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1.  Interlaboratory Variability of Caspofungin MICs for Candida spp. Using CLSI and EUCAST Methods: Should the Clinical Laboratory Be Testing This Agent? 
Antimicrobial Agents and Chemotherapy  2013;57(12):5836-5842.
Although Clinical and Laboratory Standards Institute (CLSI) clinical breakpoints (CBPs) are available for interpreting echinocandin MICs for Candida spp., epidemiologic cutoff values (ECVs) based on collective MIC data from multiple laboratories have not been defined. While collating CLSI caspofungin MICs for 145 to 11,550 Candida isolates from 17 laboratories (Brazil, Canada, Europe, Mexico, Peru, and the United States), we observed an extraordinary amount of modal variability (wide ranges) among laboratories as well as truncated and bimodal MIC distributions. The species-specific modes across different laboratories ranged from 0.016 to 0.5 μg/ml for C. albicans and C. tropicalis, 0.031 to 0.5 μg/ml for C. glabrata, and 0.063 to 1 μg/ml for C. krusei. Variability was also similar among MIC distributions for C. dubliniensis and C. lusitaniae. The exceptions were C. parapsilosis and C. guilliermondii MIC distributions, where most modes were within one 2-fold dilution of each other. These findings were consistent with available data from the European Committee on Antimicrobial Susceptibility Testing (EUCAST) (403 to 2,556 MICs) for C. albicans, C. glabrata, C. krusei, and C. tropicalis. Although many factors (caspofungin powder source, stock solution solvent, powder storage time length and temperature, and MIC determination testing parameters) were examined as a potential cause of such unprecedented variability, a single specific cause was not identified. Therefore, it seems highly likely that the use of the CLSI species-specific caspofungin CBPs could lead to reporting an excessive number of wild-type (WT) isolates (e.g., C. glabrata and C. krusei) as either non-WT or resistant isolates. Until this problem is resolved, routine testing or reporting of CLSI caspofungin MICs for Candida is not recommended; micafungin or anidulafungin data could be used instead.
doi:10.1128/AAC.01519-13
PMCID: PMC3837874  PMID: 24018263
2.  Identification and frequency of CCR5Δ32/Δ32 HIV-resistant cord blood units from Houston area hospitals 
HIV medicine  2011;12(8):481-486.
Objectives
The use of umbilical cord blood (CB) that is genetically resistant to HIV infection has been proposed as a novel stem cell therapy for the treatment of patients with AIDS. These genetically unique CB units (CBUs) should be present in public CB banks at a predicted frequency.
Methods
The chemokine (C-C motif) receptor 5 (CCR5) genotypes of CBUs donated to the M. D. Anderson CB Bank by four Houston area hospitals were determined by polymerase chain reaction (PCR) and DNA sequencing.
Results
The frequency of CCR5Δ32/Δ32 CBUs was consistent with the frequency of the CCR5Δ32 allele in human populations, and was apparently dependent on the ethnic population of the parents of the newborns from whom the CBUs were collected.
Conclusions
Routine genotyping to identify HIV-resistant CBUs could create a bank of CB-derived stem/progenitor cells with which to treat HIV infection.
doi:10.1111/j.1468-1293.2010.00911.x
PMCID: PMC4021858  PMID: 21375684
AIDS; cord blood; stem cell therapy; transplantation; virus co-receptor
3.  Glass-like recovery of antiferromagnetic spin ordering in a photo-excited manganite Pr0.7Ca0.3MnO3 
Scientific Reports  2014;4:4050.
Electronic orderings of charges, orbitals and spins are observed in many strongly correlated electron materials, and revealing their dynamics is a critical step toward undertsanding the underlying physics of important emergent phenomena. Here we use time-resolved resonant soft x-ray scattering spectroscopy to probe the dynamics of antiferromagnetic spin ordering in the manganite Pr0.7Ca0.3MnO3 following ultrafast photo-exitation. Our studies reveal a glass-like recovery of the spin ordering and a crossover in the dimensionality of the restoring interaction from quasi-1D at low pump fluence to 3D at high pump fluence. This behavior arises from the metastable state created by photo-excitation, a state characterized by spin disordered metallic droplets within the larger charge- and spin-ordered insulating domains. Comparison with time-resolved resistivity measurements suggests that the collapse of spin ordering is correlated with the insulator-to-metal transition, but the recovery of the insulating phase does not depend on the re-establishment of the spin ordering.
doi:10.1038/srep04050
PMCID: PMC3923209  PMID: 24522173
4.  Multicenter Study of Isavuconazole MIC Distributions and Epidemiological Cutoff Values for Aspergillus spp. for the CLSI M38-A2 Broth Microdilution Method 
Epidemiological cutoff values (ECVs) were established for the new triazole isavuconazole and Aspergillus species wild-type (WT) MIC distributions (organisms in a species-drug combination with no detectable acquired resistance mechanisms) that were defined with 855 Aspergillus fumigatus, 444 A. flavus, 106 A. nidulans, 207 A. niger, 384 A. terreus, and 75 A. versicolor species complex isolates; 22 Aspergillus section Usti isolates were also included. CLSI broth microdilution MIC data gathered in Europe, India, Mexico, and the United States were aggregated to statistically define ECVs. ECVs were 1 μg/ml for the A. fumigatus species complex, 1 μg/ml for the A. flavus species complex, 0.25 μg/ml for the A. nidulans species complex, 4 μg/ml for the A. niger species complex, 1 μg/ml for the A. terreus species complex, and 1 μg/ml for the A. versicolor species complex; due to the small number of isolates, an ECV was not proposed for Aspergillus section Usti. These ECVs may aid in detecting non-WT isolates with reduced susceptibility to isavuconazole due to cyp51A (an A. fumigatus species complex resistance mechanism among the triazoles) or other mutations.
doi:10.1128/AAC.00636-13
PMCID: PMC3719700  PMID: 23716059
5.  Electronic superlattice revealed by resonant scattering from random impurities in Sr3Ru2O7 
Scientific Reports  2013;3:2299.
Resonant elastic x-ray scattering (REXS) is an exquisite element-sensitive tool for the study of subtle charge, orbital, and spin superlattice orders driven by the valence electrons, which therefore escape detection in conventional x-ray diffraction (XRD). Although the power of REXS has been demonstrated by numerous studies of complex oxides performed in the soft x-ray regime, the cross section and photon wavelength of the material-specific elemental absorption edges ultimately set the limit to the smallest superlattice amplitude and periodicity one can probe. Here we show – with simulations and REXS on Mn-substituted Sr3Ru2O7 – that these limitations can be overcome by performing resonant scattering experiments at the absorption edge of a suitably-chosen, dilute impurity. This establishes that – in analogy with impurity-based methods used in electron-spin-resonance, nuclear-magnetic resonance, and Mössbauer spectroscopy – randomly distributed impurities can serve as a non-invasive, but now momentum-dependent probe, greatly extending the applicability of resonant x-ray scattering techniques.
doi:10.1038/srep02299
PMCID: PMC3730170  PMID: 23903555
6.  Genetic regulation of the ramA locus and its expression in clinical isolates of Klebsiella pneumoniae 
Tigecycline resistance has been attributed to ramA overexpression and subsequent acrA upregulation. The ramA locus, originally identified in Klebsiella pneumoniae, has homologues in Enterobacter and Salmonella spp. In this study, we identify in silico that the ramR binding site is also present in Citrobacter spp. and that Enterobacter, Citrobacter and Klebsiella spp. share key regulatory elements in the control of the romA–ramA locus. RACE (rapid amplification of cDNA ends) mapping indicated that there are two promoters from which romA–ramA expression can be regulated in K. pneumoniae. Correspondingly, electrophoretic binding studies clearly showed that purified RamA and RamR proteins bind to both of these promoters. Hence, there appear to be two RamR binding sites within the Klebsiella romA–ramA locus. Like MarA, RamA binds the promoter region, implying that it might be subject to autoregulation. We have identified changes within ramR in geographically distinct clinical isolates of K. pneumoniae. Intriguingly, levels of romA and ramA expression were not uniformly affected by changes within the ramR gene, thereby supporting the dual promoter finding. Furthermore, a subset of strains sustained no changes within the ramR gene but which still overexpressed the romA–ramA genes, strongly suggesting that a secondary regulator may control ramA expression.
doi:10.1016/j.ijantimicag.2011.02.012
PMCID: PMC3117140  PMID: 21514798
Klebsiella pneumoniae; romA; ramA; ramR; acrA; Tigecycline
7.  PCR based identification and discrimination of agents of mucormycosis and aspergillosis in paraffin wax embedded tissue 
Journal of Clinical Pathology  2005;58(11):1180-1184.
Background: Invasive fungal infections are often diagnosed by histopathology without identification of the causative fungi, which show significantly different antifungal susceptibilities.
Aims: To establish and evaluate a system of two seminested polymerase chain reaction (PCR) assays to identify and discriminate between agents of aspergillosis and mucormycosis in paraffin wax embedded tissue samples.
Methods: DNA of 52 blinded samples from five different centres was extracted and used as a template in two PCR assays targeting the mitochondrial aspergillosis DNA and the 18S ribosomal DNA of zygomycetes.
Results: Specific fungal DNA was identified in 27 of 44 samples in accordance with a histopathological diagnosis of zygomycosis or aspergillosis, respectively. Aspergillus fumigatus DNA was amplified from one specimen of zygomycosis (diagnosed by histopathology). In four of 16 PCR negative samples no human DNA was amplified, possibly as a result of the destruction of DNA before paraffin wax embedding. In addition, eight samples from clinically suspected fungal infections (without histopathological proof) were examined. The two PCR assays detected a concomitant infection with Absidia corymbifera and A fumigatus in one, and infections with Rhizopus arrhizus and A fumigatus in another two cases.
Conclusions: The two seminested PCR assays described here can support a histopathological diagnosis of mucormycosis or aspergillosis, and can identify the infective agent, thereby optimising antifungal treatment.
doi:10.1136/jcp.2004.024703
PMCID: PMC1770765  PMID: 16254108
mucormycosis; aspergillosis; zygomycetes; polymerase chain reaction
8.  Very low prevalence of bovine immunodeficiency virus infection in western Canadian cattle. 
Bovine immunodeficiency virus (BIV) is a lentivirus that causes disease in cattle. Despite the large cattle industry in western Canada, the presence of BIV has not been examined to date. Genomic DNA, derived from semen and buffy coat samples, was analyzed by nested polymerase chain reaction (PCR) using specific primers for the gag, pol, and env genes of BIV. Despite utilizing a procedure that detected a minimum of 10 proviral copies, BIV sequences were not amplified in any of 317 buffy coat and 50 semen samples that were obtained from an archive that included 27 cattle breeds, collected from different sources in Alberta (1980-1999). In the 367 DNA samples examined, there was no evidence of BIV infection, suggesting that the prevalence of BIV infection was very low.
Images
PMCID: PMC1189647  PMID: 11227201
9.  Does Horner's syndrome in infancy require investigation? 
AIMS—To evaluate whether isolated Horner's syndrome presenting in the first year of life warrants investigation.
METHOD—Retrospective review of 23 children presenting with Horner's syndrome in the first year of life.
RESULTS—In 16 patients (70%) no cause was identified. Birth trauma was the most common identifiable cause (four patients). Twenty one children (91%) had urinary vanillylmandelic acid (VMA) measured and 13 patients (57%) underwent either computed tomography or magnetic resonance imaging of the chest and neck. These investigations revealed previously undisclosed pathology in only two—one ganglioneuroma of the left pulmonary apex and one cervical neuroblastoma. A further patient was known to have abdominal neuroblastoma before presenting with Horner's syndrome. There were no cases of Horner's syndrome occurring after cardiothoracic surgery. Long term follow up of the patients (mean 9.3 years) has not revealed further pathology.
CONCLUSIONS—Routine diagnostic imaging of isolated Horner's syndrome in infancy is unnecessary. Infants should be examined for cervical or abdominal masses and involvement of other cranial nerves. If the Horner's syndrome is truly isolated then urinary VMA levels and follow up in conjunction with a paediatrician should detect any cases associated with neuroblastoma. Further investigation is warranted if the Horner's syndrome is acquired or associated with other signs such as increasing heterochromia, a cervical mass, or cranial nerve palsies.

 Keywords: Horner's syndrome; neuroblastoma
PMCID: PMC1722330  PMID: 9536881
10.  Examination of spinal cord in diseases of the craniocervical junction and high cervical spine. 
Journal of Clinical Pathology  1991;44(2):170-172.
A simple necropsy technique for the removal of the craniocervical junction was devised: a relatively small specimen comprising part of the clivus, the foramen magnum, and cervical vertebral canal is removed in one piece with the medulla and spinal cord inside, and examined systematically after fixation. This method, used in a series of patients with chronic craniocervical instability, allows both good clinicopathological correlations to be made and histological changes in the lower medulla or upper cervical cord segments to be related to sites of extrinsic compression.
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PMCID: PMC496986  PMID: 1864993
11.  Effect of lung T lymphocytes on fibroblasts in idiopathic pulmonary fibrosis and extrinsic allergic alveolitis. 
Thorax  1990;45(6):451-455.
Increased fibroblast replication and interstitial collagen accumulation occur commonly in the interstitial lung disease that progress to fibrosis. The processes controlling lung fibrogenesis are not completely understood, however. This study was designed to analyse the influence of T lymphocytes from lung tissue obtained at open lung biopsy from four patients with idiopathic pulmonary fibrosis and four patients with extrinsic allergic alveolitis on fibroblast proliferation and collagen synthesis in vitro. Lung T cell supernatants from patients with both diseases induced a moderate but significant inhibition of human lung fibroblast cell line growth. In contrast, there was a clear difference in the effect of T cells from the two groups of patients in relation to collagen production. Lung T lymphocytes from all four patients with idiopathic pulmonary fibrosis produced a substantial increase in collagen synthesis (from 371% to 514% of control values), whereas T cells from three of the four patients with extrinsic allergic alveolitis induced a significant decrease in collagen production (to 35%, 36%, and 43% of control values); in the fourth case there was an increase in collagen synthesis but this was lower than that seen with T cells from any of the patients with idiopathic pulmonary fibrosis. Peripheral T cells from six patients and control subjects caused a small increase in fibroblast proliferation and no change in collagen synthesis. The findings suggest that at least two types of interaction occur between lung T cells and fibroblasts in these disorders. A variable degree of inhibition of cell proliferation is observed in response to lung T cell supernatants from patients with both idiopathic pulmonary fibrosis and extrinsic allergic alveolitis; a substantial increase in collagen synthesis is triggered by lymphokines from patients with idiopathic pulmonary fibrosis.
PMCID: PMC462528  PMID: 2392789
12.  Characterization of motifs which are critical for activity of the cyclic AMP-responsive transcription factor CREB. 
Molecular and Cellular Biology  1991;11(3):1306-1312.
Cyclic AMP mediates the hormonal stimulation of a number of eukaryotic genes by directing the protein kinase A (PK-A)-dependent phosphorylation of transcription factor CREB. We have previously determined that although phosphorylation at Ser-133 is critical for induction, this site does not appear to participate directly in transactivation. To test the hypothesis that CREB ultimately activates transcription through domains that are distinct from the PK-A site, we constructed a series of CREB mutants and evaluated them by transient assays in F9 teratocarcinoma cells. Remarkably, a glutamine-rich region near the N terminus appeared to be important for PK-A-mediated induction of CREB since removal of this domain caused a marked reduction in CREB activity. A second region consisting of a short acidic motif (DLSSD) C terminal to the PK-A site also appeared to synergize with the phosphorylation motif to permit transcriptional activation. Biochemical experiments with purified recombinant CREB protein further demonstrate that the transactivation domain is more sensitive to trypsin digestion than are the DNA-binding and dimerization domains, suggesting that the activator region may be structured to permit interactions with other proteins in the RNA polymerase II complex.
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PMCID: PMC369401  PMID: 1671708
13.  Comparison of the abilities of different protein sources of iron to enhance Neisseria meningitidis infection in mice. 
Infection and Immunity  1989;57(8):2425-2429.
This study was done primarily to determine whether the previously observed specificity of the meningococcal transferrin and lactoferrin receptors for human proteins was maintained in vivo during meningococcal infection in mice. Preliminary experiments evaluating the choice of host strain, the age and sex of mice, and the growth conditions of the meningococci indicated that 45-day-old female Swiss Webster mice challenged with meningococci grown on low-pH, low-iron Mueller-Hinton agar plates were appropriate for this study. The comparison of transferrins and lactoferrins from different species demonstrated that only the human forms of these proteins were utilized by meningococci; there was significantly greater mortality among mice treated with iron-saturated human transferrin or lactoferrin (93 and 100%, respectively) than among those not treated or treated with iron-saturated bovine transferrin or bovine lactoferrin (0%). Provision of exogenous hemoglobin also resulted in increased mortality, although not as great as that observed with amounts of transferrin with equivalent iron content, which parallels the more effective utilization of transferrin and lactoferrin in in vitro growth experiments. In addition, unlike with transferrin and lactoferrin, there was no difference in utilization of human and bovine hemoglobin in vitro or in vivo.
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PMCID: PMC313464  PMID: 2545624
14.  FiltraCheck-UTI, a rapid, disposable system for detection of bacteriuria. 
Journal of Clinical Microbiology  1987;25(5):926-928.
The initial evaluation of the FiltraCheck-UTI bacteriuria detection system is described. The colorimetric test, which utilizes a disposable filter disk and a stable reagent system, does not require instrumentation. The test procedure is simple and may be performed in less than 1 min. Results obtained with the FiltraCheck-UTI system were compared with those obtained by conventional semiquantitative culturing. Of 1,198 urine specimens evaluated, 202 (16.9%) were determined to be significant positives at greater than or equal to 10(5) CFU/ml by the culture method. The sensitivity and specificity of the FiltraCheck-UTI system were 96.5 and 79.7%, respectively, and the negative predictive value was 99.1%. The high sensitivity, rapidity, simplicity, and unique disposable format of the FiltraCheck-UTI system offer significant advantages over other commonly used screening methods.
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PMCID: PMC266120  PMID: 3584428

Results 1-15 (15)