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1.  Using pet-ct to reduce futile thoracotomy rates in non-small-cell lung cancer: a population-based review 
Current Oncology  2014;21(6):e768-e774.
Combined positron-emission tomography and computed tomography (pet-ct) reduces futile thoracotomy (ft) rates in patients with non-small-cell lung cancer (nsclc). We sought to identify preoperative risk factors for ft in patients staged with pet-ct.
We retrospectively reviewed all patients referred to the BC Cancer Agency during 2009–2010 who underwent pet-ct and thoracotomy for nsclc. Patients with clinical N2 disease were excluded. An ft was defined as any of a benign lesion; an exploratory thoracotomy; pathologic N2 or N3, stage iiib or iv, or inoperable T3 or T4 disease; and recurrence or death within 1 year of surgery.
Of the 108 patients who met the inclusion criteria, ft occurred in 27. The main reason for ft was recurrence within 1 year (14 patients) and pathologic N2 disease (10 patients). On multivariate analysis, an Eastern Cooperative Oncology Group performance status greater than 1, a pet-ct positive N1 status, a primary tumour larger than 3 cm, and a period of more than 16 weeks from pet-ct to surgery were associated with ft. N2 disease that had been negative on pet-ct occurred in 21% of patients with a pet-ct positive N1 status and in 20% of patients with tumours larger than 3 cm and non-biopsy mediastinal staging only. The combination of pet-ct positive N1 status and a primary larger than 3 cm had 85% specificity, and the presence of either risk factor had 100% sensitivity, for ft attributable to N2 disease.
To reduce ft attributable to N2 disease, tissue biopsy for mediastinal staging should be considered for patients with pet-ct positive N1 status and with tumours larger than 3 cm even with a pet-ct negative mediastinum.
PMCID: PMC4257121  PMID: 25489265
Non-small-cell lung cancer; positron-emission tomography–computed tomography; thoracotomy; lymphatic metastasis or pathology; mediastinal staging; endobronchial ultrasonography; mediastinoscopy; endoscopic ultrasonography
2.  Genome Sequencing of an Extended Series of NDM-Producing Klebsiella pneumoniae Isolates from Neonatal Infections in a Nepali Hospital Characterizes the Extent of Community- versus Hospital-Associated Transmission in an Endemic Setting 
Antimicrobial Agents and Chemotherapy  2014;58(12):7347-7357.
NDM-producing Klebsiella pneumoniae strains represent major clinical and infection control challenges, particularly in resource-limited settings with high rates of antimicrobial resistance. Determining whether transmission occurs at a gene, plasmid, or bacterial strain level and within hospital and/or the community has implications for monitoring and controlling spread. Whole-genome sequencing (WGS) is the highest-resolution typing method available for transmission epidemiology. We sequenced carbapenem-resistant K. pneumoniae isolates from 26 individuals involved in several infection case clusters in a Nepali neonatal unit and 68 other clinical Gram-negative isolates from a similar time frame, using Illumina and PacBio technologies. Within-outbreak chromosomal and closed-plasmid structures were generated and used as data set-specific references. Three temporally separated case clusters were caused by a single NDM K. pneumoniae strain with a conserved set of four plasmids, one being a 304,526-bp plasmid carrying blaNDM-1. The plasmids contained a large number of antimicrobial/heavy metal resistance and plasmid maintenance genes, which may have explained their persistence. No obvious environmental/human reservoir was found. There was no evidence of transmission of outbreak plasmids to other Gram-negative clinical isolates, although blaNDM variants were present in other isolates in different genetic contexts. WGS can effectively define complex antimicrobial resistance epidemiology. Wider sampling frames are required to contextualize outbreaks. Infection control may be effective in terminating outbreaks caused by particular strains, even in areas with widespread resistance, although this study could not demonstrate evidence supporting specific interventions. Larger, detailed studies are needed to characterize resistance genes, vectors, and host strains involved in disease, to enable effective intervention.
PMCID: PMC4249533  PMID: 25267672
3.  Anti-resorptive Agents Reduce the Size of Resorption Cavities: A Three-Dimensional Dynamic Bone Histomorphometry Study 
Bone  2013;57(1):10.1016/j.bone.2013.08.018.
Alterations in resorption cavities and bone remodeling events during anti-resorptive treatment are believed to contribute to reductions in fracture risk. Here, we examine changes in the size of individual remodeling events associated with treatment with a selective estrogen receptor modulator (raloxifene) or a bisphosphonate (risedronate). Adult female rats (6 months of age) were submitted to ovariectomy (n = 17) or sham surgery (SHAM, n = 5). One month after surgery, the ovariectomized animals were separated into three groups: untreated (OVX, n = 5), raloxifene treated (OVX+Ral, n = 6) and risedronate treated (OVX+Ris, n = 6). At 10 months of age, the lumbar vertebrae were submitted to three-dimensional dynamic bone histomorphometry to examine the size (depth, breadth, volume) of individual resorption cavities and formation events. Maximum resorption cavity depth did not differ between the SHAM (23.66 ± 1.87 µm, mean ± SD) and OVX (22.88 ± 3.69 µm) groups but was smaller in the OVX+Ral (14.96 ± 2.30 µm) and OVX+Ris (14.94 ± 2.70 µm) groups (p < 0.01). Anti-resorptive treatment was associated with reductions in the surface area of resorption cavities and the volume occupied by each resorption cavity (p < 0.01 each). The surface area and volume of individual formation events (double-labeled events) in the OVX+Ris group were reduced as compared to other groups (p < 0.02). Raloxifene treated animals showed similar amounts of bone remodeling (ES/BS and dLS/BS) compared to sham-operated controls but smaller cavity size (depth, breadth and volume). The current study shows that anti-resorptive agents influence the size of resorption cavities and individual remodeling events and that the effect of anti-resorptives on individual remodeling events may not always be directly related to the degree of suppression of bone remodeling.
PMCID: PMC3818704  PMID: 23988275
Bone Remodeling; Bone Histomorphometry; Ovariectomy; Osteoporosis; Bisphosphonates; SERMS
4.  A National Strategy to Develop Pragmatic Clinical Trials Infrastructure 
An important challenge in comparative effectiveness research is the lack of infrastructure to support pragmatic clinical trials, which compare interventions in usual practice settings and subjects. These trials present challenges that differ from those of classical efficacy trials, which are conducted under ideal circumstances, in patients selected for their suitability, and with highly controlled protocols.
In 2012, we launched a one-year learning network to identify high priority pragmatic clinical trials and to deploy research infrastructure through the NIH Clinical and Translational Science Awards Consortium that could be used to launch and sustain them. The network and infrastructure were initiated as a learning ground and shared resource for investigators and communities interested in developing pragmatic clinical trials.
We followed a three-stage process of developing the network, prioritizing proposed trials, and implementing learning exercises that culminated in a one-day network meeting at the end of the year. The year-long project resulted in five recommendations related to developing the network, enhancing community engagement, addressing regulatory challenges, advancing information technology, and developing research methods. The recommendations can be implemented within 24 months and are designed to lead toward a sustained national infrastructure for pragmatic trials.
PMCID: PMC4126802  PMID: 24472114
trials; translational research; ethics; methodology
5.  Neurobiology of secure infant attachment and attachment despite adversity: a mouse model 
Genes, brain, and behavior  2013;12(7):673-680.
Attachment to an abusive caregiver has wide phylogenetic representation, suggesting that animal models are useful in understanding the neural basis underlying this phenomenon and subsequent behavioral outcomes. We previously developed a rat model, in which we use classical conditioning to parallel learning processes evoked during secure attachment (odor-stroke, with stroke mimicking tactile stimulation from the caregiver) or attachment despite adversity (odor-shock, with shock mimicking maltreatment). Here we extend this model to mice. We conditioned infant mice (postnatal day (PN) 7–9 or 13–14) with presentations of peppermint odor and either stroking or shock. We used 14C 2-deoxyglucose (2-DG) to assess olfactory bulb and amygdala metabolic changes following learning. PN7-9 mice learned to prefer an odor following either odor-stroke or shock conditioning, whereas odor-shock conditioning at PN13-14 resulted in aversion/fear learning. 2-DG data indicated enhanced bulbar activity in PN7-9 preference learning, whereas significant amygdala activity was present following aversion learning at PN13-14. Overall, the mouse results parallel behavioral and neural results in the rat model of attachment, and provide the foundation for the use of transgenic and knockout models to assess the impact of both genetic (biological vulnerabilities) and environmental factors (abusive) on attachment-related behaviors and behavioral development.
PMCID: PMC4047794  PMID: 23927771
Animal model; attachment; infant; learning; maltreatment; memory
6.  Expression of steroid receptor coactivator 3 in ovarian epithelial cancer is a poor prognostic factor and a marker for platinum resistance 
British Journal of Cancer  2013;108(10):2039-2044.
Steroid receptor coactivator 3 (SRC3) is an important coactivator of a number of transcription factors and is associated with a poor outcome in numerous tumours. Steroid receptor coactivator 3 is amplified in 25% of epithelial ovarian cancers (EOCs) and its expression is higher in EOCs compared with non-malignant tissue. No data is currently available with regard to the expression of SRC-3 in EOC and its influence on outcome or the efficacy of treatment.
Immunohistochemistry was performed for SRC3, oestrogen receptor-α, HER2, PAX2 and PAR6, and protein expression was quantified using automated quantitative immunofluorescence (AQUA) in 471 EOCs treated between 1991 and 2006 with cytoreductive surgery followed by first-line treatment platinum-based therapy, with or without a taxane.
Steroid receptor coactivator 3 expression was significantly associated with advanced stage and was an independent prognostic marker. High expression of SRC3 identified patients who have a significantly poorer survival with single-agent carboplatin chemotherapy, while with carboplatin/paclitaxel treatment such a difference was not seen.
Steroid receptor coactivator 3 is a poor prognostic factor in EOCs and appears to identify a population of patients who would benefit from the addition of taxanes to their chemotherapy regimen, due to intrinsic resistance to platinum therapy.
PMCID: PMC3670494  PMID: 23652306
ovarian cancer; SRC3; platinum; resistance
7.  Novel Fastidious, Partially Acid-Fast, Anaerobic Gram-Positive Bacillus Associated with Abscess Formation and Recovered from Multiple Medical Centers 
Journal of Clinical Microbiology  2013;51(11):3903-3907.
We report a novel anaerobe causing abscess in four patients at three hospitals. In the clinical specimen, bacilli were branching, Gram positive, and acid fast. The organism grew slowly and was not identified by 16S rRNA sequencing. Our findings support the description of a new genus and species of the suborder Corynebacterineae.
PMCID: PMC3889796  PMID: 24025902
8.  Prognostic and predictive value of VEGF, sVEGFR-2 and CEA in mCRC studies comparing cediranib, bevacizumab and chemotherapy 
British Journal of Cancer  2013;108(6):1316-1323.
The prognostic/predictive value of potential vascular endothelial growth factor (VEGF) signalling biomarkers was evaluated retrospectively using samples from two randomized Phase III studies (HORIZON II and III) investigating cediranib in metastatic colorectal cancer (mCRC).
Baseline levels of VEGF, soluble VEGF receptor-2 (sVEGFR-2) and carcinoembryonic antigen (CEA) were measured in plasma/serum samples collected from patients participating in HORIZON II (n=860; FOLFOX/XELOX plus cediranib 20 mg (n=502) or placebo (n=358)) and HORIZON III (n=1422; mFOLFOX6 plus cediranib 20 mg (n=709) or bevacizumab (n=713)). Median biomarker baseline levels determined cutoff values for the patient subgroups.
Baseline data were available for 88–97% of patients/study (>2000 patients). In both the studies, high baseline VEGF and CEA were associated with worse outcomes for progression-free survival (PFS) and overall survival (OS) independent of treatment (HORIZON II OS: VEGF, hazard ratio (HR)=1.35 (95% confidence interval (CI): 1.12–1.63); CEA, HR=1.63 (1.36–1.96); HORIZON III OS: VEGF, HR=1.32 (1.12–1.54); CEA, HR=1.50 (1.29–1.76)). sVEGFR-2 was not prognostic for PFS/OS. Baseline VEGF and CEA were not predictive for PFS/OS outcome to cediranib treatment; low sVEGFR-2 was associated with a trend towards improved cediranib effect in HORIZON II.
Baseline VEGF and CEA levels were treatment-independent prognostic biomarkers for PFS and OS in both the studies.
PMCID: PMC3619270  PMID: 23449351
colorectal; cediranib; bevacizumab; VEGF; biomarkers
9.  Prediction of Staphylococcus aureus Antimicrobial Resistance by Whole-Genome Sequencing 
Journal of Clinical Microbiology  2014;52(4):1182-1191.
Whole-genome sequencing (WGS) could potentially provide a single platform for extracting all the information required to predict an organism's phenotype. However, its ability to provide accurate predictions has not yet been demonstrated in large independent studies of specific organisms. In this study, we aimed to develop a genotypic prediction method for antimicrobial susceptibilities. The whole genomes of 501 unrelated Staphylococcus aureus isolates were sequenced, and the assembled genomes were interrogated using BLASTn for a panel of known resistance determinants (chromosomal mutations and genes carried on plasmids). Results were compared with phenotypic susceptibility testing for 12 commonly used antimicrobial agents (penicillin, methicillin, erythromycin, clindamycin, tetracycline, ciprofloxacin, vancomycin, trimethoprim, gentamicin, fusidic acid, rifampin, and mupirocin) performed by the routine clinical laboratory. We investigated discrepancies by repeat susceptibility testing and manual inspection of the sequences and used this information to optimize the resistance determinant panel and BLASTn algorithm. We then tested performance of the optimized tool in an independent validation set of 491 unrelated isolates, with phenotypic results obtained in duplicate by automated broth dilution (BD Phoenix) and disc diffusion. In the validation set, the overall sensitivity and specificity of the genomic prediction method were 0.97 (95% confidence interval [95% CI], 0.95 to 0.98) and 0.99 (95% CI, 0.99 to 1), respectively, compared to standard susceptibility testing methods. The very major error rate was 0.5%, and the major error rate was 0.7%. WGS was as sensitive and specific as routine antimicrobial susceptibility testing methods. WGS is a promising alternative to culture methods for resistance prediction in S. aureus and ultimately other major bacterial pathogens.
PMCID: PMC3993491  PMID: 24501024
10.  Use of low-dose CT KUB: is it becoming the easy way out? 
Critical Care  2014;18(Suppl 1):P85.
PMCID: PMC4068828
11.  Healthcare-associated outbreak of meticillin-resistant Staphylococcus aureus bacteraemia: role of a cryptic variant of an epidemic clone☆ 
New strains of meticillin-resistant Staphylococcus aureus (MRSA) may be associated with changes in rates of disease or clinical presentation. Conventional typing techniques may not detect new clonal variants that underlie changes in epidemiology or clinical phenotype.
To investigate the role of clonal variants of MRSA in an outbreak of MRSA bacteraemia at a hospital in England.
Bacteraemia isolates of the major UK lineages (EMRSA-15 and -16) from before and after the outbreak were analysed by whole-genome sequencing in the context of epidemiological and clinical data. For comparison, EMRSA-15 and -16 isolates from another hospital in England were sequenced. A clonal variant of EMRSA-16 was identified at the outbreak hospital and a molecular signature test designed to distinguish variant isolates among further EMRSA-16 strains.
By whole-genome sequencing, EMRSA-16 isolates during the outbreak showed strikingly low genetic diversity (P < 1 × 10−6, Monte Carlo test), compared with EMRSA-15 and EMRSA-16 isolates from before the outbreak or the comparator hospital, demonstrating the emergence of a clonal variant. The variant was indistinguishable from the ancestral strain by conventional typing. This clonal variant accounted for 64/72 (89%) of EMRSA-16 bacteraemia isolates at the outbreak hospital from 2006.
Evolutionary changes in epidemic MRSA strains not detected by conventional typing may be associated with changes in disease epidemiology. Rapid and affordable technologies for whole-genome sequencing are becoming available with the potential to identify and track the emergence of variants of highly clonal organisms.
PMCID: PMC3924019  PMID: 24433924
Bacteraemia; Meticillin-resistant Staphylococcus aureus; Outbreak; Whole-genome sequencing
12.  3-Dimensional Imaging Modalities for Phenotyping Genetically Engineered Mice 
Veterinary pathology  2011;49(1):10.1177/0300985811429814.
A variety of 3-dimensional (3D) digital imaging modalities are available for whole-body assessment of genetically engineered mice: magnetic resonance microscopy (MRM), X-ray microcomputed tomography (microCT), optical projection tomography (OPT), episcopic and cryoimaging, and ultrasound biomicroscopy (UBM). Embryo and adult mouse phenotyping can be accomplished at microscopy or near microscopy spatial resolutions using these modalities. MRM and microCT are particularly well-suited for evaluating structural information at the organ level, whereas episcopic and OPT imaging provide structural and functional information from molecular fluorescence imaging at the cellular level. UBM can be used to monitor embryonic development longitudinally in utero. Specimens are not significantly altered during preparation, and structures can be viewed in their native orientations. Technologies for rapid automated data acquisition and high-throughput phenotyping have been developed and continually improve as this exciting field evolves.
PMCID: PMC3857693  PMID: 22146851
mouse phenotyping; imaging; mouse embryo; MRM; UBM; OPT; microCT; cryoimaging
13.  Radiation-induced cancer: a modern view 
The British Journal of Radiology  2012;85(1020):e1166-e1173.
Diagnostic medical radiation has been the most rapidly increasing component of population background radiation exposure in Western countries over the past decade. This trend is set to increase as CT scanning is readily available with burgeoning use in everyday clinical practice. Consequently, the issue of cancer induction from the doses received during diagnostic medical exposures is highly relevant. In this review we explain current understanding of potential cancer induction at low doses of sparsely ionising radiation. For cancers that may be induced at low doses, a mechanistic description of radiation-induced cancer is discussed, which, in combination with extrapolation of data based on population cohort studies, provides the basis of the currently accepted linear no-threshold model. We explore the assumptions made in deriving risk estimates, the controversies surrounding the linear no-threshold model and the potential future challenges facing clinicians and policy-makers with regards to diagnostic medical radiation and cancer risk, most notably the uncertainties regarding deriving risk estimates from epidemiological data at low doses.
PMCID: PMC3611719  PMID: 23175483
14.  Ultrasound elastography for musculoskeletal applications 
The British Journal of Radiology  2012;85(1019):1435-1445.
Ultrasound elastography (EUS) is a method to assess the mechanical properties of tissue, by applying stress and detecting tissue displacement using ultrasound. There are several EUS techniques used in clinical practice; strain (compression) EUS is the most common technique that allows real-time visualisation of the elastographic map on the screen. There is increasing evidence that EUS can be used to measure the mechanical properties of musculoskeletal tissue in clinical practice, with the future potential for early diagnosis to both guide and monitor therapy. This review describes the various EUS techniques available for clinical use, presents the published evidence on musculoskeletal applications of EUS and discusses the technical issues, limitations and future perspectives of this method in the assessment of the musculoskeletal system.
PMCID: PMC3500785  PMID: 23091287
15.  Evaluation of image reconstruction for mouse brain imaging with synthetic collimation from highly multiplexed SiliSPECT projections 
Physics in medicine and biology  2010;55(17):10.1088/0031-9155/55/17/017.
We have performed a theoretical study to explore the potential and limitations of synthetic collimation for SPECT imaging with stacked detector acquisition (dual magnification). This study will be used to optimize SiliSPECT, a small-animal SPECT for imaging small volumes such as mouse brain at high sensitivity and resolution. The synthetic collimation enables image reconstruction with a limited number of camera views and in the presence of significant multiplexing. We also developed a new formulation to quantify the multiplexed object sensitivity and investigated how this changes for different acquisition parameters such as number of pinholes and combinations of front and back detector distances for imaging objects as large as a mouse brain. In our theoretical studies, we were not only able to demonstrate better reconstruction results by incorporating two detector magnifications in comparison to either alone, but also observed an improved image reconstruction by optimizing the detector-collimator distances to change the multiplexing ratio between the front and back detectors.
PMCID: PMC3808864  PMID: 20714046
16.  Self-assembling nanoparticles for intra-articular delivery of anti-inflammatory proteins 
Biomaterials  2012;33(30):7665-7675.
Intra-articular delivery of therapeutics to modulate osteoarthritis (OA) is challenging. Delivery of interleukin-1 receptor antagonist (IL-1Ra), the natural protein inhibitor of IL-1, to modulate IL-1-based inflammation through gene therapy or bolus protein injections has emerged as a promising therapy for OA. However, these approaches suffer from rapid clearance and reduced potency over time. Nano/microparticles represent a promising strategy for overcoming the shortcomings of intra-articular drug delivery. However, these delivery vehicles are limited for delivery of protein therapeutics due to their hydrophobic character, low drug loading efficiency, and harsh chemical conditions during particle processing. We designed a new block copolymer that assembles into submicron-scale particles and provides for covalently tethering proteins to the particle surface for controlled intra-articular protein delivery. This block copolymer self-assembles into 300 nm-diameter particles with a protein-tethering moiety for surface covalent conjugation of IL-1Ra protein. This copolymer particle system efficiently bound IL-1Ra and maintained protein bioactivity in vitro. Furthermore, particle-tethered IL-1Ra bound specifically to target synoviocyte cells via surface IL-1 receptors. Importantly, IL-1Ra-nanoparticles inhibited IL-1-mediated signaling to equivalent levels as soluble IL-1Ra. Finally, the ability of nanoparticles to retain IL-1Ra in the rat stifle joint was evaluated by in vivo imaging over 14 days. IL-1Ra-tethered nanoparticles significantly increased the retention time of IL-1Ra in the rat stifle joint over 14 days with enhanced IL-1Ra half-life (3.01 days) compared to that of soluble IL-1Ra (0.96 days) and without inducing degenerative changes in cartilage structure or composition.
PMCID: PMC3418443  PMID: 22818981
IL-1Ra; nanoparticles; block copolymer; RAFT polymerization; osteoarthritis; drug delivery
17.  Complex Mixture Discrimination and the Role of Contaminants 
Chemical Senses  2012;37(6):533-540.
Rats were trained in a 2-alternative odor choice task to discriminate between a 10-component odor mixture and the same mixture with one component removed and replaced with 1 of 3 concentrations of a different monomolecular odor (contaminant). All stimuli were presented within a training session, thus the rat essentially had to learn to discriminate the 10-component mixture from “not” the 10-component mixture. Rats performed most poorly discriminating the complete mixture from the mixture with one component removed and no contaminant added. As the concentration of the contaminant increased from 10 ppm to a concentration equal to the other components (100 ppm), discrimination improved linearly. In analyses of individual differences, rats that spent more time in the sampling port (sampling and making a decision) were more accurate than rats that spent less time. Together, these results emphasize the balance between perceptual stability and perceptual discrimination expressed by the olfactory system dealing with dynamic mixtures and the robust effects of contamination on those processes. In addition, they provide further support that modification of sampling/decision time is a strategy used by rats to deal with difficult discriminations of complex odors.
PMCID: PMC3529621  PMID: 22354907
odor object; odor mixture; odor sampling; pattern completion; sniffing; speed-accuracy trade-off
18.  Using tablet computers compared to interactive voice response to improve subject recruitment in osteoporosis pragmatic clinical trials: feasibility, satisfaction, and sample size 
Pragmatic clinical trials (PCTs) provide large sample sizes and enhanced generalizability to assess therapeutic effectiveness, but efficient patient enrollment procedures are a challenge, especially for community physicians. Advances in technology may improve methods of patient recruitment and screening in PCTs. Our study looked at a tablet computer versus an integrated voice response system (IVRS) for patient recruitment and screening for an osteoporosis PCT in community physician offices.
Materials and methods
We recruited women ≥ 65 years of age from community physician offices to answer screening questions for a hypothetical osteoporosis active comparator PCT using a tablet computer or IVRS. We assessed the feasibility of these technologies for patient recruitment as well as for patient, physician, and office staff satisfaction with the process. We also evaluated the implications of these novel recruitment processes in determining the number of primary care practices and screened patients needed to conduct the proposed trial.
A total of 160 women (80% of those approached) agreed to complete the osteoporosis screening questions in ten family physicians’ offices. Women using the tablet computer were able to complete all screening questions consistently and showed a nonsignificant trend towards greater ease of use and willingness to spend more time in their physician’s office compared to those using IVRS. Using the proportion of women found to be eligible in this study (almost 20%) and other eligibility scenarios, we determined that between 240 and 670 community physician offices would be needed to recruit ample patients for our hypothetical study.
We found good satisfaction and feasibility with a tablet computer interface for the recruitment and screening of patients for a hypothetical osteoporosis PCT in community office settings. In addition, we used this experience to estimate the number of research sites needed for such a study.
PMCID: PMC3685447  PMID: 23807841
osteoporosis; clinical trial; pragmatic clinical trials; computer applications
19.  Should Varicella-Zoster Virus Culture Be Eliminated? A Comparison of Direct Immunofluorescence Antigen Detection, Culture, and PCR, with a Historical Review 
Journal of Clinical Microbiology  2012;50(12):4120-4122.
A comparison of direct fluorescent-antibody assay (DFA), culture, and two PCR assays disclosed sensitivities of 87.8%, 46.3%, and 97.6% and 100%, respectively. We reviewed 1,150 results for clinical specimens submitted for DFA and culture and found that only 17 were culture positive/DFA negative. The incremental cost to detect these 17 positives was $3,078/specimen.
PMCID: PMC3502980  PMID: 23035203
20.  Three-Dimensional Dynamic Bone Histomorphometry 
Dynamic bone histomorphometry is the standard method for measuring bone remodeling at the level of individual events. While dynamic bone histomorphometry is an invaluable tool for understanding osteoporosis and other metabolic bone diseases, the technique’s two-dimensional nature requires the use of stereology and prevents measures of individual remodeling event number and size. Here, we use a novel three-dimensional fluorescence imaging technique to achieve measures of individual resorption cavities and formation events. We perform this three-dimensional histomorphometry approach using a common model of postmenopausal osteoporosis, the ovariectomized rat. The three-dimensional images demonstrate the spatial relationship between resorption cavities and formation events consistent with the hemi-osteonal model of cancellous bone remodeling. Established ovariectomy was associated with significant increases in the number of resorption cavities per unit bone surface (2.38 ± 0.24 mm−2 SHAM v. 3.86 ± 0.35 mm−2 OVX, mean ± SD, p < 0.05) and total volume occupied by cavities per unit bone volume (0.38 ± 0.06% SHAM v. 1.12 ± 0.18% OVX, p < 0.001), but no difference in surface area per resorption cavity, maximum cavity depth, or cavity volume. Additionally, we find that established ovariectomy is associated with increased size of bone formation events due to merging of formation events (23,700 ± 6,890 μm2 SHAM v. 33,300 ± 7,950 μm2 OVX). No differences in mineral apposition rate (determined in 3D) were associated with established ovariectomy. That established estrogen depletion is associated with increased number of remodeling events with only subtle changes in remodeling event size suggests that circulating estrogens may have their primary effect on the origination of new basic multicellular units with relatively little effect on the progression and termination of active remodeling events.
PMCID: PMC3288521  PMID: 22028195
Bone histomorphometry; Bone Remodeling; Osteoporosis; Ovariectomy; Rodent
21.  Fifth-Generation Digital Immunoassay for Prostate Specific Antigen Using Single Molecule Arrays 
Clinical Chemistry  2011;57(12):1712-1721.
Measurement of prostate specific antigen (PSA) in prostate cancer patients following radical prostatectomy (RP) has been limited by the sensitivity of available assays. Because radical prostatectomy removes the tissue responsible for PSA production, post-surgical PSA is typically undetectable with current assay methods. However, evidence suggests that more sensitive determination of PSA status following RP could improve assessment of patient prognosis, response to treatment, and better target secondary therapy to those who may benefit most. We report the development and validation of an investigational digital immunoassay with two logs greater sensitivity than today’s ultrasensitive third-generation PSA assays.
Reagents were developed for a paramagnetic bead-based ELISA for use with high-density arrays of femtoliter-volume wells. Anti-PSA capture-beads with immunocomplexes and associated enzyme labels were singulated within the wells of the arrays and interrogated for the presence of enzymatic product. Analytical performance of the assay was characterized, its accuracy compared with a commercially available test, and longitudinal serum samples from a pilot study of 33 RP patients were analyzed.
The assay exhibited a functional sensitivity (20% inter-assay CV) of less than 0.00005 ng/mL (0.05 pg/mL), total imprecision of less than 10% from 1 to 50 pg/mL, and excellent agreement with the comparator method. All RP samples were well within the assay measurement capability. PSA values following surgery were examined in the context of five-year biochemical cancer recurrence.
The assay demonstrated a robust two-log advance in measurement sensitivity relative to current ultrasensitive assays, and the analytical performance for accurate assessment of PSA status after RP.
PMCID: PMC3402036  PMID: 21998342
22.  Currently available medications may not be sufficient for lifelong treatment of HIV 
Purpose of the study
Combination antiretroviral therapy (cART) has greatly improved the life expectancy of people living with HIV (PLHIV). A series of cohort studies have predicted near-to-normal life expectancies for PLHIV receiving cART but have not considered the impact of multi-class resistance on long-term survival. Our study aims to project the future life expectancy of PLHIV in a resource-rich setting in the context of the currently available antiretroviral treatments.
Patient antiretroviral treatment data, including time on each regimen until treatment failure, were sourced from an observational cohort of 3434 predominantly male (94.2%) PLHIV in Australia over the period 1997 to 2010. These data were analyzed in an individual-based mathematical model to calculate the time until exhaustion of all treatment options and the expected impact on HIV-associated mortality. Standardized mortality ratios were used to simulate expected survival before and after treatment exhaustion.
Summary of results
The model estimated that the median time until exhaustion of currently available treatment options is 43.4 years (interquartile range = 31.4 to 58.6 years). However, the model predicts that 10% of PLHIV will use up all currently available cART options after just 22.6 years. The figure shows the survival proportions of males from age 20 years in four mortality scenarios: (1) the general population mortality rate; (2) the mortality rate in PLHIV as currently measured (without considering exhaustion of currently available treatments); (3) mortality rate in PLHIV considering additional mortality due to limited cART options; and (4) mortality rate if no cART is available. PLHIV who start currently available cART regimens at age 20 years are expected to live to a median of 64.7 (95% uncertainty bound (UB) = 61.8 to 69.3) years of age, when adjusting for treatment option exhaustion. This is a substantial improvement on no cART (median survival to 27.6 [95% UB = 27.2 to 28.1] years of age) but is lower than the expected life expectancy (82.2 years of age) of an HIV-negative male in the general population. The gap between life expectancy among PLHIV and the general population is greater for those infected at younger ages.
As treatment options are exhausted in the coming years, a substantial difference in life expectancy between PLHIV and the general population is expected, particularly for people who acquire HIV at a younger age or who are currently highly treatment-experienced.
PMCID: PMC3512450
23.  Breast MRI quality assurance in practice 
Breast Cancer Research : BCR  2012;14(Suppl 1):P58.
PMCID: PMC3542689
24.  The Synthesis and characterization of SIRT6 protein coated magnetic beads: Identification of a novel inhibitor of SIRT6 deacetylase from medicinal plant extracts 
Analytical chemistry  2011;83(19):7400-7407.
SIRT6 is a histone deacetylase that has been proposed as a potential therapeutic target for metabolic disorders and the prevention of age-associated diseases. Thus the identification of compounds that modulate SIRT6 activity could be of great therapeutic importance. The aim of this study was to develop a screening method for the identification of novel modulators of SIRT6 from a natural plant extract. We immobilized SIRT6 onto the surface of magnetic beads, and assessed SIRT6 enzymatic activity on synthetic acetylated histone tails (H3K9Ac) by measuring products of the deacetylation process. The SIRT6 coated magnetic beads were then suspended in fenugreek seed extract (Trigonella foenumgraecum) as a bait to identify active ligands suppressing SIRT6 activity. While the whole extract also inhibited SIRT6 activity in a cell-based assay, the inhibitory effect of two flavonoids from this extract, quercetin and vitexin, was only detected in vitro. This is the first report for the use of protein-coated magnetic beads for the identification of an active ligand from a botanical matrix, and sets the basis for the de novo identification of SIRT6 modulators from complex biological mixtures.
PMCID: PMC3197717  PMID: 21854049
25.  State-dependent functional connectivity of rat olfactory system assessed by fMRI 
Neuroscience letters  2011;497(2):69-73.
Functional connectivity between the piriform cortex and limbic and neocortical areas was assessed using functional magnetic resonance imaging (fMRI) of urethane anesthetized rats that spontaneously cycled between slow-wave and fast-wave states. Slow-wave and fast-wave states were determined indirectly through monitoring of respiration rate, which was confirmed to co-vary with state as determined by electrophysiological recordings. Previous electrophysiological data have suggested that the piriform cortex shifts between responsiveness to afferent odor input during fast-wave states and enhanced functional connectivity with limbic areas during slow-wave state. The present results demonstrate that fMRI-based resting state functional connectivity between the piriform cortex and both limbic and neocortical areas is enhanced during slow-wave state compared to fast-wave state using respiration as an indirect measure of state in urethane anesthetized rats. This state-dependent shift in functional connectivity may be important for sleep-dependent odor memory consolidation.
PMCID: PMC3103633  PMID: 21530613
piriform cortex; slow-wave sleep; functional magnetic resonance imaging; resting state; hippocampus; amygdala; memory consolidation

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