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1.  Uterine artery embolization immediately preceding laparoscopic myomectomy 
To determine whether performing uterine artery embolization (UAE) immediately before laparoscopic myomectomy can facilitate a minimally invasive surgical approach for larger uterine fibroids.
In a retrospective case–control study, laparoscopic myomectomy with and without preoperative UAE was examined. Data were analyzed from 26 laparoscopic myomectomies performed by a single surgeon at Northwestern University Feinberg School of Medicine between 2004 and 2010. Controls were matched for age, calendar year, surgeon, and number of fibroids removed. Surgical outcomes included preoperative clinical uterine size, operative time, operative blood loss, and postoperative myoma specimen weight. Data were analyzed via 2-tailed Student t test.
Twelve women underwent laparoscopic myomectomy within 169±16 minutes (mean±SEM) of preoperative UAE. Fourteen control patients underwent laparoscopic myomectomy alone. The UAE group had a greater mean preoperative clinical uterine size (19.7 versus 12.4 weeks, P<0.001) and a greater mean myoma specimen weight measured postoperatively (595.3 versus 153.6 grams, P<0.05). There were no significant differences in operative time or blood loss, and there were no intra-operative complications.
UAE performed immediately before laparoscopic myomectomy facilitated minimally invasive surgery for larger uteri and larger uterine myomas, with no differences in operative time or blood loss.
PMCID: PMC4034570  PMID: 22098788
Laparoscopy; Uterine artery embolization; Uterine leiomyomata
2.  Interannual variability in the timing of New England shellfish toxicity and relationships to environmental forcing 
Routine monitoring along the coast of the Gulf of Maine (GoM) reveals shellfish toxicity nearly every summer, but at varying times, locations, and magnitudes. The responsible toxin is known to be produced by the dinoflagellate Alexandrium fundyense, yet there is little apparent association between Alexandrium abundance and shellfish toxicity. One possibility is that toxic cells are persistent in offshore areas and variability in shellfish toxicity is caused not by changes in overall abundance, but rather by variability in transport processes. Measurements of offshore Alexandrium biomass are scarce, so we bypass cell abundance as an explanatory variable and focus instead on the relations between shellfish toxicity and concurrent metrics of GoM meteorology, hydrology, and oceanography. While this yields over two decades (1985–2005) of data representing a variety of interannual conditions, the toxicity data are gappy in spatial and temporal coverage. We address this through a combination of parametric curve fitting and hierarchical cluster analysis to reveal eight archetypical modes of seasonal toxicity timing. Groups of locations are then formed that have similar interannual patterns in these archetypes. Finally, the interannual patterns within each group are related to available environmental metrics using classification trees. Results indicate that a weak cross-shore sea surface temperature (SST) gradient in the summer is the strongest correlate of shellfish toxicity, likely by signifying a hydrological connection between offshore Alexandrium populations and near-shore shellfish beds. High cumulative downwelling wind strength early in the season is revealed as a precursor consistent with this mechanism. Although previous studies suggest that alongshore transport is important in moving Alexandrium from the eastern to western GoM, alongshore SST gradient is not an important correlate of toxicity in our study. We conclude by discussing the implications of our results for designing efficient and effective shellfish monitoring programs along the GoM coast.
PMCID: PMC3586711  PMID: 23391892
harmful algal blooms; red tides; paralytic shellfish poisoning; cluster analysis; CART modeling; satellite remote sensing
3.  Impact of grazing intensity on seasonal variations in soil organic carbon and soil CO2 efflux in two semiarid grasslands in southern Botswana 
Biological soil crusts (BSCs) are an important source of organic carbon, and affect a range of ecosystem functions in arid and semiarid environments. Yet the impact of grazing disturbance on crust properties and soil CO2 efflux remain poorly studied, particularly in African ecosystems. The effects of burial under wind-blown sand, disaggregation and removal of BSCs on seasonal variations in soil CO2 efflux, soil organic carbon, chlorophyll a and scytonemin were investigated at two sites in the Kalahari of southern Botswana. Field experiments were employed to isolate CO2 efflux originating from BSCs in order to estimate the C exchange within the crust. Organic carbon was not evenly distributed through the soil profile but concentrated in the BSC. Soil CO2 efflux was higher in Kalahari Sand than in calcrete soils, but rates varied significantly with seasonal changes in moisture and temperature. BSCs at both sites were a small net sink of C to the soil. Soil CO2 efflux was significantly higher in sand soils where the BSC was removed, and on calcrete where the BSC was buried under sand. The BSC removal and burial under sand also significantly reduced chlorophyll a, organic carbon and scytonemin. Disaggregation of the soil crust, however, led to increases in chlorophyll a and organic carbon. The data confirm the importance of BSCs for C cycling in drylands and indicate intensive grazing, which destroys BSCs through trampling and burial, will adversely affect C sequestration and storage. Managed grazing, where soil surfaces are only lightly disturbed, would help maintain a positive carbon balance in African drylands.
PMCID: PMC3479694  PMID: 23045706
biological soil crusts; soil CO2 efflux; grazing; soil organic carbon
4.  A Quality Assurance Method that Utilizes 3D Dosimetry and Facilitates Clinical Interpretation 
International journal of radiation oncology, biology, physics  2012;84(2):10.1016/j.ijrobp.2011.12.015.
To demonstrate a new three-dimensional (3D) quality assurance (QA) method that provides comprehensive dosimetry verification and facilitates evaluation of the clinical significance of QA data acquired in a phantom. Also to apply the method to investigate the dosimetric efficacy of base-of-skull (BOS) intensity-modulated radiotherapy (IMRT) treatment.
Methods and Materials
Two types of IMRT QA verification plans were created for 6 patients who received BOS IMRT. The first plan enabled conventional 2D planar IMRT QA using the Varian portal dosimetry system. The second plan enabled 3D verification using an anthropomorphic head phantom. In the latter, the 3D dose distribution was measured using the DLOS/Presage dosimetry system (DLOS = Duke Large-field-of-view Optical-CT System, Presage Heuris Pharma, Skillman, NJ), which yielded isotropic 2-mm data throughout the treated volume. In a novel step, measured 3D dose distributions were transformed back to the patient’s CT to enable calculation of dose–volume histograms (DVH) and dose overlays. Measured and planned patient DVHs were compared to investigate clinical significance.
Close agreement between measured and calculated dose distributions was observed for all 6 cases. For gamma criteria of 3%, 2 mm, the mean passing rate for portal dosimetry was 96.8% (range, 92.0%–98.9%), compared to 94.9% (range, 90.1%–98.9%) for 3D. There was no clear correlation between 2D and 3D passing rates. Planned and measured dose distributions were evaluated on the patient’s anatomy, using DVH and dose overlays. Minor deviations were detected, and the clinical significance of these are presented and discussed.
Two advantages accrue to the methods presented here. First, treatment accuracy is evaluated throughout the whole treated volume, yielding comprehensive verification. Second, the clinical significance of any deviations can be assessed through the generation of DVH curves and dose overlays on the patient’s anatomy. The latter step represents an important development that advances the clinical relevance of complex treatment QA.
PMCID: PMC3832997  PMID: 22361085
3D dosimetry; IMRT; Quality assurance; Treatment verification
5.  Functional mechanotransduction is required for cisplatin-induced hair cell death in the zebrafish lateral line 
Cisplatin, one of the most commonly used anti-cancer drugs, is known to cause inner ear hair cell damage and hearing loss. Despite much investigation into mechanisms of cisplatin-induced hair cell death, little is known about the mechanism whereby cisplatin is selectively toxic to hair cells. Using hair cells of the zebrafish lateral line, we found that chemical inhibition of mechanotransduction with quinine and EGTA protected against cisplatin-induced hair cell death. Furthermore, we found that the zebrafish mutants mariner (myo7aa) and sputnik (cad23) that lack functional mechanotransduction were resistant to cisplatin-induced hair cell death. Using a fluorescent analogue of cisplatin, we found that chemical or genetic inhibition of mechanotransduction prevented its uptake. These findings demonstrate that cisplatin-induced hair cell death is dependent on functional mechanotransduction in the zebrafish lateral line.
PMCID: PMC3666553  PMID: 23467357
6.  Purkinje cell dysfunction and delayed death in plasma membrane calcium ATPase 2-heterozygous mice 
Purkinje cell (PC) dysfunction or death have been implicated in a number of disorders including ataxia, autism and multiple sclerosis. Plasma membrane calcium ATPase 2 (PMCA2), an important calcium (Ca2+) extrusion pump that interacts with synaptic signaling complexes, is most abundantly expressed in PCs compared to other neurons. Using the PMCA2 heterozygous mouse as a model, we investigated whether a reduction in PMCA2 levels affects PC function. We focused on Ca2+ signaling and the expression of glutamate receptors which play a key role in PC function including synaptic plasticity. We found that the amplitude of depolarization and 2-amino-3-(5-methyl-3-oxo-1,2-oxazol-4-yl)propanoic acid receptor (AMPAR)-mediated Ca2+ transients is significantly higher in cultured PMCA2+/− PCs than in PMCA2+/+ PCs. This is due to increased Ca2+ influx, since P/Q type voltage-gated Ca2+ channel (VGCC) expression was more pronounced in PCs and cerebella of PMCA2+/− mice and VGCC blockade prevented the elevation in amplitude. Neuronal nitric oxide synthase (nNOS) activity was higher in PMCA2+/−cerebella and inhibition of nNOS or the soluble guanylate cyclase (sGC)-cyclic guanosine monophosphate (cGMP) pathway, which mediates nitric oxide (NO) signaling, reduced the amplitude of Ca2+ transients in PMCA2+/− PCs, in vitro. In addition, there was an age-dependent decrease in metabotropic glutamate receptor 1 (mGluR1) and AMPA receptor subunit GluR2/3 transcript and protein levels at 8 weeks of age. These changes were followed by PC loss in the 20-week-old PMCA2+/− mice. Our studies highlight the importance of PMCA2 in Ca2+ signaling, glutamate receptor expression and survival of Purkinje cells.
PMCID: PMC3436994  PMID: 22789621
Ataxia; autism; neurodegeneration; glutamate; AMPA; calcium channel; ion pump; nitric oxide
7.  Calcium-Dependent Physiologic and Pathologic Stimulus-Metabolic Response Coupling in Hepatocytes 
Cell Calcium  2012;52(1):93-102.
A recurrent paradigm in calcium signaling is the coordination of the target response of the calcium signal with activation of metabolic energy production to support that response. This occurs in many tissues, including cardiac and skeletal muscle where contractile activity and ATP production are coordinately regulated by the frequency and amplitude of calcium transients, endocrine and exocrine cells that use calcium to drive the secretory process, and hepatocytes where the downstream targets of calcium include both catabolic and anabolic processes. The primary mechanism by which calcium enhances the capacity for energy production is through calcium-dependent stimulation of mitochondrial oxidative metabolism, achieved by increasing NADH production and respiratory chain flux. Although this enhances energy supply, it also has the potential for deleterious consequences resulting from increased generation of reactive oxygen species (ROS). The negative consequences of calcium-dependent mitochondrial activation can be ameliorated when the underlying cytosolic calcium signals occur as brief calcium spikes or oscillations, with signal strength encoded through the spike frequency (frequency modulation). Frequency modulation increases signal fidelity, and reduces pathological effects of calcium, including excess mitochondrial ROS production and apoptotic or necrotic outcomes. The present article reviews these issues using data obtained in hepatocytes under physiologic and pathologic conditions.
PMCID: PMC3391328  PMID: 22564906
8.  Homophily and Contagion Are Generically Confounded in Observational Social Network Studies 
Sociological methods & research  2011;40(2):211-239.
The authors consider processes on social networks that can potentially involve three factors: homophily, or the formation of social ties due to matching individual traits; social contagion, also known as social influence; and the causal effect of an individual’s covariates on his or her behavior or other measurable responses. The authors show that generically, all of these are confounded with each other. Distinguishing them from one another requires strong assumptions on the parametrization of the social process or on the adequacy of the covariates used (or both). In particular the authors demonstrate, with simple examples, that asymmetries in regression coefficients cannot identify causal effects and that very simple models of imitation (a form of social contagion) can produce substantial correlations between an individual’s enduring traits and his or her choices, even when there is no intrinsic affinity between them. The authors also suggest some possible constructive responses to these results.
PMCID: PMC3328971  PMID: 22523436
contagion; social influence; homophily; causal inference; network confounding; neutral models
9.  Use of thermal melt curves to assess the quality of enzyme preparations1 
Analytical Biochemistry  2009;399(2):268-275.
This study sought to determine whether the quality of enzyme preparations can be determined from their melting curves, which may easily be obtained using a fluorescent probe and a standard RT-PCR machine. Thermal melt data on 31 recombinant enzymes from Plasmodium parasites were acquired by incrementally heating them to 90 °C and measuring unfolding with a fluorescent dye; activity assays specific to each enzyme were also performed. Four of the enzymes were denatured to varying degrees with heat and SDS prior to the thermal melt and activity assays. In general, melting curve quality correlated with enzyme activity; enzymes with high-quality curves were found almost uniformly to be active, while those with lower-quality curves were more varied in their catalytic performance. Inspection of melting curves of bovine xanthine oxidase and Entamoeba histolytica cysteine protease 1 allowed active stocks to be distinguished from inactive stocks, implying that a relationship between melting curve quality and activity persists over a wide range of experimental conditions and species. Our data suggest that melting curves can help to distinguish properly folded proteins from denatured ones and therefore may be useful in selecting stocks for further study and in optimizing purification procedures for specific proteins.
PMCID: PMC3270315  PMID: 20018159
thermal melting; malaria; protein denaturation
10.  M2 macrophages exhibit higher sensitivity to oxLDL-induced lipotoxicity than other monocyte/macrophage subtypes 
In obesity, phenotypic switches occur in macrophage populations such that the predominantly M2-polarised anti-inflammatory state seen in lean individuals changes to a predominantly M1-polarised pro-inflammatory state in those who are obese. However, the mechanisms by which these phenotypic shifts occur have not yet been fully elucidated.
The effects of oxLDL (1-40 μg/ml; 24 h) on several parameters relevant to the Unfolded Protein Response (UPR)-mediated lipotoxic effects of oxLDL (disruption of ER Ca2+ handling; activation of the UPR transcription factor XBP-1; upregulation of the UPR target genes BiP and CHOP; apoptosis; cell viability) were investigated in human primary monocyte-derived macrophages, and also in monocyte-macrophages derived from the THP-1 monocytic cell line. A consistent pattern was observed: M2-polarised macrophages were more sensitive to the lipotoxic effects of oxLDL than either non-polarised macrophages or non-differentiated monocytic cells. Specifically, M2-polarised macrophages were the only cell type to undergo significantly increased apoptosis (Primary cells: 1.23 ± 0.01 basal; THP-1-derived: 1.97 ± 0.12 basal; P < 0.05 in both cases) and decreased cell viability (Primary cells: 0.79 ± 0.04 basal; THP-1-derived: 0.67 ± 0.02 basal; P < 0.05 in both cases) when exposed to oxLDL levels similar to those seen in overweight individuals (ie. 1 μg/ml).
We propose that the enhanced susceptibility of M2-polarised macrophages to lipotoxicity seen in the present in vitro study could, over time, contribute to the phenotypic shift seen in obese individuals in vivo. This is because a higher degree of oxLDL-induced lipotoxic cell death within M2 macrophages could contribute to a decrease in numbers of M2 cells, and thus a relative increase in proportion of non-M2 cells, within macrophage populations. Given the pro-inflammatory characteristics of a predominantly M1-polarised state, the data presented here may constitute a useful contribution to our understanding of the origin of the pro-inflammatory nature of obesity, and of the pathogenesis of obesity-associated inflammatory disorders such as Type 2 Diabetes and atherosclerosis.
PMCID: PMC3281809  PMID: 22146099
alternative M2 monocyte/macrophage polarisation; UPR; oxLDL; lipotoxicity
11.  A method to correct for stray light in telecentric optical-CT imaging of radiochromic dosimeters 
Physics in medicine and biology  2011;56(14):4433-4451.
Radiochromic plastic and gel materials have recently emerged which can yield 3D dose information over clinical volumes in high resolution. These dosimeters can provide a much more comprehensive verification of complex radiation therapy treatments than can be achieved by conventional planar and point dosimeters. To achieve full clinical potential, these dosimeters require a fast and accurate read-out technology. Broad-beam optical-computed tomography (optical-CT) systems have shown promise, but can be sensitive to stray light artifacts originating in the imaging chain. In this work we present and evaluate a method to correct for stray light artifacts by deconvolving a measured, spatially invariant, point spread function (PSF). The correction was developed for the DLOS (Duke large field-of-view optical-CT scanner) in conjunction with radiochromic PRESAGE® dosimeters. The PSF was constructed from a series of acquisitions of projection images of various sized apertures placed in the optical imaging chain. Images were acquired with a range of exposure times, and for a range of aperture sizes (0.2–11 mm). The PSF is investigated under a variety of conditions, and found to be robust and spatially invariant, key factors enabling the viability of the deconvolution approach. The spatial invariance and robustness of the PSF are facilitated by telecentric imaging, which produces a collimated light beam and removes stray light originating upstream of the imaging lens. The telecentric capability of the DLOS therefore represents a significant advantage, both in keeping stray light levels to a minimum and enabling viability of an accurate PSF deconvolution method to correct for the residual. The performance of the correction method was evaluated on projection images containing known optical-density variations, and also on known 3D dose distributions. The method is shown to accurately account for stray light on small field dosimetry with corrections up to 3% in magnitude shown here although corrections of >10% have been observed in extreme cases. The dominant source of stray light was found to be within the imaging lens. Correcting for stray light extended the dynamic range of the system from ~30 to ~60 dB. The correction should be used when measurements need to be accurate within 3%.
PMCID: PMC3227692  PMID: 21719946
12.  A method to correct for spectral artifacts in optical-CT dosimetry 
Physics in medicine and biology  2011;56(11):3403-3416.
The recent emergence of radiochromic dosimeters with low inherent light-scattering presents the possibility of fast 3D dosimetry using broad-beam optical computed tomography (optical-CT). Current broad beam scanners typically employ either a single or a planar array of light-emitting diodes (LED) for the light source. The spectrum of light from LED sources is polychromatic and this, in combination with the non-uniform spectral absorption of the dosimeter, can introduce spectral artifacts arising from preferential absorption of photons at the peak absorption wavelengths in the dosimeter. Spectral artifacts can lead to large errors in the reconstructed attenuation coefficients, and hence dose measurement. This work presents an analytic method for correcting for spectral artifacts which can be applied if the spectral characteristics of the light source, absorbing dosimeter, and imaging detector are known or can be measured. The method is implemented here for a PRESAGE® dosimeter scanned with the DLOS telecentric scanner (Duke Large field-of-view Optical-CT Scanner). Emission and absorption profiles were measured with a commercial spectrometer and spectrophotometer, respectively. Simulations are presented that show spectral changes can introduce errors of 8% for moderately attenuating samples where spectral artifacts are less pronounced. The correction is evaluated by application to a 16 cm diameter PRESAGE® cylindrical dosimeter irradiated along the axis with two partially overlapping 6 × 6 cm fields of different doses. The resulting stepped dose distribution facilitates evaluation of the correction as each step had different spectral contributions. The spectral artifact correction was found to accurately correct the reconstructed coefficients to within ~1.5%, improved from ~7.5%, for normalized dose distributions. In conclusion, for situations where spectral artifacts cannot be removed by physical filters, the method shown here is an effective correction. Physical filters may be less viable if they introduce strong sensitivity to Schlieren bands in the dosimeters.
PMCID: PMC3227693  PMID: 21572184
13.  A comprehensive method for optical-emission computed tomography 
Physics in medicine and biology  2010;55(14):3947-3957.
Optical-computed tomography (CT) and optical-emission computed tomography (ECT) are recent techniques with potential for high-resolution multi-faceted 3D imaging of the structure and function in unsectioned tissue samples up to 1–4 cc. Quantitative imaging of 3D fluorophore distribution (e.g. GFP) using optical-ECT is challenging due to attenuation present within the sample. Uncorrected reconstructed images appear hotter near the edges than at the center. A similar effect is seen in SPECT/PET imaging, although an important difference is attenuation occurs for both emission and excitation photons. This work presents a way to implement not only the emission attenuation correction utilized in SPECT, but also excitation attenuation correction and source strength modeling which are unique to optical-ECT. The performance of the correction methods was investigated by the use of a cylindrical gelatin phantom whose central region was filled with a known distribution of attenuation and fluorophores. Uncorrected and corrected reconstructions were compared to a sectioned slice of the phantom imaged using a fluorescent dissecting microscope. Significant attenuation artifacts were observed in uncorrected images and appeared up to 80% less intense in the central regions due to attenuation and an assumed uniform light source. The corrected reconstruction showed agreement throughout the verification image with only slight variations (~5%). Final experiments demonstrate the correction in tissue as applied to a tumor with constitutive RFP.
PMCID: PMC3227695  PMID: 20577042
14.  The role of leukocyte-stromal interactions in chronic inflammatory joint disease 
Rheumatoid arthritis (RA) is a debilitating, chronic, persistent inflammatory disease that is characterised by painful and swollen joints. The aetiology of RA is unknown, however whereas past research has concentrated on the role of immune or inflammatory infiltrating cells in inflammation, it is becoming clear that stromal cells play a critical part in regulating the quality and duration of an inflammatory response. In this review we assess the role of fibroblasts within the inflamed synovium in modulating immune responses; in particular we examine the role of stromal cells in the switch from resolving to persistent inflammation as is found in the rheumatoid synovium.
PMCID: PMC3122102  PMID: 15681242
Rheumatoid arthritis; Cytokines; Chemokines; Synovitis; Inflammation
15.  Differential Survival of Leukocyte Subsets Mediated by Synovial, Bone Marrow, and Skin Fibroblasts 
Arthritis and rheumatism  2006;54(7):2096-2108.
Synovial fibroblasts share a number of phenotype markers with fibroblasts derived from bone marrow. In this study we investigated the role of matched fibroblasts obtained from 3 different sources (bone marrow, synovium, and skin) to test the hypothesis that synovial fibroblasts share similarities with bone marrow–derived fibroblasts in terms of their ability to support survival of T cells and neutrophils.
Matched synovial, bone marrow, and skin fibroblasts were established from 8 different patients with rheumatoid arthritis who were undergoing knee or hip surgery. Resting or activated fibroblasts were cocultured with either CD4 T cells or neutrophils, and the degree of leukocyte survival, apoptosis, and proliferation were measured.
Fibroblasts derived from all 3 sites supported increased survival of CD4 T cells, mediated principally by interferon-β. However, synovial and bone marrow fibroblasts shared an enhanced site-specific ability to maintain CD4 T cell survival in the absence of proliferation, an effect that was independent of fibroblast activation or proliferation but required direct T cell–fibroblast cell contact. In contrast, fibroblast-mediated neutrophil survival was less efficient, being independent of the site of origin of the fibroblast but dependent on prior fibroblast activation, and mediated solely by soluble factors, principally granulocyte–macrophage colony-stimulating factor.
These results suggest an important functional role for fibroblasts in the differential accumulation of leukocyte subsets in a variety of tissue microenvironments. The findings also provide a potential explanation for site-specific differences in the pattern of T cell and neutrophil accumulation observed in chronic inflammatory diseases.
PMCID: PMC3119431  PMID: 16802344
16.  Galectin 3 Induces a Distinctive Pattern of Cytokine and Chemokine Production in Rheumatoid Synovial Fibroblasts via Selective Signaling Pathways 
Arthritis and rheumatism  2009;60(6):1604-1614.
High expression of galectin 3 at sites of joint destruction in rheumatoid arthritis (RA) suggests that galectin 3 plays a role in RA pathogenesis. Previous studies have demonstrated the effects of galectins on immune cells, such as lymphocytes and macrophages. This study was undertaken to investigate the hypothesis that galectin 3 induces proinflammatory effects in RA by modulating the pattern of cytokine and chemokine production in synovial fibroblasts.
Matched samples of RA synovial and skin fibroblasts were pretreated with galectin 3 or tumor necrosis factor α (TNFα), and the levels of a panel of cytokines, chemokines, and matrix metalloproteinases (MMPs) were determined using enzyme-linked immunosorbent assays and multiplex assays. Specific inhibitors were used to dissect signaling pathways, which were confirmed by Western blotting and NF-κB activation assay.
Galectin 3 induced secretion of interleukin-6 (IL-6), granulocyte–macrophage colony-stimulating factor, CXCL8, and MMP-3 in both synovial and skin fibroblasts. By contrast, galectin 3–induced secretion of TNFα, CCL2, CCL3, and CCL5 was significantly greater in synovial fibroblasts than in skin fibroblasts. TNFα blockade ruled out autocrine TNFα-stimulated induction of chemokines. The MAPKs p38, JNK, and ERK were necessary for IL-6 production, but phosphatidylinositol 3-kinase (PI 3-kinase) was required for selective CCL5 induction. NF-κB activation was required for production of both IL-6 and CCL5.
Our findings indicate that galectin 3 promotes proinflammatory cytokine secretion by tissue fibroblasts. However, galectin 3 induces the production of mononuclear cell–recruiting chemokines uniquely from synovial fibroblasts, but not matched skin fibroblasts, via a PI 3-kinase signaling pathway. These data provide further evidence of the role of synovial fibroblasts in regulating the pattern and persistence of the inflammatory infiltrate in RA and suggest a new and important functional consequence of the observed high expression of galectin 3 in the rheumatoid synovium.
PMCID: PMC3116228  PMID: 19479862
17.  Toward acquiring comprehensive radiosurgery field commissioning data using the PRESAGE®/optical-CT 3D dosimetry system 
Physics in medicine and biology  2010;55(5):1279-1293.
Achieving accurate small field dosimetry is challenging. This study investigates the utility of a radiochromic plastic PRESAGE® read with optical-CT for the acquisition of radiosurgery field commissioning data from a Novalis Tx system with a high-definition multileaf collimator (HDMLC). Total scatter factors (Sc, p), beam profiles, and penumbrae were measured for five different radiosurgery fields (5, 10, 20, 30 and 40 mm) using a commercially available optical-CT scanner (OCTOPUS, MGS Research). The percent depth dose (PDD), beam profile and penumbra of the 10 mm field were also measured using a higher resolution in-house prototype CCD-based scanner. Gafchromic EBT® film was used for independent verification. Measurements of Sc, p made with PRESAGE® and film agreed with mini-ion chamber commissioning data to within 4% for every field (range 0.2–3.6% for PRESAGE®, and 1.6–3.6% for EBT). PDD, beam profile and penumbra measurements made with the two PRESAGE®/optical-CT systems and film showed good agreement with the high-resolution diode commissioning measurements with a competitive resolution (0.5 mm pixels). The in-house prototype optical-CT scanner allowed much finer resolution compared with previous applications of PRESAGE®. The advantages of the PRESAGE® system for small field dosimetry include 3D measurements, negligible volume averaging, directional insensitivity, an absence of beam perturbations, energy and dose rate independence.
PMCID: PMC3030986  PMID: 20134082
18.  An investigation into a new re-useable 3D radiochromic dosimetry material, PresageREU 
To investigate the dosimetric properties of a new Presage formulation which exhibits a reversible color change on exposure to radiation. PresageREU offers the intriguing possibility of the first re-useable 3D dosimetry material.
Method and Materials
Small volumes of PresageREU in 1×1×5cm optical cuvettes were irradiated and re-irradiated under a variety of conditions and times to investigate a range of properties including re-usability, dose-rate dependence, dose sensitivity, temporal response, energy sensitivity, and temperature dependence.
The radiation induced change in optical density (OD) was found to be linear with dose after initial and subsequent irradiations. After the first irradiation OD was observed to clear in ~2 weeks when stored at room temperature. 3 subsequent irradiations of the same cuvettes showed a very similar strong OD response, although there was a significant increase between this response and that achieve at initial irradiation.
The PresageREU formulation shows strong potential as the first re-useable 3D dosimetry material. When dosimeters are stored at room temperature (~22°C) clearing can occur in 2–3 weeks.
PMCID: PMC3015145  PMID: 21218168
19.  Smart Pipes—Instrumented Water Pipes, Can This Be Made a Reality? 
Sensors (Basel, Switzerland)  2011;11(8):7455-7475.
Several millions of kilometres of pipes and cables are buried beneath our streets in the UK. As they are not visible and easily accessible, the monitoring of their integrity as well as the quality of their contents is a challenge. Any information of these properties aids the utility owners in their planning and management of their maintenance regime. Traditionally, expensive and very localised sensors are used to provide irregular measurements of these properties. In order to have a complete picture of the utility network, cheaper sensors need to be investigated which would allow large numbers of small sensors to be incorporated into (or near to) the pipe leading to so-called smart pipes. This paper focuses on a novel trial where a short section of a prototype smart pipe was buried using mainly off-the-shelf sensors and communication elements. The challenges of such a burial are presented together with the limitations of the sensor system. Results from the sensors were obtained during and after burial indicating that off-the-shelf sensors can be used in a smart pipes system although further refinements are necessary in order to miniaturise these sensors. The key challenges identified were the powering of these sensors and the communication of the data to the operator using a range of different methods.
PMCID: PMC3231726  PMID: 22164027
smart pipes; intelligent water distribution networks; MEMS; smart technology; structural monitoring
20.  Rheumatoid synovial fluid interleukin-17-producing CD4 T cells have abundant tumor necrosis factor-alpha co-expression, but little interleukin-22 and interleukin-23R expression 
Arthritis Research & Therapy  2010;12(5):R184.
Th17 cells have been implicated in the pathogenesis of rheumatoid arthritis (RA). The aim of this study was to systematically analyse the phenotype, cytokine profile and frequency of interleukin-17 (IL-17) producing CD4-positive T cells in mononuclear cells isolated from peripheral blood, synovial fluid and synovial tissue of RA patients with established disease, and to correlate cell frequencies with disease activity.
Flow cytometry was used to analyse the phenotype and cytokine production of mononuclear cells isolated from peripheral blood (PBMC) (n = 44), synovial fluid (SFMC) (n = 14) and synovium (SVMC) (n = 10) of RA patients and PBMC of healthy controls (n = 13).
The frequency of IL-17-producing CD4 T cells was elevated in RA SFMC compared with RA PBMC (P = 0.04). However, the frequency of this population in RA SVMC was comparable to that in paired RA PBMC. The percentage of IL-17-producing CD4 T cells coexpressing tumor necrosis factor alpha (TNFα) was significantly increased in SFMC (P = 0.0068). The frequency of IFNγ-producing CD4 T cells was also significantly higher in SFMC than paired PBMC (P = 0.042). The majority of IL-17-producing CD4 T cells coexpressed IFNγ. IL-17-producing CD4 T cells in RA PBMC and SFMC exhibited very little IL-22 or IL-23R coexpression.
These findings demonstrate a modest enrichment of IL-17-producing CD4 T cells in RA SFMC compared to PBMC. Th17 cells in SFMC produce more TNFα than their PBMC counterparts, but are not a significant source of IL-22 and do not express IL-23R. However, the percentage of CD4 T cells which produce IL-17 in the rheumatoid joint is low, suggesting that other cells may be alternative sources of IL-17 within the joints of RA patients.
PMCID: PMC2991017  PMID: 20929536
21.  Buffer Optimization of Thermal Melt Assays of Plasmodium Proteins for Detection of Small-Molecule Ligands 
Journal of biomolecular screening  2009;14(6):700-707.
In the last decade, thermal melt/thermal shift assays have become a common tool for identifying ligands and other factors that stabilize specific proteins. Increased stability is indicated by an increase in the protein's melting temperature (Tm). In optimizing the assays for subsequent screening of compound libraries, it is important to minimize the variability of Tm measurements so as to maximize the assay's ability to detect potential ligands. Here we present an investigation of Tm variability in recombinant proteins from Plasmodium parasites. Ligands of Plasmodium proteins are particularly interesting as potential starting points for drugs for malaria, and new drugs are urgently needed. A single standard buffer (100 mM HEPES, pH 7.5, 150 mM NaCl) permitted estimation of Tm for 58 of 61 Plasmodium proteins tested. However, with several proteins, Tm could not be measured with a consistency suitable for high-throughput screening unless alternative protein-specific buffers were employed. We conclude that buffer optimization to minimize variability in Tm measurements increases the success of thermal melt screens involving proteins for which a standard buffer is suboptimal.
PMCID: PMC2819745  PMID: 19470714
thermal shift assays; protein unfolding; protein stabilization; superoxide dismutase
22.  Marine plankton phenology and life history in a changing climate: current research and future directions 
Journal of Plankton Research  2010;32(10):1355-1368.
Increasing availability and extent of biological ocean time series (from both in situ and satellite data) have helped reveal significant phenological variability of marine plankton. The extent to which the range of this variability is modified as a result of climate change is of obvious importance. Here we summarize recent research results on phenology of both phytoplankton and zooplankton. We suggest directions to better quantify and monitor future plankton phenology shifts, including (i) examining the main mode of expected future changes (ecological shifts in timing and spatial distribution to accommodate fixed environmental niches vs. evolutionary adaptation of timing controls to maintain fixed biogeography and seasonality), (ii) broader understanding of phenology at the species and community level (e.g. for zooplankton beyond Calanus and for phytoplankton beyond chlorophyll), (iii) improving and diversifying statistical metrics for indexing timing and trophic synchrony and (iv) improved consideration of spatio-temporal scales and the Lagrangian nature of plankton assemblages to separate time from space changes.
PMCID: PMC2933132  PMID: 20824042
plankton; phenology; life history; climate change
23.  Preparation of Bicyclic 1,2,4-Trioxanes from γ,δ-Unsaturated Ketones 
Organic letters  2009;11(3):507-510.
Treatment of γ,δ-unsaturated ketones with hydrogen peroxide and acid provides a rapid entry into the medicinally important 1,2,4-trioxane structure. Alkene substitution that stabilizes carbocationic intermediates proved to be important for the success of this transformation.
PMCID: PMC2657341  PMID: 19132925
24.  Calcium-dependent activation of mitochondrial metabolism in mammalian cells 
Methods (San Diego, Calif.)  2008;46(3):224-232.
Endogenous fluorophores provide a simple, but elegant means to investigate the relationship between agonist-evoked Ca2+ signals and the activation of mitochondrial metabolism. In this article, we discuss the methods and strategies to measure cellular pyridine nucleotide and flavoprotein fluorescence alone or in combination with Ca2+-sensitive indicators. These methods were developed using primary cultured hepatocytes and neurons, which contain relatively high levels of endogenous fluorophores and robust metabolic responses. Nevertheless, these methods are amendable to a wide variety of primary cell types and cell lines that maintain active mitochondrial metabolism.
PMCID: PMC2640951  PMID: 18854213
Mitochondria; calcium; inositol 1,4,5-trisphosphate; pyridine nucleotides; flavoproteins; membrane potential; digital fluorescence imaging; confocal microscopy
25.  Full Likelihood Analysis of Genetic Risk with Variable Age at Onset Disease—Combining Population-Based Registry Data and Demographic Information 
PLoS ONE  2009;4(8):e6836.
In genetic studies of rare complex diseases it is common to ascertain familial data from population based registries through all incident cases diagnosed during a pre-defined enrollment period. Such an ascertainment procedure is typically taken into account in the statistical analysis of the familial data by constructing either a retrospective or prospective likelihood expression, which conditions on the ascertainment event. Both of these approaches lead to a substantial loss of valuable data.
Methodology and Findings
Here we consider instead the possibilities provided by a Bayesian approach to risk analysis, which also incorporates the ascertainment procedure and reference information concerning the genetic composition of the target population to the considered statistical model. Furthermore, the proposed Bayesian hierarchical survival model does not require the considered genotype or haplotype effects be expressed as functions of corresponding allelic effects. Our modeling strategy is illustrated by a risk analysis of type 1 diabetes mellitus (T1D) in the Finnish population-based on the HLA-A, HLA-B and DRB1 human leucocyte antigen (HLA) information available for both ascertained sibships and a large number of unrelated individuals from the Finnish bone marrow donor registry. The heterozygous genotype DR3/DR4 at the DRB1 locus was associated with the lowest predictive probability of T1D free survival to the age of 15, the estimate being 0.936 (0.926; 0.945 95% credible interval) compared to the average population T1D free survival probability of 0.995.
The proposed statistical method can be modified to other population-based family data ascertained from a disease registry provided that the ascertainment process is well documented, and that external information concerning the sizes of birth cohorts and a suitable reference sample are available. We confirm the earlier findings from the same data concerning the HLA-DR3/4 related risks for T1D, and also provide here estimated predictive probabilities of disease free survival as a function of age.
PMCID: PMC2730012  PMID: 19718441

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