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1.  Molecular Imprint of Exposure to Naturally Occurring Genetic Variants of Human Cytomegalovirus on the T cell Repertoire 
Scientific Reports  2014;4:3993.
Exposure to naturally occurring variants of herpesviruses in clinical settings can have a dramatic impact on anti-viral immunity. Here we have evaluated the molecular imprint of variant peptide-MHC complexes on the T-cell repertoire during human cytomegalovirus (CMV) infection and demonstrate that primary co-infection with genetic variants of CMV was coincident with development of strain-specific T-cell immunity followed by emergence of cross-reactive virus-specific T-cells. Cross-reactive CMV-specific T cells exhibited a highly conserved public T cell repertoire, while T cells directed towards specific genetic variants displayed oligoclonal repertoires, unique to each individual. T cell recognition foot–print and pMHC-I structural analyses revealed that the cross-reactive T cells accommodate alterations in the pMHC complex with a broader foot-print focussing on the core of the peptide epitope. These findings provide novel molecular insight into how infection with naturally occurring genetic variants of persistent human herpesviruses imprints on the evolution of the anti-viral T-cell repertoire.
doi:10.1038/srep03993
PMCID: PMC3918921  PMID: 24509977
2.  Computer Surveillance of Patients at High Risk for and with Venous Thromboembolism 
Venous thromboembolism (VTE), including deep vein thrombosis (DVT) and pulmonary embolism (PE), may be the number one preventable cause of death associated with hospitalization. Numerous evidence-based guidelines for effective VTE prophylaxis therapy exist. However, underuse is common due to the difficulty in integrating VTE risk assessment into routine patient care. Previous studies utilizing computer decision support to identify high-risk patients report improved use of prophylaxis therapy and reduced VTE. However, those studies did not report the sensitivity, specificity or positive predictive value of their methods to identify patients at high risk. We report an evaluation of a computerized tool to identify patients at high risk for VTE that found a sensitivity of 98% and positive predictive value of 99%. Another computer program used to detect VTE had a sensitivity of 92%, specificity of 99% and a positive predictive value of 97% to identify DVT and a sensitivity of 100%, specificity of 98% and positive predictive value of 89% to identify PE. These tools were found to provide a dependable method to identify patients at high risk for and with VTE.
PMCID: PMC3041332  PMID: 21346972
3.  Genome-wide association study identifies novel breast cancer susceptibility loci 
Easton, Douglas F. | Pooley, Karen A. | Dunning, Alison M. | Pharoah, Paul D. P. | Thompson, Deborah | Ballinger, Dennis G. | Struewing, Jeffery P. | Morrison, Jonathan | Field, Helen | Luben, Robert | Wareham, Nicholas | Ahmed, Shahana | Healey, Catherine S. | Bowman, Richard | Meyer, Kerstin B. | Haiman, Christopher A. | Kolonel, Laurence K. | Henderson, Brian E. | Marchand, Loic Le | Brennan, Paul | Sangrajrang, Suleeporn | Gaborieau, Valerie | Odefrey, Fabrice | Shen, Chen-Yang | Wu, Pei-Ei | Wang, Hui-Chun | Eccles, Diana | Evans, D. Gareth | Peto, Julian | Fletcher, Olivia | Johnson, Nichola | Seal, Sheila | Stratton, Michael R. | Rahman, Nazneen | Chenevix-Trench, Georgia | Bojesen, Stig E. | Nordestgaard, Børge G. | Axelsson, Christen K. | Garcia-Closas, Montserrat | Brinton, Louise | Chanock, Stephen | Lissowska, Jolanta | Peplonska, Beata | Nevanlinna, Heli | Fagerholm, Rainer | Eerola, Hannaleena | Kang, Daehee | Yoo, Keun-Young | Noh, Dong-Young | Ahn, Sei-Hyun | Hunter, David J. | Hankinson, Susan E. | Cox, David G. | Hall, Per | Wedren, Sara | Liu, Jianjun | Low, Yen-Ling | Bogdanova, Natalia | Schürmann, Peter | Dörk, Thilo | Tollenaar, Rob A. E. M. | Jacobi, Catharina E. | Devilee, Peter | Klijn, Jan G. M. | Sigurdson, Alice J. | Doody, Michele M. | Alexander, Bruce H. | Zhang, Jinghui | Cox, Angela | Brock, Ian W. | MacPherson, Gordon | Reed, Malcolm W. R. | Couch, Fergus J. | Goode, Ellen L. | Olson, Janet E. | Meijers-Heijboer, Hanne | van den Ouweland, Ans | Uitterlinden, André | Rivadeneira, Fernando | Milne, Roger L. | Ribas, Gloria | Gonzalez-Neira, Anna | Benitez, Javier | Hopper, John L. | McCredie, Margaret | Southey, Melissa | Giles, Graham G. | Schroen, Chris | Justenhoven, Christina | Brauch, Hiltrud | Hamann, Ute | Ko, Yon-Dschun | Spurdle, Amanda B. | Beesley, Jonathan | Chen, Xiaoqing | Mannermaa, Arto | Kosma, Veli-Matti | Kataja, Vesa | Hartikainen, Jaana | Day, Nicholas E. | Cox, David R. | Ponder, Bruce A. J. | Luccarini, Craig | Conroy, Don | Shah, Mitul | Munday, Hannah | Jordan, Clare | Perkins, Barbara | West, Judy | Redman, Karen | Driver, Kristy | Aghmesheh, Morteza | Amor, David | Andrews, Lesley | Antill, Yoland | Armes, Jane | Armitage, Shane | Arnold, Leanne | Balleine, Rosemary | Begley, Glenn | Beilby, John | Bennett, Ian | Bennett, Barbara | Berry, Geoffrey | Blackburn, Anneke | Brennan, Meagan | Brown, Melissa | Buckley, Michael | Burke, Jo | Butow, Phyllis | Byron, Keith | Callen, David | Campbell, Ian | Chenevix-Trench, Georgia | Clarke, Christine | Colley, Alison | Cotton, Dick | Cui, Jisheng | Culling, Bronwyn | Cummings, Margaret | Dawson, Sarah-Jane | Dixon, Joanne | Dobrovic, Alexander | Dudding, Tracy | Edkins, Ted | Eisenbruch, Maurice | Farshid, Gelareh | Fawcett, Susan | Field, Michael | Firgaira, Frank | Fleming, Jean | Forbes, John | Friedlander, Michael | Gaff, Clara | Gardner, Mac | Gattas, Mike | George, Peter | Giles, Graham | Gill, Grantley | Goldblatt, Jack | Greening, Sian | Grist, Scott | Haan, Eric | Harris, Marion | Hart, Stewart | Hayward, Nick | Hopper, John | Humphrey, Evelyn | Jenkins, Mark | Jones, Alison | Kefford, Rick | Kirk, Judy | Kollias, James | Kovalenko, Sergey | Lakhani, Sunil | Leary, Jennifer | Lim, Jacqueline | Lindeman, Geoff | Lipton, Lara | Lobb, Liz | Maclurcan, Mariette | Mann, Graham | Marsh, Deborah | McCredie, Margaret | McKay, Michael | McLachlan, Sue Anne | Meiser, Bettina | Milne, Roger | Mitchell, Gillian | Newman, Beth | O'Loughlin, Imelda | Osborne, Richard | Peters, Lester | Phillips, Kelly | Price, Melanie | Reeve, Jeanne | Reeve, Tony | Richards, Robert | Rinehart, Gina | Robinson, Bridget | Rudzki, Barney | Salisbury, Elizabeth | Sambrook, Joe | Saunders, Christobel | Scott, Clare | Scott, Elizabeth | Scott, Rodney | Seshadri, Ram | Shelling, Andrew | Southey, Melissa | Spurdle, Amanda | Suthers, Graeme | Taylor, Donna | Tennant, Christopher | Thorne, Heather | Townshend, Sharron | Tucker, Kathy | Tyler, Janet | Venter, Deon | Visvader, Jane | Walpole, Ian | Ward, Robin | Waring, Paul | Warner, Bev | Warren, Graham | Watson, Elizabeth | Williams, Rachael | Wilson, Judy | Winship, Ingrid | Young, Mary Ann | Bowtell, David | Green, Adele | deFazio, Anna | Chenevix-Trench, Georgia | Gertig, Dorota | Webb, Penny
Nature  2007;447(7148):1087-1093.
Breast cancer exhibits familial aggregation, consistent with variation in genetic susceptibility to the disease. Known susceptibility genes account for less than 25% of the familial risk of breast cancer, and the residual genetic variance is likely to be due to variants conferring more moderate risks. To identify further susceptibility alleles, we conducted a two-stage genome-wide association study in 4,398 breast cancer cases and 4,316 controls, followed by a third stage in which 30 single nucleotide polymorphisms (SNPs) were tested for confirmation in 21,860 cases and 22,578 controls from 22 studies. We used 227,876 SNPs that were estimated to correlate with 77% of known common SNPs in Europeans at r2>0.5. SNPs in five novel independent loci exhibited strong and consistent evidence of association with breast cancer (P<10−7). Four of these contain plausible causative genes (FGFR2, TNRC9, MAP3K1 and LSP1). At the second stage, 1,792 SNPs were significant at the P<0.05 level compared with an estimated 1,343 that would be expected by chance, indicating that many additional common susceptibility alleles may be identifiable by this approach.
doi:10.1038/nature05887
PMCID: PMC2714974  PMID: 17529967
4.  Activity and kinetics of dissociation and transfer of amphotericin B from a novel delivery form 
AAPS PharmSci  1999;1(3):21-31.
Recently it has been demonstrated that moderate heat treatment of Amphotericin B/deoxycholate solutions (HAmB-DOC) leads to a therapeutically interesting supramolecular rearrangement that can be observed by significant changes in light scattering, CD, and absorbance. In this study, we continue the investigation of the physical properties of this new form by evaluating the activity and kinetics of dissociation and dispersion of HAmB-DOC and AmB-DOC in saline, serum, and in model mammalian or fungal lipid biomimetic membrane vesicles. Stopped-flow spectrophotometry combined with singular value decomposition (SVD) and global analysis were used to resolve the components of this process. The dissociation kinetics for both states are complex, requiring multiexponential fits, vet in most cases SVD indicates only two significant changing species representing the monomer and the aggregate. The kinetic mechanism could involve dissociation of monomers from coexisting spectroscopically similar but structurally distinct aggregates or sequential rearrangements in supramolecular structure of aggregates. Rate constants and amplitudes of dissociation from aggregates to monomer in buffer, whole serum, 10% cholesterol, and ergosterol membrane vesicles are generally greater for AmB-DOC, demonstrating its greater kinetic instability. In addition, at comparable low concentrations, HAmB-DOC and AmB-DOC are nearly equally active at promoting cation selective permeability in ergosterol-containing membranes; however, HAmB-DOC is much less active against mammalian mimetic cholesterol-containing vesicles, despite a higher level of self-association, supporting previous observations that there exists a specific “toxic aggregate” structure.
doi:10.1208/ps010310
PMCID: PMC2761124  PMID: 11741206
6.  Imaging patients with psychosis and a mouse model establishes a spreading pattern of hippocampal dysfunction and implicates glutamate as a pathogenic driver 
Neuron  2013;78(1):81-93.
SUMMARY
The hippocampus in schizophrenia is characterized by both hypermetabolism and reduced size. It remains unknown whether these abnormalities are mechanistically linked. Here, in addressing these questions we used MRI tools that can map hippocampal metabolism and structure in patients and mouse models. In at-risk patients, hypermetabolism was found to begin in CA1 and spread to the subiculum after psychosis onset. CA1 hypermetabolism at baseline predicted hippocampal atrophy, which occured during progression to psychosis, most prominently in similar regions. Next, we used ketamine to model conditions of acute psychosis in mice. Acute ketamine reproduced a regional pattern of hippocampal hypermetabolism, while repeated exposure shifted the hippocampus to a hypermetabolic state with concurrent atrophy and pathology in parvalbumin-expressing interneurons. Parallel in vivo experiments using LY379268 and direct measurements of extracellular glutamate showed that glutamate drives both neuroimaging abnormalities. These findings show that hippocampal hypermetabolism leads to atrophy in psychotic disorder and suggest glutamate as a pathogenic driver.
doi:10.1016/j.neuron.2013.02.011
PMCID: PMC3966570  PMID: 23583108
7.  Association of Single-Nucleotide Polymorphisms of the Tau Gene With Late-Onset Parkinson Disease 
Context
The human tau gene, which promotes assembly of neuronal microtubules, has been associated with several rare neurologic diseases that clinically include parkinsonian features. We recently observed linkage in idiopathic Parkinson disease (PD) to a region on chromosome 17q21 that contains the tau gene. These factors make tau a good candidate for investigation as a susceptibility gene for idiopathic PD, the most common form of the disease.
Objective
To investigate whether the tau gene is involved in idiopathic PD.
Design, Setting, and Participants
Among a sample of 1056 individuals from 235 families selected from 13 clinical centers in the United States and Australia and from a family ascertainment core center, we tested 5 single-nucleotide polymorphisms (SNPs) within the tau gene for association with PD, using family-based tests of association. Both affected (n = 426) and unaffected (n = 579) family members were included; 51 individuals had unclear PD status. Analyses were conducted to test individual SNPs and SNP haplotypes within the tau gene.
Main Outcome Measure
Family-based tests of association, calculated using asymptotic distributions.
Results
Analysis of association between the SNPs and PD yielded significant evidence of association for 3 of the 5 SNPs tested: SNP 3, P = .03; SNP 9i, P = .04; and SNP 11, P = .04. The 2 other SNPs did not show evidence of significant association (SNP 9ii, P = .11, and SNP 9iii, P = .87). Strong evidence of association was found with haplotype analysis, with a positive association with one haplotype (P = .009) and a negative association with another haplotype (P = .007). Substantial linkage disequilibrium (P<.001) was detected between 4 of the 5 SNPs (SNPs 3,9i, 9ii, and 11).
Conclusions
This integrated approach of genetic linkage and positional association analyses implicates tau as a susceptibility gene for idiopathic PD.
PMCID: PMC3973175  PMID: 11710889
8.  A novel application of propensity score matching to estimate Alcoholics Anonymous’ effect on drinking outcomes 
Drug and alcohol dependence  2012;129(1-2):54-59.
Background
Randomized controlled trials (RCTs) of mutual aid, including Alcoholics Anonymous (AA), are notoriously difficult to conduct and correlational studies are problematic to interpret due to potential confounds.
Methods
A secondary analysis was conducted of Project MATCH, a RCT of alcoholism treatments. Although MATCH did not randomly assign subjects to AA vs. no AA, the 12 Step Facilitation (TSF) condition did result in a higher proportion of subjects attending community AA meetings than in the other two treatment conditions. The key inference is that there exists a latent subgroup in MATCH who attended AA only because its constituents received TSF, not because of the “normal” factors leading to self-selection of AA. A novel application of propensity score matching (PSM) allowed four latent AA-related subgroups to be identified to estimate an unconfounded effect of AA on drinking outcomes.
Results
The study hypotheses were supported: subjects who consistently attended AA solely due to their exposure to TSF (the “Added AA” subgroup) had better drinking outcomes than equivalent subjects who did not consistently attend AA, but would have so attended, had they been exposed to TSF (the “Potential AA” subgroup); this indicates an AA effect on drinking.
Conclusions
The analysis presents evidence that consistent AA attendance improves drinking outcomes, independent of “normal” confounding factors that make correlations between AA attendance and outcomes difficult to interpret.
doi:10.1016/j.drugalcdep.2012.09.011
PMCID: PMC3549307  PMID: 23040721
propensity score; Alcoholics Anonymous; Project MATCH; self-help groups; alcoholism; bootstrapping
9.  A Meta-analysis of Genome-wide Association Studies for Serum Total IgE in Diverse Study Populations 
Background
Immunoglobulin E (IgE) is both a marker and mediator of allergic inflammation. Despite reported differences in serum total IgE levels by race-ethnicity, African American and Latino individuals have not been well represented in genetic studies of total IgE.
Objective
To identify the genetic predictors of serum total IgE levels.
Methods
We used genome wide association (GWA) data from 4,292 individuals (2,469 African Americans, 1,564 European Americans, and 259 Latinos) in the EVE Asthma Genetics Consortium. Tests for association were performed within each cohort by race-ethnic group (i.e., African American, Latino, and European American) and asthma status. The resulting p-values were meta-analyzed accounting for sample size and direction of effect. Top single nucleotide polymorphism (SNP) associations from the meta-analysis were reassessed in six additional cohorts comprising 5,767 individuals.
Results
We identified 10 unique regions where the combined association statistic was associated with total serum IgE levels (P-value <5.0×10−6) and the minor allele frequency was ≥5% in two or more population groups. Variant rs9469220, corresponding to HLA-DQB1, was the most significantly associated SNP with serum total IgE levels when assessed in both the replication cohorts and the discovery and replication sets combined (P-value = 0.007 and 2.45×10−7, respectively). In addition, findings from earlier GWA studies were also validated in the current meta-analysis.
Conclusion
This meta-analysis independently identified a variant near HLA-DQB1 as a predictor of total serum IgE in multiple race-ethnic groups. This study also extends and confirms the findings of earlier GWA analyses in African American and Latino individuals.
doi:10.1016/j.jaci.2012.10.002
PMCID: PMC3596497  PMID: 23146381
meta-analysis; genome wide association study; total immunoglobulin E; race-ethnicity; continental population groups
10.  Cixutumumab and temsirolimus for patients with bone and soft-tissue sarcoma: a multicentre, open-label, phase 2 trial 
The lancet oncology  2013;14(4):371-382.
Summary
Background
Preclinical studies have shown synergistic antitumour activity by inhibition of insulin-like growth factor-1 receptor (IGF-1R) and mTOR. The expression of IGF-1R seems to be crucial for this effect. We investigated the safety and efficacy of the combination of the IGF-1R antibody cixutumumab and the mTOR inhibitor temsirolimus in patients with chemotherapy-refractory bone and soft-tissue sarcomas according to IGF-1R expression by immunohistochemistry.
Methods
We undertook a multicentre, open-label, phase 2 study in 19 cancer centres in the USA. Patients aged at least 16 years with a histologically confirmed diagnosis of bone or soft-tissue sarcoma were allocated on the basis of IGF-1R expression by immunohistochemistry to one of three treatment groups: IGF-1R-positive soft-tissue sarcoma (group A), IGF-1R-positive bone sarcomas (group B), or IGF-1R-negative bone and soft-tissue sarcoma (group C). Patients received weekly treatment with cixutumumab (6 mg/kg, intravenous) and temsirolimus (25 mg, intravenous flat dose) in 6-week cycles. A Simon optimal two-stage design was used for every arm. The primary endpoint was progression-free survival (PFS) at 12 weeks by intention-to-treat analysis in the first 54 patients assigned to every treatment arm. Although patients still remain on treatment, this trial has completed enrolment and this represents the final analysis. This study is registered with ClinicalTrials.gov, number NCT01016015.
Findings
Between Nov 18, 2009, and April 11, 2012, 388 patients were screened for IGF-1R expression and 54 were assigned to each arm. 17 of 54 patients in the IGF-1R-positive soft-tissue sarcoma group (31%; one-sided 95% CI lower bound 21%; two-sided 90% CI 21–43), 19 of 54 in IGF-1R-positive bone sarcoma group (35%; one-sided 95% CI lower bound 24%; two-sided 90% CI 24–47), and 21 of 54 in the IGF-1R-negative group (39%, one-sided 95% CI lower bound 28%; two-sided 90% CI 28–51) were progression free at 12 weeks. On April 6, 2011, the protocol was amended to include three additional patients in the IGF-1R-positive soft-tissue sarcoma group (total of 57 patients) and nine more in the IGF-1R-negative group (total of 63 patients). There were 2546 adverse events reported during the study, 214 (8%) of which were grade 3–4. The most common grade 3–4 toxicities in the 174 treated patients were anaemia in 16 (9%) patients, hyperglycaemia in 18 (10%), hypophosphataemia in 16 (9%), lymphopenia in 25 (14%), oral mucositis in 19 (11%), and thrombocytopenia in 19 (11%).
Interpretation
The combination of cixutumumab and temsirolimus shows clinical activity in patients with sarcoma and forms a basis for future trials. However, IGF-1R expression by immunohistochemistry is not predictive of clinical outcome after treatment with this combination.
Funding
National Cancer Institute and Cycle for Survival Fund, Memorial Sloan-Kettering Cancer Center.
doi:10.1016/S1470-2045(13)70049-4
PMCID: PMC3766955  PMID: 23477833
11.  Abrogation of MLL-AF10 and CALM-AF10 mediated transformation through genetic inactivation or pharmacological inhibition of the H3K79 methyltransferase Dot1l 
Leukemia  2012;27(4):813-822.
The t(10;11)(p12;q23) translocation and the t(10;11)(p12;q14) translocation, which encode the MLL-AF10 and CALM-AF10 fusion oncoproteins respectively, are two recurrent chromosomal rearrangements observed in patients with acute myeloid leukemia and acute lymphoblastic leukemia. Here we demonstrate that MLL-AF10 and CALM-AF10 mediated transformation is dependent on the H3K79 methyltransferase Dot1l using genetic and pharmacological approaches in mouse models. Targeted disruption of Dot1l using a conditional knockout mouse model abolished in vitro transformation of murine bone marrow cells and in vivo initiation and maintenance of MLL-AF10 or CALM-AF10 leukemia.. Treatment of MLL-AF10 and CALM-AF10 transformed cells with EPZ004777, a specific small-molecule inhibitor of Dot1l, suppressed expression of leukemogenic genes such as Hoxa cluster genes and Meis1, and selectively suppressed proliferation of MLL-AF10 and CALM-AF10 transformed cells. Pretreatment with EPZ004777 profoundly decreased the in vivo spleen-colony forming ability of MLL-AF10 or CALM-AF10 transformed bone marrow cells. These results show that patients with leukemias bearing chromosomal translocations that involve the AF10 gene may benefit from small molecule therapeutics that inhibit H3K79 methylation.
doi:10.1038/leu.2012.327
PMCID: PMC3932800  PMID: 23138183
MLL-AF10; CALM-AF10; MLL fusions; leukemia; Dot1l; EPZ004777
12.  Effectiveness of MR Angiography for the Primary Diagnosis of Acute Pulmonary Embolism: Clinical Outcomes at 3 Months and 1 Year 
Purpose
To determine the effectiveness of MR angiography for pulmonary embolism (MRA-PE) in symptomatic patients.
Materials and Methods
We retrospectively reviewed all patients whom were evaluated for possible pulmonary embolism (PE) using MRA-PE. A 3-month and 1-year from MRA-PE electronic medical record (EMR) review was performed. Evidence for venous thromboembolism (VTE) (or death from PE) within the year of follow-up was the outcome surrogate for this study.
Results
There were 190 MRA-PE exams performed with 97.4% (185/190) of diagnostic quality. There were 148 patients (120 F: 28 M) that had both a diagnostic MRA-PE exam and 1 complete year of EMR follow-up. There were 167 patients (137 F: 30 M) with 3 months or greater follow-up. We found 83% (139/167) and 81% (120/148) MRA-PE exams negative for PE at 3 months and 1 year, respectively. Positive exams for PE were seen in 14% (23/167). During the 1-year follow-up period, five patients (false negative) were diagnosed with DVT (5/148 = 3.4 %), and one of these patients also experienced a non–life-threatening PE. The negative predictive value (NPV) for MRA-PE was 97% (92–99; 95% CI) at 3 months and 96% (90–98; 95% CI) with 1 year of follow-up.
Conclusion
The NPV of MRA-PE, when used for the primary diagnosis of pulmonary embolism in symptomatic patients, were found to be similar to the published values for CTA-PE. In addition, the technical success rate and safety of MRA-PE were excellent.
doi:10.1002/jmri.24057
PMCID: PMC3970266  PMID: 23553735
pulmonary embolism; magnetic resonance angiography; effectiveness; outcomes analysis; negative predictive value
13.  Combined Approach to Lysis Utilizing Eptifibatide and Recombinant Tissue Plasminogen Activator in Acute Ischemic Stroke–Enhanced Regimen Stroke Trial 
Background and Purpose
In a previous study, 0.3 and 0.45 mg/kg of intravenous recombinant tissue plasminogen activator (rt-PA) were safe when combined with eptifibatide 75 mcg/kg bolus and a 2-hour infusion (0.75 mcg/kg per minute). The Combined Approach to Lysis Utilizing Eptifibatide and rt-PA in Acute Ischemic Stroke–Enhanced Regimen (CLEAR-ER) trial sought to determine the safety of a higher-dose regimen and to establish evidence for a phase III trial.
Methods
CLEAR-ER was a multicenter, double-blind, randomized safety study. Ischemic stroke patients were randomized to 0.6 mg/kg rt-PA plus eptifibatide (135 mcg/kg bolus and a 2-hour infusion at 0.75 mcg/kg per minute) versus standard rt-PA (0.9 mg/kg). The primary safety end point was the incidence of symptomatic intracranial hemorrhage within 36 hours. The primary efficacy outcome measure was the modified Rankin Scale (mRS) score ≤1 or return to baseline mRS at 90 days. Analysis of the safety and efficacy outcomes was done with multiple logistic regression.
Results
Of 126 subjects, 101 received combination therapy, and 25 received standard rt-PA. Two (2%) patients in the combination group and 3 (12%) in the standard group had symptomatic intracranial hemorrhage (odds ratio, 0.15; 95% confidence interval, 0.01–1.40; P=0.053). At 90 days, 49.5% of the combination group had mRS ≤1 or return to baseline mRS versus 36.0% in the standard group (odds ratio, 1.74; 95% confidence interval, 0.70–4.31; P=0.23). After adjusting for age, baseline National Institutes of Health Stroke Scale, time to intravenous rt-PA, and baseline mRS, the odds ratio was 1.38 (95% confidence interval, 0.51–3.76; P=0.52).
Conclusions
The combined regimen of intravenous rt-PA and eptifibatide studied in this trial was safe and provides evidence that a phase III trial is warranted to determine efficacy of the regimen.
doi:10.1161/STROKEAHA.113.001059
PMCID: PMC3970761  PMID: 23887841
clinical trial; eptifibatide; ischemic stroke; tissue plasminogen activator
14.  Development of Dual PLD1/2 and PLD2 Selective Inhibitors From a Common 1,3,8-Triazaspiro[4.5]decane Core: Discovery of ML298 and ML299 that Decrease Invasive Migration in U87-MG Glioblastoma Cells 
Journal of medicinal chemistry  2013;56(6):2695-2699.
An iterative parallel synthesis effort identified a PLD2 selective inhibitor, ML298 (PLD1 IC50 >20,000 nM, PLD2 IC50 = 355 nM) and a dual PLD1/2 inhibitor, ML299 (PLD1 IC50 = 6 nM, PLD2 IC50 = 20 nM). SAR studies revealed a small structural change (incorporation of a methyl group) increased PLD1 activity within this classically PLD2-preferring core, and that the effect was enantiospecific. Both probes decreased invasive migration in U87-MG glioblastoma cells.
doi:10.1021/jm301782e
PMCID: PMC3632306  PMID: 23445448
Phospholipase D; PLD1; PLD2; ML299; ML298; MLPCN probe
15.  Moderators of Post-Binge Eating Negative Emotion in Eating Disorders 
Journal of psychiatric research  2012;47(3):323-328.
The purpose of this study was to test the impact of two variables on post-binge eating negative emotion in a combined sample of women with anorexia nervosa (AN; n = 47) and bulimia nervosa (BN; n = 121). Participants completed two weeks of an ecological momentary assessment protocol during which they provided multiple daily ratings of overall negative affect and guilt and reported eating disorder behaviors including binge eating and self-induced vomiting. The results indicate that both overall negative affect and guilt exhibited a statistically significantly decrease in the hour immediately following binge eating episodes. The decrease in guilt, but not overall negative affect, was moderated by eating disorder diagnosis and the tendency to engage in self-induced vomiting. Specifically, individuals with BN reported a greater reduction in guilt than those with AN, and individuals who did not typically engage in self-induced vomiting reported more decreases in guilt than those who typically engaged in self-induced vomiting. This study extends the existing literature on the relationship between negative affect and eating disorder behaviors, suggesting guilt as a potentially relevant facet of negative affect in the maintenance of binge eating. In addition, the findings indicate that two individual differences, eating disorder diagnosis and self-induced vomiting, may influence the trajectory of guilt following binge eating episodes.
doi:10.1016/j.jpsychires.2012.11.012
PMCID: PMC3570645  PMID: 23245289
anorexia nervosa; bulimia nervosa; negative affect; guilt; ecological momentary assessment
16.  Trait-level and momentary correlates of bulimia nervosa with a history of anorexia nervosa 
Objective
Some investigators have suggested subtyping bulimia nervosa (BN) by anorexia nervosa (AN) history. We examined trait-level and momentary eating-related and psychosocial factors in BN with and without an AN history.
Method
Interview, questionnaire, and ecological momentary assessment data of eating-related and psychological symptoms were collected from 122 women with BN, including 43 with (BN+) and 79 without an AN history (BN−).
Results
Body mass index (kg/m2) was lower in BN+ than BN− (p=.001). Groups did not differ on trait-level anxiety, shape/weight concerns, psychiatric comorbidity, or dietary restraint; or on momentary anxiety, dietary restriction, binge eating, purging, or exercise frequency, or affective patterns surrounding binge/purge behaviors. Negative affect increased prior to exercise and decreased thereafter in BN+ but not BN−, although groups did not statistically differ.
Discussion
Results do not support formally subtyping BN by AN history. Exercise in BN+ may modulate negative affect, which could have important treatment implications.
doi:10.1002/eat.22054
PMCID: PMC3570735  PMID: 22987478
eating disorders; bulimia nervosa; history of anorexia nervosa; subtyping; classification; exercise
17.  Predicting bycatch hotspots for endangered leatherback turtles on longlines in the Pacific Ocean 
Fisheries bycatch is a critical source of mortality for rapidly declining populations of leatherback turtles, Dermochelys coriacea. We integrated use-intensity distributions for 135 satellite-tracked adult turtles with longline fishing effort to estimate predicted bycatch risk over space and time in the Pacific Ocean. Areas of predicted bycatch risk did not overlap for eastern and western Pacific nesting populations, warranting their consideration as distinct management units with respect to fisheries bycatch. For western Pacific nesting populations, we identified several areas of high risk in the north and central Pacific, but greatest risk was adjacent to primary nesting beaches in tropical seas of Indo-Pacific islands, largely confined to several exclusive economic zones under the jurisdiction of national authorities. For eastern Pacific nesting populations, we identified moderate risk associated with migrations to nesting beaches, but the greatest risk was in the South Pacific Gyre, a broad pelagic zone outside national waters where management is currently lacking and may prove difficult to implement. Efforts should focus on these predicted hotspots to develop more targeted management approaches to alleviate leatherback bycatch.
doi:10.1098/rspb.2013.2559
PMCID: PMC3896015  PMID: 24403331
critically endangered species; fisheries bycatch; marine conservation; marine turtles; migratory pelagic vertebrate; satellite tracking
18.  A Biophysical Basis for Mucus Solids Concentration as a Candidate Biomarker for Airways Disease 
PLoS ONE  2014;9(2):e87681.
In human airways diseases, including cystic fibrosis (CF) and chronic obstructive pulmonary disease (COPD), host defense is compromised and airways inflammation and infection often result. Mucus clearance and trapping of inhaled pathogens constitute key elements of host defense. Clearance rates are governed by mucus viscous and elastic moduli at physiological driving frequencies, whereas transport of trapped pathogens in mucus layers is governed by diffusivity. There is a clear need for simple and effective clinical biomarkers of airways disease that correlate with these properties. We tested the hypothesis that mucus solids concentration, indexed as weight percent solids (wt%), is such a biomarker. Passive microbead rheology was employed to determine both diffusive and viscoelastic properties of mucus harvested from human bronchial epithelial (HBE) cultures. Guided by sputum from healthy (1.5–2.5 wt%) and diseased (COPD, CF; 5 wt%) subjects, mucus samples were generated in vitro to mimic in vivo physiology, including intermediate range wt% to represent disease progression. Analyses of microbead datasets showed mucus diffusive properties and viscoelastic moduli scale robustly with wt%. Importantly, prominent changes in both biophysical properties arose at ∼4 wt%, consistent with a gel transition (from a more viscous-dominated solution to a more elastic-dominated gel). These findings have significant implications for: (1) penetration of cilia into the mucus layer and effectiveness of mucus transport; and (2) diffusion vs. immobilization of micro-scale particles relevant to mucus barrier properties. These data provide compelling evidence for mucus solids concentration as a baseline clinical biomarker of mucus barrier and clearance functions.
doi:10.1371/journal.pone.0087681
PMCID: PMC3928107  PMID: 24558372
19.  Safety, tolerability, and biomarkers of the treatment of mice with aerosolized Toll-like receptor ligands 
We have previously discovered a synergistically therapeutic combination of two Toll-like receptor ligands, an oligodeoxynucleotide (ODN) and Pam2CSK4. Aerosolization of these ligands stimulates innate immunity within the lungs to prevent pneumonia from bacterial and viral pathogens. Here we examined the safety and tolerability of this treatment in mice, and characterized the expression of biomarkers of innate immune activation. We found that neutrophils appeared in lung lavage fluid 4 h after treatment, reached a peak at 48 h, and resolved by 7 days. The peak of neutrophil influx was accompanied by a small increase in lung permeability. Despite the abundance of neutrophils in lung lavage fluid, only rare neutrophils were visible histopathologically in the interstitium surrounding bronchi and veins and none were visible in alveolar airspaces. The cytokines interleukin 6 (IL-6), tumour necrosis factor, and Chemokine (C-X-C motif) ligand 2 rose several hundred-fold in lung lavage fluid 4 h after treatment in a dose-dependent and synergistic manner, providing useful biomarkers of lung activation. IL-6 rose fivefold in serum with delayed kinetics compared to its rise in lavage fluid, and might serve as a systemic biomarker of immune activation of the lungs. The dose–response relationship of lavage fluid cytokines was preserved in mice that underwent myeloablative treatment with cytosine arabinoside to model the treatment of hematologic malignancy. There were no overt signs of distress in mice treated with ODN/Pam2CSK4 in doses up to eightfold the therapeutic dose, and no changes in temperature, respiratory rate, or behavioral signs of sickness including sugar water preference, food disappearance, cage exploration or social interaction, though there was a small degree of transient weight loss. We conclude that treatment with aerosolized ODN/Pam2CSK4 is well tolerated in mice, and that innate immune activation of the lungs can be monitored by the measurement of inflammatory cytokines in lung lavage fluid and serum.
doi:10.3389/fphar.2014.00008
PMCID: PMC3915096  PMID: 24567720
pneumonia; innate immunity; Toll-like receptor; oligodeoxynucleotide; lipopeptide; aerosol; myeloablation
20.  Enhanced Bioactivity of Silybin B Methylation Products 
Bioorganic & medicinal chemistry  2012;21(3):742-747.
Flavonolignans from milk thistle (Silybum marianum) have been investigated for their cellular modulatory properties, including cancer chemoprevention and hepatoprotection, as an extract (silymarin), as partially purified mixtures (silibinin and isosilibinin), and as pure compounds (a series of seven isomers). One challenge with the use of these compounds in vivo is their relatively short half-life due to conjugation, particularly glucuronidation. In an attempt to generate analogues with improved in vivo properties, particularly reduced metabolic liability, a semi-synthetic series was prepared in which the hydroxy groups of silybin B were alkylated. A total of five methylated analogues of silybin B were synthesized using standard alkylation conditions (dimethyl sulfate and potassium carbonate in acetone), purified using preparative HPLC, and elucidated via spectroscopy and spectrometry. Of the five, one was monomethylated (3), one was dimethylated (4), two were trimethylated (2 and 6), and one was tetramethylated (5). The relative potency of all compounds was determined in a 72 hr growth-inhibition assay against a panel of three prostate cancer cell lines (DU-145, PC-3, and LNCaP) and a human hepatoma cell line (Huh7.5.1) and compared to natural silybin B. Compounds also were evaluated for inhibition of both cytochrome P450 2C9 (CYP2C9) activity in human liver microsomes and hepatitis C virus infection in Huh7.5.1 cells. The monomethyl and dimethyl analogues were shown to have enhanced activity in terms of cytotoxicity, CYP2C9 inhibitory potency, and antiviral activity (up to 6-fold increased potency) compared to the parent compound, silybin B. In total, these data suggested that methylation of flavonolignans can increase bioactivity.
doi:10.1016/j.bmc.2012.11.035
PMCID: PMC3630461  PMID: 23260576
Silybin B; Milk thistle; Silybum marianum; Flavonolignans; Methylation
21.  ACPA-positive and ACPA-negative rheumatoid arthritis differ in their requirements for combination DMARDs and corticosteroids: secondary analysis of a randomized controlled trial 
Introduction
UK guidelines recommend that all early active rheumatoid arthritis (RA) patients are offered combination disease-modifying antirheumatic drugs (DMARDs) and short-term corticosteroids. Anti-citrullinated protein antibody (ACPA)-positive and ACPA-negative RA may differ in their treatment responses. We used data from a randomized controlled trial - the Combination Anti-Rheumatic Drugs in Early RA (CARDERA) trial - to examine whether responses to intensive combination treatments in early RA differ by ACPA status.
Methods
The CARDERA trial randomized 467 early active RA patients to receive: (1) methotrexate, (2) methotrexate/ciclosporin, (3) methotrexate/prednisolone or (4) methotrexate/ciclosporin/prednisolone in a factorial-design. Patients were assessed every six months for two years. In this analysis we evaluated 431 patients with available ACPA status. To minimize multiple testing we used a mixed-effects repeated measures ANOVA model to test for an interaction between ACPA and treatment on mean changes from baseline for each outcome (Larsen, disease activity scores on a 28-joint count (DAS28), Health Assessment Questionnaire (HAQ), EuroQol, SF-36 physical component summary (PCS) and mental component summary (MCS) scores). When a significant interaction was present, mean changes in outcomes were compared by treatment group at each time point using t-tests stratified by ACPA status. Odds ratios (ORs) for the onset of new erosions with treatment were calculated stratified by ACPA.
Results
ACPA status influenced the need for combination treatments to reduce radiological progression. ACPA-positive patients had significant reductions in Larsen score progression with all treatments. ACPA-positive patients receiving triple therapy had the greatest benefits: two-year mean Larsen score increases comprised 3.66 (95% confidence interval (CI) 2.27 to 5.05) with triple therapy and 9.58 (95% CI 6.76 to 12.39) with monotherapy; OR for new erosions with triple therapy versus monotherapy was 0.32 (95% CI 0.14 to 0.72; P = 0.003). ACPA-negative patients had minimal radiological progression irrespective of treatment. Corticosteroid’s impact on improving DAS28/PCS scores was confined to ACPA-positive RA.
Conclusions
ACPA status influences the need for combination DMARDs and high-dose tapering corticosteroids in early RA. In CARDERA, combination therapy was only required to prevent radiological progression in ACPA-positive patients; corticosteroids only provided significant disease activity and physical health improvements in ACPA-positive disease. This suggests ACPA is an important biomarker for guiding treatment decisions in early RA.
Trial registration
Current Controlled Trials ISRCTN32484878
doi:10.1186/ar4439
PMCID: PMC3979097  PMID: 24433430
22.  Inflammation and Alzheimer’s disease 
Neurobiology of aging  2000;21(3):383-421.
Inflammation clearly occurs in pathologically vulnerable regions of the Alzheimer’s disease (AD) brain, and it does so with the full complexity of local peripheral inflammatory responses. In the periphery, degenerating tissue and the deposition of highly insoluble abnormal materials are classical stimulants of inflammation. Likewise, in the AD brain damaged neurons and neurites and highly insoluble amyloid β peptide deposits and neurofibrillary tangles provide obvious stimuli for inflammation. Because these stimuli are discrete, microlocalized, and present from early preclinical to terminal stages of AD, local upregulation of complement, cytokines, acute phase reactants, and other inflammatory mediators is also discrete, microlocalized, and chronic. Cumulated over many years, direct and bystander damage from AD inflammatory mechanisms is likely to significantly exacerbate the very pathogenic processes that gave rise to it. Thus, animal models and clinical studies, although still in their infancy, strongly suggest that AD inflammation significantly contributes to AD pathogenesis. By better understanding AD inflammatory and immunoregulatory processes, it should be possible to develop anti-inflammatory approaches that may not cure AD but will likely help slow the progression or delay the onset of this devastating disorder.
PMCID: PMC3887148  PMID: 10858586
Alzheimer’s disease; Inflammation; Nervous system; Neuroinflammation; Complement; Cytokine; Chemokine; Acute phase protein; Microglia; Astrocyte; Neuron
23.  ‘Transient’ Genetic Suppression Facilitates Generation of Hexose Transporter Null Mutants in Leishmania mexicana 
Molecular microbiology  2012;87(2):412-429.
Summary
The genome of Leishmania mexicana encompasses a cluster of three glucose transporter genes designated LmxGT1, LmxGT2, and LmxGT3. Functional and genetic studies of a cluster null mutant (Δlmxgt1-3) have dissected the roles of these proteins in Leishmania metabolism and virulence. However, null mutants were recovered at very low frequency, and comparative genome hybridizations revealed that Δlmxgt1-3 mutants contained a linear extrachromosomal 40 kb amplification of a region on chromosome 29 not amplified in WT parasites. These data suggested a model where this 29–40k amplicon encoded a second site suppressor contributing to parasite survival in the absence of GT1-3 function. To test this, we quantified the frequency of recovery of knockouts in the presence of individual overexpressed ORFs covering the 29–40k amplicon. The data mapped the suppressor activity to PIFTC3, encoding a component of the intraflagellar transport pathway. We discuss possible models by which PIFTC3 might act to facilitate loss of GTs specifically. Surprisingly, by plasmid segregation we showed that continued PIFTC3 overexpression was not required for Δlmxgt1-3 viability. These studies provide the first evidence that genetic suppression can occur by providing critical biological functions transiently. This novel form of genetic suppression may extend to other genes, pathways and organisms.
doi:10.1111/mmi.12106
PMCID: PMC3545093  PMID: 23170981
24.  Active MS is associated with accelerated retinal ganglion cell/inner plexiform layer thinning 
Neurology  2013;80(1):47-54.
Objective:
To determine the effect of clinical and radiologic disease activity on the rate of thinning of the ganglion cell/inner plexiform (GCIP) layer and the retinal nerve fiber layer in patients with multiple sclerosis (MS) using optical coherence tomography (OCT).
Methods:
One hundred sixty-four patients with MS and 59 healthy controls underwent spectral-domain OCT scans every 6 months for a mean follow-up period of 21.1 months. Baseline and annual contrast-enhanced brain MRIs were performed. Patients who developed optic neuritis during follow-up were excluded from analysis.
Results:
Patients with the following features of disease activity during follow-up had faster rates of annualized GCIP thinning: relapses (42% faster, p = 0.007), new gadolinium-enhancing lesions (54% faster, p < 0.001), and new T2 lesions (36% faster, p = 0.02). Annual GCIP thinning was 37% faster in those with disability progression during follow-up, and 43% faster in those with disease duration <5 years vs >5 years (p = 0.003). Annual rates of GCIP thinning were highest in patients exhibiting combinations of new gadolinium-enhancing lesions, new T2 lesions, and disease duration <5 years (70% faster in patients with vs without all 3 characteristics, p < 0.001).
Conclusions:
MS patients with clinical and/or radiologic nonocular disease activity, particularly early in the disease course, exhibit accelerated GCIP thinning. Our findings suggest that retinal changes in MS reflect global CNS processes, and that OCT-derived GCIP thickness measures may have utility as an outcome measure for assessing neuroprotective agents, particularly in early, active MS.
doi:10.1212/WNL.0b013e31827b1a1c
PMCID: PMC3589201  PMID: 23267030
25.  DSM-IV-Defined Anorexia Nervosa Versus Subthreshold Anorexia Nervosa (EDNOS-AN) 
Objectives
Eating disorder not otherwise specified (EDNOS) is the most prevalent eating disorder, yet its heterogeneity begs less reliance on this broad diagnostic category. The purpose of this study was to compare women with anorexia nervosa (AN) and EDNOS, AN type (EDNOS-AN) from a multisite study on eating-related and general psychopathology measures.
Methods
One hundred eighteen participants (n = 59 with DSM-IV AN, n = 59 with EDNOS-AN) completed structured interviews, questionnaires and a physical examination at baseline. In addition, participants carried a handheld palm pilot computer for two weeks to provide ecological momentary assessment (EMA) information about mood and eating disorder behaviors.
Results
No significant differences between AN and EDNOS-AN were found on the self-report and interview measures, or on the EMA mood assessments. The only differences to emerge were that participants with AN reported higher rates of binge eating and purging on EMA compared to those with EDNOS-AN, while EDNOS-AN reported higher rates of checking thighs and joints on EMA compared to those with AN. For the physiological parameters, AN presented with lower white blood cell counts compared to EDNOS-AN.
Conclusions
Findings highlight the clinical significance of EDNOS-AN, and support a closer look at the definition of AN as proposed by DSM-5.
doi:10.1002/erv.2192
PMCID: PMC3715616  PMID: 22847947
Anorexia nervosa; EDNOS; classification

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