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PubMed2006

Efficient amplification and cloning of near full-length hepatitis C virus genome from clinical samples.

Long RT-PCR (LRP) amplification of RNA templates is sometimes difficult compared to long PCR of DNA templates. Among RNA templates, hepatitis C virus (HCV) represents an excellent example to challenge the potential of LRP technology due to its extensive secondary structures and its difficulty to be readily cultured in vitro. The only source for viral genome amplification is clinical samples in which HCV is usually present at low titers. We have created a comprehensive optimization protocol that allows robust amplification of a 9.1 kb fragment of HCV, followed by efficient cloning into a novel vector. Detailed analyses indicate the lack of potential LRP-mediated recombination and the preservation of viral diversity. Thus, our LRP protocol could be applied for the amplification of other difficult RNA templates and may facilitate RNA virus research such as linked viral mutations and reverse genetics.

Amino Acid Sequence↗

PubMed2006

Differences in family functioning in grandparent and parent-headed households in a clinical sample of drug-using African American adolescents.

Grandparents play a critical role in African American families, providing support and important leadership functions. Little is known, however, about family functioning in grandparent-headed households with a drug-using adolescent. Such knowledge is particularly salient for researchers and therapists who work with drug-using adolescents and their families. Using a clinical sample of convenience, analyses were conducted to identify similarities and differences in adolescent substance use and behavior problems, family relationships, and family social ecology relationships between African American grandparent-headed (n=12) and parent-headed (n=54) households. Results indicated that adolescents from the 2 household types reported similar levels of problem behaviors, but that grandparents reported less delinquency with peers than did parents. Primary caregivers in grandparent-headed households reported less monitoring and supervision of peers and less within-family conflict. Implications for treatment are discussed.

Adolescent↗

PubMedDate not supplied

Factor Analysis of the Attention Deficit Scales for Adults (ADSA) with a clinical sample of outpatient substance abusers.

Individuals with adult symptoms of ADHD who are in treatment for substance abuse have been identified as being at greater risk of failure to complete treatment and relapse. The identification of such clients must thus become an important part of assessment and treatment planning. The Attention Deficit Scale for Adults (ADSA) is one device designed to assess ADHD symptomology in adults. This study investigated the application of the ADSA in a substance-abusing population by assessing its psychometric properties with a clinical sample of 268 adult patients (170 males, 92 females, gender missing for 6) in an outpatient substance abuse treatment program. The findings indicate that the ADSA is unidimensional with this population yet possess high reliability (alpha=.93 for entire sample:.89 for males,.94 for females) and correlate consistently with DSM-IV diagnostic criteria. The data tentatively support the use of the ADSA with substance-abusing populations as a reliable and valid assessment tool for clinical use and research.

Adult↗

PubMed1991

Emotional distress and its socio-political correlates in Salvadoran refugees: analysis of a clinical sample.

The emotional distress responses of refugees cannot be adequately understood using the traditional notions of stress and adaptation. In these populations it is necessary to consider the relations between emotional distress and socio-political context, particularly the processes of terror and intimidation and the conditions of migratory illegality and social marginality. This study analyses the patterns of emotional distress in a clinical sample of 71 Salvadoran refugees in an urban center of the United States. Case histories are presented and patterns of trauma, distress and associated life problems analyzed. It is argued that distress patterns reflect the particular socio-political conditions of women and men and represent the embodiment of the conflicts that refugees face. The concept of illness is used to link distress patterns and socio-political context and to avoid the reductionism of psychiatric categories.

Adult↗

PubMed1993

A rapid DNA extraction method from culture and clinical samples. Suitable for the detection of human cytomegalovirus by the polymerase chain reaction.

We propose an one-step DNA extraction method suitable for the polymerase chain reaction. This procedure utilizes Chelex 100, a chelating in exchange resin. This technique was compared with a traditional technique (proteinase K lysis, phenol-chloroform extraction and ethanol precipitation) for isolation of human cytomegalovirus DNA from clinical samples. The procedure using Chelex 100 appeared to be a simple and fast extraction method for human cytomegalovirus DNA.

Bronchoalveolar Lavage Fluid↗

PubMed1996

Comparison of solid and liquid culture media with polymerase chain reaction for detection of Mycobacterium tuberculosis in clinical samples.

The aim of this study was to determine the sensitivity of different methods--two commercial polymerase chain reaction (PCR) kits (a protocol of nested PCR and a protocol of amplification of the IS6110 insertion element), the radiometric Bactec system, the Septi-Chek AFB culture system, and culture in Löwenstein-Jensen (LJ) solid medium--for the detection of Mycobacterium tuberculosis. One hundred clinical samples from 51 patients with culture-positive tuberculosis (81 specimens) and 19 controls (19 specimens) were used. Eighty-nine percent of the samples were smear negative. In the 81 specimens obtained from patients with tuberculosis, the frequency of positivity was 66.6% for nested PCR, 63% for culture in liquid media, 38.3% for IS6110 assay, and 28.4% for culture in LJ medium. In 18 samples obtained by invasive procedures in patients with tuberculosis, mycobacterial DNA was detected by nested PCR in 83.3% (including all samples positive by culture on liquid media), by culture in liquid media in 77.7% by culture on LJ medium in 27.7%, and by the IS6110 assay in 11.1%. No false-positive results were obtained from the negative control specimens with any of the techniques tested. The sensitivity of the reamplification protocol appears to be superior to that of the IS6110 assay and similar to that of the Bactec system.

Culture Media↗

PubMed1979

Sighting-eye dominance related to composite sidedness in classroom and clinic samples.

Near-point and far-point binocular and monocular sighting tests given 20 high and 20 low achievers each from regular classrooms at Grades 4, 8, and 12 (N = 240) yielded significant chi 2 for differences of proportions of lateral agreement with sidedness in comparison to distributions unrelated to sidedness. Composite sighting congruent to sidedness yielded significant differences between classroom and reading clinic samples. The near-point binocular sighting test markedly influences distributions of combined scores in sighting.

Adolescent↗

PubMedDate not supplied

New statistical software for intralaboratory and interlaboratory quality control in clinical cytology. Validation in a simulation study on clinical samples.

OBJECTIVE: To design a statistical software package to provide automated calculations of normal and weighted and 3 indices. STUDY DESIGN: Prompted by the lack of commonly available software to compute weighted kappa and the nonproportionate workload needed to calculate our 3 variability indices manually, the new statistical software package was designed. To demonstrate the performance of the new CONQUISTADOR software, a simulation study (both intralaboratory and interlaboratory) was designed using 5,000 clinical samples randomly selected from a data file of > or = 200,000 conventional Pap smears and programmed to become "analyzed" by 12 cytologists in 5 imaginary laboratories. RESULTS: A representative set of both complete and partial outputs provided by the software, in Excel format (Microsoft, Redmond, Washington, U.S.A.) are shown to illustrate the different functions of the program. In the interlaboratory mode, the software calculates accuracy indicators (sensitivity, specificity, positive and negative predictive value, and their 95% CI), which are not common features of regular statistical packages; kappa and weighted kappa; and their 95% CI (comparison of single laboratories to all laboratories and pairwise comparisons between single laboratories). The 3 diagnostic variability indices can be computed separately for all samples or for only the positive samples. In the intralaboratory mode, the software calculates the same indices for individual cytologists. CONCLUSION: The CONQUISTADOR statistical package has properties that are useful in monitoring cytologic laboratory quality in both intralaboratory and interlaboratory settings. The software will be distributed by the National Institute of Health, Rome, for the delivery costs only.

Clinical Laboratory Techniques↗

PubMed2006

Affective disorder in the parents of a clinic sample of children with anxiety disorders.

BACKGROUND: Family history studies in adults reveal strong familiality for the anxiety disorders with some specificity. The aim of the current study was to establish whether there was an elevated rate of anxiety disorders in the parents of children with anxiety disorders, and whether there was intergenerational specificity in the form of disorder. METHODS: The mental state of a clinic sample of 85 children with anxiety disorder and their parents was systematically assessed, together with a comparison sample of 45 children with no current disorder and their parents. RESULTS: Compared to the rate of anxiety disorder amongst parents of comparison children, the rate of current anxiety disorder in mothers of anxious children was significantly raised, as was the lifetime rate of anxiety disorder for both mothers and fathers. The mothers of children with generalised anxiety disorder, social phobia, specific phobia and separation anxiety disorder all had raised lifetime rates of the corresponding disorder, but also raised rates of others disorders. LIMITATIONS: Only 60% of the fathers of the anxious children were assessed. CONCLUSIONS: Strong familiality of anxiety disorders was confirmed, especially between child and maternal anxiety disorder. All child anxiety disorders were associated with several forms of anxiety disorder in the mother. Some specificity in the form of anxiety disorder in the child and the mother was apparent for social phobia and separation anxiety disorder. The findings have implications for the management of child anxiety.

Adolescent↗

PubMed2002

Evaluation of a multiplex reverse transcription-polymerase chain reaction assay for subtyping hemagglutinin genes 1 and 3 of swine influenza type A virus in clinical samples.

A multiplex reverse transcription-polymerase chain reaction (RT-PCR) assay was developed to detect and identify subtypes of hemagglutinin (H) 1 and H3 swine influenza virus (SIV). Two oligonucleotide primer sets were prepared using published sequence data for H1N1 and H3N2. The PCR products with unique size characteristics of each subtype were sequenced, and the sequences were confirmed to be subtype specific for H gene 1 or 3. These primer sets did not amplify when RT-PCR assay was performed for genomic DNA or RNA from other common swine pathogens. The RT-PCR assay was able to detect viral RNA up to 1 tissue culture infective dose of reference SIV H1N1 or H3N2. The multiplex RT-PCR was applied to 30 SIV isolates subtyped by hemagglutination inhibition (HI) test. Forty-three positive and 20 negative swine field samples for SIV by virus isolation were also tested. Of these 73 SIV-positive samples tested, H1 and H3 were identified in 38 and 28 samples by the multiplex RT-PCR, respectively. The remaining 7 samples were positive for both H1 and H3 genes. No positive reaction was found for all 20 SIV-negative field samples. Subsequently, 235 random field samples from pigs with respiratory problems were tested by the multiplex RT-PCR, and 26 and 13 samples were found to be positive for H1 and H3, respectively. Results of these multiplex RT-PCR were comparable with those of the HI test. These results suggest that multiplex RT-PCR can be a useful test for detection and subtyping of SIV in clinical samples.

Animals↗

PubMed1993

Comparison of Wechsler vs. Mayo summary scores in a clinical sample.

Normative bases for the Wechsler Adult Intelligence Scale-Revised (WAIS-R) and the Wechsler Memory Scale-Revised (WMS-R) recently were extended through age 97 with the publication of norms that permit computation of MAYO IQs for the WAIS-R and MAYO Memory Indices for the WMS-R. This study compares traditional Wechsler summary scores with their corresponding MAYO values in a clinical sample. MAYO summary scores are correlated highly with traditional Wechsler values, and concordance rates are also strong. Despite their similarities MAYO summary scores and traditional Wechsler values are not interchangeable. Cautions are discussed relative to the use of both MAYO and traditional Wechsler IQs and Memory Indices.

Aged↗

PubMed1989

Rapid detection of HIV-1 in clinical samples by co-culture with heat-shocked cells.

A mild heat-shock (10 min at 44 degrees C), performed just before seeding on healthy PBL used for co-cultivation, allows the detection of viral markers (p24 core antigen and reverse transcriptase) in a very short time. This suggests that heat-shocked PBL can be employed routinely for the rapid detection of HIV-1 in clinical samples.

Cells, Cultured↗

PubMed2005

The design and application of DNA chips for early detection of SARS-CoV from clinical samples.

BACKGROUND: SARS coronavirus has been identified as the cause of severe acute respiratory syndrome (SARS). Few tests allow confirmation or exclusion of SARS within the first few days of infection. A gene chip is a useful tool for the study of microbial infections mainly for its capability of performing multi-target analysis in a single test. OBJECTIVES: Investigate the possibility of early detection of SARS virus from clinical samples using the gene chip-based method. STUDY DESIGN: We purified RNA from SARS-CoV obtained from routinely collected peripheral blood and sputum samples of 34 patients who had been identified as probable SARS patients by following the interim U.S. case definition. Four segments of the SARS-CoV were amplified using reverse transcription-nested PCR and the products examined using the 70-mer gene chips for SARS-CoV detection. RESULTS: A blind-test of both peripheral blood and sputum specimens lead to the positive detection of SARS-CoV in 31 out of 34 patients. SARS-CoV was not found in peripheral blood or sputum specimens from three patients. Two of the 34 patients were only 3 days post-onset of symptoms and were subsequently confirmed to be SARS positive. Our results indicate that the gene chip-based molecular test is specific for SARS-CoV and allows early detection of patients with SARS with detection rate about 8% higher than the single PCR test when the sputum sample is available.

Blood↗

PubMed1999

Microbiological characteristics and susceptibility patterns of strains of Rhodotorula isolated from clinical samples.

The members of the genus Rhodotorula show a marked ubiquity. In man, they have been isolated from faeces, nails, skin, sputum, digestive tract and adenoids, forming part of the normal human flora, although in recent years cases have been reported of both local and systemic infection by this yeast. There are virtually no studies in the literature on the sensitivity of this genus to the antifungal agents in common clinical use. Therefore, it is considered of interest to study the microbiological characteristics and the susceptibility patterns of Rhodotorula isolated from clinical samples. A total of 35 different strains of Rhodotorula were studied. In vitro susceptibility testing to 5-fluorocytosine, amphotericin B, ketoconazole, fluconazole and itraconazole was performed. All the strains were considered sensitive to 5-fluorocytosine, amphotericin B, ketoconazole and itraconazole and resistant to fluconazole. As a conclusion, we can state that all the antifungal agents tested, except fluconazole, are useful medicaments for the treatment of infections by the Rhodotorula genus.

Antifungal Agents↗

PubMed1999

PCR identification of Pseudomonas aeruginosa and direct detection in clinical samples from cystic fibrosis patients.

This report describes a PCR primer pair that targets the algD GDP mannose gene of Pseudomonas aeruginosa and produces a specific 520-bp PCR product useful for P. aeruginosa identification. This PCR assay was tested with 182 isolates of P. aeruginosa and 20 isolates of other bacterial species, and demonstrated 100% specificity and sensitivity. The test was also able to detect P. aeruginosa directly in clinical samples such as sputum or throat swabs obtained from cystic fibrosis patients. The combination of this primer with a universal bacterial primer, acting as a control to assess DNA quality in the sample, resulted in a robust PCR method that can be used for rapid P. aeruginosa detection.

Carbohydrate Dehydrogenases↗

PubMed2005

Application of horizontal staircase electrophoresis in agarose minigels to the random intergenic spacer analysis of clinical samples.

The random intergenic spacer analysis is a recently developed technique for the study of microbial populations. The bacterial intergenic spacer (ITS) is located between 16S rRNA and 23S rRNA genes and presents different length and sequence among bacterial species. Therefore, the amplicons can be separated by electrophoresis commonly performed at low voltage during several hours. Although this technique is especially useful for unculturable microorganisms, it has not been applied before to clinical sample analysis. As these samples have a limited number of bacterial species, the size of the gels may be reduced to facilitate their handling and to reduce the running time. To obtain maximum separation among the ITS bands, we analysed in this work different electrophoretical conditions including staircase electrophoresis, a technique based on the application of several voltage steps. The results obtained showed a different behaviour of the electrical resistance during the performance of submarine horizontal and vertical staircase electrophoresis. In the first case the resistance decreased during most of the running time whereas in the second case it increased. Here, we show that the performance of horizontal staircase electrophoresis reduces the running time more than 80% with respect to conventional electrophoresis at low voltages. This procedure was applied to the separation of ITS bands from bacterial DNA present in a tissue from a vocal cord biopsy. The sequencing of these bands allowed their identification. This new procedure may be very useful in the rapid diagnosis of bacteria present in human, animal and plant tissues.

Bacteria↗

PubMed2006

The relationship between rumination, avoidance and depression in a non-clinical sample.

Recent commentaries have proposed conceptualizations of rumination in terms of both cognitive and behavioral avoidance. This study examined the relationship between rumination, avoidance and depression using a newly developed self-report measure of avoidance in depression, the Cognitive-Behavioral Avoidance Scale (CBAS) [Ottenbreit, N.D., & Dobson, K.S. (2004). Avoidance and depression: The construction of the cognitive-behavioral avoidance scale. Behaviour Research and Therapy, 42, 293-313]. A non-clinical sample (N=104) of undergraduate students completed self-report measures of depression, anxiety, rumination and avoidance. Rumination, avoidance and depression were all significantly correlated. Rumination and behavioral avoidance remained intercorrelated when anxiety was controlled, confirming an association that is independent of anxiety. By contrast, the relationship between cognitive avoidance and rumination disappeared when anxiety was partialled out. Notably, avoidance predicted unique variance in depression scores, over and above anxiety and rumination. Consistent with the proposal of Ottenbreit and Dobson [Avoidance and depression: The construction of the cognitive-behavioral avoidance scale. Behaviour Research and Therapy, 42, 293-313], our findings support the value of clinicians and psychopathologists giving consideration to avoidance in their conceptualization of depression.

Adaptation, Psychological↗

PubMed1990

Enumeration of mutans streptococci in clinical samples by using monoclonal antibodies.

Mutans streptococci have been strongly associated with dental caries. Two members of this group of bacteria, Streptococcus mutans and Streptococcus sobrinus, are often found in human dental plaque. Identification of mutans streptococci on the basis of sugar fermentation is troublesome and easily leads to erroneous conclusions. Furthermore, the recovery on selective media differs for different species. This causes incorrect enumeration of S. mutans and S. sobrinus in clinical samples. The aim of this study was to develop a method for simultaneous identification and enumeration of S. mutans and S. sobrinus in dental plaque and saliva samples. With this immunoblot technique (IBT), significantly more plaque samples containing S. sobrinus were detected than on the selective medium Trypticase-yeast-cysteine-sucrose-bacitracin agar (TYCSB) (P less than 0.01). The numbers of plaque samples harboring S. mutans were equal on TYCSB and by IBT. However, the numbers of CFU of S.mutans as well as of S. sobrinus detected with the IBT were significantly higher than those obtained on TYCSB (P less than 0.001). The recovery of primary isolations of S. sobrinus on TYCSB seems to have been inhibited in 26 of the 45 S. sobrinus-containing plaque samples. False-positive or false-negative reactions with the IBT were not found.

Animals↗