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1.  Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture 
Berndt, Sonja I. | Gustafsson, Stefan | Mägi, Reedik | Ganna, Andrea | Wheeler, Eleanor | Feitosa, Mary F. | Justice, Anne E. | Monda, Keri L. | Croteau-Chonka, Damien C. | Day, Felix R. | Esko, Tõnu | Fall, Tove | Ferreira, Teresa | Gentilini, Davide | Jackson, Anne U. | Luan, Jian’an | Randall, Joshua C. | Vedantam, Sailaja | Willer, Cristen J. | Winkler, Thomas W. | Wood, Andrew R. | Workalemahu, Tsegaselassie | Hu, Yi-Juan | Lee, Sang Hong | Liang, Liming | Lin, Dan-Yu | Min, Josine L. | Neale, Benjamin M. | Thorleifsson, Gudmar | Yang, Jian | Albrecht, Eva | Amin, Najaf | Bragg-Gresham, Jennifer L. | Cadby, Gemma | den Heijer, Martin | Eklund, Niina | Fischer, Krista | Goel, Anuj | Hottenga, Jouke-Jan | Huffman, Jennifer E. | Jarick, Ivonne | Johansson, Åsa | Johnson, Toby | Kanoni, Stavroula | Kleber, Marcus E. | König, Inke R. | Kristiansson, Kati | Kutalik, Zoltán | Lamina, Claudia | Lecoeur, Cecile | Li, Guo | Mangino, Massimo | McArdle, Wendy L. | Medina-Gomez, Carolina | Müller-Nurasyid, Martina | Ngwa, Julius S. | Nolte, Ilja M. | Paternoster, Lavinia | Pechlivanis, Sonali | Perola, Markus | Peters, Marjolein J. | Preuss, Michael | Rose, Lynda M. | Shi, Jianxin | Shungin, Dmitry | Smith, Albert Vernon | Strawbridge, Rona J. | Surakka, Ida | Teumer, Alexander | Trip, Mieke D. | Tyrer, Jonathan | Van Vliet-Ostaptchouk, Jana V. | Vandenput, Liesbeth | Waite, Lindsay L. | Zhao, Jing Hua | Absher, Devin | Asselbergs, Folkert W. | Atalay, Mustafa | Attwood, Antony P. | Balmforth, Anthony J. | Basart, Hanneke | Beilby, John | Bonnycastle, Lori L. | Brambilla, Paolo | Bruinenberg, Marcel | Campbell, Harry | Chasman, Daniel I. | Chines, Peter S. | Collins, Francis S. | Connell, John M. | Cookson, William | de Faire, Ulf | de Vegt, Femmie | Dei, Mariano | Dimitriou, Maria | Edkins, Sarah | Estrada, Karol | Evans, David M. | Farrall, Martin | Ferrario, Marco M. | Ferrières, Jean | Franke, Lude | Frau, Francesca | Gejman, Pablo V. | Grallert, Harald | Grönberg, Henrik | Gudnason, Vilmundur | Hall, Alistair S. | Hall, Per | Hartikainen, Anna-Liisa | Hayward, Caroline | Heard-Costa, Nancy L. | Heath, Andrew C. | Hebebrand, Johannes | Homuth, Georg | Hu, Frank B. | Hunt, Sarah E. | Hyppönen, Elina | Iribarren, Carlos | Jacobs, Kevin B. | Jansson, John-Olov | Jula, Antti | Kähönen, Mika | Kathiresan, Sekar | Kee, Frank | Khaw, Kay-Tee | Kivimaki, Mika | Koenig, Wolfgang | Kraja, Aldi T. | Kumari, Meena | Kuulasmaa, Kari | Kuusisto, Johanna | Laitinen, Jaana H. | Lakka, Timo A. | Langenberg, Claudia | Launer, Lenore J. | Lind, Lars | Lindström, Jaana | Liu, Jianjun | Liuzzi, Antonio | Lokki, Marja-Liisa | Lorentzon, Mattias | Madden, Pamela A. | Magnusson, Patrik K. | Manunta, Paolo | Marek, Diana | März, Winfried | Mateo Leach, Irene | McKnight, Barbara | Medland, Sarah E. | Mihailov, Evelin | Milani, Lili | Montgomery, Grant W. | Mooser, Vincent | Mühleisen, Thomas W. | Munroe, Patricia B. | Musk, Arthur W. | Narisu, Narisu | Navis, Gerjan | Nicholson, George | Nohr, Ellen A. | Ong, Ken K. | Oostra, Ben A. | Palmer, Colin N.A. | Palotie, Aarno | Peden, John F. | Pedersen, Nancy | Peters, Annette | Polasek, Ozren | Pouta, Anneli | Pramstaller, Peter P. | Prokopenko, Inga | Pütter, Carolin | Radhakrishnan, Aparna | Raitakari, Olli | Rendon, Augusto | Rivadeneira, Fernando | Rudan, Igor | Saaristo, Timo E. | Sambrook, Jennifer G. | Sanders, Alan R. | Sanna, Serena | Saramies, Jouko | Schipf, Sabine | Schreiber, Stefan | Schunkert, Heribert | Shin, So-Youn | Signorini, Stefano | Sinisalo, Juha | Skrobek, Boris | Soranzo, Nicole | Stančáková, Alena | Stark, Klaus | Stephens, Jonathan C. | Stirrups, Kathleen | Stolk, Ronald P. | Stumvoll, Michael | Swift, Amy J. | Theodoraki, Eirini V. | Thorand, Barbara | Tregouet, David-Alexandre | Tremoli, Elena | Van der Klauw, Melanie M. | van Meurs, Joyce B.J. | Vermeulen, Sita H. | Viikari, Jorma | Virtamo, Jarmo | Vitart, Veronique | Waeber, Gérard | Wang, Zhaoming | Widén, Elisabeth | Wild, Sarah H. | Willemsen, Gonneke | Winkelmann, Bernhard R. | Witteman, Jacqueline C.M. | Wolffenbuttel, Bruce H.R. | Wong, Andrew | Wright, Alan F. | Zillikens, M. Carola | Amouyel, Philippe | Boehm, Bernhard O. | Boerwinkle, Eric | Boomsma, Dorret I. | Caulfield, Mark J. | Chanock, Stephen J. | Cupples, L. Adrienne | Cusi, Daniele | Dedoussis, George V. | Erdmann, Jeanette | Eriksson, Johan G. | Franks, Paul W. | Froguel, Philippe | Gieger, Christian | Gyllensten, Ulf | Hamsten, Anders | Harris, Tamara B. | Hengstenberg, Christian | Hicks, Andrew A. | Hingorani, Aroon | Hinney, Anke | Hofman, Albert | Hovingh, Kees G. | Hveem, Kristian | Illig, Thomas | Jarvelin, Marjo-Riitta | Jöckel, Karl-Heinz | Keinanen-Kiukaanniemi, Sirkka M. | Kiemeney, Lambertus A. | Kuh, Diana | Laakso, Markku | Lehtimäki, Terho | Levinson, Douglas F. | Martin, Nicholas G. | Metspalu, Andres | Morris, Andrew D. | Nieminen, Markku S. | Njølstad, Inger | Ohlsson, Claes | Oldehinkel, Albertine J. | Ouwehand, Willem H. | Palmer, Lyle J. | Penninx, Brenda | Power, Chris | Province, Michael A. | Psaty, Bruce M. | Qi, Lu | Rauramaa, Rainer | Ridker, Paul M. | Ripatti, Samuli | Salomaa, Veikko | Samani, Nilesh J. | Snieder, Harold | Sørensen, Thorkild I.A. | Spector, Timothy D. | Stefansson, Kari | Tönjes, Anke | Tuomilehto, Jaakko | Uitterlinden, André G. | Uusitupa, Matti | van der Harst, Pim | Vollenweider, Peter | Wallaschofski, Henri | Wareham, Nicholas J. | Watkins, Hugh | Wichmann, H.-Erich | Wilson, James F. | Abecasis, Goncalo R. | Assimes, Themistocles L. | Barroso, Inês | Boehnke, Michael | Borecki, Ingrid B. | Deloukas, Panos | Fox, Caroline S. | Frayling, Timothy | Groop, Leif C. | Haritunian, Talin | Heid, Iris M. | Hunter, David | Kaplan, Robert C. | Karpe, Fredrik | Moffatt, Miriam | Mohlke, Karen L. | O’Connell, Jeffrey R. | Pawitan, Yudi | Schadt, Eric E. | Schlessinger, David | Steinthorsdottir, Valgerdur | Strachan, David P. | Thorsteinsdottir, Unnur | van Duijn, Cornelia M. | Visscher, Peter M. | Di Blasio, Anna Maria | Hirschhorn, Joel N. | Lindgren, Cecilia M. | Morris, Andrew P. | Meyre, David | Scherag, André | McCarthy, Mark I. | Speliotes, Elizabeth K. | North, Kari E. | Loos, Ruth J.F. | Ingelsson, Erik
Nature genetics  2013;45(5):501-512.
Approaches exploiting extremes of the trait distribution may reveal novel loci for common traits, but it is unknown whether such loci are generalizable to the general population. In a genome-wide search for loci associated with upper vs. lower 5th percentiles of body mass index, height and waist-hip ratio, as well as clinical classes of obesity including up to 263,407 European individuals, we identified four new loci (IGFBP4, H6PD, RSRC1, PPP2R2A) influencing height detected in the tails and seven new loci (HNF4G, RPTOR, GNAT2, MRPS33P4, ADCY9, HS6ST3, ZZZ3) for clinical classes of obesity. Further, we show that there is large overlap in terms of genetic structure and distribution of variants between traits based on extremes and the general population and little etiologic heterogeneity between obesity subgroups.
doi:10.1038/ng.2606
PMCID: PMC3973018  PMID: 23563607
2.  Ensuring Quality Cancer Care: A Follow-Up Review of the Institute of Medicine’s Ten Recommendations for Improving the Quality of Cancer Care in America 
Cancer  2011;118(10):2571-2582.
Responding to growing concerns regarding the safety, quality, and efficacy of cancer care in the United States, the Institute of Medicine (IOM) of the National Academy of Sciences commissioned a comprehensive review of cancer care delivery in the US healthcare system in the late 1990s. The National Cancer Policy Board (NCPB), a twenty-member board with broad representation, performed this review. In its review, the NCPB focused on the state of cancer care delivery at that time, its shortcomings, and ways to measure and improve the quality of cancer care. The NCPB described an ideal cancer care system, where patients would have equitable access to coordinated, guideline-based care and novel therapies throughout the course of their disease. In 1999, the IOM published the results of this review in its influential report, Ensuring Quality Cancer Care. This report outlined ten recommendations, which, when implemented, would: 1) improve the quality of cancer care; 2) increase our understanding of quality cancer care; and, 3) reduce or eliminate access barriers to quality cancer care.
Despite the fervor generated by this report, there are lingering doubts regarding the safety and quality of cancer care in the United States today. Increased awareness of medical errors and barriers to quality care, coupled with escalating healthcare costs, has prompted national efforts to reform the healthcare system. These efforts by healthcare providers and policymakers should bridge the gap between the ideal state described in Ensuring Quality Cancer Care and the current state of cancer care in the United States.
doi:10.1002/cncr.26536
PMCID: PMC3272132  PMID: 22045610
Oncology Service; Hospital; Quality of Health Care; Benchmarking; Guideline Adherence; Medically Uninsured; Palliative Care; Comparative Effectiveness Research
3.  Rapid and Sustainable Detoxication of Airborne Pollutants by Broccoli Sprout Beverage: Results of a Randomized Clinical Trial in China 
Broccoli sprouts are a convenient and rich source of the glucosinolate, glucoraphanin, which can generate the chemopreventive agent, sulforaphane, an inducer of glutathione S-transferases (GSTs) and other cytoprotective enzymes. A broccoli sprout-derived beverage providing daily doses of 600 μmol glucoraphanin and 40 μmol sulforaphane was evaluated for magnitude and duration of pharmacodynamic action in a 12-week randomized clinical trial. Two hundred and ninety-one study participants were recruited from the rural He-He Township, Qidong, in the Yangtze River delta region of China, an area characterized by exposures to substantial levels of airborne pollutants. Exposure to air pollution has been associated with lung cancer and cardiopulmonary diseases. Urinary excretion of the mercapturic acids of the pollutants, benzene, acrolein, and crotonaldehyde, were measured before and during the intervention using liquid chromatography tandem mass spectrometry. Rapid and sustained, statistically significant (p ≤ 0.01) increases in the levels of excretion of the glutathione-derived conjugates of benzene (61%), acrolein (23%), but not crotonaldehyde were found in those receiving broccoli sprout beverage compared with placebo. Excretion of the benzene-derived mercapturic acid was higher in participants who were GSTT1-positive compared to the null genotype, irrespective of study arm assignment. Measures of sulforaphane metabolites in urine indicated that bioavailability did not decline over the 12-week daily dosing period. Thus, intervention with broccoli sprouts enhances the detoxication of some airborne pollutants and may provide a frugal means to attenuate their associated long-term health risks.
doi:10.1158/1940-6207.CAPR-14-0103
PMCID: PMC4125483  PMID: 24913818
Air pollution; broccoli; sulforaphane; benzene; chemoprevention
4.  PAI-1 over-expression decreases experimental post-thrombotic vein wall fibrosis by a non-vitronectin dependent mechanism 
SUMMARY
Background
Factors associated with post-thrombotic syndrome are known clinically, but the underlying cellular processes at the vein wall are not well-delineated. Prior work suggests that vein wall damage does not correlate with thrombus resolution, but rather with plasminogen activator-1 (PAI-1) and matrix metalloproteinase (MMP) activity.
Objective
We hypothesized that PAI-1 would confer post venous thrombosis (VT) vein wall protection via a Vitronectin (Vn) dependent mechanism.
Methods
A stasis model of VT was used with harvest over 2 weeks, in wild type (WT), Vn−/−, and PAI-1 overexpressing mice (PAI-1 Tg).
Results
PAI-1 Tg mice had larger VT at 6 and 14 days, compared to controls, but Vn−/−mice had no alteration of VT resolution. Gene deletion of Vn resulted in increased, rather than expected decrease in circulating PAI-1 activity. While both Vn−/− and PAI-1 Tg had attenuated intimal fibrosis, PAI-1 Tg had significantly less vein wall collagen and a compensatory increase in collagen III gene expression. Both Vn−/− and PAI-1 Tg vein wall had less monocyte chemotactic factor-1, and fewer macrophages (F4/80), with significantly less MMP-2 activity and decreased TIMP-1 antigen. Ex vivo assessment of TGFβ mediated fibrotic response showed that PAI-1 Tg vein walls had increased profibrotic gene expression (collagen I, III, MMP-2 and α-SMA) as compared with controls, opposite of the in vivo response.
Conclusions
The absence of Vn increases circulating PAI-1, which positively modulates vein wall fibrosis in a dose-dependent manner. Translationally, PAI-1 elevation may decrease vein wall damage after DVT, perhaps by decreasing macrophage-mediated activities.
doi:10.1111/jth.12644
PMCID: PMC4127110  PMID: 24943740
fibrosis; PAI-1; postthrombotic syndrome; venous thrombosis; vitronectin
5.  A Twin Study of Heritable and Shared Environmental Contributions to Autism 
The present study examined genetic and shared environment contributions to quantitatively-measured autism symptoms and categorically-defined ASD. Participants included 568 twins from the Interactive Autism Network. Autism symptoms were obtained using the Social Communication Questionnaire and Social Responsiveness Scale. Categorically-defined ASD was based on clinical diagnoses. DeFries-Fulker and liability threshold models examined etiologic influences. Very high heritability was observed for extreme autism symptom levels (h2g=.92-1.20). Extreme levels of social and repetitive behavior symptoms were strongly influenced by common genetic factors. Heritability of categorically-defined ASD diagnosis was comparatively low (.21, 95% CI=0.15-0.28). High heritability of extreme autism symptom levels confirms previous observations of strong genetic influences on autism. Future studies will require large, carefully ascertained family pedigrees and quantitative symptom measurements.
doi:10.1007/s10803-014-2081-2
PMCID: PMC4104233  PMID: 24604525
autism; twins; genetic; heritability; environment; diagnosis
6.  Weather Regulates Location, Timing, and Intensity of Dengue Virus Transmission between Humans and Mosquitoes 
PLoS Neglected Tropical Diseases  2015;9(7):e0003957.
Background
Dengue is one of the most aggressively expanding mosquito-transmitted viruses. The human burden approaches 400 million infections annually. Complex transmission dynamics pose challenges for predicting location, timing, and magnitude of risk; thus, models are needed to guide prevention strategies and policy development locally and globally. Weather regulates transmission-potential via its effects on vector dynamics. An important gap in understanding risk and roadblock in model development is an empirical perspective clarifying how weather impacts transmission in diverse ecological settings. We sought to determine if location, timing, and potential-intensity of transmission are systematically defined by weather.
Methodology/Principal Findings
We developed a high-resolution empirical profile of the local weather-disease connection across Peru, a country with considerable ecological diversity. Applying 2-dimensional weather-space that pairs temperature versus humidity, we mapped local transmission-potential in weather-space by week during 1994-2012. A binary classification-tree was developed to test whether weather data could classify 1828 Peruvian districts as positive/negative for transmission and into ranks of transmission-potential with respect to observed disease. We show that transmission-potential is regulated by temperature-humidity coupling, enabling epidemics in a limited area of weather-space. Duration within a specific temperature range defines transmission-potential that is amplified exponentially in higher humidity. Dengue-positive districts were identified by mean temperature >22°C for 7+ weeks and minimum temperature >14°C for 33+ weeks annually with 95% sensitivity and specificity. In elevated-risk locations, seasonal peak-incidence occurred when mean temperature was 26-29°C, coincident with humidity at its local maximum; highest incidence when humidity >80%. We profile transmission-potential in weather-space for temperature-humidity ranging 0-38°C and 5-100% at 1°C x 2% resolution.
Conclusions/Significance
Local duration in limited areas of temperature-humidity weather-space identifies potential locations, timing, and magnitude of transmission. The weather-space profile of transmission-potential provides needed data that define a systematic and highly-sensitive weather-disease connection, demonstrating separate but coupled roles of temperature and humidity. New insights regarding natural regulation of human-mosquito transmission across diverse ecological settings advance our understanding of risk locally and globally for dengue and other mosquito-borne diseases and support advances in public health policy/operations, providing an evidence-base for modeling, predicting risk, and surveillance-prevention planning.
Author Summary
Timing and spatial-extent of diseases such as dengue and malaria that result from transmission between humans and mosquitoes are regulated by weather in complicated ways. For Aedes aegypti mosquitoes, the primary vector of dengue, slight changes in different components of weather have important effects on population dynamics, lifespan, biting-frequency, virus incubation period and capacity to transmit the virus, thus inducing changes in transmission probability. These complicated dynamics produce a weather-disease connection that is not well-defined for different ecological settings. Understanding this connection is important to critical elements of policy development and operational control of dengue such as predicting risk, developing human-vector transmission models, and planning surveillance-intervention strategies locally and globally. The empirical profile of the weather-disease connection for dengue developed in this study provides a needed understanding of how temperature and humidity work together in regulating human-mosquito transmission. The observed likelihood of low to epidemic-level transmission was highly sensitive to local seasonal duration in limited areas of this two-dimensional weather-space. Data presented represent a resource for estimating where and when transmission-potential supports epidemics of varying magnitude. This high-resolution weather-disease profile for dengue reveals systematic relationships that are informative for mosquito-borne diseases in general and discussions of consequences of global warming.
doi:10.1371/journal.pntd.0003957
PMCID: PMC4519153  PMID: 26222979
7.  Enhanced Raman Scattering from Vibro-Polariton Hybrid States** 
Ground-state molecular vibrations can be hybridized through strong coupling with the vacuum field of a cavity optical mode in the infrared region, leading to the formation of two new coherent vibro-polariton states. The spontaneous Raman scattering from such hybridized light–matter states was studied, showing that the collective Rabi splitting occurs at the level of a single selected bond. Moreover, the coherent nature of the vibro-polariton states boosts the Raman scattering cross-section by two to three orders of magnitude, revealing a new enhancement mechanism as a result of vibrational strong coupling. This observation has fundamental consequences for the understanding of light-molecule strong coupling and for molecular science.
doi:10.1002/anie.201502979
PMCID: PMC4515085  PMID: 26037542
optical cavity; Raman scattering; strong coupling; vibrations; vibro-polariton states
8.  Increased inflammation but similar physical composition and function in older-aged, HIV-1 infected subjects 
BMC Immunology  2015;16:43.
Background
Systemic immune activation (inflammation) and immunosenescence develop in some people with advancing age. This process, known as “inflamm-aging,” is associated with physical frailty and sarcopenia. Meanwhile, successful antiretroviral therapy has led to a growing number of older HIV-1-infected individuals who face both age-related and HIV-1-related inflammation, which may synergistically promote physical decline, including frailty and sarcopenia. The purpose of our study was to determine if inflammation during treated HIV-1 infection worsens physical impairment in older individuals.
Methods
We determined the severity of HIV-associated inflammation and physical performance (strength and endurance) in 21 older HIV-infected individuals (54–69 years) receiving suppressive antiretroviral therapy, balanced for confounding variables including age, anthropometrics, and co-morbidities with 10 uninfected control individuals. Biomarkers for microbial translocation (lipopolysaccharide [LPS]), inflammation (soluble CD14 [sCD14], osteopontin, C-reactive protein [CRP], interleukin-6 [IL-6], soluble ICAM-1 [sICAM-1] and soluble VCAM-1 [sVCAM-1]), and coagulopathy (D-dimer) were assayed in plasma. Activation phenotypes of CD4+T cells, CD8+ T cells and monocytes were measured by flow cytometry. Physical performance was measured by 400 m walking speed, a short physical performance battery [SPPB], and lower extremity muscle strength and fatigue.
Results
Overall physical function was similar in the uninfected and HIV-infected groups. Compared to uninfected individuals, the HIV-infected group had elevated levels of sCD14 (P < 0.001), CRP (P < 0.001) and IL-6 (P = 0.003) and an increased frequency of CD4+ and CD8+ T cells with an immunosenescent CD57+ phenotype (P = 0.004 and P = 0.043, respectively). Neither plasma inflammatory biomarkers nor CD57+ T cells correlated with CD4+ T cell counts. Furthermore, none of the elevated inflammatory biomarkers in the HIV-infected subjects were associated with any of the physical performance results.
Conclusions
When age-related co-morbidities were carefully balanced between the uninfected and HIV-infected groups, no evidence of inflammation-associated physical impairment was detected. Despite careful balancing for age, BMI, medications and co-morbidities, the HIV-infected group still displayed evidence of significant chronic inflammation, including elevated sCD14, CRP, IL-6 and CD57+ T cells, although the magnitude of this inflammation was unrelated to physical impairment.
doi:10.1186/s12865-015-0106-z
PMCID: PMC4513956  PMID: 26204934
9.  Novel Fast Adapting Interneurons Mediate Cholinergic-Induced Fast GABAA IPSCs In Striatal Spiny Neurons 
The European journal of neuroscience  2015;42(2):1764-1774.
Previous work suggests that neostriatal cholinergic interneurons control the activity of several classes of GABAergic interneurons through fast nicotinic receptor mediated synaptic inputs. Although indirect evidence has suggested the existence of several classes of interneurons controlled by this mechanism only one such cell type, the neuropeptide-Y expressing neurogliaform neuron, has been identified to date. Here we tested the hypothesis that in addition to the neurogliaform neurons that elicit slow GABAergic inhibitory responses, another interneuron type exists in the striatum that receives strong nicotinic cholinergic input and elicits conventional fast GABAergic synaptic responses in projection neurons. We obtained in vitro slice recordings from double transgenic mice in which Channelrhodopsin-2 was natively expressed in cholinergic neurons and a population of serotonin receptor-3a-Cre expressing GABAergic interneurons were visualized with tdTomato. We show that among the targeted GABAergic interneurons a novel type of interneuron, termed the fast-adapting interneuron, can be identified that is distinct from previously known interneurons based on immunocytochemical and electrophysiological criteria. We show using optogenetic activation of cholinergic inputs that fast-adapting interneurons receive a powerful supra-threshold nicotinic cholinergic input in vitro. Moreover, fast adapting neurons are densely connected to projection neurons and elicit fast, GABAA receptor mediated inhibitory postsynaptic responses. The nicotinic receptor mediated activation of fast-adapting interneurons may constitute an important mechanism through which cholinergic interneurons control the activity of projection neurons and perhaps the plasticity of their synaptic inputs when animals encounter reinforcing or otherwise salient stimuli.
doi:10.1111/ejn.12915
PMCID: PMC4510010  PMID: 25865337
neostriatum; acetylcholine; fast inhibition; nicotinic receptors
10.  Genome sequence and comparative analysis of a putative entomopathogenic Serratia isolated from Caenorhabditis briggsae 
BMC Genomics  2015;16(1):531.
Background
Entomopathogenic associations between nematodes in the genera Steinernema and Heterorhabdus with their cognate bacteria from the bacterial genera Xenorhabdus and Photorhabdus, respectively, are extensively studied for their potential as biological control agents against invasive insect species. These two highly coevolved associations were results of convergent evolution. Given the natural abundance of bacteria, nematodes and insects, it is surprising that only these two associations with no intermediate forms are widely studied in the entomopathogenic context. Discovering analogous systems involving novel bacterial and nematode species would shed light on the evolutionary processes involved in the transition from free living organisms to obligatory partners in entomopathogenicity.
Results
We report the complete genome sequence of a new member of the enterobacterial genus Serratia that forms a putative entomopathogenic complex with Caenorhabditis briggsae. Analysis of the 5.04 MB chromosomal genome predicts 4599 protein coding genes, seven sets of ribosomal RNA genes, 84 tRNA genes and a 64.8 KB plasmid encoding 74 genes. Comparative genomic analysis with three of the previously sequenced Serratia species, S. marcescens DB11 and S. proteamaculans 568, and Serratia sp. AS12, revealed that these four representatives of the genus share a core set of ~3100 genes and extensive structural conservation. The newly identified species shares a more recent common ancestor with S. marcescens with 99 % sequence identity in rDNA sequence and orthology across 85.6 % of predicted genes. Of the 39 genes/operons implicated in the virulence, symbiosis, recolonization, immune evasion and bioconversion, 21 (53.8 %) were present in Serratia while 33 (84.6 %) and 35 (89 %) were present in Xenorhabdus and Photorhabdus EPN bacteria respectively.
Conclusion
The majority of unique sequences in Serratia sp. SCBI (South African Caenorhabditis briggsae Isolate) are found in ~29 genomic islands of 5 to 65 genes and are enriched in putative functions that are biologically relevant to an entomopathogenic lifestyle, including non-ribosomal peptide synthetases, bacteriocins, fimbrial biogenesis, ushering proteins, toxins, secondary metabolite secretion and multiple drug resistance/efflux systems. By revealing the early stages of adaptation to this lifestyle, the Serratia sp. SCBI genome underscores the fact that in EPN formation the composite end result – killing, bioconversion, cadaver protection and recolonization- can be achieved by dissimilar mechanisms. This genome sequence will enable further study of the evolution of entomopathogenic nematode-bacteria complexes.
Electronic supplementary material
The online version of this article (doi:10.1186/s12864-015-1697-8) contains supplementary material, which is available to authorized users.
doi:10.1186/s12864-015-1697-8
PMCID: PMC4506600  PMID: 26187596
Serratia; Caenorhabditis; Entomopathogen; EPN; Mutualism; Urea pathway
11.  Marburg virus infection in nonhuman primates: Therapeutic treatment by lipid-encapsulated siRNA 
Science translational medicine  2014;6(250):250ra116.
Marburg virus (MARV) and the closely related filovirus Ebola virus cause severe and often fatal hemorrhagic fever (HF) in humans and nonhuman primates with mortality rates up to 90%. There are no vaccines or drugs approved for human use, and no postexposure treatment has completely protected nonhuman primates against MARV-Angola, the strain associated with the highest rate of mortality in naturally occurring human outbreaks. Studies performed with other MARV strains assessed candidate treatments at times shortly after virus exposure, before signs of disease are detectable. We assessed the efficacy of lipid nanoparticle (LNP) delivery of anti-MARV nucleoprotein (NP)–targeting small interfering RNA (siRNA) at several time points after virus exposure, including after the onset of detectable disease in a uniformly lethal nonhuman primate model of MARV-Angola HF. Twenty-one rhesus monkeys were challenged with a lethal dose of MARV-Angola. Sixteen of these animals were treated with LNP containing anti-MARV NP siRNA beginning at 30 to 45 min, 1 day, 2 days, or 3 days after virus challenge. All 16 macaques that received LNP-encapsulated anti-MARV NP siRNA survived infection, whereas the untreated or mock-treated control subjects succumbed to disease between days 7 and 9 after infection. These results represent the successful demonstration of therapeutic anti–MARV-Angola efficacy in nonhuman primates and highlight the substantial impact of an LNP-delivered siRNA therapeutic as a countermeasure against this highly lethal human disease.
doi:10.1126/scitranslmed.3009706
PMCID: PMC4502585  PMID: 25143366
12.  Glottic Regeneration with Tissue Engineering Technique Using Acellular Extracellular Matrix Scaffold in Canine Model 
Acellular extracellular matrix scaffold derived from porcine urinary bladder (UBM) is decellularized material that has shown success for constructive remodeling of various tissues and organs. The regenerative effects of UBM were reported for the tympanic membrane, esophagus, trachea, larynx, pleura, and pericardium in animal studies with promising results. The aim of this study was to investigate regenerative effects of UBM to regenerate hemilarynx using a canine model. A left partial hemilaryngectomy was performed, and the surgical defects were reconstructed by insertion of UBM scaffold. Although local infection was observed in one dog in a week after implantation of the scaffold, all dogs showed good re-epithelialization with minimum complication in one month. The effect of regeneration of the larynx was evaluated 6 months after the operation. The excised larynx experiments were performed to measure phonation threshold pressure (PTP), normalized mucosal wave amplitude (NMWA), and normalized glottal gap (NGG). The results of the measurements showed that PTP was normal or near normal in 2 cases, NMWA was within normal range in 3 cases, although there were individual variations. Histologic examination was completed to evaluate structural changes of the scaffold with appearance of new cartilaginous structure. However the regenerated vocal fold mucosa is mostly scarred. The UBM scaffold has shown to be biocompatible, biodegradable, and useful for tissue regeneration of the hemilarynx with possible restoration of the vocal fold function. The vocal fold mucosa was scarred, which is the next challenge to improve.
doi:10.1002/term.1855
PMCID: PMC4087089  PMID: 24403099
acellular extracellular matrix; scaffold; glottic regeneration; tissue engineering; porcine urinary bladder; laryngeal function
13.  Identifying patients at high risk for venous thromboembolism requiring treatment after outpatient surgery 
Annals of surgery  2012;255(6):1093-1099.
Objective
To identify independent predictors of 30-day VTE events requiring treatment after outpatient surgery.
Summary Background Data
An increasing proportion of surgical procedures are performed in the outpatient setting. The incidence of venous thromboembolism (VTE) requiring treatment after outpatient surgery is unknown.
Methods
Prospective observational cohort study using the American College of Surgeons National Surgical Quality Improvement Program (ACS-NSQIP) database from 2005–2009. Adult patients who had outpatient surgery or surgery with subsequent 23-hour observation were included. The main outcome measure was 30-day VTE requiring treatment. Patients were randomly assigned to derivation (N=173,501) or validation (N=85,730) cohorts. Logistic regression examined independent risk factors for 30-day VTE. A weighted risk index was created and applied to the validation cohort. Stratified analyses examined 30-day VTE by risk level.
Results
30-day incidence of VTE for the overall cohort was 0.15%. Independent risk factors included current pregnancy (adjusted odds ratio (OR) 7.80, p=0.044), active cancer (OR 3.66, p=0.005), age 41–59 (OR 1.72, p=0.008), age ≥60 (OR 2.48, p<0.001), body mass index ≥40 (OR 1.81, p=0.015), operative time ≥120 minutes (OR 1.69, p=0.027), arthroscopic surgery (OR 5.16, p<0.001), sapheno-femoral junction surgery (OR 13.20, p<0.001), and venous surgery not involving the great saphenous vein (OR 15.61, p<0.001). The weighted risk index identified a 20-fold variation in 30-day VTE between low (0.06%) and highest risk (1.18%) patients.
Conclusions
30-day VTE risk after outpatient surgery can be quantified using a weighted risk index. The risk index identifies a high-risk subgroup of patients with 30-day VTE rates of 1.18%.
doi:10.1097/SLA.0b013e3182519ccf
PMCID: PMC4496245  PMID: 22584630
14.  Differential replication properties among H9N2 avian influenza viruses of Eurasian origin 
Veterinary Research  2015;46(1):75.
Avian influenza H9N2 viruses have become panzootic in Eurasia causing respiratory manifestations, great economic losses and occasionally being transmitted to humans. To evaluate the replication properties and compare the different virus quantification methods, four Eurasian H9N2 viruses from different geographical origins were propagated in embryonated chicken egg (ECE) and Madin-Darby canine kidney epithelial cell systems. The ECE-grown and cell culture-grown viruses were monitored for replication kinetics based on tissue culture infectious dose (TCID50), Hemagglutination (HA) test and quantitative real time RT-PCR (qRT-PCR). The cellular morphology was analyzed using immunofluorescence (IF) and cellular ELISA was used to screen the sensitivity of the viruses to amantadine. The Eurasian wild type-H9N2 virus produced lower titers compared to the three G1-H9N2 viruses at respective time points. Detectable titers were observed earliest at 16 h post inoculation (hpi), significant morphological changes on cells were first observed at 32 hpi. Few nucleotide and amino acid substitutions were noticed in the HA, NA and NS gene sequences but none of them are related to the known conserved region that can alter pathogenesis or virulence following a single passage in cell culture. All studied H9N2 viruses were sensitive to amantadine. The G1-H9N2 viruses have higher replication capabilities compared to the European wild bird-H9N2 probably due to their specific genetic constitutions which is prerequisite for a successful vaccine candidate. Both the ECE and MDCK cell system allowed efficient replication but the ECE system is considered as the better cultivation system for H9N2 viruses in order to get maximum amounts of virus within a short time period.
doi:10.1186/s13567-015-0198-8
PMCID: PMC4491879  PMID: 26149130
15.  The immunomodulating V and W proteins of Nipah virus determine disease course 
Nature Communications  2015;6:7483.
The viral determinants that contribute to Nipah virus (NiV)-mediated disease are poorly understood compared with other paramyxoviruses. Here we use recombinant NiVs (rNiVs) to examine the contributions of the NiV V and W proteins to NiV pathogenesis in a ferret model. We show that a V-deficient rNiV is susceptible to the innate immune response in vitro and behaves as a replicating non-lethal virus in vivo. Remarkably, rNiV lacking W expression results in a delayed and altered disease course with decreased respiratory disease and increased terminal neurological disease associated with altered in vitro inflammatory cytokine production. This study confirms the V protein as the major determinant of pathogenesis, also being the first in vivo study to show that the W protein modulates the inflammatory host immune response in a manner that determines the disease course.
Nipah virus (NiV) can be transmitted from bats and other animals to humans, causing severe encephalitis and respiratory disease. Here, Satterfield et al. show that the W protein of NiV modulates the host immune response and determines disease course in a ferret model of infection.
doi:10.1038/ncomms8483
PMCID: PMC4482017  PMID: 26105519
16.  Pros and cons of methylation-based enrichment methods for ancient DNA 
Scientific Reports  2015;5:11826.
The recent discovery that DNA methylation survives in fossil material provides an opportunity for novel molecular approaches in palaeogenomics. Here, we apply to ancient DNA extracts the probe-independent Methylated Binding Domains (MBD)-based enrichment method, which targets DNA molecules containing methylated CpGs. Using remains of a Palaeo-Eskimo Saqqaq individual, woolly mammoths, polar bears and two equine species, we confirm that DNA methylation survives in a variety of tissues, environmental contexts and over a large temporal range (4,000 to over 45,000 years before present). MBD enrichment, however, appears principally biased towards the recovery of CpG-rich and long DNA templates and is limited by the fast post-mortem cytosine deamination rates of methylated epialleles. This method, thus, appears only appropriate for the analysis of ancient methylomes from very well preserved samples, where both DNA fragmentation and deamination have been limited. This work represents an essential step toward the characterization of ancient methylation signatures, which will help understanding the role of epigenetic changes in past environmental and cultural transitions.
doi:10.1038/srep11826
PMCID: PMC4488743  PMID: 26134828
17.  Pathogenic properties of enterohepatic Helicobacter spp. isolated from rhesus macaques with intestinal adenocarcinoma 
Journal of Medical Microbiology  2014;63(Pt 7):1004-1016.
Considerable progress has been made in understanding the roles of Helicobacter pylori in inflammation and gastric cancer; however, far less is known about the roles of enterohepatic Helicobacter species (EHS) in carcinogenesis and their zoonotic or pathogenic potential. We determined the prevalence of EHS infection in a cohort of geriatric rhesus monkeys in which intestinal adenocarcinoma (IAC) is common and investigated the association between EHS infection and IAC. The cohort consisted of 36 animals, 14 of which (age 26–35 years) had IAC. Of the 36 rhesus, 35 (97 %) were positive for EHS using PCR or bacterial isolation from faeces, colonic or tumour tissues. Only a single rhesus, which had IAC, was negative for EHS by all detection methods. The EHS identified by 16S rRNA sequencing in this study were from three Helicobacter taxa: Helicobacter macacae (previously rhesus monkey taxon 1), Helicobacter sp. rhesus monkey taxon 2, previously described from strain MIT 99-5507, and Helicobacter sp. rhesus monkey taxon 4, related to Helicobacter fennelliae. Thirteen of 14 monkeys with IAC were positive for either H. macacae (7/13, 54 %), EHS rhesus monkey taxon 4 (4/13, 31 %) or a mixture of the two EHS (2/13, 15 %). These results indicate that EHS are prevalent among aged rhesus macaques with IAC. Using Helicobacter genus-specific florescent in situ hybridization, EHS were detected on the surface of colonic epithelia of infected monkeys. All Helicobacter isolates, including H. macacae, effectively adhered to, invaded, and significantly induced proinflammatory genes, including IL-8, IL-6, TNF-α and iNOS, while downregulating genes involved in the function of inflammasomes, particularly IL-1β, CASPASE-1, NRLP3, NLRP6 and NLRC4 in the human colonic T84 cell line (P<0.0001). These results suggest that EHS may represent an aetiological agent mediating diarrhoea, chronic inflammation, and possibly intestinal cancer in non-human primates, and may play a role in similar disease syndromes in humans. Downregulation of inflammasome function may represent an EHS strategy for long-term persistence in the host and play a role in inducing pathological changes in the host’s lower bowel.
doi:10.1099/jmm.0.072462-0
PMCID: PMC4064350  PMID: 24696515
18.  Complete protection against aflatoxin B1-induced liver cancer with a triterpenoid: DNA adduct dosimetry, molecular signature and genotoxicity threshold 
In experimental animals and humans, aflatoxin B1 (AFB1) is a potent hepatic toxin and carcinogen. The synthetic oleanane triterpenoid 1-[2-cyano-3-,12-dioxooleana-1,9(11)-dien-28-oyl]imidazole (CDDO-Im), a powerful activator of Keap1-Nrf2 signaling, protects against AFB1-induced toxicity and preneoplastic lesion formation (GST-P positive foci). This study assessed and mechanistically characterized the chemoprotective efficacy of CDDO-Im against AFB1-induced hepatocellular carcinoma (HCC). A lifetime cancer bioassay was undertaken in F344 rats dosed with AFB1 (200μg/kg rat/day) for 4 weeks and receiving either vehicle or CDDO-Im (three times weekly), one week prior to and throughout the exposure period. Weekly, 24-hour urine samples were collected for analysis of AFB1 metabolites. In a subset of rats, livers were analyzed for GST-P foci. The comparative response of a toxicogenomic RNA expression signature for AFB1 was examined. CDDO-Im completely protected (0/20) against AFB1-induced liver cancer compared to a 96% incidence (22/23) observed in the AFB1 group. With CDDO-Im treatment, integrated level of urinary AFB1-N7-guanine was significantly reduced (66%) and aflatoxin-N-acetylcysteine, a detoxication product, was consistently elevated (300%) after the first AFB1 dose. In AFB1-treated rats, the hepatic burden of GST-P positive foci increased substantially (0% to 13.8%) over the 4 weeks, but was largely absent with CDDO-Im intervention. The toxicogenomic RNA expression signature characteristic of AFB1 was absent in the AFB1 + CDDO-Im treated rats. The remarkable efficacy of CDDO-Im as an anticarcinogen is established even in the face of a significant aflatoxin adduct burden. Consequently, the absence of cancer requires a concept of a threshold for DNA damage for cancer development.
doi:10.1158/1940-6207.CAPR-13-0430
PMCID: PMC4082474  PMID: 24662598
aflatoxin; chemoprevention; gene expression; DNA adducts; triterpenoid
19.  Control of Acid Resistance Pathways of Enterohemorrhagic Escherichia coli Strain EDL933 by PsrB, a Prophage-Encoded AraC-Like Regulator 
Infection and Immunity  2014;83(1):346-353.
Enterohemorrhagic Escherichia coli (EHEC) O157:H7 causes bloody diarrhea and hemolytic-uremic syndrome (HUS) and is the most prevalent E. coli serotype associated with food-borne illness worldwide. This pathogen is transmitted via the fecal-oral route and has a low infectious dose that has been estimated to be between 10 and 100 cells. We and others have previously identified three prophage-encoded AraC-like transcriptional regulators, PatE, PsrA, and PsrB in the EHEC O157:H7 EDL933 strain. Our analysis showed that PatE plays an important role in facilitating survival of EHEC under a number of acidic conditions, but the contribution of PsrA and PsrB to acid resistance (AR) was unknown. Here, we investigated the involvement of PsrA and PsrB in the survival of E. coli O157:H7 in acid. Our results showed that PsrB, but not PsrA, enhanced the survival of strain EDL933 under various acidic conditions. Transcriptional analysis using promoter-lacZ reporters and electrophoretic mobility shift assays demonstrated that PsrB activates transcription of the hdeA operon, which encodes a major acid stress chaperone, by interacting with its promoter region. Furthermore, using a mouse model, we showed that expression of PsrB significantly enhanced the ability of strain EDL933 to overcome the acidic barrier of the mouse stomach. Taken together, our results indicate that EDL933 acquired enhanced acid tolerance via horizontally acquired regulatory genes encoding transcriptional regulators that activate its AR machinery.
doi:10.1128/IAI.02758-14
PMCID: PMC4288888  PMID: 25368119
20.  A Phase 3 Randomized Double-Blind Comparison of Ceftobiprole Medocaril Versus Ceftazidime Plus Linezolid for the Treatment of Hospital-Acquired Pneumonia 
In this double-blind, randomized, multicenter study, ceftobiprole was shown to be noninferior to combined ceftazidime/linezolid in patients with hospital-acquired pneumonia (HAP) for clinical cure. Ceftobiprole is considered a safe and effective bactericidal antibiotic for empiric treatment of HAP (excluding ventilator-associated pneumonia).
Background. Ceftobiprole, the active moiety of ceftobiprole medocaril, is a novel broad-spectrum cephalosporin, with bactericidal activity against a wide range of gram-positive bacteria, including Staphylococcus aureus (including methicillin-resistant strains) and penicillin- and ceftriaxone-resistant pneumococci, and gram-negative bacteria, including Enterobacteriaceae and Pseudomonas aeruginosa.
Methods. This was a double-blind, randomized, multicenter study of 781 patients with hospital-acquired pneumonia (HAP), including 210 with ventilator-associated pneumonia (VAP). Treatment was intravenous ceftobiprole 500 mg every 8 hours, or ceftazidime 2 g every 8 hours plus linezolid 600 mg every 12 hours; primary outcome was clinical cure at the test-of-cure visit.
Results. Overall cure rates for ceftobiprole vs ceftazidime/linezolid were 49.9% vs 52.8% (intent-to-treat [ITT], 95% confidence interval [CI] for the difference, −10.0 to 4.1) and 69.3% vs 71.3% (clinically evaluable [CE], 95% CI, −10.0 to 6.1). Cure rates in HAP (excluding VAP) patients were 59.6% vs 58.8% (ITT, 95% CI, −7.3 to 8.8), and 77.8% vs 76.2% (CE, 95% CI, −6.9 to 10.0). Cure rates in VAP patients were 23.1% vs 36.8% (ITT, 95% CI, −26.0 to −1.5) and 37.7% vs 55.9% (CE, 95% CI, −36.4 to 0). Microbiological eradication rates in HAP (excluding VAP) patients were, respectively, 62.9% vs 67.5% (microbiologically evaluable [ME], 95% CI, −16.7 to 7.6), and in VAP patients 30.4% vs 50.0% (ME, 95% CI, −38.8 to −0.4). Treatment-related adverse events were comparable for ceftobiprole (24.9%) and ceftazidime/linezolid (25.4%).
Conclusions. Ceftobiprole is a safe and effective bactericidal antibiotic for the empiric treatment of HAP (excluding VAP). Further investigations are needed before recommending the use of ceftobiprole in VAP patients.
Clinical Trials Registration. NCT00210964, NCT00229008.
doi:10.1093/cid/ciu219
PMCID: PMC4305133  PMID: 24723282
ceftazidime; ceftobiprole; linezolid; hospital-acquired pneumonia; ventilator-associated pneumonia
21.  The global distribution of the arbovirus vectors Aedes aegypti and Ae. albopictus 
eLife  null;4:e08347.
Dengue and chikungunya are increasing global public health concerns due to their rapid geographical spread and increasing disease burden. Knowledge of the contemporary distribution of their shared vectors, Aedes aegypti and Aedes albopictus remains incomplete and is complicated by an ongoing range expansion fuelled by increased global trade and travel. Mapping the global distribution of these vectors and the geographical determinants of their ranges is essential for public health planning. Here we compile the largest contemporary database for both species and pair it with relevant environmental variables predicting their global distribution. We show Aedes distributions to be the widest ever recorded; now extensive in all continents, including North America and Europe. These maps will help define the spatial limits of current autochthonous transmission of dengue and chikungunya viruses. It is only with this kind of rigorous entomological baseline that we can hope to project future health impacts of these viruses.
DOI: http://dx.doi.org/10.7554/eLife.08347.001
eLife digest
Mosquitoes spread many disease-causing viruses and parasites between people and other animals, including viral infections such as dengue and chikungunya. Both infections cause high fevers often accompanied with excruciating joint pain or other flu-like symptoms. Dengue and chikungunya have become growing public health problems over the last fifty years. Today about half of the world's population is at risk of dengue infection, while chikungunya outbreaks, which were previously limited to Africa and Asia, have recently been reported in the Caribbean, South America and Europe.
The dengue and chikungunya viruses are transmitted between people by two species of mosquitoes called Aedes aegypti and Ae. albopictus. Therefore it is important to work out where these mosquito species are found around the globe to identify the areas at risk. It is also important to predict where these species could become established if they were introduced, in order to identify areas that could become at risk in the future.
Kraemer et al. now provide updated predictions about the distribution of these two mosquito species around the globe. These predictions are based upon the most up-to-date data on the known locations of the species combined with information on environmental conditions across the globe. The updated maps show that these Aedes mosquitoes are now found across all continents, including North America and Europe.
Aedes albopictus mosquitoes in particular are rapidly expanding their territory around the globe. Kraemer et al. used their new maps to show that, unlike in the United States, many of the areas in Europe and China that could support this mosquito species do not yet appear to have been colonized.
These findings provide a map of the distribution of both species as it stands at the moment. Further work is now needed to better understand which factors are contributing to the rapid expansion of these mosquitoes' range and what might be done to control this spread.
DOI: http://dx.doi.org/10.7554/eLife.08347.002
doi:10.7554/eLife.08347
PMCID: PMC4493616  PMID: 26126267
Aedes; Ae. aegypti; Ae. albopictus; other
22.  EMX2 Is a Predictive Marker for Adjuvant Chemotherapy in Lung Squamous Cell Carcinomas 
PLoS ONE  2015;10(7):e0132134.
Background
Squamous cell carcinomas (SCC) account for approximately 30% of non-small cell lung cancer (NSCLC). Current staging methods do not adequately predict outcome for this disease. EMX2 is a homeo-domain containing transcription factor known to regulate a key developmental pathway. This study assessed the significance of EMX2 as a prognostic and predictive marker for resectable lung SCC.
Methods
Two independent cohorts of patients with lung SCC undergoing surgical resection were studied. EMX2 protein expression was examined by immunohistochemistry, Western blot, or immunofluorescence. EMX2 expression levels in tissue specimens were scored and correlated with patient outcomes. Chemo-sensitivity of lung SCC cell lines stably transfected with EMX2 shRNAs to cisplatin, carboplatin, and docetaxel was examined in vitro.
Results
EMX2 expression was down-regulated in lung SCC tissue samples compared to their matched adjacent normal tissues. Positive EMX2 expression was significantly associated with improved overall survival in stage I lung SCC patients, and in stage II/IIIA lung SCC patients receiving adjuvant chemotherapy. EMX2 expression was also associated with expression of EMT markers in both lung SCC cell lines and tissue samples. Knock-down of EMX2 expression in lung SCC cells promoted chemo-resistance and cell migration.
Conclusions
EMX2 expression is down-regulated in lung SCC and its down-regulation is associated with chemo-resistance in lung SCC cells, possibly through regulation of Epithelial-to-Mesenchymal Transition (EMT). EMX2 may serve as a novel prognostic marker for stage I lung SCC patients and a prediction marker for stage II/IIIA lung SCC patients receiving adjuvant chemotherapy.
doi:10.1371/journal.pone.0132134
PMCID: PMC4488446  PMID: 26132438
23.  Discovery and Fine-Mapping of Glycaemic and Obesity-Related Trait Loci Using High-Density Imputation 
Horikoshi, Momoko | Mӓgi, Reedik | van de Bunt, Martijn | Surakka, Ida | Sarin, Antti-Pekka | Mahajan, Anubha | Marullo, Letizia | Thorleifsson, Gudmar | Hӓgg, Sara | Hottenga, Jouke-Jan | Ladenvall, Claes | Ried, Janina S. | Winkler, Thomas W. | Willems, Sara M. | Pervjakova, Natalia | Esko, Tõnu | Beekman, Marian | Nelson, Christopher P. | Willenborg, Christina | Wiltshire, Steven | Ferreira, Teresa | Fernandez, Juan | Gaulton, Kyle J. | Steinthorsdottir, Valgerdur | Hamsten, Anders | Magnusson, Patrik K. E. | Willemsen, Gonneke | Milaneschi, Yuri | Robertson, Neil R. | Groves, Christopher J. | Bennett, Amanda J. | Lehtimӓki, Terho | Viikari, Jorma S. | Rung, Johan | Lyssenko, Valeriya | Perola, Markus | Heid, Iris M. | Herder, Christian | Grallert, Harald | Müller-Nurasyid, Martina | Roden, Michael | Hypponen, Elina | Isaacs, Aaron | van Leeuwen, Elisabeth M. | Karssen, Lennart C. | Mihailov, Evelin | Houwing-Duistermaat, Jeanine J. | de Craen, Anton J. M. | Deelen, Joris | Havulinna, Aki S. | Blades, Matthew | Hengstenberg, Christian | Erdmann, Jeanette | Schunkert, Heribert | Kaprio, Jaakko | Tobin, Martin D. | Samani, Nilesh J. | Lind, Lars | Salomaa, Veikko | Lindgren, Cecilia M. | Slagboom, P. Eline | Metspalu, Andres | van Duijn, Cornelia M. | Eriksson, Johan G. | Peters, Annette | Gieger, Christian | Jula, Antti | Groop, Leif | Raitakari, Olli T. | Power, Chris | Penninx, Brenda W. J. H. | de Geus, Eco | Smit, Johannes H. | Boomsma, Dorret I. | Pedersen, Nancy L. | Ingelsson, Erik | Thorsteinsdottir, Unnur | Stefansson, Kari | Ripatti, Samuli | Prokopenko, Inga | McCarthy, Mark I. | Morris, Andrew P.
PLoS Genetics  2015;11(7):e1005230.
Reference panels from the 1000 Genomes (1000G) Project Consortium provide near complete coverage of common and low-frequency genetic variation with minor allele frequency ≥0.5% across European ancestry populations. Within the European Network for Genetic and Genomic Epidemiology (ENGAGE) Consortium, we have undertaken the first large-scale meta-analysis of genome-wide association studies (GWAS), supplemented by 1000G imputation, for four quantitative glycaemic and obesity-related traits, in up to 87,048 individuals of European ancestry. We identified two loci for body mass index (BMI) at genome-wide significance, and two for fasting glucose (FG), none of which has been previously reported in larger meta-analysis efforts to combine GWAS of European ancestry. Through conditional analysis, we also detected multiple distinct signals of association mapping to established loci for waist-hip ratio adjusted for BMI (RSPO3) and FG (GCK and G6PC2). The index variant for one association signal at the G6PC2 locus is a low-frequency coding allele, H177Y, which has recently been demonstrated to have a functional role in glucose regulation. Fine-mapping analyses revealed that the non-coding variants most likely to drive association signals at established and novel loci were enriched for overlap with enhancer elements, which for FG mapped to promoter and transcription factor binding sites in pancreatic islets, in particular. Our study demonstrates that 1000G imputation and genetic fine-mapping of common and low-frequency variant association signals at GWAS loci, integrated with genomic annotation in relevant tissues, can provide insight into the functional and regulatory mechanisms through which their effects on glycaemic and obesity-related traits are mediated.
Author Summary
Human genetic studies have demonstrated that quantitative human anthropometric and metabolic traits, including body mass index, waist-hip ratio, and plasma concentrations of glucose and insulin, are highly heritable, and are established risk factors for type 2 diabetes and cardiovascular diseases. Although many regions of the genome have been associated with these traits, the specific genes responsible have not yet been identified. By making use of advanced statistical “imputation” techniques applied to more than 87,000 individuals of European ancestry, and publicly available “reference panels” of more than 37 million genetic variants, we have been able to identify novel regions of the genome associated with these glycaemic and obesity-related traits and localise genes within these regions that are most likely to be causal. This improved understanding of the biological mechanisms underlying glycaemic and obesity-related traits is extremely important because it may advance drug development for downstream disease endpoints, ultimately leading to public health benefits.
doi:10.1371/journal.pgen.1005230
PMCID: PMC4488845  PMID: 26132169
24.  Social Network Analysis for Program Implementation 
PLoS ONE  2015;10(6):e0131712.
This paper introduces the use of social network analysis theory and tools for implementation research. The social network perspective is useful for understanding, monitoring, influencing, or evaluating the implementation process when programs, policies, practices, or principles are designed and scaled up or adapted to different settings. We briefly describe common barriers to implementation success and relate them to the social networks of implementation stakeholders. We introduce a few simple measures commonly used in social network analysis and discuss how these measures can be used in program implementation. Using the four stage model of program implementation (exploration, adoption, implementation, and sustainment) proposed by Aarons and colleagues [1] and our experience in developing multi-sector partnerships involving community leaders, organizations, practitioners, and researchers, we show how network measures can be used at each stage to monitor, intervene, and improve the implementation process. Examples are provided to illustrate these concepts. We conclude with expected benefits and challenges associated with this approach.
doi:10.1371/journal.pone.0131712
PMCID: PMC4482437  PMID: 26110842
25.  Methods for measuring diffusion of a social media-based health intervention 
Social networking  2015;4(2):41-46.
This study evaluated the feasibility of measuring diffusion from a social networking community-level intervention. One year after completion of a randomized controlled HIV prevention trial on Facebook, 112 minority men who have sex with men (MSM) were asked to refer African-American and/or Latino sex partners to complete a survey. Results suggest that, compared to non-referrers, referrers spent more time online, controlling for age, race, education, and condition. Over 60% of referrals reported hearing about the intervention, and over half reported that the referrer talked to them about changing health behaviors. Results provide support and initial feasibility of using social networking for diffusing community-based HIV interventions.
doi:10.4236/sn.2015.42005
PMCID: PMC4479395  PMID: 26120501
HIV prevention; social networking technologies; diffusion of innovations

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