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1.  Whole-Genome Sequences of 80 Environmental and Clinical Isolates of Burkholderia pseudomallei 
Genome Announcements  2015;3(1):e01282-14.
Here, we present the draft genome sequences of 80 isolates of Burkholderia pseudomallei. The isolates represent clinical cases of melioidosis and environmental isolates from regions in Australia and Papua New Guinea where B. pseudomallei is endemic. The genomes provide further context for the diversity of the pathogen.
PMCID: PMC4333647  PMID: 25676747
2.  Pepsin concentrations are elevated in the bronchoalveolar lavage fluid of patients with idiopathic pulmonary fibrosis after lung transplantation 
The Journal of surgical research  2013;185(2):e101-e108.
Aspiration of gastroesophageal refluxate has been implicated in the pathogenesis of idiopathic pulmonary fibrosis (IPF) and the progression of bronchiolitis obliterans syndrome after lung transplantation. The goals of the present study were to identify lung transplant patients at the greatest risk of aspiration and to investigate the causative factors.
Materials and methods
From September 2009 to November 2011, 252 bronchoalveolar lavage fluid (BALF) samples were collected from 100 lung transplant patients. The BALF pepsin concentrations and the results of transbronchial biopsy, esophageal function testing, barium swallow, and gastric emptying scan were compared among those with the most common end-stage lung diseases requiring lung transplantation: IPF, chronic obstructive pulmonary disease, cystic fibrosis, and α1-antitrypsin deficiency.
Patients with IPF had higher BALF pepsin concentrations and a greater frequency of acute rejection than those with α1-antitrypsin deficiency, cystic fibrosis, or chronic obstructive pulmonary disease (P = 0.037). Moreover, the BALF pepsin concentrations correlated negatively with a lower esophageal sphincter pressure and distal esophageal amplitude; negatively with distal esophageal amplitude and positively with total esophageal acid time, longest reflux episode, and DeMeester score in those with chronic obstructive pulmonary disease; and negatively with the upright acid clearance time in those with IPF.
Our results suggest that patients with IPF after lung transplantation are at increased risk of aspiration and a greater frequency of acute rejection episodes, and that the risk factors for aspiration might be different among those with the most common end-stage lung diseases who have undergone lung transplantation. These results support the role of evaluating the BALF for markers of aspiration in assessing lung transplant patients as candidates for antireflux surgery.
PMCID: PMC4306555  PMID: 23845868
Gastroesophageal reflux disease; GERD; Aspiration; Lung transplantation; Bronchiolitis obliterans syndrome; BOS
3.  Copper Complexation Screen Reveals Compounds with Potent Antibiotic Properties against Methicillin-Resistant Staphylococcus aureus 
Macrophages take advantage of the antibacterial properties of copper ions in the killing of bacterial intruders. However, despite the importance of copper for innate immune functions, coordinated efforts to exploit copper ions for therapeutic interventions against bacterial infections are not yet in place. Here we report a novel high-throughput screening platform specifically developed for the discovery and characterization of compounds with copper-dependent antibacterial properties toward methicillin-resistant Staphylococcus aureus (MRSA). We detail how one of the identified compounds, glyoxal-bis(N4-methylthiosemicarbazone) (GTSM), exerts its potent strictly copper-dependent antibacterial properties on MRSA. Our data indicate that the activity of the GTSM-copper complex goes beyond the general antibacterial effects of accumulated copper ions and suggest that, in contrast to prevailing opinion, copper complexes can indeed exhibit species- and target-specific activities. Based on experimental evidence, we propose that copper ions impose structural changes upon binding to the otherwise inactive GTSM ligand and transfer antibacterial properties to the chelate. In turn, GTSM determines target specificity and utilizes a redox-sensitive release mechanism through which copper ions are deployed at or in close proximity to a putative target. According to our proof-of-concept screen, copper activation is not a rare event and even extends to already established drugs. Thus, copper-activated compounds could define a novel class of anti-MRSA agents that amplify copper-dependent innate immune functions of the host. To this end, we provide a blueprint for a high-throughput drug screening campaign which considers the antibacterial properties of copper ions at the host-pathogen interface.
PMCID: PMC4068557  PMID: 24752262
4.  AC-186, a Selective Nonsteroidal Estrogen Receptor β Agonist, Shows Gender Specific Neuroprotection in a Parkinson’s Disease Rat Model 
ACS Chemical Neuroscience  2013;4(9):1249-1255.
Drugs that selectively activate estrogen receptor β (ERβ) are potentially safer than the nonselective estrogens currently used in hormonal replacement treatments that activate both ERβ and ERα. The selective ERβ agonist AC-186 was evaluated in a rat model of Parkinson’s disease induced through bilateral 6-hydroxydopamine lesions of the substantia nigra. In this model, AC-186 prevented motor, cognitive, and sensorimotor gating deficits and mitigated the loss of dopamine neurons in the substantia nigra, in males, but not in females. Furthermore, in male rats, 17β-estradiol, which activates ERβ and ERα with equal potency, did not show the same neuroprotective benefits as AC-186. Hence, in addition to a beneficial safety profile for use in both males and females, a selective ERβ agonist has a differentiated pharmacological profile compared to 17β-estradiol in males.
PMCID: PMC3778431  PMID: 23898966
Parkinson’s disease; neuroprotection; AC-186; gender difference; buccal/sublingual administration; selective estrogen receptor beta agonist
5.  Sleep and Cytokines 
Sleep medicine clinics  2012;7(3):517-527.
PMCID: PMC4149313  PMID: 25177229
Tumor necrosis factor; Interleukin1; Sleep function; Adenosine triphosphate; Humoral regulation; Sleep homeostasis
6.  Aspiration, Localized Pulmonary Inflammation, and Predictors of Early-Onset Bronchiolitis Obliterans Syndrome after Lung Transplantation 
We hypothesized that immune mediator concentrations in the bronchoalveolar fluid (BALF) are predictive of bronchiolitis obliterans syndrome (BOS) and demonstrate specific patterns of dysregulation, depending on the presence of acute cellular rejection, BOS, aspiration, and timing of lung transplantation.
We prospectively collected 257 BALF samples from 105 lung transplant recipients. The BALF samples were assessed for absolute and differential white blood cell counts and 34 proteins implicated in pulmonary immunity, inflammation, fibrosis, and aspiration.
There were elevated BALF concentrations of interleukin (IL)-15, IL-17, basic fibroblast growth factor, tumor necrosis factor–α, and myeloperoxidase, and reduced concentrations of α1-antitrypsin, which were predictive of early-onset BOS. Patients with BOS had an increased percentage of BALF lymphocytes and neutrophils, with a reduced percentage of macrophages (p < 0.05). The BALF concentrations of IL-1β; IL-8; interferon-γ–induced protein 10; regulated upon activation, normal T-cell expressed and secreted; neutrophil elastase; and pepsin were higher in patients with BOS (p < 0.05). Among those with BOS, BALF concentrations of IL-1RA; IL-8; eotaxin; interferon-γ–induced protein 10; regulated upon activation, normal T-cell expressed and secreted; myeloperoxidase; and neutrophil elastase were positively correlated with time since transplantation (p < 0.01). Those with worse grades of acute cellular rejection had an increased percentage of lymphocytes in their BALF (p < 0.0001) and reduced BALF concentrations of IL-1β, IL-7, IL-9, IL-12, granulocyte colony-stimulating factor, granulocyte-macrophage colony-stimulating factor, interferon-γ, and vascular endothelial growth factor (p ≤ 0.001). Patients with aspiration based on detectable pepsin had increased percentage of neutrophils (p < 0.001) and reduced BALF concentrations of IL-12 (p < 0.001).
The BALF levels of IL-15, IL-17, basic fibroblast growth factor, tumor necrosis factor–α, myeloperoxidase, and α1-antitrypsin at 6 to 12 months after lung transplantation are predictive of early-onset BOS, and those with BOS and aspiration have an augmented chemotactic and inflammatory balance of pulmonary leukocytes and immune mediators. These data justify the surgical prevention of aspiration and argue for the refinement of antirejection regimens.
PMCID: PMC4135482  PMID: 23628225
7.  Selective mRNA translation during eIF2 phosphorylation induces expression of IBTKα 
Molecular Biology of the Cell  2014;25(10):1686-1697.
This study measured changes in global mRNA translation in response to ER stress. The analysis suggests that translation of a majority of gene transcripts is either repressed or resistant, whereas select key regulators are subject to preferential translation. From this last group, IBTKα is identified as a novel target of the UPR central to cell fate.
Disruption of protein folding in the endoplasmic reticulum (ER) triggers the unfolded protein response (UPR), a transcriptional and translational control network designed to restore protein homeostasis. Central to the UPR is PKR-like ER kinase (PERK/EIF2AK3) phosphorylation of the α subunit of eIF2 (eIF2α∼P), which represses global translation coincident with preferential translation of mRNAs, such as activating transcription factor 4 (ATF4) and C/EBP-homologous protein (CHOP), that serve to implement UPR transcriptional regulation. In this study, we used sucrose gradient ultracentrifugation and a genome-wide microarray approach to measure changes in mRNA translation during ER stress. Our analysis suggests that translational efficiencies vary over a broad range during ER stress, with the majority of transcripts being either repressed or resistant to eIF2α∼P, whereas a notable cohort of key regulators are subject to preferential translation. From the latter group, we identified the α isoform of inhibitor of Bruton's tyrosine kinase (IBTKα) as being subject to both translational and transcriptional induction during eIF2α∼P in both cell lines and a mouse model of ER stress. Translational regulation of IBTKα mRNA involves stress-induced relief of two inhibitory upstream open reading frames in the 5′-leader of the transcript. Depletion of IBTKα by short hairpin RNA reduced viability of cultured cells coincident with increased caspase 3/7 cleavage, suggesting that IBTKα is a key regulator in determining cell fate during the UPR.
PMCID: PMC4019499  PMID: 24648495
8.  Inhalation injury severity and systemic immune perturbations in burned adults 
Annals of surgery  2013;257(6):1137-1146.
We aimed to determine if the severity of inhalation injury evokes an immune response measurable at the systemic level and to further characterize the balance of systemic pro- and anti-inflammation early after burn and inhalation injury.
Summary Background Data
Previously we reported that the pulmonary inflammatory response is enhanced with worse grades of inhalation injury, and that those who die from their injuries have a blunted pulmonary immune profile compared to survivors.
From August 2007 to June 2011, bronchoscopy was performed on 80 patients admitted to the burn intensive care unit when smoke inhalation was suspected. Of these, inhalation injury was graded into one of five categories (0, 1, 2, 3, and 4), with Grade 0 being the absence of visible injury and Grade 4 corresponding to massive injury. Plasma was collected at the time of bronchoscopy and analyzed for 28 immunomodulating proteins via multiplex bead array or ELISA.
The concentrations of several plasma immune mediators were increased with worse inhalation injury severity, even after adjusting for age and % TBSA. These included interleukin (IL)-1RA (p=0.002), IL-6 (p=0.002), IL-8 (p=0.026), granulocyte colony stimulating factor (p=0.002), and monocyte chemotactic protein (MCP)-1 (p=0.007). Differences in plasma immune mediator concentrations in surviving and deceased patients were also identified. Briefly, plasma concentrations of IL-1RA, IL-6, IL-8, IL-15, Eotaxin, and MCP-1 were higher in deceased patients compared to survivors (p<0.05 for all), while IL-4 and IL-7 were lower (p<0.05). After adjusting for the effects of age, % TBSA, and inhalation injury grade, plasma IL-1RA remained significantly associated with mortality (OR 3.12, 95% CI 1.03–9.44). Plasma IL-1RA also correlated with % TBSA, inhalation injury grade, fluid resuscitation, Baux score, revised Baux score, Denver score, and the Sequential Organ Failure Assessment score.
The severity of smoke inhalation injury has systemically reaching effects, which argues in favor of treating inhalation injury in a graded manner. Additionally, several plasma immune mediators measured early after injury were associated with mortality. Of these, IL-1RA appeared to have the strongest correlation with injury severity and outcomes measures, which may explain the blunted pulmonary immune response we previously found in non-survivors.
PMCID: PMC3580123  PMID: 23160150
Burn; Inhalation injury; Cytokines; Chemokines; Growth Factors; Interleukin-1 receptor antagonist; Mortality
9.  Spt6 Regulates Intragenic and Antisense Transcription, Nucleosome Positioning, and Histone Modifications Genome-Wide in Fission Yeast 
Molecular and Cellular Biology  2013;33(24):4779-4792.
Spt6 is a highly conserved histone chaperone that interacts directly with both RNA polymerase II and histones to regulate gene expression. To gain a comprehensive understanding of the roles of Spt6, we performed genome-wide analyses of transcription, chromatin structure, and histone modifications in a Schizosaccharomyces pombe spt6 mutant. Our results demonstrate dramatic changes to transcription and chromatin structure in the mutant, including elevated antisense transcripts at >70% of all genes and general loss of the +1 nucleosome. Furthermore, Spt6 is required for marks associated with active transcription, including trimethylation of histone H3 on lysine 4, previously observed in humans but not Saccharomyces cerevisiae, and lysine 36. Taken together, our results indicate that Spt6 is critical for the accuracy of transcription and the integrity of chromatin, likely via its direct interactions with RNA polymerase II and histones.
PMCID: PMC3889546  PMID: 24100010
10.  Cross-Scale Interactions and the Distribution-Abundance Relationship 
PLoS ONE  2014;9(5):e97387.
Positive interspecific relationships between local abundance and extent of regional distribution are among the most ubiquitous patterns in ecology. Although multiple hypotheses have been proposed, the mechanisms underlying distribution-abundance (d-a) relationships remain poorly understood. We examined the intra- and interspecific distribution-abundance relationships for a metacommunity of 13 amphibian species sampled for 15 consecutive years. Mean density of larvae in occupied ponds was positively related to number of ponds occupied by species; employing the fraction of ponds uniquely available to each species this same relationship sharply decelerates. The latter relationship suggested that more abundant species inhabited most available habitats annually, whereas rarer species were dispersal limited. We inferred the mechanisms responsible for this pattern based on the dynamics of one species, Pseudacris triseriata, which transitioned between a rare, narrowly distributed species to a common, widely distributed species and then back again. Both transitions were presaged by marked changes in mean local densities driven by climatic effects on habitat quality. We identified threshold densities separating these population regime shifts that differed with landscape configuration. Our data suggest that these transitions were caused by strong cross-scale interactions between local resource/niche processes and larger scale metapopulation processes. The patterns we observed have relevance for understanding the mechanisms of interspecific d-a relationships and critical thresholds associated with habitat fragmentation.
PMCID: PMC4038483  PMID: 24875899
Alcohol (Fayetteville, N.Y.)  2013;47(3):223-229.
Alcohol consumption leads to an exaggerated inflammatory response after burn injury. Elevated levels of interleukin-6 (IL-6) in patients are associated with increased morbidity and mortality after injury, and high systemic and pulmonary levels of IL-6 have been observed after the combined insult of ethanol exposure and burn injury. To further investigate the role of IL-6 in the pulmonary inflammatory response, we examined leukocyte infiltration and cytokine and chemokine production in the lungs of wild-type and IL-6 knockout mice given vehicle or ethanol (1.12 g/kg) and subjected to a sham or 15% total body surface area burn injury. Levels of neutrophil infiltration and neutrophil chemoattractants were increased to a similar extent in wild-type and IL-6 knockout mice 24 hours after burn injury. When ethanol exposure preceded the burn injury however, a further increase of these inflammatory markers was seen only in the wild-type mice. Additionally, signal transducer and activator of transcription-3 (STAT3) phosphorylation did not increase in response to ethanol exposure in the IL-6 knockout mice, in contrast to their wild-type counterparts. Visual and imaging analysis of alveolar wall thickness supported these findings and similar results were obtained by blocking IL-6 with antibody. Taken together, our data suggest a causal relationship between IL-6 and the excessive pulmonary inflammation observed after the combined insult of ethanol and burn injury.
PMCID: PMC3617054  PMID: 23462222
lung; neutrophils; cytokines; alcohol; trauma; burn
This study was conducted to assess the role of AMPK in regulating meiosis in mouse oocytes from the germinal vesicle stage to metaphase II. Exposure of mouse cumulus cell-enclosed oocytes (CEO) and denuded oocytes (DO) during spontaneous maturation in vitro to AMPK-activating agents resulted in augmentation of the rate and frequency of polar body formation. Inhibitors of AMPK had an opposite, inhibitory effect. In addition, the AMPK inhibitor, compound C (Cmpd C) increased the frequency of oocyte activation. The stimulatory action of the AMPK-activating agent, AICAR, and the inhibitory action of Cmpd C were diminished if exposure was delayed, indicating an early action of AMPK on polar body formation. The frequency of spontaneous and Cmpd C-induced activation in CEO was reduced as the period of hormonal priming was increased, and AMPK stimulation eliminated the activation response. Immunostaining of oocytes with antibody to active AMPK revealed an association of active kinase with chromatin, spindle poles and midbody during maturation. Immunolocalization of the α1 catalytic subunit of AMPK showed an association with condensed chromatin and the meiotic spindle, but not in the spindle poles or midbody; α2 stained only diffusely throughout the oocyte. These data suggest that AMPK is involved in a regulatory capacity throughout maturation and helps promote the completion of meiosis while suppressing premature activation.
PMCID: PMC3995477  PMID: 20830737
13.  Hump-Shaped Density-Dependent Regulation of Mosquito Oviposition Site-Selection by Conspecific Immature Stages: Theory, Field Test with Aedes albopictus, and a Meta-Analysis 
PLoS ONE  2014;9(3):e92658.
Oviposition site selection by gravid females is an important determinant of the distribution, abundance, and dynamics of dipteran hematophagous insects. The presence of conspecific immature stages in a potential oviposition site could, on the one hand, indicate the suitability of that site but on the other hand could indicate the potential for intraspecific competition. In this paper, we present a graphic model suggesting that the trade-off between these two opposing forces could result in a hump-shaped density-dependent relationship between oviposition rate and conspecific immature stage density (hereafter, the “Hump-shaped regulation model”) with positive effects of aggregation prevailing at low densities and negative effect of intraspecific competition prevailing at higher densities. We field-tested the predictions of this model at both the egg- and the larval levels with Aedes albopictus and evaluated if and how these relationships are affected by resource enrichment. We found support for the hump-shaped regulation model at both the larval and the egg levels. Using oviposition cups containing varying numbers of conspecific larvae, we showed that the oviposition activity of Ae. albopictus first increases and then decreases with larvae number. Medium enrichment resulted in higher hatching rate, and demonstrated linear relations for the no-enrichment treatment where larvae density range was low and hump-shaped relationship for the enriched medium that had a wider larvae density range. Using pairs of oviposition cups, we showed that at low egg densities mosquitoes laid more eggs on substrates containing pre-existing eggs. However, at higher egg densities, mosquitoes laid more eggs on a virgin substrate. Based on our results and on a meta-analysis, we suggest that due to study design or methodological shortcomings the hump-shaped regulation model is often left undetected and that it is likely to be more common than currently thought.
PMCID: PMC3969363  PMID: 24681526
14.  AltitudeOmics: The Integrative Physiology of Human Acclimatization to Hypobaric Hypoxia and Its Retention upon Reascent 
PLoS ONE  2014;9(3):e92191.
An understanding of human responses to hypoxia is important for the health of millions of people worldwide who visit, live, or work in the hypoxic environment encountered at high altitudes. In spite of dozens of studies over the last 100 years, the basic mechanisms controlling acclimatization to hypoxia remain largely unknown. The AltitudeOmics project aimed to bridge this gap. Our goals were 1) to describe a phenotype for successful acclimatization and assess its retention and 2) use these findings as a foundation for companion mechanistic studies. Our approach was to characterize acclimatization by measuring changes in arterial oxygenation and hemoglobin concentration [Hb], acute mountain sickness (AMS), cognitive function, and exercise performance in 21 subjects as they acclimatized to 5260 m over 16 days. We then focused on the retention of acclimatization by having subjects reascend to 5260 m after either 7 (n = 14) or 21 (n = 7) days at 1525 m. At 16 days at 5260 m we observed: 1) increases in arterial oxygenation and [Hb] (compared to acute hypoxia: PaO2 rose 9±4 mmHg to 45±4 while PaCO2 dropped a further 6±3 mmHg to 21±3, and [Hb] rose 1.8±0.7 g/dL to 16±2 g/dL; 2) no AMS; 3) improved cognitive function; and 4) improved exercise performance by 8±8% (all changes p<0.01). Upon reascent, we observed retention of arterial oxygenation but not [Hb], protection from AMS, retention of exercise performance, less retention of cognitive function; and noted that some of these effects lasted for 21 days. Taken together, these findings reveal new information about retention of acclimatization, and can be used as a physiological foundation to explore the molecular mechanisms of acclimatization and its retention.
PMCID: PMC3962396  PMID: 24658407
15.  EGFR and EphA2 are host factors for hepatitis C virus entry and possible targets for antiviral therapy 
Nature Medicine  2011;17(5):589-595.
Hepatitis C virus (HCV) is a major cause of liver disease. Therapeutic options are limited and preventive strategies are absent. Entry is the first step of infection and requires the cooperative interaction of several host cell factors. Using a functional RNAi kinase screen we identified epidermal growth factor receptor and ephrin receptor A2 as host co-factors for HCV entry. Blocking of kinase function by approved inhibitors broadly inhibited HCV infection of all major HCV genotypes and viral escape variants in cell culture and an animal model in vivo. Receptor tyrosine kinases (RTKs) mediate HCV entry by regulating CD81-claudin-1 co-receptor associations and membrane fusion. These results identify RTKs as novel HCV entry co-factors and uncover that kinase inhibitors have significant antiviral activity. Inhibition of RTK function may constitute a novel approach for prevention and treatment of HCV infection.
PMCID: PMC3938446  PMID: 21516087
Animals; Antigens, CD; physiology; Antigens, CD81; Antiviral Agents; pharmacology; Base Sequence; Cell Line; Claudin-1; Hepacivirus; drug effects; physiology; Hepatitis C; physiopathology; prevention & control; therapy; virology; Host-Pathogen Interactions; physiology; Humans; Ligands; Membrane Proteins; physiology; Mice; Protein Kinase Inhibitors; pharmacology; Quinazolines; pharmacology; RNA Interference; RNA, Small Interfering; genetics; Receptor, EphA2; antagonists & inhibitors; genetics; physiology; Receptor, Epidermal Growth Factor; antagonists & inhibitors; genetics; physiology; Virus Internalization; drug effects; Antiviral / Cell-cell transmission / Liver / Phosphotyrosine kinase / HCV escape variants
16.  Implications of alcohol intoxication at the time of burn and smoke inhalation injury: an epidemiologic and clinical analysis 
Up to 50% of burn patient fatalities have a history of alcohol use, and for those surviving to hospitalization, alcohol intoxication may increase the risk of infection and mortality. Yet, the effect of binge drinking on burn patients specifically with inhalation injuries is not well described. We aimed to investigate the epidemiology and outcomes of this select patient population.
In a prospective study, 53 patients with an inhalation injury and a documented blood alcohol content (BAC) were grouped as: BAC negative (n=37), BAC 1–79 mg/dL (n=4), and BAC ≥ 80 mg/dL (n=12). Those in the latter group were designated as binge drinkers according to National Institute on Alcohol Abuse and Alcoholism criteria.
Binge drinkers with an inhalation injury had considerably smaller % total body surface area (TBSA) burns than did their non-drinking counterparts (mean % TBSA 10.6 vs 24.9; p = 0.065), and significantly lower revised Baux scores (mean 75.9 vs 94.9; p = 0.030). Despite binge-drinkers having smaller injuries, the groups did not differ in terms of outcomes and resource utilization. Finally, those in the binge-drinking group had considerably higher carboxyhemoglobin levels (median 5.2 vs 23.0; p=0.026) than did non-drinkers.
Binge drinkers with inhalation injuries surviving to hospitalization had less severe injuries than did non-drinkers, though their outcomes and burden to the health care infrastructure were similar to the non-drinking patients. Our findings affirm the impact of alcohol intoxication at the time of burn and smoke inhalation injury, placing renewed emphasis on injury prevention and alcohol abuse education.
PMCID: PMC3540156  PMID: 23079566
Alcohol; Burn; Smoke Inhalation
18.  Neighborhood Disparities in Prevalence of Childhood Obesity Among Low-Income Children Before and After Implementation of New York City Child Care Regulations 
New York City Article 47 regulations, implemented in 2007, require licensed child care centers to improve the nutrition, physical activity, and television-viewing behaviors of enrolled children. To supplement an evaluation of the Article 47 regulations, we conducted an exploratory ecologic study to examine changes in childhood obesity prevalence among low-income preschool children enrolled in the Nutrition Program for Women, Infants, and Children (WIC) in New York City neighborhoods with or without a district public health office. We conducted the study 3 years before (from 2004 through 2006) and after (from 2008 through 2010) the implementation of the regulations in 2007.
We used an ecologic, time-trend analysis to compare 3-year cumulative obesity prevalence among WIC-enrolled preschool children during 2004 to 2006 and 2008 to 2010. Outcome data were obtained from the New York State component of the Centers for Disease Control and Prevention’s Pediatric Nutrition Surveillance System.
Early childhood obesity prevalence declined in all study neighborhoods from 2004–2006 to 2008–2010. The greatest decline occurred in Manhattan high-risk neighborhoods where obesity prevalence decreased from 18.6% in 2004–2006 to 15.3% in 2008–2010. The results showed a narrowing of the gap in obesity prevalence between high-risk and low-risk neighborhoods in Manhattan and the Bronx, but not in Brooklyn.
The reductions in early childhood obesity prevalence in some high-risk and low-risk neighborhoods in New York City suggest that progress was made in reducing health disparities during the years just before and after implementation of the 2007 regulations. Future research should consider the built environment and markers of differential exposure to known interventions and policies related to childhood obesity prevention.
PMCID: PMC4208999  PMID: 25321632
19.  Sepsis Induces Extensive Autophagic Vacuolization in Hepatocytes –a clinical and laboratory based study 
Autophagy is the regulated process cells use to recycle non-essential, redundant, or inefficient components and is an adaptive response during times of stress. In addition to its role in enabling the cell to gain vital nutrients in times of stress, autophagy can also be involved in elimination of intracellular microorganisms, tumor suppression, and antigen presentation. Because of difficulty in diagnosing autophagy, few clinical studies have been performed. This study examined whether autophagy occurs in hepatocytes during sepsis. Electron microscopy (EM) was performed on liver samples obtained from both an observational clinical cohort of 6 septic patients and 4 control patients as well as liver specimens from mice with surgical sepsis (via cecal ligation and puncture (CLP)) or sham operation. EM demonstrated increased autophagic vacuoles in septic versus non-septic patients. Randomly selected fields (3,000 square microns) from control and septic patients contained 1.2 ± 1.5 versus 5.3 ± 3.3 (mean ± SD) complex lysosomal/autophagolysosomal structures per image respectively (P<0.001). In rare instances, hepatocytes with autophagic vacuoles appeared to be unequivocally committed to death. Membrane alterations (membrane vacuoles, invagination into adjacent organelles and myelin figure-like changes) occur in a subpopulation of mitochondria in sepsis, but other hepatocyte organelles showed no consistent ultrastructural injury. Findings in murine sepsis paralleled those of patients, with 7.2 ± 1.9 versus 38.7 ± 3.9 lysosomal/autophagolysosomal structures in sham and septic mice, respectively (P =0.002). Quantitative RT-PCR demonstrated that sepsis-induced the upregulation of select apoptosis and cytokine gene expression with minimal changes in the core autophagy genes in liver. In conclusion, hepatocyte autophagic vacuolization increases during sepsis and is associated with mitochondrial injury. However, it is not possible to determine whether the increase in autophagic vacuolization is an adaptive response or a harbinger of cell death.
PMCID: PMC3822608  PMID: 19188912
cell death; inflammation; cytokines; electron microscopy; gene expression
20.  Pulmonary immune changes early after laparoscopic antireflux surgery in lung transplant patients with gastroesophageal reflux disease☆ 
The Journal of surgical research  2012;177(2):e65-e73.
The biologic mechanisms by which laparoscopic antireflux surgery (LARS) might influence the inflammatory process leading to bronchiolitis obliterans syndrome are unknown. We hypothesized that LARS alters the pulmonary immune profile in lung transplant patients with gastroesophageal reflux disease.
In 8 lung transplant patients with gastroesophageal reflux disease, we quantified and compared the pulmonary leukocyte differential and the concentration of inflammatory mediators in the bronchoalveolar lavage fluid (BALF) 4 weeks before LARS, 4 weeks after LARS, and 12 months after lung transplantation. Freedom from bronchiolitis obliterans syndrome (graded 1–3 according to the International Society of Heart and Lung Transplantation guidelines), forced expiratory volume in 1 second trends, and survival were also examined.
At 4 weeks after LARS, the percentages of neutrophils and lymphocytes in the BALF were reduced (from 6.6% to 2.8%, P = 0.049, and from 10.4% to 2.4%, P = 0.163, respectively). The percentage of macrophages increased (from 74.8% to 94.6%, P = 0.077). Finally, the BALF concentration of myeloperoxide and interleukin-1β tended to decrease (from 2109 to 1033 U/mg, P = 0.063, and from 4.1 to 0 pg/mg protein, P = 0.031, respectively), and the concentrations of interleukin-13 and interferon-γ tended to increase (from 7.6 to 30.4 pg/mg protein, P = 0.078 and from 0 to 159.5 pg/mg protein, P = 0.031, respectively). These trends were typically similar at 12 months after transplantation. At a mean follow-up of 19.7 months, the survival rate was 75% and the freedom from bronchiolitis obliterans syndrome was 75%. Overall, the forced expiratory volume in 1 second remained stable during the first year after transplantation.
Our preliminary study has demonstrated that LARS can restore the physiologic balance of pulmonary leukocyte populations and that the BALF concentration of pro-inflammatory mediators is altered early after LARS. These results suggest that LARS could modulate the pulmonary inflammatory milieu in lung transplant patients with gastroesophageal reflux disease.
PMCID: PMC3694396  PMID: 22537841
Gastroesophageal reflux disease GERD; Laparoscopic antireflux surgery LARS; Lung transplantation; Bronchiolitis obliterans syndrome BOS; Inflammation
21.  The Prevalence and Extent of Gastroesophageal Reflux Disease Correlates to the Type of Lung Transplantation 
Evidence is increasingly convincing that lung transplantation is a risk factor of gastroesophageal reflux disease (GERD). However, it is still not known if the type of lung transplant (unilateral, bilateral, or retransplant) plays a role in the pathogenesis of GERD.
Study Design
The records of 61 lung transplant patients who underwent esophageal function tests between September 2008 and May 2010, were retrospectively reviewed. These patients were divided into 3 groups based on the type of lung transplant they received: unilateral (n=25); bilateral (n=30), and retransplant (n=6). Among these groups we compared: (1) the demographic characteristics (eg, sex, age, race, and body mass index); (2) the presence of Barrett esophagus, delayed gastric emptying, and hiatal hernia; and (3) the esophageal manometric and pH-metric profile.
Distal and proximal reflux were more prevalent in patients with bilateral transplant or retransplant and less prevalent in patients after unilateral transplant, regardless of the cause of their lung disease. The prevalence of hiatal hernia, Barrett esophagus, and the manometric profile were similar in all groups of patients.
Although our data show a discrepancy in prevalence of GERD in patients with different types of lung transplantation, we cannot determine the exact cause for these findings from this study. We speculate that the extent of dissection during the transplant places the patients at risk for GERD. On the basis of the results of this study, a higher level of suspicion of GERD should be held in patients after bilateral or retransplantation.
PMCID: PMC3709252  PMID: 22318059
gastroesophageal reflux disease (GERD); laparoscopic antireflux surgery; esophageal function testing; lung transplantation
22.  The protective role of laparoscopic antireflux surgery against aspiration of pepsin after lung transplantation 
Surgery  2011;150(4):598-606.
The goal of this study was to determine, in lung transplant patients, if laparoscopic antireflux surgery (LARS) is an effective means to prevent aspiration as defined by the presence of pepsin in the bronchoalveolar lavage fluid (BALF).
Between September 2009 and November 2010, we collected BALF from 64 lung transplant patients at multiple routine surveillance assessments for acute cellular rejection, or when clinically indicated for diagnostic purposes. The BALF was tested for pepsin by enzyme-linked immunosorbent assay (ELISA). We then compared pepsin concentrations in the BALF of healthy controls (n = 11) and lung transplant patients with and without gastroesophageal reflux disease (GERD) on pH-monitoring (n = 8 and n = 12, respectively), and after treatment of GERD by LARS (n = 19). Time to the development of bronchiolitis obliterans syndrome was contrasted between groups based on GERD status or the presence of pepsin in the BALF.
We found that lung transplant patients with GERD had more pepsin in their BALF than lung transplant patients who underwent LARS (P = .029), and that pepsin was undetectable in the BALF of controls. Moreover, those with more pepsin had quicker progression to BOS and more acute rejection episodes.
This study compared pepsin in the BALF from lung transplant patients with and without LARS. Our data show that: (1) the detection of pepsin in the BALF proves aspiration because it is not present in healthy volunteers, and (2) LARS appears effective as a measure to prevent the aspiration of gastroesophageal refluxate in the lung transplant population. We believe that these findings provide a mechanism for those studies suggesting that LARS may prevent nonallogenic injury to the transplanted lungs from aspiration of gastroesophageal contents.
PMCID: PMC3694415  PMID: 22000170
23.  A review of the role of GERD-induced aspiration after lung transplantation 
Surgical endoscopy  2011;26(5):1201-1204.
The increased prevalence of gastroesophageal reflux disease (GERD) in lung transplantation patients has been established; however, many questions persist regarding the relationship of GERD to aspiration and its potential to induce pulmonary allograft failure. Moreover, the biological implications of aspiration in lung transplantation have yet to be fully elucidated. The goal of this review was to assess the relationship between GERD and aspiration, focusing on the role of these events in the development of allograft injury after lung transplantation.
PMCID: PMC3690196  PMID: 22083335
Gastroesophageal reflux disease (GERD); Aspiration; Lung transplantation; Ambulatory pH-monitoring; Esophageal multichannel pH impedance; Laparoscopic antireflux surgery (LARS)
24.  Laparoscopic Antireflux Surgery for Gastroesophageal Reflux Disease After Lung Transplantation 
The Journal of surgical research  2011;170(2):e279-e286.
Although gastroesophageal reflux disease (GERD) is highly prevalent in lung transplantation, the pathophysiology of GERD in these patients is unknown. We hypothesize that the pathophysiology of GERD after lung transplantation differs from that of a control population, and that the 30-d morbidity and mortality of laparoscopic antireflux surgery (LARS) are equivalent in both populations.
We retrospectively compared the pathophysiology of GERD and the 30-d morbidity and mortality of 29 consecutive lung transplant patients with 23 consecutive patients without lung transplantation (control group), all of whom had LARS for GERD between November 2008 and May 2010.
Both groups had a similar prevalence of endoscopic esophagitis and Barrett’s esophagus, comparable manometric profiles, and similar prevalence of abnormal peristalsis. However, hiatal hernia was more common in controls than in lung transplant patients (57% versus 24%; P = 0.04). Lung transplant patients had a higher prevalence and severity of proximal GERD (65% versus 33%; P = 0.04). The 30-d morbidity and mortality following LARS were similar in both groups regardless of the higher surgical risk of lung transplants (median ASA class: 3 versus 2 for controls, P < 0.001).
These results show that despite similar manometric profiles, lung transplant patients are more prone to proximal reflux than the general population with GERD; the prevalence of endoscopic esophagitis and Barrett’s esophagus is the same in both groups of patients; a hiatal hernia is uncommon after lung transplantation; and the morbidity and mortality of LARS are the same for lung transplant patients as the general population with GERD.
PMCID: PMC3686158  PMID: 21816422
gastroesophageal reflux disease (GERD); laparoscopic antireflux surgery; esophageal function testing; lung transplantation
25.  Exhaled Breath Condensate Collection in the Mechanically Ventilated Patient 
Respiratory Medicine  2012;106(5):601-613.
Collection of exhaled breath condensate (EBC) is a non-invasive means of sampling the airway-lining fluid of the lungs. EBC contains numerous measurable mediators, whose analysis could change the management of patients with certain pulmonary diseases.
While initially popularized in investigations involving spontaneously breathing patients, an increasing number of studies have been performed using EBC in association with mechanical ventilation. Collection of EBC in mechanically ventilated patients follows basic principles of condensation, but is influenced by multiple factors. Effective collection requires selection of a collection device, adequate minute ventilation, low cooling temperatures, and sampling times of greater than ten minutes. Condensate can be contaminated by saliva, which needs to be filtered. Dilution of samples occurs secondary to distilled water in vapors and humidification in the ventilator circuit. Dilution factors may need to be employed when investigating non-volatile biomarkers. Storage and analysis should occur promptly at −70° C to −80° C to prevent rapid degradation of samples.
The purpose of this review is to examine and describe methodologies and problems of EBC collection in mechanically ventilated patients. A straightforward and safe framework has been established to investigate disease processes in this population, yet technical aspects of EBC collection still exist that prevent clinical practicality of this technology. These include a lack of standardization of procedure and analysis of biomarkers, and of normal reference ranges for mediators in healthy individuals. Once these procedural aspects have been addressed, EBC could serve as a non-invasive alternative to invasive evaluation of lungs in mechanically ventilated patients.
PMCID: PMC3314159  PMID: 22398157
Exhaled breath condensate; Biomarkers; Inflammation; Mechanical ventilation; Airway-lining fluid

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