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1.  Role of Four Calcium Transport Proteins, Encoded by nca-1, nca-2, nca-3, and cax, in Maintaining Intracellular Calcium Levels in Neurospora crassa ▿ 
Eukaryotic Cell  2011;10(5):654-661.
We have examined the distribution of calcium in Neurospora crassa and investigated the role of four predicted calcium transport proteins. The results of cell fractionation experiments showed 4% of cellular calcium in mitochondria, approximately 11% in a dense vacuolar fraction, 40% in an insoluble form that copurifies with microsomes, and 40% in a high-speed supernatant, presumably from large vacuoles that had broken. Strains lacking NCA-1, a SERCA-type Ca2+-ATPase, or NCA-3, a PMC-type Ca2+-ATPase, had no obvious defects in growth or distribution of calcium. A strain lacking NCA-2, which is also a PMC-type Ca2+-ATPase, grew slowly in normal medium and was unable to grow in high concentrations of calcium tolerated by the wild type. Furthermore, when grown in normal concentrations of calcium (0.68 mM), this strain accumulated 4- to 10-fold more calcium than other strains, elevated in all cell fractions. The data suggest that NCA-2 functions in the plasma membrane to pump calcium out of the cell. In this way, it resembles the PMC-type enzymes of animal cells, not the Pmc1p enzyme in Saccharomyces cerevisiae that resides in the vacuole. Strains lacking the cax gene, which encodes a Ca2+/H+ exchange protein in vacuolar membranes, accumulate very little calcium in the dense vacuolar fraction but have normal levels of calcium in other fractions. The cax knockout strain has no other observable phenotypes. These data suggest that “the vacuole” is heterogeneous and that the dense vacuolar fraction contains an organelle that is dependent upon the CAX transporter for accumulation of calcium, while other components of the vacuolar system have multiple calcium transporters.
doi:10.1128/EC.00239-10
PMCID: PMC3127652  PMID: 21335528
2.  Structure and Distribution of Organelles and Cellular Location of Calcium Transporters in Neurospora crassa▿  
Eukaryotic Cell  2009;8(12):1845-1855.
We wanted to examine the cellular locations of four Neurospora crassa proteins that transport calcium. However, the structure and distribution of organelles in live hyphae of N. crassa have not been comprehensively described. Therefore, we made recombinant genes that generate translational fusions of putative organellar marker proteins with green or red fluorescent protein. We observed putative endoplasmic reticulum proteins, encoded by grp-78 and dpm, in the nuclear envelope and associated membranes. Proteins of the vacuolar membrane, encoded by vam-3 and vma-1, were in an interconnected network of small tubules and vesicles near the hyphal tip, while in more distal regions they were in large and small spherical vacuoles. Mitochondria, visualized with tagged ARG-4, were abundant in all regions of the hyphae. Similarly, we tagged the four N. crassa proteins that transport calcium with green or red fluorescent protein to examine their cellular locations. NCA-1 protein, a homolog of the SERCA-type Ca2+-ATPase of animal cells, colocalized with the endoplasmic reticulum markers. The NCA-2 and NCA-3 proteins are homologs of Ca2+-ATPases in the vacuolar membrane in yeast or in the plasma membrane in animal cells. They colocalized with markers in the vacuolar membrane, and they also occurred in the plasma membrane in regions of the hyphae more than 1 mm from the tip. The cax gene encodes a Ca2+/H+ exchange protein found in vacuoles. As expected, the CAX protein localized to the vacuolar compartment. We observed, approximately 50 to 100 μm from the tip, a few spherical organelles that had high amounts of tagged CAX protein and tagged subunits of the vacuolar ATPase (VMA-1 and VMA-5). We suggest that this organelle, not described previously in N. crassa, may have a role in sequestering calcium.
doi:10.1128/EC.00174-09
PMCID: PMC2794220  PMID: 19801418
3.  Selective criteria for the microbiological examination of faecal specimens. 
Journal of Clinical Pathology  1992;45(9):838-839.
To assess the effectiveness of predetermined investigation criteria for the examination of faecal samples from inpatients, cultured stool specimens were prospectively examined for Salmonella spp, Shigella spp, Campylobacter spp and Clostridium difficile, and screened microscopically for intestinal parasites. Out of a total of 505 specimens, 421 (83%) fulfilled the criteria for examination for C difficile, 254 (50%) for Salmonella spp, Shigella spp, and Campylobacter spp, and 87 (17%) for intestinal parasites. Isolation rates for these organisms in those groups of patients where examination was indicated were 22.5% for C difficile and 9.1% for Salmonella spp, Shigella spp, and Campylobacter spp; the detection rate for parasites was 3.5%. In those patients where the criteria did not suggest investigation, the isolation or detection rates were 3.6% for C difficile, 0% for Salmonella spp, Shigella spp, and Campylobacter spp, and 1.7% for intestinal parasites, suggesting that the use of predetermined investigation criteria was effective.
PMCID: PMC495122  PMID: 1401225
4.  Identification and properties of an ATPase in vacuolar membranes of Neurospora crassa. 
Journal of Bacteriology  1982;151(3):1326-1337.
Using a vacuolar preparation virtually free of contamination by other organelles, we isolated vacuolar membranes and demonstrated that they contain an ATPase. Sucrose density gradient profiles of vacuolar membranes show a single peak of ATPase activity at a density of 1.11 g/cm3. Comparison of this enzyme with the two well-studied proton-pumping ATPases of Neurospora plasma membranes and mitochondria shows that it is clearly distinct. The vacuolar membrane ATPase is insensitive to the inhibitors oligomycin, azide, and vanadate, but sensitive to N,N'-dicyclohexylcarbodiimide (Ki = 2 microM). It has a pH optimum of 7.5, requires a divalent cation (Mg2+ or Mn2+) for activity, and is remarkably unaffected (+/- 20%) by a number of monovalent cations, anions, and buffers. In its substrate affinity (Km for ATP = 0.2 mM), substrate preference (ATP greater than GTP, ITP greater than UTP greater than CTP), and loss of activity with repeated 1 mM ethylene glycol-bis(beta-aminoethyl ether)-N,N,N',N'-tetraacetic acid washes, the vacuolar membrane ATPase resembles the F1F0 type of ATPase found in mitochondria and differs from the integral membrane type of ATPase in plasma membranes.
PMCID: PMC220411  PMID: 6213602
6.  Effect of Transendocardial Delivery of Autologous Bone Marrow Mononuclear Cells on Functional Capacity, Left Ventricular Function, and Perfusion in Chronic Ischemic Heart Failure: The FOCUS-CCTRN Trial 
Context
Previous studies utilizing autologous bone marrow mononuclear cells (BMCs) in patients with ischemic cardiomyopathy have demonstrated safety and suggested efficacy. The FOCUS protocol was designed to assess efficacy of a larger cell dose in an adequately well-powered phase II study.
Objective
To determine if administration of BMCs through transendocardial injections improves myocardial perfusion, reduces left ventricular (LV) end systolic volume, or enhances maximal oxygen consumption in patients with coronary artery disease (CAD), LV dysfunction, and limiting heart failure and/or angina.
Design, Setting, and Patients
This is a 100 million cell, first-in-man randomized, double-blind, placebo-controlled trial was performed by the National Heart, Lung, and Blood Institute-sponsored Cardiovascular Cell Therapy Research Network (CCTRN) in symptomatic patients (NYHA II-III and/or CCS II-IV) receiving maximal medical therapy, with a left ventricular ejection fraction (LVEF)≤45%, perfusion defect by single-photon emission tomography (SPECT), and CAD not amenable to revascularization.
Intervention
All patients underwent bone marrow aspiration, isolation of BMCs using a standardized automated system performed locally, and transendocardial injection of 100 million BMCs or placebo (2:1 BMC: placebo).
Main Outcome Measures
Three co-primary endpoints assessed at 6 months were changes in (a) LV end systolic volume (LVESV) by echocardiography, (b) maximal oxygen consumption (MVO2), and (c) reversibility on SPECT. Secondary measures included other SPECT measures, magnetic resonance imaging (MRI), echocardiography, clinical improvement, and major adverse cardiac events (MACE). Phenotypic and functional analyses of the cell product were performed by the CCTRN Biorepository lab.
Results
Of 153 consented patients, a total of 92 (82 men; average age, 63 years) were randomized (n= 61 BMC, 31 placebo) at 5 sites between April 29, 2009 and April 18, 2011. Changes in LVESV index, (−0.9 ± 11.3 mL/m2; P = 0.733; 95% CI, −6.1 to 4.3), MVO2 (1.0 ± 2.9; P = 0.169; 95% CI, −0.42 to 2.34), percent reversible defect change, (−1.2 ± 23.3; P = 0.835; 95% CI, −12.50 to 10.12), and incidence of MACEwere not statistically significant. However, in an exploratory analysis the change in LVEF across the entire cohort by therapy group was significant (2.7 ± 5.2%; P = 0.030; 95% CI, 0.27 to 5.07).
Conclusions
This is the largest cell therapy trial of autologous BMCs in patients with ischemic LV dysfunction. In patients with chronic ischemic heart disease, transendocardial injection of BMCs compared to placebo did not improve LVESV, MVO2, or reversibility on SPECT.
doi:10.1001/jama.2012.418
PMCID: PMC3600947  PMID: 22447880
Chronic CAD; Ischemic Heart Failure; Chronic Angina; bone marrow mononuclear cells; cardiac performance
7.  Effect of Intracoronary Delivery of Autolologous Bone Marrow Mononuclear Cells Two to Three Weeks Following Acute Myocardial Infarction on Left-Ventricular Function: The LateTIME Randomized Trial 
Context
Clinical trial results suggest that intracoronary delivery of autologous bone marrow mononuclear cells (BMCs) may improve left ventricular (LV) function when administered within the first week following myocardial infarction (MI). However, since a substantial number of patients may not present for early cell delivery, we investigated the efficacy of autologous BMC delivery 2–3 weeks post-MI.
Objective
To determine if intracoronary delivery of autologous BMCs improves global and regional LV function when delivered 2–3 weeks following first MI.
Design, Setting, and Patients
LateTIME is a randomized, double-blind, placebo-controlled trial of the National Heart, Lung, and Blood Institute - sponsored Cardiovascular Cell Therapy Research Network (CCTRN) of 87 patients with significant LV dysfunction (LVEF ≤ 45%) following successful primary percutaneous coronary intervention (PCI).
Interventions
Intracoronary infusion of 150 × 106 autologous BMCs (total nucleated cells) or placebo (2:1 BMC:placebo) was performed within 12 hours of bone marrow aspiration after local automated cell processing.
Main Outcome Measures
The primary endpoints were changes in global (LVEF) and regional (wall motion) LV function in the infarct and border zone from baseline to 6 months as measured by cardiac MRI at a core lab blinded to treatment assignment Secondary endpoints included changes in LV volumes and infarct size.
Results
87 patients were randomized between July 2008 and February 2011: mean age = 57 ± 11 yrs, 83% male. Harvesting, processing, and intracoronary delivery of BMCs in this setting was feasible and safe. The change from baseline to six months in the BMC group, when compared to the placebo group, for LVEF (48.7 to 49.2% vs. 45.3 to 48.8%; Difference = −3.0, 95% CI −7.0 to 0.9), wall motion in the infarct zone (6.2 to 6.5 vs. 4.9 to 5.9 mm; Difference = −0.7, 95% CI −2.8 to 1.3), and wall motion in the border zone (16.0 to 16.6 mm vs. 16.1 to 19.3 mm; Difference = −2.6; 95% CI −6.0 to 0.8) were not statistically significant. There was no significant change in LV volumes and infarct volumes decreased by a similar amount in both groups at 6 months compared to baseline.
Conclusions
Among patients with MI and LV dysfunction following reperfusion with PCI, intracoronary infusion of autologous BMCs compared to intracoronary placebo infusion, 2–3 weeks after PCI did not improve global or regional function at 6 months.
doi:10.1001/jama.2011.1670
PMCID: PMC3600981  PMID: 22084195
Acute myocardial infarction; bone marrow mononuclear cells; LVEF; cardiac MRI
8.  Predictors of yoga use among patients with breast cancer 
Explore (New York, N.Y.)  2010;6(6):359-363.
Objective
Emerging research suggests that yoga may be beneficial for reducing symptoms and improving quality of life among breast cancer patients (BCP). However, very little is known about the characteristics of BCP who use yoga; thus, this study seeks to identify the socio-demographic and clinical characteristics of yoga users among this population.
Design
Cross-sectional survey study.
Setting
Outpatient breast oncology clinic at a large university hospital
Participants
300 postmenopausal BCP currently receiving aromatase inhibitors.
Main outcome measurement
Self-reported use of yoga since the cancer diagnosis was collected along with sociodemographic and clinical data. Multivariate logistic regression was used to identify independent predictors of yoga use among BCP.
Results
Of 300 participants, 53 (17.7%) reported having used yoga since cancer diagnosis. White patients were significantly more likely to use yoga than non-white patients (p=0.02). Higher education level, lower BMI (body mass index), part-time employment status, previous chemotherapy and radiation therapy were all associated with greater yoga use (all p<0.05). Controlling for other factors, greater yoga use was independently associated with higher education level, adjusted odds ratio (AOR) 2.72, 95% confidence interval (CI), (1.15–6.46), and lower BMI, AOR, 0.25, 95% CI, (0.09–0.66).
Conclusion
Yoga use following breast cancer diagnosis was substantially higher for white patients and those with lower BMI and higher education levels. Considering its potential benefits for symptom management in cancer, more research is needed to understand the attitudes and barriers to yoga use among individuals with non-white race, lower education, and higher BMI level. Such investigation will help design yoga programs that are aligned to the needs of these populations.
doi:10.1016/j.explore.2010.08.002
PMCID: PMC3600409  PMID: 21040884
9.  3′ UTR and functional secretor haplotypes in mannose-binding lectin 2 are associated with increased colon cancer risk in African Americans 
Cancer research  2012;72(6):1467-1477.
Because chronic intestinal inflammation is a risk factor for colorectal cancer, we hypothesized that genetic variants of inflammatory mediators, such as mannose-binding lectin 2 (MBL2), are associated with colon cancer susceptibility. Here we report the association of 24 MBL2 single nucleotide polymorphisms (SNPs) and corresponding haplotypes with colon cancer risk in a case-control study. Four SNPs in the 3′-UTR region of the gene (rs10082466, rs2120132, rs2099902, and rs10450310) were associated with an increased risk of colon cancer in African Americans. Odds ratios (OR) for homozygous variants vs. wild-type ranged from 3.17 (95% CI, 1.57–6.40) to 4.51 (95% CI, 1.94–10.50), whereas the 3′-UTR region haplotype consisting of these four variants had an OR of 2.10 (95% CI, 1.42–3.12). The C allele of rs10082466 exhibited a binding affinity of miR-27a and this allele was associated with both lower MBL plasma levels and activity. We found that 5′ secretor haplotypes known to correlate with moderate and low MBL serum levels exhibited associations with increased risk of colon cancer in African Americans, specifically as driven by two haplotypes LYPA and LYQC relative to the referent HYPA haplotype (LYPA: OR 2.60; 95% CI 1.33–5.08 and LYQC: OR 2.28; 95% CI 1.20–4.30). Similar associations were not displayed in Caucasians. Together, our results support the hypothesis that genetic variations in MBL2 increase colon cancer susceptibility in African Americans.
doi:10.1158/0008-5472.CAN-11-3073
PMCID: PMC3306468  PMID: 22282660
colon cancer; single nucleotide polymorphism; mannose-binding lectin 2; innate immunity; African American
10.  Circulating microRNA Expression Profiles in Early Stage Non-Small Cell Lung Cancer 
Circulating micro-RNA (miR) profiles have been proposed as promising diagnostic and prognostic biomarkers for cancer, including lung cancer. We have developed methods to accurately and reproducibly measure microRNA levels in serum and plasma. Here we study paired serum and plasma samples from 220 patients with early stage NSCLC and 220 matched controls. We use qRT-PCR to measure the circulating levels of 30 different miRs that have previously been reported to be differently expressed in lung cancer tissue. Duplicate RNA extractions were performed for 10% of all samples and microRNA measurements were highly correlated among those duplicates. This demonstrates high reproducibility of our assay. The expression of miR-146b, miR-221, let-7a, miR-155, miR-17-5p, miR-27a and miR-106a were significantly reduced in the serum of NSCLC cases while miR-29c was significantly increased. No significant differences were observed in plasma of patients compared to controls. Overall, expression levels in serum did not correlate well with levels in plasma. In secondary analyses, reduced plasma expression of let-7b was modestly associated with worse cancer-specific mortality in all patients and reduced serum expression of miR-223 was modestly associated with cancer-specific mortality in stage IA/B patients. MiR profiles also showed considerable differences comparing African American and European Americans. In summary, we found significant differences in miR expression when comparing cases and controls and find evidence that expression of let-7b is associated with prognosis in NSCLC.
doi:10.1002/ijc.26153
PMCID: PMC3259258  PMID: 21544802
11.  Neonatal rhinovirus infection induces mucous metaplasia and airways hyperresponsiveness 
Recent studies link early rhinovirus (RV) infections to later asthma development. We hypothesized that neonatal RV infection leads to an IL-13-driven asthma-like phenotype in mice. BALB/c mice were inoculated with RV1B or sham on day 7 of life. Viral RNA persisted in the neonatal lung up to 7 days after infection. Within this time frame, IFNs-α, -β and -γ peaked 1 day after infection, whereas IFN-λ levels persisted. Next, we examined mice on day 35 of life, 28 days after initial infection. Compared to sham-treated controls, virus-inoculated mice demonstrated airways hyperresponsiveness. Lungs from RV-infected mice showed increases in several immune cell populations, as well as the percentages of CD4-positive T cells expressing IFN-γ and of NKp46/CD335+, TCR-β+ cells expressing IL-13. Periodic acid-Schiff and immunohistochemical staining revealed mucous cell metaplasia and muc5AC expression in RV1B- but not sham-inoculated lungs. Mucous metaplasia was accompanied by induction of gob-5, MUC5AC, MUC5B and IL-13 mRNA. By comparison, adult mice infected with RV1B showed no change in IL-13 expression, mucus production or airways responsiveness 28 days after infection. Intraperitoneal administration of anti-IL13 neutralizing antibody attenuated RV-induced mucous metaplasia and methacholine responses, and IL-4R null mice failed to show RV-induced mucous metaplasia. Finally, neonatal RV increased the inflammatory response to subsequent allergic sensitization and challenge. We conclude that neonatal RV1B infection leads to persistent airways inflammation, mucous metaplasia and hyperresponsiveness which are mediated, at least in part, by IL-13.
doi:10.4049/jimmunol.1101391
PMCID: PMC3294163  PMID: 22331068
asthma; BALB/c; childhood; gob-5; IL-13
12.  Ascorbic acid, cognitive function, and Alzheimer’s disease: a current review and future direction 
BioFactors (Oxford, England)  2012;38(2):114-122.
This narrative review appraises the human and animal studies implicating ascorbic acid (AA) in normal cognitive function and Alzheimer’s disease. A research framework for how nutrition affects brain aging is proposed with emphasis on AA intake, status, metabolism, and transport into brain tissue. A final synopsis highlights areas for future research regarding AA nourishment and healthy brain aging.
doi:10.1002/biof.1002
PMCID: PMC3594659  PMID: 22419527
ascorbic acid; vitamin C; cognitive function; Alzheimer’s disease; dementia; plasma; CSF; SVCT; blood–brain barrier; blood; CSF barrier; choroid plexus
13.  Phenotypes and Karyotypes of Human Malignant Mesothelioma Cell Lines 
PLoS ONE  2013;8(3):e58132.
Background
Malignant mesothelioma is an aggressive tumour of serosal surfaces most commonly pleura. Characterised cell lines represent a valuable tool to study the biology of mesothelioma. The aim of this study was to develop and biologically characterise six malignant mesothelioma cell lines to evaluate their potential as models of human malignant mesothelioma.
Methods
Five lines were initiated from pleural biopsies, and one from pleural effusion of patients with histologically proven malignant mesothelioma. Mesothelial origin was assessed by standard morphology, Transmission Electron Microscopy (TEM) and immunocytochemistry. Growth characteristics were assayed using population doubling times. Spectral karyotyping was performed to assess chromosomal abnormalities. Authentication of donor specific derivation was undertaken by DNA fingerprinting using a panel of SNPs.
Results
Most of cell lines exhibited spindle cell shape, with some retaining stellate shapes. At passage 2 to 6 all lines stained positively for calretinin and cytokeratin 19, and demonstrated capacity for anchorage-independent growth. At passage 4 to 16, doubling times ranged from 30–72 hours, and on spectral karyotyping all lines exhibited numerical chromosomal abnormalities ranging from 41 to 113. Monosomy of chromosomes 8, 14, 22 or 17 was observed in three lines. One line displayed four different karyotypes at passage 8, but only one karyotype at passage 42, and another displayed polyploidy at passage 40 which was not present at early passages. At passages 5–17, TEM showed characteristic features of mesothelioma ultrastructure in all lines including microvilli and tight intercellular junctions.
Conclusion
These six cell lines exhibit varying cell morphology, a range of doubling times, and show diverse passage-dependent structural chromosomal changes observed in malignant tumours. However they retain characteristic immunocytochemical protein expression profiles of mesothelioma during maintenance in artificial culture systems. These characteristics support their potential as in vitro model systems for studying cellular, molecular and genetic aspects of mesothelioma.
doi:10.1371/journal.pone.0058132
PMCID: PMC3597627
14.  Borrelia burgdorferi cp32 BpaB Modulates Expression of the Prophage NucP Nuclease and SsbP Single-Stranded DNA-Binding Protein 
Journal of Bacteriology  2012;194(17):4570-4578.
The Borrelia burgdorferi BpaB proteins of the spirochete's ubiquitous cp32 prophages are DNA-binding proteins, required both for maintenance of the bacteriophage episomes and for transcriptional regulation of the cp32 erp operons. Through use of DNase I footprinting, we demonstrate that BpaB binds the erp operator initially at the sequence 5′-TTATA-3′. Electrophoretic mobility shift assays indicated that BpaB also binds with high affinity to sites located in the 5′ noncoding regions of two additional cp32 genes. Characterization of the proteins encoded by those genes indicated that they are a single-stranded DNA-binding protein and a nuclease, which we named SsbP and NucP, respectively. Chromatin immunoprecipitation indicated that BpaB binds erp, ssbP, and nucP in live B. burgdorferi. A mutant bacterium that overexpressed BpaB produced significantly higher levels of ssbP and nucP transcript than did the wild-type parent.
doi:10.1128/JB.00661-12
PMCID: PMC3415502  PMID: 22730122
15.  Glycoscience: Integrating a Key Macromolecule More Fully into the Curriculum 
CBE Life Sciences Education  2013;12(1):5-8.
The recent report from the National Research Council, Transforming Glycoscience: A Roadmap for the Future, explores an important area of the life sciences. Glycoscience examples are suitable additions to many areas of the curriculum, and their inclusion will help ensure that students have an understanding of the diverse functions played by this key class of macromolecules.
doi:10.1187/cbe.12-12-0217
PMCID: PMC3587856  PMID: 23463222
16.  Arbuscular-Mycorrhizal Networks Inhibit Eucalyptus tetrodonta Seedlings in Rain Forest Soil Microcosms 
PLoS ONE  2013;8(2):e57716.
Eucalyptus tetrodonta, a co-dominant tree species of tropical, northern Australian savannas, does not invade adjacent monsoon rain forest unless the forest is burnt intensely. Such facilitation by fire of seedling establishment is known as the "ashbed effect." Because the ashbed effect might involve disruption of common mycorrhizal networks, we hypothesized that in the absence of fire, intact rain forest arbuscular mycorrhizal (AM) networks inhibit E. tetrodonta seedlings. Although arbuscular mycorrhizas predominate in the rain forest, common tree species of the northern Australian savannas (including adult E. tetrodonta) host ectomycorrhizas. To test our hypothesis, we grew E. tetrodonta and Ceiba pentandra (an AM-responsive species used to confirm treatments) separately in microcosms of ambient or methyl-bromide fumigated rain forest soil with or without severing potential mycorrhizal fungus connections to an AM nurse plant, Litsea glutinosa. As expected, C. pentandra formed mycorrhizas in all treatments but had the most root colonization and grew fastest in ambient soil. E. tetrodonta seedlings also formed AM in all treatments, but severing hyphae in fumigated soil produced the least colonization and the best growth. Three of ten E. tetrodonta seedlings in ambient soil with intact network hyphae died. Because foliar chlorosis was symptomatic of iron deficiency, after 130 days we began to fertilize half the E. tetrodonta seedlings in ambient soil with an iron solution. Iron fertilization completely remedied chlorosis and stimulated leaf growth. Our microcosm results suggest that in intact rain forest, common AM networks mediate belowground competition and AM fungi may exacerbate iron deficiency, thereby enhancing resistance to E. tetrodonta invasion. Common AM networks–previously unrecognized as contributors to the ashbed effect–probably help to maintain the rain forest–savanna boundary.
doi:10.1371/journal.pone.0057716
PMCID: PMC3584021  PMID: 23460899
17.  BSMac: A MATLAB toolbox implementing a Bayesian spatial model for brain activation and connectivity 
Journal of Neuroscience Methods  2011;204(1):133-143.
We present a statistical and graphical visualization MATLAB toolbox for the analysis of functional magnetic resonance imaging (fMRI) data, called the Bayesian Spatial Model for activation and connectivity (BSMac). BSMac simultaneously performs whole-brain activation analyses at the voxel and region of interest (ROI) levels as well as task-related functional connectivity (FC) analyses using a flexible Bayesian modeling framework (Bowman et al., 2008). BSMac allows for inputting data in either Analyze or Nifti file formats. The user provides information pertaining to subgroup memberships, scanning sessions, and experimental tasks (stimuli), from which the design matrix is constructed. BSMac then performs parameter estimation based on Markov Chain Monte Carlo (MCMC) methods and generates plots for activation and FC, such as interactive 2D maps of voxel and region-level task-related changes in neural activity and animated 3D graphics of the FC results. The toolbox can be downloaded from http://www.sph.emory.edu/bios/CBIS/. We illustrate the BSMac toolbox through an application to an fMRI study of working memory in patients with schizophrenia.
doi:10.1016/j.jneumeth.2011.10.025
PMCID: PMC3341733  PMID: 22101143
fMRI; Spatial modeling; Functional connectivity; Bayesian analysis; Neuroimaging software
19.  Comparative Study of Descemet Stripping Automated Endothelial Keratoplasty Donor Preparation by Moria CBm Microkeratome, Horizon Microkeratome, and Intralase FS60 
Cornea  2011;30(3):320-324.
Purpose
To evaluate the quality of stromal bed and the safety on endothelium in preparation of donor tissue for Descemet stripping automated endothelial keratoplasty in a masked fashion using 2 mechanical microkeratomes and a femtosecond laser.
Methods
Deep anterior lamellar dissection was performed on 15 donor corneas. Central endothelial cell density was calculated using specular microscopy before and after the dissection. One cornea from each of 5 donor pairs was cut with the Moria ALTK system with the CBm microkeratome using the 300-μm head and the mate cut with the Horizon disposable 300-μm microkeratome. Five additional donor corneas were cut with the Intralase 60-kHz FS laser. The donor corneas were then bisected with half of the cornea used for Live/Dead assay to study central endothelial viability. The other halves were sent for scanning electron microscopy of the stromal bed. Qualitative surface roughness of the scanning electron microscopy images was graded by 2 masked observers, and quantitative surface roughness was assessed using roughness evaluation software.
Results
The Horizon group showed a smoother stromal bed compared with the Moria or Intralase groups by 2 masked observers. However, the Moria group had the smoothest quantitative score of all the groups when assessed by roughness evaluation software. There was no statistically significant difference among the 3 groups in the percentage change in the central endothelial cell density or percentage of viable central endothelium by Live/Dead assay after the dissection.
Conclusions
Both mechanical microkeratomes created smoother stromal bed dissections than the femtosecond laser. All systems provided good endothelial cell viability.
doi:10.1097/ICO.0b013e3181f22cc3
PMCID: PMC3569007  PMID: 21304290
Descemet stripping automated endothelial keratoplasty; posterior lamellar keratoplasty; endothelial cell density; microkeratome; femtosecond laser; roughness; surface
20.  Patterns and Risk Factors Associated with Aromatase Inhibitor Related Arthralgia Among Breast Cancer Survivors 
Cancer  2009;115(16):3631-3639.
Purpose
Arthralgia is common in postmenopausal breast cancer survivors (BCS) receiving aromatase inhibitors (AI). This study aims to evaluate the perceived onset, characteristics, and risk factors for AI-related arthralgia (AIA).
Patients and Methods
We performed a cross-sectional survey of postmenopausal BCS receiving adjuvant AI therapy at a university-based oncology clinic. Patient-reported attribution of AIs as a cause of joint pain was used as the primary outcome. Multivariate logistic regression analyses (MVA) were performed to evaluate risk factor(s).
Results
Among 300 participants, 139 (47%) attributed AI as a cause of their current arthralgia. Of these patients, 74% recognized onset of AIA within three months since medication initiation, and 67% rated joint pain moderate or severe in the previous seven days. In a MVA, time since last menstrual period (LMP) was the only significant predictor of AIA. Controlling for covariates, those who had LMP within five years had the highest probability of reporting AIA (73%), while those with LMP beyond ten years had the lowest (35%; adjusted odds radio, 3.39, 95% confidence interval, 1.21-9.44, P=0.02). Wrists/hands, ankles/feet, elbows and knees appeared to be more strongly associated with AI-related symptoms than non-AI related joint symptoms (all p<0.01).
Conclusions
AIA is common, begins within the first three months of therapy in most patients, and appears to be inversely related to the length of time since cessation of menstrual function. These findings suggest that estrogen withdrawal may play a role in the mechanism of this disorder.
doi:10.1002/cncr.24419
PMCID: PMC3569524  PMID: 19517460
keywords: breast neoplasm; aromatase inhibitor; adverse effects; arthralgia; arthritis postmenopausal; epidemiology
21.  Uncovering the expectancy effect: the validation of Acupuncture Expectancy Scale 
Purpose
Research suggests that expectancy may modulate the response to medical interventions, including acupuncture. However, the paucity of validated tools to measure expectancy limits rigorous evaluation. We sought to validate a previously developed Acupuncture Expectancy Scale (AES) as an instrument to measure patients’ expected responses to acupuncture.
Methods
Participants were patients with stage I to III cancers seen in outpatient medical and radiation oncology clinics. They were drawn from three study cohorts that included 404 participants. We examined the reliability, validity and responsiveness of AES.
Results
The scores of AES had internal consistency (Cronbach’s α coefficient) of 0.95 and test-retest reliability of 0.62 over four weeks without acupuncture treatment. Those who had previously used acupuncture had higher AES compared to those who were acupuncture naïve (12.4 vs. 9.5, p=0.002). AES was higher in those who reported willingness to participate in an acupuncture trial compared to those who did not want to participate in an acupuncture trial (11.5 vs. 8.1, p<0.001). Those patients who enrolled in a pilot trial of acupuncture had higher AES score than the general outpatient population (13.0 vs. 9.8, p=0.02), and expectancy increased during the course of acupuncture treatment (13.0 to 16.5, p<0.017).
Conclusion
The AES is reliable and valid, and scores appear to increase during or after prior therapy. Incorporation of AES in clinical trials and outcome studies can evaluate the role of expectancy on acupuncture outcomes.
PMCID: PMC3569526  PMID: 21280459
22.  Feasibility Trial of Electro-acupuncture for Aromatase Inhibitor Related Arthralgia in Breast Cancer Survivors 
Integrative cancer therapies  2009;8(2):123-129.
Background
Arthralgia affects postmenopausal women receiving aromatase inhibitors (AI) for breast cancer. Given the existing evidence for electro-acupuncture (EA) for treatment of osteoarthritis in the general population, this study aims to establish the feasibility of studying EA for treating AI-related arthralgia.
Patients and Methods
Postmenopausal women with stage I-III breast cancer who reported AI-related arthralgia were enrolled in a single arm feasibility trial. EA was provided twice a week for two weeks followed by six weekly treatments. The protocol was based on Chinese medicine diagnosis of “Bi” syndrome with electro-stimulation of needles around the painful joint(s). Pain severity of the modified Brief Pain Inventory was used as the primary outcome. Joint stiffness, Joint interference, and Patient Global Impression of Change (PGIC) were secondary outcomes. Paired-t tests were used for analysis.
Results
Twelve women were enrolled and all provided data for analysis. From baseline to the end of intervention, patients reported reduction in pain severity (5.3 to 1.9), stiffness (6.9 to 2.4), and joint symptom interference (4.7 to 0.8), all P<0.001; 11/12 considered joint symptoms “very much better” based on PGIC. Subjects also reported significant decrease in fatigue (4.4 to 1.9, p=0.005) and anxiety (7.1 to 4.8, p=0.01). No infection or development or worsening of lymphedema was observed.
Conclusion
Preliminary data establishes the feasibility of recruitment and acceptance as well as promising preliminary safety and effectiveness. A randomized controlled trial is warranted to establish the efficacy of EA for AI-related arthralgia in breast cancer survivors.
doi:10.1177/1534735409332903
PMCID: PMC3569528  PMID: 19679620
Acupuncture; breast neoplasm; clinical trial; Aromatase inhibitors/*adverse effects; joint diseases
23.  The Sensitivity of Genetic Connectivity Measures to Unsampled and Under-Sampled Sites 
PLoS ONE  2013;8(2):e56204.
Landscape genetic analyses assess the influence of landscape structure on genetic differentiation. It is rarely possible to collect genetic samples from all individuals on the landscape and thus it is important to assess the sensitivity of landscape genetic analyses to the effects of unsampled and under-sampled sites. Network-based measures of genetic distance, such as conditional genetic distance (cGD), might be particularly sensitive to sampling intensity because pairwise estimates are relative to the entire network. We addressed this question by subsampling microsatellite data from two empirical datasets. We found that pairwise estimates of cGD were sensitive to both unsampled and under-sampled sites, and FST, Dest, and deucl were more sensitive to under-sampled than unsampled sites. We found that the rank order of cGD was also sensitive to unsampled and under-sampled sites, but not enough to affect the outcome of Mantel tests for isolation by distance. We simulated isolation by resistance and found that although cGD estimates were sensitive to unsampled sites, by increasing the number of sites sampled the accuracy of conclusions drawn from landscape genetic analyses increased, a feature that is not possible with pairwise estimates of genetic differentiation such as FST, Dest, and deucl. We suggest that users of cGD assess the sensitivity of this measure by subsampling within their own network and use caution when making extrapolations beyond their sampled network.
doi:10.1371/journal.pone.0056204
PMCID: PMC3568052  PMID: 23409155
24.  Changes in the striatal proteome of YAC128Q mice exhibit gene-environment interactions between mutant Huntingtin and manganese 
Journal of Proteome Research  2012;11(2):1118-1132.
Huntington disease (HD) is a neurodegenerative disorder caused by expansion of a CAG repeat within the Huntingtin (HTT) gene, though the clinical presentation of disease and age-of-onset are strongly influenced by ill-defined environmental factors. We recently reported a gene-environment interaction wherein expression of mutant HTT is associated with neuroprotection against manganese (Mn) toxicity. Here, we are testing the hypothesis that this interaction may be manifested by altered protein expression patterns in striatum, a primary target of both neurodegeneration in HD and neurotoxicity of Mn. To this end we compared striatal proteomes of wild-type and HD (YAC128Q) mice exposed to vehicle or Mn. Principal component analysis of proteomic data revealed that Mn exposure disrupted a segregation of WT versus mutant proteomes by the major principal component in vehicle-exposed mice. Identification of altered proteins revealed novel markers of Mn toxicity, particularly proteins involved in glycolysis, excitotoxicity and cytoskeletal dynamics. In addition, YAC128Q dependent changes suggest that axonal pathology may be an early feature in HD pathogenesis. Finally, for several proteins, genotype-specific responses to Mn were observed. These differences include increased sensitivity to exposure in YAC128Q mice (UBQLN1) and amelioration of some mutant HTT-induced alterations (SAE1, ENO1). We conclude that the interaction of Mn and mutant HTT may suppress proteomic phenotypes of YAC128Q mice, which could reveal potential targets in novel treatment strategies for HD.
doi:10.1021/pr200839d
PMCID: PMC3319668  PMID: 22191580
Huntington disease; Manganese toxicity; gene-environment interaction; striatum; mouse
25.  Trends in US Pediatric Drowning Hospitalizations, 1993–2008 
Pediatrics  2012;129(2):275-281.
BACKGROUND:
In the United States, drowning is the second leading cause of unintentional injury death in children aged 1 to 19 years, accounting for nearly 1100 deaths per year. Although a decline in overall fatal drowning deaths among children has been noted, national trends and disparities in pediatric drowning hospitalizations have not been reported.
METHODS:
To describe trends in pediatric drowning in the United States and provide national benchmarks for state and regional comparisons, we analyzed existing data (1993–2008) from the Nationwide Inpatient Sample, the largest, longitudinal, all-payer inpatient care database in the United States. Children aged 0 to 19 years were included. Annual rates of drowning-related hospitalizations were determined, stratified by age, gender, and outcome.
RESULTS:
From 1993 to 2008, the estimated annual incidence rate of pediatric hospitalizations associated with drowning declined 49% from 4.7 to 2.4 per 100 000 (P < .001). The rates declined for all age groups and for both males and females. The hospitalization rate for males remained consistently greater than for females at each point in time. Rates of fatal drowning hospitalization declined from 0.5 (95% confidence interval, 0.4–0.7) deaths per 100 000 in 1993–1994 to 0.3 (95% confidence interval, 0.2–0.4) in 2007–2008 (P < .01). No difference was observed in the mean hospital length of stay over time.
CONCLUSIONS:
Pediatric hospitalization rates for drowning have decreased over the past 16 years. Our study provides national estimates of pediatric drowning hospitalization that can be used as benchmarks to target and assess prevention strategies.
doi:10.1542/peds.2011-2491
PMCID: PMC3269118  PMID: 22250031
drowning; pediatric; hospitalization; incidence; trends

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