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Biomedical subjects

J G Hughes

Publications and source records attributed to J G Hughes.

At least 19 recordsLinked to original sources
PubMed2001

Direct identification of bacteria from positive blood cultures by amplification and sequencing of the 16S rRNA gene: evaluation of BACTEC 9240 instrument true-positive and false-positive results.

In a previous study which evaluated the BACTEC 9240 automated blood culture system (Becton Dickinson Diagnostic Instrument Systems, Sparks, Md.), we noted a 1.3% "instrument false-positive" rate. That is, the BACTEC system signaled that a bottle (BACTEC Plus Aerobic/F bottle or BACTEC Anaerobic Lytic/10 bottle) culture was positive but a Gram stain was negative and there was no growth of bacteria or yeasts on subculture to chocolate agar. Furthermore, from the same sample of blood, cultures for fungi using the Isolator blood culture system (Wampole Laboratories, Cranbury, N.J.) were negative for growth. For the present study, we evaluated 76 instrument false-positive samples for the presence of 16S ribosomal DNA using the MicroSeq 500 kit (PE Biosystems, Foster City, Calif.). These samples also were negative for fungi by the Isolator method. This kit has a PCR module and sequencing module for the amplification and sequencing of the 16S RNA gene and provides a database for sequence alignment and identification of bacteria. To optimize the assay, we evaluated the effect of adding 0.5% bovine serum albumin to the sample from blood culture bottles and found that it decreased the effects of inhibitors on the PCR. Two control groups of blood culture specimens were also evaluated. One group (n = 45) were "instrument true positives"; the instrument signaled positive, and subsequent Gram stains were positive and subcultures on chocolate agar grew bacteria. The other group (n = 20) were "instrument true negatives"; the instrument signaled negative, the Gram stain was negative, and subcultures on chocolate agar and from the Isolator tube on fungal media showed no growth. None of the 76 instrument false-positive samples had evidence for 16S rRNA gene sequences. All of the instrument true-positive samples and all of the instrument true-negative specimens were positive and negative, respectively, using the MicroSeq 500 kit. Total peripheral white blood cell counts were statistically significantly higher for patients who had instrument false-positive results than for patients who had instrument true-positive or true-negative results (P = 0.001). We conclude that instrument false positives signaled by the BACTEC 9240 system are not due to bacteria in the blood culture samples.

Bacteremia↗
PubMed2001

Culture with BACTEC Peds Plus/F bottle compared with conventional methods for detection of bacteria in synovial fluid.

An evaluation was undertaken to determine the utility of the BACTEC Peds Plus/F bottle and the BACTEC 9240 instrument (Becton Dickinson Diagnostic Instrument Systems, Sparks, Md.) for the detection of clinically significant microorganisms in synovial fluid specimens. The Peds Plus/F bottle was used because in our laboratory the quantity of synovial fluid available for culture is frequently in the range of 0.5 to 3.0 ml. The culture results obtained with the Peds Plus/F bottle were compared to those obtained by a conventional agar plate method for a total of 805 synovial fluid specimens. Microbial growth was produced by 74 cultures (9.2%) from 60 patients, yielding a total of 77 microorganisms. Organisms were classified as pathogens (n = 62), contaminants (n = 12), or indeterminate (n = 3) on the basis of a review of the patients' medical histories. Culture using BACTEC Peds Plus/F bottle detected statistically significantly more pathogens overall (62 versus 51 pathogens [P = 0.001]) and statistically fewer contaminants overall (1 versus 11 contaminants [P = 0.006]) than culture by the agar plate method. These results indicate the superior performance of the BACTEC Peds Plus/F bottle over the conventional agar plate method for the detection of clinically significant microorganisms from synovial fluid specimens.

Arthritis, Infectious↗
PubMed2001

On prognostic models, artificial intelligence and censored observations.

The development of prognostic models for assisting medical practitioners with decision making is not a trivial task. Models need to possess a number of desirable characteristics and few, if any, current modelling approaches based on statistical or artificial intelligence can produce models that display all these characteristics. The inability of modelling techniques to provide truly useful models has led to interest in these models being purely academic in nature. This in turn has resulted in only a very small percentage of models that have been developed being deployed in practice. On the other hand, new modelling paradigms are being proposed continuously within the machine learning and statistical community and claims, often based on inadequate evaluation, being made on their superiority over traditional modelling methods. We believe that for new modelling approaches to deliver true net benefits over traditional techniques, an evaluation centric approach to their development is essential. In this paper we present such an evaluation centric approach to developing extensions to the basic k-nearest neighbour (k-NN) paradigm. We use standard statistical techniques to enhance the distance metric used and a framework based on evidence theory to obtain a prediction for the target example from the outcome of the retrieved exemplars. We refer to this new k-NN algorithm as Censored k-NN (Ck-NN). This reflects the enhancements made to k-NN that are aimed at providing a means for handling censored observations within k-NN.

Algorithms↗
PubMed2000

Performance of five agar media for recovery of fungi from isolator blood cultures.

We studied the recovery of 1,270 fungal isolates from 176,144 Isolator blood cultures (0.72% positive) on bacterial and fungal media, under routine and differing incubation conditions. Except with Histoplasma capsulatum, chocolate agar incubated for only 3 days proved to be an excellent medium for the recovery of fungi from the Isolator system.

Agar↗
PubMed1999

An evaluation of intelligent prognostic systems for colorectal cancer.

In this paper we describe attempts at building a robust model for predicting the length of survival of patients with colorectal cancer. The aim of the research, reported in this paper, is to study the effective utilisation of artificial intelligence techniques in the medical domain. We suggest that an important research objective of proponents of intelligent prognostic systems must be to evaluate the additionality that AI techniques can bring to an already well-established field of medical prognosis. Towards this end, we compare a number of different AI techniques that lend themselves to the task of predicting survival in colorectal cancer patients. We describe the pros and cons of each of these methods using the usual metrics of accuracy and perspicuity. We then present the notion of intelligent hybrid systems and evaluate the role that they may potentially play in developing robust prognostic models. In particular we evaluate a hybrid system that utilises the k Nearest Neighbour technique in conjunction with Genetic Algorithms. We describe a number of innovations used within this hybrid paradigm used to build the prognostic model. We discuss the issue of censored patients and how this issue can be tackled within the various models used. In keeping with our objective of studying the additionality that AI techniques bring to building prognostic models, we use Cox's regression as a standard and compare each AI technique with it, attempting to discover their capabilities in enhancing prognostic methods in medicine. In doing so we address two main questions--which model fits the data best?, and are the results obtained by the various AI techniques significantly different from those of Cox's regression? We conclude this paper by discussing future enhancements to the work presented and lessons learned from the study to date.

Age Factors↗
PubMed1997

Analysis of 281,797 consecutive blood cultures performed over an eight-year period: trends in microorganisms isolated and the value of anaerobic culture of blood.

The results for 281,797 blood culture sets of specimens collected from adult patients at the Mayo Clinic over an approximately 8-year period (1 November 1984 through 30 November 1992) were analyzed in order to determine whether there were differences in the types of microorganisms isolated over this time and to assess the usefulness of anaerobic culturing of blood. Each blood culture set consisted of two aerobic blood cultures (Septi-Chek [Becton Dickinson, Sparks, MD] and Isolator [Wampole Laboratories, Cranbury, NJ]) and one anaerobic culture (nonvented tryptic or trypticase soy broth [NVTSB; Difco Laboratories, Detroit, or Becton Dickinson]). The relative frequency of isolation of aerobic and facultatively anaerobic gram-positive bacteria and obligately anaerobic bacteria increased over the second half of the 1984-1992 surveillance period. The value of the NVTSB anaerobic blood culture was demonstrated for diagnosing bloodstream infections caused by certain facultatively anaerobic bacteria in addition to obligately anaerobic bacteria and supported the inclusion of the NVTSB anaerobic blood culture as a standard part of the three-component blood culture set used at this institution.

Adult↗
PubMed1997

Clinical comparison of BACTEC 9240 plus aerobic/F resin bottles and the isolator aerobic culture system for detection of bloodstream infections.

The Plus Aerobic/F resin bottle of the BACTEC 9240 automated blood culture system (Becton Dickinson Diagnostic Instrument Systems, Sparks, Md.) was compared with aerobic culture of the Isolator system (Wampole Laboratories, Cranbury, N.J.) for the detection of bloodstream microorganisms from 6,145 blood cultures collected from adult patients with suspected septicemia. The BACTEC resin bottles were incubated for 7 days, and the sediment from the Isolator tube was inoculated to sheep blood and chocolate agars which were incubated for 72 h and to inhibitory mold, brain heart infusion, and Sabouraud agars which were incubated for 21 days. A total of 622 microorganisms were recovered from 583 blood cultures. The BACTEC resin bottle recovered statistically significantly more pathogens overall than the Isolator system (P = 0.0006). When individual pathogens isolated from either system for a 7-day study period were assessed, it was determined that the BACTEC resin bottle detected statistically significantly more isolates of Staphylococcus aureus (P = 0.0113) and coagulase-negative Staphylococcus spp. (P = 0.0029) than the Isolator system. The BACTEC resin bottle also detected statistically significantly more bloodstream infections (septic episodes) caused by coagulase-negative Staphylococcus spp. (P = 0.0146). The Isolator system recovered statistically significantly more contaminants overall (P < 0.0001), and among this group of microorganisms, recovered statistically significantly more Bacillus spp. (P < 0.0001), coagulase-negative Staphylococcus spp. (P < 0.0001), and viridans group Streptococcus spp. (P = 0.0156). The Isolator system detected statistically significantly more isolates of Histoplasma capsulatum (P = 0.004), but all of these isolates were detected at > or = 7 days of incubation of fungal plates, i.e., after the system to system comparison study period (7 days). In blood culture sets which produced growth of the same pathogen in both systems, there was a statistically significant difference in median time to detection for all pathogens combined favoring the BACTEC resin bottle over the Isolator tube (P < 0.05). When assessing individual microorganisms, the median times for detection of S. aureus, Enterococcus spp., and Pseudomonas spp. were all statistically significantly less for the BACTEC system (P < 0.05). The BACTEC instrument had 79 (1.3%) false positive signals. The BACTEC system required less processing time than the Isolator system and eliminates the hands-on time for detection of positive cultures required with the Isolator system.

Adult↗
PubMed1995

Evaluation of an immunoassay for direct detection of Escherichia coli O157 in stool specimens.

An enzyme-linked immunosorbent assay (ELISA) produced by LMD Laboratories, Inc., Carlsbad, Calif., was compared with culture for the detection of Escherichia coli O157. Nine of 185 stool specimens evaluated had positive results by the LMD E. coli O157 ELISA and grew E. coli O157 on culture; 174 had negative by LMD E. coli O157 ELISA results and did not grow E. coli O157 on culture. Of 174 specimens negative by LMD E. coli O157 ELISA, 117 specimens grew other enteric pathogens: Campylobacter spp. (46 isolates), Salmonella spp. (43 isolates), Yersinia spp. (20 isolates), and Shigella spp. (8 isolates). There were two indeterminant results by the LMD E. coli O157 ELISA. One stool specimen did not grow other enteric pathogens on culture, and one grew a Campylobacter sp. on culture. Both had negative LMD E. coli O157 ELISA results upon repeat testing. The LMD E. coli O157 ELISA is an accurate, easy-to-read screening method for the detection of E. coli O157 in fecal specimens.

Antibodies, Bacterial↗
PubMed1994

The long-term stability in whole blood of 14 commonly-requested hormone analytes.

Concentrations of 14 commonly-requested plasma hormones were measured in octuplicate in each of six subjects to determine their stability when unseparated from red cells for periods up to 1 week. Most of the analytes were stable when stored in this way and although statistically significant changes were recorded, in the great majority of cases the changes seen would have no bearing on the clinical interpretation of the result. In the light of these findings, we would confidently report results of analyses for these hormones in plasma that had remained in contact with red cells at ambient temperature for long periods of time.

17-alpha-Hydroxyprogesterone↗
PubMed1989

Transfer of caesium from silage to cows milk: observations and models.

The transfer of radiocaesium from silage, contaminated as a result of the Chernobyl accident, to cows milk was studied in a feeding trial at Trawsgoed Experimental Husbandry Farm. Feed and milk samples obtained from the cows were analysed for Cs-137 and Cs-134 during the 124 days cows were fed contaminated silage and for a further 32 days when cows were fed uncontaminated material. The trial also involved the addition of bentonite supplements to the diet of some animals. Supplements of 250 g and 500 g sodium bentonite per day reduced Cs-137 transfer factors to milk to 0.63 and 0.33 of the control values respectively after 78 days of feeding. No effects of bentonite supplementation on the absorption of other elements were detected. The results for animals not given a supplement are compared with the cow-milk model implemented in the SPADE suite of codes, using both default parameters and input data and parameters derived from the feeding trial. The model overpredicted observed milk concentrations by a factor of 2 to 3. Reasons for this and alternative models are discussed. The sensitivity of the model to parameter selection is also emphasized.

Accidents↗
PubMed1985

An evaluation of a leukocyte esterase/nitrite test strip and a bioluminescence assay for detection of bacteriuria.

A leukocyte esterase/nitrite (Chemstrip LNTM) and a bioluminescence assay (LumacTM) were evaluated for detection of bacteriuria in 1,000 urine specimens. Both devices provided high predictive negative values (95.4-97.8%); however, false-negative values at levels of bacteriuria greater than or equal to 10(4) CFU/ml were 22.6% and 12.3%, respectively, for the leukocyte esterase/nitrate and the bioluminescence assay tests. The corresponding false-negative values at levels of bacteriuria of greater than or equal to 10(5) CFU/ml were 16.5% and 3.9%, respectively.

Bacteriuria↗