in testing motivation and psychological distress following pretest education for BRCA1 gene testing.
OBJECTIVES: We conducted a randomized trial to investigate racial differences in response to two alternate pretest education strategies for BRCA1 genetic testing: a standard education model and an education plus counseling (E + C) model. MATERIALS AND METHODS: Two hundred twenty-eight Caucasian women and 70 African American women with a family history of breast or ovarian cancer were contacted for a baseline telephone interview to assess sociodemographic characteristics, number of relatives affected with cancer, and race before pretest education. Outcome variables included changes from baseline to 1-month follow-up in cancer-related distress and genetic testing intentions, as well as provision of a blood sample after the education session. RESULTS: African American women were found to differ significantly from Caucasian women in the effects of the interventions on testing intentions and provision of a blood sample. Specifically, in African American women, E + C led to greater increases than education only in intentions to be tested and provision of a blood sample. These effects were independent of socioeconomic status and referral mechanisms. In Caucasian women, there were no differential effects of the interventions on these outcomes. Reductions in cancer-specific distress were evidenced in all study groups. However, this decrease, although not significantly different, was smallest among African American women who received E + C. CONCLUSIONS: In low- to moderate-risk African American women, pretest education and counseling may motivate BRCA1 testing. Further research is needed to explore the mechanisms of impact of the alternate pretest education strategies and to increase the cultural sensitivity of education and counseling protocols.
Adolescent↗
A miniature analytical instrument for nucleic acids based on micromachined silicon reaction chambers.
In this paper, we describe a miniature analytical thermal cycling instrument (MATCI) to amplify and detect DNA via the polymerase chain reaction in real-time. The MATCI is an integrated, miniaturized analytical system that uses silicon-based, high-efficiency reaction chambers with integrated heaters and simple, inexpensive electronics to precisely control the reaction temperatures. Optical windows in the silicon and solid-state, diode-based detection components are employed to perform real-time fluorescence monitoring of product DNA production. The entire system fits into a briefcase and runs on rechargeable batteries. The applications of this miniaturized nucleic acid analysis system include clinical, research, environmental, and agricultural analyses as well as others which require rapid, portable, and accurate analysis of biological samples for nucleic acids. This paper describes the MATCI and presents results from ultrafast thermal cycling and real-time PCR detection. Examples include human genes and pathogenic viruses and bacteria.
Actins↗
Single photon emission computed tomography in the identification of new variant Creutzfeldt-Jakob disease: case reports.
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Adult↗
Face processing impairments after encephalitis: amygdala damage and recognition of fear.
Face processing and facial emotion recognition were investigated in five post-encephalitic people of average or above-average intelligence. Four of these people (JC, YW, RB and SE) had extensive damage in the region of the amygdala. A fifth post-encephalitic person with predominantly hippocampal damage and relative sparing of the amygdala (RS) participated, allowing us to contrast the effects of temporal lobe damage including and excluding the amygdala region. The findings showed impaired recognition of fear following bilateral temporal lobe damage when this included the amygdala. For JC, this was part of a constellation of deficits on face processing tasks, with impaired recognition of several emotions. SE, YW and RB, however, showed relatively circumscribed deficits. Although they all had some problems in recognizing or naming famous faces, and had poor memory for faces on the Warrington Recognition Memory Test, none showed a significant impairment on the Benton Test of Facial Recognition, indicating relatively good perception of the face's physical structure. In a test of recognition of basic emotions (happiness, surprise, fear, sadness, disgust and anger), SE, YW and RB achieved normal levels of performance in comparison to our control group for all emotions except fear. Their results contrast with those of RS, with relative sparing of the amygdala region and unimpaired recognition of emotion, pointing clearly toward the importance of the amygdala in the recognition of fear.
Aged↗
Early 1H magnetic resonance spectroscopy of acute head injury: four cases.
In an attempt to examine in vivo the early metabolic consequences of severe acute head injury, 1H MRS was performed in four patients from 8 to 25 h (mean 15 h) following trauma. In three of these patients, decompressive surgery was performed 4-5 h prior to the MRS. High levels of lactate (area of lactate peak >50% of the mean areas of the NAA, choline-containing, and creatine-containing compound peaks) were found at 8 h posttrauma in the one patient who was not operated on and at 10 h posttrauma in one of the patients who underwent surgery. In the other two postoperative patients, at 18 and 25 h after trauma, lactate levels were found to be low (lactate peak <20% of the mean area of the other three peaks). In the one patient who had a follow-up at 6 days and who had the largest initial lactate levels, these remained high. These findings suggest that high levels of lactate may not be an inevitable consequence of severe head injury and that similar MRS studies should be performed on each individual patient before therapies to reduce lactate are considered. There appeared to be no correlation between the relative amounts of lactate and outcome.
Acute Disease↗
Rapid pathogen detection using a microchip PCR array instrument.
An array of PCR microchips for rapid, parallel testing of samples for pathogenic microbes is described. The instrument, called the Advanced Nucleic Acid Analyzer (ANAA), utilizes 10 silicon reaction chambers with thin-film resistive heaters and solid-state optics. Features of the system include efficient heating and real-time monitoring, low power requirements for battery operation, and no moving parts for reliability and ruggedness. We analyzed cultures of Erwinia herbicola vegetative cells, Bacillus subtilis spores, and MS2 virions, which simulated pathogenic microbes such as Yersinia pestis, Bacillus anthracis spores, and Venezuelan equine encephalitis, respectively. Detection of microbes was achieved in as little as 16 min with detection limits of 10(5)-10(7) organisms/L (10(2)-10(4) organisms/mL).
Bacillus subtilis↗
Ictal regional cerebral blood flow in frontal lobe seizures.
99mTC (single photon emission computed tomography) (HMPAO SPECT) was carried out during 16 frontal-lobe seizures in 15 patients. Focal changes in regional cerebral blood flow were seen during all seizures. In 9 of 16 seizures SPECT showed hyperperfusion localized to one frontal lobe. In 1 of 16 seizures ictal hypoperfusion was seen in one frontal lobe. In 2 of 16 seizures there was hyperperfusion in both frontal lobes, and in 4 of 16 seizures hyperperfusion involved the frontal lobe or lobes plus other lobes of the brain. These changes were accompanied by hyperperfusion of subcortical structures in 13 seizures. SPECT thus localized to one frontal lobe in 10 of 16 seizures, and localized to the frontal lobes without lateralizing in two further seizures. No seizure showed a pattern of perfusion similar to that reported in mesial-temporal-lobe seizures. We conclude that ictal SPECT may provide useful localizing information in frontal-lobe seizures.
Adolescent↗
Errors in MR stereotaxy due to undetected extraneous metal objects.
MR stereotaxic procedures are being increasingly used, particularly in functional neurosurgery where very high levels of localization accuracy are required. Whilst many studies have investigated intrinsic causes of non-linearity, potential errors due to an extrinsic cause are not generally appreciated. It is not uncommon to find objects such as hair clips, paper clips and pins inside high-field magnets. They can remain undetected for long periods because they can reach positions not open to visual inspection and because they often do not produce observable deterioration in routine image quality. In this study we measured the maximum absolute positional shifts caused by such objects and found that these can be significant (> 1 mm, even up to 200 mm from one such object). Additional measurements were performed using an MR compatible Leksell stereotaxic frame to calculate actual stereotaxic coordinate errors. The encompassing nature of the frame is such that some degree of compensation for such nonlinearities is inherent, and so errors for areas of the brain more proximal to the object are found to be reduced but not eliminated. Stereotaxic coordinate errors will not be reduced in nonencompassing designs and in frameless stereotaxy. The prevalence of such objects in clinical systems and the measures required to detect their presence are discussed. The need for quality control testing before each stereotaxic procedure is highlighted.
Biophysical Phenomena↗
An STS-based radiation hybrid map of the human genome.
We have constructed a physical map of the human genome by using a panel of 83 whole genome radiation hybrids (the Stanford G3 panel) in conjunction with 10,478 sequence-tagged sites (STSs) derived from random genomic DNA sequences, previously mapped genetic markers, and expressed sequences. Of these STSs, 5049 are framework markers that fall into 1766 high-confidence bins. An additional 945 STSs are indistinguishable in their map location from one or more of the framework markers. These 5994 mapped STSs have an average spacing of 500 kb. An additional 4484 STSs are positioned with respect to the framework markers. Comparison of the orders of markers on this map with orders derived from independent meiotic and YAC STS-content maps indicates that the error rate in defining high-confidence bins is < 5%. Analysis of 322 random cDNAs indicates that the map covers the vast majority of the human genome. This STS-based radiation hybrid map of the human genome brings us one step closer to the goal of a physical map containing 30,000 unique ordered landmarks with an average marker spacing of 100 kb.
Animals↗
Ictal single photon emission computed tomography in occipital lobe seizures.
PURPOSE: Ictal single photon emission computed tomography (SPECT) has been evaluated as an adjunctive localizing technique in temporal lobe epilepsies and, to a lesser degree, in some extratemporal epilepsies. The purpose of this study was to determine whether occipital lobe seizures are associated with distinctive ictal cerebral blood perfusion (rCP) patterns. METHODS: SPECT was used with the tracer 99mTc HMPAO to image ictal rCP in 6 patients in whom clinical, EEG, and imaging data indicated occipital lobe seizures. RESULTS: Two patterns of rCP were seen. Four patients had hyperperfusion that was restricted to the occipital lobe, and two patients had hyperperfusion of the occipital lobe and the ipsilateral mesial temporal lobe, with hypoperfusion of the lateral temporal lobe. The latter 2 patients had clinical and surface EEG evidence of temporal lobe involvement in the seizure discharge. CONCLUSIONS: Ictal rCP patterns in occipital lobe seizures are distinct from those in temporal lobe seizures and may vary according to whether or not ipsilateral temporal lobe structures are involved in the ictal discharge.
Adolescent↗
Early changes in peritumorous oedema and contralateral white matter after dexamethasone: a study using proton magnetic resonance spectroscopy.
AIMS: To study the mechanism of action of steroids in patients with peritumorous oedema. METHODS: To investigate early cerebral metabolic changes proton magnetic resonance spectroscopy (1H-MRS) was used before and 11 to 14 hours after treatment with dexamethasone (12 mg oral loading and 4 mg four times daily maintenance). Nine patients (two men, seven women, mean age 54) with pronounced oedema associated with various intracranial tumours (two astrocytomas, three meningiomas, two glioblastoma, and two metastases) were examined using MRI and MRS. SE1500/135 volume selected MRS (mean volume 21 ml) were performed on an oedematous region and a contralateral region. All spectra were acquired with and without water suppression. Metabolite peak area ratios were determined. RESULTS: Regions of oedema had significantly (P < 0.01) higher unsuppressed water than the contralateral regions, as expected. There was no change at this early time point after dexamethasone. The ratio of the area of choline containing compounds to that creatine and phosphocreatine compounds was determined after which the serial ratios of these before and after were calculated (a serial ratio of 1.0 would indicate no change in the choline to creatine ratios after steroid administration). The mean serial ratios for the area of oedema were 1.02 (SEM 0.08) and 1.10 (0.08) for the contralateral volume of interest, indicating no significant changes. However, significant changes (P < 0.02) were found in the N-acetyl-aspartate (NAA)/choline serial ratios (0.86 (0.06) in the area of oedema, 1.20 (0.10) in contralateral brain) and the NAA/creatine serial ratios (0.86 (0.08) for the oedema, 1.25 (0.11) in contralateral brain). CONCLUSIONS: Such rapid changes may be explained either by relatively large alterations in the relaxation characteristics of NAA or, more controversially, by actual changes in the amounts of NAA. It is proposed that steroids act primarily by causing early metabolic changes that are later expressed in improvements in intracranial volume relations.
Antineoplastic Agents, Hormonal↗
Functional integration of PCR amplification and capillary electrophoresis in a microfabricated DNA analysis device.
Microfabricated silicon PCR reactors and glass capillary electrophoresis (CE) chips have been successfully coupled to form an integrated DNA analysis system. This construct combines the rapid thermal cycling capabilities of microfabricated PCR devices (10 degrees C/s heating, 2.5 degrees C/s cooling) with the high-speed (< 120 s) DNA separations provided by microfabricated CE chips. The PCR chamber and the CE chip were directly linked through a photolithographically fabricated channel filled with hydroxyethylcellulose sieving matrix. Electrophoretic injection directly from the PCR chamber through the cross injection channel was used as an "electrophoretic valve" to couple the PCR and CE devices on-chip. To demonstrate the functionality of this system, a 15 min PCR amplification of a beta-globin target cloned in M13 was immediately followed by high-speed CE chip separation in under 120 s, providing a rapid PCR-CE analysis in under 20 min. A rapid assay for genomic Salmonella DNA was performed in under 45 min, demonstrating that challenging amplifications of diagnostically interesting targets can also be performed. Real-time monitoring of PCR target amplification in these integrated PCR-CE devices is also feasible. Amplification of the beta-globin target as a function of cycle number was directly monitored for two different reactions starting with 4 x 10(7) and 4 x 10(5) copies of DNA template. This work establishes the feasibility of performing high-speed DNA analyses in microfabricated integrated fluidic systems.
DNA↗
A gene map of the human genome.
The human genome is thought to harbor 50,000 to 100,000 genes, of which about half have been sampled to date in the form of expressed sequence tags. An international consortium was organized to develop and map gene-based sequence tagged site markers on a set of two radiation hybrid panels and a yeast artificial chromosome library. More than 16,000 human genes have been mapped relative to a framework map that contains about 1000 polymorphic genetic markers. The gene map unifies the existing genetic and physical maps with the nucleotide and protein sequence databases in a fashion that should speed the discovery of genes underlying inherited human disease. The integrated resource is available through a site on the World Wide Web at http://www.ncbi.nlm.nih.gov/SCIENCE96/.
Amino Acid Sequence↗
Genome maps 7. The human transcript map. Wall chart.
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Chromosome Mapping↗
Analysis of chromosome 18 DNA markers in multiplex pedigrees with manic depression.
Six pedigrees segregating manic-depressive illness (MDI) were analyzed for linkage to 21 highly polymorphic microsatellite DNA markers on chromosome 18. These markers span almost the entire length of the chromosome, and gaps between markers are less than 20 cM. In particular, we analyzed several markers localizing to the pericentromeric region of chromosome 18 which generated lod scores suggestive of linkage in an independent study. Lod score analysis was performed and results were examined by family. One region produced positive lod scores, though at 18q23 and not in the pericentromeric region. We additionally used two nonparametric methods because the true mode of transmission of MDI is unknown; results were again somewhat suggestive for markers in the region of 18q23 but not in the pericentromeric region.
Adult↗
Application of exponential smoothing for nosocomial infection surveillance.
Detection of outbreaks of infection or increases in bacterial resistance to antimicrobial agents is an essential component of hospital infection control surveillance. The authors applied the method of exponential smoothing to microbiology data from 1987-1992 to investigate a suspected outbreak of gentamicin resistance among Pseudomonas aeruginosa bacteria at the Department of Veterans Affairs Medical Center, San Francisco, California, in 1991-1992. The years 1987-1990 were used to develop the baseline for the forecast model. Application of the model indicated that two observed prominent peaks in the annual cumulative incidence of gentamicin-resistant P. aeruginosa were within the upper bounds of their respective 95% confidence intervals as estimated by the forecast model--i.e., that no epidemic was in progress. This prediction was supported by investigations by the hospital's infection control team which indicated that the apparent increases were due to readmission of patients previously known to harbor these organisms. In contrast, application of a typically employed method that ignores the time series data structure indicated that there were 6 months in which incidence rates exceeded the upper bounds of their respective 95% confidence intervals, thereby erroneously suggesting that an epidemic was in progress. Recursive algorithms and some simplifying assumptions that do not affect the validity of inferences make the application of this method practical for nosocomial infection control programs.
Anti-Bacterial Agents↗
Interictal temporal hypoperfusion is related to early-onset temporal lobe epilepsy.
Previous studies of interictal regional cerebral blood flow (rCBF) in temporal lobe epilepsy have shown variable correlations with clinical measures. We used high spatial resolution hexamethyl propyleneamine oxime single photon emission computed tomography (HMPAO SPECT) in 80 consecutive patients with complex partial seizures (CPS), comparing results with those from a large series of normal subjects. Visual image analysis detected abnormalities of rCBF in 41 of 80 (51%; numeric analysis detected abnormalities in 38 of 80). Age at epilepsy onset was significantly younger in patients with temporal hypoperfusion (p = 0.002), and the frequency distribution of hypoperfusion versus age at epilepsy onset was reverse exponential. The results of numerical image analysis showed that degree of hypoperfusion did not vary with age at epilepsy onset. These data suggest a single insult operating early in life as a cause of temporal hypoperfusion, as has been shown for mesial temporal sclerosis (MTS). We could not demonstrate relationships with other clinical variables, including time since last seizure.
Adolescent↗