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Variable importance and prediction methods for longitudinal problems with missing variables

Díaz, Iván; Hubbard, Alan; Decker, Anna; Cohen, Mitchell
We present prediction and variable importance (VIM) methods for longitudinal data sets containing continuous and binary exposures subject to missingness. We demonstrate the use of these methods for prognosis of medical outcomes of severe trauma patients, a field in which current medical practice involves rules of thumb and scoring methods that only use a few variables and ignore the dynamic and high-dimensional nature of trauma recovery. Well-principled prediction and VIM methods can provide a tool to make care decisions informed by the high-dimensional patient's physiological and clinical history. Our VIM parameters are analogous to slope coefficients in adjusted regressions, but are not dependent on a specific statistical model, nor require a certain functional form of the prediction regression to be estimated. In addition, they can be causally interpreted under causal and statistical assumptions as the expected outcome under time-specific clinical interventions, related to changes in the mean of the outcome if each individual experiences a specified change in the variable (keeping other variables in the model fixed). Better yet, the targeted MLE used is doubly robust and locally efficient. Because the proposed VIM does not constrain the prediction model fit, we use a very flexible ensemble learner (the SuperLearner), which returns a linear combination of a list of user-given algorithms. Not only is such a prediction algorithm intuitive appealing, it has theoretical justification as being asymptotically equivalent to the oracle selector. The results of the analysis show effects whose size and significance would have been not been found using a parametric approach (such as stepwise regression or LASSO). In addition, the procedure is even more compelling as the predictor on which it is based showed significant improvements in cross-validated fit, for instance area under the curve (AUC) for a receiver-operator curve (ROC). Thus, given that 1) our VIM applies to any model fitting procedure, 2) under assumptions has meaningful clinical (causal) interpretations and 3) has asymptotic (influence-curve) based robust inference, it provides a compelling alternative to existing methods for estimating variable importance in high-dimensional clinical (or other) data.
PMCID:4376910
PMID: 25815719
ISSN: 1932-6203
CID: 5304432

A novel system to generate WTC dust particles for inhalation exposures

Vaughan, Joshua M; Garrett, Brittany J; Prophete, Colette; Horton, Lori; Sisco, Maureen; Soukup, Joleen M; Zelikoff, Judith T; Ghio, Andrew; Peltier, Richard E; Asgharian, Bahman; Chen, Lung-Chi; Cohen, Mitchell D
First responders (FRs) present at Ground Zero within the critical first 72 h after the World Trade Center (WTC) collapse have progressively exhibited significant respiratory injury. The majority (>96%) of WTC dusts were >10 mum and no studies have examined potential health effects of this size fraction. This study sought to develop a system to generate and deliver supercoarse (10-53 mum) WTC particles to a rat model in a manner that mimicked FR exposure scenarios. A modified Fishing Line generator was integrated onto an intratracheal inhalation (ITIH) system that allowed for a bypassing of the nasal passages so as to mimic FR exposures. Dust concentrations were measured gravimetrically; particle size distribution was measured via elutriation. Results indicate that the system could produce dusts with 23 mum mass median aerodynamic diameter (MMAD) at levels up to >/=1200 mg/m(3). To validate system utility, F344 rats were exposed for 2 h to approximately 100 mg WTC dust/m(3). Exposed rats had significantly increased lung weight and levels of select tracer metals 1 h after exposure. Using this system, it is now possible to conduct relevant inhalation exposures to determine adverse WTC dusts impacts on the respiratory system. Furthermore, this novel integrated Fishing Line-ITIH system could potentially be used in the analyses of a wide spectrum of other dusts/pollutants of sizes previously untested or delivered to the lungs in ways that did not reflect realistic exposure scenarios.
PMCID:4115325
PMID: 24220216
ISSN: 1559-0631
CID: 741342

Immunotoxicology: Fifty years of global scientific progress

McKarns, Susan C; Kerkvliet, Nancy I; Dean, Jack H; Bonn, Michael B; Cohen, Mitchell D; Franko, Jennifer; Laiosa, Michael D; Lawrence, B Paige; Luebke, Robert W; Luster, Michael I; Miller, Patrick G; Palmer, Rachel K; Pfau, Jean C; Raman, Priyadarshini; Regal, Jean F; Rodgers, Kathleen E; Schondelmeyer, Rio S; Zhang, Xiaochu; Burns-Naas, Leigh Ann
The Immunotoxicology Specialty Section of the Society of Toxicology (SOT) celebrated the 50(th) Anniversary of the SOT by constructing a poster to highlight the milestones of Immunotoxicology during that half-century period. This poster was assembled by an ad hoc committee and intertwines in words, citations, graphics, and photographs our attempts to capture a timeline reference of the development and progressive movement of immunotoxicology across the globe. This poster was displayed during the 50(th) Annual SOT Meeting in Washington DC in March, 2011. The poster can be accessed by any Reader at the SOT Website via the link http://www.toxicology.org/AI/MEET/AM2011/posters_rcsigss.asp#imss . We dedicate this poster to all of the founders and the scientists that followed them who have made the discipline of Immunotoxicology what it is today.
PMID: 23078377
ISSN: 1547-691x
CID: 185912

Comparison of WTC Dust Size on Macrophage Inflammatory Cytokine Release In vivo and In vitro

Weiden, Michael D; Naveed, Bushra; Kwon, Sophia; Segal, Leopoldo N; Cho, Soo Jung; Tsukiji, Jun; Kulkarni, Rohan; Comfort, Ashley L; Kasturiarachchi, Kusali J; Prophete, Colette; Cohen, Mitchell D; Chen, Lung-Chi; Rom, William N; Prezant, David J; Nolan, Anna
BACKGROUND: The WTC collapse exposed over 300,000 people to high concentrations of WTC-PM; particulates up to approximately 50 mm were recovered from rescue workers' lungs. Elevated MDC and GM-CSF independently predicted subsequent lung injury in WTC-PM-exposed workers. Our hypotheses are that components of WTC dust strongly induce GM-CSF and MDC in AM; and that these two risk factors are in separate inflammatory pathways. METHODOLOGY/PRINCIPAL FINDINGS: Normal adherent AM from 15 subjects without WTC-exposure were incubated in media alone, LPS 40 ng/mL, or suspensions of WTC-PM(10-53) or WTC-PM(2.5) at concentrations of 10, 50 or 100 microg/mL for 24 hours; supernatants assayed for 39 chemokines/cytokines. In addition, sera from WTC-exposed subjects who developed lung injury were assayed for the same cytokines. In the in vitro studies, cytokines formed two clusters with GM-CSF and MDC as a result of PM(10-53) and PM(2.5). GM-CSF clustered with IL-6 and IL-12(p70) at baseline, after exposure to WTC-PM(10-53) and in sera of WTC dust-exposed subjects (n = 70) with WTC lung injury. Similarly, MDC clustered with GRO and MCP-1. WTC-PM(10-53) consistently induced more cytokine release than WTC-PM(2.5) at 100 microg/mL. Individual baseline expression correlated with WTC-PM-induced GM-CSF and MDC. CONCLUSIONS: WTC-PM(10-53) induced a stronger inflammatory response by human AM than WTC-PM(2.5). This large particle exposure may have contributed to the high incidence of lung injury in those exposed to particles at the WTC site. GM-CSF and MDC consistently cluster separately, suggesting a role for differential cytokine release in WTC-PM injury. Subject-specific response to WTC-PM may underlie individual susceptibility to lung injury after irritant dust exposure.
PMCID:3399845
PMID: 22815721
ISSN: 1932-6203
CID: 174082

How environment affects drug activity: Localization, compartmentalization and reactions of a vanadium insulin-enhancing compound, dipicolinatooxovanadium(V)

Crans, Debbie C.; Trujillo, Alejandro M.; Pharazyn, Philip S.; Cohen, Mitchell D.
The chemical and biological properties of a simple and traditional V(5+) coordination complex, dipicolinatooxovanadium(V) (abbreviated [VO(2)dipic](-)), are described in order to present a hypothesis for a novel mode of action wherein a hydrophobic membrane environment plays a key role. Specifically, we propose that the compartmentalization and both chemical and biological transformations of vanadium-complexes direct whether beneficial or toxic effects will be observed with this class of compounds. This concept is based on the formation of high levels of uncontrollable reactive oxygen species (ROS) from one-electron reactions or alternative events possibly initiated by a two-electron reaction which may be directly or indirectly beneficial by reducing the high levels of ROS. The properties of dipicolinatooxovanadium(V) compounds in aqueous solution (D.C. Crans, et al., Inorg. Chem. 39 (2000) 4409-4416) are very different from those in organic solvents (S.K. Hanson, et al., J. Am. Chem. Soc. 131 (2009) 428-429) and these differences may be key for their mode of action. Since other vanadium complexes are known to hydrolyze upon administration, the low stability of the aqueous complex requires entrapment in hydrophobic environments for such a complex to exist sufficiently long to have an effect. The suggestion that the environment changes the reactivity of the compounds is consistent with the very different modes of action by which one complex act. In short, a novel hypothesis is presented for a mode of action of vanadium compounds based on differences in properties resulting from environmental conditions. These considerations are supported by recent evidence supporting a role for membranes and signal transduction events (D.A. Roess, et al. Chem. Biodivers. 5 (2008) 1558-1570) of the insulin-enhancing properties of these compounds. (C) 2011 Elsevier B.V. All rights reserved
ISI:0002952508000
ISSN: 0010-8545
CID: 139065

Interactive effect of cigarette smoke extract and world trade center dust particles on airway cell cytotoxicity

Xu, Alice; Prophete, Colette; Chen, Lung-Chi; Emala, Charles W; Cohen, Mitchell D
Rescue workers and residents exposed to the environment surrounding the collapse of the World Trade Center (WTC) on September 11, 2001, have suffered a disproportionate incidence of chronic lung disease attributed to the inhalation of airborne dust. To date, the pathophysiology of this lung disease is poorly understood. The aim of this study was to examine whether airborne dust contaminants recovered from the surrounding area 24-48 h after the collapse of the WTC demonstrate direct cytotoxicity to two airway cell types that were most directly exposed to inhaled dust, airway epithelial and smooth muscle cells. It was also of interest to determine whether the presence of these dusts could modulate the effects of cigarette smoke on these cell types in that some of the individuals who responded to the collapse site were also smokers. Human cultured airway epithelial (BEAS-2B) cells were exposed to 10% cigarette smoke extract (CSE), WTC dust particles (10-53 mum; 0.01-0.5 mug/mul), or a combination of the two for 2-24 h. Cell viability was measured by determining mitochondrial integrity (MTT assays) and apoptosis (poly-ADP-ribose polymerase [PARP] immunoblotting). Conditioned cell culture media recovered from the CSE- and/or WTC dust-exposed BEAS-2B cells were then applied to cultured human airway smooth muscle cells that were subsequently assayed for mitochondrial integrity and their ability to synthesize cyclic AMP (a regulator of airway smooth muscle constriction). BEAS-2B cells underwent necrotic cell death following exposure to WTC dust or CSE for 2-24 h without evidence of apoptosis. Smooth muscle cells demonstrated cellular toxicity and enhanced cyclic AMP synthesis following exposure to conditioned media from WTC- or CSE-exposed epithelial cells. These acute toxicity assays of WTC dust and CSE offer insights into lung cell toxicity that may contribute to the pathophysiology of chronic lung disease in workers and residents exposed to WTC dust. These studies clearly showed that WTC dust (at least the supercoarse particle fraction) or CSE alone exerted direct adverse effects on airway epithelial and smooth muscle cells, and altered the signaling properties of airway smooth muscle cells. In addition the combination of CSE and WTC exerted an interactive effect on cell toxicity. It remains to be determined whether these initial cell death events might account, in part, for the chronic lung effects associated with WTC dust exposure among First Responders and others
PMID: 21623534
ISSN: 1528-7394
CID: 135195

Roles of MAPK pathway activation during cytokine induction in BEAS-2B cells exposed to fine World Trade Center (WTC) dust

Wang, Shang; Prophete, Colette; Soukup, Joleen M; Chen, Lung-Chi; Costa, Max; Ghio, Andrew; Qu, Qingshan; Cohen, Mitchell D; Chen, Haobin
The World Trade Center (WTC) collapse on September 11, 2001 released copious amounts of particulate matter (PM) into the atmosphere of New York City. Follow-up studies on persons exposed to the dusts have revealed a severely increased rate for asthma and other respiratory illnesses. There have only been a few studies that have sought to discern the possible mechanisms underlying these untoward pathologies. In one study, an increased cytokine release was detected in cells exposed to WTC fine dusts (PM. fraction or WTC.). However, the mechanism(s) for these increases has yet to be fully defined. Because activation of the mitogen-activated protein kinase (MAPK) signaling pathways is known to cause cytokine induction, the current study was undertaken to analyze the possible involvement of these pathways in any increased cytokine formation by lung epithelial cells (as BEAS-2B cells) exposed to WTC.. Our results showed that exposure to WTC. for 5 hr increased interleukin-6 (IL-6) mRNA expression in BEAS-2B cells, as well as its protein levels in the culture media, in a dose-dependent manner. Besides IL-6, cytokine multiplex analyses revealed that formation of IL-8 and -10 was also elevated by the exposure. Both extracellular signal-regulated kinase (ERK) and p38, but not c-Jun N-terminal protein kinase, signaling pathways were found to be activated in cells exposed to WTC.. Inactivation of ERK signaling pathways by PD98059 effectively blocked IL-6, -8, and -10 induction by WTC.; the p38 kinase inhibitor SB203580 significantly decreased induction of IL-8 and -10. Together, our data demonstrated activation of MAPK signaling pathway(s) likely played an important role in the WTC.-induced formation of several inflammatory (and, subsequently, anti-inflammatory) cytokines. The results are important in that they help to define one mechanism via which the WTC dusts may have acted to cause the documented increases in asthma and other inflammation-associated respiratory dysfunctions in the individuals exposed to the dusts released from the WTC collapse
PMCID:3966203
PMID: 20731619
ISSN: 1547-6901
CID: 138258

Changes in biologic and/or immunologic parameters induced by intratracheal instillation of pregnant mice with benzo(a)pyrene are potentially confounded by anesthesia

Urso, Paul; Wirsiy, Yungri G; Cohen, Mitchell D; Adkins, Bernard Jr
Benzo(alpha)pyrene (B(alpha)P) is a potent multiorgan carcinogen released into the atmosphere from commercial, domestic, and industrial sources. Studies using animal models have shown that giving B(alpha)P parenterally to pregnant animals (i.e., dams) led to increased tumor frequency and sensitivity to tumorigenesis in their progeny. The authors' studies also showed that the progeny of the B(alpha)P-exposed dams displayed increased deficiencies in cell-mediated and humoral immune functions, changes among T-cell subsets in developing lymphoid tissues, and significant expression of B(alpha)P-7,8-dihydrodiol-9,10-epoxide (BPDE)-DNA adducts in thymic, splenic, and (fetal) liver tissues. The authors evaluated whether similar biologic/immunologic effects of B(alpha)P seen earlier in parenterally exposed mouse dams (and offspring) occurred if dams were exposed to B(alpha)P via the lungs. Pregnant dams were subjected to intratracheal instillation of B(alpha)P (at 1 mg/ml corn oil, 0.1 ml/instillate) beginning on day 11 of pregnancy (GD 11) and again on GDs 12 and 14. In each case, the dams were anesthetized with metofane. Other dams were left untreated (controls), anesthetized only, or anesthetized and then instilled with vehicle. Effects of the B(alpha)P exposures included lower dam body weights during gestation, decreased postbirth pup survival, increased pup tumor frequency, and decreased mixed-lymphocyte responses by pup lymphocytes. These studies also revealed that metofane imparted effects on the dams and progeny. These effects equaled the B(alpha)P treatments alone; in other instances, the metofane had no impact, and thus questions the observed biologic/immunologic effects of B(alpha)P induced in pregnant mice (and their progeny), which might have been confounded by use of this (or potentially other) anesthesia
PMID: 20384551
ISSN: 1091-7691
CID: 133508

Effects of metal compounds with distinct physicochemical properties on iron homeostasis and antibacterial activity in the lungs: chromium and vanadium

Cohen, Mitchell D; Sisco, Maureen; Prophete, Colette; Yoshida, Kotaro; Chen, Lung-chi; Zelikoff, Judith T; Smee, Jason; Holder, Alvin A; Stonehuerner, Jacqueline; Crans, Debbie C; Ghio, Andrew J
In situ reactions of metal ions or their compounds are important mechanisms by which particles alter lung immune responses. The authors hypothesized that major determinants of the immunomodulatory effect of any metal include its redox behavior/properties, oxidation state, and/or solubility, and that the toxicities arising from differences in physicochemical parameters are manifest, in part, via differential shifts in lung iron (Fe) homeostasis. To test the hypotheses, immunomodulatory potentials for both pentavalent vanadium (V(V); as soluble metavanadate or insoluble vanadium pentoxide) and hexavalent chromium (Cr(VI); as soluble sodium chromate or insoluble calcium chromate) were quantified in rats after inhalation (5 h/day for 5 days) of each at 100 mug metal/m(3). Differences in effects on local bacterial resistance between the two V(V), and between each Cr(VI), agents suggested that solubility might be a determinant of in situ immunotoxicity. For the soluble forms, V(V) had a greater impact on resistance than Cr(VI), indicating that redox behavior/properties was likely also a determinant. The soluble V(V) agent was the strongest immunomodulant. Regarding Fe homeostasis, both V(V) agents had dramatic effects on airway Fe levels. Both also impacted local immune/airway epithelial cell Fe levels in that there were significant increases in production of select cytokines/chemokines whose genes are subject to regulation by HIF-1 (whose intracellular longevity is related to cell Fe status). Our findings contribute to a better understanding of the role that metal compound properties play in respiratory disease pathogenesis and provide a rationale for differing pulmonary immunotoxicities of commonly encountered ambient metal pollutants
PMCID:4018818
PMID: 19757987
ISSN: 1091-7691
CID: 105696

Pulmonary immunology

Chapter by: Zelikoff, Judith T; Cohen, Mitchell D
in: Comprehensive toxicology by McQueen, Charlene A [Eds]
Oxford : Elsevier, 2010
pp. 191-202
ISBN: 0080468829
CID: 2221922