Bacteremic nosocomial pneumonia caused by Acinetobacter baumannii and Acinetobacter nosocomialis: a single or two distinct clinical entities?

The phenotypically indistinguishable Acinetobacter baumannii and Acinetobacter nosocomialis have become leading pathogens causing nosocomial pneumonia in critically ill patients. A. baumannii and A. nosocomialis nosocomial pneumonias were grouped as a single clinical entity previously. This study aimed to determine whether they are the same or a different clinical entity. A total of 121 patients with A. baumannii and 131 with A. nosocomialis bacteremic nosocomial pneumonia were included during an 8-year period. Despite the similar Charlson co-morbidity scores at admission, patients with A. baumannii pneumonia were more likely to have abnormal haematological findings, lobar pneumonia, significantly higher Acute Physiology and Chronic Health Evaluation II scores and higher frequency of shock at the onset of bacteraemia than those with A. nosocomialis pneumoni. A. baumannii isolates were resistant to more classes of antimicrobials, except colistin, and therefore the patients with A. baumannii pneumonia were more likely to receive inappropriate antimicrobial therapy. The 14-day mortality was significantly higher in patients with A. baumannii pneumonia (34.7% vs. 15.3%, p 0.001). A. baumannii was an independent risk factor for mortality (OR, 2.03; 95% CI, 1.05-3.90; p 0.035) in the overall cohort after adjustment for other risk factors for death, including inappropriate antimicrobial therapy. The results demonstrated the difference in clinical presentation, microbial characteristics and outcomes between A. baumannii and A. nosocomialis nosocomial pneumonia, and supported that they are two distinct clinical entities.

Mutations in isocitrate dehydrogenase 1 and 2 occur frequently in intrahepatic cholangiocarcinomas and share hypermethylation targets with glioblastomas.

Mutations in the genes encoding isocitrate dehydrogenase, IDH1 and IDH2, have been reported in gliomas, myeloid leukemias, chondrosarcomas and thyroid cancer. We discovered IDH1 and IDH2 mutations in 34 of 326 (10%) intrahepatic cholangiocarcinomas. Tumor with mutations in IDH1 or IDH2 had lower 5-hydroxymethylcytosine and higher 5-methylcytosine levels, as well as increased dimethylation of histone H3 lysine 79 (H3K79). Mutations in IDH1 or IDH2 were associated with longer overall survival (P=0.028) and were independently associated with a longer time to tumor recurrence after intrahepatic cholangiocarcinoma resection in multivariate analysis (P=0.021). IDH1 and IDH2 mutations were significantly associated with increased levels of p53 in intrahepatic cholangiocarcinomas, but no mutations in the p53 gene were found, suggesting that mutations in IDH1 and IDH2 may cause a stress that leads to p53 activation. We identified 2309 genes that were significantly hypermethylated in 19 cholangiocarcinomas with mutations in IDH1 or IDH2, compared with cholangiocarcinomas without these mutations. Hypermethylated CpG sites were significantly enriched in CpG shores and upstream of transcription start sites, suggesting a global regulation of transcriptional potential. Half of the hypermethylated genes overlapped with DNA hypermethylation in IDH1-mutant gliobastomas, suggesting the existence of a common set of genes whose expression may be affected by mutations in IDH1 or IDH2 in different types of tumors.

Missed diagnosis of influenza B virus due to nucleoprotein sequence mutations, Singapore, April 2011.

A new influenza B variant was discovered in Singapore in April 2011 during diagnostic testing of a 3-year-old boy with respiratory symptoms. Influenza B virus was isolated from culture and confirmed by standard immunofluorescence testing, but was not detected by the routine, in-house influenza screening reverse-transcription polymerase chain reaction assay that targets the nucleoprotein (NP) gene. Subsequent sequencing investigations demonstrated that several other published assays targeting NP could also fail to detect this novel variant.

Microstructure and crystallization kinetics analysis of the (In15Sb85)(100-x)Zn(x) phase change recording thin films.

The (In15Sb85)(100-x)Zn(x) films (x = 0 - 17.4) were deposited on nature oxidized Si wafer and glass substrate at room temperature by magnetron co-sputtering of Sb target and InZn composite target. The thermal property of the films was examined by a homemade reflectivity thermal analyzer. Microstructures of the films were analyzed by transmission electron microscope (TEM). We examined the effects of Zn addition on the thermal property, crystallization kinetics, and crystallization mechanism of the In15Sb85 recording film. As x = 0 - 17.4, thermal analysis shows that the (In15Sb85)(100-x)Zn(x) films have two phase transition temperature ranges which are 189 degrees C-215 degrees C and 300 degrees C-350 degrees C. It is found that the activation energy is increased with Zn content. This indicates that the thermal stability of amorphous state is improved by doping Zn. The optical contrasts of the films are all larger than 15%, as x = 0 - 6.2, indicating that the films have the potential in blue laser optical recording media application.

Effects of Os inserted layers on the microstructures and magnetic properties of the FePt films.

The microstructure and magnetic properties of multilayer [Os(t)/FePt(x)]n films on a glass substrate with a 10 nm Os buffer layer by ion beam sputtering have been studied as a function of the annealing temperatures between 300 and 800 degrees C. Here, t = 0.2, 1 or 5 nm and x varied from 10, 20, 25, 50, to 100 nm with its associated n value of 10, 5, 4, 2, and 1, respectively. No diffusion evidence was found in samples with a thin Os layer and t > or = 1 nm. The average grain size of the multilayer films can be well controlled by both annealing temperature and thickness of the FePt layer by a very thin Os space layer with t > or = 1 nm. The enhancement of H(c) can be understood from the fact that for a FePt film with an Os spacer layers, the increasing number of Os layer will inhibit the grain growth of FePt grains and enriches the grain boundary. We have experimentally demonstrated that even with a very thin 1 nm Os spacer layers, the [Os(t)/FePt(x)]n multilayer films can exhibit good hard magnetic properties and are attractive candidates for ultrahigh density magnetic recording media.

Crystallization mechanisms of phase change (GeSbSn)(100-x)Co(x) optical recording films.

In this study, the (GeSbSn)(100-x0Co(x) films (x = 0-13.3) were deposited on natural oxidized silicon wafer and glass substrate by dc magnetron co-sputtering of GeSbSn and Co targets. The ZnS-SiO2 films were used as protective layers. The thicknesses of the (GeSbSn)(100-x)Co(x) films and protective layer were 100 nm and 30 nm, respectively. We investigated the effects of Co addition on the thermal property, crystallization kinetics, and crystallization mechanism of the GeSbSn recording film. The crystallization temperatures of (GeSbSn)(100-x)Co(x) films were decreased with Co content. It was found that the activation energy of the (GeSbSn)(100-x)Co(x) films will decrease from 1.53 eV to 0.55 eV as Co content increased from 0 at.% to 13.3 at.%.

Protein sequence entropy is closely related to packing density and hydrophobicity.

We investigated the correlation between the Shannon information entropy, 'sequence entropy', with respect to the local flexibility of native globular proteins as described by inverse packing density. These are determined at each residue position for a total set of 130 query proteins, where sequence entropies are calculated from each set of aligned residues. For the accompanying aggregate set of 130 alignments, a strong linear correlation is observed between the calculated sequence entropy and the corresponding inverse packing density determined at an associated residue position. This region of linearity spans the range of C(alpha) packing densities from 12 to 25 amino acids within a sphere of 9 angstrom radius. Three different hydrophobicity scales all mimic the behavior of the sequence entropies. This confirms the idea that the ability to accommodate mutations is strongly dependent on the available space and on the propensity for each amino acid type to be buried. Future applications of these types of methods may prove useful in identifying both core and flexible residues within a protein.

Management of post-operative bladder spasm.

OBJECTIVE: Pain management following bladder surgery in children is often complicated by bladder spasm. The overall severity of spasm can be reduced with opioids, anticholinergic medication and sedatives, although breakthrough spasms often occur. At the Royal Children's Hospital, Melbourne, intravesical bupivacaine has been used to manage postoperative bladder spasm to good effect. The administration of intravesical bupivacaine is analysed in this prospective audit of locally applied intravesical anaesthetic and compared with other methods. METHOD: From February to August 2003, histories of 58 patients who had intravesical bupivacaine were studied and compared with six other methods of management of postoperative bladder spasm. CONCLUSION: Data showed that epidural anaesthesia was the most effective treatment of pain, with a pain score reduction of 6.6, compared with a reduction of 6.1 with intravesical bupivacaine, and 4.5 using intravenous morphine. However, intravesical bupivacaine was the most effective method for the relief of bladder spasm.

Does the endoscopic technique of ureterocele incision matter?

PURPOSE: Endoscopic ureterocele decompression is a well established procedure in children. However, an accurate endoscopic incision may be challenging in large ectopic ureteroceles. We describe a percutaneously assisted technique to facilitate the ease of ureterocele incision and review other described methods. MATERIALS AND METHODS: We reviewed the medical records of 12 children with ectopic ureteroceles subtending a double collecting system who underwent endoscopic, percutaneously assisted incision. Six ureteroceles were on the left side, 5 were on the right side and 1 child had bilateral ureteroceles. Decompression results were evaluated by ultrasound and Tc-mercaptoacetyltriglycine imaging during a mean of 2.8 years of followup. RESULTS: There were 7 girls and 5 boys. Mean age at presentation was 11.6 months (range 1 week to 6 years). The decompression success rate was 84% (11 of 13 renal units), and improved renal function and drainage was noted in 5 of 12 patients (41.6%). Seven of 12 patients had vesicoureteral reflux, of whom 2 were asymptomatic at followup and, hence, were treated conservatively. Five children underwent surgery because of recurrent urinary tract infections. CONCLUSIONS: Although our results are similar to those of other methods, percutaneously assisted cystoscopic incision of ureterocele enables easier and more accurate decompression. However, when comparing the various techniques described, it seems that postoperative results mostly reflect the anatomical and functional characteristics of the urinary system rather than the technique used.

Phylogenetic motif detection by expectation-maximization on evolutionary mixtures.

The preferential conservation of transcription factor binding sites implies that non-coding sequence data from related species will prove a powerful asset to motif discovery. We present a unified probabilistic framework for motif discovery that incorporates evolutionary information. We treat aligned DNA sequence as a mixture of evolutionary models, for motif and background, and, following the example of the MEME program, provide an algorithm to estimate the parameters by Expectation-Maximization. We examine a variety of evolutionary models and show that our approach can take advantage of phylogenic information to avoid false positives and discover motifs upstream of groups of characterized target genes. We compare our method to traditional motif finding on only conserved regions. An implementation will be made available at http://rana.lbl.gov.

Ulaanbaatar procedure for tubularization of the glans in severe hypospadias.

PURPOSE: We developed a new procedure for the repair of proximal hypospadias in which the distal urethra is constructed as part of the first of 2 stages, and reviewed the results of 34 cases. MATERIALS AND METHODS: We performed stage 1 of the Ulaanbaatar procedure in 35 children 0.6 to 11 years old (average age 2.5), and stage 2 in 20. The meatus was at the posterior third of the shaft in 14 children, at the penoscrotal junction in 16 and in the perineum in 5. Three patients had a previous operation, and none had Byars flaps formed. Followup was less than 2(1/2) years for stage 1 and less than 1(1/2) years for stage 2. In 2 stage 2 procedures a free graft was also used to augment the proximal part of the urethroplasty. RESULTS: Urethral fistula did not develop in any patient, a minor early stricture occurred in 2 patients and 1 urethral diverticulum occurred in 1 patient after stage 2. In all patients the glans and meatus were more normal compared to other 2-stage procedures after the first operation, and the cosmetic result was usually satisfactory. CONCLUSIONS: The Ulaanbaatar technique provides an alternative approach to the formation of the glans urethra in severe hypospadias. It does not have the risks associated with a single stage procedure but has the benefit of enabling tunneling of the urethra through the glans, thus facilitating a favorable cosmetic outcome and an easy stage 2.

Guide wire-assisted urethral dilatation for urethral strictures in pediatric urology.

PURPOSE: The aim of this study was to report the results of 32 cases of dilatation of urethral stricture using a guide wire and sheath dilator technique supplemented by clean intermittent catheterization if further stabilization of the urethral stricture was felt warranted. METHODS: The procedure involves insertion of a straight flexi-tip lubricated guide wire through the urethral stricture under cystoscopic guidance followed by insertion of a series of sheath dilators. Dilatation was followed by insertion of a Foley catheter, which was left in situ for 1 to 3 days. Patients underwent repeat cystoscopy to evaluate the urethra for recurrent stricture and those with a recalcitrant stricture were commenced on clean intermittent catheterization (CIC) to stabilize the narrowing. RESULTS: Thirty-two patients were included. They have been followed up for up to 2(1/2) years after their last cystoscopy (mean, 16 months). Thirteen of 32 patients had more than 4 dilatations under anesthesia. Twelve patients had undergone CIC postoperatively. Complications included a urinary tract infection in 3 boys and bladder spasms in one. No false passage or sepsis occurred with this approach. CONCLUSIONS: Guide wire-assisted urethral dilatation helps avoid risks associated with blind dilatation techniques and appears to be a safe and simple alternative for management of urethral strictures in pediatric urology.

Prediction of stone disease by discriminant analysis and artificial neural networks in genetic polymorphisms: a new method.

OBJECTIVE: To use information from genetic polymorphisms and from patients (drinking/exercise habits) to identify their association with stone disease, the main analytical and predictive tools being discriminant analysis (DA) and artificial neural networks (ANNs). PATIENTS, SUBJECTS AND METHODS: Urinary stone disease is common in Taiwan; the formation of calcium oxalate stone is reportedly associated with genetic polymorphisms but there are many of these. Genotyping requires many individuals and markers because of the complexity of gene-gene and gene-environmental factor interactions. With the development of artificial intelligence, data-mining tools like ANNs can be used to derive more from patient data in predicting disease. Thus we compared 151 patients with calcium oxalate stones and 105 healthy controls for the presence of four genetic polymorphisms; cytochrome p450c17, E-cadherin, urokinase and vascular endothelial growth factor (VEGF). Information about environmental factors, e.g. water, milk and coffee consumption, and outdoor activities, was also collected. Stepwise DA and ANNs were used as classification methods to obtain an effective discriminant model. RESULTS: With only the genetic variables, DA successfully classified 64% of the participants, but when all related factors (gene and environmental factors) were considered simultaneously, stepwise DA was successful in classifying 74%. The results for DA were best when six variables (sex, VEGF, stone number, coffee, milk, outdoor activities), found by iterative selection, were used. The ANN successfully classified 89% of participants and was better than DA when considering all factors in the model. A sensitivity analysis of the input parameters for ANN was conducted after the ANN program was trained; the most important inputs affecting stone disease were genetic (VEGF), while the second and third were water and milk consumption. CONCLUSIONS: While data-mining tools such as DA and ANN both provide accurate results for assessing genetic markers of calcium stone disease, the ANN provides a better prediction than the DA, especially when considering all (genetic and environmental) related factors simultaneously. This model provides a new way to study stone disease in combination with genetic polymorphisms and environmental factors.

Visualizing associations between genome sequences and gene expression data using genome-mean expression profiles.

The combination of genome-wide expression patterns and full genome sequences offers a great opportunity to further our understanding of the mechanisms and logic of transcriptional regulation. Many methods have been described that identify sequence motifs enriched in transcription control regions of genes that share similar gene expression patterns. Here we present an alternative approach that evaluates the transcriptional information contained by specific sequence motifs by computing for each motif the mean expression profile of all genes that contain the motif in their transcription control regions. These genome-mean expression profiles (GMEP's) are valuable for visualizing the relationship between genome sequences and gene expression data, and for characterizing the transcriptional importance of specific sequence motifs. Analysis of GMEP's calculated from a dataset of 519 whole-genome microarray experiments in Saccharomyces cerevisiae show a significant correlation between GMEP's of motifs that are reverse complements, a result that supports the relationship between GMEP's and transcriptional regulation. Hierarchical clustering of GMEP's identifies clusters of motifs that correspond to binding sites of well-characterized transcription factors. The GMEP's of these clustered motifs have patterns of variation across conditions that reflect the known activities of these transcription factors. Software that computed GMEP's from sequence and gene expression data is available under the terms of the Gnu Public License from http://rana.lbl.gov/.

Vav2 is an activator of Cdc42, Rac1, and RhoA.

Vav and Vav2 are members of the Dbl family of proteins that act as guanine nucleotide exchange factors (GEFs) for Rho family proteins. Whereas Vav expression is restricted to cells of hematopoietic origin, Vav2 is widely expressed. Although Vav and Vav2 share highly related structural similarities and high sequence identity in their Dbl homology domains, it has been reported that they are active GEFs with distinct substrate specificities toward Rho family members. Whereas Vav displayed GEF activity for Rac1, Cdc42, RhoA, and RhoG, Vav2 was reported to exhibit GEF activity for RhoA, RhoB, and RhoG but not for Rac1 or Cdc42. Consistent with their distinct substrate targets, it was found that constitutively activated versions of Vav and Vav2 caused distinct transformed phenotypes when expressed in NIH 3T3 cells. In contrast to the previous findings, we found that Vav2 can act as a potent GEF for Cdc42, Rac1, and RhoA in vitro. Furthermore, we found that NH(2)-terminally truncated and activated Vav and Vav2 caused indistinguishable transforming actions in NIH 3T3 cells that required Cdc42, Rac1, and RhoA function. In addition, like Vav and Rac1, we found that Vav2 activated the Jun NH(2)-terminal kinase cascade and also caused the formation of lamellipodia and membrane ruffles in NIH 3T3 cells. Finally, Vav2-transformed NIH 3T3 cells showed up-regulated levels of Rac-GTP. We conclude that Vav2 and Vav share overlapping downstream targets and are activators of multiple Rho family proteins. Therefore, Vav2 may mediate the same cellular consequences in nonhematopoietic cells as Vav does in hematopoietic cells.

Potential misidentification of Burkholderia pseudomallei by API 20NE.

Biochemical confirmation of the identity of Burkholderia pseudomallei in Singapore previously relied on the API 20NE panel of tests. After introducing an alternative proprietary biochemical panel, the Microbact 24E (MedVet, Adelaide, Australia), we noted that the API panel identified some presumptive B. pseudomallei isolates as other species. We therefore compared the performance of the API 20NE against the Microbact 24E with 50 distinct clinical isolates of B. pseudomallei, after 24 hours and after five days incubation of primary cultures. The API panel correctly identified 40 isolates. Four results were unacceptable or uninterpretable. Six isolates were misidentified as other species; the commonest being Chromobacterium violaceum. One of these was again identified as C. violaceum by the repeat API panel. Fourteen isolates, including the six misidentified isolates and four isolate pairs from separate sources in four separate patients, were typed using PCR amplification of repetitive extragenic palindromic sequences (REPS). The isolates identified as C. violaceum appeared to have identical REPS patterns, suggesting that some of the errant API results may be due to a single locally prevalent strain of B. pseudomallei. A previous suggestion that C. violaceum may produce a melioidosis-like illness may therefore be due to laboratory misidentification of B. pseudomallei with the API 20NE biochemical test panel.

Reaching NLM through the Internet.

Currently, many of the electronic services are still new, and there may be a need for further fine-tuning and changes. Having separate electronic addresses for each service rather than having one centralized address will make it easier for NLM to identify and isolate questions or problems. The Appendix summarizes the commands and addresses mentioned in this article.

A photometric detector based on a blue light-emitting diode.

The suitability of blue light-emitting diodes as radiation sources in molecular absorption spectroscopy was evaluated. Electronic as well as spectral considerations are discussed. A transducer based on a blue light-emitting diode and a photodiode is described which yields direct absorbance readings by passing the photocurrent to an integrated circuit logarithmic converter. The performance of this device was tested for commonly used spectrophotometric procedures for Cr, Mn, Zn, Fe and Cl and compared with conventional molecular absorption spectroscopy. Also investigated was the application of the transducer as a detector in flow-injection analysis.

Cloning and characterization of a gene required for the secretion of extracellular enzymes across the outer membrane by Xanthomonas campestris pv. campestris.

Nonpathogenic mutants of Xanthomonas campestris pv. campestris, generated from transposon mutagenesis, accumulated extracellular polygalacturonate lyase, alpha-amylase, and endoglucanase in the periplasm. The transposon Tn5 was introduced by a mobilizable, suicidal plasmid, pSUP2021 or pEYDG1. Genomic banks of wild-type X. campestris pv. campestris, constructed on the broad-host-range, mobilizable cosmid pLAFR1 or pLAFR3, were conjugated with one of the mutants, designated XC1708. Recombinant plasmids isolated by their ability to complement XC1708 can be classified into two categories. One, represented by pLASC3, can complement some mutants, whereas the other, represented by a single plasmid, pLAHH2, can complement all of the other mutants. Restriction mapping showed that the two recombinant plasmids shared an EcoRI fragment of 8.9 kb. Results from subcloning, deletion mapping, and mini-Mu insertional mutation of the 8.9-kb EcoRI fragment suggested that a 4.2-kb fragment was sufficient to complement the mutant XC1708. Sequence analysis of this 4.2-kb fragment revealed three consecutive open reading frames (ORFs), ORF1, ORF2, and ORF3. Hybridization experiments showed that Tn5 in the genome of XC1708 and other mutants complemented by pLASC3 was located in ORF3, which could code for a protein of 83.5 kDa. A signal peptidase II processing site was identified at the N terminus of the predicted amino acid sequence. Sequence homology of 51% was observed between the amino acid sequences predicted from ORF3 and the pulD gene of Klebsiella species.