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Michael O'Connell

Publications and source records attributed to Michael O'Connell.

18 recordsLinked to original sources
PubMed2006

FoxB of Pseudomonas aeruginosa functions in the utilization of the xenosiderophores ferrichrome, ferrioxamine B, and schizokinen: evidence for transport redundancy at the inner membrane.

Expression of the inner membrane protein FoxB (PA2465) of Pseudomonas aeruginosa in mutants of Sinorhizobium meliloti that are defective in the utilization of ferrichrome, ferrioxamine B, and schizokinen resulted in the restoration of siderophore utilization. Mutagenesis of foxB in P. aeruginosa did not abolish siderophore utilization, suggesting that the function is redundant.

Bacterial Proteins↗
PubMed2006

Current issues in adjuvant treatment of stage II colon cancer.

BACKGROUND: Adjuvant chemotherapy with 5-fluorouracil modulated by folinic acid, combined with oxaliplatin, has now become an accepted standard of care for patients with stage III colon cancer. In contrast, the use of adjuvant therapy for stage II patients remains controversial, and the identification of reliable prognostic factors to aid therapeutic decision making is crucial. METHODS: The authors critically review the results of clinical trials and meta-analyses investigating the value of adjuvant chemotherapy for stage II patients, emphasizing the heterogeneous nature of this population and the difficulty of performing clinical trials with sufficient power to reliably assess treatment efficacy. They also discuss the evidence concerning potential prognostic factors, particularly molecular markers. RESULTS: Available clinical trial data do not support the routine use of adjuvant chemotherapy for all stage II patients but suggest that it should be considered, particularly for certain high-risk patients. Recent guidelines advocate considering factors such as tumor differentiation, tumor perforation, number of lymph nodes examined, and T stage when assessing the likely benefit:risk ratio. Microsatellite instability and allelic imbalance seem to be strong predictors of good and poor prognosis, respectively, and in the near future, therapeutic decision-making models are likely to be further refined by the inclusion of such molecular markers. CONCLUSIONS: There is growing evidence that the prognosis of certain stage II patients with unfavorable prognostic factors can be improved by adjuvant chemotherapy, and increasingly refined tools are now available to define those most likely to benefit. Referral of stage II patients for individual assessment is strongly recommended.

Allelic Imbalance↗
PubMed2006

Identification and characterization of an iron-regulated gene, chtA, required for the utilization of the xenosiderophores aerobactin, rhizobactin 1021 and schizokinen by Pseudomonas aeruginosa.

Pseudomonas aeruginosa utilizes several xenosiderophores under conditions of iron limitation, including the citrate hydroxamate siderophore aerobactin. Analysis of the P. aeruginosa genome sequence revealed the presence of two genes, chtA (PA4675) and PA1365, encoding proteins displaying significant similarity to the aerobactin outer-membrane receptor, IutA, of Escherichia coli. The chtA and PA1365 genes were mutated by insertional inactivation and it was demonstrated that ChtA is the outer-membrane receptor for aerobactin. ChtA also mediated the utilization of rhizobactin 1021 and schizokinen, which are structurally similar to aerobactin. In contrast to the utilization of other xenosiderophores by P. aeruginosa, there was no apparent redundancy in the utilization of aerobactin, rhizobactin 1021 and schizokinen. The utilization of citrate hydroxamate siderophores by P. aeruginosa was demonstrated to be TonB1 dependent. A Fur box was identified in the region directly upstream of chtA and it was demonstrated by the in vivo Fur titration assay that this region is capable of binding Fur and accordingly that expression of chtA is iron regulated. The PA1365 mutant was unaffected in the utilization of citrate hydroxamate siderophores.

Bacterial Outer Membrane Proteins↗
PubMed2005

Disease-free survival versus overall survival as a primary end point for adjuvant colon cancer studies: individual patient data from 20,898 patients on 18 randomized trials.

PURPOSE: A traditional end point for colon adjuvant clinical trials is overall survival (OS), with 5 years demonstrating adequate follow-up. A shorter-term end point providing convincing evidence to allow treatment comparisons could significantly speed the translation of advances into practice. METHODS: Individual patient data were pooled from 18 randomized phase III colon cancer adjuvant clinical trials. Trials included 43 arms, with a pooled sample size of 20,898 patients. The primary hypothesis was that disease-free survival (DFS), with 3 years of follow-up, is an appropriate primary end point to replace OS with 5 years of follow-up. RESULTS: The recurrence rates for years 1 through 5 were 12%, 14%, 8%, 5%, and 3%, respectively. Median time from recurrence to death was 12 months. Eighty percent of recurrences were in the first 3 years; 91% of patients with recurrence by 3 years died before 5 years. Correlation between 3-year DFS and 5-year OS was 0.89. Comparing control versus experimental arms within each trial, the correlation between hazard ratios for DFS and OS was 0.92. Within-trial log-rank testing using both DFS and OS provided the same conclusion in 23 (92%) of 25 cases. Formal measures of surrogacy were satisfied. CONCLUSION: In patients treated on phase III adjuvant colon clinical trials, DFS and OS are highly correlated, both within patients and across trials. These results suggest that DFS after 3 years of median follow-up is an appropriate end point for adjuvant colon cancer clinical trials of fluorouracil-based regimens, although marginally significant DFS improvements may not translate into significant OS benefits.

Aged↗
PubMed2005

Carbon nanotubes as multifunctional biological transporters and near-infrared agents for selective cancer cell destruction.

Biological systems are known to be highly transparent to 700- to 1,100-nm near-infrared (NIR) light. It is shown here that the strong optical absorbance of single-walled carbon nanotubes (SWNTs) in this special spectral window, an intrinsic property of SWNTs, can be used for optical stimulation of nanotubes inside living cells to afford multifunctional nanotube biological transporters. For oligonucleotides transported inside living cells by nanotubes, the oligos can translocate into cell nucleus upon endosomal rupture triggered by NIR laser pulses. Continuous NIR radiation can cause cell death because of excessive local heating of SWNT in vitro. Selective cancer cell destruction can be achieved by functionalization of SWNT with a folate moiety, selective internalization of SWNTs inside cells labeled with folate receptor tumor markers, and NIR-triggered cell death, without harming receptor-free normal cells. Thus, the transporting capabilities of carbon nanotubes combined with suitable functionalization chemistry and their intrinsic optical properties can lead to new classes of novel nanomaterials for drug delivery and cancer therapy.

Cell Death↗
PubMed2005

Rank-invariant resampling based estimation of false discovery rate for analysis of small sample microarray data.

BACKGROUND: The evaluation of statistical significance has become a critical process in identifying differentially expressed genes in microarray studies. Classical p-value adjustment methods for multiple comparisons such as family-wise error rate (FWER) have been found to be too conservative in analyzing large-screening microarray data, and the False Discovery Rate (FDR), the expected proportion of false positives among all positives, has been recently suggested as an alternative for controlling false positives. Several statistical approaches have been used to estimate and control FDR, but these may not provide reliable FDR estimation when applied to microarray data sets with a small number of replicates. RESULTS: We propose a rank-invariant resampling (RIR) based approach to FDR evaluation. Our proposed method generates a biologically relevant null distribution, which maintains similar variability to observed microarray data. We compare the performance of our RIR-based FDR estimation with that of four other popular methods. Our approach outperforms the other methods both in simulated and real microarray data. CONCLUSION: We found that the SAM's random shuffling and SPLOSH approaches were liberal and the other two theoretical methods were too conservative while our RIR approach provided more accurate FDR estimation than the other approaches.

Algorithms↗
PubMed2005

RirA is the iron response regulator of the rhizobactin 1021 biosynthesis and transport genes in Sinorhizobium meliloti 2011.

The genes encoding the biosynthesis and transport of rhizobactin 1021, a siderophore produced by Sinorhizobium meliloti, are negatively regulated by iron. Mutagenesis of rirA, the rhizobial iron regulator, resulted in abolition of the iron responsive regulation of the biosynthesis and transport genes. Bioassay analysis revealed that the siderophore is produced in the presence of iron in a rirA mutant. RNA analysis and GFP fusions supported the conclusion that RirA is the mediator of iron-responsive transcriptional repression of the two transcripts encoding the biosynthesis and transport genes. RirA in S. meliloti appears to fulfil the role often observed for Fur in other bacterial species. The regulator was found to mediate the iron-responsive expression of two additional genes, smc02726 and dppA1, repressing the former while activating the latter. The rirA mutant nodulated the host plant Medicago sativa (alfalfa) and fixed nitrogen as effectively as the wild type.

Bacterial Proteins↗
PubMed2005

Novel mobilizable prokaryotic two-hybrid system vectors for high-throughput protein interaction mapping in Escherichia coli by bacterial conjugation.

Since its initial description, the yeast two-hybrid (Y2H) system has been widely used for the detection and analysis of protein-protein interactions. Mating-based strategies have been developed permitting its application for automated proteomic interaction mapping projects using both exhaustive and high-throughput strategies. More recently, a number of prokaryotic two-hybrid (P2H) systems have been developed but, despite the many advantages such Escherichia coli-based systems have over the Y2H system, they have not yet been widely implemented for proteomic interaction mapping. This may be largely due to the fact that high-throughput strategies employing bacterial transformation are not as amenable to automation as Y2H mating-based strategies. Here, we describe the construction of novel conjugative P2H system vectors. These vectors carry a mobilization element of the IncPalpha group plasmid RP4 and can therefore be mobilized with high efficiency from an E.coli donor strain encoding all of the required transport functions in trans. We demonstrate how these vectors permit the exploitation of bacterial conjugation for technically simplified and automated proteomic interaction mapping strategies in E.coli, analogous to the mating-based strategies developed for the Y2H system.

Bacterial Proteins↗
PubMed2004

Phase I dose escalation trial of feverfew with standardized doses of parthenolide in patients with cancer.

PURPOSE: Feverfew is a botanical product that contains parthenolide. Parthenolide has in vitro and in vivo anti-tumor and anti-angiogenic activity. Feverfew has been used extensively without any formal pharmacokinetic analysis. A Phase I trial was conducted to evaluate the pharmacokinetics and toxicity of parthenolide given as a component of "feverfew." PATIENTS AND METHODS: Feverfew (Tanacet trade mark ) was administered as a daily oral tablet in a 28-day cycle. A starting dose of 1 mg per day was explored with subsequent dose escalations to 2, 3, and 4 mg. Assessment of plasma pharmacokinetics was performed on patients accrued to the trial. Solid phase extraction and mass spectroscopy were used to evaluate parthenolide plasma concentrations. The limit of detection for parthenolide in plasma was 0.5 ng/ml. Patients were evaluated for response after every two cycles. RESULTS: Feverfew given on this schedule had no significant toxicity, and the maximum tolerated dose was not reached. When parthenolide was administered at doses up to 4 mg as a daily oral capsule in the feverfew preparation, there was not detectable concentration in the plasma. Because of this, parthenolide pharmacokinetics were not able to be completed. CONCLUSION: Feverfew, with up to 4 mg of parthenolide, given daily as an oral tablet is well tolerated without dose-limiting toxicity, but does not provide detectable plasma concentrations. Purification of parthenolide for administration of higher doses will be needed.

Administration, Oral↗
PubMed2004

An overview of data integration methods for regional assessment.

The U.S. Environmental Protections Agency's (U.S. EPA) Regional Vulnerability Assessment(ReVA) program has focused much of its research over the last five years on developing and evaluating integration methods for spatial data. An initial strategic priority was to use existing data from monitoring programs, model results, and other spatial data. Because most of these data were not collected with an intention of integrating into a regional assessment of conditions and vulnerabilities, issues exist that may preclude the use of some methods or require some sort of data preparation. Additionally, to support multi-criteria decision-making, methods need to be able to address a series of assessment questions that provide insights into where environmental risks are a priority. This paper provides an overview of twelve spatial integration methods that can be applied towards regional assessment, along with preliminary results as to how sensitive each method is to data issues that will likely be encountered with the use of existing data.

Animals↗
PubMed2004

Identification of rhtX and fptX, novel genes encoding proteins that show homology and function in the utilization of the siderophores rhizobactin 1021 by Sinorhizobium meliloti and pyochelin by Pseudomonas aeruginosa, respectively.

Rhizobactin 1021 is a hydroxymate siderophore produced by the soil bacterium Sinorhizobium meliloti 2011. A regulon comprising rhtA, encoding the outer membrane receptor protein for the ferrisiderophore; the biosynthesis operon rhbABCDEF; and rhrA, the Ara-C-like regulator of the receptor and biosynthesis genes has been previously described. We report the discovery of a gene, located upstream of rhbA and named rhtX (for "rhizobactin transport"), which is required, in addition to rhtA, to confer the ability to utilize rhizobactin 1021 on a strain of S. meliloti that does not naturally utilize the siderophore. Rhizobactin 1021 is structurally similar to aerobactin, which is transported in Escherichia coli via the IutA outer membrane receptor and the FhuCDB inner membrane transport system. E. coli expressing iutA and fhuCDB was found to also transport rhizobactin 1021. We demonstrated that RhtX alone could substitute for FhuCDB to transport rhizobactin 1021 in E. coli. RhtX shows similarity to a number of uncharacterized proteins which are encoded proximal to genes that are either known to be or predicted to be involved in iron acquisition. Among these is PA4218 of Pseudomonas aeruginosa, which is located close to the gene cluster that functions in pyochelin biosynthesis and outer membrane transport. PA4218 was mutated by allelic replacement, and the mutant was found to have a pyochelin utilization-defective phenotype. It is proposed that PA4218 be named fptX (for "ferripyochelin transport"). RhtX and FptX appear to be members of a novel family of permeases that function as single-subunit transporters of siderophores.

Amino Acid Sequence↗
PubMed2003

Local-pooled-error test for identifying differentially expressed genes with a small number of replicated microarrays.

MOTIVATION: In microarray studies gene discovery based on fold-change values is often misleading because error variability for each gene is heterogeneous under different biological conditions and intensity ranges. Several statistical testing methods for differential gene expression have been suggested, but some of these approaches are underpowered and result in high false positive rates because within-gene variance estimates are based on a small number of replicated arrays. RESULTS: We propose to use local-pooled-error (LPE) estimates and robust statistical tests for evaluating significance of each gene's differential expression. Our LPE estimation is based on pooling errors within genes and between replicate arrays for genes in which expression values are similar. We have applied our LPE method to compare gene expression in naïve and activated CD8+ T-cells. Our results show that the LPE method effectively identifies significant differential-expression patterns with a small number of replicated arrays. AVAILABILITY: The methodology is implemented with S-PLUS and R functions available at http://hesweb1.med.virginia.edu/bioinformatics

Algorithms↗
PubMed2003

Self-organizing maps for integrated environmental assessment of the Mid-Atlantic region.

A new method has been developed to perform environmental assessment at regional scale. This involves a combination of a self-organizing map (SOM) neural network and principal component analysis (PCA). The method is capable of clustering ecosystems in terms of environmental conditions and suggesting relative cumulative environmental impacts of multiple factors across a large region. Using data on land-cover, population, roads, streams, air pollution, and topography of the Mid-Atlantic region, the method was able to indicate areas that are in relatively poor environmental condition or vulnerable to future deterioration. Combining the strengths of SOM with those of PCA, the method offers an easy and useful way to perform a regional environmental assessment. Compared with traditional clustering and ranking approaches, the described method has considerable advantages, such as providing a valuable means for visualizing complex multidimensional environmental data at multiple scales and offering a single assessment or ranking needed for a regional environmental assessment while still facilitating the opportunity for more detailed analyses.

Environmental Monitoring↗
PubMed2003

Differences in mitochondrial and nuclear DNA status of high-density and low-density sperm fractions after density centrifugation preparation.

OBJECTIVE: To determine the mitochondrial DNA and nuclear DNA fragmentation of sperm populations separated by using discontinuous density gradient. DESIGN: Analysis of mitochondrial and nuclear DNA status of sperm from high and low density layers. SETTING: Regional fertility center. PATIENT(S): Twenty-eight men who presented for an initial infertility investigation. MAIN OUTCOME MEASURE(S): Semen was prepared by using discontinuous density gradient (90.0%:45.0%) and subjected to a modified long polymerase chain reaction to assess mitochondrial DNA deletions and to a modified single-cell alkaline gel electrophoresis assay to determine nuclear DNA fragmentation. RESULT(S): The high-density fraction displayed significantly more wild-type mitochondrial DNA (75% of samples) than did the low-density fraction (25% of samples). In the high-density fraction, the incidence of single deletions was higher than that of double or multiple deletions, and the deletions were predominantly small. A strong correlation was observed between nuclear DNA fragmentation and the number and size of mitochondrial DNA deletions. CONCLUSION(S): Density centrifugation isolates a population of sperm with high-quality mitochondrial DNA and nuclear DNA.

Adult↗
PubMed2002

The nasal base in cleft lip rhinoplasty.

The discussion on how to correct the nasal base in cleft lip (CL) rhinoplasty focuses on timing of the surgery, the type of approach, and the technique of repositioning the ala. Little attention is paid to the nasal vestibule. We compared the results of two different techniques. Forty-two patients were operated on via an endonasal approach with total mobilization of the lateral crus and fixation after repositioning. An external approach was used in 12 patients and the lateral crus freed as a medially based chondrocutaneous flap. The defect in the lateral vestibule wall was covered with an ear composite graft. The latter group showed more stable results concerning symmetry and breathing. We conclude that in most cases of unilateral CL noses there is not only a malposition and deformity of soft tissues and skin of the ala, but also a deficiency in the surface of inner lining of the nasal vestibule that needs appropriate repair. In general, the numerous procedures for repair of the nasal base in unilateral CL patients can be attributed to three principles based on different philosophies concerning the underlying pathology.

Adolescent↗
PubMedDate not supplied

Visibility of puncture sites after external osteotomy in rhinoplastic surgery.

BACKGROUND: External lateral osteotomy performed through a small puncture incision in the skin has numerous advantages, but it has been criticized by its opponents who claim it may leave visible scars. OBJECTIVE: To examine whether the external lateral osteotomy actually leaves visible scars. METHODS: Eighty-one postoperative photographs of patients who had undergone the external lateral osteotomy technique were reviewed. The photographic slides were a mixture of some taken 3 months after surgery and others taken 6 months after surgery. Scar visibility was assessed. RESULTS: Percutaneous puncture site visibility as assessed by 3 surgeons independently was 0% at 6 months after surgery and about 3% at 3 months after surgery. CONCLUSION: The external osteotomy procedure produces an excellent cosmetic result at the puncture sites in the skin.

Cicatrix↗
PubMedDate not supplied

Early self-awareness following traumatic brain injury: comparison of brain injury and orthopedic inpatients using the Functional Self-Assessment Scale (FSAS).

OBJECTIVE: To examine the Functional Self-Assessment Scale (FSAS) in hospitalized orthopedic patients with no brain dysfunction, and compare results to prior self-awareness data collected with brain injury patients. DESIGN: Comparison of patient and staff ratings on FSAS using paired sample t tests. PARTICIPANTS: Thirty-one adult volunteers hospitalized on National Rehabilitation Hospital (NRH) orthopedic treatment unit. MEASURES: FSAS was used to compare patient and staff ratings of patient performance on tasks relevant for inpatient rehabilitation. Subjects were screened to rule out brain impairment. RESULTS: Statistically significant but very small differences were found between orthopedic patients and therapist ratings using the FSAS. However, brain injury patients' ratings show a significantly larger discrepancy between self-therapist ratings than do orthopedic patients. CONCLUSION: Impaired self-awareness is related to brain injury rather than nonspecific factors in rehabilitation inpatients.

Adolescent↗